FICUS JGI-EMSL FY20 - DOE Joint Genome Institute (original) (raw)

Letters of Intent (LOI) for collaborative research applications with the Environmental Molecular Sciences Laboratory (EMSL) and the Joint Genome Institute (JGI) are being accepted until March 20, 2019 at 11:00 PM (PDT). This call is part of the Facilities Integrating Collaborations for User Science (FICUS) program – a collaboration that was developed between user facilities stewarded by the Department of Energy (DOE) Office of Biological and Environmental Research (BER). FICUS was established between EMSL and JGI in 2014 to encourage and enable researchers to more easily integrate the expertise and capabilities of these two user facilities into their research and represented a unique opportunity for researchers to combine the power of genomics and molecular characterization in a single research project.

FICUS applications follow a proposal package guidance, schedule, and review process that is tailored to meet the requirements of the facilities involved. Returning users especially are advised to carefully review the unique elements of this joint program as some of the procedures and requirements have changed.

Applications begin with a required LOI, which is evaluated by members of EMSL and JGI scientific staff and management for relevance to DOE mission areas. Submitters whose letters of intent are approved will be notified via email by April 5 to submit full proposals through EMSL’s User Portal by May 5, 2019. Proposals will be peer-reviewed and ranked following the published review criteria, using a combined panel of EMSL and JGI independent reviewers. Final decisions based on ranking for these proposals will be made by the EMSL, JGI, and NSLS-II management, and approved projects will start on October 1, 2019.

Highlights

Successful applications will address high risk/high payoff projects in the focus topic areas that can be completed in an 18-24 month timeline; use a range of the capabilities of each facility; and generate datasets beyond what users of each of these facilities could generate through separate projects. Because this program offers a diverse but integrated set of capabilities, including complementary metabolomics capabilities that each facility offers to characterize plant, soil and microbe interactions, applicants are strongly encouraged to talk to facility staff in advance to design a set of analyses that is directed at their research goals. For more details regarding the FICUS application process, sample limits or the capabilities available at the user facilities, please check our frequently asked questions (FAQ) or the contacts listed below.

Focused Topic Areas

• Biofuels and bioproducts – Projects should be aimed at characterizing biological processes that are relevant to biofuels and bioproducts production, and connecting these processes to genomics-based analyses in DOE-relevant plants, algae, fungi, bacteria, archaea and viruses. Relevant biological processes include plant polymer biosynthesis and deconstruction, especially lignocellulose and production of metabolites that are precursors of biofuels and/or non-pharmaceutical bioproducts. Proposals for projects investigating organisms and/or biological products involved in plant-microbial interactions that impact biofuel and bioproduct feedstock productivity are also encouraged.
• Biogeochemistry – Projects should focus on the cycling and transport of elements and compounds in soils, aquatic sediments and the subsurface, or on their involvement in regulatory/metabolic processes of plants, algae, fungi, bacteria, archaea and viruses. Proposals should seek to illuminate key biogeochemical processes through which these organisms and their communities influence the cycling of biogeochemical critical elements, as well as the transformation and transport of contaminants. Such projects should seek to link microbial populations, genes and traits to molecular biochemistry.
• Inter-organismal interactions – Projects should explore the exchange of carbon, nitrogen and other elements among plants, algae, fungi, bacteria, archaea and viruses in above and below ground ecosystems as well as investigate signaling, cooperation or competition via physical or chemical means. Proposals for projects studying the impact of genetic diversity within plant populations on plant-associated microbial communities and plant-microbial interactions are also encouraged, as are those structurally or functionally characterizing secondary metabolites potentially involved in cell-cell interactions.
• Novel applications of molecular techniques – Projects should be aimed at stretching the boundaries of scientific integration of EMSL and JGI capabilities. Outcomes should have long-term benefits to DOE/BER missions involving biofuels and bioproducts production, environmental processes, plant-microbe interactions, soil-atmospheric interactions, soil/subsurface/aquatic sediment biogeochemical processes, and nutrient traffic and transformations. Structural and functional characterization of novel proteins (e.g., enzymes) and compounds (e.g., secondary metabolites) produced by genes found in (meta)genomic data, as well as assignment of function to uncultivated organisms are of particular interest. For high-risk exploratory studies aimed at assessing the general feasibility or establishing proof of principle for a proposed approach or study design, the scope should be limited to a scale required to demonstrate novel results, with the possibility of expanded support after successful completion

EMSL provides a wide range of unique and state-of-the-art omics, imaging, and computational capabilities that can be applied to proposals under this call:

• proteomics & metabolomics by mass spectrometry and NMR
• bioimaging of macromolecular complexes by electron microscopy
• dynamics & quantification of biomolecules by live-cell microscopy
• nutrient flux experiments with stable isotope probes
• multimodal chemical analysis of biotic and abiotic elements
• flow and transport measurements in pore-scale micromodels
• phytotrons for controlled plant growth

Of special interest are a variety of in-situ probes for NMR, advanced electron microscopy in quiet space including a dynamic transmission electron microscope, super resolution fluorescence microscopy for live cells, high-resolution mass spectrometers including a 21 Tesla FTICR, nonlinear optical spectroscopy (sum frequency generation), a 3.4 petaflop supercomputer, interactive data visualization tools, NanoSIMS, and Atom Probe Tomography. Applications are not limited to these EMSL capabilities and may request any combination of EMSL’s capabilities, but they must provide adequate information to demonstrate the plan for integration and justify the amount of time or other resources requested. Applicants are strongly urged to discuss their resource needs with the respective Capability Lead(s) or Instrument Scientist 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.

JGI employs both next-generation short-read sequencing platforms and 3rd generation single-molecule/long-read capabilities as well as DNA synthesis and mass spectrometry-based metabolomics. The capabilities available for this call are listed below. FICUS proposals should request no more than 1 Tb of sequencing, 500 kb of synthesis and up to 200 samples for metabolomics polar analysis and 500 samples for nonpolar analysis. 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 (more details) as needed to fulfill project goals. Successful projects frequently exploit a combination of capabilities.

• De novo sequencing and annotation of plant, fungal, bacterial, and archaeal genomes
• Resequencing for variation detection
• Fluorescence activated cell sorting for targeted metagenomics and single-cell genomics
• Microbial community DNA/RNA sequencing and annotation
• Comprehensive transcriptome analysis
• Whole genome DNA methylation analysis
• Chromatin analysis including FAIRE and ChIP-seq
• Gene and pathway DNA synthesis
• Organism engineering
• High throughput metabolomics for functional genomics.

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 April 5, 2019. 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, 2019.

Questions regarding FICUS or specifics related to this Call may be directed to the contacts listed below.

Contacts:

For general LOI or full proposal inquiries –
Terry Law ([email protected], 509-371-6003)
Christa Pennacchio ([email protected])

For general EMSL inquiries – Mary Lipton ([email protected], 509-371-6589)

For Joint Genome Institute inquiries – Susannah Tringe ([email protected], 925-296-5813)

For metabolomics inquiries –
EMSL mass spectrometry capabilities – Mary Lipton ([email protected], 509-371-6589)
EMSL nuclear magnetic resonance capabilities – Nancy Washton ([email protected]; 509-371-7094)

JGI high throughput capabilities – Katherine Louie: ([email protected], 480-225-5328)
JGI high throughput capabilities – Trent Northen ([email protected], 925-927-2827)

Proposal Schedule

To respond to the FY20 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 14 – Mar 20, 2019. Applicants will be advised by email whether to prepare a full proposal, and full proposals will be due May 5, 2019. Guidance for submitting full proposals will be included in the email notification to invited applicants.

The full FY20 schedule is below: