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Archive - Oct 3, 2015

Surprisingly, Generalist Caterpillar Sequesters More of One Toxic Chemical from Vismia Poisonous Plants Than Does Specialist Caterpillar That Feeds Exclusively on These Toxic Plants

Scientists at the Smithsonian Tropical Research Institute (STRI) in Panama compared the diets of two caterpillar species, expecting that the caterpillar that exclusively consumed plants containing toxic chemicals would more easily incorporate toxins into its body than the one with a broad diet. They found just the opposite. The new finding, published online on August 20, 2015 in the Journal of Chemical Ecology, flies in the face of a long-held theory that specialist insects are better adapted to use toxic plant chemicals than non-specialists. The discovery opens new avenues for understanding plant-insect co-evolution--an ongoing arms race of plants producing new defense chemicals and insects finding ways around them. Toxic plant chemicals also have potential medical applications against microbes and cancer cells. The Journal of Chemical Ecology article is titled “Differential Sequestration of a Cytotoxic Vismione from the Host Plant Vismia baccifera by Periphoba arcaei and Pyrrhopyge thericles.” The tropical plant Vismia baccifera protects itself by producing a number of repellent chemicals, including three compounds that are toxic to living cells. Few plant-eating insects can stomach such a cocktail, but for those that can, the advantages are clear--less competition for a meal, and a chemical toolkit they can use in their own defense. Skipper butterfly, Pyrrhopyge thericles, caterpillars only eat plants in the genus Vismia. The caterpillars of a large moth, Periphoba arcaei, have a much broader diet, including Vismia plants and many others. Both are brightly colored caterpillars, one with flamboyant stripes, and the other blue-green with bristles, and they teach predators to associate their striking looks with toxicity--a defensive warning system known as aposematism.

Pacific Biosciences Launches New Nucleic Acid Sequencing Platform Based on Its Single Molecule, Real-Time (SMRT) Technology; Sequel™ System Said to Offer Significantly Higher Throughput, Reducing Project Costs and Timelines

On September 30, 2015, Pacific Biosciences of California, Inc., (NASDAQ:PACB), a pioneer and leader in long-read sequencing using its Single Molecule, Real-Time (SMRT®) Technology, announced that it has launched a new nucleic acid sequencing platform. The Sequel™ System (photo) provides higher throughput, more scalability, a reduced footprint and lower sequencing project costs compared to the PacBio® RS II System, while maintaining the existing benefits of the company’s SMRT Technology, the company said. Pacific Biosciences will showcase the new product at the American Society of Human Genetics (ASHG) 2015 annual meeting taking place in Baltimore, Maryland from October 6 through October 10. The core of the Sequel System is the capacity of its re-designed SMRT Cells, which contain one million zero-mode waveguides (ZMWs) at the product’s launch, compared to 150,000 ZMWs in the earlier SMRT Technology instrument, the PacBio RS II. Active individual polymerases are immobilized within the ZMWs, providing windows to observe and record DNA sequencing in real time. With approximately seven times as many reads per SMRT Cell as the PacBio RS II, customers should be able to realize lower costs and shorter timelines for sequencing projects, with approximately half the up-front capital investment compared to previous technology. The Sequel System also occupies a smaller footprint — less than one-third the size and weight — compared to the PacBio RS II. Because the new system is built on the Pacific Biosciences established SMRT Technology, most aspects of the sequencing workflow are unchanged.

Researchers Achieve 26-Hour Rapid Whole-Genome Sequencing In Critically Ill Infants; Fastest Turnaround Time in World; STAT-Seq Test IDs Mutations for 5,300 Genetic Diseases; Edico Data Analysis & Illumina Sequencer Among Keys to Record Speed

