Genome Insider

JGI
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Stories where genes and genomes are key to solving energy and environmental challenges. Hear diverse voices in science talk about their JGI-supported research to better understand — and harness — the superpowers encoded in plants, fungi, microalgae, environmental viruses, and bacteria to contribute to a more sustainable world. 

  1. 04/15/2025

    SIPs with Standards

    Stable Isotope Probing (SIP) is a powerful technique for studying microbial communities. These experiments can show which microbes are handling specific nutrients, or what they're doing with those nutrients, and even how quickly. But there's a catch: SIP labwork and analysis can be very demanding.  The JGI offers SIP analysis to make these experiments accessible to more researchers. Ultimately, the goal is to generate SIP data that can be useful to multiple teams and analyses. This episode, Rex Malmstrom (JGI), and Roli Wilhelm (Purdue University), share a few different ways they're working to make this technique, SIP, more standardized -- more reproducible, more reusable, and more insightful, for the future of studying microbial communities. Links from this episode: Submit your own proposal to work with the JGIFind all episode transcripts on our website JGI’s Micro-Scale Applications GroupMISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experimentHT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi Webinar: Metagenome quantitative SIP at the JGI: https://www.youtube.com/watch?v=5OgLDTw7eYA  Genome Insider: Party in the Rhizosphere Genome Insider: A Powerful Technique to Study Microbes, Now Easier  Simulating metagenomic stable isotope probing datasets with MetaSIPSim  Microbes Persist: Systems Biology of the Soil Microbiome Science Focus Area (SFA), led by Dr. Jennifer Pett-Ridge at Lawrence Livermore National Laboratory (LLNL)Our contact info:X: @JGIEmail: jgi-comms at lbl dot gov

    21 min
  2. Adopt-A-Genome

    10/11/2024

    Adopt-A-Genome

    In this episode, undergraduates adopt genomes that the JGI sequenced, but never published in the literature. These students analyze the genomes, write reports, and publish first-author papers, making the data available for future research.  Hear from Rekha Seshadri (JGI) and Matt Escobar (California State San Marcos) about how the Adopt-A-Genome project got started. Plus, Kalyani Maitra (California State Fresno) and two students, Angela and Mark Soghomonian share what it was like to take on one of these genomes. Links from this episode: Submit your own proposal to work with the JGIFind all episode transcripts on our website For more information about Adopt-A-Genome:Rekha Seshadri: rseshadri@lbl.gov Matt Escobar: mescobar@csusm.edu  Adopt-A-Genome Papers: Draft genome sequence of Nitrobacter vulgaris DSM 10236TDraft genome sequences of Butyrivibrio hungatei DSM 14810 (JK 615T) and Butyrivibrio fibrisolvens DSM 3071 (D1T)Genome sequences of key bacterial symbionts of entomopathogenic nematodes: Xenorhabdus cabanillasii DSM17905, Xenorhabdus ehlersii DSM16337, Xenorhabdus japonica DSM16522, Xenorhabdus koppenhoeferii DSM18168, and Xenorhabdus mauleonii DSM17908 Our contact info:X: @JGIEmail: jgi-comms at lbl dot gov

    27 min
  3. Gotta Catch 'Em Gall

    08/01/2024

    Gotta Catch 'Em Gall

    Kasey Markel and Patrick Shih (UC Berkeley and the Joint BioEnergy Institute) are looking for new ways to engineer plants. So they’ve looked into wasps that program oak trees to grow structures called galls. In this episode, hear from Kasey and Patrick about how this project unfolded, and how they worked with the JGI's metabolomics program to find out more about these weird little pods. Links from this episode: Submit your own proposal to work with the JGIJoin us at the 2024 JGI User Meeting Find all episode transcripts on our websitePaper: Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov Sound effects credits: oars.wav by hazureParma Park Bird Song with Stream.WAV by muneio

    25 min
  4. A Redesign for Yeast’s Genome, Chromosome by Chromosome - Jef Boeke, Weimin Zhang & Leslie Mitchell

    06/28/2024

    A Redesign for Yeast’s Genome, Chromosome by Chromosome - Jef Boeke, Weimin Zhang & Leslie Mitchell

