Environmental Molecular Sciences Laboratory

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Call for FY2021 Letters of Intent for FICUS Research with JGI and EMSL

The Call for Letters of Intent for FY2021 FICUS Research is Now Closed

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 23, 2020 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 in 2014 to encourage and enable researchers to more easily integrate the expertise and capabilities of multiple user facilities into their research and represented a unique opportunity for researchers to combine the power of genomics and molecular characterization in one proposed research project.

In addition, the call for FY2021 proposals includes two new opportunities: 1) an interdepartmental pilot program with the National Synchrotron Light Source II (NSLS-II), an Office of Basic Energy Sciences user facility, to provide limited access to the X-ray Fluorescence Microprobe (XFM) Beamline; and 2) an interagency pilot program with the National Ecological Observatory Network (NEON), a National Science Foundation observational network of terrestrial and aquatic sites across the US, for use of seasonal soil samples archived in the NEON Biorepository.

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 change each year.

Applications begin with a required LOI, which is evaluated by members of the user facilities’ scientific staff and management for relevance to DOE mission areas. Submitters whose letters of intent are approved will be notified via email by April 6 to submit full proposals through EMSL's User Portal by May 4, 2020. Proposals will be peer-reviewed and ranked following the published review criteria, using a combined panel of the user facilities’ independent reviewers. Award decisions based on ranking for these proposals will be made by the user facilities by July 31, 2020, and approved projects will start on October 1, 2020.

Highlights

Successful applications will address high risk/high payoff projects in the focus topic areas that can be completed in a 24-30 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, 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, biomaterials and bioproducts – Projects should be aimed at characterizing biological processes (including those derived via synthetic biology approaches) that are relevant to biofuels, biomaterials 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 biosynthesis and deconstruction of plant polymers, especially lignocellulose, and production of metabolites that are precursors of biofuels, biomaterials, 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 molecular compounds in soils, atmosphere, 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 biogeochemically 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 and their interfaces, 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 and their associated biosynthetic pathways potentially involved in cell-cell interactions.
  • Novel applications of molecular techniques – Projects should be aimed at stretching the boundaries of scientific integration of capabilities across the user facilities. Outcomes should have long-term benefits to DOE/BER missions involving biofuels, biomaterials and bioproducts production, plant-microbe interactions and nutrient exchange, ecosystem resilience or plasticity in response to environmental stress, and land-atmosphere exchanges and feedbacks. Structural and functional characterization of novel proteins (e.g., enzymes), compounds (e.g., secondary metabolites) or biomaterials 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.  
  • Utilize soils from the NEON Biorepository and EMSL/JGI capabilities to conduct continental scale ecosystem research – Projects should investigate the soil chemistry and soil microbial communities across NEON sites along climate/vegetation gradients or seasonal variation at specific sites. NEON, the National Ecological Observatory Network, is a national network of terrestrial and aquatic sites located across the US, including Alaska, Hawaii, and Puerto Rico that captures more than 180 data products collected either continuously or with vast seasonal standardized sampling campaigns including soils. A diversity of genomic sequencing data products capturing the soil microbiome is available from the NEON data portal for a subset of the seasonal soil sampling. The FICUS Letter of Intent must include a letter of support from NEON for the specific samples that you require. Find out more below about NEON, the NEON Biorepository and data products, such as metagenomic sequencing.

Partnering Facilities

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. Applicants should especially consider emerging cutting-edge capabilities that are available to users who coordinate their proposals with the EMSL scientists leading their development. The capabilities include but are not limited to the following: 

