Call for FICUS Research Proposals with EMSL and JGI, FY 2024
[Closed]
Timeline
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Letters of intent due
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Invitation of proposals
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Full Proposals Due
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Decision notices sent
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Projects start
*Updated: June 8, 2023
The Joint Genome Institute (JGI), a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory (Berkeley Lab), and the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science User Facility at the Pacific Northwest National Laboratory (PNNL) are seeking collaborative research applications through the Facilities Integrating Collaborations for User Science (FICUS) program. The FICUS program originally established in 2014 to encourage and enable ambitious multidisciplinary research projects, integrates expertise and experimental capabilities of multiple DOE supported user facilities.
The FY2024 FICUS proposal call will include access to expanded capabilities available at DOE supported user facilities, including Bio-SANS beamline through the Center for Structural Molecular Biology (CSMB) at Oak Ridge National Laboratory, and the Advanced Photon Source at Argonne National Laboratory. Additionally, applicants can also request access to archived biological, genomic, and geological samples and specimens from terrestrial and aquatic sites through National Science Foundation's (NSF) National Ecological Observatory Network (NEON).
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 variety of available capabilities at two or more user facilities, and generate datasets beyond what users of each of these facilities can generate through separate projects. Applicants are strongly encouraged to contact facility staff (see contact information below) in advance of submitting a Letter of Intent, for help designing a set of analyses that are directed at their research goals.
Focus topic areas
Proposals submitted to this call should be responsive to one or more of the following focus area topics aligned to the Biological and Environmental Research (BER) program . Biofuels, biomaterials, and bioproducts: Projects should be aimed at characterizing biological processes (including those novel pathways generated by synthetic biology approaches) that are relevant to biofuels, biomaterials, and bioproducts production, and connecting these processes to omics-based analyses for DOE-relevant plants, microbes, and microbial communities including viruses. Relevant biological processes include biosynthesis and deconstruction of plant biomass, especially lignocellulose, and the production of metabolites that are precursors of biofuels, biomaterials, and/or non-pharmaceutical bioproducts. Topics of interest include the discovery and characterization of enzymes and metabolic pathways for synthetic polymer breakdown and/or conversion to novel products, the microbially-mediated construction and deconstruction of plastics, secure synthetic biology and biocontainment, genome-enabled organic and inorganic material synthesis, and investigations into organisms and/or biological products involved in plant-microbial interactions that impact biofuel and bioproduct feedstock productivity.
- Hydro-biogeochemistry: Projects should focus on the cycling and transport of key elements, nutrients, and other compounds within ecosystems.. Study systems can include soils, vegetation, microbial communities, the atmosphere, the subsurface, and land/aquatic interfaces, including but not limited to river/stream systems, coastal zones, and/or urban ecosystems. Proposals should seek to illuminate key hydro-biogeochemical processes through which microorganisms influence the biogeochemical cycling of critical elements, nutrients, colloids, and other compounds under baseline or disturbance conditions. Understanding the regulatory/metabolic processes of plants, microbes, and microbial communities, including viruses, is of particular interest. Proposals that focus on aerosol particle formation and processes and/or mineral-organic matter interactions are also encouraged. Projects should seek to link microbial populations, genes, and traits to molecular biogeochemistry and to the surrounding environment.
- Inter-organismal interactions: Projects should explore the exchange of metabolites, signals and/or nutrients (carbon, nitrogen, and other elements) among plants, microbes, and viruses in above- and below-ground ecosystems and their interfaces (e.g., terrestrial-aquatic interfaces), as well as investigate signaling, cooperation, or competition via physical or chemical means under abiotic environmental stresses (e.g., drought, salinity). Proposals focused on the impacts of biological diversity and root structure within plant populations, on plant-associated microbial communities, and plant-microbial interactions are also encouraged. These investigations can include metabolite exchange, structurally or functionally characterization of transporters, surface proteins, exudates, and the enzymes, pathways and proteins and metabolites involved in secondary metabolism that affect multi-organismal and organism-environment interactions.
- Novel applications of molecular techniques: Projects should be aimed at re-defining the boundaries of scientific integration of experimental and data capabilities across the DOE User Facilities. Outcomes should have long-term benefits to DOE/BER mission involving biofuels, biomaterials, and bioproducts production, plastic bioprocessing and degradation, plant-microbe interactions, and nutrient exchange, ecosystem resilience or plasticity in response to environmental stress or disturbances, and land-atmosphere exchanges and feedbacks. Structural and functional characterization of novel proteins (e.g., enzymes), compounds (e.g., primary and secondary metabolites), or biomaterials produced by genes found in (meta)genomic data, as well as functional analysis of uncultivated organisms, are of particular interest. For high-risk, exploratory studies aimed at assessing the general feasibility or establishing proof of principle, the scope should be limited to a scale required to demonstrate novel results, with the possibility of expanded support after successful completion.
