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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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All JGI Features
Home › Items tagged with: USDA-ARS

Content Tagged "USDA-ARS"

Page 1 of 212»

September 15, 2010

HudsonAlpha involved in cacao genome project

A first draft of the cacao genome is complete, a consortium of academic, governmental, and industry scientists announced today. Indiana University Bloomington scientists performed much of the sequencing work, which is described and detailed at http://www.cacaogenomedb.org/, the official website of the Cacao Genome Database project. Despite being led and funded by a private company, Mars… [Read More]

March 4, 2010

Soybean project in GenomeWeb literature reference

A large team comprised of researchers from Purdue University, the US Department of Energy’s Joint Genome Institute, and the US Department of Agriculture’s Agricultural Research Service used whole-genome shotgun sequencing to sequence roughly 85 percent of the 1.1-gigabase soybean, Glycine max, genome. The paper describes how the team integrated the shotgun approach with physical and… [Read More]

February 25, 2010

Brachypodium genome project collaborator Oregon State’s release

“What this work provides is a highly informative roadmap to explore and improve plants of great agricultural value, like wheat,” said James Carrington, director of the Center for Genome Research and Biocomputing, and a co-author of the study. “The quality of science that can be done with plants like Brachypodium is really exceptional.” Read more… [Read More]

February 25, 2010

Brachypodium project in Biofuels Digest

In Washington, researchers at the USDA and the Joint Genome Institute today announced that they have completed sequencing the genome of Brachypodium distachyon, similar to switchgrass – as a model organism that is similar to but easier to grow and study than important agricultural crops, used by plant scientists the way other researchers use lab… [Read More]

February 24, 2010

Brachypodium genome project on CORDIS

Some grass species play a pivotal role in meeting our food supply needs. We have also seen a surge in the domestication of new grass crops for feedstock production and sustainable energy. Experts say, however, that failure to understand how genes work and a lack of knowledge about their large and complex genomes lead to… [Read More]

February 23, 2010

Brachypodium project on Huffington Post

In a study published Feb. 11 in the journal Nature, researchers from the department’s Joint Genome Institute in Walnut Creek, which is managed in part by Lawrence Berkeley National Laboratory, sequenced a form of wild grass in order to derive a genome specifically adapted for biomass and biofuel production. Read more at The Huffington Post.  [Read More]

February 19, 2010

Brachy genome project on ScienceCentric

Brachypodium is actually a wild annual grass plant, native to the Mediterranean and Middle East, with little agricultural importance and is of no major economic value itself. But it allows researchers to obtain genetic information for grasses much more easily than some of its related, but larger and more complex counterparts with much larger genomes… [Read More]

February 19, 2010

Brachy genome project on Daily Cal

In a study published Feb. 11 in the journal Nature, researchers from the department’s Joint Genome Institute in Walnut Creek, which is managed in part by Lawrence Berkeley National Laboratory, sequenced a form of wild grass in order to derive a genome specifically adapted for biomass and biofuel production.  Researchers would then be able to… [Read More]

February 19, 2010

Brachy genome project on OfficialWire

A British- and U.S.-led international consortium says it has sequenced the first member of the wheat and barley group of grasses. The scientists, led by Britain’s John Innes Center, the U.S. Department of Energy’s Joint Genome Institute, the U.S. Department of Agriculture and Oregon State University, said the genome sequencing was of the wild grass… [Read More]

February 19, 2010

Brachy project on USDA-ARS news site

A major stumbling block in using switchgrass or any perennial grass as a biofuel crop is the difficulty in breaking down its cell walls, an essential step in producing ethanol from cellulosic biomass. Brachypodium may hold the key to finding ways to produce plant cell walls that are easy to break down, Vogel said. Vogel… [Read More]
Page 1 of 212»

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