On September 21, the Biosciences Area held a welcome event to acknowledge the coming together of many new and existing research groups at the Aquatic Park facility in West Berkeley. Laboratory Director Mike Witherell and Deputy Director Horst Simon attended and shared their support. The informal program consisted of brief comments by Helen Cademartori, Biosciences Area Deputy for Operations; Louise Glass, Environmental Genomics & Systems Biology (EGSB) Division Director, who provided her perspective via videoconference; Mary Maxon, Associate Laboratory Director for Biosciences; and Mike Witherell. Witherell acknowledged the group for their shared vision for Aquatic Park and the many inter- and cross-Area collaborations that will be fostered through the colocation of these researchers.
JGI Maps Bacterial Genes That Regulate Microbe-Plant Root Interactions
A plant’s health and development is influenced by the complex community of microbes that surrounds it. Researchers at the Joint Genome Institute (JGI) and their collaborators at the Howard Hughes Medical Institute at the University of North Carolina have identified some 350 genes of the bacterium Pseudomonas simiae that positively or negatively impact how effectively this beneficial microbe colonizes plant roots. Cataloging these genes—and understanding the cellular functions that they’re involved in—is the first step toward developing targeted approaches to improving plant health and growth for a number of applications. The results of the study were published in PLOS Biology. Read more on the JGI website..
JGI Announces 2018 Community Science Program Portfolio
Among the 30 proposals selected for the 2018 Community Science Program (CSP) of the U.S. Department of Energy Joint Genome Institute (DOE JGI) is one by Jillian Banfield, a UC Berkeley professor and Berkeley Lab faculty scientist affiliated with the Environmental Genomics & System Biology (EGSB) Division. Banfield will study the impact of soil microbial communities along the East River in Colorado on the quality of water leaving the watershed. The research is part of a major DOE project to investigate how terrestrial systems respond to perturbations such as droughts, floods, and early snowmelt. The full list of accepted proposals can be viewed here.
American Society for Microbiology Honors Nikos Kyrpides
Nikos Kyrpides, head of the Prokaryote Super Program at the Department of Energy Joint Genome Institute (DOE JGI) and a senior scientist in the Biosciences Environmental Genomics and Systems Biology (EGSB) division, was selected as the 2018 USFCC/J. Roger Porter Award recipient by the American Society for Microbiology (ASM). He will be honored at the 2018 ASM Microbe Meeting in Atlanta, Ga. The award recognizes outstanding effort by a scientist in demonstrating the importance of microbial biodiversity through sustained curation or stewardship of a major resource used by the scientific community. For more than a decade, Kyrpides and his colleagues have been working toward the goal of developing a comprehensive catalog of reference genomes for every bacterial and archaeal species. Read more from JGI.
Modular Ensembles of Enhancers Regulate Ihh, Developmental Gene Expression in Mice
Biosciences researchers Axel Visel (JGI/EGSB) and Marco Osterwalder (EGSB) contributed to a study, led by researchers at the Max Planck Institute for Molecular Genetics, in which targeted genome editing and a transgenic reporter assay were used to characterize elements regulating Ihh (encoding Indian hedgehog) in mice. Indian hedgehog is a mammalian signaling protein involved with the development and proliferation of cells in cartilage. In humans, copy number variants (CNVs) upstream of Ihh cause localized phenotypes including premature fusion of the sutures of the skull and malformation of the phalanges. The study, published in Nature Genetics, showed that in mice Ihh is regulated by modular ensembles of enhancers (with individual tissue specificities) that appear to act in an additive manner. Despite apparent redundancy and overlapping function of enhancers, these ensembles—in which the correct number of each enhancer is present—are necessary for precise spatiotemporal control of developmental gene expression.
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