Publications

Goulding, M., Bollu, T., Büschges, A. Sensory Feedback and the Dynamic Control of Movement. (2025) Annual Review of Neuroscience. DOI: 10.1146/annurev-neuro-112723-042229

+ expand abstract

Mi, X., Chen, A.B., Duarte, D., Carey, E., Taylor, C.R., Braaker, P.N., Bright, M., Almeida, R.G., Lim, J.X., Ruetten, V.M.S., Wang, Y., Wang, M., Zhang, W., Zheng, W., Reitman, M.E., Huang, Y., Wang, X., Li, L., Deng, H., Shi, S.H., Poskanzer, K.E., Lyons, D.A., Nimmerjahn, A., Ahrens, M.B., Yu, G. Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals. (2025) Cell. DOI: 10.1016/j.cell.2025.03.012

+ expand abstract

Bartol, T.M., Ordyan, M., Sejnowski, T.J., Rangamani, P., Kennedy, M.B. A spatial model of autophosphorylation of CaMKII predicts that the lifetime of phospho-CaMKII after induction of synaptic plasticity is greatly prolonged by CaM-trapping. (2025) Front Synaptic Neurosci. 17:1547948. DOI: 10.3389/fnsyn.2025.1547948

+ expand abstract

Long-term potentiation (LTP) is a biochemical process that underlies learning in excitatory glutamatergic synapses in the Central Nervous System (CNS). A critical early driver of LTP is autophosphorylation of the abundant postsynaptic enzyme, Ca/calmodulin-dependent protein kinase II (CaMKII). Autophosphorylation is initiated by Ca flowing through NMDA receptors activated by strong synaptic activity. Its lifetime is ultimately determined by the balance of the rates of autophosphorylation and of dephosphorylation by protein phosphatase 1 (PP1). Here we have modeled the autophosphorylation and dephosphorylation of CaMKII during synaptic activity in a spine synapse using MCell4, an open source computer program for creating particle-based stochastic, and spatially realistic models of cellular microchemistry. The model integrates four earlier detailed models of separate aspects of regulation of spine Ca and CaMKII activity, each of which incorporate experimentally measured biochemical parameters and have been validated against experimental data. We validate the composite model by showing that it accurately predicts previous experimental measurements of effects of NMDA receptor activation, including high sensitivity of induction of LTP to phosphatase activity and persistence of autophosphorylation for a period of minutes after the end of synaptic stimulation. We then use the model to probe aspects of the mechanism of regulation of autophosphorylation of CaMKII that are difficult to measure . We examine the effects of "CaM-trapping," a process in which the affinity for Ca/CaM increases several hundred-fold after autophosphorylation. We find that CaM-trapping does not increase the proportion of autophosphorylated subunits in holoenzymes after a complex stimulus, as previously hypothesized. Instead, CaM-trapping may dramatically prolong the lifetime of autophosphorylated CaMKII through steric hindrance of dephosphorylation by protein phosphatase 1. The results provide motivation for experimental measurement of the extent of suppression of dephosphorylation of CaMKII by bound Ca/CaM. The composite MCell4 model of biochemical effects of complex stimuli in synaptic spines is a powerful new tool for realistic, detailed dissection of mechanisms of synaptic plasticity.

Gage, F.H. New neurons are born in the adult human brain. (2025) Nature Medicine. DOI: 10.1038/s41591-025-03497-x

Gage, F.H. Adult Neurogenesis in the Human Dentate Gyrus. (2025) Hippocampus. 35(1):e23655. DOI: 10.1002/hipo.23655

+ expand abstract

Rungratsameetaweemana, N., Kim, R., Chotibut, T., Sejnowski, T.J. Random noise promotes slow heterogeneous synaptic dynamics important for robust working memory computation. (2025) Proceedings of the National Academy of Sciences of the United States of America. 122(3):e2316745122. DOI: 10.1073/pnas.2316745122

+ expand abstract

Cassidy, R.M., Macias, A.V., Lagos, W.N., Ugorji, C., Callaway, E.M. Complementary Organization of Mouse Driver and Modulator Cortico-Thalamo-Cortical Circuits. (2025) Journal of Neuroscience. DOI: 10.1523/JNEUROSCI.1167-24.2024

+ expand abstract

Corticocortical (CC) projections in the visual system facilitate hierarchical processing of sensory information. In addition to direct CC connections, indirect cortico-thalamo-cortical (CTC) pathways through the pulvinar nucleus of the thalamus can relay sensory signals and mediate cortical interactions according to behavioral demands. While the pulvinar connects extensively to the entire visual cortex, it is unknown whether transthalamic pathways link all cortical areas or whether they follow systematic organizational rules. Because mouse pulvinar neurons projecting to different areas are spatially intermingled, their input/output relationships have been difficult to characterize using traditional anatomical methods. To determine the organization of CTC circuits, we mapped the higher visual areas (HVAs) of male and female mice with intrinsic signal imaging and targeted five pulvinar→HVA pathways for projection-specific rabies tracing. We aligned post-mortem cortical tissue to in vivo maps for precise quantification of the areas and cell types projecting to each pulvinar→HVA population. Layer 5 corticothalamic (L5CT) "driver" inputs to the pulvinar originate predominantly from primary visual cortex (V1), consistent with the CC hierarchy. L5CT inputs from lateral HVAs specifically avoid driving reciprocal connections, consistent with the "no-strong-loops" hypothesis. Conversely, layer 6 corticothalamic (L6CT) "modulator" inputs are distributed across areas and are biased toward reciprocal connections. Unlike previous studies in primates, we find that every HVA receives disynaptic input from the superior colliculus. CTC circuits in the pulvinar thus depend on both target HVA and input cell type, such that driving and modulating higher-order pathways follow complementary connection rules similar to those governing first-order CT circuits. Understanding the function of the pulvinar will require knowledge of its anatomical connections. Using state-of-the-art rabies tracing, we establish a map of brain-wide and CTC pulvinar connections. While the primate tectopulvinar pathway selectively targets dorsal visual areas, we find ubiquitous SC input in the mouse. This extrageniculate projection supports unconscious visually-guided behavior, suggesting that all visual cortical areas contribute to such functions in mice. Our results also unify longstanding anatomical hypotheses. Namely, "driver" CTC inputs are feedforward relays and adhere to the "no-strong-loops" hypothesis. "Modulator" L6CT inputs are overrepresented in the target HVA, reflecting the reciprocal connectivity described in previous bulk tracing studies. Together, these findings constitute a comprehensive map to guide future experimental and theoretical studies of pulvinar function.

Pașca, S.P., Arlotta, P., Bateup, H.S., Camp, J.G., Cappello, S., Gage, F.H., Knoblich, J.A., Kriegstein, A.R., Lancaster, M.A., Ming, G.L., Novarino, G., Okano, H., Parmar, M., Park, I.H., Reiner, O., Song, H., Studer, L., Takahashi, J., Temple, S., Testa, G., Treutlein, B., Vaccarino, F.M., Vanderhaeghen, P., Young-Pearse, T. A framework for neural organoids, assembloids and transplantation studies. (2024) Nature. DOI: 10.1038/s41586-024-08487-6

+ expand abstract

Praturu, A., Sharpee, T.O. Adaptive data embedding for curved spaces. (2024) iScience. 27(12):111266. DOI: 10.1016/j.isci.2024.111266

+ expand abstract

Hirakis, S.P., Bartol, T.M., Autin, L., Amaro, R.E., Sejnowski, T.J. Electrophysical cardiac remodeling at the molecular level: insights into Ryanodine Receptor activation and calcium-induced calcium release from a stochastic explicit-particle model. (2024) Biophysical Journal. DOI: 10.1016/j.bpj.2024.09.029

+ expand abstract

We present the first-ever, fully-discrete, stochastic model of triggered cardiac calcium dynamics. Using anatomically accurate subcellular cardiac myocyte geometries, we simulate the molecular players involved in calcium handling using high-resolution stochastic and explicit-particle methods at the level of an individual cardiac dyadic junction. Integrating data from multiple experimental sources, the model not only replicates the findings of traditional in silico studies and complements in vitro experimental data, but also reveals new insights into the molecular mechanisms driving cardiac dysfunction under stress and disease conditions. We improve upon older, non-discrete models using the same realistic geometry by incorporating molecular mechanisms for spontaneous, as well as triggered Calcium-Induced Calcium Release (CICR). Action potentials are used to activate L-type calcium channels (LTCCs), triggering CICR through Ryanodine receptors (RyR) on the surface of the sarcoplasmic reticulum. These improvements allow for the specific focus on the couplon: the structure-function relationship between LTCC and RyR. We investigate the electrophysical effects of normal and diseased action potentials on CICR and interrogate the effects of dyadic junction deformation through detubulation and orphaning of RyR. Our work demonstrates the importance of the electrophysical integrity of the CRU on CICR fidelity, giving insights into the molecular basis of heart disease. Finally, we provide a unique, detailed, molecular view of the CICR process using advanced rendering techniques. This easy-to-use model comes complete with tutorials and all necessary software for use and analysis so as to maximize usability and reproducibility. Our work focuses on quantifying, qualifying, and visualizing the behavior of the molecular species that underlie the function and dysfunction of subcellular cardiomyocyte systems.

Patel, D., Sejnowski, T., Siegelmann, H. Optimizing Attention and Cognitive Control Costs Using Temporally Layered Architectures. (2024) Neural Computation.:1-30 DOI: 10.1162/neco_a_01718

+ expand abstract

Son, G., Na, Y., Kim, Y., Son, J.H., Clemenson, G.D., Schafer, S.T., Yoo, J.Y., Parylak, S.L., Paquola, A., Do, H., Kim, D., Ahn, I., Ju, M., Kang, C.S., Ju, Y., Jung, E., McDonald, A.H., Park, Y., Kim, G., Paik, S.B., Hur, J., Kim, J., Han, Y.M., Lee, S.H., Gage, F.H., Kim, J.S., Han, J. miR-124 coordinates metabolic regulators acting at early stages of human neurogenesis. (2024) Communications Biology. 7(1):1393. DOI: 10.1038/s42003-024-07089-2

+ expand abstract

Barykina, N.V., Carey, E.M., Oliinyk, O.S., Nimmerjahn, A., Verkhusha, V.V. Destabilized near-infrared fluorescent nanobodies enable background-free targeting of GFP-based biosensors for imaging and manipulation. (2024) Nature Communications. 15(1):7788. DOI: 10.1038/s41467-024-51857-x

+ expand abstract

Muller, L., Churchland, P.S., Sejnowski, T.J. Transformers and cortical waves: encoders for pulling in context across time. (2024) Trends in Neurosciences. DOI: 10.1016/j.tins.2024.08.006

+ expand abstract

Comstock, L., Carvalho, V.R., Lainscsek, C., Fallah, A., Sejnowski, T.J. Transcranial Magnetic Stimulation Facilitates Neural Speech Decoding. (2024) Brain Sci. 14(9). DOI: 10.3390/brainsci14090895

+ expand abstract

Patiño, M., Rossa, M.A., Lagos, W.N., Patne, N.S., Callaway, E.M. Transcriptomic cell-type specificity of local cortical circuits. (2024) Neuron. DOI: 10.1016/j.neuron.2024.09.003

+ expand abstract

Fernandes, S., Revanna, J., Pratt, J., Hayes, N., Marchetto, M.C., Gage, F.H. Modeling Alzheimer's disease using human cell derived brain organoids and 3D models. (2024) Frontiers in Neuroscience. 18:1434945. DOI: 10.3389/fnins.2024.1434945

+ expand abstract

Minhas, P.S., Jones, J.R., Latif-Hernandez, A., Sugiura, Y., Durairaj, A.S., Wang, Q., Mhatre, S.D., Uenaka, T., Crapser, J., Conley, T., Ennerfelt, H., Jung, Y.J., Liu, L., Prasad, P., Jenkins, B.C., Ay, Y.A., Matrongolo, M., Goodman, R., Newmeyer, T., Heard, K., Kang, A., Wilson, E.N., Yang, T., Ullian, E.M., Serrano, G.E., Beach, T.G., Wernig, M., Rabinowitz, J.D., Suematsu, M., Longo, F.M., McReynolds, M.R., Gage, F.H., Andreasson, K.I. Restoring hippocampal glucose metabolism rescues cognition across Alzheimer's disease pathologies. (2024) Science. 385(6711):eabm6131. DOI: 10.1126/science.abm6131

+ expand abstract

Alvarez-Kuglen, M., Ninomiya, K., Qin, H., Rodriguez, D., Fiengo, L., Farhy, C., Hsu, W.M., Kirk, B., Havas, A., Feng, G.S., Roberts, A.J., Anderson, R.M., Serrano, M., Adams, P.D., Sharpee, T.O., Terskikh, A.V. ImAge quantitates aging and rejuvenation. (2024) Nat Aging. DOI: 10.1038/s43587-024-00685-1

+ expand abstract

Su, Y., Xu, J., Zhu, Z., Chin, J., Xu, L., Yu, H., Nudell, V., Dash, B., Moya, E.A., Ye, L., Nimmerjahn, A., Sun, X. Brainstem Dbh neurons control allergen-induced airway hyperreactivity. (2024) Nature. DOI: 10.1038/s41586-024-07608-5

+ expand abstract

Schmidt, T.T., Tyer, C., Rughani, P., Haggblom, C., Jones, J.R., Dai, X., Frazer, K.A., Gage, F.H., Juul, S., Hickey, S., Karlseder, J. High resolution long-read telomere sequencing reveals dynamic mechanisms in aging and cancer. (2024) Nature Communications. 15(1):5149. DOI: 10.1038/s41467-024-48917-7

+ expand abstract

Chen, Y., Zhang, H., Cameron, M., Sejnowski, T. Predictive sequence learning in the hippocampal formation. (2024) Neuron. DOI: 10.1016/j.neuron.2024.05.024

+ expand abstract

Phang, H.J., Heimler, S.R., Scandalis, L.M., Wing, D., Moran, R., Nichols, J.F., Moreno, D., Shadel, G.S., Gage, F.H., Molina, A.J.A. Protocol for the San Diego Nathan Shock Center Clinical Cohort: a new resource for studies of human aging. (2024) BMJ Open. 14(6):e082659. DOI: 10.1136/bmjopen-2023-082659

+ expand abstract

Herdy, J.R., Mertens, J., Gage, F.H. Neuronal senescence may drive brain aging. LINK TO FREE FULL-TEXT https://www.science.org/stoken/author-tokens/ST-1962/full [Pubmed] (2024) Science. 384(6703):1404-1406. DOI: 10.1126/science.adi3450

+ expand abstract

Minhas, P.S., Jones, J.R., Latif-Hernandez, A., Sugiura, Y., Durairaj, A.S., Uenaka, T., Wang, Q., Mhatre, S.D., Liu, L., Conley, T., Ennerfelt, H., Jung, Y.J., Prasad, P., Jenkins, B.C., Goodman, R., Newmeyer, T., Heard, K., Kang, A., Wilson, E.N., Ullian, E.M., Serrano, G.E., Beach, T.G., Rabinowitz, J.D., Wernig, M., Suematsu, M., Longo, F.M., McReynolds, M.R., Gage, F.H., Andreasson, K.I. Restoring hippocampal glucose metabolism rescues cognition across Alzheimer's disease pathologies. (2024) bioRxiv. DOI: 10.1101/2024.06.23.598940

+ expand abstract

Stern, S., Zhang, L., Wang, M., Wright, R., Rosh, I., Hussein, Y., Stern, T., Choudhary, A., Tripathi, U., Reed, P., Sadis, H., Nayak, R., Shemen, A., Agarwal, K., Cordeiro, D., Peles, D., Hang, Y., Mendes, A.P.D., Baul, T.D., Roth, J.G., Coorapati, S., Boks, M.P., McCombie, W.R., Hulshoff Pol, H., Brennand, K.J., Réthelyi, J.M., Kahn, R.S., Marchetto, M.C., Gage, F.H. Monozygotic twins discordant for schizophrenia differ in maturation and synaptic transmission. (2024) Molecular Psychiatry. DOI: 10.1038/s41380-024-02561-1

+ expand abstract

Wu, Y., Temple, B.A., Sevilla, N., Zhang, J., Zhu, H., Zolotavin, P., Jin, Y., Duarte, D., Sanders, E., Azim, E., Nimmerjahn, A., Pfaff, S.L., Luan, L., Xie, C. Ultraflexible electrodes for recording neural activity in the mouse spinal cord during motor behavior. (2024) Cell Reports. 43(5):114199. DOI: 10.1016/j.celrep.2024.114199

+ expand abstract

Tripathi, U., Rosh, I., Ben Ezer, R., Nayak, R., Hussein, Y., Choudhary, A., Djamus, J., Manole, A., Houlden, H., Gage, F.H., Stern, S. Upregulated ECM genes and increased synaptic activity in Parkinson's human DA neurons with PINK1/ PRKN mutations. (2024) NPJ Parkinsons Dis. 10(1):103. DOI: 10.1038/s41531-024-00715-0

+ expand abstract

Mi, X., Chen, A.B., Duarte, D., Carey, E., Taylor, C.R., Braaker, P.N., Bright, M., Almeida, R.G., Lim, J.X., Rutten, V.M., Zheng, W., Wang, M., Reitman, M.E., Wang, Y., Poskanzer, K.E., Lyons, D.A., Nimmerjahn, A., Ahrens, M.B., Yu, G. Fast, Accurate, and Versatile Data Analysis Platform for the Quantification of Molecular Spatiotemporal Signals. (2024) bioRxiv. DOI: 10.1101/2024.05.02.592259

+ expand abstract

Zocher, S., McCloskey, A., Karasinsky, A., Schulte, R., Friedrich, U., Lesche, M., Rund, N., Gage, F.H., Hetzer, M.W., Toda, T. Lifelong persistence of nuclear RNAs in the mouse brain. (2024) Science. 384(6691):53-59. DOI: 10.1126/science.adf3481

+ expand abstract

Samavat, M., Bartol, T.M., Harris, K.M., Sejnowski, T.J. Synaptic Information Storage Capacity Measured With Information Theory. (2024) Neural Computation. 36(5):781-802. DOI: 10.1162/neco_a_01659

+ expand abstract

Husar, A., Ordyan, M., Garcia, G.C., Yancey, J.G., Saglam, A.S., Faeder, J.R., Bartol, T.M., Kennedy, M.B., Sejnowski, T.J. MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface. (2024) PLOS Computational Biology. 20(4):e1011800. DOI: 10.1371/journal.pcbi.1011800

+ expand abstract

Adusei, M., Callaway, E.M., Usrey, W.M., Briggs, F. Parallel streams of direct corticogeniculate feedback from mid-level extrastriate cortex in the macaque monkey. (2024) eNeuro. DOI: 10.1523/ENEURO.0364-23.2024

+ expand abstract

First order thalamic nuclei receive feedforward signals from peripheral receptors and relay these signals to primary sensory cortex. Primary sensory cortex, in turn, provides reciprocal feedback to first order thalamus. Because the vast majority of sensory thalamocortical inputs target primary sensory cortex, their complementary corticothalamic neurons are assumed to be similarly restricted to primary sensory cortex. We upend this assumption by characterizing morphologically diverse neurons in multiple mid-level visual cortical areas of the primate () brain that provide direct feedback to the primary visual thalamus, the dorsal lateral geniculate nucleus (LGN). Although the majority of geniculocortical neurons project to primary visual cortex (V1), a minority, located mainly in the koniocellular LGN layers, provide direct input to extrastriate visual cortex. These "V1-bypassing" projections may be implicated in blindsight. We hypothesized that geniculocortical inputs directly targeting extrastriate cortex should be complemented by reciprocal corticogeniculate circuits. Using virus-mediated circuit tracing, we discovered corticogeniculate neurons throughout three mid-level extrastriate areas: MT, MST, and V4. Quantitative morphological analyses revealed non-uniform distributions of unique cell types across areas. Many extrastriate corticogeniculate neurons had spiny stellate morphology, suggesting possible targeting of koniocellular LGN layers. Importantly though, multiple morphological types were observed across areas. Such morphological diversity could suggest parallel streams of V1-bypassing corticogeniculate feedback at multiple stages of the visual processing hierarchy. Furthermore, the presence of corticogeniculate neurons across visual cortex necessitates a reevaluation of the LGN as a hub for visual information rather than a simple relay. First order thalamic nuclei are most strongly connected in feedforward and feedback directions with primary sensory cortex. In the visual system, direct feedforward circuits link the visual thalamus with higher-order, extrastriate visual areas, although the function of these less-common pathways remains unknown. Here we demonstrate for the first time the presence of complementary direct feedback connections between multiple extrastriate visual cortical areas and the visual thalamus in the primate brain. Although sparse, extrastriate corticogeniculate circuits are consistently present and contain morphologically diverse neurons, suggesting parallel streams of extrastriate feedback. These findings indicate an evolutionary conservation of circuits that integrate information from throughout the visual processing hierarchy within the visual thalamus.

Podvin, S., Jones, J., Kang, A., Goodman, R., Reed, P., Lietz, C.B., Then, J., Lee, K.C., Eyler, L.T., Jeste, D.V., Gage, F.H., Hook, V. Human iN neuronal model of schizophrenia displays dysregulation of chromogranin B and related neuropeptide transmitter signatures. (2024) Molecular Psychiatry. DOI: 10.1038/s41380-024-02422-x

+ expand abstract

Toda, T., Bedrosian, T.A., Schafer, S.T., Cuoco, M.S., Linker, S.B., Ghassemzadeh, S., Mitchell, L., Whiteley, J.T., Novaresi, N., McDonald, A.H., Gallina, I.S., Yoon, H., Hester, M.E., Pena, M., Lim, C., Suljic, E., AlFatah Mansour, A., Boulard, M., Parylak, S.L., Gage, F.H. Long interspersed nuclear elements safeguard neural progenitors from precocious differentiation. (2024) Cell Reports. 43(2):113774. DOI: 10.1016/j.celrep.2024.113774

+ expand abstract

Bartol, T.M., Ordyan, M., Sejnowski, T.J., Rangamani, P., Kennedy, M.B. A spatial model of autophosphorylation of CaMKII in a glutamatergic spine suggests a network-driven kinetic mechanism for bistable changes in synaptic strength. (2024) bioRxiv. DOI: 10.1101/2024.02.02.578696

+ expand abstract

Rosh, I., Tripathi, U., Hussein, Y., Rike, W.A., Djamus, J., Shklyar, B., Manole, A., Houlden, H., Winkler, J., Gage, F.H., Stern, S. Synaptic dysfunction and extracellular matrix dysregulation in dopaminergic neurons from sporadic and E326K-GBA1 Parkinson's disease patients. (2024) NPJ Parkinsons Dis. 10(1):38. DOI: 10.1038/s41531-024-00653-x

+ expand abstract

Wang, H., Dey, O., Lagos, W.N., Behnam, N., Callaway, E.M., Stafford, B.K. Parallel pathways carrying direction-and orientation-selective retinal signals to layer 4 of the mouse visual cortex. (2024) Cell Reports. 43(3):113830. DOI: 10.1016/j.celrep.2024.113830

+ expand abstract

Wang, M., Zhang, L., Novak, S.W., Yu, J., Gallina, I.S., Xu, L.L., Lim, C.K., Fernandes, S., Shokhirev, M.N., Williams, A.E., Saxena, M.D., Coorapati, S., Parylak, S.L., Quintero, C., Molina, E., Andrade, L.R., Manor, U., Gage, F.H. Morphological diversification and functional maturation of human astrocytes in glia-enriched cortical organoid transplanted in mouse brain. (2024) Nature Biotechnology. DOI: 10.1038/s41587-024-02157-8

+ expand abstract

Sameni, S., Bartol, T.M., Corey-Bloom, J., Sejnowski, T.J. Computer simulations predict the impact of neuronal atrophy on the calcium dynamics in Huntington's disease. (2024) PNAS Nexus. 3(1):pgad443. DOI: 10.1093/pnasnexus/pgad443

+ expand abstract

Samavat, M., Bartol, T.M., Bromer, C., Hubbard, D.D., Hanka, D.C., Kuwajima, M., Mendenhall, J.M., Parker, P.H., Bowden, J.B., Abraham, W.C., Sejnowski, T.J., Harris, K.M. Long-Term Potentiation Produces a Sustained Expansion of Synaptic Information Storage Capacity in Adult Rat Hippocampus. (2024) bioRxiv. DOI: 10.1101/2024.01.12.574766

+ expand abstract

Zhang, L.A., Li, P., Callaway, E.M. High-Resolution Laminar Identification in Macaque Primary Visual Cortex Using Neuropixels Probes. (2024) bioRxiv. DOI: 10.1101/2024.01.23.576944

+ expand abstract

Zhou, J., Zhang, Z., Wu, M., Liu, H., Pang, Y., Bartlett, A., Peng, Z., Ding, W., Rivkin, A., Lagos, W.N., Williams, E., Lee, C.T., Miyazaki, P.A., Aldridge, A., Zeng, Q., Salinda, J.L.A., Claffey, N., Liem, M., Fitzpatrick, C., Boggeman, L., Yao, Z., Smith, K.A., Tasic, B., Altshul, J., Kenworthy, M.A., Valadon, C., Nery, J.R., Castanon, R.G., Patne, N.S., Vu, M., Rashid, M., Jacobs, M., Ito, T., Osteen, J., Emerson, N., Lee, J., Cho, S., Rink, J., Huang, H.H., Pinto-Duartec, A., Dominguez, B., Smith, J.B., O'Connor, C., Zeng, H., Chen, S., Lee, K.F., Mukamel, E.A., Jin, X., Margarita Behrens, M., Ecker, J.R., Callaway, E.M. Brain-wide correspondence of neuronal epigenomics and distant projections. (2023) Nature. 624(7991):355-365. DOI: 10.1038/s41586-023-06823-w

+ expand abstract

Zemke, N.R., Armand, E.J., Wang, W., Lee, S., Zhou, J., Li, Y.E., Liu, H., Tian, W., Nery, J.R., Castanon, R.G., Bartlett, A., Osteen, J.K., Li, D., Zhuo, X., Xu, V., Chang, L., Dong, K., Indralingam, H.S., Rink, J.A., Xie, Y., Miller, M., Krienen, F.M., Zhang, Q., Taskin, N., Ting, J., Feng, G., McCarroll, S.A., Callaway, E.M., Wang, T., Lein, E.S., Behrens, M.M., Ecker, J.R., Ren, B. Conserved and divergent gene regulatory programs of the mammalian neocortex. (2023) Nature. 624(7991):390-402. DOI: 10.1038/s41586-023-06819-6

+ expand abstract

Patiño, M., Lagos, W.N., Patne, N.S., Miyazaki, P.A., Bhamidipati, S.K., Collman, F., Callaway, E.M. Postsynaptic cell type and synaptic distance do not determine efficiency of monosynaptic rabies virus spread measured at synaptic resolution. (2023) Elife. 12. DOI: 10.7554/eLife.89297

+ expand abstract

Chung, B., Zia, M., Thomas, K.A., Michaels, J.A., Jacob, A., Pack, A., Williams, M.J., Nagapudi, K., Teng, L.H., Arrambide, E., Ouellette, L., Oey, N., Gibbs, R., Anschutz, P., Lu, J., Wu, Y., Kashefi, M., Oya, T., Kersten, R., Mosberger, A.C., O'Connell, S., Wang, R., Marques, H., Mendes, A.R., Lenschow, C., Kondakath, G., Kim, J.J., Olson, W., Quinn, K.N., Perkins, P., Gatto, G., Thanawalla, A., Coltman, S., Kim, T., Smith, T., Binder-Markey, B., Zaback, M., Thompson, C.K., Giszter, S., Person, A., Goulding, M., Azim, E., Thakor, N., O'Connor, D., Trimmer, B., Lima, S.Q., Carey, M.R., Pandarinath, C., Costa, R.M., Pruszynski, J.A., Bakir, M., Sober, S.J. Myomatrix arrays for high-definition muscle recording. (2023) Elife. 12. DOI: 10.7554/eLife.88551

+ expand abstract

Lainscsek, C., Salami, P., Carvalho, V.R., Mendes, E.M.A.M., Fan, M., Cash, S.S., Sejnowski, T.J. Network-motif delay differential analysis of brain activity during seizures. (2023) Chaos. 33(12). DOI: 10.1063/5.0165904

+ expand abstract

Garrison, M.A., Jang, Y., Bae, T., Cherskov, A., Emery, S.B., Fasching, L., Jones, A., Moldovan, J.B., Molitor, C., Pochareddy, S., Peters, M.A., Shin, J.H., Wang, Y., Yang, X., Akbarian, S., Chess, A., Gage, F.H., Gleeson, J.G., Kidd, J.M., McConnell, M., Mills, R.E., Moran, J.V., Park, P.J., Sestan, N., Urban, A.E., Vaccarino, F.M., Walsh, C.A., Weinberger, D.R., Wheelan, S.J., Abyzov, A. Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. (2023) Sci Data. 10(1):813. DOI: 10.1038/s41597-023-02645-7

+ expand abstract

Tsuda, B., Richmond, B.J., Sejnowski, T.J. Exploring strategy differences between humans and monkeys with recurrent neural networks. (2023) PLOS Computational Biology. 19(11):e1011618. DOI: 10.1371/journal.pcbi.1011618

+ expand abstract

Manole, A., Wong, T., Rhee, A., Novak, S., Chin, S.M., Tsimring, K., Paucar, A., Williams, A., Newmeyer, T.F., Schafer, S.T., Rosh, I., Kaushik, S., Hoffman, R., Chen, S., Wang, G., Snyder, M., Cuervo, A.M., Andrade, L., Manor, U., Lee, K., Jones, J.R., Stern, S., Marchetto, M.C., Gage, F.H. NGLY1 mutations cause protein aggregation in human neurons. (2023) Cell Reports. 42(12):113466. DOI: 10.1016/j.celrep.2023.113466

+ expand abstract

Alvarez-Kuglen, M., Rodriguez, D., Qin, H., Ninomiya, K., Fiengo, L., Farhy, C., Hsu, W.M., Havas, A., Feng, G.S., Roberts, A.J., Anderson, R.M., Serrano, M., Adams, P.D., Sharpee, T.O., Terskikh, A.V. Imaging-based chromatin and epigenetic age, ImAge, quantitates aging and rejuvenation. (2023) Res Sq. DOI: 10.21203/rs.3.rs-3479973/v1

+ expand abstract

Jorstad, N.L., Close, J., Johansen, N., Yanny, A.M., Barkan, E.R., Travaglini, K.J., Bertagnolli, D., Campos, J., Casper, T., Crichton, K., Dee, N., Ding, S.L., Gelfand, E., Goldy, J., Hirschstein, D., Kiick, K., Kroll, M., Kunst, M., Lathia, K., Long, B., Martin, N., McMillen, D., Pham, T., Rimorin, C., Ruiz, A., Shapovalova, N., Shehata, S., Siletti, K., Somasundaram, S., Sulc, J., Tieu, M., Torkelson, A., Tung, H., Callaway, E.M., Hof, P.R., Keene, C.D., Levi, B.P., Linnarsson, S., Mitra, P.P., Smith, K., Hodge, R.D., Bakken, T.E., Lein, E.S. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. (2023) Science. 382(6667):eadf6812. DOI: 10.1126/science.adf6812

+ expand abstract

Lainscsek, C., Mendes, E.M.A.M., Salgado, G.H.O., Sejnowski, T.J. Transformations that preserve the uniqueness of the differential form for Lorenz-like systems. (2023) Chaos. 33(10). DOI: 10.1063/5.0156237

+ expand abstract

Klug, J.R., Yan, X., Hoffman, H.A., Engelhardt, M.D., Osakada, F., Callaway, E.M., Jin, X. Asymmetric cortical projections to striatal direct and indirect pathways distinctly control actions. (2023) bioRxiv. DOI: 10.1101/2023.10.02.560589

+ expand abstract

Daboussi, L., Costaguta, G., Gullo, M., Jasinski, N., Pessino, V., O'Leary, B., Lettieri, K., Driscoll, S., Pfaff, S.L. Mitf is a Schwann cell sensor of axonal integrity that drives nerve repair. (2023) Cell Reports. 42(11):113282. DOI: 10.1016/j.celrep.2023.113282

+ expand abstract

Garcia, G.C., Gupta, K., Bartol, T.M., Sejnowski, T.J., Rangamani, P. Mitochondrial morphology governs ATP production rate. (2023) J Gen Physiol. 155(9). DOI: 10.1085/jgp.202213263

+ expand abstract

Globig, A.M., Zhao, S., Roginsky, J., Maltez, V.I., Guiza, J., Avina-Ochoa, N., Heeg, M., Araujo Hoffmann, F., Chaudhary, O., Wang, J., Senturk, G., Chen, D., O'Connor, C., Pfaff, S., Germain, R.N., Schalper, K.A., Emu, B., Kaech, S.M. The β-adrenergic receptor links sympathetic nerves to T cell exhaustion. (2023) Nature. DOI: 10.1038/s41586-023-06568-6

+ expand abstract

Li, J.S., Sarma, A.A., Sejnowski, T.J., Doyle, J.C. Internal feedback in the cortical perception-action loop enables fast and accurate behavior. (2023) Proceedings of the National Academy of Sciences of the United States of America. 120(39):e2300445120. DOI: 10.1073/pnas.2300445120

+ expand abstract

Wang, H., Dey, O., Lagos, W.N., Behnam, N., Callaway, E.M., Stafford, B.K. Parallel pathways carrying direction and orientation selective retinal signals to layer 4 of mouse visual cortex. (2023) bioRxiv. DOI: 10.1101/2023.09.18.558281

+ expand abstract

Mizrahi, L., Choudhary, A., Ofer, P., Goldberg, G., Milanesi, E., Kelsoe, J.R., Gurwitz, D., Alda, M., Gage, F.H., Stern, S. Immunoglobulin genes expressed in lymphoblastoid cell lines discern and predict lithium response in bipolar disorder patients. (2023) Molecular Psychiatry. DOI: 10.1038/s41380-023-02183-z

+ expand abstract

Traxler, L., Lucciola, R., Herdy, J.R., Jones, J.R., Mertens, J., Gage, F.H. Neural cell state shifts and fate loss in ageing and age-related diseases. (2023) Nat Rev Neurol. DOI: 10.1038/s41582-023-00815-0

+ expand abstract

Schafer, S.T., Mansour, A.A., Schlachetzki, J.C.M., Pena, M., Ghassemzadeh, S., Mitchell, L., Mar, A., Quang, D., Stumpf, S., Ortiz, I.S., Lana, A.J., Baek, C., Zaghal, R., Glass, C.K., Nimmerjahn, A., Gage, F.H. An in vivo neuroimmune organoid model to study human microglia phenotypes. (2023) Cell. 186(10):2111-2126.e20. DOI: 10.1016/j.cell.2023.04.022

+ expand abstract

Arlotta, P., Gage, F.H. Neural Organoids and the Quest to Understand and Treat Psychiatric Disease. (2023) Biological Psychiatry. 93(7):588-589. DOI: 10.1016/j.biopsych.2023.01.021

Zemke, N.R., Armand, E.J., Wang, W., Lee, S., Zhou, J., Li, Y.E., Liu, H., Tian, W., Nery, J.R., Castanon, R.G., Bartlett, A., Osteen, J.K., Li, D., Zhuo, X., Xu, V., Miller, M., Krienen, F.M., Zhang, Q., Taskin, N., Ting, J., Feng, G., McCarroll, S.A., Callaway, E.M., Wang, T., Behrens, M.M., Lein, E.S., Ecker, J.R., Ren, B. Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex. (2023) bioRxiv. DOI: 10.1101/2023.04.08.536119

+ expand abstract

Kobayashi, Y., Shigyo, M., Platoshyn, O., Marsala, S., Kato, T., Takamura, N., Yoshida, K., Kishino, A., Bravo-Hernandez, M., Juhas, S., Juhasova, J., Studenovska, H., Proks, V., Driscoll, S.P., Glenn, T.D., Pfaff, S.L., Ciacci, J.D., Marsala, M. Expandable Sendai-Virus-Reprogrammed Human iPSC-Neuronal Precursors: Post-Grafting Safety Characterization in Rats and Adult Pig. (2023) Cell Transplantation. 32:9636897221107009. DOI: 10.1177/09636897221107009

+ expand abstract

Mishra, H.K., Wei, H., Rohr, K.E., Ko, I., Nievergelt, C.M., Maihofer, A.X., Shilling, P.D., Alda, M., Berrettini, W.H., Brennand, K.J., Calabrese, J.R., Coryell, W.H., Frye, M., Gage, F., Gershon, E., McInnis, M.G., Nurnberger, J., Oedegaard, K.J., Zandi, P.P., Kelsoe, J.R., McCarthy, M.J. Contributions of circadian clock genes to cell survival in fibroblast models of lithium-responsive bipolar disorder. (2023) Eur Neuropsychopharmacol. 74:1-14. DOI: 10.1016/j.euroneuro.2023.04.009

+ expand abstract

Shekhtmeyster, P., Duarte, D., Carey, E.M., Ngo, A., Gao, G., Olmstead, J.A., Nelson, N.A., Nimmerjahn, A. Trans-segmental imaging in the spinal cord of behaving mice. (2023) Nature Biotechnology. DOI: 10.1038/s41587-023-01700-3

+ expand abstract

Kempermann, G., Song, H., Gage, F.H. Adult neurogenesis in the hippocampus. (2023) Hippocampus. DOI: 10.1002/hipo.23525

Shekhtmeyster, P., Carey, E.M., Duarte, D., Ngo, A., Gao, G., Nelson, N.A., Clark, C.L., Nimmerjahn, A. Multiplex translaminar imaging in the spinal cord of behaving mice. (2023) Nature Communications. 14(1):1427. DOI: 10.1038/s41467-023-36959-2

+ expand abstract

Zador, A., Escola, S., Richards, B., Ölveczky, B., Bengio, Y., Boahen, K., Botvinick, M., Chklovskii, D., Churchland, A., Clopath, C., DiCarlo, J., Ganguli, S., Hawkins, J., Körding, K., Koulakov, A., LeCun, Y., Lillicrap, T., Marblestone, A., Olshausen, B., Pouget, A., Savin, C., Sejnowski, T., Simoncelli, E., Solla, S., Sussillo, D., Tolias, A.S., Tsao, D. Catalyzing next-generation Artificial Intelligence through NeuroAI. (2023) Nature Communications. 14(1):1597. DOI: 10.1038/s41467-023-37180-x

+ expand abstract

Niemsiri, V., Rosenthal, S.B., Nievergelt, C.M., Maihofer, A.X., Marchetto, M.C., Santos, R., Shekhtman, T., Alliey-Rodriguez, N., Anand, A., Balaraman, Y., Berrettini, W.H., Bertram, H., Burdick, K.E., Calabrese, J.R., Calkin, C.V., Conroy, C., Coryell, W.H., DeModena, A., Eyler, L.T., Feeder, S., Fisher, C., Frazier, N., Frye, M.A., Gao, K., Garnham, J., Gershon, E.S., Goes, F.S., Goto, T., Harrington, G.J., Jakobsen, P., Kamali, M., Kelly, M., Leckband, S.G., Lohoff, F.W., McCarthy, M.J., McInnis, M.G., Craig, D., Millett, C.E., Mondimore, F., Morken, G., Nurnberger, J.I., Donovan, C.O., Øedegaard, K.J., Ryan, K., Schinagle, M., Shilling, P.D., Slaney, C., Stapp, E.K., Stautland, A., Tarwater, B., Zandi, P.P., Alda, M., Fisch, K.M., Gage, F.H., Kelsoe, J.R. Focal adhesion is associated with lithium response in bipolar disorder: evidence from a network-based multi-omics analysis. (2023) Molecular Psychiatry. DOI: 10.1038/s41380-022-01909-9

+ expand abstract

Little, J.C., Kaaronen, R.O., Hukkinen, J.I., Xiao, S., Sharpee, T., Farid, A.M., Nilchiani, R., Barton, C.M. Earth Systems to Anthropocene Systems: An Evolutionary, System-of-Systems, Convergence Paradigm for Interdependent Societal Challenges. (2023) Environ Sci Technol. DOI: 10.1021/acs.est.2c06203

+ expand abstract

Ren, X., Liu, S., Virlogeux, A., Kang, S.J., Brusch, J., Liu, Y., Dymecki, S.M., Han, S., Goulding, M., Acton, D. Identification of an essential spinoparabrachial pathway for mechanical itch. (2023) Neuron. DOI: 10.1016/j.neuron.2023.03.013

+ expand abstract

Hayashi, M., Gullo, M., Senturk, G., Di Costanzo, S., Nagasaki, S.C., Kageyama, R., Imayoshi, I., Goulding, M., Pfaff, S.L., Gatto, G. A spinal synergy of excitatory and inhibitory neurons coordinates ipsilateral body movements. (2023) bioRxiv. DOI: 10.1101/2023.03.21.533603

+ expand abstract

Sejnowski, T.J. Large Language Models and the Reverse Turing Test. (2023) Neural Computation.:1-34 DOI: 10.1162/neco_a_01563

+ expand abstract

Parylak, S.L., Qiu, F., Linker, S.B., Gallina, I.S., Lim, C.K., Preciado, D., McDonald, A.H., Zhou, X., Gage, F.H. Neuronal activity-related transcription is blunted in immature compared to mature dentate granule cells. (2023) Hippocampus. DOI: 10.1002/hipo.23515

+ expand abstract

Yang, J.Y., O'Connell, T.F., Hsu, W.M., Bauer, M.S., Dylla, K.V., Sharpee, T.O., Hong, E.J. Restructuring of olfactory representations in the fly brain around odor relationships in natural sources. (2023) bioRxiv. DOI: 10.1101/2023.02.15.528627

+ expand abstract

Bermperidis, T., Schafer, S., Gage, F.H., Sejnowski, T., Torres, E.B. Dynamic Interrogation of Stochastic Transcriptome Trajectories Using Disease Associated Genes Reveals Distinct Origins of Neurological and Psychiatric Disorders. (2023) Frontiers in Neuroscience. 16:884707. DOI: 10.3389/fnins.2022.884707

+ expand abstract

Fischer, K.B., Collins, H.K., Pang, Y., Roy, D.S., Zhang, Y., Feng, G., Li, S.J., Kepecs, A., Callaway, E.M. Monosynaptic restriction of the anterograde herpes simplex virus strain H129 for neural circuit tracing. (2023) Journal of Comparative Neurology. DOI: 10.1002/cne.25451

+ expand abstract

Perez-Garcia, G., Bicak, M., Haure-Mirande, J.V., Perez, G.M., Otero-Pagan, A., Gama Sosa, M.A., De Gasperi, R., Sano, M., Barlow, C., Gage, F.H., Readhead, B., Ehrlich, M.E., Gandy, S., Elder, G.A. BCI-838, an orally active mGluR2/3 receptor antagonist pro-drug, rescues learning behavior deficits in the PS19 MAPT mouse model of tauopathy. (2023) Neurosci Lett.:137080 DOI: 10.1016/j.neulet.2023.137080

+ expand abstract

Wang, M., Gage, F.H., Schafer, S.T. Transplantation Strategies to Enhance Maturity and Cellular Complexity in Brain Organoids. (2023) Biological Psychiatry. DOI: 10.1016/j.biopsych.2023.01.004

+ expand abstract

Herdy, J.R., Traxler, L., Agarwal, R.K., Karbacher, L., Schlachetzki, J.C.M., Boehnke, L., Zangwill, D., Galasko, D., Glass, C.K., Mertens, J., Gage, F.H. Increased post-mitotic senescence in aged human neurons is a pathological feature of Alzheimer's disease. (2022) Cell Stem Cell. 29(12):1637-1652.e6. DOI: 10.1016/j.stem.2022.11.010

+ expand abstract

Fu, C., Ngo, J., Zhang, S., Lu, L., Miron, A., Schafer, S., Gage, F.H., Jin, F., Schumacher, F.R., Wynshaw-Boris, A. Novel correlative analysis identifies multiple genomic variations impacting ASD with macrocephaly. (2022) Human Molecular Genetics. DOI: 10.1093/hmg/ddac300

+ expand abstract

Ronzano, R., Skarlatou, S., Barriga, B.K., Bannatyne, B.A., Bhumbra, G.S., Foster, J.D., Moore, J.D., Lancelin, C., Pocratsky, A.M., Özyurt, M.G., Smith, C.C., Todd, A.J., Maxwell, D.J., Murray, A.J., Pfaff, S.L., Brownstone, R.M., Zampieri, N., Beato, M. Spinal premotor interneurons controlling antagonistic muscles are spatially intermingled. (2022) Elife. 11. DOI: 10.7554/eLife.81976

+ expand abstract

Wilson, M.N., Thunemann, M., Liu, X., Lu, Y., Puppo, F., Adams, J.W., Kim, J.H., Ramezani, M., Pizzo, D.P., Djurovic, S., Andreassen, O.A., Mansour, A.A., Gage, F.H., Muotri, A.R., Devor, A., Kuzum, D. Multimodal monitoring of human cortical organoids implanted in mice reveal functional connection with visual cortex. (2022) Nature Communications. 13(1):7945. DOI: 10.1038/s41467-022-35536-3

+ expand abstract

Zhang, H., Rich, P.D., Lee, A.K., Sharpee, T.O. Hippocampal spatial representations exhibit a hyperbolic geometry that expands with experience. (2022) Nature Neuroscience. DOI: 10.1038/s41593-022-01212-4

+ expand abstract

Rungratsameetaweemana, N., Lainscsek, C., Cash, S.S., Garcia, J.O., Sejnowski, T.J., Bansal, K. Brain network dynamics codify heterogeneity in seizure evolution. (2022) Brain Commun. 4(5):fcac234. DOI: 10.1093/braincomms/fcac234

+ expand abstract

Dynamic functional brain connectivity facilitates adaptive cognition and behaviour. Abnormal alterations within such connectivity could result in disrupted functions observed across various neurological conditions. As one of the most common neurological disorders, epilepsy is defined by the seemingly random occurrence of spontaneous seizures. A central but unresolved question concerns the mechanisms by which extraordinarily diverse propagation dynamics of seizures emerge. Here, we applied a graph-theoretical approach to assess dynamic reconfigurations in the functional brain connectivity before, during and after seizures that display heterogeneous propagation patterns despite sharing similar cortical onsets. We computed time-varying functional brain connectivity networks from human intracranial recordings of 67 seizures (across 14 patients) that had a focal origin-49 of these focal seizures remained focal and 18 underwent a bilateral spread (focal to bilateral tonic-clonic seizures). We utilized functional connectivity networks estimated from interictal periods across patients as control. Our results characterize network features that quantify the underlying functional dynamics associated with the observed heterogeneity of seizure propagation across these two types of focal seizures. Decoding these network features demonstrate that bilateral propagation of seizure activity is an outcome of the imbalance of global integration and segregation in the brain prior to seizure onset. We show that there exist intrinsic network signatures preceding seizure onset that are associated with the extent to which an impending seizure will propagate throughout the brain (i.e. staying within one hemisphere versus spreading transcallosally). Additionally, these features characterize an increase in segregation and a decrease in excitability within the brain network (i.e. high modularity and low spectral radius). Importantly, seizure-type-specific differences in these features emerge several minutes prior to seizure onset, suggesting the potential utility of such measures in intervention strategies. Finally, our results reveal network characteristics the onset that are unique to the propagation mechanisms of two most common focal seizure subtypes, indicative of distinct reconfiguration processes that may assist termination of each seizure type. Together, our findings provide insights into the relationship between the temporal evolution of seizure activity and the underlying functional connectivity dynamics. These results offer exciting avenues where graph-theoretical measures could potentially guide personalized clinical interventions for epilepsy and other neurological disorders in which extensive heterogeneity is observed across subtypes as well as across and within individual patients.

Linker, S.B., Narvaiza, I., Hsu, J.Y., Wang, M., Qiu, F., Mendes, A.P.D., Oefner, R., Kottilil, K., Sharma, A., Randolph-Moore, L., Mejia, E., Santos, R., Marchetto, M.C., Gage, F.H. Human-specific regulation of neural maturation identified by cross-primate transcriptomics. (2022) Current Biology. DOI: 10.1016/j.cub.2022.09.028

+ expand abstract

Martins, L.F., Brambilla, I., Motta, A., de Pretis, S., Bhat, G.P., Badaloni, A., Malpighi, C., Amin, N.D., Imai, F., Almeida, R.D., Yoshida, Y., Pfaff, S.L., Bonanomi, D. Motor neurons use push-pull signals to direct vascular remodeling critical for their connectivity. (2022) Neuron. DOI: 10.1016/j.neuron.2022.09.021

+ expand abstract

van den Hurk, M., Lau, S., Marchetto, M.C., Mertens, J., Stern, S., Corti, O., Brice, A., Winner, B., Winkler, J., Gage, F.H., Bardy, C. Druggable transcriptomic pathways revealed in Parkinson's patient-derived midbrain neurons. (2022) NPJ Parkinsons Dis. 8(1):134. DOI: 10.1038/s41531-022-00400-0

+ expand abstract

Complex genetic predispositions accelerate the chronic degeneration of midbrain substantia nigra neurons in Parkinson's disease (PD). Deciphering the human molecular makeup of PD pathophysiology can guide the discovery of therapeutics to slow the disease progression. However, insights from human postmortem brain studies only portray the latter stages of PD, and there is a lack of data surrounding molecular events preceding the neuronal loss in patients. We address this gap by identifying the gene dysregulation of live midbrain neurons reprogrammed in vitro from the skin cells of 42 individuals, including sporadic and familial PD patients and matched healthy controls. To minimize bias resulting from neuronal reprogramming and RNA-seq methods, we developed an analysis pipeline integrating PD transcriptomes from different RNA-seq datasets (unsorted and sorted bulk vs. single-cell and Patch-seq) and reprogramming strategies (induced pluripotency vs. direct conversion). This PD cohort's transcriptome is enriched for human genes associated with known clinical phenotypes of PD, regulation of locomotion, bradykinesia and rigidity. Dysregulated gene expression emerges strongest in pathways underlying synaptic transmission, metabolism, intracellular trafficking, neural morphogenesis and cellular stress/immune responses. We confirmed a synaptic impairment with patch-clamping and identified pesticides and endoplasmic reticulum stressors as the most significant gene-chemical interactions in PD. Subsequently, we associated the PD transcriptomic profile with candidate pharmaceuticals in a large database and a registry of current clinical trials. This study highlights human transcriptomic pathways that can be targeted therapeutically before the irreversible neuronal loss. Furthermore, it demonstrates the preclinical relevance of unbiased large transcriptomic assays of reprogrammed patient neurons.

Li, P., Garg, A.K., Zhang, L.A., Rashid, M.S., Callaway, E.M. Cone opponent functional domains in primary visual cortex combine signals for color appearance mechanisms. (2022) Nature Communications. 13(1):6344. DOI: 10.1038/s41467-022-34020-2

+ expand abstract

Wang, H., Dey, O., Lagos, W.N., Callaway, E.M. Diversity in spatial frequency, temporal frequency, and speed tuning across mouse visual cortical areas and layers. (2022) Journal of Comparative Neurology. DOI: 10.1002/cne.25404

+ expand abstract

Pașca, S.P., Arlotta, P., Bateup, H.S., Camp, J.G., Cappello, S., Gage, F.H., Knoblich, J.A., Kriegstein, A.R., Lancaster, M.A., Ming, G.L., Muotri, A.R., Park, I.H., Reiner, O., Song, H., Studer, L., Temple, S., Testa, G., Treutlein, B., Vaccarino, F.M. A nomenclature consensus for nervous system organoids and assembloids. (2022) Nature. 609(7929):907-910. DOI: 10.1038/s41586-022-05219-6

+ expand abstract

Stern, S., Lau, S., Manole, A., Rosh, I., Percia, M.M., Ben Ezer, R., Shokhirev, M.N., Qiu, F., Schafer, S., Mansour, A.A., Mangan, K.P., Stern, T., Ofer, P., Stern, Y., Diniz Mendes, A.P., Djamus, J., Moore, L.R., Nayak, R., Laufer, S.H., Aicher, A., Rhee, A., Wong, T.L., Nguyen, T., Linker, S.B., Winner, B., Freitas, B.C., Jones, E., Sagi, I., Bardy, C., Brice, A., Winkler, J., Marchetto, M.C., Gage, F.H. Reduced synaptic activity and dysregulated extracellular matrix pathways in midbrain neurons from Parkinson's disease patients. (2022) NPJ Parkinsons Dis. 8(1):103. DOI: 10.1038/s41531-022-00366-z

+ expand abstract

Traxler, L., Herdy, J.R., Stefanoni, D., Eichhorner, S., Pelucchi, S., Szücs, A., Santagostino, A., Kim, Y., Agarwal, R.K., Schlachetzki, J.C.M., Glass, C.K., Lagerwall, J., Galasko, D., Gage, F.H., D'Alessandro, A., Mertens, J. Warburg-like metabolic transformation underlies neuronal degeneration in sporadic Alzheimer's disease. (2022) Cell Metabolism. DOI: 10.1016/j.cmet.2022.07.014

+ expand abstract

Ghaninia, M., Zhou, Y., Knauer, A.C., Schiestl, F.P., Sharpee, T.O., Smith, B.H. Hyperbolic odorant mixtures as a basis for more efficient signaling between flowering plants and bees. (2022) PLOS One. 17(7):e0270358. DOI: 10.1371/journal.pone.0270358

+ expand abstract

van Niekerk, E.A., Kawaguchi, R., Marques de Freria, C., Groeniger, K., Marchetto, M.C., Dupraz, S., Bradke, F., Geschwind, D.H., Gage, F.H., Tuszynski, M.H. Methods for culturing adult CNS neurons reveal a CNS conditioning effect. (2022) Cell Rep Methods. 2(7):100255. DOI: 10.1016/j.crmeth.2022.100255

+ expand abstract

Bae, T., Fasching, L., Wang, Y., Shin, J.H., Suvakov, M., Jang, Y., Norton, S., Dias, C., Mariani, J., Jourdon, A., Wu, F., Panda, A., Pattni, R., Chahine, Y., Yeh, R., Roberts, R.C., Huttner, A., Kleinman, J.E., Hyde, T.M., Straub, R.E., Walsh, C.A., , Urban, A.E., Leckman, J.F., Weinberger, D.R., Vaccarino, F.M., Abyzov, A., Walsh, C.A., Park, P.J., Sestan, N., Weinberger, D., Moran, J.V., Gage, F.H., Vaccarino, F.M., Gleeson, J., Mathern, G., Courchesne, E., Roy, S., Chess, A.J., Akbarian, S., Bizzotto, S., Coulter, M., Dias, C., D'Gama, A., Ganz, J., Hill, R., Huang, A.Y., Khoshkhoo, S., Kim, S., Lee, A., Lodato, M., Maury, E.A., Miller, M., Borges-Monroy, R., Rodin, R., Zhou, Z., Bohrson, C., Chu, C., Cortes-Ciriano, I., Dou, Y., Galor, A., Gulhan, D., Kwon, M., Luquette, J., Sherman, M., Viswanadham, V., Jones, A., Rosenbluh, C., Cho, S., Langmead, B., Thorpe, J., Erwin, J., Jaffe, A., McConnell, M., Narurkar, R., Paquola, A., Shin, J., Straub, R., Abyzov, A., Bae, T., Jang, Y., Wang, Y., Molitor, C., Peters, M., Linker, S., Reed, P., Wang, M., Urban, A., Zhou, B., Zhu, X., Pattni, R., Serres Amero, A., Juan, D., Lobon, I., Marques-Bonet, T., Solis Moruno, M., Garcia Perez, R., Povolotskaya, I., Soriano, E., Antaki, D., Averbuj, D., Ball, L., Breuss, M., Yang, X., Chung, C., Emery, S.B., Flasch, D.A., Kidd, J.M., Kopera, H.C., Kwan, K.Y., Mills, R.E., Moldovan, J.B., Sun, C., Zhao, X., Zhou, W., Frisbie, T.J., Cherskov, A., Fasching, L., Jourdon, A., Pochareddy, S., Scuderi, S. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. (2022) Science. 377(6605):511-517. DOI: 10.1126/science.abm6222

+ expand abstract

Lecoin, L., Dempsey, B., Garancher, A., Bourane, S., Ruffault, P.L., Morin-Surun, M.P., Rocques, N., Goulding, M., Eychène, A., Pouponnot, C., Fortin, G., Champagnat, J. Mafa-dependent GABAergic activity promotes mouse neonatal apneas. (2022) Nature Communications. 13(1):3284. DOI: 10.1038/s41467-022-30825-3

+ expand abstract

Ward, S., Riley, C., Carey, E.M., Nguyen, J., Esener, S., Nimmerjahn, A., Sirbuly, D.J. Electro-optical mechanically flexible coaxial microprobes for minimally invasive interfacing with intrinsic neural circuits. (2022) Nature Communications. 13(1):3286. DOI: 10.1038/s41467-022-30275-x

+ expand abstract

Zhang, Y., Roy, D.S., Zhu, Y., Chen, Y., Aida, T., Hou, Y., Shen, C., Lea, N.E., Schroeder, M.E., Skaggs, K.M., Sullivan, H.A., Fischer, K.B., Callaway, E.M., Wickersham, I.R., Dai, J., Li, X.M., Lu, Z., Feng, G. Targeting thalamic circuits rescues motor and mood deficits in PD mice. (2022) Nature. DOI: 10.1038/s41586-022-04806-x

+ expand abstract

Chen, Y., Rosen, B.Q., Sejnowski, T.J. Dynamical differential covariance recovers directional network structure in multiscale neural systems. (2022) Proceedings of the National Academy of Sciences of the United States of America. 119(24):e2117234119. DOI: 10.1073/pnas.2117234119

+ expand abstract

Grün, S., Li, J., McNaughton, B., Petersen, C., McCormick, D., Robson, D., Buzsáki, G., Harris, K., Sejnowski, T., Mrsic-Flogel, T., Lindén, H., Roland, P.E. Emerging principles of spacetime in brains: Meeting report on spatial neurodynamics. (2022) Neuron. 110(12):1894-1898. DOI: 10.1016/j.neuron.2022.05.018

+ expand abstract

Chen, Y., Bukhari, Q., Lin, T.W., Sejnowski, T.J. Functional connectivity of fMRI using differential covariance predicts structural connectivity and behavioral reaction times. (2022) Network neuroscience. 6(2):614-633. DOI: 10.1162/netn_a_00239

+ expand abstract

Zhou, Y., Sharpee, T.O. Using Global t-SNE to Preserve Intercluster Data Structure. (2022) Neural Computation.:1-15 DOI: 10.1162/neco_a_01504

+ expand abstract

Tadokoro, T., Bravo-Hernandez, M., Agashkov, K., Kobayashi, Y., Platoshyn, O., Navarro, M., Marsala, S., Miyanohara, A., Yoshizumi, T., Shigyo, M., Krotov, V., Juhas, S., Juhasova, J., Nguyen, D., Skalnikova, H.K., Motlik, J., Studenovska, H., Proks, V., Reddy, R., Driscoll, S.P., Glenn, T.D., Kemthong, T., Malaivijitnond, S., Tomori, Z., Vanicky, I., Kakinohana, M., Pfaff, S.L., Ciacci, J., Belan, P., Marsala, M. Precision spinal gene delivery-induced functional switch in nociceptive neurons reverses neuropathic pain. (2022) Molecular Therapy. DOI: 10.1016/j.ymthe.2022.04.023

+ expand abstract

Garcia, J.W., Bartol, T.M., Sejnowski, T.J. Multiscale modeling of presynaptic dynamics from molecular to mesoscale. (2022) PLOS Computational Biology. 18(5):e1010068. DOI: 10.1371/journal.pcbi.1010068

+ expand abstract

Chemical synapses exhibit a diverse array of internal mechanisms that affect the dynamics of transmission efficacy. Many of these processes, such as release of neurotransmitter and vesicle recycling, depend strongly on activity-dependent influx and accumulation of Ca2+. To model how each of these processes may affect the processing of information in neural circuits, and how their dysfunction may lead to disease states, requires a computationally efficient modelling framework, capable of generating accurate phenomenology without incurring a heavy computational cost per synapse. Constructing a phenomenologically realistic model requires the precise characterization of the timing and probability of neurotransmitter release. Difficulties arise in that functional forms of instantaneous release rate can be difficult to extract from noisy data without running many thousands of trials, and in biophysical synapses, facilitation of per-vesicle release probability is confounded by depletion. To overcome this, we obtained traces of free Ca2+ concentration in response to various action potential stimulus trains from a molecular MCell model of a hippocampal Schaffer collateral axon. Ca2+ sensors were placed at varying distance from a voltage-dependent calcium channel (VDCC) cluster, and Ca2+ was buffered by calbindin. Then, using the calcium traces to drive deterministic state vector models of synaptotagmin 1 and 7 (Syt-1/7), which respectively mediate synchronous and asynchronous release in excitatory hippocampal synapses, we obtained high-resolution profiles of instantaneous release rate, to which we applied functional fits. Synchronous vesicle release occurred predominantly within half a micron of the source of spike-evoked Ca2+ influx, while asynchronous release occurred more consistently at all distances. Both fast and slow mechanisms exhibited multi-exponential release rate curves, whose magnitudes decayed exponentially with distance from the Ca2+ source. Profile parameters facilitate on different time scales according to a single, general facilitation function. These functional descriptions lay the groundwork for efficient mesoscale modelling of vesicular release dynamics.

Li, J., Pinto-Duarte, A., Zander, M., Cuoco, M.S., Lai, C.Y., Osteen, J., Fang, L., Luo, C., Lucero, J.D., Gomez-Castanon, R., Nery, J.R., Silva-Garcia, I., Pang, Y., Sejnowski, T.J., Powell, S.B., Ecker, J.R., Mukamel, E.A., Behrens, M.M. Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3. (2022) Elife. 11. DOI: 10.7554/eLife.66909

+ expand abstract

Patiño, M., Lagos, W.N., Patne, N.S., Tasic, B., Zeng, H., Callaway, E.M. Single-cell transcriptomic classification of rabies-infected cortical neurons. (2022) Proceedings of the National Academy of Sciences of the United States of America. 119(22):e2203677119. DOI: 10.1073/pnas.2203677119

+ expand abstract

Oliinyk, O.S., Baloban, M., Clark, C.L., Carey, E., Pletnev, S., Nimmerjahn, A., Verkhusha, V.V. Single-domain near-infrared protein provides a scaffold for antigen-dependent fluorescent nanobodies. (2022) Nature Methods. DOI: 10.1038/s41592-022-01467-6

+ expand abstract

Nimmerjahn, A., Hirrlinger, J. Astrocyte regulation of neural circuit function and animal behavior. (2022) Glia. DOI: 10.1002/glia.24223

Shi, Y., Evans, R.M., Gage, F.H. Oleic acid regulates hippocampal neurogenesis as a TLX ligand. (2022) Proceedings of the National Academy of Sciences of the United States of America. 119(15):e2203038119. DOI: 10.1073/pnas.2203038119

+ expand abstract

Amin, N.D., Senturk, G., Hayashi, M., Driscoll, S.P., Pfaff, S.L. Detecting microRNA-mediated gene regulatory effects in murine neuronal subpopulations. (2022) STAR Protoc. 3(1):101130. DOI: 10.1016/j.xpro.2022.101130

+ expand abstract

Cook, J.R., Li, H., Nguyen, B., Huang, H.H., Mahdavian, P., Kirchgessner, M.A., Strassmann, P., Engelhardt, M., Callaway, E.M., Jin, X. Secondary auditory cortex mediates a sensorimotor mechanism for action timing. (2022) Nature Neuroscience. 25(3):330-344. DOI: 10.1038/s41593-022-01025-5

+ expand abstract

Hirrlinger, J., Nimmerjahn, A. A perspective on astrocyte regulation of neural circuit function and animal behavior. (2022) Glia. DOI: 10.1002/glia.24168

+ expand abstract

Zhang, Z., Cisneros, E., Lee, H.Y., Vu, J.P., Chen, Q., Benadof, C.N., Whitehill, J., Rouzbehani, R., Sy, D.T., Huang, J.S., Sejnowski, T.J., Jankovic, J., Factor, S., Goetz, C.G., Barbano, R.L., Perlmutter, J.S., Jinnah, H.A., Berman, B.D., Richardson, S.P., Stebbins, G.T., Comella, C.L., Peterson, D.A. Hold that pose: capturing cervical dystonia's head deviation severity from video. (2022) Ann Clin Transl Neurol. DOI: 10.1002/acn3.51549

+ expand abstract

Budzinski, R.C., Nguyen, T.T., Đoàn, J., Mináč, J., Sejnowski, T.J., Muller, L.E. Geometry unites synchrony, chimeras, and waves in nonlinear oscillator networks. (2022) Chaos. 32(3):031104. DOI: 10.1063/5.0078791

+ expand abstract

Nowotny, T., van Albada, S.J., Fellous, J.M., Haas, J.S., Jolivet, R.B., Metzner, C., Sharpee, T. Editorial: Advances in Computational Neuroscience. (2022) Frontiers in Computational Neuroscience. 15:824899. DOI: 10.3389/fncom.2021.824899

Abdelfattah, A.S., Ahuja, S., Akkin, T., Allu, S.R., Brake, J., Boas, D.A., Buckley, E.M., Campbell, R.E., Chen, A.I., Cheng, X., Čižmár, T., Costantini, I., De Vittorio, M., Devor, A., Doran, P.R., El Khatib, M., Emiliani, V., Fomin-Thunemann, N., Fainman, Y., Fernandez-Alfonso, T., Ferri, C.G.L., Gilad, A., Han, X., Harris, A., Hillman, E.M.C., Hochgeschwender, U., Holt, M.G., Ji, N., Kılıç, K., Lake, E.M.R., Li, L., Li, T., Mächler, P., Miller, E.W., Mesquita, R.C., Nadella, K.M.N.S., Nägerl, U.V., Nasu, Y., Nimmerjahn, A., Ondráčková, P., Pavone, F.S., Perez Campos, C., Peterka, D.S., Pisano, F., Pisanello, F., Puppo, F., Sabatini, B.L., Sadegh, S., Sakadzic, S., Shoham, S., Shroff, S.N., Silver, R.A., Sims, R.R., Smith, S.L., Srinivasan, V.J., Thunemann, M., Tian, L., Tian, L., Troxler, T., Valera, A., Vaziri, A., Vinogradov, S.A., Vitale, F., Wang, L.V., Uhlířová, H., Xu, C., Yang, C., Yang, M.H., Yellen, G., Yizhar, O., Zhao, Y. Neurophotonic tools for microscopic measurements and manipulation: status report. (2022) Neurophotonics. 9(Suppl 1):013001. DOI: 10.1117/1.NPh.9.S1.013001

+ expand abstract

Gage, F.H. Adult neurogenesis in neurological diseases. [Pubmed] (2021) Science. 374(6571):1049-1050. DOI: 10.1126/science.abm7468

+ expand abstract

Heard, K.J., Shokhirev, M.N., Becronis, C., Fredlender, C., Zahid, N., Le, A.T., Ji, Y., Skime, M., Nelson, T., Hall-Flavin, D., Weinshilboum, R., Gage, F.H., Vadodaria, K.C. Chronic cortisol differentially impacts stem cell-derived astrocytes from major depressive disorder patients. (2021) Transl Psychiatry. 11(1):608. DOI: 10.1038/s41398-021-01733-9

+ expand abstract

Wagner, M., Bartol, T.M., Sejnowski, T.J., Cauwenberghs, G. Markov Chain Abstractions of Electrochemical Reaction-Diffusion in Synaptic Transmission for Neuromorphic Computing. (2021) Frontiers in Neuroscience. 15:698635. DOI: 10.3389/fnins.2021.698635

+ expand abstract

Mendelsohn, R., Garcia, G.C., Bartol, T.M., Lee, C.T., Khandelwal, P., Liu, E., Spencer, D.J., Husar, A., Bushong, E.A., Phan, S., Perkins, G., Ellisman, M.H., Skupin, A., Sejnowski, T.J., Rangamani, P. Morphological principles of neuronal mitochondria. (2021) Journal of Comparative Neurology. DOI: 10.1002/cne.25254

+ expand abstract

Liu, H., Zhou, J., Tian, W., Luo, C., Bartlett, A., Aldridge, A., Lucero, J., Osteen, J.K., Nery, J.R., Chen, H., Rivkin, A., Castanon, R.G., Clock, B., Li, Y.E., Hou, X., Poirion, O.B., Preissl, S., Pinto-Duarte, A., O'Connor, C., Boggeman, L., Fitzpatrick, C., Nunn, M., Mukamel, E.A., Zhang, Z., Callaway, E.M., Ren, B., Dixon, J.R., Behrens, M.M., Ecker, J.R. DNA methylation atlas of the mouse brain at single-cell resolution. (2021) Nature. 598(7879):120-128. DOI: 10.1038/s41586-020-03182-8

+ expand abstract

Zhang, Z., Zhou, J., Tan, P., Pang, Y., Rivkin, A.C., Kirchgessner, M.A., Williams, E., Lee, C.T., Liu, H., Franklin, A.D., Miyazaki, P.A., Bartlett, A., Aldridge, A.I., Vu, M., Boggeman, L., Fitzpatrick, C., Nery, J.R., Castanon, R.G., Rashid, M., Jacobs, M.W., Ito-Cole, T., O'Connor, C., Pinto-Duartec, A., Dominguez, B., Smith, J.B., Niu, S.Y., Lee, K.F., Jin, X., Mukamel, E.A., Behrens, M.M., Ecker, J.R., Callaway, E.M. Epigenomic diversity of cortical projection neurons in the mouse brain. (2021) Nature. 598(7879):167-173. DOI: 10.1038/s41586-021-03223-w

+ expand abstract

Neuronal cell types are classically defined by their molecular properties, anatomy and functions. Although recent advances in single-cell genomics have led to high-resolution molecular characterization of cell type diversity in the brain, neuronal cell types are often studied out of the context of their anatomical properties. To improve our understanding of the relationship between molecular and anatomical features that define cortical neurons, here we combined retrograde labelling with single-nucleus DNA methylation sequencing to link neural epigenomic properties to projections. We examined 11,827 single neocortical neurons from 63 cortico-cortical and cortico-subcortical long-distance projections. Our results showed unique epigenetic signatures of projection neurons that correspond to their laminar and regional location and projection patterns. On the basis of their epigenomes, intra-telencephalic cells that project to different cortical targets could be further distinguished, and some layer 5 neurons that project to extra-telencephalic targets (L5 ET) formed separate clusters that aligned with their axonal projections. Such separation varied between cortical areas, which suggests that there are area-specific differences in L5 ET subtypes, which were further validated by anatomical studies. Notably, a population of cortico-cortical projection neurons clustered with L5 ET rather than intra-telencephalic neurons, which suggests that a population of L5 ET cortical neurons projects to both targets. We verified the existence of these neurons by dual retrograde labelling and anterograde tracing of cortico-cortical projection neurons, which revealed axon terminals in extra-telencephalic targets including the thalamus, superior colliculus and pons. These findings highlight the power of single-cell epigenomic approaches to connect the molecular properties of neurons with their anatomical and projection properties.

Davis, Z.W., Benigno, G.B., Fletterman, C., Desbordes, T., Steward, C., Sejnowski, T.J., Reynolds, J.H., Muller, L. Spontaneous traveling waves naturally emerge from horizontal fiber time delays and travel through locally asynchronous-irregular states. (2021) Nature Communications. 12(1):6057. DOI: 10.1038/s41467-021-26175-1

+ expand abstract

Li, Y., Kim, R., Sejnowski, T.J. Learning the Synaptic and Intrinsic Membrane Dynamics Underlying Working Memory in Spiking Neural Network Models. (2021) Neural Computation.:1-24 DOI: 10.1162/neco_a_01409

+ expand abstract

Lainscsek, C., Cash, S.S., Sejnowski, T.J., Kurths, J. Dynamical ergodicity DDA reveals causal structure in time series. (2021) Chaos. 31(10):103108. DOI: 10.1063/5.0063724

+ expand abstract

Kirchgessner, M.A., Franklin, A.D., Callaway, E.M. Distinct "driving" versus "modulatory" influences of different visual corticothalamic pathways. (2021) Current Biology. DOI: 10.1016/j.cub.2021.09.025

+ expand abstract

Gorbunova, V., Seluanov, A., Mita, P., McKerrow, W., Fenyö, D., Boeke, J.D., Linker, S.B., Gage, F.H., Kreiling, J.A., Petrashen, A.P., Woodham, T.A., Taylor, J.R., Helfand, S.L., Sedivy, J.M. The role of retrotransposable elements in ageing and age-associated diseases. https://rdcu.be/ct1i3 Full-text provided by the Springer Nature SharedIt content-sharing initiative [Pubmed] (2021) Nature. 596(7870):43-53. DOI: 10.1038/s41586-021-03542-y

+ expand abstract

Shadel, G.S., Adams, P.D., Berggren, W.T., Diedrich, J.K., Diffenderfer, K.E., Gage, F.H., Hah, N., Hansen, M., Hetzer, M.W., Molina, A.J.A., Manor, U., Marek, K., O'Keefe, D.D., Pinto, A.F.M., Sacco, A., Sharpee, T.O., Shokriev, M.N., Zambetti, S. The San Diego Nathan Shock Center: tackling the heterogeneity of aging. (2021) Geroscience. DOI: 10.1007/s11357-021-00426-x

+ expand abstract

Understanding basic mechanisms of aging holds great promise for developing interventions that prevent or delay many age-related declines and diseases simultaneously to increase human healthspan. However, a major confounding factor in aging research is the heterogeneity of the aging process itself. At the organismal level, it is clear that chronological age does not always predict biological age or susceptibility to frailty or pathology. While genetics and environment are major factors driving variable rates of aging, additional complexity arises because different organs, tissues, and cell types are intrinsically heterogeneous and exhibit different aging trajectories normally or in response to the stresses of the aging process (e.g., damage accumulation). Tackling the heterogeneity of aging requires new and specialized tools (e.g., single-cell analyses, mass spectrometry-based approaches, and advanced imaging) to identify novel signatures of aging across scales. Cutting-edge computational approaches are then needed to integrate these disparate datasets and elucidate network interactions between known aging hallmarks. There is also a need for improved, human cell-based models of aging to ensure that basic research findings are relevant to human aging and healthspan interventions. The San Diego Nathan Shock Center (SD-NSC) provides access to cutting-edge scientific resources to facilitate the study of the heterogeneity of aging in general and to promote the use of novel human cell models of aging. The center also has a robust Research Development Core that funds pilot projects on the heterogeneity of aging and organizes innovative training activities, including workshops and a personalized mentoring program, to help investigators new to the aging field succeed. Finally, the SD-NSC participates in outreach activities to educate the general community about the importance of aging research and promote the need for basic biology of aging research in particular.

Amin, N.D., Senturk, G., Costaguta, G., Driscoll, S., O'Leary, B., Bonanomi, D., Pfaff, S.L. A hidden threshold in motor neuron gene networks revealed by modulation of miR-218 dose. (2021) Neuron. DOI: 10.1016/j.neuron.2021.07.028

+ expand abstract

Hayes, T.L., Krishnan, G.P., Bazhenov, M., Siegelmann, H.T., Sejnowski, T.J., Kanan, C. Replay in Deep Learning: Current Approaches and Missing Biological Elements. (2021) Neural Computation.:1-44 DOI: 10.1162/neco_a_01433

+ expand abstract

Johnston, S., Parylak, S., Kim, S., Mac, N., Lim, C., Gallina, I., Bloyd, C., Newberry, A., Saavedra, C.D., Novak, O., Goncalves, J.T., Gage, F.H., Shtrahman, M. AAV ablates neurogenesis in the adult murine hippocampus. (2021) Elife. 10. DOI: 10.7554/eLife.59291

+ expand abstract

Nakahira, Y., Liu, Q., Sejnowski, T.J., Doyle, J.C. Diversity-enabled sweet spots in layered architectures and speed-accuracy trade-offs in sensorimotor control. (2021) Proceedings of the National Academy of Sciences of the United States of America. 118(22). DOI: 10.1073/pnas.1916367118

+ expand abstract

Tan, K., Kim, M.E., Song, H.W., Skarbrevik, D., Babajanian, E., Bedrosian, T.A., Gage, F.H., Wilkinson, M.F. The Rhox gene cluster suppresses germline LINE1 transposition. (2021) Proceedings of the National Academy of Sciences of the United States of America. 118(23). DOI: 10.1073/pnas.2024785118

+ expand abstract

Faulkner, R.L., Wall, N.R., Callaway, E.M., Cline, H.T. Application of Recombinant Rabies Virus to Xenopus Tadpole Brain. (2021) eNeuro. DOI: 10.1523/ENEURO.0477-20.2021

+ expand abstract

The Xenopus laevis experimental system has provided significant insight into the development and plasticity of neural circuits. Xenopus neuroscience research would be enhanced by additional tools to study neural circuit structure and function. Rabies viruses are powerful tools to label and manipulate neural circuits and have been widely used to study mesoscale connectomics. Whether rabies virus can be used to transduce neurons and express transgenes in Xenopus has not been systematically investigated. Glycoprotein-deleted rabies virus transduces neurons at the axon terminal and retrogradely labels their cell bodies. We show that glycoprotein-deleted rabies virus infects local and projection neurons in the Xenopus tadpole when directly injected into brain tissue. Pseudotyping glycoprotein-deleted rabies with EnvA restricts infection to cells with exogenous expression of the EnvA receptor, TVA. EnvA pseudotyped virus specifically infects tadpole neurons with promoter-driven expression of TVA, demonstrating its utility to label targeted neuronal populations. Neuronal cell types are defined by a combination of features including anatomical location, expression of genetic markers, axon projection sites, morphology, and physiological properties. We show that driving TVA expression in one hemisphere and injecting EnvA pseudotyped virus into the contralateral hemisphere, retrogradely labels neurons defined by cell body location and axon projection site. Using this approach, rabies can be used to identify cell types in Xenopus brain and simultaneously to express transgenes which enable monitoring or manipulation of neuronal activity. This makes rabies a valuable tool to study the structure and function of neural circuits in Xenopus.Studies in Xenopus have contributed a great deal to our understanding of brain circuit development and plasticity, regeneration, and hormonal regulation of behavior and metamorphosis. Here, we show that recombinant rabies virus transduces neurons in the Xenopus tadpole, enlarging the toolbox that can be applied to studying Xenopus brain. Rabies can be used for retrograde labeling and expression of a broad range of transgenes including fluorescent proteins for anatomical tracing and studying neuronal morphology, voltage or calcium indicators to visualize neuronal activity, and photo- or chemosensitive channels to control neuronal activity. The versatility of these tools enables diverse experiments to analyze and manipulate Xenopus brain structure and function, including mesoscale connectivity.

Schafer, S.T., Gage, F.H. To eat, or not to eat, that is the question: Neural stem cells escape phagocytosis in autism with macrocephaly. (2021) Proceedings of the National Academy of Sciences of the United States of America. 118(19). DOI: 10.1073/pnas.2104888118

Compans, B., Camus, C., Kallergi, E., Sposini, S., Martineau, M., Butler, C., Kechkar, A., Klaassen, R.V., Retailleau, N., Sejnowski, T.J., Smit, A.B., Sibarita, J.B., Bartol, T.M., Perrais, D., Nikoletopoulou, V., Choquet, D., Hosy, E. NMDAR-dependent long-term depression is associated with increased short term plasticity through autophagy mediated loss of PSD-95. (2021) Nature Communications. 12(1):2849. DOI: 10.1038/s41467-021-23133-9

+ expand abstract

Dias, G.P., Murphy, T., Stangl, D., Ahmet, S., Morisse, B., Nix, A., Aimone, L.J., Aimone, J.B., Kuro-O, M., Gage, F.H., Thuret, S. Intermittent fasting enhances long-term memory consolidation, adult hippocampal neurogenesis, and expression of longevity gene Klotho. (2021) Molecular Psychiatry. DOI: 10.1038/s41380-021-01102-4

+ expand abstract

Hsu, W.M., Kastner, D.B., Baccus, S.A., Sharpee, T.O. How inhibitory neurons increase information transmission under threshold modulation. (2021) Cell Reports. 35(8):109158. DOI: 10.1016/j.celrep.2021.109158

+ expand abstract

Reid, D.A., Reed, P.J., Schlachetzki, J.C.M., Nitulescu, I.I., Chou, G., Tsui, Chandran, S., Jones, J.R., Lu, A.T., McClain, C.A., Ooi, J.H., Wang, T.W., Lana, Linker, S.B., Ricciardulli, A.S., Lau, S., Schafer, S., Horvath, S., Dixon, J.R., Hah, N., Glass, C.K., Gage, F.H. Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons. (2021) Science. 372(6537):91-94. DOI: 10.1126/science.abb9032

+ expand abstract

Huang, Y., Happonen, K.E., Burrola, P.G., O'Connor, C., Hah, N., Huang, L., Nimmerjahn, A., Lemke, G. Microglia use TAM receptors to detect and engulf amyloid β plaques. (2021) Nature Immunology. DOI: 10.1038/s41590-021-00913-5

+ expand abstract

Osseward, P.J., Amin, N.D., Moore, J.D., Temple, B.A., Barriga, B.K., Bachmann, L.C., Beltran, F., Gullo, M., Clark, R.C., Driscoll, S.P., Pfaff, S.L., Hayashi, M. Conserved genetic signatures parcellate cardinal spinal neuron classes into local and projection subsets. (2021) Science. 372(6540):385-393. DOI: 10.1126/science.abe0690

+ expand abstract

Mertens, J., Herdy, J.R., Traxler, L., Schafer, S.T., Schlachetzki, J.C.M., Böhnke, L., Reid, D.A., Lee, H., Zangwill, D., Fernandes, D.P., Agarwal, R.K., Lucciola, R., Zhou-Yang, L., Karbacher, L., Edenhofer, F., Stern, S., Horvath, S., Paquola, A.C.M., Glass, C.K., Yuan, S.H., Ku, M., Szücs, A., Goldstein, L.S.B., Galasko, D., Gage, F.H. Age-dependent instability of mature neuronal fate in induced neurons from Alzheimer's patients. (2021) Cell Stem Cell. DOI: 10.1016/j.stem.2021.04.004

+ expand abstract

Schafer, S.T., Gage, F.H. The When and Where: Molecular and Cellular Convergence in Autism. (2021) Biological Psychiatry. 89(5):419-420. DOI: 10.1016/j.biopsych.2020.12.016

Mishra, H.K., Ying, N.M., Luis, A., Wei, H., Nguyen, M., Nakhla, T., Vandenburgh, S., Alda, M., Berrettini, W.H., Brennand, K.J., Calabrese, J.R., Coryell, W.H., Frye, M.A., Gage, F.H., Gershon, E.S., McInnis, M.G., Nievergelt, C.M., Nurnberger, J.I., Shilling, P.D., Oedegaard, K.J., Zandi, P.P., , Kelsoe, J.R., Welsh, D.K., McCarthy, M.J. Circadian rhythms in bipolar disorder patient-derived neurons predict lithium response: preliminary studies. (2021) Molecular Psychiatry. DOI: 10.1038/s41380-021-01048-7

+ expand abstract

Zhou, Y., Sharpee, T.O. Hyperbolic geometry of gene expression. (2021) iScience. 24(3):102225. DOI: 10.1016/j.isci.2021.102225

+ expand abstract

Nakatsuka, N., Heard, K.J., Faillétaz, A., Momotenko, D., Vörös, J., Gage, F.H., Vadodaria, K.C. Sensing serotonin secreted from human serotonergic neurons using aptamer-modified nanopipettes. (2021) Molecular Psychiatry. DOI: 10.1038/s41380-021-01066-5

+ expand abstract

Bedrosian, T.A., Houtman, J., Eguiguren, J.S., Ghassemzadeh, S., Rund, N., Novaresi, N.M., Hu, L., Parylak, S.L., Denli, A.M., Randolph-Moore, L., Namba, T., Gage, F.H., Toda, T. Lamin B1 decline underlies age-related loss of adult hippocampal neurogenesis. (2021) EMBO Journal. 40(3):e105819. DOI: 10.15252/embj.2020105819

+ expand abstract

Fukuda, S., Varshney, A., Fowler, B.J., Wang, S.B., Narendran, S., Ambati, K., Yasuma, T., Magagnoli, J., Leung, H., Hirahara, S., Nagasaka, Y., Yasuma, R., Apicella, I., Pereira, F., Makin, R.D., Magner, E., Liu, X., Sun, J., Wang, M., Baker, K., Marion, K.M., Huang, X., Baghdasaryan, E., Ambati, M., Ambati, V.L., Pandey, A., Pandya, L., Cummings, T., Banerjee, D., Huang, P., Yerramothu, P., Tolstonog, G.V., Held, U., Erwin, J.A., Paquola, A.C.M., Herdy, J.R., Ogura, Y., Terasaki, H., Oshika, T., Darwish, S., Singh, R.K., Mozaffari, S., Bhattarai, D., Kim, K.B., Hardin, J.W., Bennett, C.L., Hinton, D.R., Hanson, T.E., Röver, C., Parang, K., Kerur, N., Liu, J., Werner, B.C., Sutton, S.S., Sadda, S.R., Schumann, G.G., Gelfand, B.D., Gage, F.H., Ambati, J. Cytoplasmic synthesis of endogenous complementary DNA via reverse transcription and implications in age-related macular degeneration. (2021) Proceedings of the National Academy of Sciences of the United States of America. 118(6). DOI: 10.1073/pnas.2022751118

+ expand abstract

Singh, N., Bartol, T., Levine, H., Sejnowski, T., Nadkarni, S. Presynaptic endoplasmic reticulum regulates short-term plasticity in hippocampal synapses. (2021) Communications Biology. 4(1):241. DOI: 10.1038/s42003-021-01761-7

+ expand abstract

Vadodaria, K.C., Mendes, A.P.D., Mei, A., Racha, V., Erikson, G., Shokhirev, M.N., Oefner, R., Heard, K.J., McCarthy, M.J., Eyler, L., Kelsoe, J.R., Santos, R., Marchetto, M.C., Gage, F.H. Altered Neuronal Support and Inflammatory Response in Bipolar Disorder Patient-Derived Astrocytes. (2021) Stem Cell Reports. DOI: 10.1016/j.stemcr.2021.02.004

+ expand abstract

Santos, R., Linker, S.B., Stern, S., Mendes, A.P.D., Shokhirev, M.N., Erikson, G., Randolph-Moore, L., Racha, V., Kim, Y., Kelsoe, J.R., Bang, A.G., Alda, M., Marchetto, M.C., Gage, F.H. Deficient LEF1 expression is associated with lithium resistance and hyperexcitability in neurons derived from bipolar disorder patients. (2021) Molecular Psychiatry. DOI: 10.1038/s41380-020-00981-3

+ expand abstract

Zholudeva, L.V., Abraira, V.E., Satkunendrarajah, K., McDevitt, T.C., Goulding, M.D., Magnuson, D.S.K., Lane, M.A. Spinal Interneurons as Gatekeepers to Neuroplasticity after Injury or Disease. (2021) Journal of Neuroscience. DOI: 10.1523/JNEUROSCI.1654-20.2020

+ expand abstract

Trujillo, C.A., Adams, J.W., Negraes, P.D., Carromeu, C., Tejwani, L., Acab, A., Tsuda, B., Thomas, C.A., Sodhi, N., Fichter, K.M., Romero, S., Zanella, F., Sejnowski, T.J., Ulrich, H., Muotri, A.R. Pharmacological reversal of synaptic and network pathology in human MECP2-KO neurons and cortical organoids. (2021) EMBO Molecular Medicine. 13(1):e12523. DOI: 10.15252/emmm.202012523

+ expand abstract

Kim, R., Sejnowski, T.J. Strong inhibitory signaling underlies stable temporal dynamics and working memory in spiking neural networks. (2020) Nature Neuroscience. DOI: 10.1038/s41593-020-00753-w

+ expand abstract

Tsuda, B., Tye, K.M., Siegelmann, H.T., Sejnowski, T.J. A modeling framework for adaptive lifelong learning with transfer and savings through gating in the prefrontal cortex. (2020) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.2009591117

+ expand abstract

Peirs, C., Williams, S.G., Zhao, X., Arokiaraj, C.M., Ferreira, D.W., Noh, M.C., Smith, K.M., Halder, P., Corrigan, K.A., Gedeon, J.Y., Lee, S.J., Gatto, G., Chi, D., Ross, S.E., Goulding, M., Seal, R.P. Mechanical Allodynia Circuitry in the Dorsal Horn Is Defined by the Nature of the Injury. (2020) Neuron. DOI: 10.1016/j.neuron.2020.10.027

+ expand abstract

Gatto, G., Bourane, S., Ren, X., Di Costanzo, S., Fenton, P.K., Halder, P., Seal, R.P., Goulding, M.D. A Functional Topographic Map for Spinal Sensorimotor Reflexes. (2020) Neuron. DOI: 10.1016/j.neuron.2020.10.003

+ expand abstract

Wang, Q.W., Lu, S.Y., Liu, Y.N., Chen, Y., Wei, H., Shen, W., Chen, Y.F., Fu, C.L., Wang, Y.H., Dai, A., Huang, X., Gage, F.H., Xu, Q., Yao, J. Synaptotagmin-7 deficiency induces mania-like behavioral abnormalities through attenuating GluN2B activity. (2020) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.2016416117

+ expand abstract

Roome, R.B., Bourojeni, F.B., Mona, B., Rastegar-Pouyani, S., Blain, R., Dumouchel, A., Salesse, C., Thompson, W.S., Brookbank, M., Gitton, Y., Tessarollo, L., Goulding, M., Johnson, J.E., Kmita, M., Chédotal, A., Kania, A. Phox2a Defines a Developmental Origin of the Anterolateral System in Mice and Humans. (2020) Cell Reports. 33(8):108425. DOI: 10.1016/j.celrep.2020.108425

+ expand abstract

Davis, W., Muller, L., Martinez-Trujillo, J., Sejnowski, T., Reynolds, J.H. Spontaneous travelling cortical waves gate perception in behaving primates (2020) Nature. DOI: https://www.nature.com/articles/s41586-020-2802-y.

+ expand abstract

Sejnowski, T. Charles Gross: Mentor, Maestro, Mensch. (2020) Progress in Neurobiology.:101926 DOI: 10.1016/j.pneurobio.2020.101926

Choi, S., Hachisuka, J., Brett, M.A., Magee, A.R., Omori, Y., Iqbal, N.U., Zhang, D., DeLisle, M.M., Wolfson, R.L., Bai, L., Santiago, C., Gong, S., Goulding, M., Heintz, N., Koerber, H.R., Ross, S.E., Ginty, D.D. Parallel ascending spinal pathways for affective touch and pain. [Pubmed] (2020) Nature.:https://rdcu.be/b9ulT DOI: 10.1038/s41586-020-2860-1

+ expand abstract

Linker, S.B., Randolph-Moore, L., Kottilil, K., Qiu, F., Jaeger, B.N., Barron, J., Gage, F.H. Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus. (2020) Genome Research. DOI: 10.1101/gr.262196.120

+ expand abstract

Gonzalez, C.E., Lainscsek, C., Sejnowski, T.J., Letellier, C. Assessing observability of chaotic systems using Delay Differential Analysis. (2020) Chaos. 30(10):103113. DOI: 10.1063/5.0015533

+ expand abstract

Sobczak, F., He, Y., Sejnowski, T.J., Yu, X. Predicting the fMRI Signal Fluctuation with Recurrent Neural Networks Trained on Vascular Network Dynamics. (2020) Cerebral Cortex . DOI: 10.1093/cercor/bhaa260

+ expand abstract

Abbott, L.F., Bock, D.D., Callaway, E.M., Denk, W., Dulac, C., Fairhall, A.L., Fiete, I., Harris, K.M., Helmstaedter, M., Jain, V., Kasthuri, N., LeCun, Y., Lichtman, J.W., Littlewood, P.B., Luo, L., Maunsell, J.H.R., Reid, R.C., Rosen, B.R., Rubin, G.M., Sejnowski, T.J., Seung, H.S., Svoboda, K., Tank, D.W., Tsao, D., Van Essen, D.C. The Mind of a Mouse. (2020) Cell. 182(6):1372-1376. DOI: 10.1016/j.cell.2020.08.010

+ expand abstract

Lin, T.W., Chen, Y., Bukhari, Q., Krishnan, G.P., Bazhenov, M., Sejnowski, T.J. Differential Covariance: A New Method to Estimate Functional Connectivity in fMRI. (2020) Neural Computation.:1-33 DOI: 10.1162/neco_a_01323

+ expand abstract

Yang, C.F., Kim, E.J., Callaway, E.M., Feldman, J.L. Monosynaptic Projections to Excitatory and Inhibitory preBötzinger Complex Neurons. (2020) Frontiers in Neuroanatomy. 14:58. DOI: 10.3389/fnana.2020.00058

+ expand abstract

Figueiredo, T., Mendes, A.P.D., Moreira, D.P., Goulart, E., Oliveira, D., Kobayashi, G.S., Stern, S., Kok, F., Marchetto, M.C., Santos, R., Gage, F.H., Zatz, M. Inositol monophosphatase 1 (IMPA1) mutation in intellectual disability patients impairs neurogenesis but not gliogenesis. (2020) Molecular Psychiatry. DOI: 10.1038/s41380-020-00862-9

+ expand abstract

Kerman, B.E., Genoud, S., Kurt Vatandaslar, B., Denli, A.M., Ghosh, S.G., Xu, X., Yeo, G.W., Aimone, J.B., Gage, F.H. Motoneuron expression profiling identifies an association between an axonal splice variant of HDGF-related protein 3 and peripheral myelination. (2020) Journal of Biological Chemistry. DOI: 10.1074/jbc.RA120.014329

+ expand abstract

Ordyan, M., Bartol, T., Kennedy, M., Rangamani, P., Sejnowski, T. Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator. (2020) PLOS Computational Biology. 16(7):e1008015. DOI: 10.1371/journal.pcbi.1008015

+ expand abstract

Calmodulin-dependent kinase II (CaMKII) has long been known to play an important role in learning and memory as well as long term potentiation (LTP). More recently it has been suggested that it might be involved in the time averaging of synaptic signals, which can then lead to the high precision of information stored at a single synapse. However, the role of the scaffolding molecule, neurogranin (Ng), in governing the dynamics of CaMKII is not yet fully understood. In this work, we adopt a rule-based modeling approach through the Monte Carlo method to study the effect of Ca2+ signals on the dynamics of CaMKII phosphorylation in the postsynaptic density (PSD). Calcium surges are observed in synaptic spines during an EPSP and back-propagating action potential due to the opening of NMDA receptors and voltage dependent calcium channels. Using agent-based models, we computationally investigate the dynamics of phosphorylation of CaMKII monomers and dodecameric holoenzymes. The scaffolding molecule, Ng, when present in significant concentration, limits the availability of free calmodulin (CaM), the protein which activates CaMKII in the presence of calcium. We show that Ng plays an important modulatory role in CaMKII phosphorylation following a surge of high calcium concentration. We find a non-intuitive dependence of this effect on CaM concentration that results from the different affinities of CaM for CaMKII depending on the number of calcium ions bound to the former. It has been shown previously that in the absence of phosphatase, CaMKII monomers integrate over Ca2+ signals of certain frequencies through autophosphorylation (Pepke et al, Plos Comp. Bio., 2010). We also study the effect of multiple calcium spikes on CaMKII holoenzyme autophosphorylation, and show that in the presence of phosphatase, CaMKII behaves as a leaky integrator of calcium signals, a result that has been recently observed in vivo. Our models predict that the parameters of this leaky integrator are finely tuned through the interactions of Ng, CaM, CaMKII, and PP1, providing a mechanism to precisely control the sensitivity of synapses to calcium signals. Author Summary not valid for PLOS ONE submissions.

