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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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Our Projects
Home › Our Projects › Approved User Proposals › Approved Proposals FY15

Approved Proposals FY15

Following are the approved user proposals for fiscal year 2015 including CSP and JGI-EMSL Collaborative Science Initiative projects.

FY 2015 Community Science Program (CSP) Plans

Proposer Affiliation Project Description
Baliga, Nitin Institute of Systems Biology Genome-wide analysis of chromatin accessibility and miRNA-mediated transcriptional regulation of lipid accumulation in Chlamydomonas reinhardtii
Banfield, Jill University of California, Berkeley Genome-resolved metagenomic analysis of microbial function in the subsurface
Banfield, Jill University of California, Berkeley Tree-driven diel microbial carbon dynamics in the vadose zone
Barrasa, Jose Maria University of Alcala  (Spain) Study of the lignocellulolytic machinery in saprobic wood and leaf litter degrading Agaricales
Busby, Posy University of Washington Mechanisms of interaction in the foliar fungal microbiome of Populus trichocarpa
Cadillo-Quiroz, Hinsby Arizona State University Microbial composition and metagenomic functional potential across tropical peatlands: comparative evaluation and modeling of C decomposition to greenhouse gases
Campbell, Barbara Clemson University Biogeochemical cycling links between terrestrial and marine systems
Cavicchioli, Rick University of New South Wales (Australia) Seasonal variation in Antarctic microbial communities: ecology, stability and susceptibility to ecosystem change
Chistoserdova, Ludmila University of Washington Methane oxidation as a community function: defining partnerships and strategies through sequencing metagenomes and metatranscriptomes of laboratory manipulated microcosms
DiFazio, Steven West Virginia University Sex determination in the Salicaceae
Frank, Carolin University of California, Merced Diazotrophic aboveground endophytes in native pines, poplar and willow
Fredrickson, Jim PNNL Spatio-temporal functional profiling in model microbial communities
Hallam, Steven University of British Columbia (Canada) Microbial engines driving organic matter transformations in the dark ocean: an integrated biological and chemical perspective
James, Timothy University of Michigan Revealing the ecological function of uncultured fungal dark matter in freshwater ecosystems using single cell genomics
Klassen, Jonathan University of Connecticut Metagenomic mining of natural product diversity and understanding its contribution to ecosystem function in the cellulolytic fungus-growing ant symbiosis
Klenk, Hans-Peter; Goker, Markus University of Newcastle (UK); DSMZ (Germany) Exploiting the genomes of the Actinobacteria: plant growth promoters and producers of natural products and energy relevant enzymes united in a taxonomically unresolved phylum
Lamendella, Regina Juniata College Systems biology approach to fracking for environmental monitoring
Laudencia-Chingcuanco, Debbie USDA-ARS Creating a genome-wide sequence-indexed collection of grass mutants
Liu, Wen-Tso University of Illinois Shedding light on the anaerobic wastewater treatment “black-box” in anthropogenic carbon cycling: exploring the uncharted ecological function of uncultured microbial taxa through next-generation sequencing technology
Loper, Joyce USDA-ARS Exploring the genomic diversity of the Pseudomonas fluorescens group
Medina-Munoz, Monica Penn State University How do coral hosts communicate with their associated microbial community?
Peay, Kabir Stanford University Coprophilous fungi as a model system for understanding the metagenomics of carbon cycling in microbial eukaryote communities
Simon, Holly Oregon Health & Science University A systems approach to evaluate physical constraints and microbial controls on fluxes of nutrients and energy in a coastal ecosystem
Sorek, Rotem Weizmann Institute of Science (Israel) Comparative genomics of a single organism: In search of acquired immunity in trees
Swaminathan, Kankshita University of Illinois Understanding variance in allele specific expression in the polyploid Saccharinae
Thon, Michael University of Salamanca (Spain) Evolution and adaptation of carbohydrate utilization in the Colletotrichum acutatum species complex
Treseder, Kathleen University of California, Irvine Genomes and transcriptomes of decomposer fungi responding to warming in Alaskan boreal forest
Wildermuth, Mary University of California, Berkeley Comparative genomics of powdery mildews and associated host plants
Wosten, Han Utrecht University (Netherlands) Functional genomics of lignocellulose degradation by Agaricomycete fungi
Wurzbacher, Christian IGB (Germany) Whole genome sequencing of aquatic fungi responsible for the degradation of recalcitrant substrates in liquid environments
Young, Erica University of Wisconsin Metagenome and metatranscriptome of complex algal communities growing in wastewater: Bioremediation, nutrient transformation, carbon sequestration
Zhang, Baohong East Carolina University Panicum virgatum small RNA sequencing to identify gene expression changes related to biofuel traits

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

Proposer Affiliation Project Description
Colwell, Frederick Oregon State University Integrated Biogeochemical Modeling of Microbial Consortia Mediating Anaerobic Oxidation of Methane in Dynamic Methane Hydrate-bearing Sediments
Crump, Byron Oregon State University Decoding DOM Degradation: How Does Carbon Source and Sunlight Exposure Alter Microbial Metabolism and Expression of Genome-Encoded Metabolic Degradation of Permafrost Organic Matter?
Cumming, Jonathan West Virginia University Mapping the Metabolism of Nutrient and Carbon Exchange in the Plant-Microbe Symbiosis
de Vries, Ronald CBS-KNAW Fungal Biodiversity Centre Dissecting Intraspecies Diversity in Fungal Wood Decay
DiChristina, Thomas Georgia Institute of Technology Sensing External Metals by Outer Membrane Beta-Barrel Proteins
Lebeis, Sarah University of Tennessee Uncovering the Composition and Function of the Aquatic Microbiome for Duckweeds
Luthey-Schulten, Zaida University of Illinois at Urbana-Champaign Quantifying Differential Expression and Identifying Bottlenecks in Methanogenic Pathways
Magnuson, Jon Pacific Northwest National Laboratory Elucidating the Influences of Engineered N-glycosylation Motifs in Bacterial Biomass Hydrolyzing Enzymes upon Heterologous and Native Gene Expression, Secretion and Degradation in Aspergillus niger
Rich, Virginia University of Arizona Systems-level Insights into Carbon Transformations in Thawing Permafrost by Parallel High-resolution Organic Matter and Microbial Community Characterizations
Stegen, James Pacific Northwest National Laboratory Coupling Microbial Communities to Carbon and Contaminant Biogeochemistry in the Groundwater-Surface Water Interaction Zone
Vilgalys, Rytas Duke University Integrated Genomic/Transcriptomic/Secretomic Study of Plant-Fungal Interactions Between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Mushroom Genus Suillus
Wrighton, Kelly The Ohio State University Microbial Controls on Biogeochemical Cycling in Deep Subsurface Shale Carbon Reservoirs
  • Approved Proposals FY21
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  • 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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