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Genomic Science Program

User Facilities Enabling Science

DOE Environmental Molecular Sciences Laboratory

EMSL Campus
Cyanothece sp. PCC 7822, a marine unicelluar cyanobacterium, imaged with a helium ion microscope located in EMSL’s Quiet Wing (image colorized). This and other Cyanothece strains perform photosynthesis during the day and nitrogen fixation at night and are metabolically diverse. The image is part of an EMSL user project characterizing the cellular response network that governs bioenergy production and cell morphology of cyanobacteria under different environmental conditions. Louis Sherman, Purdue University, is the principal investigator, and Himadri Pakrasi, Washington University, is co-investigator. The cells were grown and prepared by David Welkie, a graduate student in Sherman’s laboratory.

The mission of the Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy (DOE) scientific user facility, is to lead molecular-level discoveries for DOE and its Office of Biological and Environmental Research (BER) that translate to predictive understanding and accelerated solutions for national energy and environmental challenges.

EMSL’s unique and state-of-the-art capabilities and staff expertise can help scientists gain a predictive understanding of the molecular-to-mesoscale processes in biological, climate, environmental, and energy systems. EMSL offers scientists access to more than 60 major experimental and computational systems, including many one-of-a-kind analytical instruments for studying atomic to molecular to larger-scale processes, and a supercomputing management and storage platform with associated molecular and network modeling capacities. In-house scientists collaborate with users to generate high-quality and timely results. By co-locating capabilities and expertise, EMSL is ideal for research teams interested in integrating theory with experiment and for individual investigators conducting studies using multiple techniques.

Biosystem Dynamics and Design Science Theme

Within EMSL, its Biosystem Dynamics and Design (BDD) Science Theme focuses on dynamic processes in archaea, bacteria, and eukaryotes such as algae, fungi, and plants. EMSL users can generate a variety of data to integrate into metabolic flux/bioinformatics/molecular dynamics/other types of models, and improve strategies for exploring and modifying plants, fungi, and microbes to discover and better understand biological processes and advance systems biology for biofuel and bio-based products.

Transformational Capabilities

Capabilities available to advance your genomic science research include:

Microscopy and In Situ Dynamic Imaging

Super resolution fluorescence microscopy: Stochastic optical reconstruction microscopy (STORM) and structured illumination microscopy (SIM) enable imaging of intact hydrated cells and cell communities or tissues with nanometer resolution to achieve unprecedented insights to subcellular structures and molecular patterns, as well as interactions and processes within cell communities.

Multi-photon fluorescence microscope: Seamlessly integrates nonlinear two-photon excitation, laser scanning confocal microscopy, and fluorescence lifetime imaging for minimally invasive and deep-penetrating laser excitation, enabling 3D imaging of living cells and tissues as well as quantitative investigation of molecular interaction dynamics using fluorescence resonance energy transfer (FRET).

Biomolecular mass spectrometry imaging systems: Effectively identifies and characterizes a diverse range of biomolecules and the spatial distribution of these biomolecules in complex systems.

Cryogenic transmission electron microscopes: The 120kV cryoTEM supports imaging and 3D tomographic reconstruction of biological samples for morphological and immunocytochemistry studies. The 300kV liquid helium cryoTEM provides a platform for low-damage imaging of proteins and supramolecular complexes with 2 Å level spatial resolution.

Helium ion microscope: A cutting-edge instrument not available at any other user facility for large depth-of-field, surface sensitive imaging of uncoated cells and biological networks with extremely high spatial resolution (down to 0.35 nm).

Aberration corrected transmission electron microscopes: The capabilities of the environmental TEM and scanning/TEM permit high-resolution imaging of biological samples. Combined with liquid stages, these systems enable in situ dynamic imaging of molecular-level biological processes.

Single Cell and Organelle Analysis and Transcriptomics

The Influx™ flowcytometer cell sorter, and a high-resolution laser capture microdissection microscope enable the isolation of distinct cell populations or single cells from complex microbial communities and single cells or organelles from plant and animal tissues for further analyses.

Chinook Supercomputer
EMSL scientist Shuttha Shutthanandan studies biological transformations with the helium ion microscope, known for its high-resolution imaging of native microstructures and chemical analysis suing its sub-nanometer probe. This microscope is located in EMSL’s Quiet Wing, a unique research environment housing a suite of ultrasensitive microscopy and scanning instruments.

Next-generation RNA sequencing (RNA-Seq) is achieved using the SOLiD® 5500 series sequencing systems together with the Ion Proton™ system for massively parallel unbiased sequencing to enable metatranscriptome analysis of complex microbial communities, including plant rhizopheric and phyllospheric microbiomes, whole transcriptome and novel transcript identification, as well as RNA-Seq of single eukaryotic cells.

