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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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May 22, 2015

The Most Complete Functional Map of an Entire Enzyme Family

Overlay of SacteLam55A onto PcLam55A (Image from Bianchetti CM et al, J Biol Chem. 2015 May 8. doi: 10.1074/jbc.M114.623579. )DOE-funded researchers develop a new process for annotating cellulose-degrading enzymes. The Science: Researchers at two Department of Energy-funded Scientific User Facilities collaborated with one of three Bioenergy Research Centers to develop and analyze high-resolution crystal structures of an enzyme from the cellulose-degrading GH55 family. They then went further and were able to apply a variety… [Read More]

May 1, 2015

Understanding the [Non-Coding] Spaces Between

The golden-brown surface mats that indicate a Trichodesmium erythaeum bloom have led to them being called “sea sawdust.” (Image by FWC Fish and Wildlife Research Institute via Flickr CC BY-NC-ND 2.0)DOE JGI researchers sequenced and analyzed a cyanobacterium with known nitrogen-fixing capabilities. The Science: Researchers sequenced and analyzed the uncommonly large genome of a nitrogen-fixing cyanobacterial strain, comparing it to the more than 150 extant cyanobacterial genomes. The Impact: Unlike many of the existing cyanobacterial genome sequences, the genome of Trichodesmium erythaeum IMS 101 is… [Read More]

April 15, 2015

Big Plant Genomes: Formerly Intractable, No Longer Insurmountable

wheat image by Jordi Paya Canal via Flickr, CC-BY-SA-2.0DOE JGI researchers have developed an assembly and mapping strategy for any species, including large and complex genomes. The Science: Through a combination of high-throughput sequencing, high performance computing, and genetic mapping, DOE JGI researchers have derived a sequence assembly for the highly repetitive plant genome of bread wheat (Triticum aestivum). The Impact: The researchers… [Read More]

March 27, 2015

Targeted Sorting of Microbial Cells

DOE JGI is enabling collaborators to develop a universally applicable technique for studying microbial metabolic activities. The Science: A team led by University of Vienna researchers has developed a way to identify and sort single microbial cells through a probe-independent process that uses heavy water (laced with deuterium) which is then incorporated into mostly lipids… [Read More]

March 24, 2015

Identifying causes of poplar canker

Cankers caused by the fungal tree pathogen M. populorum on poplar stems. (T.H. Filer Jr., USDA, Bugwood.org CC BY-NC-3.0)Researchers compared two fungal tree pathogens to find out how one of them has gained the capability to significantly damage hybrid poplar plantations. [Read More]

February 3, 2015

Complete Genomes from Single Cells Still Elusive

Clingenpeel et al image from Frontiers in Microbiology articleDOE JGI researchers describe the current challenges in single-cell genomics. The Science: DOE JGI researchers review the status of single-cell genomics, and how close scientists are to being able to reconstruct an individual cell’s genome. The Impact: As an alternative method of studying microbial communities, single-cell genomics allows researchers to link function to phylogeny without… [Read More]

January 20, 2015

Enhancing Microbial Pathways for Biofuel Production

refueling a car with biodiesel. image from Flickr CC United Soybean BoardDOE JGI, JBEI researchers collaborate on improving terpene production in E. coli. Science: Researchers from the DOE JGI and the Joint Bioenergy Institute identified genes in an E. coli microbial metabolism pathway that could improve the production of terpenes. The Impact: Terpenes are high-energy compounds produced in microbes and plants that could be used for… [Read More]

December 22, 2014

How a White Rot Tackles Freshly-Cut Wood

Scanning electron microscopy (SEM) image of pine that was substantially eroded by the white rot P. gigantea. Bar = 40 µm. (Image from Hori et al. PloS Genet. doi:10.1371/journal.pgen.1004759.g002)Unlike many other white rot fungi, P. gigantea prefers to colonize freshly-harvested wood. The Science: Researchers sequenced and analyzed the white rot fungus Phlebiopsis gigantea, which can break down fresh-cut conifer sapwood. They also sequenced and analyzed the set of P. gigantea’s secreted proteins (secretome) and the set of all of its RNA molecules (transcriptome)…. [Read More]

November 26, 2014

Eucalyptus grandis Genome 2.0—Community Resource

eucalyptus plantation courtesy of the University of PretoriaGenetic maps improve the reference genome assembly of the candidate bioenergy feedstock The Science: A team of French researchers developed an array that allowed them to produce high-resolution genetic maps of two eucalyptus species that they then compared to the reference genome of eucalyptus produced by a team including DOE JGI researchers. The Impact: The… [Read More]

November 19, 2014

Noteworthy DOE JGI papers in Nature Methods

GenePRIMP figure from Nature Methods paperThree publications are featured in the Special 10th Anniversary issue. The Science: To mark its 10th anniversary, the journal Nature Methods released a Special Issue highlighting impactful articles. Among these noteworthy articles are three from DOE JGI researchers. The Impact: Microbial Sequencing is one of the areas of methods development highlighted by the journal, and… [Read More]
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