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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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User Programs
Home › User Programs › Special Initiatives & Programs › Partnerships Development Team (PDT)

Partnerships Development Team (PDT)

Through the Partnerships Development Team (PDT), strategic outreach efforts are targeting companies and other institutions without any prior JGI collaborations. The PDT is comprised of Director Nigel Mouncey, Chief Informatics Officer Kjiersten Fagnan, User Program Deputy Susannah Tringe, DNA Synthesis Science Program Head Yasuo Yoshikuni, Senior Manager of Communications & Outreach David Gilbert, and Robin Johnston, the Joint BioEnergy Institute (JBEI) Director of Commercialization, Biosciences Strategic Industry Engagements and Entrepreneurship Lead. The PDT also draws the expertise of Genomics Technologies Deputy Len Pennacchio, as needed. The PDT enables industry engagement through three primary routes: the Community Science Program call as well as less-explored mechanisms of Strategic Partnership Projects (SPP) and Cooperative Research and Development Agreements (CRADA), see below. The Business Development Team works closely with Berkeley Lab’s Intellectual Property Office to facilitate these new interactions. To set up a call or meeting to discuss partnering opportunities, contact Debbie Wendt.

Recent Partnerships

On June 11, 2020, the Department of Energy announced the 2020 Technology Commercialization Fund (TCF) projects. One of them supports a project between JGI and LanzaTech, a Skokie, Illinois-based company that recycles carbon emissions to make fuels and chemicals, improving air quality and promoting a circular economy.

Acetogenic Clostridium is considered the most efficient method of converting abundant low-cost gas feedstock into valuable bioproducts, but many Clostridium strains are difficult to engineer.

Yasuo Yoshikuni and his JGI colleagues have developed a technology called chassis-independent recombinase-assisted genome engineering (CRAGE), which offers single-step genomic integration and prototyping of complex pathways. The team will be working with LanzaTech to rapidly engineer a Clostridium strain for the production of biofuels and bioproducts from low-cost gas feedstock. For more information about the supported Berkeley Lab TCG projects, visit the Intellectual Property Office here.

Case Study

A recent case study describing a collaboration between the JGI Metabolomics Technology Group and Brightseed can be found here.

Strategic Partnership Projects (SPPs)

SPPs enable research funded by an Industry partner to perform a defined scope of work using JGI’s unique facilities, equipment, and personnel. Sponsor may elect to obtain the entire right, title, and interest to any intellectual property generated under the agreement.

Cooperative Research and Development Agreements (CRADAs)

CRADAs enable research jointly sponsored by the Berkeley Lab and one or more partners for shared benefit. Industry partners can retain rights to their own inventions and have the first right to license Lab inventions generated through the CRADA.

For additional information about these partnering mechanisms, visit Berkeley Lab’s Innovation and Partnership Office (IPO) and read the Guide to Partnering with DOE’s National Laboratories.

  • Partnerships Development Team (PDT)
    • JGI Partnership Case Study: Brightseed

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