Biosingularity

Archive for August 2011

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.

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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.

 


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