DOE Joint Genome Institute

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    (PXFuel)
    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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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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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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    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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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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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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User Programs
Home › User Programs › Special Initiatives & Programs

Special Initiatives & Programs

Biological and Environmental Research Support Science (BERSS) | Emerging Technologies Opportunity Program (ETOP) | Visiting Scientist Program

Partnerships Development Team (PDT)

The vast majority of the JGI’s over 2,000 Users come from the public sector – academic and government institutions. As such, the capabilities and expertise of the JGI are largely unknown and underutilized by industry. With the arrival of JGI Director Nigel Mouncey, who joined the JGI with 20 years of industry experience in 2017, an opportunity emerged to expand JGI’s portfolio of user companies by establishing a Partnerships Development Team (PDT). Other targets of PDT’s activities include other academic, governmental, and non-governmental institutions that have not yet partnered with the JGI. Learn more about the PDT.

Bioenergy Research Centers (BRCs):

The JGI performs sequencing on behalf of the U.S. Department of Energy Bioenergy Research Centers. The Centers are intended to accelerate basic research in the development of cellulosic ethanol and other biofuels, advancing the federal initiative that seeks to reduce U.S. gasoline consumption by 20% within 10 years through increased efficiency and diversification of clean energy sources. The four Centers are located in geographically distinct areas and use different plants both for laboratory research and for improving feedstock crops.

Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) led by University of Illinois at Urbana-Champaign. Announced in July 2017, CABBI is a collaboration between Illinois’ Institute for Sustainability, Energy, and Environment (iSEE) and the Carl R. Woese Institute for Genomic Biology (IGB), and it will include 17 partner institutions. CABBI researchers will develop fuels and products by integrating three highly interconnected DOE priority areas of Feedstock Development, Conversion, and Sustainability.

Center for Bioenergy Innovation (CBI) led by DOE’s Oak Ridge National Laboratory in Oak Ridge, Tennessee. CBI will pursue a host of new technologies to alleviate critical cost barriers to sustainable, economically viable production of bio-based products and advanced biofuels. The center will focus on creating robust high-yielding feedstock plants, using advanced genetic technology to accelerate the domestication of perennials. CBI will create methods for high-yield production of advanced biofuels that can be blended with existing transportation fuels. Researchers will also study ways to develop valuable byproducts from lignin left over after biomass processing.

Great Lakes Bioenergy Research Center (GLBRC) led by the University of Wisconsin in Madison, Wisconsin, in close collaboration with Michigan State University in East Lansing, Michigan. This center is studying a range of plants and, in addition to exploring plant fiber breakdown, aims to increase plant production of starches and oils, which are more easily converted to fuels. This Center also has a major focus on sustainability, examining the environmental and socioeconomic implications of moving to a biofuels economy.

Joint BioEnergy Institute (JBEI) led by DOE’s Lawrence Berkeley National Laboratory. This center will concentrate on “model” crops of rice and Arabidopsis, in the search for game-changing breakthroughs in basic science, and is exploring microbial-based synthesis of fuels beyond ethanol.

Biological and Environmental Research Support Science (BERSS):

Overview

JGI provides sequencing, synthesis, and targeted metabolomics support for DOE-BER funded awards, including awards funded through BER Funding Opportunity Announcements, Science Focus Areas (SFA) opportunities, and the Office of Science Early Career Research Program.

Available Resources

Eligible product types include those listed here:  https://jgi.doe.gov/our-science/product-offerings/

Proposals may not exceed 3 Tbp sequencing, 500 kbp synthesis, and 200 polar/500 nonpolar metabolomics samples, and should generally conform to the guidelines for current annual Community Science Program proposals.

Process

Proposals may be submitted at any time.  Support is limited to work included in the BER-funded proposal, and PIs must provide an award number and contact information for their DOE program officer. Submitters are strongly encouraged to contact JGI to determine general feasibility prior to submitting a BER proposal that includes a JGI request. Proposals whose scope was not previously negotiated with the JGI will only be accepted pending available capacity, technical review, and scope negotiation at JGI.

Investigators with grants funded by DOE-BER requiring support from JGI capabilities may submit proposals here.

Investigators preparing grant applications to DOE-BER and requesting an optional letter of feasibility to accompany their proposal may contact Tanja Woyke (twoyke@lbl.gov), Deputy for User Programs, with a proposed scope.

Investigators wishing to expand on their DOE-BER funded work with additional sequencing, synthesis, or metabolomics should apply to one of the JGI’s calls for user proposals.

 

Emerging Technologies Opportunity Program (ETOP)

The ETOP identifies and funds partnerships to develop new technical capabilities that could be provided to JGI users.  Projects targeted for 2018 include development of methods for rapid prototyping of gene and pathway function targeting organisms found in natural environments:

  • High-throughput cell-based systems for biological and metabolic characterization
  • Cell-free technologies that enable scaleable in vitro gene and pathway functional analyses
  • Sensor-based technologies, biological or non-biological, that enable in vivo reporting of metabolic activity and/or activity-based cell sorting

Deadline for proposal submission has passed. For more information, check out the solicitation.

See a list of previously supported projects.

 

Visiting Scientist Program

The JGI Visiting Scientist Program (VSP) provides an opportunity for faculty-level scientists who are seeking to build upon their line of scientific inquiry by leveraging JGI experimental, computational, and personnel resources for genomic research and sequence-based science. Projects include de novo generation of genome data, assistance in interpreting and/or building on an existing data set, or the refining of new technology (e.g., single-cell genomics; metagenomics, etc.). Length of stay depends on complexity of the project being considered and availability of data and other resources. Investigators, postdocs, and graduate students participating in approved JGI User Projects are also invited to apply for on-site access to JGI resources and capabilities. For more information, contact Tanja Woyke (twoyke@lbl.gov), Deputy for User Programs.

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