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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 FY06

Approved Proposals FY06

Following are the approved user proposals for fiscal year 2006.

Community Science Program (CSP) Plans

Large Eukaryotes

Organism Proposer Affiliation
Arabidopsis lyrata and Capsella rubella (pink shepherd’s-purse) Weigel Max Planck Inst. for Developmental Biology
Mimulus guttatus (monkey flower) Willis Duke Univ.
Sorghum bicolor Paterson Univ. of Georgia

Small Eukaryotes

Organism Proposer Affiliation
Batrachochytrium dendrobatidis (frog-infecting chytrid fungus ) Taylor UC Berkeley
Bicyclus anynana (a butterfly) Long UC Irvine
Campanulales (Grammathotheca bergiana, Isotoma petraea, Lobelia anceps, L. angolenis, L. baumannii, L. cardinalis, L. erinus, L. galpinii, L. gregoriana, L. inflata, L. jasionoides, L. malowensis, L. laxa, L. linearis chloroplast, L. patula, L. siphilitica, L. spicata, L. thermalis, L. boninensis, L. morogoroensis chloroplast
L. holstii chloroplast, Monopsis alba, M. debilis, M. flava, M. stellaroides, Pratia angulata, P. nummularia, Wimmerella hederacea chloroplast, Carpodetus serratus Chloroplast, Cyphia volubilis chloroplast, Cyphia dentariifolia chloroplast, Cyphia angustiloba, Cyphia crenata Chloroplast, Cyphia digitata chloroplast, Cyphia tortilis chloroplast, Cyphia phyteuma chloroplast, Cyphia belfastica chloroplast, Brighamia insignis chloroplast, Porterella carnosula, Cyanea fissa chloroplast)
Knox Indiana Univ.
Ciona intestinalis (sea squirt) Lemaire CNRS, France
Crassostrea gigas (oyster) Hedgecock Univ. of Sourthern California
Hydractinia symbiolongicarpus Buss Yale Univ
Ictalurus punctatus and I. Furcatus (catfish) Liu-J Auburn Univ.
Melampsora larici-populina (poplar rust) Martin Institut National de la Recherche Agronomique
Lake Malawi cichlid fish (Metriaclima zebra, Labeotropheus fuelleborni, Melanochromis auratus, Copadichromis conophorus, Rhamphochromis esox) Kocher Univ. of New Hampshire
Mycosphaerella fijiensis (cause of black Sigatoka ) Goodwin USDA-ARS, Purdue Univ
Mytilus californianus (California mussel) Gracey Stanford Univ.
Ostreococcus (green unicellular alga, low-light strain) Palenik UC San Diego
Parhyale hawaiensis and Jassa slatteryi (amphipod crustaceans) Patel UC Berkeley
Petrolisthes cinctipes (porcelain crab) Stillman San Francisco State Univ.
Phycomyces blakesleeanus Corrochano Univ. of Seville
Phytophthora capsici (root and crown rot) Kingsmore Natl. Ctr. for Genome Resources
Piromyces sp. E2 (a chytrid fungus) Baker, S Pacific Northwest Natl. Lab.
Trichoderma virens Ebbole Texas A&M Univ.
Triphysaria versicolor (a parasitic wildflower) Yoder UC Davis
Xanthoria parietina (a lichen fungus) Crittendon Univ. of Nottingham

Bacteria and Archaea

Organism Proposer Affiliation
Acidovorax avenae subsp. Citrulli AAC00-1, Acidovorax JS42, Thermotoga RQ2, and Acidovorax symbiont (Verminephrobacter eiseniae EF01-2) Stahl Univ. of Washington
Verrucomicrobia (Akkermansia muciniphila, Chthoniobacter flavus Ellin428, bacterium Ellin 514, Opitutus terrae, and Victivallis vadensis ATCC BAA-548) Smidt Wageningen Univ.
Alaskan soil microbial community Handelsman Univ. of Wisconsin- Madison
Antarctic marine bacterioplankton Murray Desert Research Inst.
Bacillus coagulans 36D1 Shanmugam Univ. of Florida
Two caulobacter (Caulobacter sp. K31 and Maricaulis maris MCS10) Stephens Santa Clara Univ.
Crenarchaeote community (phylotype C1b.A1) Simon Oregon Health & Science Univ.
Euryarchaeota community Baker, B UC Berkeley
Six archaea (Halorubrum lacusprofundi ATCC 49239, Methanocorpusculum labreanum Z, Methanoculleus marisnigri JR1, Staphylothermus marinus F1, and Thermofilum pendens Woese/ Anderson Univ. of Illinois at Urbana- Champaign
Thermotogales (hyperthermophiles including Fervidobacterium nodosum Rt17-B1, Petrotoga mobilis SJ95, Thermosipho melanesiensis BI429, Thermotoga lettingae TMO, Thermotoga naphthophila, and Thermotoga petrophila RKU-1) Noll Univ. of Connecticut
Hypersaline microbial mats Pace Univ. of Colorado
Korarchaeota community (Candidatus Korarchaeum cryptofilum OPF8, two others) Stetter/ Elkins Univ. Regensberg, Diversa Corp.
Nitrosomonas (isolate IS-79 and oligotropha Nm45) Norton Utah State Univ.
Polynucleobacter necessarius STIR1 and Polynucleobacter sp. QWL-P1DMWA-1 pol_q Hahn Instit. for Limnology, Austria
Salinispora tropica CNB-440 and S. arenicola CNS205 (marine actinomycetes) Jensen Scripps Inst., UC San Diego
Sinorhizobium medicae WSM 419 Reeve Murdoch Univ.
Termite gut microbial community Leadbetter Caltech
Terephthalate (TA) degrading community Liu/ Hugenholtz Natl. Univ. of Singapore
Hyperthermophilic Archaeal Species (Thermoproteus neutrophilus V24Sta , Pyrobaculum aresenaticum DSM 13514, P. calidifontis, P. islandicum, Caldivirga maquilingensis IC-167) Lowe UC Santa Cruz
Opitutaceae bacterium TAV2 (ex. Verrucomicrobium sp. TAV2) Schmidt/ Rodrigues Michigan State Univ.
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