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Archive - 2013

March 17th

Nuclear DNA Sequencing Clarifies Relationship Between Polar Bears and Brown Bears

At the end of the last ice age, a population of polar bears was stranded by the receding ice on a few islands in southeastern Alaska. Male brown bears swam across to the islands from the Alaskan mainland and mated with female polar bears, eventually transforming the polar bear population into brown bears. Evidence for this surprising scenario emerged from a new genetic study of polar bears and brown bears led by researchers at the University of California (UC), Santa Cruz. The findings,published on March 14, 2013 in the open-access journal PLOS Genetics, upend prevailing ideas about the evolutionary history of the two species, which are closely related and known to produce fertile hybrids. Previous studies suggested that past hybridization had resulted in all polar bears having genes that came from brown bears. But the new study indicates that episodes of gene flow between the two species occurred only in isolated populations and did not affect the larger polar bear population, which remains free of brown bear genes. At the center of the confusion is a population of brown bears that lives on Alaska's Admiralty, Baranof, and Chicagof Islands, known as the ABC Islands. These bears--clearly brown bears in appearance and behavior--have striking genetic similarities to polar bears. "This population of brown bears stood out as being really weird genetically, and there's been a long controversy about their relationship to polar bears. We can now explain it, and instead of the convoluted history some have proposed, it's a very simple story," said coauthor Dr. Beth Shapiro, associate professor of ecology and evolutionary biology at the UC Santa Cruz (UCSC). Dr. Shapiro and her colleagues analyzed genome-wide DNA sequence data from seven polar bears, an ABC Islands brown bear, a mainland Alaskan brown bear, and a black bear.

March 15th

Tapeworm Genome Sequencing Reveals Potential Weaknesses to Existing Human Drugs

For the first time, researchers have mapped the genomes of tapeworms to reveal potential drug targets on which existing drugs could act. The genome sequences provide a new resource that offers faster ways to develop urgently needed and effective treatments for these debilitating diseases. The results were published online in an open-access article in Nature on March 13, 2013 by Wellcome Trust Sanger Institute scientists and collaborators. Tapeworms cause two of the World Health Organization's 17 neglected tropical diseases; echinococcosis and cysticercosis. The research team sequenced the genomes of four species of tapeworm to explore the genetics and underlying biology of this unusual parasite. As an adult it can live relatively harmlessly in the gut, but its larvae can spread through the body with devastating effects. The larvae form cysts in the internal organs or tissues of humans and other animals. These cysts proliferate or grow in the body, much like cancer. In some species this can cause complications such as blindness and epilepsy; with others it may lead to death. "Tapeworm infections are prevalent across the world and their devastating burden is comparable to that of multiple sclerosis or malignant melanoma," says Dr. Matthew Berriman, senior author from the Wellcome Trust Sanger Institute. "These genome sequences are helping us to immediately identify new targets for much-needed drug treatment. In addition, exploring the parasites' full DNA sequences is driving our understanding of its complex biology, helping the research community to focus on the most effective drug candidates." Normally, researchers identify new targets for drugs to combat diseases by comparing a pathogen's genome sequence with the human host's DNA to find differences between them.

March 11th

Gene Expression Studies Show Antarctic and Arctic Insects Use Different Genetic Mechanisms to Cope With Lack of Water

Although they live in similarly extreme ecosystems at opposite ends of the world, Antarctic insects appear to employ entirely different methods at the genetic level to cope with extremely dry conditions than their counterparts that live north of the Arctic Circle, according to National Science Foundation (NSF)-funded researchers. Writing in the December 11, 2012 issue of PNAS, the researchers concluded, "Polar arthropods have developed distinct... mechanisms to cope with similar desiccating conditions." The researchers noted that aside from the significance of the specific discovery about the genetics of how creatures cope in polar environments, the new finding is important because it shows how relatively new and developing scientific techniques, including genomics, are opening new scientific vistas in the Polar Regions, which were once thought to be relatively uniform and, relatively speaking, scientifically sterile environments. "It's great to have an Antarctic animal that has entered the genomic era," said David Denlinger, a distinguished professor of entomology at Ohio State University and a co-author of the paper. "This paper, which analyzed the expression of thousands of genes in response to the desiccating environment of Antarctica, is just one example of the power that the genomic revolution offers for advancing polar science." The collaborative research--which included contributions from scientists at Ohio State University, the Centre National de la Recherche Scientifique (National Center for Scientific Research) in France, Catholic University of Louvain in Belgium, Stanford University, and Miami University in Ohio--was supported in part by the Division of Polar Programs in NSF's Geosciences Directorate. Polar Programs manages the U.S. Antarctic Program, through which it coordinates all U.S.

