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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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News & Publications
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February 27, 2017

Revealing Aspergillus Diversity for Industrial Applications

Comparative growth of aspergilli. (Ad Wiebenga & Ronald de Vries, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands)Comparative analysis of Aspergillus species provides genus-wide view of fungal diversity In the world of fungi, Aspergillus is an industrial superstar. Aspergillus niger, for example, has been used for decades to produce citric acid—a compound frequently added to foods and pharmaceuticals —through fermentation at an industrial scale. Other species in this genus play critical roles… [Read More]

January 19, 2017

Seeking Structure With Metagenome Sequences

From sample to structure. Top: Researchers gathering samples from Great Boiling Spring in Nevada. Left: a snapshot of aligned metagenomic sequences. Each row is a different sequence (the different colors are the different amino acid groups). Each position (or column) is compared to all other positions to detect patterns of co-evolution. Bottom: the strength of the top co-evolving residues is shown as blue dots, these are also shown as colored lines on the structure above. The goal is to make a structure that makes as many of these contacts as possible. Right: a cartoon of the protein structure predicted. The protein domain shown is from Pfam DUF3794, this domain is part of a Spore coat assembly protein SafA. (Image of Great Boiling Spring by Brian Hedlund, UNLV. Protein structure and composite image by Sergey Ovchinnikov, UW)Metagenomics database helps fill in 10 percent of previously unknown protein structures For proteins, appearance matters. These important molecules largely form a cell’s structures and carry out its functions: proteins control growth and influence mobility, serve as catalysts, and transport or store other molecules. Comprised of long amino acid chains, the one-dimensional amino acid sequence… [Read More]

January 16, 2017

Tracking Antarctic Adaptations in Diatoms

Scanning electron micrograph of two cells of Fragilariopsis cylindrus. Shown are two silica shells (Frustules) in valve view. Magnification: 15,000X; scale bar: 5 μm (Image credit: Gerhard S. Dieckmann)Comparative genome analysis provides clues on how climate change might impact evolutionary adaptation limits Diatoms are a common type of photosynthetic microorganism, found in many environments from marine to soil; in the oceans, they are responsible for more than a third of the global ocean carbon captured during photosynthesis. This leads to a significant amount… [Read More]

January 10, 2017

Industrial Biotechnology Leader to Assume the Helm of the DOE Joint Genome Institute

Nigel MounceyAfter a 9-month national search, Nigel Mouncey, currently Research and Development Director for Bioengineering and Bioprocessing at Dow AgroSciences LLC, has been selected as the Director of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility. “Nigel brings the perfect set of scientific and management skills as… [Read More]

November 17, 2016

Engineering a More Efficient System for Harnessing Carbon Dioxide

A MPI video featuring study senior author Tobias Erb discussing this project may be viewed at http://bit.ly/ErbCETCH.Despite the vast diversity of organisms on the planet that express enzymes for the conversion of carbon dioxide into such organic compounds as sugars – as plants do through photosynthesis – the efforts to harness these capabilities to transform CO2 into high-value products such as biofuel and renewable chemicals have met with limited success. While… [Read More]

November 2, 2016

2017 DOE Joint Genome Institute Community Science Program Allocations Announced

John Cushman of the University of Nevada seeks to establish the common or crystalline ice plant (Mesembryanthemum crystallinum L.) as a DOE JGI Flagship Genome species. (Image by Krzysztof Ziarnek, Kenraiz CC BY-SA 4.0 Wikipedia)Portfolio additions build upon contributions in sustainable biofuels, plant microbiomes and biogeochemistry. From deep within the Earth to the upper atmosphere, the organisms and ecosystems highlighted in the 37 projects selected for the 2017 Community Science Program (CSP) of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User… [Read More]

September 7, 2016

How Fungi Help Trees Tolerate Drought

The crosscut shows the fungal tissues - the fungal mantle around the root tip and the the fungal network of tendrils that penetrates the root of plants, or Hartig Net, between Pinus sylvestris plant root cells - in green. (Image by Maira de Freitas Pereira, INRA Nancy.)Genome of world’s most common fungal symbiont sheds light on drought resistance role The mutualistic relationship between tree roots and ectomycorrhizal (ECM) fungi has been shaping forest ecosystems since their inception. ECM fungi are key players supporting the growth, health and stress tolerance of forest trees globally, such as oak, pine, spruce, birch and beech,… [Read More]

September 6, 2016

10 New Projects to be Supported Under Joint DOE User Facility Initiative

This diagram from Petr Baldrian’s proposal shows the seasonal differences in the carbon cycle processes in the temperate and boreal coniferous forests. During vegetation seasons, depicted by September on the left, photosynthesis products are allocated to soil via tree roots. When photosynthesis stops in winter, depicted by March on the right, decomposition is the most important carbon cycle process. (Image courtesy of Petr Baldrian)The U.S. Department of Energy Joint Genome Institute (DOE JGI) and the Environmental Molecular Sciences Laboratory (EMSL) have accepted 10 projects submitted during the 2017 call for proposals for their joint “Facilities Integrating Collaborations for User Science” (FICUS) initiative. These new research projects all involve collaboration between two user facilities that are stewarded by the DOE Office… [Read More]

August 17, 2016

Unveiled: Earth’s Viral Diversity

virome-graphic_art-by-Z-Rostomian-LBNLEnvironmental datasets help researchers double the number of microbial phyla known to be infected by viruses. The number of microbes in, on, and around the planet – on the order of a nonillion, or 1030 – is estimated to outnumber the stars in the Milky Way. Microbes are known to play crucial roles in regulating… [Read More]

August 15, 2016

Expanding the Stable of Workhorse Yeasts

One of the genomes sequenced for this study was of the yeast Scheffersomyces stipitis. (Courtesy of Tom Jeffries, University of Wisconsin-Madison)New genome sequences target next generation of yeasts with improved biotech uses The yeast Saccharomyces cerevisiae was a part of human civilization before history was recorded. It is essential for making bread, beer and wine, and it is ubiquitous. It is not, however, typical of the more than 1,500 yeast species found around the world…. [Read More]
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