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TACC to Serve as Key Collaborator on NeuroNex Grant to Advance Understanding of Brain Structure

Published on August 2, 2017 by Faith Singer-Villalobos

Figure: Image from an electron micrograph through a single section plane illustrating spiny dendrites (yellow), nonspiny dendrites (orange), excitatory axons (green), excitatory synapses (red), astroglia (light blue), microglia (dark brown). Image courtesy of Kristen Harris.

The National Science Foundation (NSF) has awarded The University of Texas at Austin, the Texas Advanced Computing Center (TACC), and the Salk Institute a $9 million NeuroNex grant to explore the brain in microscopic detail and understand the cell biology of the nervous system. The grant will allow researchers to image and map synapses, the tiny points of contact between neurons throughout the brain, in detail and to model synapse function and share the data publically for use by colleagues throughout the world. TACC's portion of the grant is $2 million over five years.

Kristin Harris, principal investigator and professor in the Department of Neuroscience at The University of Texas at Austin
Kristin Harris, the principal investigator of the grant and a professor in the Department of Neuroscience at The University of Texas at Austin, says that the funding from NSF's Next Generation Networks for Neuroscience (NeuroNex) program allows her to expand her expertise through collaborations with James Carson of TACC and Terrence Sejnowski of the Salk Institute.

"I've been working to understand synapse structure and function for my whole academic life," Harris says. "We have created accurate three-dimensional reconstructions of all the synapses and their associated structures (dendrites, axons and glia) using sophisticated electron microscopy. We discovered, for example, that in brain volumes as tiny as a single red blood cell, there are more than 500 synapses. With this grant, we will collect new images more quickly from a variety of brain regions and taxa from mice to humans and share them more easily with the scientific community."

Part of the funding will enable the team to design a new electron microscope capable of imaging at a greater volume while simultaneously peeking inside the tiniest substructure of individual synapses using a new tomographic approach (tomography uses penetrating waves travelling through sections of material to determine the material's physical structure). As the images are collected, they will be shared with collaborators at the Salk Institute to expand existing computational modeling tools and build new ones to understand how synapse ultrastructure supports brain function.

"Our team at the Salk Institute will build a computational microscope to animate the electron microscope data from the NeuroNex project and probe the function of synapses at the molecular level," says Sejnowski, laboratory head of Salk's Computational Neurobiology Laboratory and a Howard Hughes Medical Institute investigator.

The images and tools will be shared with the scientific community through a portal being developed at TACC.

Left: Terrence Sejnowski of the Salk Institute; Right: James Carson, co-principal investigator and research associate in Life Sciences Computing at TACC

"Electron microscopy is a powerful tool for understanding the tiny details of the brain that are critical to how advanced organisms learn and remember," says Carson, co-principal investigator and research associate in Life Sciences Computing at TACC. "Yet the amount of data collected is not currently limited by the microscope itself, but instead the ability to process the data and interpret it. By leveraging TACC's high-performance computing, we intend to greatly speed up the rate of knowledge discovery in this field. By creating a public portal for other researchers, we provide the foundation for collaboration and sharing of data and analysis methods, thus further accelerating our ability to learn about how our brains work."

TACC will build on its experience with DesignSafe-CI, a platform for natural hazards engineering research, to construct a significantly customized portal for three-dimensional electron microscopy (3DEM) images of the brain, according to Carson. This includes not only making this resource available, but also training researchers to use 3DEM in conjunction with the portal. Disseminating the 3DEM technology is a big part of the project, and having an online portal to learn about the instrument and the software tools is important as well.

"TACC's role is a result of TACC's commitment to developing user-friendly interfaces for high-performance computing that encourage collaboration and sharing," says Carson. "Though the focus is neuroscience, the tools and technology could be leveraged by other research fields."

The award is part of a major public-private joint endeavor, the Brain Initiative, which is pursuing one of science's grandest challenges: understanding the brain. NSF states that the overall goal of the NeuroNex program within the Brian Initiative is to establish a coherent national infrastructure to enhance understanding of brain function across organizational levels and a diversity of species. The initiative focuses on interdisciplinary approaches and new technologies, with the promise of ushering in new ways of conducting neuroscience research.

"Through the development of advanced instrumentation to observe and model the brain, we're closer to our goal of building a more complete knowledge base about how neural activity produces behavior," says Jim Olds, NSF's assistant director for biological sciences. "NeuroNex seeks to take that progress forward by creating an ecosystem of new tools, resources and theories. Most importantly, NeuroNex aims to ensure their broad dissemination to the neuroscience community. With these awards, NSF is building a foundation for the next generation of research into the brain."


Faith Singer-Villalobos

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