Biosingularity

Mice don’t have tails on their backs, and their ribs don’t grow from lumbar vertebrae. And for a good reason. EPFL scientists have discovered the mechanism that determines the shape that many animals take – including humans, blue whales, and insects.

Why don’t our arms grow from the middle of our bodies? The question isn’t as trivial as it appears. Vertebrae, limbs, ribs, tailbone … in only two days, all these elements take their place in the embryo, in the right spot and with the precision of a Swiss watch. Intrigued by the extraordinary reliability of this mechanism, biologists have long wondered how it works. Now, researchers at EPFL (Ecole Polytechnique Fédérale de Lausanne) and the University of Geneva (Unige) have solved the mystery. Their discovery will be published October 13, 2011 in the journal Science.

via From whales to earthworms, the mechanism that gives shape to life.

Scientists working at the Medical Research Council have identified changes in the patterns of sugar molecules that line pre-cancerous cells in the esophagus, a condition called Barrett’s dysplasia, making it much easier to detect and remove these cells before they develop into esophageal cancer. These findings, reported in the journal Nature Medicine, have important implications for patients and may help to monitor their condition and prevent the development of cancer.
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Researchers Find Unique Protein Organization In Arteries Associated with Cardiovascular Disease. Knowledge could assist in tissue replacements, treatments for high blood pressure and diabetes.

..Human arteries – some smaller than a strand of hair – stiffen as a person ages. This stiffening is a factor in cardiovascular disease, the leading cause of death in the United States, because it contributes to the circulatory complications in disorders such as high blood pressure and diabetes. University of Missouri researchers have now used advanced 3-D microscopic imaging technology to identify and monitor the proteins involved in this stiffening process. These findings could eventually help researchers and physicians understand and treat complications associated with cardiovascular disease.

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Have you ever wondered what a virus sounds like? Or what noise a bacterium makes when it moves between hosts? If the answer is yes, you may soon get your chance to find out, thanks to the development of the world’s tiniest ear. The “nano-ear,” a microscopic particle of gold trapped by a laser beam, can detect sound a million times fainter than the threshold for human hearing. Researchers suggest the work could open up a whole new field of “acoustic microscopy,” in which organisms are studied using the sound they emit.

The concept of the nano-ear began with a 1986 invention known as optical tweezers. The tweezers use a laser beam focused to a point with a lens to grab hold of tiny particles and move them around. They’ve become a standard tool in molecular biology and nanotechnology, helping researchers inject DNA into cells and even manipulate it once inside. Optical tweezers can also be used to measure minuscule forces acting on microscopic particles; once you’ve grabbed hold of your particle with the laser beam, instead of moving it yourself, you simply use a microscope or other suitable monitoring apparatus to watch whether it moves of its own accord. That’s where the nano-ear comes in.

via Scientists Create World’s Tiniest Ear – ScienceNOW.

The compound—delta-12-protaglandin J3, or D12-PGJ3—targeted and killed the stem cells of chronic myelogenous leukemia, or CML, in mice, says Sandeep Prabhu, associate professor of immunology and molecular toxicology at Penn State.

The compound is produced from EPA—Eicosapentaenoic Acid—an omega-3 fatty acid found in fish and in fish oil.

“Research in the past on fatty acids has shown the health benefits of fatty acids on cardiovascular system and brain development, particularly in infants, but we have shown that some metabolites of omega-3 have the ability to selectively kill the leukemia-causing stem cells in mice,” says Prabhu. “The important thing is that the mice were completely cured of leukemia with no relapse.”

via Futurity.org – Fish oil compound stops leukemia in mice.

Anyone who’s passed basic biology knows that we get one copy of a gene from our mother, a second from our father. But few people realize that not all of these genes end up being treated equally. Imprinted genes are expressed from only the maternal or paternal allele, rather than both. And, when this process goes wrong, it can actually lead to diseases. Now, researchers have identified a possible way to treat imprinting errors.

In the brain, Ube3a is an imprinted gene; only the maternal allele is expressed, even if it is mutated and the paternal allele is normal. This is the case in Angelman syndrome, a severe neurodevelopmental disorder caused by mutation or deletion of the maternal allele of Ube3a. Ube3a is imprinted only in the brain, though; in other tissues, the paternal allele is expressed along with the maternal one.

This led Benjamin Philpot and his colleagues at UNC Chapel Hill to wonder: wouldn’t it be great if we could get the normal, paternal version of Ube3a to work in the brain—to unsilence it? Maybe this could help kids with Angelman syndrome.

via A drug that activates only your father’s version of a gene may treat neural disorder.

A mysterious bony growth found in elephants’ feet is actually a sixth “toe”, scientists report.

For more than 300 years, the structure has puzzled researchers, but this study suggests that it helps to support elephants’ colossal weight.

Fossils reveal that this “pre-digit” evolved about 40 million years ago, at a point when early elephants became larger and more land-based.

The research is published in the journal Science.

Lead author Professor John Hutchinson, from the UK’s structure and motion laboratory at the Royal Veterinary College, said: “It’s a cool mystery that goes back to 1706, when the first elephant was dissected by a Scottish surgeon.”

via BBC News – Elephant’s sixth ‘toe’ discovered.

