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How to Edit the Genes of Nature’s Master Manipulators

December 5, 2022

CRISPR-Cas13 creates an evolutionary bottleneck by targeting the RNA of diverse phages, allowing for edited phages (orange) to be specifically enriched. (Credit: Davian Ho)

A team led by CRISPR pioneer Jennifer Doudna and her longtime collaborator Jill Banfield has developed a clever tool to edit the genomes of bacteria-infecting viruses called bacteriophages using a rare form of CRISPR. The ability to easily engineer custom-designed phages—which has long eluded the research community—could help researchers control microbiomes without antibiotics or harsh chemicals, and treat dangerous drug-resistant infections. A paper describing the work was recently published in Nature Microbiology.

Methane-Eating ‘Borgs’ Have Been Assimilating Earth’s Microbes

October 19, 2022

A digital illustration inspired by methane-eating archaea and the Borgs that assimilate them (Credit: Jenny Nuss/Berkeley Lab)

A team led by UC Berkeley’s Jill Banfield discovered DNA structures within a methane-consuming microbe that appear to supercharge the organism’s metabolic rate. In a nod to the Star Trek universe, they named the genetic elements “Borgs” because the DNA within contains genes assimilated from many organisms.

All-star Scientific Team Seeks to Edit Entire Microbiomes with CRISPR

December 20, 2021

A rendering of Lactobacillus, a type of beneficial bacteria found in the human intestine microbiome. (Credit: nopparit/iStock)

CRISPR enzymes are like super scissors: they cut, delete, and add genes to a specific kind of cell, one at a time. But now, UC Berkeley faculty and Biosciences Area researchers have figured out how to add or modify genes within a microbial community of many different species, coining the phrase, “community editing.”

Study Finds ‘Missing Link’ in the Evolutionary History of Carbon-Fixing Protein Rubisco

October 8, 2020

A ribbon diagram (L) and molecular surface representation (R) of carbon-fixing form I’ rubisco, showing eight molecular subunits without the small subunits. An x-ray diffraction pattern of the enzyme, also generated by the research team, is in the background. (Credit: Henrique Pereira/Berkeley Lab)

In a study appearing in Nature Plants, researchers from UC Davis, UC Berkeley, and Berkeley Lab report the discovery and characterization of a previously undescribed lineage of form I rubisco – one that the researchers suspect diverged from form I rubisco prior to the evolution of cyanobacteria. The novel lineage, called form I’ rubisco, gives researchers new insights into the structural evolution of form I rubisco, potentially providing clues as to how this enzyme changed the planet.

The work was led by Patrick Shih, a UC Davis assistant professor and the director of Plant Biosystems Design at the Joint BioEnergy Institute (JBEI), and Doug Banda, a postdoctoral scholar in his lab.

Banfield Team Studies Huge Bacteria-eating Viruses

February 26, 2020

Jill Banfield

Jill Banfield, an Earth and Environmental Sciences Area faculty scientist with a secondary appointment in the Environmental Genomics & Systems Biology Division, co-led a team to discover 351 different huge bacteria-eating phages. One of these is the largest bacteriophage known to date–with a genome that at 735,000 pairs long–is nearly 15 times longer than the average phage.

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