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On the show
Recent episodes
SIPs with Standards
Apr 15, 2025
21m 00s
Adopt-A-Genome
Oct 11, 2024
26m 45s
Gotta Catch 'Em Gall
Aug 1, 2024
24m 31s
A Redesign for Yeast’s Genome, Chromosome by Chromosome - Jef Boeke, Weimin Zhang & Leslie Mitchell
Jun 28, 2024
20m 53s
Forest Fungi, Seagrass, and a New View of Symbiosis
Jun 13, 2024
26m 34s
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| Date | Episode | Description | Length | ||||||
|---|---|---|---|---|---|---|---|---|---|
| 4/15/25 | 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 episo... | 21m 00s | ||||||
| 10/11/24 |  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... | 26m 45s | ||||||
| 8/1/24 |  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 Meetin... | 24m 31s | ||||||
| 6/28/24 |  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 20... | 20m 53s | ||||||
| 6/13/24 |  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 U... | 26m 34s | ||||||
| 5/30/24 |  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 ... | 22m 53s | ||||||
| 12/21/23 | 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 websiteR... | 24m 38s | ||||||
| 12/7/23 | 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 cal... | 22m 06s | ||||||
| 11/21/23 | The Megadata of Lake Mendota - Part 1: Many, Many Mers | Lake 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 ... | 26m 16s | ||||||
| 11/9/23 | Experimenting with EcoFABs for Student Labs - Jill Bouchard & Ying Wang | To 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... | 22m 15s | ||||||
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| 10/19/23 | JGIota: A Surprise for Chloroflexota — The First Flagella! | To understand how organisms adapt to extreme environments, Marike Palmer and Brian Hedlund study organisms living in hot springs. Hear how their recent work revealed more about the history of the Chloroflexota phylum and a new way of moving: a tail-like flagella. Submit your own proposal to work with the JGIJoin us at the 2023 JGI User MeetingLinks from this episode: Find all episode transcripts on our websitePublication: Palmer, M, et al.Thermophilic Dehalococcoidia with unusual traits... | 8m 26s | ||||||
| 9/20/23 | JGIota: A Tool to Find the Nomadic Genes that Help Microbes Adapt - geNomad | A quick snippet on Antonio Camargo and Simon Roux, a few of the JGI researchers behind software that finds plasmids and viruses within microbial genomes. As mobile genetic elements like viruses spread their DNA, they can affect how microbes cycle nutrients and adapt to climate change. Find all episode transcripts on our websitePublication: Camargo, A.P., et al. “Identification of mobile genetic elements with geNomad,” Nature Biotechnology. (2023). doi: 10.1038/s41587-023-01953-yScience Hig... | 5m 51s | ||||||
| 6/29/23 | Methane Makers in Yosemite's Lakes - Mike Beman and Elisabet Perez Coronel | Meet researchers who have hiked, rafted and met local wildlife (a marmot!) as they’ve sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains. These lakes are isolated, but varied. They’re a great way to see how climate change affects freshwater ecosystems, and how those ecosystems work. Links from this episode: Submit your own proposal to work with the JGI http://jointgeno.me/proposals Join us at the 2023 JGI User Meeting http://jointg... | 27m 16s | ||||||
| 6/22/23 | A Shrubbier Version of Rubber - Andrew Nelson and Colleen McMahan | Right now, our natural rubber comes from just one tree species: Hevea brasiliensis. It’s great at producing latex that becomes rubber, but it’s vulnerable to disease and climate shifts. So researchers are looking into a desert shrub that’s native to North America: guayule. This episode was made in collaboration with our friends at the HudsonAlpha Institute for Biotechnology. Links from this episode: Submit your own proposal to work with the JGI : http://jointgeno.me/proposals &nb... | 20m 37s | ||||||
| 6/15/23 | The Busy World of Deep Sea Eruptions - Anna-Louise Reysenbach and Emily St. John | The ocean depths are vast and dark. But there are hotspots on the ocean floor — underwater volcanoes and hydrothermal vents — where lively microbial communities thrive, and even support entire ecosystems. Hear from researchers Anna-Louise Reysenbach, Emily St. John, Gilberto Flores, and Peter Girguis about sampling these communities, and understanding how they’ve adapted to this extreme environment. Links from this episode: Submit your own proposal to work with the JGI: http://jointgen... | 30m 44s | ||||||