Ceto, S., Sekiguchi, K.J., Takashima, Y., Nimmerjahn, A., Tuszynski, M.H. Neural Stem Cell Grafts Form Extensive Synaptic Networks that Integrate with Host Circuits after Spinal Cord Injury. (2020) Cell Stem Cell. DOI: 10.1016/j.stem.2020.07.007

+ expand abstract

Goncalves, J., Bartol, T.M., Camus, C., Levet, F., Menegolla, A.P., Sejnowski, T.J., Sibarita, J.B., Vivaudou, M., Choquet, D., Hosy, E. Nanoscale co-organization and coactivation of AMPAR, NMDAR, and mGluR at excitatory synapses. (2020) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1922563117

+ expand abstract

Mansour, A.A., Schafer, S.T., Gage, F.H. Cellular complexity in brain organoids: Current progress and unsolved issues. (2020) Seminars in Cell & Developmental Biology. DOI: 10.1016/j.semcdb.2020.05.013

+ expand abstract

Filimon, F., Nelson, J.D., Sejnowski, T.J., Sereno, M.I., Cottrell, G.W. The ventral striatum dissociates information expectation, reward anticipation, and reward receipt. (2020) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1911778117

+ expand abstract

Kim, E.J., Zhang, Z., Huang, L., Ito-Cole, T., Jacobs, M.W., Juavinett, A.L., Senturk, G., Hu, M., Ku, M., Ecker, J.R., Callaway, E.M. Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population. (2020) Neuron. DOI: 10.1016/j.neuron.2020.04.018

+ expand abstract

Kirchgessner, M.A., Franklin, A.D., Callaway, E.M. Context-dependent and dynamic functional influence of corticothalamic pathways to first- and higher-order visual thalamus. (2020) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.2002080117

+ expand abstract

Wenderski, W., Wang, L., Krokhotin, A., Walsh, J.J., Li, H., Shoji, H., Ghosh, S., George, R.D., Miller, E.L., Elias, L., Gillespie, M.A., Son, E.Y., Staahl, B.T., Baek, S.T., Stanley, V., Moncada, C., Shipony, Z., Linker, S.B., Marchetto, M.C.N., Gage, F.H., Chen, D., Sultan, T., Zaki, M.S., Ranish, J.A., Miyakawa, T., Luo, L., Malenka, R.C., Crabtree, G.R., Gleeson, J.G. Loss of the neural-specific BAF subunit ACTL6B relieves repression of early response genes and causes recessive autism. (2020) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1908238117

+ expand abstract

Sun, G., Chiuppesi, F., Chen, X., Wang, C., Tian, E., Nguyen, J., Kha, M., Trinh, D., Zhang, H., Marchetto, M.C., Song, H., Ming, G.L., Gage, F.H., Diamond, D.J., Wussow, F., Shi, Y. Modeling Human Cytomegalovirus-Induced Microcephaly in Human iPSC-Derived Brain Organoids. (2020) Cell Reports Medicine. 1(1):100002. DOI: 10.1016/j.xcrm.2020.100002

+ expand abstract

DAS, A., Cash, S.S., Sejnowski, T.J. Heterogeneity of Preictal Dynamics in Human Epileptic Seizures. (2020) IEEE Access. 8:52738-52748. DOI: 10.1109/access.2020.2981017

+ expand abstract

It is generally understood that there is a preictal phase in the development of a seizure and this precictal period is the basis for seizure prediction attempts. The focus of this study is the preictal global spatiotemporal dynamics and its intra-patient variability. We analyzed preictal broadband brain connectivity from human electrocorticography (ECoG) recordings of 185 seizures (which included 116 clinical seizures) collected from 12 patients. ECoG electrodes record from only a part of the cortex, leaving large regions of the brain unobserved. Brain connectivity was therefore estimated using the sparse-plus-latent-regularized precision matrix (SLRPM) method, which calculates connectivity from partial correlations of the conditional statistics of the observed regions given the unobserved latent regions. Brain connectivity was quantified using eigenvector centrality (EC), from which a degree of heterogeneity was calculated for the preictal periods of all seizures in each patient. Results from the SLRPM method are compared to those from the sparse-regularized precision matrix (SRPM) and correlation methods, which do not account for the unobserved inputs when estimating brain connectivity. The degree of heterogeneity estimated by the SLRPM method is higher than those estimated by the SRPM and correlation methods for the preictal periods in most patients. These results reveal substantial heterogeneity or desynchronization among brain areas in the preictal period of human epileptic seizures. Furthermore, the SLRPM method identifies more onset channels from the preictal active electrodes compared to the SRPM and correlation methods. Finally, the correlation between the degree of heterogeneity and seizure severity of patients for SLRPM and SRPM methods were lower than that obtained from the correlation method. These results support recent findings suggesting that inhibitory neurons can have anti-seizure effects by inducing variability or heterogeneity across seizures. Understanding how this variability is linked to seizure initiation may lead to better predictions and controlling therapies.

Shen, W., Wang, Q.W., Liu, Y.N., Marchetto, M.C., Linker, S., Lu, S.Y., Chen, Y., Liu, C., Guo, C., Xing, Z., Shi, W., Kelsoe, J.R., Alda, M., Wang, H., Zhong, Y., Sui, S.F., Zhao, M., Yang, Y., Mi, S., Cao, L., Gage, F.H., Yao, J. Synaptotagmin-7 is a key factor for bipolar-like behavioral abnormalities in mice. (2020) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1918165117

+ expand abstract

Stern, S., Sarkar, A., Galor, D., Stern, T., Mei, A., Stern, Y., Mendes, A.P.D., Randolph-Moore, L., Rouleau, G., Bang, A.G., Santos, R., Alda, M., Marchetto, M.C., Gage, F.H. A Physiological Instability Displayed in Hippocampal Neurons Derived From Lithium-Nonresponsive Bipolar Disorder Patients. (2020) Biological Psychiatry. DOI: 10.1016/j.biopsych.2020.01.020

+ expand abstract

Sejnowski, T.J. The unreasonable effectiveness of deep learning in artificial intelligence. (2020) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1907373117

+ expand abstract

Wang, M., Wei, P.C., Lim, C.K., Gallina, I.S., Marshall, S., Marchetto, M.C., Alt, F.W., Gage, F.H. Increased Neural Progenitor Proliferation in a hiPSC Model of Autism Induces Replication Stress-Associated Genome Instability. (2020) Cell Stem Cell. 26(2):221-233.e6 . DOI: 10.1016/j.stem.2019.12.013

+ expand abstract

Nimmerjahn, A. Monitoring neuronal health. (2020) Science. 367(6477):510-511. DOI: 10.1126/science.aba4472

Fischer, K.B., Collins, H.K., Callaway, E.M. Sources of off-target expression from recombinase-dependent AAV vectors and mitigation with cross-over insensitive ATG-out vectors. (2019) Proceedings of the National Academy of Sciences of the United States of America. 116(52):27001–27010. DOI: 10.1073/pnas.1915974116

+ expand abstract

Marsala, M., Kamizato, K., Tadokoro, T., Navarro, M., Juhas, S., Juhasova, J., Marsala, S., Studenovska, H., Proks, V., Hazel, T., Johe, K., Kakinohana, M., Driscoll, S., Thomas, G., Pfaff, S., Ciacci, J. Spinal parenchymal occupation by neural stem cells after subpial delivery in adult immunodeficient rats. (2019) Stem Cells Translational Medicine. DOI: 10.1002/sctm.19-0156

+ expand abstract

Garcia, G.C., Bartol, T.M., Phan, S., Bushong, E.A., Perkins, G., Sejnowski, T.J., Ellisman, M.H., Skupin, A. Mitochondrial morphology provides a mechanism for energy buffering at synapses. (2019) Scientific Reports. 9(1):18306. DOI: 10.1038/s41598-019-54159-1

+ expand abstract

Jullié, D., Stoeber, M., Sibarita, J.B., Zieger, H.L., Bartol, T.M., Arttamangkul, S., Sejnowski, T.J., Hosy, E., von Zastrow, M. A Discrete Presynaptic Vesicle Cycle for Neuromodulator Receptors. (2019) Neuron. DOI: 10.1016/j.neuron.2019.11.016

+ expand abstract

Reichenstein, I., Eitan, C., Diaz-Garcia, S., Haim, G., Magen, I., Siany, A., Hoye, M.L., Rivkin, N., Olender, T., Toth, B., Ravid, R., Mandelbaum, A.D., Yanowski, E., Liang, J., Rymer, J.K., Levy, R., Beck, G., Ainbinder, E., Farhan, S.M.K., Lennox, K.A., Bode, N.M., Behlke, M.A., Möller, T., Saxena, S., Moreno, C.A.M., Costaguta, G., van Eijk, K.R., Phatnani, H., Al-Chalabi, A., Başak, A.N., van den Berg, L.H., Hardiman, O., Landers, J.E., Mora, J.S., Morrison, K.E., Shaw, P.J., Veldink, J.H., Pfaff, S.L., Yizhar, O., Gross, C., Brown, R.H., Ravits, J.M., Harms, M.B., Miller, T.M., Hornstein, E. Human genetics and neuropathology suggest a link between miR-218 and amyotrophic lateral sclerosis pathophysiology. (2019) Science Translational Medicine. 11(523). DOI: 10.1126/scitranslmed.aav5264

+ expand abstract

Pharris, M.C., Patel, N.M., VanDyk, T.G., Bartol, T.M., Sejnowski, T.J., Kennedy, M.B., Stefan, M.I., Kinzer-Ursem, T.L. A Multi-State Model of the CaMKII Dodecamer Suggests a Role for Calmodulin in Maintenance of Autophosphorylation. (2019) PLOS Computational Biology. 15(12):e1006941. DOI: 10.1371/journal.pcbi.1006941

+ expand abstract

Bravo-Hernandez, M., Tadokoro, T., Navarro, M.R., Platoshyn, O., Kobayashi, Y., Marsala, S., Miyanohara, A., Juhas, S., Juhasova, J., Skalnikova, H., Tomori, Z., Vanicky, I., Studenovska, H., Proks, V., Chen, P., Govea-Perez, N., Ditsworth, D., Ciacci, J.D., Gao, S., Zhu, W., Ahrens, E.T., Driscoll, S.P., Glenn, T.D., McAlonis-Downes, M., Da Cruz, S., Pfaff, S.L., Kaspar, B.K., Cleveland, D.W., Marsala, M. Spinal subpial delivery of AAV9 enables widespread gene silencing and blocks motoneuron degeneration in ALS. (2019) Nature Medicine. DOI: 10.1038/s41591-019-0674-1

+ expand abstract

Lainscsek, C., Rungratsameetaweemana, N., Cash, S.S., Sejnowski, T.J. Cortical chimera states predict epileptic seizures. (2019) Chaos. 29(12):121106. DOI: 10.1063/1.5139654

+ expand abstract

Ruiz-Martínez, , Bartol, T.M., Sejnowski, T.J., Tartakovsky, D.M. Stochastic self-tuning hybrid algorithm for reaction-diffusion systems. (2019) Journal of Chemical Physics. 151(24):244117. DOI: 10.1063/1.5125022

+ expand abstract

Zhu, Z., Mesci, P., Bernatchez, J.A., Gimple, R.C., Wang, X., Schafer, S.T., Wettersten, H.I., Beck, S., Clark, A.E., Wu, Q., Prager, B.C., Kim, L.J.Y., Dhanwani, R., Sharma, S., Garancher, A., Weis, S.M., Mack, S.C., Negraes, P.D., Trujillo, C.A., Penalva, L.O., Feng, J., Lan, Z., Zhang, R., Wessel, A.W., Dhawan, S., Diamond, M.S., Chen, C.C., Wechsler-Reya, R.J., Gage, F.H., Hu, H., Siqueira-Neto, J.L., Muotri, A.R., Cheresh, D.A., Rich, J.N. Zika Virus Targets Glioblastoma Stem Cells through a SOX2-Integrin αβ Axis. (2019) Cell Stem Cell. 26(2):187-204. DOI: 10.1016/j.stem.2019.11.016

+ expand abstract

Siddharth, S., Jung, T.P., Sejnowski, T.J. Impact of Affective Multimedia Content on the Electroencephalogram and Facial Expressions. (2019) Scientific Reports. 9(1):16295. DOI: 10.1038/s41598-019-52891-2

+ expand abstract

De la Fuente, I.M., Bringas, C., Malaina, I., Regner, B., Pérez-Samartín, A., Boyano, M.D., Fedetz, M., López, J.I., Pérez-Yarza, G., Cortes, J.M., Sejnowski, T. The nucleus does not significantly affect the migratory trajectories of amoeba in two-dimensional environments. (2019) Scientific Reports. 9(1):16369. DOI: 10.1038/s41598-019-52716-2

+ expand abstract

Nott, A., Holtman, I.R., Coufal, N.G., Schlachetzki, J.C.M., Yu, M., Hu, R., Han, C.Z., Pena, M., Xiao, J., Wu, Y., Keulen, Z., Pasillas, M.P., O'Connor, C., Nickl, C.K., Schafer, S.T., Shen, Z., Rissman, R.A., Brewer, J.B., Gosselin, D., Gonda, D.D., Levy, M.L., Rosenfeld, M.G., McVicker, G., Gage, F.H., Ren, B., Glass, C.K. Brain cell type-specific enhancer-promoter interactome maps and disease risk association. (2019) Science. 366(6469):1134-1139. DOI: 10.1126/science.aay0793

+ expand abstract

Patriarchi, T., Cho, J.R., Merten, K., Marley, A., Broussard, G.J., Liang, R., Williams, J., Nimmerjahn, A., von Zastrow, M., Gradinaru, V., Tian, L. Imaging neuromodulators with high spatiotemporal resolution using genetically encoded indicators. (2019) Nature Protocols. 14(12):3471–3505. DOI: 10.1038/s41596-019-0239-2

+ expand abstract

Vadodaria, K.C., Jones, J.R., Linker, S., Gage, F.H. Modeling Brain Disorders Using Induced Pluripotent Stem Cells. (2019) Cold Spring Harbor Perspectives in Biology. DOI: 10.1101/cshperspect.a035659

+ expand abstract

Sharpee, T.O., Berkowitz, J.A. Linking neural responses to behavior with information-preserving population vectors (2019) Current Opinion in Behavioral Sciences. 29:37-44. DOI: https://doi.org/10.1016/j.cobeha.2019.03.004

+ expand abstract

Litvina, E., Adams, A., Barth, A., Bruchez, M., Carson, J., Chung, J.E., Dupre, K.B., Frank, L.M., Gates, K.M., Harris, K.M., Joo, H., William Lichtman, J., Ramos, K.M., Sejnowski, T., Trimmer, J.S., White, S., Koroshetz, W. BRAIN Initiative: Cutting-Edge Tools and Resources for the Community. (2019) Journal of Neuroscience. 39(42):8275-8284. DOI: 10.1523/JNEUROSCI.1169-19.2019

+ expand abstract

The overarching goal of the NIH BRAIN (Brain Research through Advancing Innovative Neurotechnologies) Initiative is to advance the understanding of healthy and diseased brain circuit function through technological innovation. Core principles for this goal include the validation and dissemination of the myriad innovative technologies, tools, methods, and resources emerging from BRAIN-funded research. Innovators, BRAIN funding agencies, and non-Federal partners are working together to develop strategies for making these products usable, available, and accessible to the scientific community. Here, we describe several early strategies for supporting the dissemination of BRAIN technologies. We aim to invigorate a dialogue with the neuroscience research and funding community, interdisciplinary collaborators, and trainees about the existing and future opportunities for cultivating groundbreaking research products into mature, integrated, and adaptable research systems. Along with the accompanying Society for Neuroscience 2019 Mini-Symposium, "BRAIN Initiative: Cutting-Edge Tools and Resources for the Community," we spotlight the work of several BRAIN investigator teams who are making progress toward providing tools, technologies, and services for the neuroscience community. These tools access neural circuits at multiple levels of analysis, from subcellular composition to brain-wide network connectivity, including the following: integrated systems for EM- and florescence-based connectomics, advances in immunolabeling capabilities, and resources for recording and analyzing functional connectivity. Investigators describe how the resources they provide to the community will contribute to achieving the goals of the NIH BRAIN Initiative. Finally, in addition to celebrating the contributions of these BRAIN-funded investigators, the Mini-Symposium will illustrate the broader diversity of BRAIN Initiative investments in cutting-edge technologies and resources.

Kim, R., Li, Y., Sejnowski, T.J. Simple framework for constructing functional spiking recurrent neural networks. (2019) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1905926116

+ expand abstract

Lainscsek, C., Gonzalez, C.E., Sampson, A.L., Cash, S.S., Sejnowski, T.J. Causality detection in cortical seizure dynamics using cross-dynamical delay differential analysis. (2019) Chaos. 29(10):101103. DOI: 10.1063/1.5126125

+ expand abstract

Stern, S., Sarkar, A., Stern, T., Mei, A., Mendes, A.P.D., Stern, Y., Goldberg, G., Galor, D., Nguyen, T., Randolph-Moore, L., Kim, Y., Rouleau, G., Bang, A., Alda, M., Santos, R., Marchetto, M.C., Gage, F.H. Mechanisms Underlying the Hyperexcitability of CA3 and Dentate Gyrus Hippocampal Neurons Derived From Patients With Bipolar Disorder. (2019) Biological Psychiatry. DOI: 10.1016/j.biopsych.2019.09.018

+ expand abstract

Paixão, S., Loschek, L., Gaitanos, L., Alcalà Morales, P., Goulding, M., Klein, R. Identification of Spinal Neurons Contributing to the Dorsal Column Projection Mediating Fine Touch and Corrective Motor Movements. (2019) Neuron. 104(4):749-764. DOI: 10.1016/j.neuron.2019.08.029

+ expand abstract

Hafner, G., Witte, M., Guy, J., Subhashini, N., Fenno, L.E., Ramakrishnan, C., Kim, Y.S., Deisseroth, K., Callaway, E.M., Oberhuber, M., Conzelmann, K.K., Staiger, J.F. Mapping Brain-Wide Afferent Inputs of Parvalbumin-Expressing GABAergic Neurons in Barrel Cortex Reveals Local and Long-Range Circuit Motifs. (2019) Cell Reports. 28(13):3450-3461.e8. DOI: 10.1016/j.celrep.2019.08.064

+ expand abstract

Cugno, A., Bartol, T.M., Sejnowski, T.J., Iyengar, R., Rangamani, P. Geometric principles of second messenger dynamics in dendritic spines. (2019) Scientific Reports. 9(1):11676. DOI: 10.1038/s41598-019-48028-0

+ expand abstract

Amatya, D.N., Linker, S.B., Mendes, A.P.D., Santos, R., Erikson, G., Shokhirev, M.N., Zhou, Y., Sharpee, T., Gage, F.H., Marchetto, M.C., Kim, Y. Dynamical Electrical Complexity Is Reduced during Neuronal Differentiation in Autism Spectrum Disorder. (2019) Stem Cell Reports. DOI: 10.1016/j.stemcr.2019.08.001

+ expand abstract

Sharpee, T.O. An argument for hyperbolic geometry in neural circuits. (2019) Current Opinion in Neurobiology. 58:101-104. DOI: 10.1016/j.conb.2019.07.008

+ expand abstract

Juavinett, A.L., Kim, E.J., Collins, H.C., Callaway, E.M. A systematic topographical relationship between mouse lateral posterior thalamic neurons and their visual cortical projection targets. (2019) Journal of Comparative Neurology. 528(1):95-107. DOI: 10.1002/cne.24737

+ expand abstract

Wang, H.P., Garcia, J.W., Sabottke, C.F., Spencer, D., Sejnowski, T.J. Feedforward thalamocortical connectivity preserves stimulus timing information in sensory pathways. (2019) Journal of Neuroscience. DOI: 10.1523/JNEUROSCI.3165-17.2019

+ expand abstract

Reliable timing of cortical spikes in response to visual events is crucial in representing visual inputs to the brain. Spikes in the primary visual cortex need to occur at the same time within a repeated visual stimulus. Two classical mechanisms are employed by the cortex to enhance reliable timing. First, cortical neurons respond reliably to a restricted set of stimuli through their preference for certain patterns of membrane potential due to their intrinsic properties. Second, intracortical networking of excitatory and inhibitory neurons induces lateral inhibition that, through the timing and strength of IPSCs and EPSCs, produces sparse and reliably timed cortical neuron spike trains to be transmitted downstream. Here we describe a third mechanism that, through preferential thalamocortical synaptic connectivity, enhances the trial-to-trial timing precision of cortical spikes in the presence of spike train variability within each trial that is introduced between LGN neurons in the retino-thalamic pathway. Applying experimentally recorded LGN spike trains from the anesthetized cat to a detailed model of a spiny stellate V1 neuron, we found that output spike timing precision improved with increasing numbers of convergent LGN inputs. The improvement was consistent with the predicted proportionality of √???? for ???? LGN source neurons. We also found connectivity configurations that maximize reliability and that generate V1 cell output spike trains quantitatively similar to the experimental recordings. Our findings suggest a general principle, namely intra-trial variability among converging inputs, that increases stimulus response precision and is widely applicable to synaptically connected spiking neurons.The early visual pathway of the cat is favorable for studying the effects of trial-to-trial variability of synaptic inputs and intra-trial variability of thalamocortical connectivity on information transmission into the visual cortex. We have used a detailed model to show that there are preferred combinations of the number of thalamic afferents and the number of synapses per afferent that maximize the output reliability and spike-timing precision of cortical neurons. This provides additional insights into how synchrony in thalamic spike trains can reduce trial-to-trial variability to produce highly reliable reporting of sensory events to the cortex. The same principles may apply to other converging pathways where temporally jittered spike trains can reliably drive the downstream neuron and improve temporal precision.

Acton, D., Ren, X., Di Costanzo, S., Dalet, A., Bourane, S., Bertocchi, I., Eva, C., Goulding, M. Spinal Neuropeptide Y1 Receptor-Expressing Neurons Form an Essential Excitatory Pathway for Mechanical Itch. (2019) Cell Reports. 28(3):625-639.e6. DOI: 10.1016/j.celrep.2019.06.033

+ expand abstract

Bell, M., Bartol, T., Sejnowski, T., Rangamani, P. Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium. (2019) J. Gen. Physiol. DOI: 10.1085/jgp.201812261

+ expand abstract

Quraishi, I.H., Stern, S., Mangan, K.P., Zhang, Y., Ali, S.R., Mercier, M.R., Marchetto, M.C., McLachlan, M.J., Jones, E.M., Gage, F.H., Kaczmarek, L.K. An epilepsy-associated KCNT1 mutation enhances excitability of human iPSC-derived neurons by increasing Slack K currents. (2019) Journal of Neuroscience. DOI: 10.1523/JNEUROSCI.1628-18.2019

+ expand abstract

Mutations in the KCNT1 (Slack, K1.1) sodium-activated potassium channel produce severe epileptic encephalopathies. Expression in heterologous systems has shown that the disease-causing mutations give rise to channels that have increased current amplitude. It is not known, however, whether such gain of function occurs in human neurons, nor whether such increased K current is expected to suppress or increase the excitability of cortical neurons. Using genetically-engineered human iPSC-derived neurons, we have now found that sodium-dependent potassium currents are increased several-fold in neurons bearing a homozygous P924L mutation. In current clamp recordings, the increased K current in neurons with the P924L mutation acts to shorten the duration of action potentials and to increase the amplitude of the afterhyperpolarization that follows each action potential. Strikingly, the number of action potentials that were evoked by depolarizing currents as well as maximal firing rates were increased in neurons expressing the mutant channel. In networks of spontaneously active neurons, the mean firing rate, the occurrence of rapid bursts of action potentials, and the intensity of firing during the burst were all increased in neurons with the P924L Slack mutation. The feasibility of an increased K current to increase firing rates independent of any compensatory changes was validated by numerical simulations. Our findings indicate that gain-of-function in Slack K channels causes hyperexcitability in both isolated neurons and in neural networks and occurs by a cell-autonomous mechanism that does not require network interactions.KCNT1 mutations lead to severe epileptic encephalopathies for which there are no effective treatments. This study is the first demonstration that a KCNT1 mutation increases the Slack current in neurons. It also provides the first explanation for how this increased potassium current induces hyperexcitability, which could be the underlining factor causing seizures.

Pinto-Duarte, A., Roberts, A.J., Ouyang, K., Sejnowski, T.J. Impairments in remote memory caused by the lack of Type 2 IP receptors. (2019) Glia. DOI: 10.1002/glia.23679

+ expand abstract

Stern, S., Linker, S., Vadodaria, K.C., Marchetto, M.C., Gage, F.H. Prediction of Response to Drug Therapy in Psychiatric Disorders. (2019) Focus (American Psychiatric Publishing). 17(3):294-307. DOI: 10.1176/appi.focus.17304

+ expand abstract

Vadodaria, K.C., Ji, Y., Skime, M., Paquola, A., Nelson, T., Hall-Flavin, D., Fredlender, C., Heard, K.J., Deng, Y., Le, A.T., Dave, S., Fung, L., Li, X., Marchetto, M.C., Weinshilboum, R., Gage, F.H. Studying treatment resistance in depression using patient derived neurons in vitro. (2019) Molecular Psychiatry. 24(6):775. DOI: 10.1038/s41380-019-0424-2

Sommer, A., Marxreiter, F., Krach, F., Fadler, T., Grosch, J., Maroni, M., Graef, D., Eberhardt, E., Riemenschneider, M.J., Yeo, G.W., Kohl, Z., Xiang, W., Gage, F.H., Winkler, J., Prots, I., Winner, B. Th17 Lymphocytes Induce Neuronal Cell Death in a Human iPSC-Based Model of Parkinson's Disease. (2019) Cell Stem Cell. 24(6):1006. DOI: 10.1016/j.stem.2019.04.019

Nelson, N.A., Wang, X., Cook, D., Carey, E.M., Nimmerjahn, A. Imaging spinal cord activity in behaving animals. (2019) Experimental Neurology. 230:112974. DOI: 10.1016/j.expneurol.2019.112974

+ expand abstract

Zhou, J., Ma, J., Chen, Y., Cheng, C., Bao, B., Peng, J., Sejnowski, T.J., Dixon, J.R., Ecker, J.R. Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation. (2019) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1901423116

+ expand abstract

Oakley, B.A., Sejnowski, T.J. What we learned from creating one of the world's most popular MOOCs. (2019) NPJ Sci Learn. 4:7. DOI: 10.1038/s41539-019-0046-0

+ expand abstract

Garg, A.K., Li, P., Rashid, M.S., Callaway, E.M. Color and orientation are jointly coded and spatially organized in primate primary visual cortex. (2019) Science. 364(6447):1275-1279. DOI: 10.1126/science.aaw5868

+ expand abstract

Ernst, O.K., Bartol, T.M., Sejnowski, T.J., Mjolsness, E. Learning moment closure in reaction-diffusion systems with spatial dynamic Boltzmann distributions. (2019) Phys Rev E. 99(6-1):063315. DOI: 10.1103/PhysRevE.99.063315

+ expand abstract

Herdy, J., Schafer, S., Kim, Y., Ansari, Z., Zangwill, D., Ku, M., Paquola, A., Lee, H., Mertens, J., Gage, F.H. Chemical modulation of transcriptionally enriched signaling pathways to optimize the conversion of fibroblasts into neurons. (2019) Elife. 8. DOI: 10.7554/eLife.41356

+ expand abstract

Das, A., Sexton, D., Lainscsek, C., Cash, S.S., Sejnowski, T.J. Characterizing Brain Connectivity from Human Electrocorticography Recordings with Unobserved Inputs during Epileptic Seizures. (2019) Neural Computation.:1-56 DOI: 10.1162/neco_a_01205

+ expand abstract

Epilepsy is a neurological disorder characterized by the sudden occurrence of unprovoked seizures. There is extensive evidence of significantly altered brain connectivity during seizure periods in the human brain. Research on analyzing human brain functional connectivity during epileptic seizures has been limited predominantly to the use of the correlation method. However, spurious connectivity can be measured between two brain regions without having direct connection or interaction between them. Correlations can be due to the apparent interactions of the two brain regions resulting from common input from a third region, which may or may not be observed. Hence, researchers have recently proposed a sparse-plus-latent-regularized precision matrix (SLRPM) when there are unobserved or latent regions interacting with the observed regions. The SLRPM method yields partial correlations of the conditional statistics of the observed regions given the latent regions, thus identifying observed regions that are conditionally independent of both the observed and latent regions. We evaluate the performance of the methods using a spring-mass artificial network and assuming that some nodes cannot be observed, thus constituting the latent variables in the example. Several cases have been considered, including both sparse and dense connections, short-range and long-range connections, and a varying number of latent variables. The SLRPM method is then applied to estimate brain connectivity during epileptic seizures from human ECoG recordings. Seventy-four clinical seizures from five patients, all having complex partial epilepsy, were analyzed using SLRPM, and brain connectivity was quantified using modularity index, clustering coefficient, and eigenvector centrality. Furthermore, using a measure of latent inputs estimated by the SLRPM method, it was possible to automatically detect 72 of the 74 seizures with four false positives and find six seizures that were not marked manually.

Wang, M., Zhang, L., Gage, F.H. Modeling neuropsychiatric disorders using human induced pluripotent stem cells. (2019) Protein & Cell. 11(1):45-59. DOI: 10.1007/s13238-019-0638-8

+ expand abstract

Schafer, S.T., Gage, F.H. Nerve cells from the brain invade prostate tumours. (2019) Nature. 569(7758):637-638. DOI: 10.1038/d41586-019-01461-7

Gage, F.H. Adult neurogenesis in mammals. (2019) Science. 364(6443):827-828. DOI: 10.1126/science.aav6885

Siddharth, Patel, A.N., Jung, T.P., Sejnowski, T.J. A Wearable Multi-Modal Bio-Sensing System Towards Real-World Applications. (2019) IEEE Trans Biomed Eng. 66(4):1137-1147. DOI: 10.1109/TBME.2018.2868759

+ expand abstract

Tapia, J.J., Saglam, A.S., Czech, J., Kuczewski, R., Bartol, T.M., Sejnowski, T.J., Faeder, J.R. MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework. (2019) Methods in Molecular Biology. 1945:203-229. DOI: 10.1007/978-1-4939-9102-0_9

+ expand abstract

Gatto, G., Smith, K.M., Ross, S.E., Goulding, M. Neuronal diversity in the somatosensory system: bridging the gap between cell type and function. (2019) Current Opinion in Neurobiology. 56:167-174. DOI: 10.1016/j.conb.2019.03.002

+ expand abstract

Osseward, P.J., Pfaff, S.L. Cell type and circuit modules in the spinal cord. (2019) Current Opinion in Neurobiology. 56:175-184. DOI: 10.1016/j.conb.2019.03.003

+ expand abstract

Berkowitz, J.A., Sharpee, T.O. Quantifying Information Conveyed by Large Neuronal Populations. (2019) Neural Computation.:1-33 DOI: 10.1162/neco_a_01193

+ expand abstract

McBride, E.G., Lee, S.J., Callaway, E.M. Local and Global Influences of Visual Spatial Selection and Locomotion in Mouse Primary Visual Cortex. (2019) Current Biology. 29(10):1592-1605. DOI: 10.1016/j.cub.2019.03.065

+ expand abstract

Nudell, V., Wei, H., Nievergelt, C., Maihofer, A.X., Shilling, P., Alda, M., Berrettini, W.H., Brennand, K.J., Calabrese, J.R., Coryell, W.H., Covault, J.M., Frye, M.A., Gage, F., Gershon, E., McInnis, M.G., Nurnberger, J.I., Oedegaard, K.J., Shekhtman, T., Zandi, P.P., Kelsoe, J.R., McCarthy, M.J. Entrainment of Circadian Rhythms to Temperature Reveals Amplitude Deficits in Fibroblasts from Patients with Bipolar Disorder and Possible Links to Calcium Channels. (2019) Molecular Neuropsychiatry. 5(2):115-124. DOI: 10.1159/000497354

+ expand abstract

Wang, M., Zhang, L., Gage, F.H. Microglia, complement and schizophrenia. (2019) Nature Neuroscience. 22(3):333-334. DOI: 10.1038/s41593-019-0343-1

Farrelly, L.A., Thompson, R.E., Zhao, S., Lepack, A.E., Lyu, Y., Bhanu, N.V., Zhang, B., Loh, Y.E., Ramakrishnan, A., Vadodaria, K.C., Heard, K.J., Erikson, G., Nakadai, T., Bastle, R.M., Lukasak, B.J., Zebroski, H., Alenina, N., Bader, M., Berton, O., Roeder, R.G., Molina, H., Gage, F.H., Shen, L., Garcia, B.A., Li, H., Muir, T.W., Maze, I. Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3. (2019) Nature. DOI: 10.1038/s41586-019-1024-7

+ expand abstract

Bohaciakova, D., Hruska-Plochan, M., Tsunemoto, R., Gifford, W.D., Driscoll, S.P., Glenn, T.D., Wu, S., Marsala, S., Navarro, M., Tadokoro, T., Juhas, S., Juhasova, J., Platoshyn, O., Piper, D., Sheckler, V., Ditsworth, D., Pfaff, S.L., Marsala, M. A scalable solution for isolating human multipotent clinical-grade neural stem cells from ES precursors. (2019) Stem Cell Research & Therapy. 10(1):83. DOI: 10.1186/s13287-019-1163-7

+ expand abstract

Vadodaria, K.C., Ji, Y., Skime, M., Paquola, A.C., Nelson, T., Hall-Flavin, D., Heard, K.J., Fredlender, C., Deng, Y., Elkins, J., Dani, K., Le, A.T., Marchetto, M.C., Weinshilboum, R., Gage, F.H. Altered serotonergic circuitry in SSRI-resistant major depressive disorder patient-derived neurons. (2019) Molecular Psychiatry. DOI: 10.1038/s41380-019-0377-5

+ expand abstract

Bonanomi, D., Valenza, F., Chivatakarn, O., Sternfeld, M.J., Driscoll, S.P., Aslanian, A., Lettieri, K., Gullo, M., Badaloni, A., Lewcock, J.W., Hunter, T., Pfaff, S.L. p190RhoGAP Filters Competing Signals to Resolve Axon Guidance Conflicts. (2019) Neuron. DOI: 10.1016/j.neuron.2019.02.034

+ expand abstract

Marchetto, M.C., Hrvoj-Mihic, B., Kerman, B.E., Yu, D.X., Vadodaria, K.C., Linker, S.B., Narvaiza, I., Santos, R., Denli, A.M., Mendes, A.P., Oefner, R., Cook, J., McHenry, L., Grasmick, J.M., Heard, K., Fredlender, C., Randolph-Moore, L., Kshirsagar, R., Xenitopoulos, R., Chou, G., Hah, N., Muotri, A.R., Padmanabhan, K., Semendeferi, K., Gage, F.H. Species-specific maturation profiles of human, chimpanzee and bonobo neural cells. (2019) Elife. 8. DOI: 10.7554/eLife.37527

+ expand abstract

Aimon, S., Katsuki, T., Jia, T., Grosenick, L., Broxton, M., Deisseroth, K., Sejnowski, T.J., Greenspan, R.J. Fast near-whole-brain imaging in adult Drosophila during responses to stimuli and behavior. (2019) PLOS Biology. 17(2):e2006732. DOI: 10.1371/journal.pbio.2006732

+ expand abstract

Lainscsek, C., Sampson, A.L., Kim, R., Thomas, M.L., Man, K., Lainscsek, X., , Swerdlow, N.R., Braff, D.L., Sejnowski, T.J., Light, G.A. Nonlinear dynamics underlying sensory processing dysfunction in schizophrenia. (2019) Proceedings of the National Academy of Sciences of the United States of America. 116(9):3847-3852. DOI: 10.1073/pnas.1810572116

+ expand abstract

Bennett, C., Gale, S.D., Garrett, M.E., Newton, M.L., Callaway, E.M., Murphy, G.J., Olsen, S.R. Higher-Order Thalamic Circuits Channel Parallel Streams of Visual Information in Mice. (2019) Neuron. 102(2):477-492. DOI: 10.1016/j.neuron.2019.02.010

+ expand abstract

Lucassen, P.J., Toni, N., Kempermann, G., Frisen, J., Gage, F.H., Swaab, D.F. Limits to human neurogenesis-really? (2019) Molecular Psychiatry. DOI: 10.1038/s41380-018-0337-5

+ expand abstract

Schafer, S.T., Paquola, A.C.M., Stern, S., Gosselin, D., Ku, M., Pena, M., Kuret, T.J.M., Liyanage, M., Mansour, A.A., Jaeger, B.N., Marchetto, M.C., Glass, C.K., Mertens, J., Gage, F.H. Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons. (2019) Nature Neuroscience. DOI: 10.1038/s41593-018-0295-x

+ expand abstract

Eftekharzadeh, B., Daigle, J.G., Kapinos, L.E., Coyne, A., Schiantarelli, J., Carlomagno, Y., Cook, C., Miller, S.J., Dujardin, S., Amaral, A.S., Grima, J.C., Bennett, R.E., Tepper, K., DeTure, M., Vanderburg, C.R., Corjuc, B.T., DeVos, S.L., Gonzalez, J.A., Chew, J., Vidensky, S., Gage, F.H., Mertens, J., Troncoso, J., Mandelkow, E., Salvatella, X., Lim, R.Y.H., Petrucelli, L., Wegmann, S., Rothstein, J.D., Hyman, B.T. Tau Protein Disrupts Nucleocytoplasmic Transport in Alzheimer's Disease. (2019) Neuron. 101(2):349. DOI: 10.1016/j.neuron.2018.12.031

Padmanabhan, K., Osakada, F., Tarabrina, A., Kizer, E., Callaway, E.M., Gage, F.H., Sejnowski, T.J. Centrifugal Inputs to the Main Olfactory Bulb Revealed Through Whole Brain Circuit-Mapping. (2019) Frontiers in Neuroanatomy. 12:115. DOI: 10.3389/fnana.2018.00115

+ expand abstract

Yetman, M.J., Washburn, E., Hyun, J.H., Osakada, F., Hayano, Y., Zeng, H., Callaway, E.M., Kwon, H.B., Taniguchi, H. Intersectional monosynaptic tracing for dissecting subtype-specific organization of GABAergic interneuron inputs. (2019) Nature Neuroscience. 22:492-502. DOI: 10.1038/s41593-018-0322-y

+ expand abstract

Vadodaria, K.C., Ji, Y., Skime, M., Paquola, A., Nelson, T., Hall-Flavin, D., Fredlender, C., Heard, K.J., Deng, Y., Le, A.T., Dave, S., Fung, L., Li, X., Marchetto, M.C., Weinshilboum, R., Gage, F.H. Serotonin-induced hyperactivity in SSRI-resistant major depressive disorder patient-derived neurons. (2019) Molecular Psychiatry. DOI: 10.1038/s41380-019-0363-y

+ expand abstract

Sampson, A.L., Lainscsek, C., Gonzalez, C.E., Ulbert, I., Devinsky, O., Fabó, D., Halgren, E., Cash, S.S., Sejnowski, T.J. Delay Differential Analysis for Dynamical Sleep Spindle Detection. (2019) Journal of Neuroscience Methods. DOI: 10.1016/j.jneumeth.2019.01.009

+ expand abstract

Huang, T., Lin, S.H., Malewicz, N.M., Zhang, Y., Zhang, Y., Goulding, M., LaMotte, R.H., Ma, Q. Identifying the pathways required for coping behaviours associated with sustained pain. (2018) Nature. 565(7737):86-90. DOI: 10.1038/s41586-018-0793-8

+ expand abstract

Kim, Y., Vadodaria, K.C., Lenkei, Z., Kato, T., Gage, F.H., Marchetto, M.C., Santos, R. MITOCHONDRIA, METABOLISM AND REDOX MECHANISMS IN PSYCHIATRIC DISORDERS. (2018) Antioxidants & Redox Signaling. DOI: 10.1089/ars.2018.7606

+ expand abstract

McCarthy, M.J., Wei, H., Nievergelt, C.M., Stautland, A., Maihofer, A.X., Welsh, D.K., Shilling, P., Alda, M., Alliey-Rodriguez, N., Anand, A., Andreasson, O.A., Balaraman, Y., Berrettini, W.H., Bertram, H., Brennand, K.J., Calabrese, J.R., Calkin, C.V., Claasen, A., Conroy, C., Coryell, W.H., Craig, D.W., D'Arcangelo, N., Demodena, A., Djurovic, S., Feeder, S., Fisher, C., Frazier, N., Frye, M.A., Gage, F.H., Gao, K., Garnham, J., Gershon, E.S., Glazer, K., Goes, F., Goto, T., Harrington, G., Jakobsen, P., Kamali, M., Karberg, E., Kelly, M., Leckband, S.G., Lohoff, F., McInnis, M.G., Mondimore, F., Morken, G., Nurnberger, J.I., Obral, S., Oedegaard, K.J., Ortiz, A., Ritchey, M., Ryan, K., Schinagle, M., Schoeyen, H., Schwebel, C., Shaw, M., Shekhtman, T., Slaney, C., Stapp, E., Szelinger, S., Tarwater, B., Zandi, P.P., Kelsoe, J.R. Chronotype and cellular circadian rhythms predict the clinical response to lithium maintenance treatment in patients with bipolar disorder. (2018) Neuropsychopharmacology . DOI: 10.1038/s41386-018-0273-8

+ expand abstract

Suh, H., Zhou, Q.G., Fernandez-Carasa, I., Clemenson, G.D., Pons-Espinal, M., Ro, E.J., Marti, M., Raya, A., Gage, F.H., Consiglio, A. Long-Term Labeling of Hippocampal Neural Stem Cells by a Lentiviral Vector. (2018) Frontiers in Molecular Neuroscience. 11:415. DOI: 10.3389/fnmol.2018.00415

+ expand abstract

Dhande, O.S., Stafford, B.K., Franke, K., El-Danaf, R., Percival, K.A., Phan, A.H., Li, P., Hansen, B.J., Nguyen, P.L., Berens, P., Taylor, W.R., Callaway, E., Euler, T., Huberman, A.D. Molecular fingerprinting of On-Off direction selective retinal ganglion cells across species and relevance to primate visual circuits. (2018) Journal of Neuroscience. DOI: 10.1523/JNEUROSCI.1784-18.2018

+ expand abstract

The ability to detect moving objects is an ethologically salient function. Direction selective neurons have been identified in the retina, thalamus, and cortex of many species, but their homology has remained opaque. For instance, it is unknown whether direction-selective retinal ganglion cells (DSGCs) exist in primates, and if so, whether they are the equivalent to mouse and rabbit DSGCs. Here, we used a molecular/circuit approach in both sexes to address these issues. In mice, we identify the transcription factor Satb2 (Special AT-rich sequence-binding protein 2) as a selective marker for three RGC types: On-Off DSGCs encoding motion in either the anterior or posterior direction, a newly identified type of Off-DSGC and an Off-sustained RGC type. In rabbits, we find that expression of Satb2 is conserved in On-Off DSGCs; however, has evolved to include On-Off DSGCs encoding upward and downward motion, in addition to anterior and posterior motion. Next, we show that macaque RGCs express Satb2 most likely in a single type. We used rabies-virus based circuit mapping tools to reveal the identity of macaque Satb2-RGCs and discovered their dendritic arbors are relatively large and monostratified. Together, these data indicate Satb2-expressing On-Off DSGCs are likely not present in the primate retina. Moreover, if DSGCs are present in the primate retina, it is unlikely that they express Satb2.The ability to detect object-motion is a fundamental feature of almost all visual systems. Here we identify a novel marker for retinal ganglion cells encoding directional motion that is evolutionarily conserved in mice and rabbits, but not in primates. We show that in macaque monkeys the retinal ganglion cells that express this marker comprise a single type and are morphologically distinct from mouse and rabbit direction-selective retinal ganglion cells. Our findings indicate that On-Off direction-selective retinal neurons may have evolutionarily diverged in primates and more generally provide novel insight into the identity and organization of primate parallel visual pathways.

Kuhn, H.G., Toda, T., Gage, F.H. Adult hippocampal neurogenesis: a coming-of-age story. (2018) Journal of Neuroscience. DOI: 10.1523/JNEUROSCI.2144-18.2018

+ expand abstract

Reddy, G., Wong-Ng, J., Celani, A., Sejnowski, T.J., Vergassola, M. Glider soaring via reinforcement learning in the field. (2018) Nature. DOI: 10.1038/s41586-018-0533-0

+ expand abstract

Eftekharzadeh, B., Daigle, J.G., Kapinos, L.E., Coyne, A., Schiantarelli, J., Carlomagno, Y., Cook, C., Miller, S.J., Dujardin, S., Amaral, A.S., Grima, J.C., Bennett, R.E., Tepper, K., DeTure, M., Vanderburgh, C.R., Corjuc, B.T., DeVos, S.L., Gonzalez, J.A., Chew, J., Vidensky, S., Gage, F.H., Mertens, J., Troncoso, J., Mandelkow, E., Salvatella, X., Lim, R.Y.H., Petrucelli, L., Wegmann, S., Rothstein, J.D., Hyman, B.T. Tau Protein Disrupts Nucleocytoplasmic Transport in Alzheimer's Disease. (2018) Neuron. 99(5):925-940.e7. DOI: 10.1016/j.neuron.2018.07.039

+ expand abstract

Choi, S.H., Bylykbashi, E., Chatila, Z.K., Lee, S.W., Pulli, B., Clemenson, G.D., Kim, E., Rompala, A., Oram, M.K., Asselin, C., Aronson, J., Zhang, C., Miller, S.J., Lesinski, A., Chen, J.W., Kim, D.Y., van Praag, H., Spiegelman, B.M., Gage, F.H., Tanzi, R.E. Combined adult neurogenesis and BDNF mimic exercise effects on cognition in an Alzheimer's mouse model. (2018) Science. 361(6406). DOI: 10.1126/science.aan8821

+ expand abstract

Mertens, J., Reid, D., Lau, S., Kim, Y., Gage, F.H. Aging in a Dish: iPSC-Derived and Directly Induced Neurons for Studying Brain Aging and Age-Related Neurodegenerative Diseases. (2018) Annual Review of Genetics. 52:271-293. DOI: 10.1146/annurev-genet-120417-031534

+ expand abstract

Sejnowski, T. The prophet who foretold our future. (2018) Brain : A Journal of Neurology. 141(9):2820-2822. DOI: 10.1093/brain/awy212

Jaeger, B.N., Linker, S.B., Parylak, S.L., Barron, J.J., Gallina, I.S., Saavedra, C.D., Fitzpatrick, C., Lim, C.K., Schafer, S.T., Lacar, B., Jessberger, S., Gage, F.H. A novel environment-evoked transcriptional signature predicts reactivity in single dentate granule neurons. (2018) Nature Communications. 9(1):3084. DOI: 10.1038/s41467-018-05418-8

+ expand abstract

Zhang, Y., Liu, S., Zhang, Y.Q., Goulding, M., Wang, Y.Q., Ma, Q. Timing Mechanisms Underlying Gate Control by Feedforward Inhibition. (2018) Neuron. 99(5):941-955.e4. DOI: 10.1016/j.neuron.2018.07.026

+ expand abstract

van den Hurk, M., Erwin, J.A., Yeo, G.W., Gage, F.H., Bardy, C. Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells. (2018) Frontiers in Molecular Neuroscience. 11:261. DOI: 10.3389/fnmol.2018.00261

+ expand abstract

Zhou, Y., Smith, B.H., Sharpee, T.O. Hyperbolic geometry of the olfactory space. (2018) Science Advances. 4(8):eaaq1458. DOI: 10.1126/sciadv.aaq1458

+ expand abstract

Sommer, A., Maxreiter, F., Krach, F., Fadler, T., Grosch, J., Maroni, M., Graef, D., Eberhardt, E., Riemenschneider, M.J., Yeo, G.W., Kohl, Z., Xiang, W., Gage, F.H., Winkler, J., Prots, I., Winner, B. Th17 Lymphocytes Induce Neuronal Cell Death in a Human iPSC-Based Model of Parkinson's Disease. (2018) Cell Stem Cell. 23(1):123-131.e6. DOI: 10.1016/j.stem.2018.06.015

+ expand abstract

Linker, S.B., Hsu, J.Y., Pfaff, A., Amatya, D., Ko, S.M., Voter, S., Wong, Q., Gage, F.H. BrainImageR: Spatiotemporal gene set analysis referencing the human brain. (2018) Bioinformatics. DOI: 10.1093/bioinformatics/bty618

+ expand abstract

Ernst, O.K., Bartol, T., Sejnowski, T., Mjolsness, E. Learning dynamic Boltzmann distributions as reduced models of spatial chemical kinetics. (2018) J Chem Phys. 149(3):034107. DOI: 10.1063/1.5026403

+ expand abstract

Haas, K.T., Compans, B., Letellier, M., Bartol, T.M., Grillo-Bosch, D., Sejnowski, T.J., Sainlos, M., Choquet, D., Thoumine, O., Hosy, E. Pre-post synaptic alignment through neuroligin-1 tunes synaptic transmission efficiency. (2018) Elife. 7. DOI: 10.7554/eLife.31755

+ expand abstract

Siddharth, Jung, T.P., Sejnowski, T.J. Multi-modal Approach for Affective Computing. (2018) Conf Proc IEEE Eng Med Biol Soc. 2018:291-294. DOI: 10.1109/EMBC.2018.8512320

+ expand abstract

Kronenberg, Z.N., Fiddes, I.T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O.S., Underwood, J.G., Nelson, B.J., Chaisson, M.J.P., Dougherty, M.L., Munson, K.M., Hastie, A.R., Diekhans, M., Hormozdiari, F., Lorusso, N., Hoekzema, K., Qiu, R., Clark, K., Raja, A., Welch, A.E., Sorensen, M., Baker, C., Fulton, R.S., Armstrong, J., Graves-Lindsay, T.A., Denli, A.M., Hoppe, E.R., Hsieh, P., Hill, C.M., Pang, A.W.C., Lee, J., Lam, E.T., Dutcher, S.K., Gage, F.H., Warren, W.C., Shendure, J., Haussler, D., Schneider, V.A., Cao, H., Ventura, M., Wilson, R.K., Paten, B., Pollen, A., Eichler, E.E. High-resolution comparative analysis of great ape genomes. (2018) Science. 360(6393). DOI: 10.1126/science.aar6343

+ expand abstract

Krishnan, G.P., Rosen, B.Q., Chen, J.Y., Muller, L., Sejnowski, T.J., Cash, S.S., Halgren, E., Bazhenov, M. Thalamocortical and intracortical laminar connectivity determines sleep spindle properties. (2018) PLOS Computational Biology. 14(6):e1006171. DOI: 10.1371/journal.pcbi.1006171

+ expand abstract

Ueno, M., Nakamura, Y., Li, J., Gu, Z., Niehaus, J., Maezawa, M., Crone, S.A., Goulding, M., Baccei, M.L., Yoshida, Y. Corticospinal Circuits from the Sensory and Motor Cortices Differentially Regulate Skilled Movements through Distinct Spinal Interneurons. (2018) Cell Reports. 23(5):1286-1300.e7. DOI: 10.1016/j.celrep.2018.03.137

+ expand abstract

Sarkar, A., Mei, A., Paquola, A.C.M., Stern, S., Bardy, C., Klug, J.R., Kim, S., Neshat, N., Kim, H.J., Ku, M., Shokhirev, M.N., Adamowicz, D.H., Marchetto, M.C., Jappelli, R., Erwin, J.A., Padmanabhan, K., Shtrahman, M., Jin, X., Gage, F.H. Efficient Generation of CA3 Neurons from Human Pluripotent Stem Cells Enables Modeling of Hippocampal Connectivity In Vitro. (2018) Cell Stem Cell. 22(5):684-697.e9. DOI: 10.1016/j.stem.2018.04.009

+ expand abstract

Strnadel, J., Carromeu, C., Bardy, C., Navarro, M., Platoshyn, O., Glud, A.N., Marsala, S., Kafka, J., Miyanohara, A., Kato, T., Tadokoro, T., Hefferan, M.P., Kamizato, K., Yoshizumi, T., Juhas, S., Juhasova, J., Ho, C.S., Kheradmand, T., Chen, P., Bohaciakova, D., Hruska-Plochan, M., Todd, A.J., Driscoll, S.P., Glenn, T.D., Pfaff, S.L., Klima, J., Ciacci, J., Curtis, E., Gage, F.H., Bui, J., Yamada, K., Muotri, A.R., Marsala, M. Survival of syngeneic and allogeneic iPSC-derived neural precursors after spinal grafting in minipigs. (2018) Science Translational Medicine. 10(440). DOI: 10.1126/scitranslmed.aam6651

+ expand abstract

Stern, S., Linker, S., Vadodaria, K.C., Marchetto, M.C., Gage, F.H. Prediction of response to drug therapy in psychiatric disorders. (2018) Open Biology. 8(5). DOI: 10.1098/rsob.180031

+ expand abstract

Personalized medicine has become increasingly relevant to many medical fields, promising more efficient drug therapies and earlier intervention. The development of personalized medicine is coupled with the identification of biomarkers and classification algorithms that help predict the responses of different patients to different drugs. In the last 10 years, the Food and Drug Administration (FDA) has approved several genetically pre-screened drugs labelled as pharmacogenomics in the fields of oncology, pulmonary medicine, gastroenterology, haematology, neurology, rheumatology and even psychiatry. Clinicians have long cautioned that what may appear to be similar patient-reported symptoms may actually arise from different biological causes. With growing populations being diagnosed with different psychiatric conditions, it is critical for scientists and clinicians to develop precision medication tailored to individual conditions. Genome-wide association studies have highlighted the complicated nature of psychiatric disorders such as schizophrenia, bipolar disorder, major depression and autism spectrum disorder. Following these studies, association studies are needed to look for genomic markers of responsiveness to available drugs of individual patients within the population of a specific disorder. In addition to GWAS, the advent of new technologies such as brain imaging, cell reprogramming, sequencing and gene editing has given us the opportunity to look for more biomarkers that characterize a therapeutic response to a drug and to use all these biomarkers for determining treatment options. In this review, we discuss studies that were performed to find biomarkers of responsiveness to different available drugs for four brain disorders: bipolar disorder, schizophrenia, major depression and autism spectrum disorder. We provide recommendations for using an integrated method that will use available techniques for a better prediction of the most suitable drug.

Kim, Y., Zheng, X., Ansari, Z., Bunnell, M.C., Herdy, J.R., Traxler, L., Lee, H., Paquola, A.C.M., Blithikioti, C., Ku, M., Schlachetzki, J.C.M., Winkler, J., Edenhofer, F., Glass, C.K., Paucar, A.A., Jaeger, B.N., Pham, S., Boyer, L., Campbell, B.C., Hunter, T., Mertens, J., Gage, F.H. Mitochondrial Aging Defects Emerge in Directly Reprogrammed Human Neurons due to Their Metabolic Profile. (2018) Cell Reports. 23(9):2550-2558. DOI: 10.1016/j.celrep.2018.04.105

+ expand abstract

Patriarchi, T., Cho, J.R., Merten, K., Howe, M.W., Marley, A., Xiong, W.H., Folk, R.W., Broussard, G.J., Liang, R., Jang, M.J., Zhong, H., Dombeck, D., von Zastrow, M., Nimmerjahn, A., Gradinaru, V., Williams, J.T., Tian, L. Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors. (2018) Science. DOI: 10.1126/science.aat4422

+ expand abstract

Mansour, A.A., Gonçalves, J.T., Bloyd, C.W., Li, H., Fernandes, S., Quang, D., Johnston, S., Parylak, S.L., Jin, X., Gage, F.H. An in vivo model of functional and vascularized human brain organoids. (2018) Nature Biotechnology. DOI: 10.1038/nbt.4127

+ expand abstract

Luo, L., Callaway, E.M., Svoboda, K. Genetic Dissection of Neural Circuits: A Decade of Progress. (2018) Neuron. 98(2):256-281. DOI: 10.1016/j.neuron.2018.03.040

+ expand abstract

Toda, T., Parylak, S.L., Linker, S.B., Gage, F.H. The role of adult hippocampal neurogenesis in brain health and disease. (2018) Molecular Psychiatry. DOI: 10.1038/s41380-018-0036-2

+ expand abstract

Kempermann, G., Gage, F.H., Aigner, L., Song, H., Curtis, M.A., Thuret, S., Kuhn, H.G., Jessberger, S., Frankland, P.W., Cameron, H.A., Gould, E., Hen, R., Abrous, D.N., Toni, N., Schinder, A.F., Zhao, X., Lucassen, P.J., Frisén, J. Human Adult Neurogenesis: Evidence and Remaining Questions. (2018) Cell Stem Cell. DOI: 10.1016/j.stem.2018.04.004

+ expand abstract

Ruiz-Martínez, , Bartol, T.M., Sejnowski, T.J., Tartakovsky, D.M. Efficient models of polymerization applied to FtsZ ring assembly in . (2018) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1719391115

+ expand abstract

Moldakarimov, S., Bazhenov, M., Feldman, D.E., Sejnowski, T.J. Structured networks support sparse traveling waves in rodent somatosensory cortex. (2018) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1710202115

+ expand abstract

Wang, X., Pinto-Duarte, A., Behrens, M.M., Zhou, X., Sejnowski, T.J. Ketamine independently modulated power and phase-coupling of theta oscillations in Sp4 hypomorphic mice. (2018) PLOS One. 13(3):e0193446. DOI: 10.1371/journal.pone.0193446

+ expand abstract

Reduced expression of Sp4, the murine homolog of human SP4, a risk gene of multiple psychiatric disorders, led to N-methyl-D-aspartate (NMDA) hypofunction in mice, producing behavioral phenotypes reminiscent of schizophrenia, including hypersensitivity to ketamine. As accumulating evidence on molecular mechanisms and behavioral phenotypes established Sp4 hypomorphism as a promising animal model, systems-level neural circuit mechanisms of Sp4 hypomorphism, especially network dynamics underlying cognitive functions, remain poorly understood. We attempted to close this gap in knowledge in the present study by recording multi-channel epidural electroencephalogram (EEG) from awake behaving wildtype and Sp4 hypomorphic mice. We characterized cortical theta-band power and phase-coupling phenotypes, a known neural circuit substrate underlying cognitive functions, and further studied the effects of a subanesthetic dosage of ketamine on theta abnormalities unique to Sp4 hypomorphism. Sp4 hypomorphic mice had markedly elevated theta power localized frontally and parietally, a more pronounced theta phase progression along the neuraxis, and a stronger frontal-parietal theta coupling. Acute subanesthetic ketamine did not affect theta power in wildtype animals but significantly reduced it in Sp4 hypomorphic mice, nearly completely neutralizing their excessive frontal/parietal theta power. Ketamine did not significantly alter cortical theta phase progression in either wildtype or Sp4 hypomorphic animals, but significantly strengthened cortical theta phase-coupling in wildtype, but not in Sp4 hypomorphic animals. Our results suggested that the resting-state phenotypes of cortical theta oscillations unique to Sp4 hypomorphic mice closely mimicked a schizophrenic endophenotype. Further, ketamine independently modulated Sp4 hypomorphic anomalies in theta power and phase-coupling, suggesting separate underlying neural circuit mechanisms.

Mo, Z., Zhao, X., Liu, H., Hu, Q., Chen, X.Q., Pham, J., Wei, N., Liu, Z., Zhou, J., Burgess, R.W., Pfaff, S.L., Caskey, C.T., Wu, C., Bai, G., Yang, X.L. Aberrant GlyRS-HDAC6 interaction linked to axonal transport deficits in Charcot-Marie-Tooth neuropathy. (2018) Nature Communications. 9(1):1007. DOI: 10.1038/s41467-018-03461-z

+ expand abstract

Gatto, G., Goulding, M. Locomotion Control: Brainstem Circuits Satisfy the Need for Speed. (2018) Current Biology. 28(6):R256-R259. DOI: 10.1016/j.cub.2018.01.068

+ expand abstract

Muller, L., Chavane, F., Reynolds, J., Sejnowski, T.J. Cortical travelling waves: mechanisms and computational principles. (2018) Nature Reviews Neuroscience. DOI: 10.1038/nrn.2018.20

+ expand abstract

Bedrosian, T.A., Quayle, C., Novaresi, N., Gage, F.H. Early life experience drives structural variation of neural genomes in mice. (2018) Science. 359(6382):1395-1399. DOI: 10.1126/science.aah3378

+ expand abstract

Zhang, Y., Kastner, D.B., Baccus, S.A., Sharpee, T.O. Optimal Information Transmission by Overlapping Retinal Cell Mosaics. (2018) Proc Conf Inf Sci Syst. 2018. DOI: 10.1109/ciss.2018.8362310

+ expand abstract

Zheng, Y., Shen, W., Zhang, J., Yang, B., Liu, Y.N., Qi, H., Yu, X., Lu, S.Y., Chen, Y., Xu, Y.Z., Li, Y., Gage, F.H., Mi, S., Yao, J. CRISPR interference-based specific and efficient gene inactivation in the brain. (2018) Nature Neuroscience. DOI: 10.1038/s41593-018-0077-5

+ expand abstract

Kaya, C., Cheng, M.H., Block, E.R., Bartol, T.M., Sejnowski, T.J., Sorkin, A., Faeder, J.R., Bahar, I. Heterogeneities in Axonal Structure and Transporter Distribution Lower Dopamine Reuptake Efficiency. (2018) eNeuro. 5(1). DOI: 10.1523/ENEURO.0298-17.2017

+ expand abstract

Bromer, C., Bartol, T.M., Bowden, J.B., Hubbard, D.D., Hanka, D.C., Gonzalez, P.V., Kuwajima, M., Mendenhall, J.M., Parker, P.H., Abraham, W.C., Sejnowski, T.J., Harris, K.M. Long-term potentiation expands information content of hippocampal dentate gyrus synapses. (2018) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1716189115

+ expand abstract

Vadodaria, K.C., Amatya, D.N., Marchetto, M.C., Gage, F.H. Modeling psychiatric disorders using patient stem cell-derived neurons: a way forward. (2018) Genome Medicine. 10(1):1. DOI: 10.1186/s13073-017-0512-3

+ expand abstract

Wang, M., He, Y., Sejnowski, T.J., Yu, X. Brain-state dependent astrocytic Ca2+ signals are coupled to both positive and negative BOLD-fMRI signals. (2018) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1711692115

+ expand abstract

Hayashi, M., Hinckley, C.A., Driscoll, S.P., Moore, N.J., Levine, A.J., Hilde, K.L., Sharma, K., Pfaff, S.L. Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control. (2018) Neuron. DOI: 10.1016/j.neuron.2018.01.023

+ expand abstract

Sharpee, T.O. (2018) Oxford Research Encyclopedias, Neuroscience.:1-23 DOI: doi.org/10.1093/acrefore/9780190264086.013.110

+ expand abstract

Sensory systems exist to provide an organism with information about the state of the environment that can be used to guide future actions and decisions. Remarkably, two conceptually simple yet general theorems from information theory can be used to evaluate the performance of any sensory system. One theorem states that there is a minimal amount of energy that an organism has to spend in order to capture a given amount of information about the environment. The second theorem states that the maximum rate with which the organism can acquire resources from the environment, relative to its competitors, is limited by the information this organism collects about the environment, also relative to its competitors. These two theorems provide a scaffold for formulating and testing general principles of sensory coding but leave unanswered many important practical questions of implementation in neural circuits. These implementation questions have guided thinking in entire subfields of sensory neuroscience, and include: What features in the sensory environment should be measured? Given that we make decisions on a variety of time scales, how should one solve trade-offs between making simpler measurements to guide minimal decisions vs. more elaborate sensory systems that have to overcome multiple delays between sensation and action. Once we agree on the types of features that are important to represent, how should they be represented? How should resources be allocated between different stages of processing, and where is the impact of noise most damaging? Finally, one should consider trade-offs between implementing a fixed strategy vs. an adaptive scheme that readjusts resources based on current needs. Where adaptation is considered, under what conditions does it become optimal to switch strategies? Research over the past 60 years has provided answers to almost all of these questions but primarily in early sensory systems. Joining these answers into a comprehensive framework is a challenge that will help us understand who we are and how we can make better use of limited natural resources.

Koch, S.C., Del Barrio, M.G., Dalet, A., Gatto, G., Günther, T., Zhang, J., Seidler, B., Saur, D., Schüle, R., Goulding, M. RORβ Spinal Interneurons Gate Sensory Transmission during Locomotion to Secure a Fluid Walking Gait. (2017) Neuron. DOI: 10.1016/j.neuron.2017.11.011

+ expand abstract

Jaeger, B.N., Parylak, S.L., Gage, F.H. Mechanisms of dietary flavonoid action in neuronal function and neuroinflammation. (2017) Molecular Aspects of Medicine. DOI: 10.1016/j.mam.2017.11.003

+ expand abstract

Callaway, E.M., Garg, A.K. Brain technology: Neurons recorded en masse. (2017) Nature. 551(7679):172-173. DOI: 10.1038/551172a

Toda, T., Gage, F.H. Review: adult neurogenesis contributes to hippocampal plasticity. (2017) Cell and Tissue Research. DOI: 10.1007/s00441-017-2735-4

+ expand abstract

O'Donnell, C., Gonçalves, J.T., Portera-Cailliau, C., Sejnowski, T.J. Beyond excitation/inhibition imbalance in multidimensional models of neural circuit changes in brain disorders. (2017) Elife. 6. DOI: 10.7554/eLife.26724

+ expand abstract

Snijders, C., de Nijs, L., Baker, D.G., Hauger, R.L., van den Hove, D., Kenis, G., Nievergelt, C.M., Boks, M.P., Vermetten, E., Gage, F.H., Rutten, B.P.F. MicroRNAs in Post-traumatic Stress Disorder. (2017) Current Topics in Behavioral Neurosciences. DOI: 10.1007/7854_2017_32

+ expand abstract

Atencio, C.A., Sharpee, T.O. Multidimensional receptive field processing by cat primary auditory cortical neurons. (2017) Neuroscience. 359:130-141. DOI: 10.1016/j.neuroscience.2017.07.003

+ expand abstract

Topol, A., Zhu, S., Hartley, B.J., English, J., Hauberg, M.E., Tran, N., Rittenhouse, C.A., Simone, A., Ruderfer, D.M., Johnson, J., Readhead, B., Hadas, Y., Gochman, P.A., Wang, Y.C., Shah, H., Cagney, G., Rapoport, J., Gage, F.H., Dudley, J.T., Sklar, P., Mattheisen, M., Cotter, D., Fang, G., Brennand, K.J. Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. (2017) Cell Reports. 20(10):2525. DOI: 10.1016/j.celrep.2017.08.073

Wu, J., Capelli, P., Bouvier, J., Goulding, M., Arber, S., Fortin, G. A V0 core neuronal circuit for inspiration. (2017) Nature Communications. 8(1):544. DOI: 10.1038/s41467-017-00589-2

+ expand abstract

Toda, T., Hsu, J.Y., Linker, S.B., Hu, L., Schafer, S.T., Mertens, J., Jacinto, F.V., Hetzer, M.W., Gage, F.H. Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor Cells. (2017) Cell Stem Cell. 21:618–634. DOI: 10.1016/j.stem.2017.08.012

+ expand abstract

Shahsavani, M., Pronk, R.J., Falk, R., Lam, M., Moslem, M., Linker, S.B., Salma, J., Day, K., Schuster, J., Anderlid, B.M., Dahl, N., Gage, F.H., Falk, A. An in vitro model of lissencephaly: expanding the role of DCX during neurogenesis. (2017) Molecular Psychiatry. DOI: 10.1038/mp.2017.175

+ expand abstract

Koch, S.C., Acton, D., Goulding, M. Spinal Circuits for Touch, Pain, and Itch. (2017) Annual Review of Physiology. DOI: 10.1146/annurev-physiol-022516-034303

+ expand abstract

Sharpee, T.O. On texture, form, and fixational eye movements. (2017) Current Opinion in Neurobiology. 46:228-233. DOI: 10.1016/j.conb.2017.09.002

+ expand abstract

Li, Y., Wang, F., Chen, Y., Cichocki, A., Sejnowski, T. The Effects of Audiovisual Inputs on Solving the Cocktail Party Problem in the Human Brain: An fMRI Study. (2017) Cerebral Cortex .:1-15 DOI: 10.1093/cercor/bhx235

+ expand abstract

Holter, K.E., Kehlet, B., Devor, A., Sejnowski, T.J., Dale, A.M., Omholt, S.W., Ottersen, O.P., Nagelhus, E.A., Mardal, K.A., Pettersen, K.H. Interstitial solute transport in 3D reconstructed neuropil occurs by diffusion rather than bulk flow. (2017) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1706942114

+ expand abstract

Vadodaria, K.C., Stern, S., Marchetto, M.C., Gage, F.H. Serotonin in psychiatry: in vitro disease modeling using patient-derived neurons. (2017) Cell and Tissue Research. DOI: 10.1007/s00441-017-2670-4

+ expand abstract

Linker, S.B., Marchetto, M.C., Narvaiza, I., Denli, A.M., Gage, F.H. Examining non-LTR retrotransposons in the context of the evolving primate brain. (2017) BMC Biology. 15(1):68. DOI: 10.1186/s12915-017-0409-z

+ expand abstract

Luo, C., Keown, C.L., Kurihara, L., Zhou, J., He, Y., Li, J., Castanon, R., Lucero, J., Nery, J.R., Sandoval, J.P., Bui, B., Sejnowski, T.J., Harkins, T.T., Mukamel, E.A.*, Behrens, M.M.*, Ecker, J.R.* Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. (2017) Science. 357(6351):600-604. DOI: 10.1126/science.aan3351

+ expand abstract

Lainscsek, C., Weyhenmeyer, J., Cash, S.S., Sejnowski, T.J. Delay Differential Analysis of Seizures in Multichannel Electrocorticography Data. (2017) Neural Computation.:1-38 DOI: 10.1162/neco_a_01009

+ expand abstract

Lin, T.W., Das, A., Krishnan, G.P., Bazhenov, M., Sejnowski, T.J. Differential Covariance: A New Class of Methods to Estimate Sparse Connectivity from Neural Recordings. (2017) Neural Computation.:1-52 DOI: 10.1162/neco_a_01008

+ expand abstract

Kaardal, J.T., Theunissen, F.E., Sharpee, T.O. A Low-Rank Method for Characterizing High-Level Neural Computations. (2017) Frontiers in Computational Neuroscience. 11:68. DOI: 10.3389/fncom.2017.00068

+ expand abstract

Newkirk, S.J., Lee, S., Grandi, F.C., Gaysinskaya, V., Rosser, J.M., Vanden Berg, N., Hogarth, C.A., Marchetto, M.C.N., Muotri, A.R., Griswold, M.D., Ye, P., Bortvin, A., Gage, F.H., Boeke, J.D., An, W. Intact piRNA pathway prevents L1 mobilization in male meiosis. (2017) Proceedings of the National Academy of Sciences of the United States of America. 114(28):E5635-E5644. DOI: 10.1073/pnas.1701069114

+ expand abstract

Lainscsek, C., Muller, L.E., Sampson, A.L., Sejnowski, T.J. Analytical Derivation of Nonlinear Spectral Effects and 1/f Scaling Artifact in Signal Processing of Real-World Data. (2017) Neural Computation. 29(7):2004-2020. DOI: 10.1162/NECO_a_00979

+ expand abstract

Veit, J., Hakim, R., Jadi, M.P., Sejnowski, T.J., Adesnik, H. Cortical gamma band synchronization through somatostatin interneurons. (2017) Nature Neuroscience. 20(7):951-959. DOI: 10.1038/nn.4562

+ expand abstract

Hurtado-López, J., Ramirez-Moreno, D.F., Sejnowski, T.J. Decision-making neural circuits mediating social behaviors : An attractor network model. (2017) Journal of Computational Neuroscience. DOI: 10.1007/s10827-017-0654-8

+ expand abstract

Sharpee, T.O. Optimizing Neural Information Capacity through Discretization. (2017) Neuron. 94(5):954-960. DOI: 10.1016/j.neuron.2017.04.044

+ expand abstract

Rowekamp, R.J., Sharpee, T.O. Cross-orientation suppression in visual area V2. (2017) Nature Communications. 8:15739. DOI: 10.1038/ncomms15739

+ expand abstract

Santos, R., Vadodaria, K.C., Jaeger, B.N., Mei, A., Lefcochilos-Fogelquist, S., Mendes, A.P.D., Erikson, G., Shokhirev, M., Randolph-Moore, L., Fredlender, C., Dave, S., Oefner, R., Fitzpatrick, C., Pena, M., Barron, J.J., Ku, M., Denli, A.M., Kerman, B.E., Charnay, P., Kelsoe, J.R., Marchetto, M.C., Gage, F.H. Differentiation of Inflammation-Responsive Astrocytes from Glial Progenitors Generated from Human Induced Pluripotent Stem Cells. (2017) Stem Cell Reports. 8(6):1757-1769. DOI: 10.1016/j.stemcr.2017.05.011

+ expand abstract

Gosselin, D., Skola, D., Coufal, N.G., Holtman, I.R., Schlachetzki, J.C.M., Sajti, E., Jaeger, B.N., O'Connor, C., Fitzpatrick, C., Pasillas, M.P., Pena, M., Adair, A., Gonda, D.D., Levy, M.L., Ransohoff, R.M., Gage, F.H., Glass, C.K. An environment-dependent transcriptional network specifies human microglia identity. (2017) Science. 356(6344). DOI: 10.1126/science.aal3222

+ expand abstract

Cheng, L., Duan, B., Huang, T., Zhang, Y., Chen, Y., Britz, O., Garcia-Campmany, L., Ren, X., Vong, L., Lowell, B.B., Goulding, M., Wang, Y., Ma, Q. Identification of spinal circuits involved in touch-evoked dynamic mechanical pain. (2017) Nature Neuroscience. 20(6):804-814. DOI: 10.1038/nn.4549

+ expand abstract

Marchetto, M.C., Belinson, H., Tian, Y., Freitas, B.C., Fu, C., Vadodaria, K., Beltrao-Braga, P., Trujillo, C.A., Mendes, A.P.D., Padmanabhan, K., Nunez, Y., Ou, J., Ghosh, H., Wright, R., Brennand, K., Pierce, K., Eichenfield, L., Pramparo, T., Eyler, L., Barnes, C.C., Courchesne, E., Geschwind, D.H., Gage, F.H., Wynshaw-Boris, A., Muotri, A.R. Altered proliferation and networks in neural cells derived from idiopathic autistic individuals. (2017) Molecular Psychiatry. 22(6):820-835. DOI: 10.1038/mp.2016.95

+ expand abstract

Ishii, S., Torii, M., Son, A.I., Rajendraprasad, M., Morozov, Y.M., Kawasawa, Y.I., Salzberg, A.C., Fujimoto, M., Brennand, K., Nakai, A., Mezger, V., Gage, F.H., Rakic, P., Hashimoto-Torii, K. Variations in brain defects result from cellular mosaicism in the activation of heat shock signalling. (2017) Nature Communications. 8:15157. DOI: 10.1038/ncomms15157

+ expand abstract

McConnell, M.J., Moran, J.V., Abyzov, A., Akbarian, S., Bae, T., Cortes-Ciriano, I., Erwin, J.A., Fasching, L., Flasch, D.A., Freed, D., Ganz, J., Jaffe, A.E., Kwan, K.Y., Kwon, M., Lodato, M.A., Mills, R.E., Paquola, A.C.M., Rodin, R.E., Rosenbluh, C., Sestan, N., Sherman, M.A., Shin, J.H., Song, S., Straub, R.E., Thorpe, J., Weinberger, D.R., Urban, A.E., Zhou, B., Gage, F.H., Lehner, T., Senthil, G., Walsh, C.A., Chess, A., Courchesne, E., Gleeson, J.G., Kidd, J.M., Park, P.J., Pevsner, J., Vaccarino, F.M. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. (2017) Science. 356(6336). DOI: 10.1126/science.aal1641

+ expand abstract

Peterson, D.A., Sejnowski, T.J. A Dynamic Circuit Hypothesis for the Pathogenesis of Blepharospasm. (2017) Frontiers in Computational Neuroscience. 11:11. DOI: 10.3389/fncom.2017.00011

+ expand abstract

Blepharospasm (sometimes called "benign essential blepharospasm," BEB) is one of the most common focal dystonias. It involves involuntary eyelid spasms, eye closure, and increased blinking. Despite the success of botulinum toxin injections and, in some cases, pharmacologic or surgical interventions, BEB treatments are not completely efficacious and only symptomatic. We could develop principled strategies for preventing and reversing the disease if we knew the pathogenesis of primary BEB. The objective of this study was to develop a conceptual framework and dynamic circuit hypothesis for the pathogenesis of BEB. The framework extends our overarching theory for the multifactorial pathogenesis of focal dystonias (Peterson et al., 2010) to incorporate a two-hit rodent model specifically of BEB (Schicatano et al., 1997). We incorporate in the framework three features critical to cranial motor control: (1) the joint influence of motor cortical regions and direct descending projections from one of the basal ganglia output nuclei, the substantia nigra pars reticulata, on brainstem motor nuclei, (2) nested loops composed of the trigeminal blink reflex arc and the long sensorimotor loop from trigeminal nucleus through thalamus to somatosensory cortex back through basal ganglia to the same brainstem nuclei modulating the reflex arc, and (3) abnormalities in the basal ganglia dopamine system that provide a sensorimotor learning substrate which, when combined with patterns of increased blinking, leads to abnormal sensorimotor mappings manifest as BEB. The framework explains experimental data on the trigeminal reflex blink excitability (TRBE) from Schicatano et al. and makes predictions that can be tested in new experimental animal models based on emerging genetics in dystonia, including the recently characterized striatal-specific D1R dopamine transduction alterations caused by the GNAL mutation. More broadly, the model will provide a guide for future efforts to mechanistically link multiple factors in the pathogenesis of BEB and facilitate simulations of how exogenous manipulations of the pathogenic factors could ultimately be used to prevent and reverse the disorder.

Das, A., Sampson, A.L., Lainscsek, C., Muller, L., Lin, W., Doyle, J.C., Cash, S.S., Halgren, E., Sejnowski, T.J. Interpretation of the Precision Matrix and Its Application in Estimating Sparse Brain Connectivity during Sleep Spindles from Human Electrocorticography Recordings. (2017) Neural Computation. 29(3):603-642. DOI: 10.1162/NECO_a_00936

+ expand abstract

Kim, Y., Santos, R., Gage, F.H., Marchetto, M.C. Molecular Mechanisms of Bipolar Disorder: Progress Made and Future Challenges. (2017) Frontiers in Cellular Neuroscience. 11:30. DOI: 10.3389/fncel.2017.00030

+ expand abstract

Ramsay, L., Marchetto, M.C., Caron, M., Chen, S.H., Busche, S., Kwan, T., Pastinen, T., Gage, F.H., Bourque, G. Conserved expression of transposon-derived non-coding transcripts in primate stem cells. (2017) BMC Genomics. 18(1):214. DOI: 10.1186/s12864-017-3568-y

+ expand abstract

Stern, S., Santos, R., Marchetto, M.C., Mendes, A.P., Rouleau, G.A., Biesmans, S., Wang, Q.W., Yao, J., Charnay, P., Bang, A.G., Alda, M., Gage, F.H. Neurons derived from patients with bipolar disorder divide into intrinsically different sub-populations of neurons, predicting the patients' responsiveness to lithium. (2017) Molecular Psychiatry. DOI: 10.1038/mp.2016.260

+ expand abstract

Bipolar disorder (BD) is a progressive psychiatric disorder with more than 3% prevalence worldwide. Affected individuals experience recurrent episodes of depression and mania, disrupting normal life and increasing the risk of suicide greatly. The complexity and genetic heterogeneity of psychiatric disorders have challenged the development of animal and cellular models. We recently reported that hippocampal dentate gyrus (DG) neurons differentiated from induced pluripotent stem cell (iPSC)-derived fibroblasts of BD patients are electrophysiologically hyperexcitable. Here we used iPSCs derived from Epstein-Barr virus-immortalized B-lymphocytes to verify that the hyperexcitability of DG-like neurons is reproduced in this different cohort of patients and cells. Lymphocytes are readily available for research with a large number of banked lines with associated patient clinical description. We used whole-cell patch-clamp recordings of over 460 neurons to characterize neurons derived from control individuals and BD patients. Extensive functional analysis showed that intrinsic cell parameters are very different between the two groups of BD neurons, those derived from lithium (Li)-responsive (LR) patients and those derived from Li-non-responsive (NR) patients, which led us to partition our BD neurons into two sub-populations of cells and suggested two different subdisorders. Training a Naïve Bayes classifier with the electrophysiological features of patients whose responses to Li are known allows for accurate classification with more than 92% success rate for a new patient whose response to Li is unknown. Despite their very different functional profiles, both populations of neurons share a large, fast after-hyperpolarization (AHP). We therefore suggest that the large, fast AHP is a key feature of BD and a main contributor to the fast, sustained spiking abilities of BD neurons. Confirming our previous report with fibroblast-derived DG neurons, chronic Li treatment reduced the hyperexcitability in the lymphoblast-derived LR group but not in the NR group, strengthening the validity and utility of this new human cellular model of BD.Molecular Psychiatry advance online publication, 28 February 2017; doi:10.1038/mp.2016.260.

Flynn, J.R., Conn, V.L., Boyle, K.A., Hughes, D.I., Watanabe, M., Velasquez, T., Goulding, M.D., Callister, R.J., Graham, B.A. Anatomical and Molecular Properties of Long Descending Propriospinal Neurons in Mice. (2017) Frontiers in Neuroanatomy. 11:5. DOI: 10.3389/fnana.2017.00005

+ expand abstract

Sternfeld, M.J., Hinckley, C.A., Moore, N.J., Pankratz, M.T., Hilde, K.L., Driscoll, S.P., Hayashi, M., Amin, N.D., Bonanomi, D., Gifford, W.D., Sharma, K., Goulding, M., Pfaff, S.L. Speed and segmentation control mechanisms characterized in rhythmically-active circuits created from spinal neurons produced from genetically-tagged embryonic stem cells. (2017) Elife. 6. DOI: 10.7554/eLife.21540

+ expand abstract

Tufail, Y., Cook, D., Fourgeaud, L., Powers, C.J., Merten, K., Clark, C.L., Hoffman, E., Ngo, A., Sekiguchi, K.J., O'Shea, C.C., Lemke, G., Nimmerjahn, A. Phosphatidylserine Exposure Controls Viral Innate Immune Responses by Microglia. (2017) Neuron. 93(3):574-586.e8. DOI: 10.1016/j.neuron.2016.12.021

+ expand abstract

Adamowicz, D.H., Roy, S., Salmon, D.P., Galasko, D.R., Hansen, L.A., Masliah, E., Gage, F.H. Hippocampal α-Synuclein in Dementia with Lewy Bodies Contributes to Memory Impairment and Is Consistent with Spread of Pathology. (2017) Journal of Neuroscience. 37(7):1675-1684. DOI: 10.1523/JNEUROSCI.3047-16.2016

+ expand abstract

Despite considerable research to uncover them, the anatomic and neuropathologic correlates of memory impairment in dementia with Lewy bodies (DLB) remain unclear. While some studies have implicated Lewy bodies in the neocortex, others have pointed to α-synuclein pathology in the hippocampus. We systematically examined hippocampal Lewy pathology and its distribution in hippocampal subfields in 95 clinically and neuropathologically characterized human cases of DLB, finding that α-synuclein pathology was highest in two hippocampal-related subregions: the CA2 subfield and the entorhinal cortex (EC). While the EC had numerous classic somatic Lewy bodies, CA2 contained mainly Lewy neurites in presumed axon terminals, suggesting the involvement of the EC → CA2 circuitry in the pathogenesis of DLB symptoms. Clinicopathological correlations with measures of verbal and visual memory supported a role for EC Lewy pathology, but not CA2, in causing these memory deficits. Lewy pathology in CA1-the main output region for CA2-correlated best with results from memory testing despite a milder pathology. This result indicates that CA1 may be more functionally relevant than CA2 in the context of memory impairment in DLB. These correlations remained significant after controlling for several factors, including concurrent Alzheimer's pathology (neuritic plaques and neurofibrillary tangles) and the interval between time of testing and time of death. Our data suggest that although hippocampal Lewy pathology in DLB is predominant in CA2 and EC, memory performance correlates most strongly with CA1 burden.SIGNIFICANCE STATEMENT This study provides a detailed neuropathologic analysis of hippocampal Lewy pathology in human patients with autopsy-confirmed dementia with Lewy bodies. The approach-informed by regional molecular markers, concurrent Alzheimer's pathology analysis, and relevant clinical data-helps tease out the relative contribution of Lewy pathology to memory dysfunction in the disease. Levels of Lewy pathology were found to be highest in the hippocampal CA2 subregion and entorhinal cortex, implicating a potentially overlooked circuit in disease pathogenesis. However, correlation with memory performance was strongest with CA1. This unexpected finding suggests that Lewy pathology must reach a critical burden across hippocampal circuitry to contribute to memory dysfunction beyond that related to other factors, notably coexisting Alzheimer's disease tau pathology.

Sarkar, A., Marchetto, M.C., Gage, F.H. Synaptic activity: An emerging player in schizophrenia. (2017) Brain Research. 1656:68-75. DOI: 10.1016/j.brainres.2015.12.028

+ expand abstract

Paquola, A.C.M., Erwin, J.A., Gage, F.H. Insights into the role of somatic mosaicism in the brain. (2017) Current Opinion in Systems Biology. 1:90-94. DOI: 10.1016/j.coisb.2016.12.004

+ expand abstract

Juavinett, A.L., Nauhaus, I., Garrett, M.E., Zhuang, J., Callaway, E.M. Automated identification of mouse visual areas with intrinsic signal imaging. (2017) Nature Protocols. 12(1):32-43. DOI: 10.1038/nprot.2016.158

+ expand abstract

O'Donnell, C., Gonçalves, J.T., Whiteley, N., Portera-Cailliau, C., Sejnowski, T.J. The Population Tracking Model: A Simple, Scalable Statistical Model for Neural Population Data. (2017) Neural Computation. 29(1):50-93. DOI: 10.1162/NECO_a_00910

+ expand abstract

Han, J., Gage, F.H. A role for miR-19 in the migration of adult-born neurons and schizophrenia. (2016) Neurogenesis. 3(1):e1251873. DOI: 10.1080/23262133.2016.1251873

+ expand abstract

Williams, A.H., O'Donnell, C., Sejnowski, T.J., O'Leary, T. Dendritic trafficking faces physiologically critical speed-precision tradeoffs. (2016) Elife. 5. DOI: 10.7554/eLife.20556

+ expand abstract

Sharpee, T.O. Plasticity to the Rescue. (2016) Neuron. 92(5):935-936. DOI: 10.1016/j.neuron.2016.11.042

+ expand abstract

Suzuki, K., Tsunekawa, Y., Hernandez-Benitez, R., Wu, J., Zhu, J., Kim, E.J., Hatanaka, F., Yamamoto, M., Araoka, T., Li, Z., Kurita, M., Hishida, T., Li, M., Aizawa, E., Guo, S., Chen, S., Goebl, A., Soligalla, R.D., Qu, J., Jiang, T., Fu, X., Jafari, M., Esteban, C.R., Berggren, W.T., Lajara, J., Nuñez-Delicado, E., Guillen, P., Campistol, J.M., Matsuzaki, F., Liu, G.H., Magistretti, P., Zhang, K., Callaway, E.M., Zhang, K., Belmonte, J.C. In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. (2016) Nature. 540(7631):144-149. DOI: 10.1038/nature20565

+ expand abstract

Dimidschstein, J., Chen, Q., Tremblay, R., Rogers, S.L., Saldi, G.A., Guo, L., Xu, Q., Liu, R., Lu, C., Chu, J., Grimley, J.S., Krostag, A.R., Kaykas, A., Avery, M.C., Rashid, M.S., Baek, M., Jacob, A.L., Smith, G.B., Wilson, D.E., Kosche, G., Kruglikov, I., Rusielewicz, T., Kotak, V.C., Mowery, T.M., Anderson, S.A., Callaway, E.M., Dasen, J.S., Fitzpatrick, D., Fossati, V., Long, M.A., Noggle, S., Reynolds, J.H., Sanes, D.H., Rudy, B., Feng, G., Fishell, G. A viral strategy for targeting and manipulating interneurons across vertebrate species. (2016) Nature Neuroscience. 19(12):1743-1749. DOI: 10.1038/nn.4430

+ expand abstract

Erwin, J.A., Paquola, A.C., Singer, T., Gallina, I., Novotny, M., Quayle, C., Bedrosian, T.A., Alves, F.I., Butcher, C.R., Herdy, J.R., Sarkar, A., Lasken, R.S., Muotri, A.R., Gage, F.H. L1-associated genomic regions are deleted in somatic cells of the healthy human brain. (2016) Nature Neuroscience. 19(12):1583-1591. DOI: 10.1038/nn.4388

+ expand abstract

Kuczala, A., Sharpee, T.O. Eigenvalue spectra of large correlated random matrices. (2016) Phys Rev E. 94(5-1):050101. DOI: 10.1103/PhysRevE.94.050101

+ expand abstract

Muller, L., Piantoni, G., Koller, D., Cash, S.S., Halgren, E., Sejnowski, T.J. Rotating waves during human sleep spindles organize global patterns of activity that repeat precisely through the night. (2016) Elife. 5. DOI: 10.7554/eLife.17267

+ expand abstract

Gonçalves, J.T., Schafer, S.T., Gage, F.H. Adult Neurogenesis in the Hippocampus: From Stem Cells to Behavior. (2016) Cell. 167(4):897-914. DOI: 10.1016/j.cell.2016.10.021

+ expand abstract

Vadodaria, K.C., Marchetto, M.C., Mertens, J., Gage, F.H. Generating human serotonergic neurons in vitro: Methodological advances. (2016) Bioessays. 38(11):1123-1129. DOI: 10.1002/bies.201600127

+ expand abstract

Xu, C., Krabbe, S., Gründemann, J., Botta, P., Fadok, J.P., Osakada, F., Saur, D., Grewe, B.F., Schnitzer, M.J., Callaway, E.M., Lüthi, A. Distinct Hippocampal Pathways Mediate Dissociable Roles of Context in Memory Retrieval. (2016) Cell. 167(4):961-972. DOI: 10.1016/j.cell.2016.09.051

+ expand abstract

Peterson, D.A., Littlewort, G.C., Bartlett, M.S., Macerollo, A., Perlmutter, J.S., Jinnah, H.A., Hallett, M., Sejnowski, T.J. Objective, computerized video-based rating of blepharospasm severity. (2016) Neurology. 87(20):2146-2153. DOI: 10.1212/WNL.0000000000003336

+ expand abstract

Bardy, C., van den Hurk, M., Kakaradov, B., Erwin, J.A., Jaeger, B.N., Hernandez, R.V., Eames, T., Paucar, A.A., Gorris, M., Marchand, C., Jappelli, R., Barron, J., Bryant, A.K., Kellogg, M., Lasken, R.S., Rutten, B.P., Steinbusch, H.W., Yeo, G.W., Gage, F.H. Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology. (2016) Molecular Psychiatry. 21(11):1573-1588. DOI: 10.1038/mp.2016.158

+ expand abstract

Churchland, P.S., Sejnowski, T.J. Blending computational and experimental neuroscience. (2016) Nature Reviews Neuroscience. 17(11):667-668. DOI: 10.1038/nrn.2016.114

+ expand abstract

Tian, J., Huang, R., Cohen, J.Y., Osakada, F., Kobak, D., Machens, C.K., Callaway, E.M., Uchida, N., Watabe-Uchida, M. Distributed and Mixed Information in Monosynaptic Inputs to Dopamine Neurons. (2016) Neuron. 91(6):1374-1389. DOI: 10.1016/j.neuron.2016.08.018

+ expand abstract

Barth, L., Burkhalter, A., Callaway, E.M., Connors, B.W., Cauli, B., DeFelipe, J., Feldmeyer, D., Freund, T., Kawaguchi, Y., Kisvarday, Z., Kubota, Y., McBain, C., Oberlaender, M., Rossier, J., Rudy, B., Staiger, J.F., Somogyi, P., Tamas, G., Yuste, R. Comment on "Principles of connectivity among morphologically defined cell types in adult neocortex". (2016) Science. 353(6304):1108. DOI: 10.1126/science.aaf5663

+ expand abstract

Du, H., Deng, W., Aimone, J.B., Ge, M., Parylak, S., Walch, K., Zhang, W., Cook, J., Song, H., Wang, L., Gage, F.H., Mu, Y. Dopaminergic inputs in the dentate gyrus direct the choice of memory encoding. (2016) Proceedings of the National Academy of Sciences of the United States of America. 113(37):E5501-10. DOI: 10.1073/pnas.1606951113

+ expand abstract

Smith, J.B., Klug, J.R., Ross, D.L., Howard, C.D., Hollon, N.G., Ko, V.I., Hoffman, H., Callaway, E.M., Gerfen, C.R., Jin, X. Genetic-Based Dissection Unveils the Inputs and Outputs of Striatal Patch and Matrix Compartments. (2016) Neuron. 91(5):1069-1084. DOI: 10.1016/j.neuron.2016.07.046

+ expand abstract

Sharpee, T.O. How Invariant Feature Selectivity Is Achieved in Cortex. (2016) Front Synaptic Neurosci. 8:26. DOI: 10.3389/fnsyn.2016.00026

+ expand abstract

Grillner, S., Ip, N., Koch, C., Koroshetz, W., Okano, H., Polachek, M., Poo, M.M., Sejnowski, T.J. Worldwide initiatives to advance brain research. (2016) Nature Neuroscience. 19(9):1118-22. DOI: 10.1038/nn.4371

Kosik, K.S., Sejnowski, T.J., Raichle, M.E., Ciechanover, A., Baltimore, D. A path toward understanding neurodegeneration. (2016) Science. 353(6302):872-3. DOI: 10.1126/science.aai7622

Nauhaus, I., Nielsen, K.J., Callaway, E.M. Efficient Receptive Field Tiling in Primate V1. (2016) Neuron. 91(4):893-904. DOI: 10.1016/j.neuron.2016.07.015

+ expand abstract

Reddy, G., Celani, A., Sejnowski, T.J., Vergassola, M. Learning to soar in turbulent environments. (2016) Proceedings of the National Academy of Sciences of the United States of America. 113(33):E4877-84. DOI: 10.1073/pnas.1606075113

+ expand abstract

Hilde, K.L., Levine, A.J., Hinckley, C.A., Hayashi, M., Montgomery, J.M., Gullo, M., Driscoll, S.P., Grosschedl, R., Kohwi, Y., Kohwi-Shigematsu, T., Pfaff, S.L. Satb2 Is Required for the Development of a Spinal Exteroceptive Microcircuit that Modulates Limb Position. (2016) Neuron. 91(4):763-776. DOI: 10.1016/j.neuron.2016.07.014

+ expand abstract

van den Hurk, M., Kenis, G., Bardy, C., van den Hove, D.L., Gage, F.H., Steinbusch, H.W., Rutten, B.P. Transcriptional and epigenetic mechanisms of cellular reprogramming to induced pluripotency. (2016) Epigenomics. 8(8):1131-49. DOI: 10.2217/epi-2016-0032

+ expand abstract

Huh, D., Sejnowski, T.J. Conservation law for self-paced movements. (2016) Proceedings of the National Academy of Sciences of the United States of America. 113(31):8831-6. DOI: 10.1073/pnas.1608724113

+ expand abstract

Gage, F.H., Guarente, L.P., Wagers, A.J. Aging and Rejuvenation: Insights from Rusty Gage, Leonard Guarente, and Amy Wagers. (2016) Trends in Molecular Medicine. 22(8):633-4. DOI: 10.1016/j.molmed.2016.06.011

Chailangkarn, T., Trujillo, C.A., Freitas, B.C., Hrvoj-Mihic, B., Herai, R.H., Yu, D.X., Brown, T.T., Marchetto, M.C., Bardy, C., McHenry, L., Stefanacci, L., Järvinen, A., Searcy, Y.M., DeWitt, M., Wong, W., Lai, P., Ard, M.C., Hanson, K.L., Romero, S., Jacobs, B., Dale, A.M., Dai, L., Korenberg, J.R., Gage, F.H., Bellugi, U., Halgren, E., Semendeferi, K., Muotri, A.R. A human neurodevelopmental model for Williams syndrome. (2016) Nature. 536(7616):338-43. DOI: 10.1038/nature19067

+ expand abstract

Nuttle, X., Giannuzzi, G., Duyzend, M.H., Schraiber, J.G., Narvaiza, I., Sudmant, P.H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H.A., Marchetto, M.C., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., Tang, W.J., Ventura, M., Banci, L., Antonacci, F., Akey, J.M., Amemiya, C.T., Gage, F.H., Reymond, A., Eichler, E.E. Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. (2016) Nature. 536(7615):205-9. DOI: 10.1038/nature19075

+ expand abstract

Padmanabhan, K., Osakada, F., Tarabrina, A., Kizer, E., Callaway, E.M., Gage, F.H., Sejnowski, T.J. Diverse Representations of Olfactory Information in Centrifugal Feedback Projections. (2016) Journal of Neuroscience. 36(28):7535-45. DOI: 10.1523/JNEUROSCI.3358-15.2016

+ expand abstract

Ruiz-Martinez, A., Bartol, T.M., Sejnowski, T.J., Tartakovsky, D.M. Efficient Multiscale Models of Polymer Assembly. (2016) Biophysical Journal. 111(1):185-96. DOI: 10.1016/j.bpj.2016.05.022

+ expand abstract

Han, J., Kim, H.J., Schafer, S.T., Paquola, A., Clemenson, G.D., Toda, T., Oh, J., Pankonin, A.R., Lee, B.S., Johnston, S.T., Sarkar, A., Denli, A.M., Gage, F.H. Functional Implications of miR-19 in the Migration of Newborn Neurons in the Adult Brain. (2016) Neuron. 91(1):79-89. DOI: 10.1016/j.neuron.2016.05.034

+ expand abstract

Mertens, J., Marchetto, M.C., Bardy, C., Gage, F.H. Evaluating cell reprogramming, differentiation and conversion technologies in neuroscience. (2016) Nature Reviews Neuroscience. 17(7):424-37. DOI: 10.1038/nrn.2016.46

+ expand abstract

Ettle, B., Kerman, B.E., Valera, E., Gillmann, C., Schlachetzki, J.C., Reiprich, S., Büttner, C., Ekici, A.B., Reis, A., Wegner, M., Bäuerle, T., Riemenschneider, M.J., Masliah, E., Gage, F.H., Winkler, J. α-Synuclein-induced myelination deficit defines a novel interventional target for multiple system atrophy. (2016) Acta Neuropathologica. 132(1):59-75. DOI: 10.1007/s00401-016-1572-y

+ expand abstract

Multiple system atrophy (MSA) is a rare atypical parkinsonian disorder characterized by a rapidly progressing clinical course and at present without any efficient therapy. Neuropathologically, myelin loss and neurodegeneration are associated with α-synuclein accumulation in oligodendrocytes, but underlying pathomechanisms are poorly understood. Here, we analyzed the impact of oligodendrocytic α-synuclein on the formation of myelin sheaths to define a potential interventional target for MSA. Post-mortem analyses of MSA patients and controls were performed to quantify myelin and oligodendrocyte numbers. As pre-clinical models, we used transgenic MSA mice, a myelinating stem cell-derived oligodendrocyte-neuron co-culture, and primary oligodendrocytes to determine functional consequences of oligodendrocytic α-synuclein overexpression on myelination. We detected myelin loss accompanied by preserved or even increased numbers of oligodendrocytes in post-mortem MSA brains or transgenic mouse forebrains, respectively, indicating an oligodendrocytic dysfunction in myelin formation. Corroborating this observation, overexpression of α-synuclein in primary and stem cell-derived oligodendrocytes severely impaired myelin formation, defining a novel α-synuclein-linked pathomechanism in MSA. We used the pro-myelinating activity of the muscarinic acetylcholine receptor antagonist benztropine to analyze the reversibility of the myelination deficit. Transcriptome profiling of primary pre-myelinating oligodendrocytes demonstrated that benztropine readjusts myelination-related processes such as cholesterol and membrane biogenesis, being compromised by oligodendrocytic α-synuclein. Additionally, benztropine restored the α-synuclein-induced myelination deficit of stem cell-derived oligodendrocytes. Strikingly, benztropine also ameliorated the myelin deficit in transgenic MSA mice, resulting in a prevention of neuronal cell loss. In conclusion, this study defines the α-synuclein-induced myelination deficit as a novel and crucial pathomechanism in MSA. Importantly, the reversible nature of this oligodendrocytic dysfunction opens a novel avenue for an intervention in MSA.

