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Archive - Dec 11, 2014

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Ground-Breaking Studies of Bird Evolution Published in Science

A University of Nebraska-Lincoln (UNL) researcher has contributed to discoveries about bird evolution as part of a new study that sequenced the complete genomes of 45 avian species. Published as the cover story of the December 12, 2014 issue of Science, the study found that avian genomes -- the complete archive of genetic material present in cells -- have exhibited surprisingly slow rates of evolution when compared with their mammalian counterparts. Dr. Jay Storz, a Susan J. Rosowski Associate Professor of Biological Sciences, led a research group that assisted the study by examining the evolution of multi-gene families shared by birds and mammals. Each family comprises a collection of genes related to one another through a history of duplication, with all members of a given family descending from a single ancient gene. Dr. Storz and his colleagues used computational methods to measure "gene turnover," the rate at which genes are gained or lost over time. The researchers reported that the rate of turnover in avian gene families is roughly two times slower than in mammals. This finding reflects a larger-scale pattern of evolutionary stasis in avian genomes, according to Dr. Storz. "In mammals, there's this continual turnover -- it's like a genomic turnstile. With birds, it's far more conservative," Dr. Storz said. "There might be a gene family that consists of, say, 10 members in the common ancestor of birds and mammals. In mammals, that gene family has probably expanded and contracted in different lineages, and this results in dramatic differences in gene family size and membership composition among contemporary species. In birds, those 10 ancestral gene copies will remain intact and are inherited by all descendant lineages, so very little variation accumulates among species."

Scientist Use “Hi-C” Method to Map the Folded Human Genome; Shed Additional Light on Gene Regulation; Loops and CTCF Proteins Crucial

In a triumph for cell biology, researchers have assembled the first high-resolution, 3D maps of entire folded genomes and found a structural basis for gene regulation—a kind of "genomic origami" that allows the same genome to produce different types of cells. The research appears online on December 11, 2014 in Cell. A central goal of the five-year project, a collaboration among researchers at Harvard University, Baylor College of Medicine, Rice University, and the Broad Institute of Harvard and MIT, was to identify the loops in the human genome. Loops form when two bits of DNA that are far apart in the genome sequence end up in close contact in the folded version of the genome in a cell's nucleus. Researchers used a technology called "in situ Hi-C" to collect billions of snippets of DNA that were later analyzed for signs of loops. The team found that loops and other genome folding patterns are an essential part of genetic regulation. "More and more, we're realizing that folding is regulation," said study co-first author Suhas Rao, a researcher at Baylor's Center for Genome Architecture and a 2012 graduate of Harvard College. "When you see genes turn on or off, what lies behind that is a change in folding. It's a different way of thinking about how cells work." Co-first author Miriam Huntley, a doctoral student at the Harvard School of Engineering and Applied Sciences (SEAS), said, "Our maps of looping have revealed thousands of hidden switches that scientists didn't know about before. In the case of genes that can cause cancer or other diseases, knowing where these switches are is vital."

Study Finds Connection between Gut Microbiota and Parkinson's Disease

Parkinson's disease sufferers have a different microbiota in their intestines than their healthy counterparts, according to a study conducted at the University of Helsinki and the Helsinki University Central Hospital (HUCH). "Our most important observation was that patients with Parkinson's have much less bacteria from the Prevotellaceae family; unlike the control group, practically no one in the patient group had a large quantity of bacteria from this family," states Filip Scheperjans, M.D., Ph.D., neurologist at the HUCH Neurology Clinic. The researchers have not yet determined what the lack of Prevotellaceae bacteria in Parkinson's sufferers means - do these bacteria perhaps have a property which protects their host from the disease? Or does this discovery merely indicate that intestinal dysfunction is part of the pathology? "It's an interesting question which we are trying to answer," Dr. Sheperjans says. Another interesting discovery was that the amount of bacteria from the Enterobacteriaceae family in the intestine was connected to the degree of severity of balance and walking problems in the patients. The more Enterobacteriaceae patients had, the more severe the symptoms. The results were published online on December 5, 2014 in Moverment Disorders. "We are currently re-examining these same subjects to determine whether the differences are permanent and whether intestinal bacteria are associated with the progression of the disease and therefore its prognosis," explains Dr. Sheperjans. "In addition, we will have to see if these changes in the bacterial ecosystem are apparent before the onset of motor symptoms. We will of course also try to establish the basis of this connection between intestinal microbiota and Parkinson's disease - what kind of mechanism binds them."

Bird Study Indicates Mother Contributes Much to Telomere Length in Chicks; Differing from Humans, Where Father’s Role Is Key

In the hunt for better knowledge on the aging process, researchers from Lund University in Sweden have now enlisted the help of small birds. A new study investigates various factors which affect whether chicks are born with long or short chromosome ends, called telomeres. The genetic make-up of our cells consists of genes lined up on chromosomes. The ends of the chromosomes are called telomeres, and they protect the chromosomes from sticking to each other. The longer the telomeres, the longer time the chromosomes are able to function. And conversely, the shorter these ends, the less time left for the chromosomes, and therefore also less time for the cells to function properly. More knowledge of telomeres can therefore be valuable in understanding the aging process in humans and other animals. In the present study, published online on December 10, 2014 in an open-access article in the Proceedings of the Royal Society B, researchers from Lund University looked for explanations for the large variation in telomere length in newborn individuals. This is curious because it should be advantageous to start life with longer telomeres rather than shorter telomeres. "It is remarkable that already, so early on in life, there are already such major differences between individuals, both in humans and in animals," says Dr. Asghar Muhammad, one of the researchers behind the study. The researchers used data from a 30-year-long study of individually recognizable ringed great reed warblers at Lake Kvismaren, south Central Sweden. The aim of the study was to find out which inheritance factors affect the length of the chromosome ends in chicks. Thanks to the long series of measurements, it was possible to compare the length of telomeres in newborn individuals with that of their parents when these were newly hatched chicks.