Waking From a Coma

March 5th, 2010 by kjkurtz

Popular Science recently published an article describing a novel approach to treating traumatic brain injuries with an 84% success rate of waking patients from a vegetative state. Neuroscientist Philip De Fina and colleagues at the International Brain Research Foundation (IBRF) use various neurological tests, such as Functional Magnetic Resonance Imaging (fMRI) and Electroencephalography (EEG), to identify “functional neuromarkers” following traumatic brain injury.  These neuromarkers are structural and molecular cues that allow the doctors to assess the damage and devise a treatment program aimed toward promoting neural plasticity. While tissue damage and cell death cannot be reversed, De Fina and colleagues administer drugs to alter the concentration and efficacy of various neurotransmitters to prevent the death of synapses and to stimulate alternative routes of neural connectivity.  In addition, electrical impulses are used to increase blood flow to the brain and patients are given a cocktail of vitamins and nutrients to promote optimal neural health.

Although De Fina’s innovative treatment method has proven effective, very little is known about the precise neurophysiological mechanisms that are responsible for its success. The US Department of Defense recently granted $6.4 million to IBRF, funding research that will elucidate and advance this treatment. In addition to its immediate clinical application, De Fina’s medical breakthrough could lead to a new, expanded understanding of the dynamic nature of neural development and function.

It seems unorthodox that a treatment would be clinically administered and deemed successful before anyone can actually explain how and why it works.  However, this method has been incredibly successful, and even if its development was some sort of fluke, it could lead to major advancements in the treatment of various neurological damage and disorders.

Building Complex Biological Machines

February 25th, 2010 by kjkurtz

The National Science Foundation recently awarded $25 million to the creation of the Emergent Behaviors of Integrated Cellular Systems Center (EBICS), a new research and education center dedicated to the development of complex biological machines. As part of NSF’s Science and Technology Centers Integrative Partnership program, EBICS will include participation from the University of Illinois at Urbana-Champaign and the Georgia Institute of Technology and will hold its headquarters at the Massachusetts Institute of Technology.

EBICS will be a multidisciplinary research unit where engineers and biological scientists work collaboratively toward the construction of complex biological machines. This newly evolving field aims to elucidate the complex relationships and interactions between cells and cellular systems by building high-tech mechanical units (sensors, processors, and actuators) that can be assembled into machines to simulate the behavior of biological systems.  If successful, the creation of biological machines could become a key method of study for neuroscience, particularly contributing to research on neural connectivity. The technology used to construct such machines could also have major implications for the future of medicine.

NSF’s support of EBICS illustrates current trends toward interdisciplinary scientific investigation and remote collaboration.  As neuroscience evolves, it becomes increasingly clear that the mysteries of the brain cannot be understood without extensive cooperation between various academic fields. If all is successful, the new “biological machines” should help to shed some light on cognition as an emergent property of the complex biological organization and computational power of the brain.

For more information, see the NSF Press Release.

When you need to forget

February 22nd, 2010 by gnwood

Last week’s issue of the journal Cell describes research that explains why and how the brain erases certain memories, long a topic of interest to scientists. The research suggests that short-term memory is erased by the brain on purpose, so that new, more relevant memories can be recorded.

At least in fruit flies.

Researchers from China and the United States have found that flies have a protein called Rac that erodes a memory when needed. The researchers subjected the flies to two circumstances: a foul smelling odor and a foul smelling odor that also came with an electric shock.

After being exposed to both situations, flies picked the lesser of the two evils — the foul odor without the shock. They changed the shock to be tied with the first odor instead of the second. The flies noted this new information, and erased their original memory. The shock, in their minds, was now correctly tied to the first odor. When exposed to both odors, they again correctly picked the odor without the shock.

But when the experiment was repeated after the memory-eroding protein was blocked, there was utter confusion. The flies had not erased their first memory, and had made a second memory. Unable to pick which odor to fly toward, they zigzagged back and forth.

