DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    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.

    More

    (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.

    More

    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.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    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.

    More

    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.

    More

    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.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    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.”

    More

    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.

    More

    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.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • 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.

    More

    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.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    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.

    More

    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.

    More

    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.

    More

User Programs
Home › User Programs › User Program Info › Closed Calls › CSP DNA Synthesis

CSP DNA Synthesis

(status: CLOSED)

About The DNA Synthesis Call

The mission of the DNA Synthesis Science Program is to enable users to perform state-of-the-art functional genomics research and to help them translate genomic information into biological function. Our strategies are to provide users:

  • Access to large-scale DNA synthesis and assembly capabilities
  • Access to integrated genome technologies and informatics pipelines — from sequencing data generation and database mining including JGI genome databases (Genome portal; bacteria: IMG; fungi: MycoCosm; plants: Phytozome), to construct design, DNA synthesis, and microbial strain engineering.

Additionally, our value proposition is to enable users to study the function of genes that are otherwise difficult to source from environmental samples, including uncultured microbes and higher plants. For consortium-type projects, we can help coordinate the consortiums to publish articles on the highest impact journals.

Proposals to access these capabilities may be submitted to the JGI at any time in the form of brief white papers.  Proposals are reviewed twice a year for scientific merit, DOE relevance, proposed usage by the applicant/community, and the applicant’s track record.  Applicants are encouraged to review Synthetic Biology Internal Review Process guidelines, as insufficient information will delay or potentially defer approval for the proposal.

For questions about whether your project is appropriate, or for program specifics or technical guidance, please contact Yasuo Yoshikuni (program head) and Miranda Harmon-Smith (project manager).  For questions about the application process, please contact Miranda Harmon-Smith.

Current Call

The current call for proposals offers multiple capabilities, as described below:

1. Synthesis of genes and pathways for functional characterization.  DNA synthesis technology has advanced to the point that now it allows access to many genes and pathways within diverse, large, and rapidly expanding sequence spaces for heterologous expression. The technology could facilitate discovery and characterization of gene products with novel and/or desired biochemical function at an unprecedented scale. To support this work, the JGI solicits proposals requesting large-scale DNA synthesis and construct assembly of genes and pathways for functional characterization.

The JGI also supports sequence data mining through the JGI’s genome portals and selection of target genes and pathways for synthesis. These selections are made with criteria including phylogenetic distributions and Pfam compositions in pathways. All constructs are synthesized and assembled into user-defined plasmids, sequence validated, and transformed into an E. coli strain before shipment to users. The products are delivered to users as glycerol stocks.

The program accepts proposals from single investigators and consortiums. A consortium must include participation of principal investigators from at least three different institutions and a plan to disseminate materials synthesized by the program to the scientific community. A single investigator can request a total of 50 to 500 kbp of DNA synthesis capacity per proposal. A consortium can request large-scale synthesis capacity (50 to 1,500 kbp in total per proposal).

2. Synthesis of combinatorial pathway libraries for fast-track metabolic engineering.  Metabolic engineering traditionally approaches strain development stepwise, requiring cycles of construct design, building, and characterization. However, pathway efficiency may be optimized more efficiently if multiple pathway variations are tested simultaneously. The JGI recently developed the ability to efficiently build more than 400 pathway variations comprising promoters, RBSs, gene variations, and terminators with different strengths and/or activities. Each proposal may request up to 4,000 kbp of DNA synthesis capacity. The JGI will also help identify a panel of each pathway component and design final constructs. All constructs are assembled using type II restriction-enzyme-based technologies (e.g., golden gate assembly) into user-defined plasmids and are transformed into E. coli strains before shipment to users; no sequencing validations will be performed for the constructs. The products are delivered to users as glycerol stocks.

3. Synthesis of sgRNA libraries. CRISPR/CAS9 technologies facilitate genome editing (deletion, insertion, and point mutation) and transcriptional regulation (activation and inhibition) of any genes of interest at an unprecedented scale and are therefore useful for high throughput functional genomics studies. Each proposal may request up to four libraries comprising up to 12,000 sgRNA sequences. The JGI can help design sgRNA sequences based on the genome sequences of targeted microbes. All sgRNA constructs are synthesized, cloned into user-defined plasmids, and transformed into an E. coli strain as pools. The quality of these libraries is evaluated with sequencing-based analysis using MiSeq before shipment to users. The JGI will create at least 10 replicates of each library to minimize variations in experiments, and will deliver them to users as glycerol stocks. The sgRNA libraries are purified and subsequently transformed into the targeted microbes. These transformants are subjected to user-defined functional screenings. The JGI can further evaluate enriched sgRNA libraries with sequencing-based analysis using MiSeq.

Proposal Schedule

DNA Synthesis Science proposals are accepted on a continuous basis and will be reviewed twice a year. Submission deadline for reach review process is listed below. Letters of intent are not required.

Submission deadlines:

  • July 31, 2019 (review date September 2019)
  • January 31, 2020 (review date March 2020)

Synthetic Biology Internal Review

Proposals are evaluated by at least three external reviewers in a process known as Synthetic Biology Internal Review (SBIR). SBIR encourages investigators to extensively consider broader aspects of their research (e.g., biosafety, biosecurity, bio-containment and environmental issues) to evaluate both positive and negative impacts and to propose strategies to mitigate concerns. If issues are not sufficiently addressed, users will be asked to modify their proposal. If issues are not resolved, the proposal may be rejected. SBIR generally takes three weeks.

Investigators should not merely write “None” or “All research will be conducted in a safe manner according to Federal regulations” in the broader implications statement, as this will lead to requests for proposal modifications, incurring delays of three weeks or longer.

Investigators must explicitly state whether their proposed research would:

  • Demonstrate how to make a vaccine ineffective
  • Confer resistance to antibiotics or antiviral agents
  • Enhance a pathogen’s virulence or make a non-virulent microbe virulent
  • Increase transmissibility of a pathogen
  • Alter the host range of a pathogen
  • Enable a pathogen’s ability to evade diagnostic or detection modalities
  • Enable the weaponization of a biological agent or toxin
  • Calls for User Proposals
  • CSP Overview
  • FICUS Overview
  • Closed Calls
    • CSP FY23
    • FICUS JGI-EMSL FY23
    • CSP Small-scale
    • CSP DNA Synthesis
    • CSP FY22
    • CSP FY21
    • CSP FY20
    • CSP FY19
    • CSP FY18
    • CSP FY17
    • CSP FY16
    • CSP FY15
    • FICUS JGI-NERSC-KBase FY19
    • FICUS JGI-EMSL FY22
    • FICUS JGI-EMSL FY21
    • FICUS JGI-EMSL FY20
    • FICUS JGI-EMSL FY19
    • FICUS JGI-EMSL FY18
    • FICUS JGI-NERSC FY17
    • FICUS JGI-EMSL FY17
    • FICUS JGI-EMSL FY16
    • FICUS JGI-EMSL FY15
  • Review Process and Scoring Criteria
  • DOE Mission Relevance
  • FAQ

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California