DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • 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

Upcoming Events
Home › Past Events › 2016 Microbial and Plant Systems Modulated by Secondary Metabolites Meeting › Agenda

Agenda

Microbial and Plant Systems Modulated by Secondary Metabolites Meeting

Monday, May 2   (Walnut Creek Marriott)

5:00 – 5:10 PM Opening Remarks Host: Susannah Tringe, JGI
5:10 – 6:00 PM Opening key Note: Niche adaptation of the Arabidopsis leaf microbiota Julia Vorholt, ETH Zurich
6:00 – 9:00 PM  Poster Session and Reception

*Refreshments served

Tuesday, May 3   (JGI Room 149A)

9:00 – 10:10 AM Overview of the JGI Capabilities

*Will include morning break & working lunch

Chair: Yasuo Yoshikuni, JGI
9:00 – 9:10 AM Welcome and Introduction

*Morning refreshments served

Susannah Tringe JGI
9:10 – 9:25 AM JGI Synthesis Science Yasuo Yoshikuni, JGI
9:25 – 9:40 AM JGI Synthesis Platform Sam Deutsch, JGI
9:40 – 9:55 AM JGI IMG-ABC Michalis Hadjithomas,  JGI
9:55 – 10:10 AM JGI Metabolomics Trent Northen, JGI
10:10 – 10:30 AM Break
10:30 – 12:05 PM Session I: Science from the JGI User Communities
10:30 – 10:35 AM Introduction Yasuo Yoshikuni, JGI
10:35 – 11:05 AM Investigating Plant Terpene Metabolic Diversity for Pharmaceutical and Agricultural Applications Philipp Zerbe, University of California, Davis
11:05 – 11:35 AM Volatile Metabolites as Chemical Modulators of Plant-Microbe Interactions Dorothea Tholl, Virginia Tech University
11:35 – 12:05 PM Assessing the Role of Biotic and Abiotic Interactions in Determining the Community Composition of the Root Microbiome Omri Finkel, University of North Carolina, Chapel Hill
12:05 – 1:05 PM  Group Discussion and Picture

*Working lunch served

 1:05 – 2:40 PM  Session II
 1:05 – 1:10 PM  Introduction  Sam Deutsch, JGI
 1:10 – 1:40 PM  Chemical Discovery in the Microbial World  Emily Balskus, Harvard
 1:40 – 2:10 PM  Biosynthetic Gene Clusters: Nature’s Gift to Discovery and Application  Bradley Moore, Scripps Institution of Oceanography
 2:10 – 2:40 PM  Metabolic Regulation of Community Behavior in Pseudomonas aeruginosa  Lars Dietrich, Columbia University
 2:40 – 3:00 PM  Break
 3:00 – 5:00 PM Panel Discussion  Kellye Eversole, Phytobiome Initiative
Randy Verka, Novozymes
Daniel Van der Lelie, FMC
Steve Evans, Dow AgroScience
Dilara Ally, Bayer CropScience
Rich Broglie, DuPont Pioneer

Wednesday, May 4   (JGI Room 149A)

9:10 – 10:45 AM Session III 

*Will include morning break & working lunch

*Morning refreshments served

 9:10 – 9:15 AM Introduction Elizabeth Sattely, Stanford University
 9:15 – 9:45 AM Specialized Cell Types and the Rise of Chemical Diversity in Plants Mark Lange, Washington State University
 9:45 – 10:15 AM Integrated Metabolomics for Triterpenoid Gene Discovery in the Model Legume Medicago truncatula Lloyd Sumner, University of Missouri
 10:15 – 10:45 AM Botanicals and Experimental Pharmacology in the Post-Genomic Era: New Directions Larry Walker, University of Mississippi National Center for Natural Products Research University
 10:45 – 11:05 AM Break
11:05 – 12:40 PM Session IV
11:05 – 11:10 AM Introduction: Secondary Metabolites–Chemical Warfare in Plant-Pathogen-Antagonist Interactions David Weller
 11:10 – 11:40 AM Rhizosphere Diversity of Fluorescent Pseudomonads and Cyclic Lipopeptides Correlates with Cocoyam (Xanthosoma sagittifolium) Resilience to the Pythium Root Rot Disease Monica Höfte, Ghent University
 11:40 – 12:10 PM Crossfire: Diterpenoids in the Chemical Warfare Between Rice and a Bacterial Pathogen Reuben Peters, Iowa State University
 12:10 – 12:40 PM Secondary Metabolites Have Primary Roles in the Lifestyle of the Soil Bacterium Pseudomonas protegens Joyce Loper, USDA-ARS, Oregon State University
12:40 – 1:40 PM Group Discussion and Facility Tour

*Working lunch served

 1:40 – 3:15 PM Session V: Parts, Pathways and Performance: Discovery and Deployment of Plant Specialized Metabolic Pathways 
 1:40 – 1:45 PM Introduction: Parts, Pathways and Performance–Discovery and Deployment of Plant Specialize Metabolic Pathways Peter Facchini, University of Calgary
 1:45 – 2:15 PM Harnessing Plant Metabolic Diversity Anne Osbourn, John Innes Centre, UK
 2:15 – 2:45 PM How Do Plants Mediate Crosstalk Between Biochemical Pathways? Clint Chapple, Purdue University
 2:45 – 3:15 PM Gene Centric Discovery of Plant Metabolic Pathways Elizabeth Sattely, Stanford University
 3:15 – 3:30 PM Break
 3:30 – 4:55 PM Session VI
 3:30 – 3:35 PM Introduction Eoin Brodie, LBNL
 3:35 – 4:05 PM Exploiting the Role of Secondary Metabolites in Plant-Microbe Interactions for Biotechnology Gabriele Berg, Graz University of Technology
 4:05 – 4:55 PM  Closing key note: TBD  Jos Raaijmakers, NIOO Wageningen
 4:55 – 5:00 PM  Closing Remarks  Axel Visel, JGI

** Note: AM and PM refreshments will be served after the meeting begins, while work is being performed. Attendance is required during these times.

  • 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