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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 FY14

Approved Proposals FY14

Following are the approved user proposals for fiscal year 2014 including CSP and JGI-EMSL “Facilities Integrating Collaborations for User Science” (FICUS) initiative projects.

Community Science Program (CSP) Plans

Proposer Affiliation Project Description
Banfield, Jillian UC Berkeley, LBNL Community metagenomic and transcriptomic analyses of microbial carbon turnover in grassland soil profiles under two rainfall regimes
Bonito, Gregory Duke University Comparative genomics of early diverging terrestrial fungi and their bacterial endosymbionts
Brem, Rachel UC Berkeley Pioneering fungal mutagenesis using Tn-seq
Brutnell, Thomas Donald Danforth Plant Science Center Doubling the number of Panicoideae genome sequences
Canovas, David University of Seville, Spain Global genomic consequences of the deletion of the Aspergilli non-homologous end joining DNA repair mechanism employed as a genetic tool worldwide
Chen, Jay Oak Ridge National Laboratory RNA-seq-Enabled Expression Quantitative Trait Locus (eQTL) in Populus
Coleman, Jeffrey Alpert Medical School of Brown University/Rhode Island Hospital Exploring the supernumerary chromosomes of the Fusarium solani and Fusarium oxysporum species complexes: Reservoirs for functional genetic diversity
Duplessis, Sébastien INRA, France Combined population genomics and transcriptomics to decipher the molecular bases of virulence and host adaptation in the poplar leaf rust fungus Melampsora larici-populina
Goodwin, Stephen Purdue University Stress responses of fungal saprobes and plant pathogens of the Dothideomycetes
Hammond, Ming UC Berkeley Synthesis and parallel construction of a library of large binary vectors for the screening of suicide exons for multi-gene pathway engineering in plants
Hazen, Samuel University of Massachusetts Synthesis of grass transcription factors for functional characterization in the energy crop model system Brachypodium distachyon
Isaacs, Farren Yale University Harvesting recombinases from metagenomes to develop multiplex genome engineering technologies in microorganisms
Konstantinidis, Kostas Georgia Institute of Technology The microbiome of the upper troposphere and its role in the chemistry of the atmosphere.
Libault, Marc University of Oklahoma Use of a single cell type model, the root hair cell, to advance our understanding of the soybean and sorghum transcriptomic and epigenomic responses to various environmental stresses
Lilleskov, Erik USDA Forest Service, Northern Research Station Fungal, bacterial, and archaeal communities mediating C cycling and trace gas flux in peatland ecosystems subject to climate change
Mockler, Todd Donald Danforth Plant Science Center From sequence to function: Predicting physiological responses in Brachypodium to facilitate engineering of biofuel crops
Molnar, Istvan University of Arizona Leveraging the JGI MycoCosm to functionally characterize orphan polyketide synthase clusters and their predicted bioactive small molecule natural products using comparative metaparvomics and synthetic biology
Mullet, John Texas A&M University Sorghum GENCODE Project
Nelson, Rebecca Cornell University MetaMaize: Characterizing Aboveground Maize-Endophyte Associations Influenced By Host Genotype, Climatic Region, Seed Source, and Tissue Type
Pelletier, Dale Oak Ridge National Laboratory Defining the functional diversity of the Populus root microbiome
Pett-Ridge, Jennifer Lawrence Livermore National Laboratory Unraveling the rhizosphere carbon cycle: Using comparative metatranscriptomics to identify key processes involved in root-enhanced decomposition of organic matter
Schmitz, Robert University of Georgia Harnessing epigenomic reprogramming to improve bioenergy trait performance
Shaw, Jonathan Duke University Development of a Comparative Genomics Resource for Sphagnum magellanicum
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Microbial Dark Matter project phase II – stepping deeper into unknown territory
Stewart, Frank Georgia Institute of Technology Microbial and viral regulation of community carbon cycling across diverse low-oxygen zones
Taylor, John UC Berkeley Fungal response to global change: Adaption to global change and determination of rates of mutation and recombination
Wagner, Michael University of Vienna, Austria Raman-based microcolony genomics and transcriptomics for studying microevolution and ecology of nitrifiers
Whitman, William University of Georgia Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

JGI-EMSL Facilities Integrating Collaborations for User Science (FICUS) Plans

Proposer Affiliation Project Description
Firestone, Mary Kathryn UC Berkeley Mapping soil carbon from cradle to grave: using comparative transcriptomics, proteomics and metabolite analysis to identify the microbial blueprint for root-enhanced decomposition of organic matter
Hansel, Colleen Woods Hole Oceanographic Institution Genome-enabled Investigations of the Role of Secreted Proteins and Reactive Metabolites in Carbon Degradation by Pure and Mixed Ascomycete Fungal Communities
Harris, Steven University of Nebraska-Lincoln Engineering morphology and secretion to enhance the productivity of fungal fermentations
Hess, Matthias Washington State University Tri-Cities FECB: A Functional Encyclopedia of Cyanobacteria – Building the knowledge framework for an enhanced understanding of carbon and nitrogen cycling
Hofmockel, Kirsten Iowa State University Development of novel approaches to target microbial drivers of C cycling in soil aggregates
Kistler, Harold USDA ARS Cereal Disease Laboratory Organelles promoting high level terpenoid biosynthesis in filamentous fungi
O’Malley, Michelle Ann UC Santa Barbara Identification and Regulation of Cellulases within Novel Anaerobic Gut Fungi
Weyman, Philip J. Craig Venter Institute Functional genomics of moss-cyanobacteria interactions in boreal forest ecosystems
  • Approved Proposals FY23
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  • Approved Proposals FY21
  • Approved Proposals FY20
  • Approved Proposals FY19
  • Approved Proposals FY18
  • Approved Proposals FY17
  • Approved Proposals FY16
  • Approved Proposals FY15
  • Approved Proposals FY14
  • Approved Proposals FY13
  • Approved Proposals FY12
  • Approved Proposals FY11
  • Approved Proposals FY10
  • Approved Proposals FY09
  • Approved Proposals FY08
  • Approved Proposals FY07
  • Approved Proposals FY06
  • Approved Proposals FY05
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