Humans also have the protein Rac, and Yi Zhong, the paper’s lead author, believes that further study may reveal how human memories are made. There is also hope that once they are better understood, Rac levels can be controlled to help people with abnormal memory, said Dr. Zhong of Tsinghua University in China and Cold Spring Harbor Laboratory in New York.

For more information: http://www.cell.com/abstract/S0092-8674%2809%2901630-4

The Search for Pannexin Expression: An Application of the Whole Brain Catalog

February 16th, 2010 by kjkurtz

AngelaSlide2Identifying molecular patterns within nervous tissue is a key method of understanding large-scale neurological function. It is extremely difficult to compare separate whole brain sections to one another at a large scale and comparison of protein labeling to gene expression is complicated in the nervous system, because it requires knowledge of where the processes of neurons are located and their connectivity.  I have begun to use the Whole Brain Catalog (WBC) to overcome this interoperability problem in my current research on the newly discovered pannexin (Panx) family of gap junction-like proteins.

The spatial framework of the WBC is helping me work towards the ability to co-navigate separate data pieces in a meaningful way and in three dimensions by taking advantage of the spatial registration tools I have used in the Cell Centered Database (CCDB) resource.

To identify Panx expression patterns and interactive partners within the brain I am using wide-scale high resolution mouse brain tissue imaging.  I upload all data to the CCDB, where it can be normalized to a standard spatial framework, the Allen Reference Atlas. By this process, the brain maps can be compared with one another and against other data in neuroinformatics image-based databases such as GENSAT and the Allen Brain Atlas. When I do find inconsistency between comparative data, the WBC eases the problem by providing metadata and original images so that discrepancies can be resolved or more fully understood.

The WBC functions as both tool and inspiration in the quest for the ability to map Panx expression and interactions through a high resolution 3D model of the mouse brain. The Catalog provides a multi-dimensional workspace in which the high resolution data can be incorporated into a more complete representation of Panx expression. And while the WBC does not yet contain the complete multi-scale connectivity data that would significantly illuminate the function of the Panx protein family, it does provide an ideal environment into which this data will soon be integrated.

This neuroinformatics approach to the Panx problem has broader impact for how to use shared frameworks to facilitate neuroscience research.  The WBC is at the cutting edge of this field working towards the integration of all the necessary tools into one resource.

Angela C. Cone, Ph.D.

Post Doctoral Fellow

National Center for Microscopy and Imaging Research

University of California San Diego

Identification Of Brain Protein For Synapse Development

February 3rd, 2010 by Sarah

The UC Davis Health System recently identified a brain protein called SynDIG1 that has a critical role in creating and sustaining synapses, the complex chemical signaling system responsible for communication between neurons. The research, published in the Jan.14 issue of the journal Neuron, fills a major gap in understanding the molecular foundations of higher cognitive abilities as well as some brain disorders.
“We know that synapses are essential for learning, memory and perception and suspect that imbalances in synapse formation impact disorders of the brain such as autism and schizophrenia,” said Elva Diaz, assistant professor of pharmacology and senior author of the study. “Our study is the first to identify SynDIG1 as a critical regulator of these important brain connections.”

The majority of synapses in the brain use glutamate as a neurotransmitter. While past research revealed that regulation of a certain class of glutamate receptor — AMPA receptors — are critical to communication between neurons, Diaz set out to discover novel molecular mechanisms of AMPA receptors that could support the formation and vitality of synapses.

Full story at http://www.medicalnewstoday.com/articles/177716.php

Severe sleep apnea linked to “Reduced Brain Gray Matter Concentration”

February 1st, 2010 by Sarah

A study in the Feb. 1 issue of the journal SLEEP found gray matter concentration deficits are associated with severe obstructive sleep apnea (OSA). The study suggests that the memory loss, heart problems, and lack of respiratory control frequently observed in OSA patients may be related to physical changes in brain structure.

Optimized voxel-based morphometry, an automated processing technique for magnetic resonance imaging (MRI), was used to evaluate structural differences in gray matter by examining the entire brain, rather than a particular region. “Gray matter” refers to the cerebral cortex, where most information processing in the brain takes place: a layer of tissue that coats the surface of the cerebrum and the cerebellum and is gray in appearance, lacking the myelin insulation that makes most other parts of the brain appear to be white.

