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Archive - Jan 2014

January 22nd

De Novo Schizophrenia Mutations Cluster in Specific Sets of Proteins in Key Brain Pathways

Genetic mutations in people with schizophrenia cluster in specific proteins offering a new window into the disorder, according to a team of scientists from major institutions around the world. In the largest genetic study of its kind, published online on January 22, 2014 in Nature, an international team led by scientists from Cardiff University examined the occurrence of new “de novo” genetic mutations in people with schizophrenia. Their study was entitled, “De Novo Mutations in Schizophrenia Implicate Synaptic Pathways:” lead author: Dr. Menachem Fromer—see link below). Working alongside teams from leading research institutions including the Icahn School of Medicine at Mount Sinai, New York, the Broad Institute of the Massachusetts Institute of Technology (MIT), and Harvard and Cambridge Universities, the scientists examined DNA blood samples from 623 schiophrenia sufferers and their parents. The study showed that de novo mutations, which are found in affected individuals, but not their parents, play a role in triggering the disorder but more importantly that they preferentially disrupt specific sets of proteins which have related functions in the brain. These pathways are involved in modulating the strength of connections between nerve cells and play important roles in brain development, learning, memory, and cognition. “We already had evidence from previous work in Cardiff supporting the importance of these pathways but the new findings, together with those from a related study published on the same day in Nature (“A Polygenic Burden of Rare Disruptive Mutations in Schizophrenia;” lead author: Dr.

January 21st

Pathogenic RNA Plant Virus Jumps to Honeybees

A viral pathogen that typically infects plants has been found in honeybees and could help explain their decline. Researchers working in the United States and Beijing, China reported their findings on January 21, 2014 in mBio, the online open-access journal of the American Society for Microbiology. The routine screening of bees for frequent and rare viruses "resulted in the serendipitous detection of Tobacco Ringspot Virus (image), or TRSV, and prompted an investigation into whether this plant-infecting virus could also cause systemic infection in the bees," says Dr. Yan Ping Chen from the U.S. Department of Agriculture's Agricultural Research Service (ARS) laboratory in Beltsville, Maryland, an author on the study. "The results of our study provide the first evidence that honeybees exposed to virus-contaminated pollen can also be infected and that the infection becomes widespread in their bodies," says lead author Dr. Ji Lian Li, from the Chinese Academy of Agricultural Science in Beijing. "We already know that honeybees, Apis melllifera, can transmit TRSV when they move from flower to flower, likely spreading the virus from one plant to another," Dr. Chen adds. Notably, about 5% of known plant viruses are pollen-transmitted and thus potential sources of host-jumping viruses. RNA viruses tend to be particularly dangerous because they lack the 3'-5' proofreading function which edits out errors in replicated genomes. As a result, viruses such as TRSV generate a flood of variant copies with differing infective properties. One consequence of such high replication rates are populations of RNA viruses thought to exist as "quasispecies," clouds of genetically related variants that appear to work together to determine the pathology of their hosts.

Arctic Warmth Unprecedented in 44,000 Years, Reveal Samples of Ancient Moss

When the temperature rises on Baffin Island, in the Canadian high Arctic, ancient Polytrichum mosses (image), trapped beneath the ice for thousands of years, are exposed. Using radiocarbon dating, new research in the November 16, 2013 issue of Geophysical Research Letters has calculated the age of relic moss samples that have been exposed by modern Arctic warming. Because the moss samples would have been destroyed by erosion had they been previously exposed, the authors suggest that the temperatures in the Arctic now must be warmer than during any sustained period since the mosses were originally buried. The authors collected 365 samples of recently exposed biological material from 110 different locations, cutting a 1,000-kilometers-long transect across Baffin Island, with samples representing a range of altitudes. From their samples, the authors obtained 145 viable measurements through radiocarbon dating. They found that most of their samples date from the past 5,000 years, when a period of strong cooling overtook the Arctic. However, the authors also found even older samples that were buried from 24,000 to 44,000 years ago. The records suggest that, in general, the eastern Canadian Arctic is warmer now than in any century in the past 5,000 years, and in some places, modern temperatures are unprecedented in at least the past 44,000 years. The observations, the authors suggest, show that modern Arctic warming far exceeds the bounds of historical natural variability. “The great time these plants have been entombed in ice, and their current exposure, is the first direct evidence that present summer warmth in the Eastern Canadian Arctic now exceeds the peak warmth there in the Early Holocene era,” said Dr. Gifford Miller, from the University of Colorado.

