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    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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    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
    Researchers combined expertise at the National Labs to screen, characterize, sequence and then analyze the genomes and multi-omics datasets for algae that can be used for large-scale production of biofuels and bioproducts.

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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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    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

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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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    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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    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

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Our Science
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April 11, 2022

The Power of One, Amplified

One of the pools at Dewar Creek hot springs in British Columbia, Canada. (Allyson Brady)Researchers showed that large-scale single cell genomics can add significant value when used in complementarity with metagenomic sequencing. [Read More]

March 9, 2022

Fungal Friends or Foes in Plant Roots

41 fungal isolates representative of the A. thaliana root mycobiomeFungi colonizing Arabidopsis thaliana roots have gene families that help determine if these fungi act as friends or foes. [Read More]

November 18, 2021

Marine Microbe Contains Multitudes

Boeuf and colleagues collected samples of SAR324 microbial communities from this research vessel, the Kilo Moana. (School of Ocean And Earth Science And Technology at University of Hawaii at Manoa)A deep dive into microbial genomics reveals one bacterial species is made of four ecologically distinct groups with different lifestyles. [Read More]

November 17, 2021

When “The Blob” Made It Hotter Under the Water

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)With genomic samples collected before, during and after The Blob, researchers developed a preliminary model of how marine microbial communities are affected by warming events. [Read More]

October 26, 2021

The Case for Conservation

Female (left) and male (right) Ceratodon purpureus plants. Females typically grow larger than males in several traits, like the length of leaves. Males often turn red when developing antheridiophores, which in mosses are the structures that produce sperm (seen in the bottom right. (Sarah Carey)High-quality reference genome sequences of the male and female fire moss plants are now available, and lessons from their sex chromosomes could help improve crop yields. [Read More]

September 22, 2021

Plotting a Model for Virus-Host Warfare Deep Below Ground

Image of biofilm with both Altiarchaea (blue) and viruses (red). (Victoria Turzynksi and Lea Griesdorn)Researchers describe how viruses repeatedly attempt to infect and destroy their hosts – and how the microbes resist. [Read More]

June 25, 2021

A Natural Mechanism Can Turbocharge Viral Evolution

Virus tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— don't allow the virus to attach to a purple tinted cell type.A genetic element that enables rapid, targeted mutation is surprisingly widespread and appears to allow viruses to hunt new microbial prey. [Read More]

June 3, 2021

Refining the Process of Identifying Algae Biotechnology Candidates

Algae growing in a bioreactor. (Dennis Schroeder, NREL)A collaborative approach highlights how a screening and characterization pipeline could help accelerate algae biotechnology research efforts. [Read More]

April 30, 2021

Bacteria and Fungi Divvy Up the Work in Forest Floor

The study site in the coniferous forest located in the Bohemian Forest National Park, Czech Republic. (Petr Baldrian)While thousands of species of fungi and bacteria dwell on — and within — the forest floor, who’s recycling the plant biomass? [Read More]

April 28, 2021

Gut Fungi: Unexpected Source of Novel Chemicals

The anaerobic fungus Anaeroromyces robustus growing on reed canary grass. (Vaithiyalingam Shutthanandan, PNNL/EMSL)Combing through the genomes of four anaerobic fungal species has revealed, for the first time, that this group is unexpectedly powerful: they can whip up dozens of complex natural products, including new ones. [Read More]
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