The computer assisted design (CAD) tools that made it possible to fabricate integrated circuits with millions of transistors may soon be coming to the biological sciences. Researchers at the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) have developed CAD-type models and simulations for RNA molecules that make it possible to engineer biological components or “RNA devices” for controlling genetic expression  in microbes. This holds enormous potential for microbial-based sustainable production of advanced biofuels, biodegradable plastics, therapeutic drugs and a host of other goods now derived from petrochemicals.

JBEI researchers have developed CAD-type tools for engineering RNA components that hold enormous potential for microbial-based production of advanced biofuels and other goods now derived from petrochemicals. (Image by Zosia Rostomian, Berkeley Lab)

“Because biological systems exhibit functional complexity at multiple scales, a big question has been whether effective design tools can be created to increase the sizes and complexities of the microbial systems we engineer to meet specific needs,” says Jay Keasling, director of JBEI and a world authority on synthetic biology and metabolic engineering. “Our work establishes a foundation for developing CAD platforms to engineer complex RNA-based control systems that can process cellular information and program the expression of very large numbers of genes. Perhaps even more importantly, we have provided a framework for studying RNA functions and demonstrated the potential of using biochemical and biophysical modeling to develop rigorous design-driven engineering strategies for biology.” Read the rest of this entry »

Do we finally have a miracle weight loss drug? I mean, for real this time? The data seems to support such a claim, at least for overweight monkeys that simply can’t drop those extra pounds no matter what they try. After receiving the drug for just four weeks, the monkeys lost between 7 and 15 percent of the body weight, and averaged a more than 38 percent loss of total body fat.

The study, published November 9th in the journal Science Translational Medicine, was headed by husband-and-wife team Wadih Arap and Renata Pasqualini at the M.D. Anderson Cancer Center in Houston. Their drug, called Adipotide, targets the blood vessels that feed fat cells, or adipocytes. Attacking those blood vessels chokes off the nutrient supply that the fat cells need to survive and they either die or become stressed to the point that they don’t function.

Of course, blood vessels are needed to keep all cells alive. But the major medical advancement that adipotide brings is its ability to kill blood vessels associated with fat cells while leaving other blood vessels alone. The strategy has been long sought after by cancer biologists trying to kill cancer cells while leaving normal cells unharmed. Where others had failed, Arap and Pasqualini, cancer biologists themselves, succeeded by taking an approach that was novel in multiple ways.

via Obese Monkeys Given Miracle Weight Loss Pill (video) | Singularity Hub.

Simulating How Proteins Self-Assemble, Or Fold – YouTube.

Faster, longer, further… fatter? Knocking out a particular gene in muscle lets mice run twice as far as normal. Knocking out the same gene in fat cells allows the animals to put on weight without developing type-2 diabetes.The discoveries could lead to new treatments for diabetes or for invigorating muscles in elderly people and in those with wasting diseases, say Johan Auwerx of the Federal Polytechnic School of Lausanne, Switzerland, and colleagues. Auwerx warns that cheats may exploit the potential for increase athletic performance, however.Auwerx and his colleagues used a targeted virus to knock out the gene that makes a protein called nuclear receptor corepressor 1 NCoR1 in the muscle of mice. Without NCoR1, mitochondria, which power cells, keep working at full speed. “Effectively, the mice go further, faster, on the same amount of gas,” says Auwerx.

via Gene tweak creates supermouse – and prevents diabetes – life – 11 November 2011 – New Scientist.

Since 1928, the way breast cancer characteristics are evaluated and categorized has remained largely unchanged. It is done by hand, under a microscope. Pathologists examine the tumors visually and score them according to a scale first developed eight decades ago. These scores help doctors assess the type and severity of the cancer and, accordingly, to calculate the patient’s prognosis and course of treatment.

In a paper published Nov. 9 in Science Translational Medicine, computer scientists at the Stanford School of Engineering and pathologists at the Stanford School of Medicine report their collaboration to train computers to analyze breast cancer microscopic images. The computer analyses were more accurate than those conducted by humans.

via Stanford team trains computer to evaluate breast cancer – Office of Communications & Public Affairs – Stanford University School of Medicine.

The red wine ingredient resveratrol mimicked the metabolic effects of dieting and exercising in obese men, a small study found.

Although it didn’t lead to weight loss, a daily 150-milligram dose of resveratrol lowered blood pressure as well as blood glucose levels and liver fat in obese men after 30 days, Dutch researchers reported today in the journal Cell Metabolism.

“It seems to make you metabolically healthier without weight loss,” said study author Patrick Schrauwen of Maastricht University in the Netherlands. “I don’t think it’s a weight-loss drug.”

via Red Wine Ingredient Resveratrol Mimics Calorie Restriction in Obese Men – ABC News.

BGI, the world’s largest genomic organization, announced that an international team of researchers from Korea, China and USA, for the first time, demonstrated the physiology and longevity of the naked mole rats (NMR) in terms of genomics and transcriptomics. The results, published online today in the international journal Nature, provide an excellent opportunity to better understand the unique traits of naked mole rats and advance its use in biological and biomedical studies.