Anti-Swine Flu Vaccination Linked to Increased Risk of Narcolepsy in Children and Adolescents

Pandemrix is an influenza vaccination, created in 2009 to combat H1N1 virus (image), known as Swine Flu. Now, according to a January 21, 2014 press release from the Journal of Internal Medicine, a team of Swedish clinicians testing the vaccine for links to immune-related or neurological diseases has linked Pandemrix to an increased risk of narcolepsy in young adults. Using a population-based prospective cohort study, the team analyzed data from regional vaccination registries and national health registries, covering seven healthcare regions and 61% of the Swedish population. While the team did not identify any link to a large number of immune-related or neurological diseases, they did confirm an increased risk in diagnosis of narcolepsy in individuals younger than 20 years of age, and observed a trend towards an increased risk amongst young adults between 21 and 30. “The follow-up of Pandemrix vaccinations in a large registry based study in Sweden confirms an increased risk of narcolepsy in children and adolescents, while also providing reassuring results for a large number of other neurological and immune related diseases,” said Dr. I. Persson from the Karolinska Institutet, Stockholm. [Press release]

Zone in with Zon—Will Wooly Mammoths and Passenger Pigeons Return?

Dr. Gerald Zon’s latest blog post, dated January 20, 2014, and published by TriLink BioTechnologies of San Diego, focuses on the issue of “De-Extinction: Hope or Hype?” In this thought-provoking post, Dr. Zon asks if the wooly mammoth can be revived and if the passenger pigeon might be returned to flight. He then suggests that “facilitated adaptation” might be a more realistic approach. Initially, Dr. Zon describes a CBS News interview with Dr. Hendrik Poinar on the possibility of reestablishing wooly mammoths. Dr. Poinar specializes in the novel techniques to extract and analyze “molecular information (DNA and/or protein sequences)” from ancient samples and has already sequenced the mitochondrial genome of the long-extinct wooly mammoth. Dr. Poinar believes that it might indeed be possible to bring these extinct creatures back to life in 30 to 50 years time. When asked to describe how this would be done, he said, “First thing you have to do is to get the entire blueprint. We have mapped the genome of the woolly mammoth. We’re almost completely done with that as well as a couple other extinct animals. We can look at the discrete differences between a mammoth and an Asian elephant. We would take an Asian elephant chromosome and modify it with mammoth information. Technology at Harvard can actually do that. Take the modified chromosomes and put them into an Asian elephant egg. Inseminate that egg and put that into an Asian elephant and take it to term. It could be as soon as 20 years.” Dr. Zon next described the work of a determined young ecologist with no graduate degree, Ben Novak, who has devoted all his recent efforts to resurrecting the exinct passenger pigeon. This was once the United States’ most numerous bird at approximately 5 billion strong, according to Audubon, but died out completely by 1914.

January 20th

Hot Pepper Genome Sequenced

An article by Pat Bailey in the January 19 issue of The Davis Enterprise reports on the sequencing of the hot pepper (Capsicum annuum)(image) genome by a large international team, which included scientists from the University of California-Davis and Seoul National University in Korea. The research was published online on January 19, 2014 in an open-access article in Nature Genetics. According to Bailey, the new genome sheds light on the biology of the pepper’s characteristic spiciness, as well as its fruit-ripening and disease-resistance mechanisms. In addition, the genome data reveals new information v ital. for improving the horticultural, nutritional, and medicinal qualities of these peppers, for which the annual global production has grown more than 40-fold in the last two decades and now is greater than $14.4 billion. According to Bailey’s article, the researchers sequenced a hot pepper landrace, or domesticated variety, from the Mexican state of Morelos. The variety, known as Criolo de Morelos 334, has consistently exhibited high levels of disease resistance and has been extensively used in hot-pepper research and breeding. The research team also provided sequencing data for the Perennial and Dempsey cultivated pepper varieties and for the related habanero pepper species (Capsicum chinense). The sequencing also uncovered evidence suggesting that the pungency, or “heat,” of the hot pepper originated through the evolution of new genes by duplication of existing genes and changes in gene expression after the peppers evolved into species. Bailey said that it was already known that pepper pungency was caused by the accumulation of naturally occurring chemicals called capsaicinoids, unique to the Capsicum genus.

Hookworm Genome Decoded; Insights May Aid Development of Therapies

Going barefoot in parts of Africa, Asia, and South America contributes to hookworm infections, which afflict an estimated 700 million of the world's poor. The parasitic worm lives in the soil and enters the body through the feet. By feeding on victims' blood, the worms cause anemia and, in children, stunted growth and learning problems. Now, researchers at Washington University School of Medicine in St. Louis, together with colleagues, have decoded the genome of the hookworm, Necator americanus, finding clues to how it infects and survives in humans and to aid in development of new therapies to combat hookworm disease. The research was published online on January 19, 2014 in an open-access article in Nature Genetics. "We now have a more complete picture of just how this worm invades the body, begins feeding on the blood, and successfully evades the host immune defenses," said senior author Makedonka Mitreva, Ph.D., assistant professor of medicine and of genetics and a member of The Genome Institute at the School of Medicine. "This information will accelerate development of new diagnostic tools and vaccines against the infection." Necator americanus causes about 85 percent of human hookworm infections, which are not usually fatal. However, in pregnant women, the worm can cause severe anemia, leading to maternal deaths and low birth weights that contribute to newborn deaths. The deworming drug albendazole typically is given as part of mass treatment programs in areas with endemic infection, but its repeated and excessive use is leading to treatment failures and drug resistance in some regions, Dr. Mitreva said. Hookworms are common in areas of extreme poverty that lack indoor plumbing. The worm's eggs are excreted in the feces of infected individuals, contaminating the soil.

