Assembling viral genomes from metagenomes is challenging and often results in highly fragmented data, which limits the ability of researchers to accurately perform functional assessment, host prediction, and phylogenetic analysis. As reported in Nature Biotechnology, a team including JGI’s Stephen Nayfach, Frederik Schulz, Emiley Eloe-Fadrosh, Simon Roux and Nikos Kyrpides developed an automated tool called CheckV (pronounced “Check-Vee”) to help researchers assess and improve the quality of metagenome-assembled viral genomes. CheckV has already been applied to over 2.4 million viral genomes available in the latest release of IMG/VR, a database that is part of the Integrated Microbial Genomes & Microbiomes (IMG/M) suite. Learn more here on the JGI website.
JGI Launches Data Portal for Algae
A JGI team led by Algal Genomics Program lead Igor Grigoriev and data scientist Alan Kuo have unveiled PhycoCosm in the Nucleic Acids Research journal. The genome portal reinforces the JGI’s new strategic focus on exploring algal biology, diversity, and ecology. Read more here on the JGI website.
New Refinement Technique Promises Greater Protein Structure Accuracy
X-ray free-electron lasers (XFELs) came into use in 2010 for protein crystallography, allowing scientists to study fully hydrated specimens at room temperature without radiation damage. Researchers have developed many new experimental and computational techniques to optimize the technology and draw the most accurate picture of proteins from crystals. Now scientists in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division have developed a new program, diffBragg, which can process every pixel collected from an XFEL for a protein structure independently. In a recent IUCrJ paper, the team led by MBIB Senior Scientist Nicholas Sauter proposed a new processing framework for more accurate determination of protein structures.
SARS-CoV-2/COVID-19 Strategic Research Plan Released
Strategic Programs Development Group (SPDG) Lead Katy Christiansen spearheaded the Lab-wide effort to develop, write, and distribute a Berkeley Lab SARS-CoV-2/COVID-19 10-Year Multidisciplinary Strategic Research Plan. The plan builds on our current capabilities and creates a solid vision for the future. Katy led a brown bag about the plan on December 15; watch the video or plan to attend a reprise on January 7, 2021.
Cataloging Nature’s Hidden Arsenal: Viruses that Infect Bacteria
Viruses that infect bacteria, or phages, are continually evolving ways to target and exploit their specific hosts. Their bacterial hosts, in turn, are continually evolving means to evade the phages. These perpetual battles for survival yield incredibly diverse molecular arsenals that researchers are itching to study, yet doing so can be tedious and labor-intensive.
A team led by Berkeley Lab scientists has developed an efficient and inexpensive new method to gain insight into these defensive strategies. They reported in PLOS Biology that a combination of three recently developed techniques can reveal which bacterial receptors phages exploit to infect the cell, as well as what cellular mechanisms the bacteria use to respond to a phage infection.
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