- Ecosystem-scale research using samples from the NEON Biorepository: 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. Projects should investigate the biogeochemistry and microbial communities across NEON sites along climate/vegetation gradients or seasonal variation at specific sites but could also include sites that have experienced disturbance. Several genomic sequencing data products, capturing the composition of soil microbiomes, are 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 (e.g., megapit samples) and/or the NEON Biorepository (all other samples) for the specific samples that are required. Additional information is listed below about NEON, as well as the NEON Biorepository and data products, such as metagenomic sequences.
Proposals submitted to this call should be responsive to one or more of the following focus area topics aligned to the Biological and Environmental Research (BER) program . Biofuels, biomaterials, and bioproducts: Projects should be aimed at characterizing biological processes (including those novel pathways generated by synthetic biology approaches) that are relevant to biofuels, biomaterials, and bioproducts production, and connecting these processes to omics-based analyses for DOE-relevant plants, microbes, and microbial communities including viruses. Relevant biological processes include biosynthesis and deconstruction of plant biomass, especially lignocellulose, and the production of metabolites that are precursors of biofuels, biomaterials, and/or non-pharmaceutical bioproducts. Topics of interest include the discovery and characterization of enzymes and metabolic pathways for synthetic polymer breakdown and/or conversion to novel products, the microbially-mediated construction and deconstruction of plastics, secure synthetic biology and biocontainment, genome-enabled organic and inorganic material synthesis, and investigations into organisms and/or biological products involved in plant-microbial interactions that impact biofuel and bioproduct feedstock productivity.
- Hydro-biogeochemistry: Projects should focus on the cycling and transport of key elements, nutrients, and other compounds within ecosystems.. Study systems can include soils, vegetation, microbial communities, the atmosphere, the subsurface, and land/aquatic interfaces, including but not limited to river/stream systems, coastal zones, and/or urban ecosystems. Proposals should seek to illuminate key hydro-biogeochemical processes through which microorganisms influence the biogeochemical cycling of critical elements, nutrients, colloids, and other compounds under baseline or disturbance conditions. Understanding the regulatory/metabolic processes of plants, microbes, and microbial communities, including viruses, is of particular interest. Proposals that focus on aerosol particle formation and processes and/or mineral-organic matter interactions are also encouraged. Projects should seek to link microbial populations, genes, and traits to molecular biogeochemistry and to the surrounding environment.
- Inter-organismal interactions: Projects should explore the exchange of metabolites, signals and/or nutrients (carbon, nitrogen, and other elements) among plants, microbes, and viruses in above- and below-ground ecosystems and their interfaces (e.g., terrestrial-aquatic interfaces), as well as investigate signaling, cooperation, or competition via physical or chemical means under abiotic environmental stresses (e.g., drought, salinity). Proposals focused on the impacts of biological diversity and root structure within plant populations, on plant-associated microbial communities, and plant-microbial interactions are also encouraged. These investigations can include metabolite exchange, structurally or functionally characterization of transporters, surface proteins, exudates, and the enzymes, pathways and proteins and metabolites involved in secondary metabolism that affect multi-organismal and organism-environment interactions.
- Novel applications of molecular techniques: Projects should be aimed at re-defining the boundaries of scientific integration of experimental and data capabilities across the DOE User Facilities. Outcomes should have long-term benefits to DOE/BER mission involving biofuels, biomaterials, and bioproducts production, plastic bioprocessing and degradation, plant-microbe interactions, and nutrient exchange, ecosystem resilience or plasticity in response to environmental stress or disturbances, and land-atmosphere exchanges and feedbacks. Structural and functional characterization of novel proteins (e.g., enzymes), compounds (e.g., primary and secondary metabolites), or biomaterials produced by genes found in (meta)genomic data, as well as functional analysis of uncultivated organisms, are of particular interest. For high-risk, exploratory studies aimed at assessing the general feasibility or establishing proof of principle, the scope should be limited to a scale required to demonstrate novel results, with the possibility of expanded support after successful completion.
- Ecosystem-scale research using samples from the NEON Biorepository: 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. Projects should investigate the biogeochemistry and microbial communities across NEON sites along climate/vegetation gradients or seasonal variation at specific sites but could also include sites that have experienced disturbance. Several genomic sequencing data products, capturing the composition of soil microbiomes, are 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 (e.g., megapit samples) and/or the NEON Biorepository (all other samples) for the specific samples that are required. Additional information is listed below about NEON, as well as the NEON Biorepository and data products, such as metagenomic sequences.
Highlighted Capabilities
Proposals should make use of capabilities from two or more of the participating user facilities, where at least one of the facilities must be EMSL and/or JGI.
