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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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  • User Programs
    • Calls for Proposals
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    • Submit a Proposal
    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 Program Info › FAQ

FAQ

Where can I find instructions and templates for submitting proposals?

Review the list of open calls; click on the call link to see specific details including project types supported, sample/capacity limits, and instructions.  Many of the submissions are done using web-based forms.  To view the proposal templates, go to the proposal submission page in WIP, login using your JGI account (create one here if you don’t already have an account) and click the “begin” button for the call you are interested in.

All proposals must be written in English.

Are there example proposals that I can view?

Yes.  While the details of the proposal templates may have changed slightly since these were submitted, the format is largely the same.  These proposals were shared with the permission of the PI.

CSP New Investigator proposal – example

CSP Annual Letter of Intent – example 1, example 2, example 3

CSP Functional Genomics proposal – example

FICUS proposal (JGI/EMSL) – example 1, example 2

Who is eligible to submit CSP and FICUS proposals?

The CSP and FICUS calls are open to both domestic and international applicants from any institution type and at any career stage. Generally, most users are able to work with Berkeley Lab. However, users from certain countries (Iran, North Korea, Cuba, and Syria), need DOE permission and authorization from other U.S. Government agencies to work with Berkeley Lab, a process which can take 6 months or longer to obtain with no guarantee of approval.   JGI staff are not eligible to submit proposals, or to be listed as co-PIs or collaborators.  JGI’s standard User Agreement must be signed before work can begin, and all CSP proposals are subject to JGI policies on Data Release and Publication.  Except for applicants to the CSP New Investigator call, investigators may have existing proposals with the JGI.

How can I increase my chance of success?

Get tips on how to submit an effective proposal here: https://jgi.doe.gov/webinar-successfully-apply-for-csp-proposal/  This webinar is targeted to the New Investigator call, but many of the suggestions can be applied to JGI’s other calls as well.  The number one tip: contact us in advance for advice!

What can I request from the CSP and FICUS programs?

The deliverables can range from raw sequence data to well-annotated assembled genomes to synthesized DNA constructs to metabolomics data, depending on the specific product types covered in the call.   If you have technical questions, we encourage you to contact us in advance for advice.

How much will it cost me to sequence or synthesize my target or obtain metabolomics data?

For accepted proposals, sequencing, synthesis, metabolomics and analysis will be paid for by the Department of Energy’s funding of the JGI.

Should I include budget information in my proposal?

No, the proposal is only for sequencing, metabolomics and/or synthesis effort at JGI. There is no cost to the user and no granting of funds.

Where do I go to get sequence data from an approved proposal?

A complete listing of approved proposals can be found here.  All sequence data will be accessible on the JGI Portal.

I am applying for a research grant. I would like to request genomic resources from the JGI for this research grant. Can I get technical information, deliverables, and perhaps a support letter from the JGI?

Yes. You should indicate this in the proposal so we can select the project provisionally. If your project makes it successfully through the scientific review and is selected, we will provide you with the information you need for the grant.

If I have ongoing research funding to carry out functional studies using the proposed sequencing data, should I mention it in the proposal?

Yes. You should use it to demonstrate that you have the capability to perform the plans described in your proposal.

Will the JGI provide other types of genomic resources such as construction of cDNA libraries, BAC libraries, or genotyping?

While, in general, requests will be for sequencing and its analysis, investigators are encouraged to contact the JGI concerning other genomic resource needs.

Am I allowed to submit NIH-oriented projects to the CSP and FICUS calls?

Scientific merit is the major criteria used in evaluating proposals; however, the proposal must demonstrate relevance to DOE missions.  USDA, NSF, and NIH operate sequencing programs, and potential users are urged to contact these agencies for projects when appropriate.

I am in a competitive field. I do not want my competitors to know that I am submitting a proposal to the JGI. What degree of confidentiality do I have?

The review process is confidential. Once a project is selected, however, we will post the PIs’ names and the proposal title. All data will be released in accordance with the JGI Data Release Policy.

What are the JGI’s sample material requirements?

Sample requirements for sequencing projects can be found here.  The quality of the starting material is one of the greatest predictors of a successful sequencing project.

What should be included in the “sample regulatory compliance” section of the proposal?

Utilization or transfer of any genetic resource may be covered by local, national or international regulation.  These requirements apply whether the use is for non-profit or for-profit activity. A few examples include:

Convention on Biological Diversity Nagoya Protocol on Access and Benefit Sharing

Benefits sharing in the US National Parks

USDA Animal and Plant Health Inspection Service permits

US Fish and Wildlife permits

These examples may apply to your samples, but do not serve as a comprehensive list of regulatory requirements. The user is responsible for determining which regulations or permit requirements are appropriate and ensuring compliance before any materials are transferred to JGI.

What format should I use for my CV?

JGI does not require a specific format; many investigators use a format similar to the NIH or NSF biosketches.  In general, CVs should not exceed three pages.

Who can I contact with questions?

We encourage submitters to contact JGI to discuss their proposals prior to submission!  Specific contact info is available on the individual call pages, or please contact us with your general questions.

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