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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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September 22, 2017

Daily Cycles of Microbial Decomposition

Marine and freshwater microbial communities and activities vary over the course of the day. In contrast, researchers know little about whether these same patterns exist on land. The team aims to profile the activity of surface soil microbes (those on dead leaf litter) of an arid ecosystem over the course of three days. The leaf… [Read More]

September 22, 2017

Microbes That Impact the Soil Carbon Cycle

This project will identify and characterize the dominant uncultivated microorganisms that mediate major transformations in the soil carbon cycle. The genetic capacity of microbial communities can be studied through genomic approaches but it remains difficult to make direct links between the genetic capacity of microorganisms and their function in the soil carbon cycle. Proposer: Dan… [Read More]

September 22, 2017

River Microbes and the Carbon Cycle

River microbes play a key role in transforming and metabolizing dissolved organic matter (DOM) and thus have an important impact on global carbon cycles. However, scientists’ understanding of the relationship between the chemical composition of DOM and the genomic functional activity of microbial communities remains limited. Here, researchers aim to produce an extensive metagenomic and… [Read More]

September 22, 2017

Meet a JGI Postdoc: Estelle Schaefer

Estelle Schaefer is a postdoc in John Vogel's Plant Functional Genomics groupFrom September 18-22, 2017, we introduce you to 5 postdocs at the JGI in honor of National Postdoc Appreciation Week, which recognizes the contributions of these early career researchers. Through a series of hard-hitting questions, we find out what drives each one.   What do you work on? Plant and microbe interactions. I’m setting up… [Read More]

September 21, 2017

Meet a JGI Postdoc: Adam Session

From September 18-22, 2017, we introduce you to 5 postdocs at the JGI in honor of National Postdoc Appreciation Week, which recognizes the contributions of these early career researchers. Through a series of hard-hitting questions, we find out what drives each one.   What do you work on? I work in the Eukaryote Super Program… [Read More]

September 20, 2017

Meet a JGI Postdoc: Kateryna Zhalnina

From September 18-22, 2017, we introduce you to 5 postdocs at the JGI in honor of National Postdoc Appreciation Week, which recognizes the contributions of these early career researchers. Through a series of hard-hitting questions, we find out what drives each one.   What do you work on? I study how plants use their exudation… [Read More]

September 19, 2017

Meet a JGI Postdoc: Hiroshi Otani

Hiroshi Otani, postdoc in Sam Deutsch's Synthetic Biology groupFrom September 18-22, 2017, we introduce you to 5 postdocs at the JGI in honor of National Postdoc Appreciation Week, which recognizes the contributions of these early career researchers. Through a series of hard-hitting questions, we find out what drives each one.   What do you work on? The products of microbial metabolism have biotechnological… [Read More]

September 18, 2017

Meet a JGI Postdoc: Jess Jarett

Jess Jarett, postdoc with Tanja Woyke in Single Cell MethodsFrom September 18-22, 2017, we introduce you to 5 postdocs at the JGI in honor of National Postdoc Appreciation Week, which recognizes the contributions of these early career researchers. Through a series of hard-hitting questions, we find out what drives each one.   What do you work on? I work on the Microbial Dark Matter… [Read More]

September 13, 2017

National Microbiome Data Collaborative Now on Trellis

NMDC workshop at JGI in February 2017“At the dawn of the third decade of microbial genomics, and well into the information age, the establishment of a national microbiome data center can pave the way to understanding the Earth’s microbiome.” –Nikos Kyrpides Following the June 2017 ASM Microbe Town Hall on “Envisioning a National Microbiome Data Collaborative,” everyone interested is encouraged to… [Read More]

September 11, 2017

Nikos Kyrpides Named 2018 ASM USFCC/J. Roger Porter Awardee

Nikos KyrpidesCongratulations to Nikos Kyrpides, JGI’s Prokaryote Super Program head, who was recently selected as the 2018 USFCC/J. Roger Porter Award recipient by the American Society for Microbiology (ASM). This award recognizes outstanding efforts by a scientist who has demonstrated the importance of microbial biodiversity through sustained curatorial or stewardship activities for a major resource by… [Read More]
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