With its wrinkled skin and double-saber buck teeth, the naked mole rat may not be among the most beautiful animals, but they are exceptional in other ways. They are the longest-lived rodent known till now and are exceptionally resistant to cancer; they can live in full darkness, at low oxygen and high carbon dioxide concentrations; and they are unable to sustain thermogenesis or feel certain types of pain. These unique features make naked mole rats particularly attractive to scientists as emerging models for research on aging and cancer, as well as other biological activities or conditions (e.g. metabolic regulation, development, pain and behavior).

In this study, researchers utilized the whole-genome shotgun (WGS) sequencing strategy and next-generation sequencing system to sequence the genome of an individual male naked mole rat. The NMR genome is approximately 2.6 Gb, and the predicted NMR gene set includes 22,561 genes. By sequencing the genome, the researchers demonstrated that the ancestor of NMR split from the ancestors of mice and rats about 73 million years ago, and 93% of the NMR genome shows synteny to human, mouse or rat genomes. Utilizing comparative transcriptome analysis, some genes related to anti-aging and adaptation to a low oxygen environment were identified based on the different expression levels of NMR transcripts between different age groups and at exposure to different levels of oxygen concentration.

The researchers made further investigation and found several important genes related to the exceptional traits of NMR. The stable gene expression of TERT and other genes, regardless of age, may be related to NMR’s longevity mechanism. In addition, the unusual regulatory involvement of tumor suppressor p16Ink4a and p19Arf may be the key factor in NMR’s cancer resistance, and mutation in the specificity of HIF1a and VHL may contribute to NMR’s high tolerance to a low oxygen environment. At least 10% of the approximately 200 genes associated with visual perception in humans and mice were found to be inactivated or missing in NMR, implicating that NMR’s poor visual function may be caused by the deterioration of genes coding for various critical components of the visual system.

The genomic information of NMR provides a rich resource for researchers working in aging, cancer, eusociality and many other areas. The data can be mined in numerous ways to uncover the molecular basis for the extraordinary traits of this most unusual mammal. To achieve a more comprehensive insight into NMR’s exceptional traits, the international team will continue to explore the molecular mechanisms of anti-aging, anti-cancer, adaptation to low oxygen environment and eusociality, with approaches of comparative genomics, comparative transcriptomics, and comparative methylation.

“The NMR genome will play an important role in functional studies of NMR, which also will provide unprecedented opportunities for exploring some of the most challenging questions in biology and medicine,” stated Xiaodong Fang, Leader of non-model organisms group at BGI and the co-leading author of the study. “We believe that NMR will become a new model in biological and biomedical research in the near future.”

New York University biologists have identified a new mechanism for regulating color vision by studying a mutant fly named after Frank (‘Ol Blue Eyes) Sinatra. Their findings, which appear in the journal Nature, focus on how the visual system functions in order to preserve the fidelity of color discrimination throughout the life of an organism. They also offer new insights into how genes controlling color detection are turned on and off.

Many biologists study how different cells develop to acquire their fate. The NYU research team, headed by Claude Desplan, a professor of biology, examined how they stay the same. Cells have complex functions that must be maintained through extensive coordination, and failure to do so could lead to “confused” cells whose function is not clear. This is particularly important for cells, such as neurons, which live for a long time—usually the entire lifetime of an animal. Read the rest of this entry »

The brain learns through changes in the strength of its synapses — the connections between neurons — in response to stimuli.

Now, in a discovery that challenges conventional wisdom on the brain mechanisms of learning, UCLA neuro-physicists have found there is an optimal brain “rhythm,” or frequency, for changing synaptic strength. And further, like stations on a radio dial, each synapse is tuned to a different optimal frequency for learning.

Mehta-Brain

The image shows a neuron with a tree trunk-like dendrite. Each triangular shape touching the dendrite represents a synapse, where inputs from other neurons, called spikes, arrive (the squiggly shapes). Synapses that are further away on the dendritic tree from the cell body require a higher spike frequency (spikes that come closer together in time) and spikes that arrive with perfect timing to generate maximal learning.

The findings, which provide a grand-unified theory of the mechanisms that underlie learning in the brain, may lead to possible new therapies for treating learning disabilities. Read the rest of this entry »

Broken biological clocks in blood vessels may contribute to hardened arteries, even if the main timer in the brain works fine. The finding, from transplant experiments with mice, suggests that throwing off the daily rhythms of the body’s organs can have serious health consequences.

A wealth of evidence shows that skimping on sleep and working against the body’s natural daily, or circadian, rhythms can raise the risk of developing illnesses such as heart disease and diabetes. Scientists assumed that the diseases resulted from malfunctions in a master clock in the brain, which synchronizes sleeping, waking and other body functions with the rising and setting of the sun.

via Heart Disease Has Its Own Clock – Science News.

Fewer women are dying from breast cancer, largely because of advances in screening and treatment. Poorer women, however, are seeing a slower and later decline in their risk of dying from breast cancer, in part because they don’t have as much access to these life-saving advances.