Environmental Molecular Sciences Laboratory
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 who lead their development. The capabilities include but are not limited to the following:
- New single-cell transcriptomic workflows for elucidating intercellular signaling, communication and ensuing heterogeneity that underpin the behavior of complex multicellular/multispecies assemblages, including microbial communities and host-microbe systems (Contact: Alex Beliaev)
- Developing capabilities in chemical biology to probe enzyme function and characterize biochemical pathways. For example, users are sought for a recently developed probe library to broadly profile amidase activity, which targets both canonical (peptide-like) and non-canonical amide hydrolase activity, and for developing probes for other activities (Contact: Sankar Krishnamoorthy)
- Stable isotope probing and analysis platform that includes labeled CO2 plant growth facilities, NMR, IRMS, and NanoSIMS (Contact: Mary Lipton, or Pubudu Handakumbura)
- Small sample omics analysis 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: Sarai Williams or Ljiljana Pasa-Tolic)
- Spatial metabolomics, used to investigate the spatial distribution of molecules within biological samples (Contact: Chris Anderton, Dusan Velickovic, and Kristin Burnum-Johnson)
- Structural biology approaches utilizing cell-free expression, native mass spectrometry, and NMR capabilities for characterization of protein complexes (Contact: Irina Novikova or Mowei Zhou)
- Krios cryoTEM for atomic resolution structural analysis of proteins, protein complexes, and/or small molecule crystals or for high resolution tomographic analysis of whole cells and tissues (Contact: James Evans, Irina Novikova, or Amar Parvate)
- Aquilos cryo-FIB/SEM for site-selective sample preparation for cryo-EM/tomography or serial section slice-and-view 3D imaging of large tissue or plant/microbe interactions. (Contact: James Evans or Trevor Moser) [More...]
- Tender 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 biogeochemical samples such as soil, rhizosphere, and sediment samples to investigate porous microstructure, plant root architecture, hydrology, etc. Two resolution options are available; 0.8 µm resolution and 0.2 µm (Contact: Tamas Varga)
- Noninvasive root imaging platform for monitoring and characterizing plant root systems in transparent growth medium (Contact: Amir Ahkami or Thomas Wietsma)
- Optical Coherence Tomography for a non-invasive approach for in situ, 3D imaging of living tissues. The approach can be applied to static samples or deployed in various growth chambers to provide time-series imaging of plants or other systems. (Contact: Amir Ahkami)
- Liquid and Solid state NMR-based metabolomics to define the metabolite profile in a biological system, including primary and secondary metabolites and plant cell wall components.(Contact: David Hoyt and Andrew Lipton) [More…]
- Interactive data visualization tools that support the exploration of complex natural organic matter or proteomics data, and comparison of data across treatment groups. (Contact: Satish Karra) [More…]
- Tahoma, BER’s heterogeneous (CPU/GPU) computing system for highly parallel modeling/simulation and data processing needs (Contact: Satish Karra). [More…]
- Investigations using plant- and soil-based EcoFAB devices supplied by EMSL to conduct experiments to uncover the molecular mechanisms in microbial communities in soils and rhizosphere (root-microbe interactions). (Contact: Arunima Bhattacharjee or Amir Ahkami) [More...]
- A suite of synthetic soil habitats to measure the impact of target soil parameters on ecological interactions, including pore scale micromodels, mineral-amended microfluidic habitats, RhizoChip, and Bioprinted Synthetic Soil Aggregates. These synthetic habitats are ideal for multiomics characterization and multimodal imaging of the spatial organization of soil and rhizosphere communities (plant, bacteria, and fungi) and mapping molecular exchanges between organisms. (Contact: Arunima Bhattacharjee and Jayde Aufrecht)
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. Learn more about these and other EMSL capabilities.
Joint Genome Institute
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; more details can be found about JGI products here. FICUS proposals should request no more than 3 Tb of sequencing, 500 kb of synthesis, and up to 200 samples for metabolomics polar analysis and 500 samples for nonpolar analysis. Requests for Pacific Biosciences long read sequencing are capped at 1 Tp, while requests for DAP-seq should include a minimum of 70 transcription factors. For EcoFab experiments, up to 50 EcoFabs are available. 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.
- 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 and/or viral community DNA/RNA sequencing and annotation (i.e., metagenomes and metatranscriptomes)
- Stable isotope probing-enabled metagenomics
- Transcriptome analysis including coding transcript annotation and expression profiling
- Prokaryotic whole genome DNA methylation analysis
- Transcription factor binding site discovery with DAP-seq
- Gene and pathway DNA synthesis
- Whole genome gRNA library construction and QC
- Organism engineering
- LC-MS/MS based metabolomic analysis of polar (e.g., amino acids, organic acids, sugars, nucleobases, etc.) and non-polar metabolites (e.g., secondary metabolites, lipids, etc.)
- Integrated metabolomic and genomic analyses
- Investigations using EcoFAB devices and, if desired, a defined microbiome supplied by JGI to conduct experiments to uncover the mechanisms underlying the interactions between plants and their root microbiomes. [More...]
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.
