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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 Projects
Home › Our Projects › Approved User Proposals › Approved Proposals FY12

Approved Proposals FY12

Following are the approved user proposals for fiscal year 2012.

Community Science Program (CSP) Plans

Proposer Affiliation Project Description
Acinas, Silvia ICM-CSIC, Spain Microbial metagenomics and transcriptomics from a global deep-ocean expedition
Andresson, Olafur University of Iceland Sequencing of the three cultured partners of the lichen Lobaria pulmonaria and the sequencing of the transcriptomes from the natural tripartite lichen under selected and controlled conditions.
Banfield, Jill University of California, Berkeley Terabase sequencing for comprehensive genome reconstruction to assess metabolic potential for environmental bioremediation
Brodie, Eoin DOE JGI Mediterranean Grassland Soil Metagenome (MGSM): Enabling a systems view of soil carbon and nitrogen biogeochemistry under a changing climate.
Brutnell, Thomas Boyce Thompson Institute for Plant Research Development of sequence-based community tools for Setaria viridis-a model genetic system for C4 grasses
Bucking, Heike South Dakota State University Exploring the transcriptome of perennial grasses in association with beneficial microorganisms to increase biomass production and environmental sustainability of bioenergy production
Cary, Stephen University of Delaware Understanding terrestrial microbial biocomplexity in an Antarctic desert landscape: resolving universal drivers of community structure and function in a trophically simple system
Crouch, Jo Anne USDA-ARS Genomic signatures of pathogenicity and endophytism in five species of grass-associated Colletotrichum impacting the health and production of bioenergy feedstocks, agriculture and the environment
Dangl, Jeff University of North Carolina at Chapel Hill Plant associated metagenomes–Microbial community diversity and host control of community assembly across model and emerging plant ecological genomics systems.
DeAngelis, Kristen University of Massachusetts Microbial ecology and genomics of carbon-storing bacteria in rhizosphere soils
Dubilier, Nicole & Kleiner, Manuel Max Planck Institute for Marine Microbiology, Germany Understanding novel pathways for energy and carbon use in bacterial symbionts of gutless marine worms
Emerson, David Bigelow Laboratory for Ocean Sciences Single cell genome sequencing of biomineralizing bacteria
Fierer, Noah University of Colorado Cross-site metagenomic analyses to assess the impacts of experimental nitrogen additions on belowground carbon dynamics
Fredrickson, Jim Pacific Northwest National Laboratory Microbial Interactions in Extremophilic Mat Communities
Gilbert, Jack Argonne National Laboratory Creating a successional model for carbon remediation in the Gulf of Mexico
Gross, Stephen DOE JGI The Agave Microbiome: Exploring the role of microbial communities in plant adaptations to desert environments
Hazen, Samuel University of Massachusetts Creating a multi-functional library of grass transcription factors for the energy crop model system Brachypodium distachyon
Hess, Matthias Washington State University Expression profile of biomass-degrading fungi inhabiting the cow rumen
Kelly, William AgResearch, New Zealand The Hungate 1000. A catalogue of reference genomes from the rumen microbiome.
Kerfeld, Cheryl DOE JGI Enhancing Bacterial Carbon Capture and Sequestration: Synthesis of Building Blocks for the Carboxysome, A Metabolic Module for CO2 Fixation
Kyrpides, Nikos DOE JGI Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project
Laplaze, Laurent Institut de Recherche pour le Developpement (IRD), France Transcriptome Analysis of Salt Tolerance in Casuarina trees
Martin, Francis INRA, France Metatranscriptomics of Soil Forest Ecosystems
McKay, Robert Bowling Green State University Metagenomics and metatranscriptomics of the Lake Erie ‘dead zone’: a seasonal source of greenhouse gases
McMahon, Katherine University of Wisconsin, Madison Dynamics of microbial carbon processing pathways across a decade in a freshwater eutrophic lake revealed through metagenomic sequencing
Mock, Thomas University of East Anglia, UK Sea of Change: Eukaryotic Phytoplankton Communities in the Arctic Ocean
Mohn, William University of British Columbia, Canada Metagenomic and metatranscriptomic analysis of forest soil communities across North America
Moran, Mary Ann University of Georgia The Genetic Basis for Heterotrophic Carbon Processing in the Sea
Murray, Alison Desert Research Institute Lake Vida brine microbial community (LVBMCo) genomics and transcriptomics – a window into diversity, adaptation and processes in extreme cold
Gerard Muyzer Delft University of Technology Genome sequencing of 100 strains of the haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacterium Thioalkalivibrio
Nealson, Kenneth University of Southern California Life at the edge: community cooperation and success in a very extreme (ultrabasic and ultra-reducing) environment
Ohm, Robin DOE JGI Towards functional genomics: development of Schizophyllum commune as a model system to study lignocellulose degradation
Pester, Michael University of Vienna, Austria Targeted metagenomics and metatranscriptomics of a sulfate-reducing rare biosphere member and potentially novel sulfate reducers that impact methane emission from peatlands
Powell, Amy Sandia National Laboratories A Phylogenomic Framework to Investigate Fungal Thermophily
Pukkila, Patricia University of North Carolina at Chapel Hill Functional genomics in the model mushroom Coprinopsis cinerea
Rodrigues, Jorge University of Texas at Arlington Profiling metagenomic consequences of Amazon deforestation at different spatial scales
Schadt, Christopher Oak Ridge National Laboratory Defining the Populus Microbiome: Role of Genotype by Environment Interactions in Shaping the Rhizosphere Microbiome of Populus trichocarpa
Schrenk, Matthew East Carolina University Metagenome-enabled Investigations of Carbon and Hydrogen Fluxes within the Serpentinite-hosted Subsurface Biosphere
Spatafora, Joseph Oregon State University 1000 Fungal Genomes
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Dark ocean microbial single cell genomics
Wing, Rod University of Arizona Empowering functional plant genomics with genomes and transcriptomes of the top 20 Brassicales
  • Approved Proposals FY23
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