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Archive - Sep 19, 2015

Nanopore DNA Sequencing Offers Four Times More Rapid Characterization of Bacteria Causing Urinary Tract Infections (UTIs) Than Conventional Culturing When Testing Heavily Infected Urine; Approach Can Also Detect Antibiotic Resistance

Urinary tract infections (UTIs) could be treated more quickly and efficiently by analyzing urine with a DNA sequencing device the size of a USB stick (see image), according to research from the University of East Anglia (UEA). Researchers used a new device called MinION to perform nanopore sequencing to characterize bacteria from urine samples four times more quickly than can be done using traditional culture methods. The new method can also detect antibiotic resistance, allowing patients to be treated more effectively and improving stewardship of diminishing antibiotic reserves. The findings will be unveiled today, Saturday, September 19, 2015, at an international four-day medical conference in San Diego, California, run jointly by the American Society for Microbiology's Interscience Conference of Antimicrobial Agents and Chemotherapy (ICAAC) and the International Society of Chemotherapy (ICC). The pertinent presentation is titled “MinION Nanopore Sequencing to Identify Pathogens and Resistance Genes Directly from Urine Specimens” and will be presented by Katarzyna Schmidt and Dr. Justin O'Grady, both of the UEA. Professor David Livermore, from UEA's Norwich Medical School, said: "Urinary tract infections are among the most common reasons for prescribing antibiotics. Most are mild and only affect the lower urinary tract, but a few are more troublesome. These 'ascending' UTIs cause a growing burden of hospitalizations, mostly of elderly patients.” "At worst, infection spills into the bloodstream, leading to a condition called urosepsis, which can be fatal. There were more than 30,000 cases of Escherichia coli bloodstream infection recorded in England in 2014, mostly with a urinary origin. "Antibiotics are vital, especially if bacteria have entered the bloodstream, and must be given urgently.

Genome of Darwin’s “Living Fossil” Is Sequenced in Japan; Surprisingly, This Ancient Brachiopod Genome Is Found to Be Evolving Rapidly

A group of scientists from Okinawa Institute of Science and Technology Graduate University (OIST), Nagoya University, and the University of Tokyo have sequenced the first lingulid brachiopod genome, from Lingula anatina collected at Amami Island, Japan. (Note that this press release is also available in Japanese at (http://www.eurekalert.org/pub_releases_ml/2015-09/aaft-_1091715.php). Their paper was published online on September 18, 2015 in an open-access article in Nature Communications and presents the results of their analysis of over 34,000 genes comprising the L. anatina genome and shows that, despite Lingula's reputation as a "living fossil," its genome is actively evolving. The article is titled “The Lingula Genome Provides Insights into Brachiopod Evolution and the Origin of Phosphate Biomineralization.” Brachiopods are marine invertebrates with external shells and a stalk. They are often confused with molluscs; however, the resemblance is superficial. Unlike bivalves (clams and mussels) that have shells on the sides of their bodies, brachiopod shells are on the top and bottom. As a result, the plane of symmetry in a bivalve runs along the hinge; hence the two valves are mirror images of one another. In brachiopods the plane of symmetry is perpendicular to the hinge, so that the halves of the valves mirror each other. Brachiopods are one of the first known examples of animal biomineralization, a process whereby living organisms stiffen or harden tissues with minerals. The earliest discovered brachiopod fossils date back to the early Cambrian period, approximately 520 million years ago. Brachiopods quickly spread all over the world and dominated the seas during the Paleozoic era (542-251 million years ago) and, by virtue of their mineralized shells, left an abundance of fossils.

Three Genetic Variants That Modify Huntington’s Disease Age of Onset Are Located; Two on Chromosome 15 and One on Chromosome 8; GWAS of Over 4,000 HD Patients Provides New Clues to Possible Disease Intervention

A study that took a novel approach to investigating factors affecting the emergence of symptoms of Huntington’s disease (HD) has identified at least two genome sites that house variants that can hasten or delay symptom onset. In its report in the July 30, 2015 issue of Cell, the multi-institutional research team describes how genome-wide association analysis of samples from more than 4,000 HD patients found that particular variants on two chromosomes were more common in individuals who first exhibited HD-associated movement disorders either earlier or later than would otherwise have been expected. The article is titled “Identification of Genetic Factors that Modify Clinical Onset of Huntington’s Disease.” “Most previous research into ways of delaying the onset of HD symptoms have focused on studying the mutant protein in cells or in animal models, but the relevance of abnormalities in those systems to what actually happens in patients remains a huge assumption,” says James Gusella, Ph.D., Director of the Center for Human Genetic Research (CHGR) at Massachusetts General Hospital (MGH), and corresponding author of the Cell paper. “Our approach does not rely on model systems, but on DNA samples and clinical data from human patients. In essence, we are analyzing the results of a ‘clinical trial’ conducted by nature, a trial in which naturally occurring variations in genes other than the HD gene intervened to influence the course of the disease. Now it is up to scientists to figure out how those genetic interventions work and to build on them to develop effective therapies based on understanding how these processes operate in humans.” Dr.

58,000 Fruit Flies Help Answer 100-Year-Old Question on Limits of Evolution

Why do certain body shape and size relationships remain consistent over long periods? One such example is found in flies, where small wings are normally rounder than large wings. Researchers from Norway and the United States bred fruit flies to change that relationship as a way to explore the limits of evolution and shed light on a question that biologists have puzzled over for the last 100 years. Throughout the natural world, shape, physiology and behavior are strongly related to the size of the organisms. These relationships are found both within species and between species, and often remain unchanged in species separated for millions of years. For example, the hearts of small species beat much faster than those of large species, and the antlers of small deer species are smaller, relative to body size, compared to antlers of large species. Sometimes these relationships are so strong that they are considered to be laws of nature, so much so that generations of biologists over the last 100 years have wondered whether or not these relationships can be changed by natural selection. In a paper published online on September 14, 2015 in PNAS, researchers from the Norwegian University of Science and Technology's Center for Biodiversity Dynamics (CBD), the Centre for Evolutionary and Ecological Synthesis at the University of Oslo, and Florida State University now say that the answer to this question is both yes (in principle), but no (in practice). The article is titled “Complex Constraints on Allometry Revealed by Artificial Selection on the Wing of Drosophila melanogaster.” "Our results suggest that these traits can evolve, but changing these relationships creates deleterious side effects for the organism.