    To engineer yeast to do more, and understand genomes in general, Jef Boeke, Weimin Zhang (NYU Langone Health) and Leslie Mitchell (Neochromosome) have worked to replace yeast’s native chromosomes with synthetic versions. This project has turned out to be an international collaboration, with some artistic endeavors along the way. Eventually, the goal is to create an entirely human-generated yeast genome. Links from this episode: Submit your own proposal to work with the JGIJoin us at the 2024 JGI User Meeting Find all episode transcripts on our websitePaper: Manipulating the 3D organization of the largest synthetic yeast chromosomeNYU Release: Researchers Assemble Nine Synthetic Yeast Chromosomes Our contact info:X: @JGIEmail: jgi-comms at lbl dot gov

    21 min
  5. Forest Fungi, Seagrass, and a New View of Symbiosis

    06/13/2024

    Forest Fungi, Seagrass, and a New View of Symbiosis

    Three stories of JGI-supported research, connected to nutrient cycles. Francis Martin and Lucas Auer discuss their work on communities of forest floor fungi. Allison Joy looks into seagrass meadows' carbon sequestration with insights from Adam Healey and Xiao Ma. And Karen Serrano and Benjamin Cole explain their research on the symbiotic relationship between mycorrhizal fungi and plant roots.  Links from this episode: Submit your own proposal to work with the JGIJoin us at the 2024 JGI User MeetingFind all episode transcripts on our website Feature: Getting to the Bottom of Fungal Functions Across Earth’s ForestsPaper: Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems Feature: Eelgrass proves to be much younger than we thoughtPaper: Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)Paper: Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment Paper: Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

    27 min
  6. What Happens To a Rainforest When You Dial Up Drought? - Linnea Honeker and Malak Tfaily

    05/30/2024

    What Happens To a Rainforest When You Dial Up Drought? - Linnea Honeker and Malak Tfaily

    Rainforests store a big fraction of all the carbon on Earth, and soil microbes play a key role in pulling that carbon out of the atmosphere. This episode, researchers take a look at what happens to that storage when a rainforest hits a drought. Tag along with their experiments in a fully enclosed, human-made ecosystem: Biosphere 2.  Links from this episode: Submit your own proposal to work with the JGIJoin us at the 2024 JGI User MeetingFICUS program Find all episode transcripts on our websitePaper: Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest  https://doi.org/10.1038/s41564-023-01507-7 Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

    23 min

  7. 12/21/2023

    The Megadata of Lake Mendota - Part 3: Boating Out to David Buoy

    This is the third and final episode of our series on a giant metagenome assembly from Wisconsin’s Lake Mendota. In the last two episodes, we’ve covered the specialized software and supercomputers behind this project. But every part of this project depends on lakewater samples — so this episode is a look at how researchers get these specialized snapshots of a freshwater ecosystem. Links from this episode: Submit your own proposal to work with the JGIFind all episode transcripts on our websiteRelated papers: Species invasions shift microbial phenology in a two-decade freshwater time seriesTerabase-Scale Coassembly of a Tropical Soil MicrobiomeOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

    25 min

  8. 12/07/2023

    The Megadata of Lake Mendota - Part 2: Souped Up Computing

    This series is the story of a giant metagenome assembly from Wisconsin’s Lake Mendota. In this episode: a look at the supercomputing that stitches together large datasets with the assembler program MetaHipMer2. Oak Ridge National Lab is home to two supercomputers — Summit and Frontier — that process terabytes of data with MetaHipMer2. And the National Energy Research Scientific Computing (NERSC) has another supercomputer, Perlmutter that works at large scale. But nearby the JGI, a cluster called Dori is also capable of running smaller assemblies — so we head there for a sense of what this supercomputing looks like. Links from this episode: Submit your own proposal to work with the JGIFind all episode transcripts on our websiteRobert Riley at the 2016 DOE JGI Genomics of Energy & Environment MeetingMetaHipMerThe ExaBiome ProjectOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

    22 min
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About

Stories where genes and genomes are key to solving energy and environmental challenges. Hear diverse voices in science talk about their JGI-supported research to better understand — and harness — the superpowers encoded in plants, fungi, microalgae, environmental viruses, and bacteria to contribute to a more sustainable world. 

Information

  • Creator
    JGI
  • Years Active
    2020 - 2025
  • Episodes
    51
  • Rating
    Clean
  • Copyright
    © 2025 U.S. Department of Energy Joint Genome Institute
  • Show Website
    Genome Insider