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    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
    Researchers combined expertise at the National Labs to screen, characterize, sequence and then analyze the genomes and multi-omics datasets for algae that can be used for large-scale production of biofuels and bioproducts.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

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News & Publications
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May 5, 2022

JGI at 25: Solving the Mystery of the Missing Oil

A surface slick in the Gulf of Mexico, taken ~1.5 km from the Deepwater Horizon wellhead (Olivia Mason, LBNL).JGI at 25 revisits our contributions to a systems biology approach understanding how waves of microbial communities dispersed the 2010 Deepwater Horizon oil spill. [Read More]

April 26, 2022

JGI at 25: The Human Genome Project, or the JGI’s Origin Story

JGI contributions detailed in DOE Human Genome Project posterJGI at 25 revisits our contributions to the Human Genome Project, and our origins in DOE bringing together the people and resources from three national labs. [Read More]

April 20, 2022

JGI at 25: A Single Cell, Myriad Microbial Discoveries

Artistic rendering of a microbial genome layered over a dark forest. (Composition by Zosia Rostomian/Berkeley Lab)JGI at 25 charts the development of single cell genomics from proof of principle to a crucial tool for mapping microbial diversity. [Read More]

April 12, 2022

Calculating the Costs of Multiple Switchgrass Gene Copies

: Documented occurrences of different switchgrass cytotypes (4X in blue and 8X in orange) throughout the United States. One of the early interests in exploring 8X switchgrass was because the noticeable occurrence of 8X in 4X distribution gaps. (Joseph Napier)In the following guest piece on a recent PNAS article, researchers describe the costs associated with switchgrass adaptations to expand its habitat range. [Read More]

March 15, 2022

JGI at 25: Roots of a Mutualist Relationship

Laccaria bicolorAs part of JGI’s 25th anniversary, a look back on the first genome sequence of a mycorrhizal fungus, Laccaria bicolor. [Read More]

March 9, 2022

From Intern to Published Scientist: The Journey of a JGI-UC Merced Intern

Rhondene Wint’s summer project through the JGI-UC Merced internship program grew into a three-year research endeavor, resulting in a recent publication. [Read More]

March 7, 2022

A Plant Root Atlas for Tracking Developmental Trajectories

February 2022 cover of the Development Cell journalResearchers have developed an atlas that maps gene expression patterns in the Arabidopsis root from single root cell profiles. [Read More]

February 22, 2022

Jane Grimwood Named HudsonAlpha Genomics Chair

Jane Grimwood standing with plants behind her on the left and a wooden column behind her on the rightJane Grimwood was named the Loretta Purdy Spencer Chair in Genomics at the HudsonAlpha Institute for Biotechnology. Co-director of the HudsonAlpha Genome Sequencing Center, she also heads the JGI Library Construction group. [Read More]

February 14, 2022

Digging into Microbial Ecosystems Deep Underground

screencap from Amundson and Wilkins subsurface microbiome videoMicrobiome researchers Mike Wilkins and Kaela Amundson at Colorado State University are studying microbial ecosystems deep underground. [Read More]

January 13, 2022

Introducing New Members of the JGI User Executive Committee

New User Executive Committee Members as of January 2022Roland Hatzenpichler, Teresa Pawlowska, and Jana U’Ren have joined the JGI User Executive Committee (UEC). [Read More]
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