BSE News

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.

The prevalence of anxiety disorders, already the most common mental illness in many countries, including the U.S., has surged during the novel coronavirus pandemic. A study led by researchers in Berkeley Lab’s Biosciences Area provides evidence that taking care of our gut microbiome may help mitigate some of that anxiety.

Chemotherapy and radiation treatments can be life-saving for patients with cancer, but they have harsh side effects that can been felt and seen throughout the body. There can also be unseen consequences: These important treatments can mutate DNA and damage chromosomes in patients’ cancerous and noncancerous cells alike. When this occurs in a germline cell (eggs in women and sperm in men), it can lead to serious fetal and birth defects in a resulting pregnancy. In a study published in PLOS One, a team led by Biological Systems and Engineering (BSE) Division senior scientist Andrew Wyrobek reported success adapting an established cellular DNA analysis technique called fluorescence in situ hybridization (FISH) to probe sperm DNA for a wide variety of chromosomal defects simultaneously.

The protein CheY plays a role in relaying sensory signals from chemoreceptors to the rotary motor at the base of the tail-like appendage, or flagellum, that protrudes from the cell body of certain bacteria and eukaryotic cells. It has been studied as a model for dissecting the mechanism of allostery—the process by which the binding of biological macromolecules (mainly proteins) at one location regulates activity at another, often distant, functional site. When it is transiently phosphorylated in response to chemotactic cues, CheY’s binding affinity for a flagellar motor switch protein called FliM is enhanced. CheY binding to FliM changes the direction of flagellar rotation from counterclockwise to clockwise.

Using X-ray footprinting with mass spectroscopy (XFMS), a team led by Shahid Khan, a senior scientist with the Molecular Biology Consortium, established that CheY changes shape when it tethers to the motor, and further parsed the contribution of phosphorylation to this shape change. The results of the XFMS experiments validated atomistic molecular dynamics (MD) predictions of the architecture of the allosteric communication network, marking the first time that XFMS has been used to validate protein dynamics simulations at single-residue resolution sampled over the complete protein.

The American Association for the Advancement of Science (AAAS), which was founded in 1848 and is the world’s largest general scientific society, announced that 489 of its members—among them nine scientists at Berkeley Lab—have been named Fellows. This lifetime honor, which follows a nomination and review process, recognizes scientists, engineers, and innovators for their distinguished achievements toward the advancement or applications of science.

The three newly named Fellows from the Biosciences Area are: Sanjay Kumar, a faculty scientist in the Biological Systems and Engineering (BSE) Division; Mary Maxon, the Associate Laboratory Director for the Biosciences Area; and Len Pennacchio, a senior scientist in the Environmental Genomics and Systems Biology (EGSB) Division and the Deputy of Genomic Technologies at the DOE Joint Genome Institute (JGI).