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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 Program Info › CSP Overview › CSP New Investigator

CSP New Investigator

About This Call

The CSP New Investigator call seeks to target investigators and research initiatives new to the JGI, with an emphasis on providing pilot data to assess feasibility of a novel approach or form the foundation for a large-scale CSP proposal submission.  Projects must be independent of ongoing JGI proposals, and lead PIs cannot have been lead PI on any previously accepted JGI CSP or FICUS proposal.  Sequence requests should not exceed 1 Tb in total.

Proposals for this call may be submitted at any time as brief white papers and will be reviewed every six months.  Applicants may submit up to two proposals per cycle (but may be listed as co-PI on an unlimited number of proposals).  Proposals must be submitted using the web form available at  (begin a new proposal document at http://proposals.jgi.doe.gov/ to see the proposal format).

All proposals will undergo an internal pre-review to ensure technical feasibility and alignment with JGI and DOE missions.  Screened proposals will then be reviewed for scientific merit, DOE relevance, proposed data usage by the applicant/community, and track record of the applicant. It is highly recommended that samples meeting JGI’s sample requirements be in-hand at the time of proposal submission.  Samples that are not immediately available, or are of insufficient quality or quantity, may delay or potentially defer approval for sequencing.

For accepted proposals, sequencing, synthesis, metabolomics and analysis will be paid for by the Department of Energy’s funding of the JGI. There is no cost to the user and no granting of funds.

For details on JGI product offerings see https://jgi.doe.gov/user-program-info/product-offerings/.

For general questions, please contact Christa Pennacchio, Project Management Office.  For questions about the appropriateness of projects or experimental design, please contact Tanja Woyke, Deputy for User Programs.  Technical and Scientific Leads will also be available to answer any questions prior to proposal submission.  

Get tips on how to submit an effective New Investigator proposal: https://jgi.doe.gov/webinar-successfully-apply-for-csp-proposal/

Current Call (OPEN)

Bacterial, archaeal, and viral isolates and single cell draft genomes

The JGI will accept proposals for sequencing of collections of bacterial, archaeal, and viral genomes from cultivated isolates or physically isolated single cells. Proposed organisms should broaden phylogenetic representation among sequenced representatives or participate in processes directly relevant to DOE missions. Type strains, including proposed strains prior to publication, are highly encouraged. Between 48 and 184 isolates may be proposed.  For single-cell sequencing projects, JGI will sort up to 8 samples and sequence up to 384 single particle sorts (unverified by 16S) per proposal.  For single virus sort sequencing projects, the amplified DNA needs to be provided by the PI, as JGI does not sort and genome amplify viral particles. Between 48 and 384 single virus sorts may be proposed for sequencing. For projects with larger numbers of genomes, please refer to the CSP Annual Call.

Genome resequencing

The JGI seeks proposals centered on resequencing of bacterial, archaeal, fungal, algal and plant isolates for which a reference genome exists. Projects may focus on natural population structure, understanding gene function under selective pressure or in mutagenized strains, or developing pan and core genomes. We will also consider collections of highly related strains from nature that display differences in phenotypes related to DOE missions, e.g. lignocellulose decomposition, fermentation of sugar substrates or degradation of environmental toxins for bacteria and fungi or biomass composition for plants. Between 22 and 92 samples may be proposed for bacteria, fungi, plants, or algae. For projects with larger numbers of samples, please refer to the CSP Annual Call.

Fungal draft genomes

Proposals will be considered for long-read sequencing of fungal genomes <60 Mb in size, including RNA for annotation. Between 1-6 genomes may be proposed. For larger numbers, please refer to the CSP Annual Call.

Plant/algal genome size estimation

Proposals will be considered for low-pass short-read sequencing of plant and algal genomes to assess genome size and complexity in preparation for large-scale genome sequencing projects.  PacBio may not be requested.  Between 1-6 samples may be proposed.  For larger number of samples, please refer to the CSP Annual Call.

RNA sequencing

The JGI solicits RNA sequencing projects for bacterial, archaeal, fungal, algal and plant genomes for which a reference genome is available. RNA-seq data may be used for improvement of genome annotation or for transcript counting applications (e.g. gene expression profiling of a bacterium during growth on an array of cellulosic substrates to decipher degradation pathways). Projects should be directly relevant to DOE missions; for plants, projects using the standard conditions defined by the Plant Gene Atlas are specifically encouraged. Between 22 and 92 samples (including replicates) may be proposed. For projects with >92 samples, please refer to the CSP Annual Call.

Bacterial and archaeal epigenomes and high-quality draft genomes

Single molecule real time sequencing enables greater genome contiguity as well as assessment of DNA base modifications (6mA, 5mC, 4mC and others) of potential importance in host defense and gene regulation. The JGI will accept proposals including up to 12 samples for improved draft or epigenome sequencing. For projects with >12 samples, please refer to the CSP Annual Call.

Metagenomes and metatranscriptomes

JGI is accepting proposals that include up to 92 metagenomes or metatranscriptomes (in any combination) from environmental samples, laboratory enrichments or synthetic communities. Up to 8 long-read metagenome samples may be also proposed, which will not count toward the 1 Tb cap, but should be discussed with JGI staff prior to requesting. Projects examining sample series across time or space as well as those targeting viruses are particularly encouraged.

The JGI has limited capacity (≤16 biomass samples for sorting) for targeted sorting and metagenomic analysis of specific populations that can be fluorescently labeled, e.g. naturally pigmented cells, cells labeled with Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT), etc. This ‘mini-metagenomic’ approach does not require whole genome amplification assuming >10,000 target cells can be recovered, and target populations should be >1% of cells. Sequencing of up to 92 cell enrichments (mini-metagenomes) can be requested.

DNA synthesis for functional assays

DNA/gene synthesis linked to sequence data generation, including codon optimization, refactoring, and assembly of biosynthetic pathways into appropriate vector systems for expression in heterologous hosts. (Use of this capability is encouraged, but synthesis-only projects should be directed to the Functional Genomics call). JGI is accepting proposals for synthesis of up to 500 kb.

Metabolomics based functional analyses

Targeted and untargeted metabolomic technologies at JGI enable users to examine diverse polar and non-polar metabolites from plants, microbes, and environments. In addition, users may request targeted analysis of stable isotope labeling for specific metabolites. JGI is accepting proposals for up to 50 polar metabolite sample analyses and up to 150 non-polar metabolite sample analyses.

EcoFAB pilot projects

The JGI can provide up to 50 EcoFAB devices (https://eco-fab.org/) to study plant-microbiome interactions. These devices allow for non-destructive root imaging and sampling of the growth media while maintaining a sterile environment. In addition, the JGI can provide a standardized defined microbial community that colonizes plant roots and Brachypodium germplasm, if desired. Users would conduct experiments using these resources and return samples to the JGI for analysis by existing JGI capabilities e.g. metabolomics and transcriptomics.

Proposal Schedule

Proposals are accepted on a continuous basis and will be reviewed twice a year. Letters of intent are not required. Deadline for submission is 60 days prior to the review date. This call replaces the “Small Scale Microbial CSP call” which is no longer active.

Upcoming submission deadlines:

  • March 3, 2023 (review in May 2023)

 

 

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