In 2008, 51.4% of poor women aged 40 and older had a screening mammogram in the past two years. By contrast, 72.8% of wealthier women had a mammogram in the past two years.

These are some of the findings from the American Cancer Society’s Breast Cancer Facts & Figures 2011-2012 report. It appears in CA: A Cancer Journal for Clinicians in time for National Breast Cancer Awareness Month, which takes place every October.

In 2011, an estimated 230,480 women will be diagnosed with breast cancer, according to the new report. About 39,520 women will die from the disease in 2011. Beside skin cancer, breast cancer is the most common cancer seen among American women.

via Breast Cancer Death Rates Decline.

Johns Hopkins scientists investigating chemical modifications across the genomes of adult mice have discovered that DNA modifications in non-dividing brain cells, thought to be inherently stable, instead underwent large-scale dynamic changes as a result of stimulated brain activity. Their report, in the October issue of Nature Neuroscience, has major implications for treating psychiatric diseases, neurodegenerative disorders, and for better understanding learning, memory and mood regulation. Read the rest of this entry »

Laughter is regularly promoted as a source of health and well being, but it has been hard to pin down exactly why laughing until it hurts feels so good.RSS Feed Get Science News From The New York Times »The answer, reports Robin Dunbar, an evolutionary psychologist at Oxford, is not the intellectual pleasure of cerebral humor, but the physical act of laughing. The simple muscular exertions involved in producing the familiar ha, ha, ha, he said, trigger an increase in endorphins, the brain chemicals known for their feel-good effect.

via Laughter Produces Endorphins, Study Finds – NYTimes.com.

A gene responsible for chronic pain has been identified, with scientists saying this could lead to drugs for treating long-lasting back pain.Writing in the journal Science, University of Cambridge researchers removed the HCN2 gene from pain-sensitive nerves in mice.Deleting the gene stopped any chronic pain but did not affect acute pain.

via BBC News – Gene find could lead to drug for chronic back pain.

Each taste, from sweet to salty, is sensed by a unique set of neurons in the brains of mice, new research reveals. The findings demonstrate that neurons that respond to specific tastes are arranged discretely in what the scientists call a “gustotopic map.” This is the first map that shows how taste is represented in the mammalian brain.

There’s no mistaking the sweetness of a ripe peach for the saltiness of a potato chip – in part due to highly specialized, selectively-tuned cells in the tongue that detect each unique taste. Now, Howard Hughes Medical Institute and NIH scientists have added to our understanding of how we perceive taste, showing that four of our basic tastes—sweet, bitter, salty, and “umami,” or savory—are also processed by distinct areas of the brain. The researchers published their work in the September 2, 2011, issue of the journal Science.

via HHMI News: New Map Shows Where Tastes are Coded in the Brain: How Does the Brain Know What the Tongue Knows?.

Like explorers mapping a new planet, scientists probing the brain need every type of landmark they can get. Each mountain, river or forest helps scientists find their way through the intricacies of the human brain.

Researchers at Washington University School of Medicine in St. Louis have developed a new technique that provides rapid access to brain landmarks formerly only available at autopsy. Better brain maps will result, speeding efforts to understand how the healthy brain works and potentially aiding in future diagnosis and treatment of brain disorders, the researchers report in The Journal of Neuroscience Aug. 10

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Scientists have found a way to use MRI scanning data to map myelin, a white sheath that covers some brain cell branches. Such maps, previously only available via dissection, help scientists detemine precisely where they are at in the brain. Red and yellow indicate regions with high myelin levels; blue, purple and black areas have low myelin levels.  

via Scientists have new help finding brain’s nooks and crannies | Newsroom | Washington University in St. Louis.

Engineers from the Beckman Institute at the University of Illinois recently reported in the Proceedings of the National Academy of Sciences using small changes in the optical properties of  single living cells to measure their growth.

“Determining the growth patterns of single cells,” the researchers write, “offers answers to some of the most elusive questions in contemporary cell biology: how cell growth is regulated and how cell size distributions are maintained.”

via Futurity.org – Optics used to track single cell’s growth.

Multiple lifestyle factors such as obesity and alcohol consumption increase a person’s risk of diabetes. But new research suggests that a person’s odds of developing the disease may decrease for each positive lifestyle change they make.

Lifestyle factors that can influence the risk of developing type 2 diabetes include diet, weight, physical activity, smoking, and alcohol use.

Researchers, who surveyed about 200,000 people, say diabetes risk can be reduced by 31% for men and 39% for women for each positive lifestyle change, such as quitting smoking or regularly exercising. Also, alcohol use should not exceed one drink daily for women and two drinks daily for men.

via Improving Lifestyle Reduces Diabetes Risk.

Researchers at the University of Leeds have discovered a pain-free way of tackling dental decay that reverses the damage of acid attack and re-builds teeth as new.

The pioneering treatment promises to transform the approach to filling teeth forever.