Protein and Metabolite Profiling and Analysis

High-field Fourier transform ion cyclotron resonance mass spectrometry: 15 Tesla FT-ICR MS offers the highest mass resolving power and mass accuracy available on any commercial mass spectrometer, is a key technology for analyzing intact proteins (top-down mass spectrometry), and offers higher specificity for identifying metabolites and peptides from very complex mixtures (e.g., microbial communities and plant cells) in a high-throughput fashion.

Advanced mass spectrometry capability: Orbitrap Velos ETD/H-ESI combines three different and complementary fragmentation techniques and represents the most comprehensive solution for analysis of post-translationally modified peptides and metabolites and for quantitative proteomics measurements.

Ion mobility spectrometry-mass spectrometry proteomics system: A next-generation proteomics platform that combines liquid chromatography, IMS, and time-of-flight MS for increased throughput and sensitivity for systems biology research.

Metallomics mass spectrometry capability: Combines ICP and ESI ionization with independent TOF-MS detection channels for the study of metals and their interactions and transformations in biological and environmental systems.

600 MHz Metabolomics System for metabolomics characterization: For high resolution, high sensitivity studies of complex biofluids by a combination of 1- and 2D methods, EMSL features a 600-MHz NMR platform with an HCN cold probe and cold carbon preamplifier, allowing direct detection of 13C, and a robot for high-throughput studies.

Solids 850-MHz WB NMR system: The first of its kind in North America, this system is dedicated to solid-state NMR and is applicable to biosolids and biosolids/surface interactions allowing the highest resolution of complex biological systems in the solid state. The atomic-level resolution of structure and dynamics of biomolecules translates to system function and emergent properties.

High-field EPR (95-GHz) system: One of only three systems of its kind with high-power capability worldwide, this system is designed not only for high field but high power (1 kW vs. 70-400 mW), sharply reducing acquisition time. The high pulsed power enables structure determination of biomolecules that cannot be accomplished by traditional methods. This includes the overall 3D macromolecular structure as well as atomic-scale structure of the active sites of proteins and catalysts.


To create controlled fluidic microenvironments for bioenergy and carbon cycling research, such as investigating cellulose breakdown using microbial communities; integrated bioanalytical microfluidic devices to combine sample handling, separation, and detection of biomolecules, as well as analysis of single cells.

High-Performance Computing

EMSL is home to a 3.4 petaflop supercomputer, called Cascade, that is specially designed for studies in biology, climate research, chemistry, and materials science.

Protein Dynamics, Single-Molecule Disection of Complex Systems, and Plant Phenotyping

EMSL and BER are investing in the development of two new instruments that will enable researchers to advance their understanding of biosystems and their design. They include:

  • Dynamic transmission electron microscope: With its pulsed electron source, this instrument will provide unprecedented in situ imaging of the structural dynamics of proteins with submolecular detail on the nsec to μsec time scale. Upon development, this capability will enable milestone advancements in our understanding of dynamic biological processes, such as enzymatic reactions, cell-signaling protein-protein interactions, and interfacial electron transfer processes.
  • High-resolution FTICR mass spectrometry system: Next-generation FTICR mass spectrometry will provide unequivocal abilities to discern and identify molecular species in complex systems. Will enable previously intractable sample types and difficult scientific problems to be resolved, such as application to microbial and plant proteomics and metabolomics, atmospheric aerosol analysis, imaging, and natural organic matter and biofuel characterization.
  • Plant phenotyping: To permit EMSL users and staff to leverage existing omics and imaging capabilities in exploring and exploiting the vast resources available in plant genomics databases, EMSL is currently considering options for a plant phenotyping pipeline for high-throughput, noninvasive screening of plant germplasm.

Accessing EMSL Capabilities

To provide a scientific focus for user research and to match appropriate EMSL resources and scientific expertise, EMSL categorizes most user research within four science themes:

Researchers may submit a general proposal to use EMSL capabilities through the EMSL website at any time. DOE’s EMSL supports both open and proprietary research proposals, all of which are externally peer reviewed. In addition to general proposals, EMSL issues an annual Science Theme call and periodic calls for specific types of proposals.

More than half of EMSL’s 700 annual users are from academia; the rest are from DOE national laboratories, other federally sponsored labs, and industry.

Visiting Scientist Program and Fellowships

DOE’s EMSL seeks to attract new, highly qualified users and honor their major contributions through fellowships and awards:

For more information about EMSL, contact:

Paul Bayer
Climate and Environmental Sciences Division
U.S. Department of Energy Office of Science


Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment [9/17]

Advanced Technologies for Biology brochure

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DOE JGI Strategic Planning for the Genomic Sciences [8/12]

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Applications of New DOE National User Facilities in Biology report