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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
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April 11, 2011

Brown mercury-producing bacterium in Medical News Today

“What is not known are the genes or the proteins that allow these bacteria to mediate the transformation,” said ORNL’s Steven Brown, who led a research team to sequence the genome of a bacterium in the Desulfovibrio genus that is capable of methylating mercury. The new genome, sequenced at the California-based DOE Joint Genome Institute… [Read More]

April 10, 2011

Brown mercury-producing bacterium in ScienceDaily

Desulfovibrio desulfuricans strain ND132 is an organism that thrives in sediments and soils without oxygen — the places in lakes, streams and wetlands where mercury contamination is converted to methylmercury. It is representative of a group of organisms that “breathe” sulfate instead of oxygen and are largely responsible for mercury methylation in nature. “This is… [Read More]

April 8, 2011

ORNL collaboration to understand methylmercury production

Mercury pollution in aquatic environments has been a concern, though the contaminants are mainly sourced from industrial processes and fossil fuel combustion. Isolated from Chesapeake Bay sediment, the sulfate-reducing bacterium, Desulfovibriodesulfuricansstrain ND132, can also produce the human neurotoxin methylmercury. “What is not known are the genes or the proteins that allow these bacteria to mediate… [Read More]

April 7, 2011

Cheryl Kerfeld presents ASBMB award lecture

Cheryl A. Kerfeld, a structural biologist and the head of the U.S. Department of Energy Joint Genome Institute’s Education and Structural Genomics Programs, has won the American Society for Biochemistry and Molecular Biology’s Award for Exemplary Contributions to Education. Kerfeld will present her award lecture, titled “Sequence and Consequence,” at 12:30 p.m. on April 10… [Read More]

April 7, 2011

DOE JGI’s Cheryl Kerfeld among 2011 ASBMB awardees in Washington DC

Cheryl A. Kerfeld, a structural biologist and the head of the Department of Energy Joint Genome Institute’s Education and Structural Genomics Program, won the ASBMB Award for Exemplary Contributions to Education. Kerfeld, who also serves as an adjunct professor at the University of California, Berkeley, was named the winner for encouraging effective teaching and learning… [Read More]

March 28, 2011

Fungal Genomics blog re DOE JGI User Meeting

Personally, my favorite talk at the last 6th Annual DOE JGI Users Meeting at Walnut Creek was Rob Knight‘s contribution on ‘Spatially and Temporally Resolved Studies of the Human Microbiome‘. Rob was creative and integrative. Displaying the biogeography of bacterial communities on the human body using UniFrac and QUIME was astounding. Read more at the… [Read More]

March 26, 2011

Eisen blogs Twitter wrap-up of the DOE JGI User Meeting

Off to another meeting so don’t have time to write up details of the JGI User Meeting that just ended.  But I am posting my tweets and some related tweets here.  Also, apparently videos of the talks will be available soon. Will try to clean up the style of the posts ASAP but on the… [Read More]

March 25, 2011

Finding cellulases in sediment from a paper mill

During the DOE JGI User Meeting held in Walnut Creek, Calif. from March 22-24, 2011, collaborator Daniel Distel noted that more than 20 enzymes are needed to break down cellulose. To assist in identifying novel cellulose degraders and thus improve cellulosic biofuel production processes, a team of DOE JGI researchers including Microbial Program head TanjaWoyke… [Read More]

March 25, 2011

Tasmanian devils at DOE JGI User Meeting in GenomeWeb

As part of the large-scale conservation effort he calls “Project Ark,” Schuster and his team intend to genotype hundreds of Tasmanian devils, he told attendees of the sixth annual Department of Energy Joint Genome Institute User Meeting held in Walnut Creek, Calif., this week. To date, he said, devil tumor facial disease does not seem… [Read More]

March 24, 2011

Alfred University selected for DOE JGI Undergraduate Research Program in Microbial Genome Annotation

Alfred University is one of only 21 institutions in the country to be selected for the federal Joint Genome Institution (JGI) Undergraduate Research Program in Microbial Genome Collaboration. What that means, explains Jean Cardinale, professor of biology in the College of Liberal Arts & Sciences, is Alfred University students will have a unique opportunity to… [Read More]
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