Biosciences News

A cross-disciplinary effort by Berkeley Lab scientists has yielded a new algorithmic approach for determining 3D molecular structures from single-particle X-ray free-electron laser (XFEL) imaging. Peter Zwart of the Molecular Biophysics & Integrated Bioimaging Division (MBIB) worked with James Sethian and Jeffrey Donatelli of the Computational Research Division’s Mathematics Group to create the multi-tiered iterative phasing (M-TIP) framework, which uses advanced mathematical techniques to extract nano-scale biological structures from sparse and noisy diffraction data. A paper detailing the approach was published in the Proceedings of the National Academy of Sciences.

Miniaturized, microfluidic-based metagenomics technology developed under the aegis of U.S. Department of Energy Joint Genome Institute’s (DOE JGI’s) Emerging Technology Opportunity Program (ETOP) has enabled researchers to shine a light on so-called microbial “dark matter”—the majority of the planet’s microbial diversity that remains uncultivated. Researchers from Stanford University demonstrated the efficacy of the new technique, extracting 29 novel microbial genomes from Yellowstone hot spring samples while still preserving single-cell resolution to enable accurate analysis of genome function and abundance. Read more in this JGI Science Highlight.

A decade after the complete representative genomes of three Ostreococcus groups were sequenced, an international team of researchers including scientists at the Department of Energy Joint Genome Institute (DOE JGI) have resequenced and analyzed the genomes of 13 members of a natural population from the northwest Mediterranean Sea. The analysis revealed that the O. tauri population is larger than anticipated, with high genetic and phenotypic diversity that is influenced by the algae’s natural resistance to ocean viruses. Understanding the genetic variability of various Ostreococcus strains will help researchers understand how environmental changes affect their abundance and ability to photosynthesize. The work was reported in Science Advances. Read more in this DOE JGI Science Highlight.

Using a combination of crystallographic, biochemical, and genetic analyses, Berkeley Lab researchers have shown that the actions of FEN1, an enzyme involved in DNA replication and repair, are guided by electrostatic forces known as phosphate steering. Susan Tsutakawa and John Tainer in the Biosciences Area’s Molecular Biophysics and Integrated Bioimaging (MBIB) Division were the lead and corresponding authors, respectively, on the report published this week in Nature Communications. The work reveals key details of this previously unknown mechanism controlling the specificity of FEN1 in healthy cells and provides new directions for cancer treatment research. Read more from the Berkeley Lab News Center.

With funding from the Department of Energy’s  (DOE’s) Laboratory Directed Research and Development (LDRD) program, Berkeley Lab researchers from the Computational Research Division (CRD) and the Biosciences Area are collaborating to explore how brain-inspired computer chips might benefit science.