Tooth decay begins when acid produced by bacteria in plaque dissolves the mineral in the teeth, causing microscopic holes or ‘pores’ to form. As the decay process progresses these micro-pores increase in size and number. Eventually the damaged tooth may have to be drilled and filled to prevent toothache, or even removed.
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We make decisions all our lives—so you’d think we’d get better and better at it. Yet research has shown that younger adults are better decision makers than older ones. Some Texas psychologists, puzzled by these findings, suspected the experiments were biased toward younger brains.

So, rather than testing the ability to make decisions one at a time without regard to past or future, as earlier research did, these psychologists designed a model requiring participants to evaluate each result in order to strategize the next choice, more like decision making in the real world.

The results: The older decision makers trounced their juniors. The findings will be published in an upcoming issue of Psychological Science, a journal of the Association for Psychological Science. Read the rest of this entry »

A team of scientists from The Scripps Research Institute have successfully reengineered an important antibiotic to kill the deadliest antibiotic-resistant bacteria. The compound could one day be used clinically to treat patients with life-threatening and highly resistant bacterial infections.

The results were published in an advanced online issue of the Journal of the American Chemical Society.
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RNA molecules have long been known for their role in translating genes to proteins inside a cell, but more recently, scientists have found large numbers of RNA molecules that don’t code for proteins but seem to have other cellular roles. Most research in mammals has focused on tiny RNA molecules called microRNAs, but a new study, published this week in Nature, describes the far-reaching effects of much larger and relatively unstudied RNA molecules called lincRNAs (short for large intergenic noncoding RNAs). The study identifies lincRNAs that play a role in the function of embryonic stem cells, and suggests trying to use lincRNAs to manipulate these cells to spawn other cell types.

via An RNA Switch for Stem Cells – Technology Review.

An experimental pill to prevent blood clots exceeded already high expectations as a better therapy for millions of people with atrial fibrillation, according to final results of a worldwide study released Sunday.

The study was featured at the European Society of Cardiology in Paris and simultaneously published on the Web site of The New England Journal of Medicine.

“It’s a remarkable achievement,” said Dr. Valentin Fuster, a past president of American and world heart associations, who was not involved with the trial. “This is one of the most significant advances in cardiovascular medicine in the last five years, no question,” Dr. Fuster, chairman of federal and medical panels on atrial fibrillation and director of the heart center at Mount Sinai Medical Center in New York, said in an interview.

The twice-daily pill, to be called Eliquis, prevented 21 percent more strokes than the blood thinner warfarin, a standard treatment for heart arrhythmia, and resulted in 31 percent fewer incidents of major bleeding over an average of 1.8 years in the study.

via Trial Shows Blockbuster Potential for Blood Clot Pill Eliquis – NYTimes.com.

A diet that incorporates cholesterol-lowering foods like soy, nuts, and plant sterols may work better at lowering cholesterol levels than a traditional low-fat diet.

A new study shows that people with high cholesterol who followed the portfolio diet, which includes a combination of cholesterol-lowering foods, lowered their low-density lipoprotein (LDL) cholesterol levels by about 13% after six months on the diet. That’s compared with a 3% LDL reduction among those who followed a traditional diet low in saturated fat.

“Given that cardiovascular disease is our major killer, we feel that a lot of people will benefit to a greater or lesser extent by adopting this diet, which is basically a plant-based approach,” says researcher David Jenkins, MD, Canada Research Chair at the University of Toronto. “Those who may want to follow the diet more specifically are those who are on the cusp for statin treatment.”

via Portfolio Diet Beats Low-Fat Diet at Lowering Cholesterol.

Researchers in Canada have shown that a special cholesterol-lowering diet works well – even with only two nutritional counseling sessions over six months.

Making dietary changes like eating oat bran for breakfast, drinking soy milk instead of dairy, soy burgers in place of hamburgers, and fruit and nuts instead of a full lunch prompted a double-digit drop in both total cholesterol and LDL or “bad” cholesterol.

The study was published Tuesday in the Journal of the American Medical Association.

Lead author Dr. David Jenkins, Canada research chair in nutrition and metabolism at the University of Toronto and St. Michael’s Hospital, had previously shown the effectiveness of a cholesterol-lowering diet when all the meals were provided to participants.

via Bran, soy help cut cholesterol – The Chart – CNN.com Blogs.

Nine years after getting gene therapy for a rare, inherited immune system disorder often called “bubble boy disease,” 14 out of 16 children are doing well, researchers report.

The children were born with severe combined immunodeficiency disease (SCID). They got an experimental gene therapy in the U.K.

A new report shows that nine years later, 14 of the 16 children had working immune systems and were leading normal lives.

“These children, who would have died very young without treatment, are participating in life as fully as their brothers and sisters,” researcher H. Bobby Gaspar, MD, PhD, tells WebMD. “Most of them are going to school, playing ball, and going to parties.”

via Gene Therapy Works for ‘Bubble Boy’ Disease.

A new atlas of gene expression in the mouse brain provides insight into how genes work in the outer part of the brain called the cerebral cortex. In humans, the cerebral cortex is the largest part of the brain, and the region responsible for memory, sensory perception and language.