Center for Structural Molecular Biology
CSMB supports the user access and science program of the Biological Small-Angle Neutron Scattering (Bio-SANS) instrument at the High-Flux Isotope Reactor located at Oak Ridge National Laboratory. Neutrons provide unique structural information due to their sensitivity to hydrogen and deuterium that is unattainable by other means. Through this FICUS partnership, CSMB is providing access to resources for studies of hierarchical and complex biological systems.
- Small-angle neutron scattering at Bio-SANS provides structural information about a range of biological systems across length scales from 1 – 100 nm. Examples include biomacromolecules and their complexes in solution, biomembranes, and hierarchical and complex systems such as plant cell walls and soils.
- Deuterium labeling of biological macromolecules including, proteins, lipids, nucleic acids, biopolymers.
These tools help researchers understand how macromolecular systems are formed and how they interact with other systems in living cells. For further information about the CSMB and Bio-SANS please visit https://www.ornl.gov/facility/csmb (Contact: Hugh O’Neill).
Advanced Photon Source
Advanced Photon Source (APS) at Argonne National Laboratory (ANL) is being upgraded with new transformative accelerator technology. The new design of the storage ring, the beamline improvement program and new feature beamlines will offer a wide range of x-ray - based tools that will provide novel opportunities for research pertinent to the BER mission, including biological, geological, geochemical and environmental sciences, to address existing and new scientific challenges. eBERlight program is currently being developed as a virtual Collaborative Access Team (CAT) at APS. It will serve as a liaison between user community and the APS after the upgrade, offering an integrated platform enhancing user science through focused communication with users and coordinated activities among the relevant APS beamlines.
In addition to APS x-ray beamlines and techniques, eBERlight will offer expertise and additional infrastructure available at ANL (i) Advanced Protein Characterization Facility (APCF, sector 84 of APS, sample preparation), (ii) Advanced Leadership Computing Facility (ALCF, exascale computing for data processing using supercomputers), (iii) APS cryolab (sample preparation), and (iv) Molecular Environmental Science and Biogeochemical Process Group (MESBPG) laboratories (sample preparation).
In the first year of the FICUS proposal, eBERlight will work with the users on sample preparations, handling and environment. The x-ray measurements will be generally planned for the second year, when APS-U and eBERlight-available beamlines are expected to be able to accept novice users. Exceptions can be made if the capabilities are available sooner.
Specific capabilities/resources include:
- Protein production and structural characterization recourses/services in the Advanced Protein Characterization Facility for gene cloning, recombinant protein expression, purification, characterization, crystallization (access to the lab to perform the work or mail-in service for gene-to-structure pipeline). (Contact Karolina Michalska)
- APS capabilities (Contact Zou Finfrock)
- Macromolecular crystallography is for determination of 3D structures of macromolecules: proteins, nucleic acids and their complexes
- Full-field x-ray imaging is for micro- and nano-computed x-ray tomography (CT) to enable visualization of soil cores or aggregates, plant structures etc., Sample size ranges from microns to centimeters.
- Scanning x-ray microscopy enables the visualization of elemental distribution in 2D/3D (X-Ray Fluorescence (XRF)) and structural information in 3D (ptychography). XRF approaches are applicable for mapping of elements with an atomic number of 13 (Aluminum) and higher; ptychography is a computational scanning microscopy technique for acquiring structural information with resolutions beyond the limits of x-ray optics. Both techniques can be applied to a variety of samples in both, biological and environmental research, such as soils, plants, rhizosphere, aerosol particles, and microorganisms. Sample size ranges for XRF are from microns to centimeter with spatial resolution ranges from 5 nm to 30 microns. The highest achievable spatial resolution for ptychography is 5 nm.
For general questions, please contact Karolina Michalska.
National Ecological Observatory Network
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 measurements and cyberinfrastructure that deliver standardized, calibrated data to the scientific community through a single, openly accessible data portal. In addition to its openly available data products NEON provides access to hundreds of thousands of archived biological, genomic, and geological samples and specimens from terrestrial and aquatic sites. NEON infrastructure is geographically distributed across the United States and will generate data for ecological research over a 30-year period. The network 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. Requests for large numbers of samples or that require additional sample processing may incur a service fee. Additional information about the network is available below:
- NEON Field Sites
- NEON Research Support and Assignable Assets
- NEON Letters of support
- Biorepository website
- NEON Megapit Archive
- NEON Metagenomic sequencing
National Microbiome Data Collaborative (NMDC) and DOE Systems Biology Knowledgebase (KBase)
Applicants are encouraged to interface with NMDC and KBase, as appropriate, for the registration and processing of their data (NMDC) and advanced analysis and data integration (KBase).
The National Microbiome Data Collaborative (NMDC) is an integrated microbiome data ecosystem hosting high-quality, consistently processed multi-omics microbiome data to enable data sharing, management, and cross-comparison across studies in accordance with the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. Applicants interested in collaborating with the NMDC team and having their data hosted within the NMDC Data Portal should indicate so in their proposal.