March 11th

Study Shows How Fruit Fly Gained Its Wings

Scientists have delved more deeply into the evolutionary history of the fruit fly than ever before to reveal the genetic activity that led to the development of wings – a key to the insect’s ability to survive. The wings themselves are common research models for this and other species’ appendages. But until now, scientists did not know how the fruit fly,Drosophila melanogaster, first sprouted tiny buds that became flat wings. A cluster of only 20 or so cells present in the fruit fly’s first day of larval life was analyzed to connect a gene known to be active in the embryo and the gene that triggers the growth of wings. Researchers determined that the known embryonic gene, called Dpp, sends the first signal to launch the activation of a gene called vn. That signal alone is dramatic, because it crosses cell layers. The activation of the vn gene lasts just long enough to turn on a target gene that combines with additional signals to activate genes responsible for cell growth and completion of wing development. “Our work shows how when you add a gene into the equation, you get a wing. The clue is that one growth factor, Dpp, turns on another growth factor, vn, but just for a short period of time. You absolutely need a pulse of this activity to turn on yet another gene cascade that gives you a wing, but if vn is active for too long, a wing wouldn’t form,” said Dr. Amanda Simcox, professor of molecular genetics at The Ohio State University and lead author of the study. “We learned all this from investigating 20 tiny cells. The events could be responsible for this big event in evolutionary history, when the insect got its wing.

Single MicroRNA Keeps Segmentation “Clock” Running in Embryos

New research shows that a tiny piece of RNA has an essential role in ensuring that embryonic tissue segments form properly. The study, conducted in chicken embryos, determined that this piece of RNA regulates cyclical gene activity that defines the timing of the formation of tissue segments that later become muscle and vertebrae. Genes involved in this activity are turned on and off in an oscillating pattern that matches the formation of each tissue segment. If the timing of these genes’ activity doesn’t remain tightly regulated, the tissue either won’t form at all or will form with defects. One gene long associated with this segmentation “clock” is called Lfng. Researchers established in this study that a single microRNA – a tiny segment of RNA that has no role in producing any protein – is key to turning off Lfng at precisely the right time as tissues form in this oscillating pattern. When the microRNA was deleted or manipulated so that it wouldn’t bind when it was supposed to, the oscillatory pattern of the genetic clock was broken and tissue development was abnormal. “It’s a big deal to find that a single interaction between a microRNA and its target has this very profound effect when you interfere with its function,” said Dr. Susan Cole, associate professor of molecular genetics at The Ohio State University and lead author of the study. “There are very few cases where interfering with just one microRNA during development can make this much of a difference. But here, this regulation is so tight that this turns out to be incredibly important.

March 10th

Selectively Manipulating Protein Modifications

Protein activity is strictly regulated. Incorrect or poor protein regulation can lead to uncontrolled growth and thus cancer or chronic inflammation. Members of the Institute of Veterinary Biochemistry and Molecular Biology from the University of Zurich have identified enzymes that can regulate the activity of medically important proteins. Their discovery enables these proteins to be manipulated very selectively, opening up new treatment methods for inflammations and cancer. The work was published online on March 10, 2013 in Nature Structural & Molecular Biology. A related article was also published online at the same time in the same journal. For a healthy organism, it is crucial for proteins to be active or inactive at the right time. The corresponding regulation is often based on a chemical modification of the protein structure: Enzymes attach small molecules to particular sites on a protein or remove them, thereby activating or deactivating the protein. Members of the Institute of Veterinary Biochemistry and Molecular Biology from the University of Zurich, in collaboration with researches at other institutes, have now discovered how the inactivation of a protein, which is important for medicine, can be reversed. An important protein modification is ADP-ribosylation, which is involved in certain types of breast cancer, cellular stress reactions, and gene regulation. So-called ADP-ribosyltransferases attach the ADP ribose molecule to proteins, thereby altering their function. In recent years, many ADP-ribosyltransferases have been discovered that can convey single or several ADP-riboses to different proteins. Enzymes that can remove these riboses again, however, are less well known. Professor Michael Hottiger's team of researchers has now identified a new group of such ADP-ribosylhydrolases.

Telomere Length in Heart Disease Patients Can Predict Life Expectancy

Can the length of strands of DNA in patients with heart disease predict their life expectancy? Researchers from the Intermountain Heart Institute at Intermountain Medical Center in Salt Lake City, who studied the DNA of more that 3,500 patients with heart disease, say yes it can. In the new study, presented Saturday, March 9, 2013, at the American College of Cardiology's Annual Scientific Session in San Francisco, the researchers were able to predict survival rates among patients with heart disease based on the length of strands of DNA found at the ends of chromosomes known as telomeres—the longer the patient's telomeres, the greater the chance of living a longer life. The study is one of 17 studies from the Intermountain Heart Institute at Intermountain Medical Center that are being presented at the scientific session, which is being attended by thousands of cardiologists and heart experts from around the world. Previous research has shown that telomere length can be used as a measure of age, but these expanded findings suggest that telomere length may also predict the life expectancy of patients with heart disease. Telomeres protect the ends of chromosome from becoming damaged. As people get older, their telomeres get shorter until the cell is no longer able to divide. Shortened telomeres are associated with age-related diseases such as heart disease or cancer, as well as exposure to oxidative damage from stress, smoking, air pollution, or conditions that accelerate biologic aging. "Chromosomes by their nature get shorter as we get older," said John Carlquist, Ph.D., director of the Intermountain Heart Institute Genetics Lab. "Once they become too short, they no longer function properly, signaling the end of life for the cell. And when cells reach this stage, the patient's risk for age-associated diseases increases dramatically." Dr.

