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Uncovered: 1000 New Microbial Genomes

JUNE 12, 2017 Joint Genome Institute
The number of microbes in a handful of soil exceeds the number of stars in the Milky Way galaxy, but researchers know less about what’s on Earth because they have only recently had the tools to deeply explore what is just underfoot. Now scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, have taken a decisive step forward in uncovering the planet’s microbial diversity. In a paper published June 12, 2017 in Nature Biotechnology, DOE JGI’s Prokaryotic Super Program head Nikos Kyrpides and his team of researchers report the release of 1,003 phylogenetically diverse bacterial and archaeal reference genomes—the single largest release to date.

With the release of high quality genomic information from the 1,003 reference genomes, DOE JGI is providing a wealth of new sequences that will be invaluable to scientists interested in experiments such as characterizing biotechnologically relevant secondary metabolites or studying enzymes that work under specific conditions, Seshadri said. And because Kyrpides’ research team sequenced type strains that are readily available from culture collections, scientists can perform follow-up experiments with them in the lab, she added.

Source: Joint Genome Institute



Finding A New Major Gene Expression Regulator in Fungi

MAY 8, 2017, Joint Genome Institute

In the May 8, 2017 issue of Nature Genetics, a team led by scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, report the prevalence of 6mA modifications in the earliest branches of the fungal kingdom. Though fungi have been around for a billion years and collectively are capable of degrading nearly all naturally-occurring polymers and even some human-made ones, most of the species that have been studied belong to just two phyla, the Ascomycota and Basidiomycota. The remaining 6 groups of fungi are classified as “early diverging lineages,” the earliest branches in fungal genealogy. They comprise a little-explored realm of fungi, providing a repertoire of important and valuable gene products for DOE missions in bioenergy and environment.

Source: The U.S. Department of Energy Joint Genome Institute



DNA Methylation Status Predicts Mortality

20. March 2017, dkfz 
Methyl labels in the DNA regulate the activity of our genes and, thus, have a great influence on health and disease. Scientists from the German Cancer Research Center and from the Saarland cancer registry have now revealed that an altered methylation status at only ten specific sites in the genome can indicate that mortality is increased by up to seven times. Smoking has a particularly unfavorable impact on the methylation status.

In their present study, the researchers investigated the cases of 1,900 participants of two epidemiological studies called ESTHER and KORA*. They used DNA from blood cells as the basis of their investigation. All study subjects were older adults and had provided blood samples when they entered the study. This was up to 14 years ago and many of them had died since then.

Of the 58 CpGs, the scientists selected those ten with the strongest correlation with mortality. This epigenetic risk profile alone enabled them to predict the so-called all-cause mortality (cancer, cardiovascular diseases, and others). Study participants whose genome exhibited an "unfavorable" methylation status at five or more of these sites had a risk of death within the 14-year observation period that was seven times that of study participants whose methylation at these positions showed no abnormalities.

Source: dkfz German Cancer Research Center




21. March 2017, SIB 
Recent advances in the fight against type 2 diabetes (T2D) result from a pan-European collaborative project, called IMIDIA, in which the SIB Swiss Institute of Bioinformatics is closely involved since 2010. SIB was in charge of both coordinating the large amount of patients’ data (acting as Data Coordination Centre, DCC) as well as analysing the data to find biomarkers for early detection of the disease. The major findings of the research include the discovery of molecules, which could serve as biomarkers to detect the disease up to nine years before its diagnosis.

In a first study, coordinated by senior author Mark Ibberson of SIB’s Vital-IT group and published in Molecular Metabolism, the team identified a key gene associated with T2D. Using a network analysis that integrated transcriptomic and phenotypic data, the gene Elovl2 appeared to be related to insulin secretion in mice. The finding was confirmed in human pancreatic beta-cell lines, i.e. cells resembling those affected in T2D.