Faget, L., Osakada, F., Duan, J., Ressler, R., Johnson, A.B., Proudfoot, J.A., Yoo, J.H., Callaway, E.M., Hnasko, T.S. Afferent Inputs to Neurotransmitter-Defined Cell Types in the Ventral Tegmental Area. (2016) Cell Reports. 15(12):2796-2808. DOI: 10.1016/j.celrep.2016.05.057

+ expand abstract

Zheng, X., Boyer, L., Jin, M., Mertens, J., Kim, Y., Ma, L., Ma, L., Hamm, M., Gage, F.H., Hunter, T. Metabolic reprogramming during neuronal differentiation from aerobic glycolysis to neuronal oxidative phosphorylation. (2016) Elife. 5. DOI: 10.7554/eLife.13374

+ expand abstract

Gonçalves, J.T., Bloyd, C.W., Shtrahman, M., Johnston, S.T., Schafer, S.T., Parylak, S.L., Tran, T., Chang, T., Gage, F.H. In vivo imaging of dendritic pruning in dentate granule cells. (2016) Nature Neuroscience. 19(6):788-91. DOI: 10.1038/nn.4301

+ expand abstract

Bedrosian, T.A., Linker, S., Gage, F.H. Environment-driven somatic mosaicism in brain disorders. (2016) Genome Medicine. 8(1):58. DOI: 10.1186/s13073-016-0317-9

+ expand abstract

Franks, T.M., Benner, C., Narvaiza, I., Marchetto, M.C., Young, J.M., Malik, H.S., Gage, F.H., Hetzer, M.W. Evolution of a transcriptional regulator from a transmembrane nucleoporin. (2016) Genes & Development. 30(10):1155-71. DOI: 10.1101/gad.280941.116

+ expand abstract

Poo, M.M., Pignatelli, M., Ryan, T.J., Tonegawa, S., Bonhoeffer, T., Martin, K.C., Rudenko, A., Tsai, L.H., Tsien, R.W., Fishell, G., Mullins, C., Gonçalves, J.T., Shtrahman, M., Johnston, S.T., Gage, F.H., Dan, Y., Long, J., Buzsáki, G., Stevens, C. What is memory? The present state of the engram. (2016) BMC Biology. 14:40. DOI: 10.1186/s12915-016-0261-6

+ expand abstract

Oedegaard, K.J., Alda, M., Anand, A., Andreassen, O.A., Balaraman, Y., Berrettini, W.H., Bhattacharjee, A., Brennand, K.J., Burdick, K.E., Calabrese, J.R., Calkin, C.V., Claasen, A., Coryell, W.H., Craig, D., DeModena, A., Frye, M., Gage, F.H., Gao, K., Garnham, J., Gershon, E., Jakobsen, P., Leckband, S.G., McCarthy, M.J., McInnis, M.G., Maihofer, A.X., Mertens, J., Morken, G., Nievergelt, C.M., Nurnberger, J., Pham, S., Schoeyen, H., Shekhtman, T., Shilling, P.D., Szelinger, S., Tarwater, B., Yao, J., Zandi, P.P., Kelsoe, J.R. The Pharmacogenomics of Bipolar Disorder study (PGBD): identification of genes for lithium response in a prospective sample. (2016) BMC Psychiatry. 16:129. DOI: 10.1186/s12888-016-0732-x

+ expand abstract

Topol, A., Zhu, S., Hartley, B.J., English, J., Hauberg, M.E., Tran, N., Rittenhouse, C.A., Simone, A., Ruderfer, D.M., Johnson, J., Readhead, B., Hadas, Y., Gochman, P.A., Wang, Y.C., Shah, H., Cagney, G., Rapoport, J., Gage, F.H., Dudley, J.T., Sklar, P., Mattheisen, M., Cotter, D., Fang, G., Brennand, K.J. Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. (2016) Cell Reports. 15(5):1024-1036. DOI: 10.1016/j.celrep.2016.03.090

+ expand abstract

Jadi, M.P., Behrens, M.M., Sejnowski, T.J. Abnormal Gamma Oscillations in N-Methyl-D-Aspartate Receptor Hypofunction Models of Schizophrenia. (2016) Biological Psychiatry. 79(9):716-26. DOI: 10.1016/j.biopsych.2015.07.005

+ expand abstract

Saremi, S., Sejnowski, T.J. Correlated Percolation, Fractal Structures, and Scale-Invariant Distribution of Clusters in Natural Images. (2016) IEEE Trans Pattern Anal Mach Intell. 38(5):1016-20. DOI: 10.1109/TPAMI.2015.2481402

+ expand abstract

Kim, E.J., Jacobs, M.W., Ito-Cole, T., Callaway, E.M. Improved Monosynaptic Neural Circuit Tracing Using Engineered Rabies Virus Glycoproteins. (2016) Cell Reports. 15(4):692-699. DOI: 10.1016/j.celrep.2016.03.067

+ expand abstract

Sharpee, T.O. Taking a close look at electrosensing. (2016) Elife. 5. DOI: 10.7554/eLife.16209

+ expand abstract

Sekiguchi, K.J., Shekhtmeyster, P., Merten, K., Arena, A., Cook, D., Hoffman, E., Ngo, A., Nimmerjahn, A. Imaging large-scale cellular activity in spinal cord of freely behaving mice. (2016) Nature Communications. 7:11450. DOI: 10.1038/ncomms11450

+ expand abstract

Lacar, B., Linker, S.B., Jaeger, B.N., Krishnaswami, S., Barron, J., Kelder, M., Parylak, S., Paquola, A., Venepally, P., Novotny, M., O'Connor, C., Fitzpatrick, C., Erwin, J., Hsu, J.Y., Husband, D., McConnell, M.J., Lasken, R., Gage, F.H. Nuclear RNA-seq of single neurons reveals molecular signatures of activation. (2016) Nature Communications. 7:11022. DOI: 10.1038/ncomms11022

+ expand abstract

Harrison, B.J., Venkat, G., Lamb, J.L., Hutson, T.H., Drury, C., Rau, K.K., Bunge, M.B., Mendell, L.M., Gage, F.H., Johnson, R.D., Hill, C.E., Rouchka, E.C., Moon, L.D., Petruska, J.C. The Adaptor Protein CD2AP Is a Coordinator of Neurotrophin Signaling-Mediated Axon Arbor Plasticity. (2016) Journal of Neuroscience. 36(15):4259-75. DOI: 10.1523/JNEUROSCI.2423-15.2016

+ expand abstract

Zhang, Y., Sharpee, T.O. A Robust Feedforward Model of the Olfactory System. (2016) PLOS Computational Biology. 12(4):e1004850. DOI: 10.1371/journal.pcbi.1004850

+ expand abstract

Wall, N.R., De La Parra, M., Sorokin, J.M., Taniguchi, H., Huang, Z.J., Callaway, E.M. Brain-Wide Maps of Synaptic Input to Cortical Interneurons. (2016) Journal of Neuroscience. 36(14):4000-4009. DOI: 10.1523/JNEUROSCI.3967-15.2016

+ expand abstract

Fourgeaud, L., Través, P.G., Tufail, Y., Leal-Bailey, H., Lew, E.D., Burrola, P.G., Callaway, P., Zagórska, A., Rothlin, C.V., Nimmerjahn, A., Lemke, G. TAM receptors regulate multiple features of microglial physiology. (2016) Nature. 532(7598):240-244. DOI: 10.1038/nature17630

+ expand abstract

Otani, T., Marchetto, M.C., Gage, F.H., Simons, B.D., Livesey, F.J. 2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size. (2016) Cell Stem Cell. 18(4):467-80. DOI: 10.1016/j.stem.2016.03.003

+ expand abstract

Briggs, F., Kiley, C.W., Callaway, E.M., Usrey, W.M. Morphological Substrates for Parallel Streams of Corticogeniculate Feedback Originating in Both V1 and V2 of the Macaque Monkey. (2016) Neuron. 90(2):388-399. DOI: 10.1016/j.neuron.2016.02.038

+ expand abstract

Zheng, X., Boyer, L., Jin, M., Kim, Y., Fan, W., Bardy, C., Berggren, T., Evans, R.M., Gage, F.H., Hunter, T. Alleviation of neuronal energy deficiency by mTOR inhibition as a treatment for mitochondria-related neurodegeneration. (2016) Elife. 5. DOI: 10.7554/eLife.13378

+ expand abstract

Mishra, H.K., Prots, I., Havlicek, S., Kohl, Z., Perez-Branguli, F., Boerstler, T., Anneser, L., Minakaki, G., Wend, H., Hampl, M., Leone, M., Brückner, M., Klucken, J., Reis, A., Boyer, L., Schuierer, G., Behrens, J., Lampert, A., Engel, F.B., Gage, F.H., Winkler, J., Winner, B. GSK3ß-dependent dysregulation of neurodevelopment in SPG11-patient iPSC model. (2016) Ann. Neurol. DOI: 10.1002/ana.24633

+ expand abstract

Krishnaswami, S.R., Grindberg, R.V., Novotny, M., Venepally, P., Lacar, B., Bhutani, K., Linker, S.B., Pham, S., Erwin, J.A., Miller, J.A., Hodge, R., McCarthy, J.K., Kelder, M., McCorrison, J., Aevermann, B.D., Fuertes, F.D., Scheuermann, R.H., Lee, J., Lein, E.S., Schork, N., McConnell, M.J., Gage, F.H., Lasken, R.S. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. (2016) Nature Protocols. 11(3):499-524. DOI: 10.1038/nprot.2016.015

+ expand abstract

Johnston, S.T., Shtrahman, M., Parylak, S., Gonçalves, J.T., Gage, F.H. Paradox of pattern separation and adult neurogenesis: A dual role for new neurons balancing memory resolution and robustness. (2016) Neurobiology of Learning and Memory. 129:60-8. DOI: 10.1016/j.nlm.2015.10.013

+ expand abstract

Zarrinpar, A., Callaway, E.M. Functional Local Input to Layer 5 Pyramidal Neurons in the Rat Visual Cortex. (2016) Cereb. Cortex. 26(3):991-1003. DOI: 10.1093/cercor/bhu268

+ expand abstract

Aljadeff, J., Renfrew, D., Vegué, M., Sharpee, T.O. Low-dimensional dynamics of structured random networks. (2016) Phys Rev E. 93(2):022302. DOI: 10.1103/PhysRevE.93.022302

+ expand abstract

Weissman, I.L., Gage, F.H. A Mechanism for Somatic Brain Mosaicism. (2016) Cell. 164(4):593-5. DOI: 10.1016/j.cell.2016.01.048

+ expand abstract

Rodrigues, S., Desroches, M., Krupa, M., Cortes, J.M., Sejnowski, T.J., Ali, A.B. Time-coded neurotransmitter release at excitatory and inhibitory synapses. (2016) Proceedings of the National Academy of Sciences of the United States of America. 113(8):E1108-15. DOI: 10.1073/pnas.1525591113

+ expand abstract

Tuncdemir, S.N., Wamsley, B., Stam, F.J., Osakada, F., Goulding, M., Callaway, E.M., Rudy, B., Fishell, G. Early Somatostatin Interneuron Connectivity Mediates the Maturation of Deep Layer Cortical Circuits. (2016) Neuron. 89(3):521-35. DOI: 10.1016/j.neuron.2015.11.020

+ expand abstract

Hasenstaub, A., Otte, S., Callaway, E. Cell Type-Specific Control of Spike Timing by Gamma-Band Oscillatory Inhibition. (2016) Cereb. Cortex. 26(2):797-806. DOI: 10.1093/cercor/bhv044

+ expand abstract

Agre, P., Bertozzi, C., Bissell, M., Campbell, K.P., Cummings, R.D., Desai, U.R., Estes, M., Flotte, T., Fogleman, G., Gage, F., Ginsburg, D., Gordon, J.I., Hart, G., Hascall, V., Kiessling, L., Kornfeld, S., Lowe, J., Magnani, J., Mahal, L.K., Medzhitov, R., Roberts, R.J., Sackstein, R., Sarkar, R., Schnaar, R., Schwartz, N., Varki, A., Walt, D., Weissman, I. Training the next generation of biomedical investigators in glycosciences. (2016) Journal of Clinical Investigation. 126(2):405-8. DOI: 10.1172/JCI85905

+ expand abstract

Wasson, J.A., Simon, A.K., Myrick, D.A., Wolf, G., Driscoll, S., Pfaff, S.L., Macfarlan, T.S., Katz, D.J. Maternally provided LSD1/KDM1A enables the maternal-to-zygotic transition and prevents defects that manifest postnatally. (2016) Elife. 5. DOI: 10.7554/eLife.08848

+ expand abstract

O'Donnell, C., Sejnowski, T.J. Street View of the Cognitive Map. (2016) Cell. 164(1-2):13-5. DOI: 10.1016/j.cell.2015.12.051

+ expand abstract

Tang, X., Kim, J., Zhou, L., Wengert, E., Zhang, L., Wu, Z., Carromeu, C., Muotri, A.R., Marchetto, M.C., Gage, F.H., Chen, G. KCC2 rescues functional deficits in human neurons derived from patients with Rett syndrome. (2016) Proceedings of the National Academy of Sciences of the United States of America. 113(3):751-6. DOI: 10.1073/pnas.1524013113

+ expand abstract

Vadodaria, K.C., Mertens, J., Paquola, A., Bardy, C., Li, X., Jappelli, R., Fung, L., Marchetto, M.C., Hamm, M., Gorris, M., Koch, P., Gage, F.H. The different moods of human serotonergic neurons. (2016) Molecular Psychiatry. 21(1):3. DOI: 10.1038/mp.2015.202

Duricki, D.A., Hutson, T.H., Kathe, C., Soleman, S., Gonzalez-Carter, D., Petruska, J.C., Shine, H.D., Chen, Q., Wood, T.C., Bernanos, M., Cash, D., Williams, S.C., Gage, F.H., Moon, L.D. Delayed intramuscular human neurotrophin-3 improves recovery in adult and elderly rats after stroke. (2016) Brain. 139(Pt 1):259-75. DOI: 10.1093/brain/awv341

+ expand abstract

Vadodaria, K.C., Mertens, J., Paquola, A., Bardy, C., Li, X., Jappelli, R., Fung, L., Marchetto, M.C., Hamm, M., Gorris, M., Koch, P., Gage, F.H. Generation of functional human serotonergic neurons from fibroblasts. (2016) Molecular Psychiatry. 21(1):49-61. DOI: 10.1038/mp.2015.161

+ expand abstract

Geeven, G., Zhu, Y., Kim, B.J., Bartholdy, B.A., Yang, S.M., Macfarlan, T.S., Gifford, W.D., Pfaff, S.L., Verstegen, M.J., Pinto, H., Vermunt, M.W., Creyghton, M.P., Wijchers, P.J., Stamatoyannopoulos, J.A., Skoultchi, A.I., de Laat, W. Local compartment changes and regulatory landscape alterations in histone H1-depleted cells. (2015) Genome Biology. 16:289. DOI: 10.1186/s13059-015-0857-0

+ expand abstract

Harrison, B.J., Venkat, G., Hutson, T., Rau, K.K., Bunge, M.B., Mendell, L.M., Gage, F.H., Johnson, R.D., Hill, C., Rouchka, E.C., Moon, L., Petruska, J.C. Transcriptional changes in sensory ganglia associated with primary afferent axon collateral sprouting in spared dermatome model. (2015) Genomics Data. 6:249-52. DOI: 10.1016/j.gdata.2015.10.005

+ expand abstract

Amin, N.D., Bai, G., Klug, J.R., Bonanomi, D., Pankratz, M.T., Gifford, W.D., Hinckley, C.A., Sternfeld, M.J., Driscoll, S.P., Dominguez, B., Lee, K.F., Jin, X., Pfaff, S.L. Loss of motoneuron-specific microRNA-218 causes systemic neuromuscular failure. (2015) Science. 350(6267):1525-9. DOI: 10.1126/science.aad2509

+ expand abstract

Kim, E.J., Juavinett, A.L., Kyubwa, E.M., Jacobs, M.W., Callaway, E.M. Three Types of Cortical Layer 5 Neurons That Differ in Brain-wide Connectivity and Function. (2015) Neuron. 88(6):1253-1267. DOI: 10.1016/j.neuron.2015.11.002

+ expand abstract

Brennand, K.J., Marchetto, M.C., Benvenisty, N., Brüstle, O., Ebert, A., Izpisua Belmonte, J.C., Kaykas, A., Lancaster, M.A., Livesey, F.J., McConnell, M.J., McKay, R.D., Morrow, E.M., Muotri, A.R., Panchision, D.M., Rubin, L.L., Sawa, A., Soldner, F., Song, H., Studer, L., Temple, S., Vaccarino, F.M., Wu, J., Vanderhaeghen, P., Gage, F.H., Jaenisch, R. Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders. (2015) Stem Cell Reports. 5(6):933-45. DOI: 10.1016/j.stemcr.2015.10.011

+ expand abstract

Veltz, R., Sejnowski, T.J. Periodic Forcing of Inhibition-Stabilized Networks: Nonlinear Resonances and Phase-Amplitude Coupling. (2015) Neural Computation. 27(12):2477-509. DOI: 10.1162/NECO_a_00786

+ expand abstract

Mertens, J., Paquola, A.C., Ku, M., Hatch, E., Böhnke, L., Ladjevardi, S., McGrath, S., Campbell, B., Lee, H., Herdy, J.R., Gonçalves, J.T., Toda, T., Kim, Y., Winkler, J., Yao, J., Hetzer, M.W., Gage, F.H. Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects. (2015) Cell Stem Cell. 17(6):705-18. DOI: 10.1016/j.stem.2015.09.001

+ expand abstract

Bartol, T.M., Bromer, C., Kinney, J., Chirillo, M.A., Bourne, J.N., Harris, K.M., Sejnowski, T.J. Nanoconnectomic upper bound on the variability of synaptic plasticity. (2015) Elife. 4:e10778. DOI: 10.7554/eLife.10778

+ expand abstract

Kim, H.J., Denli, A.M., Wright, R., Baul, T.D., Clemenson, G.D., Morcos, A.S., Zhao, C., Schafer, S.T., Gage, F.H., Kagalwala, M.N. REST Regulates Non-Cell-Autonomous Neuronal Differentiation and Maturation of Neural Progenitor Cells via Secretogranin II. (2015) Journal of Neuroscience. 35(44):14872-84. DOI: 10.1523/JNEUROSCI.4286-14.2015

+ expand abstract

Pan, F.C., Brissova, M., Powers, A.C., Pfaff, S., Wright, C.V. Inactivating the permanent neonatal diabetes gene Mnx1 switches insulin-producing β-cells to a δ-like fate and reveals a facultative proliferative capacity in aged β-cells. (2015) Development. 142(21):3637-48. DOI: 10.1242/dev.126011

+ expand abstract

Mertens, J., Wang, Q.W., Kim, Y., Yu, D.X., Pham, S., Yang, B., Zheng, Y., Diffenderfer, K.E., Zhang, J., Soltani, S., Eames, T., Schafer, S.T., Boyer, L., Marchetto, M.C., Nurnberger, J.I., Calabrese, J.R., Ødegaard, K.J., McCarthy, M.J., Zandi, P.P., Alda, M., Alba, M., Nievergelt, C.M., , Mi, S., Brennand, K.J., Kelsoe, J.R., Gage, F.H., Yao, J. Differential responses to lithium in hyperexcitable neurons from patients with bipolar disorder. (2015) Nature. 527(7576):95-9. DOI: 10.1038/nature15526

+ expand abstract

Bipolar disorder is a complex neuropsychiatric disorder that is characterized by intermittent episodes of mania and depression; without treatment, 15% of patients commit suicide. Hence, it has been ranked by the World Health Organization as a top disorder of morbidity and lost productivity. Previous neuropathological studies have revealed a series of alterations in the brains of patients with bipolar disorder or animal models, such as reduced glial cell number in the prefrontal cortex of patients, upregulated activities of the protein kinase A and C pathways and changes in neurotransmission. However, the roles and causation of these changes in bipolar disorder have been too complex to exactly determine the pathology of the disease. Furthermore, although some patients show remarkable improvement with lithium treatment for yet unknown reasons, others are refractory to lithium treatment. Therefore, developing an accurate and powerful biological model for bipolar disorder has been a challenge. The introduction of induced pluripotent stem-cell (iPSC) technology has provided a new approach. Here we have developed an iPSC model for human bipolar disorder and investigated the cellular phenotypes of hippocampal dentate gyrus-like neurons derived from iPSCs of patients with bipolar disorder. Guided by RNA sequencing expression profiling, we have detected mitochondrial abnormalities in young neurons from patients with bipolar disorder by using mitochondrial assays; in addition, using both patch-clamp recording and somatic Ca(2+) imaging, we have observed hyperactive action-potential firing. This hyperexcitability phenotype of young neurons in bipolar disorder was selectively reversed by lithium treatment only in neurons derived from patients who also responded to lithium treatment. Therefore, hyperexcitability is one early endophenotype of bipolar disorder, and our model of iPSCs in this disease might be useful in developing new therapies and drugs aimed at its clinical treatment.

Bourane, S., Duan, B., Koch, S.C., Dalet, A., Britz, O., Garcia-Campmany, L., Kim, E., Cheng, L., Ghosh, A., Ma, Q., Goulding, M. Gate control of mechanical itch by a subpopulation of spinal cord interneurons. (2015) Science. 350(6260):550-4. DOI: 10.1126/science.aac8653

+ expand abstract

He, W., Bai, G., Zhou, H., Wei, N., White, N.M., Lauer, J., Liu, H., Shi, Y., Dumitru, C.D., Lettieri, K., Shubayev, V., Jordanova, A., Guergueltcheva, V., Griffin, P.R., Burgess, R.W., Pfaff, S.L., Yang, X.L. CMT2D neuropathy is linked to the neomorphic binding activity of glycyl-tRNA synthetase. (2015) Nature. 526(7575):710-4. DOI: 10.1038/nature15510

+ expand abstract

Bartol, T.M., Keller, D.X., Kinney, J.P., Bajaj, C.L., Harris, K.M., Sejnowski, T.J., Kennedy, M.B. Computational reconstitution of spine calcium transients from individual proteins. (2015) Front Synaptic Neurosci. 7:17. DOI: 10.3389/fnsyn.2015.00017

+ expand abstract

Denli, A.M., Narvaiza, I., Kerman, B.E., Pena, M., Benner, C., Marchetto, M.C., Diedrich, J.K., Aslanian, A., Ma, J., Moresco, J.J., Moore, L., Hunter, T., Saghatelian, A., Gage, F.H. Primate-specific ORF0 contributes to retrotransposon-mediated diversity. (2015) Cell. 163(3):583-93. DOI: 10.1016/j.cell.2015.09.025

+ expand abstract

Mu, Y., Zhao, C., Toni, N., Yao, J., Gage, F.H. Distinct roles of NMDA receptors at different stages of granule cell development in the adult brain. (2015) Elife. 4:e07871. DOI: 10.7554/eLife.07871

+ expand abstract

Britz, O., Zhang, J., Grossmann, K.S., Dyck, J., Kim, J.C., Dymecki, S., Gosgnach, S., Goulding, M. A genetically defined asymmetry underlies the inhibitory control of flexor-extensor locomotor movements. (2015) Elife. 4. DOI: 10.7554/eLife.04718

+ expand abstract

Wang, X., Pinto-Duarte, A., Behrens, M.M., Zhou, X., Sejnowski, T.J. Characterization of spatio-temporal epidural event-related potentials for mouse models of psychiatric disorders. (2015) Scientific Reports. 5:14964. DOI: 10.1038/srep14964

+ expand abstract

Barnes, S.A., Pinto-Duarte, A., Kappe, A., Zembrzycki, A., Metzler, A., Mukamel, E.A., Lucero, J., Wang, X., Sejnowski, T.J., Markou, A.*, Behrens, M.M.* Disruption of mGluR5 in parvalbumin-positive interneurons induces core features of neurodevelopmental disorders. (2015) Molecular Psychiatry. 20(10):1161-72. DOI: 10.1038/mp.2015.113

+ expand abstract

Pawar, K., Cummings, B.J., Thomas, A., Shea, L.D., Levine, A., Pfaff, S., Anderson, A.J. Biomaterial bridges enable regeneration and re-entry of corticospinal tract axons into the caudal spinal cord after SCI: Association with recovery of forelimb function. (2015) Biomaterials. 65:1-12. DOI: 10.1016/j.biomaterials.2015.05.032

+ expand abstract

Tashiro, A., Zhao, C., Suh, H., Gage, F.H. Preparation and Use of Retroviral Vectors for Labeling, Imaging, and Genetically Manipulating Cells. (2015) Cold Spring Harbor Protocols. 2015(10):883-8. DOI: 10.1101/pdb.top086363

+ expand abstract

Tashiro, A., Zhao, C., Suh, H., Gage, F.H. Analysis of Spine Motility of Newborn Granule Cells in Acute Brain Slices. (2015) Cold Spring Harbor Protocols. 2015(10):934-6. DOI: 10.1101/pdb.prot086397

+ expand abstract

Tashiro, A., Zhao, C., Suh, H., Gage, F.H. Imaging Newborn Granule Cells in Fixed Sections. (2015) Cold Spring Harbor Protocols. 2015(10):932-3. DOI: 10.1101/pdb.prot086389

+ expand abstract

Tashiro, A., Zhao, C., Suh, H., Gage, F.H. Purification and Injection of Retroviral Vectors. (2015) Cold Spring Harbor Protocols. 2015(10):925-31. DOI: 10.1101/pdb.prot086371

+ expand abstract

González, O.C., Krishnan, G.P., Chauvette, S., Timofeev, I., Sejnowski, T., Bazhenov, M. Modeling of Age-Dependent Epileptogenesis by Differential Homeostatic Synaptic Scaling. (2015) Journal of Neuroscience. 35(39):13448-62. DOI: 10.1523/JNEUROSCI.5038-14.2015

+ expand abstract

Prescott, S.L., Srinivasan, R., Marchetto, M.C., Grishina, I., Narvaiza, I., Selleri, L., Gage, F.H., Swigut, T., Wysocka, J. Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. (2015) Cell. 163(1):68-83. DOI: 10.1016/j.cell.2015.08.036

+ expand abstract

Hinckley, C.A., Alaynick, W.A., Gallarda, B.W., Hayashi, M., Hilde, K.L., Driscoll, S.P., Dekker, J.D., Tucker, H.O., Sharpee, T.O., Pfaff, S.L. Spinal Locomotor Circuits Develop Using Hierarchical Rules Based on Motorneuron Position and Identity. (2015) Neuron. 87(5):1008-21. DOI: 10.1016/j.neuron.2015.08.005

+ expand abstract

Kempermann, G., Song, H., Gage, F.H. Neurogenesis in the Adult Hippocampus. (2015) Cold Spring Harbor Perspectives in Biology. 7(9):a018812. DOI: 10.1101/cshperspect.a018812

+ expand abstract

Jovičić, A., Mertens, J., Boeynaems, S., Bogaert, E., Chai, N., Yamada, S.B., Paul, J.W., Sun, S., Herdy, J.R., Bieri, G., Kramer, N.J., Gage, F.H., Van Den Bosch, L., Robberecht, W., Gitler, A.D. Modifiers of C9orf72 dipeptide repeat toxicity connect nucleocytoplasmic transport defects to FTD/ALS. (2015) Nature Neuroscience. 18(9):1226-9. DOI: 10.1038/nn.4085

+ expand abstract

Firth, A.L., Menon, T., Parker, G.S., Qualls, S.J., Lewis, B.M., Ke, E., Dargitz, C.T., Wright, R., Khanna, A., Gage, F.H., Verma, I.M. Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs. (2015) Cell Reports. 12(9):1385-90. DOI: 10.1016/j.celrep.2015.07.062

+ expand abstract

Wang, J., Telese, F., Tan, Y., Li, W., Jin, C., He, X., Basnet, H., Ma, Q., Merkurjev, D., Zhu, X., Liu, Z., Zhang, J., Ohgi, K., Taylor, H., White, R.R., Tazearslan, C., Suh, Y., Macfarlan, T.S., Pfaff, S.L., Rosenfeld, M.G. LSD1n is an H4K20 demethylase regulating memory formation via transcriptional elongation control. (2015) Nature Neuroscience. 18(9):1256-64. DOI: 10.1038/nn.4069

+ expand abstract

Deng, W., Gage, F.H. The effect of immature adult-born dentate granule cells on hyponeophagial behavior is related to their roles in learning and memory. (2015) Frontiers in Systems Neuroscience. 9:34. DOI: 10.3389/fnsys.2015.00034

+ expand abstract

Coggan, J.S., Sejnowski, T.J., Prescott, S.A. Cooperativity between remote sites of ectopic spiking allows afterdischarge to be initiated and maintained at different locations. (2015) Journal of Computational Neuroscience. 39(1):17-28. DOI: 10.1007/s10827-015-0562-8

+ expand abstract

Huh, D., Sejnowski, T.J. Spectrum of power laws for curved hand movements. (2015) Proceedings of the National Academy of Sciences of the United States of America. 112(29):E3950-8. DOI: 10.1073/pnas.1510208112

+ expand abstract

Han, J., Sarkar, A., Gage, F.H. MIR137: big impacts from small changes. (2015) Nature Neuroscience. 18(7):931-3. DOI: 10.1038/nn.4045

Schultz, M.D., He, Y., Whitaker, J.W., Hariharan, M., Mukamel, E.A., Leung, D., Rajagopal, N., Nery, J.R., Urich, M.A., Chen, H., Lin, S., Lin, Y., Jung, I., Schmitt, A.D., Selvaraj, S., Ren, B., Sejnowski, T.J., Wang, W., Ecker, J.R. Human body epigenome maps reveal noncanonical DNA methylation variation. (2015) Nature. 523(7559):212-6. DOI: 10.1038/nature14465

+ expand abstract

Lainscsek, C., Weyhenmeyer, J., Sejnowski, T.J., Letellier, C. Discovering independent parameters in complex dynamical systems. (2015) Chaos Solitons Fractals. 76:182-189. DOI: 10.1016/j.chaos.2015.04.001

+ expand abstract

Lee, H., Kim, M., Kim, N., Macfarlan, T., Pfaff, S.L., Mastick, G.S., Song, M.R. Slit and Semaphorin signaling governed by Islet transcription factors positions motor neuron somata within the neural tube. (2015) Experimental Neurology. 269:17-27. DOI: 10.1016/j.expneurol.2015.03.024

+ expand abstract

Zhao, C., Jou, J., Wolff, L.J., Sun, H., Gage, F.H. Spine morphogenesis in newborn granule cells is differentially regulated in the outer and middle molecular layers. (2015) Journal of Comparative Neurology. 523(10):1588. DOI: 10.1002/cne.23800

Krzisch, M., Temprana, S.G., Mongiat, L.A., Armida, J., Schmutz, V., Virtanen, M.A., Kocher-Braissant, J., Kraftsik, R., Vutskits, L., Conzelmann, K.K., Bergami, M., Gage, F.H., Schinder, A.F., Toni, N. Pre-existing astrocytes form functional perisynaptic processes on neurons generated in the adult hippocampus. (2015) Brain Structure & Function. 220(4):2027-42. DOI: 10.1007/s00429-014-0768-y

+ expand abstract

Mo, A., Mukamel, E.A., Davis, F.P., Luo, C., Henry, G.L., Picard, S., Urich, M.A., Nery, J.R., Sejnowski, T.J., Lister, R., Eddy, S.R., Ecker, J.R., Nathans, J. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. (2015) Neuron. 86(6):1369-84. DOI: 10.1016/j.neuron.2015.05.018

+ expand abstract

Callaway, E.M., Luo, L. Monosynaptic Circuit Tracing with Glycoprotein-Deleted Rabies Viruses. (2015) Journal of Neuroscience. 35(24):8979-8985. DOI: 10.1523/JNEUROSCI.0409-15.2015

Juavinett, A.L., Callaway, E.M. Pattern and Component Motion Responses in Mouse Visual Cortical Areas. (2015) Current Biology. 25(13):1759-1764. DOI: 10.1016/j.cub.2015.05.028

+ expand abstract

Kerman, B.E., Kim, H.J., Padmanabhan, K., Mei, A., Georges, S., Joens, M.S., Fitzpatrick, J.A., Jappelli, R., Chandross, K.J., August, P., Gage, F.H. In vitro myelin formation using embryonic stem cells. (2015) Development. 142(12):2213-25. DOI: 10.1242/dev.116517

+ expand abstract

Nimmerjahn, A., Bergles, D.E. Large-scale recording of astrocyte activity. (2015) Current Opinion in Neurobiology. 32:95-106. DOI: 10.1016/j.conb.2015.01.015

+ expand abstract

Johnson, T., Bartol, T., Sejnowski, T., Mjolsness, E. Model reduction for stochastic CaMKII reaction kinetics in synapses by graph-constrained correlation dynamics. (2015) Phys Biol. 12(4):045005. DOI: 10.1088/1478-3975/12/4/045005

+ expand abstract

Mukherjee, S., Hsieh, W.L., Smith, N., Goulding, M., Heikenfeld, J. Electrokinetic pixels with biprimary inks for color displays and color-temperature-tunable smart windows. (2015) Appl Opt. 54(17):5603-5609.

+ expand abstract

Sejnowski, T.J. Vernon Mountcastle: Father of neuroscience. (2015) Proceedings of the National Academy of Sciences of the United States of America. 112(21):6523-4. DOI: 10.1073/pnas.1506644112

Izpisua Belmonte, J.C., Callaway, E.M., Caddick, S.J., Churchland, P., Feng, G., Homanics, G.E., Lee, K.F., Leopold, D.A., Miller, C.T., Mitchell, J.F., Mitalipov, S., Moutri, A.R., Movshon, J.A., Okano, H., Reynolds, J.H., Ringach, D., Sejnowski, T.J., Silva, A.C., Strick, P.L., Wu, J., Zhang, F. Brains, genes, and primates. (2015) Neuron. 86(3):617-31. DOI: 10.1016/j.neuron.2015.03.021

+ expand abstract

Bardy, C., van den Hurk, M., Eames, T., Marchand, C., Hernandez, R.V., Kellogg, M., Gorris, M., Galet, B., Palomares, V., Brown, J., Bang, A.G., Mertens, J., Böhnke, L., Boyer, L., Simon, S., Gage, F.H. Neuronal medium that supports basic synaptic functions and activity of human neurons in vitro. (2015) Proceedings of the National Academy of Sciences of the United States of America. 112(20):E2725-34. DOI: 10.1073/pnas.1504393112

+ expand abstract

Jorgenson, L.A., Newsome, W.T., Anderson, D.J., Bargmann, C.I., Brown, E.N., Deisseroth, K., Donoghue, J.P., Hudson, K.L., Ling, G.S., MacLeish, P.R., Marder, E., Normann, R.A., Sanes, J.R., Schnitzer, M.J., Sejnowski, T.J., Tank, D.W., Tsien, R.Y., Ugurbil, K., Wingfield, J.C. The BRAIN Initiative: developing technology to catalyse neuroscience discovery. (2015) Philos. Trans. R. Soc. Lond., B, Biol. Sci. 370(1668). DOI: 10.1098/rstb.2014.0164

+ expand abstract

Calhoun, A.J., Tong, A., Pokala, N., Fitzpatrick, J.A., Sharpee, T.O., Chalasani, S.H. Neural Mechanisms for Evaluating Environmental Variability in Caenorhabditis elegans. (2015) Neuron. 86(2):428-41. DOI: 10.1016/j.neuron.2015.03.026

+ expand abstract

Pei, L., Mu, Y., Leblanc, M., Alaynick, W., Barish, G.D., Pankratz, M., Tseng, T.W., Kaufman, S., Liddle, C., Yu, R.T., Downes, M., Pfaff, S.L., Auwerx, J., Gage, F.H., Evans, R.M. Dependence of hippocampal function on ERRγ-regulated mitochondrial metabolism. (2015) Cell Metabolism. 21(4):628-36. DOI: 10.1016/j.cmet.2015.03.004

+ expand abstract

Adamowicz, D.H., Mertens, J., Gage, F.H. Alzheimer's disease: distinct stages in neurogenic decline? (2015) Biological Psychiatry. 77(8):680-2. DOI: 10.1016/j.biopsych.2015.02.021

Amador-Arjona, A., Cimadamore, F., Huang, C.T., Wright, R., Lewis, S., Gage, F.H., Terskikh, A.V. SOX2 primes the epigenetic landscape in neural precursors enabling proper gene activation during hippocampal neurogenesis. (2015) Proceedings of the National Academy of Sciences of the United States of America. 112(15):E1936-45. DOI: 10.1073/pnas.1421480112

+ expand abstract

Schafer, S.T., Han, J., Pena, M., von Bohlen Und Halbach, O., Peters, J., Gage, F.H. The Wnt adaptor protein ATP6AP2 regulates multiple stages of adult hippocampal neurogenesis. (2015) Journal of Neuroscience. 35(12):4983-98. DOI: 10.1523/JNEUROSCI.4130-14.2015

+ expand abstract

Li, P.H., Gauthier, J.L., Schiff, M., Sher, A., Ahn, D., Field, G.D., Greschner, M., Callaway, E.M., Litke, A.M., Chichilnisky, E.J. Anatomical identification of extracellularly recorded cells in large-scale multielectrode recordings. (2015) Journal of Neuroscience. 35(11):4663-4675. DOI: 10.1523/JNEUROSCI.3675-14.2015

+ expand abstract

Lainscsek, C., Sejnowski, T.J. Delay differential analysis of time series. (2015) Neural Computation. 27(3):594-614. DOI: 10.1162/NECO_a_00706

+ expand abstract

Nonlinear dynamical system analysis based on embedding theory has been used for modeling and prediction, but it also has applications to signal detection and classification of time series. An embedding creates a multidimensional geometrical object from a single time series. Traditionally either delay or derivative embeddings have been used. The delay embedding is composed of delayed versions of the signal, and the derivative embedding is composed of successive derivatives of the signal. The delay embedding has been extended to nonuniform embeddings to take multiple timescales into account. Both embeddings provide information on the underlying dynamical system without having direct access to all the system variables. Delay differential analysis is based on functional embeddings, a combination of the derivative embedding with nonuniform delay embeddings. Small delay differential equation (DDE) models that best represent relevant dynamic features of time series data are selected from a pool of candidate models for detection or classification. We show that the properties of DDEs support spectral analysis in the time domain where nonlinear correlation functions are used to detect frequencies, frequency and phase couplings, and bispectra. These can be efficiently computed with short time windows and are robust to noise. For frequency analysis, this framework is a multivariate extension of discrete Fourier transform (DFT), and for higher-order spectra, it is a linear and multivariate alternative to multidimensional fast Fourier transform of multidimensional correlations. This method can be applied to short or sparse time series and can be extended to cross-trial and cross-channel spectra if multiple short data segments of the same experiment are available. Together, this time-domain toolbox provides higher temporal resolution, increased frequency and phase coupling information, and it allows an easy and straightforward implementation of higher-order spectra across time compared with frequency-based methods such as the DFT and cross-spectral analysis.

Clemenson, G.D., Lee, S.W., Deng, W., Barrera, V.R., Iwamoto, K.S., Fanselow, M.S., Gage, F.H. Enrichment rescues contextual discrimination deficit associated with immediate shock. (2015) Hippocampus. 25(3):385-92. DOI: 10.1002/hipo.22380

+ expand abstract

Lainscsek, C., Hernandez, M.E., Poizner, H., Sejnowski, T.J. Delay differential analysis of electroencephalographic data. (2015) Neural Computation. 27(3):615-27. DOI: 10.1162/NECO_a_00656

+ expand abstract

Brennand, K., Savas, J.N., Kim, Y., Tran, N., Simone, A., Hashimoto-Torii, K., Beaumont, K.G., Kim, H.J., Topol, A., Ladran, I., Abdelrahim, M., Matikainen-Ankney, B., Chao, S.H., Mrksich, M., Rakic, P., Fang, G., Zhang, B., Yates, J.R., Gage, F.H. Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia. (2015) Molecular Psychiatry. 20(3):361-8. DOI: 10.1038/mp.2014.22

+ expand abstract

Aljadeff, J., Stern, M., Sharpee, T. Transition to chaos in random networks with cell-type-specific connectivity. (2015) Phys. Rev. Lett. 114(8):088101. DOI: 10.1103/PhysRevLett.114.088101

+ expand abstract

Moldakarimov, S., Bazhenov, M., Sejnowski, T.J. Feedback stabilizes propagation of synchronous spiking in cortical neural networks. (2015) Proceedings of the National Academy of Sciences of the United States of America. 112(8):2545-50. DOI: 10.1073/pnas.1500643112

+ expand abstract

Kastner, D.B., Baccus, S.A., Sharpee, T.O. Critical and maximally informative encoding between neural populations in the retina. (2015) Proceedings of the National Academy of Sciences of the United States of America. 112(8):2533-8. DOI: 10.1073/pnas.1418092112

+ expand abstract

Tanaka, H., Sejnowski, T.J. Motor adaptation and generalization of reaching movements using motor primitives based on spatial coordinates. (2015) Journal of Neurophysiology. 113(4):1217-33. DOI: 10.1152/jn.00002.2014

+ expand abstract

Frost, W.N., Brandon, C.J., Bruno, A.M., Humphries, M.D., Moore-Kochlacs, C., Sejnowski, T.J., Wang, J., Hill, E.S. Monitoring Spiking Activity of Many Individual Neurons in Invertebrate Ganglia. (2015) Advances in Experimental Medicine and Biology. 859:127-45. DOI: 10.1007/978-3-319-17641-3_5

+ expand abstract

Sejnowski, T.J. Consciousness. (2015) Daedalus. 144(1):123-132. DOI: 10.1162/DAED_a_00321

+ expand abstract

Bourane, S., Grossmann, K.S., Britz, O., Dalet, A., Del Barrio, M.G., Stam, F.J., Garcia-Campmany, L., Koch, S., Goulding, M. Identification of a spinal circuit for light touch and fine motor control. (2015) Cell. 160(3):503-15. DOI: 10.1016/j.cell.2015.01.011

+ expand abstract

Duan, B., Cheng, L., Bourane, S., Britz, O., Padilla, C., Garcia-Campmany, L., Krashes, M., Knowlton, W., Velasquez, T., Ren, X., Ross, S., Lowell, B.B., Wang, Y., Goulding, M., Ma, Q. Identification of spinal circuits transmitting and gating mechanical pain. (2014) Cell. 159(6):1417-1432. DOI: 10.1016/j.cell.2014.11.003

+ expand abstract

Ritaccio, A., Brunner, P., Gunduz, A., Hermes, D., Hirsch, L.J., Jacobs, J., Kamada, K., Kastner, S., Knight, R.T., Lesser, R.P., Miller, K., Sejnowski, T., Worrell, G., Schalk, G. Proceedings of the Fifth International Workshop on Advances in Electrocorticography. (2014) Epilepsy Behav. 41:183-92. DOI: 10.1016/j.yebeh.2014.09.015

+ expand abstract

Calhoun, A.J., Chalasani, S.H., Sharpee, T.O. Maximally informative foraging by Caenorhabditis elegans. (2014) Elife. 3. DOI: 10.7554/eLife.04220

+ expand abstract

Pankevich, D.E., Altevogt, B.M., Dunlop, J., Gage, F.H., Hyman, S.E. Improving and accelerating drug development for nervous system disorders. (2014) Neuron. 84(3):546-53. DOI: 10.1016/j.neuron.2014.10.007

+ expand abstract

Regner, B.M., Tartakovsky, D.M., Sejnowski, T.J. Identifying transport behavior of single-molecule trajectories. (2014) Biophysical Journal. 107(10):2345-51. DOI: 10.1016/j.bpj.2014.10.005

+ expand abstract

Carcagno, A.L., Di Bella, D.J., Goulding, M., Guillemot, F., Lanuza, G.M. Neurogenin3 restricts serotonergic neuron differentiation to the hindbrain. (2014) Journal of Neuroscience. 34(46):15223-33. DOI: 10.1523/JNEUROSCI.3403-14.2014

+ expand abstract

Sejnowski, T.J., Churchland, P.S., Movshon, J.A. Putting big data to good use in neuroscience. (2014) Nature Neuroscience. 17(11):1440-1. DOI: 10.1038/nn.3839

+ expand abstract

Kim, S.H., Steele, J.W., Lee, S.W., Clemenson, G.D., Carter, T.A., Treuner, K., Gadient, R., Wedel, P., Glabe, C., Barlow, C., Ehrlich, M.E., Gage, F.H., Gandy, S. Proneurogenic Group II mGluR antagonist improves learning and reduces anxiety in Alzheimer Aβ oligomer mouse. (2014) Molecular Psychiatry. 19(11):1235-42. DOI: 10.1038/mp.2014.87

+ expand abstract

Hook, V., Brennand, K.J., Kim, Y., Toneff, T., Funkelstein, L., Lee, K.C., Ziegler, M., Gage, F.H. Human iPSC neurons display activity-dependent neurotransmitter secretion: aberrant catecholamine levels in schizophrenia neurons. (2014) Stem Cell Reports. 3(4):531-8. DOI: 10.1016/j.stemcr.2014.08.001

+ expand abstract

Aimone, J.B., Li, Y., Lee, S.W., Clemenson, G.D., Deng, W., Gage, F.H. Regulation and function of adult neurogenesis: from genes to cognition. (2014) Physiological Reviews. 94(4):991-1026. DOI: 10.1152/physrev.00004.2014

+ expand abstract

Jessberger, S., Gage, F.H. Adult neurogenesis: bridging the gap between mice and humans. (2014) Trends in Cell Biology. 24(10):558-63. DOI: 10.1016/j.tcb.2014.07.003

+ expand abstract

Fields, R.D., Araque, A., Johansen-Berg, H., Lim, S.S., Lynch, G., Nave, K.A., Nedergaard, M., Perez, R., Sejnowski, T., Wake, H. Glial biology in learning and cognition. (2014) The Neuroscientist. 20(5):426-431. DOI: 10.1177/1073858413504465

+ expand abstract

Mak-McCully, R.A., Deiss, S.R., Rosen, B.Q., Jung, K.Y., Sejnowski, T.J., Bastuji, H., Rey, M., Cash, S.S., Bazhenov, M., Halgren, E. Synchronization of isolated downstates (K-complexes) may be caused by cortically-induced disruption of thalamic spindling. (2014) PLOS Computational Biology. 10(9):e1003855. DOI: 10.1371/journal.pcbi.1003855

+ expand abstract

Sleep spindles and K-complexes (KCs) define stage 2 NREM sleep (N2) in humans. We recently showed that KCs are isolated downstates characterized by widespread cortical silence. We demonstrate here that KCs can be quasi-synchronous across scalp EEG and across much of the cortex using electrocorticography (ECOG) and localized transcortical recordings (bipolar SEEG). We examine the mechanism of synchronous KC production by creating the first conductance based thalamocortical network model of N2 sleep to generate both spontaneous spindles and KCs. Spontaneous KCs are only observed when the model includes diffuse projections from restricted prefrontal areas to the thalamic reticular nucleus (RE), consistent with recent anatomical findings in rhesus monkeys. Modeled KCs begin with a spontaneous focal depolarization of the prefrontal neurons, followed by depolarization of the RE. Surprisingly, the RE depolarization leads to decreased firing due to disrupted spindling, which in turn is due to depolarization-induced inactivation of the low-threshold Ca2+ current (IT). Further, although the RE inhibits thalamocortical (TC) neurons, decreased RE firing causes decreased TC cell firing, again because of disrupted spindling. The resulting abrupt removal of excitatory input to cortical pyramidal neurons then leads to the downstate. Empirically, KCs may also be evoked by sensory stimuli while maintaining sleep. We reproduce this phenomenon in the model by depolarization of either the RE or the widely-projecting prefrontal neurons. Again, disruption of thalamic spindling plays a key role. Higher levels of RE stimulation also cause downstates, but by directly inhibiting the TC neurons. SEEG recordings from the thalamus and cortex in a single patient demonstrated the model prediction that thalamic spindling significantly decreases before KC onset. In conclusion, we show empirically that KCs can be widespread quasi-synchronous cortical downstates, and demonstrate with the first model of stage 2 NREM sleep a possible mechanism whereby this widespread synchrony may arise.

Stefan, M.I., Bartol, T.M., Sejnowski, T.J., Kennedy, M.B. Multi-state modeling of biomolecules. (2014) PLOS Computational Biology. 10(9):e1003844. DOI: 10.1371/journal.pcbi.1003844

+ expand abstract

Sharpee, T.O. Toward functional classification of neuronal types. (2014) Neuron. 83(6):1329-34. DOI: 10.1016/j.neuron.2014.08.040

+ expand abstract

Garrett, M.E., Nauhaus, I., Marshel, J.H., Callaway, E.M. Topography and areal organization of mouse visual cortex. (2014) Journal of Neuroscience. 34(37):12587-12600. DOI: 10.1523/JNEUROSCI.1124-14.2014

+ expand abstract

Winner, B., Marchetto, M.C., Winkler, J., Gage, F.H. Human-induced pluripotent stem cells pave the road for a better understanding of motor neuron disease. (2014) Human Molecular Genetics. 23(R1):R27-34. DOI: 10.1093/hmg/ddu205

+ expand abstract

Gage, F., Nair, P. QnAs with Fred Gage. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(36):12958-9. DOI: 10.1073/pnas.1412625111

Moldakarimov, S., Bazhenov, M., Sejnowski, T.J. Top-down inputs enhance orientation selectivity in neurons of the primary visual cortex during perceptual learning. (2014) PLOS Computational Biology. 10(8):e1003770. DOI: 10.1371/journal.pcbi.1003770

+ expand abstract

Lee, H.S., Ghetti, A., Pinto-Duarte, A., Wang, X., Dziewczapolski, G., Galimi, F., Huitron-Resendiz, S., Piña-Crespo, J.C., Roberts, A.J., Verma, I.M., Sejnowski, T.J., Heinemann, S.F. Astrocytes contribute to gamma oscillations and recognition memory. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(32):E3343-52. DOI: 10.1073/pnas.1410893111

+ expand abstract

Erwin, J.A., Marchetto, M.C., Gage, F.H. Mobile DNA elements in the generation of diversity and complexity in the brain. (2014) Nature Reviews Neuroscience. 15(8):497-506. DOI: 10.1038/nrn3730

+ expand abstract

Gage, F., Pariente, N. On jumping genes and other things: Interview with Fred Gage, Adler Professor at the Salk Institute. (2014) EMBO Reports. 15(8):822-6. DOI: 10.15252/embr.201439088

Zhao, C., Jou, J., Wolff, L.J., Sun, H., Gage, F.H. Spine morphogenesis in newborn granule cells is differentially regulated in the outer and middle molecular layers. (2014) Journal of Comparative Neurology. 522(12):2756-66. DOI: 10.1002/cne.23581

+ expand abstract

Weyhenmeyer, J., Hernandez, M.E., Lainscsek, C., Sejnowski, T.J., Poizner, H. Muscle artifacts in single trial EEG data distinguish patients with Parkinson's disease from healthy individuals. (2014) Conf Proc IEEE Eng Med Biol Soc. 2014:3292-3295. DOI: 10.1109/EMBC.2014.6944326

+ expand abstract

Broccard, F.D., Mullen, T., Chi, Y.M., Peterson, D., Iversen, J.R., Arnold, M., Kreutz-Delgado, K., Jung, T.P., Makeig, S., Poizner, H., Sejnowski, T., Cauwenberghs, G. Closed-loop brain-machine-body interfaces for noninvasive rehabilitation of movement disorders. (2014) Ann Biomed Eng. 42(8):1573-1593. DOI: 10.1007/s10439-014-1032-6

+ expand abstract

Bekinschtein, P., Kent, B.A., Oomen, C.A., Clemenson, G.D., Gage, F.H., Saksida, L.M., Bussey, T.J. Brain-derived neurotrophic factor interacts with adult-born immature cells in the dentate gyrus during consolidation of overlapping memories. (2014) Hippocampus. 24(8):905-11. DOI: 10.1002/hipo.22304

+ expand abstract

Hatori, M., Gill, S., Mure, L.S., Goulding, M., O'Leary, D.D., Panda, S. Lhx1 maintains synchrony among circadian oscillator neurons of the SCN. (2014) Elife. 3:e03357. DOI: 10.7554/eLife.03357

+ expand abstract

Ni, Y., Nawabi, H., Liu, X., Yang, L., Miyamichi, K., Tedeschi, A., Xu, B., Wall, N.R., Callaway, E.M., He, Z. Characterization of long descending premotor propriospinal neurons in the spinal cord. (2014) Journal of Neuroscience. 34(28):9404-9417. DOI: 10.1523/JNEUROSCI.1771-14.2014

+ expand abstract

Stein, J.L., de la Torre-Ubieta, L., Tian, Y., Parikshak, N.N., Hernández, I.A., Marchetto, M.C., Baker, D.K., Lu, D., Hinman, C.R., Lowe, J.K., Wexler, E.M., Muotri, A.R., Gage, F.H., Kosik, K.S., Geschwind, D.H. A quantitative framework to evaluate modeling of cortical development by neural stem cells. (2014) Neuron. 83(1):69-86. DOI: 10.1016/j.neuron.2014.05.035

+ expand abstract

Saremi, S., Sejnowski, T.J. On criticality in high-dimensional data. (2014) Neural Computation. 26(7):1329-1339. DOI: 10.1162/NECO_a_00607

+ expand abstract

Yu, D.X., Marchetto, M.C., Gage, F.H. How to make a hippocampal dentate gyrus granule neuron. (2014) Development. 141(12):2366-75. DOI: 10.1242/dev.096776

+ expand abstract

Solstad, T., Yousif, H.N., Sejnowski, T.J. Place cell rate remapping by CA3 recurrent collaterals. (2014) PLOS Computational Biology. 10(6):e1003648. DOI: 10.1371/journal.pcbi.1003648

+ expand abstract

Episodic-like memory is thought to be supported by attractor dynamics in the hippocampus. A possible neural substrate for this memory mechanism is rate remapping, in which the spatial map of place cells encodes contextual information through firing rate variability. To test whether memories are stored as multimodal attractors in populations of place cells, recent experiments morphed one familiar context into another while observing the responses of CA3 cell ensembles. Average population activity in CA3 was reported to transition gradually rather than abruptly from one familiar context to the next, suggesting a lack of attractive forces associated with the two stored representations. On the other hand, individual CA3 cells showed a mix of gradual and abrupt transitions at different points along the morph sequence, and some displayed hysteresis which is a signature of attractor dynamics. To understand whether these seemingly conflicting results are commensurate with attractor network theory, we developed a neural network model of the CA3 with attractors for both position and discrete contexts. We found that for memories stored in overlapping neural ensembles within a single spatial map, position-dependent context attractors made transitions at different points along the morph sequence. Smooth transition curves arose from averaging across the population, while a heterogeneous set of responses was observed on the single unit level. In contrast, orthogonal memories led to abrupt and coherent transitions on both population and single unit levels as experimentally observed when remapping between two independent spatial maps. Strong recurrent feedback entailed a hysteretic effect on the network which diminished with the amount of overlap in the stored memories. These results suggest that context-dependent memory can be supported by overlapping local attractors within a spatial map of CA3 place cells. Similar mechanisms for context-dependent memory may also be found in other regions of the cerebral cortex.

Sharpee, T.O. Function determines structure in complex neural networks. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(23):8327-8. DOI: 10.1073/pnas.1407198111

Goulding, M., Bourane, S., Garcia-Campmany, L., Dalet, A., Koch, S. Inhibition downunder: an update from the spinal cord. (2014) Current Opinion in Neurobiology. 26:161-6. DOI: 10.1016/j.conb.2014.03.006

+ expand abstract

Lacar, B., Parylak, S.L., Vadodaria, K.C., Sarkar, A., Gage, F.H. Increasing the resolution of the adult neurogenesis picture. (2014) F1000 Prime Reports. 6:8. DOI: 10.12703/P6-8

+ expand abstract

Hrvoj-Mihic, B., Marchetto, M.C., Gage, F.H., Semendeferi, K., Muotri, A.R. Novel tools, classic techniques: evolutionary studies using primate pluripotent stem cells. (2014) Biological Psychiatry. 75(12):929-35. DOI: 10.1016/j.biopsych.2013.08.007

+ expand abstract

Sejnowski, T.J. Summary: Cognition in 2014. (2014) Cold Spring Harbor Symposia on Quantitative Biology. 79:237-41. DOI: 10.1101/sqb.2014.79.024885

+ expand abstract

Sejnowski, T.J., Poizner, H., Lynch, G., Gepshtein, S., Greenspan, R.J. Prospective Optimization. (2014) Proceedings of the IEEE. Institute of Electrical and Electronics Engineers. 102(5). DOI: 10.1109/JPROC.2014.2314297

+ expand abstract

Knowland, D., Arac, A., Sekiguchi, K.J., Hsu, M., Lutz, S.E., Perrino, J., Steinberg, G.K., Barres, B.A., Nimmerjahn, A., Agalliu, D. Stepwise recruitment of transcellular and paracellular pathways underlies blood-brain barrier breakdown in stroke. (2014) Neuron. 82(3):603-17. DOI: 10.1016/j.neuron.2014.03.003

+ expand abstract

Jadi, M.P., Sejnowski, T.J. Cortical oscillations arise from contextual interactions that regulate sparse coding. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(18):6780-5. DOI: 10.1073/pnas.1405300111

+ expand abstract

Hashimoto-Torii, K., Torii, M., Fujimoto, M., Nakai, A., El Fatimy, R., Mezger, V., Ju, M.J., Ishii, S., Chao, S.H., Brennand, K.J., Gage, F.H., Rakic, P. Roles of heat shock factor 1 in neuronal response to fetal environmental risks and its relevance to brain disorders. (2014) Neuron. 82(3):560-72. DOI: 10.1016/j.neuron.2014.03.002

+ expand abstract

Cetin, A., Callaway, E.M. Optical control of retrogradely infected neurons using drug-regulated "TLoop" lentiviral vectors. (2014) Journal of Neurophysiology. 111(10):2150-2159. DOI: 10.1152/jn.00495.2013

+ expand abstract

Wang, L., Mongera, A., Bonanomi, D., Cyganek, L., Pfaff, S.L., Nüsslein-Volhard, C., Marquardt, T. A conserved axon type hierarchy governing peripheral nerve assembly. (2014) Development. 141(9):1875-83. DOI: 10.1242/dev.106211

+ expand abstract

McDonnell, M.D., Boahen, K., Ijspeert, A., Sejnowski, T.J. Engineering Intelligent Electronic Systems Based on Computational Neuroscience. (2014) Proceedings of the IEEE. Institute of Electrical and Electronics Engineers. 102(5):646-651. DOI: 10.1109/JPROC.2014.2314776

Rockenstein, E., Nuber, S., Overk, C.R., Ubhi, K., Mante, M., Patrick, C., Adame, A., Trejo-Morales, M., Gerez, J., Picotti, P., Jensen, P.H., Campioni, S., Riek, R., Winkler, J., Gage, F.H., Winner, B., Masliah, E. Accumulation of oligomer-prone α-synuclein exacerbates synaptic and neuronal degeneration in vivo. (2014) Brain. 137(Pt 5):1496-513. DOI: 10.1093/brain/awu057

+ expand abstract

In Parkinson's disease and dementia with Lewy bodies, α-synuclein aggregates to form oligomers and fibrils; however, the precise nature of the toxic α-synuclein species remains unclear. A number of synthetic α-synuclein mutations were recently created (E57K and E35K) that produce species of α-synuclein that preferentially form oligomers and increase α-synuclein-mediated toxicity. We have shown that acute lentiviral expression of α-synuclein E57K leads to the degeneration of dopaminergic neurons; however, the effects of chronic expression of oligomer-prone α-synuclein in synapses throughout the brain have not been investigated. Such a study could provide insight into the possible mechanism(s) through which accumulation of α-synuclein oligomers in the synapse leads to neurodegeneration. For this purpose, we compared the patterns of neurodegeneration and synaptic damage between a newly generated mThy-1 α-synuclein E57K transgenic mouse model that is prone to forming oligomers and the mThy-1 α-synuclein wild-type mouse model (Line 61), which accumulates various forms of α-synuclein. Three lines of α-synuclein E57K (Lines 9, 16 and 54) were generated and compared with the wild-type. The α-synuclein E57K Lines 9 and 16 were higher expressings of α-synuclein, similar to α-synuclein wild-type Line 61, and Line 54 was a low expressing of α-synuclein compared to Line 61. By immunoblot analysis, the higher-expressing α-synuclein E57K transgenic mice showed abundant oligomeric, but not fibrillar, α-synuclein whereas lower-expressing mice accumulated monomeric α-synuclein. Monomers, oligomers, and fibrils were present in α-synuclein wild-type Line 61. Immunohistochemical and ultrastructural analyses demonstrated that α-synuclein accumulated in the synapses but not in the neuronal cells bodies, which was different from the α-synuclein wild-type Line 61, which accumulates α-synuclein in the soma. Compared to non-transgenic and lower-expressing mice, the higher-expressing α-synuclein E57K mice displayed synaptic and dendritic loss, reduced levels of synapsin 1 and synaptic vesicles, and behavioural deficits. Similar alterations, but to a lesser extent, were seen in the α-synuclein wild-type mice. Moreover, although the oligomer-prone α-synuclein mice displayed neurodegeneration in the frontal cortex and hippocampus, the α-synuclein wild-type only displayed neuronal loss in the hippocampus. These results support the hypothesis that accumulating oligomeric α-synuclein may mediate early synaptic pathology in Parkinson's disease and dementia with Lewy bodies by disrupting synaptic vesicles. This oligomer-prone model might be useful for evaluating therapies directed at oligomer reduction.

Havlicek, S., Kohl, Z., Mishra, H.K., Prots, I., Eberhardt, E., Denguir, N., Wend, H., Plötz, S., Boyer, L., Marchetto, M.C., Aigner, S., Sticht, H., Groemer, T.W., Hehr, U., Lampert, A., Schlötzer-Schrehardt, U., Winkler, J., Gage, F.H., Winner, B. Gene dosage-dependent rescue of HSP neurite defects in SPG4 patients' neurons. (2014) Human Molecular Genetics. 23(10):2527-41. DOI: 10.1093/hmg/ddt644

+ expand abstract

Jadi, M.P., Sejnowski, T.J. Regulating Cortical Oscillations in an Inhibition-Stabilized Network. (2014) Proceedings of the IEEE. Institute of Electrical and Electronics Engineers. 102(5). DOI: 10.1109/JPROC.2014.2313113

+ expand abstract

O'Donnell, C., Sejnowski, T.J. Selective memory generalization by spatial patterning of protein synthesis. (2014) Neuron. 82(2):398-412. DOI: 10.1016/j.neuron.2014.02.028

+ expand abstract

Sharpee, T.O., Calhoun, A.J., Chalasani, S.H. Information theory of adaptation in neurons, behavior, and mood. (2014) Current Opinion in Neurobiology. 25:47-53. DOI: 10.1016/j.conb.2013.11.007

+ expand abstract

Morris, R., Sancho-Martinez, I., Sharpee, T.O., Izpisua Belmonte, J.C. Mathematical approaches to modeling development and reprogramming. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(14):5076-82. DOI: 10.1073/pnas.1317150111

+ expand abstract

Firth, A.L., Dargitz, C.T., Qualls, S.J., Menon, T., Wright, R., Singer, O., Gage, F.H., Khanna, A., Verma, I.M. Generation of multiciliated cells in functional airway epithelia from human induced pluripotent stem cells. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(17):E1723-30. DOI: 10.1073/pnas.1403470111

+ expand abstract

Zhang, J., Lanuza, G.M., Britz, O., Wang, Z., Siembab, V.C., Zhang, Y., Velasquez, T., Alvarez, F.J., Frank, E., Goulding, M. V1 and v2b interneurons secure the alternating flexor-extensor motor activity mice require for limbed locomotion. (2014) Neuron. 82(1):138-50. DOI: 10.1016/j.neuron.2014.02.013

+ expand abstract

Sun, Y., Nguyen, A.Q., Nguyen, J.P., Le, L., Saur, D., Choi, J., Callaway, E.M., Xu, X. Cell-type-specific circuit connectivity of hippocampal CA1 revealed through Cre-dependent rabies tracing. (2014) Cell Reports. 7(1):269-280. DOI: 10.1016/j.celrep.2014.02.030

+ expand abstract

Pao, G.M., Zhu, Q., Perez-Garcia, C.G., Chou, S.J., Suh, H., Gage, F.H., O'Leary, D.D., Verma, I.M. Role of BRCA1 in brain development. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(13):E1240-8. DOI: 10.1073/pnas.1400783111

+ expand abstract

Levine, A.J., Hinckley, C.A., Hilde, K.L., Driscoll, S.P., Poon, T.H., Montgomery, J.M., Pfaff, S.L. Identification of a cellular node for motor control pathways. (2014) Nature Neuroscience. 17(4):586-93. DOI: 10.1038/nn.3675

+ expand abstract

Crotti, A., Benner, C., Kerman, B.E., Gosselin, D., Lagier-Tourenne, C., Zuccato, C., Cattaneo, E., Gage, F.H., Cleveland, D.W., Glass, C.K. Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors. (2014) Nature Neuroscience. 17(4):513-21. DOI: 10.1038/nn.3668

+ expand abstract

Edwards, J., Daniel, E., Kinney, J., Bartol, T., Sejnowski, T., Johnston, D., Harris, K., Bajaj, C. VolRoverN: enhancing surface and volumetric reconstruction for realistic dynamical simulation of cellular and subcellular function. (2014) Neuroinformatics. 12(2):277-289. DOI: 10.1007/s12021-013-9205-2

+ expand abstract

Yu, D.X., Di Giorgio, F.P., Yao, J., Marchetto, M.C., Brennand, K., Wright, R., Mei, A., McHenry, L., Lisuk, D., Grasmick, J.M., Silberman, P., Silberman, G., Jappelli, R., Gage, F.H. Modeling hippocampal neurogenesis using human pluripotent stem cells. (2014) Stem Cell Reports. 2(3):295-310. DOI: 10.1016/j.stemcr.2014.01.009

+ expand abstract

Cruz-Martín, A., El-Danaf, R.N., Osakada, F., Sriram, B., Dhande, O.S., Nguyen, P.L., Callaway, E.M., Ghosh, A., Huberman, A.D. A dedicated circuit links direction-selective retinal ganglion cells to the primary visual cortex. (2014) Nature. 507(7492):358-361. DOI: 10.1038/nature12989

+ expand abstract

Wright, R., Réthelyi, J.M., Gage, F.H. Enhancing induced pluripotent stem cell models of schizophrenia. (2014) JAMA Psychiatry. 71(3):334-5. DOI: 10.1001/jamapsychiatry.2013.4239

Yang, L., Leung, H., Peterson, D.A., Sejnowski, T.J., Poizner, H. Toward a semi-self-paced EEG brain computer interface: decoding initiation state from non-initiation state in dedicated time slots. (2014) PLOS One. 9(2):e88915. DOI: 10.1371/journal.pone.0088915

+ expand abstract

Brain computer interfaces (BCIs) offer a broad class of neurologically impaired individuals an alternative means to interact with the environment. Many BCIs are "synchronous" systems, in which the system sets the timing of the interaction and tries to infer what control command the subject is issuing at each prompting. In contrast, in "asynchronous" BCIs subjects pace the interaction and the system must determine when the subject's control command occurs. In this paper we propose a new idea for BCI which draws upon the strengths of both approaches. The subjects are externally paced and the BCI is able to determine when control commands are issued by decoding the subject's intention for initiating control in dedicated time slots. A single task with randomly interleaved trials was designed to test whether it can be used as stimulus for inducing initiation and non-initiation states when the sensory and motor requirements for the two types of trials are very nearly identical. Further, the essential problem on the discrimination between initiation state and non-initiation state was studied. We tested the ability of EEG spectral power to distinguish between these two states. Among the four standard EEG frequency bands, beta band power recorded over parietal-occipital cortices provided the best performance, achieving an average accuracy of 86% for the correct classification of initiation and non-initiation states. Moreover, delta band power recorded over parietal and motor areas yielded a good performance and thus could also be used as an alternative feature to discriminate these two mental states. The results demonstrate the viability of our proposed idea for a BCI design based on conventional EEG features. Our proposal offers the potential to mitigate the signal detection challenges of fully asynchronous BCIs, while providing greater flexibility to the subject than traditional synchronous BCIs.

Vadodaria, K.C., Gage, F.H. SnapShot: adult hippocampal neurogenesis. (2014) Cell. 156(5):1114-1114.e1. DOI: 10.1016/j.cell.2014.02.029

Rangel, L.M., Alexander, A.S., Aimone, J.B., Wiles, J., Gage, F.H., Chiba, A.A., Quinn, L.K. Temporally selective contextual encoding in the dentate gyrus of the hippocampus. (2014) Nature Communications. 5:3181. DOI: 10.1038/ncomms4181

+ expand abstract

Parylak, S.L., Deng, W., Gage, F.H. Mother's milk programs offspring's cognition. (2014) Nature Neuroscience. 17(1):8-9. DOI: 10.1038/nn.3611

Marchetto, M.C., Gage, F.H. Your brain under the microscope: the promise of stem cells. (2014) Cerebrum. 2014:1.

+ expand abstract

Lainscsek, C., Weyhenmeyer, J., Hernandez, M.E., Poizner, H., Sejnowski, T.J. Non-linear dynamical classification of short time series of the rössler system in high noise regimes. (2013) Frontiers in Neurology. 4:182. DOI: 10.3389/fneur.2013.00182

+ expand abstract

Time series analysis with delay differential equations (DDEs) reveals non-linear properties of the underlying dynamical system and can serve as a non-linear time-domain classification tool. Here global DDE models were used to analyze short segments of simulated time series from a known dynamical system, the Rössler system, in high noise regimes. In a companion paper, we apply the DDE model developed here to classify short segments of encephalographic (EEG) data recorded from patients with Parkinson's disease and healthy subjects. Nine simulated subjects in each of two distinct classes were generated by varying the bifurcation parameter b and keeping the other two parameters (a and c) of the Rössler system fixed. All choices of b were in the chaotic parameter range. We diluted the simulated data using white noise ranging from 10 to -30 dB signal-to-noise ratios (SNR). Structure selection was supervised by selecting the number of terms, delays, and order of non-linearity of the model DDE model that best linearly separated the two classes of data. The distances d from the linear dividing hyperplane was then used to assess the classification performance by computing the area A' under the ROC curve. The selected model was tested on untrained data using repeated random sub-sampling validation. DDEs were able to accurately distinguish the two dynamical conditions, and moreover, to quantify the changes in the dynamics. There was a significant correlation between the dynamical bifurcation parameter b of the simulated data and the classification parameter d from our analysis. This correlation still held for new simulated subjects with new dynamical parameters selected from each of the two dynamical regimes. Furthermore, the correlation was robust to added noise, being significant even when the noise was greater than the signal. We conclude that DDE models may be used as a generalizable and reliable classification tool for even small segments of noisy data.

Lainscsek, C., Hernandez, M.E., Weyhenmeyer, J., Sejnowski, T.J., Poizner, H. Non-linear dynamical analysis of EEG time series distinguishes patients with Parkinson's disease from healthy individuals. (2013) Frontiers in Neurology. 4:200. DOI: 10.3389/fneur.2013.00200

+ expand abstract

The pathophysiology of Parkinson's disease (PD) is known to involve altered patterns of neuronal firing and synchronization in cortical-basal ganglia circuits. One window into the nature of the aberrant temporal dynamics in the cerebral cortex of PD patients can come from analysis of the patients electroencephalography (EEG). Rather than using spectral-based methods, we used data models based on delay differential equations (DDE) as non-linear time-domain classification tools to analyze EEG recordings from PD patients on and off dopaminergic therapy and healthy individuals. Two sets of 50 1-s segments of 64-channel EEG activity were recorded from nine PD patients on and off medication and nine age-matched controls. The 64 EEG channels were grouped into 10 clusters covering frontal, central, parietal, and occipital brain regions for analysis. DDE models were fitted to individual trials, and model coefficients and error were used as features for classification. The best models were selected using repeated random sub-sampling validation and classification performance was measured using the area under the ROC curve A'. In a companion paper, we show that DDEs can uncover hidden dynamical structure from short segments of simulated time series of known dynamical systems in high noise regimes. Using the same method for finding the best models, we found here that even short segments of EEG data in PD patients and controls contained dynamical structure, and moreover, that PD patients exhibited a greater dynamic range than controls. DDE model output on the means from one set of 50 trials provided nearly complete separation of PD patients off medication from controls: across brain regions, the area under the receiver-operating characteristic curves, A', varied from 0.95 to 1.0. For distinguishing PD patients on vs. off medication, classification performance A' ranged from 0.86 to 1.0 across brain regions. Moreover, the generalizability of the model to the second set of 50 trials was excellent, with A' ranging from 0.81 to 0.94 across brain regions for controls vs. PD off medication, and from 0.62 to 0.82 for PD on medication vs. off. Finally, model features significantly predicted individual patients' motor severity, as assessed with standard clinical rating scales.

Pfaff, S., Shaham, S. Development of neurons and glia. (2013) Current Opinion in Neurobiology. 23(6):901-2.

Grindberg, R.V., Yee-Greenbaum, J.L., McConnell, M.J., Novotny, M., O'Shaughnessy, A.L., Lambert, G.M., Araúzo-Bravo, M.J., Lee, J., Fishman, M., Robbins, G.E., Lin, X., Venepally, P., Badger, J.H., Galbraith, D.W., Gage, F.H., Lasken, R.S. RNA-sequencing from single nuclei. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(49):19802-7. DOI: 10.1073/pnas.1319700110

+ expand abstract

Borowska, J., Jones, C.T., Zhang, H., Blacklaws, J., Goulding, M., Zhang, Y. Functional subpopulations of V3 interneurons in the mature mouse spinal cord. (2013) Journal of Neuroscience. 33(47):18553-65. DOI: 10.1523/JNEUROSCI.2005-13.2013

+ expand abstract

Del Barrio, M.G., Bourane, S., Grossmann, K., Schüle, R., Britsch, S., O'Leary, D.D., Goulding, M. A transcription factor code defines nine sensory interneuron subtypes in the mechanosensory area of the spinal cord. (2013) PLOS One. 8(11):e77928. DOI: 10.1371/journal.pone.0077928

+ expand abstract

Reilly, M.T., Faulkner, G.J., Dubnau, J., Ponomarev, I., Gage, F.H. The role of transposable elements in health and diseases of the central nervous system. (2013) Journal of Neuroscience. 33(45):17577-86. DOI: 10.1523/JNEUROSCI.3369-13.2013

+ expand abstract

McConnell, M.J., Lindberg, M.R., Brennand, K.J., Piper, J.C., Voet, T., Cowing-Zitron, C., Shumilina, S., Lasken, R.S., Vermeesch, J.R., Hall, I.M., Gage, F.H. Mosaic copy number variation in human neurons. (2013) Science. 342(6158):632-7. DOI: 10.1126/science.1243472

+ expand abstract

Marchetto, M.C.N., Narvaiza, I., Denli, A.M., Benner, C., Lazzarini, T.A., Nathanson, J.L., Paquola, A.C.M., Desai, K.N., Herai, R.H., Weitzman, M.D., Yeo, G.W., Muotri, A.R., Gage, F.H. Differential L1 regulation in pluripotent stem cells of humans and apes. (2013) Nature. 503(7477):525-529. DOI: 10.1038/nature12686

+ expand abstract

Identifying cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic understanding of the evolution and diversity of our own species. Until now, preserved tissues have been the main source for most comparative studies between humans, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). However, these tissue samples do not fairly represent the distinctive traits of live cell behaviour and are not amenable to genetic manipulation. We propose that induced pluripotent stem (iPS) cells could be a unique biological resource to determine relevant phenotypical differences between human and NHPs, and that those differences could have potential adaptation and speciation value. Here we describe the generation and initial characterization of iPS cells from chimpanzees and bonobos as new tools to explore factors that may have contributed to great ape evolution. Comparative gene expression analysis of human and NHP iPS cells revealed differences in the regulation of long interspersed element-1 (L1, also known as LINE-1) transposons. A force of change in mammalian evolution, L1 elements are retrotransposons that have remained active during primate evolution. Decreased levels of L1-restricting factors APOBEC3B (also known as A3B) and PIWIL2 (ref. 7) in NHP iPS cells correlated with increased L1 mobility and endogenous L1 messenger RNA levels. Moreover, results from the manipulation of A3B and PIWIL2 levels in iPS cells supported a causal inverse relationship between levels of these proteins and L1 retrotransposition. Finally, we found increased copy numbers of species-specific L1 elements in the genome of chimpanzees compared to humans, supporting the idea that increased L1 mobility in NHPs is not limited to iPS cells in culture and may have also occurred in the germ line or embryonic cells developmentally upstream to germline specification during primate evolution. We propose that differences in L1 mobility may have differentially shaped the genomes of humans and NHPs and could have continuing adaptive significance.

Bekinschtein, P., Kent, B.A., Oomen, C.A., Clemenson, G.D., Gage, F.H., Saksida, L.M., Bussey, T.J. BDNF in the dentate gyrus is required for consolidation of "pattern-separated" memories. (2013) Cell Reports. 5(3):759-68. DOI: 10.1016/j.celrep.2013.09.027

+ expand abstract

Miller, J.A., Nathanson, J., Franjic, D., Shim, S., Dalley, R.A., Shapouri, S., Smith, K.A., Sunkin, S.M., Bernard, A., Bennett, J.L., Lee, C.K., Hawrylycz, M.J., Jones, A.R., Amaral, D.G., Šestan, N., Gage, F.H., Lein, E.S. Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates. (2013) Development. 140(22):4633-44. DOI: 10.1242/dev.097212

+ expand abstract

Gage, F.H., Temple, S. Neural stem cells: generating and regenerating the brain. (2013) Neuron. 80(3):588-601. DOI: 10.1016/j.neuron.2013.10.037

+ expand abstract

Deshmukh, V.A., Tardif, V., Lyssiotis, C.A., Green, C.C., Kerman, B., Kim, H.J., Padmanabhan, K., Swoboda, J.G., Ahmad, I., Kondo, T., Gage, F.H., Theofilopoulos, A.N., Lawson, B.R., Schultz, P.G., Lairson, L.L. A regenerative approach to the treatment of multiple sclerosis. (2013) Nature. 502(7471):327-332. DOI: 10.1038/nature12647

+ expand abstract

Devor, A., Bandettini, P.A., Boas, D.A., Bower, J.M., Buxton, R.B., Cohen, L.B., Dale, A.M., Einevoll, G.T., Fox, P.T., Franceschini, M.A., Friston, K.J., Fujimoto, J.G., Geyer, M.A., Greenberg, J.H., Halgren, E., Hämäläinen, M.S., Helmchen, F., Hyman, B.T., Jasanoff, A., Jernigan, T.L., Judd, L.L., Kim, S.G., Kleinfeld, D., Kopell, N.J., Kutas, M., Kwong, K.K., Larkum, M.E., Lo, E.H., Magistretti, P.J., Mandeville, J.B., Masliah, E., Mitra, P.P., Mobley, W.C., Moskowitz, M.A., Nimmerjahn, A., Reynolds, J.H., Rosen, B.R., Salzberg, B.M., Schaffer, C.B., Silva, G.A., So, P.T., Spitzer, N.C., Tootell, R.B., Van Essen, D.C., Vanduffel, W., Vinogradov, S.A., Wald, L.L., Wang, L.V., Weber, B., Yodh, A.G. The challenge of connecting the dots in the B.R.A.I.N. (2013) Neuron. 80(2):270-4. DOI: 10.1016/j.neuron.2013.09.008

+ expand abstract

Cortes, J.M., Desroches, M., Rodrigues, S., Veltz, R., Muñoz, M.A., Sejnowski, T.J. Short-term synaptic plasticity in the deterministic Tsodyks-Markram model leads to unpredictable network dynamics. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(41):16610-5. DOI: 10.1073/pnas.1316071110

+ expand abstract

Herzog, C.D., Brown, L., Kruegel, B.R., Wilson, A., Tansey, M.G., Gage, F.H., Johnson, E.M., Bartus, R.T. Enhanced neurotrophic distribution, cell signaling and neuroprotection following substantia nigral versus striatal delivery of AAV2-NRTN (CERE-120). (2013) Neurobiol. Dis. 58:38-48. DOI: 10.1016/j.nbd.2013.04.011

+ expand abstract

This paper reassesses the currently accepted viewpoint that targeting the terminal fields (i.e. striatum) of degenerating nigrostriatal dopamine neurons with neurotrophic factors in Parkinson's disease (PD) is sufficient for achieving an optimal neurotrophic response. Recent insight indicating that PD is an axonopathy characterized by axonal transport deficits prompted this effort. We tested whether a significantly greater neurotrophic response might be induced in SN neurons when the neurotrophic factor neurturin (NRTN) is also targeted to the substantia nigra (SN), compared to the more conventional, striatum-only target. While recognizing the importance of maintaining the integrity of nigrostriatal fibers and terminals (especially for achieving optimal function), we refocused attention to the fate of SN neurons. Under conditions of axonal degeneration and neuronal transport deficits, this component of the nigrostriatal system is most vulnerable to the lack of neurotrophic exposure following striatal-only delivery. Given the location of repair genes induced by neurotrophic factors, achieving adequate neurotrophic exposure to the SN neurons is essential for an optimal neurotrophic response, while the survival of these neurons is essential to the very survival of the fibers. Two separate studies were performed using the 6-OHDA model of nigrostriatal degeneration, in conjunction with delivery of the viral vector AAV2-NRTN (CERE-120) to continuously express NRTN to either striatum or nigra alone or combined striatal/nigral exposure, including conditions of ongoing axonopathy. These studies provide additional insight for reinterpreting past animal neurotrophic/6-OHDA studies conducted under conditions where axon transport deficiencies were generally not accounted for, which suggested that targeting the striatum was both necessary and sufficient. The current data demonstrate that delivering NRTN directly to the SN produces 1) expanded NRTN distribution within the terminal field and cell bodies of targeted nigrostriatal neurons, 2) enhanced intracellular neurotrophic factor signaling in the nigrostriatal neurons, and 3) produced greater numbers of surviving dopamine neurons against 6-OHDA-induced toxicity, particularly under the conditions of active axonopathy. Thus, these data provide empirical support that targeting the SN with neurotrophic factors (in addition to striatum) may help enhance the neurotrophic response in midbrain neurons, particularly under conditions of active neurodegeneration which occurs in PD patients.

Aljadeff, J., Segev, R., Berry, M.J., Sharpee, T.O. Spike triggered covariance in strongly correlated gaussian stimuli. (2013) PLOS Computational Biology. 9(9):e1003206. DOI: 10.1371/journal.pcbi.1003206

+ expand abstract

Ruiz, O., Lustig, B.R., Nassi, J.J., Cetin, A., Reynolds, J.H., Albright, T.D., Callaway, E.M., Stoner, G.R., Roe, A.W. Optogenetics through windows on the brain in the nonhuman primate. (2013) Journal of Neurophysiology. 110(6):1455-67. DOI: 10.1152/jn.00153.2013

+ expand abstract

Hsu, C.C., White, N.M., Hayashi, M., Lin, E.C., Poon, T., Banerjee, I., Chen, J., Pfaff, S.L., Macagno, E.R., Dorrestein, P.C. Microscopy ambient ionization top-down mass spectrometry reveals developmental patterning. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(37):14855-60. DOI: 10.1073/pnas.1310618110

+ expand abstract

Timofeev, I., Sejnowski, T.J., Bazhenov, M., Chauvette, S., Grand, L.B. Age dependency of trauma-induced neocortical epileptogenesis. (2013) Frontiers in Cellular Neuroscience. 7:154. DOI: 10.3389/fncel.2013.00154

+ expand abstract

Tang, X., Zhou, L., Wagner, A.M., Marchetto, M.C., Muotri, A.R., Gage, F.H., Chen, G. Astroglial cells regulate the developmental timeline of human neurons differentiated from induced pluripotent stem cells. (2013) Stem Cell Research. 11(2):743-57. DOI: 10.1016/j.scr.2013.05.002

+ expand abstract

Osakada, F., Callaway, E.M. Design and generation of recombinant rabies virus vectors. (2013) Nature Protocols. 8(8):1583-1601. DOI: 10.1038/nprot.2013.094

+ expand abstract

Lister, R.*, Mukamel, E.A., Nery, J.R., Urich, M., Puddifoot, C.A., Johnson, N.D., Lucero, J., Huang, Y., Dwork, A.J., Schultz, M.D., Yu, M., Tonti-Filippini, J., Heyn, H., Hu, S., Wu, J.C., Rao, A., Esteller, M., He, C., Haghighi, F.G., Sejnowski, T.J., Behrens, M.M.*, Ecker, J.R.* Global epigenomic reconfiguration during mammalian brain development. (2013) Science. 341(6146):1237905. DOI: 10.1126/science.1237905

+ expand abstract

Francius, C., Harris, A., Rucchin, V., Hendricks, T.J., Stam, F.J., Barber, M., Kurek, D., Grosveld, F.G., Pierani, A., Goulding, M., Clotman, F. Identification of multiple subsets of ventral interneurons and differential distribution along the rostrocaudal axis of the developing spinal cord. (2013) PLOS One. 8(8):e70325. DOI: 10.1371/journal.pone.0070325

+ expand abstract

Sung, T.C., Chen, Z., Thuret, S., Vilar, M., Gage, F.H., Riek, R., Lee, K.F. P45 forms a complex with FADD and promotes neuronal cell survival following spinal cord injury. (2013) PLOS One. 8(7):e69286. DOI: 10.1371/journal.pone.0069286

+ expand abstract

Sharpee, T.O. Computational identification of receptive fields. (2013) Annual Review of Neuroscience. 36:103-20. DOI: 10.1146/annurev-neuro-062012-170253

+ expand abstract

Nienborg, H., Hasenstaub, A., Nauhaus, I., Taniguchi, H., Huang, Z.J., Callaway, E.M. Contrast dependence and differential contributions from somatostatin- and parvalbumin-expressing neurons to spatial integration in mouse V1. (2013) Journal of Neuroscience. 33(27):11145-11154. DOI: 10.1523/JNEUROSCI.5320-12.2013

+ expand abstract

Wall, N.R., De La Parra, M., Callaway, E.M., Kreitzer, A.C. Differential innervation of direct- and indirect-pathway striatal projection neurons. (2013) Neuron. 79(2):347-360. DOI: 10.1016/j.neuron.2013.05.014

+ expand abstract

Sharpee, T.O., Kouh, M., Reynolds, J.H. Trade-off between curvature tuning and position invariance in visual area V4. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(28):11618-23. DOI: 10.1073/pnas.1217479110

+ expand abstract

Kaardal, J., Fitzgerald, J.D., Berry, M.J., Sharpee, T.O. Identifying functional bases for multidimensional neural computations. (2013) Neural Computation. 25(7):1870-90. DOI: 10.1162/NECO_a_00465

+ expand abstract

Current dimensionality-reduction methods can identify relevant subspaces for neural computations but do not favor one basis over the other within the relevant subspace. Finding the appropriate basis can simplify the description of the nonlinear computation with respect to the relevant variables, making it easier to elucidate the underlying neural computation and make hypotheses about the neural circuitry, giving rise to the observed responses. Part of the problem is that although some of the dimensionality reduction methods can identify many of the relevant dimensions, it is usually difficult to map out or interpret the nonlinear transformation with respect to more than a few relevant dimensions simultaneously without some simplifying assumptions. While recent approaches make it possible to create predictive models based on many relevant dimensions simultaneously, there still remains the need to relate such predictive models to the mechanistic descriptions of the operation of underlying neural circuitry. Here we demonstrate that transforming to a basis within the relevant subspace where the neural computation is best described by a given nonlinear function often makes it easier to interpret the computation and describe it with a small number of parameters. We refer to the corresponding basis as the functional basis, and illustrate the utility of such transformation in the context of logical OR and logical AND functions. We show that although dimensionality-reduction methods such as spike-triggered covariance are able to find a relevant subspace, they often produce dimensions that are difficult to interpret and do not correspond to a functional basis. The functional features can be found using a maximum likelihood approach. The results are illustrated using simulated neurons and recordings from retinal ganglion cells. The resulting features are uniquely defined and nonorthogonal, and they make it easier to relate computational and mechanistic models to each other.