A study published on September 30, 2015 in an open-access article in Genome Medicine describes how researchers at Children's Mercy Kansas City, and colleagues, have cut in half the time needed for rapid whole-genome sequencing and genetic diagnosis in critically-ill infants, using a test that is called STAT-Seq. Through a variety of enhancements, the Center for Pediatric Genomic Medicine at Children's Mercy completed the STAT-Seq test in 26 hours compared to 50 hours, improving on a turnaround time that was already the fastest available in the world. The STAT-Seq test can identify mutations across the genome associated with approximately 5,300 known genetic diseases, and in some cases even identify previously unknown genetic diseases. In contrast, standard clinical practice calls for an array of genetic tests to be performed, which are time-consuming, costly and can only test for a limited set of disorders. The Genome Medicine article is titled “A 26-Hour System of Highly Sensitive Whole genome sequencing for emergency management of genetic diseases.” Lead authors of the study were Neil Millerand Emily Farrow, Ph.D., C.G.C., of Children's Mercy Kansas City, and senior author was Stephen Kingsmore, D.Sc., who was previously also at Children’s Mercy, but recently became the inaugural CEO of the Genomics Institute at Rady Children’s Hospital San Diego. "We believe rapid genome sequencing of critically-ill infants with suspected genetic diseases is a breakthrough application for genomic medicine," said Dr. Farrow, Director of Laboratory Operations and a genetic research scientist at the Center for Pediatric Genomic Medicine at Children's Mercy.

20 miRNAs in Exosome-Enriched Plasma Identified As Potential Biomarkers for Alzheimer’s Disease

Researchers at the University of Illinois at Chicago (UIC), and collaborators, have identified 20 potentially useful microRNA biomarkers for Alzheimer’s disease (AD) in their analysis of plasma fractions, enriched in exosomes by differential centrifugation, from 35 AD patients and 35 controls. Seven of these miRNAs were highly informative in a machine learning model for predicting AD status of individual samples with 83–89% accuracy. The researchers noted that perhaps the most interesting single miRNA was miR-342-3p, which was (a) expressed in the AD group at about 60% of control levels, (b) highly correlated with several of the other miRNAs that were significantly down-regulated in AD, and (c) also reported to be down-regulated in AD in two previous studies. The miRNAs were analyzed by expression measurement using Illumina deep sequencing technology. The scientists said that their findings warrant replication and follow-up with a larger cohort of patients and controls who have been carefully characterized in terms of cognitive and imaging data, other biomarkers (e.g., CSF amyloid and tau levels) and risk factors (e.g., apoE4 status), and who are sampled repeatedly over time. They further noted their belief that integrating miRNA expression data with other data is likely to provide informative and robust biomarkers in Alzheimer disease. This work was published on October 1, 2015 in the open-access journal PLOS ONE. The article is titled “Plasma Exosomal miRNAs in Persons with and without Alzheimer Disease: Altered Expression and Prospects for Biomarkers.” This BioQuick summary was written by Editor & Publisher Michael D. O’Nell. This research has also been reported by Genome Web (see link below). The image shows exsomes released by a cell.

International Team Seeks to Revolutionize Understanding of How Gene Variants Affect Organ Transplant Outcomes

Nearly 30,000 organ transplants are performed in the United States every year. These operations routinely extend lives, but the success of these procedures continues to be limited by problems that arise when the recipient's immune system rejects the new organ and by other complications. Now, a large international team of transplant surgeons and scientists, co-led by researchers from the Perelman School of Medicine at the University of Pennsylvania (Penn), has come together to investigate the genetic factors behind transplant successes and failures. The project, involving more than three dozen research institutions around the world, is called the International Genetics & Translational Research in Transplantation Network (iGeneTRAiN). Their efforts are detailed in a pair of papers published in Genome Medicine (open-access article) on October 1, 2015 and in Transplantation (in press). The Genome Medicine article is titled “Concept and Design of a Genome-Wide Association Genotyping Array Tailored for Transplantation-Specific Studies.” The Transplantation article is titled “Design and Implementation of the International Genetics & Translational Research in Transplantation Network (iGeneTRAiN). "The genetic datasets we've put together in this project are by far the largest ever assembled in transplant genomics," said Brendan J. Keating, D.Phil., an Assistant Professor of Transplant Surgery at Penn Medicine. "We want to revolutionize our understanding of how genetic variants affect transplant outcomes, and use those findings to improve these outcomes in the future." Dr. Keating is senior author of the Genome Medicine publication and first author of the Transplantation publication.