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.
‘Magic Pools’ Approach Accelerates Study of Novel Bacteria
To characterize the functions of genes in newly discovered bacteria, microbiologists introduce mutations using mobile DNA snippets called transposons delivered via a vector. But finding an effective transposon mutagenesis system for a novel microorganism through trial and error can be a time-consuming and expensive endeavor.
To streamline the process, Environmental Genomics and Systems Biology (EGSB) Division researchers, led by Adam Deutschbauer and Adam Arkin, have developed a new technique to test hundreds of different transposon vector variants in parallel within what the investigators term “magic pools.”
The approach was detailed in mSystems, an open access journal from the American Society for Microbiology.
Dub-seq Wins 2017 R&D100 Award
A high-throughput, cost effective method for discovering gene function in microbes under various environmental conditions is among the winners of R&D Magazine’s 2017 R&D 100 Award. The technology, called Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), was developed by Adam Arkin, Adam Deutschbauer, Vivek Mutalik, and Pavel Novichkov of the Environmental Genomics and Systems Biology (EGSB) Division. Dub-seq … Read more »
Dub-seq Named a Finalist for R&D 100 Awards
A method for discovering gene function in microbes developed by Adam Arkin, Adam Deutschbauer, Vivek Mutalik, and Pavel Novichkov of the Environmental Genomics and Systems Biology division has been shortlisted for R&D Magazine’s 2017 R&D 100 Award. The technology, called Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), combines the shotgun expression library method and next generation sequencing method developed through the ENIGMA program. Now in its 55th year, the prestigious R&D 100 Awards program recognizes the most innovative inventions of the prior year. The winners will be announced and honored at a black-tie ceremony to be held this fall in conjunction with the annual R&D 100 Conference.
Division Leadership Team Changes in EGSB and BSE
The Biosciences Area is pleased to announce that Adam Deutschbauer and Diane Dickel have agreed to take on new leadership positions in the Environmental Genomics & Systems Biology (EGSB) Division. Deutschbauer, previously the department head of Functional Genomics, is rising to the position of EGSB co-deputy for science, and Dickel will assume the role of … Read more »
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