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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 FY10

Approved Proposals FY10

Following are the approved user proposals for fiscal year 2010.

Community Science Program (CSP) Plans

Eukaryotes

Proposer Affiliation Organism
Collier, Jackie Stony Brook University Four Labyrinthulomycete species
Cullen, Daniel US Forest Service, Forest Products Laboratory Homkaryotic derivative of Postia placenta
Cullen, Daniel US Forest Service, Forest Products Laboratory Lignin-degrading fungus Phlebiopsis gigantea
Goodwin, Stephen USDA-ARS and Purdue University Dothideomycetes plant pathogens
Grossniklaus, Ueli University of Zurich Apomictic plant Boechera holboellii
Koppisch, Andy Los Alamos National Laboratory Colony forming microalga Botryococcus braunii var Showa
Kubisiak, Thomas US Forest Service, Southern Research Station Fusiform rust fungus Cronartium quercuum f.sp. fusiforme
Martin, Francis Institut National de la Recherche Agronomique Pan-global basidiomycetes Pisolithus tinctorius and Pisolithus microcarpus
McDaniel, Stuart University of Florida Ceratodon purpureus(moss)
Moreau, Herve CNRS and UPMC Resequencing Ostreococcus tauri
Paterson, Andrew University of Georgia Resequencing sorghum
Phister, Trevor North Carolina State University Completion of the Dekkera (Brettanomyces) bruxellensis genome sequence
Pringle, Anne Harvard University Cellulose degrading fungus Amanita thiersii
Reeve, Wayne Murdoch University Phytopathogenic oomycete Phytophthora cinnamomi
Roossinck, Marilyn Samuel Roberts Noble Foundation Alteration of Curvularia protuberata transcripts due to presence of Curvularia thermal tolerance virus
Vyverman, Wim Ghent University Diatom transcriptome and genome
Weeks, Donald University of Nebraska-Lincoln Transcriptome analyses of Chlamydomonas and Chlorella
Zhong, Shaobin North Dakota State University Fungal pathogen Cochliobolus sativus