Golomb, B.A., Brenner, S., Chalfie, M., Glashow, S.L., Glauber, R.J., Hubel, D.H., Maskin, E.S., Greengard, P., Gross, D.J., Roberts, R., Tonegawa, S., Wilczek, F.A., Brown, E.M., Sejnowski, T.J. Chocolate habits of Nobel prizewinners. (2013) Nature. 499(7459):409. DOI: 10.1038/499409a

Lainscsek, C., Sejnowski, T.J. Electrocardiogram classification using delay differential equations. (2013) Chaos. 23(2):023132. DOI: 10.1063/1.4811544

+ expand abstract

Nandy, A.S., Sharpee, T.O., Reynolds, J.H., Mitchell, J.F. The fine structure of shape tuning in area V4. (2013) Neuron. 78(6):1102-15. DOI: 10.1016/j.neuron.2013.04.016

+ expand abstract

Yu, D.X., Marchetto, M.C., Gage, F.H. Therapeutic translation of iPSCs for treating neurological disease. (2013) Cell Stem Cell. 12(6):678-88. DOI: 10.1016/j.stem.2013.05.018

+ expand abstract

Vilchez, D., Boyer, L., Lutz, M., Merkwirth, C., Morantte, I., Tse, C., Spencer, B., Page, L., Masliah, E., Berggren, W.T., Gage, F.H., Dillin, A. FOXO4 is necessary for neural differentiation of human embryonic stem cells. (2013) Aging Cell. 12(3):518-22. DOI: 10.1111/acel.12067

+ expand abstract

Ji, B., Wang, X., Pinto-Duarte, A., Kim, M., Caldwell, S., Young, J.W., Behrens, M.M., Sejnowski, T.J., Geyer, M.A., Zhou, X. Prolonged Ketamine Effects in Sp4 Hypomorphic Mice: Mimicking Phenotypes of Schizophrenia. (2013) PLOS One. 8(6):e66327. DOI: 10.1371/journal.pone.0066327

+ expand abstract

Chukoskie, L., Snider, J., Mozer, M.C., Krauzlis, R.J., Sejnowski, T.J. Learning where to look for a hidden target. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110 Suppl :10438-10445. DOI: 10.1073/pnas.1301216110

+ expand abstract

Egawa, N., Kitaoka, S., Tsukita, K., Naitoh, M., Takahashi, K., Yamamoto, T., Adachi, F., Kondo, T., Okita, K., Asaka, I., Aoi, T., Watanabe, A., Yamada, Y., Morizane, A., Takahashi, J., Ayaki, T., Ito, H., Yoshikawa, K., Yamawaki, S., Suzuki, S., Watanabe, D., Hioki, H., Kaneko, T., Makioka, K., Okamoto, K., Takuma, H., Tamaoka, A., Hasegawa, K., Nonaka, T., Hasegawa, M., Kawata, A., Yoshida, M., Nakahata, T., Takahashi, R., Marchetto, M.C., Gage, F.H., Yamanaka, S., Inoue, H. Response to comment on "Drug screening for ALS using patient-specific induced pluripotent stem cells". (2013) Science Translational Medicine. 5(188):188lr2. DOI: 10.1126/scitranslmed.3005697

+ expand abstract

Li, Y., Stam, F.J., Aimone, J.B., Goulding, M., Callaway, E.M., Gage, F.H. Molecular layer perforant path-associated cells contribute to feed-forward inhibition in the adult dentate gyrus. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(22):9106-11. DOI: 10.1073/pnas.1306912110

+ expand abstract

Stiefel, K.M., Englitz, B., Sejnowski, T.J. Origin of intrinsic irregular firing in cortical interneurons. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(19):7886-7891. DOI: 10.1073/pnas.1305219110

+ expand abstract

Gifford, W.D., Pfaff, S.L., Macfarlan, T.S. Transposable elements as genetic regulatory substrates in early development. (2013) Trends in Cell Biology. 23(5):218-26. DOI: 10.1016/j.tcb.2013.01.001

+ expand abstract

Yin, L., Geng, Y., Osakada, F., Sharma, R., Cetin, A.H., Callaway, E.M., Williams, D.R., Merigan, W.H. Imaging light responses of retinal ganglion cells in the living mouse eye. (2013) Journal of Neurophysiology. 109(9):2415-2421. DOI: 10.1152/jn.01043.2012

+ expand abstract

Gire, D.H., Restrepo, D., Sejnowski, T.J., Greer, C., De Carlos, J.A., Lopez-Mascaraque, L. Temporal processing in the olfactory system: can we see a smell? (2013) Neuron. 78(3):416-432. DOI: 10.1016/j.neuron.2013.04.033

+ expand abstract

Rangel, L.M., Quinn, L.K., Chiba, A.A., Gage, F.H., Aimone, J.B. A hypothesis for temporal coding of young and mature granule cells. (2013) Frontiers in Neuroscience. 7:75. DOI: 10.3389/fnins.2013.00075

+ expand abstract

Saremi, S., Sejnowski, T.J., Sharpee, T.O. Double-gabor filters are independent components of small translation-invariant image patches. (2013) Neural Computation. 25(4):922-39. DOI: 10.1162/NECO_a_00418

+ expand abstract

Wang, X., Pinto-Duarte, A., Sejnowski, T.J., Behrens, M.M. How Nox2-containing NADPH oxidase affects cortical circuits in the NMDA receptor antagonist model of schizophrenia. (2013) Antioxidants & Redox Signaling. 18(12):1444-62. DOI: 10.1089/ars.2012.4907

+ expand abstract

Jeanne, J.M., Sharpee, T.O., Gentner, T.Q. Associative learning enhances population coding by inverting interneuronal correlation patterns. (2013) Neuron. 78(2):352-63. DOI: 10.1016/j.neuron.2013.02.023

+ expand abstract

Regner, B.M., Vučinić, D., Domnisoru, C., Bartol, T.M., Hetzer, M.W., Tartakovsky, D.M., Sejnowski, T.J. Anomalous diffusion of single particles in cytoplasm. (2013) Biophysical Journal. 104(8):1652-60. DOI: 10.1016/j.bpj.2013.01.049

+ expand abstract

Wang, X., Zhao, Y., Zhang, X., Badie, H., Zhou, Y., Mu, Y., Loo, L.S., Cai, L., Thompson, R.C., Yang, B., Chen, Y., Johnson, P.F., Wu, C., Bu, G., Mobley, W.C., Zhang, D., Gage, F.H., Ranscht, B., Zhang, Y.W., Lipton, S.A., Hong, W., Xu, H. Loss of sorting nexin 27 contributes to excitatory synaptic dysfunction by modulating glutamate receptor recycling in Down's syndrome. (2013) Nature Medicine. 19(4):473-80. DOI: 10.1038/nm.3117

+ expand abstract

Deng, W., Mayford, M., Gage, F.H. Selection of distinct populations of dentate granule cells in response to inputs as a mechanism for pattern separation in mice. (2013) Elife. 2:e00312. DOI: 10.7554/eLife.00312

+ expand abstract

Hinckley, C.A., Pfaff, S.L. Imaging spinal neuron ensembles active during locomotion with genetically encoded calcium indicators. (2013) Ann. N. Y. Acad. Sci. 1279:71-9. DOI: 10.1111/nyas.12092

+ expand abstract

Rowe, H.M., Kapopoulou, A., Corsinotti, A., Fasching, L., Macfarlan, T.S., Tarabay, Y., Viville, S., Jakobsson, J., Pfaff, S.L., Trono, D. TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. (2013) Genome Research. 23(3):452-61. DOI: 10.1101/gr.147678.112

+ expand abstract

Alivisatos, A.P., Andrews, A.M., Boyden, E.S., Chun, M., Church, G.M., Deisseroth, K., Donoghue, J.P., Fraser, S.E., Lippincott-Schwartz, J., Looger, L.L., Masmanidis, S., McEuen, P.L., Nurmikko, A.V., Park, H., Peterka, D.S., Reid, C., Roukes, M.L., Scherer, A., Schnitzer, M., Sejnowski, T.J., Shepard, K.L., Tsao, D., Turrigiano, G., Weiss, P.S., Xu, C., Yuste, R., Zhuang, X. Nanotools for neuroscience and brain activity mapping. (2013) ACS Nano. 7(3):1850-66. DOI: 10.1021/nn4012847

+ expand abstract

Alivisatos, A.P., Chun, M., Church, G.M., Deisseroth, K., Donoghue, J.P., Greenspan, R.J., McEuen, P.L., Roukes, M.L., Sejnowski, T.J., Weiss, P.S., Yuste, R. Neuroscience. The brain activity map. (2013) Science. 339(6125):1284-5. DOI: 10.1126/science.1236939

Liang, Y., Franks, T.M., Marchetto, M.C., Gage, F.H., Hetzer, M.W. Dynamic association of NUP98 with the human genome. (2013) PLOS Genetics. 9(2):e1003308. DOI: 10.1371/journal.pgen.1003308

+ expand abstract

Saremi, S., Sejnowski, T.J. Hierarchical model of natural images and the origin of scale invariance. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(8):3071-3076. DOI: 10.1073/pnas.1222618110

+ expand abstract

Tanaka, H., Sejnowski, T.J. Computing reaching dynamics in motor cortex with Cartesian spatial coordinates. (2013) Journal of Neurophysiology. 109(4):1182-1201. DOI: 10.1152/jn.00279.2012

+ expand abstract

Kinney, J.P., Spacek, J., Bartol, T.M., Bajaj, C.L., Harris, K.M., Sejnowski, T.J. Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil. (2013) Journal of Comparative Neurology. 521(2):448-464. DOI: 10.1002/cne.23181

+ expand abstract

Srinivasan, L., Asaad, W.F., Ginat, D.T., Gale, J.T., Dougherty, D.D., Williams, Z.M., Sejnowski, T.J., Eskandar, E.N. Action initiation in the human dorsal anterior cingulate cortex. (2013) PLOS One. 8(2):e55247. DOI: 10.1371/journal.pone.0055247

+ expand abstract

Shimozaki, K., Clemenson, G.D., Gage, F.H. Paired related homeobox protein 1 is a regulator of stemness in adult neural stem/progenitor cells. (2013) Journal of Neuroscience. 33(9):4066-75. DOI: 10.1523/JNEUROSCI.4586-12.2013

+ expand abstract

Volman, V., Bazhenov, M., Sejnowski, T.J. Divide and conquer: functional segregation of synaptic inputs by astrocytic microdomains could alleviate paroxysmal activity following brain trauma. (2013) PLOS Computational Biology. 9(1):e1002856. DOI: 10.1371/journal.pcbi.1002856

+ expand abstract

Kurian, L., Sancho-Martinez, I., Nivet, E., Aguirre, A., Moon, K., Pendaries, C., Volle-Challier, C., Bono, F., Herbert, J.M., Pulecio, J., Xia, Y., Li, M., Montserrat, N., Ruiz, S., Dubova, I., Rodriguez, C., Denli, A.M., Boscolo, F.S., Thiagarajan, R.D., Gage, F.H., Loring, J.F., Laurent, L.C., Izpisua Belmonte, J.C. Conversion of human fibroblasts to angioblast-like progenitor cells. (2013) Nature Methods. 10(1):77-83. DOI: 10.1038/nmeth.2255

+ expand abstract

Nauhaus, I., Nielsen, K.J., Disney, A.A., Callaway, E.M. Orthogonal micro-organization of orientation and spatial frequency in primate primary visual cortex. (2012) Nature Neuroscience. 15(12):1683-1690. DOI: 10.1038/nn.3255

+ expand abstract

Brennand, K.J., Simone, A., Tran, N., Gage, F.H. Modeling psychiatric disorders at the cellular and network levels. (2012) Molecular Psychiatry. 17(12):1239-53. DOI: 10.1038/mp.2012.20

+ expand abstract

Fava, M., Targum, S.D., Nierenberg, A.A., Bleicher, L.S., Carter, T.A., Wedel, P.C., Hen, R., Gage, F.H., Barlow, C. An exploratory study of combination buspirone and melatonin SR in major depressive disorder (MDD): a possible role for neurogenesis in drug discovery. (2012) J Psychiatr Res. 46(12):1553-63. DOI: 10.1016/j.jpsychires.2012.08.013

+ expand abstract

Marshel, J.H., Kaye, A.P., Nauhaus, I., Callaway, E.M. Anterior-posterior direction opponency in the superficial mouse lateral geniculate nucleus. (2012) Neuron. 76(4):713-720. DOI: 10.1016/j.neuron.2012.09.021

+ expand abstract

Goulding, M. Motor neurons that multitask. (2012) Neuron. 76(4):669-70. DOI: 10.1016/j.neuron.2012.11.011

+ expand abstract

Winner, B., Regensburger, M., Schreglmann, S., Boyer, L., Prots, I., Rockenstein, E., Mante, M., Zhao, C., Winkler, J., Masliah, E., Gage, F.H. Role of α-synuclein in adult neurogenesis and neuronal maturation in the dentate gyrus. (2012) Journal of Neuroscience. 32(47):16906-16. DOI: 10.1523/JNEUROSCI.2723-12.2012

+ expand abstract

Bellin, M., Marchetto, M.C., Gage, F.H., Mummery, C.L. Induced pluripotent stem cells: the new patient? (2012) Nature Reviews Molecular Cell Biology. 13(11):713-26. DOI: 10.1038/nrm3448

+ expand abstract

Levine, A.J., Lewallen, K.A., Pfaff, S.L. Spatial organization of cortical and spinal neurons controlling motor behavior. (2012) Current Opinion in Neurobiology. 22(5):812-21. DOI: 10.1016/j.conb.2012.07.002

+ expand abstract

Toups, J.V., Fellous, J.M., Thomas, P.J., Sejnowski, T.J., Tiesinga, P.H. Multiple spike time patterns occur at bifurcation points of membrane potential dynamics. (2012) PLOS Computational Biology. 8(10):e1002615. DOI: 10.1371/journal.pcbi.1002615

+ expand abstract

Catterall, W.A., Raman, I.M., Robinson, H.P., Sejnowski, T.J., Paulsen, O. The Hodgkin-Huxley heritage: from channels to circuits. (2012) Journal of Neuroscience. 32(41):14064-14073. DOI: 10.1523/JNEUROSCI.3403-12.2012

+ expand abstract

Vilchez, D., Boyer, L., Morantte, I., Lutz, M., Merkwirth, C., Joyce, D., Spencer, B., Page, L., Masliah, E., Berggren, W.T., Gage, F.H., Dillin, A. Increased proteasome activity in human embryonic stem cells is regulated by PSMD11. (2012) Nature. 489(7415):304-8. DOI: 10.1038/nature11468

+ expand abstract

Eickenberg, M., Rowekamp, R.J., Kouh, M., Sharpee, T.O. Characterizing responses of translation-invariant neurons to natural stimuli: maximally informative invariant dimensions. (2012) Neural Computation. 24(9):2384-421. DOI: 10.1162/NECO_a_00330

+ expand abstract

The human visual system is capable of recognizing complex objects even when their appearances change drastically under various viewing conditions. Especially in the higher cortical areas, the sensory neurons reflect such functional capacity in their selectivity for complex visual features and invariance to certain object transformations, such as image translation. Due to the strong nonlinearities necessary to achieve both the selectivity and invariance, characterizing and predicting the response patterns of these neurons represents a formidable computational challenge. A related problem is that such neurons are poorly driven by randomized inputs, such as white noise, and respond strongly only to stimuli with complex high-order correlations, such as natural stimuli. Here we describe a novel two-step optimization technique that can characterize both the shape selectivity and the range and coarseness of position invariance from neural responses to natural stimuli. One step in the optimization is finding the template as the maximally informative dimension given the estimated spatial location where the response could have been triggered within each image. The estimates of the locations that triggered the response are updated in the next step. Under the assumption of a monotonic relationship between the firing rate and stimulus projections on the template at a given position, the most likely location is the one that has the largest projection on the estimate of the template. The algorithm shows quick convergence during optimization, and the estimation results are reliable even in the regime of small signal-to-noise ratios. When we apply the algorithm to responses of complex cells in the primary visual cortex (V1) to natural movies, we find that responses of the majority of cells were significantly better described by translation-invariant models based on one template compared with position-specific models with several relevant features.

Nadkarni, S., Bartol, T.M., Stevens, C.F., Sejnowski, T.J., Levine, H. Short-term plasticity constrains spatial organization of a hippocampal presynaptic terminal. (2012) Proceedings of the National Academy of Sciences of the United States of America. 109(36):14657-14662. DOI: 10.1073/pnas.1211971109

+ expand abstract

Volman, V., Bazhenov, M., Sejnowski, T.J. Computational models of neuron-astrocyte interaction in epilepsy. (2012) Frontiers in Computational Neuroscience. 6:58. DOI: 10.3389/fncom.2012.00058

+ expand abstract

Boyer, L.F., Campbell, B., Larkin, S., Mu, Y., Gage, F.H. Dopaminergic differentiation of human pluripotent cells. (2012) Curr Protoc Stem Cell Biol. Chapter 1:Unit1H.6. DOI: 10.1002/9780470151808.sc01h06s22

+ expand abstract

Callaway, E.M., Marder, E. Common features of diverse circuits. (2012) Current Opinion in Neurobiology. 22(4):565-567. DOI: 10.1016/j.conb.2012.07.003

Egawa, N., Kitaoka, S., Tsukita, K., Naitoh, M., Takahashi, K., Yamamoto, T., Adachi, F., Kondo, T., Okita, K., Asaka, I., Aoi, T., Watanabe, A., Yamada, Y., Morizane, A., Takahashi, J., Ayaki, T., Ito, H., Yoshikawa, K., Yamawaki, S., Suzuki, S., Watanabe, D., Hioki, H., Kaneko, T., Makioka, K., Okamoto, K., Takuma, H., Tamaoka, A., Hasegawa, K., Nonaka, T., Hasegawa, M., Kawata, A., Yoshida, M., Nakahata, T., Takahashi, R., Marchetto, M.C., Gage, F.H., Yamanaka, S., Inoue, H. Drug screening for ALS using patient-specific induced pluripotent stem cells. (2012) Science Translational Medicine. 4(145):145ra104. DOI: 10.1126/scitranslmed.3004052

+ expand abstract

Macfarlan, T.S., Gifford, W.D., Driscoll, S., Lettieri, K., Rowe, H.M., Bonanomi, D., Firth, A., Singer, O., Trono, D., Pfaff, S.L. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. (2012) Nature. 487(7405):57-63. DOI: 10.1038/nature11244

+ expand abstract

Giorgetti, A., Marchetto, M.C., Li, M., Yu, D., Fazzina, R., Mu, Y., Adamo, A., Paramonov, I., Cardoso, J.C., Monasterio, M.B., Bardy, C., Cassiani-Ingoni, R., Liu, G.H., Gage, F.H., Izpisua Belmonte, J.C. Cord blood-derived neuronal cells by ectopic expression of Sox2 and c-Myc. (2012) Proceedings of the National Academy of Sciences of the United States of America. 109(31):12556-61. DOI: 10.1073/pnas.1209523109

+ expand abstract

Nielsen, K.J., Callaway, E.M., Krauzlis, R.J. Viral vector-based reversible neuronal inactivation and behavioral manipulation in the macaque monkey. (2012) Frontiers in Systems Neuroscience. 6:48. DOI: 10.3389/fnsys.2012.00048

+ expand abstract

Marchetto, M.C., Gage, F.H. Modeling brain disease in a dish: really? (2012) Cell Stem Cell. 10(6):642-5. DOI: 10.1016/j.stem.2012.05.008

+ expand abstract

Zhao, C., Warner-Schmidt, J., Duman, R.S., Gage, F.H. Electroconvulsive seizure promotes spine maturation in newborn dentate granule cells in adult rat. (2012) Developmental Neurobiology. 72(6):937-42. DOI: 10.1002/dneu.20986

+ expand abstract

Atencio, C.A., Sharpee, T.O., Schreiner, C.E. Receptive field dimensionality increases from the auditory midbrain to cortex. (2012) Journal of Neurophysiology. 107(10):2594-603. DOI: 10.1152/jn.01025.2011

+ expand abstract

Nimmerjahn, A. Two-photon imaging of microglia in the mouse cortex in vivo. (2012) Cold Spring Harbor Protocols. 2012(5). DOI: 10.1101/pdb.prot069294

+ expand abstract

Nimmerjahn, A. Optical window preparation for two-photon imaging of microglia in mice. (2012) Cold Spring Harbor Protocols. 2012(5). DOI: 10.1101/pdb.prot069286

+ expand abstract

Nimmerjahn, A. Surgical implantation of a head plate in mice in preparation for in vivo two-photon imaging of microglia. (2012) Cold Spring Harbor Protocols. 2012(5). DOI: 10.1101/pdb.prot069278

+ expand abstract

Yao, J., Mu, Y., Gage, F.H. Neural stem cells: mechanisms and modeling. (2012) Protein & Cell. 3(4):251-61. DOI: 10.1007/s13238-012-2033-6

+ expand abstract

Bonjean, M., Baker, T., Bazhenov, M., Cash, S., Halgren, E., Sejnowski, T. Interactions between core and matrix thalamocortical projections in human sleep spindle synchronization. (2012) Journal of Neuroscience. 32(15):5250-5263. DOI: 10.1523/JNEUROSCI.6141-11.2012

+ expand abstract

Tanaka, H., Krakauer, J.W., Sejnowski, T.J. Generalization and multirate models of motor adaptation. (2012) Neural Computation. 24(4):939-966. DOI: 10.1162/NECO_a_00262

+ expand abstract

Gage, F.H. Transplantation in the future. (2012) Progress in Brain Research. 200:7-13. DOI: 10.1016/B978-0-444-59575-1.00001-6

+ expand abstract

Gage, F.H., Muotri, A.R. What makes each brain unique. (2012) Sci. Am. 306(3):26-31.

Li, Y., Aimone, J.B., Xu, X., Callaway, E.M., Gage, F.H. Development of GABAergic inputs controls the contribution of maturing neurons to the adult hippocampal network. (2012) Proceedings of the National Academy of Sciences of the United States of America. 109(11):4290-5. DOI: 10.1073/pnas.1120754109

+ expand abstract

Nimmerjahn, A., Helmchen, F. In vivo labeling of cortical astrocytes with sulforhodamine 101 (SR101). (2012) Cold Spring Harbor Protocols. 2012(3):326-34. DOI: 10.1101/pdb.prot068155

+ expand abstract

Ramirez-Moreno, D.F., Sejnowski, T.J. A computational model for the modulation of the prepulse inhibition of the acoustic startle reflex. (2012) Biol Cybern. 106(3):169-176. DOI: 10.1007/s00422-012-0485-7

+ expand abstract

Powell, S.B., Sejnowski, T.J., Behrens, M.M. Behavioral and neurochemical consequences of cortical oxidative stress on parvalbumin-interneuron maturation in rodent models of schizophrenia. (2012) Neuropharmacology. 62(3):1322-31. DOI: 10.1016/j.neuropharm.2011.01.049

+ expand abstract

Ge, W.P., Miyawaki, A., Gage, F.H., Jan, Y.N., Jan, L.Y. Local generation of glia is a major astrocyte source in postnatal cortex. (2012) Nature. 484(7394):376-80. DOI: 10.1038/nature10959

+ expand abstract

Bracko, O., Singer, T., Aigner, S., Knobloch, M., Winner, B., Ray, J., Clemenson, G.D., Suh, H., Couillard-Despres, S., Aigner, L., Gage, F.H., Jessberger, S. Gene expression profiling of neural stem cells and their neuronal progeny reveals IGF2 as a regulator of adult hippocampal neurogenesis. (2012) Journal of Neuroscience. 32(10):3376-87. DOI: 10.1523/JNEUROSCI.4248-11.2012

+ expand abstract

Thuret, S., Thallmair, M., Horky, L.L., Gage, F.H. Enhanced functional recovery in MRL/MpJ mice after spinal cord dorsal hemisection. (2012) PLOS One. 7(2):e30904. DOI: 10.1371/journal.pone.0030904

+ expand abstract

Bonanomi, D., Chivatakarn, O., Bai, G., Abdesselem, H., Lettieri, K., Marquardt, T., Pierchala, B.A., Pfaff, S.L. Ret is a multifunctional coreceptor that integrates diffusible- and contact-axon guidance signals. (2012) Cell. 148(3):568-82. DOI: 10.1016/j.cell.2012.01.024

+ expand abstract

Shimozaki, K., Zhang, C.L., Suh, H., Denli, A.M., Evans, R.M., Gage, F.H. SRY-box-containing gene 2 regulation of nuclear receptor tailless (Tlx) transcription in adult neural stem cells. (2012) Journal of Biological Chemistry. 287(8):5969-78. DOI: 10.1074/jbc.M111.290403

+ expand abstract

Nauhaus, I., Nielsen, K.J., Callaway, E.M. Nonlinearity of two-photon Ca2+ imaging yields distorted measurements of tuning for V1 neuronal populations. (2012) Journal of Neurophysiology. 107(3):923-936. DOI: 10.1152/jn.00725.2011

+ expand abstract

Lee, S.W., Clemenson, G.D., Gage, F.H. New neurons in an aged brain. (2012) Behavioural Brain Research. 227(2):497-507. DOI: 10.1016/j.bbr.2011.10.009

+ expand abstract

Kerr, J.N., Nimmerjahn, A. Functional imaging in freely moving animals. (2012) Current Opinion in Neurobiology. 22(1):45-53. DOI: 10.1016/j.conb.2011.12.002

+ expand abstract

Vivar, C., Potter, M.C., Choi, J., Lee, J.Y., Stringer, T.P., Callaway, E.M., Gage, F.H., Suh, H., van Praag, H. Monosynaptic inputs to new neurons in the dentate gyrus. (2012) Nature Communications. 3:1107. DOI: 10.1038/ncomms2101

+ expand abstract

Sharpee, T.O. Adaptive switches in midbrain circuits. (2012) Neuron. 73(1):6-7. DOI: 10.1016/j.neuron.2011.12.017

+ expand abstract

Gage, F.H. ISSCR: beginning the next chapter. (2012) Cell Stem Cell. 10(1):29-31. DOI: 10.1016/j.stem.2011.12.009

Han, J., Denli, A.M., Gage, F.H. The enemy within: intronic miR-26b represses its host gene, ctdsp2, to regulate neurogenesis. (2012) Genes & Development. 26(1):6-10. DOI: 10.1101/gad.184416.111

+ expand abstract

Stam, F.J., Hendricks, T.J., Zhang, J., Geiman, E.J., Francius, C., Labosky, P.A., Clotman, F., Goulding, M. Renshaw cell interneuron specialization is controlled by a temporally restricted transcription factor program. (2012) Development. 139(1):179-90. DOI: 10.1242/dev.071134

+ expand abstract

Brennand, K.J., Gage, F.H. Modeling psychiatric disorders through reprogramming. (2012) Dis Model Mech. 5(1):26-32. DOI: 10.1242/dmm.008268

+ expand abstract

Nhan, H.L., Callaway, E.M. Morphology of superior colliculus- and middle temporal area-projecting neurons in primate primary visual cortex. (2012) Journal of Comparative Neurology. 520(1):52-80. DOI: 10.1002/cne.22685

+ expand abstract

Ikrar, T., Shi, Y., Velasquez, T., Goulding, M., Xu, X. Cell-type specific regulation of cortical excitability through the allatostatin receptor system. (2012) Front Neural Circuits. 6:2. DOI: 10.3389/fncir.2012.00002

+ expand abstract

Israel, M.A., Yuan, S.H., Bardy, C., Reyna, S.M., Mu, Y., Herrera, C., Hefferan, M.P., Van Gorp, S., Nazor, K.L., Boscolo, F.S., Carson, C.T., Laurent, L.C., Marsala, M., Gage, F.H., Remes, A.M., Koo, E.H., Goldstein, L.S. Probing sporadic and familial Alzheimer's disease using induced pluripotent stem cells. (2012) Nature. 482(7384):216-20. DOI: 10.1038/nature10821

+ expand abstract

Our understanding of Alzheimer's disease pathogenesis is currently limited by difficulties in obtaining live neurons from patients and the inability to model the sporadic form of the disease. It may be possible to overcome these challenges by reprogramming primary cells from patients into induced pluripotent stem cells (iPSCs). Here we reprogrammed primary fibroblasts from two patients with familial Alzheimer's disease, both caused by a duplication of the amyloid-β precursor protein gene (APP; termed APP(Dp)), two with sporadic Alzheimer's disease (termed sAD1, sAD2) and two non-demented control individuals into iPSC lines. Neurons from differentiated cultures were purified with fluorescence-activated cell sorting and characterized. Purified cultures contained more than 90% neurons, clustered with fetal brain messenger RNA samples by microarray criteria, and could form functional synaptic contacts. Virtually all cells exhibited normal electrophysiological activity. Relative to controls, iPSC-derived, purified neurons from the two APP(Dp) patients and patient sAD2 exhibited significantly higher levels of the pathological markers amyloid-β(1-40), phospho-tau(Thr 231) and active glycogen synthase kinase-3β (aGSK-3β). Neurons from APP(Dp) and sAD2 patients also accumulated large RAB5-positive early endosomes compared to controls. Treatment of purified neurons with β-secretase inhibitors, but not γ-secretase inhibitors, caused significant reductions in phospho-Tau(Thr 231) and aGSK-3β levels. These results suggest a direct relationship between APP proteolytic processing, but not amyloid-β, in GSK-3β activation and tau phosphorylation in human neurons. Additionally, we observed that neurons with the genome of one sAD patient exhibited the phenotypes seen in familial Alzheimer's disease samples. More generally, we demonstrate that iPSC technology can be used to observe phenotypes relevant to Alzheimer's disease, even though it can take decades for overt disease to manifest in patients.

Boyce, V.S., Park, J., Gage, F.H., Mendell, L.M. Differential effects of brain-derived neurotrophic factor and neurotrophin-3 on hindlimb function in paraplegic rats. (2012) Eur. J. Neurosci. 35(2):221-32. DOI: 10.1111/j.1460-9568.2011.07950.x

+ expand abstract

We compared the effect of viral administration of brain-derived neurotrophic factor (BDNF) or neurotrophin 3 (NT-3) on locomotor recovery in adult rats with complete thoracic (T10) spinal cord transection injuries, in order to determine the effect of chronic neurotrophin expression on spinal plasticity. At the time of injury, BDNF, NT-3 or green fluorescent protein (GFP) (control) was delivered to the lesion via adeno-associated virus (AAV) constructs. AAV-BDNF was significantly more effective than AAV-NT-3 in eliciting locomotion. In fact, AAV-BDNF-treated rats displayed plantar, weight-supported hindlimb stepping on a stationary platform, that is, without the assistance of a moving treadmill and without step training. Rats receiving AAV-NT-3 or AAV-GFP were incapable of hindlimb stepping during this task, despite provision of balance support. AAV-NT-3 treatment did promote the recovery of treadmill-assisted stepping, but this required continuous perineal stimulation. In addition, AAV-BDNF-treated rats were sensitized to noxious heat, whereas AAV-NT-3-treated and AAV-GFP-treated rats were not. Notably, AAV-BDNF-treated rats also developed hindlimb spasticity, detracting from its potential clinical applicability via the current viral delivery method. Intracellular recording from triceps surae motoneurons revealed that AAV-BDNF significantly reduced motoneuron rheobase, suggesting that AAV-BDNF promoted the recovery of over-ground stepping by enhancing neuronal excitability. Elevated nuclear c-Fos expression in interneurons located in the L2 intermediate zone after AAV-BDNF treatment indicated increased activation of interneurons in the vicinity of the locomotor central pattern generator. AAV-NT-3 treatment reduced motoneuron excitability, with little change in c-Fos expression. These results support the potential for BDNF delivery at the lesion site to reorganize locomotor circuits.

Marshel, J.H., Garrett, M.E., Nauhaus, I., Callaway, E.M. Functional specialization of seven mouse visual cortical areas. (2011) Neuron. 72(6):1040-1054. DOI: 10.1016/j.neuron.2011.12.004

+ expand abstract

Mu, Y., Gage, F.H. Adult hippocampal neurogenesis and its role in Alzheimer's disease. (2011) Mol Neurodegener. 6:85. DOI: 10.1186/1750-1326-6-85

+ expand abstract

Volman, V., Behrens, M.M., Sejnowski, T.J. Downregulation of parvalbumin at cortical GABA synapses reduces network gamma oscillatory activity. (2011) Journal of Neuroscience. 31(49):18137-48. DOI: 10.1523/JNEUROSCI.3041-11.2011

+ expand abstract

Coufal, N.G., Garcia-Perez, J.L., Peng, G.E., Marchetto, M.C., Muotri, A.R., Mu, Y., Carson, C.T., Macia, A., Moran, J.V., Gage, F.H. Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells. (2011) Proceedings of the National Academy of Sciences of the United States of America. 108(51):20382-7. DOI: 10.1073/pnas.1100273108

+ expand abstract

Coggan, J.S., Ocker, G.K., Sejnowski, T.J., Prescott, S.A. Explaining pathological changes in axonal excitability through dynamical analysis of conductance-based models. (2011) J Neural Eng. 8(6):065002. DOI: 10.1088/1741-2560/8/6/065002

+ expand abstract

Brennand, K.J., Gage, F.H. Concise review: the promise of human induced pluripotent stem cell-based studies of schizophrenia. (2011) Stem Cells. 29(12):1915-22. DOI: 10.1002/stem.762

+ expand abstract

Choi, J., Callaway, E.M. Monosynaptic inputs to ErbB4-expressing inhibitory neurons in mouse primary somatosensory cortex. (2011) Journal of Comparative Neurology. 519(17):3402-3414. DOI: 10.1002/cne.22680

+ expand abstract

Kuwabara, T., Kagalwala, M.N., Onuma, Y., Ito, Y., Warashina, M., Terashima, K., Sanosaka, T., Nakashima, K., Gage, F.H., Asashima, M. Insulin biosynthesis in neuronal progenitors derived from adult hippocampus and the olfactory bulb. (2011) EMBO Molecular Medicine. 3(12):742-54. DOI: 10.1002/emmm.201100177

+ expand abstract

Tremblay, M., Stevens, B., Sierra, A., Wake, H., Bessis, A., Nimmerjahn, A. The role of microglia in the healthy brain. (2011) Journal of Neuroscience. 31(45):16064-9. DOI: 10.1523/JNEUROSCI.4158-11.2011

+ expand abstract

Wei, H., Bonjean, M., Petry, H.M., Sejnowski, T.J., Bickford, M.E. Thalamic burst firing propensity: a comparison of the dorsal lateral geniculate and pulvinar nuclei in the tree shrew. (2011) Journal of Neuroscience. 31(47):17287-17299. DOI: 10.1523/JNEUROSCI.6431-10.2011

+ expand abstract

Brenner, S., Sejnowski, T.J. Understanding the human brain. (2011) Science. 334(6056):567. DOI: 10.1126/science.1215674

Fitzgerald, J.D., Rowekamp, R.J., Sincich, L.C., Sharpee, T.O. Second order dimensionality reduction using minimum and maximum mutual information models. (2011) PLOS Computational Biology. 7(10):e1002249. DOI: 10.1371/journal.pcbi.1002249

+ expand abstract

Bai, G., Pfaff, S.L. Protease regulation: the Yin and Yang of neural development and disease. (2011) Neuron. 72(1):9-21. DOI: 10.1016/j.neuron.2011.09.012

+ expand abstract

Kawakami, Y., Marti, M., Kawakami, H., Itou, J., Quach, T., Johnson, A., Sahara, S., O'Leary, D.D., Nakagawa, Y., Lewandoski, M., Pfaff, S., Evans, S.M., Izpisua Belmonte, J.C. Islet1-mediated activation of the β-catenin pathway is necessary for hindlimb initiation in mice. (2011) Development. 138(20):4465-73. DOI: 10.1242/dev.065359

+ expand abstract

Marchetto, M.C., Brennand, K.J., Boyer, L.F., Gage, F.H. Induced pluripotent stem cells (iPSCs) and neurological disease modeling: progress and promises. (2011) Human Molecular Genetics. 20(R2):R109-15. DOI: 10.1093/hmg/ddr336

+ expand abstract

Volman, V., Sejnowski, T.J., Bazhenov, M. Topological basis of epileptogenesis in a model of severe cortical trauma. (2011) Journal of Neurophysiology. 106(4):1933-1942. DOI: 10.1152/jn.00458.2011

+ expand abstract

Sharpee, T.O., Nagel, K.I., Doupe, A.J. Two-dimensional adaptation in the auditory forebrain. (2011) Journal of Neurophysiology. 106(4):1841-61. DOI: 10.1152/jn.00905.2010

+ expand abstract

Sharpee, T.O., Atencio, C.A., Schreiner, C.E. Hierarchical representations in the auditory cortex. (2011) Current Opinion in Neurobiology. 21(5):761-7. DOI: 10.1016/j.conb.2011.05.027

+ expand abstract

Hester, M.E., Murtha, M.J., Song, S., Rao, M., Miranda, C.J., Meyer, K., Tian, J., Boulting, G., Schaffer, D.V., Zhu, M.X., Pfaff, S.L., Gage, F.H., Kaspar, B.K. Rapid and efficient generation of functional motor neurons from human pluripotent stem cells using gene delivered transcription factor codes. (2011) Mol. Ther. 19(10):1905-12. DOI: 10.1038/mt.2011.135

+ expand abstract

Yu, T., Sejnowski, T.J., Cauwenberghs, G. Biophysical Neural Spiking, Bursting, and Excitability Dynamics in Reconfigurable Analog VLSI. (2011) IEEE Trans Biomed Circuits Syst. 5(5):420-429. DOI: 10.1109/TBCAS.2011.2169794

+ expand abstract

Zhu, Q., Pao, G.M., Huynh, A.M., Suh, H., Tonnu, N., Nederlof, P.M., Gage, F.H., Verma, I.M. BRCA1 tumour suppression occurs via heterochromatin-mediated silencing. (2011) Nature. 477(7363):179-84. DOI: 10.1038/nature10371

+ expand abstract

Volman, V., Bazhenov, M., Sejnowski, T.J. Pattern of trauma determines the threshold for epileptic activity in a model of cortical deafferentation. (2011) Proceedings of the National Academy of Sciences of the United States of America. 108(37):15402-15407. DOI: 10.1073/pnas.1112066108

+ expand abstract

Ghosh, K.K., Burns, L.D., Cocker, E.D., Nimmerjahn, A., Ziv, Y., Gamal, A.E., Schnitzer, M.J. Miniaturized integration of a fluorescence microscope. (2011) Nature Methods. 8(10):871-8. DOI: 10.1038/nmeth.1694

+ expand abstract

Dang-Vu, T.T., Bonjean, M., Schabus, M., Boly, M., Darsaud, A., Desseilles, M., Degueldre, C., Balteau, E., Phillips, C., Luxen, A., Sejnowski, T.J., Maquet, P. Interplay between spontaneous and induced brain activity during human non-rapid eye movement sleep. (2011) Proceedings of the National Academy of Sciences of the United States of America. 108(37):15438-15443. DOI: 10.1073/pnas.1112503108

+ expand abstract

Toups, J.V., Fellous, J.M., Thomas, P.J., Sejnowski, T.J., Tiesinga, P.H. Finding the event structure of neuronal spike trains. (2011) Neural Computation. 23(9):2169-2208. DOI: 10.1162/NECO_a_00173

+ expand abstract

Osakada, F., Mori, T., Cetin, A.H., Marshel, J.H., Virgen, B., Callaway, E.M. New rabies virus variants for monitoring and manipulating activity and gene expression in defined neural circuits. (2011) Neuron. 71(4):617-631. DOI: 10.1016/j.neuron.2011.07.005

+ expand abstract

Shen, B., Xiang, Z., Miller, B., Louie, G., Wang, W., Noel, J.P., Gage, F.H., Wang, L. Genetically encoding unnatural amino acids in neural stem cells and optically reporting voltage-sensitive domain changes in differentiated neurons. (2011) Stem Cells. 29(8):1231-40. DOI: 10.1002/stem.679

+ expand abstract

Rowekamp, R.J., Sharpee, T.O. Analyzing multicomponent receptive fields from neural responses to natural stimuli. (2011) Network. 22(1-4):45-73. DOI: 10.3109/0954898X.2011.566303

+ expand abstract

Alaynick, W.A., Jessell, T.M., Pfaff, S.L. SnapShot: spinal cord development. (2011) Cell. 146(1):178-178.e1. DOI: 10.1016/j.cell.2011.06.038

Woods, N.B., Parker, A.S., Moraghebi, R., Lutz, M.K., Firth, A.L., Brennand, K.J., Berggren, W.T., Raya, A., Izpisúa Belmonte, J.C., Gage, F.H., Verma, I.M. Brief report: efficient generation of hematopoietic precursors and progenitors from human pluripotent stem cell lines. (2011) Stem Cells. 29(7):1158-64. DOI: 10.1002/stem.657

+ expand abstract

Liang, X., Song, M.R., Xu, Z., Lanuza, G.M., Liu, Y., Zhuang, T., Chen, Y., Pfaff, S.L., Evans, S.M., Sun, Y. Isl1 is required for multiple aspects of motor neuron development. (2011) Molecular and Cellular Neurosciences. 47(3):215-22. DOI: 10.1016/j.mcn.2011.04.007

+ expand abstract

Bonjean, M., Baker, T., Lemieux, M., Timofeev, I., Sejnowski, T., Bazhenov, M. Corticothalamic feedback controls sleep spindle duration in vivo. (2011) Journal of Neuroscience. 31(25):9124-9134. DOI: 10.1523/JNEUROSCI.0077-11.2011

+ expand abstract

Aimone, J.B., Deng, W., Gage, F.H. Resolving new memories: a critical look at the dentate gyrus, adult neurogenesis, and pattern separation. (2011) Neuron. 70(4):589-96. DOI: 10.1016/j.neuron.2011.05.010

+ expand abstract

Callaway, E.M., Borrell, V. Developmental sculpting of dendritic morphology of layer 4 neurons in visual cortex: influence of retinal input. (2011) Journal of Neuroscience. 31(20):7456-7470. DOI: 10.1523/JNEUROSCI.5222-10.2011

+ expand abstract

Brennand, K.J., Simone, A., Jou, J., Gelboin-Burkhart, C., Tran, N., Sangar, S., Li, Y., Mu, Y., Chen, G., Yu, D., McCarthy, S., Sebat, J., Gage, F.H. Modelling schizophrenia using human induced pluripotent stem cells. (2011) Nature. 473(7346):221-5. DOI: 10.1038/nature09915

+ expand abstract

Bruno, I.G., Karam, R., Huang, L., Bhardwaj, A., Lou, C.H., Shum, E.Y., Song, H.W., Corbett, M.A., Gifford, W.D., Gecz, J., Pfaff, S.L., Wilkinson, M.F. Identification of a microRNA that activates gene expression by repressing nonsense-mediated RNA decay. (2011) Molecular Cell. 42(4):500-10. DOI: 10.1016/j.molcel.2011.04.018

+ expand abstract

Miyamichi, K., Amat, F., Moussavi, F., Wang, C., Wickersham, I., Wall, N.R., Taniguchi, H., Tasic, B., Huang, Z.J., He, Z., Callaway, E.M., Horowitz, M.A., Luo, L. Cortical representations of olfactory input by trans-synaptic tracing. (2011) Nature. 472(7342):191-196. DOI: 10.1038/nature09714

+ expand abstract

Fitzgerald, J.D., Sincich, L.C., Sharpee, T.O. Minimal models of multidimensional computations. (2011) PLOS Computational Biology. 7(3):e1001111. DOI: 10.1371/journal.pcbi.1001111

+ expand abstract

Mu, Y., Zhao, C., Gage, F.H. Dopaminergic modulation of cortical inputs during maturation of adult-born dentate granule cells. (2011) Journal of Neuroscience. 31(11):4113-23. DOI: 10.1523/JNEUROSCI.4913-10.2011

+ expand abstract

Aimone, J.B., Gage, F.H. Modeling new neuron function: a history of using computational neuroscience to study adult neurogenesis. (2011) European Journal of Neuroscience. 33(6):1160-9. DOI: 10.1111/j.1460-9568.2011.07615.x

+ expand abstract

Winner, B., Kohl, Z., Gage, F.H. Neurodegenerative disease and adult neurogenesis. (2011) Eur. J. Neurosci. 33(6):1139-51. DOI: 10.1111/j.1460-9568.2011.07613.x

+ expand abstract

Macfarlan, T.S., Gifford, W.D., Agarwal, S., Driscoll, S., Lettieri, K., Wang, J., Andrews, S.E., Franco, L., Rosenfeld, M.G., Ren, B., Pfaff, S.L. Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. (2011) Genes & Development. 25(6):594-607. DOI: 10.1101/gad.2008511

+ expand abstract

Winner, B., Jappelli, R., Maji, S.K., Desplats, P.A., Boyer, L., Aigner, S., Hetzer, C., Loher, T., Vilar, M., Campioni, S., Tzitzilonis, C., Soragni, A., Jessberger, S., Mira, H., Consiglio, A., Pham, E., Masliah, E., Gage, F.H., Riek, R. In vivo demonstration that alpha-synuclein oligomers are toxic. (2011) Proceedings of the National Academy of Sciences of the United States of America. 108(10):4194-9. DOI: 10.1073/pnas.1100976108

+ expand abstract

Winner, B., Melrose, H.L., Zhao, C., Hinkle, K.M., Yue, M., Kent, C., Braithwaite, A.T., Ogholikhan, S., Aigner, R., Winkler, J., Farrer, M.J., Gage, F.H. Adult neurogenesis and neurite outgrowth are impaired in LRRK2 G2019S mice. (2011) Neurobiol. Dis. 41(3):706-16. DOI: 10.1016/j.nbd.2010.12.008

+ expand abstract

Romani, S., Sejnowski, T.J., Tsodyks, M. Intracellular dynamics of virtual place cells. (2011) Neural Computation. 23(3):651-5. DOI: 10.1162/NECO_a_00087

+ expand abstract

Yuan, S.H., Martin, J., Elia, J., Flippin, J., Paramban, R.I., Hefferan, M.P., Vidal, J.G., Mu, Y., Killian, R.L., Israel, M.A., Emre, N., Marsala, S., Marsala, M., Gage, F.H., Goldstein, L.S., Carson, C.T. Cell-surface marker signatures for the isolation of neural stem cells, glia and neurons derived from human pluripotent stem cells. (2011) PLOS One. 6(3):e17540. DOI: 10.1371/journal.pone.0017540

+ expand abstract

Garudadri, S., Gallarda, B., Pfaff, S., Alaynick, W. Spinal cord electrophysiology II: extracellular suction electrode fabrication. (2011) J Vis Exp.(48) DOI: 10.3791/2580

+ expand abstract

Jeanne, J.M., Thompson, J.V., Sharpee, T.O., Gentner, T.Q. Emergence of learned categorical representations within an auditory forebrain circuit. (2011) Journal of Neuroscience. 31(7):2595-606. DOI: 10.1523/JNEUROSCI.3930-10.2011

+ expand abstract

Kim, J.E., O'Sullivan, M.L., Sanchez, C.A., Hwang, M., Israel, M.A., Brennand, K., Deerinck, T.J., Goldstein, L.S., Gage, F.H., Ellisman, M.H., Ghosh, A. Investigating synapse formation and function using human pluripotent stem cell-derived neurons. (2011) Proceedings of the National Academy of Sciences of the United States of America. 108(7):3005-10. DOI: 10.1073/pnas.1007753108

+ expand abstract

Bai, G., Chivatakarn, O., Bonanomi, D., Lettieri, K., Franco, L., Xia, C., Stein, E., Ma, L., Lewcock, J.W., Pfaff, S.L. Presenilin-dependent receptor processing is required for axon guidance. (2011) Cell. 144(1):106-18. DOI: 10.1016/j.cell.2010.11.053

+ expand abstract

Meng, X., Arocena, M., Penninger, J., Gage, F.H., Zhao, M., Song, B. PI3K mediated electrotaxis of embryonic and adult neural progenitor cells in the presence of growth factors. (2011) Exp. Neurol. 227(1):210-7. DOI: 10.1016/j.expneurol.2010.11.002

+ expand abstract

Peterson, D.A., Lotz, D.T., Halgren, E., Sejnowski, T.J., Poizner, H. Choice modulates the neural dynamics of prediction error processing during rewarded learning. (2011) Neuroimage. 54(2):1385-1394. DOI: 10.1016/j.neuroimage.2010.09.051

+ expand abstract

Ruiz, S., Brennand, K., Panopoulos, A.D., Herrerías, A., Gage, F.H., Izpisua-Belmonte, J.C. High-efficient generation of induced pluripotent stem cells from human astrocytes. (2010) PLOS One. 5(12):e15526. DOI: 10.1371/journal.pone.0015526

+ expand abstract

Wall, N.R., Wickersham, I.R., Cetin, A., De La Parra, M., Callaway, E.M. Monosynaptic circuit tracing in vivo through Cre-dependent targeting and complementation of modified rabies virus. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(50):21848-21853. DOI: 10.1073/pnas.1011756107

+ expand abstract

Timofeev, I., Bazhenov, M., Seigneur, J., Sejnowski, T. Neocortical synchronization. (2010) Epilepsia. 51(Suppl 5):18. DOI: 10.1111/j.1528-1167.2010.02804.x

+ expand abstract

Weible, A.P., Schwarcz, L., Wickersham, I.R., Deblander, L., Wu, H., Callaway, E.M., Seung, H.S., Kentros, C.G. Transgenic targeting of recombinant rabies virus reveals monosynaptic connectivity of specific neurons. (2010) Journal of Neuroscience. 30(49):16509-16513. DOI: 10.1523/JNEUROSCI.2442-10.2010

+ expand abstract

Hill, E.S., Moore-Kochlacs, C., Vasireddi, S.K., Sejnowski, T.J., Frost, W.N. Validation of independent component analysis for rapid spike sorting of optical recording data. (2010) Journal of Neurophysiology. 104(6):3721-3731. DOI: 10.1152/jn.00691.2010

+ expand abstract

Sejnowski, T.J. Learning optimal strategies in complex environments. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(47):20151-2. DOI: 10.1073/pnas.1014954107

Marchetto, M.C., Carromeu, C., Acab, A., Yu, D., Yeo, G.W., Mu, Y., Chen, G., Gage, F.H., Muotri, A.R. A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells. (2010) Cell. 143(4):527-39. DOI: 10.1016/j.cell.2010.10.016

+ expand abstract

Coggan, J.S., Prescott, S.A., Bartol, T.M., Sejnowski, T.J. Imbalance of ionic conductances contributes to diverse symptoms of demyelination. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(48):20602-20609. DOI: 10.1073/pnas.1013798107

+ expand abstract

Mathews, E.A., Morgenstern, N.A., Piatti, V.C., Zhao, C., Jessberger, S., Schinder, A.F., Gage, F.H. A distinctive layering pattern of mouse dentate granule cells is generated by developmental and adult neurogenesis. (2010) Journal of Comparative Neurology. 518(22):4479-90. DOI: 10.1002/cne.22489

+ expand abstract

Heider, B., Nathanson, J.L., Isacoff, E.Y., Callaway, E.M., Siegel, R.M. Two-photon imaging of calcium in virally transfected striate cortical neurons of behaving monkey. (2010) PLOS One. 5(11). DOI: 10.1371/journal.pone.0013829

+ expand abstract

Haubensak, W., Kunwar, P.S., Cai, H., Ciocchi, S., Wall, N.R., Ponnusamy, R., Biag, J., Dong, H.W., Deisseroth, K., Callaway, E.M., Fanselow, M.S., Lüthi, A., Anderson, D.J. Genetic dissection of an amygdala microcircuit that gates conditioned fear. (2010) Nature. 468(7321):270-276. DOI: 10.1038/nature09553

+ expand abstract

Tiesinga, P.H., Sejnowski, T.J. Mechanisms for Phase Shifting in Cortical Networks and their Role in Communication through Coherence. (2010) Frontiers in Human Neuroscience. 4:196. DOI: 10.3389/fnhum.2010.00196

+ expand abstract

Nadkarni, S., Bartol, T.M., Sejnowski, T.J., Levine, H. Modelling vesicular release at hippocampal synapses. (2010) PLOS Computational Biology. 6(11):e1000983. DOI: 10.1371/journal.pcbi.1000983

+ expand abstract

Volman, V., Levine, H., Sejnowski, T.J. Shunting inhibition controls the gain modulation mediated by asynchronous neurotransmitter release in early development. (2010) PLOS Computational Biology. 6(11):e1000973. DOI: 10.1371/journal.pcbi.1000973

+ expand abstract

Sejnowski, T.J. QnAs with Terrence J. Sejnowski. [Interviewed by Prashant Nair]. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(48):20601. DOI: 10.1073/pnas.1015459107

Muotri, A.R., Marchetto, M.C., Coufal, N.G., Oefner, R., Yeo, G., Nakashima, K., Gage, F.H. L1 retrotransposition in neurons is modulated by MeCP2. (2010) Nature. 468(7322):443-6. DOI: 10.1038/nature09544

+ expand abstract

Long interspersed nuclear elements-1 (LINE-1 or L1s) are abundant retrotransposons that comprise approximately 20% of mammalian genomes. Active L1 retrotransposons can impact the genome in a variety of ways, creating insertions, deletions, new splice sites or gene expression fine-tuning. We have shown previously that L1 retrotransposons are capable of mobilization in neuronal progenitor cells from rodents and humans and evidence of massive L1 insertions was observed in adult brain tissues but not in other somatic tissues. In addition, L1 mobility in the adult hippocampus can be influenced by the environment. The neuronal specificity of somatic L1 retrotransposition in neural progenitors is partially due to the transition of a Sox2/HDAC1 repressor complex to a Wnt-mediated T-cell factor/lymphoid enhancer factor (TCF/LEF) transcriptional activator. The transcriptional switch accompanies chromatin remodelling during neuronal differentiation, allowing a transient stimulation of L1 transcription. The activity of L1 retrotransposons during brain development can have an impact on gene expression and neuronal function, thereby increasing brain-specific genetic mosaicism. Further understanding of the molecular mechanisms that regulate L1 expression should provide new insights into the role of L1 retrotransposition during brain development. Here we show that L1 neuronal transcription and retrotransposition in rodents are increased in the absence of methyl-CpG-binding protein 2 (MeCP2), a protein involved in global DNA methylation and human neurodevelopmental diseases. Using neuronal progenitor cells derived from human induced pluripotent stem cells and human tissues, we revealed that patients with Rett syndrome (RTT), carrying MeCP2 mutations, have increased susceptibility for L1 retrotransposition. Our data demonstrate that L1 retrotransposition can be controlled in a tissue-specific manner and that disease-related genetic mutations can influence the frequency of neuronal L1 retrotransposition. Our findings add a new level of complexity to the molecular events that can lead to neurological disorders.

Ma, D.K., Marchetto, M.C., Guo, J.U., Ming, G.L., Gage, F.H., Song, H. Epigenetic choreographers of neurogenesis in the adult mammalian brain. (2010) Nature Neuroscience. 13(11):1338-44. DOI: 10.1038/nn.2672

+ expand abstract

Aimone, J.B., Deng, W., Gage, F.H. Put them out to pasture? What are old granule cells good for, anyway...? (2010) Hippocampus. 20(10):1124-5. DOI: 10.1002/hipo.20867

+ expand abstract

Miller, K.J., Hermes, D., Honey, C.J., Sharma, M., Rao, R.P., den Nijs, M., Fetz, E.E., Sejnowski, T.J., Hebb, A.O., Ojemann, J.G., Makeig, S., Leuthardt, E.C. Dynamic modulation of local population activity by rhythm phase in human occipital cortex during a visual search task. (2010) Frontiers in Human Neuroscience. 4:197. DOI: 10.3389/fnhum.2010.00197

+ expand abstract

Liu, D., Ou, L., Clemenson, G.D., Chao, C., Lutske, M.E., Zambetti, G.P., Gage, F.H., Xu, Y. Puma is required for p53-induced depletion of adult stem cells. (2010) Nature Cell Biology. 12(10):993-8. DOI: 10.1038/ncb2100

+ expand abstract

Hasenstaub, A.R., Callaway, E.M. Paint it black (or red, or green): optical and genetic tools illuminate inhibitory contributions to cortical circuit function. (2010) Neuron. 67(5):681-684. DOI: 10.1016/j.neuron.2010.08.039

+ expand abstract

Choi, J., Young, J.A., Callaway, E.M. Selective viral vector transduction of ErbB4 expressing cortical interneurons in vivo with a viral receptor-ligand bridge protein. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(38):16703-16708. DOI: 10.1073/pnas.1006233107

+ expand abstract

Petruska, J.C., Kitay, B., Boyce, V.S., Kaspar, B.K., Pearse, D.D., Gage, F.H., Mendell, L.M. Intramuscular AAV delivery of NT-3 alters synaptic transmission to motoneurons in adult rats. (2010) Eur. J. Neurosci. 32(6):997-1005. DOI: 10.1111/j.1460-9568.2010.07392.x

+ expand abstract

Hao, J., Lee, T.W., Sejnowski, T.J. Speech Enhancement Using Gaussian Scale Mixture Models. (2010) IEEE Trans Audio Speech Lang Process. 18(6):1127-1136. DOI: 10.1109/TASL.2009.2030012

+ expand abstract

Marshel, J.H., Mori, T., Nielsen, K.J., Callaway, E.M. Targeting single neuronal networks for gene expression and cell labeling in vivo. (2010) Neuron. 67(4):562-574. DOI: 10.1016/j.neuron.2010.08.001

+ expand abstract

Fröhlich, F., Sejnowski, T.J., Bazhenov, M. Network bistability mediates spontaneous transitions between normal and pathological brain states. (2010) Journal of Neuroscience. 30(32):10734-10743. DOI: 10.1523/JNEUROSCI.1239-10.2010

+ expand abstract

Mu, Y., Lee, S.W., Gage, F.H. Signaling in adult neurogenesis. (2010) Current Opinion in Neurobiology. 20(4):416-23. DOI: 10.1016/j.conb.2010.04.010

+ expand abstract

Singer, T., McConnell, M.J., Marchetto, M.C., Coufal, N.G., Gage, F.H. LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes? (2010) Trends in Neurosciences. 33(8):345-54. DOI: 10.1016/j.tins.2010.04.001

+ expand abstract

Valdez, G., Tapia, J.C., Kang, H., Clemenson, G.D., Gage, F.H., Lichtman, J.W., Sanes, J.R. Attenuation of age-related changes in mouse neuromuscular synapses by caloric restriction and exercise. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(33):14863-8. DOI: 10.1073/pnas.1002220107

+ expand abstract

Mira, H., Andreu, Z., Suh, H., Lie, D.C., Jessberger, S., Consiglio, A., San Emeterio, J., Hortigüela, R., Marqués-Torrejón, M.A., Nakashima, K., Colak, D., Götz, M., Fariñas, I., Gage, F.H. Signaling through BMPR-IA regulates quiescence and long-term activity of neural stem cells in the adult hippocampus. (2010) Cell Stem Cell. 7(1):78-89. DOI: 10.1016/j.stem.2010.04.016

+ expand abstract

Hasenstaub, A., Otte, S., Callaway, E., Sejnowski, T.J. Metabolic cost as a unifying principle governing neuronal biophysics. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(27):12329-34. DOI: 10.1073/pnas.0914886107

+ expand abstract

Aimone, J.B., Deng, W., Gage, F.H. Adult neurogenesis: integrating theories and separating functions. (2010) Trends in Cognitive Sciences. 14(7):325-37. DOI: 10.1016/j.tics.2010.04.003

+ expand abstract

Imaizumi, K., Priebe, N.J., Sharpee, T.O., Cheung, S.W., Schreiner, C.E. Encoding of temporal information by timing, rate, and place in cat auditory cortex. (2010) PLOS One. 5(7):e11531. DOI: 10.1371/journal.pone.0011531

+ expand abstract

Qu, Y., Glasco, D.M., Zhou, L., Sawant, A., Ravni, A., Fritzsch, B., Damrau, C., Murdoch, J.N., Evans, S., Pfaff, S.L., Formstone, C., Goffinet, A.M., Chandrasekhar, A., Tissir, F. Atypical cadherins Celsr1-3 differentially regulate migration of facial branchiomotor neurons in mice. (2010) Journal of Neuroscience. 30(28):9392-401. DOI: 10.1523/JNEUROSCI.0124-10.2010

+ expand abstract

Nelson, J.D., McKenzie, C.R., Cottrell, G.W., Sejnowski, T.J. Experience matters: information acquisition optimizes probability gain. (2010) Psychol Sci. 21(7):960-969. DOI: 10.1177/0956797610372637

+ expand abstract

Grossmann, K.S., Giraudin, A., Britz, O., Zhang, J., Goulding, M. Genetic dissection of rhythmic motor networks in mice. (2010) Progress in Brain Research. 187:19-37. DOI: 10.1016/B978-0-444-53613-6.00002-2

+ expand abstract

Gallarda, B.W., Sharpee, T.O., Pfaff, S.L., Alaynick, W.A. Defining rhythmic locomotor burst patterns using a continuous wavelet transform. (2010) Ann. N. Y. Acad. Sci. 1198:133-9. DOI: 10.1111/j.1749-6632.2010.05437.x

+ expand abstract

Hao, J., Lee, I., Lee, T.W., Sejnowski, T.J. Independent vector analysis for source separation using a mixture of gaussians prior. (2010) Neural Computation. 22(6):1646-1673. DOI: 10.1162/neco.2010.11-08-906

+ expand abstract

Deng, W., Aimone, J.B., Gage, F.H. New neurons and new memories: how does adult hippocampal neurogenesis affect learning and memory? (2010) Nature Reviews Neuroscience. 11(5):339-50. DOI: 10.1038/nrn2822

+ expand abstract

Moldakarimov, S., Bazhenov, M., Sejnowski, T.J. Representation sharpening can explain perceptual priming. (2010) Neural Computation. 22(5):1312-32. DOI: 10.1162/neco.2009.04-09-999

+ expand abstract

Zhang, M., Liu, J., Kim, Y., Dixon, J.E., Pfaff, S.L., Gill, G.N., Noel, J.P., Zhang, Y. Structural and functional analysis of the phosphoryl transfer reaction mediated by the human small C-terminal domain phosphatase, Scp1. (2010) Protein Science. 19(5):974-86. DOI: 10.1002/pro.375

+ expand abstract

Modchang, C., Nadkarni, S., Bartol, T.M., Triampo, W., Sejnowski, T.J., Levine, H., Rappel, W.J. A comparison of deterministic and stochastic simulations of neuronal vesicle release models. (2010) Phys Biol. 7(2):026008. DOI: 10.1088/1478-3975/7/2/026008

+ expand abstract

Marchetto, M.C., Winner, B., Gage, F.H. Pluripotent stem cells in neurodegenerative and neurodevelopmental diseases. (2010) Human Molecular Genetics. 19(R1):R71-6. DOI: 10.1093/hmg/ddq159

+ expand abstract

Wang, H.P., Spencer, D., Fellous, J.M., Sejnowski, T.J. Synchrony of thalamocortical inputs maximizes cortical reliability. (2010) Science. 328(5974):106-109. DOI: 10.1126/science.1183108

+ expand abstract

Tronel, S., Fabre, A., Charrier, V., Oliet, S.H., Gage, F.H., Abrous, D.N. Spatial learning sculpts the dendritic arbor of adult-born hippocampal neurons. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(17):7963-8. DOI: 10.1073/pnas.0914613107

+ expand abstract

Gage, F.H. Molecular and cellular mechanisms contributing to the regulation, proliferation and differentiation of neural stem cells in the adult dentate gyrus. (2010) Keio J Med. 59(3):79-83.

+ expand abstract

Stiefel, K.M., Fellous, J.M., Thomas, P.J., Sejnowski, T.J. Intrinsic subthreshold oscillations extend the influence of inhibitory synaptic inputs on cortical pyramidal neurons. (2010) European Journal of Neuroscience. 31(6):1019-26. DOI: 10.1111/j.1460-9568.2010.07146.x

+ expand abstract

Bonanomi, D., Pfaff, S.L. Motor axon pathfinding. (2010) Cold Spring Harbor Perspectives in Biology. 2(3):a001735. DOI: 10.1101/cshperspect.a001735

+ expand abstract

Moldakarimov, S., Bazhenov, M., Sejnowski, T.J. Perceptual priming leads to reduction of gamma frequency oscillations. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(12):5640-5645. DOI: 10.1073/pnas.0907525107

+ expand abstract

Drion, G., Bonjean, M., Waroux, O., Scuvée-Moreau, J., Liégeois, J.F., Sejnowski, T.J., Sepulchre, R., Seutin, V. M-type channels selectively control bursting in rat dopaminergic neurons. (2010) European Journal of Neuroscience. 31(5):827-835. DOI: 10.1111/j.1460-9568.2010.07107.x

+ expand abstract

Peterson, D.A., Sejnowski, T.J., Poizner, H. Convergent evidence for abnormal striatal synaptic plasticity in dystonia. (2010) Neurobiol. Dis. 37(3):558-73. DOI: 10.1016/j.nbd.2009.12.003

+ expand abstract

Dystonia is a functionally disabling movement disorder characterized by abnormal movements and postures. Although substantial recent progress has been made in identifying genetic factors, the pathophysiology of the disease remains a mystery. A provocative suggestion gaining broader acceptance is that some aspect of neural plasticity may be abnormal. There is also evidence that, at least in some forms of dystonia, sensorimotor "use" may be a contributing factor. Most empirical evidence of abnormal plasticity in dystonia comes from measures of sensorimotor cortical organization and physiology. However, the basal ganglia also play a critical role in sensorimotor function. Furthermore, the basal ganglia are prominently implicated in traditional models of dystonia, are the primary targets of stereotactic neurosurgical interventions, and provide a neural substrate for sensorimotor learning influenced by neuromodulators. Our working hypothesis is that abnormal plasticity in the basal ganglia is a critical link between the etiology and pathophysiology of dystonia. In this review we set up the background for this hypothesis by integrating a large body of disparate indirect evidence that dystonia may involve abnormalities in synaptic plasticity in the striatum. After reviewing evidence implicating the striatum in dystonia, we focus on the influence of two neuromodulatory systems: dopamine and acetylcholine. For both of these neuromodulators, we first describe the evidence for abnormalities in dystonia and then the means by which it may influence striatal synaptic plasticity. Collectively, the evidence suggests that many different forms of dystonia may involve abnormal plasticity in the striatum. An improved understanding of these altered plastic processes would help inform our understanding of the pathophysiology of dystonia, and, given the role of the striatum in sensorimotor learning, provide a principled basis for designing therapies aimed at the dynamic processes linking etiology to pathophysiology of the disease.

Glass, C.K., Saijo, K., Winner, B., Marchetto, M.C., Gage, F.H. Mechanisms underlying inflammation in neurodegeneration. (2010) Cell. 140(6):918-34. DOI: 10.1016/j.cell.2010.02.016

+ expand abstract

Gage, F. The promise and the challenge of modelling human disease in a dish. (2010) EMBO Molecular Medicine. 2(3):77-8. DOI: 10.1002/emmm.201000060

Otte, S., Hasenstaub, A., Callaway, E.M. Cell type-specific control of neuronal responsiveness by gamma-band oscillatory inhibition. (2010) Journal of Neuroscience. 30(6):2150-2159. DOI: 10.1523/JNEUROSCI.4818-09.2010

+ expand abstract

Garcia-Campmany, L., Stam, F.J., Goulding, M. From circuits to behaviour: motor networks in vertebrates. (2010) Current Opinion in Neurobiology. 20(1):116-25. DOI: 10.1016/j.conb.2010.01.002

+ expand abstract

Xu, X., Roby, K.D., Callaway, E.M. Immunochemical characterization of inhibitory mouse cortical neurons: three chemically distinct classes of inhibitory cells. (2010) Journal of Comparative Neurology. 518(3):389-404. DOI: 10.1002/cne.22229

+ expand abstract

Lyon, D.C., Nassi, J.J., Callaway, E.M. A disynaptic relay from superior colliculus to dorsal stream visual cortex in macaque monkey. (2010) Neuron. 65(2):270-279. DOI: 10.1016/j.neuron.2010.01.003

+ expand abstract

Meyer, A., Gallarda, B.W., Pfaff, S., Alaynick, W. Spinal cord electrophysiology. (2010) J Vis Exp.(35) DOI: 10.3791/1660

+ expand abstract

Qu, Q., Sun, G., Li, W., Yang, S., Ye, P., Zhao, C., Yu, R.T., Gage, F.H., Evans, R.M., Shi, Y. Orphan nuclear receptor TLX activates Wnt/beta-catenin signalling to stimulate neural stem cell proliferation and self-renewal. (2010) Nature Cell Biology. 12(1):31-40; sup pp 1-9. DOI: 10.1038/ncb2001

+ expand abstract

Sejnowski, T.J. Consequences of non-uniform active currents in dendrites. (2009) Frontiers in Neuroscience. 3(3):332-333. DOI: 10.3389/neuro.01.038.2009

Atencio, C.A., Sharpee, T.O., Schreiner, C.E. Hierarchical computation in the canonical auditory cortical circuit. (2009) Proceedings of the National Academy of Sciences of the United States of America. 106(51):21894-9. DOI: 10.1073/pnas.0908383106

+ expand abstract

Volman, V., Levine, H., Ben-Jacob, E., Sejnowski, T.J. Locally balanced dendritic integration by short-term synaptic plasticity and active dendritic conductances. (2009) Journal of Neurophysiology. 102(6):3234-3250. DOI: 10.1152/jn.00260.2009

+ expand abstract

Nathanson, J.L., Jappelli, R., Scheeff, E.D., Manning, G., Obata, K., Brenner, S., Callaway, E.M. Short Promoters in Viral Vectors Drive Selective Expression in Mammalian Inhibitory Neurons, but do not Restrict Activity to Specific Inhibitory Cell-Types. (2009) Front Neural Circuits. 3:19. DOI: 10.3389/neuro.04.019.2009

+ expand abstract

Tanaka, H., Sejnowski, T.J., Krakauer, J.W. Adaptation to visuomotor rotation through interaction between posterior parietal and motor cortical areas. (2009) Journal of Neurophysiology. 102(5):2921-32. DOI: 10.1152/jn.90834.2008

+ expand abstract

Nakashima, K., Kohyama, J., Namihira, M., Gage, F.H., Okano, H., Sawamoto, K. [Epigenetic mechanisms regulating neural cell fate determination]. (2009) No To Hattatsu. 41(6):411-4.

+ expand abstract

Jessberger, S., Gage, F.H., Eisch, A.J., Lagace, D.C. Making a neuron: Cdk5 in embryonic and adult neurogenesis. (2009) Trends in Neurosciences. 32(11):575-82. DOI: 10.1016/j.tins.2009.07.002

+ expand abstract

Peterson, D.A., Elliott, C., Song, D.D., Makeig, S., Sejnowski, T.J., Poizner, H. Probabilistic reversal learning is impaired in Parkinson's disease. (2009) Neuroscience. 163(4):1092-1101. DOI: 10.1016/j.neuroscience.2009.07.033

+ expand abstract

Deng, W., Saxe, M.D., Gallina, I.S., Gage, F.H. Adult-born hippocampal dentate granule cells undergoing maturation modulate learning and memory in the brain. (2009) Journal of Neuroscience. 29(43):13532-42. DOI: 10.1523/JNEUROSCI.3362-09.2009

+ expand abstract

Muotri, A.R., Zhao, C., Marchetto, M.C., Gage, F.H. Environmental influence on L1 retrotransposons in the adult hippocampus. (2009) Hippocampus. 19(10):1002-7. DOI: 10.1002/hipo.20564

+ expand abstract

Wehr, M., Hostick, U., Kyweriga, M., Tan, A., Weible, A.P., Wu, H., Wu, W., Callaway, E.M., Kentros, C. Transgenic silencing of neurons in the mammalian brain by expression of the allatostatin receptor (AlstR). (2009) Journal of Neurophysiology. 102(4):2554-2562. DOI: 10.1152/jn.00480.2009

+ expand abstract

Fitzgerald, J.D., Sharpee, T.O. Maximally informative pairwise interactions in networks. (2009) Phys Rev E Stat Nonlin Soft Matter Phys. 80(3 Pt 1):031914. DOI: 10.1103/PhysRevE.80.031914

+ expand abstract

Liu, Y.S., Stevens, C.F., Sharpee, T.O. Predictable irregularities in retinal receptive fields. (2009) Proceedings of the National Academy of Sciences of the United States of America. 106(38):16499-504. DOI: 10.1073/pnas.0908926106

+ expand abstract

Marchetto, M.C., Yeo, G.W., Kainohana, O., Marsala, M., Gage, F.H., Muotri, A.R. Transcriptional signature and memory retention of human-induced pluripotent stem cells. (2009) PLOS One. 4(9):e7076. DOI: 10.1371/journal.pone.0007076

+ expand abstract

Behrens, M.M., Sejnowski, T.J. Does schizophrenia arise from oxidative dysregulation of parvalbumin-interneurons in the developing cortex? (2009) Neuropharmacology. 57(3):193-200. DOI: 10.1016/j.neuropharm.2009.06.002

+ expand abstract

Lin, W., Metzakopian, E., Mavromatakis, Y.E., Gao, N., Balaskas, N., Sasaki, H., Briscoe, J., Whitsett, J.A., Goulding, M., Kaestner, K.H., Ang, S.L. Foxa1 and Foxa2 function both upstream of and cooperatively with Lmx1a and Lmx1b in a feedforward loop promoting mesodiencephalic dopaminergic neuron development. (2009) Developmental Biology. 333(2):386-96. DOI: 10.1016/j.ydbio.2009.07.006

+ expand abstract

Song, M.R., Sun, Y., Bryson, A., Gill, G.N., Evans, S.M., Pfaff, S.L. Islet-to-LMO stoichiometries control the function of transcription complexes that specify motor neuron and V2a interneuron identity. (2009) Development. 136(17):2923-32. DOI: 10.1242/dev.037986

+ expand abstract

Mukamel, E.A., Nimmerjahn, A., Schnitzer, M.J. Automated analysis of cellular signals from large-scale calcium imaging data. (2009) Neuron. 63(6):747-60. DOI: 10.1016/j.neuron.2009.08.009

+ expand abstract

Tiesinga, P., Sejnowski, T.J. Cortical enlightenment: are attentional gamma oscillations driven by ING or PING? (2009) Neuron. 63(6):727-732. DOI: 10.1016/j.neuron.2009.09.009

+ expand abstract

Conner, J.M., Franks, K.M., Titterness, A.K., Russell, K., Merrill, D.A., Christie, B.R., Sejnowski, T.J., Tuszynski, M.H. NGF is essential for hippocampal plasticity and learning. (2009) Journal of Neuroscience. 29(35):10883-10889. DOI: 10.1523/JNEUROSCI.2594-09.2009

+ expand abstract

Tamaki, S.J., Jacobs, Y., Dohse, M., Capela, A., Cooper, J.D., Reitsma, M., He, D., Tushinski, R., Belichenko, P.V., Salehi, A., Mobley, W., Gage, F.H., Huhn, S., Tsukamoto, A.S., Weissman, I.L., Uchida, N. Neuroprotection of host cells by human central nervous system stem cells in a mouse model of infantile neuronal ceroid lipofuscinosis. (2009) Cell Stem Cell. 5(3):310-9. DOI: 10.1016/j.stem.2009.05.022

+ expand abstract

Kuwabara, T., Hsieh, J., Muotri, A., Yeo, G., Warashina, M., Lie, D.C., Moore, L., Nakashima, K., Asashima, M., Gage, F.H. Wnt-mediated activation of NeuroD1 and retro-elements during adult neurogenesis. (2009) Nature Neuroscience. 12(9):1097-105. DOI: 10.1038/nn.2360

+ expand abstract

Coufal, N.G., Garcia-Perez, J.L., Peng, G.E., Yeo, G.W., Mu, Y., Lovci, M.T., Morell, M., O'Shea, K.S., Moran, J.V., Gage, F.H. L1 retrotransposition in human neural progenitor cells. (2009) Nature. 460(7259):1127-31. DOI: 10.1038/nature08248

+ expand abstract

Makeig, S., Gramann, K., Jung, T.P., Sejnowski, T.J., Poizner, H. Linking brain, mind and behavior. (2009) Int J Psychophysiol. 73(2):95-100. DOI: 10.1016/j.ijpsycho.2008.11.008

+ expand abstract

Overall, R.W., Kempermann, G., Peirce, J., Lu, L., Goldowitz, D., Gage, F.H., Goodwin, S., Smit, A.B., Airey, D.C., Rosen, G.D., Schalkwyk, L.C., Sutter, T.R., Nowakowski, R.S., Whatley, S., Williams, R.W. Genetics of the hippocampal transcriptome in mouse: a systematic survey and online neurogenomics resource. (2009) Frontiers in Neuroscience. 3:55. DOI: 10.3389/neuro.15.003.2009

+ expand abstract

Clelland, C.D., Choi, M., Romberg, C., Clemenson, G.D., Fragniere, A., Tyers, P., Jessberger, S., Saksida, L.M., Barker, R.A., Gage, F.H., Bussey, T.J. A functional role for adult hippocampal neurogenesis in spatial pattern separation. (2009) Science. 325(5937):210-3. DOI: 10.1126/science.1173215

+ expand abstract

Goulding, M. Circuits controlling vertebrate locomotion: moving in a new direction. (2009) Nature Reviews Neuroscience. 10(7):507-18. DOI: 10.1038/nrn2608

+ expand abstract

Thuret, S., Toni, N., Aigner, S., Yeo, G.W., Gage, F.H. Hippocampus-dependent learning is associated with adult neurogenesis in MRL/MpJ mice. (2009) Hippocampus. 19(7):658-69. DOI: 10.1002/hipo.20550

+ expand abstract

Destexhe, A., Sejnowski, T.J. The Wilson-Cowan model, 36 years later. (2009) Biol Cybern. 101(1):1-2. DOI: 10.1007/s00422-009-0328-3

+ expand abstract

Meltzoff, A.N., Kuhl, P.K., Movellan, J., Sejnowski, T.J. Foundations for a new science of learning. (2009) Science. 325(5938):284-288. DOI: 10.1126/science.1175626

+ expand abstract

Fortun, J., Puzis, R., Pearse, D.D., Gage, F.H., Bunge, M.B. Muscle injection of AAV-NT3 promotes anatomical reorganization of CST axons and improves behavioral outcome following SCI. (2009) J. Neurotrauma. 26(7):941-53. DOI: 10.1089/neu.2008.0807

+ expand abstract

Nathanson, J.L., Yanagawa, Y., Obata, K., Callaway, E.M. Preferential labeling of inhibitory and excitatory cortical neurons by endogenous tropism of adeno-associated virus and lentivirus vectors. (2009) Neuroscience. 161(2):441-450. DOI: 10.1016/j.neuroscience.2009.03.032

+ expand abstract

Jagasia, R., Steib, K., Englberger, E., Herold, S., Faus-Kessler, T., Saxe, M., Gage, F.H., Song, H., Lie, D.C. GABA-cAMP response element-binding protein signaling regulates maturation and survival of newly generated neurons in the adult hippocampus. (2009) Journal of Neuroscience. 29(25):7966-77. DOI: 10.1523/JNEUROSCI.1054-09.2009

+ expand abstract

Li, Y., Mu, Y., Gage, F.H. Development of neural circuits in the adult hippocampus. (2009) Current Topics in Developmental Biology. 87:149-74. DOI: 10.1016/S0070-2153(09)01205-8

+ expand abstract

Sincich, L.C., Horton, J.C., Sharpee, T.O. Preserving information in neural transmission. (2009) Journal of Neuroscience. 29(19):6207-16. DOI: 10.1523/JNEUROSCI.3701-08.2009

+ expand abstract

Nassi, J.J., Callaway, E.M. Parallel processing strategies of the primate visual system. (2009) Nature Reviews Neuroscience. 10(5):360-372. DOI: 10.1038/nrn2619

+ expand abstract

Nimmerjahn, A., Mukamel, E.A., Schnitzer, M.J. Motor behavior activates Bergmann glial networks. (2009) Neuron. 62(3):400-12. DOI: 10.1016/j.neuron.2009.03.019

+ expand abstract

Suh, H., Deng, W., Gage, F.H. Signaling in adult neurogenesis. (2009) Annual Review of Cell and Developmental Biology. 25:253-75. DOI: 10.1146/annurev.cellbio.042308.113256

+ expand abstract

Stiefel, K.M., Gutkin, B.S., Sejnowski, T.J. The effects of cholinergic neuromodulation on neuronal phase-response curves of modeled cortical neurons. (2009) Journal of Computational Neuroscience. 26(2):289-301. DOI: 10.1007/s10827-008-0111-9

+ expand abstract

Sharpee, T.O., Victor, J.D. Contextual modulation of V1 receptive fields depends on their spatial symmetry. (2009) Journal of Computational Neuroscience. 26(2):203-18. DOI: 10.1007/s10827-008-0107-5

+ expand abstract

Nimmerjahn, A. Astrocytes going live: advances and challenges. (2009) Journal of Physiology. 587(Pt 8):1639-47. DOI: 10.1113/jphysiol.2008.167171

+ expand abstract

Schwartz, O., Sejnowski, T.J., Dayan, P. Perceptual organization in the tilt illusion. (2009) Journal of Vision. 9(4):19.1-20. DOI: 10.1167/9.4.19

+ expand abstract

Andrews, M.R., Czvitkovich, S., Dassie, E., Vogelaar, C.F., Faissner, A., Blits, B., Gage, F.H., ffrench-Constant, C., Fawcett, J.W. Alpha9 integrin promotes neurite outgrowth on tenascin-C and enhances sensory axon regeneration. (2009) Journal of Neuroscience. 29(17):5546-57. DOI: 10.1523/JNEUROSCI.0759-09.2009

+ expand abstract

Saijo, K., Winner, B., Carson, C.T., Collier, J.G., Boyer, L., Rosenfeld, M.G., Gage, F.H., Glass, C.K. A Nurr1/CoREST pathway in microglia and astrocytes protects dopaminergic neurons from inflammation-induced death. (2009) Cell. 137(1):47-59. DOI: 10.1016/j.cell.2009.01.038

+ expand abstract

Denli, A.M., Cao, X., Gage, F.H. miR-9 and TLX: chasing tails in neural stem cells. (2009) Nature Structural & Molecular Biology. 16(4):346-7. DOI: 10.1038/nsmb0409-346

Zhao, C., Suh, H., Gage, F.H. Notch keeps ependymal cells in line. (2009) Nature Neuroscience. 12(3):243-5. DOI: 10.1038/nn0309-243

Bazhenov, M., Timofeev, I., Fröhlich, F., Sejnowski, T.J. Cellular and network mechanisms of electrographic seizures. (2009) Drug Discov Today Dis Models. 5(1):45-57. DOI: 10.1016/j.ddmod.2008.07.005

+ expand abstract

Jessberger, S., Clark, R.E., Broadbent, N.J., Clemenson, G.D., Consiglio, A., Lie, D.C., Squire, L.R., Gage, F.H. Dentate gyrus-specific knockdown of adult neurogenesis impairs spatial and object recognition memory in adult rats. (2009) Learn. Mem. 16(2):147-54. DOI: 10.1101/lm.1172609

+ expand abstract

Yeo, G.W., Coufal, N.G., Liang, T.Y., Peng, G.E., Fu, X.D., Gage, F.H. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. (2009) Nature Structural & Molecular Biology. 16(2):130-7. DOI: 10.1038/nsmb.1545

+ expand abstract

Jessberger, S., Gage, F.H. Fate plasticity of adult hippocampal progenitors: biological relevance and therapeutic use. (2009) Trends in Pharmacological Sciences. 30(2):61-5. DOI: 10.1016/j.tips.2008.11.003

+ expand abstract

Kouh, M., Sharpee, T.O. Estimating linear-nonlinear models using Renyi divergences. (2009) Network. 20(2):49-68. DOI: 10.1080/09548980902950891

+ expand abstract

Aimone, J.B., Wiles, J., Gage, F.H. Computational influence of adult neurogenesis on memory encoding. (2009) Neuron. 61(2):187-202. DOI: 10.1016/j.neuron.2008.11.026

+ expand abstract

Xu, X., Callaway, E.M. Laminar specificity of functional input to distinct types of inhibitory cortical neurons. (2009) Journal of Neuroscience. 29(1):70-85. DOI: 10.1523/JNEUROSCI.4104-08.2009

+ expand abstract

Marumoto, T., Tashiro, A., Friedmann-Morvinski, D., Scadeng, M., Soda, Y., Gage, F.H., Verma, I.M. Development of a novel mouse glioma model using lentiviral vectors. (2009) Nature Medicine. 15(1):110-6. DOI: 10.1038/nm.1863

+ expand abstract

Hao, J., Attias, H., Nagarajan, S., Lee, T.W., Sejnowski, T.J. Speech Enhancement, Gain, and Noise Spectrum Adaptation Using Approximate Bayesian Estimation. (2009) IEEE Trans Audio Speech Lang Process. 17(1):24-37. DOI: 10.1109/TASL.2008.2005342

+ expand abstract

Rose, J.B., Crews, L., Rockenstein, E., Adame, A., Mante, M., Hersh, L.B., Gage, F.H., Spencer, B., Potkar, R., Marr, R.A., Masliah, E. Neuropeptide Y fragments derived from neprilysin processing are neuroprotective in a transgenic model of Alzheimer's disease. (2009) Journal of Neuroscience. 29(4):1115-25. DOI: 10.1523/JNEUROSCI.4220-08.2009

+ expand abstract

Callaway, E.M. Transneuronal circuit tracing with neurotropic viruses. (2008) Current Opinion in Neurobiology. 18(6):617-623. DOI: 10.1016/j.conb.2009.03.007

+ expand abstract

Stiefel, K.M., Gutkin, B.S., Sejnowski, T.J. Cholinergic neuromodulation changes phase response curve shape and type in cortical pyramidal neurons. (2008) PLOS One. 3(12):e3947. DOI: 10.1371/journal.pone.0003947

+ expand abstract

Prescott, S.A., Sejnowski, T.J. Spike-rate coding and spike-time coding are affected oppositely by different adaptation mechanisms. (2008) Journal of Neuroscience. 28(50):13649-13661. DOI: 10.1523/JNEUROSCI.1792-08.2008

+ expand abstract

Marchetto, M.C., Muotri, A.R., Mu, Y., Smith, A.M., Cezar, G.G., Gage, F.H. Non-cell-autonomous effect of human SOD1 G37R astrocytes on motor neurons derived from human embryonic stem cells. (2008) Cell Stem Cell. 3(6):649-57. DOI: 10.1016/j.stem.2008.10.001

+ expand abstract

Cao, X., Pfaff, S.L., Gage, F.H. YAP regulates neural progenitor cell number via the TEA domain transcription factor. (2008) Genes & Development. 22(23):3320-34. DOI: 10.1101/gad.1726608

+ expand abstract

Prescott, S.A., Ratté, S., De Koninck, Y., Sejnowski, T.J. Pyramidal neurons switch from integrators in vitro to resonators under in vivo-like conditions. (2008) Journal of Neurophysiology. 100(6):3030-42. DOI: 10.1152/jn.90634.2008

+ expand abstract

Jessberger, S., Gage, F.H. Stem-cell-associated structural and functional plasticity in the aging hippocampus. (2008) Psychol Aging. 23(4):684-91. DOI: 10.1037/a0014188

+ expand abstract

Thompson, C.L., Pathak, S.D., Jeromin, A., Ng, L.L., MacPherson, C.R., Mortrud, M.T., Cusick, A., Riley, Z.L., Sunkin, S.M., Bernard, A., Puchalski, R.B., Gage, F.H., Jones, A.R., Bajic, V.B., Hawrylycz, M.J., Lein, E.S. Genomic anatomy of the hippocampus. (2008) Neuron. 60(6):1010-21. DOI: 10.1016/j.neuron.2008.12.008

+ expand abstract

Jessberger, S., Aigner, S., Clemenson, G.D., Toni, N., Lie, D.C., Karalay, O., Overall, R., Kempermann, G., Gage, F.H. Cdk5 regulates accurate maturation of newborn granule cells in the adult hippocampus. (2008) PLOS Biology. 6(11):e272. DOI: 10.1371/journal.pbio.0060272

+ expand abstract

Flusberg, B.A., Nimmerjahn, A., Cocker, E.D., Mukamel, E.A., Barretto, R.P., Ko, T.H., Burns, L.D., Jung, J.C., Schnitzer, M.J. High-speed, miniaturized fluorescence microscopy in freely moving mice. (2008) Nature Methods. 5(11):935-8. DOI: 10.1038/nmeth.1256

+ expand abstract

Spencer, B., Marr, R.A., Rockenstein, E., Crews, L., Adame, A., Potkar, R., Patrick, C., Gage, F.H., Verma, I.M., Masliah, E. Long-term neprilysin gene transfer is associated with reduced levels of intracellular Abeta and behavioral improvement in APP transgenic mice. (2008) BMC Neurosci. 9:109. DOI: 10.1186/1471-2202-9-109

+ expand abstract

Kohyama, J., Kojima, T., Takatsuka, E., Yamashita, T., Namiki, J., Hsieh, J., Gage, F.H., Namihira, M., Okano, H., Sawamoto, K., Nakashima, K. Epigenetic regulation of neural cell differentiation plasticity in the adult mammalian brain. (2008) Proceedings of the National Academy of Sciences of the United States of America. 105(46):18012-7. DOI: 10.1073/pnas.0808417105

+ expand abstract

Fröhlich, F., Bazhenov, M., Iragui-Madoz, V., Sejnowski, T.J. Potassium dynamics in the epileptic cortex: new insights on an old topic. (2008) The Neuroscientist. 14(5):422-433. DOI: 10.1177/1073858408317955

+ expand abstract

Zhang, Y., Narayan, S., Geiman, E., Lanuza, G.M., Velasquez, T., Shanks, B., Akay, T., Dyck, J., Pearson, K., Gosgnach, S., Fan, C.M., Goulding, M. V3 spinal neurons establish a robust and balanced locomotor rhythm during walking. (2008) Neuron. 60(1):84-96. DOI: 10.1016/j.neuron.2008.09.027

+ expand abstract

Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.C., Baden, S.B., Sejnowski, T.J., Stiles, J.R. FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES. (2008) SIAM Journal on Scientific Computing. 30(6):3126. DOI: 10.1137/070692017

+ expand abstract

Prescott, S.A., De Koninck, Y., Sejnowski, T.J. Biophysical basis for three distinct dynamical mechanisms of action potential initiation. (2008) PLOS Computational Biology. 4(10):e1000198. DOI: 10.1371/journal.pcbi.1000198

+ expand abstract

Transduction of graded synaptic input into trains of all-or-none action potentials (spikes) is a crucial step in neural coding. Hodgkin identified three classes of neurons with qualitatively different analog-to-digital transduction properties. Despite widespread use of this classification scheme, a generalizable explanation of its biophysical basis has not been described. We recorded from spinal sensory neurons representing each class and reproduced their transduction properties in a minimal model. With phase plane and bifurcation analysis, each class of excitability was shown to derive from distinct spike initiating dynamics. Excitability could be converted between all three classes by varying single parameters; moreover, several parameters, when varied one at a time, had functionally equivalent effects on excitability. From this, we conclude that the spike-initiating dynamics associated with each of Hodgkin's classes represent different outcomes in a nonlinear competition between oppositely directed, kinetically mismatched currents. Class 1 excitability occurs through a saddle node on invariant circle bifurcation when net current at perithreshold potentials is inward (depolarizing) at steady state. Class 2 excitability occurs through a Hopf bifurcation when, despite net current being outward (hyperpolarizing) at steady state, spike initiation occurs because inward current activates faster than outward current. Class 3 excitability occurs through a quasi-separatrix crossing when fast-activating inward current overpowers slow-activating outward current during a stimulus transient, although slow-activating outward current dominates during constant stimulation. Experiments confirmed that different classes of spinal lamina I neurons express the subthreshold currents predicted by our simulations and, further, that those currents are necessary for the excitability in each cell class. Thus, our results demonstrate that all three classes of excitability arise from a continuum in the direction and magnitude of subthreshold currents. Through detailed analysis of the spike-initiating process, we have explained a fundamental link between biophysical properties and qualitative differences in how neurons encode sensory input.

