Podcast
Genome Insider
Hosted by JGI · EN
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.
10episodes
Episodes
Newest firstAll episodes
SIPs with Standards
Apr 15, 202500:21:00Tap to summarizeStable 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 websiteJGI’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 fungiWebinar: 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
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Adopt-A-Genome
Oct 11, 202400:26:45Tap to summarizeIn 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 websiteFor 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 DSM17908Our contact info:X: @JGIEmail: jgi-comms at lbl dot gov
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Gotta Catch 'Em Gall
Aug 1, 202400:24:31Tap to summarizeKasey 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 MeetingFind all episode transcripts on our websitePaper: Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing gallsOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot govSound effects credits: oars.wav by hazureParma Park Bird Song with Stream.WAV by muneio
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A Redesign for Yeast’s Genome, Chromosome by Chromosome - Jef Boeke, Weimin Zhang & Leslie Mitchell
Jun 28, 202400:20:53Tap to summarizeTo 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 MeetingFind all episode transcripts on our websitePaper: Manipulating the 3D organization of the largest synthetic yeast chromosomeNYU Release: Researchers Assemble Nine Synthetic Yeast ChromosomesOur contact info:X: @JGIEmail: jgi-comms at lbl dot gov
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Forest Fungi, Seagrass, and a New View of Symbiosis
Jun 13, 202400:26:34Tap to summarizeThree 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 websiteFeature: 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 ecosystemsFeature: 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 environmentPaper: Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosisOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov
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What Happens To a Rainforest When You Dial Up Drought? - Linnea Honeker and Malak Tfaily
May 30, 202400:22:53Tap to summarizeRainforests 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 programFind 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/s41564-023-01507-7Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov
Transcribe →The Megadata of Lake Mendota - Part 3: Boating Out to David Buoy
Dec 21, 202300:24:38Tap to summarizeThis 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
Transcribe →The Megadata of Lake Mendota - Part 2: Souped Up Computing
Dec 7, 202300:22:06Tap to summarizeThis 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
Transcribe →The Megadata of Lake Mendota - Part 1: Many, Many Mers
Nov 21, 202300:26:16Tap to summarizeLake Mendota sits right next to the University of Wisconsin, Madison. And Trina McMahon's lab has been sampling the microbes of that lake for over 20 years, to understand how the freshwater ecosystem works. So a few years ago, when they set out to analyze 500 metagenomes, it was the biggest project the JGI had ever put together. The next 3 episodes are the story behind that giant assembly from Lake Mendota. In this episode: the software evolution that made metagenome assemblies like this possible.Links from this episode:Submit your own proposal to work with the JGIFind all episode transcripts on our websiteThe ExaBiome ProjectPaper: Hofmeyr, S., Egan, R., Georganas, E. et al. Terabase-scale metagenome coassembly with MetaHipMer. Sci Rep 10, 10689 (2020). https://doi.org/10.1038/s41598-020-67416-5 Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov
Transcribe →Experimenting with EcoFABs for Student Labs - Jill Bouchard & Ying Wang
Nov 9, 202300:22:15Tap to summarizeTo set up flexible, repeatable experiments on plants and microbes, Trent Northen’s group at Berkeley Lab created a fabricated ecosystem – an EcoFAB. These small plastic growth chambers let researchers around the world compare their work consistently. And EcoFABs also work well in the classroom. This episode, we visit Los Medanos College to see EcoFABs in action in Jill Bouchard’s BIO 21 lab course. Links from this episode:Submit your own proposal to work with the JGIFind out more about EcoFABsConnect with Ying Wang about her lab at Texas A&MFind all episode transcripts on our websiteOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov
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