Brain atlas

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Brain atlas

Postby dignan » Tue Sep 26, 2006 7:40 am

This sounds like a significant new tool for researchers.

Paul Allen's "brain atlas" unlocking mysteries of the ultimate computer

September 26, 2006 -- Seattle Times -- The type of brain map that used to grace high-school biology texts looked like a quilt: A pink chunk labeled "vision" bumped up against a blue blob that was the seat of language and a yellow swath representing motor perception.

Those crude representations were the result of centuries' worth of painstaking dissection, coupled with case studies of people suffering from brain damage and disease.

It took only three years for a Seattle lab founded by Microsoft mogul and philanthropist Paul Allen to revolutionize the landscape of neuroscience by creating a map of the brain that goes far beyond topography to pinpoint the workings of individual cells.

Allen, who donated $100 million to the lab, said he is so pleased with the results that he will consider similar, large-scale science projects in the future.

"This was a great opportunity to do something here that made a difference, and that we could do quickly," he said. "We'll certainly look for more opportunities like this."

Experts say the Allen Brain Atlas, which will be formally unveiled today, will boost understanding of brain circuits and chemistry — and what goes wrong in conditions ranging from schizophrenia and autism to Parkinson's disease and drug addiction.

The map is of the mouse brain, but that doesn't mean it's not applicable to humans. The two species share nearly 99 percent of their genes, and much brain research is conducted in mice.

Neurosurgeons at Swedish Medical Center in Seattle are already using the atlas to study the genetics of fatal brain cancers.

"This really just bolts us ahead in our ability to understand brain function and brain disorder," said neuroscientist Marc Tessier-Lavigne, who discovered the molecules that trigger connections between nerve cells, and serves as a science adviser for the Allen Institute for Brain Science. "It's cool, and it's important as well."

Allan Jones, the institute's chief scientific officer, likens the advance to leaping from a 19th-century map of Seattle that showed land masses and bodies of water, to zooming in on a single house with Google's interactive mapping system.

The project builds on the explosion of information from gene sequencing projects, like the Human Genome Initiative. Having lists of genes is valuable but doesn't necessarily reveal much about what those genes do in the body — or where they are active.

The atlas fills in those blanks for the brain, the body's most complex organ.

Using a robotic system to analyze 16,000 paper-thin mouse brain slices a week, the institute determined where in the brain each of the mouse's 21,000 genes is switched on, or expressed.

Almost every cell of the mouse body contains a full complement of all genes. What a particular type of cell looks like and how it functions is determined by which genes are switched on, so that a liver cell is different from a skin cell — or a brain cell.

The gene expression map provides unprecedented detail about the types of neurotransmitters and other chemicals produced in different regions of the brain and in different types of brain cells.

"The way brain cells are programmed to do their job is through the expression of specific genes," said Tessier-Lavigne, vice president of research drug discovery for the biotech firm Genentech.

Scientists were surprised to discover that 80 percent of all mouse genes are switched on somewhere in the brain, Jones said.

"We think there are probably more cell types within the brain than in all the other organs of the body combined," he said.

The free, online mouse atlas has been getting 250 hits a day from researchers working on a wide range of neuroscience problems.

"I really can't live without it," said Ben Barres, professor of neurobiology and developmental biology at Stanford University. He studies a little-understood class of brain cells called glia. The atlas allows him to quickly confirm which genes are switched on in various types of glial cells.

Mapping the genes himself would be far too time-consuming, he said.

Researchers studying Parkinson's disease can use the atlas to learn more about the genetics of the brain cells that are destroyed by the disease, leading to tremors. Multiple-sclerosis experts can explore why the crippling disease attacks some parts of the brain more than others.

As a programmer, Allen said he has long been fascinated by the ultimate computer: the human brain. When he was considering a brain project, he convened a meeting of top neuroscientists to find out what would be most valuable.

The resulting atlas is one of his biggest philanthropic endeavors. And though it lacks the pizzazz of some of Allen's higher-profile projects, like the search for extraterrestrial life or his X Prize-winning Space Ship One, it similarly blends the billionaire's interests in science and technology.

The atlas also generated staggering amounts of data, and much of the project focused on computer programs to make the information easily accessible.

The federal government would have been reluctant to fund a project on such a scale, said Dr. Thomas Insel, director of the National Institute of Mental Health.

"For a private donor to build this kind of a spectacular electronic atlas and just say to the world: 'Have at it' — I can't think of a precedent for that," he said.

Completing the atlas cost about $40 million, leaving the institute $60 million while it works to become self-sufficient. Jones said he hopes to bring in federal grants and forge partnerships with other scientists. The only outside money the institute has received so far is a $1.8 million grant from the U.S. Army to study the brain effects of sleep deprivation.

With its remaining Allen money, the institute plans to map the human neocortex — the wrinkled outer layer that is the seat of higher thought and emotion. Jones said they'll use cadaver brains and pea-sized bits of living tissue excised by surgeons during brain tumor removal or aneurysm repair.