The Department of Energy Systems Biology Knowledgebase (KBase) is a free, open source data analysis platform for system biology research that supports the FAIR data principles, reproducible analysis workflows, and sharing and publishing of data sets and knowledge generated from your analysis. Please explore the analyses supported by KBase, available at www.kbase.us/learn, and reach out to the KBase staff to discuss how they can support your project.
Data Policies:
EMSL: https://www.emsl.pnnl.gov/data-management-policy
JGI: https://jgi.doe.gov/user-programs/pmo-overview/policies/
NEON: https://www.neonscience.org/data-samples/data-policies-citation
Proposals should make use of capabilities from two or more of the participating user facilities, where at least one of the facilities must be EMSL and/or JGI.
Environmental Molecular Sciences Laboratory
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 who lead their development. The capabilities include but are not limited to the following:
- New single-cell transcriptomic workflows for elucidating intercellular signaling, communication and ensuing heterogeneity that underpin the behavior of complex multicellular/multispecies assemblages, including microbial communities and host-microbe systems (Contact: Alex Beliaev)
- Developing capabilities in chemical biology to probe enzyme function and characterize biochemical pathways. For example, users are sought for a recently developed probe library to broadly profile amidase activity, which targets both canonical (peptide-like) and non-canonical amide hydrolase activity, and for developing probes for other activities (Contact: Sankar Krishnamoorthy)
- Stable isotope probing and analysis platform that includes labeled CO2 plant growth facilities, NMR, IRMS, and NanoSIMS (Contact: Mary Lipton, or Pubudu Handakumbura)
- Small sample omics analysis 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: Sarai Williams or Ljiljana Pasa-Tolic)
- Spatial metabolomics, used to investigate the spatial distribution of molecules within biological samples (Contact: Chris Anderton, Dusan Velickovic, and Kristin Burnum-Johnson)
- Structural biology approaches utilizing cell-free expression, native mass spectrometry, and NMR capabilities for characterization of protein complexes (Contact: Irina Novikova or Mowei Zhou)
- Krios cryoTEM for atomic resolution structural analysis of proteins, protein complexes, and/or small molecule crystals or for high resolution tomographic analysis of whole cells and tissues (Contact: James Evans, Irina Novikova, or Amar Parvate)
- Aquilos cryo-FIB/SEM for site-selective sample preparation for cryo-EM/tomography or serial section slice-and-view 3D imaging of large tissue or plant/microbe interactions. (Contact: James Evans or Trevor Moser) [More...]
- Tender 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 biogeochemical samples such as soil, rhizosphere, and sediment samples to investigate porous microstructure, plant root architecture, hydrology, etc. Two resolution options are available; 0.8 µm resolution and 0.2 µm (Contact: Tamas Varga)
- Noninvasive root imaging platform for monitoring and characterizing plant root systems in transparent growth medium (Contact: Amir Ahkami or Thomas Wietsma)
- Optical Coherence Tomography for a non-invasive approach for in situ, 3D imaging of living tissues. The approach can be applied to static samples or deployed in various growth chambers to provide time-series imaging of plants or other systems. (Contact: Amir Ahkami)
- Liquid and Solid state NMR-based metabolomics to define the metabolite profile in a biological system, including primary and secondary metabolites and plant cell wall components.(Contact: David Hoyt and Andrew Lipton) [More…]
- Interactive data visualization tools that support the exploration of complex natural organic matter or proteomics data, and comparison of data across treatment groups. (Contact: Satish Karra) [More…]
- Tahoma, BER’s heterogeneous (CPU/GPU) computing system for highly parallel modeling/simulation and data processing needs (Contact: Satish Karra). [More…]
- Investigations using plant- and soil-based EcoFAB devices supplied by EMSL to conduct experiments to uncover the molecular mechanisms in microbial communities in soils and rhizosphere (root-microbe interactions). (Contact: Arunima Bhattacharjee or Amir Ahkami) [More...]
- A suite of synthetic soil habitats to measure the impact of target soil parameters on ecological interactions, including pore scale micromodels, mineral-amended microfluidic habitats, RhizoChip, and Bioprinted Synthetic Soil Aggregates. These synthetic habitats are ideal for multiomics characterization and multimodal imaging of the spatial organization of soil and rhizosphere communities (plant, bacteria, and fungi) and mapping molecular exchanges between organisms. (Contact: Arunima Bhattacharjee and Jayde Aufrecht)
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. Learn more about these and other EMSL capabilities.
Joint Genome Institute
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; more details can be found about JGI products here. FICUS proposals should request no more than 3 Tb of sequencing, 500 kb of synthesis, and up to 200 samples for metabolomics polar analysis and 500 samples for nonpolar analysis. Requests for Pacific Biosciences long read sequencing are capped at 1 Tp, while requests for DAP-seq should include a minimum of 70 transcription factors. For EcoFab experiments, up to 50 EcoFabs are available. 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.