Barbour, D.L., Callaway, E.M. Excitatory local connections of superficial neurons in rat auditory cortex. (2008) Journal of Neuroscience. 28(44):11174-11185. DOI: 10.1523/JNEUROSCI.2093-08.2008

+ expand abstract

Pagliardini, S., Ren, J., Gray, P.A., Vandunk, C., Gross, M., Goulding, M., Greer, J.J. Central respiratory rhythmogenesis is abnormal in lbx1- deficient mice. (2008) Journal of Neuroscience. 28(43):11030-41. DOI: 10.1523/JNEUROSCI.1648-08.2008

+ expand abstract

Li, X., Barkho, B.Z., Luo, Y., Smrt, R.D., Santistevan, N.J., Liu, C., Kuwabara, T., Gage, F.H., Zhao, X. Epigenetic regulation of the stem cell mitogen Fgf-2 by Mbd1 in adult neural stem/progenitor cells. (2008) Journal of Biological Chemistry. 283(41):27644-52. DOI: 10.1074/jbc.M804899200

+ expand abstract

Pfaff, S.L. Developmental neuroscience: Hox and Fox. (2008) Nature. 455(7211):295-7. DOI: 10.1038/455295a

Lopreore, C.L., Bartol, T.M., Coggan, J.S., Keller, D.X., Sosinsky, G.E., Ellisman, M.H., Sejnowski, T.J. Computational modeling of three-dimensional electrodiffusion in biological systems: application to the node of Ranvier. (2008) Biophysical Journal. 95(6):2624-2635. DOI: 10.1529/biophysj.108.132167

+ expand abstract

Gage, F.H., Selzer, M.E. Experts provide insights into emerging field of brain and spine repair. Interview by Bridget M. Kuehn. (2008) JAMA. 300(9):1013-4. DOI: 10.1001/jama.300.9.1013

Toni, N., Laplagne, D.A., Zhao, C., Lombardi, G., Ribak, C.E., Gage, F.H., Schinder, A.F. Neurons born in the adult dentate gyrus form functional synapses with target cells. (2008) Nature Neuroscience. 11(8):901-7. DOI: 10.1038/nn.2156

+ expand abstract

Jessberger, S., Toni, N., Clemenson, G.D., Ray, J., Gage, F.H. Directed differentiation of hippocampal stem/progenitor cells in the adult brain. (2008) Nature Neuroscience. 11(8):888-93. DOI: 10.1038/nn.2148

+ expand abstract

Low, P.S., Shank, S.S., Sejnowski, T.J., Margoliash, D. Mammalian-like features of sleep structure in zebra finches. (2008) Proceedings of the National Academy of Sciences of the United States of America. 105(26):9081-9086. DOI: 10.1073/pnas.0703452105

+ expand abstract

Wang, Z., Li, L., Goulding, M., Frank, E. Early postnatal development of reciprocal Ia inhibition in the murine spinal cord. (2008) Journal of Neurophysiology. 100(1):185-96. DOI: 10.1152/jn.90354.2008

+ expand abstract

Atencio, C.A., Sharpee, T.O., Schreiner, C.E. Cooperative nonlinearities in auditory cortical neurons. (2008) Neuron. 58(6):956-66. DOI: 10.1016/j.neuron.2008.04.026

+ expand abstract

Lee, S., Lee, B., Joshi, K., Pfaff, S.L., Lee, J.W., Lee, S.K. A regulatory network to segregate the identity of neuronal subtypes. (2008) Developmental Cell. 14(6):877-89. DOI: 10.1016/j.devcel.2008.03.021

+ expand abstract

Sharpee, T.O., Miller, K.D., Stryker, M.P. On the importance of static nonlinearity in estimating spatiotemporal neural filters with natural stimuli. (2008) Journal of Neurophysiology. 99(5):2496-509. DOI: 10.1152/jn.01397.2007

+ expand abstract

Tan, W., Janczewski, W.A., Yang, P., Shao, X.M., Callaway, E.M., Feldman, J.L. Silencing preBötzinger complex somatostatin-expressing neurons induces persistent apnea in awake rat. (2008) Nature Neuroscience. 11(5):538-540. DOI: 10.1038/nn.2104

+ expand abstract

Yeo, G.W., Coufal, N., Aigner, S., Winner, B., Scolnick, J.A., Marchetto, M.C., Muotri, A.R., Carson, C., Gage, F.H. Multiple layers of molecular controls modulate self-renewal and neuronal lineage specification of embryonic stem cells. (2008) Human Molecular Genetics. 17(R1):R67-75. DOI: 10.1093/hmg/ddn065

+ expand abstract

Keller, D.X., Franks, K.M., Bartol, T.M., Sejnowski, T.J. Calmodulin activation by calcium transients in the postsynaptic density of dendritic spines. (2008) PLOS One. 3(4):e2045. DOI: 10.1371/journal.pone.0002045

+ expand abstract

Finelli, L.A., Haney, S., Bazhenov, M., Stopfer, M., Sejnowski, T.J. Synaptic learning rules and sparse coding in a model sensory system. (2008) PLOS Computational Biology. 4(4):e1000062. DOI: 10.1371/journal.pcbi.1000062

+ expand abstract

Gallarda, B.W., Bonanomi, D., Müller, D., Brown, A., Alaynick, W.A., Andrews, S.E., Lemke, G., Pfaff, S.L., Marquardt, T. Segregation of axial motor and sensory pathways via heterotypic trans-axonal signaling. (2008) Science. 320(5873):233-6. DOI: 10.1126/science.1153758

+ expand abstract

Xu, Y., Lopes, C., Qian, Y., Liu, Y., Cheng, L., Goulding, M., Turner, E.E., Lima, D., Ma, Q. Tlx1 and Tlx3 coordinate specification of dorsal horn pain-modulatory peptidergic neurons. (2008) Journal of Neuroscience. 28(15):4037-46. DOI: 10.1523/JNEUROSCI.4126-07.2008

+ expand abstract

Ma, Y.C., Song, M.R., Park, J.P., Henry Ho, H.Y., Hu, L., Kurtev, M.V., Zieg, J., Ma, Q., Pfaff, S.L., Greenberg, M.E. Regulation of motor neuron specification by phosphorylation of neurogenin 2. (2008) Neuron. 58(1):65-77. DOI: 10.1016/j.neuron.2008.01.037

+ expand abstract

Larsen, D.D., Wickersham, I.R., Callaway, E.M. Retrograde tracing with recombinant rabies virus reveals correlations between projection targets and dendritic architecture in layer 5 of mouse barrel cortex. (2008) Front Neural Circuits. 1:5. DOI: 10.3389/neuro.04.005.2007

+ expand abstract

Luo, L., Callaway, E.M., Svoboda, K. Genetic dissection of neural circuits. (2008) Neuron. 57(5):634-660. DOI: 10.1016/j.neuron.2008.01.002

+ expand abstract

Zhao, C., Deng, W., Gage, F.H. Mechanisms and functional implications of adult neurogenesis. (2008) Cell. 132(4):645-60. DOI: 10.1016/j.cell.2008.01.033

+ expand abstract

Fröhlich, F., Bazhenov, M., Sejnowski, T.J. Pathological effect of homeostatic synaptic scaling on network dynamics in diseases of the cortex. (2008) Journal of Neuroscience. 28(7):1709-1720. DOI: 10.1523/JNEUROSCI.4263-07.2008

+ expand abstract

Zhang, C.L., Zou, Y., He, W., Gage, F.H., Evans, R.M. A role for adult TLX-positive neural stem cells in learning and behaviour. (2008) Nature. 451(7181):1004-7. DOI: 10.1038/nature06562

+ expand abstract

Chen, E., Stiefel, K.M., Sejnowski, T.J., Bullock, T.H. Model of traveling waves in a coral nerve network. (2008) J. Comp. Physiol. A Neuroethol. Sens. Neural. Behav. Physiol. 194(2):195-200. DOI: 10.1007/s00359-007-0305-z

+ expand abstract

Tiesinga, P., Fellous, J.M., Sejnowski, T.J. Regulation of spike timing in visual cortical circuits. (2008) Nature Reviews Neuroscience. 9(2):97-107. DOI: 10.1038/nrn2315

+ expand abstract

Ghosh, S., Marquardt, T., Thaler, J.P., Carter, N., Andrews, S.E., Pfaff, S.L., Hunter, T. Instructive role of aPKCzeta subcellular localization in the assembly of adherens junctions in neural progenitors. (2008) Proceedings of the National Academy of Sciences of the United States of America. 105(1):335-40. DOI: 10.1073/pnas.0705713105

+ expand abstract

Nielsen, K.J., Callaway, E.M. More than a feeling: sensation from cortical stimulation. (2008) Nature Neuroscience. 11(1):10-11. DOI: 10.1038/nn0108-10

+ expand abstract

Englitz, B., Stiefel, K.M., Sejnowski, T.J. Irregular firing of isolated cortical interneurons in vitro driven by intrinsic stochastic mechanisms. (2008) Neural Computation. 20(1):44-64. DOI: 10.1162/neco.2008.20.1.44

+ expand abstract

Cezar, G.G., Quam, J.A., Smith, A.M., Rosa, G.J., Piekarczyk, M.S., Brown, J.F., Gage, F.H., Muotri, A.R. Identification of small molecules from human embryonic stem cells using metabolomics. (2007) Stem Cells Dev. 16(6):869-82. DOI: 10.1089/scd.2007.0022

+ expand abstract

Yao, W., Nathanson, J., Lian, I., Gage, F.H., Sung, L.A. Mouse erythrocyte tropomodulin in the brain reported by lacZ knocked-in downstream from the E1 promoter. (2007) Gene Expr. Patterns. 8(1):36-46. DOI: 10.1016/j.modgep.2007.08.002

+ expand abstract

Suh, H., Consiglio, A., Ray, J., Sawai, T., D'Amour, K.A., Gage, F.H. In vivo fate analysis reveals the multipotent and self-renewal capacities of Sox2+ neural stem cells in the adult hippocampus. (2007) Cell Stem Cell. 1(5):515-28. DOI: 10.1016/j.stem.2007.09.002

+ expand abstract

Lewcock, J.W., Genoud, N., Lettieri, K., Pfaff, S.L. The ubiquitin ligase Phr1 regulates axon outgrowth through modulation of microtubule dynamics. (2007) Neuron. 56(4):604-20. DOI: 10.1016/j.neuron.2007.09.009

+ expand abstract

Clifford, C.W., Webster, M.A., Stanley, G.B., Stocker, A.A., Kohn, A., Sharpee, T.O., Schwartz, O. Visual adaptation: neural, psychological and computational aspects. (2007) Vision Research. 47(25):3125-31. DOI: 10.1016/j.visres.2007.08.023

+ expand abstract

Yeo, G.W., Xu, X., Liang, T.Y., Muotri, A.R., Carson, C.T., Coufal, N.G., Gage, F.H. Alternative splicing events identified in human embryonic stem cells and neural progenitors. (2007) PLOS Computational Biology. 3(10):1951-67. DOI: 10.1371/journal.pcbi.0030196

+ expand abstract

Human embryonic stem cells (hESCs) and neural progenitor (NP) cells are excellent models for recapitulating early neuronal development in vitro, and are key to establishing strategies for the treatment of degenerative disorders. While much effort had been undertaken to analyze transcriptional and epigenetic differences during the transition of hESC to NP, very little work has been performed to understand post-transcriptional changes during neuronal differentiation. Alternative RNA splicing (AS), a major form of post-transcriptional gene regulation, is important in mammalian development and neuronal function. Human ESC, hESC-derived NP, and human central nervous system stem cells were compared using Affymetrix exon arrays. We introduced an outlier detection approach, REAP (Regression-based Exon Array Protocol), to identify 1,737 internal exons that are predicted to undergo AS in NP compared to hESC. Experimental validation of REAP-predicted AS events indicated a threshold-dependent sensitivity ranging from 56% to 69%, at a specificity of 77% to 96%. REAP predictions significantly overlapped sets of alternative events identified using expressed sequence tags and evolutionarily conserved AS events. Our results also reveal that focusing on differentially expressed genes between hESC and NP will overlook 14% of potential AS genes. In addition, we found that REAP predictions are enriched in genes encoding serine/threonine kinase and helicase activities. An example is a REAP-predicted alternative exon in the SLK (serine/threonine kinase 2) gene that is differentially included in hESC, but skipped in NP as well as in other differentiated tissues. Lastly, comparative sequence analysis revealed conserved intronic cis-regulatory elements such as the FOX1/2 binding site GCAUG as being proximal to candidate AS exons, suggesting that FOX1/2 may participate in the regulation of AS in NP and hESC. In summary, a new methodology for exon array analysis was introduced, leading to new insights into the complexity of AS in human embryonic stem cells and their transition to neural stem cells.

Muotri, A.R., Marchetto, M.C., Coufal, N.G., Gage, F.H. The necessary junk: new functions for transposable elements. (2007) Human Molecular Genetics. 16 Spec No:R159-67. DOI: 10.1093/hmg/ddm196

+ expand abstract

Nassi, J.J., Callaway, E.M. Specialized circuits from primary visual cortex to V2 and area MT. (2007) Neuron. 55(5):799-808. DOI: 10.1016/j.neuron.2007.07.037

+ expand abstract

Sharpee, T.O. Comparison of information and variance maximization strategies for characterizing neural feature selectivity. (2007) Stat Med. 26(21):4009-31. DOI: 10.1002/sim.2931

+ expand abstract

Jessberger, S., Zhao, C., Toni, N., Clemenson, G.D., Li, Y., Gage, F.H. Seizure-associated, aberrant neurogenesis in adult rats characterized with retrovirus-mediated cell labeling. (2007) Journal of Neuroscience. 27(35):9400-7. DOI: 10.1523/JNEUROSCI.2002-07.2007

+ expand abstract

Vucinić, D., Sejnowski, T.J. A compact multiphoton 3D imaging system for recording fast neuronal activity. (2007) PLOS One. 2(8):e699. DOI: 10.1371/journal.pone.0000699

+ expand abstract

Lanctot, P.M., Gage, F.H., Varki, A.P. The glycans of stem cells. (2007) Current Opinion in Chemical Biology. 11(4):373-80. DOI: 10.1016/j.cbpa.2007.05.032

+ expand abstract

Sharpee, T., Bialek, W. Neural decision boundaries for maximal information transmission. (2007) PLOS One. 2(7):e646. DOI: 10.1371/journal.pone.0000646

+ expand abstract

Aigner, S., Denli, A.M., Gage, F.H. A novel model for an older remodeler: the BAF swap in neurogenesis. (2007) Neuron. 55(2):171-3. DOI: 10.1016/j.neuron.2007.07.004

+ expand abstract

Tour, O., Adams, S.R., Kerr, R.A., Meijer, R.M., Sejnowski, T.J., Tsien, R.W., Tsien, R.Y. Calcium Green FlAsH as a genetically targeted small-molecule calcium indicator. (2007) Nature Chemical Biology. 3(7):423-31. DOI: 10.1038/nchembio.2007.4

+ expand abstract

Stiefel, K.M., Sejnowski, T.J. Mapping function onto neuronal morphology. (2007) Journal of Neurophysiology. 98(1):513-26. DOI: 10.1152/jn.00865.2006

+ expand abstract

Smrt, R.D., Eaves-Egenes, J., Barkho, B.Z., Santistevan, N.J., Zhao, C., Aimone, J.B., Gage, F.H., Zhao, X. Mecp2 deficiency leads to delayed maturation and altered gene expression in hippocampal neurons. (2007) Neurobiol. Dis. 27(1):77-89. DOI: 10.1016/j.nbd.2007.04.005

+ expand abstract

Garcia-Perez, J.L., Marchetto, M.C., Muotri, A.R., Coufal, N.G., Gage, F.H., O'Shea, K.S., Moran, J.V. LINE-1 retrotransposition in human embryonic stem cells. (2007) Human Molecular Genetics. 16(13):1569-77. DOI: 10.1093/hmg/ddm105

+ expand abstract

Toni, N., Teng, E.M., Bushong, E.A., Aimone, J.B., Zhao, C., Consiglio, A., van Praag, H., Martone, M.E., Ellisman, M.H., Gage, F.H. Synapse formation on neurons born in the adult hippocampus. (2007) Nature Neuroscience. 10(6):727-34. DOI: 10.1038/nn1908

+ expand abstract

El-Amouri, S.S., Zhu, H., Yu, J., Gage, F.H., Verma, I.M., Kindy, M.S. Neprilysin protects neurons against Abeta peptide toxicity. (2007) Brain Research. 1152:191-200. DOI: 10.1016/j.brainres.2007.03.072

+ expand abstract

Wachtler, T., Doi, E., Lee, T., Sejnowski, T.J. Cone selectivity derived from the responses of the retinal cone mosaic to natural scenes. (2007) Journal of Vision. 7(8):6. DOI: 10.1167/7.8.6

+ expand abstract

Parent, J.M., Jessberger, S., Gage, F.H., Gong, C. Is neurogenesis reparative after status epilepticus? (2007) Epilepsia. 48 Suppl 8:69-71.

Jessberger, S., Nakashima, K., Clemenson, G.D., Mejia, E., Mathews, E., Ure, K., Ogawa, S., Sinton, C.M., Gage, F.H., Hsieh, J. Epigenetic modulation of seizure-induced neurogenesis and cognitive decline. (2007) Journal of Neuroscience. 27(22):5967-75. DOI: 10.1523/JNEUROSCI.0110-07.2007

+ expand abstract

van Praag, H., Lucero, M.J., Yeo, G.W., Stecker, K., Heivand, N., Zhao, C., Yip, E., Afanador, M., Schroeter, H., Hammerstone, J., Gage, F.H. Plant-derived flavanol (-)epicatechin enhances angiogenesis and retention of spatial memory in mice. (2007) Journal of Neuroscience. 27(22):5869-78. DOI: 10.1523/JNEUROSCI.0914-07.2007

+ expand abstract

Laplagne, D.A., Kamienkowski, J.E., Espósito, M.S., Piatti, V.C., Zhao, C., Gage, F.H., Schinder, A.F. Similar GABAergic inputs in dentate granule cells born during embryonic and adult neurogenesis. (2007) European Journal of Neuroscience. 25(10):2973-81. DOI: 10.1111/j.1460-9568.2007.05549.x

+ expand abstract

Jessberger, S., Clemenson, G.D., Gage, F.H. Spontaneous fusion and nonclonal growth of adult neural stem cells. (2007) Stem Cells. 25(4):871-4. DOI: 10.1634/stemcells.2006-0620

+ expand abstract

Fox, M.A., Sanes, J.R., Borza, D.B., Eswarakumar, V.P., Fässler, R., Hudson, B.G., John, S.W., Ninomiya, Y., Pedchenko, V., Pfaff, S.L., Rheault, M.N., Sado, Y., Segal, Y., Werle, M.J., Umemori, H. Distinct target-derived signals organize formation, maturation, and maintenance of motor nerve terminals. (2007) Cell. 129(1):179-93. DOI: 10.1016/j.cell.2007.02.035

+ expand abstract

Mishra, J., Martinez, A., Sejnowski, T.J., Hillyard, S.A. Early cross-modal interactions in auditory and visual cortex underlie a sound-induced visual illusion. (2007) Journal of Neuroscience. 27(15):4120-4131. DOI: 10.1523/JNEUROSCI.4912-06.2007

+ expand abstract

Tashiro, A., Makino, H., Gage, F.H. Experience-specific functional modification of the dentate gyrus through adult neurogenesis: a critical period during an immature stage. (2007) Journal of Neuroscience. 27(12):3252-9. DOI: 10.1523/JNEUROSCI.4941-06.2007

+ expand abstract

Leingärtner, A., Thuret, S., Kroll, T.T., Chou, S.J., Leasure, J.L., Gage, F.H., O'Leary, D.D. Cortical area size dictates performance at modality-specific behaviors. (2007) Proceedings of the National Academy of Sciences of the United States of America. 104(10):4153-8. DOI: 10.1073/pnas.0611723104

+ expand abstract

Cao, X., Pfaff, S.L., Gage, F.H. A functional study of miR-124 in the developing neural tube. (2007) Genes & Development. 21(5):531-6. DOI: 10.1101/gad.1519207

+ expand abstract

Wickersham, I.R., Lyon, D.C., Barnard, R.J., Mori, T., Finke, S., Conzelmann, K.K., Young, J.A., Callaway, E.M. Monosynaptic restriction of transsynaptic tracing from single, genetically targeted neurons. (2007) Neuron. 53(5):639-647. DOI: 10.1016/j.neuron.2007.01.033

+ expand abstract

Peng, C.Y., Yajima, H., Burns, C.E., Zon, L.I., Sisodia, S.S., Pfaff, S.L., Sharma, K. Notch and MAML signaling drives Scl-dependent interneuron diversity in the spinal cord. (2007) Neuron. 53(6):813-27. DOI: 10.1016/j.neuron.2007.02.019

+ expand abstract

Eagleman, D.M., Sejnowski, T.J. Motion signals bias localization judgments: a unified explanation for the flash-lag, flash-drag, flash-jump, and Frohlich illusions. (2007) Journal of Vision. 7(4):3. DOI: 10.1167/7.4.3

+ expand abstract

Pereira, A.C., Huddleston, D.E., Brickman, A.M., Sosunov, A.A., Hen, R., McKhann, G.M., Sloan, R., Gage, F.H., Brown, T.R., Small, S.A. An in vivo correlate of exercise-induced neurogenesis in the adult dentate gyrus. (2007) Proceedings of the National Academy of Sciences of the United States of America. 104(13):5638-43. DOI: 10.1073/pnas.0611721104

+ expand abstract

Delorme, A., Sejnowski, T., Makeig, S. Enhanced detection of artifacts in EEG data using higher-order statistics and independent component analysis. (2007) Neuroimage. 34(4):1443-1449. DOI: 10.1016/j.neuroimage.2006.11.004

+ expand abstract

Odani, N., Pfaff, S.L., Nakamura, H., Funahashi, J. Cloning and developmental expression of a chick G-protein-coupled receptor SCGPR1. (2007) Gene Expression Patterns. 7(4):375-80. DOI: 10.1016/j.modgep.2006.12.003

+ expand abstract

Siegel, R.M., Duann, J.R., Jung, T.P., Sejnowski, T. Spatiotemporal dynamics of the functional architecture for gain fields in inferior parietal lobule of behaving monkey. (2007) Cerebral Cortex . 17(2):378-390. DOI: 10.1093/cercor/bhj155

+ expand abstract

Suzuki, S., Gerhold, L.M., Böttner, M., Rau, S.W., Dela Cruz, C., Yang, E., Zhu, H., Yu, J., Cashion, A.B., Kindy, M.S., Merchenthaler, I., Gage, F.H., Wise, P.M. Estradiol enhances neurogenesis following ischemic stroke through estrogen receptors alpha and beta. (2007) Journal of Comparative Neurology. 500(6):1064-75. DOI: 10.1002/cne.21240

+ expand abstract

Wickersham, I.R., Finke, S., Conzelmann, K.K., Callaway, E.M. Retrograde neuronal tracing with a deletion-mutant rabies virus. (2007) Nature Methods. 4(1):47-49. DOI: 10.1038/nmeth999

+ expand abstract

Pillai, A., Mansouri, A., Behringer, R., Westphal, H., Goulding, M. Lhx1 and Lhx5 maintain the inhibitory-neurotransmitter status of interneurons in the dorsal spinal cord. (2007) Development. 134(2):357-66. DOI: 10.1242/dev.02717

+ expand abstract

Jessberger, S., Gage, F.H. ZOOMING IN: a new high-resolution gene expression atlas of the brain. (2007) Mol. Syst. Biol. 3:75. DOI: 10.1038/msb4100122

Zhang, Y., Kim, Y., Genoud, N., Gao, J., Kelly, J.W., Pfaff, S.L., Gill, G.N., Dixon, J.E., Noel, J.P. Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1. (2006) Molecular Cell. 24(5):759-70. DOI: 10.1016/j.molcel.2006.10.027

+ expand abstract

Nassi, J.J., Callaway, E.M. Multiple circuits relaying primate parallel visual pathways to the middle temporal area. (2006) Journal of Neuroscience. 26(49):12789-12798. DOI: 10.1523/JNEUROSCI.4044-06.2006

+ expand abstract

Song, M.R., Shirasaki, R., Cai, C.L., Ruiz, E.C., Evans, S.M., Lee, S.K., Pfaff, S.L. T-Box transcription factor Tbx20 regulates a genetic program for cranial motor neuron cell body migration. (2006) Development. 133(24):4945-55. DOI: 10.1242/dev.02694

+ expand abstract

Sceniak, M.P., Chatterjee, S., Callaway, E.M. Visual spatial summation in macaque geniculocortical afferents. (2006) Journal of Neurophysiology. 96(6):3474-3484. DOI: 10.1152/jn.00734.2006

+ expand abstract

Miller, T.M., Kim, S.H., Yamanaka, K., Hester, M., Umapathi, P., Arnson, H., Rizo, L., Mendell, J.R., Gage, F.H., Cleveland, D.W., Kaspar, B.K. Gene transfer demonstrates that muscle is not a primary target for non-cell-autonomous toxicity in familial amyotrophic lateral sclerosis. (2006) Proceedings of the National Academy of Sciences of the United States of America. 103(51):19546-51. DOI: 10.1073/pnas.0609411103

+ expand abstract

Suhonen, J., Ray, J., Blömer, U., Gage, F.H., Kaspar, B. Ex vivo and in vivo gene delivery to the brain. (2006) Current Protocols in Human Genetics. Chapter 13:Unit 13.3. DOI: 10.1002/0471142905.hg1303s51

+ expand abstract

Schwartz, O., Sejnowski, T.J., Dayan, P. Soft mixer assignment in a hierarchical generative model of natural scene statistics. (2006) Neural Computation. 18(11):2680-718. DOI: 10.1162/neco.2006.18.11.2680

+ expand abstract

Xu, X., Roby, K.D., Callaway, E.M. Mouse cortical inhibitory neuron type that coexpresses somatostatin and calretinin. (2006) Journal of Comparative Neurology. 499(1):144-160. DOI: 10.1002/cne.21101

+ expand abstract

Thallmair, M., Ray, J., Stallcup, W.B., Gage, F.H. Functional and morphological effects of NG2 proteoglycan deletion on hippocampal neurogenesis. (2006) Exp. Neurol. 202(1):167-78. DOI: 10.1016/j.expneurol.2006.05.025

+ expand abstract

NG2-expressing cells are the largest proliferating cell population in the adult central nervous system. The function of NG2 proteoglycan or NG2-expressing cells in the adult brain, however, is unknown. So far, NG2-positive cells are thought to be mainly oligodendrocyte precursor cells. This view was recently challenged when NG2+/CNP-EGFP-positive cells were identified as multipotent progenitor cells in the postnatal and adult CNS (e.g., [Belachew, S., Chittajallu, R., Aguirre, A.A., Yuan, X., Kirby, M., Anderson, S., Gallo, V., 2003. Postnatal NG2 proteoglycan-expressing progenitor cells are intrinsically multipotent and generate functional neurons. J. Cell Biol. 161, 169-186]). In addition, purified NG2-expressing progenitor cells, were shown to differentiate into neurons and astrocytes in vitro [Sellers, D.L., Horner, P.J., 2005. Instructive niches: environmental instructions that confound NG2 proteoglycan expression and the fate-restriction of CNS progenitors J. Anat. 207, 727-734]. In this study, we focus on the influence of NG2 ablation on neurogenesis in the hippocampus, where putative multipotent NG2-positive cells reside, and on hippocampus-dependent behavior using NG2 knockout mice. Using the thymidine analogue bromodeoxyuridine (BrdU) to label dividing cells in vivo we show that the number of BrdU-positive cells was unchanged in the hippocampus of NG2 knockout mice 1 day after a series of BrdU injections. This finding suggests that the proliferation rate of hippocampal progenitor cells is not influenced by NG2. A few BrdU-positive cells were found in deeper layers of the granule zone 1 day after a series of BrdU injections, which is different from the wild type. The presence and the phenotype of newborn hippocampal cells were studied 4 weeks after a series of BrdU injections. The survival and differentiation of BrdU-positive cells in NG2 knockout hippocampus did not significantly differ from wild-type mice. Concurrently, the water maze task did not reveal obvious differences compared to wild-type animals. These results suggest that the null mutation for NG2 does not influence adult hippocampal neurogenesis or hippocampal-dependent behavioral tasks.

Borrell, V., Kaspar, B.K., Gage, F.H., Callaway, E.M. In vivo evidence for radial migration of neurons by long-distance somal translocation in the developing ferret visual cortex. (2006) Cereb. Cortex. 16(11):1571-83. DOI: 10.1093/cercor/bhj094

+ expand abstract

Mishra, J., Fellous, J.M., Sejnowski, T.J. Selective attention through phase relationship of excitatory and inhibitory input synchrony in a model cortical neuron. (2006) Neural Networks. 19(9):1329-1346. DOI: 10.1016/j.neunet.2006.08.005

+ expand abstract

Ramirez-Amaya, V., Marrone, D.F., Gage, F.H., Worley, P.F., Barnes, C.A. Integration of new neurons into functional neural networks. (2006) Journal of Neuroscience. 26(47):12237-41. DOI: 10.1523/JNEUROSCI.2195-06.2006

+ expand abstract

Although it is established that new granule cells can be born and can survive in the adult mammalian hippocampus, there remains some question concerning the functional integration of these neurons into behaviorally relevant neural networks. By using high-resolution confocal microscopy, we have applied a new strategy to address the question of functional integration of newborn neurons into networks that mediate spatial information processing and memory formation. Exploration-induced expression of the immediate-early gene Arc in hippocampal cells has been linked to cellular activity observed in electrophysiological recordings under the same behavioral conditions. We investigated whether mature (5-month-old), newborn granule cells express Arc in response to a discrete spatial experience by detecting the expression of Arc in combination with NeuN (neuron-specific nuclear protein)-positive and bromodeoxyuridine-positive cells. We found that mature new granule cells do indeed express Arc in response to an exploration experience, supporting the idea that these cells are well integrated into hippocampal circuits. The proportion of mature newborn neurons that expressed Arc in response to exploration, however, was significantly higher (approximately 2.8%) than the proportion of cells that expressed Arc in the already existing population of granule cells (approximately 1.6%; p < 0.01). This finding extends previous data suggesting that the cellular physiology of newborn granule neurons differs from that of the existing population by indicating that these properties are retained in mature adult-generated neurons. Thus, these data have interesting implications for network models of spatial information processing and the role of hippocampal circuits in memory, indicating that mature new neurons are selectively recruited into hippocampal cell assemblies in higher proportions than older cells.

Laplagne, D.A., Espósito, M.S., Piatti, V.C., Morgenstern, N.A., Zhao, C., van Praag, H., Gage, F.H., Schinder, A.F. Functional convergence of neurons generated in the developing and adult hippocampus. (2006) PLOS Biology. 4(12):e409. DOI: 10.1371/journal.pbio.0040409

+ expand abstract

Carson, C.T., Aigner, S., Gage, F.H. Stem cells: the good, bad and barely in control. (2006) Nature Medicine. 12(11):1237-8. DOI: 10.1038/nm1106-1237

Prescott, S.A., Sejnowski, T.J., De Koninck, Y. Reduction of anion reversal potential subverts the inhibitory control of firing rate in spinal lamina I neurons: towards a biophysical basis for neuropathic pain. (2006) Mol Pain. 2:32. DOI: 10.1186/1744-8069-2-32

+ expand abstract

Horky, L.L., Galimi, F., Gage, F.H., Horner, P.J. Fate of endogenous stem/progenitor cells following spinal cord injury. (2006) Journal of Comparative Neurology. 498(4):525-38. DOI: 10.1002/cne.21065

+ expand abstract

Callaway, E.M., Sanes, J.R. New technologies. (2006) Current Opinion in Neurobiology. 16(5):540-542. DOI: 10.1016/j.conb.2006.08.014

Prescott, S.A., Ratté, S., De Koninck, Y., Sejnowski, T.J. Nonlinear interaction between shunting and adaptation controls a switch between integration and coincidence detection in pyramidal neurons. (2006) Journal of Neuroscience. 26(36):9084-97. DOI: 10.1523/JNEUROSCI.1388-06.2006

+ expand abstract

Jagasia, R., Song, H., Gage, F.H., Lie, D.C. New regulators in adult neurogenesis and their potential role for repair. (2006) Trends in Molecular Medicine. 12(9):400-5. DOI: 10.1016/j.molmed.2006.07.006

+ expand abstract

Tashiro, A., Sandler, V.M., Toni, N., Zhao, C., Gage, F.H. NMDA-receptor-mediated, cell-specific integration of new neurons in adult dentate gyrus. (2006) Nature. 442(7105):929-33. DOI: 10.1038/nature05028

+ expand abstract

Vucinić, D., Bartol, T.M., Sejnowski, T.J. Hybrid reflecting objectives for functional multiphoton microscopy in turbid media. (2006) Opt Lett. 31(16):2447-2449.

+ expand abstract

Kashani, A.H., Qiu, Z., Jurata, L., Lee, S.K., Pfaff, S., Goebbels, S., Nave, K.A., Ghosh, A. Calcium activation of the LMO4 transcription complex and its role in the patterning of thalamocortical connections. (2006) Journal of Neuroscience. 26(32):8398-408. DOI: 10.1523/JNEUROSCI.0618-06.2006

+ expand abstract

Zhao, Y., Morales, D.C., Hermesz, E., Lee, W.K., Pfaff, S.L., Westphal, H. Reduced expression of the LIM-homeobox gene Lhx3 impairs growth and differentiation of Rathke's pouch and increases cell apoptosis during mouse pituitary development. (2006) Mechanisms of Development. 123(8):605-13. DOI: 10.1016/j.mod.2006.06.005

+ expand abstract

Anemüller, J., Duann, J.R., Sejnowski, T.J., Makeig, S. Spatio-temporal dynamics in fMRI recordings revealed with complex independent component analysis. (2006) Neurocomputing. 69(13-15):1502-1512. DOI: 10.1016/j.neucom.2005.12.029

+ expand abstract

Bhardwaj, R.D., Curtis, M.A., Spalding, K.L., Buchholz, B.A., Fink, D., Björk-Eriksson, T., Nordborg, C., Gage, F.H., Druid, H., Eriksson, P.S., Frisén, J. Neocortical neurogenesis in humans is restricted to development. (2006) Proceedings of the National Academy of Sciences of the United States of America. 103(33):12564-8. DOI: 10.1073/pnas.0605177103

+ expand abstract

Thuret, S., Moon, L.D., Gage, F.H. Therapeutic interventions after spinal cord injury. (2006) Nature Reviews Neuroscience. 7(8):628-43. DOI: 10.1038/nrn1955

+ expand abstract

Tan, E.M., Yamaguchi, Y., Horwitz, G.D., Gosgnach, S., Lein, E.S., Goulding, M., Albright, T.D., Callaway, E.M. Selective and quickly reversible inactivation of mammalian neurons in vivo using the Drosophila allatostatin receptor. (2006) Neuron. 51(2):157-70. DOI: 10.1016/j.neuron.2006.06.018

+ expand abstract

Suzuki, A., Raya, A., Kawakami, Y., Morita, M., Matsui, T., Nakashima, K., Gage, F.H., Rodríguez-Esteban, C., Izpisúa Belmonte, J.C. Nanog binds to Smad1 and blocks bone morphogenetic protein-induced differentiation of embryonic stem cells. (2006) Proceedings of the National Academy of Sciences of the United States of America. 103(27):10294-9. DOI: 10.1073/pnas.0506945103

+ expand abstract

Tashiro, A., Zhao, C., Gage, F.H. Retrovirus-mediated single-cell gene knockout technique in adult newborn neurons in vivo. (2006) Nature Protocols. 1(6):3049-55. DOI: 10.1038/nprot.2006.473

+ expand abstract

Muotri, A.R., Gage, F.H. Generation of neuronal variability and complexity. (2006) Nature. 441(7097):1087-93. DOI: 10.1038/nature04959

+ expand abstract

Cao, X., Yeo, G., Muotri, A.R., Kuwabara, T., Gage, F.H. Noncoding RNAs in the mammalian central nervous system. (2006) Annual Review of Neuroscience. 29:77-103. DOI: 10.1146/annurev.neuro.29.051605.112839

+ expand abstract

Shirasaki, R., Lewcock, J.W., Lettieri, K., Pfaff, S.L. FGF as a target-derived chemoattractant for developing motor axons genetically programmed by the LIM code. (2006) Neuron. 50(6):841-53. DOI: 10.1016/j.neuron.2006.04.030

+ expand abstract

Fröhlich, F., Bazhenov, M., Timofeev, I., Steriade, M., Sejnowski, T.J. Slow state transitions of sustained neural oscillations by activity-dependent modulation of intrinsic excitability. (2006) Journal of Neuroscience. 26(23):6153-6162. DOI: 10.1523/JNEUROSCI.5509-05.2006

+ expand abstract

Aimone, J.B., Wiles, J., Gage, F.H. Potential role for adult neurogenesis in the encoding of time in new memories. (2006) Nature Neuroscience. 9(6):723-7. DOI: 10.1038/nn1707

+ expand abstract

Mizuguchi, R., Kriks, S., Cordes, R., Gossler, A., Ma, Q., Goulding, M. Ascl1 and Gsh1/2 control inhibitory and excitatory cell fate in spinal sensory interneurons. (2006) Nature Neuroscience. 9(6):770-8. DOI: 10.1038/nn1706

+ expand abstract

Barkho, B.Z., Song, H., Aimone, J.B., Smrt, R.D., Kuwabara, T., Nakashima, K., Gage, F.H., Zhao, X. Identification of astrocyte-expressed factors that modulate neural stem/progenitor cell differentiation. (2006) Stem Cells Dev. 15(3):407-21. DOI: 10.1089/scd.2006.15.407

+ expand abstract

Zhang, C.L., Zou, Y., Yu, R.T., Gage, F.H., Evans, R.M. Nuclear receptor TLX prevents retinal dystrophy and recruits the corepressor atrophin1. (2006) Genes & Development. 20(10):1308-20. DOI: 10.1101/gad.1413606

+ expand abstract

Nassi, J.J., Lyon, D.C., Callaway, E.M. The parvocellular LGN provides a robust disynaptic input to the visual motion area MT. (2006) Neuron. 50(2):319-327. DOI: 10.1016/j.neuron.2006.03.019

+ expand abstract

Callaway, E.M. Should I stay or should I go? Presynaptic boutons in the adult cortex still haven't made up their minds. (2006) Neuron. 49(6):780-783. DOI: 10.1016/j.neuron.2006.03.007

+ expand abstract

Gosgnach, S., Lanuza, G.M., Butt, S.J., Saueressig, H., Zhang, Y., Velasquez, T., Riethmacher, D., Callaway, E.M., Kiehn, O., Goulding, M. V1 spinal neurons regulate the speed of vertebrate locomotor outputs. (2006) Nature. 440(7081):215-9. DOI: 10.1038/nature04545

+ expand abstract

Jacobs, S., Lie, D.C., DeCicco, K.L., Shi, Y., DeLuca, L.M., Gage, F.H., Evans, R.M. Retinoic acid is required early during adult neurogenesis in the dentate gyrus. (2006) Proceedings of the National Academy of Sciences of the United States of America. 103(10):3902-7. DOI: 10.1073/pnas.0511294103

+ expand abstract

Suzuki, A., Raya, A., Kawakami, Y., Morita, M., Matsui, T., Nakashima, K., Gage, F.H., Rodríguez-Esteban, C., Izpisúa Belmonte, J.C. Maintenance of embryonic stem cell pluripotency by Nanog-mediated reversal of mesoderm specification. (2006) Nature Clinical Practice. Cardiovascular Medicine. 3 Suppl 1:S114-22. DOI: 10.1038/ncpcardio0442

+ expand abstract

Ray, J., Gage, F.H. Differential properties of adult rat and mouse brain-derived neural stem/progenitor cells. (2006) Molecular and Cellular Neurosciences. 31(3):560-73. DOI: 10.1016/j.mcn.2005.11.010

+ expand abstract

Zarrinpar, A., Callaway, E.M. Local connections to specific types of layer 6 neurons in the rat visual cortex. (2006) Journal of Neurophysiology. 95(3):1751-1761. DOI: 10.1152/jn.00974.2005

+ expand abstract

Nakahira, E., Kagawa, T., Shimizu, T., Goulding, M.D., Ikenaka, K. Direct evidence that ventral forebrain cells migrate to the cortex and contribute to the generation of cortical myelinating oligodendrocytes. (2006) Developmental Biology. 291(1):123-31. DOI: 10.1016/j.ydbio.2005.12.010

+ expand abstract

Sejnowski, T.J., Paulsen, O. Network oscillations: emerging computational principles. (2006) Journal of Neuroscience. 26(6):1673-6. DOI: 10.1523/JNEUROSCI.3737-05d.2006

Sharpee, T.O., Sugihara, H., Kurgansky, A.V., Rebrik, S.P., Stryker, M.P., Miller, K.D. Adaptive filtering enhances information transmission in visual cortex. (2006) Nature. 439(7079):936-42. DOI: 10.1038/nature04519

+ expand abstract

Paulsen, O., Sejnowski, T.J. From invertebrate olfaction to human cognition: emerging computational functions of synchronized oscillatory activity. (2006) Journal of Neuroscience. 26(6):1661-1662. DOI: 10.1523/JNEUROSCI.3737-05a.2006

Yang, H., Lu, P., McKay, H.M., Bernot, T., Keirstead, H., Steward, O., Gage, F.H., Edgerton, V.R., Tuszynski, M.H. Endogenous neurogenesis replaces oligodendrocytes and astrocytes after primate spinal cord injury. (2006) Journal of Neuroscience. 26(8):2157-66. DOI: 10.1523/JNEUROSCI.4070-05.2005

+ expand abstract

Zhao, C., Teng, E.M., Summers, R.G., Ming, G.L., Gage, F.H. Distinct morphological stages of dentate granule neuron maturation in the adult mouse hippocampus. (2006) Journal of Neuroscience. 26(1):3-11. DOI: 10.1523/JNEUROSCI.3648-05.2006

+ expand abstract

Kerr, R.A., Levine, H., Sejnowski, T.J., Rappel, W.J. Division accuracy in a stochastic model of Min oscillations in Escherichia coli. (2006) Proceedings of the National Academy of Sciences of the United States of America. 103(2):347-352. DOI: 10.1073/pnas.0505825102

+ expand abstract

Larsen, D.D., Callaway, E.M. Development of layer-specific axonal arborizations in mouse primary somatosensory cortex. (2006) Journal of Comparative Neurology. 494(3):398-414. DOI: 10.1002/cne.20754

+ expand abstract

Victor, J.D., Mechler, F., Repucci, M.A., Purpura, K.P., Sharpee, T. Responses of V1 neurons to two-dimensional hermite functions. (2006) Journal of Neurophysiology. 95(1):379-400. DOI: 10.1152/jn.00498.2005

+ expand abstract

Battista, D., Ferrari, C.C., Gage, F.H., Pitossi, F.J. Neurogenic niche modulation by activated microglia: transforming growth factor beta increases neurogenesis in the adult dentate gyrus. (2006) European Journal of Neuroscience. 23(1):83-93. DOI: 10.1111/j.1460-9568.2005.04539.x

+ expand abstract

Alisch, R.S., Garcia-Perez, J.L., Muotri, A.R., Gage, F.H., Moran, J.V. Unconventional translation of mammalian LINE-1 retrotransposons. (2006) Genes & Development. 20(2):210-24. DOI: 10.1101/gad.1380406

+ expand abstract

Kempermann, G., Chesler, E.J., Lu, L., Williams, R.W., Gage, F.H. Natural variation and genetic covariance in adult hippocampal neurogenesis. (2006) Proceedings of the National Academy of Sciences of the United States of America. 103(3):780-5. DOI: 10.1073/pnas.0510291103

+ expand abstract

Warashina, M., Min, K.H., Kuwabara, T., Huynh, A., Gage, F.H., Schultz, P.G., Ding, S. A synthetic small molecule that induces neuronal differentiation of adult hippocampal neural progenitor cells. (2006) Angew. Chem. Int. Ed. Engl. 45(4):591-3. DOI: 10.1002/anie.200503089

Pizzo, D.P., Coufal, N.G., Lortie, M.J., Gage, F.H., Thal, L.J. Regulatable acetylcholine-producing fibroblasts enhance cognitive performance. (2006) Mol. Ther. 13(1):175-82. DOI: 10.1016/j.ymthe.2005.08.001

+ expand abstract

Moon, L.D., Leasure, J.L., Gage, F.H., Bunge, M.B. Motor enrichment sustains hindlimb movement recovered after spinal cord injury and glial transplantation. (2006) Restorative Neurology and Neuroscience. 24(3):147-61.

+ expand abstract

Muotri, A.R., Nakashima, K., Toni, N., Sandler, V.M., Gage, F.H. Development of functional human embryonic stem cell-derived neurons in mouse brain. (2005) Proceedings of the National Academy of Sciences of the United States of America. 102(51):18644-8. DOI: 10.1073/pnas.0509315102

+ expand abstract

Quina, L.A., Pak, W., Lanier, J., Banwait, P., Gratwick, K., Liu, Y., Velasquez, T., O'Leary, D.D., Goulding, M., Turner, E.E. Brn3a-expressing retinal ganglion cells project specifically to thalamocortical and collicular visual pathways. (2005) Journal of Neuroscience. 25(50):11595-604. DOI: 10.1523/JNEUROSCI.2837-05.2005

+ expand abstract

Alvarez, F.J., Jonas, P.C., Sapir, T., Hartley, R., Berrocal, M.C., Geiman, E.J., Todd, A.J., Goulding, M. Postnatal phenotype and localization of spinal cord V1 derived interneurons. (2005) Journal of Comparative Neurology. 493(2):177-92. DOI: 10.1002/cne.20711

+ expand abstract

Hsieh, J., Gage, F.H. Chromatin remodeling in neural development and plasticity. (2005) Current Opinion in Cell Biology. 17(6):664-71. DOI: 10.1016/j.ceb.2005.09.002

+ expand abstract

Song, M.R., Pfaff, S.L. Hox genes: the instructors working at motor pools. (2005) Cell. 123(3):363-5. DOI: 10.1016/j.cell.2005.10.014

+ expand abstract

Yoshimura, Y., Callaway, E.M. Fine-scale specificity of cortical networks depends on inhibitory cell type and connectivity. (2005) Nature Neuroscience. 8(11):1552-1559. DOI: 10.1038/nn1565

+ expand abstract

Genoud, S., Maricic, I., Kumar, V., Gage, F.H. Targeted expression of IGF-1 in the central nervous system fails to protect mice from experimental autoimmune encephalomyelitis. (2005) Journal of Neuroimmunology. 168(1-2):40-5. DOI: 10.1016/j.jneuroim.2005.06.033

+ expand abstract

Cheng, L., Samad, O.A., Xu, Y., Mizuguchi, R., Luo, P., Shirasawa, S., Goulding, M., Ma, Q. Lbx1 and Tlx3 are opposing switches in determining GABAergic versus glutamatergic transmitter phenotypes. (2005) Nature Neuroscience. 8(11):1510-5. DOI: 10.1038/nn1569

+ expand abstract

Lie, D.C., Colamarino, S.A., Song, H.J., Désiré, L., Mira, H., Consiglio, A., Lein, E.S., Jessberger, S., Lansford, H., Dearie, A.R., Gage, F.H. Wnt signalling regulates adult hippocampal neurogenesis. (2005) Nature. 437(7063):1370-5. DOI: 10.1038/nature04108

+ expand abstract

Singer, O., Marr, R.A., Rockenstein, E., Crews, L., Coufal, N.G., Gage, F.H., Verma, I.M., Masliah, E. Targeting BACE1 with siRNAs ameliorates Alzheimer disease neuropathology in a transgenic model. (2005) Nature Neuroscience. 8(10):1343-9. DOI: 10.1038/nn1531

+ expand abstract

Sample, P.A., Boden, C., Zhang, Z., Pascual, J., Lee, T.W., Zangwill, L.M., Weinreb, R.N., Crowston, J.G., Hoffmann, E.M., Medeiros, F.A., Sejnowski, T., Goldbaum, M. Unsupervised machine learning with independent component analysis to identify areas of progression in glaucomatous visual fields. (2005) Investigative Ophthalmology & Visual Science. 46(10):3684-3692. DOI: 10.1167/iovs.04-1168

+ expand abstract

Goldbaum, M.H., Sample, P.A., Zhang, Z., Chan, K., Hao, J., Lee, T.W., Boden, C., Bowd, C., Bourne, R., Zangwill, L., Sejnowski, T., Spinak, D., Weinreb, R.N. Using unsupervised learning with independent component analysis to identify patterns of glaucomatous visual field defects. (2005) Investigative Ophthalmology & Visual Science. 46(10):3676-3683. DOI: 10.1167/iovs.04-1167

+ expand abstract

Gage, F.H., McAllister, A.K. Neuronal and glial cell biology. (2005) Current Opinion in Neurobiology. 15(5):497-9. DOI: 10.1016/j.conb.2005.08.010

van Praag, H., Shubert, T., Zhao, C., Gage, F.H. Exercise enhances learning and hippocampal neurogenesis in aged mice. (2005) Journal of Neuroscience. 25(38):8680-5. DOI: 10.1523/JNEUROSCI.1731-05.2005

+ expand abstract

Cummings, B.J., Uchida, N., Tamaki, S.J., Salazar, D.L., Hooshmand, M., Summers, R., Gage, F.H., Anderson, A.J. Human neural stem cells differentiate and promote locomotor recovery in spinal cord-injured mice. (2005) Proceedings of the National Academy of Sciences of the United States of America. 102(39):14069-74. DOI: 10.1073/pnas.0507063102

+ expand abstract

Aigner, S., Gage, F.H. A small gem with great powers: geminin keeps neural progenitors thriving. (2005) Developmental Cell. 9(2):171-2. DOI: 10.1016/j.devcel.2005.07.005

+ expand abstract

Sullivan, M.R., Nimmerjahn, A., Sarkisov, D.V., Helmchen, F., Wang, S.S. In vivo calcium imaging of circuit activity in cerebellar cortex. (2005) Journal of Neurophysiology. 94(2):1636-44. DOI: 10.1152/jn.01013.2004

+ expand abstract

Gillette, M.U., Sejnowski, T.J. Physiology. Biological clocks coordinately keep life on time. (2005) Science. 309(5738):1196-1198. DOI: 10.1126/science.1111420

Prank, K., Schulze, E., Eckert, O., Nattkemper, T.W., Bettendorf, M., Maser-Gluth, C., Sejnowski, T.J., Grote, A., Penner, E., von Zur Mühlen, A., Brabant, G. Machine learning approaches for phenotype-genotype mapping: predicting heterozygous mutations in the CYP21B gene from steroid profiles. (2005) Eur. J. Endocrinol. 153(2):301-305. DOI: 10.1530/eje.1.01957

+ expand abstract

Zupanc, G.K., Hinsch, K., Gage, F.H. Proliferation, migration, neuronal differentiation, and long-term survival of new cells in the adult zebrafish brain. (2005) Journal of Comparative Neurology. 488(3):290-319. DOI: 10.1002/cne.20571

+ expand abstract

Coggan, J.S., Bartol, T.M., Esquenazi, E., Stiles, J.R., Lamont, S., Martone, M.E., Berg, D.K., Ellisman, M.H., Sejnowski, T.J. Evidence for ectopic neurotransmission at a neuronal synapse. (2005) Science. 309(5733):446-451. DOI: 10.1126/science.1108239

+ expand abstract

Kriks, S., Lanuza, G.M., Mizuguchi, R., Nakafuku, M., Goulding, M. Gsh2 is required for the repression of Ngn1 and specification of dorsal interneuron fate in the spinal cord. (2005) Development. 132(13):2991-3002. DOI: 10.1242/dev.01878

+ expand abstract

Callaway, E.M. Structure and function of parallel pathways in the primate early visual system. (2005) Journal of Physiology. 566(Pt 1):13-19. DOI: 10.1113/jphysiol.2005.088047

+ expand abstract

Muotri, A.R., Chu, V.T., Marchetto, M.C., Deng, W., Moran, J.V., Gage, F.H. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. (2005) Nature. 435(7044):903-10. DOI: 10.1038/nature03663

+ expand abstract

Fröhlich, F., Bazhenov, M., Timofeev, I., Sejnowski, T.J. Maintenance and termination of neocortical oscillations by dynamic modulation of intrinsic and synaptic excitability. (2005) Thalamus Relat Syst. 3(2):147-156. DOI: 10.1017/S147292880700015

+ expand abstract

Houweling, A.R., Bazhenov, M., Timofeev, I., Steriade, M., Sejnowski, T.J. Homeostatic synaptic plasticity can explain post-traumatic epileptogenesis in chronically isolated neocortex. (2005) Cerebral Cortex . 15(6):834-845. DOI: 10.1093/cercor/bhh184

+ expand abstract

Kuwabara, T., Hsieh, J., Nakashima, K., Warashina, M., Taira, K., Gage, F.H. The NRSE smRNA specifies the fate of adult hippocampal neural stem cells. (2005) Nucleic Acids Symp Ser (Oxf).(49):87-8 DOI: 10.1093/nass/49.1.87

+ expand abstract

Lin, W., Dominguez, B., Yang, J., Aryal, P., Brandon, E.P., Gage, F.H., Lee, K.F. Neurotransmitter acetylcholine negatively regulates neuromuscular synapse formation by a Cdk5-dependent mechanism. (2005) Neuron. 46(4):569-79. DOI: 10.1016/j.neuron.2005.04.002

+ expand abstract

Bazhenov, M., Stopfer, M., Sejnowski, T.J., Laurent, G. Fast odor learning improves reliability of odor responses in the locust antennal lobe. (2005) Neuron. 46(3):483-492. DOI: 10.1016/j.neuron.2005.03.022

+ expand abstract

Kaspar, B.K., Frost, L.M., Christian, L., Umapathi, P., Gage, F.H. Synergy of insulin-like growth factor-1 and exercise in amyotrophic lateral sclerosis. (2005) Ann. Neurol. 57(5):649-55. DOI: 10.1002/ana.20451

+ expand abstract

Scheel, J.R., Ray, J., Gage, F.H., Barlow, C. Quantitative analysis of gene expression in living adult neural stem cells by gene trapping. (2005) Nature Methods. 2(5):363-70. DOI: 10.1038/nmeth755

+ expand abstract

Briggs, F., Callaway, E.M. Laminar patterns of local excitatory input to layer 5 neurons in macaque primary visual cortex. (2005) Cereb. Cortex. 15(5):479-488. DOI: 10.1093/cercor/bhh154

+ expand abstract

Nimmerjahn, A., Kirchhoff, F., Helmchen, F. Resting microglial cells are highly dynamic surveillants of brain parenchyma in vivo. (2005) Science. 308(5726):1314-8. DOI: 10.1126/science.1110647

+ expand abstract

Duann, J.R., Jung, T.P., Makeig, S., Sejnowski, T. Repeated decompositions reveal the stability of infomax decomposition of fMRI data. (2005) Conf Proc IEEE Eng Med Biol Soc. 5:5324-5327. DOI: 10.1109/IEMBS.2005.1615683

+ expand abstract

Miller, T.M., Kaspar, B.K., Kops, G.J., Yamanaka, K., Christian, L.J., Gage, F.H., Cleveland, D.W. Virus-delivered small RNA silencing sustains strength in amyotrophic lateral sclerosis. (2005) Ann. Neurol. 57(5):773-6. DOI: 10.1002/ana.20453

+ expand abstract

Lilley, C.E., Carson, C.T., Muotri, A.R., Gage, F.H., Weitzman, M.D. DNA repair proteins affect the lifecycle of herpes simplex virus 1. (2005) Proceedings of the National Academy of Sciences of the United States of America. 102(16):5844-9. DOI: 10.1073/pnas.0501916102

+ expand abstract

Myers, C.P., Lewcock, J.W., Hanson, M.G., Gosgnach, S., Aimone, J.B., Gage, F.H., Lee, K.F., Landmesser, L.T., Pfaff, S.L. Cholinergic input is required during embryonic development to mediate proper assembly of spinal locomotor circuits. (2005) Neuron. 46(1):37-49. DOI: 10.1016/j.neuron.2005.02.022

+ expand abstract

Marquardt, T., Shirasaki, R., Ghosh, S., Andrews, S.E., Carter, N., Hunter, T., Pfaff, S.L. Coexpressed EphA receptors and ephrin-A ligands mediate opposing actions on growth cone navigation from distinct membrane domains. (2005) Cell. 121(1):127-39. DOI: 10.1016/j.cell.2005.01.020

+ expand abstract

Borrell, V., Yoshimura, Y., Callaway, E.M. Targeted gene delivery to telencephalic inhibitory neurons by directional in utero electroporation. (2005) Journal of Neuroscience Methods. 143(2):151-158. DOI: 10.1016/j.jneumeth.2004.09.027

+ expand abstract

Callaway, E.M. A molecular and genetic arsenal for systems neuroscience. (2005) Trends in Neurosciences. 28(4):196-201. DOI: 10.1016/j.tins.2005.01.007

+ expand abstract

Lein, E.S., Callaway, E.M., Albright, T.D., Gage, F.H. Redefining the boundaries of the hippocampal CA2 subfield in the mouse using gene expression and 3-dimensional reconstruction. (2005) Journal of Comparative Neurology. 485(1):1-10. DOI: 10.1002/cne.20426

+ expand abstract

Bowd, C., Medeiros, F.A., Zhang, Z., Zangwill, L.M., Hao, J., Lee, T.W., Sejnowski, T.J., Weinreb, R.N., Goldbaum, M.H. Relevance vector machine and support vector machine classifier analysis of scanning laser polarimetry retinal nerve fiber layer measurements. (2005) Investigative Ophthalmology & Visual Science. 46(4):1322-1329. DOI: 10.1167/iovs.04-1122

+ expand abstract

Galimi, F., Summers, R.G., van Praag, H., Verma, I.M., Gage, F.H. A role for bone marrow-derived cells in the vasculature of noninjured CNS. (2005) Blood. 105(6):2400-2. DOI: 10.1182/blood-2004-02-0612

+ expand abstract

Yoshimura, Y., Dantzker, J.L., Callaway, E.M. Excitatory cortical neurons form fine-scale functional networks. (2005) Nature. 433(7028):868-873. DOI: 10.1038/nature03252

+ expand abstract

Goulding, M., Pfaff, S.L. Development of circuits that generate simple rhythmic behaviors in vertebrates. (2005) Current Opinion in Neurobiology. 15(1):14-20. DOI: 10.1016/j.conb.2005.01.017

+ expand abstract

Lee, S.K., Jurata, L.W., Nowak, R., Lettieri, K., Kenny, D.A., Pfaff, S.L., Gill, G.N. The LIM domain-only protein LMO4 is required for neural tube closure. (2005) Molecular and Cellular Neurosciences. 28(2):205-14. DOI: 10.1016/j.mcn.2004.04.010

+ expand abstract

Martin, M.J., Muotri, A., Gage, F., Varki, A. Human embryonic stem cells express an immunogenic nonhuman sialic acid. (2005) Nature Medicine. 11(2):228-32. DOI: 10.1038/nm1181

+ expand abstract

Callaway, E.M. Neural substrates within primary visual cortex for interactions between parallel visual pathways. (2005) Progress in Brain Research. 149:59-64. DOI: 10.1016/S0079-6123(05)49005-6

Lee, S.K., Lee, B., Ruiz, E.C., Pfaff, S.L. Olig2 and Ngn2 function in opposition to modulate gene expression in motor neuron progenitor cells. (2005) Genes & Development. 19(2):282-94. DOI: 10.1101/gad.1257105

+ expand abstract

Yeo, M., Lee, S.K., Lee, B., Ruiz, E.C., Pfaff, S.L., Gill, G.N. Small CTD phosphatases function in silencing neuronal gene expression. (2005) Science. 307(5709):596-600. DOI: 10.1126/science.1100801

+ expand abstract

Cepeda-Nieto, A.C., Pfaff, S.L., Varela-Echavarría, A. Homeodomain transcription factors in the development of subsets of hindbrain reticulospinal neurons. (2005) Molecular and Cellular Neurosciences. 28(1):30-41. DOI: 10.1016/j.mcn.2004.06.016

+ expand abstract

Lehky, S.R., Sejnowski, T.J., Desimone, R. Selectivity and sparseness in the responses of striate complex cells. (2005) Vision Research. 45(1):57-73. DOI: 10.1016/j.visres.2004.07.021

+ expand abstract

Fuentealba, P., Timofeev, I., Bazhenov, M., Sejnowski, T.J., Steriade, M. Membrane bistability in thalamic reticular neurons during spindle oscillations. (2005) Journal of Neurophysiology. 93(1):294-304. DOI: 10.1152/jn.00552.2004

+ expand abstract

Siegel, R.M., Callaway, E.M. Francis Crick's legacy for neuroscience: between the alpha and the Omega. (2004) PLOS Biology. 2(12). DOI: 10.1371/journal.pbio.0020419

Dittgen, T., Nimmerjahn, A., Komai, S., Licznerski, P., Waters, J., Margrie, T.W., Helmchen, F., Denk, W., Brecht, M., Osten, P. Lentivirus-based genetic manipulations of cortical neurons and their optical and electrophysiological monitoring in vivo. (2004) Proceedings of the National Academy of Sciences of the United States of America. 101(52):18206-11. DOI: 10.1073/pnas.0407976101

+ expand abstract

Hashimoto, M., Rockenstein, E., Mante, M., Crews, L., Bar-On, P., Gage, F.H., Marr, R., Masliah, E. An antiaggregation gene therapy strategy for Lewy body disease utilizing beta-synuclein lentivirus in a transgenic model. (2004) Gene Therapy. 11(23):1713-23. DOI: 10.1038/sj.gt.3302349

+ expand abstract

Hsieh, J., Nakashima, K., Kuwabara, T., Mejia, E., Gage, F.H. Histone deacetylase inhibition-mediated neuronal differentiation of multipotent adult neural progenitor cells. (2004) Proceedings of the National Academy of Sciences of the United States of America. 101(47):16659-64. DOI: 10.1073/pnas.0407643101

+ expand abstract

Pak, W., Hindges, R., Lim, Y.S., Pfaff, S.L., O'Leary, D.D. Magnitude of binocular vision controlled by islet-2 repression of a genetic program that specifies laterality of retinal axon pathfinding. (2004) Cell. 119(4):567-78. DOI: 10.1016/j.cell.2004.10.026

+ expand abstract

Göbel, W., Kerr, J.N., Nimmerjahn, A., Helmchen, F. Miniaturized two-photon microscope based on a flexible coherent fiber bundle and a gradient-index lens objective. (2004) Opt Lett. 29(21):2521-3.

+ expand abstract

Chin, V.I., Taupin, P., Sanga, S., Scheel, J., Gage, F.H., Bhatia, S.N. Microfabricated platform for studying stem cell fates. (2004) Biotechnol. Bioeng. 88(3):399-415. DOI: 10.1002/bit.20254

+ expand abstract

Platforms that allow parallel, quantitative analysis of single cells will be integral to realizing the potential of postgenomic biology. In stem cell biology, the study of clonal stem cells in multiwell formats is currently both inefficient and time-consuming. Thus, to investigate low-frequency events of interest, large sample sizes must be interrogated. We report a simple, versatile, and efficient micropatterned arraying system conducive to the culture and dynamic monitoring of stem cell proliferation. This platform enables: 1) parallel, automated, long-term ( approximately days to weeks), live-cell microscopy of single cells in culture; 2) tracking of individual cell fates over time (proliferation, apoptosis); and 3) correlation of differentiated progeny with founder clones. To achieve these goals, we used microfabrication techniques to create an array of approximately 10,000 microwells on a glass coverslip. The dimensions of the wells are tunable, ranging from 20 to >500 microm in diameter and 10-500 microm in height. The microarray can be coated with adhesive proteins and is integrated into a culture chamber that permits rapid (approximately min), addressable monitoring of each well using a standard programmable microscope stage. All cells share the same media (including paracrine survival signals), as opposed to cells in multiwell formats. The incorporation of a coverslip as a substrate also renders the platform compatible with conventional, high-magnification light and fluorescent microscopy. We validated this approach by analyzing the proliferation dynamics of a heterogeneous adult rat neural stem cell population. Using this platform, one can further interrogate the response of distinct stem cell subpopulations to microenvironmental cues (mitogens, cell-cell interactions, and cell-extracellular matrix interactions) that govern their behavior. In the future, the platform may also be adapted for the study of other cell types by tailoring the surface coatings, microwell dimensions, and culture environment, thereby enabling parallel investigation of many distinct cellular responses.

Shihabuddin, L.S., Numan, S., Huff, M.R., Dodge, J.C., Clarke, J., Macauley, S.L., Yang, W., Taksir, T.V., Parsons, G., Passini, M.A., Gage, F.H., Stewart, G.R. Intracerebral transplantation of adult mouse neural progenitor cells into the Niemann-Pick-A mouse leads to a marked decrease in lysosomal storage pathology. (2004) Journal of Neuroscience. 24(47):10642-51. DOI: 10.1523/JNEUROSCI.3584-04.2004

+ expand abstract

Hsieh, J., Gage, F.H. Epigenetic control of neural stem cell fate. (2004) Current Opinion in Genetics & Development. 14(5):461-9. DOI: 10.1016/j.gde.2004.07.006

+ expand abstract

Horwitz, G.D., Callaway, E.M. Antisense inhibition of reward learning. (2004) Nature Neuroscience. 7(10):1023-1024. DOI: 10.1038/nn1004-1023

Nimmerjahn, A., Kirchhoff, F., Kerr, J.N., Helmchen, F. Sulforhodamine 101 as a specific marker of astroglia in the neocortex in vivo. (2004) Nature Methods. 1(1):31-7. DOI: 10.1038/nmeth706

+ expand abstract

Consiglio, A., Gritti, A., Dolcetta, D., Follenzi, A., Bordignon, C., Gage, F.H., Vescovi, A.L., Naldini, L. Robust in vivo gene transfer into adult mammalian neural stem cells by lentiviral vectors. (2004) Proceedings of the National Academy of Sciences of the United States of America. 101(41):14835-40. DOI: 10.1073/pnas.0404180101

+ expand abstract

Schinder, A.F., Gage, F.H. A hypothesis about the role of adult neurogenesis in hippocampal function. (2004) Physiology (Bethesda). 19:253-61. DOI: 10.1152/physiol.00012.2004

+ expand abstract

Aimone, J.B., Leasure, J.L., Perreau, V.M., Thallmair, M., Gage Spatial and temporal gene expression profiling of the contused rat spinal cord. (2004) Exp. Neurol. 189(2):204-21. DOI: 10.1016/j.expneurol.2004.05.042

+ expand abstract

Sejnowski, T.J. In memoriam: Francis H.C. Crick. (2004) Neuron. 43(5):619-621. DOI: 10.1016/j.neuron.2004.08.022

Goulding, M. How early is firing required for wiring? (2004) Neuron. 43(5):601-3. DOI: 10.1016/j.neuron.2004.08.027

+ expand abstract

Schwander, M., Shirasaki, R., Pfaff, S.L., Müller, U. Beta1 integrins in muscle, but not in motor neurons, are required for skeletal muscle innervation. (2004) Journal of Neuroscience. 24(37):8181-91. DOI: 10.1523/JNEUROSCI.1345-04.2004

+ expand abstract

Weiner, J.A., Koo, S.J., Nicolas, S., Fraboulet, S., Pfaff, S.L., Pourquié, O., Sanes, J.R. Axon fasciculation defects and retinal dysplasias in mice lacking the immunoglobulin superfamily adhesion molecule BEN/ALCAM/SC1. (2004) Molecular and Cellular Neurosciences. 27(1):59-69. DOI: 10.1016/j.mcn.2004.06.005

+ expand abstract

Zangwill, L.M., Chan, K., Bowd, C., Hao, J., Lee, T.W., Weinreb, R.N., Sejnowski, T.J., Goldbaum, M.H. Heidelberg retina tomograph measurements of the optic disc and parapapillary retina for detecting glaucoma analyzed by machine learning classifiers. (2004) Investigative Ophthalmology & Visual Science. 45(9):3144-3151. DOI: 10.1167/iovs.04-0202

+ expand abstract

Bazhenov, M., Timofeev, I., Steriade, M., Sejnowski, T.J. Potassium model for slow (2-3 Hz) in vivo neocortical paroxysmal oscillations. (2004) Journal of Neurophysiology. 92(2):1116-1132. DOI: 10.1152/jn.00529.2003

+ expand abstract

In slow neocortical paroxysmal oscillations, the de- and hyperpolarizing envelopes in neocortical neurons are large compared with slow sleep oscillations. Increased local synchrony of membrane potential oscillations during seizure is reflected in larger electroencephalographic oscillations and the appearance of spike- or polyspike-wave complex recruitment at 2- to 3-Hz frequencies. The oscillatory mechanisms underlying this paroxysmal activity were investigated in computational models of cortical networks. The extracellular K(+) concentration ([K(+)](o)) was continuously computed based on neuronal K(+) currents and K(+) pumps as well as glial buffering. An increase of [K(+)](o) triggered a transition from normal awake-like oscillations to 2- to 3-Hz seizure-like activity. In this mode, the cells fired periodic bursts and nearby neurons oscillated highly synchronously; in some cells depolarization led to spike inactivation lasting 50-100 ms. A [K(+)](o) increase, sufficient to produce oscillations could result from excessive firing (e.g., induced by external stimulation) or inability of K(+) regulatory system (e.g., when glial buffering was blocked). A combination of currents including high-threshold Ca(2+), persistent Na(+) and hyperpolarization-activated depolarizing (I(h)) currents was sufficient to maintain 2- to 3-Hz activity. In a network model that included lateral K(+) diffusion between cells, increase of [K(+)](o) in a small region was generally sufficient to maintain paroxysmal oscillations in the whole network. Slow changes of [K(+)](o) modulated the frequency of bursting and, in some case, led to fast oscillations in the 10- to 15-Hz frequency range, similar to the fast runs observed during seizures in vivo. These results suggest that modifications of the intrinsic currents mediated by increase of [K(+)](o) can explain the range of neocortical paroxysmal oscillations in vivo.

Sample, P.A., Chan, K., Boden, C., Lee, T.W., Blumenthal, E.Z., Weinreb, R.N., Bernd, A., Pascual, J., Hao, J., Sejnowski, T., Goldbaum, M.H. Using unsupervised learning with variational bayesian mixture of factor analysis to identify patterns of glaucomatous visual field defects. (2004) Investigative Ophthalmology & Visual Science. 45(8):2596-2605. DOI: 10.1167/iovs.03-0343

+ expand abstract

Shon, A.P., Rao, R.P., Sejnowski, T.J. Motion detection and prediction through spike-timing dependent plasticity. (2004) Network. 15(3):179-198.

+ expand abstract

Callaway, E.M. Close encounters: how cortical neurons find and connect to their correct synaptic partners depends on the cell type. (2004) Neuron. 43(2):156-158. DOI: 10.1016/j.neuron.2004.07.006

+ expand abstract

Wurmser, A.E., Nakashima, K., Summers, R.G., Toni, N., D'Amour, K.A., Lie, D.C., Gage, F.H. Cell fusion-independent differentiation of neural stem cells to the endothelial lineage. (2004) Nature. 430(6997):350-6. DOI: 10.1038/nature02604

+ expand abstract

Lee, S.K., Jurata, L.W., Funahashi, J., Ruiz, E.C., Pfaff, S.L. Analysis of embryonic motoneuron gene regulation: derepression of general activators function in concert with enhancer factors. (2004) Development. 131(14):3295-306. DOI: 10.1242/dev.01179

+ expand abstract

Tiesinga, P.H., Fellous, J.M., Salinas, E., José, J.V., Sejnowski, T.J. Inhibitory synchrony as a mechanism for attentional gain modulation. (2004) Journal of Physiology, Paris. 98(4-6):296-314. DOI: 10.1016/j.jphysparis.2005.09.002

+ expand abstract

Recordings from area V4 of monkeys have revealed that when the focus of attention is on a visual stimulus within the receptive field of a cortical neuron, two distinct changes can occur: The firing rate of the neuron can change and there can be an increase in the coherence between spikes and the local field potential (LFP) in the gamma-frequency range (30-50 Hz). The hypothesis explored here is that these observed effects of attention could be a consequence of changes in the synchrony of local interneuron networks. We performed computer simulations of a Hodgkin-Huxley type neuron driven by a constant depolarizing current, I, representing visual stimulation and a modulatory inhibitory input representing the effects of attention via local interneuron networks. We observed that the neuron's firing rate and the coherence of its output spike train with the synaptic inputs was modulated by the degree of synchrony of the inhibitory inputs. When inhibitory synchrony increased, the coherence of spiking model neurons with the synaptic input increased, but the firing rate either increased or remained the same. The mean number of synchronous inhibitory inputs was a key determinant of the shape of the firing rate versus current (f-I) curves. For a large number of inhibitory inputs (approximately 50), the f-I curve saturated for large I and an increase in input synchrony resulted in a shift of sensitivity-the model neuron responded to weaker inputs I. For a small number (approximately 10), the f-I curves were non-saturating and an increase in input synchrony led to an increase in the gain of the response-the firing rate in response to the same input was multiplied by an approximately constant factor. The firing rate modulation with inhibitory synchrony was highest when the input network oscillated in the gamma frequency range. Thus, the observed changes in firing rate and coherence of neurons in the visual cortex could be controlled by top-down inputs that regulated the coherence in the activity of a local inhibitory network discharging at gamma frequencies.

Fuentealba, P., Crochet, S., Timofeev, I., Bazhenov, M., Sejnowski, T.J., Steriade, M. Experimental evidence and modeling studies support a synchronizing role for electrical coupling in the cat thalamic reticular neurons in vivo. (2004) European Journal of Neuroscience. 20(1):111-9. DOI: 10.1111/j.1460-9568.2004.03462.x

+ expand abstract

Bowd, C., Zangwill, L.M., Medeiros, F.A., Hao, J., Chan, K., Lee, T.W., Sejnowski, T.J., Goldbaum, M.H., Sample, P.A., Crowston, J.G., Weinreb, R.N. Confocal scanning laser ophthalmoscopy classifiers and stereophotograph evaluation for prediction of visual field abnormalities in glaucoma-suspect eyes. (2004) Investigative Ophthalmology & Visual Science. 45(7):2255-2262.

+ expand abstract

Pizzo, D.P., Paban, V., Coufal, N.G., Gage, F.H., Thal, L.J. Long-term production of choline acetyltransferase in the CNS after transplantation of fibroblasts modified with a regulatable vector. (2004) Brain Research. Molecular Brain Research. 126(1):1-13. DOI: 10.1016/j.molbrainres.2004.03.006

+ expand abstract

Farmer, J., Zhao, X., van Praag, H., Wodtke, K., Gage, F.H., Christie, B.R. Effects of voluntary exercise on synaptic plasticity and gene expression in the dentate gyrus of adult male Sprague-Dawley rats in vivo. (2004) Neuroscience. 124(1):71-9. DOI: 10.1016/j.neuroscience.2003.09.029

+ expand abstract

Callaway, E.M. Feedforward, feedback and inhibitory connections in primate visual cortex. (2004) Neural Networks. 17(5-6):625-632. DOI: 10.1016/j.neunet.2004.04.004

+ expand abstract

Brandon, E.P., Mellott, T., Pizzo, D.P., Coufal, N., D'Amour, K.A., Gobeske, K., Lortie, M., López-Coviella, I., Berse, B., Thal, L.J., Gage, F.H., Blusztajn, J.K. Choline transporter 1 maintains cholinergic function in choline acetyltransferase haploinsufficiency. (2004) Journal of Neuroscience. 24(24):5459-66. DOI: 10.1523/JNEUROSCI.1106-04.2004

+ expand abstract

Gage, F.H. Structural plasticity of the adult brain. (2004) Dialogues Clin Neurosci. 6(2):135-41.

+ expand abstract

Schwartz, O., Movellan, J.R., Wachtler, T., Albright, T.D., Sejnowski, T.J. Spike count distributions, factorizability, and contextual effects in area V1. (2004) Neurocomputing. 58-60:893-900. DOI: 10.1016/j.neucom.2004.01.143

+ expand abstract

Arnold, M., Sejnowski, T., Hammerstrom, D., Jabri, M. Neural systems integration. (2004) Neurocomputing. 58-60:1123-1128. DOI: 10.1016/j.neucom.2004.01.176

+ expand abstract

Lie, D.C., Song, H., Colamarino, S.A., Ming, G.L., Gage, F.H. Neurogenesis in the adult brain: new strategies for central nervous system diseases. (2004) Annual Review of Pharmacology and Toxicology. 44:399-421. DOI: 10.1146/annurev.pharmtox.44.101802.121631

+ expand abstract

Marr, R.A., Guan, H., Rockenstein, E., Kindy, M., Gage, F.H., Verma, I., Masliah, E., Hersh, L.B. Neprilysin regulates amyloid Beta peptide levels. (2004) J. Mol. Neurosci. 22(1-2):5-11. DOI: 10.1385/JMN:22:1-2:5

+ expand abstract

Goulding, M. Neurobiology: a matter of balance. (2004) Nature. 429(6991):515-7. DOI: 10.1038/429515a

Göbel, W., Nimmerjahn, A., Helmchen, F. Distortion-free delivery of nanojoule femtosecond pulses from a Ti:sapphire laser through a hollow-core photonic crystal fiber. (2004) Optics Letters. 29(11):1285-7.

+ expand abstract

Makeig, S., Delorme, A., Westerfield, M., Jung, T.P., Townsend, J., Courchesne, E., Sejnowski, T.J. Electroencephalographic brain dynamics following manually responded visual targets. (2004) PLOS Biology. 2(6):e176. DOI: 10.1371/journal.pbio.0020176

+ expand abstract

Tiesinga, P.H., Fellous, J.M., Salinas, E., José, J.V., Sejnowski, T.J. Synchronization as a mechanism for attentional gain modulation. (2004) Neurocomputing. 58-60:641-646. DOI: 10.1016/j.neucom.2004.01.108

+ expand abstract

Schaffer, D.V., Gage, F.H. Neurogenesis and neuroadaptation. (2004) Neuromolecular Med. 5(1):1-9. DOI: 10.1385/NMM:5:1:001

+ expand abstract

Sharpee, T., Sugihara, H., Kurgansky, A.V., Rebrik, S., Stryker, M.P., Miller, K.D. Probing feature selectivity of neurons in primary visual cortex with natural stimuli. (2004) Proc SPIE Int Soc Opt Eng.(5467):212-222

+ expand abstract

Wurmser, A.E., Palmer, T.D., Gage, F.H. Neuroscience. Cellular interactions in the stem cell niche. (2004) Science. 304(5675):1253-5. DOI: 10.1126/science.1099344

Lanuza, G.M., Gosgnach, S., Pierani, A., Jessell, T.M., Goulding, M. Genetic identification of spinal interneurons that coordinate left-right locomotor activity necessary for walking movements. (2004) Neuron. 42(3):375-86.

+ expand abstract

Aimone, J.B., Gage, F.H. Unbiased characterization of high-density oligonucleotide microarrays using probe-level statistics. (2004) Journal of Neuroscience Methods. 135(1-2):27-33. DOI: 10.1016/j.jneumeth.2003.11.016

+ expand abstract

Cheng, L., Arata, A., Mizuguchi, R., Qian, Y., Karunaratne, A., Gray, P.A., Arata, S., Shirasawa, S., Bouchard, M., Luo, P., Chen, C.L., Busslinger, M., Goulding, M., Onimaru, H., Ma, Q. Tlx3 and Tlx1 are post-mitotic selector genes determining glutamatergic over GABAergic cell fates. (2004) Nature Neuroscience. 7(5):510-7. DOI: 10.1038/nn1221

+ expand abstract

Lein, E.S., Zhao, X., Gage, F.H. Defining a molecular atlas of the hippocampus using DNA microarrays and high-throughput in situ hybridization. (2004) Journal of Neuroscience. 24(15):3879-89. DOI: 10.1523/JNEUROSCI.4710-03.2004

+ expand abstract

Yates, P.A., Holub, A.D., McLaughlin, T., Sejnowski, T.J., O'Leary, D.D. Computational modeling of retinotopic map development to define contributions of EphA-ephrinA gradients, axon-axon interactions, and patterned activity. (2004) Journal of Neurobiology. 59(1):95-113. DOI: 10.1002/neu.10341

+ expand abstract

The topographic projection of retinal ganglion cell (RGC) axons to mouse superior colliculus (SC) or chick optic tectum (OT) is formed in three phases: RGC axons overshoot their termination zone (TZ); they exhibit interstitial branching along the axon that is topographically biased for the correct location of their future TZ; and branches arborize preferentially at the TZ and the initial exuberant projection refines through axon and branch elimination to generate a precise retinotopic map. We present a computational model of map development that demonstrates that the countergradients of EphAs and ephrinAs in retina and the OT/SC and bidirectional repellent signaling between RGC axons and OT/SC cells are sufficient to direct an initial topographic bias in RGC axon branching. Our model also suggests that a proposed repellent action of EphAs/ephrinAs present on RGC branches and arbors added to that of EphAs/ephrinAs expressed by OT/SC cells is required to progressively restrict branching and arborization to topographically correct locations and eliminate axon overshoot. Simulations show that this molecular framework alone can develop considerable topographic order and refinement, including axon elimination, a feature not programmed into the model. Generating a refined map with a condensed TZ as in vivo requires an additional parameter that enhances branch formation along an RGC axon near sites that it has a higher branch density, and resembles an assumed role for patterned neural activity. The same computational model generates the phenotypes reported in ephrinA deficient mice and Isl2-EphA3 knockin mice. This modeling suggests that gradients of counter-repellents can establish a substantial degree of topographic order in the OT/SC, and that repellents present on RGC axon branches and arbors make a substantial contribution to map refinement. However, competitive interactions between RGC axons that enhance the probability of continued local branching are required to generate precise retinotopy.

Eagleman, D.M., Jacobson, J.E., Sejnowski, T.J. Perceived luminance depends on temporal context. (2004) Nature. 428(6985):854-856. DOI: 10.1038/nature02467

+ expand abstract

Kempermann, G., Wiskott, L., Gage, F.H. Functional significance of adult neurogenesis. (2004) Current Opinion in Neurobiology. 14(2):186-91. DOI: 10.1016/j.conb.2004.03.001

+ expand abstract

Fellous, J.M., Tiesinga, P.H., Thomas, P.J., Sejnowski, T.J. Discovering spike patterns in neuronal responses. (2004) Journal of Neuroscience. 24(12):2989-3001. DOI: 10.1523/JNEUROSCI.4649-03.2004

+ expand abstract

Kuwabara, T., Hsieh, J., Nakashima, K., Taira, K., Gage, F.H. A small modulatory dsRNA specifies the fate of adult neural stem cells. (2004) Cell. 116(6):779-93.

+ expand abstract

Markakis, E.A., Palmer, T.D., Randolph-Moore, L., Rakic, P., Gage, F.H. Novel neuronal phenotypes from neural progenitor cells. (2004) Journal of Neuroscience. 24(12):2886-97. DOI: 10.1523/JNEUROSCI.4161-03.2004

+ expand abstract

Thaler, J.P., Koo, S.J., Kania, A., Lettieri, K., Andrews, S., Cox, C., Jessell, T.M., Pfaff, S.L. A postmitotic role for Isl-class LIM homeodomain proteins in the assignment of visceral spinal motor neuron identity. (2004) Neuron. 41(3):337-50.

+ expand abstract

Sapir, T., Geiman, E.J., Wang, Z., Velasquez, T., Mitsui, S., Yoshihara, Y., Frank, E., Alvarez, F.J., Goulding, M. Pax6 and engrailed 1 regulate two distinct aspects of renshaw cell development. (2004) Journal of Neuroscience. 24(5):1255-64. DOI: 10.1523/JNEUROSCI.3187-03.2004

+ expand abstract

Sharpee, T., Rust, N.C., Bialek, W. Analyzing neural responses to natural signals: maximally informative dimensions. (2004) Neural Computation. 16(2):223-50. DOI: 10.1162/089976604322742010

+ expand abstract

Brivanlou, I.H., Dantzker, J.L., Stevens, C.F., Callaway, E.M. Topographic specificity of functional connections from hippocampal CA3 to CA1. (2004) Proceedings of the National Academy of Sciences of the United States of America. 101(8):2560-2565.

+ expand abstract

Kim, J., Dittgen, T., Nimmerjahn, A., Waters, J., Pawlak, V., Helmchen, F., Schlesinger, S., Seeburg, P.H., Osten, P. Sindbis vector SINrep(nsP2S726): a tool for rapid heterologous expression with attenuated cytotoxicity in neurons. (2004) Journal of Neuroscience Methods. 133(1-2):81-90.

+ expand abstract

Tiesinga, P.H., Sejnowski, T.J. Rapid temporal modulation of synchrony by competition in cortical interneuron networks. (2004) Neural Computation. 16(2):251-75. DOI: 10.1162/089976604322742029

+ expand abstract

Hsieh, J., Aimone, J.B., Kaspar, B.K., Kuwabara, T., Nakashima, K., Gage, F.H. IGF-I instructs multipotent adult neural progenitor cells to become oligodendrocytes. (2004) Journal of Cell Biology. 164(1):111-22. DOI: 10.1083/jcb.200308101

+ expand abstract

Shi, Y., Chichung Lie, D., Taupin, P., Nakashima, K., Ray, J., Yu, R.T., Gage, F.H., Evans, R.M. Expression and function of orphan nuclear receptor TLX in adult neural stem cells. (2004) Nature. 427(6969):78-83. DOI: 10.1038/nature02211

+ expand abstract

Schreiber, S., Fellous, J.M., Tiesinga, P., Sejnowski, T.J. Influence of ionic conductances on spike timing reliability of cortical neurons for suprathreshold rhythmic inputs. (2004) Journal of Neurophysiology. 91(1):194-205. DOI: 10.1152/jn.00556.2003

+ expand abstract

Nakashima, K., Colamarino, S., Gage, F.H. Embryonic stem cells: staying plastic on plastic. (2004) Nature Medicine. 10(1):23-4. DOI: 10.1038/nm0104-23

Chatterjee, S., Callaway, E.M. Parallel colour-opponent pathways to primary visual cortex. (2003) Nature. 426(6967):668-671. DOI: 10.1038/nature02167

+ expand abstract

Cai, C.L., Liang, X., Shi, Y., Chu, P.H., Pfaff, S.L., Chen, J., Evans, S. Isl1 identifies a cardiac progenitor population that proliferates prior to differentiation and contributes a majority of cells to the heart. (2003) Developmental Cell. 5(6):877-89.

+ expand abstract

Fellous, J.M., Sejnowski, T.J. Regulation of persistent activity by background inhibition in an in vitro model of a cortical microcircuit. (2003) Cerebral Cortex . 13(11):1232-1241.

+ expand abstract

Anemüller, J., Sejnowski, T.J., Makeig, S. Complex independent component analysis of frequency-domain electroencephalographic data. (2003) Neural Networks. 16(9):1311-1323. DOI: 10.1016/j.neunet.2003.08.003

+ expand abstract

Muotri, A.R., Gage, F.H. Vibrating in the background. (2003) Nature Genetics. 35(3):205-7. DOI: 10.1038/ng1103-205

Sejnowski, T. The computational self. (2003) Ann. N. Y. Acad. Sci. 1001:262-271.

+ expand abstract

Rhodes, J.S., van Praag, H., Jeffrey, S., Girard, I., Mitchell, G.S., Garland, T., Gage, F.H. Exercise increases hippocampal neurogenesis to high levels but does not improve spatial learning in mice bred for increased voluntary wheel running. (2003) Behavioral Neuroscience. 117(5):1006-16. DOI: 10.1037/0735-7044.117.5.1006

+ expand abstract

Dziewczapolski, G., Lie, D.C., Ray, J., Gage, F.H., Shults, C.W. Survival and differentiation of adult rat-derived neural progenitor cells transplanted to the striatum of hemiparkinsonian rats. (2003) Exp. Neurol. 183(2):653-64.

+ expand abstract

Destexhe, A., Sejnowski, T.J. Interactions between membrane conductances underlying thalamocortical slow-wave oscillations. (2003) Physiological Reviews. 83(4):1401-1453. DOI: 10.1152/physrev.00012.2003

+ expand abstract

Gage, F.H. Brain, repair yourself. (2003) Sci. Am. 289(3):46-53.

D'Amour, K.A., Gage, F.H. Genetic and functional differences between multipotent neural and pluripotent embryonic stem cells. (2003) Proceedings of the National Academy of Sciences of the United States of America. 100 Suppl :11866-72. DOI: 10.1073/pnas.1834200100

+ expand abstract

Gage, F.H., Verma, I.M. Stem cells at the dawn of the 21st century. (2003) Proceedings of the National Academy of Sciences of the United States of America. 100 Suppl :11817-8. DOI: 10.1073/pnas.1834433100

Laughlin, S.B., Sejnowski, T.J. Communication in neuronal networks. (2003) Science. 301(5641):1870-1874. DOI: 10.1126/science.1089662

+ expand abstract

Aberg, M.A., Aberg, N.D., Palmer, T.D., Alborn, A.M., Carlsson-Skwirut, C., Bang, P., Rosengren, L.E., Olsson, T., Gage, F.H., Eriksson, P.S. IGF-I has a direct proliferative effect in adult hippocampal progenitor cells. (2003) Molecular and Cellular Neurosciences. 24(1):23-40.

+ expand abstract

Arvanian, V.L., Horner, P.J., Gage, F.H., Mendell, L.M. Chronic neurotrophin-3 strengthens synaptic connections to motoneurons in the neonatal rat. (2003) Journal of Neuroscience. 23(25):8706-12.

+ expand abstract

Eagleman, D.M., Sejnowski, T.J. The line-motion illusion can be reversed by motion signals after the line disappears. (2003) Perception. 32(8):963-968. DOI: 10.1068/p3314a

+ expand abstract

Kaspar, B.K., Lladó, J., Sherkat, N., Rothstein, J.D., Gage, F.H. Retrograde viral delivery of IGF-1 prolongs survival in a mouse ALS model. (2003) Science. 301(5634):839-42. DOI: 10.1126/science.1086137

+ expand abstract

Sejnowski, T.J. Perceptions of science. Tap into science 24-7. (2003) Science. 301(5633):601. DOI: 10.1126/science.1084463

Dickinson-Anson, H., Winkler, J., Fisher, L.J., Song, H.J., Poo, M.m., Gage, F.H. Acetylcholine-secreting cells improve age-induced memory deficits. (2003) Molecular Therapy. 8(1):51-61.

+ expand abstract

Lee, S.K., Pfaff, S.L. Synchronization of neurogenesis and motor neuron specification by direct coupling of bHLH and homeodomain transcription factors. (2003) Neuron. 38(5):731-45.

+ expand abstract

Kretzberg, J., Sejnowski, T., Warzecha, A.K., Egelhaaf, M. Variability of postsynaptic responses depends non-linearly on the number of synaptic inputs. (2003) Neurocomputing. 52-54:313-320. DOI: 10.1016/S0925-2312(02)00797-X

+ expand abstract

Schreiber, S., Fellous, J.M., Whitmer, D., Tiesinga, P., Sejnowski, T.J. A new correlation-based measure of spike timing reliability. (2003) Neurocomputing. 52-54:925-931. DOI: 10.1016/S0925-2312(02)00838-X

+ expand abstract

Rao, R.P., Sejnowski, T.J. Self-organizing neural systems based on predictive learning. (2003) Philos Trans A Math Phys Eng Sci. 361(1807):1149-1175. DOI: 10.1098/rsta.2003.1190

+ expand abstract

Thomas, P.J., Tiesinga, P.H., Fellous, J.M., Sejnowski, T.J. Reliability and bifurcation in neurons driven by multiple sinusoids. (2003) Neurocomputing. 52-54:955-961. DOI: 10.1016/S0925-2312(02)00856-1

+ expand abstract

South, S.M., Kohno, T., Kaspar, B.K., Hegarty, D., Vissel, B., Drake, C.T., Ohata, M., Jenab, S., Sailer, A.W., Malkmus, S., Masuyama, T., Horner, P., Bogulavsky, J., Gage, F.H., Yaksh, T.L., Woolf, C.J., Heinemann, S.F., Inturrisi, C.E. A conditional deletion of the NR1 subunit of the NMDA receptor in adult spinal cord dorsal horn reduces NMDA currents and injury-induced pain. (2003) Journal of Neuroscience. 23(12):5031-40.

+ expand abstract

Zhao, X., Ueba, T., Christie, B.R., Barkho, B., McConnell, M.J., Nakashima, K., Lein, E.S., Eadie, B.D., Willhoite, A.R., Muotri, A.R., Summers, R.G., Chun, J., Lee, K.F., Gage, F.H. Mice lacking methyl-CpG binding protein 1 have deficits in adult neurogenesis and hippocampal function. (2003) Proceedings of the National Academy of Sciences of the United States of America. 100(11):6777-82. DOI: 10.1073/pnas.1131928100

+ expand abstract

Scheel, J.R., Garrett, L.J., Allen, D.M., Carter, T.A., Randolph-Moore, L., Gambello, M.J., Gage, F.H., Wynshaw-Boris, A., Barlow, C. An inbred 129SvEv GFPCre transgenic mouse that deletes loxP-flanked genes in all tissues. (2003) Nucleic Acids Research. 31(10):e57.

+ expand abstract

Klassen, H.J., Imfeld, K.L., Kirov, I.I., Tai, L., Gage, F.H., Young, M.J., Berman, M.A. Expression of cytokines by multipotent neural progenitor cells. (2003) Cytokine. 22(3-4):101-6.

+ expand abstract

Brown, J., Cooper-Kuhn, C.M., Kempermann, G., Van Praag, H., Winkler, J., Gage, F.H., Kuhn, H.G. Enriched environment and physical activity stimulate hippocampal but not olfactory bulb neurogenesis. (2003) European Journal of Neuroscience. 17(10):2042-6.

+ expand abstract

Brivanlou, A.H., Gage, F.H., Jaenisch, R., Jessell, T., Melton, D., Rossant, J. Stem cells. Setting standards for human embryonic stem cells. (2003) Science. 300(5621):913-6. DOI: 10.1126/science.1082940

Neubig, M., Destexhe, A., Sejnowski, T.J. Variability of quantal synaptic currents in thalamocortical neurons. (2003) Thalamus Relat Syst. 2(2):153-168. DOI: 10.1016/S1472-9288(03)00008-6

+ expand abstract

Franks, K.M., Stevens, C.F., Sejnowski, T.J. Independent sources of quantal variability at single glutamatergic synapses. (2003) Journal of Neuroscience. 23(8):3186-3195.

+ expand abstract

Klassen, H., Imfeld, K.L., Ray, J., Young, M.J., Gage, F.H., Berman, M.A. The immunological properties of adult hippocampal progenitor cells. (2003) Vision Research. 43(8):947-56.

+ expand abstract

Fellous, J.M., Rudolph, M., Destexhe, A., Sejnowski, T.J. Synaptic background noise controls the input/output characteristics of single cells in an in vitro model of in vivo activity. (2003) Neuroscience. 122(3):811-829.

+ expand abstract

Marr, R.A., Rockenstein, E., Mukherjee, A., Kindy, M.S., Hersh, L.B., Gage, F.H., Verma, I.M., Masliah, E. Neprilysin gene transfer reduces human amyloid pathology in transgenic mice. (2003) Journal of Neuroscience. 23(6):1992-6.

+ expand abstract

Wachtler, T., Sejnowski, T.J., Albright, T.D. Representation of color stimuli in awake macaque primary visual cortex. (2003) Neuron. 37(4):681-691.

+ expand abstract

Doi, E., Inui, T., Lee, T.W., Wachtler, T., Sejnowski, T.J. Spatiochromatic receptive field properties derived from information-theoretic analyses of cone mosaic responses to natural scenes. (2003) Neural Computation. 15(2):397-417. DOI: 10.1162/089976603762552960

+ expand abstract

Kreutz-Delgado, K., Murray, J.F., Rao, B.D., Engan, K., Lee, T.W., Sejnowski, T.J. Dictionary learning algorithms for sparse representation. (2003) Neural Computation. 15(2):349-96. DOI: 10.1162/089976603762552951

+ expand abstract

Brandon, E.P., Lin, W., D'Amour, K.A., Pizzo, D.P., Dominguez, B., Sugiura, Y., Thode, S., Ko, C.P., Thal, L.J., Gage, F.H., Lee, K.F. Aberrant patterning of neuromuscular synapses in choline acetyltransferase-deficient mice. (2003) Journal of Neuroscience. 23(2):539-49.