Dr. Gregory Foltz, a neurosurgeon at Swedish, is partnering with the institute to help zero in on the genetic abnormalities glioblastomas — a type of brain cancer that usually kills within 18 months. Understanding why some genes are switched off in the tumors may lead to better treatments, he said. ... in26m.html
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brain picture

Postby gwa » Tue Sep 26, 2006 9:43 am

Fantastic article! Thanks for the post.

It is very encouraging and I now no longer believe that we are still in the Dark Ages as far as brain knowledge.

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Postby dignan » Wed Dec 06, 2006 12:45 pm

Here's an update on the brain atlas:

Genomic atlas of the mouse brain revealed

06 December 2006 - news service - It is a brain map like no other, has been three years in the making, and promises a revolution in neuroscience: a genomic atlas of the mouse brain has been crafted.

Unveiled in its full glory today, the Allen Brain Atlas contains 85 million images, and enough data to fill 20,000 iPods. It documents the activity of more than 21,000 genes across the entire mouse brain in such fine detail that it is possible pick out individual cells. Already, the atlas has revealed that the mammalian brain contains “hidden” structures, defined by common patterns of gene activity.

“It is a profound enabling tool that is going to dramatically facilitate and accelerate research,” says Marc Tessier-Lavigne, senior vice-president of the biotech firm Genentech in South San Francisco, US. “By having all of the information collated in one place, you can do all of the searching that would not otherwise be possible.”

Ed Lein and colleagues at the Allen Institute Brain Science in Seattle, US, created the atlas using a technique called "in situ hybridisation". This involves bathing thin slices of brain tissue in chemically labelled RNA probes that bind to sequences, called messenger RNA, produced by individual genes.

The process had to be repeated for each gene, and for slices of tissue taken from different parts of the brain, to build a 3D map of gene activity that can be navigated using software available on the web.

To standardise the results, the researchers used inbred male mice from a strain commonly used in brain research, which were all sacrificed at exactly the same age and time of day. “It’s a snapshot,” says neuroscientist Kelly Overly, who worked on the project.

While factors such as age, sex and daily cycles of biological activity are known to affect gene expression, the researchers are confident that many of the patterns of gene activity they have discovered are common features of the mammalian brain.

The map has already revealed that at least 80% of the genes studied are active in the brain – more than had been predicted. Some are “housekeeping” genes, expressed across most of the brain, but most seem to be active in only subsets of cells.

By studying patterns of activity for these genes, the team has identified structures that are invisible to conventional neuroanatomical methods, and more revelations are expected as neuroscientists get to grips with the atlas.

You can query the Brain Atlas and download the Brain Explorer software at ... ealed.html
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Postby dignan » Thu Mar 13, 2008 8:08 am

Another update on the brain atlas...

Allen Institute for Brain Science Launches Three New Landmark Atlas Projects Focusing on the Human Brain, Developing Brain and Spinal Cord

March 13 /PRNewswire/ -- The Allen Institute for Brain Science announced today that it is undertaking three major projects designed to accelerate brain, and spinal cord research, and help scientists worldwide gain new insight into numerous diseases and disorders.

The Institute will create three new Web-based atlas resources that map gene activity in the brain and spinal cord. These include an atlas designed to provide insight into gene expression in the human brain; an atlas of the developing mouse brain designed to illustrate and enhance understanding of gene activity across multiple stages of development from birth through adulthood; and an atlas of the mouse spinal cord designed to inform research into spinal injuries due to disease, disorder or trauma.

The new atlases will be officially known as the Allen Brain Atlas (ABA)- Human Brain, ABA-Developing Mouse Brain, and ABA-Mouse Spinal Cord. Upon completion, the atlases will be made publicly available on the Internet at no charge to users to encourage widespread use and scientific collaboration.

"Building on the success of our inaugural Allen Brain Atlas project, we are inspired to take on projects at the leading edge of science -- creating large-scale resources that will fuel innovation for countless discoveries in brain research," said Allan Jones, Chief Scientific Officer at the Allen Institute. "Scientists in the research community agree that these projects will provide a transformative catalyst for advancing and promoting innovation, ultimately allowing for the most positive impact worldwide. The Institute is uniquely suited to successfully complete these projects because of its established technology platforms and multidisciplinary reach."

Recognizing that the atlases can exponentially advance the global understanding of many diseases and disorders that afflict millions, the Allen Institute has been successful in bringing diverse groups together to fund a common project by providing centralized databases of information that an individual researcher might spend a lifetime trying to gather.

"By putting our data in the hands of scientists studying devastating diseases and disorders such as autism, obesity, epilepsy, schizophrenia and Amyotrophic Lateral Sclerosis (ALS), these new projects will enable the work of many researchers, industries and organizations," said Elaine Jones, Chief Operating Officer at the Allen Institute. "We believe that free access to our unique resources is the best way to encourage widespread use and collaboration, which ultimately could expedite progress toward life-changing medical breakthroughs."