- 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 and/or viral community DNA/RNA sequencing and annotation (i.e., metagenomes and metatranscriptomes)
- Stable isotope probing-enabled metagenomics
- Transcriptome analysis including coding transcript annotation and expression profiling
- Prokaryotic whole genome DNA methylation analysis
- Transcription factor binding site discovery with DAP-seq
- Gene and pathway DNA synthesis
- Whole genome gRNA library construction and QC
- Organism engineering
- LC-MS/MS based metabolomic analysis of polar (e.g., amino acids, organic acids, sugars, nucleobases, etc.) and non-polar metabolites (e.g., secondary metabolites, lipids, etc.)
- Integrated metabolomic and genomic analyses
- Investigations using EcoFAB devices and, if desired, a defined microbiome supplied by JGI to conduct experiments to uncover the mechanisms underlying the interactions between plants and their root microbiomes. [More...]
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.
Center for Structural Molecular Biology
CSMB supports the user access and science program of the Biological Small-Angle Neutron Scattering (Bio-SANS) instrument at the High-Flux Isotope Reactor located at Oak Ridge National Laboratory. Neutrons provide unique structural information due to their sensitivity to hydrogen and deuterium that is unattainable by other means. Through this FICUS partnership, CSMB is providing access to resources for studies of hierarchical and complex biological systems.
- Small-angle neutron scattering at Bio-SANS provides structural information about a range of biological systems across length scales from 1 – 100 nm. Examples include biomacromolecules and their complexes in solution, biomembranes, and hierarchical and complex systems such as plant cell walls and soils.
- Deuterium labeling of biological macromolecules including, proteins, lipids, nucleic acids, biopolymers.
These tools help researchers understand how macromolecular systems are formed and how they interact with other systems in living cells. For further information about the CSMB and Bio-SANS please visit https://www.ornl.gov/facility/csmb (Contact: Hugh O’Neill).
Advanced Photon Source
Advanced Photon Source (APS) at Argonne National Laboratory (ANL) is being upgraded with new transformative accelerator technology. The new design of the storage ring, the beamline improvement program and new feature beamlines will offer a wide range of x-ray - based tools that will provide novel opportunities for research pertinent to the BER mission, including biological, geological, geochemical and environmental sciences, to address existing and new scientific challenges. eBERlight program is currently being developed as a virtual Collaborative Access Team (CAT) at APS. It will serve as a liaison between user community and the APS after the upgrade, offering an integrated platform enhancing user science through focused communication with users and coordinated activities among the relevant APS beamlines.
In addition to APS x-ray beamlines and techniques, eBERlight will offer expertise and additional infrastructure available at ANL (i) Advanced Protein Characterization Facility (APCF, sector 84 of APS, sample preparation), (ii) Advanced Leadership Computing Facility (ALCF, exascale computing for data processing using supercomputers), (iii) APS cryolab (sample preparation), and (iv) Molecular Environmental Science and Biogeochemical Process Group (MESBPG) laboratories (sample preparation).
In the first year of the FICUS proposal, eBERlight will work with the users on sample preparations, handling and environment. The x-ray measurements will be generally planned for the second year, when APS-U and eBERlight-available beamlines are expected to be able to accept novice users. Exceptions can be made if the capabilities are available sooner.
Specific capabilities/resources include:
- Protein production and structural characterization recourses/services in the Advanced Protein Characterization Facility for gene cloning, recombinant protein expression, purification, characterization, crystallization (access to the lab to perform the work or mail-in service for gene-to-structure pipeline). (Contact Karolina Michalska)
- APS capabilities (Contact Zou Finfrock)
- Macromolecular crystallography is for determination of 3D structures of macromolecules: proteins, nucleic acids and their complexes
- Full-field x-ray imaging is for micro- and nano-computed x-ray tomography (CT) to enable visualization of soil cores or aggregates, plant structures etc., Sample size ranges from microns to centimeters.
- Scanning x-ray microscopy enables the visualization of elemental distribution in 2D/3D (X-Ray Fluorescence (XRF)) and structural information in 3D (ptychography). XRF approaches are applicable for mapping of elements with an atomic number of 13 (Aluminum) and higher; ptychography is a computational scanning microscopy technique for acquiring structural information with resolutions beyond the limits of x-ray optics. Both techniques can be applied to a variety of samples in both, biological and environmental research, such as soils, plants, rhizosphere, aerosol particles, and microorganisms. Sample size ranges for XRF are from microns to centimeter with spatial resolution ranges from 5 nm to 30 microns. The highest achievable spatial resolution for ptychography is 5 nm.
For general questions, please contact Karolina Michalska.