Mice and people share 90 percent of their genes so the atlas, which is based on the study of normal mice, lays a foundation for future studies of mouse models for human diseases and, eventually, the development of treatments. Researchers from the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, and from Oxford University in the United Kingdom, published a description of the new atlas in the Aug. 25, 2011, journal Neuron. The study describes the activity of more than 11,000 genes in the six layers of brain cells that make up the cerebral cortex.

“This study shows the power of genomic technologies for making unexpected discoveries about the basic biology of life,” said NHGRI Director Eric D. Green, M.D., Ph.D. “The brain is our most complex organ. Until we understand how it is built and how it functions based on our genetic blueprint, we will be hampered in keeping the brain healthy or dealing with its terrible diseases.”

To map gene activity in all six layers of the mouse cerebral cortex, the research team first micro-dissected the brains of eight adult mice, separating the layers of the cortex. They then purified processed RNAs, including messenger RNA, from each cortical layer.

The cell creates messenger RNA (mRNA) when genes are switched on and the DNA code is read out to make proteins. The presence of an mRNA indicates that a gene is turned on, and the amount of mRNA shows the extent to which the gene is active.

To determine which genes were turned on and to what extent, the researchers used a relatively new sequencing technology called RNA-seq. The technique depends on two steps. The researchers first copy processed RNA into a form of DNA, and then sequence the resulting DNA on a second-generation, DNA sequencing instrument. The resulting massive data set must then be analyzed by a cluster of computers to determine which genes have been turned on in the brain cells and to what extent.

The international collaborators have made the new atlas freely available at http://genserv.anat.ox.ac.uk/layers.

By determining the gene activity in each layer, researchers believe it will be possible to connect brain anatomy, genetics and disease processes with greater precision. The research team found that more than half of the genes expressed in the mouse cerebral cortex showed different levels of activity in different layers. These differences point to the areas where specific genes play important roles.

“We found that genes associated with some human diseases were more active in certain layers. For example, we detected genes previously associated with Parkinson’s disease in layer five and Alzheimer’s disease in layers two and three. These are correlations, not necessarily causal, but they do suggest directions for future research,” said T. Grant Belgard, lead author of the paper and an NIH-Oxford fellow in NHGRI’s Genome Technology Branch. “Knowing the detailed pattern of expression of all genes in the cortex and how this fits into the overall brain architecture will help us understand how genes act together to sustain the cells and circuits that underlie behavior and disease.”

Using the technique, researchers detected a vast array of noncoding RNAs. These are RNAs produced from DNA that do not encode proteins, but probably play a critical role in regulating genes and controlling biological processes. Some of these were active in specific layers, and many had not previously been discovered.

The study also further demonstrated the importance of alternative splicing in gene function within the brain. Messenger RNA includes segments called exons that can be stitched together in different ways to produce a mature message that the cell uses to produce proteins. The alternative splicing process allows a single gene to produce many different proteins that can have different functions in different cells or at different times in a cell’s life.

Many alternatively spliced genes showed different distributions of the alternative forms between layers. This includes the Mtap4 gene, whose activity is altered in Alzheimer’s disease.

Next year, Belgard and others will be involved in an effort to replicate the mouse brain atlas for parts of the human brain.

A relatively simple combination of naturally occurring sugars and amino acids offers a plausible route to the building blocks of life, according to a paper published in Nature Chemistry co-authored by a professor at the University of California, Merced.

The study, “A Route to Enantiopure RNA Precursors from Nearly Racemic Starting Materials,” shows how the precursors to RNA could have formed on Earth before any life existed. It was authored by Jason E. Hein, Eric Tse and Donna G. Blackmond, a team of researchers with the Scripps Research Institute. Hein is now a chemistry professor with UC Merced. The paper was published online Sunday.

Biological molecules, such as RNA and proteins, can exist in either a natural or unnatural form, called enantiomers. By studying the chemical reactions carefully, the research team found that it was possible to generate only the natural form of the necessary RNA precursors by including simple amino acids.

“These amino acids changed how the reactions work and allowed only the naturally occurring RNA precursors to be generated in a stable form,” said Hein. “In the end, we showed that an amazingly simple result emerged from some very complex and interconnected chemistry.”

The natural enantiomer of the RNA precursor molecules formed a crystal structure visible to the naked eye. The crystals are stable and avoid normal chemical breakdown. They can exist until the conditions are right for them to change into RNA.

Tiny particles made of polymers hold great promise for targeted delivery of drugs and as structural scaffolds for building artificial tissues. However, current production methods for such microparticles yield a limited array of shapes and can only be made with certain materials, restricting their usefulness.

In an advance that could broadly expand the possible applications for such particles, MIT engineers have developed a way to make microparticles of nearly any shape, using a micromold that changes shape in response to temperature. They can also precisely place drugs into different compartments of the particles, making it easier to control the timing of drug release, or arrange different cells into layers to create tissue that closely mimics the structure of natural tissues.

The new technique, described in a paper published online July 18 in the Journal of the American Chemical Society, also allows researchers to create microparticles from a much more diverse range of materials, says Halil Tekin, an MIT graduate student in electrical engineering and computer science and lead author of the paper.

via Mimicking biological complexity, in a tiny particle – MIT News Office.

