FY18 JGI-EMSL Collaborative Science Call (status: CLOSED)
Applications for collaborative research with the Environmental Molecular Sciences Laboratory (EMSL) and the Joint Genome Institute (JGI) are being accepted from January 3, 2017 to April 3, 2017. This call is part of the Facilities Integrating Collaborations for User Science initiative (FICUS) – a collaboration between user facilities that are stewarded by the Department of Energy Office of Biological and Environmental Research. FICUS was established three years ago to encourage and enable researchers to more easily integrate the expertise and capabilities of multiple user facilities into their research. The FICUS call between EMSL and DOE JGI represents a unique opportunity for researchers to combine the power of genomics and molecular characterization in one proposed research project.
FICUS applications follow a proposal package guidance, schedule, and review process that is tailored to meet the requirements of the facilities involved. Applications begin with Letters of Intent (LOI), and requests for full proposals will be issued by April 18. Returning users especially are advised to carefully review the unique elements of this joint program as some of the procedures have changed.
Highlights
Successful applications will focus on high risk/high payoff projects in the focused topic areas that can be completed on an accelerated timeline, as compared to the standard DOE JGI CSP or EMSL science theme projects; utilize a broad range of the capabilities of each facility; and generate datasets beyond what each of these facilities could generate by itself. In addition to the EMSL resources necessary for the proposed work, an individual application should not request more than 600 Gb of DOE JGI sequencing and 250 Mb of DOE JGI synthesis. Accepted projects must address or be aligned with DOE/BER missions, but proof of concept for the demonstration of a technology that would be applicable to a DOE mission is appropriate.
Focused Topic Areas
- Airborne biological particles – Identification and abundance of airborne biological particles, particularly as a function of altitude, season, and location, and their ability to act as ice nucleating particles. Viability of these biological particles after atmospheric transport and processing is also of interest.
- Biofuels and bioproducts – Projects should be aimed at characterizing biological processes that are relevant to biofuels and bioproducts, and connecting these processes to genotypes in organisms of interest (plants, fungi, microbes and algae). Relevant biological processes include plant polymer biosynthesis and deconstruction, especially lignin and production of metabolites that are biofuels, bioproducts or biofuel/bioproduct precursors. Proposals for projects investigating organisms (including under-represented groups such as arbuscular mycorrhizal fungi) and/or biological products involved in plant-microbial interactions that impact biofuel feedstock productivity are also encouraged.
- Biogeochemistry – Projects should focus on the cycling and transport of elements and molecular compounds in soils, aquatic sediments and the subsurface, or on their involvement in microbial regulatory/metabolic processes. Proposals should seek to illuminate critical biogeochemical processes, including those through which bacteria, archaea, fungi, and/or microbial communities/consortia influence the fate and transport of radionuclides and heavy metals or the release/cycling of CO2 and CH4. Such projects should seek to link microbial genes and populations to molecular biochemistry.
- Plant-microbe interactions – Projects should explore the exchange of carbon, nitrogen and other elements between plants and microbes in above and below ground ecosystems, particularly in response to abiotic stresses such as micronutrient limitation, increased temperature, and drought. Examples of approaches include but are not limited to studies that explore the importance of volatile organic compounds (VOCs) in plant-microbe and microbe-microbe interactions and implications for atmospheric secondary organic aerosol formation. Proposals for projects studying the impact of genetic diversity within plant populations on plant-associated microbial communities (including under-represented groups such as arbuscular mycorrhizal fungi) and plant-microbial interactions are also encouraged.
EMSL provides a wide range of new capabilities that offer opportunities to obtain novel and exciting experimental data to advance scientific objectives.Details about these are available on the EMSL capabilities web page. They include a variety of in-situ probes for NMR, advanced electron and dynamic transmission electron microscopy in a specialized “quiet” facility, super resolution fluorescence microscopy for live cell imaging, high-resolution mass spectrometry including a 21 Tesla FTICR, advanced ‘omics and microfluidic capabilities, a 3.4 petaflop supercomputer, NanoSIMS, Atom Probe Tomography, and Imaging XPS. Users also have access to the EMSL phytotron for plant growth and imaging. Applications may request any combination of resources, but must provide adequate information to demonstrate the plan for integration and justify the amount of time or other resources requested. If you’re uncertain which instruments would be best for your project, you can search by research area to view a list of commonly used instruments.
