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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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Our Science
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February 10, 2020

Viruses Reprogram Cells into Different Virocells

How a cell behaves as virocell largely depends on the infecting virus and the genomic similarity between host and virus. Pseudoalteromonas was infected with two unrelated viruses: siphovirus PSA-HS2 and podovirus PSA-HP1. The infections transformed the same bacterial host into two very different virocells, HS2-virocell and HP1-virocell. The HS2 siphovirus genome was much more similar to the host than the genome of HP1 podovirus and had better access to recycle existing host resources. In contrast, the HP1 podovirus needed to work harder at obtaining the resources needed for infection, and reprogrammed multiple host metabolisms. HS2 virocells had a comparatively higher fitness than HP1 virocells. (Figure by Cristina Howard-Varona)If it looks like a duck and quacks like a duck, so the adage goes, it must be a duck. But if the duck gets infected by a virus so that it no longer looks or quacks like one, is it still a duck? For a team led by researchers from The Ohio State University and the University of Michigan studying how virus infections cause significant metabolic changes in marine microbes, the answer is no. They refer to the infected microbial cells as virocells, a change in name which reflects the metabolic changes they’ve undergone. [Read More]

December 20, 2019

Fishing for Novel Cellulose Degraders

Graphical representation of the cellulose hook approach. (Devin Doud)A “bait and hook” single-cell genomic approach to bioprospecting. The Science One of the most vital pieces of equipment for fly fishing is a boxful of lures. Designed with feathers or wires to mimic an insect or a particular movement, each of these lures are the bait designed to attract specific catches. A similar technique… [Read More]

December 2, 2019

Dealing with Drought: Uncovering Sorghum’s Secrets

Sorghum variety BTx642 grown in Central Valley at temperatures around 100 degrees for 65 days without water. It is still green and filling grain to almost the same extent as plants that were watered weekly. (Jeffrey Dahlberg, UC ANR Agricultural Research and Extension Center)Over 40 percent of the cereal crop’s genes respond to drought stress. The Science Fields of drooping stalks and cracked earth are becoming common images in many regions due to more extreme weather events such as heat waves, droughts and floods. The planet’s resources are being stretched by a growing human population and increasing demand… [Read More]

November 20, 2019

Making a Lichen Together

The lichen Gray’s Cup (Cladonia grayi), with its namesake goblet structures. (Thomas Barlow)For the first time, a team analyzes the transcriptomes of a lichen fungus and alga to understand their partnership more clearly. The Science The humble lichen is a superorganism: one being that is actually comprised of two (or more) participants. One is a fungus (usually belonging to the ascomycetes, one of the two main branches… [Read More]

August 20, 2019

Fungus Fuels Tree Growth

Poplar cuttings inoculated with M. elongata strain PM193 (far right) grow larger in 30 percent forest soil / 70 percent sand than without PM193 (middle). On the left are controls grown in sterile sand. (Chih-Ming Hsu)A better understanding of how poplar responds to endophyte associations with endophytes enables scientists to fine-tune their engineering efforts. [Read More]

July 15, 2019

Better Genome Editing for Bioenergy

The lipid producing yeast, Yarrowia lipolytica, examined with light microscopy (left) and fluorescence microscopy (right), after being stained with Nile Red to visualize the lipid droplets inside (shown here in white). (Courtesy of Hal Alper)A team has optimized a crucial part of CRISPR-Cas9 technology to enable improvements in microbial oil production. The Science CRISPR-Cas9 is a powerful, high-throughput gene-editing tool that can help scientists engineer organisms for bioenergy applications. Cas9 needs guide RNA to lead it to the correct sequence to snip — but not all guides are effective…. [Read More]

July 10, 2019

Cultivating Symbiotic Antarctic Microbes

FISH of Nha-C enrichment with Hrr. lacusprofundi ACAM34-hmgA. Fluorescence micrograph shows individual Nha-C cells amongst Hrr. lacusprofundi cells. Nha-C cells labelled with a Cy5 (red fluorescence) conjugated probe; Hrr. lacusprofundi cells labelled with a Cy3 (yellow fluorescence, recolored to green to improve contrast) probe; all nucleic-acid containing cells stained with DAPI (blue fluorescence). Composite image of all three filters. Scale bars represent 2 µm. (Josh Hamm, UNSW)Nanohaloarchaeota cultures reveal they are symbionts and not free-living organisms. The Science Researchers employed multiple microbiology and ‘omics techniques to experimentally determine that Nanohaloarchaeota are symbionts, rather than free-living organisms as had been originally thought. The Impact The Antarctic lakes are a “treasure trove” of unknown microbes that play critical roles in environmental processes (related… [Read More]

June 11, 2019

Developing Switchgrass for Biomass Production

Left to Right: Jerry Jenkins, JGI Plant Program head Jeremy Schmutz, Adam Healey and study senior author Tom Juenger of UT-Austin.Switchgrass community gardens help distinguish genetic bases of fitness traits from climactic influence. The Science To better understand the genetic basis of local adaptation, researchers established community gardens of switchgrass plants in 10 different field sites on a north-south gradient across the United States. Hundreds of the switchgrass plants in these gardens are clonally propagated… [Read More]

February 25, 2019

Evolution of a Fungal Gene Expression Regulator

Parasitella parasitica (ZyGoLife Research Consortium on Flickr, CC BY-SA 2.0)5mC is an important piece of how many organisms regulate their genomes, but it is not well understood in fungi. Researchers reported on the largest analysis of 5mC distribution across the fungal tree of life to date, involving more than 500 species of fungi. [Read More]

December 7, 2018

A Model System for Perennial Grasses

Field researchers studying drought responses in Panicum hallii at the UT Austin Brackenridge Field Lab. (David Gilbert)Panicum hallii genomes offer insights to drought tolerance. The Science Researchers have developed a genomic model to study drought tolerance in perennial grasses using Panicum hallii (Hall’s panicgrass), by generating two complete genomes from varieties that diverged over a million years ago. The hallii variety thrives in desert environments, while the filipes variety is less… [Read More]
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