National Ecological Observatory Network
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 measurements and cyberinfrastructure that deliver standardized, calibrated data to the scientific community through a single, openly accessible data portal. In addition to its openly available data products NEON provides access to hundreds of thousands of archived biological, genomic, and geological samples and specimens from terrestrial and aquatic sites. NEON infrastructure is geographically distributed across the United States and will generate data for ecological research over a 30-year period. The network 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. Requests for large numbers of samples or that require additional sample processing may incur a service fee. Additional information about the network is available below:
- NEON Field Sites
- NEON Research Support and Assignable Assets
- NEON Letters of support
- Biorepository website
- NEON Megapit Archive
- NEON Metagenomic sequencing
National Microbiome Data Collaborative (NMDC) and DOE Systems Biology Knowledgebase (KBase)
Applicants are encouraged to interface with NMDC and KBase, as appropriate, for the registration and processing of their data (NMDC) and advanced analysis and data integration (KBase).
The National Microbiome Data Collaborative (NMDC) is an integrated microbiome data ecosystem hosting high-quality, consistently processed multi-omics microbiome data to enable data sharing, management, and cross-comparison across studies in accordance with the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. Applicants interested in collaborating with the NMDC team and having their data hosted within the NMDC Data Portal should indicate so in their proposal.
The Department of Energy Systems Biology Knowledgebase (KBase) is a free, open source data analysis platform for system biology research that supports the FAIR data principles, reproducible analysis workflows, and sharing and publishing of data sets and knowledge generated from your analysis. Please explore the analyses supported by KBase, available at www.kbase.us/learn, and reach out to the KBase staff to discuss how they can support your project.
Data Policies:
EMSL: https://www.emsl.pnnl.gov/data-management-policy
JGI: https://jgi.doe.gov/user-programs/pmo-overview/policies/
NEON: https://www.neonscience.org/data-samples/data-policies-citation
Partnering User Facilities
Environmental Molecular Sciences Laboratory
The Environmental Molecular Sciences Laboratory (EMSL) is a Department of Energy, Office of Science, user facility sponsored by the Biological and Environmental Research (BER) program. EMSL seeks to gain a predictive understanding of the molecular and atomic processes that control the continuous changes underpinning biological and ecosystem functions. This means, in support of BER's mission, we advance and integrate the process-level understanding of complex systems across wide temporal and spatial scales by coupling observations, experiments, and theory with modeling and simulation. Proposals submitted to this research call will be supported under the new Terrestrial–Atmospheric Processes Integrated Research Platform.
EMSL Contacts
- General inquiries: EMSL User Program Services, emsl@pnnl.gov, 509-371-6003
- Detailed research questions: Swarup China, swarup.china@pnnl.gov, 509-371-7329
Data resulting from projects awarded under a FICUS call are made available in accordance with each user facility’s data policies.
EMSL Data Management Policy: https://www.emsl.pnnl.gov/data-management-policy
Joint Genome Institute
The mission of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility of Lawrence Berkeley National Laboratory (Berkeley Lab) and part of the Biosciences Area, is to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. Supported by the DOE Office of Science, JGI unites the expertise at Berkeley Lab, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology. Located in the Integrative Genomics Building in the heart of the Berkeley Lab campus, atop the hills above Berkeley, California, the JGI is operated by the University of California for the U.S. Department of Energy. JGI provides integrated high-throughput sequencing, DNA design and synthesis, metabolomics and computational analysis that enable systems-based scientific approaches to these challenges.
JGI Contacts
- General inquiries: Christa Pennacchio, jgi-jira+pmosupport@lbl.gov
- Research questions: Tanja Woyke, TWoyke@lbl.gov, 510-495-8506
National Ecological Observatory Network
The National Science Foundation's National Ecological Observatory Network (NEON) is a continental-scale observation facility operated by Battelle and designed to collect long-term open access ecological data to better understand how U.S. ecosystems are changing. NEON monitors ecosystems across the United States.
NEON Contacts
- Letters of Support information
- Research questions: Michael SanClements, msanclements@battelleecology.org, 720-836-2499
Center for Structural Molecular Biology
The Center for Structural Molecular Biology (CSMB) at Oak Ridge National Laboratory is an open access user program dedicated to advancing instrumentation and methods for determining the three-dimensional structures of biomacromolecules and their assemblies as well as hierarchical structures and biomimetic systems.
CSMB Contacts
- General inquiries: Janell Thomson, thomsonji@ornl.gov, 865-576-2281
- Research questions: Hugh O’Neill, oneillhm@ornl.gov, 865-574-5283
Review criteria
FICUS proposals are reviewed for technical feasibility by scientific staff at each facility. Proposals also undergo external peer review against four scientific criteria. For each criterion, the reviewer rates the proposal Extraordinary, Excellent, Good, Fair, or Poor and provides detailed comments on the quality of the proposal to support each rating, noting specifically the proposal's strengths and weaknesses. The reviewer also provides overall comments and recommendations to support the ratings given. These scores and comments serve as the starting point for Proposal Review Panel (PRP) discussions. The PRP is responsible for the final score and recommendation to the facilities’ managements.
Criterion 1: Scientific merit and quality of the proposed research (25%)
Potential Considerations: How important is the proposed activity to advancing knowledge and understanding within its own field or across different fields? To what extent does the proposed activity suggest and explore creative and original concepts? How well conceived and organized is the proposed activity?
