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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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    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)
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    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 Science › Science Programs & Platforms Leads › John Vogel

John Vogel

John Vogel

John Vogel, DOE Joint Genome Institute

Dr. Vogel joined JGI in 2014 to establish a plant functional genomics program. Prior to this, he served as a Research Molecular Biologist at the USDA for 12 years where he was a driving force behind the development of numerous genomic resources that fostered the widespread adoption of Brachypodium distachyon as an experimental model for the grasses. In addition to this fundamental work, he established an efficient switchgrass transformation pipeline and, in collaboration with industrial partners, generated hundreds of transgenic switchgrass lines in an effort to create improved varieties for biomass production. He did his postdoctoral studies at the Carnegie Institution for Science where he studied the molecular basis of a plant host’s susceptibility to pathogens. Dr. Vogel’s current research is focused on developing plant functional genomic resources (e.g. sequenced mutant collections, transformation technology, epigenetic analysis techniques) and utilizing these resources to understand genome organization and regulation, abiotic stress tolerance, and the mechanisms by which plants interact with their microbiomes. In addition, his group conducts comparative genomic research to understand the evolutionary and practical significance of plant pan-genomes including understanding polyploid genome evolution in a pan-genomic context. Dr. Vogel also serves as an adjunct professor at UC Berkeley in the department of Plant and Microbial Biology.

Education

  • BS in Plant Science, Cornell University, NY
  • PhD in Biology, University of Illinois at Chicago, IL

Awards and Service

  • 2018-present  Member ,EcoFAB steering committee
  • 2014-present  Chair, International Brachypodium Steering Committee
  • 2013  USDA Award for Outstanding Performance
  • 2005-2012  USDA Awards for Superior Performance
  • 2008 CSIRO  McMaster Visiting Fellowship Australia

Research Interests

Dr. Vogel’s research is focused on developing plant functional genomic resources and utilizing these resources to understand genome organization and regulation, abiotic stress tolerance and the molecular basis of perenniality. Most projects in his lab utilize B. distachyon and related species as model systems to develop knowledge that will ultimately be used to improve biomass crops like switchgrass. Major projects currently underway include: 1) Using a trio of Brachypodium species as a model for polyploidy in order to understand polyploidy genome evolution and regulation 2) Determining the molecular mechanism of engineered resistance to multiple abiotic stresses and the molecular basis of perenniality using the perennial model grass Brachypodium sylvaticum 3) Developing a comprehensive collection of grass mutants by sequencing chemical and radiation induced mutants.

  • Brachypodium resources

Select Publications

  1. Gordon, et. al. 2020 Gradual polyploid genome evolution revealed by a pan-genomic analysis of Brachypodium hybridum and its diploid progenitors. Nature Communications 11 (1), 1-16 https://doi.org/10.1038/s41467-020-17302-5
  2. Varoquaux, et. al.N. 2019 Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. Natl. Acad. Sci. 116 (52) 27124-27132
  3. Sasse, et. al.J. 2019 Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass New Phytologist 222: 1149-1160 https://doi.org/10.1111/nph.15662
  4. Gordon, et. al. 2017 Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Comm. 8(1), 2184 doi: 10.1038/s41467-017-02292-8
  5. Genetics and Genomics of Brachypodium. 2016 Vogel, J.P., Springer, Switzerland. ISBN: 978-3-319-26942-9
  6. Gordon, et. al. 2014 Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Inbred Lines 2014 Plant Journal 79: 361–374 DOI: 10.1111/tpj.12569
  7. Hsia, et. al. 2017 Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection. Plant Journal 91(3): p. 361-370.
  8. Vogel, et. al., 2010 Genome Sequencing and Analysis of The Model Grass Brachypodium distachyon. Nature. 463: 763-768

 

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