Bacteria and Archaea

Proposer Affiliation Organism
Auchtung, Jennifer Michigan State University Role of population microdiversity in adaptation to environmental redox gradients
Anderson, Iain DOE Joint Genome Institute Xylan degraders
Anderson, Iain DOE Joint Genome Institute Genomic survey of haloarchaeal genomes
Bayer, Travis University of California, San Francisco Actinotalea fermentans
Bollmann, Annette Miami University Five isolates from the contaminated subsurface sediment of Oak Ridge’s FRC area
Brown, Igor NASA Johnson Space Center Two strains of Cyanobacteria for biological remediation
Bryant, Donald Penn State University Representative photosynthetic purple sulfur bacteria
Cavicchioli, Rick University of New South Wales Novel haloarchaea from Deep Lake
Coleman, Nicholas University of Sydney Ethene and vinyl chloride-oxidizing Mycobacterium strains
Cooper, Vaughn University of New Hampshire Adaptive mechanisms in Burkholderia biofilms
Copley, Shelley University of Colorado at Boulder Sphingobium chlorophenolicum
Daly, Michael Uniformed Services University of the Health Sciences Radiation-resistant bacterium Deinococcus grandis
Dopson, Mark Umeå University Psychrotolerant Acidithiobacillus species
Dvornyk, Volodymyr University of Hong Kong Nostoc linckia from “Evolution Canyon”
Edwards, Elizabeth University of Toronto Novel acetogenic bacterial isolates from dechlorinating microbial mixed cultures
Emerson, David Bigelow Laboratory for Ocean Sciences Two novel ‘Zetaproteobacteria’ from the ocean
Green, Stefan Florida State University Denitrifying bacterial isolates
Grzymski, Joseph Desert Research Institute Microbes integral to the cycling of sulfate and iron
Haggblom, Max Rutgers University Acidobacterium species from Arctic tundra soils
Hedlund, Brian University of Nevada Las Vegas Thermophiles in Great Basin hot springs
Kappler, Ulrike The University of Queensland Alkaliphilic sulfur oxidizing bacteria for sulfur pollution remediation
Lewis, Gillian University of Auckland Freshwater manganese depositing β-proteobacterium (Siderocapsaceae)
Liao, James University of California, Los Angeles Reverse metabolic engineering of Escherichia coli
Liu, Wen-Tso University of Illinois at Urbana-Champaign Comparison of novel methanogens from peatlands and bioreactors
Liu, Wen-Tso University of Illinois at Urbana-Champaign Obligate syntrophic bacteria capable of phthalate isomer compound degradation in methanogenic conditions
Martinez, Robert University of Alabama ORFRC Rahnella sp. Y9602
Mavrommatis, Konstantinos DOE Joint Genome Institute Cyanobacteria (Synechocystis) transcriptome
Mayali, Xavier Lawrence Livermore National Laboratory Marine Roseobacter RCA cluster bacterial strain LE17
Mills, David University of California, Davis Acetobacter aceti ATCC 23746
Muyzer, Gerard Delft University of Technology Haloalkaliphilic chemolithoautotrophic Thioalkalivibrio bacteria
Nesbø, Camilla University of Oslo Thermotogales strain mesG1.Ag.4.1
Norton, Jeanette M. Utah State University Nitrosomonas cryotolerans and Nitrosospira briensis for comparative phylogenomics of ammonia-oxidizing bacteria
Pappas, Katherine University of Athens Zymomonas mobilis transcriptomes and resequencing Z. mobilis industrial strain ZM4
Reeve, Wayne Murdoch University Rhizobia of clover, pea/bean and
lupin microsymbionts
Robb, Frank Center of Marine Biotechnology Carbon monoxide oxidizing thermophiles
Rodrigues, Jorge University of Texas at Arlington Genome closure of lignocellulosic degrader Verrucomicrobium sp. strain TAV2.
Sanchez Amat, Antonio University of Murcia Marine bacterial genus Marinomonas
Sello, Jason Brown University Biomass-degrading bacteria Streptomyces viridosporus ATCC 39115 and Streptomyces setonii ATCC 39116
Smidt, Hauke Wageningen University Halorespiring Firmicutes
Stabb, Eric The University of Georgia Research Foundation Mutations in Vibrio fischeri
Stein, Lisa University of Alberta Methanotrophic Bacteria from diverse environments
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Single cell genome sequencing of mesopelagic bacterioplankton
Tisa, Louis University of New Hampshire An atypical Frankia isolate and Non-Frankia Actinobacteria from Actinorhizal Plants
Vieille, Claire Michigan State University Resequencing of Actinobacillus succinogene
Ward, David Montana State University Synechococcus cyanobacterial isolates

Metagenomes

Proposer Affiliation Organism
Breitbart, Mya University of South Florida Modern freshwater microbialites
Chistoserdova, Ludmila University of Washington Functional metagenomics of methane and nitrogen cycles in freshwater lakes
Davidson, Seana University of Washington Metagenome function of the Earthworm egg capsule bacterial community
Deng, Li University of Arizona Viruses that infect freshwater cyanobacteria
Edwards, Elizabeth University of Toronto Dehalobacter-containing dechlorinating community
Hedlund, Brian University of Nevada, Las Vegas Great Boiling Spring sediment and water microbial communities
Kirchman, David University of Delaware Metagenomic analysis of methane degradation in Arctic coastal waters and sediments
Madsen, Eugene Cornell University Naphthalene biodegrading microbial community
Mincer, Tracy Woods Hole Oceanographic Institute Natural microbial community associated with the cyanobacteria Trichodesmium
Moon, Christina AgResearch Limited Lignocellulolytic enzyme discovery from the rumen
Powell, Amy Sandia National Laboratories Eukaryotic microbial metatranscriptome of blue grama grass rhizosphere soils
Sullivan, Matthew University of Arizona Viral community in the Subarctic Pacific Ocean
Sullivan, Matthew University of Arizona Viral community in the Mediterranean Sea
Taylor, Mike University of Auckland Microbial symbionts of New Zealand’s endemic wood-degrading insects
Waldrop, Mark US Geological Services Permafrost Soil Microbiota
Ward, Naomi University of Wyoming Metatranscriptomic analysis of bacterial-algal interactions
Warnecke, Falk Friedrich Schiller University of Jena Desert locust (Schistocerca gregaria)
Worden, Alexandra Monterey Bay Aquarium Research Institute Metagenomics of uncultured marine eukaryotes
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