Sunlight Causes NO to Move from Skin to Circulation, Reducing Heart Attack Risk

Exposing skin to sunlight may help to reduce blood pressure and thus cut the risk of heart attack and stroke, a study published in the Journal of Investigative Dermatology suggests. Research carried out at the Universities of Southampton and Edinburgh shows that sunlight alters levels of the small messenger molecule, nitric oxide (NO) (image) in the skin and blood, reducing blood pressure. Dr. Martin Feelisch, Professor of Experimental Medicine and Integrative Biology at the University of Southampton, comments: "NO along with its breakdown products, known to be abundant in skin, is involved in the regulation of blood pressure. When exposed to sunlight, small amounts of NO are transferred from the skin to the circulation, lowering blood vessel tone; as blood pressure drops, so does the risk of heart attack and stroke." While limiting sunlight exposure is important to prevent skin cancer, the authors of the study, including Dr. Richard Weller of the University of Edinburgh, suggest that minimizing exposure may be disadvantageous by increasing the risk of prevalent conditions related to cardiovascular disease. Cardiovascular disease, often associated with high blood pressure, accounts for 30 per cent of deaths globally each year. Blood pressure and cardiovascular disease are known to vary according to season and latitude, with higher levels observed in winter and in countries farther from the equator, where ultraviolet radiation from the sun is lower. During the study, the skin of 24 healthy individuals was exposed to ultraviolet (UVA) light from tanning lamps for two sessions of 20 minutes each. In one session, the volunteers were exposed to both the UVA rays and the heat of the lamps. In another, the UV rays were blocked so that only the heat of the lamps affected the skin.

New Drug Targets/Epigenetic Changes Found in Cocaine Addiction

Researchers from the Icahn School of Medicine at Mount Sinai in New York have identified a new molecular mechanism by which cocaine alters the brain's reward circuits and causes addiction. Published online in PNAS by Dr. Eric J. Nestler, M.D., Ph.D., and colleagues, the preclinical research reveals how an abundant enzyme and synaptic gene affect a key reward circuit in the brain, changing the ways genes are expressed in the nucleus accumbens. The DNA itself does not change, but its "mark" activates or represses certain genes encoding synaptic proteins within the DNA. The marks indicate epigenetic changes—changes made by enzymes—that alter the activity of the nucleus accumbens. In a mouse model, the research team found that chronic cocaine administration increased levels of an enzyme called PARP-1 or poly(ADP-ribosyl)ation polymerase-1 (image). This increase in PARP-1 leads to an increase in its PAR marks at genes in the nucleus accumbens, contributing to long-term cocaine addiction. Although this is the first time PARP-1 has been linked to cocaine addiction, PARP-1 has been under investigation for cancer treatment. "This discovery provides new leads for the development of anti-addiction medications," said the study's senior author, Dr. Nestler, Nash Family Professor of Neuroscience and Director of the Friedman Brain Institute, at the Icahn School of Medicine at Mount Sinai. Dr. Nestler said that the research team is using PARP to identify other proteins regulated by cocaine. PARP inhibitors may also prove valuable in changing cocaine's addictive power. Kimberly Scobie, Ph.D., the lead investigator and postdoctoral fellow in Dr. Nestler's laboratory, underscored the value of implicating PARP-1 in mediating the brain's reward center.

Illumina’s NextSeq™ 500 Brings Next-Gen Sequencing to the Desktop

In a January 14, 2014 press release, Illumina, Inc. (NASDAQ:ILMN) announced the immediate availability of a transformative addition to its industry-leading next-generation sequencing portfolio with the launch of the NextSeq 500 System. The new sequencer packs high-throughput performance into an affordable desktop form factor, enabling researchers to perform the most popular sequencing applications in less than a day. The NextSeq 500 System is priced at $250,000. “Illumina’s sequencing portfolio is the most comprehensive in the world, and the addition of the NextSeq 500 System furthers this distinction by enabling next-generation sequencing to become an everyday tool,” said Jay Flatley, CEO of Illumina. “The NextSeq 500 was reimagined from the ground up and uses technology breakthroughs in optics, fluidics, and chemistry to bring high-throughput power to the desktop at a significantly reduced cost.” The NextSeq 500 System delivers the power of high-throughput sequencing with the load-and-go simplicity of a desktop sequencer, effectively transforming a broad range of high-throughput applications into affordable, everyday research tools. Its push-button operation delivers a one-day turnaround for a number of popular sequencing applications, including one whole human genome and up to 16 exomes, up to 20 non-invasive prenatal testing samples, up to 20 transcriptomes, up to 48 gene expression samples and up to 96 targeted panels. With its streamlined informatics, sequencing data can be run through a range of open-source or commercial pipelines or instantly transferred, analyzed, and stored securely in BaseSpace® or the new BaseSpace® OnSite for researchers needing an on-premises solution.