Criterion 2: Qualifications of the proposed research team to achieve proposal goals and contribute to high-impact science (25%)
Potential Considerations: Does the proposal team, combined with relevant EMSL and JGI staff expertise, possess the appropriate breadth of skill/knowledge to successfully perform the proposed research and drive progress in this science area? Proposals will be evaluated on whether scientists with expertise and the necessary skills will be ready to perform follow-up research and publications. If successful, would the proposed research deliver high-impact products (for example, be publishable in high-impact journals)? The size and productivity of the user community will also be considered.
Note: Impact factors are a measure of the average number of citations per published articles. Journals with higher impact factors reflect a higher average of citations per article and are considered more influential within their scientific field.
Criterion 3: Relevance of the proposed research to DOE missions (25%)
EMSL and JGI are managed by the Department of Energy’s Office of Biological and Environmental Research, and both play critical roles in supporting DOE’s energy, environment and basic research missions. They provide integrated experimental and computational data and analysis, as well as high-throughput DNA sequencing, synthesis and analysis in support of BER’s missions in plant/fungal/microbial bioenergy feedstocks, carbon and nutrient cycling, and biogeochemistry.
Potential Considerations: What is the relationship of the proposed research to DOE missions? Does the research project significantly advance the mission goals? Proof of concept proposals for the demonstration of a technology that would be applicable to a DOE mission are acceptable. How well does the project plan represent a unique or innovative demonstration and to what extent does it advance the mission area?
Criterion 4: Appropriateness and reasonableness of the request for resources for the proposed research (25%)
Potential Considerations: Are EMSL and JGI capabilities and resources essential to performing this research? Does the project generate a dataset unique to these facilities and beyond what each could generate by itself? Are the proposed methods/approaches optimal for achieving the scientific objectives of the proposal? Are the requested resources reasonable and appropriate for the proposed research? Does the complexity and/or scope of effort justify the duration of the proposed project? Is the specified work plan practical and achievable within the shortened project timeframe (less than JGI’s CSP projects)?
FICUS proposals are reviewed for technical feasibility by scientific staff at each facility. Proposals also undergo external peer review against four scientific criteria. For each criterion, the reviewer rates the proposal Extraordinary, Excellent, Good, Fair, or Poor and provides detailed comments on the quality of the proposal to support each rating, noting specifically the proposal's strengths and weaknesses. The reviewer also provides overall comments and recommendations to support the ratings given. These scores and comments serve as the starting point for Proposal Review Panel (PRP) discussions. The PRP is responsible for the final score and recommendation to the facilities’ managements.
Criterion 1: Scientific merit and quality of the proposed research (25%)
Potential Considerations: How important is the proposed activity to advancing knowledge and understanding within its own field or across different fields? To what extent does the proposed activity suggest and explore creative and original concepts? How well conceived and organized is the proposed activity?
Criterion 2: Qualifications of the proposed research team to achieve proposal goals and contribute to high-impact science (25%)
Potential Considerations: Does the proposal team, combined with relevant EMSL and JGI staff expertise, possess the appropriate breadth of skill/knowledge to successfully perform the proposed research and drive progress in this science area? Proposals will be evaluated on whether scientists with expertise and the necessary skills will be ready to perform follow-up research and publications. If successful, would the proposed research deliver high-impact products (for example, be publishable in high-impact journals)? The size and productivity of the user community will also be considered.
Note: Impact factors are a measure of the average number of citations per published articles. Journals with higher impact factors reflect a higher average of citations per article and are considered more influential within their scientific field.
Criterion 3: Relevance of the proposed research to DOE missions (25%)
EMSL and JGI are managed by the Department of Energy’s Office of Biological and Environmental Research, and both play critical roles in supporting DOE’s energy, environment and basic research missions. They provide integrated experimental and computational data and analysis, as well as high-throughput DNA sequencing, synthesis and analysis in support of BER’s missions in plant/fungal/microbial bioenergy feedstocks, carbon and nutrient cycling, and biogeochemistry.
Potential Considerations: What is the relationship of the proposed research to DOE missions? Does the research project significantly advance the mission goals? Proof of concept proposals for the demonstration of a technology that would be applicable to a DOE mission are acceptable. How well does the project plan represent a unique or innovative demonstration and to what extent does it advance the mission area?
Criterion 4: Appropriateness and reasonableness of the request for resources for the proposed research (25%)
Potential Considerations: Are EMSL and JGI capabilities and resources essential to performing this research? Does the project generate a dataset unique to these facilities and beyond what each could generate by itself? Are the proposed methods/approaches optimal for achieving the scientific objectives of the proposal? Are the requested resources reasonable and appropriate for the proposed research? Does the complexity and/or scope of effort justify the duration of the proposed project? Is the specified work plan practical and achievable within the shortened project timeframe (less than JGI’s CSP projects)?