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Inside Salk 12 |15

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light fluorescent and electron microscopy—a

broad range of availability not common in a

single core. This range allows what’s called

multi-scaled imaging: a researcher can not

only image a whole organism (e.g., the brain

of a worm) but can go down to single cells

and molecules to understand what happens in

genes and proteins and how they impact the

whole organism in disease.

The core focuses not just on the development

of new microscopes, but rather new computa-

tional methods to analyze images. The field of

microscopy and imaging has become, like other

technologies, data-driven science, as a single

image can produce a terabyte or more of data

to analyze.

“We very much see this as not a classic core

where a staff of technicians assists scientists,

but rather a center actively involved in devel-

oping new technology to enable people to do

experiments that they couldn’t otherwise do,”

says

Martin Hetzer

, Salk professor and faculty

director of the biophotonics center. “Biopho-

tonics is one of the hottest and most rapidly

developing areas in biomedical research. Our

ability to visualize things in animals and cells

is improving through techniques in physics and

optics, allowing us to dig deeper into cells.”

This core also has a unique model: it operates

under the Waitt Advanced Biophotonics Center,

which includes a group of award-winning

faculty whose specialties span many fields: bio-

medicine, physics, chemistry and engineering.

“The center really enabled the core to take

off,” says Hetzer. “The idea was to have a

core with the broadest impact on the Institute,

while the biophotonics faculty—

Hu Cang

,

Björn Lillemeier

and

Axel Nimmerjahn

—push

the new technology and develop imaging

approaches that don’t exist yet.”

INTEGRATING DATA

As technology becomes more advanced, so

does the need to contextualize new data.

The Integrative Genomics and Bioinformatics

Core, started in 2012, processes raw data

from sequencing and develops techniques to

combine different types of genomics data,

such as linking mutations to the molecular

pathways and epigenetic changes involved in

research. In addition to providing technologi-

cal tools, it also offers innovative methods in

bioinformatics, network analysis, molecular

dynamics and computational data integration.

“Over the course of the last three years, I’ve

learned how to analyze sequencing data

through this core,” says

Julie Law

, a Salk

assistant professor who studies the genome

of plants to better understand epigenetic

regulation and DNA packaging. “I started

with a cursory understanding of genomics

analyses, and after working with the core my

lab is now at a point where we can do more

sophisticated interpretations of sequencing

data to maximize what we can learn from the

experiments we do.”

Researchers who are doing anything with big

data—whether it’s next generation sequencing,

mass spectrometry, proteomics or biophoton-

ics—need new ways to interpret the reams

and reams of information. For scientists that

have huge data sets, a regular, off-the-shelf

computer cannot process—let alone organize—

the information within a reasonable time-

frame. “Expanding in this area, and relatedly,

high-performance computing in general,

is one of our biggest needs for the future,”

says Berggren.

A data resource center at Salk has already

been constructed, with high-end fiber optic

data transmission cables and other infrastruc-

ture that supports moving and analyzing data

for the cores and labs. The next steps, says

Berggren, are to secure equipment and, most

importantly, staff who not only understand

biological research questions, but are also able

to leverage the latest approaches in computer

science and informatics.

“We have a truly dedicated group of some

40 scientists and core staff researchers that

routinely give that extra effort,” says Berggren.

“It’s that extra effort, combined with powerful

new technologies, that makes core facilities

at Salk such exceptional standouts.”

In this network representation of genes involved in lymphoma, each circle is a gene

and the connections indicate a variety of biological interactions. Darker colors indicate

a stronger association with the disease.

Image courtesy of Max Chang, Integrated Genomics Core