In Nature, researchers in Berkeley Lab’s Biosciences Area, the Gladstone Institutes, and the Chan-Zuckerberg Biohub presented nearly 61,000 microbial genomes that were computationally reconstructed from 3,810 publicly available human gut metagenomes, which are datasets of all the genetic material present in a microbiome sample. The metagenome-assembled genomes (MAGs) included 2,058 previously unknown species, bringing the number of known human gut species to 4,558 and increasing the phylogenetic diversity of sequenced gut bacteria by 50 percent. This work helps answer the question of why certain microbes have not been cultivated in the lab. Read more in the Berkeley Lab News Center.
New Computational Biosciences Group Formed
Researchers from Biosciences and the Computational Research Division (CRD) have formed a new integrated Computational Biosciences Group to develop tools for addressing a range of scientific problems that cross organizational lines. Members of the group include (pictured, from left): Héctor García Martin of the Biological Systems and Engineering and the Environmental Genomics and Systems Biology Divisions (BSE/EGSB), acting group lead Kris Bouchard (BSE), Chris Mungall (EGSB), Andrew Tritt of the Computational Research Division(CRD), Oliver Rübel (CRD), and Ben Brown (EGSB). Additional members not pictured are: Aydın Buluç (CRD), Silvia Crivelli (CRD), Hans Johansen (CRD), Talita Perciano (CRD), and Peter Zwart of the Molecular Biophysics and Integrated Bioimaging Division (MBIB).
Read more on the Computing Sciences website.
Beetle’s Gut Microbiome is Nature’s Biorefinery
A study led by Eoin Brodie and Javier Ceja-Navarro in Berkeley Lab’s Earth and Environmental Sciences Area (EESA) provides new insights into how the wood-eating passalid beetle’s complex digestive tract and resident microbes are able to efficiently turn tough plant polymers like lignin and cellulose into food and fuel. By bringing together a team of experts—including collaborators at Pacific Northwest National Laboratory and Lawrence Livermore National Laboratory—and using advanced molecular biology tools combined with spectrometry and tiny sensors, they discovered that the beetle’s gut is made up of specialized compartments, each with a distinct microbiome, that work together in a manner similar to a factory production line. “The key innovation that nature has provided here is a way to combine biochemical processes that are otherwise incompatible,” said Brodie, deputy director of EESA’s Climate and Ecosystem Sciences Division, who has a secondary affiliation in Biosciences’ Environmental Genomics and Systems Biology (EGSB) Division. The study was published in Nature Microbiology.
Read more in the Berkeley Lab News Center.
Sloan Fellowship Will Help Patrick Shih Investigate Ancient Origins of Photosynthesis
Patrick Shih, JBEI’s Director of Plant Biosystems Design who also serves as an assistant professor at the department of plant biology at UC Davis and is a Environmental Genomics and Systems Biology (EGSB) affiliate, was recently selected as a 2019 Alfred P. Sloan Research Fellow in Computational and Evolutionary Molecular Biology.
Shih, will use this fellowship to help fund his research to reconstruct the evolution of photosynthesis, a process that originated billions of years ago.
Read more in the UC Davis News Center.
Two New Additions to CRISPR Toolkit
UC Berkeley and Berkeley Lab scientists have expanded the CRISPR gene-editing toolkit with the addition of a new, compact CRISPR-associated (Cas) protein—the RNA-guided “scissors” that snip DNA—and a modification of the Cas9 protein to give it an “on” switch for better control.
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