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Archive - Jan 20, 2014

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.

New Sequencing System from Illumina May Enable World’s First $1,000 Genomes

In a January 14, 2014 press release, Illumina, Inc. (NASDAQ:ILMN) announced that it had broken the ‘sound barrier’ of human genomics by enabling the $1,000 genome. This achievement is made possible by the Illumina’s new HiSeq X Ten Sequencing System. This platform includes dramatic technology breakthroughs that enable researchers to undertake studies of unprecedented scale by providing the throughput to sequence tens of thousands of human whole genomes in a single year in a single lab. Initial customers for the transformative HiSeq X Ten System include Macrogen, a global next-generation sequencing service organization based in Seoul, South Korea and its CLIA laboratory in Rockville, Maryland, the Broad Institute in Cambridge, Massachusetts, the world’s leading research institute in genomic medicine, and the Garvan Institute of Medical Research in Sydney, Australia, a world leader in biomedical research. “The sequencing capacity and economies of scale of the HiSeq X Ten facility will also allow Garvan to accelerate the introduction of clinical genomics and next-generation medicine in Australia,” said Professor John Mattick, Executive Director of the Garvan Institute of Medical Research. “We expect the HiSeq X Ten to underpin a new phase of collaboration between government, industry, and other medical research stakeholders.” “For the first time, it looks like it will be possible to deliver the $1,000 genome, which is tremendously exciting,” said Dr. Eric Lander, founding director of the Broad Institute and a professor of biology at MIT. “The HiSeq X Ten should give us the ability to analyze complete genomic information from huge sample populations.