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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)
    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
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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 › User Programs › Special Initiatives & Programs › Partnerships Development Team (PDT) › JGI Partnership Case Study: Brightseed

JGI Partnership Case Study: Brightseed

Katherine Louie (foreground), JGI Metabolomics Platform Group Lead.

In response to varying environmental conditions, plants produce a panoply of chemical compounds, the vast majority of which have yet to be characterized. Therein lies an opportunity: to identify specialized metabolic pathways that can be engineered for ecological, agronomic, specialty chemical, or human health applications. The question is: can the analysis of advanced multi-omic data, such as those generated by high-throughput DNA sequencing and liquid chromatography-mass spectrometry (LC/MS), be brought to bear on natural product discovery?

Brightseed, a San Francisco-based biosciences company founded in 2017, has developed Forager™, a computational intelligence whose learning objective is to understand nature more profoundly than humans can.  Forager is fueled by Brightseed’s growing proprietary data on the world’s plant life and deep knowledge of human biology.  Forager interrogates and learns with unprecedented speed and scale, discovering natural compounds that solve unmet human needs, including addressing chronic health indications and other emerging market opportunities. To drive this effort forward, Brightseed sought a partner that could help them determine how best to integrate large-scale metabolomic and transcriptomic data sets into Brightseed’s discovery process. That’s where the U.S. Department of Energy Joint Genome Institute (JGI) factored into the equation.

“We were in need of a unique combination of expert domain knowledge of plant natural products, with access to mass spectrometry characterization of plant tissue, and the specialized bioinformatics tools to interpret the most complex data sets,” said Lee Chae (PhD, UC Berkeley, Plant Biology, Computational and Genomic Biology, 2008), Brightseed Co-Founder and Chief Technology Officer. He turned to Trent Northen and his colleagues in the JGI’s Metabolomics Technology Group.

JGI performed a secondary metabolite analysis on a subset of Brightseed’s plant compound library to enable the company to gauge detection capabilities and limitations, compound abundance, and to identify and annotate secondary metabolites from plant extracts from three underrepresented flowering plant families with a history of human consumption.

“What particularly accelerated progress toward achieving Brightseed’s goals was gaining access to MAGI, and the sage interpretation of the results by Ben,” said Gabriel Navarro, (PhD, UC Santa Cruz, Natural Products Chemistry, 2013), Brightseed’s program lead for the collaboration with JGI. MAGI, the Metabolite Annotation and Gene Integration tool, is the brainchild of Ben Bowen in the Northen Lab. MAGI provides a fundamentally different approach for directly linking novel sequences to their biochemical functions and products by generating a metabolite-gene association score using a biochemical reaction network.

“Metagenomics and single-cell sequencing have provided us a glimpse into the vast metabolic potential of Earth’s complex biological systems,” Bowen said. “Yet, we’ve been stymied in our ability to accurately predict and identify the products of most biosynthetic pathways. Most of what we have known of microbial biochemistry was based on characterization of a few model microorganisms, and through sequence correlations based on publicly-available data. We saw this as an opportunity, so we built MAGI to make connecting metabolomics data with genes easier for researchers.”

MAGI also enabled Brightseed to identify critical knowledge gaps and to quickly close them.

“JGI’s team was very knowledgeable in guiding Brightseed through the project, helping us understand their technology platform and providing us what we needed to know so that we could consider investing in our own instrument,” Navarro said. “Our overall positive experience with JGI—clear communication, rapid turn-around, and high-quality results—encourages us to pursue a future project in the near-term.”

Bowen, Northen and other colleagues from the Lawrence Berkeley National Laboratory’s Environmental Genomics and Systems Biology Division in the Biosciences Area, the Data Analytics and Visualization Group of the Computational Research Division, and the National Energy Research Scientific Computing Center (NERSC) recently published an article about MAGI in ACS Chemical Biology.

MAGI is freely available for academic use, both as an online tool at https://magi.nersc.gov, and with source code available at https://github.com/biorack/magi. For more information about how to partner with the JGI, see the different mechanisms described here. To learn more about Brightseed here.

  • Partnerships Development Team (PDT)
    • JGI Partnership Case Study: Brightseed

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