Applicants are strongly urged to discuss their resource needs with the respective Capability Lead or Instrument Scientists prior to responding to the Call. Contact information for these individuals is available on the resource description pages, or interested applicants may contact the User Support Office for assistance.
Researchers interested in learning more about EMSL and specific instruments can view a dozen different instruments in four of EMSL’s laboratories through a panning 360-degree virtual tour. The tour includes lab and instrument overviews available through text, images, video and web pages. It features EMSL’s surface science instruments, nuclear magnetic resonance spectrometers, ion mobility mass spectrometers, and cell isolation and surface analysis tools.
DOE JGI primarily employs next-generation short-read sequencing platforms augmented by 3rd generation single-molecule/long-read capabilities (read lengths in the 6-10kb range). The capabilities available for this call are listed below. Researchers are encouraged to review JGI’s sample submission guidelines to obtain additional information about the amounts of material that are required for various product types. Individual proposals may draw from one or more of these capabilities as needed to fulfill project goals. Successful projects frequently exploit a combination of capabilities:
- Core Capabilities Include:
- De novo sequencing of plant, fungal, bacterial, and archaeal genomes
- Resequencing for variation detection
- Fluorescence activated cell sorting, including single-cell sorting and amplification of genomic DNA
- Single-cell DNA sequencing
- Microbial community DNA/RNA sequencing
- Comprehensive transcriptome analysis including coding transcript annotation, non-coding RNA (both small and long ncRNA) characterization and expression profiling
- Target enriched re-sequencing
- Whole genome DNA methylation analysis
- Chromatin analysis including FAIRE, and histone modifications through ChIP-seq
- DNA/gene synthesis
- Analysis pipelines for the datasets above
- DOE JGI also has limited capacity for the following developing capabilities:
- Custom genome analysis of generated datasets
- Mass spectrometry-based metabolomics analysis of primary and secondary metabolites from plants and microorganisms
- Access to high-performance computing at the National Energy Research Scientific Computing Center (NERSC)
Submitted LOIs will be reviewed by members of both EMSL and DOE JGI scientific staff and management for relevance to DOE mission areas. Submitters whose letters of intent are approved will be notified via email to submit full proposals through EMSL’s User Portal by May 22, 2017. Proposals will be peer-reviewed and ranked following the published review criteria for EMSL and DOE JGI, using a combined panel of EMSL and DOE JGI independent reviewers. Final decisions based on ranking for these proposals will be made by EMSL and DOE JGI management, and approved projects will start on October 1, 2017.
Questions regarding FICUS or specifics related to this Call may be directed to the contacts listed below.
Contacts:
For general proposal inquiries – Terry Law
(emsl@pnnl.gov, 509-371-6003)
For EMSL’s science program –Ljiljana Paša-Tolić
(ljiljana.pasatolic@pnnl.gov, 509-371-6733)
For atmospheric systems – John Shilling
(John.Shilling@pnnl.gov, 509-375-6874)
For biofuels and bioproducts – Scott Baker
(Scott.Baker@pnnl.gov, 509-372-4759)
For plant-microbe interactions and biogeochemistry – Nancy Hess
(Nancy.Hess@pnnl.gov, 509-371-6385)
For multi-scale modeling and high-performance computing – Tim Scheibe
(Tim.Scheibe@pnnl.gov, 509-372-6065)
For Joint Genome Institute inquiries – Susannah Tringe
(SGTringe@lbl.gov, 925-296-5813)
Proposal Schedule
To respond to the FY18 call, a Letter of Intent (LOI) is required before submitting a proposal. Letters of intent will only be accepted electronically and should be submitted via the EMSL Portal from Jan 3 – April 3, 2017. Applicants will be advised by email whether to prepare a full proposal, and full proposals will be due May 22, 2017. Guidance for submitting full proposals will be included in the email notification to invited applicants.
The full FY18 schedule is below:
| Calls for proposals issued | January 3, 2017 |
|---|---|
| Letters of intent received | April 3, 2017 |
| Invitation of proposals | April 18, 2017 |
| Proposals received | May 22, 2017 |
| Technical and scientific review | June 21-23, 2017 |
| Approval and rejection notices sent | July 31, 2017 |
| Prepare user agreements | September 2017 |
| Projects start | As soon as user agreement is finalized |