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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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News & Publications
Home › News & Publications › Podcasts

Podcasts

The JGI launched two podcasts in March 2020. Check out these audio stories, complete with transcripts.

Genome Insider hosted by Menaka Wilhelm

Menaka WIlhelm

“Genome Insider” is a podcast that showcases the work of JGI collaborators in brief forays, connecting audiences with the people behind the science. Hear diverse voices in science talk about their groundbreaking research to better understand — and harness — the superpowers encoded in plants, fungi, microalgae, environmental viruses, and bacteria to contribute to a more sustainable world. Learn about JGI-supported projects, delving into the researchers’ motivations, the insights that amaze them, and how their work contributes to solving energy and environmental challenges.

Natural Prodcast hosted by Dan Udwary

Dan Udwary

“Natural Prodcast” is a “fireside chat”-style podcast about natural products and the science and scientists of secondary metabolism. Natural products, secondary metabolites, and specialized metabolites all refer to the chemicals that make species unique and different from one another. They are incredibly important to medicine, the environment, and human health. As the JGI acts on its goals in — and builds out its capabilities for — secondary metabolism research, “Natural Prodcast” serves as an important line of communication to the scientific community. Host Dan Udwary talks to luminaries in the field about current and future developments, and how the JGI can be part of that space.

 

Recent and Past Podcasts from JGI

Listen to all the latest episodes of Genome Insider and Natural Prodcast.

Genome Insider is available on Apple Podcasts, Google Play, Spotify, iHeart Radio, and TuneIn Radio – Subscribe today! Natural Prodcast is available on Apple Podcasts, Google Play, and Spotify – Subscribe today!

  • JGIota: Sequencing Shiitakes with David Hibbett (3/2/2023) - David Hibbett (Clark University) fills us in on the kind of decay that makes shiitake mushrooms special. This week, he 39 collaborators published a paper tracing how these mushrooms have evolved.
  • Natural Prodcast Episode 19 – Bill Fenical (2/9/2023) - Natural Prodcast guest William Fenical of the Scripps Institution of Oceanography on the beginnings of marine natural products, his experiences in drug discovery, and exploring marine bacteria for novel chemistry.
  • Natural Prodcast Episode 18 – A CSP Primer (1/25/2023) - A crossover podcast on the JGI's Community Science Program: what a CSP is, how you apply for and get one, and what happens once you do.
  • Genome Insider S3 Episode 5: Work With the JGI! Tips for a Winning CSP Proposal (12/8/2022) - The JGI’s Community Science Program gives researchers access to all kinds of sequencing, ‘omics and bioinformatics capabilities — and it’s open to scientists at any career stage, anywhere in the world, for free. We accept new projects related to energy and the environment several times a year. A few proposal calls have deadlines coming up – in January, March, and later on in the spring. In this episode, hear proposal tips from Tanja Woyke, who runs user programs at the JGI, and project manager Miranda Harmon-Smith, who helps shepherd CSP projects along.
  • JGIota: Looking back at how our cow rumen study drives higher learning (11/17/2022) - Hear from CSU-San Marcos course instructor Matt Escobar and UC Davis Associate Professor Matthias Hess, also the chair of the JGI User Executive Committee, on how a JGI study on cow rumen went from the lab to the classroom.
  • Genome Insider S3 Episode 4: From Sample Shipments to Sequences – A Tour of the JGI’s Sequencing Pipeline (11/3/2022) - Every year, the JGI sequences around 35,000 samples — from plants, algae, bacteria, archaea, fungi, viruses — to support scientists around the world. Most of those researchers send their samples in from afar, without ever hearing much about the sequencing lab. So today, Chris Daum walks through the JGI’s sequencing pipeline, where there are freezers with names — but not doors — and robots handle a bunch of benchwork.
  • JGIota: Looking Back at Methane-Making Microbes (10/6/2022) - Since 2010, the JGI has supported researchers studying microbial methane-makers. Eventually, that could help us dial back their emissions, while still producing things like meat, milk, and wool.
  • Genome Insider S3 Episode 3: The Fungi That Survive in Antarctica (9/22/2022) - Black fungi are microscopic and mighty. They survive everywhere from Antarctica to Joshua Tree National Park, despite extremely harsh conditions. And their survival secrets could one day help other organisms survive hotter, drier climates. So University of Tuscia researchers Laura Selbmann and Claudia Coleine are working with scientists from around the world – and the JGI – to understand them better.
  • JGIota: Looking Back at Sequencing for Soybeans (9/15/2022) - In honor of the JGI's 25th anniversary, a JGIota episode on soybean, a crop that could boost biofuels and fertilize fields.
  • Genome Insider S3 Episode 2: Better Crops With a Pointillist Approach to Plant Genomics (8/25/2022) - In this episode, we peer into plant cells. Researchers are using measurements from single cells to understand which genes help plants grow, get nutrients, weather drought, and more. And eventually, their findings could help us grow better crops, with less impact on our planet.
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