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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 FY19

Approved Proposals FY19

Following are the approved user proposals for fiscal year 2019, including CSP, CSP New Investigator, Synthesis, and FICUS JGI-EMSL.

Community Science Program (CSP)

Proposer Affiliation Project Description
Airo, Alessandro Berlin Institute of Technology (Germany) Past and modern microbial communities in million-year-old Atacama Desert and their role in biogeochemical cycling in hyperarid environments
Blanchard, Jeffrey University of Massachusetts-Amherst Molecular responses to a short-term temperature shift in a long-term soil warming experiment at Harvard Forest
Bowen, Jennifer Northeastern University Nitrate in coastal waters: shifting the balance from carbon sink to carbon source
Brown, Judith The University of Arizona Characterizing infections and host-pathogen interactions of Chlorella spp. by the predatory algal bacterial pathogen, Vampirovibrio chlorellavorus
Carini, Paul The University of Arizona Adaptive strategies in a cosmopolitan and abundant soil bacterium: metabolic flexibility or genome divergence?
D’Hont, Angelique CIRAD (France) Genomic diversity in the Saccharum complex for improvement of sugarcane as an energy crop
Freitag, Michael Oregon State University The curse of being first meets the need to be complete: Finishing genomes to leverage additional information from completed and ongoing JGI CSPs
Gladieux, Pierre INRA (France) Comparative genomics and association mapping in Sordariales: insights into functional diversity in Neurospora and its relatives
Greenham, Katie University of Minnesota Leveraging pan-genomes to investigate diel transcriptomic and metabolomic responses to abiotic stress in B. rapa and B. napus diversity panels.
Hazen, Samuel University Of Massachusetts-Amherst Regulatory Genomics of Plant Biomass Accumulation
Leakey, Andrew University of Illinois at Urbana-Champaign Transcriptomics of water use efficiency traits in Sorghum and Setaria
Liao, Hui-Ling NFREC/University of Florida Genetic, community, and ecosystem consequences of co-introduction of mycorrhizal fungi with exotic pines
Malagnac, Fabienne University Paris Sud (France) Linking epigenomic regulation of carbon acquisition to nutrient use in fungi
McMahon, Trina University of Wisconsin-Madison Extended temporal dynamics of microbially-mediated freshwater carbon processing as revealed through time-series metagenomes
Moore, Bradley University of California, San Diego Exploring algal biodiversity for the production of chemical feedstocks and other biotechnological applications
Nagy, Laszlo Biological Research Center (Hungary) Fungal Comparative ENCODE Project: FUNCODE
Rodrigues, Jorge University of California, Davis Partitioning the Biological Causes of Methane Flux Variation in the Amazon Rainforest
Salome, Patrice University of California, Los Angeles Control of mRNA half-life Across the Diurnal Cycle in the Model Alga Chlamydomonas
Van de Peer, Yves Ghent University/VIB (Belgium) Marine Angiosperm Genome Initiative (MAGI)
Weston, David Oak Ridge National Laboratory Elucidating Sphagnum Microbiome Genetic Interactions for Improved Plant Growth to Warming
Whitman, William University of Georgia Genome Encyclopedia of Bacteria and Archaea VI: Functional Genomics of Type Strains
Wilhelm, Steven The University of Tennessee Algal, Bacterial and Viral Interactions as the Backdrop to Marine Carbon and Trace Metal Cycling
Wrighton, Kelly Colorado State University From genomes to updated biogeochemical models: Targeting critical knowledge gaps in methanogenesis from soil systems

CSP New Investigator

Proposer Affiliation Project Description
Bouskill, Nicholas Lawrence Berkeley National Laboratory Microbial environmental feedbacks and the evolution of soil organic matter
Carlos-Shanley, Camila Texas State Univeristy Functional genomics of gut bacteria from endangered species of beetles from the Edwards Aquifer
Dassanayake, Maheshi Louisiana State University A transcriptome atlas enabling discovery of genes evolved as adaptations to environmental stress in a model extremophyte, Schrenkiella parvula
Davis, Richard Jacobs Engineering/JETS Temporal and Spatial Exploration of Fumarolic Ice Cave Microbial Communities
Emerson, Joanne University of California, Davis Elucidating depth-resolved viral links to soil carbon chemistry and crop yields in agricultural systems
Fabiano, Elena IIBCE Searching for New Bacterial Functions in Antarctic Lithobionts
Hughes, Karen University of Tennessee Utilizing microbial functional responses to follow soil carbon and nutrient cycling recovery and resilience following the November 2016 fire in the Great Smoky Mountains National Park
Kluge, Mariana SLU – Swedish University of Agricultural Sciences (Sweden) The fungal contribution to the carbon cycle of Subarctic and Arctic permafrost areas
Moghe, Gaurav Cornell University High-throughput annotation of metabolic enzymes in Brachypodium distachyon using correlated transcriptomics and metabolomics
Rivers, Adam USDA – Agricultural Research Service Developing probabilistic graphical models and analysis software to integrate multi-omics data
 

Schultzhaus, Zachary

Naval Research Laboratory Functional Genomics and Transcriptomics to Target Mechanisms of Radiation Resistance in Melanized Fungi
Searcy, Christopher University of Miami Fire selection and the carbon cycling potential of the soil microbiome
Strack, Maria University of Waterloo (Canada) Microbial processes in restored and unrestored post-extraction peatlands: key to understanding greenhouse gas emissions from managed wetland ecosystems

FY 2019 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Plans

Proposer Affiliation Project Description
Boye, Kristin Stanford Linear Accelerator Center Microbial Metabolic Activity and Biogeochemical Reaction Networks in Redox Cycled Alluvial Systems
de Vries, Ron Westerdijk Fungal Biodiversity Institute Validation of The Transfer of Metabolic Models From Aspergillus niger to Other Fungi Using an Orthology-Based Approach
Hom, Erik University of Mississippi Probing Microbial Interactions and Coordinated Trophic Responses in Biological Soil Crusts
Moran, James Pacific Northwest National Laboratory Linking Phosphorus and Carbon in Rhizosphere Nutrient Cycling
O’Malley, Michelle University of California, Santa Barbara Deciphering the Structure & Function of Secondary Metabolites from Anaerobic Fungi
Oono, Ryoko University of California, Santa Barbara Plant Litter Degradation and Microbial Defense by Host-Specific Fungal Endophytes
Shaked, Yeala Hebrew University of Jerusalem Interactive Mechanisms of Mineral Dissolution by A Microbial Consortia
Solomon, Kevin Purdue University Epigenetic Regulation of Anaerobic Fungi for Increased Lignocellulose Degradation
Trinh, Cong University of Tennessee Understanding and Harnessing the Robustness of Undomesticated Yarrowia lipolytica Strains for Biosynthesis of Designer Bioesters
Weston, David Oak Ridge National Laboratory Consequences of Plant Genetic Variation and The Surrounding Microbiome on Nitrogen Fixation
Wilkins, Michael Colorado State University Hydrobiogeochemical Feedbacks Across Seasonal and Decadal Time-Scales: Implications For Solute Fate and Transport in Riverbed Ecosystems
Zimmerman, Richard Old Dominion University Experimental Impacts of Climate Warming and Ocean Acidification on Metabolic Function and Blue Carbon Accumulation by Eelgrass

 

  • Approved Proposals FY23
  • Approved Proposals FY22
  • 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
  • ETOP Projects

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