A PI professor of neurology at the Samsung Medical Center in Sungkyunkwan University School of Medicine in Seoul, South Korea, said the study emphasizes the importance of diagnosing and effectively treating severe OSA.

“Poor sleep quality and progressive brain damage induced by OSA could be responsible for poor memory, emotional problems, decreased cognitive functioning and increased cardiovascular disturbances,” said Hong. “The use of continuous positive airway pressure – CPAP – therapy could stop further progression of brain damage in patients with severe OSA.”

Full story at http://www.medicalnewstoday.com/articles/177728.php

New Release: 0.7.5

January 27th, 2010 by slarson

A new beta edition of the Whole Brain Catalog has arrived!  Version 0.7.5 was released today, just three months after the first public debut of version 0.7 at the Society for Neuroscience 2009 annual meeting in Chicago.  The new version integrates substantial new data and features to improve the Catalog’s usability and intuitiveness.

With these new enhancements, the multi-scale resolution of the Catalog’s Google Earth-like brain model is richer.  As mentioned in our last post, over 200 Allen atlas brain regions were recently added to the Whole Brain Catalog.  Version 0.7.5 provides full Allen region support, which allows users to explore more detailed models of the mouse brain.  Better 3D controls make the 3D models more accessible and easier for researchers to view their data in the context of the brain regions.

Our developers have been working hard to fix the bugs that have been reported since the initial release.  Our developers have added better logging of bugs to help with bug reporting.  As more of the worldwide neuroscience community makes new connections in the Catalog, we’re growing a fertile open-access virtual environment for sharing and collaborations.  The Whole Brain Catalog is a work in progress, so stay tuned and watch this space for more news and updates.

A complete list of the updates are available online.

Jumping Neural DNA Key to Brain Plasticity?

January 21st, 2010 by gnwood

We understand that every one of our body’s cells contains the same genome, or pattern of DNA—but it turns out that this is not true of the brain. Researchers here at the Salk Institute for Biological Studies recently found that the DNA sequence in human neurons can vary not only from that of the rest of the body but even from one brain cell to the next.

The reason is “jumping genes,” DNA elements that can copy and reinsert themselves in different places within the genome. These mutations increase the total amount of DNA in each neuron. Geneticist Fred H. Gage and his team at Salk looked at a type of mobile element called LINE-1. Although LINE-1s are present in all cells of the body, they appeared to be active only in developing brain cells, the researchers found.

The jumping genes generate neuronal diversity, which might help the brain adapt, Gage speculates. “Many of the things that we are going to be presented with throughout our lives are unanticipated,” he says. The higher the neuronal variety in the brain, the higher the chances that it contains some cells that are capable of rising to these cognitive challenges.

For more information check out the Scientific American article.

New year! New features! New releases!

January 8th, 2010 by Sarah

We have been a bit dormant on here, but doesn’t mean we haven’t been busy! We have been making plans for future releases (look out for our next beta release at the end of January) and focusing on improving the usability of the Whole Brain Catalog. As always, we would love to hear from you. You can join discussions on our google groups mailing lists and if you have any troubles, be sure to report the bug.

One very exciting development, is we have added over two hundred Allen Atlas brain regions to the latest version of the Whole Brain Catalog. The addition of the Allen Atlas brain regions gives a more a detailed and elegant view of the mouse brain, but visualizing over 200 brain meshes at once has proven to be challenging. Take a look at a post from Jesus Martinez, who has been tackling this challenging problem on the developers blog if you would like to learn more about some of the challenges we have encountered.

Further, we are looking to feature some neuroscience bloggers so stay tuned for updates! Also, be sure to follow us on twitter for more updates!

Tutorial videos – how to use the Whole Brain Catalog

November 19th, 2009 by slarson

We wanted to direct your attention at some  new videos on our YouTube channel that help to illustrate how to perform basic functionality in the Whole Brain Catalog.  A tutorial on basic navigation is available, as well as one on loading simulation time series.   Please let us know if you have questions by posting on our forum.