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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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Home › Our Projects › Approved User Proposals › Approved Proposals FY11

Approved Proposals FY11

Following are the approved user proposals for fiscal year 2011.

Community Science Program (CSP) Plans

Algae

Proposer Affiliation Organism
Kerfeld, Cheryl DOE JGI Genome and Transcriptome Analyses of Two Extremely Acidophilic and One Neutrophilic Eukaryotic Algal Species with Diverse Mechanism for CO2 Acquisition
Lovejoy, Connie Laval University, Canada Small planktonic single celled eukaryotes from the Arctic Ocean

Plants

Proposer Affiliation Organism
Muehlbauer, Gary University of Minnesota Whole genome shotgun sequencing of the barley genome
Vogel, John USDA-ARS Surveying natural diversity of the model grass Brachypodium distachyon

Fungi

Proposer Affiliation Organism
de Vries, Ronald CBS-KNAW Fungal Biodiversity Centre, the Netherlands Comparative analysis of Aspergilli to facilitate novel strategies in fungal biotechnology
Goodwin, Stephen Purdue University Sequencing of pathogens and extremophiles in the Dothideomycetes
Hibbett, David S. Clark University Community proposal to sequence a diverse assemblage of saprotrophic Basidiomycota (Agaricomycotina)
Jeffries, Thomas Forest Products Laboratory Yeasts of Biotechnological, Taxonomic and Physiological Interest
Martin, Francis INRA, France Exploring the Genome Diversity of Mycorrhizal Fungi to Understand the Evolution and Functioning of Symbiosis in Woody Shrubs and Trees
Pisabarro, Antonio Public University of Navarre, Spain Comparative transcriptomics pipeline for saprophytic basidiomycota
Pringle, Anne Harvard University Comparative transcriptomics of closely related saprotrophic and ectomycorrhizal Amanita species.
Spatafora, Joseph Oregon State University Phylogenomics and the origin and diversification of Kingdom Fungi
Turgeon, Gillian Cornell University Cochliobolus: expanded and deepened
Turk, Martina University of Ljubljana, Slovenia The varieties of the black yeast-like fungus Aureobasidium pullulans: evolution and use in biotechnology

Bacteria/Archaea

Proposer Affiliation Organism
Bertilsson, Stefan Uppsala University, Sweden Genome wide diversity and population genetics in uncultured aquatic bacteria: single cell genomics of the freshwater SAR11 group and the ubiquitous Actinobacteria ac1 lineage
Chistoserdova, Ludmila University of Washington Genomes of fifty methylotrophs isolated from Lake Washington
Eichorst, Stephanie Los Alamos National Laboratory Populating the branches of the Phylum Acidobacteria with relevant soil strains
Eisen, Jonathan DOE JGI Continuation of the Genomic Encyclopedia of Bacteria and Archaea pilot project
Kalyuzhnaya, Marina University of Washington Coupling function to genomics via single-cell phenotyping and genome sequencing
Liu, Wen-Tso University of Illinois Single cells genomics for uncultured Archaea dominating in a terrestrial subsurface aquifer abundantly containing methane
Sievert, Stefan Woods Hole Oceanographic Institute Shedding Light on the Dark: Single-cell Genomics of Uncultivated Epsilonproteobacteria Inhabiting the Subseafloor Biosphere at Deep-Sea Hydrothermal Vents
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Generating reference genomes for marine ecosystem research: Single cell sequencing of ubiquitous, uncultured bacterioplankton clades
Tsiamis, George University of Ioannina, Greece Unraveling the unique microbial diversity of the Etoliko lagoon in Western Greece through a single cell genomics approach

Metagenomes

Proposer Affiliation Organism
Bryant, Donald Penn State University Metagenomic and metatranscriptomic analysis of anoxygenic, chlorophototrophic microbial mat communities in Yellowstone National Park
Campbell, Barbara University of Delaware Metagenomic and metatranscriptomic analysis of carbon cycling in Delaware coastal waters
Dionisi, Hebe Patagonian National Research Center, Argentina Microbial Community Structure and Metabolic Potential of Chronically Polluted Marine Sediments from Cold Regions of the Northern and Southern Hemispheres
Distel, Dan Ocean Genome Legacy Foundation, Center for Marine Research The complete shipworm microbiome: a comparative genomic and metagenomic analysis of lignocellulose-degrading microbial communities from multiple species of wood-boring bivalves.
Girguis, Peter Harvard University Linking mantle to microbe: a community-wide effort to ally hydrothermal vent microbial identity and ecology to geochemical cycles via metagenomics
Hallam, Steven University of British Columbia, Canada Microbial Systems Ecology of Expanding Oxygen Minimum Zones in the Eastern Subtropical North Pacific Ocean
Kerfeld, Cheryl DOE JGI Metagenomic Sequencing for Understanding Microbial Carbon Cycling by Biological Soil Crusts of Arid Lands
Macalady, Jennifer Penn State University Uncultivated and novel microbial lineages in terrestrial subsurface biofilms from a sulfidic aquifer
McMahon, Katherine University of Wisconsin High-resolution temporal and spatial dynamics of microbially-mediated carbon processing revealed though time-series metagenomics in freshwater lakes
Moran, Mary Ann University of Georgia Transcriptional analysis of a marine bacteria-phytoplankton binary model system
Muyzer, Gerard Delft University of Technology, the Netherlands Metagenomics of microbial communities from soda lakes and soda solonchak soils
Tringe, Susannah DOE JGI Microbial community impact on carbon sequestration in managed wetland “carbon farming”
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