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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
Home › News Releases
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June 1, 2005

DOE JGI Releases Latest Version of IMG

WALNUT CREEK, CA–An enhanced version of the Integrated Microbial Genomes (IMG) data management system has been released by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI). IMG 1.1 contains 32 new public genomes and 14 new genomes sequenced by DOE JGI, bringing the total of genomes in IMG to 337.  These include 301… [Read More]

May 12, 2005

DOE JGI Announces 2006 Community Sequencing Program Portfolio

WALNUT CREEK, CA–Embedded in the language of DNA, the common link among all living things, are lessons for interpreting the complex systems that regulate the health of planet Earth. Now, rounding out this global lesson plan are more than 40 new genome projects, representing a cornucopia of life forms, from the important grain sorghum to… [Read More]

April 21, 2005

Study Reveals New Technique for Fingerprinting Environmental Samples

WALNUT CREEK, CA–Groundbreaking research led by the U.S. Department of Energy Joint Genome Institute (DOE JGI) demonstrates for the first time that the signatures of the genes alone in terrestrial and aquatic samples can accurately diagnose the health of the sampled environments.  This study, published in the April 22nd edition of the journal Science, positions… [Read More]

March 1, 2005

DOE JGI Launches IMG Public Online Microbial Genome Data Clearinghouse

WALNUT CREEK, CA–As the microbial world comes to light through DNA sequencing, the new Integrated Microbial Genomes (IMG) data management system of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) will deliver valuable information for the benefit of the global research community. “The IMG system is an essential enhancement to the computational toolkit… [Read More]

December 22, 2004

Chromosome 16 Publication Fulfills DOE’s Human Genome Commitment

WALNUT CREEK, CA–The U.S. Department of Energy Joint Genome Institute (JGI), culminating a 16-year effort, has completed its share of the Human Genome Project with the publication of the DNA sequence and analysis of chromosome 16 in the Dec. 23 issue of Nature. “The Department of Energy is very proud of its historic role in… [Read More]

October 20, 2004

Mice Thrive Despite Massive Genetic Makeover

WALNUT CREEK, CA–Can you lose scores of pages from a novel and still follow the story line? In the case of the mouse’s genome, or “book of life” — and perhaps even our own — the answer appears to be, astonishingly, “yes.” Researchers from the U.S. Department of Energy Joint Genome Institute (JGI) and Lawrence… [Read More]

September 30, 2004

Diatom Genome Reveals Key Role in Biosphere’s Carbon Cycle

WALNUT CREEK, CA–The first genetic instruction manual of a diatom, from a family of microscopic ocean algae that are among the Earth’s most prolific carbon dioxide assimilators, has yielded important insights on how the creature uses nitrogen, fats, and silica to thrive. The diatom DNA sequencing project, funded by the U.S. Department of Energy (DOE)… [Read More]

September 21, 2004

The Book Opens on the First Tree Genome

WALNUT CREEK, CA–An international consortium including the U.S. Department of Energy (DOE), Genome Canada, and the Umeå Plant Science Centre in Sweden has released the first complete DNA sequence of a tree, Populus trichocarpa, the Black Cottonwood or poplar, one member of the most ecologically and commercially valuable group of trees in North America. The… [Read More]

September 15, 2004

Human Chromosome 5 Final Sequence Analysis Released to Public

WALNUT CREEK, CA–Four years after publicly revealing the official draft human genetic sequence, researchers have reached the halfway point in dotting the i’s and crossing the t’s of the genetic sentences describing how to build a human. The newly finalized chromosome 5 is the 12th chromosome polished off, with 12 more to go. As the… [Read More]

August 24, 2004

JGI Announces Community Sequencing Program Portfolio

WALNUT CREEK, CA–Despite the perception that the genetic diversity among animals–ranging from humans to worms–is enormous, the reality is that it pales in comparison to the diversity between the microbes that make up the bulk of the biomass on the planet. Accordingly, to close conspicuous gaps in our understanding of the tree of life, the… [Read More]
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