Mapping the Human Brain

Building on new technology and information gained in the development of its inaugural project, the ABA-Mouse Brain, which was completed in 2006, the Institute will develop the ABA-Human Brain, the world's first human brain atlas that overlays information about gene activity onto a three-dimensional anatomic map. For the first time and using a fresh approach to human brain mapping, the Institute will create a unique resource for understanding genes at work in the human brain and combining information about gene activity with existing anatomic and functional knowledge.

Currently, about 26 percent of American adults -- close to 58 million people -- suffer from a diagnosable mental disorder in a given year. This atlas will enable researchers and clinicians worldwide to advance understanding of brain diseases and disorders and speed progress toward breakthrough therapies.

"Ultimately, understanding the anatomic basis of gene expression in the normal brain will enable us to more effectively target abnormal gene expression in individual patients with brain cancer," said Dr. Greg Foltz, a neurosurgeon at Swedish Medical Center in Seattle, Wash. "As we move into the new era of personalized medicine, understanding the variability between individuals with highly heterogeneous diseases will be fundamental to developing effective treatment strategies. The human brain atlas will provide a critical resource for any scientist or physician interested in treating diseases of the brain."

When completed in approximately four years, the ABA-Human Brain will provide the scientific community with a comprehensive map of gene activity in the human brain. The key features include a quantitative inventory of which genes are turned on in each brain structure and a finer-resolution image database pinpointing to the cellular level where a selected list of high-value genes are turned on.

Understanding the Developing Brain

The ABA-Developing Mouse Brain will provide new insights into how a brain develops and matures. For this two-year project, the Institute will develop a highly detailed map of gene activity in the developing mouse brain. The resulting atlas will comprise an extensive image database showing where several thousand genes are expressed, or "turned on," in the mouse brain at multiple stages of development, from before birth through adulthood. In addition, it will show gene expression in various organs within the embryo.

"The developing brain atlas provides a molecular narrative of how the genetic map of the brain unfolds in space and time," said Dr. David Anderson, professor of biology and Howard Hughes Medical Institute investigator at the California Institute of Technology. "The atlas will be invaluable in gaining insight into the origins of certain behavioral disorders, such as schizophrenia and autism, which are increasingly thought to result from abnormalities of brain development."

This new atlas holds promise for furthering understanding of human developmental disorders such as autism and other age-associated conditions including schizophrenia and Alzheimer's disease. In addition, it is likely to uncover new opportunities for therapeutic intervention, as genes that are important for healthy brain development and maintenance may be helpful in slowing progress of degenerative diseases, preventing life-changing secondary brain damage from stroke or other brain injuries and repairing brain tissue already damaged by injury or disease.

Analyzing the Spinal Cord

In response to specific requests from the spinal cord research community and advocacy groups, and with support from a diverse consortium of funders, the Institute is following its successful ABA-Mouse Brain project with an atlas mapping gene expression in the mouse spinal cord. Expected to be complete in a one-year timeframe, the ABA-Spinal Cord will be a comprehensive genome-wide survey of gene expression that pinpoints where each gene is expressed -- or "turned on" -- in both juvenile and adult mouse spinal cord.

"The spinal cord is relatively small, compared to the brain, but it is a crucial highway for transmitting signals between the brain and the rest of the body in order to make everything work the way we need it to," said Dr. Jane Roskams, associate professor at the Brain Research Center and iCord at the University of British Columbia. "It may be small, but can be catastrophic when it becomes broken. The problem is that we know very little about the genes that control different functions in the spinal cord. This mouse spinal cord atlas will absolutely help researchers advance their work in this area in quantum leaps, and maybe it will help us discover how to make spinal cord patients take leaps of their own."

The Institute hopes this unique database will support the entire spinal cord research community, offering an essential baseline of the normal mouse spinal cord for comparison with models of injuries or diseases found in humans. The atlas holds great promise for furthering understanding of diseases and disorders affecting the spinal cord -- including ALS, multiple sclerosis, Spinal Muscular Atrophy and spinal cord injuries -- and pointing the way for effective treatments.

The ABA-Spinal Cord is funded by a group of disease organizations, foundations, and corporate and private donors. The Institute will continue seeking support from individuals and organizations for the spinal cord atlas project.

"We are excited to see such a diverse array of funders come forward with the shared goal of supporting this project to advance spinal cord research," said Elaine Jones. "This is an example of individuals and organizations coming together to fund an important project that will empower scientists and have far-reaching impacts on spinal cord research in the future. We look forward to building similar funding groups for our human brain atlas, developing brain atlas and other projects moving forward."

Link to press release
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Postby dignan » Tue Apr 12, 2011 1:49 pm

They have finished the human brain atlas: ... -gene.html
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Postby Lyon » Tue Apr 12, 2011 1:53 pm

Last edited by Lyon on Sun Nov 20, 2011 4:24 pm, edited 1 time in total.
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Postby patientx » Wed Apr 13, 2011 11:04 am

Slide show with some images from the atlas and photos showing how it was made - pretty cool:
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