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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 FY09

Approved Proposals FY09

Following are the approved user proposals for fiscal year 2009.

Community Science Program (CSP) Plans

Eukaryotes

Organism Proposer Affiliation
Resequencing Trichoderma reesei Scott Baker Pacific Northwest National Lab
Rhizopogon salebrosus (ectomycorrhizal fungus) Thomas Bruns University of California, Berkeley
Ceriporiopsis subvermispora (lignin-degrading fungus) Daniel Cullen USDA Forest Products Laboratory
Gene expression in Chlamydomonas reinhardtii Maria Ghirardi Natl. Renewable Energy Lab.
Paralvinella sulfincola (polychaete worm) Peter Girguis Harvard Univ.
Thalassiosira rotula (diatom) Bethany Jenkins Univ. of Rhode Island
Dendroctonus frontalis (southern pine beetle) ESTs Scott Kelley San Diego State Univ.
Botryococcus braunii (Oil-Producing Green Microalga) cDNA Andrew Koppisch Los Alamos Natl. Lab.
Chlamydomonas and Volvox transcriptomes Sabeeha Merchant Univ. of California, Los Angeles
Spirodela polyrhiza (duckweed) Todd Michael Rutgers
Zostera marina (seagrass) Jeanine Olsen University of Groningen
Gossypium (cotton) Andrew Paterson Univ. of Georgia
Pine BAC Sequencing Daniel Peterson Mississippi State Univ.
Hansenula polymorpha strain NCYC 495 leu1.1 (ATCC MYA-335) Andriy Sibirny Institute of Cell Biology, Ukraine
Resequencing of Brachypodium distachyon John Vogel USDA-ARS Western Regional Research Center
Nanoflagellates: Paraphysomonas, Ochromonas, and Spumella Alexandra Worden Monterey Bay Aquarium Research Institute

Bacteria and Archaea

Organism Proposer Affiliation
Four diverse cellulose degrading microbes Iain Anderson DOE JGI
Escherichia coli MG1655 John Battista Lousiana State Univ.
Sinorhizobium meliloti strains AK83 and BL225C Emanuele Biondi Universita’ di Firenze
Methylotenera species Ludmila Chistoserdova Univ. of Washington
SAR11 Genome Evolution Stephen Giovannoni Oregon State Univ.
Rhodopseudomonas palustris strain DX-1 Caroline Harwood Univ. of Washington
Cycloclasticus pugetii (a PAH-Degrading Bacterium) Russell Herwig Univ. of Washington
Burkholderia sp. Ch1-1 and Burkholderia sp. Cs1-4 William Hickey Univ. of Wisconsin
Sphaerochaeta pleomorpha and Sphaerochaeta globus Frank Loeffler Georgia Inst. of Technology
Archaeal transcriptomes Todd Lowe Univ. of California Santa Cruz
Dehalogenimonas lykanthroporepellens William Moe Louisiana State Univ.
Desulfurococcus (hyperthermophilic archaeon) Biswarup Mukhopadhyay Virginia Bioinformatics Inst., Virginia Polytechnic Inst. and State Univ.
Mesorhizobium ciceri bv biserrulae (strains WSM1271, WSM2073 and WSM2075) (legume symbionts) Kemanthi Nandasena Murdoch Univ.
Thermoacidophiles of deep-sea hydrothermal vents Anna-Louise Reysenbach Portland State Univ.
Alicycliphilus denitrificans strain BC Alfons Stams Wageningen Univ.
Desulfotomaculum species Alfons Stams Wageningen Univ.
Freshwater Actinobacteria belonging to the acI lineage Falk Warnecke DOE JGI

Metagenomes

Organism Proposer Affiliation
Novel subsurface microbial phylotypes Jennifer Biddle Univ. of North Carolina, Chapel Hill
Highly efficient, highly stable, reductive dechlorinating bioreactor Eoin Brodie Lawrence Berkeley National Lab
Bankia setacea (shipworm) metagenome. Daniel Distel Ocean Genome Legacy
Hoatzin crop microbiome Maria Dominguez-Bello Univ. of Puerto Rico
Ammonia-oxidizing archaeal enrichment culture Christopher Francis Stanford Univ.
Subarctic Pacific Ocean Steven Hallam Univ. of British Columbia
Lake Vostok accretion ice Philip Hugenholtz DOE JGI
Microbial communities at the Hanford 300A IFC Site. Allan Konopka Pacific Northwest Natl. Lab.
PCE-dechlorinating mixed communities Ruth Richardson Cornell Univ.
Uncultivated marine viruses Grieg Steward Univ. of Hawaii
Great Salt Lake Bart Weimer Utah State Univ.
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