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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.

    Read more

    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 › User Support › Institutional User Agreements

Institutional User Agreements

Welcome to the Department of Energy (DOE) Joint Genome Institute!  Before work can start on any approved proposal – including the submission of samples for sequencing, or the submission of sequencing data for synthesis – the DOE requires that all work performed in its User Facilities be covered by a legally binding contract, which is the User Agreement.  All User researchers must have their home/employing institution sign a JGI Non-Proprietary User Agreement and Appendix. An Appendix identifies the type of work or specific proposal to be covered under the Agreement.

The signing official must have the legal authority to commit your institution/organization to the terms and conditions in the User Agreement.  These include, among others, indemnification, patent rights, rights in technical data, project reporting to the DOE, and publication requirements.  An official with authority is usually an individual in a central office, such as President, Rector, CEO, Sponsored Projects Officer/Director or Legal Representative. Please check with your unit director or supervisor for the appropriate contact name, email address and phone number for the signing official.

*User Institutions with an active JGI User Agreement older than June 2017 will be required to execute a 2018 version.  The recent updates were approved by the DOE to address the DNA Synthesis program.  When fully executed, the new User Agreement will replace the active version. For those with an active 2017 version, an amendment to update the agreement terms will be required.

*For researchers with a Howard Hughes Medical Institution (HHMI) appointment, a version of the User Agreement between HHMI, your Host Institution and LBNL is required.

If you have any questions, please contact Contracts Officer, Chevon LeDree at cledree@lbl.gov.      

User Agreement Process

After your proposal is approved, the Contracts Officer (CO) will send required paperwork to your institution.  See samples of the JGI User Agreement, JGI User Agreement for Federal Agencies, DNA Synthesis Appendix and DNA Sequencing Appendix.  After your home institution has signed, all documents can be emailed to the CO.  The CO will sign on behalf of LBNL, and will notify all parties when work may begin.

*DNA SYNTHESIS PROPOSALS – ADDITIONAL REQUIREMENTS:

  •    ACADEMIC, NON-PROFIT OR COMMERCIAL PROPOSALS with MULTIPLE COLLABORATORS: The submitting researcher’s home institution will be identified as the lead institution.  *This applies only when the lead institution is academic (includes HHMI researchers), non-profit or commercial.

o   Only the lead institution will be required to execute User Agreement paperwork and an MTA.

o   The lead institution will be required to flow down the User Agreement terms to the collaborators.

o   The lead institution will be required to assume responsibility for all material transfers.

o   *University of California Campus: An Appendix for the synthesis proposal and MTA must be in place with the submitting researcher’s home campus.  The home campus will have the same requirements as other academic lead institutions.

  •    OTHER DOE NATIONAL LABORATORIES:  A version of the Bilateral DOE Laboratory Utilization Agreement (BDLUA) specifically for JGI’s DNA Synthesis Program has been implemented.  Before work can begin on proposals submitted by researchers from another DOE National Laboratory, a JGI-BDLUA, BDLUA Synthesis Appendix and BDLUA MTA must be in place.

o   For multiple collaborator proposals, all collaborating institutions must execute User Agreement and MTA documents.

  •  OTHER FEDERAL AGENCIES:  For multiple collaborator proposals submitted by researchers from another Federal Agency, all collaborating institutions must execute User Agreement and MTA documents (the UBMTA Implementing Letter is used).
  • SYNTHESIS APPENDIX: Before work can begin, an Appendix for the synthesis proposal must be in place.  This is in addition to an active 2018 User Agreement or JGI BDLUA.
  • MATERIAL TRANSFER AGREEMENT (MTA):  Before work can begin, an MTA must be in place for the constructs that will be sent from JGI when their technical work is completed.  Having the MTA in place before work starts will prevent delays when JGI is ready to send the constructs.

o   The MTA requires signatures by an institution’s authorized representative, the submitting researcher, and by LBNL.

o   The Uniform Biological Material Transfer Agreement (UBMTA) and UBMTA Implementing Letter will be used for academic institutions, non-profits and other federal agencies.

o   MTA for commercial organizations.

o   JGI-BDLUA MTA for other DOE National Laboratories.

o   For proposals with multiple collaborators, the lead institution must assume responsibility for the transfer of constructs to the proposal collaborators and any third party recipients.  If a transfer is requested, a Third Party MTA Letter – executed between the lead institution and LBNL – is required.

  •    After all required documents are fully executed, the Contracts Officer will notify all that work may begin.

Standard practice requires completion of work on all approved proposals within 36 months from the approved start date.  Additional time requires the Project Manager’s approval. An amendment to extend the performance period for a proposal approved on an appendix for only that proposal is required.

Please email all institution-signed paperwork or, if signed originals are needed, send to:

Chevon LeDree, Contracts Officer
Lawrence Berkeley National Laboratory
1 Cyclotron Road, MS 56A0120
Berkeley, CA 94720 USA
Phone: 510-495-2022
email: CLeDree@lbl.gov

NOTE:  If a PI changes academic institutions or a new PI is named during the performance period, your Project Manager must be notified immediately. Either of these changes may require new signed paperwork, and getting new documents in place early will prevent disruption and delays on the work. The transfer of a proposal from one commercial institution to a new commercial institution requires approval by all parties.

 

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