Working closely with a team of researchers from Duke University, scientists from the Florida campus of The Scripps Research Institute have helped identify a molecular pathway that plays a key role in stress-related damage to the genome, the entirety of an organism’s hereditary information.

The new findings, published in the journal Nature on August 21, 2011, could not only explain the development of certain human disorders, they could also offer a potential model for prevention and therapy. Read the rest of this entry »

Aneuploidy—when the cells of an organism contain more or fewer than the standard number of chromosomes for its species—is found in greater than 90 percent of all human cancers. But how exactly it relates to cancer, and whether it is a cause or merely a consequence of genomic instability, has long been a mystery. Two new studies published today (August 18) in Science show that it’s probably both, pointing to a gene defect that can cause aneuploidy, and elucidating the disastrous effects of aneuploidy on a cell’s genome.

“Aneuploidy is found in virtually all cancers, yet very little is known about its origins or its effects,” said a cancer biologist Bert Vogelstein at Johns Hopkins Medicine, who was not involved in the research. “These two papers provide some really excellent clues to what’s going on.”

via Chromosomes and Cancer | The Scientist.

A new microscope has allowed researchers to watch molecules move within a cell on a millisecond-by-millisecond time scale for the first time. The novel method, which combines two preëxisting microscopic techniques, opens a window onto cellular processes that had previously been undetectable, unveiling molecular activity within a cell at a much finer level than ever before possible.

“This allows us to look at interactions of molecules, and their mobility,” says Malte Wachsmuth, a cell biophysicist at the European Molecular Biology Laboratory in Heidelberg, Germany, who helped develop the new microscope. Current microscopy techniques can home in on a single spot within a cell, but they can miss vital information when the focus moves from one spot to another. “A typical protein might spend one to two milliseconds in such a spot,” Wachsmuth says. “Molecules are quite mobile, diffusing all around, and it’s a very fast process. A lot can happen in a few tens of milliseconds.”

via Watching the Protein Tango – Technology Review.

Obese people who are otherwise healthy live as long as normal-weight people, new research from Canada suggests.

Some obese but healthy people actually are less likely to die of heart problems than normal-weight people who have some medical conditions, the researchers found.

“You shouldn’t just look at body weight alone,” says researcher Jennifer Kuk, PhD, assistant professor of kinesiology and health science at York University in Toronto.

“A healthy lifestyle, including being physically active and eating a healthy diet, is probably more important than your body weight and focusing on weight loss, if you are otherwise healthy,” she tells WebMD.

Kuk and her colleagues used a new tool that helps identify which people would benefit from weight loss and from weight loss surgery. Called the Edmonton Obesity Staging System (EOSS), it grades or stages obese people depending on whether they have diseases such as heart disease or cancer.

via Study: Obese People Live as Long as Slimmer People.

The study was led by Lori Daiello, PharmD, a research scientist at the Rhode Island Hospital Alzheimer’s Disease and Memory Disorders Center. Data for the analyses was obtained from the Alzheimer’s Disease Neuroimaging Initiative (ADNI), a large multi-center, NIH-funded study that followed older adults with normal cognition, mild cognitive impairment, and Alzheimer’s Disease for over three years with periodic memory testing and brain MRIs.

The study included 819 individuals, 117 of whom reported regular use of fish oil supplements before entry and during study follow-up. The researchers compared cognitive functioning and brain atrophy for patients who reported routinely using these supplements to those who were not using fish oil supplements.

Daiello reports that compared to non-users, use of fish oil supplements was associated with better cognitive functioning during the study. However, this association was significant only in those individuals who had a normal baseline cognitive function and in individuals who tested negative for a genetic risk factor for Alzheimer’s Disease known as APOE4. This is consistent with previous research.
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Continuity of sleep, not just the total hours of nightly slumber, is crucial to forming and retaining memories, a new study in mice suggests.

Mice couldn’t remember objects they’d seen before after a night of interrupted sleep, Asya Rolls of Stanford and her colleagues report online July 25 in the Proceedings of the National Academy of Sciences. Even though the mice got just as much sleep as normal and slept as intensely as usual, breaking that sleep into one-minute chunks was enough to erase the memory of toys the animal had seen before.

The results emphasize that sleep is a process, says Paul Shaw, a neuroscientist at Washington University in St. Louis who was not involved in the study. “Whatever biological function sleep serves takes time,” he says. “So if you wake up, you disrupt that process and have to start from scratch again.”

via Tossing, Turning, Forgetting – Science News.

For the last decade cancer research has been guided by a common vision of how a single cell, outcompeting its neighbors, evolves into a malignant tumor.

Through a series of random mutations, genes that encourage cellular division are pushed into overdrive, while genes that normally send growth-restraining signals are taken offline.

With the accelerator floored and the brake lines cut, the cell and its progeny are free to rapidly multiply. More mutations accumulate, allowing the cancer cells to elude other safeguards and to invade neighboring tissue and metastasize.

