Biosciences Area

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.

Using Tiny Organisms to Unlock Big Environmental Mysteries

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.

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.

‘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.

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