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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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July 7, 2017

Tiny Green Algae Reveal Large Genomic Variation

TEM image of O. tauri strain RCC4221. Credit: Herve MoreauFirst complete picture of standing genetic variation within a natural population. The Science Ostreococcus are tiny green algae that are the bases of many marine food webs. A decade after the complete representative genomes of three Ostreococcus picoplankton groups were sequenced, researchers have sequenced and analyzed the genomes of 13 members of a natural Ostreococcus… [Read More]

July 5, 2017

Mutant Rice Database for Bioenergy Research

Genome-wide distribution of fast neutron-induced mutations in the Kitaake rice mutant population. (Guotian Li and Rashmi Jain)Genome-wide rice studies yield first major, large-scale collection of mutations for grass models. The Science Fast-neutron irradiation, exposure to high energy neutrons, induces a wide variety of mutations by making changes in DNA. Using this approach, rice researchers were able to create the first major, large-scale collection of mutations for grass models. Resequencing the 1,504… [Read More]

June 30, 2017

Lessons from Simulating A Deep Ocean Oil Spill

The oil slick in the Gulf of Mexico from the Deepwater Horizon oil spill as seen on April 29, 2010. (NASA Earth Observatory image created by Jesse Allen, using data provided courtesy of the University of Wisconsin’s Space Science and Engineering Center MODIS Direct Broadcast system)Metagenome pipeline helps researchers resolve near-complete microbial genomes involved in Deepwater Horizon oil spill. The Science The 2010 Deepwater Horizon oil spill released 4.1 million barrels of oil into the Gulf of Mexico and was the first major release of oil and natural gases into the deep ocean (1,500 meters). Due to the depth of… [Read More]

April 28, 2017

A Gene that Influences Grain Yields in Grasses

Field of Setaria viridis growing in western Nebraska. In the current issue of Nature Plants Huang and colleagues use Setaria viridis to identify the inflorescence mutant, sparse panicle 1. A mutation in the maize ortholog conditions a very similar panicle defect, demonstrating the utility of S. viridis for gene discovery in the panicoids. (Pu Huang)Genetic screen identifies mutations that impact green foxtail panicle formation. The Science Through deep sequencing of the model grass green foxtail (Setaria viridis), researchers pinpointed a gene critical for the development of flowers that give rise to the grain. Using this information, a homologous gene in maize was identified as playing a similar role highlighting… [Read More]

April 3, 2017

Speciation Driven by Alleles Adapted to Local Conditions

For this study, researchers planted a test population in a mountain-top meadow near the Lost Trail Pass ski resort in the mountains of Montana. To water these transplants, they lugged nine empty garbage cans up the mountain and filled them with snow to water the plants throughout the summer. (Tom Mitchell-Olds)Genome sequence analysis provides first evidence that linked, locally adapted alleles exist first, and subsequently are captured within a new, selectively-favored inversion. The Science A team of scientists investigated the pathway by which chromosomal inversions – in which a segment of the chromosome was removed, flipped and then re-inserted – contribute to speciation in nature…. [Read More]

March 29, 2017

Grasses: The Secrets behind Their Stomatal Success

John Vogel with Brachypodium plants at the DOE JGI. (Roy Kaltschmidt, Berkeley Lab)Finding a grass gene impacting stomatal morphology underscores importance of developing mutant gene index. The Science The evolution of adjustable pores, stomata, allows plants to control the amount of CO2 that enters the plant and water that escapes by modifying the stomatal pore size. Plants have evolved two kidney shaped guard cells that swell to… [Read More]

March 14, 2017

New Software Tools Streamline DNA Sequence Design-and-Build Process

DOE JGI BOOST logoImprove on existing biological computer-aided design and manufacture (bioCAD/CAM) tools The Science Synthetic DNA allows scientists to expand the breadth and depth of their genomic research. In this study researchers from the U.S. Department of Energy Joint Genome Institute (JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in… [Read More]

March 6, 2017

Nitrogen Uptake Between Fungi and Orchids

Researchers investigated Tulasnella calospora as both a free-living mycelium and in symbiosis with the photosynthetic orchid long-lipped serapias. (Ziegler175, Wikimedia Commons, CC BY-SA 3.0)Fungal and plant gene expression provides clues to nitrogen pathways. The Science Orchids are an example of an experimentally tractable plant that is highly dependent on its relationship with its mycorrhizal fungal partners for nutrient supply. In this recent study, researchers for the first time identified some genetic determinants potentially involved in nitrogen uptake and… [Read More]

February 6, 2017

Metagenomics Leads to New CRISPR-Cas Systems

The newly discovered CRISPR-CasY system was found in bacteria from deep underground at Crystal Geyser in California. (Jill Banfield, UC Berkeley)First CRISPR-Cas9 system in archaea discovered The Science Through metagenomic data generated by the DOE Joint Genome Institute, researchers analyzed 155 million protein coding genes from uncultivated microbial communities, leading to the discovery of the first CRISPR-Cas9 protein in the archaeal domain, and of two previously unknown simple bacterial CRISPR-Cas systems. The Impact Microbes play… [Read More]

December 19, 2016

Of Mutualism and Lipid Metabolism in Fungi

Hyphae and asexual sporangia of Rhizopus microsporus (photo by Stephen Mondo). Inset shows a hypha with YFP-labeled Burkholderia endobacteria in green and DAPI-stained fungal nuclei in blue; scale bar, 5 um (photo by Olga Lastovetsky)Novel mechanism in bacterial-fungal symbiosis could have biodiesel production applications The Science To answer the challenge of producing renewable, sustainable alternative fuels, researchers aren’t just looking at developing candidate bioenergy crops but are also reviewing other natural sources of energy-dense oils such as fungi. To learn more about how bacteria interact with fungi in a… [Read More]
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