Biosciences News

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.

A group of researchers at Washington University School of Medicine have used the capabilities available at the Advanced Light Source’s SIBYLS beamline to gain insight into an enzyme that functions in blood clotting. ADAMTS13, which stands for a disintegrin and metalloproteinase with thrombospondin-1 repeats, member 13, is a multi-domain protease enzyme whose catalytic mechanism involves a metal. It is the only known protein to regulate the adhesive function of von Willebrand factor (VWF), a blood clotting protein involved in hemostasis.

The crystallographic study of STING (stimulator of interferon genes), a transmembrane protein that plays a key role in innate immunity, in complex with TBK1 (serine/threonine-protein kinase), an enzyme that regulates the inflammatory response to foreign DNA, is extremely challenging due to weakly diffracting crystals. But thanks to the expertise of Berkeley Center for Structural Biology (BCSB) scientists, researchers from Texas A&M University (TAMU) were able to pinpoint the conserved motif of STING that mediates the recruitment and activation of TBK1. They published their results in Nature.

Researchers led by Ivaylo Ivanov of Georgia State University have produced a comprehensive model of the human transcription preinitiation complex (PIC), a vital assembly of proteins responsible for regulating gene expression. The new model is the most complete to date and provides mechanistic insights into how mutations affecting one component—human transcription initiation factor IIH, or TFIIH—lead to three inherited genetic diseases. Berkeley Lab Biosciences’ Susan Tsutakawa, a research scientist in Molecular Biophysics and Integrated Bioimaging (MBIB), and John Tainer, a professor at the University of Texas MD Anderson Cancer Center and visiting faculty in MBIB, were part of the team. Results from this work were recently published in Nature Structural & Molecular Biology.

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.