| 6/8/23 | Crops as Tough as World Cup Turf - James Schnable and Guangchao Sun | In our warming world, we’ll need corn, sorghum and other crops to grow well in worse conditions: with more heat, less water and less fertilizer. Grasses do better in these conditions, so plant biologists James Schable, Guangchao Sun and Vladimir Torrres have looked into traits that could transfer from grasses into other crops. One grass they studied just happened to be the same species that covered World Cup pitches in 2022. Links from this episode: Submit your own proposal to work ... | 28m 16s | ||||||
| 6/6/23 | Season 4 Trailer (and sneak peek!) | On June 8th, Genome Insider is back! We've got a batch of 4 new episodes where researchers discover the expertise encoded in our environment — in the genomes of plants, fungi, bacteria, archaea, algae, and environmental viruses — to power a more sustainable future. Stick around for a snippet of the next episode. Join us at our User Meeting: jointgeno.me/JGI2023 Find out how to become a JGI user here: jointgeno.me/proposals Our contact info: Twitter: @JGIEmail: jgi-comms at lbl dot go... | 3m 14s | ||||||
| 3/30/23 | JGIota: A Biofuel Breakthrough in Anaerobic Fungi with Michelle O'Malley and Tom Lankiewicz | Michelle O'Malley and Tom Lankiewicz of UC-Santa Barbara discuss the importance of studying anaerobic fungi, as well as a recent discovery that turns scientific presumption on its head and opens up a new avenue to explore for efficient biofuel production. Find all episode transcripts on our websitePublication: Lankiewicz, T.S., Choudhary, H., Gao, Y. et al. Lignin deconstruction by anaerobic fungi. Nat Microbiol 8, 596–610 (2023). doi: 10.1038/s41564-023-01336-8 | 4m 31s | ||||||
| 3/2/23 | JGIota: Sequencing Shiitakes with David Hibbett | 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. Find all episode transcripts on our websitePublication: Sierra-Patev S et al. A global phylogenomic analysis of the shiitake genus Lentinula. Proc Natl Acad Sci U S A. 2023 Mar 7;120(10):e2214076120. doi: 10.1073/pnas.2214076120. The Lentinula genomes are publicly available on JGI’s MycoCosm ... | 5m 40s | ||||||
| 12/16/22 | Work With the JGI! Tips for a Winning CSP Proposal | 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 manage... | 30m 19s | ||||||
| 11/17/22 | JGIota: Looking Back at How Cow Rumen Samples Landed on a Syllabus | Back in 2011, JGI-supported researchers published a paper in the journal Science. They’d used metagenomics to sift for microbial genes encoding carbohydrate-chomping enzymes in cow rumen — and found 27,000 candidates. The data from that study is now used across California State University campuses for biotechnology education as part of a course-based undergraduate resource experience. Hear from CSU San Marcos Professor Matt Escobar and UC Davis Associate Professor Matthias Hess, also the chai... | 8m 15s | ||||||
| 11/3/22 | From Sample Shipments to Sequences – A Tour of the JGI’s Sequencing Pipeline | 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. Links from this episode: Find all episode transcripts on our websiteSubmit a... | 18m 58s | ||||||
| 10/6/22 | JGIota: Looking Back at Methane-Making Microbes | We count on livestock for food and fiber, but raising these animals also produces an atmosphere-warming gas: methane. Those emissions mainly come from gut microbes — the bacteria and archaea breaking down plant matter. So since 2010, the JGI has supported researchers studying those microbial methane-makers. Eventually, that could help us dial back their emissions, while still producing things like meat, milk, and wool. Hear more from JGI collaborators Sinead Leahy (New Zealand Agricultural Gr... | 7m 03s | ||||||
| 9/22/22 | The Fungi That Survive In Antarctica | 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. Links from this episode: Find all episode transcripts on our websiteIntegrated Microbial Ge... | 18m 07s | ||||||
| 9/15/22 | JGIota: Looking Back at Sequencing for Soybeans | The soybean is a crop that could boost biofuels and fertilize fields. So in 2010, the JGI helped publish the original genome sequence for the soybean, Glycine max. With a full genome sequence, researchers have been able to look into soybean’s strengths – along with a fungus that threatens this important crop. Hear more about that work from researchers Gary Stacey (University of Missouri), Peter van Esse (The Sainsbury Laboratory) and Sebastien Duplessis (INRAE). Links from this episode: Find... | 6m 12s | ||||||
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Chart Positions
4 placements across 4 markets.
Chart Positions
4 placements across 4 markets.