+ expand abstract

Rao, R.P., Sejnowski, T.J. Complex Cell-like Direction Selectivity through Spike-Timing Dependent Plasticity. (2003) IETE Journal of Research. 49(2-3):97-111.

+ expand abstract

Lai, K., Kaspar, B.K., Gage, F.H., Schaffer, D.V. Sonic hedgehog regulates adult neural progenitor proliferation in vitro and in vivo. (2003) Nature Neuroscience. 6(1):21-7. DOI: 10.1038/nn983

+ expand abstract

Kempermann, G., Gast, D., Kronenberg, G., Yamaguchi, M., Gage, F.H. Early determination and long-term persistence of adult-generated new neurons in the hippocampus of mice. (2003) Development. 130(2):391-9.

+ expand abstract

Callaway, E.M. Orientation tuning--a crooked path to the straight and narrow. (2002) Neuron. 36(5):783-785.

+ expand abstract

Suri, R.E., Sejnowski, T.J. Spike propagation synchronized by temporally asymmetric Hebbian learning. (2002) Biol Cybern. 87(5-6):440-5. DOI: 10.1007/s00422-002-0355-9

+ expand abstract

Franks, K.M., Sejnowski, T.J. Complexity of calcium signaling in synaptic spines. (2002) BioEssays. 24(12):1130-1144. DOI: 10.1002/bies.10193

+ expand abstract

Destexhe, A., Sejnowski, T.J. The initiation of bursts in thalamic neurons and the cortical control of thalamic sensitivity. (2002) Philos. Trans. R. Soc. Lond., B, Biol. Sci. 357(1428):1649-57. DOI: 10.1098/rstb.2002.1154

+ expand abstract

Bartlett, M.S., Movellan, J.R., Sejnowski, T.J. Face recognition by independent component analysis. (2002) IEEE Trans Neural Netw. 13(6):1450-1464. DOI: 10.1109/TNN.2002.804287

+ expand abstract

Franks, K.M., Bartol, T.M., Sejnowski, T.J. A Monte Carlo model reveals independent signaling at central glutamatergic synapses. (2002) Biophysical Journal. 83(5):2333-2348. DOI: 10.1016/S0006-3495(02)75248-X

+ expand abstract

Bowd, C., Chan, K., Zangwill, L.M., Goldbaum, M.H., Lee, T.W., Sejnowski, T.J., Weinreb, R.N. Comparing neural networks and linear discriminant functions for glaucoma detection using confocal scanning laser ophthalmoscopy of the optic disc. (2002) Investigative Ophthalmology & Visual Science. 43(11):3444-3454.

+ expand abstract

Horner, P.J., Gage, F.H. Regeneration in the adult and aging brain. (2002) Archives of Neurology. 59(11):1717-20.

Callaway, E.M., Yuste, R. Stimulating neurons with light. (2002) Current Opinion in Neurobiology. 12(5):587-592.

+ expand abstract

Goulding, M., Lanuza, G., Sapir, T., Narayan, S. The formation of sensorimotor circuits. (2002) Current Opinion in Neurobiology. 12(5):508-15.

+ expand abstract

Bazhenov, M., Timofeev, I., Steriade, M., Sejnowski, T.J. Model of thalamocortical slow-wave sleep oscillations and transitions to activated States. (2002) Journal of Neuroscience. 22(19):8691-704.

+ expand abstract

Zhao, X., Gage, F.H. Expressing the central nervous system. (2002) Neurochem. Res. 27(10):953-4.

Chatterjee, S., Callaway, E.M. S cone contributions to the magnocellular visual pathway in macaque monkey. (2002) Neuron. 35(6):1135-1146.

+ expand abstract

Taupin, P., Gage, F.H. Adult neurogenesis and neural stem cells of the central nervous system in mammals. (2002) Journal of Neuroscience Research. 69(6):745-9. DOI: 10.1002/jnr.10378

Chan, K., Lee, T.W., Sample, P.A., Goldbaum, M.H., Weinreb, R.N., Sejnowski, T.J. Comparison of machine learning and traditional classifiers in glaucoma diagnosis. (2002) IEEE Trans Biomed Eng. 49(9):963-74. DOI: 10.1109/TBME.2002.802012

+ expand abstract

Salinas, E., Sejnowski, T.J. Integrate-and-fire neurons driven by correlated stochastic input. (2002) Neural Computation. 14(9):2111-2155. DOI: 10.1162/089976602320264024

+ expand abstract

Tamaki, S., Eckert, K., He, D., Sutton, R., Doshe, M., Jain, G., Tushinski, R., Reitsma, M., Harris, B., Tsukamoto, A., Gage, F., Weissman, I., Uchida, N. Engraftment of sorted/expanded human central nervous system stem cells from fetal brain. (2002) Journal of Neuroscience Research. 69(6):976-86. DOI: 10.1002/jnr.10412

+ expand abstract

Direct isolation of human central nervous system stem cells (CNS-SC) based on cell surface markers yields a highly purified stem cell population that can extensively expand in vitro and exhibit multilineage differentiation potential both in vitro and in vivo. The CNS-SC were isolated from fetal brain tissue using the cell surface markers CD133(+), CD34(-), CD45(-), and CD24(-/lo) (CD133(+) cells). Fluorescence-activated cell sorted (FACS) CD133(+) cells continue to expand exponentially as neurospheres while retaining multipotential differentiation capacity for >10 passages. CD133(-), CD34(-), and CD45(-) sorted cells (approximately 95% of total fetal brain tissue) fail to initiate neurospheres. Neurosphere cells transplanted into neonatal immunodeficient NOD-SCID mice proliferated, migrated, and differentiated in a site-specific manner. However, it has been difficult to evaluate human cell engraftment, because many of the available monoclonal antibodies against neural cells (beta-tubulin III and glial fibrillary acidic protein) are not species specific. To trace the progeny of human cells after transplantation, CD133(+)-derived neurosphere cells were transduced with lentiviral vectors containing enhanced green fluorescent protein (eGFP) expressed downstream of the phosphoglycerate kinase promoter. After transduction, GFP(+) cells were enriched by FACS, expanded, and transplanted into the lateral ventricular space of neonatal immunodeficient NOD-SCID brain. The progeny of transplanted cells were detected by either GFP fluorescence or antibody against GFP. GFP(+) cells were present in the subventricular zone-rostral migrating stream, olfactory bulb, and hippocampus as well as nonneurogenic sites, such as cerebellum, cerebral cortex, and striatum. Antibody against GFP revealed that some of the cells displayed differentiating dendrites and processes with neurons or glia cells. Thus, marking human CNS-SC with reporter genes introduced by lentiviral vectors is a useful tool with which to characterize migration and differentiation of human cells in this mouse transplantation model.

Koo, S.J., Pfaff, S.L. Fine-tuning motor neuron properties: signaling from the periphery. (2002) Neuron. 35(5):823-6.

+ expand abstract

Borrell, V., Callaway, E.M. Reorganization of exuberant axonal arbors contributes to the development of laminar specificity in ferret visual cortex. (2002) Journal of Neuroscience. 22(15):6682-6695. DOI: 20026663

+ expand abstract

Lie, D.C., Dziewczapolski, G., Willhoite, A.R., Kaspar, B.K., Shults, C.W., Gage, F.H. The adult substantia nigra contains progenitor cells with neurogenic potential. (2002) Journal of Neuroscience. 22(15):6639-49. DOI: 20026700

+ expand abstract

Chan, K., Lee, T.W., Sejnowski, T.J. Variational Learning of Clusters of Undercomplete Nonsymmetric Independent Components. (2002) J Mach Learn Res. 3:99-114.

+ expand abstract

Hu, W.Y., Myers, C.P., Kilzer, J.M., Pfaff, S.L., Bushman, F.D. Inhibition of retroviral pathogenesis by RNA interference. (2002) Current Biology. 12(15):1301-11.

+ expand abstract

Lee, T.W., Wachtler, T., Sejnowski, T.J. Color opponency is an efficient representation of spectral properties in natural scenes. (2002) Vision Research. 42(17):2095-2103.

+ expand abstract

Sample, P.A., Goldbaum, M.H., Chan, K., Boden, C., Lee, T.W., Vasile, C., Boehm, A.G., Sejnowski, T., Johnson, C.A., Weinreb, R.N. Using machine learning classifiers to identify glaucomatous change earlier in standard visual fields. (2002) Investigative Ophthalmology & Visual Science. 43(8):2660-2665.

+ expand abstract

Kempermann, G., Gast, D., Gage, F.H. Neuroplasticity in old age: sustained fivefold induction of hippocampal neurogenesis by long-term environmental enrichment. (2002) Ann. Neurol. 52(2):135-43. DOI: 10.1002/ana.10262

+ expand abstract

Thaler, J.P., Lee, S.K., Jurata, L.W., Gill, G.N., Pfaff, S.L. LIM factor Lhx3 contributes to the specification of motor neuron and interneuron identity through cell-type-specific protein-protein interactions. (2002) Cell. 110(2):237-49.

+ expand abstract

Houweling, A.R., Bazhenov, M., Timofeev, I., Grenier, F., Steriade, M., Sejnowski, T.J. Frequency-selective augmenting responses by short-term synaptic depression in cat neocortex. (2002) Journal of Physiology. 542(Pt 2):599-617.

+ expand abstract

Lechner, H.A., Lein, E.S., Callaway, E.M. A genetic method for selective and quickly reversible silencing of Mammalian neurons. (2002) Journal of Neuroscience. 22(13):5287-5290. DOI: 20026527

+ expand abstract

Tiesinga, P.H., Fellous, J.M., Sejnowski, T.J. Attractor reliability reveals deterministic structure in neuronal spike trains. (2002) Neural Computation. 14(7):1629-1650. DOI: 10.1162/08997660260028647

+ expand abstract

Timofeev, I., Grenier, F., Bazhenov, M., Houweling, A.R., Sejnowski, T.J., Steriade, M. Short- and medium-term plasticity associated with augmenting responses in cortical slabs and spindles in intact cortex of cats in vivo. (2002) Journal of Physiology. 542(Pt 2):583-598.

+ expand abstract

Plastic changes in the synaptic responsiveness of neocortical neurones, which occur after rhythmic stimuli within the frequency range of sleep spindles (10 Hz), were investigated in isolated neocortical slabs and intact cortex of anaesthetized cats by means of single, dual and triple simultaneous intracellular recordings in conjunction with recordings of local field potential responses. In isolated cortical slabs (10 mm long, 6 mm wide and 4-5 mm deep), augmenting responses to pulse-trains at 10 Hz (responses with growing amplitudes from the second stimulus in a train) were elicited only by relatively high-intensity stimuli. At low intensities, responses were decremental. The largest augmenting responses were evoked in neurones located close to the stimulation site. Quantitative analyses of the number of action potentials and the amplitude and area of depolarization during augmenting responses in a population of neurones recorded from slabs showed that the most dramatic increases in the number of spikes with successive stimuli, and the greatest increase in depolarization amplitude, were found in conventional fast-spiking (FS) neurones. The largest increase in the area of depolarization was found in regular-spiking (RS) neurones. Dual intracellular recordings from a pair of FS and RS neurones in the slab revealed more action potentials in the FS neurone during augmenting responses and a significant increase in the depolarization area of the RS neurone that was dependent on the firing of the FS neurone. Self-sustained seizures could occur in the slab after rhythmic stimuli at 10 Hz. In the intact cortex, repeated sequences of stimuli generating augmenting responses or spontaneous spindles could induce an increased synaptic responsiveness to single stimuli, which lasted for several minutes. A similar time course of increased responsiveness was obtained with induction of cellular plasticity. These data suggest that augmenting responses elicited by stimulation, as well as spontaneously occurring spindles, may induce short- and medium-term plasticity of neuronal responses.

Timofeev, I., Bazhenov, M., Sejnowski, T., Steriade, M. Cortical hyperpolarization-activated depolarizing current takes part in the generation of focal paroxysmal activities. (2002) Proceedings of the National Academy of Sciences of the United States of America. 99(14):9533-9537. DOI: 10.1073/pnas.132259899

+ expand abstract

Kempermann, G., Gage, F.H. Genetic determinants of adult hippocampal neurogenesis correlate with acquisition, but not probe trial performance, in the water maze task. (2002) European Journal of Neuroscience. 16(1):129-36.

+ expand abstract

Eagleman, D.M., Sejnowski, T.J. Untangling spatial from temporal illusions. (2002) Trends in Neurosciences. 25(6):293; author reply 294.

Horner, P.J., Thallmair, M., Gage, F.H. Defining the NG2-expressing cell of the adult CNS. (2002) Journal of Neurocytology. 31(6-7):469-80.

+ expand abstract

Gross, M.K., Dottori, M., Goulding, M. Lbx1 specifies somatosensory association interneurons in the dorsal spinal cord. (2002) Neuron. 34(4):535-49.

+ expand abstract

Shirasaki, R., Pfaff, S.L. Transcriptional codes and the control of neuronal identity. (2002) Annual Review of Neuroscience. 25:251-81. DOI: 10.1146/annurev.neuro.25.112701.142916

+ expand abstract

Song, H., Stevens, C.F., Gage, F.H. Astroglia induce neurogenesis from adult neural stem cells. (2002) Nature. 417(6884):39-44. DOI: 10.1038/417039a

+ expand abstract

Song, H.J., Stevens, C.F., Gage, F.H. Neural stem cells from adult hippocampus develop essential properties of functional CNS neurons. (2002) Nature Neuroscience. 5(5):438-45. DOI: 10.1038/nn844

+ expand abstract

Wiskott, L., Sejnowski, T.J. Slow feature analysis: unsupervised learning of invariances. (2002) Neural Computation. 14(4):715-770. DOI: 10.1162/089976602317318938

+ expand abstract

Duann, J.R., Jung, T.P., Kuo, W.J., Yeh, T.C., Makeig, S., Hsieh, J.C., Sejnowski, T.J. Single-trial variability in event-related BOLD signals. (2002) Neuroimage. 15(4):823-835. DOI: 10.1006/nimg.2001.1049

+ expand abstract

Wurmser, A.E., Gage, F.H. Stem cells: cell fusion causes confusion. (2002) Nature. 416(6880):485-7. DOI: 10.1038/416485a

Callaway, E.M. Cell type specificity of local cortical connections. (2002) Journal of Neurocytology. 31(3-5):231-237.

+ expand abstract

Kempermann, G., Gage, F.H. Genetic influence on phenotypic differentiation in adult hippocampal neurogenesis. (2002) Brain Res. Dev. Brain Res. 134(1-2):1-12.

+ expand abstract

van Praag, H., Gage, F.H. Genetics of childhood disorders: XXXVI. Stem cell research, part 1: New neurons in the adult brain. (2002) J Am Acad Child Adolesc Psychiatry. 41(3):354-6.

D'Amour, K.A., Gage, F.H. Are somatic stem cells pluripotent or lineage-restricted? (2002) Nature Medicine. 8(3):213-4. DOI: 10.1038/nm0302-213

Tiesinga, P.H., Fellous, J.M., José, J.V., Sejnowski, T.J. Information transfer in entrained cortical neurons. (2002) Network. 13(1):41-66.

+ expand abstract

van Praag, H., Schinder, A.F., Christie, B.R., Toni, N., Palmer, T.D., Gage, F.H. Functional neurogenesis in the adult hippocampus. (2002) Nature. 415(6875):1030-4. DOI: 10.1038/4151030a

+ expand abstract

Kaspar, B.K., Vissel, B., Bengoechea, T., Crone, S., Randolph-Moore, L., Muller, R., Brandon, E.P., Schaffer, D., Verma, I.M., Lee, K.F., Heinemann, S.F., Gage, F.H. Adeno-associated virus effectively mediates conditional gene modification in the brain. (2002) Proceedings of the National Academy of Sciences of the United States of America. 99(4):2320-5. DOI: 10.1073/pnas.042678699

+ expand abstract

Gage, F.H. Neurogenesis in the adult brain. (2002) Journal of Neuroscience. 22(3):612-3.

Makeig, S., Westerfield, M., Jung, T.P., Enghoff, S., Townsend, J., Courchesne, E., Sejnowski, T.J. Dynamic brain sources of visual evoked responses. (2002) Science. 295(5555):690-4. DOI: 10.1126/science.1066168

+ expand abstract

Kaspar, B.K., Erickson, D., Schaffer, D., Hinh, L., Gage, F.H., Peterson, D.A. Targeted retrograde gene delivery for neuronal protection. (2002) Mol. Ther. 5(1):50-6. DOI: 10.1006/mthe.2001.0520

+ expand abstract

Vallières, L., Campbell, I.L., Gage, F.H., Sawchenko, P.E. Reduced hippocampal neurogenesis in adult transgenic mice with chronic astrocytic production of interleukin-6. (2002) Journal of Neuroscience. 22(2):486-92.

+ expand abstract

Goldbaum, M.H., Sample, P.A., Chan, K., Williams, J., Lee, T.W., Blumenthal, E., Girkin, C.A., Zangwill, L.M., Bowd, C., Sejnowski, T., Weinreb, R.N. Comparing machine learning classifiers for diagnosing glaucoma from standard automated perimetry. (2002) Investigative Ophthalmology & Visual Science. 43(1):162-9.

+ expand abstract

Zhao, X., Lein, E.S., He, A., Smith, S.C., Aston, C., Gage, F.H. Transcriptional profiling reveals strict boundaries between hippocampal subregions. (2001) Journal of Comparative Neurology. 441(3):187-96.

+ expand abstract

Flash, T., Sejnowski, T.J. Computational approaches to motor control. (2001) Current Opinion in Neurobiology. 11(6):655-62.

+ expand abstract

Callaway, E.M. Neural mechanisms for the generation of visual complex cells. (2001) Neuron. 32(3):378-380.

+ expand abstract

Lee, S.K., Pfaff, S.L. Transcriptional networks regulating neuronal identity in the developing spinal cord. (2001) Nature Neuroscience. 4 Suppl:1183-91. DOI: 10.1038/nn750

+ expand abstract

Dottori, M., Gross, M.K., Labosky, P., Goulding, M. The winged-helix transcription factor Foxd3 suppresses interneuron differentiation and promotes neural crest cell fate. (2001) Development. 128(21):4127-38.

+ expand abstract

Destexhe, A., Rudolph, M., Fellous, J.M., Sejnowski, T.J. Fluctuating synaptic conductances recreate in vivo-like activity in neocortical neurons. (2001) Neuroscience. 107(1):13-24.

+ expand abstract

Jung, T.P., Makeig, S., Westerfield, M., Townsend, J., Courchesne, E., Sejnowski, T.J. Analysis and visualization of single-trial event-related potentials. (2001) Hum Brain Mapp. 14(3):166-85.

+ expand abstract

In this study, a linear decomposition technique, independent component analysis (ICA), is applied to single-trial multichannel EEG data from event-related potential (ERP) experiments. Spatial filters derived by ICA blindly separate the input data into a sum of temporally independent and spatially fixed components arising from distinct or overlapping brain or extra-brain sources. Both the data and their decomposition are displayed using a new visualization tool, the "ERP image," that can clearly characterize single-trial variations in the amplitudes and latencies of evoked responses, particularly when sorted by a relevant behavioral or physiological variable. These tools were used to analyze data from a visual selective attention experiment on 28 control subjects plus 22 neurological patients whose EEG records were heavily contaminated with blink and other eye-movement artifacts. Results show that ICA can separate artifactual, stimulus-locked, response-locked, and non-event-related background EEG activities into separate components, a taxonomy not obtained from conventional signal averaging approaches. This method allows: (1) removal of pervasive artifacts of all types from single-trial EEG records, (2) identification and segregation of stimulus- and response-locked EEG components, (3) examination of differences in single-trial responses, and (4) separation of temporally distinct but spatially overlapping EEG oscillatory activities with distinct relationships to task events. The proposed methods also allow the interaction between ERPs and the ongoing EEG to be investigated directly. We studied the between-subject component stability of ICA decomposition of single-trial EEG epochs by clustering components with similar scalp maps and activation power spectra. Components accounting for blinks, eye movements, temporal muscle activity, event-related potentials, and event-modulated alpha activities were largely replicated across subjects. Applying ICA and ERP image visualization to the analysis of sets of single trials from event-related EEG (or MEG) experiments can increase the information available from ERP (or ERF) data.

Salinas, E., Sejnowski, T.J. Gain modulation in the central nervous system: where behavior, neurophysiology, and computation meet. (2001) The Neuroscientist. 7(5):430-40. DOI: 10.1177/107385840100700512

+ expand abstract

Marquardt, T., Pfaff, S.L. Cracking the transcriptional code for cell specification in the neural tube. (2001) Cell. 106(6):651-4.

+ expand abstract

Pfeifer, A., Brandon, E.P., Kootstra, N., Gage, F.H., Verma, I.M. Delivery of the Cre recombinase by a self-deleting lentiviral vector: efficient gene targeting in vivo. (2001) Proceedings of the National Academy of Sciences of the United States of America. 98(20):11450-5. DOI: 10.1073/pnas.201415498

+ expand abstract

Rao, R.P., Sejnowski, T.J. Predictive learning of temporal sequences in recurrent neocortical circuits. (2001) Novartis Found. Symp. 239:208-229; discussion 229-240.

+ expand abstract

Salinas, E., Sejnowski, T.J. Correlated neuronal activity and the flow of neural information. (2001) Nature Reviews Neuroscience. 2(8):539-50. DOI: 10.1038/35086012

Chu, V.T., Gage, F.H. Chipping away at stem cells. (2001) Proceedings of the National Academy of Sciences of the United States of America. 98(14):7652-3. DOI: 10.1073/pnas.141244198

Jung, T.P., Makeig, S., McKeown, M.J., Bell, A.J., Lee, T.W., Sejnowski, T.J. Imaging Brain Dynamics Using Independent Component Analysis. (2001) Proceedings of the IEEE. Institute of Electrical and Electronics Engineers. 89(7):1107-1122. DOI: 10.1109/5.939827

+ expand abstract

Pouget, A., Sejnowski, T.J. Simulating a lesion in a basis function model of spatial representations: comparison with hemineglect. (2001) Psychol Rev. 108(3):653-73.

+ expand abstract

Läer, L., Kloppstech, M., Schöfl, C., Sejnowski, T.J., Brabant, G., Prank, K. Noise enhanced hormonal signal transduction through intracellular calcium oscillations. (2001) Biophysical Chemistry. 91(2):157-66.

+ expand abstract

Tiesinga, P.H., Fellous, J.M., José, J.V., Sejnowski, T.J. Computational model of carbachol-induced delta, theta, and gamma oscillations in the hippocampus. (2001) Hippocampus. 11(3):251-274. DOI: 10.1002/hipo.1041

+ expand abstract

Zhang, K., Sejnowski, T.J. Accuracy and learning in neuronal populations. (2001) Progress in Brain Research. 130:333-342.

van Praag, H., Barlow, C., Gage, F.H. Are drug targets missed owing to lack of physical activity? - Reply. (2001) Drug Discov. Today. 6(12):615-617.

Ray, J., Gage, F.H. Construction of cells expressing neurotrophins. (2001) Methods in Molecular Biology. 169:115-33.

Matsuura, N., Lie, D.C., Hoshimaru, M., Asahi, M., Hojo, M., Ishizaki, R., Hashimoto, N., Noji, S., Ohuchi, H., Yoshioka, H., Gage, F.H. Sonic hedgehog facilitates dopamine differentiation in the presence of a mesencephalic glial cell line. (2001) Journal of Neuroscience. 21(12):4326-35.

+ expand abstract

Rao, R.P., Eagleman, D.M., Sejnowski, T.J. Optimal smoothing in visual motion perception. (2001) Neural Computation. 13(6):1243-53.

+ expand abstract

Nicholson, L.F., Ma, L., Goulding, M. Cloning and expression of Munc 30: a member of the paired -like homeodomain gene family. (2001) Cell Biology International. 25(4):351-65. DOI: 10.1006/cbir.2000.0638

+ expand abstract

Tiesinga, P.H., Sejnowski, T.J. Precision of pulse-coupled networks of integrate-and-fire neurons. (2001) Network. 12(2):215-33.

+ expand abstract

Bazhenov, M., Stopfer, M., Rabinovich, M., Abarbanel, H.D., Sejnowski, T.J., Laurent, G. Model of cellular and network mechanisms for odor-evoked temporal patterning in the locust antennal lobe. (2001) Neuron. 30(2):569-81.

+ expand abstract

Bazhenov, M., Stopfer, M., Rabinovich, M., Huerta, R., Abarbanel, H.D., Sejnowski, T.J., Laurent, G. Model of transient oscillatory synchronization in the locust antennal lobe. (2001) Neuron. 30(2):553-567.

+ expand abstract

Briggs, F., Callaway, E.M. Layer-specific input to distinct cell types in layer 6 of monkey primary visual cortex. (2001) Journal of Neuroscience. 21(10):3600-3608.

+ expand abstract

Wachtler, T., Albright, T.D., Sejnowski, T.J. Nonlocal interactions in color perception: nonlinear processing of chromatic signals from remote inducers. (2001) Vision Research. 41(12):1535-1546.

+ expand abstract

Palmer, T.D., Schwartz, P.H., Taupin, P., Kaspar, B., Stein, S.A., Gage, F.H. Cell culture. Progenitor cells from human brain after death. (2001) Nature. 411(6833):42-3. DOI: 10.1038/35075141

Simon, H.H., Saueressig, H., Wurst, W., Goulding, M.D., O'Leary, D.D. Fate of midbrain dopaminergic neurons controlled by the engrailed genes. (2001) Journal of Neuroscience. 21(9):3126-34.

+ expand abstract

Lin, W., Burgess, R.W., Dominguez, B., Pfaff, S.L., Sanes, J.R., Lee, K.F. Distinct roles of nerve and muscle in postsynaptic differentiation of the neuromuscular synapse. (2001) Nature. 410(6832):1057-64. DOI: 10.1038/35074025

+ expand abstract

Suhr, S.T., Senut, M.C., Whitelegge, J.P., Faull, K.F., Cuizon, D.B., Gage, F.H. Identities of sequestered proteins in aggregates from cells with induced polyglutamine expression. (2001) Journal of Cell Biology. 153(2):283-94.

+ expand abstract

Yabuta, N.H., Sawatari, A., Callaway, E.M. Two functional channels from primary visual cortex to dorsal visual cortical areas. (2001) Science. 292(5515):297-300. DOI: 10.1126/science.1057916

+ expand abstract

Fellous, J.M., Houweling, A.R., Modi, R.H., Rao, R.P., Tiesinga, P.H., Sejnowski, T.J. Frequency dependence of spike timing reliability in cortical pyramidal cells and interneurons. (2001) Journal of Neurophysiology. 85(4):1782-1787.

+ expand abstract

Lamar, E., Kintner, C., Goulding, M. Identification of NKL, a novel Gli-Kruppel zinc-finger protein that promotes neuronal differentiation. (2001) Development. 128(8):1335-46.

+ expand abstract

Anderson, D.J., Gage, F.H., Weissman, I.L. Can stem cells cross lineage boundaries? (2001) Nature Medicine. 7(4):393-5. DOI: 10.1038/86439

Allen, D.M., van Praag, H., Ray, J., Weaver, Z., Winrow, C.J., Carter, T.A., Braquet, R., Harrington, E., Ried, T., Brown, K.D., Gage, F.H., Barlow, C. Ataxia telangiectasia mutated is essential during adult neurogenesis. (2001) Genes & Development. 15(5):554-66. DOI: 10.1101/gad.869001

+ expand abstract

Dykman, M.I., Sharpee, T., Platzman, P.M. Enhancement of tunneling from a correlated 2D electron system by a many-electron Mössbauer-type recoil in a magnetic field. (2001) Phys. Rev. Lett. 86(11):2408-11. DOI: 10.1103/PhysRevLett.86.2408

+ expand abstract

Weissman, I.L., Anderson, D.J., Gage, F.H. Stem and progenitor cells: origins, phenotypes, lineage commitments, and transdifferentiations. (2001) Annual Review of Cell and Developmental Biology. 17:387-403. DOI: 10.1146/annurev.cellbio.17.1.387

+ expand abstract

Butler, A.K., Dantzker, J.L., Shah, R.B., Callaway, E.M. Development of visual cortical axons: layer-specific effects of extrinsic influences and activity blockade. (2001) Journal of Comparative Neurology. 430(3):321-331.

+ expand abstract

Moran-Rivard, L., Kagawa, T., Saueressig, H., Gross, M.K., Burrill, J., Goulding, M. Evx1 is a postmitotic determinant of v0 interneuron identity in the spinal cord. (2001) Neuron. 29(2):385-99.

+ expand abstract

Pierani, A., Moran-Rivard, L., Sunshine, M.J., Littman, D.R., Goulding, M., Jessell, T.M. Control of interneuron fate in the developing spinal cord by the progenitor homeodomain protein Dbx1. (2001) Neuron. 29(2):367-384.

+ expand abstract

Vissel, B., Royle, G.A., Christie, B.R., Schiffer, H.H., Ghetti, A., Tritto, T., Perez-Otano, I., Radcliffe, R.A., Seamans, J., Sejnowski, T., Wehner, J.M., Collins, A.C., O'Gorman, S., Heinemann, S.F. The role of RNA editing of kainate receptors in synaptic plasticity and seizures. (2001) Neuron. 29(1):217-227.

+ expand abstract

Brown, G.D., Yamada, S., Sejnowski, T.J. Independent component analysis at the neural cocktail party. (2001) Trends in Neurosciences. 24(1):54-63.

+ expand abstract

Wachtler, T., Lee, T.W., Sejnowski, T.J. Chromatic structure of natural scenes. (2001) J Opt Soc Am A Opt Image Sci Vis. 18(1):65-77.

+ expand abstract

Seamans, J.K., Durstewitz, D., Christie, B.R., Stevens, C.F., Sejnowski, T.J. Dopamine D1/D5 receptor modulation of excitatory synaptic inputs to layer V prefrontal cortex neurons. (2001) Proceedings of the National Academy of Sciences of the United States of America. 98(1):301-306. DOI: 10.1073/pnas.011518798

+ expand abstract

van Praag, H., Kempermann, G., Gage, F.H. Neural consequences of environmental enrichment. (2000) Nature Reviews Neuroscience. 1(3):191-8. DOI: 10.1038/35044558

+ expand abstract

Kempermann, G., van Praag, H., Gage, F.H. Activity-dependent regulation of neuronal plasticity and self repair. (2000) Progress in Brain Research. 127:35-48.

+ expand abstract

Tiesinga, P.H., José, J.V., Sejnowski, T.J. Comparison of current-driven and conductance-driven neocortical model neurons with Hodgkin-Huxley voltage-gated channels. (2000) Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 62(6 Pt B):8413-8419.

+ expand abstract

Uchida, N., Buck, D.W., He, D., Reitsma, M.J., Masek, M., Phan, T.V., Tsukamoto, A.S., Gage, F.H., Weissman, I.L. Direct isolation of human central nervous system stem cells. (2000) Proceedings of the National Academy of Sciences of the United States of America. 97(26):14720-5. DOI: 10.1073/pnas.97.26.14720

+ expand abstract

Sejnowski, T.J., Destexhe, A. Why do we sleep? (2000) Brain Research. 886(1-2):208-223.

+ expand abstract

Shihabuddin, L.S., Horner, P.J., Ray, J., Gage, F.H. Adult spinal cord stem cells generate neurons after transplantation in the adult dentate gyrus. (2000) Journal of Neuroscience. 20(23):8727-35.

+ expand abstract

Makeig, S., Jung, T.P., Sejnowski, T.J. Awareness during drowsiness: dynamics and electrophysiological correlates. (2000) Can J Exp Psychol. 54(4):266-273.

+ expand abstract

Christie, B.R., Franks, K.M., Seamans, J.K., Saga, K., Sejnowski, T.J. Synaptic plasticity in morphologically identified CA1 stratum radiatum interneurons and giant projection cells. (2000) Hippocampus. 10(6):673-683. DOI: 10.1002/1098-1063(2000)10:6<673::AID-HIPO1005>3.0.

+ expand abstract

Timofeev, I., Grenier, F., Bazhenov, M., Sejnowski, T.J., Steriade, M. Origin of slow cortical oscillations in deafferented cortical slabs. (2000) Cerebral Cortex . 10(12):1185-1199.

+ expand abstract

Taupin, P., Ray, J., Fischer, W.H., Suhr, S.T., Hakansson, K., Grubb, A., Gage, F.H. FGF-2-responsive neural stem cell proliferation requires CCg, a novel autocrine/paracrine cofactor. (2000) Neuron. 28(2):385-97.

+ expand abstract

Durstewitz, D., Seamans, J.K., Sejnowski, T.J. Neurocomputational models of working memory. (2000) Nature Neuroscience. 3 Suppl:1184-91. DOI: 10.1038/81460

+ expand abstract

Shults, C.W., Ray, J., Tsuboi, K., Gage, F.H. Fibroblast growth factor-2-producing fibroblasts protect the nigrostriatal dopaminergic system from 6-hydroxydopamine. (2000) Brain Research. 883(2):192-204.

+ expand abstract

We tested the hypothesis that fibroblasts, which had been genetically engineered to produce fibroblast growth factor-2 (FGF-2), can protect nigrostriatal dopaminergic neurons. Three groups of rats received either a burr hole only (n=5) or implantation of fibroblasts, which had been genetically engineered to produce beta-galactosidase (beta-gal) (n=8) or FGF-2 (n=8), at two sites in the right striatum. Two weeks later, the animals received an injection of 25 microg of 6-hydroxydopamine hydrobromide (6-OHDA) midway between the two implant sites. The group that received FGF-2-fibroblasts had significantly fewer apomorphine-induced rotations than the groups that received a burr hole only or beta-gal-fibroblasts at weeks 2 and 3 following lesioning with 6-OHDA. Testing for amphetamine-induced rotation revealed a mild reduction in rotation in the beta-gal-fibroblast group compared to the burr hole only group, but a striking attenuation of amphetamine-induced rotation in the FGF-2-fibroblast group. There was also preservation of TH-IR neurons on the lesioned side relative to both control groups. The size of the grafts and the gliosis surrounding the injection sites did not differ between the FGF-2-fibroblast and beta-gal-fibroblast groups. To further characterize the production of FGF-2 by the FGF-2-fibroblasts, we implanted FGF-2-fibroblasts and beta-gal-fibroblast into the striatum of rats but did not lesion the animals with 6-OHDA. The animals were then sacrificed at 1, 2 and 5 weeks following implantation. Prior to implantation the FGF-2 fibroblasts contained 148 ng/mg of FGF-2-immunoreactive (FGF-2-IR) material per mg of protein of cell lysate. After implantation FGF-2-IR material was noted in the grafts of FGF-2-fibroblasts, most conspicuously at 1 and 2 weeks following implantation. We also noted FGF-2-IR material in the nuclei of reactive astrocytes adjacent to the implants, and OX-42-immunoreactive (OX-42-IR) cells adjacent and occasionally within the implants. Our work indicates that fibroblasts genetically engineered to produce FGF-2 and implanted in the striatum can protect the nigrostriatal dopaminergic system and may be useful in the treatment of Parkinson's disease.

Horner, P.J., Gage, F.H. Regenerating the damaged central nervous system. (2000) Nature. 407(6807):963-70. DOI: 10.1038/35039559

+ expand abstract

Zoghbi, H.Y., Gage, F.H., Choi, D.W. Neurobiology of disease. (2000) Current Opinion in Neurobiology. 10(5):655-60.

+ expand abstract

Gage, F.H. Structural plasticity: cause, result, or correlate of depression. (2000) Biological Psychiatry. 48(8):713-4.

Palmer, T.D., Willhoite, A.R., Gage, F.H. Vascular niche for adult hippocampal neurogenesis. (2000) Journal of Comparative Neurology. 425(4):479-94.

+ expand abstract

Jung, T.P., Makeig, S., Westerfield, M., Townsend, J., Courchesne, E., Sejnowski, T.J. Removal of eye activity artifacts from visual event-related potentials in normal and clinical subjects. (2000) Clin Neurophysiol. 111(10):1745-58.

+ expand abstract

Young, M.J., Ray, J., Whiteley, S.J., Klassen, H., Gage, F.H. Neuronal differentiation and morphological integration of hippocampal progenitor cells transplanted to the retina of immature and mature dystrophic rats. (2000) Molecular and Cellular Neurosciences. 16(3):197-205. DOI: 10.1006/mcne.2000.0869

+ expand abstract

Sharma, K., Leonard, A.E., Lettieri, K., Pfaff, S.L. Genetic and epigenetic mechanisms contribute to motor neuron pathfinding. (2000) Nature. 406(6795):515-9. DOI: 10.1038/35020078

+ expand abstract

Bazhenov, M., Timofeev, I., Steriade, M., Sejnowski, T. Spiking-bursting activity in the thalamic reticular nucleus initiates sequences of spindle oscillations in thalamic networks. (2000) Journal of Neurophysiology. 84(2):1076-87.

+ expand abstract

Salinas, E., Sejnowski, T.J. Impact of correlated synaptic input on output firing rate and variability in simple neuronal models. (2000) Journal of Neuroscience. 20(16):6193-209.

+ expand abstract

Yabuta, N.H., Butler, A.K., Callaway, E.M. Laminar specificity of local circuits in barrel cortex of ephrin-A5 knockout mice. (2000) Journal of Neuroscience. 20(15):RC88.

+ expand abstract

Krekelberg, B., Lappe, M., Whitney, D., Cavanagh, P., Eagleman, D.M., Sejnowski, T.J. The position of moving objects. (2000) Science. 289(5482):1107a. DOI: 10.1126/science.289.5482.1107a

Verma, I.M., Gage, F.H. Genome and gene therapy. (2000) Molecular Therapy. 2(2):95. DOI: 10.1006/mthe.2000.0109

Goulding, M., Lamar, E. Neuronal patterning: Making stripes in the spinal cord. (2000) Current Biology. 10(15):565-568.

Brown, A., Yates, P.A., Burrola, P., Ortuño, D., Vaidya, A., Jessell, T.M., Pfaff, S.L., O'Leary, D.D., Lemke, G. Topographic mapping from the retina to the midbrain is controlled by relative but not absolute levels of EphA receptor signaling. (2000) Cell. 102(1):77-88.

+ expand abstract

Mah, S.P., Saueressig, H., Goulding, M., Kintner, C., Dressler, G.R. Kidney development in cadherin-6 mutants: delayed mesenchyme-to-epithelial conversion and loss of nephrons. (2000) Developmental Biology. 223(1):38-53. DOI: 10.1006/dbio.2000.9738

+ expand abstract

Dantzker, J.L., Callaway, E.M. Laminar sources of synaptic input to cortical inhibitory interneurons and pyramidal neurons. (2000) Nature Neuroscience. 3(7):701-707. DOI: 10.1038/76656

+ expand abstract

Kempermann, G., Gage, F.H. Neurogenesis in the adult hippocampus. (2000) Novartis Found. Symp. 231:220-35; discussion 235-41, 302.

+ expand abstract

Kafri, T., van Praag, H., Gage, F.H., Verma, I.M. Lentiviral vectors: regulated gene expression. (2000) Molecular Therapy. 1(6):516-21. DOI: 10.1006/mthe.2000.0083

+ expand abstract

Makeig, S., Enghoff, S., Jung, T.P., Sejnowski, T.J. A natural basis for efficient brain-actuated control. (2000) IEEE Trans Rehabil Eng. 8(2):208-11.

+ expand abstract

Zhang, K., Sejnowski, T.J. A universal scaling law between gray matter and white matter of cerebral cortex. (2000) Proceedings of the National Academy of Sciences of the United States of America. 97(10):5621-6. DOI: 10.1073/pnas.090504197

+ expand abstract

Jacobs, B.L., van Praag, H., Gage, F.H. Adult brain neurogenesis and psychiatry: a novel theory of depression. (2000) Molecular Psychiatry. 5(3):262-9.

+ expand abstract

D'Amour, K., Gage, F.H. New tools for human developmental biology. (2000) Nature Biotechnology. 18(4):381-2. DOI: 10.1038/74429

Paulsen, O., Sejnowski, T.J. Natural patterns of activity and long-term synaptic plasticity. (2000) Current Opinion in Neurobiology. 10(2):172-9.

+ expand abstract

Fellous, J.M., Sejnowski, T.J. Cholinergic induction of oscillations in the hippocampal slice in the slow (0.5-2 Hz), theta (5-12 Hz), and gamma (35-70 Hz) bands. (2000) Hippocampus. 10(2):187-97. DOI: 10.1002/(SICI)1098-1063(2000)10:2<187::AID-HIPO8>3

+ expand abstract

Jung, T.P., Makeig, S., Humphries, C., Lee, T.W., McKeown, M.J., Iragui, V., Sejnowski, T.J. Removing electroencephalographic artifacts by blind source separation. (2000) Psychophysiology. 37(2):163-78.

+ expand abstract

Eagleman, D.M., Sejnowski, T.J. Motion integration and postdiction in visual awareness. (2000) Science. 287(5460):2036-8.

+ expand abstract

Durstewitz, D., Seamans, J.K., Sejnowski, T.J. Dopamine-mediated stabilization of delay-period activity in a network model of prefrontal cortex. (2000) Journal of Neurophysiology. 83(3):1733-50.

+ expand abstract

The prefrontal cortex (PFC) is critically involved in working memory, which underlies memory-guided, goal-directed behavior. During working-memory tasks, PFC neurons exhibit sustained elevated activity, which may reflect the active holding of goal-related information or the preparation of forthcoming actions. Dopamine via the D1 receptor strongly modulates both this sustained (delay-period) activity and behavioral performance in working-memory tasks. However, the function of dopamine during delay-period activity and the underlying neural mechanisms are only poorly understood. Recently we proposed that dopamine might stabilize active neural representations in PFC circuits during tasks involving working memory and render them robust against interfering stimuli and noise. To further test this idea and to examine the dopamine-modulated ionic currents that could give rise to increased stability of neural representations, we developed a network model of the PFC consisting of multicompartment neurons equipped with Hodgkin-Huxley-like channel kinetics that could reproduce in vitro whole cell and in vivo recordings from PFC neurons. Dopaminergic effects on intrinsic ionic and synaptic conductances were implemented in the model based on in vitro data. Simulated dopamine strongly enhanced high, delay-type activity but not low, spontaneous activity in the model network. Furthermore the strength of an afferent stimulation needed to disrupt delay-type activity increased with the magnitude of the dopamine-induced shifts in network parameters, making the currently active representation much more stable. Stability could be increased by dopamine-induced enhancements of the persistent Na(+) and N-methyl-D-aspartate (NMDA) conductances. Stability also was enhanced by a reduction in AMPA conductances. The increase in GABA(A) conductances that occurs after stimulation of dopaminergic D1 receptors was necessary in this context to prevent uncontrolled, spontaneous switches into high-activity states (i.e., spontaneous activation of task-irrelevant representations). In conclusion, the dopamine-induced changes in the biophysical properties of intrinsic ionic and synaptic conductances conjointly acted to highly increase stability of activated representations in PFC networks and at the same time retain control over network behavior and thus preserve its ability to adequately respond to task-related stimuli. Predictions of the model can be tested in vivo by locally applying specific D1 receptor, NMDA, or GABA(A) antagonists while recording from PFC neurons in delayed reaction-type tasks with interfering stimuli.

Horner, P.J., Power, A.E., Kempermann, G., Kuhn, H.G., Palmer, T.D., Winkler, J., Thal, L.J., Gage, F.H. Proliferation and differentiation of progenitor cells throughout the intact adult rat spinal cord. (2000) Journal of Neuroscience. 20(6):2218-28.

+ expand abstract

Barabash-Sharpee, T., Dykman, M.I., Platzman, P.M. Tunneling transverse to a magnetic field and its occurrence in correlated 2D electron systems. (2000) Phys. Rev. Lett. 84(10):2227-30. DOI: 10.1103/PhysRevLett.84.2227

+ expand abstract

Sawatari, A., Callaway, E.M. Diversity and cell type specificity of local excitatory connections to neurons in layer 3B of monkey primary visual cortex. (2000) Neuron. 25(2):459-471.

+ expand abstract

Gage, F.H. Mammalian neural stem cells. (2000) Science. 287(5457):1433-8.

+ expand abstract

Jurata, L.W., Thomas, J.B., Pfaff, S.L. Transcriptional mechanisms in the development of motor control. (2000) Current Opinion in Neurobiology. 10(1):72-9.

+ expand abstract

Moortgat, K.T., Bullock, T.H., Sejnowski, T.J. Gap junction effects on precision and frequency of a model pacemaker network. (2000) Journal of Neurophysiology. 83(2):984-97.

+ expand abstract

Moortgat, K.T., Bullock, T.H., Sejnowski, T.J. Precision of the pacemaker nucleus in a weakly electric fish: network versus cellular influences. (2000) Journal of Neurophysiology. 83(2):971-83.

+ expand abstract

We investigated the relative influence of cellular and network properties on the extreme spike timing precision observed in the medullary pacemaker nucleus (Pn) of the weakly electric fish Apteronotus leptorhynchus. Of all known biological rhythms, the electric organ discharge of this and related species is the most temporally precise, with a coefficient of variation (CV = standard deviation/mean period) of 2 x 10(-4) and standard deviation (SD) of 0.12-1.0 micros. The timing of the electric organ discharge is commanded by neurons of the Pn, individual cells of which we show in an in vitro preparation to have only a slightly lesser degree of precision. Among the 100-150 Pn neurons, dye injection into a pacemaker cell resulted in dye coupling in one to five other pacemaker cells and one to three relay cells, consistent with previous results. Relay cell fills, however, showed profuse dendrites and contacts never seen before: relay cell dendrites dye-coupled to one to seven pacemaker and one to seven relay cells. Moderate (0.1-10 nA) intracellular current injection had no effect on a neuron's spiking period, and only slightly modulated its spike amplitude, but could reset the spike phase. In contrast, massive hyperpolarizing current injections (15-25 nA) could force the cell to skip spikes. The relative timing of subthreshold and full spikes suggested that at least some pacemaker cells are likely to be intrinsic oscillators. The relative amplitudes of the subthreshold and full spikes gave a lower bound to the gap junctional coupling coefficient of 0.01-0.08. Three drugs, called gap junction blockers for their mode of action in other preparations, caused immediate and substantial reduction in frequency, altered the phase lag between pairs of neurons, and later caused the spike amplitude to drop, without altering the spike timing precision. Thus we conclude that the high precision of the normal Pn rhythm does not require maximal gap junction conductances between neurons that have ordinary cellular precision. Rather, the spiking precision can be explained as an intrinsic cellular property while the gap junctions act to frequency- and phase-lock the network oscillations.

Lewicki, M.S., Sejnowski, T.J. Learning overcomplete representations. (2000) Neural Computation. 12(2):337-65.

+ expand abstract

Senut, M.C., Suhr, S.T., Kaspar, B., Gage, F.H. Intraneuronal aggregate formation and cell death after viral expression of expanded polyglutamine tracts in the adult rat brain. (2000) Journal of Neuroscience. 20(1):219-29.

+ expand abstract

Gross, M.K., Moran-Rivard, L., Velasquez, T., Nakatsu, M.N., Jagla, K., Goulding, M. Lbx1 is required for muscle precursor migration along a lateral pathway into the limb. (2000) Development. 127(2):413-424.

+ expand abstract

Murthy, V.N., Sejnowski, T.J., Stevens, C.F. Dynamics of dendritic calcium transients evoked by quantal release at excitatory hippocampal synapses. (2000) Proceedings of the National Academy of Sciences of the United States of America. 97(2):901-6.

+ expand abstract

Sejnowski, T.J. The book of Hebb. (1999) Neuron. 24(4):773-6.

Spain, B.H., Larson, C.J., Shihabuddin, L.S., Gage, F.H., Verma, I.M. Truncated BRCA2 is cytoplasmic: implications for cancer-linked mutations. (1999) Proceedings of the National Academy of Sciences of the United States of America. 96(24):13920-5.

+ expand abstract

van Praag, H., Christie, B.R., Sejnowski, T.J., Gage, F.H. Running enhances neurogenesis, learning, and long-term potentiation in mice. (1999) Proceedings of the National Academy of Sciences of the United States of America. 96(23):13427-31.

+ expand abstract

Shihabuddin, L.S., Palmer, T.D., Gage, F.H. The search for neural progenitor cells: prospects for the therapy of neurodegenerative disease. (1999) Mol Med Today. 5(11):474-80.

+ expand abstract

McKeown, M.J., Humphries, C., Iragui, V., Sejnowski, T.J. Spatially fixed patterns account for the spike and wave features in absence seizures. (1999) Brain Topogr. 12(2):107-16.

+ expand abstract

Sailer, A., Swanson, G.T., Pérez-Otaño, I., O'Leary, L., Malkmus, S.A., Dyck, R.H., Dickinson-Anson, H., Schiffer, H.H., Maron, C., Yaksh, T.L., Gage, F.H., O'Gorman, S., Heinemann, S.F. Generation and analysis of GluR5(Q636R) kainate receptor mutant mice. (1999) Journal of Neuroscience. 19(20):8757-64.

+ expand abstract

Palmer, T.D., Markakis, E.A., Willhoite, A.R., Safar, F., Gage, F.H. Fibroblast growth factor-2 activates a latent neurogenic program in neural stem cells from diverse regions of the adult CNS. (1999) Journal of Neuroscience. 19(19):8487-97.

+ expand abstract

Saueressig, H., Burrill, J., Goulding, M. Engrailed-1 and netrin-1 regulate axon pathfinding by association interneurons that project to motor neurons. (1999) Development. 126(19):4201-4212.

+ expand abstract

Donato, G., Bartlett, M.S., Hager, J.C., Ekman, P., Sejnowski, T.J. Classifying Facial Actions. (1999) IEEE Trans Pattern Anal Mach Intell. 21(10):974. DOI: 10.1109/34.799905

+ expand abstract

Sakurada, K., Ohshima-Sakurada, M., Palmer, T.D., Gage, F.H. Nurr1, an orphan nuclear receptor, is a transcriptional activator of endogenous tyrosine hydroxylase in neural progenitor cells derived from the adult brain. (1999) Development. 126(18):4017-26.

+ expand abstract

Takahashi, M., Miyoshi, H., Verma, I.M., Gage, F.H. Rescue from photoreceptor degeneration in the rd mouse by human immunodeficiency virus vector-mediated gene transfer. (1999) Journal of Virology. 73(9):7812-6.

+ expand abstract

Smith, D.E., Roberts, J., Gage, F.H., Tuszynski, M.H. Age-associated neuronal atrophy occurs in the primate brain and is reversible by growth factor gene therapy. (1999) Proceedings of the National Academy of Sciences of the United States of America. 96(19):10893-8.

+ expand abstract

Harrison, K.A., Thaler, J., Pfaff, S.L., Gu, H., Kehrl, J.H. Pancreas dorsal lobe agenesis and abnormal islets of Langerhans in Hlxb9-deficient mice. (1999) Nature Genetics. 23(1):71-5. DOI: 10.1038/12674

+ expand abstract

Thaler, J., Harrison, K., Sharma, K., Lettieri, K., Kehrl, J., Pfaff, S.L. Active suppression of interneuron programs within developing motor neurons revealed by analysis of homeodomain factor HB9. (1999) Neuron. 23(4):675-87.

+ expand abstract

Bang, A.G., Papalopulu, N., Goulding, M.D., Kintner, C. Expression of Pax-3 in the lateral neural plate is dependent on a Wnt-mediated signal from posterior nonaxial mesoderm. (1999) Developmental Biology. 212(2):366-80. DOI: 10.1006/dbio.1999.9319

+ expand abstract

Lehky, S.R., Sejnowski, T.J. Seeing white: Qualia in the context of decoding population codes. (1999) Neural Computation. 11(6):1261-80.

+ expand abstract

Makeig, S., Westerfield, M., Townsend, J., Jung, T.P., Courchesne, E., Sejnowski, T.J. Functionally independent components of early event-related potentials in a visual spatial attention task. (1999) Philos. Trans. R. Soc. Lond., B, Biol. Sci. 354(1387):1135-44. DOI: 10.1098/rstb.1999.0469

+ expand abstract

Kempermann, G., Gage, F.H. Experience-dependent regulation of adult hippocampal neurogenesis: effects of long-term stimulation and stimulus withdrawal. (1999) Hippocampus. 9(3):321-32. DOI: 10.1002/(SICI)1098-1063(1999)9:3<321::AID-HIPO11>3

+ expand abstract

Kempermann, G., Gage, F.H. New nerve cells for the adult brain. (1999) Sci. Am. 280(5):48-53.

Steward, O., Schauwecker, P.E., Guth, L., Zhang, Z., Fujiki, M., Inman, D., Wrathall, J., Kempermann, G., Gage, F.H., Saatman, K.E., Raghupathi, R., McIntosh, T. Genetic approaches to neurotrauma research: opportunities and potential pitfalls of murine models. (1999) Experimental Neurology. 157(1):19-42. DOI: 10.1006/exnr.1999.7040

+ expand abstract

Senut, M.C., Gage, F.H. Prenatal gene therapy: can the technical hurdles be overcome? (1999) Mol Med Today. 5(4):152-6.

+ expand abstract

Markakis, E.A., Gage, F.H. Adult-generated neurons in the dentate gyrus send axonal projections to field CA3 and are surrounded by synaptic vesicles. (1999) Journal of Comparative Neurology. 406(4):449-60.

+ expand abstract

Zhang, K., Sejnowski, T.J. A theory of geometric constraints on neural activity for natural three-dimensional movement. (1999) Journal of Neuroscience. 19(8):3122-45.

+ expand abstract

Ueba, T., Kaspar, B., Zhao, X., Gage, F.H. Repression of human fibroblast growth factor 2 by a novel transcription factor. (1999) Journal of Biological Chemistry. 274(15):10382-7.

+ expand abstract

Makeig, S., Westerfield, M., Jung, T.P., Covington, J., Townsend, J., Sejnowski, T.J., Courchesne, E. Functionally independent components of the late positive event-related potential during visual spatial attention. (1999) Journal of Neuroscience. 19(7):2665-80.

+ expand abstract

van Praag, H., Kempermann, G., Gage, F.H. Running increases cell proliferation and neurogenesis in the adult mouse dentate gyrus. (1999) Nature Neuroscience. 2(3):266-70. DOI: 10.1038/6368

+ expand abstract

Suhr, S.T., Gage, F.H. Gene therapy in the central nervous system: the use of recombinant retroviruses. (1999) Archives of Neurology. 56(3):287-92.

+ expand abstract

Bartlett, M.S., Hager, J.C., Ekman, P., Sejnowski, T.J. Measuring facial expressions by computer image analysis. (1999) Psychophysiology. 36(2):253-63.

+ expand abstract

Bazhenov, M., Timofeev, I., Steriade, M., Sejnowski, T.J. Self-sustained rhythmic activity in the thalamic reticular nucleus mediated by depolarizing GABAA receptor potentials. (1999) Nature Neuroscience. 2(2):168-74. DOI: 10.1038/5729

+ expand abstract

Lee, T.W., Girolami, M., Sejnowski, T.J. Independent component analysis using an extended infomax algorithm for mixed subgaussian and supergaussian sources. (1999) Neural Computation. 11(2):417-41.

+ expand abstract

Peterson, D.A., Dickinson-Anson, H.A., Leppert, J.T., Lee, K.F., Gage, F.H. Central neuronal loss and behavioral impairment in mice lacking neurotrophin receptor p75. (1999) Journal of Comparative Neurology. 404(1):1-20.

+ expand abstract

Furuta, T., Wang, S.S., Dantzker, J.L., Dore, T.M., Bybee, W.J., Callaway, E.M., Denk, W., Tsien, R.Y. Brominated 7-hydroxycoumarin-4-ylmethyls: photolabile protecting groups with biologically useful cross-sections for two photon photolysis. (1999) Proceedings of the National Academy of Sciences of the United States of America. 96(4):1193-1200.

+ expand abstract

Ernst, U., Pawelzik, K., Tsodyks, M., Sejnowski, T.J. Relation between retinotopical and orientation maps in visual cortex. (1999) Neural Computation. 11(2):375-9.

+ expand abstract

Takahashi, J., Palmer, T.D., Gage, F.H. Retinoic acid and neurotrophins collaborate to regulate neurogenesis in adult-derived neural stem cell cultures. (1999) Journal of Neurobiology. 38(1):65-81.

+ expand abstract

Zhang, K., Sejnowski, T.J. Neuronal tuning: To sharpen or broaden? (1999) Neural Computation. 11(1):75-84.

+ expand abstract

Shihabuddin, L.S., Ray, J., Gage, F.H. Stem cell technology for basic science and clinical applications. (1999) Archives of Neurology. 56(1):29-32.

Kafri, T., van Praag, H., Ouyang, L., Gage, F.H., Verma, I.M. A packaging cell line for lentivirus vectors. (1999) Journal of Virology. 73(1):576-84.

+ expand abstract

Mandel, R.J., Gage, F.H., Clevenger, D.G., Spratt, S.K., Snyder, R.O., Leff, S.E. Nerve growth factor expressed in the medial septum following in vivo gene delivery using a recombinant adeno-associated viral vector protects cholinergic neurons from fimbria-fornix lesion-induced deg (1999) Experimental Neurology. 155(1):59-64. DOI: 10.1006/exnr.1998.6961

+ expand abstract

Destexhe, A., McCormick, D.A., Sejnowski, T.J. Thalamic and thalamocortical mechanisms underlying 3 Hz spike-and-wave discharges. (1999) Progress in Brain Research. 121:289-307.

Pouget, A., Deneve, S., Sejnowski, T.J. Frames of reference in hemineglect: a computational approach. (1999) Progress in Brain Research. 121:81-97.

Chiang, M.Y., Misner, D., Kempermann, G., Schikorski, T., Giguère, V., Sucov, H.M., Gage, F.H., Stevens, C.F., Evans, R.M. An essential role for retinoid receptors RARbeta and RXRgamma in long-term potentiation and depression. (1998) Neuron. 21(6):1353-61.

+ expand abstract

Sharma, K., Sheng, H.Z., Lettieri, K., Li, H., Karavanov, A., Potter, S., Westphal, H., Pfaff, S.L. LIM homeodomain factors Lhx3 and Lhx4 assign subtype identities for motor neurons. (1998) Cell. 95(6):817-28.

+ expand abstract

Takahashi, M., Palmer, T.D., Takahashi, J., Gage, F.H. Widespread integration and survival of adult-derived neural progenitor cells in the developing optic retina. (1998) Molecular and Cellular Neurosciences. 12(6):340-8. DOI: 10.1006/mcne.1998.0721

+ expand abstract

Takuma, N., Sheng, H.Z., Furuta, Y., Ward, J.M., Sharma, K., Hogan, B.L., Pfaff, S.L., Westphal, H., Kimura, S., Mahon, K.A. Formation of Rathke's pouch requires dual induction from the diencephalon. (1998) Development. 125(23):4835-40.

+ expand abstract

Goulding, M. Specifying motor neurons and their connections. (1998) Neuron. 21(5):943-946.

Yabuta, N.H., Callaway, E.M. Cytochrome-oxidase blobs and intrinsic horizontal connections of layer 2/3 pyramidal neurons in primate V1. (1998) Visual Neuroscience. 15(6):1007-1027.

+ expand abstract

Pyramidal neurons in superficial layers of cerebral cortex have extensive horizontal axons that provide a substrate for lateral interactions across cortical columns. These connections are believed to link functionally similar regions, as suggested by the observation that cytochrome-oxidase blobs in the monkey primary visual cortex (V1) are preferentially connected to blobs and interblobs to interblobs. To better understand the precise relationship between horizontal connections and blobs, we intracellularly labeled 20 layer 2/3 pyramidal neurons in tangential living brain slices from V1 of macaque monkeys. The locations of each cell body and the cell's synaptic boutons relative to blobs were quantitatively analyzed. We found evidence for two cell types located at characteristic distances from blob centers: (1) neurons lacking long-distance, clustered axons (somata 130-200 microm from blob centers) and (2) cells with clustered, long-distance axon collaterals (somata < 130 microm or >200 microm from blob centers). For all cells, synaptic boutons close to the cell body were located at similar distances from blob centers as the cell body. The majority of boutons from cells lacking distal axon clusters were close to their cell bodies. Cells located more than 200 microm from blob centers were in interblobs and had long-distance clustered axon collaterals selectively targeting distant interblob regions. Cells located less than 130 microm from blob centers were found within both blobs and interblobs, but many were close to traditionally defined borders. The distant synaptic boutons from these cells were generally located relatively near to blob centers, but the neurons closest to blob centers had synaptic boutons closer to blob centers than those farther away. There was not a sharp transition that would suggest specificity for blobs and interblobs as discrete, binary entities. Instead they appear to be extremes along a continuum. These observations have important implications for the function of lateral interactions within V1.

Yabuta, N.H., Callaway, E.M. Functional streams and local connections of layer 4C neurons in primary visual cortex of the macaque monkey. (1998) Journal of Neuroscience. 18(22):9489-9499.

+ expand abstract

The primate visual system is composed of multiple, functionally specialized cortical areas. The functional diversity among areas is thought to reflect different contributions from early parallel visual pathways to the area V1 neurons providing input to "higher" cortical areas. The M pathway is believed to provide information about motion and contrast, via layer 4B of V1, to dorsal visual areas. The P pathway is believed to provide information about shape and color, via layer 2/3 of V1, to ventral visual areas, with specialized contributions from cytochrome-oxidase (CO) blob versus interblob neurons. However, the detailed anatomical relationships between the M and P pathways and the neurons in V1 that provide input to higher extrastriate cortical areas are poorly understood. To study these relationships, spiny stellate neurons in the M- and P-recipient layers of V1, 4Calpha and 4Cbeta, respectively, were intracellularly labeled, and their axonal and dendritic arbors were reconstructed. We find that neurons with dendrites in upper layer 4Calpha project axons to layer 4B and CO blobs in layer 2/3, thus relaying M input to these regions. Other neurons in lower layer 4Calpha provide M input to interblobs. These cells have either (1) dendrites restricted to lower layer 4Calpha and axons specifically targeting layer 2/3 interblobs, or (2) dendrites in lower 4Calpha and 4Cbeta and axons targeting blobs and interblobs. P-recipient layer 4Cbeta neurons have dense axonal arbors in both blobs and interblobs but not layer 4B. Quantitative analyses reveal that 4Calpha cells provide approximately five times more synapses than 4Cbeta cells to layer 4B, whereas 4Cbeta cells provide five times more synapses than 4Calpha cells to layer 2/3. These observations imply that M input is dominant in layer 4B. In layer 2/3, both blobs and interblobs receive M and P input, but the P input is dominant, and M input to interblobs derives exclusively from a subpopulation of M afferents that targets lower 4Calpha, not from afferents targeting only upper 4Calpha (cf. Blasdel and Lund, 1983). We speculate that the M and P pathways to interblobs are "X-like" linear systems, whereas blobs also receive nonlinear "Y-like" M input.

Eriksson, P.S., Perfilieva, E., Björk-Eriksson, T., Alborn, A.M., Nordborg, C., Peterson, D.A., Gage, F.H. Neurogenesis in the adult human hippocampus. (1998) Nature Medicine. 4(11):1313-7. DOI: 10.1038/3305

+ expand abstract

Kempermann, G., Kuhn, H.G., Winkler, J., Gage, F.H. [New nerve cells for the adult brain. Adult neurogenesis and stem cell concepts in neurologic research]. (1998) Nervenarzt. 69(10):851-7.

+ expand abstract

Gage, F.H. Stem cells of the central nervous system. (1998) Current Opinion in Neurobiology. 8(5):671-6.

+ expand abstract

Miyoshi, H., Blömer, U., Takahashi, M., Gage, F.H., Verma, I.M. Development of a self-inactivating lentivirus vector. (1998) Journal of Virology. 72(10):8150-7.

+ expand abstract

Varki, A., Wills, C., Perlmutter, D., Woodruff, D., Gage, F.H., Moore, J., Semendeferi, K., Bernirschke, K., Katzman, R., Doolittle, R., Bullock, T. Great Ape Phenome Project? (1998) Science. 282(5387):239-40.

McKeown, M.J., Sejnowski, T.J. Independent component analysis of fMRI data: examining the assumptions. (1998) Hum Brain Mapp. 6(5-6):368-72.

+ expand abstract

Aubert, I., Ridet, J.L., Schachner, M., Rougon, G., Gage, F.H. Expression of L1 and PSA during sprouting and regeneration in the adult hippocampal formation. (1998) Journal of Comparative Neurology. 399(1):1-19.

+ expand abstract

Berger, F., Gage, F.H., Vijayaraghavan, S. Nicotinic receptor-induced apoptotic cell death of hippocampal progenitor cells. (1998) Journal of Neuroscience. 18(17):6871-81.

+ expand abstract

McKeown, M.J., Humphries, C., Achermann, P., Borbély, A.A., Sejnowski, T.J. A new method for detecting state changes in the EEG: exploratory application to sleep data. (1998) Journal of Sleep Research. 7 Suppl 1:48-56.

+ expand abstract

Bartlett, M.S., Sejnowski, T.J. Learning viewpoint-invariant face representations from visual experience in an attractor network. (1998) Network. 9(3):399-417.

+ expand abstract

Gage, F.H., Kempermann, G., Palmer, T.D., Peterson, D.A., Ray, J. Multipotent progenitor cells in the adult dentate gyrus. (1998) Journal of Neurobiology. 36(2):249-66.

+ expand abstract

Bazhenov, M., Timofeev, I., Steriade, M., Sejnowski, T.J. Computational models of thalamocortical augmenting responses. (1998) Journal of Neuroscience. 18(16):6444-65.

+ expand abstract

McKeown, M.J., Makeig, S., Brown, G.G., Jung, T.P., Kindermann, S.S., Bell, A.J., Sejnowski, T.J. Analysis of fMRI data by blind separation into independent spatial components. (1998) Hum Brain Mapp. 6(3):160-88.

+ expand abstract

Current analytical techniques applied to functional magnetic resonance imaging (fMRI) data require a priori knowledge or specific assumptions about the time courses of processes contributing to the measured signals. Here we describe a new method for analyzing fMRI data based on the independent component analysis (ICA) algorithm of Bell and Sejnowski ([1995]: Neural Comput 7:1129-1159). We decomposed eight fMRI data sets from 4 normal subjects performing Stroop color-naming, the Brown and Peterson work/number task, and control tasks into spatially independent components. Each component consisted of voxel values at fixed three-dimensional locations (a component "map"), and a unique associated time course of activation. Given data from 144 time points collected during a 6-min trial, ICA extracted an equal number of spatially independent components. In all eight trials, ICA derived one and only one component with a time course closely matching the time course of 40-sec alternations between experimental and control tasks. The regions of maximum activity in these consistently task-related components generally overlapped active regions detected by standard correlational analysis, but included frontal regions not detected by correlation. Time courses of other ICA components were transiently task-related, quasiperiodic, or slowly varying. By utilizing higher-order statistics to enforce successively stricter criteria for spatial independence between component maps, both the ICA algorithm and a related fourth-order decomposition technique (Comon [1994]: Signal Processing 36:11-20) were superior to principal component analysis (PCA) in determining the spatial and temporal extent of task-related activation. For each subject, the time courses and active regions of the task-related ICA components were consistent across trials and were robust to the addition of simulated noise. Simulated movement artifact and simulated task-related activations added to actual fMRI data were clearly separated by the algorithm. ICA can be used to distinguish between nontask-related signal components, movements, and other artifacts, as well as consistently or transiently task-related fMRI activations, based on only weak assumptions about their spatial distributions and without a priori assumptions about their time courses. ICA appears to be a highly promising method for the analysis of fMRI data from normal and clinical populations, especially for uncovering unpredictable transient patterns of brain activity associated with performance of psychomotor tasks.

Lin, J.K., Pawelzik, K., Ernst, U., Sejnowski, T.J. Irregular synchronous activity in stochastically-coupled networks of integrate-and-fire neurons. (1998) Network. 9(3):333-44.

+ expand abstract

Sejnowski, T.J. Neurobiology. Making smooth moves. (1998) Nature. 394(6695):725-6. DOI: 10.1038/29404

Suhr, S.T., Gil, E.B., Senut, M.C., Gage, F.H. High level transactivation by a modified Bombyx ecdysone receptor in mammalian cells without exogenous retinoid X receptor. (1998) Proceedings of the National Academy of Sciences of the United States of America. 95(14):7999-8004.

+ expand abstract

Winkler, J., Thal, L.J., Gage, F.H., Fisher, L.J. Cholinergic strategies for Alzheimer's disease. (1998) Journal of Molecular Medicine. 76(8):555-67.

+ expand abstract

Alzheimer's disease is a devastating degenerative disorder of the central nervous system that results in gradual deterioration of cognitive function and severe alteration of personality. Degeneration of neurons in the nucleus basalis Meynert, the origin of the major cholinergic projections to the neocortex, occurs early in the course of the disease, and is correlated with the cognitive decline. This link between cholinergic dysfunction in the basal-cortical system and cognitive deficits has focused scientific efforts on developing tools to elucidate the neurobiological role of the cholinergic system in cognition and to develop therapeutic interventions in the disorder. An important step in understanding the mechanisms underlying cognitive dysfunction has been the development of in vivo rodent models that mimic some of the features of Alzheimer's disease. Acute excitotoxic or immunotoxic lesions of the nucleus basalis in rodents have revealed a role of the basal-cortical system in attention, learning and memory. More recent advances in developing mouse gene technology offer newer models to systematically examine the underlying neuropathological cascade leading to dysfunctions in mnemonic processing. Using in vivo rodent models, several cholinergic enhancement strategies have been tested and proven to be effective in alleviating lesion-induced cognitive deficits, including neuropharmacological approaches (acetylcholinesterase inhibitors), neurotrophic factor administration (nerve growth factor), and transplantation of cholinergic-enriched fetal grafts. Successful results have also been obtained using ex vivo gene transfer to deliver nerve growth factor or acetylcholine to compromised regions of the basal-cortical system. Gene therapy may be of particular interest for clinical applications, because this approach provides a method for topographically restricted and selective delivery of therapeutic genes and their products to afflicted areas of the brain. Advanced techniques in molecular biology (e.g., exogenous regulatable gene transfer) and newly developed tools of modern neuroscience (e.g., neural precursor cells) will be important contributions for deciphering the biological bases of neuronal degeneration and for refining therapeutic strategies for Alzheimer's disease.

McTigue, D.M., Horner, P.J., Stokes, B.T., Gage, F.H. Neurotrophin-3 and brain-derived neurotrophic factor induce oligodendrocyte proliferation and myelination of regenerating axons in the contused adult rat spinal cord. (1998) Journal of Neuroscience. 18(14):5354-65.

+ expand abstract

Pfaff, S.L., Taylor, W.L. Xenopus TFIIIA gene transcription is dependent on cis-element positioning and chromatin structure. (1998) Molecular and Cellular Biology. 18(7):3811-8.

+ expand abstract

Kempermann, G., Brandon, E.P., Gage, F.H. Environmental stimulation of 129/SvJ mice causes increased cell proliferation and neurogenesis in the adult dentate gyrus. (1998) Current Biology. 8(16):939-42.

+ expand abstract

Dantzker, J.L., Callaway, E.M. The development of local, layer-specific visual cortical axons in the absence of extrinsic influences and intrinsic activity. (1998) Journal of Neuroscience. 18(11):4145-4154.

+ expand abstract

Dickinson-Anson, H., Aubert, I., Gage, F.H., Fisher, L.J. Hippocampal grafts of acetylcholine-producing cells are sufficient to improve behavioural performance following a unilateral fimbria-fornix lesion. (1998) Neuroscience. 84(3):771-81.

+ expand abstract

Bazhenov, M., Timofeev, I., Steriade, M., Sejnowski, T.J. Cellular and network models for intrathalamic augmenting responses during 10-Hz stimulation. (1998) Journal of Neurophysiology. 79(5):2730-48.

+ expand abstract

Kempermann, G., Kuhn, H.G., Gage, F.H. Experience-induced neurogenesis in the senescent dentate gyrus. (1998) Journal of Neuroscience. 18(9):3206-12.

+ expand abstract

Kempermann, G., Gage, F.H. Closer to neurogenesis in adult humans. (1998) Nature Medicine. 4(5):555-7.

Gray, M.S., Pouget, A., Zemel, R.S., Nowlan, S.J., Sejnowski, T.J. Reliable disparity estimation through selective integration. (1998) Visual Neuroscience. 15(3):511-28.

+ expand abstract

Senut, M.C., Suhr, S.T., Gage, F.H. Gene transfer to the rodent placenta in situ. A new strategy for delivering gene products to the fetus. (1998) Journal of Clinical Investigation. 101(8):1565-71. DOI: 10.1172/JCI1959

+ expand abstract

Moortgat, K.T., Keller, C.H., Bullock, T.H., Sejnowski, T.J. Submicrosecond pacemaker precision is behaviorally modulated: the gymnotiform electromotor pathway. (1998) Proceedings of the National Academy of Sciences of the United States of America. 95(8):4684-9.

+ expand abstract

Mulle, C., Sailer, A., Pérez-Otaño, I., Dickinson-Anson, H., Castillo, P.E., Bureau, I., Maron, C., Gage, F.H., Mann, J.R., Bettler, B., Heinemann, S.F. Altered synaptic physiology and reduced susceptibility to kainate-induced seizures in GluR6-deficient mice. (1998) Nature. 392(6676):601-5. DOI: 10.1038/33408

+ expand abstract

Gage, F.H. Cell therapy. (1998) Nature. 392(6679 Suppl):18-24.

+ expand abstract

Callaway, E.M. Visual scenes and cortical neurons: what you see is what you get. (1998) Proceedings of the National Academy of Sciences of the United States of America. 95(7):3344-3345.

Blömer, U., Kafri, T., Randolph-Moore, L., Verma, I.M., Gage, F.H. Bcl-xL protects adult septal cholinergic neurons from axotomized cell death. (1998) Proceedings of the National Academy of Sciences of the United States of America. 95(5):2603-8.

+ expand abstract

Pfaff, S., Kintner, C. Neuronal diversification: development of motor neuron subtypes. (1998) Current Opinion in Neurobiology. 8(1):27-36.

+ expand abstract

Zhang, K., Ginzburg, I., McNaughton, B.L., Sejnowski, T.J. Interpreting neuronal population activity by reconstruction: unified framework with application to hippocampal place cells. (1998) Journal of Neurophysiology. 79(2):1017-1044.

+ expand abstract

Physical variables such as the orientation of a line in the visual field or the location of the body in space are coded as activity levels in populations of neurons. Reconstruction or decoding is an inverse problem in which the physical variables are estimated from observed neural activity. Reconstruction is useful first in quantifying how much information about the physical variables is present in the population and, second, in providing insight into how the brain might use distributed representations in solving related computational problems such as visual object recognition and spatial navigation. Two classes of reconstruction methods, namely, probabilistic or Bayesian methods and basis function methods, are discussed. They include important existing methods as special cases, such as population vector coding, optimal linear estimation, and template matching. As a representative example for the reconstruction problem, different methods were applied to multi-electrode spike train data from hippocampal place cells in freely moving rats. The reconstruction accuracy of the trajectories of the rats was compared for the different methods. Bayesian methods were especially accurate when a continuity constraint was enforced, and the best errors were within a factor of two of the information-theoretic limit on how accurate any reconstruction can be and were comparable with the intrinsic experimental errors in position tracking. In addition, the reconstruction analysis uncovered some interesting aspects of place cell activity, such as the tendency for erratic jumps of the reconstructed trajectory when the animal stopped running. In general, the theoretical values of the minimal achievable reconstruction errors quantify how accurately a physical variable is encoded in the neuronal population in the sense of mean square error, regardless of the method used for reading out the information. One related result is that the theoretical accuracy is independent of the width of the Gaussian tuning function only in two dimensions. Finally, all the reconstruction methods considered in this paper can be implemented by a unified neural network architecture, which the brain feasibly could use to solve related problems.

Callaway, E.M. Prenatal development of layer-specific local circuits in primary visual cortex of the macaque monkey. (1998) Journal of Neuroscience. 18(4):1505-1527.

+ expand abstract

Previous studies have demonstrated that axonal arbors specific for the four main cortical layers - 2/3, 4, 5, and 6 - develop precisely from the outset using activity-independent cues. In macaque primary visual cortex (V1), layer 2/3 is subdivided into layers named 2/3A, 3B, 4A, and 4B, and layer 4 is subdivided into 4Calpha and 4Cbeta. Individual neurons in V1 of mature macaques have axonal arbors that are highly specific for these sublayers. We have studied the prenatal development of laminar and sublaminar specificity of local circuits in macaque V1. Two-hundred thirty-eight neurons were labeled intracellularly in living brain slices prepared from V1 of five prenatal macaque monkeys aged 100 to 145 d postconception (E100-E145). Axonal and dendritic arbors of labeled neurons were reconstructed to assess their relationships to the cortical layers. We find that developing spiny neurons in layers 2-4B and layer 5 specifically target superficial and deep layers without forming "incorrect" branches in layer 4C. Similarly, layer 6 pyramidal neurons that target layer 4C do not form "incorrect" branches in layer 5. These results indicate that specific projections to the main cortical layers develop with a high degree of selectivity, as in other species. However, the development of sublayer-specific projections was not always precise from the outset. Unlike postnatal animals, axons of some prenatal layer 4Cbeta spiny neurons branch in layer 4B. At similar ages, many pyramidal neurons in the upper half of layer 6 have axonal branches in layer 4Calpha as well as 4Cbeta; these projections are specific for 4Cbeta in more mature animals. Also, there is similar "exuberance" in axonal arbors of other layer 6 cell types. Transient projections were also observed in the subplate and to the white matter for cells from all layers, except 4Cbeta. These observations indicate that at least some sublayer-specific projections emerge by elimination of exuberant axonal branches and suggest that they may use activity-dependent mechanisms to identify "correct" target layers. Such cues could be provided by laminar differences in the patterns of spontaneous prenatal activity in the retino-geniculo-cortical network.

McKeown, M.J., Jung, T.P., Makeig, S., Brown, G., Kindermann, S.S., Lee, T.W., Sejnowski, T.J. Spatially independent activity patterns in functional MRI data during the stroop color-naming task. (1998) Proceedings of the National Academy of Sciences of the United States of America. 95(3):803-810.

+ expand abstract

Jurata, L.W., Pfaff, S.L., Gill, G.N. The nuclear LIM domain interactor NLI mediates homo- and heterodimerization of LIM domain transcription factors. (1998) Journal of Biological Chemistry. 273(6):3152-7.

+ expand abstract

Callaway, E.M. Local circuits in primary visual cortex of the macaque monkey. (1998) Annual Review of Neuroscience. 21:47-74. DOI: 10.1146/annurev.neuro.21.1.47

+ expand abstract

Zemel, R.S., Sejnowski, T.J. A model for encoding multiple object motions and self-motion in area MST of primate visual cortex. (1998) Journal of Neuroscience. 18(1):531-547.

+ expand abstract

Berns, G.S., Sejnowski, T.J. A computational model of how the basal ganglia produce sequences. (1998) Journal of Cognitive Neuroscience. 10(1):108-121.

+ expand abstract

Quartz, S.R., Sejnowski, T.J. The neural basis of cognitive development: a constructivist manifesto. (1997) Behavioral and Brain Sciences. 20(4):537-56; discussion 556-96.

+ expand abstract

Shihabuddin, L.S., Ray, J., Gage, F.H. FGF-2 is sufficient to isolate progenitors found in the adult mammalian spinal cord. (1997) Exp. Neurol. 148(2):577-86. DOI: 10.1006/exnr.1997.6697

+ expand abstract

Ridet, J.L., Malhotra, S.K., Privat, A., Gage, F.H. Reactive astrocytes: cellular and molecular cues to biological function. (1997) Trends in Neurosciences. 20(12):570-7.

+ expand abstract

Bell, A.J., Sejnowski, T.J. The "independent components" of natural scenes are edge filters. (1997) Vision Research. 37(23):3327-3338.

+ expand abstract

Burrill, J.D., Moran, L., Goulding, M.D., Saueressig, H. PAX2 is expressed in multiple spinal cord interneurons, including a population of EN1+ interneurons that require PAX6 for their development. (1997) Development. 124(22):4493-4503.

+ expand abstract

Kafri, T., Blömer, U., Peterson, D.A., Gage, F.H., Verma, I.M. Sustained expression of genes delivered directly into liver and muscle by lentiviral vectors. (1997) Nature Genetics. 17(3):314-7. DOI: 10.1038/ng1197-314

+ expand abstract

Pouget, A., Sejnowski, T.J. A new view of hemineglect based on the response properties of parietal neurones. (1997) Philos. Trans. R. Soc. Lond., B, Biol. Sci. 352(1360):1449-1459. DOI: 10.1098/rstb.1997.0131

+ expand abstract

Kempermann, G., Kuhn, H.G., Gage, F.H. Genetic influence on neurogenesis in the dentate gyrus of adult mice. (1997) Proceedings of the National Academy of Sciences of the United States of America. 94(19):10409-14.

+ expand abstract

Miyoshi, H., Takahashi, M., Gage, F.H., Verma, I.M. Stable and efficient gene transfer into the retina using an HIV-based lentiviral vector. (1997) Proceedings of the National Academy of Sciences of the United States of America. 94(19):10319-23.

+ expand abstract

Tang, A.C., Bartels, A.M., Sejnowski, T.J. Effects of cholinergic modulation on responses of neocortical neurons to fluctuating input. (1997) Cerebral Cortex . 7(6):502-509.

+ expand abstract

Blömer, U., Naldini, L., Kafri, T., Trono, D., Verma, I.M., Gage, F.H. Highly efficient and sustained gene transfer in adult neurons with a lentivirus vector. (1997) Journal of Virology. 71(9):6641-9.

+ expand abstract

McWhirter, J.R., Goulding, M., Weiner, J.A., Chun, J., Murre, C. A novel fibroblast growth factor gene expressed in the developing nervous system is a downstream target of the chimeric homeodomain oncoprotein E2A-Pbx1. (1997) Development. 124(17):3221-3232.

+ expand abstract

Makeig, S., Jung, T.P., Bell, A.J., Ghahremani, D., Sejnowski, T.J. Blind separation of auditory event-related brain responses into independent components. (1997) Proceedings of the National Academy of Sciences of the United States of America. 94(20):10979-10984.

+ expand abstract

Ritz, R., Sejnowski, T.J. Synchronous oscillatory activity in sensory systems: new vistas on mechanisms. (1997) Current Opinion in Neurobiology. 7(4):536-546.

+ expand abstract

Kuhn, H.G., Winkler, J., Kempermann, G., Thal, L.J., Gage, F.H. Epidermal growth factor and fibroblast growth factor-2 have different effects on neural progenitors in the adult rat brain. (1997) Journal of Neuroscience. 17(15):5820-9.

+ expand abstract

Peterson, D.A., Leppert, J.T., Lee, K.F., Gage, F.H. Basal forebrain neuronal loss in mice lacking neurotrophin receptor p75. (1997) Science. 277(5327):837-9.

Spitzer, N.C., Sejnowski, T.J. Biological information processing: bits of progress. (1997) Science. 277(5329):1060-1061.

Grill, R., Murai, K., Blesch, A., Gage, F.H., Tuszynski, M.H. Cellular delivery of neurotrophin-3 promotes corticospinal axonal growth and partial functional recovery after spinal cord injury. (1997) Journal of Neuroscience. 17(14):5560-72.

+ expand abstract

Schinstine, M., Ray, J., Gage, F.H. Potential effect of cytokines on transgene expression in primary fibroblasts implanted into the rat brain. (1997) Brain Res. Mol. Brain Res. 47(1-2):195-201.

+ expand abstract

Ray, J., Baird, A., Gage, F.H. A 10-amino acid sequence of fibroblast growth factor 2 is sufficient for its mitogenic activity on neural progenitor cells. (1997) Proceedings of the National Academy of Sciences of the United States of America. 94(13):7047-52.

+ expand abstract

Palmer, T.D., Takahashi, J., Gage, F.H. The adult rat hippocampus contains primordial neural stem cells. (1997) Molecular and Cellular Neurosciences. 8(6):389-404. DOI: 10.1006/mcne.1996.0595

+ expand abstract

Sah, D.W., Ray, J., Gage, F.H. Bipotent progenitor cell lines from the human CNS. (1997) Nature Biotechnology. 15(6):574-80. DOI: 10.1038/nbt0697-574

+ expand abstract

Tsodyks, M.V., Skaggs, W.E., Sejnowski, T.J., McNaughton, B.L. Paradoxical effects of external modulation of inhibitory interneurons. (1997) Journal of Neuroscience. 17(11):4382-4388.

+ expand abstract

Bang, A.G., Papalopulu, N., Kintner, C., Goulding, M.D. Expression of Pax-3 is initiated in the early neural plate by posteriorizing signals produced by the organizer and by posterior non-axial mesoderm. (1997) Development. 124(10):2075-85.

+ expand abstract

Kempermann, G., Kuhn, H.G., Gage, F.H. More hippocampal neurons in adult mice living in an enriched environment. (1997) Nature. 386(6624):493-5. DOI: 10.1038/386493a0

+ expand abstract

Murthy, V.N., Sejnowski, T.J., Stevens, C.F. Heterogeneous release properties of visualized individual hippocampal synapses. (1997) Neuron. 18(4):599-612.

+ expand abstract

Fagan, A.M., Suhr, S.T., Lucidi-Phillipi, C.A., Peterson, D.A., Holtzman, D.M., Gage, F.H. Endogenous FGF-2 is important for cholinergic sprouting in the denervated hippocampus. (1997) Journal of Neuroscience. 17(7):2499-511.

+ expand abstract

Maroto, M., Reshef, R., Münsterberg, A.E., Koester, S., Goulding, M., Lassar, A.B. Ectopic Pax-3 activates MyoD and Myf-5 expression in embryonic mesoderm and neural tissue. (1997) Cell. 89(1):139-148.

+ expand abstract

Raymon, H.K., Thode, S., Gage, F.H. Application of ex vivo gene therapy in the treatment of Parkinson's disease. (1997) Exp. Neurol. 144(1):82-91. DOI: 10.1006/exnr.1996.6392

+ expand abstract

Wiser, A.K., Callaway, E.M. Ocular dominance columns and local projections of layer 6 pyramidal neurons in macaque primary visual cortex. (1997) Developmental Biology. 14(2):241-251.

+ expand abstract

Pouget, A., Sejnowski, T.J. Spatial transformations in the parietal cortex using basis functions. (1997) Journal of Cognitive Neuroscience. 9(2):222-237. DOI: 10.1162/jocn.1997.9.2.222

+ expand abstract

Contreras, D., Destexhe, A., Sejnowski, T.J., Steriade, M. Spatiotemporal patterns of spindle oscillations in cortex and thalamus. (1997) Journal of Neuroscience. 17(3):1179-1196.

+ expand abstract

Spindle oscillations (7-14 Hz) appear in the thalamus and cortex during early stages of sleep. They are generated by the combination of intrinsic properties and connectivity patterns of thalamic neurons and distributed to cortical territories by thalamocortical axons. The corticothalamic feedback is a major factor in producing coherent spatiotemporal maps of spindle oscillations in widespread thalamic territories. Here we have investigated the spatiotemporal patterns of spontaneously occurring and evoked spindles by means of multisite field potential and unit recordings in intact cortex and decorticated animals. We show that (1) spontaneous spindle oscillations are synchronized over large cortical areas during natural sleep and barbiturate anesthesia; (2) under barbiturate anesthesia, the cortical coherence is not disrupted by transection of intracortical synaptic linkages; (3) in intact cortex animals, spontaneously occurring barbiturate spindle sequences occur nearly simultaneously over widespread thalamic territories; (4) in the absence of cortex, the spontaneous spindle oscillations throughout the thalamus are less organized, but the local coherence (within 2-4 mm) is still maintained; and (5) spindling propagation is observed in intact cortex animals only when elicited by low intensity cortical stimulation, applied shortly before the initiation of a spontaneous spindle sequence; propagation velocities are between 1 and 3 mm/sec, measured in the anteroposterior axis of the thalamus; increasing the intensity of cortical stimulation triggers spindle oscillations, which start simultaneously in all leads. We propose that, in vivo, the coherence of spontaneous spindle oscillations in corticothalamic networks is attributable to the combined action of continuous background corticothalamic input initiating spindle sequences in several thalamic sites at the same time and divergent corticothalamic and intrathalamic connectivity.

Sejnowski, T.J. The year of the dendrite. (1997) Science. 275(5297):178-179.

Jung, T.P., Makeig, S., Stensmo, M., Sejnowski, T.J. Estimating alertness from the EEG power spectrum. (1997) IEEE Trans Biomed Eng. 44(1):60-69. DOI: 10.1109/10.553713

+ expand abstract

Ahlgren, U., Pfaff, S.L., Jessell, T.M., Edlund, T., Edlund, H. Independent requirement for ISL1 in formation of pancreatic mesenchyme and islet cells. (1997) Nature. 385(6613):257-60. DOI: 10.1038/385257a0

+ expand abstract

Winkler, J., Ramirez, G.A., Kuhn, H.G., Peterson, D.A., Day-Lollini, P.A., Stewart, G.R., Tuszynski, M.H., Gage, F.H., Thal, L.J. Reversible Schwann cell hyperplasia and sprouting of sensory and sympathetic neurites after intraventricular administration of nerve growth factor. (1997) Annals of Neurology. 41(1):82-93. DOI: 10.1002/ana.410410114

+ expand abstract

Sah, D.W., Ray, J., Gage, F.H. Regulation of voltage- and ligand-gated currents in rat hippocampal progenitor cells in vitro. (1997) Journal of Neurobiology. 32(1):95-110.

+ expand abstract

Callaway, E.M., Lieber, J.L. Development of axonal arbors of layer 6 pyramidal neurons in ferret primary visual cortex. (1996) Journal of Comparative Neurology. 376(2):295-305. DOI: 10.1002/(SICI)1096-9861(19961209)376:2<295::AID

+ expand abstract

Senut, M.C., Suhr, S.T., Gage, F.H. Intracerebral xenografts: Sertoli cells to the rescue? (1996) Nature Biotechnology. 14(13):1650-1. DOI: 10.1038/nbt1296-1650

Contreras, D., Destexhe, A., Sejnowski, T.J., Steriade, M. Control of spatiotemporal coherence of a thalamic oscillation by corticothalamic feedback. (1996) Science. 274(5288):771-774.

+ expand abstract

Suhonen, J.O., Peterson, D.A., Ray, J., Gage, F.H. Differentiation of adult hippocampus-derived progenitors into olfactory neurons in vivo. (1996) Nature. 383(6601):624-7. DOI: 10.1038/383624a0

+ expand abstract

Naldini, L., Blömer, U., Gage, F.H., Trono, D., Verma, I.M. Efficient transfer, integration, and sustained long-term expression of the transgene in adult rat brains injected with a lentiviral vector. (1996) Proceedings of the National Academy of Sciences of the United States of America. 93(21):11382-8.

+ expand abstract

Lipkin, S.M., Grider, T.L., Heyman, R.A., Glass, C.K., Gage, F.H. Constitutive retinoid receptors expressed from adenovirus vectors that specifically activate chromosomal target genes required for differentiation of promyelocytic leukemia and teratocarcinoma cells. (1996) Journal of Virology. 70(10):7182-9.

+ expand abstract

Sufficient knowledge of transcription factor structure and function has accumulated to allow attempts at the rational design of novel transcription factors for the study of gene regulation and potential application in gene therapy. In the present studies, we have systematically evaluated the function of chimeric retinoid receptors generated by fusion with the transactivation domain of VP16 and expression in adenovirus vectors. By varying the location of fusion of the VP16 transactivation domain with the retinoic acid receptor (RAR) or retinoid X receptor (RXR), marked differences in the specificity of gene activation were obtained. Although several chimeric proteins activated both RAR and RXR target genes, fusion of the NT16 transactivation domain to the N terminus of RAR permitted specific activation of reporter genes containing retinoic acid response elements. In contrast, fusion of the VP16 transactivation domain to the C terminus of RXR permitted specific activation of reporter genes containing RXR response elements. When tested for their ability to activate chromosomal targets, the chimera consisting of VP16 linked to the N terminus of PAR was much more active in promoting the differentiation of HL-60 cells and NTera-2 cells than the chimera consisting of VP16 linked to the C terminus of RXR. These observations support the existence of two distinct retinoid signalling pathways predicted on the basis of biochemical and pharmacologic studies and provide direct evidence that the programs of differentiation elicited by retinoic acid in these cells are mediated by a specific subset of binding sites for RAR-RXR heterodimers. VP16-RAR and VP16-RXR fusion proteins should be of further use in dissecting the relative contributions of RARs and RXRs to specific programs of gene expression. Constitutive retinoid receptors may also be considered for use as novel tumor suppressor genes for genetically based treatment of retinoid-responsive cancers.

Choi, D.W., Gage, F.H. Disease, transplantation and regeneration. (1996) Current Opinion in Neurobiology. 6(5):635-7.

Varela-Echavarría, A., Pfaff, S.L., Guthrie, S. Differential expression of LIM homeobox genes among motor neuron subpopulations in the developing chick brain stem. (1996) Molecular and Cellular Neurosciences. 8(4):242-57. DOI: 10.1006/mcne.1996.0061

+ expand abstract

Callaway, E.M., Wiser, A.K. Contributions of individual layer 2-5 spiny neurons to local circuits in macaque primary visual cortex. (1996) Visual Neuroscience. 13(5):907-922.

+ expand abstract

Minger, S.L., Fisher, L.J., Ray, J., Gage, F.H. Long-term survival of transplanted basal forebrain cells following in vitro propagation with fibroblast growth factor-2. (1996) Exp. Neurol. 141(1):12-24. DOI: 10.1006/exnr.1996.0134

+ expand abstract

The intracerebral transplantation of freshly dissected fetal tissue containing cholinergic neurons of the developing basal forebrain has been reported to reverse lesion-induced or age-related cognitive deficits in animal models of cholinergic neuronal degeneration. Grafts of cultured fetal neurons, however, have generally shown poor cellular survival and limited therapeutic benefit. We tested the hypothesis that recent advances in the identification of growth factors that promote the survival and propagation of fetal precursor cells in vitro would improve the long-term survival of cultured neurons following intracerebral implantation. Dissociated cells from gestational Day 14 rodent basal forebrain were grown in chemically defined media supplemented with 20 ng/ml basic fibroblast growth factor. Two weeks postplating, numerous cells were present in the cultures and showed immunoreactive labeling for a variety of markers, including glutamic acid decarboxylase, neuron-specific enolase, neurofilament proteins, glial fibrillary acidic protein and, occasionally, choline acetyltransferase. To determine if cultured basal forebrain cells would survive intracerebral implantation, the cells were implanted homotypically into the nucleus basalis magnocellularis. To enhance the potential for graft survival in vivo, cells were also implanted into the nucleus basalis magnocellularis following an ibotenic acid lesion and into the denervated frontal cortex. Animals sacrificed between 2 weeks and 7 months following transplantation showed good and comparable graft survival in all sites. Immunocytochemical analysis revealed that representative populations of cells observed in vitro survived for prolonged periods in vivo, even in sites distal from their normal cellular targets. Thus, neuronal populations expanded in vitro can successfully survive and maintain cellular phenotypes post-transplantation. These results suggest a potential for isolating and growing specific neuronal populations in vitro for intracerebral transplantation.