These basic principles — laid out 11 years ago in a landmark paper, “The Hallmarks of Cancer,” by Douglas Hanahan and Robert A. Weinberg, and revisited in a follow-up article this year — still serve as the reigning paradigm, a kind of Big Bang theory for the field.

But recent discoveries have been complicating the picture with tangles of new detail. Cancer appears to be even more willful and calculating than previously imagined.

via Beyond the Genome, Cancer’s Secrets Come Into Sharper Focus – NYTimes.com.

Scientists have pinpointed a rare gene variant that increases a woman’s risk of developing ovarian cancer six-fold. The discovery will lead to new diagnostic tests to identify the cancer earlier and provides better information to help doctors choose targeted anti-cancer drugs.

Ovarian cancer can develop without many clear symptoms and is the fifth most common cancer in women. In the UK, 6,500 cases are diagnosed every year and, of those, almost 4,000 end in death.

In the latest study, scientists found that, in around 60 cases of ovarian cancer every year in the UK, the women had faults in a gene called RAD51D. Anyone who inherits a faulty version of this gene, they calculated, therefore had a one in 11 chance of developing ovarian cancer, compared with one in 70 for the general population.

via Ovarian cancer risk gene pinpointed | Science | guardian.co.uk.

Sleep apnea, a fairly common, treatable disorder that causes people to stop breathing momentarily while they sleep, may lead to cognitive impairment and even dementia, according to a new study of elderly women.

Women in the study with sleep apnea or other sleep disorders that affected their breathing were much more likely than those with normal sleep habits to develop cognition problems within five years, said researchers at UCSF and California Pacific Medical Center, who published the results in the Journal of the American Medical Association today.

via Sleep apnea may raise dementia risk, study finds.

German and Spanish mice have rapidly evolved the trait by breeding with an Algerian species from which they have been separate for over a million years.

The researchers say this type of gene transfer is highly unusual and normally found in plants and bacteria.

The Current Biology report says this process could yield mice resistant to almost any form of pest control.

Warfarin is a drug widely used in medicine as an anti-coagulant to prevent the build-up of harmful blood clots. It works through inhibiting a protein called VKORC1. This protein turns on our ability to produce vitamin K, which is essential for clotting.

via BBC News – ‘Super’ mouse evolves resistance to most poisons.

The newly approved drug Xarelto appears to prevent strokes at least as well as the standard treatment warfarin in people who have a heart condition that puts them at high risk for blood clots, a study shows.

Xarelto was approved by the FDA in July to prevent dangerous blood clots in people having hip and knee replacement surgery.

Next month, a panel of experts will consider whether the agency should also approve its use as a once-daily treatment for atrial fibrillation.

Atrial fibrillation causes the heart to pump in an irregular, uncoordinated way that may allow blood to pool and clot in its upper chambers. Those clots can travel to the brain, causing a stroke.

Patients with atrial fibrillation are commonly prescribed the blood-thinning drug warfarin, which is also sold under the brand names Coumadin and Jantoven.

via New Blood Thinner Prevents Strokes in Heart Patients.

Red meat, particularly processed red meats like bacon, sausage, and hot dogs, may increase a person’s risk of developing type 2 diabetes. The more processed or unprocessed red meat a person eats, the greater the risk, according to a new study in the American Journal of Clinical Nutrition.

Type 2 diabetes is linked with obesity. It occurs when they body does not produce enough of the hormone insulin, or the cells do not use insulin properly. Insulin helps the body use glucose or blood sugar for energy. When blood sugar remains elevated with diabetes, complications such as heart disease, blindness, and nerve and kidney damage can occur.

In the study, participants who ate one 3.5-ounce serving of non-processed red meat a day, such as steak or hamburger, were almost 20% more likely to develop type 2 diabetes.

Those who ate half of this amount of processed meat, such as two slices of bacon or one hot dog, had a 51% increased risk for developing diabetes.

“The amount is not huge, but the risk is pretty high,” says Frank B. Hu, MD, PhD, a professor of nutrition and epidemiology at Harvard School of Public Health in Boston. “Regular consumption of red meat, especially processed, is associated with an increased risk for type 2 diabetes. The findings are important given the rising epidemic of diabetes and the increasing consumption of red meat.”

But an industry group disputes the findings of the study.

via Red Meat, Processed Meat Linked to Diabetes Risk.

A biochemical pathway long associated with diarrhea and intestinal function may provide a new therapeutic target for treating ADHD (Attention Deficit Hyperactivity Disorder) other neuropsychiatric disorders, according to a team of scientists from China and the United States reporting Aug. 11 in Science.

Scientists have for the last quarter century studied the intestinal membrane receptor protein, guanylyl cyclase-C (GC-C) for its role in diarrheal disease and other intestinal functions, according to Mitchell Cohen, M.D., U.S. author on the study and director of Gastroenterology, Hepatology and Nutrition at Cincinnati Children’s Hospital Medical Center. In fact, it had been thought that GC-C was found primarily in the intestine.

In the current study, scientists in China who collaborated with Dr. Cohen discovered that the receptor is also expressed in critical areas of the brain. Read the rest of this entry »