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A Detailed Gene Map of the Human Brain

The Allen Institute for Brain Science has released the most comprehensive catalogue yet of the brain's biochemistry, providing an important new resource for neuroscientists.

Emily Singer 04/13/2011

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A tale of two brains. On the left, a 3D viewer shows two brains; the stripes on outer surface represent expression of a gene in different areas of the cortex, while the dots (most of which are hidden under the surface in this view), reflect expression of the gene in deeper areas of the brain. Users can a dive deeper into the massive amount of quantitative and other data, as shown on the right.


Scientists have mapped the biochemistry and anatomy of two human brains in comprehensive detail, compiling the data into a publicly accessible database called the Allen Human Brain Atlas. In addition to maps highlighting where in the brain each gene in the genome is expressed, the atlas includes brain imaging data derived from magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI).

According to a release from the institute, the data "reveal a striking 94 percent similarity between human brains". In addition, "data analysis from the two human brains indicate that at least 82 percent of all human genes are expressed in the brain, highlighting its tremendous complexity while also providing an essential genetic blueprint to understand brain functionality better and propel research in neurologic disease and other brain disorders."

Pinky and the brain. A researcher examines a cross-section of the human brain stained to determine the quality and integrity of the specimen.


The human map follows release of a mouse version that the institute released in 2006. The human data will likely be used in studies examining a broad range of neurological disorders and cognitive functions, such as Parkinson's disease, schizophrenia, multiple sclerosis and even obesity. According to the institute, about 4,000 unique visitors are accessing the new Atlas each month.

A happy brain. The dots on this brain image indicate where the antidepressant Prozac acts on the internal structures of the brain. Researchers can drill down deeper for each dot and retrieve a detailed picture of the biochemistry at that location (analogous to a detailed view of everything in a particular neighborhood in a GPS).


"Until now, a definitive map of the human brain, at this level of detail, simply hasn't existed," said Allan Jones, Ph.D., Chief Executive Officer of the Allen Institute for Brain Science. "The Allen Human Brain Atlas provides never-before-seen views into our most complex and most important organ. Understanding how our genes are used in our brains will help scientists and the medical community better understand and discover new treatments for the full spectrum of brain diseases and disorders, from mental illness and drug addiction, to Alzheimer's and Parkinson's diseases, multiple sclerosis, autism and more."

Similar to a high-powered, multi-functional GPS navigation system, the Allen Human Brain Atlas identifies 1,000 anatomical sites in the human brain, backed by more than 100 million data points that indicate the particular gene expression and underlying biochemistry of each site. Scientists can use the Allen Human Brain Atlas to explore the human brain and identify how disease and trauma, including physical brain injuries and mental health disorders, affect specific areas of the brain. This powerful resource makes it possible to pinpoint where a particular drug acts anatomically in the brain, to ultimately better control the successful outcome of numerous therapies.

It is anticipated that the Allen Human Brain Atlas will be used in small and large-scale applications to examine diseases and disorders, such as obesity, Parkinson's disease, autism, schizophrenia, Alzheimer's disease and multiple sclerosis — as well as those exploring how the healthy brain works.

Biomedical News in Brief

GM cows that produce human milk, meditating away pain, and the genes behind your love affair with caffeine.

Emily Singer 04/07/2011

Cows that Produce Human-like Milk

Scientists from China Agricultural University have genetically engineered cows to produce human-like milk. According to an article in the Telegraph,

The scientists behind the research believe milk from herds of genetically modified cows could provide an alternative to human breast milk and formula milk for babies, which is often criticised as being an inferior substitute.

...

China is now leading the way in research on genetically modified food and the rules on the technology are more relaxed than those in place in Europe.

The cows produced milk containing a human antimicrobial protein that helps protect newborns from bacterial infections as well as a protein known to boosts infants' immune systems. The research was published in the Public Library of Science One.

Professor Ning Li, the scientist who led the research and director of the State Key Laboratories for AgroBiotechnology at the China Agricultural University, told the Telegraph that the GM milk tastes stronger than normal milk and that it would be as safe to drink as milk from ordinary dairy cows.

"We aim to commercialize some research in this area in coming three years," he told the Telegraph. "For the 'human-like milk', 10 years or maybe more time will be required to finally pour this enhanced milk into the consumer's cup."


Mediation to Control Pain

Meditating can significantly reduce pain, possibly by reducing activity in part of the brain responsible for sensation, according to research published this week in the Journal of Neuroscience.

