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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 16, 2011

Maize genomics at DOE JGI User Meeting in Genome Technology

Speaking at the Department of Energy Joint Genome Institute’s sixth annual User Meeting, held in Walnut Creek, Calif., in March, Buckler said that while they may not have realized it at the time, maize breeders in Thailand, Mexico, and elsewhere have, since the turn of the 20th century, captured a great deal more genomic diversity… [Read More]

May 14, 2011

Eucalyptus genome sequence in ScienceDaily

According to Prof Myburg, these scientists, as well as countries with commercial eucalypt plantations will be the primary beneficiaries of the genome sequence now available on the Internet (http://www.phytozome.net/eucalyptus.php). The Eucalyptus research community will continue to add value to the genome sequence in order to make it more accessible to the broader scientific community. Publication of the… [Read More]

May 13, 2011

Tringe DOE Award in BioPortfolio

DOE’s Office of Science awarded the Early Career Research grant to Susannah Green Tringe, a researcher in the Lawrence Berkeley National Laboratory’s Genomics Division, to study how microbial communities in restored wetlands may impact long-term carbon sequestration, from a genomic perspective. Read more in BioPortfolio [Read More]

May 12, 2011

Eucalyptus genome in FirstScience News

A team of international researchers, led by Prof Zander Myburg from the Department of Genetics and the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria (UP) – in collaboration with the US Department of Energy (DOE) Joint Genome Institute (JGI) – making available the complete genome sequence of the forest tree species, Eucalyptus… [Read More]

May 12, 2011

Tringe DOE Award in GenomeWeb

DOE’s Office of Science awarded the Early Career Research grant to Susannah Green Tringe, a researcher in the Lawrence Berkeley National Laboratory’s Genomics Division, to study how microbial communities in restored wetlands may impact long-term carbon sequestration, from a genomic perspective. Read more on GenomeWeb [Read More]

May 11, 2011

Tringe DOE Award in Technology Today

Susannah Tringe of the Genomics Division and DOE’s Joint Genome Institute. Tringe investigates the sequencing and characterization of natural communities of microbes and their roles in processes ranging from biomass degradation to efficient production of biofuels from non-food crops. Her Early Career award from the Office of Biological and Environmental Research is for her proposal “Microbial… [Read More]

May 11, 2011

Berkeley lab second campus in the Daily Californian

The six sites that made the final cut from a list of more than 20 potential sites in the Bay Area are Alameda Point in the city of Alameda, Berkeley Aquatic Park West in West Berkeley, Brooklyn Basin in Oakland, properties already occupied by the lab in Emeryville and Berkeley, Golden Gate Fields and Richmond… [Read More]

May 11, 2011

Poplar rust fungal genome project in Western Farm Press

The sequencing of the genetic codes of wheat stem rust pathogen (Puccinia graminis) and poplar leaf rust pathogen (Melampsora larici-populina) is expected to help researchers develop control strategies to address worldwide threats to wheat fields and tree plantations. The study, published in the Proceedings of the National Academy of Sciences, was a six-year collaborative effort of… [Read More]

May 10, 2011

Poplar leaf rust fungal genome project on KRVN

Wheat stem rust causes major epidemics of both barley and wheat worldwide. A strain known as Ug99 has spread across Africa and into Central Asia, and has been able to overcome most of the stem-rust-resistant wheat varieties developed over the past 50 years. Poplar leaf rust can cause significant losses in poplar tree plantations. Poplar… [Read More]

May 10, 2011

JGI Science @ the Lesher in The Oakland Tribune

The researchers, who will speak Monday evening at the Lesher Center for the Arts in Walnut Creek, are working with the Joint Genome Institute in Walnut Creek, a federal facility for genetic sequencing of microbes and other life-forms. The terrestrial ecosystem, meaning everything on land — from plants to soil and other geological features —… [Read More]
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