Environmental Genomics and Systems Biology Division Director Susannah Tringe announced a change in leadership of the Comparative and Functional Genomics (CFG) Department, effective January 4, 2022. Diane Dickel is stepping down as the Department Head; Adam Deutschbauer has agreed to take on the role.
New Protein Functions from Beneficial Human Gut Bacterium
Researchers in the Environmental Genomics and Systems Biology (EGSB) and Biological Systems and Engineering (BSE) Divisions at Berkeley Lab employed a large-scale functional genomics approach to systematically characterize Bacteroides thetaiotaomicron, a beneficial bacterium prevalent in the human gut. They performed hundreds of genome-wide fitness assays and identified new functions for 40 proteins, including antibiotic tolerance, polysaccharide degradation, and colonization of the GI tract in germ-free mice.
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.
Dub-seq Flagship Paper Published in Nature Communications
Dual barcoded shotgun expression library sequencing, or Dub-seq, is a novel high-throughput method for discovering gene function in microbes under various environmental conditions. It was developed by scientists in the Environmental Genomics and Systems Biology (EGSB) Division under the aegis of the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) program. In a seminal paper published January 18 in Nature Communications, the Dub-seq team presented details of the technique and proof-of-concept work showing that the approach is reproducible, economical, scalable, and identifies both known and novel gene functions.
New Workflow Accelerates Experiment-based Gene Function Assignment
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.
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