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

All JGI Features
Home › Archives for Leila Hornick
Page 1 of 6412345...102030...»Last »

August 27, 2021

New JGI Data Policy Announcement

Read our JGI Data Policy [Read More]

July 9, 2015

Matthew Sullivan, The Ohio State University

Matthew Sullivan, The Ohio State UniversityDepartments of Microbiology, and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH Collaborated with JGI since 2001 How long have you collaborated with the JGI and on which projects? Since 2009 as head of my own lab, and since 2001 as a PhD student (with Penny Chisholm at MIT) working on the initial marine Prochlorococcus and… [Read More]

May 14, 2015

Jillian Banfield, University of California, Berkeley

Jillian Banfield, PhD is a prominent geomicrobiologist and biochemist, a UC Berkeley Professor, a Berkeley Lab Earth Sciences Division staff scientist, and a long time user of the DOE Joint Genome Institute’s resources through the Community Science Program (CSP) and the Emerging Technologies Opportunities Program (ETOP). In this short interview, Jill shares her perspective how… [Read More]

November 20, 2014

NCBI Genomes Reprocessed using IMG’s Annotation Pipelines and Distributed via JGI’s Genome Portals

The Integrated Microbial Genomes (IMG) system provides tools for analyzing the structural and functional annotations of metagenomes and single genomes in a comparative context. At the core of the IMG system is a data warehouse that contains genome and metagenome datasets (sets of genome sequence fragments from microbial communities) sequenced at the DOE Joint Genome… [Read More]

August 12, 2014

Fungal Response to Global Change

Fungi play a key role in global warming because they bioconvert most of the plant-produced carbon sequestered in soil. Models of global change that incorporate biological feedback hinge on whether fungi will show enhanced bioconversion of recalcitrant carbon as temperatures rise. The first part of this project deals with learning more about fungi that have… [Read More]

April 28, 2014

Steven Hallam, University of British Columbia

Steven HallamCIFAR Scholar and Associate Professor, University of British Columbia Department of Microbiology & Immunology, Life Sciences Institute I have collaborated with the JGI since 2002 before the CSP program came online. These collaborations have spanned my postdoctoral years with Ed DeLong [now at the University of Hawai’i, Mānoa] and my time as an independent investigator at the University… [Read More]

April 22, 2014

Every Day is Earth Day @JGI

Earth Day at JGIMore than four decades ago, the first celebration of Earth Day raised the idea of protecting the environment to a greater public awareness. Today, the annual event is a reminder of the longstanding goal to provide a cleaner, healthier and sustainable environment for everyone to live in. Here at the U.S. Department of Energy Joint… [Read More]

April 10, 2014

The Genomics of Energy & Environment – in Poetry

In honor of National Poetry Month, we’re celebrating an underutilized method of communicating our science: poetry. According to Merriam-Webster, poetry is defined as, “writing that formulates a concentrated imaginative awareness of experience in language chosen and arranged to create a specific emotional response through meaning, sound, and rhythm.” As proof that science can (and has)… [Read More]

April 7, 2014

Sponges that sponge off bacteria

Medical compounds harvested from a marine sponge are actually produced by symbiotic bacteria living in the sponges. The Science: The research team used single-cell genome analysis, and metagenomic sequencing to find that just two bacterial tenants of a marine sponge, Theonella swinhoei, make medically important compounds called polyketides. Both bacteria belong an uncultivated genus, Enthotheonella. The research… [Read More]

March 10, 2014

A Tale of Two Data Sets: New DNA Analysis Strategy Helps Researchers Cut through the Dirt

The sampling site located at the A.C. and Lela Morris Prairie Reserve, located in Jasper County Iowa. (Jim Tiedje)For soil microbiology, it is the best of times. While no one has undertaken an accurate census, a spoonful of soil holds hundreds of billions of microbial cells, encompassing thousands of species. “It’s one of the most diverse microbial habitats on Earth, yet we know surprisingly little about the identities and functions of the microbes… [Read More]
Page 1 of 6412345...102030...»Last »

More topics:

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