Biosciences Area researchers have developed a new DNA analysis technique that reveals a very interesting, and previously hard-to-study, aspect of a microbial community’s genome. As described in the journal mBio, a team led by Aindrila Mukhopadhyay of the Biological Systems and Engineering (BSE) Division has optimized existing methods to isolate plasmids—the small packages of DNA that enable microorganisms like bacteria to quickly acquire and share genes. Often, these DNA molecules, which are separate from the chromosomes, encode functions that can confer a survival advantage in certain situations. The work was conducted as part of ENIGMA, in collaboration with groups at Oak Ridge Field Research Center and the DOE Systems Biology Knowledgebase (KBase). Read the press release in the Berkeley Lab News Center.
Two teams of Biosciences Area researchers are representing Berkeley Lab as part of cohort eight of the U.S. Department of Energy’s I-Corps program, an intensive two-month training course that pairs national laboratory researchers with industry mentors to develop viable market pathways for their technologies. The teams, led by Deepti Tanjore and Esther Singer, presented their projects during the opening session held October 1–5 in Golden, Colorado.
In a letter to the editor published July 6 in Nature Biotechnology, the KBase team presented a comprehensive overview of the platform and an assessment of its scientific impact. The paper describes the unique features and infrastructure of the platform, in addition to highlighting scientific use cases that demonstrate its significance for biology research.
While advances in sequencing technologies have enabled researchers to access the genomes of thousands of microbes and make them publicly available, the task of assigning functions to the genes uncovered has lagged behind due to the limited capacity of functional analysis approaches. To help overcome this bottleneck, Berkeley Lab researchers, led by Adam Arkin and Adam Deutschbauer in Biosciences’ Environmental Genomics and Systems Biology (EGSB) Division and Matthew Blow at the DOE Joint Genome Institute (JGI), have developed a workflow that enables large-scale, genome-wide assays of gene importance across many conditions.
The groundbreaking for the Integrative Genomics Building (IGB), the future home of the DOE Joint Genome Institute (JGI) and the Systems Biology Knowledgebase (KBase), took place under sunny skies yesterday, January 31, at the former site of the Bevatron particle accelerator. Notables in attendance included Sharlene Weatherwax, associate director of science for Biological and Environmental Research (BER) at DOE Office of Science; Pier Oddone, former Fermilab director and former Berkeley Lab deputy director; and Kimberley Budil, vice president for national laboratories in the University of California Office of the President. To symbolize their future partnership and signify some of the vast and complex communities of microorganisms that provide the foundation for the research that will be conducted in the IGB, JGI Director-Designate Nigel Mouncey and KBase Principal Investigator Adam Arkin mixed soil samples in beaker mugs and toasted to their shared vision for the Biosciences future colocation on the Hill.