Department of Energy Joint Genome Institute (DOE JGI) and Biosciences Environmental Genomics and Systems Biology (EGSB) division researchers have released 1,003 reference genomes for diverse bacteria and archea isolated from environments ranging from sea water and soil, to plants, and to cow rumen and termite guts. The release is the largest to date from JGI’s Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, which seeks to fill in unexplored branches of the tree of microbial life. JGI’s Supratim Mukherjee and Rekha Seshadri were co-first authors on the paper published in Nature Biotechnology; senior author Nikos Kyrpides and co-authors Natalia Ivanova, Axel Visel, Tanja Woyke, and Yasuo Yoshikuni have secondary affiliations with EGSB. The genomes are publicly available through the Integrated Microbial Genomes with Microbiomes (IMG/M) system. Read more on the JGI website.
Finding Our Way Around DNA
Biosciences researchers collaborated with a team at the Salk Institute that developed a computational algorithm that integrates two different data types to make locating key regions within the genome more precise and accurate than other tools. The team’s method, recently described in Proceedings of the National Academy of Sciences, could help researchers conduct vastly more targeted searches for disease-causing genetic variants in the human genome, such as ones that promote cancer or cause metabolic disorders. Joseph Ecker, a Howard Hughes Medical Institute investigator and director of Salk’s Genomic Analysis Laboratory, was senior author of the study. Diane Dickel, Axel Visel and Len Pennacchio of the Environmental Genomics & Systems Biology Division, were co-authors, along with other researchers at the Salk Institute, UC San Diego, and UC San Francisco. Read more about the study in the Salk Institute press release.
Berkeley Lab Gets $4.6M in Functional Genomics Catalog Project
The Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) is set to receive close to $4.6 million over four years as part of an ongoing federally funded project to create a comprehensive catalog for fundamental genomics research. This work will be part of the National Human Genome Research Institute’s Encyclopedia of DNA Elements ENCODE project.
The new Berkeley Lab grant, awarded at more than $1.1 million per year, will be used to establish the Center for In Vivo Characterization of ENCODE Elements (CIViC). It will be one of five characterization centers tasked with investigating how genomic elements function in vivo. CIViC will be led by principal investigators Len Pennacchio and Axel Visel, senior scientists at Berkeley Lab’s Environmental Genomics and Systems Biology Division. Research scientist Diane Dickel will be the center’s project manager. Read more in the Berkeley Lab News Center.
Industrial Biotechnology Leader Selected as New DOE JGI Director
After 9-month national search, Nigel Mouncey, currently Research and Development Director for Bioengineering and Bioprocessing at Dow AgroSciences LLC, has been selected as the Director of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility. Mouncey will be the DOE JGI’s fourth Director in its 20-year history. He succeeds Eddy Rubin, who announced his retirement in March 2016 after a dozen years as Director, and DOE JGI Strategic Planning Deputy Axel Visel, who has served as Interim Director since then. Read more about Mouncey’s selection on the DOE JGI website.
Understanding the Genes Behind Some of Evolution’s Most Dramatic Changes
A research team led by biologist senior staff scientist Axel Visel, affiliated with the Environmental Genomics & Systems Biology Division, delved into the genetic basis for why snakes have no legs. The team’s research results demonstrated changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution.
Their findings, published in the journal Cell on October 20, have been widely covered in both national and international news media. The publication coincided with a Current Biology article in press (2016) by Leal and Cohn from the University of Florida who also looked at the mystery of how snake limbs vanished. This Washington Post article describes the approaches both teams took to come up with corroborating results.
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