Source: SIB Swiss Institute of Bioinformatics



New Goat Genome Assembly Breaks Continuity Record, Expands Breeding Tools

Tuesday, March 21, 2017, PACBIO 
Efforts to produce a reference-grade goat genome assembly for improved breeding programs have paid off. A new Nature Genetics publication reports a high-quality, highly contiguous assembly that can be used to develop genotyping tools for quick, reliable analysis of traits such as milk and meat quality or adaptation to harsh environments. The program also offers a look at how different scaffolding approaches perform with SMRT Sequencing data.

The project was motivated by a clear need to develop methods for high-quality livestock genome assemblies to benefit breeding communities. Goat offers a particular boost to developing countries, where these animals are a primary source of textile fiber, milk, and meat.

They chose SMRT Sequencing because its long reads could characterize even the most difficult genomic regions. “Initial assembly of the PacBio data alone resulted in a contig NG50 ... of 3.8 Mb,” the team reports. PacBio contigs were then connected with optical mapping and Hi-C data to create extremely long scaffolds in the final 2.92 Gb assembly. “These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps,” they write. The assembly is 400 times more continuous than the previous short-read assembly.

Source: PACBIO 



New molecular barcode technology reduces error rate in genomic sequencing to 1 in 10,000

 9. March 2017, Toronto, Ontario Institute for Cancer Research (OICR) 

Researchers at the Ontario Institute for Cancer Research (OICR), together with international collaborators, have invented a technique to avoid a major problem with common laboratory techniques and improve the sensitivity of important cancer tests.

The findings, recently published in the journal Nature Protocols, describe a process by which the sensitivity of DNA sequencing can be improved. The technology, called SiMSen-Seq, could aid in detecting the recurrence of cancers, catching possible disease relapses faster than current methods and improving patient outcomes.

“We created a DNA barcode with a hairpin structure that opens up to be read when heated and contracts when cooled. This allows us to ‘hide’ the barcode and analyze more patient DNA fragments in a single reaction,” said Dr. Paul Krzyzanowski, Program Manager of OICR’s Genome Technologies Program. Krzyzanowski led the development of analysis pipeline software used in SiMSen-Seq. This software flags errors in sequencing results and corrects them computationally.

Source: OICR News



NIH-funded preclinical study suggests a possible treatment for Alzheimer’s disease and other neurodegenerative disorders

February 8, 2017, National Institute of Neurological Disorders and Stroke (NINDS)
In a study of mice and monkeys, National Institutes of Health funded researchers showed that they could prevent and reverse some of the brain injury caused by the toxic form of a protein called tau. The results, published in Science Translational Medicine, suggest that the study of compounds, called tau antisense oligonucleotides, that are genetically engineered to block a cell’s assembly line production of tau, might be pursued as an effective treatment for a variety of disorders.

Cells throughout the body normally manufacture tau proteins. In several disorders, toxic forms of tau clump together inside dying brain cells and form neurofibrillary tangles, including Alzheimer’s disease, tau-associated frontotemporal dementia, chronic traumatic encephalopathy and progressive supranuclear palsy. Currently there are no effective treatments for combating toxic tau.

"This compound may literally help untangle the brain damage caused by tau,” said Timothy Miller, M.D., Ph.D., the David Clayson Professor of Neurology at Washington University, St. Louis, and the study's senior author.

Source: National Institute of Health NIH



NIH Funding Opportunity: Development of Highly Innovative Tools and Technology for Analysis of Single Cells 

This funding opportunity announcement (FOA) encourages Small Business Technology Transfer Research (STTR) grant applications from small business concerns (SBCs) to develop and validate next-generation single cell analysis technologies and tools. The purpose is to foster the commercialization of innovative single cell analysis technologies for their broad use in biomedical research. The novel single-cell analysis technologies will aid in obtaining a fine-grained and dynamic view of heterogeneous cellular states and intercellular interactions, thereby providing new mechanistic insight into biological processes in health and disease. Applications should define the current state of technologies and tools as a benchmark against which the new approach(es) will be measured. The new approach(es) should provide substantially improved performance in sensitivity, selectivity, spatiotemporal resolution, scalability, multiplexing capability, or non-destructive analysis of molecular or functional measures of single cells.