Biosciences News

University of California San Francisco (UCSF), UC Davis, and Lawrence Berkeley National Laboratory (Berkeley Lab) have formed a Tri-Institutional Partnership in Microbiome Research (TrIP Microbiome) to catalyze and fund novel, bold, and potentially transformative collaborative microbiome research projects. A unique aspect of the partnership is its data-driven focus and data infrastructure, brought through the participation of the Berkeley Lab-led National Microbiome Data Collaborative (NMDC). The NMDC is working with TrIP Microbiome researchers to catalyze experimental co-design between biologists and computational scientists, adoption of data management best practices, and open science to enable cross-study comparison and machine learning.

The Encyclopedia of DNA Elements (ENCODE) collaboration was launched 17 years ago by the National Human Genome Research Institute with the goal of developing the tools and expertise needed to shed light on the 98% of our genome that does not code for proteins. Now in its final year, ENCODE has made huge advances thanks to the combined scientific and technological prowess of several hundred researchers at dozens of institutions. Leading the project for Berkeley Lab are Diane Dickel, Len Pennacchio, and Axel Visel, co-PIs of the Mammalian Functional Genomics Laboratory in Biosciences’ Environmental Genomics and Systems Biology (EGSB) Division. They are co-authors on 4 of the 15 new ENCODE papers published this week as part of a special collection in Nature.

Combining cryo-electron microscopy, biochemical assays, and protein crystallography at Advanced Light Source (ALS) Beamline 5.0.2 (part of the Berkeley Center for Structural Biology), researchers from the Baylor College of Medicine discovered that rotavirus VP3 incorporates in one place all the enzymatic activities required to effectively cap rotavirus mRNA, making it unique among viral-capping enzymes.

Molecular Biophysics and Integrated Bioimaging (MBIB) Division Director Paul Adams has announced a number of changes in the Division leadership, effective July 21.

A team led by JGI researchers has generated a more accurate phylogenetic tree tracking the evolution of Dothideomycetes fungi.  This work was enabled in part through JGI’s Community Science Program (CSP), as several approved proposals have contributed toward filling gaps on the fungal Tree of Life, including the 1000 Fungal Genomes Project. Researchers had access to over 100 Dothideomycetes genomes, just enough of a sample size to test if a computer algorithm could distinguish between fungal lifestyles of saprobes and pathogens based on the data provided. The work appeared in the June issue of Studies in Mycology. The work appeared in the June issue of Studies in Mycology.  Read more on the JGI website.