In the study, researchers from Wake Forest Baptist Medical Center used magnetic resonance imaging (MRI) to scan the brain of 15 volunteers as a device heated a small area of their skin to a painful 120° Fahrenheit. The volunteers, who had never previously meditated, then took 20-minute meditation classes and were scanned again, this time meditating when experiencing the painful heat.

According to a release from the center,

Meditation significantly reduced brain activity in the primary somatosensory cortex, an area that is crucially involved in creating the feeling of where and how intense a painful stimulus is. The scans taken before meditation training showed activity in this area was very high. However, when participants were meditating during the scans, activity in this important pain-processing region could not be detected.

"This is the first study to show that only a little over an hour of meditation training can dramatically reduce both the experience of pain and pain-related brain activation," said Fadel Zeidan, Ph.D., lead author of the study and post-doctoral research fellow at Wake Forest Baptist Medical Center.

"We found a big effect - about a 40 percent reduction in pain intensity and a 57 percent reduction in pain unpleasantness. Meditation produced a greater reduction in pain than even morphine or other pain-relieving drugs, which typically reduce pain ratings by about 25 percent."


Genes for Caffeine Fiends

Researchers found that mutations in two different genes, one involved in the metabolism of caffeine and the other involved in regulating that gene, influence how much caffeine people drink. According to a press release from the National Institutes of Health, "Individuals with the highest-consumption genotype for either gene consumed ~40 mg more caffeine than those with the lowest-consumption genotype, equivalent to the amount of 1/3 cup of caffeinated coffee, or 1 can of cola."

To identify the genes, researchers scanned the genomes of nearly 50,000 people who had participated in previous studies analyzing caffeine intake. While it's not yet clear why mutations in these genes would lead to great caffeine intake, it's possible that these people metabolize caffeine so quickly that they drink a lot of it to maintain their buzz.

According to an article on ScienceNow, twin studies have shown that genetics accounts for between 43% and 58% of the variability in coffee-drinking habits. However, these two variants are responsible for just a small fraction—less than 1%—of the variation in caffeine intake among the subjects, suggesting that rarer variants, which this study didn't search for, are still out there.

When trying to tease out the genetics of behaviors such as overeating or alcoholism, researchers commonly ask whether the genes at play are ones that regulate how a substance is metabolized or ones that mediate the body's response. With caffeine, there is now a clear answer: "It's in the liver, not in your brain," says [Neil Caporaso of the National Cancer Institute in Bethesda, Maryland].

That's a marked difference from smoking, the only other consumption behavior that has been linked to certain genes, says Abraham Palmer, a pharmacogeneticist at the University of Chicago in Illinois who studies how genes regulate the effects of amphetamine. The genes linked with smoking were ones that regulated nicotine receptors in the brain. This study's results are "really a contrast" and for that reason "very interesting," he says.

The research was published in PLoS Genetics.

A Genetic Determinant of Biological Aging in Humans?

Researchers have found a genetic variant linked to the length of telomeres.

Emily Singer 02/08/2010

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Some people may be genetically programmed to age at a faster rate, according to new research. Scientists have identified a genetic variant linked to the length of telomeres--a region of repetitive DNA that caps the chromosomes. Previous research has shown that telomeres shorten with age and are considered a marker of biological aging. The research was published this week in the journal Nature Genetics.

Other scientists have identified genetic variants that appear linked to healthy aging and longevity, including a variation that causes people to produce less of a protein called cholesterol ester transfer protein (CETP). These people have higher levels of so-called good cholesterol or high-density lipoprotein (HDL), as well as better cognitive function in old age and lower risk of Alzheimer's.

In the new study,

"what we found was that those individuals carrying a particular genetic variant had shorter telomeres i.e. looked biologically older," said Nilesh Samani, of the University of Leicester of the Department of Cardiovascular Sciences, who co-led the project, in a statement. "Given the association of shorter telomeres with age-associated diseases, the finding raises the question whether individuals carrying the variant are at greater risk of developing such diseases."

"The variants identified lies near a gene called TERC which is already known to play an important role in maintaining telomere length," added Tim Spector from King's College London and director of the TwinsUK study, and co-leader of the project. "What our study suggests is that some people are genetically programmed to age at a faster rate. The effect was quite considerable in those with the variant, equivalent to between 3-4 years of 'biological aging" as measured by telomere length loss. Alternatively genetically susceptible people may age even faster when exposed to proven 'bad' environments for telomeres like smoking, obesity or lack of exercise - and end up several years biologically older or succumbing to more age-related diseases. "

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