  • Stable isotope probing and analysis platform that includes labeled CO2plant growth facilities, NMR, IRMS, and NanoSIMS (Contact: Jim Moran, Mary Lipton, or Pubudu Handakumbura)
  • Transcriptomics and proteomics from single or a small number of cells detected and isolated by flow cytometry, fluorescence microscopy and/or laser capture micro-dissection and enabled by microfluidics and nanoPOTS (Contact: Galya Orr or Ying Zhu)
  • New Krios cryoTEM in combination with native mass spectrometry and cell-free expression capabilities for characterization of protein complexes (Contact: Irina Novikova or Mowei Zhou)
  • Soft X-ray nanotomography system for 3D nanoscale imaging of cells and biological materials (Contact: James Evans or Scott Lea)
  • High-resolution micro-X-ray computed tomography system for characterization of plant root architecture and soil pore structure (Contact: Tamas Varga or Mark Bowden)
  • Noninvasive root imaging platform for monitoring and characterizing plant root systems in transparent growth medium (Contact: Amir Ahkami or Thomas Wietsma)
  • Interactive data visualization tools that support exploration of complex natural organic matter or proteomics data and comparison of data across treatment groups (Contact: Allison Thompson)
  • Tahoma, BER’s new heterogeneous computing system for highly parallel modeling/simulation and data processing needs. Tahoma is a combination of 160 CPU nodes and 24 GPU nodes, with an estimated peak performance of 0.57 PetaFLOPs. This system will support computational research requiring significant memory (384 or 1536 GByte per node RAM) as well as processing speed to enable data mining, image processing, and multiscale modeling. (Contact: Lee Ann McCue).

Other capabilities that offer opportunities for novel and exciting experimental data include a variety of in-situ probes for NMR, advanced electron microscopy in a specialized “quiet” facility, high-resolution mass spectrometry including a 21 Tesla FTICR, and Atom Probe Tomography. Details about each of these are available on the EMSL capabilities web page. Applications may request any combination of these or other EMSL 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, algal, fungal, bacterial, archaeal, and viral genomes
  • Resequencing for variation detection
  • Fluorescence activated cell sorting for targeted metagenomics and single-cell genomics
  • Microbial community DNA/RNA sequencing and annotation
  • Stable isotope probing enabled metagenomics
  • Comprehensive transcriptome analysis
  • Whole genome DNA methylation analysis
  • Chromatin analysis including FAIRE and ChIP-seq
  • Gene and pathway DNA synthesis
  • Whole genome gRNA library construction and QC
  • Organism engineering
  • High throughput metabolomics for functional genomics.

NSLS-II, a DOE Basic Energy Sciences (BES) Scientific User Facility located at Brookhaven National Laboratory, is providing limited access to the X-ray Fluorescence Microprobe (XFM) Beamline through a partnership with EMSL and JGI. XFM provides characterization of elemental abundances and chemical speciation in heterogeneous samples.  It is optimized for spatially-resolved spectroscopy (EXAFS & XANES) in the 4 - 20 keV energy range, and also offers a polychromatic "pink" mode ideal for rapid 2D and 3D fluorescence imaging and tomography. It employs compound focusing to achieve a user-tunable spot size from 2 to 10 microns while maintaining a long working distance for physically large samples and custom in situ environmental cells.

*NEW* Through a 2.5-day, hands-on training workshop at NSLS-II on March 18-20, 2020, researchers have a unique opportunity to learn more about applying tender-energy, spatially resolved X-ray absorption spectroscopy and X-ray fluorescence imaging to their current or proposed projects.  Participants are encouraged to bring their own samples and utilize this time to explore the capabilities of the instrument.

For more details about the scheduled activities or about applying the XFM to your FICUS proposal, please contact Ryan Tappero and refer to the XFM website at https://www.bnl.gov/ps/beamlines/beamline.php?r=4-BMTo register: Contact Vivian Stojanoff at stojanof@bnl.gov, or 631-344-8375.

NEON, a large facility project funded by the National Science Foundation (NSF), is a continental-scale platform for ecological research. It comprises terrestrial, aquatic, atmospheric, and remote sensing measurement infrastructure and cyberinfrastructure that deliver standardized, calibrated data to the scientific community through a single, openly accessible data portal. NEON infrastructure is geographically-distributed across the United States and will generate data for ecological research over a 30 year period. It is designed to enable the research community to ask and address their own questions on a regional to continental scale around a variety of environmental challenges. Additional information about the network is available below:

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 

For EMSL inquiries

For Joint Genome Institute inquiries