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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.

    Read more

    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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User Programs
Home › User Programs › User Support › Project Management Office (PMO)

Project Management Office (PMO)

The Project Management Office (PMO) Team:

Christa Pennacchio Special Projects
Christa Pennacchio, PMO Lead, Metabolomics Program
Kerrie Barry Plant and Fungal Genomics Programs
Kerrie Barry, Plant and Algal Genomics
Natasha Brown, Supply Chain Manager
Natasha Brown, Supply Chain Manager
Tijana Glavina del Rio Metagenomics Program
Tijana Glavina del Rio, Metagenomics
Danielle Graham, Workflow Project Manager

Nancy Hammon, Workflow Planning Manager
Miranda Harmon-Smith DNA Synthesis and Single-Cell Genomics
Miranda Harmon-Smith, DNA Synthesis and Single-Cell Genomics
Vivian Ng Project Manager
Vivian Ng, Fungal Genomics
Nicole Shapiro Microbial Genomics Program
Nicole Shapiro, Microbial Genomics

How PMO Works

JGI Project Managers work with users and JGI scientists and technical staff to prepare a Statement of Work (SOW) document that defines the scope of sequencing and analysis and lays out roles and responsibilities. The SOW includes the following items:

  • Defined source, protocols, and timeline for the provision of DNA/RNA material, libraries, and any other resources needed to initiate the project, including required ancillary documentation (e.g., experimental data supporting genome size estimates, community resources, etc.).
  • Platform and approximate quantity of JGI sequencing to address the scientific goals of the project, and timeline for the generation of this data, including responsibilities for analysis of pilot sample data to assess sequence for contamination, uniformity, and other quality control checks at the initial stages of the project. If contamination is a problem at this stage, the project may be suspended until suitable materials are available.
  • Defined plan for maintaining regular communication between the JGI and collaborators through the duration of the project.
  • Defined responsibilities for collaborators and the JGI after the completion of sequencing, including genome assembly, automated and/or manual annotation, and other analyses, and initial plan for experimental and/or computational studies needed to address the specific scientific aims of the project.
  • The initial publication plan, including a provisional timeline and anticipated authorship. To the extent that JGI scientists contribute scientific and/or technical expertise or leadership to the project, it is expected that they will participate in the publication.
  • Acknowledgment of JGI Data Release policies, and affirmation that the project will conform to applicable safety regulations, including regulations that govern organisms that are pathogenic or could potentially be used as bioweapons.

Additionally, before work can begin, users must sign a formal User Agreement that defines legal responsibilities of the JGI and the User.   Depending on the type of project, additional agreements may be needed.

Once a proposal has been approved through the review process, and the Statement of Work and User Agreement documents (if applicable) have been signed, the project may begin. Essential elements of the project are entered into JGI’s LIMS (Integrated Tracking System, or ITS) to allow staff to understand the requirements, history and status of any JGI project.  Active project management involves the following considerations:

  • Designation of a Project Manager within the JGI.
  • Designation of a principal collaborator or “Project Representative,” not necessarily the original applicant, who will be the JGI’s main point of contact throughout the duration of the sequencing project.
  • The collaborator will provide DNA or RNA, libraries, and other materials as described in the Statement of Work. Detailed guidelines for DNA/RNA submission are available. All materials described in the project proposal must be available with the appropriate documentation and should be submitted to the JGI as specified by the Project Manager. Failure to provide materials described in the proposal in a timely fashion may lead to cancellation of the project and/or return of the proposal to the review panels.
  • All source materials must pass the JGI QC process. Work will not commence on a new or resubmitted project component until the source material has passed the QC process.
  • The JGI’s Project Manager will communicate with the Project Representative to confirm, in a timely manner, when the initial sample data is of appropriate quality, free of contamination, etc.
  • Samples from approved projects will enter the production queue. This queue is managed primarily on a first-in/first-out basis, so it can take weeks or months for actual production to begin on a project, depending on the current workload and the length of time required to prepare and quality control representative libraries. Scheduling of the sequencing will be at the discretion of the JGI, given the overall production sequencing queue and the need to optimize available resources.

The post-sequencing analysis and publication plans must be coordinated and scheduled as specified in the Statement of Work.

  • Institutional User Agreements
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  • Sequence Submission Requirements - DNA Synthesis Program
  • Project Management Office (PMO)
  • Project Management FAQ
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