Maternal Care: How Mother Deer Protect Their Future Leaders

Do mothers invest more care in their sons if they believe their child is destined to be a king, president, or a high-powered leader? The answer is definitively yes – as long as those mothers and their sons happen to have hooves. New research from Brigham Young University (BYU) in Utah reports that, just like the classic tale of Bambi, females from the deer family are more likely to invest more in the survival and health of their male offspring if there is a good chance those sons will become a “Great Prince of the Forest.” “Our research demonstrates clearly that a mother’s investment in her offspring was evident during adulthood, even though offspring live independently of their mothers from a very young age,” said Dr. Brock McMillan, associate professor of wildlife ecology at BYU. The comprehensive study of deer and elk from the Intermountain West found that the most dominant males at the time of death were those who were born into the most favorable maternal conditions 5 to 15 years before. While favorable maternal conditions are largely tied to the health of the expectant mother, there are additional elements at play. A mother’s investment happens both in the womb and during the first few months of life. During those early stages of life, mothers take care to provide more excellent nourishment through lactation as well as better habitats for the baby. “Male deer and elk live independently of their mothers for several years in highly variable environments,” Dr. McMillan said. “They live through severe winters with deep snow and little to eat, dry summers with poor quality food, and years of injuries and ailments associated with everyday life.

March 9th

Genetic Defect Affecting Mechanosensitive Ion Channel Is Cause of a Hereditary Anemia

A genetic mutation that alters the kinetics of an ion channel in red blood cells has been identified as the cause of a hereditary anemia, according to a paper published online on March 4, 2013 in PNAS by University at Buffalo (UB) scientists and colleagues. The research team was led by Frederick Sachs, Ph.D., State University of New York Distinguished Professor in the UB Department of Physiology and Biophysics, who discovered in the 1980s that some ion channels are mechanosensitive, that is, they convert mechanical stress into electrical or biochemical signals. The findings of the new study are significant, Dr. Sachs says, because it is the first time that defects in a mechanosensitive ion channel have been implicated as the cause of a disease. “We found that the mutations in the gene that codes for the ion channel called PIEZO1 causes the channel to stay open too long, causing an ion leak in red cells,” explains Dr. Sachs. “Calcium and sodium enter, and potassium leaves, and that affects the ability of the red cell to regulate its volume. The cells become dehydrated and can break open, releasing their hemoglobin into the blood, and causing symptoms, such as the shortness of breath seen in anemic patients.” The anemia that results from the mutations in PIEZO1 is called familial xerocytosis, a mild to moderate form of anemia. The ion channel, PIEZO1, is about 10 nanometers across, and it increases its dimensions significantly upon opening; that change in dimensions is what is responsible for its mechanical sensitivity. Mechanosensitive ion channels are likely to play a role in many diseases, because all cells are mechanically sensitive. Dr.

Temperature-Controlled Nanopores May Enable Detailed Blood Analysis

Tiny biomolecular chambers called nanopores that can be selectively heated may help doctors diagnose disease more effectively if recent research by a team at the National Institute of Standards and Technology (NIST), Wheaton College, and Virginia Commonwealth University (VCU) proves effective. Though the findings may be years away from application in the clinic, they may one day improve doctors' ability to search the bloodstream quickly for indicators of disease—a longstanding goal of medical research. The work was published online on January 24, 2013 in the Journal of the American Chemical Society. The team has pioneered work on the use of nanopores—tiny chambers that mimic the ion channels in the membranes of cells—for the detection and identification of a wide range of molecules, including DNA. Ion channels are the gateways by which the cell admits and expels materials like proteins, ions, and nucleic acids. The typical ion channel is so small that only one molecule can fit inside at a time. Previously, team members inserted a nanopore into an artificial cell membrane, which they placed between two electrodes. With this setup, they could drive individual molecules into the nanopore and trap them there for a few milliseconds, enough to explore some of their physical characteristics. "A single molecule creates a marked change in current that flows through the pore, which allows us to measure the molecule's mass and electrical charge with high accuracy," says Dr. Joseph Reiner, a physicist at VCU who previously worked at NIST. "This enables discrimination between different molecules at high resolution.