EGSB News

In a Nature Communications report, a team of Berkeley Lab Biosciences Area scientists detail the first-ever successful use of a technique called BONCAT to isolate active microbes present in a sample of soil. Working within a Berkeley Lab-led scientific focus area called ENIGMA (for Ecosystems and Networks Integrated with Genes and Molecular Assemblies), Trent Northen’s lab in the Environmental Genomics and Systems Biology (EGSB) division teamed with JGI researchers on the work.

Researchers at Berkeley Lab and Michigan State University (MSU), led by Corie Ralston and Cheryl Kerfeld, performed X-ray footprinting mass spectrometry (XFMS) experiments at the Advanced Light Source (ALS) beamline 5.3.1, which revealed new mechanistic details of the key events in orange carotenoid protein (OCP) photoprotection. XFMS is ideally suited to probing conformational dynamics at the single residue level, providing both a spatial and temporal view of site-specific changes in the OCP and its interaction with the fluorescence recovery protein (FRP). The experiments showed that FRP provides an extended binding region that holds the OCP together and forces proximity of the two domains that accelerate relaxation of OCP to its native state.

To better understand the cause of high counts of potentially pathogenic fecal indicator bacteria (FIB) in the watersheds of the Mahaulepu Valley and Waikomo Stream in southeast Kauai, the Hawaii Department of Health (DOH) commissioned a study by Berkeley Lab microbial ecologists Gary Andersen and Eric Dubinsky. The duo is frequently invited to lead microbial water assessment projects thanks to their expertise and the PhyloChip, a credit card-sized microbial detection technology invented by Andersen and others at Berkeley Lab.

Researchers led by Diane Dickel have successfully adapted an open-source RNA analysis platform to study gene expression in individual plant cells. The method, called Drop-seq, was developed at Harvard Medical School in 2015 and had previously been used only in animal cells. Dickel and her colleagues at the DOE Joint Genome Institute (JGI) teamed up with researchers from UC Davis who had perfected a protoplasting technique for root tissue from Arabidopsis thaliana (mouse-ear cress). After preparing samples of more than 12,000 Arabidopsis root cells, the group was thrilled when the Drop-seq process went smoother than expected. Their results were published in Cell Reports.

Researchers at Berkeley Lab and Michigan State University (MSU), led by Cheryl Kerfeld, have created a genetically engineered bacterial microcompartment (BMC) shell based on natural structures and the principles of protein evolution. The new shell is smaller and simpler, made of only a single designed protein (natural BMCs are made of up to three), making it easier to work with in the lab.