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    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.

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    (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.

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    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.

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    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.

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    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.

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    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.

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    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.”

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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News & Publications
Home › News Releases
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October 8, 2020

2021 JGI Proposal Call Brings New Investigators into Community Science Program

Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)For the first time, 63 percent of the 27 accepted annual large-scale CSP proposals come from investigators who have not previously been a principal investigator on an approved JGI proposal. [Read More]

October 5, 2020

Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet

Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)For the first time in wild populations, researchers have identified a gene in green millet related seed dispersal. [Read More]

August 25, 2020

The More the Merrier: Making the Case for Plant Pan-genomes

Brachypodium distachyon, the model species for temperate cereals and biofuel crop grasses with a growing pangenome of one hundred genomes. Spain: Huesca, Ibieca, San Miguel de Foces. (Photography credits: Pilar Catalán)Researchers relied on a model grass system and pan-genomes to learn the origins, evolution and development of plant polyploids. [Read More]

April 20, 2020

Picking Up Threads of Cotton Genomics

cotton boll G. hirsutum (Cotton Inc)In Nature Genetics, a multi-institutional team has sequenced and assembled the genomes of the major cotton lineages. [Read More]

January 22, 2020

Here, There and Everywhere: Large and Giant Viruses Abound Globally

Art illustration capturing giant virus genomic diversity. (Zosia Rostomian/Berkeley Lab)JGI-led team significantly expands the global diversity of large and giant viruses. While the microbes in a single drop of water could outnumber a small city’s population, the number of viruses in the same drop—the vast majority not harmful to humans could be even larger. Viruses infect bacteria, archaea and eukaryotes, and they range in… [Read More]

January 21, 2020

Inspiring STEM Careers Through a Hands-on Everglades Microbiome Study

Students in the 2018 Boca Raton Community High School A-Level Advanced International Certificate of Education (AICE) Biology class collected samples from the Arthur R. Marshall Loxahatchee National Wildlife Refuge for the pilot project between the class and the JGI. (Image courtesy of Jon Benskin)Journal publication caps JGI pilot project with fledgling Florida high school scientists. The Florida Everglades evokes images of fanboats skimming over swamps, while alligators peer through the waters and clouds of insects hover just above. Described as a “river of grass” that stretches some 580,000 square miles across southern Florida, they encompass a wide range… [Read More]

October 1, 2019

Characterizing Communities: JGI Announces Latest CSP Portfolio

Proposals aim to sequence and annotate genomes from Antarctica to Africa to global oceans. Through the Community Science Program of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility, 24 large-scale proposals have been accepted from 70 full submissions based on 92 letters of intent. Additionally, 40… [Read More]

September 10, 2019

What Happens Underground Influences Global Nutrient Cycles

DOE user facilities EMSL and JGI announce FY 2020 collaborative FICUS projects. Through the Facilities Integrating Collaborations for User Science (FICUS) program, two Department of Energy (DOE) Office of Science national user facilities—the Environmental Molecular Sciences Laboratory (EMSL) and the DOE Joint Genome Institute (JGI)—have selected 11 proposals for support from 53 received through a… [Read More]

July 22, 2019

Learning to Look

Machine learning approach significantly expands inovirus diversity. To answer the question, “Where’s Waldo?” readers need to look for a number of distinguishing features. Several characters may be spotted with a striped scarf, striped hat, round-rimmed glasses, or a cane, but only Waldo will have all of these features. As described July 22, 2019, in Nature… [Read More]

December 17, 2018

Defining Quality Virus Data(sets)

Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)International consortium offers guidelines, best practices for characterizing uncultivated viruses. Microbes in, on and around the planet are said to outnumber the stars in the Milky Way Galaxy. The total number of viruses is expected to vastly exceed even that calculation. While many viruses remain unknown and uncultivated, advances in genome sequencing and analyses have… [Read More]
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