DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

    More

    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

    More

    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

    More

    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

    More

    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

    More

    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

    More

    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

    More

    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

    More

    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

    More

    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

    More

News & Publications
Home › Blog › Advancing Awareness of User Science

July 9, 2018

Advancing Awareness of User Science

Berkeley Lab User Facilities Prominent in SSURF Annual Meeting & Capitol Hill Office Visits.

SSURF 2018 attendees

2018 SSURF Annual Meeting attendees.

Like roads, water and energy systems, ports, and other critical infrastructure, scientific user facilities enable the innovation at the heart of U.S. economic competitiveness and national security. The Society for Science at User Research Facilities (SSURF) is a not-for-profit organization working to advance awareness of user science. Under the umbrella of “America’s Evolving Scientific Infrastructure,” SSURF convened its 2018 Annual Meeting at the American Center for Physics, University of Maryland, College Park, June 26-28, 2018.

Paul Runci, Senior Policy Advisor with Pacific Northwest National Laboratory and Chair of the SSURF Board of Directors, kicked off the meeting, which was attended by 65 participants, many of whom represented 25 user facilities that are SSURF members thus far. Individual memberships are welcome as well. The agenda focused on opportunities to build a coherent network of user facilities, users, and supporting agencies, identify relevant metrics and mechanisms such as digital object identifiers (DOIs) to track impact, and ORCID unique identifiers to track users, and effective ways to capture the success stories of the users and facilities and convey them to stakeholders.

Brian Landes, Technology Leader, Dow Chemical (left) and PNNL’s Paul Runci, Chair of the SSURF Board of Directors.

Brian Landes, Technology Leader, Dow Chemical (left) and PNNL’s Paul Runci, Chair of the SSURF Board of Directors.

Representatives from Berkeley Lab’s five user facilities were in attendance: Susan Bailey and Andrea Jones of the Advanced Light Source (ALS); Lauren Rotman of the Energy Sciences Network (ESnet); Nigel Mouncey and David Gilbert of the Joint Genome Institute (JGI); Alison Hatt of The Molecular Foundry; and, Richard Gerber and David Skinner of the National Energy Research Scientific Computing Center (NERSC). Also present was Francesca Toma of the Joint Center for Artificial Photosynthesis (JCAP).

JGI Director Nigel Mouncey presented,“How Facilities Can Partner with Industry to Strengthen the Scientific Infrastructure.” Alison Hatt, who also serves on the SSURF Board of Directors, moderated a session entitled, “Engaging User Groups to Enhance Facility Ties and Communication.”

ASCR’s Laura Biven, with BES’s George Maracas and BER’s Dan Drell and Paul Bayer, describe how their programs and the facilities they manage have responded to the shifting landscape of how science is performed.

ASCR’s Laura Biven, with BES’s George Maracas and BER’s Dan Drell and Paul Bayer, describe how their programs and the facilities they manage have responded to the shifting landscape of how science is performed.

Laura Biven of the Advanced Scientific Computing Research (ASCR) program convened a panel that included JGI’s Program Manager Daniel Drell and the Environmental Molecular Sciences Laboratory (EMSL) Program Manager, Paul Bayer, from the DOE Office of Biological and Environmental Research, and George Maracas of the Office of Basic Energy Sciences, who oversees the Nanoscale Science Research Centers. The panelists contributed their observations about the shifting landscape of how science is performed and how their programs and the facilities they manage have responded.

On Thursday, June 28, after several dry runs with feedback provided by Capitol Hill frequenters, selected participants took their stories to Congress with the goal of raising awareness of the enabling role that national user facilities play in support of the nation’s research infrastructure. Don Medley, Berkeley Lab Head of Government and Community Relations, coordinated the visit and led one of the groups which included JGI’s Nigel Mouncey, JCAP’s Francesca Toma, Jen Bohon of Case Western University (a user of the National Synchrotron Light Source II at Brookhaven National Laboratory), and Nicholas Schwarz of the Advanced Photon Source at Argonne National Laboratory.

Left to right: SSURF Congressional office visits Team 3 consisted of APS’ Nicholas Schwarz, JCAP’s Francesca Toma, Case Western University’s Jen Bohon, and JGI’s Nigel Mouncey.

Left to right: SSURF Congressional office visits Team 3 consisted of APS’ Nicholas Schwarz, JCAP’s Francesca Toma, Case Western University’s Jen Bohon, and JGI’s Nigel Mouncey.

The team made a whirlwind tour of Congressional offices, visiting with Senator Mike Rounds (R-SD) and Representative Gary Palmer (R-AL) and with staffers from the offices of Senator John Kennedy (R-LA), Senator Joni Ernst (R-IA), Senator Kamala Harris (D-CA), Representative Bob Gibbs (R-OH), and Representative Marcia Fudge (D-OH).

JGI’s Nigel Mouncey reflected on his first foray into the halls of Congress remarking, “it’s both humbling and energizing to meet with those responsible for setting science policy and funding directions for the nation and representing districts where JGI’s users make a tangible impact. It’s a bit of a challenge to summarize what may amount to be a collaborator’s life work in non-technical language and tell a compelling story that can resonate with a Senator, Representative, or staffer in less than two minutes. But what an amazing opportunity to speak to the value of the National Laboratories and User Facilities in driving the nation’s innovations and how we enable groundbreaking science.”

Berkeley Lab Head of Government and Community Relations Don Medley (left) led Team 3 on the Congressional office visits.

Berkeley Lab Head of Government and Community Relations Don Medley (left) led Team 3 on the Congressional office visits.

JGI Director Nigel Mouncey describes the “Facilities Integrating Collaborations for User Science” (FICUS) initiative that enables access to multiple user facilities with one proposal.

JGI Director Nigel Mouncey describes the “Facilities Integrating Collaborations for User Science” (FICUS) initiative that enables access to multiple user facilities with one proposal.

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

Filed Under: Blog

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

JGI at 25: Mapping Switchgrass Traits with Common Gardens

Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)

JGI at 25: Following Fungi that Pry Apart Plant Polymers

A brown goat with white horns looks at green hay

Exploring Possibilities: 2022 JGI-UC Merced Interns

2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)

JGI at 25: Using team science to build communities around data

JGI at 25: Expanding Metagenomics to Capture Viral Diversity

Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California