Destexhe, A., Bal, T., McCormick, D.A., Sejnowski, T.J. Ionic mechanisms underlying synchronized oscillations and propagating waves in a model of ferret thalamic slices. (1996) Journal of Neurophysiology. 76(3):2049-2070.

+ expand abstract

1. A network model of thalamocortical (TC) and thalamic reticular (RE) neurons was developed based on electrophysiological measurements in ferret thalamic slices. Single-compartment TC and RE cells included voltage- and calcium-sensitive currents described by Hodgkin-Huxley type of kinetics. Synaptic currents were modeled by kinetic models of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), gamma-aminobutyric acid-A (GABAA) and GABAB receptors. 2. The model reproduced successfully the characteristics of spindle and slow bicuculline-induced oscillations observed in vitro. The characteristics of these two types of oscillations depended on both the intrinsic properties of TC and RE cells and their pattern of interconnectivity. 3. The oscillations were organized by the reciprocal recruitment between TC and RE cells, due to their manual connectivity and bursting properties. TC cells elicited AMPA-mediated excitatory postsynaptic potentials (EPSPs) in RE cells, whereas RE cells elicited a mixture of GABAA and GABAB inhibitory postsynaptic potentials (IPSPs) in TC cells. Because of the presence of a T current, sufficiently strong EPSPs could elicit a burst in RE cells, and TC cells could generate a rebound burst following GABAergic IPSPs. Under these conditions, interaction between the TC and RE cells produced sustained oscillations. 4. In the absence of spontaneous oscillation in any cell, the TC-RE network remained quiescent. Spindle oscillations with a frequency of 9-11 Hz could be initiated by stimulation of either TC or RE neurons. A few spontaneously oscillating TC neurons recruited the entire network model into a "waxing-and waning" oscillation. These "initiator" cells could be an extremely small proportion of TC cells. 5. In intracellular recordings, TC cells display a reduced ability for burst firing after a sequence of bursts. The "waning" phase of spindles was reproduced in the network model by assuming an activity-dependent upregulation of Ih operating via a calcium-binding protein in TC cells, as shown previously in a two-cell model. 6. Following the global suppression of GABAA inhibition, the disinhibited RE cells produced prolonged burst discharges that elicited strong GABAB-mediated currents in TC cells. The enhancement of slow IPSPs in TC cells was also due to cooperativity in the activation of GABAB-mediated current. These slow IPSPs recruited TC and RE cells into slower waxing-and-waning oscillations (3-4 HZ) that were even more highly synchronized. 7. Local axonal arborization of the TC to RE and RE to TC projections allowed oscillations to propagate through the network. An oscillation starting at a single focus induced a propagating wavefront as more cells were recruited progressively. The waning of the oscillation also propagated due to upregulation of Ih in TC cells, leading to waves of spindle activity as observed in experiments. 8. The spatiotemporal properties of propagating waves in the model were highly dependent on the intrinsic properties of TC cells. The spatial pattern of spiking activity was markedly different for spindles compared with bicuculline-induced oscillations and depended on the rebound burst behavior of TC cells. The upregulation of Ih produced a refractory period so that colliding spindle waves merged into a single oscillation and extinguished. Finally, reducing the Ih conductance led to sustained oscillations. 9. Two key properties of cells in the thalamic network may account for the initiation, propagation, and termination of spindle oscillations, the activity-dependent upregulation of Ih in TC cells, and the localized axonal projections between TC and RE cells. In addition, the model predicts that a nonlinear stimulus dependency of GABAB responses accounts for the genesis of prolonged synchronized discharges following block of GABAA receptors.

Nakajima, T., Fukamizu, A., Takahashi, J., Gage, F.H., Fisher, T., Blenis, J., Montminy, M.R. The signal-dependent coactivator CBP is a nuclear target for pp90RSK. (1996) Cell. 86(3):465-74.

+ expand abstract

Sejnowski, T.J. Synapses get smarter. (1996) Nature. 382(6594):759-760. DOI: 10.1038/382759a0

Prank, K., Kloppstech, M., Nowlan, S.J., Sejnowski, T.J., Brabant, G. Random Secretion of Growth Hormone in Humans. (1996) Phys. Rev. Lett. 77(9):1909-1911. DOI: 10.1103/PhysRevLett.77.1909

Mainen, Z.F., Sejnowski, T.J. Influence of dendritic structure on firing pattern in model neocortical neurons. (1996) Nature. 382(6589):363-366. DOI: 10.1038/382363a0

+ expand abstract

Chalmers, G.R., Peterson, D.A., Gage, F.H. Sprouting adult CNS cholinergic axons express NILE and associate with astrocytic surfaces expressing neural cell adhesion molecule. (1996) Journal of Comparative Neurology. 371(2):287-99. DOI: 10.1002/(SICI)1096-9861(19960722)371:2<287::AID

+ expand abstract

Nakahara, Y., Gage, F.H., Tuszynski, M.H. Grafts of fibroblasts genetically modified to secrete NGF, BDNF, NT-3, or basic FGF elicit differential responses in the adult spinal cord. (1996) Cell Transplantation. 5(2):191-204.

+ expand abstract

Prank, K., Kloppstech, M., Nowlan, S.J., Sejnowski, T.J., Brabant, G. Self-organized segmentation of time series: separating growth hormone secretion in acromegaly from normal controls. (1996) Biophysical Journal. 70(6):2540-2547. DOI: 10.1016/S0006-3495(96)79825-9

+ expand abstract

Tsodyks, M.V., Skaggs, W.E., Sejnowski, T.J., McNaughton, B.L. Population dynamics and theta rhythm phase precession of hippocampal place cell firing: a spiking neuron model. (1996) Hippocampus. 6(3):271-280. DOI: 10.1002/(SICI)1098-1063(1996)6:3<271::AID-HIPO5

+ expand abstract

Bell, A.J., Sejnowski, T.J. Learning the higher-order structure of a natural sound. (1996) Network. 7(2):261-267. DOI: 10.1088/0954-898X/7/2/005

+ expand abstract

Naldini, L., Blömer, U., Gallay, P., Ory, D., Mulligan, R., Gage, F.H., Verma, I.M., Trono, D. In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector. (1996) Science. 272(5259):263-7.

+ expand abstract

Sawatari, A., Callaway, E.M. Convergence of magno- and parvocellular pathways in layer 4B of macaque primary visual cortex. (1996) Nature. 380(6573):442-446. DOI: 10.1038/380442a0

+ expand abstract

Wiser, A.K., Callaway, E.M. Contributions of individual layer 6 pyramidal neurons to local circuitry in macaque primary visual cortex. (1996) Journal of Neuroscience. 16(8):2724-2739.

+ expand abstract

Tuszynski, M.H., Roberts, J., Senut, M.C., U, H.S., Gage, F.H. Gene therapy in the adult primate brain: intraparenchymal grafts of cells genetically modified to produce nerve growth factor prevent cholinergic neuronal degeneration. (1996) Gene Therapy. 3(4):305-14.

+ expand abstract

Kuhn, H.G., Dickinson-Anson, H., Gage, F.H. Neurogenesis in the dentate gyrus of the adult rat: age-related decrease of neuronal progenitor proliferation. (1996) Journal of Neuroscience. 16(6):2027-33.

+ expand abstract

Lucidi-Phillipi, C.A., Clary, D.O., Reichardt, L.F., Gage, F.H. TrkA activation is sufficient to rescue axotomized cholinergic neurons. (1996) Neuron. 16(3):653-63.

+ expand abstract

Daston, G., Lamar, E., Olivier, M., Goulding, M. Pax-3 is necessary for migration but not differentiation of limb muscle precursors in the mouse. (1996) Development. 122(3):1017-1027.

+ expand abstract

Tuszynski, M.H., Gage, F.H. Somatic gene therapy for nervous system disease. (1996) Ciba Foundation Symposium. 196:85-94; discussion 94-7.

+ expand abstract

Montague, P.R., Dayan, P., Sejnowski, T.J. A framework for mesencephalic dopamine systems based on predictive Hebbian learning. (1996) Journal of Neuroscience. 16(5):1936-1947.

+ expand abstract

Hoshimaru, M., Ray, J., Sah, D.W., Gage, F.H. Differentiation of the immortalized adult neuronal progenitor cell line HC2S2 into neurons by regulatable suppression of the v-myc oncogene. (1996) Proceedings of the National Academy of Sciences of the United States of America. 93(4):1518-23.

+ expand abstract

Bang, A.G., Goulding, M.D. Regulation of vertebrate neural cell fate by transcription factors. (1996) Current Opinion in Neurobiology. 6(1):25-32.

+ expand abstract

Peterson, D.A., Lucidi-Phillipi, C.A., Murphy, D.P., Ray, J., Gage, F.H. Fibroblast growth factor-2 protects entorhinal layer II glutamatergic neurons from axotomy-induced death. (1996) Journal of Neuroscience. 16(3):886-98.

+ expand abstract

Lytton, W.W., Destexhe, A., Sejnowski, T.J. Control of slow oscillations in the thalamocortical neuron: a computer model. (1996) Neuroscience. 70(3):673-684.

+ expand abstract

We investigated computer models of a single thalamocortical neuron to assess the interaction of intrinsic voltage-sensitive channels and cortical synaptic input in producing the range of oscillation frequencies observed in these cells in vivo. A morphologically detailed model with Hodgkin-Huxley-like ion channels demonstrated that intrinsic properties would be sufficient to readily produce 3 to 6 Hz oscillations. Hyperpolarization of the model cell reduced its oscillation frequency monotonically whether through current injection or modulation of a potassium conductance, simulating the response to a neuromodulatory input. We performed detailed analysis of highly reduced models to determine the mechanism of this frequency control. The interburst interval was controlled by two different mechanisms depending on whether or not the pacemaker current, IH, was present. In the absence of IH, depolarization during the interburst interval occurred at the same rate with different current injections. The voltage difference from the nadir to threshold for the low-threshold calcium current, IT, determined the interburst interval. In contrast, with IH present, the rate of depolarization depended on injected current. With the full model, simulated repetitive cortical synaptic input entrained oscillations up to approximately double the natural frequency. Cortical input readily produced phase resetting as well. Our findings suggest that neither ascending brainstem control altering underlying hyperpolarization, nor descending drive by repetitive cortical inputs, would alone be sufficient to produce the range of oscillation frequencies seen in thalamocortical neurons. Instead, intrinsic neuronal mechanisms would dominate for generating the delta range (0.5-4 Hz) oscillations seen during slow wave sleep, whereas synaptic interactions with cortex and the thalamic reticular nucleus would be required for faster oscillations in the frequency range of spindling (7-14 Hz).

Blömer, U., Naldini, L., Verma, I.M., Trono, D., Gage, F.H. Applications of gene therapy to the CNS. (1996) Human Molecular Genetics. 5 Spec No:1397-404.

+ expand abstract

Kilpatrick, T.J., Brown, A., Lai, C., Gassmann, M., Goulding, M., Lemke, G. Expression of the Tyro4/Mek4/Cek4 gene specifically marks a subset of embryonic motor neurons and their muscle targets. (1996) Molecular and Cellular Neurosciences. 7(1):62-74. DOI: 10.1006/mcne.1996.0005

+ expand abstract

Destexhe, A., Contreras, D., Steriade, M., Sejnowski, T.J., Huguenard, J.R. In vivo, in vitro, and computational analysis of dendritic calcium currents in thalamic reticular neurons. (1996) Journal of Neuroscience. 16(1):169-185.

+ expand abstract

Pfaff, S.L., Mendelsohn, M., Stewart, C.L., Edlund, T., Jessell, T.M. Requirement for LIM homeobox gene Isl1 in motor neuron generation reveals a motor neuron-dependent step in interneuron differentiation. (1996) Cell. 84(2):309-20.

+ expand abstract

Tuszynski, M.H., Gabriel, K., Gage, F.H., Suhr, S., Meyer, S., Rosetti, A. Nerve growth factor delivery by gene transfer induces differential outgrowth of sensory, motor, and noradrenergic neurites after adult spinal cord injury. (1996) Experimental Neurology. 137(1):157-73. DOI: 10.1006/exnr.1996.0016

+ expand abstract

Eagle, K.S., Chalmers, G.R., Clary, D.O., Gage, F.H. Axonal regeneration and limited functional recovery following hippocampal deafferentation. (1995) Journal of Comparative Neurology. 363(3):377-88. DOI: 10.1002/cne.903630304

+ expand abstract

Gage, F.H., Coates, P.W., Palmer, T.D., Kuhn, H.G., Fisher, L.J., Suhonen, J.O., Peterson, D.A., Suhr, S.T., Ray, J. Survival and differentiation of adult neuronal progenitor cells transplanted to the adult brain. (1995) Proceedings of the National Academy of Sciences of the United States of America. 92(25):11879-83.

+ expand abstract

Mainen, Z.F., Joerges, J., Huguenard, J.R., Sejnowski, T.J. A model of spike initiation in neocortical pyramidal neurons. (1995) Neuron. 15(6):1427-1439.

+ expand abstract

Ray, J., Raymon, H.K., Gage, F.H. Generation and culturing of precursor cells and neuroblasts from embryonic and adult central nervous system. (1995) Methods in Enzymology. 254:20-37.

Gray, M.S., Lawrence, D.T., Golomb, B.A., Sejnowski, T.J. A perceptron reveals the face of sex. (1995) Neural Computation. 7(6):1160-1164.

Bell, A.J., Sejnowski, T.J. An information-maximization approach to blind separation and blind deconvolution. (1995) Neural Computation. 7(6):1129-1159.

+ expand abstract

Destexhe, A., Sejnowski, T.J. G protein activation kinetics and spillover of gamma-aminobutyric acid may account for differences between inhibitory responses in the hippocampus and thalamus. (1995) Proceedings of the National Academy of Sciences of the United States of America. 92(21):9515-9519.

+ expand abstract

Palmer, T.D., Ray, J., Gage, F.H. FGF-2-responsive neuronal progenitors reside in proliferative and quiescent regions of the adult rodent brain. (1995) Molecular and Cellular Neurosciences. 6(5):474-86. DOI: 10.1006/mcne.1995.1035

+ expand abstract

Aubert, I., Ridet, J.L., Gage, F.H. Regeneration in the adult mammalian CNS: guided by development. (1995) Current Opinion in Neurobiology. 5(5):625-35.

+ expand abstract

Montague, P.R., Dayan, P., Person, C., Sejnowski, T.J. Bee foraging in uncertain environments using predictive hebbian learning. (1995) Nature. 377(6551):725-728. DOI: 10.1038/377725a0

+ expand abstract

Senut, M.C., Tuszynski, M.H., Raymon, H.K., Suhr, S.T., Liou, N.H., Jones, K.R., Reichardt, L.F., Gage, F.H. Regional differences in responsiveness of adult CNS axons to grafts of cells expressing human neurotrophin 3. (1995) Experimental Neurology. 135(1):36-55. DOI: 10.1006/exnr.1995.1064

+ expand abstract

Chen, K.S., Masliah, E., Mallory, M., Gage, F.H. Synaptic loss in cognitively impaired aged rats is ameliorated by chronic human nerve growth factor infusion. (1995) Neuroscience. 68(1):19-27.

+ expand abstract

Sejnowski, T.J. Neural networks. Sleep and memory. (1995) Current Biology. 5(8):832-834.

+ expand abstract

Fisher, L.J., Gage, F.H. Novel therapeutic directions for Parkinson's disease. (1995) Mol Med Today. 1(4):181-7.

+ expand abstract

Sejnowski, T.J. Pattern recognition. Time for a new neural code? (1995) Nature. 376(6535):21-22. DOI: 10.1038/376021a0

Mainen, Z.F., Sejnowski, T.J. Reliability of spike timing in neocortical neurons. (1995) Science. 268(5216):1503-1506.

+ expand abstract

Prank, K., Nowlan, S.J., Harms, H.M., Kloppstech, M., Brabant, G., Hesch, R.D., Sejnowski, T.J. Time series prediction of plasma hormone concentration. Evidence for differences in predictability of parathyroid hormone secretion between osteoporotic patients and normal controls. (1995) Journal of Clinical Investigation. 95(6):2910-2919. DOI: 10.1172/JCI117998

+ expand abstract

Winkler, J., Suhr, S.T., Gage, F.H., Thal, L.J., Fisher, L.J. Essential role of neocortical acetylcholine in spatial memory. (1995) Nature. 375(6531):484-7. DOI: 10.1038/375484a0

+ expand abstract

Tuszynski, M.H., Gage, F.H. Maintaining the neuronal phenotype after injury in the adult CNS. Neurotrophic factors, axonal growth substrates, and gene therapy. (1995) Molecular Neurobiology. 10(2-3):151-67. DOI: 10.1007/BF02740673

+ expand abstract

Gage, F.H., Ray, J., Fisher, L.J. Isolation, characterization, and use of stem cells from the CNS. (1995) Annual Review of Neuroscience. 18:159-92. DOI: 10.1146/annurev.ne.18.030195.001111

+ expand abstract

The nervous system of adult mammals, unlike the rest of the organs in the body, has been considered unique in its apparent inability to replace neurons following injury. However, in certain regions of the brain, neurogenesis occurs postnatally and continues through adulthood. The nature, fate, and longevity of cells undergoing proliferation within the CNS are unknown. These cells are increasingly becoming the focus of intense scrutiny; this is a recent development that has led to considerable controversy over the appropriate terminology to describe neural cells as they pass through different stages of proliferation, migration, and differentiation. Continuing studies detailing the properties of mitotic populations in the adult CNS will provide a better understanding of the nature of these cells during their development and should lead to a more consistent nomenclature. Studies of neural precursors isolated from the embryonic brain have indicated that many subgroups of cells undergo mitosis and subsequent differentiation into neurons and glia in vitro. A number of substances, such as growth factors and substrate molecules, are essential for these processes and also for lineage restriction and fate determination of these cells. Recent studies have shown that cells with proliferative capabilities can also be isolated from the adult brain. The nature of these cells is unknown, but there is evidence that both multipotent cells (stem cells) and lineage-restricted cells (neuroblasts or glioblasts) are resident within the mature CNS and that they can be maintained and induced to divide and differentiate in response to many of the same factors that influence their embryonic counterparts. Presently, it is unclear how many potentially quiescent precursor cells exist in the adult brain or what combination of growth factors and substrate molecules is involved in the proliferation and differentiation of these cells. Some of these questions are currently being addressed by using immortalized neural precursors or growth factor-expanded populations of primary precursors to model precursor responsiveness to environmental manipulations. Because in vitro culture conditions are unlikely to provide all of the factors necessary for inducing the proliferation and differentiation of neural precursors, recent studies have explored the properties of well-characterized precursor populations after implantation back into specific regions of the developing or adult CNS. These studies have highlighted the importance of the microenvironment in precursor differentiation and further suggested that precursor plasticity is a characteristic that is probably common to neural precursors throughout the CNS.(ABSTRACT TRUNCATED AT 400 WORDS)

du Lac, S., Raymond, J.L., Sejnowski, T.J., Lisberger, S.G. Learning and memory in the vestibulo-ocular reflex. (1995) Annual Review of Neuroscience. 18:409-441. DOI: 10.1146/annurev.ne.18.030195.002205

Jester, J.M., Campbell, L.W., Sejnowski, T.J. Associative EPSP--spike potentiation induced by pairing orthodromic and antidromic stimulation in rat hippocampal slices. (1995) Journal of Physiology. 484 ( Pt 3:689-705.

+ expand abstract

Tuszynski, M.H., Gage, F.H. Bridging grafts and transient nerve growth factor infusions promote long-term central nervous system neuronal rescue and partial functional recovery. (1995) Proceedings of the National Academy of Sciences of the United States of America. 92(10):4621-5.

+ expand abstract

Chalmers, G.R., Fisher, L.J., Niijima, K., Patterson, P.H., Gage, F.H. Adrenal chromaffin cells transdifferentiate in response to basic fibroblast growth factor and show directed outgrowth to a nerve growth factor source in vivo. (1995) Exp. Neurol. 133(1):32-42. DOI: 10.1006/exnr.1995.1005

+ expand abstract

Chromaffin cells exposed to basic fibroblast growth factor (bFGF) in vitro express characteristics of sympathetic neurons, extend neurites, and become dependent on nerve growth factor (NGF) for survival. We explored whether the growth factor responsiveness of chromaffin cells could be exploited to enhance the transdifferentiation, neurite outgrowth and functional efficacy of chromaffin cells implanted into rats with unilateral 6-hydroxydopamine lesions. Cografts of neonatal chromaffin cells and fibroblasts genetically modified to produce bFGF were placed into the dopamine-depleted striatum of adult rats. Either control-transfected or NGF-producing fibroblasts were then transplanted 1 mm distal to the cograft. Chromaffin cells transdifferentiated under the influence of bFGF, as indicated by the growth of neurites and the expression of neuron-specific proteins. Distal grafts of NGF-producing fibroblasts successfully induced chromaffin neurites to traverse through the host parenchyma to the NGF source. In the absence of NGF fibroblast grafts, neither neurite extension nor good, long-term survival of the chromaffin-derived neurons was observed. Assessments of apomorphine-induced rotational behavior 2- and 4-weeks postgrafting revealed no behavior improvements in any of the groups. These results indicate that localized sources of growth factors are effective in inducing the transdifferentiation of grafted chromaffin cells as well as the extension of chromaffin-derived neurites into the host parenchyma. Such chromaffin cell-derived neurons are, however, functionally ineffective in this rat model of Parkinson's disease. Whether the lack of behavioral improvement reflected the tropic growth of neurites to an inappropriate striatal region or the noradrenergic nature of the chromaffin cell-derived neurons remains to be clarified. Nonetheless, these results caution that promoting transdifferentiation and neurite extension from engrafted chromaffin cells may not be sufficient to achieve desired functional effects of such grafts.

Lucidi-Phillipi, C.A., Gage, F.H., Shults, C.W., Jones, K.R., Reichardt, L.F., Kang, U.J. Brain-derived neurotrophic factor-transduced fibroblasts: production of BDNF and effects of grafting to the adult rat brain. (1995) Journal of Comparative Neurology. 354(3):361-76. DOI: 10.1002/cne.903540306

+ expand abstract

Chen, K.S., Gage, F.H. Somatic gene transfer of NGF to the aged brain: behavioral and morphological amelioration. (1995) Journal of Neuroscience. 15(4):2819-25.

+ expand abstract

Fisher, L.J., Gage, F.H. Radical directions in Parkinson's disease. (1995) Nature Medicine. 1(3):201-3.

Nowlan, S.J., Sejnowski, T.J. A selection model for motion processing in area MT of primates. (1995) Journal of Neuroscience. 15(2):1195-1214.

+ expand abstract

Niijima, K., Chalmers, G.R., Peterson, D.A., Fisher, L.J., Patterson, P.H., Gage, F.H. Enhanced survival and neuronal differentiation of adrenal chromaffin cells cografted into the striatum with NGF-producing fibroblasts. (1995) Journal of Neuroscience. 15(2):1180-94.

+ expand abstract

Ray, J., Hogg, J., Beutler, A.S., Takayama, H., Baird, A., Gage, F.H. Expression of biologically active basic fibroblast growth factor by genetically modified rat primary skin fibroblasts. (1995) Journal of Neurochemistry. 64(2):503-13.

+ expand abstract

Beutler, A.S., Banck, M.S., Bach, F.W., Gage, F.H., Porreca, F., Bilsky, E.J., Yaksh, T.L. Retrovirus-mediated expression of an artificial beta-endorphin precursor in primary fibroblasts. (1995) J. Neurochem. 64(2):475-81.

+ expand abstract

Takayama, H., Ray, J., Raymon, H.K., Baird, A., Hogg, J., Fisher, L.J., Gage, F.H. Basic fibroblast growth factor increases dopaminergic graft survival and function in a rat model of Parkinson's disease. (1995) Nature Medicine. 1(1):53-8.

+ expand abstract

Tsuchida, T., Ensini, M., Morton, S.B., Baldassare, M., Edlund, T., Jessell, T.M., Pfaff, S.L. Topographic organization of embryonic motor neurons defined by expression of LIM homeobox genes. (1994) Cell. 79(6):957-70.

+ expand abstract

Gonzalez, A.M., Carman, L.S., Ong, M., Ray, J., Gage, F.H., Shults, C.W., Baird, A. Storage, metabolism, and processing of 125I-fibroblast growth factor-2 after intracerebral injection. (1994) Brain Research. 665(2):285-92.

+ expand abstract

Callaway, E.M. Caged neurotransmitters. Shedding light on neural circuits. (1994) Current Biology. 4(11):1010-1012.

+ expand abstract

Peterson, D.A., Lucidi-Phillipi, C.A., Eagle, K.L., Gage, F.H. Perforant path damage results in progressive neuronal death and somal atrophy in layer II of entorhinal cortex and functional impairment with increasing postdamage age. (1994) Journal of Neuroscience. 14(11 Pt 2):6872-85.

+ expand abstract

Destexhe, A., Contreras, D., Sejnowski, T.J., Steriade, M. Modeling the control of reticular thalamic oscillations by neuromodulators. (1994) Neuroreport. 5(17):2217-2220.

+ expand abstract

Choi, D., Gage, F.H. Disease, transplantation and regeneration. (1994) Current Opinion in Neurobiology. 4(5):693-5.

Tuszynski, M.H., Gage, F.H. Neurotrophic factors and diseases of the nervous system. (1994) Annals of Neurology. 35 Suppl:S9-12.

+ expand abstract

Destexhe, A., Mainen, Z.F., Sejnowski, T.J. Synthesis of models for excitable membranes, synaptic transmission and neuromodulation using a common kinetic formalism. (1994) Journal of Computational Neuroscience. 1(3):195-230.

+ expand abstract

Destexhe, A., Contreras, D., Sejnowski, T.J., Steriade, M. A model of spindle rhythmicity in the isolated thalamic reticular nucleus. (1994) Journal of Neurophysiology. 72(2):803-818.

+ expand abstract

1. The oscillatory properties of the isolated reticular (RE) thalamus were modeled with the use of compartmental models of RE cells. Hodgkin-Huxley type kinetic models of ionic channels were derived from voltage- and current-clamp data from RE cells. Interactions between interconnected RE cells were simulated with the use of a kinetic model of gamma-aminobutyric acid (GABA) inhibitory synapses. 2. The intrinsic bursting properties of RE cells in the model were due to the presence of a low-threshold Ca2+ current and two Ca(2+)-activated currents. The properties of these model RE cells were compared with RE neurons recorded intracellularly in vivo in cats. 3. Model RE cells densely interconnected with GABAA synapses produced synchronous oscillations at a frequency close to that of spindles (7-14 Hz). Networks of RE neurons organized in a two-dimensional array with only proximal connectivity also exhibited synchronized oscillations in the spindle range. In addition, the proximally connected network showed periods of high and low synchronicity, giving rise to waxing and waning oscillations in the population of RE cells. 4. The spatiotemporal behavior of the network was investigated during waxing and waning oscillations. The waxing and waning emerged as an alternation between periods of desynchronized and synchronized activity, corresponding to periods of irregular and coherent spatial activity. During synchronized periods, the network displayed propagating coherent waves of synchronous activity that had a tendency to form spirals. 5. Networks of model RE neurons fully connected through GABAB synapses exhibited perfectly synchronous oscillations at lower frequencies (0.5-1 Hz), but two-dimensional networks with proximal GABAB connectivity failed to synchronize. 6. These simulations demonstrate that networks of model neurons that include the main intrinsic currents found in RE cells can generate waxing and waning oscillatory activity similar to the spindle rhythmicity observed in the isolated RE nucleus in vivo. The model reveals the interplay between the intrinsic rhythmic properties of RE cells and the fast synaptic interactions in organizing synchronized rhythmicity.

Ray, J., Gage, F.H. Spinal cord neuroblasts proliferate in response to basic fibroblast growth factor. (1994) Journal of Neuroscience. 14(6):3548-64.

+ expand abstract

Trophic factors may function as one of the epigenic signals responsible for the proliferation, growth, migration, and differentiation of neurons and glia during embryogenesis. The present study reports that basic fibroblast growth factor (bFGF) at high concentrations (10-100 ng/ml) is a mitogen for embryonic spinal cord cells that have already committed to a neuronal pathway and are expressing neuronal phenotypes (neuroblasts). Neuroblasts proliferate with a doubling time of 2.5 d. To characterize the nature of cells proliferating in response to bFGF, we have established long-term cultures of neuroblasts that can be passaged, freeze thawed, and recultured. In cultures the proportion of astrocytes remained the same, indicating limited survival and proliferation of these cells in response to bFGF. These results indicate that bFGF has mitogenic effects preferably on neuroblasts. The morphological and biochemical characterizations of the neuronal populations present in the long-term neuroblast cultures are presented here. The presence of cholinergic and GABAergic neurons in the cultures was established by immunocytochemical analysis. The cultures contain a small number of motoneurons as judged by their immunostaining with ChAT, low-affinity NGF receptor (LNGFR), and large size. Among all other growth factors tested for their mitogenic effects on embryonic spinal cord cells in culture, only epidermal growth factor (EGF) showed such effects, but to a lesser degree. The proliferative nature of neuroblasts has made it possible to transduce the Escherichia coli beta-galactosidase (LacZ) gene stably into these cells in vitro using a retroviral vector. The transfected cells expressing the foreign gene can be passaged, freeze thawed, and recultured without the loss of transgenes. The ability to transduce foreign genes stably into these cells permits implantation of these cells in the spinal cord to study cellular and biochemical behaviors and gene expression in defined neuronal populations in in vivo environments.

Gage, F.H. Neuronal stem cells: their characterization and utilization. (1994) Neurobiology of Aging. 15 Suppl 2:S191.

Bush, P.C., Sejnowski, T.J. Effects of inhibition and dendritic saturation in simulated neocortical pyramidal cells. (1994) Journal of Neurophysiology. 71(6):2183-2193.

+ expand abstract

1. We have used compartmental models of reconstructed pyramidal neurons from layers 2 and 5 of cat visual cortex to investigate the nonlinear summation of excitatory synaptic input and the effectiveness of inhibitory input in countering this excitation. 2. In simulations that match the conditions of a recent experiment, dendritic saturation was significant for physiological levels of synaptic activation: a compound excitatory postsynaptic potential (EPSP) electrically evoked during a depolarization caused by physiological synaptic activation was decreased by up to 80% compared with an EPSP evoked at rest. 3. Synaptic inhibition must be coactivated with excitation to quantitatively match the experimental results. The experimentally observed coactivation of inhibition with excitation produced additional current shunts that amplified the decrease in test EPSP amplitude. About 30% of the experimentally observed decrease in EPSP amplitude was caused by decreases in input resistance (Rin) due to synaptic conductance changes; a reduced driving force accounted for the remaining decrease. 4. The amount of inhibition was then increased by nearly an order of magnitude, to approximately 10% of the total number of inhibitory synapses on a typical cortical pyramidal cell. The sustained firing of this many inhibitory inputs was sufficient to completely suppress the firing of a neuron receiving strong excitatory input. However, this level of inhibition produced a very large reduction in Rin. Such large reductions in Rin have not been observed experimentally, suggesting that inhibition in cortex does not act to veto (shunt) strong, sustained excitatory input (of order 100 ms). 5. We propose instead that strong, transient activation (< 10 ms) of a neuron's inhibitory inputs, sufficient to briefly prevent firing, is used to shape the temporal structure of the cell's output spike train. Specifically, cortical inhibition may serve to synchronize the firing of groups of pyramidal cells during optimal stimulation.

Pouget, A., Sejnowski, T.J. A neural model of the cortical representation of egocentric distance. (1994) Cerebral Cortex. 4(3):314-329.

+ expand abstract

Barba, D., Hardin, J., Sadelain, M., Gage, F.H. Development of anti-tumor immunity following thymidine kinase-mediated killing of experimental brain tumors. (1994) Proceedings of the National Academy of Sciences of the United States of America. 91(10):4348-52.

+ expand abstract

Fisher, L.J., Gage, F.H. Intracerebral transplantation: basic and clinical applications to the neostriatum. (1994) FASEB Journal. 8(8):489-96.

+ expand abstract

Dekker, A.J., Winkler, J., Ray, J., Thal, L.J., Gage, F.H. Grafting of nerve growth factor-producing fibroblasts reduces behavioral deficits in rats with lesions of the nucleus basalis magnocellularis. (1994) Neuroscience. 60(2):299-309.

+ expand abstract

Rats received bilateral lesions of the nucleus basalis magnocellularis by infusion of biotenic acid. Two weeks after the lesion, a suspension of genetically modified primary rat fibroblasts was grafted dorsal to the nucleus basalis magnocellularis (2 x 10(5) cells per side). The fibroblasts were either infected with the gene for human beta-nerve growth factor or Escherichia coli beta-galactosidase. The nerve growth factor-producing fibroblasts released 67 ng nerve growth factor/10(5) cells per day in vitro. Two weeks after implantation of the fibroblasts, spatial learning was tested in the Morris water-maze. Nerve growth factor-producing fibroblasts, but not beta-galactosidase-producing fibroblasts ameliorated the deficit in acquisition of the water-maze task. In addition, spatial acuity was improved to near-normal levels by the nerve growth factor-producing grafts. Choline acetyltransferase activity in cortical areas and hippocampus was not affected by the nerve growth factor-producing grafts. Both grafted groups showed a similar reduction in the level of dopamine, but not homovanillic acid or 3-methoxytyramine, in the frontal cortex. Levels of norepinephrine, epinephrine and serotonin and their metabolites in the neocortex and hippocampus were not affected by the lesion or the grafts. Nerve growth factor-producing grafts increased the size of remaining nerve growth factor-receptor (p75) immunoreactive neurons in the nucleus basalis magnocellularis by 25%. Nucleus basalis magnocellularis lesions reduced the integrated optic density of choline acetyltransferase-positive fiber staining in the ventral neocortex by 46%, but nerve growth factor-producing grafts restored this area to 86% of control. These data suggest that nerve growth factor-producing grafts can cause a marked behavioral improvement, probably through the partial restoration of the lesioned projection from nucleus basalis magnocellularis to neocortex.

Montague, P.R., Sejnowski, T.J. The predictive brain: temporal coincidence and temporal order in synaptic learning mechanisms. (1994) Learning & Memory. 1(1):1-33.

+ expand abstract

Goulding, M., Lumsden, A., Paquette, A.J. Regulation of Pax-3 expression in the dermomyotome and its role in muscle development. (1994) Development. 120(4):957-971.

+ expand abstract

Chalepakis, G., Goulding, M., Read, A., Strachan, T., Gruss, P. Molecular basis of splotch and Waardenburg Pax-3 mutations. (1994) Proceedings of the National Academy of Sciences of the United States of America. 91(9):3685-3689.

+ expand abstract

Beeson, J.G., Shelton, E.R., Chan, H.W., Gage, F.H. Differential distribution of amyloid protein precursor immunoreactivity in the rat brain studied by using five different antibodies. (1994) Journal of Comparative Neurology. 342(1):78-96. DOI: 10.1002/cne.903420109

+ expand abstract

Beeson, J.G., Shelton, E.R., Chan, H.W., Gage, F.H. Age and damage induced changes in amyloid protein precursor immunohistochemistry in the rat brain. (1994) Journal of Comparative Neurology. 342(1):69-77. DOI: 10.1002/cne.903420108

+ expand abstract

Dekker, A.J., Fagan, A.M., Gage, F.H., Thal, L.J. Effects of brain-derived neurotrophic factor and nerve growth factor on remaining neurons in the lesioned nucleus basalis magnocellularis. (1994) Brain Research. 639(1):149-55.

+ expand abstract

Tuszynski, M.H., Peterson, D.A., Ray, J., Baird, A., Nakahara, Y., Gage, F.H. Fibroblasts genetically modified to produce nerve growth factor induce robust neuritic ingrowth after grafting to the spinal cord. (1994) Experimental Neurology. 126(1):1-14.

+ expand abstract

Fagan, A.M., Gage, F.H. Mechanisms of sprouting in the adult central nervous system: cellular responses in areas of terminal degeneration and reinnervation in the rat hippocampus. (1994) Neuroscience. 58(4):705-25.

+ expand abstract

Neurons of the adult mammalian central nervous system are limited in their ability to regenerate in response to injury. In certain circumstances, however, such neurons can exhibit morphological plasticity (e.g. sprouting). Unilateral transection of the perforant path in the adult rat induces terminal degeneration of entorhinal axons within the molecular layer of the ipsilateral hippocampal dentate gyrus. Cholinergic (and other) afferents subsequently sprout within the denervated zone. We show that despite the breach in the blood-brain barrier at the site of the aspirative lesion, the barrier remains intact in the areas of terminal degeneration (and reinnervation), and peripheral monocytic macrophages do not infiltrate this area to participate in the degenerative and/or regenerative events. Perforant path transection does not induce expression of major histocompatibility antigens on reactive cells within the denervated zone, nor are T lymphocytes recruited to this area. T lymphocyte-deficient Nude rats exhibit normal cholinergic sprouting. Perforant path transection does induce rapid and robust proliferation of microglia, and astrocytes to a lesser extent, in areas undergoing terminal degeneration. Histological evaluation after antimitotic administration shows that this glial proliferation is not required for the subsequent neuronal sprouting events. These results show that the reparative process in this model system involves interactions between cells endogenous to the brain in a non-immune context. Knowledge of these cellular responses provides a framework from which to further investigate putative molecular signals involved in initiating the neuronal sprouting events. Discovering the cellular and molecular interactions taking place under sprouting conditions is likely to be critical for understanding the mechanisms of reactive neuronal growth and, furthermore, may provide insights as to why regeneration is so limited in the central nervous system.

Goulding, M., Paquette, A. Pax genes and neural tube defects in the mouse. (1994) Ciba Found. Symp. 181:103-113; discussion 113-117.

+ expand abstract

Holtzman, D.M., Li, Y., Chen, K., Gage, F.H., Epstein, C.J., Mobley, W.C. Nerve growth factor reverses neuronal atrophy in a Down syndrome model of age-related neurodegeneration. (1993) Neurology. 43(12):2668-73.

+ expand abstract

Kang, U.J., Fisher, L.J., Joh, T.H., O'Malley, K.L., Gage, F.H. Regulation of dopamine production by genetically modified primary fibroblasts. (1993) Journal of Neuroscience. 13(12):5203-11.

+ expand abstract

Destexhe, A., McCormick, D.A., Sejnowski, T.J. A model for 8-10 Hz spindling in interconnected thalamic relay and reticularis neurons. (1993) Biophysical Journal. 65(6):2473-2477. DOI: 10.1016/S0006-3495(93)81297-9

+ expand abstract

Barba, D., Hardin, J., Ray, J., Gage, F.H. Thymidine kinase-mediated killing of rat brain tumors. (1993) Journal of Neurosurgery. 79(5):729-35. DOI: 10.3171/jns.1993.79.5.0729

+ expand abstract

Gene therapy has many potential applications in central nervous system (CNS) disorders, including the selective killing of tumor cells in the brain. A rat brain tumor model was used to test the herpes simplex virus (HSV)-thymidine kinase (TK) gene for its ability to selectively kill C6 and 9L tumor cells in the brain following systemic administration of the nucleoside analog ganciclovir. The HSV-TK gene was introduced in vitro into tumor cells (C6-TK and 9L-TK), then these modified tumor cells were evaluated for their sensitivity to cell killing by ganciclovir. In a dose-response assay, both C6-TK and 9L-TK cells were 100 times more sensitive to killing by ganciclovir (median lethal dose: C6-TK, 0.1 microgram ganciclovir/ml; C6, 5.0 micrograms ganciclovir/ml) than unmodified wild-type tumor cells or cultured fibroblasts. In vivo studies confirmed the ability of intraperitoneal ganciclovir administration to kill established brain tumors in rats as quantified by both stereological assessment of brain tumor volumes and studies of animal survival over 90 days. Rats with brain tumors established by intracerebral injection of wild-type or HSV-TK modified tumor cells or by a combination of wild-type and HSV-TK-modified cells were studied with and without ganciclovir treatments. Stereological methods determined that ganciclovir treatment eliminated tumors composed of HSV-TK-modified cells while control tumors grew as expected (p < 0.001). In survival studies, all 10 rats with 9L-TK tumors treated with ganciclovir survived 90 days while all untreated rats died within 25 days. Curiously, tumors composed of combinations of 9L and 9L-TK cells could be eliminated by ganciclovir treatments even when only one-half of the tumor cells carried the HSV-TK gene. While not completely understood, this additional tumor cell killing appears to be both tumor selective and local in nature. It is concluded that HSV-TK gene therapy with ganciclovir treatment does selectively kill tumor cells in the brain and has many potential applications in CNS disorders, including the treatment of cancer.

Suhr, S.T., Gage, F.H. Gene therapy for neurologic disease. (1993) Archives of Neurology. 50(11):1252-68.

+ expand abstract

Fisher, L.J., Schinstine, M., Salvaterra, P., Dekker, A.J., Thal, L., Gage, F.H. In vivo production and release of acetylcholine from primary fibroblasts genetically modified to express choline acetyltransferase. (1993) Journal of Neurochemistry. 61(4):1323-32.

+ expand abstract

Steriade, M., McCormick, D.A., Sejnowski, T.J. Thalamocortical oscillations in the sleeping and aroused brain. (1993) Science. 262(5134):679-685.

+ expand abstract

Destexhe, A., Babloyantz, A., Sejnowski, T.J. Ionic mechanisms for intrinsic slow oscillations in thalamic relay neurons. (1993) Biophysical Journal. 65(4):1538-1552. DOI: 10.1016/S0006-3495(93)81190-1

+ expand abstract

Berns, G.S., Dayan, P., Sejnowski, T.J. A correlational model for the development of disparity selectivity in visual cortex that depends on prenatal and postnatal phases. (1993) Proceedings of the National Academy of Sciences of the United States of America. 90(17):8277-8781.

+ expand abstract

Fisher, L.J., Raymon, H.K., Gage, F.H. Cells engineered to produce acetylcholine: therapeutic potential for Alzheimer's disease. (1993) Annals of the New York Academy of Sciences. 695:278-84.

+ expand abstract

Alzheimer's disease (AD) is a debilitating disorder of the central nervous system which may affect up to 50% of the population over the age of 85 years. The etiology of AD is unknown and there is currently no cure for the disease. Well-documented losses in cholinergic and other neurotransmitter systems have provided a focal point for attempting pharmacological interventions in AD to ameliorate some of the cognitive deficits that occur. However, current systemic strategies have met with limited success. An alternative strategy, that has been pursued in animal models of neurodegenerative disease, is to augment neurotransmitter function within the brain through tissue transplantation. Such implants have an advantage over conventional drug therapies in that the cells can be precisely placed within compromised areas of the brain. We have pursued a strategy of designing cells, through the use of molecular biology techniques, to produce neurotrophic factors and neurotransmitters. Recently, we developed a primary fibroblast cell line that was genetically modified to express choline acetyltransferase (ChAT). In vitro, these cells produced and released acetylcholine at levels that varied with the amount of choline in the culture media. When implanted into the hippocampus of rats, the in vivo microdialysis technique revealed that the ChAT-expressing fibroblasts continued to produce and release acetylcholine after grafting. Most importantly, the levels of acetylcholine synthesized by the cells could be regulated by the localized infusion of choline in the vicinity of the grafts. These results confirmed previous work which indicated that engineered fibroblasts provide an effective delivery vehicle of different substances to the brain. While the intracerebral implantation of genetically modified cells will not cure AD, the continuing development of this strategy may ultimately provide a powerful approach for ameliorating the devastating cognitive impairments which are a hallmark of this disease.

Callaway, E.M., Katz, L.C. Photostimulation using caged glutamate reveals functional circuitry in living brain slices. (1993) Proceedings of the National Academy of Sciences of the United States of America. 90(16):7661-7665.

+ expand abstract

Goulding, M., Sterrer, S., Fleming, J., Balling, R., Nadeau, J., Moore, K.J., Brown, S.D., Steel, K.P., Gruss, P. Analysis of the Pax-3 gene in the mouse mutant splotch. (1993) Genomics. 17(2):355-363. DOI: 10.1006/geno.1993.1332

+ expand abstract

Lockery, S.R., Sejnowski, T.J. The computational leech. (1993) Trends in Neurosciences. 16(7):283-290.

+ expand abstract

Hammond, R.R., Gage, F.H., Terry, R.D. Alzheimer's disease and spirochetes; a questionable relationship. (1993) Neuroreport. 4(7):840.

Fisher, L.J., Gage, F.H. Grafting in the mammalian central nervous system. (1993) Physiological Reviews. 73(3):583-616.

Nilsson, O.G., Gage, F.H. Anticholinergic sensitivity in the aging rat septohippocampal system as assessed in a spatial memory task. (1993) Neurobiology of Aging. 14(5):487-97.

+ expand abstract

Shimohama, S., Fisher, L.J., Gage, F.H. Intracerebral grafting of genetically modified cells. Applications to a rat model of Parkinson's disease. (1993) Advances in Neurology. 60:744-8.

Lockery, S.R., Sejnowski, T.J. A lower bound on the detectability of nonassociative learning in the local bending reflex of the medicinal leech. (1993) Behav. Neural Biol. 59(3):208-224.

+ expand abstract

Yamada, T., Pfaff, S.L., Edlund, T., Jessell, T.M. Control of cell pattern in the neural tube: motor neuron induction by diffusible factors from notochord and floor plate. (1993) Cell. 73(4):673-86.

+ expand abstract

Schinstine, M., Gage, F.H. Factors affecting proviral expression in primary cells grafted into the CNS. (1993) Res Publ Assoc Res Nerv Ment Dis. 71:311-23.

Ray, J., Peterson, D.A., Schinstine, M., Gage, F.H. Proliferation, differentiation, and long-term culture of primary hippocampal neurons. (1993) Proceedings of the National Academy of Sciences of the United States of America. 90(8):3602-6.

+ expand abstract

Pouget, A., Fisher, S.A., Sejnowski, T.J. Egocentric spaw representation in early vision. (1993) Journal of Cognitive Neuroscience. 5(2):150-161. DOI: 10.1162/jocn.1993.5.2.150

+ expand abstract

Goulding, M.D., Lumsden, A., Gruss, P. Signals from the notochord and floor plate regulate the region-specific expression of two Pax genes in the developing spinal cord. (1993) Development. 117(3):1001-1016.

+ expand abstract

Bush, P.C., Sejnowski, T.J. Reduced compartmental models of neocortical pyramidal cells. (1993) Journal of Neuroscience Methods. 46(2):159-166.

+ expand abstract

Gage, F.H. Parkinson's disease. Fetal implants put to the test. (1993) Nature. 361(6411):405-6. DOI: 10.1038/361405a0

Shimohama, S., Saitoh, T., Gage, F.H. Changes in protein kinase C isozymes in the rat hippocampal formation following hippocampal lesion. (1993) Hippocampus. 3(1):43-55. DOI: 10.1002/hipo.450030105

+ expand abstract

The cellular and regional distribution of the four protein kinase C (PKC) isoforms in the rat hippocampal formation and the response of PKC to lesions were determined by employing immunohistochemical and immunochemical techniques with antibodies specific to PKC(alpha), -(beta I), -(beta II), and -(gamma). PKC(alpha) intensely stained the periphery of the pyramidal cell in the stratum pyramidale. The granule cells, glial cells, and mossy fibers were anti-PKC(alpha) negative. The cytoplasm, axons, and dendrites of basket cells and interneurons in the hilus were labeled with anti-PKC(alpha). Anti-PKC(beta I) immunoreactivity was localized on the periphery of pyramidal cells and interneurons of the hilus, as well as the oriens, radiatum, and molecular layers of the CA regions. Anti-PKC(beta II) immunoreactivity was mainly cytoplasmic, extending into the dendrites in the hippocampal pyramidal cells and the dentate granule cells, and also in some glial cells. In the stratum radiatum of the CA1, anti-PKC(gamma) immunoreactivity localized to the pyramidal cell cytoplasm, extending into the dendrites. Following fimbria-fornix (FF) lesions, the anti-PKC(alpha) and -(beta I) staining of the pyramidal cell periphery was markedly reduced. The anti-PKC(gamma) staining of the pyramidal and granular cells of the dentate gyrus was reduced whereas the interneuron staining in the hilus was increased. In the FF-lesioned hippocampus, anti-PKC(alpha) and anti-PKC(beta II) labeled reactive glial cells, whereas anti-PKC(beta I) and -(gamma) did not. Quantitative Western blot analysis revealed a dramatic increase in the particulate/total PKC for all isozyme forms, although the total levels of PKC, except PKC(gamma), did not change following FF lesions. The PKC(gamma) concentration doubled after FF lesions. Perforant path lesions resulted in a marked alteration in the neuronal staining in dentate gyrus with anti-PKC(alpha) and -(beta I) and in increased numbers of anti-PKC(alpha)- and anti-PKC(beta II)-positive glial cells. Anti-PKC(gamma) staining did not change noticeably. The total PKC concentration did not change for isozymes alpha, beta I, and gamma, but PKC (beta II) concentration increased by 48% following perforant path lesions as detected by Western blot analysis. The particulate/total PKC decreased for all four isozymes although the reduction in PKC(beta I) concentration was not statistically significant. This change in PKC compartmentalization is in marked contrast to an increased level of particulate PKC following FF lesions. Thus, the effects of deafferentation and deafferentation for each PKC isoform were different.

Chowdhury, K., Goulding, M., Walther, C., Imai, K., Fickenscher, H. The ubiquitous transactivator Zfp-38 is upregulated during spermatogenesis with differential transcription. (1992) Mech. Dev. 39(3):129-42.

+ expand abstract

Lisberger, S.G., Sejnowski, T.J. Motor learning in a recurrent network model based on the vestibulo-ocular reflex. (1992) Nature. 360(6400):159-161. DOI: 10.1038/360159a0

+ expand abstract

Lockery, S.R., Sejnowski, T.J. Distributed processing of sensory information in the leech. III. A dynamical neural network model of the local bending reflex. (1992) Journal of Neuroscience. 12(10):3877-3895.

+ expand abstract

Ray, J., Gage, F.H. Gene transfer into established and primary fibroblast cell lines: comparison of transfection methods and promoters. (1992) BioTechniques. 13(4):598-603.

+ expand abstract

Fischer, W., Chen, K.S., Gage, F.H., Björklund, A. Progressive decline in spatial learning and integrity of forebrain cholinergic neurons in rats during aging. (1992) Neurobiology of Aging. 13(1):9-23.

+ expand abstract

Rats distributed over five different age groups, 3, 12, 18, 24 and 30 months of age, were screened for their spatial learning and memory ability in the Morris water maze, and the degree of place navigational impairments was correlated with morphological changes in the four major forebrain cholinergic cell groups (medial septum, MS; vertical limb of the diagonal band of Broca, VDB; nucleus basalis magnocellularis, NBM; and striatum) using choline acetyltransferase (ChAT) and nerve growth factor receptor (NGFr) histochemistry. Impaired place navigation developed progressively with age, such that 8% of the 12-month-old rats, 45% of the 18-month-old, 53% of the 24-month-old, and over 90% of the 30-month-old rats were behaviorally impaired. Significant reductions in the number of ChAT/NGFr-positive cell bodies, amounting to between 19 and 45%, were observed in all four cell groups, and the remaining cells were reduced in size (6-24% reduction in cross-sectional area in the oldest age groups). Although the morphological changes were less severe and tended to develop later than the behavioral impairments, there was overall a significant correlation between water maze performance and ChAT/NGFr-positive cell counts, and to a lesser degree also cell size in all four cell groups. These changes were also highly correlated with age. The highest correlations were seen in MS, VDB and NBM, which are known to play a role in spatial memory performance in young rats. The results indicate that degenerative and/or atrophic changes in the forebrain cholinergic system and decline in spatial learning ability are parallel processes during aging. Although the magnitude of the morphological changes does not appear to be substantial enough, by itself, to explain the severe spatial learning impairments that develop in the oldest animals, the present data are consistent with the view that impaired function in the forebrain cholinergic system can contribute to age-dependent cognitive decline in rodents.

Lehky, S.R., Sejnowski, T.J., Desimone, R. Predicting responses of nonlinear neurons in monkey striate cortex to complex patterns. (1992) Journal of Neuroscience. 12(9):3568-3581.

+ expand abstract

Yoshida, K., Kakihana, M., Chen, L.S., Ong, M., Baird, A., Gage, F.H. Cytokine regulation of nerve growth factor-mediated cholinergic neurotrophic activity synthesized by astrocytes and fibroblasts. (1992) Journal of Neurochemistry. 59(3):919-31.

+ expand abstract

The neurotrophic activity of astrocytes and fibroblasts and its regulation by various cytokines were investigated. Astrocyte conditioned medium (ACM) enhanced the survival of neurons and the proliferation of astrocytes in embryonic cortical cultures grown in serum-free defined medium. However, these results were not affected by acidic fibroblast growth factor, interleukin-1 beta (IL-1 beta), tumor necrosis factor-alpha (TNF alpha), and transforming growth factor-beta 1. In contrast, ACM induced choline acetyltransferase expression in septal cholinergic neurons via nerve growth factor (NGF)-dependent and -independent mechanisms. However, neither acidic nor basic fibroblast growth factor is involved in this biological activity in ACM. The cytokines listed above mainly stimulate NGF-mediated cholinergic neurotrophic activity in ACM. A combination of IL-1 beta and TNF alpha significantly enhanced choline acetyltransferase activity in septal neurons co-cultured with astrocytes, and this effect was found to be mediated by NGF produced by activated astrocytes. Effects of astrocytes on GABAergic neurons were also examined. ACM was found to increase glutamate decarboxylase activity in neuronal cultures from septum in the presence of Ara-C. However, the cytokines did not enhance this activity in ACM. Moreover, a combination of IL-1 beta and TNF alpha had no effect on glutamate decarboxylase activity in septal neurons co-cultured with astrocytes. In a final set of experiments, cholinergic neurotrophic activity in skin-derived fibroblast conditioned medium (FCM) was examined. FCM was found to possess biological activity similar to that of ACM on septal neurons grown in serum-free defined medium with Ara-C. The cytokines also enhanced NGF-mediated cholinergic neurotrophic activity in FCM. Astrocytes and fibroblasts were found to possess NGF-type and non-NGF-type cholinergic neurotrophic activity, and various cytokines were found to regulate the NGF-type cholinergic neurotrophic activity in both types of cells. NGF produced by astrocytes and fibroblasts that are activated by cytokines is likely to be important for development and regeneration of NGF-sensitive neurons in the central and peripheral nervous systems.

Thal, L.J., Gilbertson, E., Armstrong, D.M., Gage, F.H. Development of the basal forebrain cholinergic system: phenotype expression prior to target innervation. (1992) Neurobiology of Aging. 13(1):67-72.

+ expand abstract

Holtzman, D.M., Li, Y., Gage, F.H., Epstein, C.J., Mobley, W.C. Neurodegeneration and gene dysregulation: studies utilizing the mouse trisomy 16 model of Down syndrome. (1992) Progress in Clinical and Biological Research. 379:227-44.

Lytton, W.W., Sejnowski, T.J. Computer model of ethosuximide's effect on a thalamic neuron. (1992) Ann. Neurol. 32(2):131-139. DOI: 10.1002/ana.410320204

+ expand abstract

Sejnowski, T.J. Models of vision. (1992) Science. 257(5070):687-688. DOI: 10.1126/science.257.5070.687

Kawaja, M.D., Rosenberg, M.B., Yoshida, K., Gage, F.H. Somatic gene transfer of nerve growth factor promotes the survival of axotomized septal neurons and the regeneration of their axons in adult rats. (1992) Journal of Neuroscience. 12(7):2849-64.

+ expand abstract

Katz, L.C., Callaway, E.M. Development of local circuits in mammalian visual cortex. (1992) Annual Review of Neuroscience. 15:31-56. DOI: 10.1146/annurev.ne.15.030192.000335

Schinstine, M., Rosenberg, M.B., Routledge-Ward, C., Friedmann, T., Gage, F.H. Effects of choline and quiescence on Drosophila choline acetyltransferase expression and acetylcholine production by transduced rat fibroblasts. (1992) Journal of Neurochemistry. 58(6):2019-29.

+ expand abstract

Pfaff, S.L., Taylor, W.L. Characterization of a Xenopus oocyte factor that binds to a developmentally regulated cis-element in the TFIIIA gene. (1992) Developmental Biology. 151(1):306-16.

+ expand abstract

Gage, F.H. Repopulating the mortal brain with immortal cells. (1992) Current Biology. 2(5):232-4.

Lyden, P.D., Zivin, J.A., Chabolla, D.R., Jacobs, M.A., Gage, F.H. Quantitative effects of cerebral infarction on spatial learning in rats. (1992) Experimental Neurology. 116(2):122-32.

+ expand abstract

Kawaja, M.D., Gage, F.H. Morphological and neurochemical features of cultured primary skin fibroblasts of Fischer 344 rats following striatal implantation. (1992) Journal of Comparative Neurology. 317(1):102-16. DOI: 10.1002/cne.903170108

+ expand abstract

In order to assess the feasibility of using primary skin fibroblasts as a donor population for genetic modification and subsequent intracerebral grafting, the present study examines the structural and neurochemical characteristics of intrastriatal grafts of isogeneic primary fibroblasts over a period of 6 months. In culture, primary skin fibroblasts obtained from a female Fischer 344 rat display robust growth, but once confluent these cells exhibit contact inhibition. Following the implantation of cultured primary cells within the striatum of other adult rats from the same inbred strain, isologous grafts stain immunohistochemically for fibronectin at 1 week, and this immunostaining persists up to 6 months. Immunoreactivity for laminin is intense within the grafts from 1 to 8 weeks, but decreases by 6 months. Astrocytes within the striatum respond dramatically to the implantation of primary fibroblasts, such that immunohistochemical staining for glial fibrillary acidic protein increases markedly from 1 to 8 weeks after implantation. Although the intensity of immunostaining for glial fibrillary acidic protein diminishes among striatal astrocytes between 8 weeks and 6 months, the astrocytic border between the grafts and striatal neuropil remains intensely immunoreactive. Capillaries within the grafts stain immunohistochemically for glucose transporter (a facilitated glucose uptake carrier) as early as 3 weeks after implantation. Following intravenous infusions of peroxidase, capillaries within fibroblast grafts do not permit the extravasation of this macromolecule at 8 weeks and 6 months. Thus, capillaries formed within intracerebral grafts of primary skin fibroblasts exhibit a functional impermeable barrier to macromolecules similar to those capillaries of the host striatum. At the ultrastructural level, grafts possess numerous fibroblasts and have an extracellular matrix filled with collagen. Reactive astrocytic processes filled with intermediate filaments are found throughout the grafts. Hypertrophied astrocytes and their processes also appear to form a continuous border between the grafts and striatal neuropil. Grafts of primary fibroblasts also possess an extensive vasculature that is composed of capillaries with nonfenestrated endothelial cells; the occurrence of reactive astrocytic processes closely associated with or enveloping capillaries is variable. These results provide direct morphological and neurochemical evidence for the long-term survival of isologous fibroblasts after implantation within the rat striatum. From these data, we propose that isologous skin fibroblasts can be considered as donor candidates for successful intracerebral grafting following gene transfer.

Buzsáki, G., Gage, F.H. Fetal brain tissue grafts modulate neuronal excitability in a chronic model of epilepsy. (1992) Epilepsy Res. Suppl. 8:271-81.

Wathey, J.C., Lytton, W.W., Jester, J.M., Sejnowski, T.J. Computer simulations of EPSP-spike (E-S) potentiation in hippocampal CA1 pyramidal cells. (1992) Journal of Neuroscience. 12(2):607-618.

+ expand abstract

Callaway, E.M., Katz, L.C. Development of axonal arbors of layer 4 spiny neurons in cat striate cortex. (1992) Journal of Neuroscience. 12(2):570-582.

+ expand abstract

Spiny neurons in layer 4 of cat striate cortex are the primary recipients of geniculocortical afferents and provide crucial links to other cortical layers for processing visual information. Using intracellular staining, we examined the development of the local axonal projections of these neurons to determine (1) whether the laminar specificity of their projections emerged specifically or was sculpted from transient exuberant projections and (2) whether the emergence of excitatory connections from layer 4 to layer 2/3 could contribute to the activity-dependent development of clustered horizontal connections of layer 2/3 pyramidal neurons. Differences in the extent of projections to infragranular (layers 5 and 6, which receive sparse projections) versus superficial layers (layers 2/3 and 4, which receive extensive projections) developed specifically from the outset. By postnatal day 15 (P15) projections to infragranular layers matured and were indistinguishable from those in the oldest animal studied (P33). In contrast, projections to superficial layers continued to increase in complexity after P15. Projections within layer 4, which were the most elaborate at all ages studied, reached maturity at about P20, while those to layer 2/3 continued to increase in complexity through P33. No evidence for exuberant projections to any of these cortical layers was observed. At very early postnatal ages (P5) projections to the subplate region were evident. These disappeared by P8-P11, suggesting the presence of transient connections from layer 4 spiny neurons to subplate neurons. Binocular deprivation did not prevent the emergence of projections from layer 4 spiny neurons into layer 2/3 or development of normal laminar differences in projection density. Connections from layer 4 to layer 2/3 emerged after horizontal connections in layer 2/3 were crudely clustered, but in synchrony with the later refinement of clusters. Collaterals from layer 4 cells first crossed into layer 3 at P11, but were extremely short (extending only 50-200 microns beyond the laminar boundary) and uncommon (only 4 of 19 cells). Since by P8 horizontal projections of layer 2/3 pyramidal neurons are already crudely clustered, the emergence of crude clustering is probably independent of layer 4 to layer 2/3 excitatory projections. The proportion of cells projecting to layer 2/3 and the complexity of their arbors both increased in the subsequent weeks, closely matching the timing of both the refinement of crudely clustered horizontal connections and the emergence of visual responsiveness in layer 2/3.(ABSTRACT TRUNCATED AT 400 WORDS)

Holtzman, D.M., Li, Y.W., DeArmond, S.J., McKinley, M.P., Gage, F.H., Epstein, C.J., Mobley, W.C. Mouse model of neurodegeneration: atrophy of basal forebrain cholinergic neurons in trisomy 16 transplants. (1992) Proceedings of the National Academy of Sciences of the United States of America. 89(4):1383-7.

+ expand abstract

Jinnah, H.A., Hess, E.J., Wilson, M.C., Gage, F.H., Friedmann, T. Localization of hypoxanthine-guanine phosphoribosyltransferase mRNA in the mouse brain by in situ hybridization. (1992) Molecular and Cellular Neurosciences. 3(1):64-78.

+ expand abstract

Gage, F.H., Chen, K.S. Neural transplants: prospects for Alzheimer's disease. (1992) Current Opinion in Neurology and Neurosurgery. 5(1):94-9.

+ expand abstract

Dekker, A.J., Gage, F.H., Thal, L.J. Delayed treatment with nerve growth factor improves acquisition of a spatial task in rats with lesions of the nucleus basalis magnocellularis: evaluation of the involvement of different neurotransmitt (1992) Neuroscience. 48(1):111-9.

+ expand abstract

Yoshida, K., Gage, F.H. Cooperative regulation of nerve growth factor synthesis and secretion in fibroblasts and astrocytes by fibroblast growth factor and other cytokines. (1992) Brain Research. 569(1):14-25.

+ expand abstract

Acidic fibroblast growth factor (aFGF) enhances nerve growth factor (NGF) synthesis by astrocytes obtained from various brain regions. NGF secretion by fibrous-shaped astrocytes transformed by dibutyryl-cAMP (db-cAMP) pretreatment was less than that by untreated astrocytes. However, aFGF also enhanced NGF secretion by fibrous-shaped astrocytes. The effects of various kinds of intracellular signaling modulators on NGF synthesis were examined. None of the following second messenger effectors had an effect on NGF synthesis: protein kinase C (PKC) agonist (phorbol myristate acetate (PMA)) or antagonist (sphingosine (SP)). LiCl, and ionomycin (Iono). Further, increases of intracellular cAMP by forskolin (FK) or db-cAMP have no significant effect on NGF synthesis in astrocytes under a standard culture condition. However, NGF synthesis by astrocytes in the presence of aFGF was significantly enhanced by db-cAMP, but not by FK or sodium butyrate. These results indicate that an excessive amount of cAMP enhances the effect of aFGF on NGF synthesis in astrocytes. NGF synthesis in astrocytes was not affected by treatment with anti-aFGF or anti-bFGF neutralizing antibodies, indicating that FGFs are not involved in the autocrine regulation of NGF synthesis in astrocytes. Transforming growth factor-beta 1 (TGF-beta 1), which inhibits some effects of FGFs, increased NGF synthesis in concert with aFGF. Furthermore, the highest NGF synthesis was observed when astrocytes were stimulated by all of the following cytokines: aFGF, interleukin-1 beta (IL-1 beta), tumor necrosis factor-alpha (TNF-alpha) and TGF-beta 1. The mechanism regulating NGF synthesis in fibroblasts obtained from prenatal rat skin was also investigated. Acidic FGF, basic FGF (bFGF), epidermal growth factor (EGF), platelet-derived growth factor (PDGF), transforming growth factor-alpha (TGF-alpha), TGF-beta 1, IL-1 beta, and TNF-alpha were found to be regulators of NGF synthesis in skin fibroblasts. Among these cytokines, aFGF is the most potent regulator of NGF synthesis in fibroblasts. NGF synthesis by skin fibroblasts, either in the presence or absence of aFGF, was not modified by any of the following: FK, PMA, SP, LiCl, and Iono. However, db-cAMP significantly enhanced NGF synthesis in both conditions. Sodium butyrate enhanced NGF synthesis in the presence of aFGF, but not in the absence of aFGF. These results suggest that an excessive amount of cAMP and butyrate moiety regulate NGF synthesis in skin fibroblasts in different ways.(ABSTRACT TRUNCATED AT 400 WORDS)

Buzsáki, G., Hsu, M., Horváth, Z., Gage, F.H. Physiological and behavioral consequences of delayed septal grafts in the subcortically denervated hippocampus. (1992) Restor. Neurol. Neurosci. 4(6):369-80. DOI: 10.3233/RNN-1992-4602

+ expand abstract

Johnson, P.A., Yoshida, K., Gage, F.H., Friedmann, T. Effects of gene transfer into cultured CNS neurons with a replication-defective herpes simplex virus type 1 vector. (1992) Brain Research. Molecular Brain Research. 12(1-3):95-102.

+ expand abstract

Jinnah, H.A., Gage, F.H., Friedmann, T. Amphetamine-induced behavioral phenotype in a hypoxanthine-guanine phosphoribosyltransferase-deficient mouse model of Lesch-Nyhan syndrome. (1991) Behavioral Neuroscience. 105(6):1004-12.

+ expand abstract

Kawaja, M.D., Gage, F.H. Reactive astrocytes are substrates for the growth of adult CNS axons in the presence of elevated levels of nerve growth factor. (1991) Neuron. 7(6):1019-30.

+ expand abstract

Holliday, J., Adams, R.J., Sejnowski, T.J., Spitzer, N.C. Calcium-induced release of calcium regulates differentiation of cultured spinal neurons. (1991) Neuron. 7(5):787-796.

+ expand abstract

Tuszynski, M.H., Sang, H., Yoshida, K., Gage, F.H. Recombinant human nerve growth factor infusions prevent cholinergic neuronal degeneration in the adult primate brain. (1991) Annals of Neurology. 30(5):625-36. DOI: 10.1002/ana.410300502

+ expand abstract

Kawaja, M.D., Ray, J., Gage, F.H. Employment of fibroblasts for gene transfer: applications for grafting into the central nervous system. (1991) Genetic Engineering. 13:205-20.

+ expand abstract

Walther, C., Guenet, J.L., Simon, D., Deutsch, U., Jostes, B., Goulding, M.D., Plachov, D., Balling, R., Gruss, P. Pax: a murine multigene family of paired box-containing genes. (1991) Genomics. 11(2):424-434.

+ expand abstract

Gage, F.H., Kang, U.J., Fisher, L.J. Intracerebral grafting in the dopaminergic system: issues and controversy. (1991) Current Opinion in Neurobiology. 1(3):414-9.

+ expand abstract

Dekker, A.J., Langdon, D.J., Gage, F.H., Thal, L.J. NGF increases cortical acetylcholine release in rats with lesions of the nucleus basalis. (1991) Neuroreport. 2(10):577-80.

+ expand abstract

Schinstine, M., Kawaja, M.D., Gage, F.H. Intracerebral delivery of growth factors: potential application of genetically modified fibroblasts. (1991) Progress in Growth Factor Research. 3(1):57-66.

+ expand abstract

Lytton, W.W., Sejnowski, T.J. Simulations of cortical pyramidal neurons synchronized by inhibitory interneurons. (1991) Journal of Neurophysiology. 66(3):1059-1079.

+ expand abstract

1. The interaction between inhibitory interneurons and cortical pyramidal neurons was studied by use of computer simulations to test whether inhibitory interneurons could assist in phase-locking postsynaptic cells. Two models were used: a simplified model, which included only 3 membrane channels, and a detailed 11-channel model. 2. The 11-channel model included most of the ion channels known to be present in neocortical pyramidal neurons as well as calcium diffusion and other membrane mechanisms. The kinetics for the channels were obtained from voltage-clamp studies in a variety of preparations. The parameters were then adjusted to produce repetitive bursting similar to that seen in some cortical pyramidal cells entrained during visual stimulation. 3. Phase-locking to a train of inhibitory postsynaptic potentials (IPSPs) located on or near the soma was observed in the 3-channel model cell subjected to random synaptic bombardment. In the 11-channel model, phase-locking due to multiple IPSPs was compared with phase-locking due to multiple excitatory postsynaptic potentials (EPSPs). Phase-locking began to occur when 20% of the IPSPs (20/100) or 40% of the EPSPs (4,000/10,000) were synchronized. The exact percentages differed with different 11-channel models, but either EPSPs or IPSPs would generally produce entrainment with approximately 40% synchronization. Thus 40 inhibitory boutons had an effect equivalent to 4,000 excitatory boutons in producing phase-locking. 4. Phase-locking with IPSPs in these models was possible because the IPSPs could cause either an increase or a decrease in firing rate over a limited range. The IPSPs served a modulatory role, increasing the rate of firing in some cases and decreasing it in others, depending on the state of the cell. 5. We examined frequency entrainment by IPSPs. In the 3-channel model, frequency entrainment of a postsynaptic cell was observed with a rapid train of strong (20-100 nS), brief, compound IPSPs. A 40-Hz compound IPSP train of 60 nS entrained cells having initial firing rates between 32 and 47 Hz. Below this range, cells could be partially entrained. Above the range, entrainment would fail. Frequency entrainment in the 3-channel model generally occurred on the first cycle after onset of the IPSPs. 6. Phase-locking and frequency entrainment were less robust in the 11-channel model. This was partly because bursts rather than individual spikes were being entrained. A 40-Hz, 90-nS compound IPSP train entrained a model cell upward from 34 Hz. Downward frequency entrainment also occurred.(ABSTRACT TRUNCATED AT 400 WORDS)

Chalepakis, G., Fritsch, R., Fickenscher, H., Deutsch, U., Goulding, M., Gruss, P. The molecular basis of the undulated/Pax-1 mutation. (1991) Cell. 66(5):873-884.

+ expand abstract

Bush, P.C., Sejnowski, T.J. Simulations of a Reconstructed Cerebellar Purkinje Cell Based on Simplified Channel Kinetics. (1991) Neural Computation. 3(3):321-332. DOI: 10.1162/neco.1991.3.3.321

+ expand abstract

Sejnowski, T.J. Neuroscience. Back together again. (1991) Nature. 352(6337):669-670. DOI: 10.1038/352669a0

Masliah, E., Fagan, A.M., Terry, R.D., DeTeresa, R., Mallory, M., Gage, F.H. Reactive synaptogenesis assessed by synaptophysin immunoreactivity is associated with GAP-43 in the dentate gyrus of the adult rat. (1991) Experimental Neurology. 113(2):131-42.

+ expand abstract

Reactive synaptogenesis and terminal proliferation are known to occur in the dentate gyrus of the rat hippocampus following removal of specific afferents. In the present study we have examined the relation of synaptophysin immunoreactivity to the immunohistochemical staining pattern of GAP-43, a putative marker of neuritic growth. Within the molecular layer of the normal dentate gyrus, synaptophysin immunolabeling shows a trilaminar pattern, with the inner and outer layers having the greatest density of staining. Within the first week following denervation, there was a significant decrease in the staining density in the outer two-thirds of the molecular layer, followed by a moderate recovery at 14 days and 80% recovery by 30 days. This pattern is consistent with the time course of denervation and reinnervation in this system as determined previously by electron microscopy. By comparison, the staining pattern for GAP-43 in the intact dentate gyrus showed the middle and outer thirds of the molecular layer to be less densely stained than the inner third. Within a week following deafferentation, the outer two-thirds of the molecular layer displayed decreased levels of GAP-43 immunoreactivity, followed by recovery to normal levels by 30 days. By 84 days postlesion, patterns of both synaptophysin and GAP-43 immunostaining reflected an increased width of the inner molecular layer. Laser confocal imaging of double-immunolabeled sections at 14 days postlesion showed a 370% increase in the number of GAP-43-positive terminals in the molecular layer as compared to unoperated controls. Many of these GAP 43-positive terminals were synaptophysin negative. We conclude that GAP-43 may play a role in the synaptic remodeling that occurs in the denervated rat hippocampus and that quantitative morphometry of synaptophysin immunolabeling accurately reflects the fate of presynaptic terminals in this model of degeneration and reinnervation.

Gage, F.H., Kawaja, M.D., Fisher, L.J. Genetically modified cells: applications for intracerebral grafting. (1991) Trends in Neurosciences. 14(8):328-33.

+ expand abstract

Buzsáki, G., Masliah, E., Chen, L.S., Horváth, Z., Terry, R., Gage, F.H. Hippocampal grafts into the intact brain induce epileptic patterns. (1991) Brain Research. 554(1-2):30-7.

+ expand abstract

Carman, L.S., Gage, F.H., Shults, C.W. Partial lesion of the substantia nigra: relation between extent of lesion and rotational behavior. (1991) Brain Research. 553(2):275-83.

+ expand abstract

Fischer, W., Björklund, A., Chen, K., Gage, F.H. NGF improves spatial memory in aged rodents as a function of age. (1991) Journal of Neuroscience. 11(7):1889-906.

+ expand abstract

Pfaff, S.L., Hall, R.K., Hart, G.C., Taylor, W.L. Regulation of the Xenopus laevis transcription factor IIIA gene during oogenesis and early embryogenesis: negative elements repress the O-TFIIIA promoter in embryonic cells. (1991) Developmental Biology. 145(2):241-54.

+ expand abstract

Stanton, P.K., Chattarji, S., Sejnowski, T.J. 2-Amino-3-phosphonopropionic acid, an inhibitor of glutamate-stimulated phosphoinositide turnover, blocks induction of homosynaptic long-term depression, but not potentiation, in rat hippocampus. (1991) Neurosci. Lett. 127(1):61-66.

+ expand abstract

Gage, F.H., Tuszynski, M.H., Chen, K.S., Fagan, A.M., Higgins, G.A. Nerve growth factor function in the central nervous system. (1991) Current Topics in Microbiology and Immunology. 165:71-93.

Holtzman, D.M., Li, Y.W., Gage, F.H., DeArmond, S.J., Epstein, C.J., McKinley, M.P., Mobley, W.C. Modeling cholinergic abnormalities in Down syndrome and Alzheimer's disease. (1991) Progress in Clinical and Biological Research. 373:189-202.

Gonzalez, A.M., Lappi, D.A., Buscaglia, M.L., Carman, L.S., Gage, F.H., Baird, A. Basic FGF-SAP mitotoxin in the hippocampus. Specific lethal effect on cells expressing the basic FGF receptor. (1991) Annals of the New York Academy of Sciences. 638:442-4.

Goulding, M.D., Chalepakis, G., Deutsch, U., Erselius, J.R., Gruss, P. Pax-3, a novel murine DNA binding protein expressed during early neurogenesis. (1991) EMBO Journal. 10(5):1135-1147.

+ expand abstract

Kawaja, M.D., Fagan, A.M., Firestein, B.L., Gage, F.H. Intracerebral grafting of cultured autologous skin fibroblasts into the rat striatum: an assessment of graft size and ultrastructure. (1991) Journal of Comparative Neurology. 307(4):695-706. DOI: 10.1002/cne.903070414

+ expand abstract

Masliah, E., Yoshida, K., Shimohama, S., Gage, F.H., Saitoh, T. Differential expression of protein kinase C isozymes in rat glial cell cultures. (1991) Brain Research. 549(1):106-11.

+ expand abstract

Kawaja, M.D., Gage, F.H. Nerve growth factor receptor immunoreactivity in the rat septohippocampal pathway: a light and electron microscope investigation. (1991) J. Comp. Neurol. 307(3):517-29. DOI: 10.1002/cne.903070313

+ expand abstract

Nerve growth factor receptor immunoreactivity in the septohippocampal pathway of adult Fischer 344 rats was assessed at the light and electron microscope level. The medial septum possesses immunoreactive somata, dendrites, axons, and terminals. Immunostained somata are either bipolar or multipolar in appearance. Dendritic processes of immunoreactive septal neurons are categorized into two groups: proximal dendrites with smooth plasma membranes and distal dendrites with numerous swellings. Immunoreactive axons within the septum are long and slender and do not possess varicosities. At the electron microscope level, immunoreactivity is confined predominantly to the plasma membrane of cell bodies and dendrites of septal neurons, as well as to the plasma membrane of axons and terminals. Both immunoreactive and nonimmunoreactive terminals that contain clear, spherical vesicles are observed contacting immunoreactive dendrites and somata. Although accumulations of vesicles are evident within these terminals at sites of contact, distinct synaptic specializations are difficult to distinguish due to the localization of reaction product on the apposing plasma membranes. Axons possessing immunoreactivity are also observed in the fimbria-fornix pathway, a major source of afferent inputs to the hippocampus. Immunoreactive axons and terminals are topographically organized in the hippocampal dentate gyrus. The density of immunostained axons and terminals is highest immediately adjacent to the granular layer. In comparison, a moderate density of immunoreactive axons is found in the outer molecular layer and a weak density in the inner molecular, granular, and polymorphic layers. Immunoreactivity is found on the plasma membrane of small unmyelinated axons and terminals aggregated into clusters throughout the dentate gyrus. Definitive examples of axosomatic and axodendritic synapses possessing immunoreactivity presynaptically are not observed. Immunoreactive profiles within the medial septum and hippocampus also circumfuse a small number of intracerebral vessels. Ultrastructural examination reveals that immunoreactivity is present within a narrowed extension of the subarachnoid space and appears to be closely associated with the plasma membrane of leptomeningeal cell processes. The present study provides direct evidence for the cellular distribution of nerve growth factor receptor immunoreactivity in the medial septum and dentate gyrus in the adult rat and offers new insight into the ultrastructural localization of nerve growth factor receptor among septal cholinergic neurons and their efferent projections to the hippocampus.

Tuszynski, M.H., Gage, F.H. In vivo assay of neuron-specific effects of nerve growth factor. (1991) Methods in Enzymology. 198:35-48.

Buzsáki, G., Hsu, M., Slamka, C., Gage, F.H., Horváth, Z. Emergence and propagation of interictal spikes in the subcortically denervated hippocampus. (1991) Hippocampus. 1(2):163-80. DOI: 10.1002/hipo.450010205

+ expand abstract

Spontaneous and evoked field potentials and cellular discharges of the subcortically denervated dorsal hippocampus were studied by multisite recordings in the freely behaving rat. Characteristic short-duration (< 100 ms), large-amplitude (up to 10 mV) transients, termed interictal spikes (IIS), were seen after fimbria-fornix (FF) lesion. Both pyramidal cells and putative interneurons fired maximally during IIS, with some interneurons sustaining long bursts (up to 400 ms) of high-frequency discharges (400-600 Hz) after the IIS. The speed of propagation of IIS along the longitudinal axis of the hippocampus varied from 0.2 m/s to > 3 m/s. The majority of IIS (type 1) could be accounted for by an enhanced activity of the intrahippocampal associational systems; a second class of IIS (type 2) had positive polarities in the stratum radiatum of CA1 and CA3 and propagated very rapidly (> 1.5 m/s). The authors propose that type 2 IIS reflect somatic depolarization and discharge of pyramidal neurons due to nonsynaptic (probably ephaptic) effects. Ephaptic interactions may also explain the longitudinal propagation of IIS at speeds higher than the conduction velocities (0.5 m/s) of hippocampal fiber systems. IIS emerged during the first 3 weeks after fimbria-fornix lesion, their incidence reaching a plateau of 2/min thereafter. During the same time period, paired-pulse suppression increased in the dentate gyrus. The amplitude of test responses to angular bundle stimulation was potentiated by small-amplitude IIS but suppressed by large-amplitude IIS. The incidence of IIS was significantly suppressed during walking relative to standing still. Tetanic stimulation of the angular bundle or handling-induced stress resulted in a 10- to 20-fold increase in the incidence of IIS that lasted for about 30 minutes. There was a negative correlation between evoked field PSP slope and population spike amplitude in the dentate gyrus of FF-lesioned rats; this correlation was positive in intact rats. The authors attribute the above pathophysiological changes to sprouting of both excitatory and inhibitory GABAergic pathways as a result of denervation of the intrahippocampal circuitry. They hypothesize that the majority of the observed physiological alterations can be traced to a weakening of feedforward inhibition coupled with an enhancement of feedback inhibition and excitation.

Chen, L.S., Ray, J., Fisher, L.J., Kawaja, M.D., Schinstine, M., Kang, U.J., Gage, F.H. Cellular replacement therapy for neurologic disorders: potential of genetically engineered cells. (1991) Journal of Cellular Biochemistry. 45(3):252-7. DOI: 10.1002/jcb.240450305

+ expand abstract

Shults, C.W., O'Connor, D.T., Baird, A., Hill, R., Goetz, C.G., Watts, R.L., Klawans, H.L., Carvey, P.M., Bakay, R.A., Gage, F.H. Clinical improvement in parkinsonian patients undergoing adrenal to caudate transplantation is not reflected by chromogranin A or basic fibroblast growth factor in ventricular fluid. (1991) Exp. Neurol. 111(3):276-81.

+ expand abstract

Dawson, T.M., Dawson, V.L., Gage, F.H., Fisher, L.J., Hunt, M.A., Wamsley, J.K. Functional recovery of supersensitive dopamine receptors after intrastriatal grafts of fetal substantia nigra. (1991) Experimental Neurology. 111(3):282-92.

+ expand abstract

Interruption of the ascending dopamine neurons of the nigrostriatal pathway, by 6-hydroxydopamine (6-OHDA) lesion in rats, produced a significant loss of the dopamine transport complexes labeled with the phencyclidine derivative [3H]BTCP. This loss of dopamine innervation in the striatum was present at least 12 to 14 months after lesioning and was functionally manifested by ipsilateral rotation of the animals in response to amphetamine. In these same animals, in comparison to controls, there was a significant increase in the number (Bmax) of [3H]SCH 23390-labeled D-1 receptors in the striatum (36.7%) and the substantia nigra (35.1%) and a 54.4% increase in the number (Bmax) of [3H]sulpiride-labeled striatal D-2 receptors without an apparent change in affinity (Kd). Ten to twelve months after the transplantation of homologous fetal substantia nigra into the denervated striatum, there was a significant decrease in amphetamine-induced turning behavior. In these animals, there was an ingrowth of dopamine nerve terminals in the striatum as demonstrated by a return of [3H]BTCP binding. Accompanying this reinnervation was the normalization of D-1 and D-2 receptors to control values in the striatum as well as the return of D-1 receptors to prelesion densities in the substantia nigra. In a subgroup of transplanted rats, amphetamine continued to induce ipsilateral turning. In these animals both D-1 and D-2 receptors remained supersensitive. These results support the hypothesis that the functional recovery of transplanted animals is due, in part, to reinnervation of the striatum. In addition, long-term alterations in receptor density may be related to the behavioral deficits that are associated with the 6-OHDA-lesioned rat. Furthermore, dopamine receptor plasticity may play a role in the functional recovery of substantia nigra transplanted animals and graft viability seems to be a prerequisite for behavioral recovery as well as receptor normalization.

Fisher, L.J., Jinnah, H.A., Kale, L.C., Higgins, G.A., Gage, F.H. Survival and function of intrastriatally grafted primary fibroblasts genetically modified to produce L-dopa. (1991) Neuron. 6(3):371-80.

+ expand abstract

Fisher, L.J., Young, S.J., Tepper, J.M., Groves, P.M., Gage, F.H. Electrophysiological characteristics of cells within mesencephalon suspension grafts. (1991) Neuroscience. 40(1):109-22.

+ expand abstract

Both spontaneous and evoked extracellular electrophysiological activity of neurons within fetal mesencephalon suspension grafts to the dopamine-depleted striatum of rats were examined. In some cases, extracellular recording was combined with intracellular labeling to identify recorded neurons. Grafted rats displaying a complete cessation of ipsilateral rotations following amphetamine administration were examined at post-implantation time intervals of two, four, five, eight and nine months. Four separate classes of neurons were distinguished within the transplanted striatum based on electrophysiological properties. The first of these groups, the type I cells, appeared to be non-grafted striatal neurons. When spontaneously active, these striatal-like cells fired bursts of action potentials separated by periods of decreased activity. Evoked responses in these cells were characteristic of striatal cells. Type I cells which were intracellularly labeled were found outside the grafts and displayed the characteristic morphology of the medium spiny neuron of the neostriatum. The other three cell classes displayed electrophysiological properties similar to neurons recorded in situ within the reticular formation, substantia nigra pars compacta and substantia nigra pars reticulata. Neurons from these three groups which were labeled with an intracellular marker were found to lie within the suspension grafts. The spontaneous activity of the pars compacta dopaminergic-like neurons was predominantly irregular, with some cells also firing in a regular or pacemaker-like pattern. Infrequently, irregular firing dopaminergic-like neurons displayed episodes of doublet bursting. Many of the grafted neurons responded to electrical stimulation of prefrontal cortex and striatum, indicating that the graft was receiving functional inputs from host neurons. Comparison of the firing rate and pattern of grafted neurons to in situ mesencephalic neurons as a function of time following grafting suggested that the grafted neurons and/or the neuronal circuitry is slowly developing within the host environment. A prolonged time-course for the maturation of the graft may be reflected in the time required to achieve improvements in some behavioral deficits following transplantation. However, the relatively rapid recovery of drug-induced rotational asymmetry following grafting suggests that this form of recovery may not require mature functioning of the grafted neurons.

Wamsley, J.K., Dawson, T.M., Dawson, V.L., Hunt, M.A., Fisher, L.J., Gage, F.H. Reversal of nigrostriatal-lesion-induced receptor alterations by grafting of fetal mesencephalic dopaminergic neurons. (1991) Advances in Experimental Medicine and Biology. 287:221-35.

Sejnowski, T.J. Synaptic mechanisms for long-term depression. (1991) Current Biology. 1(1):38-40.

Dawson, T.M., Dawson, V.L., Gage, F.H., Fisher, L.J., Hunt, M.A., Wamsley, J.K. Downregulation of muscarinic receptors in the rat caudate-putamen after lesioning of the ipsilateral nigrostriatal dopamine pathway with 6-hydroxydopamine (6-OHDA): normalization by fetal mesencephali (1991) Brain Research. 540(1-2):145-52.

+ expand abstract

Yoshida, K., Gage, F.H. Fibroblast growth factors stimulate nerve growth factor synthesis and secretion by astrocytes. (1991) Brain Research. 538(1):118-26.

+ expand abstract

Gage, F.H., Fisher, L.J. Intracerebral grafting: a tool for the neurobiologist. (1991) Neuron. 6(1):1-12.

Hellweg, R., Fischer, W., Hock, C., Gage, F.H., Björklund, A., Thoenen, H. Nerve growth factor levels and choline acetyltransferase activity in the brain of aged rats with spatial memory impairments. (1990) Brain Research. 537(1-2):123-30.

+ expand abstract

Tuszynski, M.H., U, H.S., Amaral, D.G., Gage, F.H. Nerve growth factor infusion in the primate brain reduces lesion-induced cholinergic neuronal degeneration. (1990) Journal of Neuroscience. 10(11):3604-14.

+ expand abstract

Gage, F.H. Intracerebral grafting of genetically modified cells acting as biological pumps. (1990) Trends in Pharmacological Sciences. 11(11):437-9.

Qian, N., Sejnowski, T.J. When is an inhibitory synapse effective? (1990) Proceedings of the National Academy of Sciences of the United States of America. 87(20):8145-8149.

+ expand abstract

Erselius, J.R., Goulding, M.D., Gruss, P. Structure and expression pattern of the murine Hox-3.2 gene. (1990) Development. 110(2):629-642.

+ expand abstract

Fagan, A.M., Gage, F.H. Cholinergic sprouting in the hippocampus: a proposed role for IL-1. (1990) Exp. Neurol. 110(1):105-20.

+ expand abstract

Jinnah, H.A., Gage, F.H., Friedmann, T. Animal models of Lesch-Nyhan syndrome. (1990) Brain Research Bulletin. 25(3):467-75.

+ expand abstract

Foster, G.A., Brodin, E., Gage, F.H., Maxwell, D.J., Roberts, M.H., Sharp, T. Restoration of function to the denervated spinal cord after implantation of embryonic 5HT- and substance P-containing raphe neurones. (1990) Progress in Brain Research. 82:247-59.

Pfaff, S.L., Tamkun, M.M., Taylor, W.L. pOEV: a Xenopus oocyte protein expression vector. (1990) Analytical Biochemistry. 188(1):192-9.

+ expand abstract

Lehky, S.R., Sejnowski, T.J. Neural model of stereoacuity and depth interpolation based on a distributed representation of stereo disparity. (1990) Journal of Neuroscience. 10(7):2281-2299.

+ expand abstract

Hatzopoulos, A.K., Stoykova, A.S., Erselius, J.R., Goulding, M., Neuman, T., Gruss, P. Structure and expression of the mouse Oct2a and Oct2b, two differentially spliced products of the same gene. (1990) Development. 109(2):349-362.

+ expand abstract

Lehky, S.R., Sejnowski, T.J. Neural network model of visual cortex for determining surface curvature from images of shaded surfaces. (1990) Proceedings of the Royal Society of London. Series B, Biological sciences. 240(1298):251-278.

+ expand abstract

Lehky, S.R., Pouget, A., Sejnowski, T.J. Neural models of binocular depth perception. (1990) Cold Spring Harbor Symposia on Quantitative Biology. 55:765-777.

Shimohama, S., Saitoh, T., Gage, F.H. Differential expression of protein kinase C isozymes in rat cerebellum. (1990) J. Chem. Neuroanat. 3(5):367-75.

+ expand abstract

Buzsáki, G., Chen, L.S., Gage, F.H. Spatial organization of physiological activity in the hippocampal region: relevance to memory formation. (1990) Progress in Brain Research. 83:257-68.

+ expand abstract

Fisher, L.J., Young, S.J., Groves, P.M., Gage, F.H. Extracellular properties of cells within mesencephalon suspension grafts in rat striatum. (1990) Progress in Brain Research. 82:473-9.

Higgins, G.A., Koh, S., Neve, R.L., Mufson, E.J., Chen, K.S., Gage, F.H. Trophic regulation of basal forebrain gene expression in aging and Alzheimer's disease. (1990) Progress in Brain Research. 86:239-55.

Callaway, E.M., Katz, L.C. Emergence and refinement of clustered horizontal connections in cat striate cortex. (1990) Journal of Neuroscience. 10(4):1134-1153.

+ expand abstract

Pyramidal cells in layer 2/3 of adult cat striate cortex have long, intrinsic horizontal axon collaterals within both layer 2/3 and layer 5. These collaterals form periodic "clusters" of finer axon branches that link columns of similar orientation selectivity. We have investigated the sequence of events and possible mechanisms underlying the development of these clustered intrinsic horizontal connections using a combination of neuronal tracers and intracellular staining. Small injections of fluorescent latex microspheres made during the first postnatal week (at P4-6), when examined in tangential sections, produced an even, unclustered distribution of retrogradely labeled cells up to 2 mm from the injection site. At P8, retrograde labeling extended over a larger area and clustering was discernible, primarily among the most distant labeled cells. At both P6 and P8, labeling was similar in layers 2/3 and 5, indicating that the transition from clustered to unclustered connections occurred simultaneously for cells in superficial and deep laminae. By the end of the second postnatal week (P12-15), retrogradely labeled cells were far more clustered both within and beyond the extent of P6 label; the density of labeled cells was high throughout the labeled region, but much higher within clusters. The periodicity of these nascent clusters was similar to that in the adult. Despite obvious clustering, the pattern of retrograde label observed following injections at 2-3 weeks (P12-21) differed markedly from the adult, in that the regions between clusters contained many labeled cells. Over the next 3 weeks, the connections were refined, so that by the sixth postnatal week (P36-38), regions between clusters contained very few retrogradely labeled cells and the overall pattern of retrograde label was indistinguishable from that in adults. Despite differences in postmigratory ages of neurons from the superficial and deep laminae, clustering of retrogradely labeled cells from these 2 populations was similar at all ages. Experiments in which 2-3 weeks elapsed between the time microsphere injections were made and animals were killed demonstrated that neither the initial formation of crude clusters nor their refinement was due to cell death. Instead, cluster refinement resulted from specific process elimination. When a red microsphere injection at P15 was followed by a green microsphere injection at exactly the same location on P29, the earlier injection resulted in crude clustering, as expected. Virtually all of the cells double-labeled by the later injection were within the densest clusters of label from the early injection.(ABSTRACT TRUNCATED AT 400 WORDS)

Thal, L.J., Mandel, R.J., Terry, R.D., Buzsaki, G., Gage, F.H. Nucleus basalis lesions fail to induce senile plaques in the rat. (1990) Experimental Neurology. 108(1):88-90.

