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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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    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.
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    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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    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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    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)
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    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)
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    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)
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    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)
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Home › Webinars › Engagement Webinar: How to Successfully Apply for a CSP Proposal

September 8, 2020

Engagement Webinar: How to Successfully Apply for a CSP Proposal

Tips:

  • Contact us with your questions (jgi-jira+pmosupport@lbl.gov)
  • Carefully read our proposal call description and ensure your idea is aligned
  • Discuss your proposal idea with JGI staff to clarify key points about JGI’s capabilities, technical feasibility, and relevance to the DOE’s mission. 
  • Have someone proofread your proposal to make sure the goals, experimental design, and plan for data utilization are clear.
  • Contact JGI staff for feedback before submitting a proposal.
  • Describe in detail what you will do with the data! Ideally, you or someone on your team will have expertise in this area, or can demonstrate how competencies can be built.
  • We recommend exploring how KBase (www.kbase.us) can support biological data analysis. It is a free, open source analytics platform provided to the research community by DOE. Email engage@kbase.us if you have questions about how KBase can support your CSP data.

On September 1, JGI held a JGI Engagement: Pro Tips for Successful Community Science Program (CSP) Applications Webinar inviting researchers to submit white papers to the CSP New Investigator call for proposals. The proposal call is open year-round, but proposals submitted by September 21, 2020, will be included in the next review.

Q&A from the Webinar:

Q(uestion): Can people can mix and match options in their proposal as long as they’re staying under the sequence cap?
A(nswer): Proposals that are looking at multiple areas or multiple ways to answer questions are definitely encouraged. There’s multiple ways to can mix and match synthesis, metabolomics, sequencing. The only requirements are that you stay under the 500-gigabase cap and that you don’t request outside of the sample range that’s listed.

Q: What are the pros and cons of proposing a truly exploratory small proposal that might not max out the whole 500 gigabases? Is it better to try to reach that maximum with broader questions and broader project scope?
A: Focus on strong science and well-thought-out questions. We are looking for projects that can’t easily be done at a core facility, but you don’t need to necessarily just add samples in order to max out the gigabase allocation.

Q: Can PhD candidates be considered for the CSP New Investigative Proposal?
A: At most institutions, a PhD student can be considered a principal investigator (PI). There is no restriction from JGI’s side, but do check with your institution, as there are some that won’t allow this. It’s really important to show that your team has the necessary experience to handle the data, either by adding team members as co-PIs or collaborators on the proposal, or at the very least providing letters of support saying that they will support this work.

Q: Someone submitted a proposal that received good reviews but faced questions about their ability to analyze the data. How can they better demonstrate their capability for being able to carry out the work and utilize the data they were requesting?
A: The reviewers do look at the PI’s track record to make sure that they have already worked with this type of data set. Having a co-PI with complementary skills can show reviewers the team is really able to take advantage of the data and work with the data.

Q: How would you include a reference or citation in a proposal?
A: If you’re presenting preliminary data that’s been published, or if you want to give some background of the field, references would be encouraged. And you can either put those in the individual text section if you have space, or you can upload everything as a supplementary file.

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Filed Under: Blog, Webinars

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