+ expand abstract

Higgins, G.A., Oyler, G.A., Neve, R.L., Chen, K.S., Gage, F.H. Altered levels of amyloid protein precursor transcripts in the basal forebrain of behaviorally impaired aged rats. (1990) Proceedings of the National Academy of Sciences of the United States of America. 87(8):3032-6.

+ expand abstract

Tuszyński, M.H., Gage, F.H. Potential use of neurotrophic agents in the treatment of neurodegenerative disorders. (1990) Acta Neurobiologiae Experimentalis. 50(4-5):311-22.

+ expand abstract

Dragunow, M., Goulding, M., Faull, R.L., Ralph, R., Mee, E., Frith, R. Induction of c-fos mRNA and protein in neurons and glia after traumatic brain injury: pharmacological characterization. (1990) Exp. Neurol. 107(3):236-248.

+ expand abstract

Tuszynski, M.H., Buzsaki, G., Gage, F.H. Nerve growth factor infusions combined with fetal hippocampal grafts enhance reconstruction of the lesioned septohippocampal projection. (1990) Neuroscience. 36(1):33-44.

+ expand abstract

Tuszynski, M.H., Armstrong, D.M., Gage, F.H. Basal forebrain cell loss following fimbria/fornix transection. (1990) Brain Research. 508(2):241-8.

+ expand abstract

Buzsáki, G., Smith, A., Berger, S., Fisher, L.J., Gage, F.H. Petit mal epilepsy and parkinsonian tremor: hypothesis of a common pacemaker. (1990) Neuroscience. 36(1):1-14.

+ expand abstract

Short, M.P., Rosenberg, M.B., Ezzedine, Z.D., Gage, F.H., Friedmann, T., Breakefield, X.O. Autocrine differentiation of PC12 cells mediated by retroviral vectors. (1990) Developmental Neuroscience. 12(1):34-45.

+ expand abstract

Shults, C.W., Hashimoto, R., Brady, R.M., Gage, F.H. Dopaminergic cells align along radial glia in the developing mesencephalon of the rat. (1990) Neuroscience. 38(2):427-36.

+ expand abstract

Mahanthappa, N.K., Gage, F.H., Patterson, P.H. Adrenal chromaffin cells as multipotential neurons for autografts. (1990) Progress in Brain Research. 82:33-9.

Gage, F.H., Buzsáki, G., Armstrong, D.M. NGF-dependent sprouting and regeneration in the hippocampus. (1990) Progress in Brain Research. 83:357-70.

+ expand abstract

Gage, F.H., Rosenberg, M.B., Tuszynski, M.H., Yoshida, K., Armstrong, D.M., Hayes, R.C., Friedmann, T. Gene therapy in the CNS: intracerebral grafting of genetically modified cells. (1990) Progress in Brain Research. 86:205-17.

+ expand abstract

Gage, F.H., Fisher, L.J., Jinnah, H.A., Rosenberg, M.B., Tuszynski, M.H., Friedmann, T. Grafting genetically modified cells to the brain: conceptual and technical issues. (1990) Progress in Brain Research. 82:1-10.

Goulding, M.D., Gruss, P. The homeobox in vertebrate development. (1989) Current Opinion in Cell Biology. 1(6):1088-93.

Dawson, V.L., Gage, F.H., Hunt, M.A., Wamsley, J.K. Normalization of subtype-specific muscarinic receptor binding in the denervated hippocampus by septodiagonal band grafts. (1989) Exp. Neurol. 106(2):115-24.

+ expand abstract

Chen, K.S., Tuszynski, M.H., Gage, F.H. Role of neurotrophic factors in Alzheimer's disease. (1989) Neurobiology of Aging. 10(5):545-6; discussion 552-3.

+ expand abstract

Chattarji, S., Stanton, P.K., Sejnowski, T.J. Commissural synapses, but not mossy fiber synapses, in hippocampal field CA3 exhibit associative long-term potentiation and depression. (1989) Brain Research. 495(1):145-50.

+ expand abstract

Higgins, G.A., Koh, S., Chen, K.S., Gage, F.H. NGF induction of NGF receptor gene expression and cholinergic neuronal hypertrophy within the basal forebrain of the adult rat. (1989) Neuron. 3(2):247-56.

+ expand abstract

Dragunow, M., Abraham, W.C., Goulding, M., Mason, S.E., Robertson, H.A., Faull, R.L. Long-term potentiation and the induction of c-fos mRNA and proteins in the dentate gyrus of unanesthetized rats. (1989) Neurosci. Lett. 101(3):274-80.

+ expand abstract

Buzsáki, G., Bayardo, F., Miles, R., Wong, R.K., Gage, F.H. The grafted hippocampus: an epileptic focus. (1989) Exp. Neurol. 105(1):10-22.

+ expand abstract

Field potentials and unitary activity were investigated in the grafted and the host hippocampi in freely moving rats and in vitro. The subcortical afferents and efferents of the hippocampus (fimbria-fornix, FF) were removed by aspiration. Solid pieces of hippocampal grafts derived from 15- to 16-day-old fetuses were placed in the lesion cavity in rats with unilateral FF lesions, and cell suspensions prepared from fetal hippocampi were grafted directly into the host hippocampi in animals with bilateral FF lesions. Reciprocal communication between the grafted and the host hippocampi was monitored with a 16-microelectrode probe from 7 to 10 months after grafting. The fluorescent retrograde tracer, Fluorogold, was used to examine graft-host projections and acetylcholinesterase staining to reveal host-derived fibers in the graft. The most typical neuronal pattern of the hippocampal graft was a highly synchronous population burst with concurrent EEG spike. The speed of propagation of the EEG spike within the graft and across the graft-host interface was either fast (greater than 3 m/s) or slow (less than 0.5 m/s). Large amplitude, short duration EEG spikes usually propagated with a high speed, while smaller amplitude, wider spikes with broad population bursts spread at a lower velocity. The direction of propagation was usually uniform indicating that the population burst was triggered by a localized subgroup of highly excitable neurons ("focus"). Spontaneous seizures were also present in the solid graft which frequently invaded the host hippocampus. The incidence of EEG spikes was three times higher in rats with bilateral suspension grafts than in animals with FF lesion only. In about half of the grafted rats spontaneous behavioral seizures were also observed. Intracellular recordings from putative pyramidal cells in the graft and in the host revealed large amplitude (10-12 mV), spontaneously occurring EPSPs. IPSPs were difficult to detect even during depolarizations of up to 20 mV from rest. We suggest that the increased excitability of the hippocampal graft is due to the high incidence of recurrent excitatory collaterals terminating on or close to the somata of pyramidal neurons. Population bursts may spread fast via extensively arborizing axon collaterals or slowly by successively activating new sets of neighboring neurons. Spontaneous behavioral convulsions are explained by assuming that the grafted hippocampus serves as an epileptic focus which is capable of kindling the host brain by repeated seizure induction.(ABSTRACT TRUNCATED AT 400 WORDS)

Batchelor, P.E., Armstrong, D.M., Blaker, S.N., Gage, F.H. Nerve growth factor receptor and choline acetyltransferase colocalization in neurons within the rat forebrain: response to fimbria-fornix transection. (1989) Journal of Comparative Neurology. 284(2):187-204. DOI: 10.1002/cne.902840204

+ expand abstract

Although it is well known that magnocellular cholinergic basal forebrain neurons are trophically responsive to nerve growth factor (NGF) and contain NGF receptors (NGFr), the exact distribution of forebrain NGFr-immunoreactive neurons and the degree to which cholinergic neurons are colocalized with them have remained in question. In this study we employed a very sensitive double-labelling method and examined in the same tissue section the distribution and cellular features of NGFr-positive and choline acetyltransferase (ChAT)-immunolabelled neurons within the rat basal forebrain. Throughout this region the majority of magnocellular basal forebrain neurons were immunoreactive for both NGFr and ChAT. However, a small percentage of neurons in the ventral portion of the vertical limb of the diagonal band of Broca were immunoreactive only for NGFr, whereas a larger population of magnocellular neurons in the substantia innominata exhibited only ChAT immunoreactivity. No NGFr-immunoreactive cells were found associated with ChAT-positive neurons in the striatum, neocortex, or hippocampus, and no single-labelled NGFr-immunoreactive neurons were found outside the basal forebrain area, except for a large number of positive-labelled cells along the ventricular walls of the third ventricle. In addition to its function in maintaining the normal integrity of the basal forebrain and cholinergic, peripheral sympathetic, and neural-crest-derived sensory neurons, NGF may also have a role in the growth of these neurons after damage to the nervous system. To examine this postulate the hippocampus was denervated of its septal input and examined 8 weeks later. Two populations of neurons were found to have undergone collateral sprouting--namely, the midline magnocellular cholinergic neurons of the dorsal hippocampus and the sympathetic noradrenergic neurons of the superior cervical ganglion. Both of these neuronal populations also stained strongly for NGFr. In contrast, the small intrinsic cholinergic neurons of the hippocampus exhibited neither sprouting response nor staining for NGFr. In view of these results, we suggest that the differing sprouting responses demonstrated by these three neuronal populations may be due to their responsiveness to NGF, as indicated by the presence or absence of NGF receptors.

Buzsàki, G., Bickford, R.G., Ryan, L.J., Young, S., Prohaska, O., Mandel, R.J., Gage, F.H. Multisite recording of brain field potentials and unit activity in freely moving rats. (1989) Journal of Neuroscience Methods. 28(3):209-17.

+ expand abstract

Mandel, R.J., Gage, F.H., Thal, L.J. Spatial learning in rats: correlation with cortical choline acetyltransferase and improvement with NGF following NBM damage. (1989) Exp. Neurol. 104(3):208-17.

+ expand abstract

Shimohama, S., Rosenberg, M.B., Fagan, A.M., Wolff, J.A., Short, M.P., Breakefield, X.O., Friedmann, T., Gage, F.H. Grafting genetically modified cells into the rat brain: characteristics of E. coli beta-galactosidase as a reporter gene. (1989) Brain Res. Mol. Brain Res. 5(4):271-8.

+ expand abstract

Buzsáki, G., Ponomareff, G.L., Bayardo, F., Ruiz, R., Gage, F.H. Neuronal activity in the subcortically denervated hippocampus: a chronic model for epilepsy. (1989) Neuroscience. 28(3):527-38.

+ expand abstract

Spontaneous and evoked field potentials and cellular discharges were studied in the subcortically denervated hippocampus of the freely moving rat. The fimbria fornix, the ventral hippocampal commissure, and the supracallosal afferent fibers were removed by aspiration, and recordings were made 3-5 months after the lesion. Two types of spontaneous interictal spikes were observed. Type 1 interictal spike had identical depth distribution to physiological sharp waves but they were shorter in duration (less than 40 ms), larger in amplitude (greater than 2.5 mV) and population spikes were riding on the main deflection. Type 2 interictal spikes were negative in the stratum oriens and positive in the pyramidal layer and stratum radiatum of both CA1 and CA3. The amplitude of both types of interictal spikes could exceed 6 mV. We suggest that interictal spikes were initiated randomly in different subpopulations of the CA2-3 region and the location of the initiating population burst determined the polarity and amplitude of the extracellular interictal spike. Repetitive stimulation of the perforant path (5 Hz, 6 s) evoked markedly uniform afterdischarges in both intact and fimbria fornix-deprived rats. The threshold of afterdischarges was significantly lower, the seizure spread to the contralateral hippocampus was slower, and secondary afterdischarges lasted significantly longer in the lesioned rats. We suggest that under physiological conditions the electrical stability of the hippocampus is ensured by the feed-forward inhibitory action of subcortical afferents. Removal of tonic inhibitory influences and/or sprouting of local axon collaterals allows extreme synchronization and reverberation of information in the entorhinal-hippocampal-entorhinal cortex circuitry. The presence of interictal spikes and increased susceptibility to seizures for several months after the lesion offers the fimbria-fornix-deprived hippocampus a useful chronic preparation to study the mechanisms of limbic epilepsy.

Shapiro, M.L., Simon, D.K., Olton, D.S., Gage, F.H., Nilsson, O., Björklund, A. Intrahippocampal grafts of fetal basal forebrain tissue alter place fields in the hippocampus of rats with fimbria-fornix lesions. (1989) Neuroscience. 32(1):1-18.

+ expand abstract

Gage, F.H., Tuszynski, M.H., Chen, K.S., Armstrong, D., Buzsáki, G. Survival, growth and function of damaged cholinergic neurons. (1989) EXS. 57:259-74.

+ expand abstract

Buzsàki, G., Gage, F.H. The cholinergic nucleus basalis: a key structure in neocortical arousal. (1989) EXS. 57:159-71.

+ expand abstract

Callaway, E.M., Soha, J.M., Van Essen, D.C. Differential loss of neuromuscular connections according to activity level and spinal position of neonatal rabbit soleus motor neurons. (1989) Journal of Neuroscience. 9(5):1806-1824.

+ expand abstract

We have tested whether the ability of synapses to compete for occupancy of endplates during neuromuscular synapse elimination is affected by differences in the spinal position or in the activity level of the parent motor neuron. To test the role of spinal position, the relative sizes of motor units for motor neurons from middle and extreme (rostral/caudal) positions in the rabbit soleus motor pool were determined at 3 postnatal ages: 4-5 d ("early" ages, when the soleus is heavily polyinnervated), 8-9 d ("intermediate"), and 11-15 d ("late," when the soleus has just reached singly innervated state). Average motor unit sizes from extreme ventral roots were similar to those from middle ventral roots in early-aged soleus muscles but were significantly smaller (by 18-27%) for both intermediate and late muscles. Thus, motor neurons from extreme positions evidently compete less effectively for retention of synapses than those from middle positions. To test the role of differential activity, inactive and active synapses were pitted directly against one another by implanting Silastic plugs laden with tetrodotoxin (TTX) into one of the spinal nerves containing a minority of the soleus motor axons. Differential activity was maintained during a period of extensive synapse loss, from the time of the implant at day 4 or 5 until the intermediate age (day 8-9). Motor unit twitch tensions were subsequently measured to determine the relative number of synapses retained by individual active and inactive motor neurons. The inactivated motor units were on average significantly larger (by more than 50%) than the corresponding group from normal and control-implanted animals. The abnormally large size of inactivated motor units persisted in animals allowed to recover from the TTX block and examined after multiple innervation had disappeared. Hence, the effect of the TTX block cannot be attributed to a simple slowing of synapse elimination specifically among the inactive motor neurons. We conclude that complete presynaptic inactivity improves the chances of survival relative to that for normal activity during synapse elimination in the neonatal rabbit soleus muscle. This difference in competitive ability may contribute to the development of an important characteristic of adult muscles, the correlation between motor unit size and recruitment threshold.

Stanton, P.K., Sejnowski, T.J. Associative long-term depression in the hippocampus induced by hebbian covariance. (1989) Nature. 339(6221):215-8. DOI: 10.1038/339215a0

+ expand abstract

Tuszynski, M.H., Jinnah, H.A., Gage, F.H. Delivery of neuroactive compounds to the brain: potential utility of genetically modified cells. (1989) Neurobiology of Aging. 10(5):644-5; discussion 648-50.

+ expand abstract

Gage, F.H., Dunnett, S.B., Bjorklund, A. Age-related impairments in spatial memory are independent of those in sensorimotor skills. (1989) Neurobiology of Aging. 10(4):347-52.

+ expand abstract

Phelps, C.H., Gage, F.H., Growdon, J.H., Hefti, F., Harbaugh, R., Johnston, M.V., Khachaturian, Z.S., Mobley, W.C., Price, D.L., Raskind, M. Potential use of nerve growth factor to treat Alzheimer's disease. (1989) Neurobiology of Aging. 10(2):205-7.

Buzsáki, G., Wiesner, J., Henriksen, S.J., Gage, F.H. Long-term potentiation of evoked and spontaneous neuronal activity in the grafted hippocampus. (1989) Exp Brain Res. 76(2):401-8.

+ expand abstract

Buzsáki, G., Gage, F.H. Absence of long-term potentiation in the subcortically deafferented dentate gyrus. (1989) Brain Research. 484(1-2):94-101.

+ expand abstract

Callaway, E.M., Van Essen, D.C. Slowing of synapse elimination by alpha-bungarotoxin superfusion of the neonatal rabbit soleus muscle. (1989) Developmental Biology. 131(2):356-365.

+ expand abstract

Soha, J.M., Callaway, E.M., Van Essen, D.C. Lack of fiber type selectivity during reinnervation of neonatal rabbit soleus muscle. (1989) Developmental Biology. 131(2):401-414.

+ expand abstract

Gage, F.H., Batchelor, P., Chen, K.S., Chin, D., Higgins, G.A., Koh, S., Deputy, S., Rosenberg, M.B., Fischer, W., Bjorklund, A. NGF receptor reexpression and NGF-mediated cholinergic neuronal hypertrophy in the damaged adult neostriatum. (1989) Neuron. 2(2):1177-84.

+ expand abstract

Fischer, W., Gage, F.H., Björklund, A. Degenerative Changes in Forebrain Cholinergic Nuclei Correlate with Cognitive Impairments in Aged Rats. (1989) European Journal of Neuroscience. 1(1):34-45.

+ expand abstract

Goulding, M.D., Ralph, R.K. Cyclic-AMP-induced c-fos expression and its relevance to differentiation of a transformed mast cell line. (1989) Biochimica et Biophysica Acta. 1007(1):99-108.

+ expand abstract

Mandel, R.J., Gage, F.H., Thal, L.J. Enhanced detection of nucleus basalis magnocellularis lesion-induced spatial learning deficit in rats by modification of training regimen. (1989) Behavioural Brain Research. 31(3):221-9.

+ expand abstract

Foster, G.A., Roberts, M.H., Wilkinson, L.S., Björklund, A., Gage, F.H., Hökfelt, T., Schultzberg, M., Sharp, T. Structural and functional analysis of raphe neurone implants into denervated rat spinal cord. (1989) Brain Research Bulletin. 22(1):131-7.

+ expand abstract

Rosenberg, M.B., Friedmann, T., Robertson, R.C., Tuszynski, M., Wolff, J.A., Breakefield, X.O., Gage, F.H. Grafting genetically modified cells to the damaged brain: restorative effects of NGF expression. (1988) Science. 242(4885):1575-8.

+ expand abstract

Buzsáki, G., Ponomareff, G., Bayardo, F., Shaw, T., Gage, F.H. Suppression and induction of epileptic activity by neuronal grafts. (1988) Proceedings of the National Academy of Sciences of the United States of America. 85(23):9327-30.

+ expand abstract

Churchland, P.S., Sejnowski, T.J. Perspectives on cognitive neuroscience. (1988) Science. 242(4879):741-5.

+ expand abstract

Buzsaki, G., Bickford, R.G., Ponomareff, G., Thal, L.J., Mandel, R., Gage, F.H. Nucleus basalis and thalamic control of neocortical activity in the freely moving rat. (1988) Journal of Neuroscience. 8(11):4007-26.

+ expand abstract

EEG and single-unit techniques have been used to study the EEG correlates of cellular firing in the neocortex, n. reticularis (RT) and "specific" thalamic nuclei, and the cholinergic forebrain area (nucleus basalis, NB). Neuronal firing was related to the ongoing behavior of the rat. In addition, using a 16-channel neocortical recording/mapping system, we studied the effects of ibotenic acid lesion of NB, RT, and other thalamic nuclei on the patterns and spatial distribution of neocortical electrical activity. The majority of neurons in neocortex, NB, and RT increased their firing rates during walking, as compared to during immobility, with concurrent decrease of delta power in the neocortical EEG. During immobility, high-voltage spindles (HVS; greater than 1 mV) were occasionally recorded from the neocortex. Depth profiles of HVS and slow delta waves were different in the neocortex. Neocortical cells decreased their discharge frequency during the positive portion of delta waves recorded in layers V and VI. All cells in the neocortex and specific thalamic nuclei fired rhythmically and phase-locked to the spike component of HVS. RT neurons showed an opposite phase relationship and fired mainly during the wave component of HVS. Half of the NB neurons also showed phasic modulation with HVS. Circumscribed lesion of RT and extensive damage of other thalamic regions, including the intralaminar nuclei, suppressed HVS but had no effect on the neocortical EEG correlates of behavior. In sharp contrast, damage to the NB resulted in a dramatic increase of slow delta waves on the side of the lesion, mimicking the effect of scopolamine administration. We suggest that the NB plays a key role in neocortical arousal by directly activating the neocortex and by suppressing the rhythm generation in the RT-thalamocortical circuitry. We further suggest that the NB system may serve as a structural basis for the concept of the generalized ascending activation of Moruzzi and Magoun (1949).

Pfaff, S.L., Duesberg, P.H. Two autonomous myc oncogenes in avian carcinoma virus OK10. (1988) Journal of Virology. 62(10):3703-9.

+ expand abstract

Gage, F.H., Olejniczak, P., Armstrong, D.M. Astrocytes are important for sprouting in the septohippocampal circuit. (1988) Exp. Neurol. 102(1):2-13.

+ expand abstract

Sejnowski, T.J., Koch, C., Churchland, P.S. Computational neuroscience. (1988) Science. 241(4871):1299-306.

+ expand abstract

Buzsáki, G., Bickford, R.G., Armstrong, D.M., Ponomareff, G., Chen, K.S., Ruiz, R., Thal, L.J., Gage, F.H. Electric activity in the neocortex of freely moving young and aged rats. (1988) Neuroscience. 26(3):735-44.

+ expand abstract

Brundin, P., Strecker, R.E., Gage, F.H., Lindvall, O., Björklund, A. Intracerebral transplantation of dopamine neurons: understanding the functional role of the mesolimbocortical dopamine system and developing a therapy for Parkinson's disease. (1988) Annals of the New York Academy of Sciences. 537:148-60.

Qian, N., Sejnowski, T.J. Predicting the secondary structure of globular proteins using neural network models. (1988) Journal of Molecular Biology. 202(4):865-84.

+ expand abstract

Armstrong, D.M., Hersh, L.B., Gage, F.H. Morphologic alterations of cholinergic processes in the neocortex of aged rats. (1988) Neurobiology of Aging. 9(2):199-205.

+ expand abstract

Lehky, S.R., Sejnowski, T.J. Network model of shape-from-shading: neural function arises from both receptive and projective fields. (1988) Nature. 333(6172):452-4. DOI: 10.1038/333452a0

+ expand abstract

Gage, F.H., Chen, K.S., Buzsaki, G., Armstrong, D. Experimental approaches to age-related cognitive impairments. (1988) Neurobiology of Aging. 9(5-6):645-55.

+ expand abstract

Rats exhibit morphological, biochemical, and metabolic changes in their brains, as well as cognitive deficits, with aging. Aged rats were found to be significantly impaired compared to young rats in a water maze task and test of motor coordination, and show reduced locomotor activity and exploration. Although aged rats did exhibit deficits as a group, not all aged rats were impaired. Additionally, the subgroup that was impaired on one task was not necessarily the subgroup that was impaired on another task. The cholinergic projection neurons in the basal forebrain region were significantly atrophied in the aged rodent. The degree of atrophy was highly correlated with the cognitive impairment exhibited on the Morris water maze task. Swollen choline acetyltransferase (ChAT)-positive "plaque-like" structures were observed in the neocortex of the aged but not the young rats. Declines in cholinergic activity in the brain has also been observed during aging. Biochemical measurements of ChAT in the basal forebrain region of aged rats revealed small but consistent decreases in ChAT activity compared to young rats. General metabolic activity, measured by the 2-deoxyglucose method, was also decreased in the hippocampal CA1 and CA3 fields, the dentate gyrus, the medial septal-diagonal band area, and the prefrontal cortex of aged rats. There was a significant correlation between the decrease in glucose utilization and deficits on the Morris water maze. Most aged rats exhibit pathological EEG patterns as reflected by frequent long-duration high voltage neocortical spindles (HVS) during immobility. Bilateral lesions of the nucleus basalis and scopolamine treatment increased the incidence of HVS, thereby mimicking changes in the aged brain. We attempted to ameliorate the cognitive deficits observed in subgroups or impaired rats by either: (1) implanting fetal cells of basal forebrain origin into the hippocampus, or (2) infusing nerve growth factor (NGF) chronically into the lateral ventricle. The grafts appeared to facilitate an improvement in the ability of the impaired aged rats to perform in the Morris water maze. This improved performance was reversed by injections of atropine at doses that did not affect the behavior of young animals that performed well in the same task. These results suggest that enhancement of the cholinergic system could have an effect on the performance of the impaired aged animals. The study of the effects of infusions of NGF clearly demonstrate that the ability of impaired aged rats to remember what they had previously learned was increased after NGF treatment.(ABSTRACT TRUNCATED AT 400 WORDS)

Blaker, S.N., Armstrong, D.M., Gage, F.H. Cholinergic neurons within the rat hippocampus: response to fimbria-fornix transection. (1988) Journal of Comparative Neurology. 272(1):127-38. DOI: 10.1002/cne.902720109

+ expand abstract

The distribution and morphologic characteristics of choline acetyltransferase (ChAT)-containing neurons were studied throughout the rostrocaudal extent of the rat hippocampus and in a midline area just dorsal to the dorsal hippocampus. Peroxidase reaction product was observed with the aid of immunohistochemical methods and a high-titer polyclonal antibody against ChAT, the acetylcholine biosynthetic enzyme. ChAT-positive cells in the hippocampus were characterized by small, round or oval perikarya with two or more proximal processes. They were located within the caudal and temporal hippocampal formation, predominantly within the subiculum, in the stratum lacunosum moleculare, at the border of the stratum lacunosum moleculare and the stratum radiatum, and in the molecular layer of the dentate gyrus. The cells resembled in morphology the small, bipolar and multipolar neocortical ChAT-immunoreactive cells. In addition to the hippocampus, ChAT-positive neurons were observed caudally in a region just above the dorsal hippocampal commissure and rostrally in the columns of the fornix. These cells were large with an oval perikarya and darkly labeled compared to neurons in the hippocampus. They more closely resembled the ChAT-positive neurons in the midline raphe of the medial septal nucleus. Examination of the rat hippocampus 2 and 8 weeks following unilateral lesioning of the fimbria-fornix and supracallosal striae revealed a sparse innervation of ChAT-positive fibers in the hippocampus ipsilateral to the lesion. ChAT-labeled neurons in the hippocampus did not appear to sprout in response to the lesion. In contrast, ChAT-positive cells in the midline did appear to sprout into the medial dorsal subiculum and dorsal medial hippocampus. We conclude that these two populations of cells are distinct with respect to their response to hippocampal denervation and, furthermore, that this distinction may be attributed to a differential response to nerve growth factor.

Gage, F.H., Blaker, S.N., Davis, G.E., Engvall, E., Varon, S., Manthorpe, M. Human amnion membrane matrix as a substratum for axonal regeneration in the central nervous system. (1988) Experimental Brain Research. 72(2):371-80.

+ expand abstract

Human Amnion Membrane Matrix (HAMM) was used as a substratum for the regeneration of neuronal axons in the central nervous system. A large piece of HAMM was bound to nitrocellulose paper (NCP) as a supporting material, and cut into small strips. Aspirative lesions of the fimbria-fornix were made in adult rats leaving a cavity separating the septum from the hippocampus. In the same operation a small piece of HAMM-NCP was placed into the cavity with one end abutting the axotomized septum and the other end abutting the denervated hippocampus. At times between 2 weeks and 3 months after surgery the brains of the animals were examined histologically for 1) host response to the implant; 2) maintenance of HAMM-NCP in the originally implanted orientation; 3) growth of acetylcholinesterase (AChE)-positive fibers on the HAMM; 4) growth of the AChE-positive fibers into the denervated hippocampus; and 5) non-neuronal cells on the HAMM. The NCP remained in place over the 3-month period. In most cases the HAMM and NCP remained apposed and caused no greater reaction in the brain beyond that created in response to the aspirative lesion alone. AChE-positive fibers grew out from the septum onto the HAMM by 2 weeks, and by 8 weeks more extensive growth was observed on the HAMM. By 8-weeks, AChE fibers could be clearly seen coming off the membrane and entering the host hippocampus. By double-labelling for the basement membrane side of the HAMM (using anti-human laminin antibodies) and for cholinergic fibers (using AChE histochemistry) in the same sections, it was possible to see fibers clearly growing on the laminin-positive side of the HAMM but little or no growth on the opposing laminin-negative stromal side. The most important variables for extensive growth appeared to be the accurate placement of the implant and the amount of time following the lesions. The placement of the matrix on NCP prior to implantation in the brain made it easier to orient the membrane between the septum and the hippocampus, and seemed to assist in maintaining the membrane in that orientation. The HAMM represents a useful, regeneration-promoting grafting material for central nervous system repair studies.

Buzsáki, G., Freund, T., Björklund, A., Gage, F.H. Restoration and deterioration of function by brain grafts in the septohippocampal system. (1988) Progress in Brain Research. 78:69-77.

Blaker, S.N., Davis, G.E., Manthorpe, M., Engvall, E., Varon, S., Gage, F.H. Human amnion membrane as a substratum for axonal elongation in vitro and in vivo. (1988) Progress in Brain Research. 78:435-8.

Foster, G.A., Schultzberg, M., Gage, F.H., Björklund, A., Hökfelt, T., Cuello, A.C., Verhofstad, A.A., Visser, T.J., Emson, P.C. Transmitter expression and morphological development of embryonic medullary and mesencephalic raphé neurones after transplantation to the adult rat central nervous system. III. Grafts to the striatum. (1988) Exp Brain Res. 70(2):242-55.

+ expand abstract

Foster, G.A., Schultzberg, M., Gage, F.H., Björklund, A., Hökfelt, T., Cuello, A.C., Verhofstad, A.A., Visser, T.J., Emson, P.C. Transmitter expression and morphological development of embryonic medullary and mesencephalic raphé neurones after transplantation to the adult rat central nervous system. II. Grafts to the hippocampu (1988) Experimental Brain Research. 70(2):225-41.

+ expand abstract

Suspensions of cells taken from the mesencephalic or medullary raphé regions of the 13-14 day old embryonic rat brain were injected into the hippocampus of adult rats which had previously been denervated of its serotoninergic input by 5,7-dihydroxytryptamine. At periods of up to 14 months after implantation, the brains were taken for immunohistochemical analysis of 5-hydroxytryptamine (5HT)-, substance P (SP)- and thyrotropin releasing hormone (TRH)-like immunoreactivity. Surviving grafts were found in all animals. The implants derived from mesencephalic raphé contained neurones immunoreactive to 5HT, SP or both substances together. On average 19% of the potential number of mesencephalic 5HT neurones were found in the grafts. Outgrowth of 5HT-immunoreactive fibres was extensive, and displayed the typical pattern of 5HT innervation in the normal hippocampus-the densest plexuses were found in the dentate gyrus, with sparser networks in the CA1 and CA2 regions. SP-positive processes were principally found only in the graft itself. Transplants of medullary raphé cells contained 5HT-immunoreactive neurones, some of which also contained SP-and/or TRH-like immunoreactivity, thereby mirroring the situation found in the caudal raphé complex in situ. An average of 18% of the total available medullary serotoninergic neurones were found at each graft site. A rich outgrowth of 5HT-immunoreactive varicose processes was evident, with the same pattern as the 5HT innervation by the mesencephalic raphé grafts, and as in the normal hippocampus. SP- and TRH-positive fibres were essentially detectable only in the graft, but not in the host hippocampus. The present studies indicate that the milieu of the hippocampus does not preferentially attenuate the survival of the serotoninergic cells which do not normally project to it. Nor is the fibre outgrowth of these medullary raphé 5HT neurones significantly different from that of the mesencephalic raphé. However, the hippocampal environment may be responsible for the appearance of SP-LI in the otherwise apparently solely 5HT-containing mesencephalic raphé neurones, and for repressing the outgrowth of fibres containing TRH-, or SP-like immunoreactivity, regardless of their origin.

Buzsáki, G., Gage, F.H. Mechanisms of action of neural grafts in the limbic system. (1988) Can J Neurol Sci. 15(2):99-105.

+ expand abstract

Gage, F.H., Wolff, J.A., Rosenberg, M.B., Xu, L., Yee, J.K., Shults, C., Friedmann, T. Implantation of genetically engineered cells to the brain. (1988) Progress in Brain Research. 78:651-8.

Bengtsson, F., Nobin, A., Falck, B., Gage, F.H., Jeppsson, B. Effect of oral branched chain amino acids on behavior and brain serotonin metabolism in portacaval shunted rats. (1988) World Journal of Surgery. 12(2):246-54.

Sejnowski, T.J. Neural populations revealed. (1988) Nature. 332(6162):308. DOI: 10.1038/332308a0

Gage, F.H., Armstrong, D.M., Williams, L.R., Varon, S. Morphological response of axotomized septal neurons to nerve growth factor. (1988) Journal of Comparative Neurology. 269(1):147-55. DOI: 10.1002/cne.902690112

+ expand abstract

Gage, F.H., Brundin, P., Strecker, R., Dunnett, S.B., Isacson, O., Bjorklund, A. Intracerebral neuronal grafting in experimental animal models of age-related motor dysfunction. (1988) Annals of the New York Academy of Sciences. 515:383-94.

+ expand abstract

The combined morphological, biochemical, electrophysiological, and behavioral data summarized above show that implanted embryonic nerve cells in some cases can substitute quite well for a lost intrinsic neuronal system in mammals. The intracerebral implants probably exert their effects in several ways. The functional effects seen with grafts placed into one of the cerebral ventricles (such as those described in the studies of Perlow et al., Freed et al., and Gash et al.) are thus probably explained on the basis of a diffuse release of an active amine or peptide into the host CSF and adjacent brain tissue. In other instances, as in animals with DA-rich grafts reinnervating the neostriatum, we believe that the available data provide quite substantial evidence that the behavioral recovery is caused by the ability of the grafted neurons to reinnervate relevant parts of the host brain. This is illustrated by the studies mentioned above that show that the degree of functional recovery in 6-OHDA-lesioned rats with nigral transplants is directly correlated with the extent of striatal DA reinnervation and that the "profile" of functional recovery is dependent on that area of the striatal complex that is reinnervated by the graft. This point is particularly well illustrated in a further study in which rats with electrodes implanted into the center of intracortical nigral grafts were allowed to "self-stimulate" via the graft. The results show that the graft can indeed sustain self-stimulation behavior and that the rate of lever-pressing is related to the proximity between the electrode tip and the DA-containing neurons in the graft. This strongly supports the notion that the implanted DA neurons can transmit behaviorally meaningful and temporally organized information to the host brain via their efferent connections. To what extent the intracerebral implants can be functionally integrated with the host brain is still poorly known, though, and it therefore remains an interesting question for further investigation. The chances for extensive integration may be greatest for neuronal suspension grafts implanted as deposits directly into the depth of the brain, but even solid grafts inserted as whole pieces into the brain have, in several cases, been seen to become reinnervated from the host brain in adult and developing recipients. Nevertheless, a recent HRP study failed to detect any host afferents to intracortical solid nigral grafts, despite the fact that these grafts had themselves formed extensive DA connections in the host striatum and had produced behavioral recovery.(ABSTRACT TRUNCATED AT 400 WORDS)

Armstrong, D.M., Bruce, G., Hersh, L.B., Gage, F.H. Development of cholinergic neurons in the septal/diagonal band complex of the rat. (1987) Brain Research. 433(2):249-56.

+ expand abstract

Gage, F.H., Wolff, J.A., Rosenberg, M.B., Xu, L., Yee, J.K., Shults, C., Friedmann, T. Grafting genetically modified cells to the brain: possibilities for the future. (1987) Neuroscience. 23(3):795-807.

+ expand abstract

Shults, C.W., Johnston, P., Gage, F.H. Comparison of substance K-like and substance P-like fibers and cells in the rat hippocampus. (1987) Brain Research. 426(2):290-6.

+ expand abstract

Isacson, O., Pritzel, M., Dawbarn, D., Brundin, P., Kelly, P.A., Wiklund, L., Emson, P.C., Gage, F.H., Dunnett, S.B., Björklund, A. Striatal neural transplants in the ibotenic acid-lesioned rat neostriatum. Cellular and functional aspects. (1987) Annals of the New York Academy of Sciences. 495:537-55.

Armstrong, D.M., Terry, R.D., Deteresa, R.M., Bruce, G., Hersh, L.B., Gage, F.H. Response of septal cholinergic neurons to axotomy. (1987) Journal of Comparative Neurology. 264(3):421-36. DOI: 10.1002/cne.902640309

+ expand abstract

In the present study we employed quantitative morphometric techniques to assay the response of septal cholinergic neurons following unilateral transection of the fimbria/fornix and supracallosal stria. Analysis of 50-micron-thick tissue sections with a Quantimet 920 image analysis system demonstrated a reduction in ChAT immunoreactivity as early as 1 day following denervation. This decrease was associated with a drop in the number of labeled cells ipsilateral to the lesion and a decrease in the area of cholinergic perikarya on the lesioned and nonlesioned side of the septum. The response at 1 day, however, was transient, and at 4 days the number of labeled neurons was not significantly different from controls. By 8 days we observed a dramatic reduction in the number and size of ChAT-positive cells ipsilateral to the lesion and a reduction in the size of cholinergic perikarya on the contralateral (i.e., nonlesioned) side. These values persisted throughout the remainder of the study. To assess more completely the morphologic response of neurons to axotomy than can be determined in 50-micron-thick tissue sections, we embedded the adjacent immunolabeled tissue section in Epon and then serially sectioned it to a thickness of 0.75-1.0 micron. By using this method, we were able to measure the area, length, and width of the cell, the area of the nucleus and nucleolus, and the position of the nucleus (i.e., eccentricity). Measurements were performed on ChAT-labeled and nonlabeled cells. The results of our studies demonstrate that cholinergic and noncholinergic cells responded to axotomy in a characteristic yet different fashion from each other and that this response could be quantitatively assayed. In general, labeled and nonlabeled cells on the lesioned side of the septum shrink in response to denervation. This shrunken state was reflected in measurements of cellular area, length, width, and nuclear area. Moreover, other measurements of cellular morphology (i.e., area of the nucleolus, position of the nucleus) indicate that none of the neuronal populations examined in the present study displayed morphologic evidence of regeneration. Our results indicate a dramatic loss of cholinergic perikarya ipsilateral to the lesion. Moreover, although a few neurons do persist they do so in a shrunken state. These data provide an essential baseline for the second study in this series, which will evaluate the effect of nerve growth factor on the survival of denervated septal neurons.

Buzsàki, G., Czopf, J., Kondàkor, I., Björklund, A., Gage, F.H. Cellular activity of intracerebrally transplanted fetal hippocampus during behavior. (1987) Neuroscience. 22(3):871-83.

+ expand abstract

Hippocampal tissue derived from 12-, 20-, 25- and 34-mm rat fetuses was placed in a cavity formed by unilateral aspiration of the fimbria-fornix and the overlying neocortical tissue in adult rats. From 4 to 6 months after transplantation the rats were equipped with chronic recording and stimulating electrodes. Single cell activity of the transplant was monitored during running in a wheel, drinking, and sleeping. Both complex-spike cells (n = 151) and single-spike cells (n = 80) were recorded from the graft. A portion of the neurons changed their firing rates and discharge patterns as a function of ongoing behavior. About half of the single-spike cells increased their firing frequency during running. Fifteen per cent of the single-spike cells fired rhythmically at about 8 Hz during running, and the paradoxical phase of sleep and the discharge pattern correlated with rhythmic slow activity (theta) recorded concurrently from the contralateral (intact) hippocampus. These patterns were most frequently obtained from grafts of 20- and 25-mm (16 to 18 embryonic days) fetuses. Graft neurons could be activated by stimulating the ipsilateral hippocampus or the ipsilateral perforant path, with latencies of 8-30 ms. The most common electrical pattern in grafts of all groups was the synchronous bursts of several neighboring cells and concurrent electroencephalogram sharp-waves. Sharp-waves occurred during all behaviors. Large amplitude, high-frequency electroencephalogram spindles (14-18 Hz and 30-50 Hz) and associated neuronal bursts were recorded in grafts of 12-, 20-, and 25-mm fetuses. Based on these findings we suggest that both subcortical afferents and host hippocampal afferents send axons to hippocampal grafts and form viable synaptic connections with a portion of the neurons in the graft. The frequently encountered population bursts are explained by assuming that excitatory collaterals in the graft are more potent in the graft than in the normal hippocampus, and/or GABAergic inhibition is less efficient in the graft.

Isacson, O., Dawbarn, D., Brundin, P., Gage, F.H., Emson, P.C., Björklund, A. Neural grafting in a rat model of Huntington's disease: striosomal-like organization of striatal grafts as revealed by acetylcholinesterase histochemistry, immunocytochemistry and receptor autoradiogr (1987) Neuroscience. 22(2):481-97.

+ expand abstract

Grafts of fetal striatum were implanted in the form of a cell suspension into the brains of rats with prior ibotenic acid lesions of the caudate-putamen. The grafts were placed in three different sites: the lesioned caudate-putamen, or the denervated (but otherwise undamaged) globus pallidus and substantia nigra. After 3-6 months survival the grafts were investigated by means of immunohistochemistry and receptor autoradiography in combination with routine histology and acetylcholinesterase histochemistry. The grafts placed within the lesioned caudate-putamen were at least 10-fold larger larger than those placed in the substantia nigra region, with the grafts placed in the globus pallidus being of intermediate size. In all locations the acetylcholinesterase staining had an uneven, patchy distribution, which was most pronounced in the grafts located within the caudate-putamen. These patches did not bear any obvious relationship to variations in density of the neuronal perikarya within the grafted tissue. Many of the neuropeptide-immunoreactive neuron types present in the normal striatum, such as those containing substance P, [Met]enkephalin, somatostatin, cholecystokinin and neuropeptide Y were also detected in the grafted striatum along with acetylcholinesterase-positive staining. Acetylcholinesterase-positive, [Met]enkephalin-positive, substance P-positive and tyrosine hydroxylase-positive markers all showed uneven, patchy distributions in the grafts. This was also the case for the distribution of dopamine D2 and opiate receptors (as revealed by [3H]spiroperidol and [3H]diprenorphine autoradiography, respectively), whereas muscarinic receptor binding was even throughout the grafts. As is the case in the so-called striosomal patches (neurochemically defined compartments) in the immature intact striatum during the early postnatal period, patches of high acetylcholinesterase staining in the grafts showed partial correspondence with patches of high [Met]enkephalin fibre staining, and dopamine receptor density, and (although to a lesser degree) also with patches of high opiate receptor density and high substance P-immunoreactivity. This correspondence of patches also occurred between tyrosine hydroxylase fibre staining and acetylcholinesterase staining as revealed by grafts placed into the substantia nigra. These results suggest that the fetal striatal cell suspension grafts will give rise to a fairly normal range of striatal neuron and receptor types and that they develop at least some of the striosomal features characteristic for the normal striatum.(ABSTRACT TRUNCATED AT 400 WORDS)

Kesslak, J.P., Frederickson, C.J., Gage, F.H. Quantification of hippocampal noradrenaline and zinc changes after selective cell destruction. (1987) Exp Brain Res. 67(1):77-84.

+ expand abstract

Callaway, E.M., Soha, J.M., Van Essen, D.C. Competition favouring inactive over active motor neurons during synapse elimination. (1987) Nature. 328(6129):422-426. DOI: 10.1038/328422a0

+ expand abstract

Nilsson, O.G., Shapiro, M.L., Gage, F.H., Olton, D.S., Björklund, A. Spatial learning and memory following fimbria-fornix transection and grafting of fetal septal neurons to the hippocampus. (1987) Experimental Brain Research. 67(1):195-215.

+ expand abstract

The ability of intrahippocampal grafts of fetal septal-diagonal band tissue, rich in developing cholinergic neurons, to ameliorate cognitive impairments induced by bilateral fimbria-fornix transections in rats was examined in three experiments using the Morris water-maze to test different aspects of spatial memory. Experiment 1. Rats with fimbriafornix lesions received either septal cell suspension grafts or solid septal grafts; normal rats and rats with lesions alone were used as controls. Sixteen weeks after surgery, the rats' spatial learning and memory were tested in the water-maze using a place test, designed to investigate place navigation performance, in which rats learned to escape from the water by swimming to a platform hidden beneath the water's surface. After 5 days of training, the rats were given a spatial probe test in which the platform was removed from the tank to test spatial reference memory. Experiment 2. The same rats used in Exp. 1 were tested in a delayed-match-to-sample, working memory version of the water-maze task. The platform was located in one of two possible locations during each trial, which was composed of 2 swims. If the rat remembered the location of the platform on the 2nd swim of a trial, it should find the platform more quickly on that swim, and thereby demonstrate working memory. Experiment 3. Prior to receiving fimbria-fornix lesions, normal rats were trained in a modification of the water-maze task using alternating cue navigation and place navigation trials (i.e., with visible or non-visible escape platforms). The retention and reacquisition of the place task and the spatial probe test were examined in repeated tests up to 6 months after the lesion and intrahippocampal grafting of septal cell suspensions. The effects of central muscarinic cholinergic receptor blockade with atropine were also tested. Normal rats performed well in both the place and spatial probe tests. In contrast, rats with fimbria-fornix lesions only were unable to acquire or retain spatial information in any test. Instead, these rats adopted a random, non-spatial search strategy, whereby their latencies to find the platform decreased in the place navigation tasks. Sixty to 80% of the rats with septal suspension or solid grafts had recovered place navigation, i.e., the ability to locate the platform site in the tank, in Exp. 1 and 3, and they showed a significantly improved performance in the working memory test in Exp. 2. Atropine abolished the recovered place navigation in the grafted rats, whereas normal rats were impaired to a lesser extent.(ABSTRACT TRUNCATED AT 400 WORDS)

Björklund, A., Gage, F.H. Grafts of fetal septal cholinergic neurons to the hippocampal formation in aged or fimbria-fornix lesioned rats. (1987) Progress in Brain Research. 72:333-42.

Gage, F.H., Buzsaki, G., Nilsson, O., Björklund, A. Grafts of fetal cholinergic neurons to the deafferented hippocampus. (1987) Progress in Brain Research. 71:335-47.

Varon, S., Williams, L.R., Gage, F.H. Exogenous administration of neuronotrophic factors in vivo protects central nervous system neurons against axotomy induced degeneration. (1987) Progress in Brain Research. 71:191-201.

Davis, G.E., Blaker, S.N., Engvall, E., Varon, S., Manthorpe, M., Gage, F.H. Human amnion membrane serves as a substratum for growing axons in vitro and in vivo. (1987) Science. 236(4805):1106-9.

+ expand abstract

Peterson, G.M., Williams, L.R., Varon, S., Gage, F.H. Loss of GABAergic neurons in medial septum after fimbria-fornix transection. (1987) Neuroscience Letters. 76(2):140-4.

+ expand abstract

Gage, F.H., Björklund, A. Denervation-induced enhancement of graft survival and growth. A trophic hypothesis. (1987) Annals of the New York Academy of Sciences. 495:378-95.

Clarke, D.J., Gage, F.H., Dunnett, S.B., Nilsson, O.G., Björklund, A. Synaptogenesis of grafted cholinergic neurons. (1987) Annals of the New York Academy of Sciences. 495:268-83.

Steinbusch, H.W., Beek, A., Frankhuyzen, A.L., Tonnaer, J.A., Gage, F.H., Björklund, A. Functional activity of raphe neurons transplanted to the hippocampus and caudate-putamen. An immunohistochemical and neurochemical analysis in adult and aged rats. (1987) Annals of the New York Academy of Sciences. 495:169-84.

+ expand abstract

Björklund, A., Gage, F.H. Grafts of fetal septal cholinergic neurons to the hippocampal formation in aged or fimbria-fornix-lesioned rats. (1987) Annals of the New York Academy of Sciences. 495:120-37.

Gage, F.H., Björklund, A. Trophic and growth-regulating mechanisms in the central nervous system monitored by intracerebral neural transplants. (1987) Ciba Foundation Symposium. 126:143-59.

+ expand abstract

Williams, L.R., Vahlsing, H.L., Lindamood, T., Varon, S., Gage, F.H., Manthorpe, M. A small-gauge cannula device for continuous infusion of exogenous agents into the brain. (1987) Exp. Neurol. 95(3):743-54.

+ expand abstract

Fischer, W., Wictorin, K., Björklund, A., Williams, L.R., Varon, S., Gage, F.H. Amelioration of cholinergic neuron atrophy and spatial memory impairment in aged rats by nerve growth factor. (1987) Nature. 329(6134):65-8. DOI: 10.1038/329065a0

+ expand abstract

Buzsáki, G., Gage, F.H., Czopf, J., Björklund, A. Restoration of rhythmic slow activity (theta) in the subcortically denervated hippocampus by fetal CNS transplants. (1987) Brain Research. 400(2):334-47.

+ expand abstract

Solid pieces of the fetal septal region (SG) or hippocampus (HPC) were implanted in a cavity formed by aspiration of the fimbria fornix (FF) and the overlying cingulate cortex on one side in adult rats. In other lesioned animals cell suspensions obtained from the fetal septal area (SS) or the locus coeruleus region of the brainstem (LC) were injected stereotaxically into the deafferented host hippocampus. Six to 9 months after transplantation the animals had chronic recording electrodes implanted into both hippocampi. EEG and unit activity were monitored during running in a wheel, drinking and immobility. Unilateral fimbria-fornix lesions abolished rhythmic slow activity (RSA or theta, theta) in the ipsilateral hippocampus and no recovery was seen up to 9 months later in either the control FF-lesioned animals or in the rats with LC suspension grafts. Recovery of RSA, however, was observed in all animals with solid septal grafts and in some rats with solid HPC grafts. Similar to normal rats, RSA was present only during running and absent during drinking and sitting still. Coherence measurements of RSA between the transplanted and intact hemispheres resulted in high values (0.70-0.95). Concurrent with RSA, interneurons and granule cells in the host hippocampus fired rhythmically at RSA frequency (6-9 Hz). The depth profile and the antero-posterior distribution of the power of RSA correlated with the amount and distribution of the graft-induced acetylcholinesterase-positive reinnervation of the host hippocampus. In contrast to the animals with solid septal grafts, placed within the FF lesion cavity, the rats with intrahippocampal septal suspension grafts displayed only short duration bursts of RSA, and mainly during immobility. Based on these findings it is suggested that at least a proportion of the RSA 'pacemaker' cells of the host septum survives the transection of the fimbria-fornix fibers and that a graft of fetal septal or hippocampal tissue implanted into the lesion cavity may be capable of relaying this pacemaker activity to the host hippocampus. This effect may be due to the ability of the grafted tissue to promote the regeneration of new, direct or indirect, septo-hippocampal connections across the lesion cavity.

Buzsáki, G., Gage, F.H., Kellényi, L., Björklund, A. Behavioral dependence of the electrical activity of intracerebrally transplanted fetal hippocampus. (1987) Brain Research. 400(2):321-33.

+ expand abstract

Williams, L.R., Varon, S., Peterson, G.M., Wictorin, K., Fischer, W., Bjorklund, A., Gage, F.H. Continuous infusion of nerve growth factor prevents basal forebrain neuronal death after fimbria fornix transection. (1986) Proceedings of the National Academy of Sciences of the United States of America. 83(23):9231-5.

+ expand abstract

Clarke, D.J., Gage, F.H., Nilsson, O.G., Björklund, A. Grafted septal neurons form cholinergic synaptic connections in the dentate gyrus of behaviorally impaired aged rats. (1986) Journal of Comparative Neurology. 252(4):483-92. DOI: 10.1002/cne.902520405

+ expand abstract

Gage, F.H., Björklund, A. Cholinergic septal grafts into the hippocampal formation improve spatial learning and memory in aged rats by an atropine-sensitive mechanism. (1986) Journal of Neuroscience. 6(10):2837-47.

+ expand abstract

Behaviorally impaired old rats were selected from a population of 75 21- to 23-month-old rats on the basis of the place-investigated abilities in the Morris' water-maze task. After the pretransplant test, half of the old impaired rats received bilateral intrahippocampal cell suspension grafts prepared from the fetal septal-diagonal band region, which is rich in developing cholinergic neurons; the other half were left as sham-operated controls. Twelve weeks after grafting, the rats were retested in the water-maze using alternating cue-navigation and place-navigation trials (i.e., with visible or nonvisible escape platform). While the old impaired controls had deteriorated further between the 2 tests and showed poor retention of the pretransplant performance level, the grafted rats were significantly improved in comparison with both their pretransplant performance and the performance of the old impaired controls in the posttransplant test. The graft-induced effect was due both to an improved retention of the performance level acquired in the test performed prior to transplantation surgery, and to an improved acquisition of spatial memory of the escape platform site during the posttransplant test week (measured as an improved focusing of search over the platform site after platform removal). The acetylcholine esterase inhibitor physostigmine had no or only marginal effects on the performance of any of the young or aged rat groups. By contrast, the recovered navigational abilities and spatial memory in the grafted animals were completely abolished after administration of the muscarinic receptor antagonist atropine. A similar atropine-sensitivity was seen in behaviorally nonimpaired aged rats but not in the well-trained young control rats. The results show that cholinergic septal grafts, implanted into the hippocampal formation, improved spatial learning in the impaired aged rats primarily, or perhaps exclusively, by a recovery of the rats' ability to use spatial cues for place-navigation in the water-maze, while other aspects of the performance deficits in the water-maze task in the aged rats were left unaffected by the septal grafts. On the basis of parallel morphological studies, it is proposed that the effects of the septal grafts on the spatial learning impairments in the aged rats are critically dependent on the direct action of cholinergic neurons in the grafts via synapses formed onto neuronal elements in the host by their ingrowing axons.

Gage, F.H., Wictorin, K., Fischer, W., Williams, L.R., Varon, S., Bjorklund, A. Retrograde cell changes in medial septum and diagonal band following fimbria-fornix transection: quantitative temporal analysis. (1986) Neuroscience. 19(1):241-55.

+ expand abstract

Complete unilateral fimbria-fornix transections, including the overlying cingulate cortex, were administered to female rats. At time points from 1 day to 6 weeks, the septal-diagonal band region was examined using acetylcholinesterase histochemistry, Cresyl Violet cell staining, and choline acetyltransferase biochemistry. As early as 1 day following the transection a decrease in acetylcholinesterase positive cell body staining was observed in the medial septum; however, no loss of Nissl-stained neurons was measured in Cresyl Violet stained sections until 1 week after the lesion. Maximal loss of acetylcholinesterase-positive cells, as visualized after irreversible acetylcholinesterase inhibition, was measured at 1 week, and no further change was observed at time points up to 6 weeks after operation. The loss of acetyltransferase-positive cells was greatest in the medial septal area (-65%) and the vertical limb of the diagonal band (-55%). Little cell loss was measured in the horizontal limb of the diagonal band. This is consistent with the known projections of these cell bodies. Remaining acetylcholinesterase-positive cell bodies in the medial septum had shrunk by about 20% (measured as the diameter along the major axis). A marked neuronal cell loss (about 50%) was demonstrable in the medial septum and vertical limb of the diagonal band in the Cresyl Violet-stained sections, too. A pile-up of acetylcholinesterase-stained material was observed in the dorsal-lateral quadrant of the septal area just proximal to the lesion at 1 day following transection. This pile-up occurred in the medial septum and diagonal band area up to 1 week following the transection, and had nearly disappeared by 2 weeks post-transection. Choline acetyltransferase biochemical activity, measured in samples of whole septum, decreased significantly at 1 day but subsequently returned to control levels. By 2 weeks following transection, an increase in acetylcholinesterase-positive stained fibers was observed in the dorsal-lateral quadrant of the septum, ipsilateral to the lesion relative to the contralateral septum. This response, which was interpreted as sprouting from the lesioned axons proximal to the transection, probably accounted for the rise in choline acetyltransferase biochemical activity in the whole septum following the reduction on the first day.

Gage, F.H., Björklund, A. Neural grafting in the aged rat brain. (1986) Annual Review of Physiology. 48:447-59. DOI: 10.1146/annurev.ph.48.030186.002311

Björklund, A., Nornes, H., Gage, F.H. Cell suspension grafts of noradrenergic locus coeruleus neurons in rat hippocampus and spinal cord: reinnervation and transmitter turnover. (1986) Neuroscience. 18(3):685-98.

+ expand abstract

Fetal noradrenergic neurons from the brain stem locus coeruleus region can be successfully grafted as a dissociated cell suspension provided that the dissociation is done in the absence of any trypsin digestion step. The survival, fiber outgrowth and biochemical function of locus coeruleus neurons, taken from 13- to 15-day-old rat embryos, have been studied after injection into the dorsal hippocampal formation and the thoracolumbar spinal cord in adult rats. All rats were treated with an i.v. injection of 6-hydroxydopamine prior to grafting to remove the intrinsic locus coeruleus projections to these areas, and they were taken for fluorescence histochemical or biochemical analyses 2-7 months after transplantation. Up to 330 surviving noradrenaline neurons were found at each implantation site (injected with 2-3 microliters of cell suspension) which represents an estimated survival rate of about 40%. In the most successful cases the entire dorsal hippocampal formation, and an approximately 4 cm long segment of the thoracolumbar spinal cord, was supplied with a new noradrenaline-containing terminal network, which reached normal densities in the regions closest to the grafts. In the hippocampal formation, in particular, the ingrowing axons re-established a laminar innervation pattern which resembled that of the normal locus coeruleus afferents. In the hippocampus, two 2-microliters injections of locus coeruleus cell suspension restored the total hippocampal noradrenaline content to an average of 55%, and the noradrenaline synthesis rate (as assessed by the rate of DOPA accumulation after synthesis inhibition) was found to be close to normal in the graft-reinnervated specimens. In the spinal cord, two 3-microliters injections restored the noradrenaline level in the thoracolumbar cord (a 4.5 cm long segment) to an average of 22% of normal, with the highest individual levels being close to normal. Determinations of the noradrenaline metabolite 3,4-dihydroxy-phenylethyleneglycol indicated that the rate of noradrenaline metabolism in the graft-reinnervated spinal cord was close to that of the normal intact spinal cord. The results demonstrate the potential of the suspension grafting technique for extensive noradrenergic reinnervation of the hippocampal formation or large portions of the spinal cord. Fetal locus coeruleus neurons implanted in this way can re-establish fairly normal terminal innervation patterns and reinstate noradrenaline turnover and metabolism in a previously denervated central target.

Bengtsson, F., Nobin, A., Falck, B., Gage, F.H., Jeppsson, B. Portacaval shunt in the rat: selective alterations in behavior and brain serotonin. (1986) Pharmacology, Biochemistry, and Behavior. 24(6):1611-6.

+ expand abstract

Björklund, A., Gage, F.H. Transplantation of basal forebrain cholinergic neurons in the aged rat brain. (1986) Progress in Brain Research. 70:499-512.

Acsádi, G., Buzsáki, G., Keszthelyi, T., Királyfalvi, L., Gage, F.H. Effects of confinement, previous experience and hippocampal damage on the DRL schedule. (1986) Behavioural Brain Research. 20(2):241-8.

+ expand abstract

Lindvall, O., Ingvar, M., Gage, F.H. Short term status epilepticus in rats causes specific behavioral impairments related to substantia nigra necrosis. (1986) Experimental Brain Research. 64(1):143-8.

+ expand abstract

Schultzberg, M., Foster, G.A., Gage, F.H., Björklund, A., Hökfelt, T. Coexistence during ontogeny and transplantation. (1986) Progress in Brain Research. 68:129-45.

Kesslak, J.P., Gage, F.H. Recovery of spatial alternation deficits following selective hippocampal destruction with kainic acid. (1986) Behavioral Neuroscience. 100(2):280-3.

+ expand abstract

Clarke, D.J., Gage, F.H., Björklund, A. Formation of cholinergic synapses by intrahippocampal septal grafts as revealed by choline acetyltransferase immunocytochemistry. (1986) Brain Research. 369(1-2):151-62.

+ expand abstract

Brundin, P., Isacson, O., Gage, F.H., Prochiantz, A., Björklund, A. The rotating 6-hydroxydopamine-lesioned mouse as a model for assessing functional effects of neuronal grafting. (1986) Brain Research. 366(1-2):346-9.

+ expand abstract

Kienker, P.K., Sejnowski, T.J., Hinton, G.E., Schumacher, L.E. Separating figure from ground with a parallel network. (1986) Perception. 15(2):197-216. DOI: 10.1068/p150197

+ expand abstract

Zetterström, T., Brundin, P., Gage, F.H., Sharp, T., Isacson, O., Dunnett, S.B., Ungerstedt, U., Björklund, A. In vivo measurement of spontaneous release and metabolism of dopamine from intrastriatal nigral grafts using intracerebral dialysis. (1986) Brain Research. 362(2):344-9.

+ expand abstract

Gage, F.H., Björklund, A. Enhanced graft survival in the hippocampus following selective denervation. (1986) Neuroscience. 17(1):89-98.

+ expand abstract

The trophic effects of denervation on the survival of fetal cholinergic neuronal cell suspensions grafted to the hippocampal formation of the rat were assessed in the present study. Young adult female rats were injected with cell suspensions of neurons obtained from the fetal basal forebrain region into the hippocampal formation simultaneously with (or without) a fimbria-fornix transection, which removes the hippocampal cholinergic afferents. Four to six months later, one group of grafted animals was evaluated histochemically for: transplant volume; number of acetylcholinesterase-positive cells, and size of acetylcholinesterase-positive cells in the graft. A parallel study was conducted to determine the total number and size of the acetylcholinesterase-positive cells in the septal-diagonal band-substantia innominata complex of the adult rat, to match with the cell survival and growth in the grafts. A second group of grafted rats was taken in parallel for biochemical analysis of choline acetyltransferase activity in the grafted hippocampus. The transplant volume in the rats with fimbria-fornix transection was greater than twice the volume seen in animals without fimbria-fornix lesion. In addition, the number of acetylcholinesterase-positive cells in the transplant was twice as great in the denervated animals as in the non-denervated ones. However, the number of acetylcholinesterase-positive cells per mm3 of graft volume did not differ between the two groups, suggesting that the trophic effect of the denervation was not specific for the cholinergic neurons, but affected the entire grafted tissue. The hippocampal choline acetyltransferase activity of the animals that received the fimbria-fornix lesion simultaneously with transplantation was about three times higher than that of the rats that received grafts but no simultaneous fimbria-fornix transection. A control experiment with animals that received an aspirative lesion of the retrosplenial cortex, transecting the perforant path input, revealed no enhancing effect of hippocampal choline acetyltransferase activity over non-lesioned grafted animals. Thus, the denervation-enhancing effects of the fimbria-fornix lesion appear to be selective and not the result of a general wound-induced mechanism. These results strongly support the contention that neurotrophic factors are released as a result of denervation in the adult hippocampal formation, and that these neurotrophic factors can support survival and growth of central cholinergic neurons. However, the factors involved do not appear to be specific for the cholinergic neurons, but rather have their trophic effects on many types of cells.

Brundin, P., Isacson, O., Gage, F.H., Björklund, A. Intrastriatal grafting of dopamine-containing neuronal cell suspensions: effects of mixing with target or non-target cells. (1986) Brain Research. 389(1-2):77-84.

+ expand abstract

Isacson, O., Brundin, P., Gage, F.H., Björklund, A. Neural grafting in a rat model of Huntington's disease: progressive neurochemical changes after neostriatal ibotenate lesions and striatal tissue grafting. (1985) Neuroscience. 16(4):799-817.

+ expand abstract

The acute and long-term changes following large neostriatal ibotenic acid lesions and intrastriatal striatal neuronal grafting have been studied neurochemically by determinations of the gamma-aminobutyrate (GABA) and acetylcholine-synthetic enzymes, glutamate decarboxylase and choline acetyltransferase, and of dopamine and its primary acidic metabolite, 3,4-dihydroxyphenylacetic acid. The neurochemical data have been matched with estimates of tissue volume changes and striatal graft development through tissue weight and protein content analysis and histological volumetric measurements. Injections of 20 micrograms ibotenic acid, deposited over four injection sites in the head of the caudate-putamen, had by one week caused a 70-85% reduction in glutamate decarboxylase and choline acetyltransferase activity. With time there was a progressive recovery of the specific enzyme activities in the lesioned areas (expressed per microgram protein or per mg wet weight) to 40-60% of control levels as determined at 20 weeks post-lesion in the caudate-putamen. This increase was, however, largely if not exclusively due to the long-term shrinkage of the lesioned caudate-putamen, amounting to 50-70% at 20 weeks. Thus, the total glutamate decarboxylase and choline acetyltransferase activity levels in the lesioned caudate-putamen remained virtually unchanged (between 15 and 25% of control) over the 20 week experimental period. Glutamate decarboxylase activity was also markedly reduced (35-70%) in the two primary striatal projection areas, globus pallidus and substantia nigra, and there were no signs of recovery over time. Striatal dopamine levels, which were acutely unaffected by the lesion, showed a slow decline so that the total dopamine content in the area was reduced by about 80% at 20 weeks. Suspended striatal neurons obtained from the striatal primordia of 14-15-day-old rat fetuses, injected into the previously lesioned caudate-putamen, survived and established a new striatum-like structure at the site of the ibotenic acid lesion. The final volume of the graft tissue reached up to about 10 mm3 in volume and reduced striatal atrophy on average from about 50 to 70% of normal control in the rats with lesions to about 30-40% in the animals with grafts. In the rats with grafts, there was a significant recovery of glutamate decarboxylase and choline acetyltransferase activities not only in the lesioned caudate-putamen, containing the graft (from 20-25% to 40-50%, when expressed as total enzyme activity levels), but also the glutamate decarboxylase activity in the globus pallidus, a structure located at a distance from the graft.(ABSTRACT TRUNCATED AT 400 WORDS)

Pfaff, S.L., Zhou, R.P., Young, J.C., Hayflick, J., Duesberg, P.H. Defining the borders of the chicken proto-fps gene, a precursor of Fujinami sarcoma virus. (1985) Virology. 146(2):307-14.

+ expand abstract

The transforming (onc) genes of retroviruses contain specific sequences, derived from as yet poorly defined, normal cellular genes, termed proto-onc genes. Proto-onc genes must be defined to explain their docility compared to the oncogenicity of the viral derivatives. Here we set out to determine the borders of the chicken proto-fps gene from which the onc genes of avian Fujinami (FSV) and PRC sarcoma viruses (PRCSV) are derived. These onc genes are hybrids of an element from the gag gene of retroviruses (delta gag) linked to a 2.8-kb domain from proto-fps. To identify the 5' border of proto-fps we have sequenced 1.5 kb beyond the 5' border of overlap with viral fps utilizing a proto-fps clone derived previously. A possible promoter was identified that maps 736 nucleotides from this border. The 736 nucleotides contain two possible exons with 121 codons, and short regions of homology with the delta gag termini of FSV and PRCII. A translation stop codon and an adjacent polyadenylation signal were identified just prior to the 3' border of overlap with viral fps within a 1.15-kb sequence of a newly isolated proto-fps clone. Comparing four exons within this 1.15 kb proto-fps sequence with known fps equivalents of FSV and PRCSV, we have detected strain-specific, but no common point mutations in each viral genome. A 3.3-kb polyadenylated proto-fps mRNA was detected in chicken liver RNA by gel electrophoresis and hybridization with proto-fps DNA. We conclude that the coding capacity of proto-fps is just over 3 kb, consistent with the size of the putative proto-fps protein of 98 kDa and hence slightly larger than that of viral fps. Thus proto-fps and the viral delta gag-fps genes each contain distinct 5' regulatory and coding sequences and share the 3' terminal fps domains. It is suggested that this difference, rather than scattered point mutations, is responsible for the oncogenic function of the viral genes and the unknown cellular function of proto-fps.

Brundin, P., Barbin, G., Isacson, O., Mallat, M., Chamak, B., Prochiantz, A., Gage, F.H., Björklund, A. Survival of intracerebrally grafted rat dopamine neurons previously cultured in vitro. (1985) Neurosci. Lett. 61(1-2):79-84.

+ expand abstract

Bengtsson, F., Gage, F.H., Jeppsson, B., Nobin, A., Rosengren, E. Brain monoamine metabolism and behavior in portacaval-shunted rats. (1985) Experimental Neurology. 90(1):21-35.

+ expand abstract

Gage, F.H., Brundin, P., Isacson, O., Björklund, A. Rat fetal brain tissue grafts survive and innervate host brain following five day pregraft tissue storage. (1985) Neuroscience Letters. 60(2):133-7.

+ expand abstract

Segal, M., Bjorklund, A., Gage, F.H. Transplanted septal neurons make viable cholinergic synapses with a host hippocampus. (1985) Brain Research. 336(2):302-7.

+ expand abstract

Brundin, P., Nilsson, O.G., Gage, F.H., Björklund, A. Cyclosporin A increases survival of cross-species intrastriatal grafts of embryonic dopamine-containing neurons. (1985) Experimental Brain Research. 60(1):204-8.

+ expand abstract

Shapiro, M.L., Simon, D., Olton, D.S., Gage, F.H., Bjorklund, A., Stenevi, U. Brain transplants: can they restore single unit activity in the hippocampus? (1985) Annals of the New York Academy of Sciences. 444:536-7.

Foster, G.A., Schultzberg, M., Gage, F.H., Björklund, A., Hökfelt, T., Nornes, H., Cuello, A.C., Verhofstad, A.A., Visser, T.J. Transmitter expression and morphological development of embryonic medullary and mesencephalic raphé neurones after transplantation to the adult rat central nervous system. I. Grafts to the spinal cord (1985) Experimental Brain Research. 60(3):427-44.

+ expand abstract

Suspensions of cells derived from the mesencephalic raphé or medullary raphé regions of the 13-14 day old embryonic rat brain were injected into the spinal cord of adult rats which had been previously denervated with 5,7-dihydroxytryptamine. At periods of up to 12 months after grafting, the spinal cords were taken for immunohistochemical analysis of 5-hydroxytryptamine (5HT), substance P (SP) and thyrotropin releasing hormone (TRH). In nearly all cases, surviving transplants were found. The grafts derived from mesencephalic raphé cells contained neurones which were immunoreactive to 5HT, or SP, but not both together. On average 4% of the total possible number of the available embryonic mesencephalic serotoninergic cells were found. A very dense outgrowth of 5HT positive fibres from the transplant was observed, extending up to 1.5 cm in both the caudal and rostral directions from the graft locus. Some SP immunoreactive fibres were also apparent near the implant. The grafts derived from the medullary transplant also contained 5HT-immunoreactive cells, comprising on average 25% of the total 5HT neurones available from the embryonic medullary primordium. In addition, neurones co-localizing 5HT together with SP and TRH were visible, closely reflecting the situation found in the medullary raphé in situ. Dense plexi of fibres containing 5HT-LI extended both caudally and rostrally up to 12-15 mm from the transplant. Outgrowth of SP and TRH varicose fibres was also demonstrable, although to a lesser degree than for 5HT. It was also possible to find many motoneurones surrounded by varicose fibres containing both 5HT and SP, in contrast to the situation with the mesencephalic grafts, where no such patterns of innervation were seen. The experiments indicate that the milieu of the spinal cord may compromise the survival of mesencephalic raphé 5HT neurones far more than of medullary serotonin cells. However, despite this effect on cell survival, the outgrowth of fibres from the remaining mesencephalic 5HT neurones was apparently unaffected by their ectopic position. Similarly, the transmitter content of both classes of raphé cells was largely unaltered, either by the transplantation process or by the environment into which they were placed. It is concluded that although the adult denervated spinal cord can selectively affect neuronal survival, it is incapable either of inducing in other serotoninergic cells placed within it the transmitter phenotype typical of medullary raphé neurones, or of causing those ectopically located 5HT cells to form connections appropriate to the descending serotonin fibres.

Goulding, M., Ralph, R.K. Cyclic AMP, nuclear protein kinase and the PY815 cell cycle. (1985) Molecular and Cellular Biochemistry. 67(1):31-8.

+ expand abstract

Wieloch, T., Lindvall, O., Blomqvist, P., Gage, F.H. Evidence for amelioration of ischaemic neuronal damage in the hippocampal formation by lesions of the perforant path. (1985) Neuroscience Letters. 7(1):24-6.

+ expand abstract

Kelly, P.A., Gage, F.H., Ingvar, M., Lindvall, O., Stenevi, U., Björklund, A. Functional reactivation of the deafferented hippocampus by embryonic septal grafts as assessed by measurements of local glucose utilization. (1985) Experimental Brain Research. 58(3):570-9.

+ expand abstract

Transection of the septo-hippocampal connections through fimbria-fornix damage in the rat results in profound hippocampal cholinergic deafferentation, and, when applied bilaterally, leads to severe and long-lasting impairments in learning and memory. Previous studies have shown that intrahippocampal septal grafts can reestablish a new cholinergic in the initially denervated hippocampal formation and at least partly compensate for the lesion-induced learning impairments in fimbria-fornix lesioned rats. The purpose of the present study was to determine the magnitude of lesion-induced alterations in cerebral function as reflected in local glucose use measured by (14C)-2-deoxyglucose (2-DG) autoradiography, and the degree to which this index of functional activity could be normalized following reinnervation from transplants of fetal cerebral tissue from the primordial septal region. Six months after unilateral fimbria-fornix transection the rate of glucose utilization was reduced markedly throughout the ipsilateral hippocampus when compared to the intact contralateral side, while in the neocortex only the cingulate cortex showed long-lasting reductions in glucose use. Rats that received a transplant of fetal septal-diagonal band tissue at the time of fimbria-fornix transection, and were sacrificed 6 months later, displayed significantly greater glucose utilization in the ipsilateral hippocampus and cingulate cortex than was measured in these areas in rats with lesion alone. The recovery in glucose use was paralleled by a significant increase in acetylcholinesterase (AChE) staining in several areas of the ipsilateral hippocampal formation and cingulate cortex. This index of graft-induced cholinergic reinnervation was, moreover, significantly correlated with the rate of glucose use. Thus, in the fimbria-fornix transected animals the magnitude of glucose depression correlated with the extent of reduction in AChE staining, and in the grafted animals the degree of normalization of glucose use was correlated with the graft-induced increase in AChE-staining density. These results thus indicate that the 2-DG autoradiographic technique can provide a unique opportunity to map both altered functional activity in localized areas of the brain following specific lesions and the extent to which transplant-derived reinnervation of the host may induce a return to normal functional levels in the target site.

Björklund, A., Gage, F.H., Stenevi, U., Dunnett, S.B., Kelly, P.A. Intracerebral neural grafting in animal models of aging brain: strategies, rationale and preliminary results. (1985) Danish Medical Bulletin. 32 Suppl 1:35-9.

Gage, F.H., Stenevi, U., Carlstedt, T., Foster, G., Björklund, A., Aguayo, A.J. Anatomical and functional consequences of grafting mesencephalic neurons into a peripheral nerve "bridge" connected to the denervated striatum. (1985) Exp Brain Res. 60(3):584-9.

+ expand abstract

Björklund, A., Gage, F.H. Neural grafting in animal models of neurodegenerative diseases. (1985) Annals of the New York Academy of Sciences. 457:53-81.

Gage, F.H., Kelly, P.A., Björklund, A. Regional changes in brain glucose metabolism reflect cognitive impairments in aged rats. (1984) Journal of Neuroscience. 4(11):2856-65.

+ expand abstract

Aged rats (22 to 24 months) and young control rats (3 months) were tested in a battery of behavioral tests which included tests of learning, place navigation, sensorimotor integration, motor coordination, activity, and exploration. Following testing all animals were analyzed in an unanesthetized state for their local glucose utilization. Significant differences in glucose utilization were found between the aged and young groups on some behaviors and in some brain regions. There was considerable variability in the aged group in both their behavioral performance and their glucose utilization scores; thus, attempts were made to determine whether the variability in the degree of impairment within any particular behavioral test was correlated to the regional glucose utilization scores in any of the 45 brain regions analyzed. In two of the behavioral tests employed (i.e., one for learning and one for place navigation), the decline in performance correlated significantly with the decrement in regional glucose utilization. Moreover, the performance in these two tests showed significant correlation with glucose use in only five regions (dentate gyrus, medial septum-diagonal band area, hippocampal CA1, hippocampal CA3, and prefrontal cortex). These results show that the learning impairments in the aged rats are related to the extent of decrease in glucose utilization in restricted areas of the limbic system. In addition, the results show that the individual rats within an aged rat population develop cognitive impairments to a variable degree and that the aged rats with the most pronounced learning impairments are the ones exhibiting the most severe functional decrements, in terms of glucose utilization, in the septohippocampal system and the prefrontal cortex. This suggests that aging rats may be interesting not only for the study of the normal aging process, but also as a model of dementia.

Isacson, O., Brundin, P., Kelly, P.A., Gage, F.H., Björklund, A. Functional neuronal replacement by grafted striatal neurones in the ibotenic acid-lesioned rat striatum. (1984) Nature. 311(5985):458-60.

+ expand abstract

Evans, S.H., Chafetz, M.D., Gage, F.H. Taxonomic abstraction in psychobiology. (1984) Journal of General Psychology. 111(2ND Half):209-27. DOI: 10.1080/00221309.1984.9921111

+ expand abstract

Gage, F.H., Björklund, A. Intracerebral grafting of neuronal cell suspensions into the adult brain. (1984) Central Nervous System Trauma. 1(1):47-56.

+ expand abstract

Gage, F.H., Björklund, A., Stenevi, U., Dunnett, S.B., Kelly, P.A. Intrahippocampal septal grafts ameliorate learning impairments in aged rats. (1984) Science. 225(4661):533-6.

+ expand abstract

Dunnett, S.B., Bunch, S.T., Gage, F.H., Björklund, A. Dopamine-rich transplants in rats with 6-OHDA lesions of the ventral tegmental area. I. Effects on spontaneous and drug-induced locomotor activity. (1984) Behavioural Brain Research. 13(1):71-82.

+ expand abstract

Gage, F.H., Björklund, A., Stenevi, U. Denervation releases a neuronal survival factor in adult rat hippocampus. (1984) Nature. 308(5960):637-9.

+ expand abstract

Gage, F.H., Dunnett, S.B., Björklund, A. Spatial learning and motor deficits in aged rats. (1984) Neurobiology of Aging. 5(1):43-8.

+ expand abstract

Dunnett, S.B., Gage, F.H., Björklund, A., Stenevi, U., Low, W.C., Iversen, S.D. Hippocampal deafferentation: transplant-derived reinnervation and functional recovery. (1984) Acta psychiatrica Scandinavica. Supplementum. 313:46-56.

+ expand abstract

Gage, F.H., Björklund, A., Stenevi, U. Cells of origin of the ventral cholinergic septohippocampal pathway undergoing compensatory collateral sprouting following fimbria-fornix transection. (1984) Neuroscience Letters. 44(2):211-6.

+ expand abstract

Barker, D.J., Howard, A.J., Gage, F.H. Functional significance of sympathohippocampal sprouting: changes in single cell spontaneous activity. (1984) Brain Research. 291(2):357-63.

+ expand abstract

Stewart, G.R., Frederickson, C.J., Howell, G.A., Gage, F.H. Cholinergic denervation-induced increase of chelatable zinc in mossy-fiber region of the hippocampal formation. (1984) Brain Research. 290(1):43-51.

+ expand abstract

Ballard, D.H., Hinton, G.E., Sejnowski, T.J. Parallel visual computation. (1983) Nature. 306(5938):21-6.

+ expand abstract

Kuffler, S.W., Sejnowski, T.J. Peptidergic and muscarinic excitation at amphibian sympathetic synapses. (1983) Journal of Physiology. 341:257-78.

+ expand abstract

A single-electrode voltage clamp was used to study the slow muscarinic and late slow peptidergic excitatory post-synaptic currents (e.p.s.c.s) in B cells of the paravertebral sympathetic ganglia of the bull-frog. Conductance decreases were measured during peptidergic e.p.s.c.s in nearly all cells at clamped potentials near the resting level. In about half of the cells the size of the peptidergic e.p.s.c.s increased with hyperpolarization and in some of these cells conductance increases were found at hyperpolarized levels. In the remaining cells conductance decreases occurred at all levels of membrane potential tested, and in a few of these the polarity of the e.p.s.c.s reversed at hyperpolarized potentials. A similar diversity was observed among muscarinic e.p.s.c.s. At least two simple ionic mechanisms are required to explain the heterogeneous voltage dependencies observed: a conductance decrease primarily to K+ that dominates at depolarized potentials and a conductance increase to other ions that is more prominent at hyperpolarized potentials. The proportion of these two mechanisms appears to differ among B cells. The two slow e.p.s.c.s recorded in the same neurone had the same voltage dependence and were accompanied by the same conductance changes in each of eight cells despite differences between cells. The muscarinic e.p.s.c. was reduced during the peptidergic e.p.s.c. in each of twenty-five neurones tested over a range of membrane potentials. Externally-applied luteinizing hormone releasing hormone (LHRH) produced currents with the same voltage dependence and conductance changes as the nerve-evoked peptidergic e.p.s.c. in each of fifteen cells tested. Bethanechol, a muscarinic agonist, and LHRH produced currents with the same voltage dependence and conductance changes in each of the twelve cells studied. In several cells a saturating response to a prolonged application of LHRH completely occluded the response to bethanechol, and vice versa. Slow currents were recorded from dissociated cell bodies in response to bethanechol and LHRH; these responses exhibited the same diversity of voltage dependence and conductance changes as was observed in intact ganglia. Activation of muscarinic and peptidergic receptors may control shared ionic mechanisms in single ganglion cells.

Gage, F.H., Björklund, A., Stenevi, U. Local regulation of compensatory noradrenergic hyperactivity in the partially denervated hippocampus. (1983) Nature. 303(5920):819-21.

+ expand abstract

Björklund, A., Stenevi, U., Schmidt, R.H., Dunnett, S.B., Gage, F.H. Intracerebral grafting of neuronal cell suspensions. II. Survival and growth of nigral cell suspensions implanted in different brain sites. (1983) Acta physiologica Scandinavica. Supplementum. 522:9-18.

+ expand abstract

Gage, F.H., Björklund, A., Stenevi, U., Dunnett, S.B. Intracerebral grafting of neuronal cell suspensions. VIII. Survival and growth of implants of nigral and septal cell suspensions in intact brains of aged rats. (1983) Acta physiologica Scandinavica. Supplementum. 522:67-75.

+ expand abstract

Björklund, A., Gage, F.H., Schmidt, R.H., Stenevi, U., Dunnett, S.B. Intracerebral grafting of neuronal cell suspensions. VII. Recovery of choline acetyltransferase activity and acetylcholine synthesis in the denervated hippocampus reinnervated by septal suspension imp (1983) Acta physiologica Scandinavica. Supplementum. 522:59-66.

+ expand abstract

Björklund, A., Gage, F.H., Stenevi, U., Dunnett, S.B. Intracerebral grafting of neuronal cell suspensions. VI. Survival and growth of intrahippocampal implants of septal cell suspensions. (1983) Acta physiologica Scandinavica. Supplementum. 522:49-58.

+ expand abstract

Björklund, A., Stenevi, U., Schmidt, R.H., Dunnett, S.B., Gage, F.H. Intracerebral grafting of neuronal cell suspensions. I. Introduction and general methods of preparation. (1983) Acta physiologica Scandinavica. Supplementum. 522:1-7.

+ expand abstract

Gage, F.H., Dunnett, S.B., Brundin, P., Isacson, O., Björklund, A. Intracerebral grafting of embryonic neural cells into the adult host brain: an overview of the cell suspension method and its application. (1983) Developmental Neuroscience. 6(3):137-51.

+ expand abstract

Gage, F.H., Björklund, A., Stenevi, U., Dunnett, S.B. Functional correlates of compensatory collateral sprouting by aminergic and cholinergic afferents in the hippocampal formation. (1983) Brain Research. 268(1):39-47.

+ expand abstract

Selective lesions of discrete aminergic and cholinergic afferent pathways to the hippocampal formation have been studied as an experimental model of behavioral recovery after partial hippocampal deafferentation in adult rats. The noradrenergic, serotoninergic and cholinergic afferents reach the hippocampal formation along three routes: a supracallosal pathway, a subcallosal pathway (along the fimbria-fornix), and a ventral pathway (along the ansa lenticularis and the ventral amygdaloid pathway). Bi-lateral lesion of the supracallosal pathway resulted in significant reductions in biochemical markers of the hippocampal noradrenergic, serotoninergic and cholinergic innervations. Within 6 weeks following lesion these markers were found to have recovered to levels close to normal. A more substantial deafferentation, obtained by a bilateral lesion of both dorsal pathways, resulted in a more profound initial decrease in the biochemical marker levels, and a less complete recovery in the long-term animals. Concomitant with the initial phase of deafferentation, rats with lesions of one or both of the dorsal afferent pathways exhibited an equally profound behavioral deficit in acquisition of a forced choice alternation learning task in a T-maze. However, while rats subjected to the combined supracallosal-fimbria-fornix lesion remained impaired, the ones with lesions of the supracallosal pathway alone exhibited a significant recovery of the capacity to perform the maze task. The correlation between behavioral recovery and recovery of the biochemical markers in the supracallosal pathway-lesioned group was significant for the serotoninergic innervation of the hippocampus. The present results suggest that reinnervation of the partially deafferented hippocampus through compensatory collateral sprouting is a valuable new experimental model system within which to analyze mechanisms underlying functional recovery after lesions in the CNS.

Gage, F.H., Björklund, A., Stenevi, U. Reinnervation of the partially deafferented hippocampus by compensatory collateral sprouting from spared cholinergic and noradrenergic afferents. (1983) Brain Research. 268(1):27-37.

+ expand abstract

Whipple, M.R., Reinecke, M.G., Gage, F.H. Inhibition of synaptosomal neurotransmitter uptake by hallucinogens. (1983) Journal of Neurochemistry. 40(4):1185-8.

+ expand abstract

Chafetz, M.D., Gage, F.H. Pineal and habenula innervation altered by septal lesions. (1983) Brain Research Bulletin. 10(1):27-31.

+ expand abstract

Schmidt, R.H., Björklund, A., Stenevi, U., Dunnett, S.B., Gage, F.H. Intracerebral grafting of neuronal cell suspensions. III. Activity of intrastriatal nigral suspension implants as assessed by measurements of dopamine synthesis and metabolism. (1983) Acta physiologica Scandinavica. Supplementum. 522:19-28.

+ expand abstract

Sejnowski, T.J., Yodlowski, M.L. A freeze-fracture study of the skate electroreceptor. (1982) Journal of Neurocytology. 11(6):897-912.

+ expand abstract

Sejnowski, T.J. Peptidergic synaptic transmission in sympathetic ganglia. (1982) Federation Proceedings. 41(13):2923-8.

+ expand abstract

Turner, F.D., Gage, F.H. Behavioral kinetics: dynamics of the unconditioned response to footshock. (1982) Physiology & Behavior. 29(5):957-60.

+ expand abstract

Paton, J.A., Kelley, D.B., Sejnowski, T.J., Yodlowski, M.L. Mapping the auditory central nervous system of Xenopus laevis with 2-deoxyglucose autoradiography. (1982) Brain Research. 249(1):15-22.

Chafetz, M.D., Evans, S., Gage, F.H. Fluorescence measurement of lesion-induced fiber growth. II. Measurement of sympathohippocampal sprouting using a new microfluorometric method. (1982) Brain Research. 247(2):217-25.

+ expand abstract

Chafetz, M.D., Gage, F.H. Fluorescence measurement of lesion-induced fiber growth. I. A microfluorometric technique to measure density and intensity of varicosities and fibers. (1982) Brain Research. 247(2):209-16.

+ expand abstract

Björklund, A., Stenevi, U., Dunnett, S.B., Gage, F.H. Cross-species neural grafting in a rat model of Parkinson's disease. (1982) Nature. 298(5875):652-4.

Dunnett, S.B., Gage, F.H., Björklund, A., Stenevi, U., Low, W.C., Iversen, S.D. Hippocampal deafferentation: transplant-derived reinnervation and functional recovery. (1982) Scandinavian Journal of Psychology. Suppl 1:104-11.

Gage, F.H., Dunnett, S.B., Björklund, A., Stenevi, U. Functional recovery following brain damage: conceptual frameworks and biological mechanisms. (1982) Scandinavian Journal of Psychology. Suppl 1:112-20.

Thompson, R.G., Valdes, J.J., Gage, F.H. Reversible alterations in hypothalamic uptake of biogenic amines after septal lesions. (1981) Experimental Neurology. 74(2):356-69.

Gage, F.H., Springer, J.E. Behavioral assessment of norepinephrine and serotonin function and interaction in the hippocampal formation. (1981) Pharmacology, Biochemistry, and Behavior. 14(6):815-21.

+ expand abstract

Chafetz, M.D., Thompson, R.G., Evans, S.H., Gage, F.H. Biochemical specificity of septal hyperreactivity: a behavioral discrimination. (1981) Behavioural Brain Research. 2(3):409-20.

+ expand abstract

Reingold, S.C., Sejnowski, T.J., Gelperin, A., Kelley, D.B. [3H]-2-deoxyglucose autoradiography in a molluscan nervous system. (1981) Brain Research. 208(2):416-20.

+ expand abstract

Gage, F.H., Thompson, R.G. Differential distribution of norepinephrine and serotonin along the dorsal-ventral axis of the hippocampal formation. (1980) Brain Research Bulletin. 5(6):771-3.

+ expand abstract

Sejnowski, T.J., Reingold, S.C., Kelley, D.B., Gelperin, A. Localization of[3H]-2-deoxyglucose in single molluscan neurones. (1980) Nature. 287(5781):449-51.

+ expand abstract

Gage, F.H., Valdes, J.J., Thompson, R.G. Morphine injections into the periaqueductal-periventricular gray attenuate septal hyperreactivity. (1980) Psychopharmacology. 70(1):113-4.

+ expand abstract

Valdes, J.J., Cameron, W.R., Evans, S., Gage, F.H. Regional brain morphine injections selectively attenuate aspects of septal hyperreactivity: a multivariate assessment. (1980) Pharmacology, Biochemistry, and Behavior. 12(4):563-72.

Gage, F.H., Armstrong, D.R., Thompson, R.G. Behavioral kinetics: a method for deriving qualitative and quantitative changes in sensory responsiveness following septal nuclei damage. (1980) Physiology & Behavior. 24(3):479-84.

Cameron, W.R., Gage, F.H., Hitt, J.C., Popolow, H.B. The influence of the anterodorsal hippocampus on feminine sexual behavior in rats. (1979) Behavioral and Neural Biology. 27(1):72-86.

Babitch, J.A., Gage, F.H., Valdes, J.J. Effects of phalloidin on K+-dependent, Ca2+-independent neurotransmitter efflux and K+-facilitated, Ca2+-dependent neurotransmitter release. (1979) Life Sciences. 24(2):117-24.

Gage, F.H., Thompson, R.G., Valdes, J.J. Endogenous norepinephrine and serotonin within the hippocampal formation during the development and recovery from septal hyperreactivity. (1978) Pharmacology, Biochemistry, and Behavior. 9(3):359-67.

+ expand abstract

Gage, F.H., Olton, D.S., Bolanowski, D. Activity, reactivity, and dominance following septal lesions in rats. (1978) Behavioral Biology. 22(2):203-10.

Olton, D.S., Walker, J.A., Gage, F.H. Hippocampal connections and spatial discrimination. (1978) Brain Research. 139(2):295-308.

+ expand abstract

Sejnowski, T.J. Statistical constraints on synaptic plasticity. (1977) Journal of Theoretical Biology. 69(2):385-9.

Sejnowski, T.J. Storing covariance with nonlinearly interacting neurons. (1977) Journal of Mathematical Biology. 4(4):303-21.

+ expand abstract

Johnson, C.T., Olton, D.S., Gage, F.H., Jenko, P.G. Damage to hippocampus and hippocampal connections: effects on DRL and spontaneous alternation. (1977) Journal of Comparative and Physiological Psychology. 91(3):508-22.

+ expand abstract

Jenko, P.G., Gage, F.H., Olton, D.S. Time-dependent fornix influence on increased light aversion induced by septal lesions. (1976) Behavioral Biology. 17(4):607-14.

Gage, F.H., Olton, D.S. L-Dopa reduces hyperreactivity induced by septal lesions in rats. (1976) Behavioral Biology. 17(2):213-8.

Sejnowski, T.J. On the stochastic dynamics of neuronal interaction. (1976) Biological Cybernetics. 22(4):203-11.

Sejnowski, T.J. On global properties of neuronal interaction. (1976) Biol Cybern. 22(2):85-95.

Gage, F.H., Olton, D.S. Hippocampal influence on hyperreactivity induced by septal lesions. (1975) Brain Research. 98(2):311-25.

+ expand abstract

Olton, D.S., Gage, F.H. Role of the fornix in the septal syndrome. (1974) Physiology & Behavior. 13(2):269-79.

Woodruff, M.L., Gage, F.H., Isaacson, R.L. Changes in focal epileptic activity produced by brain-stem sections in the rabbit. (1973) Electroencephalography and Clinical Neurophysiology. 35(5):475-86.

Isaacson, R.L., Gage, F.H. Hypothalamic stimulation and the persistence of epileptiform discharges. (1973) Brain Research. 49(1):194-9.

Miao, S., Fourgeaud, L., Burrola, P.G., Stern, S., Zhang, Y., Happonen, K.E., Novak, S.W., Gage, F.H., Lemke, G. Tyro3 promotes the maturation of glutamatergic synapses. (n.d.) Frontiers in Neuroscience. 18:1327423. DOI: 10.3389/fnins.2024.1327423

+ expand abstract

Carvalho, V.R., Mendes, E.M.A.M., Fallah, A., Sejnowski, T.J., Comstock, L., Lainscsek, C. Decoding imagined speech with delay differential analysis. (n.d.) Frontiers in Human Neuroscience. 18:1398065. DOI: 10.3389/fnhum.2024.1398065

+ expand abstract

Perez Garcia, G., Bicak, M., Buros, J., Haure-Mirande, J.V., Perez, G.M., Otero-Pagan, A., Gama Sosa, M.A., De Gasperi, R., Sano, M., Gage, F.H., Barlow, C., Dudley, J.T., Glicksberg, B.S., Wang, Y., Readhead, B., Ehrlich, M.E., Elder, G.A., Gandy, S. Beneficial effects of physical exercise and an orally active mGluR2/3 antagonist pro-drug on neurogenesis and behavior in an Alzheimer's amyloidosis model. (n.d.) Front Dement. 2:1198006. DOI: 10.3389/frdem.2023.1198006

+ expand abstract

Publications

2025
2024
2023
2022
2021
2020
2019
2018
2017
2016
2015
2014
2013
2012
2011
2010

Waitt Advanced Biophotonics Center

Salk Institute for Biological Studies - Waitt Advanced Biophotonics Center - Research

PUBLICATIONS

Publications