Genome Insider (original) (raw)

Adopt-A-Genome 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.

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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.

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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:

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.

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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:

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:

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:

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:

Links from this episode:

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Sound Effects Credits: Marmot sound courtesy of slunali, freesound.org

]]> 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.

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Sound Effects Credits: Marmot sound courtesy of slunali, freesound.org

]]> JGI Buzzsprout-13119814 Thu, 29 Jun 2023 04:00:00 -0700 1636 4 4 full false A Shrubbier Version of Rubber - Andrew Nelson and Colleen McMahan 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.

This episode was made in collaboration with our friends at the HudsonAlpha Institute for Biotechnology.

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One grass they studied just happened to be the same species that covered World Cup pitches in 2022.

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One grass they studied just happened to be the same species that covered World Cup pitches in 2022.

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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:

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:

Episode Transcript

Episode Transcript

This work was supported by the JGI’s Community Science Program. Find out how to become a JGI User here: https://jgi.doe.gov/user-programs/

]]> 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.

This work was supported by the JGI’s Community Science Program. Find out how to become a JGI User here: https://jgi.doe.gov/user-programs/

]]> Buzzsprout-12357931 Thu, 02 Mar 2023 07:00:00 -0800 340 3 10 full false Work With the JGI! Tips for a Winning CSP Proposal 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 manager Miranda Harmon-Smith, who helps shepherd CSP projects along.

Find more information about proposal calls and capabilities on the JGI website, jgi.doe.gov.

Episode Transcript

Links from this episode:

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.

Find more information about proposal calls and capabilities on the JGI website, jgi.doe.gov.

Episode Transcript

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Genome Insider is a production of the Joint Genome Institute.

]]> 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 chair of the JGI User Executive Committee, on how that study went from the lab to the classroom.

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Genome Insider is a production of the Joint Genome Institute.

]]> JGI Buzzsprout-11714715 Thu, 17 Nov 2022 09:00:00 -0800 495 3 8 full false From Sample Shipments to Sequences – A Tour of the JGI’s Sequencing Pipeline 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:

Genome Insider is a production of the Joint Genome Institute.

Sound Effects Credits: George Hopkins “Mechanical keyboard typing”

]]> 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:

Genome Insider is a production of the Joint Genome Institute.

Sound Effects Credits: George Hopkins “Mechanical keyboard typing”

]]> JGI Buzzsprout-11618974 Thu, 03 Nov 2022 04:00:00 -0700 1138 3 7 full false JGIota: Looking Back at Methane-Making Microbes 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 Greenhouse Gas Research Centre) and Bill Kelly (AgResearch).

Links from this episode:

Genome Insider is a production of the Joint Genome Institute.

]]> 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 Greenhouse Gas Research Centre) and Bill Kelly (AgResearch).

Links from this episode:

Genome Insider is a production of the Joint Genome Institute.

]]> JGI Buzzsprout-11451656 Thu, 06 Oct 2022 10:00:00 -0700 423 3 6 full false The Fungi That Survive In Antarctica 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:

Genome Insider is a production of the Joint Genome Institute.

Some audio in the opening scene comes from an expedition Laura took to Antarctica. Laura.Selbmann©PNRA

All the sampling activities in Antarctica have been performed in the frame of italian expeditions of the Italian National Program for Antarctic Researches (PNRA), funded by the Italian Ministry of University and Research; all specimens collected and fungi isolated are preserved in the Culture Collection of Fungi from Extreme Environment, the Italian National Antarctic Museum (MNA-CCFEE)

]]> 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:

Genome Insider is a production of the Joint Genome Institute.

Some audio in the opening scene comes from an expedition Laura took to Antarctica. Laura.Selbmann©PNRA

All the sampling activities in Antarctica have been performed in the frame of italian expeditions of the Italian National Program for Antarctic Researches (PNRA), funded by the Italian Ministry of University and Research; all specimens collected and fungi isolated are preserved in the Culture Collection of Fungi from Extreme Environment, the Italian National Antarctic Museum (MNA-CCFEE)

]]> JGI Buzzsprout-11363298 Thu, 22 Sep 2022 04:00:00 -0700 1087 3 5 full false JGIota: Looking Back at Sequencing for Soybeans 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:

Genome Insider is a production of the Joint Genome Institute.

]]> 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:

Genome Insider is a production of the Joint Genome Institute.

]]> JGI Buzzsprout-11321331 Thu, 15 Sep 2022 04:00:00 -0700 372 3 4 full false Better Crops With a Pointillist Approach to Plant Genomics Better Crops With a Pointillist Approach to Plant Genomics 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.

Links from this episode:

Monet’s Waterloo Bridge at Sunset (1904)

Serat’s A Sunday on La Grande Jatte (1884)

Submit a proposal to work with the JGI: https://jointgeno.me/proposals

Margot’s 2021 Berkeley Lab SLAM talk

The JGI’s Genomics of Plant-Microbial Interactions group

Plant Single-cell Solutions for Energy and the Environment (Workshop report)

JGI Blog: A Plant Root Atlas for Tracking Developmental Trajectories

Ben Cole’s DOE Early Career Award

Genome Insider is a production of the Joint Genome Institute.

This episode uses two pieces of music from Free Music Archive:

Sad French Accordion by Dana Boulé (CC BY-NC 4.0)

Sonata No. 20 in G Major, Op. 49 No. 2 - I. Allegro ma non troppo by Daniel Veesey (Public Domain)

]]> 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.

Links from this episode:

Monet’s Waterloo Bridge at Sunset (1904)

Serat’s A Sunday on La Grande Jatte (1884)

Submit a proposal to work with the JGI: https://jointgeno.me/proposals

Margot’s 2021 Berkeley Lab SLAM talk

The JGI’s Genomics of Plant-Microbial Interactions group

Plant Single-cell Solutions for Energy and the Environment (Workshop report)

JGI Blog: A Plant Root Atlas for Tracking Developmental Trajectories

Ben Cole’s DOE Early Career Award

Genome Insider is a production of the Joint Genome Institute.

This episode uses two pieces of music from Free Music Archive:

Sad French Accordion by Dana Boulé (CC BY-NC 4.0)

Sonata No. 20 in G Major, Op. 49 No. 2 - I. Allegro ma non troppo by Daniel Veesey (Public Domain)

]]> JGI Buzzsprout-11197636 Thu, 25 Aug 2022 06:00:00 -0700 1130 3 3 full false JGIota: The Algae Nicknamed ‘Chlamy’ JGIota: The Algae Nicknamed ‘Chlamy’ This shorter episode is about a tiny, single-celled alga – Chlamydomonas reinhardtii – that’s managed to have a big impact. UC Berkeley plant biologist Sabeeha Merchant explains why she works on this alga, how researchers managed to sequence its genome, and what it has to teach us about other organisms – like plants.

Links from this episode

Genome Insider is a production of the Joint Genome Institute.

]]> This shorter episode is about a tiny, single-celled alga – Chlamydomonas reinhardtii – that’s managed to have a big impact. UC Berkeley plant biologist Sabeeha Merchant explains why she works on this alga, how researchers managed to sequence its genome, and what it has to teach us about other organisms – like plants.

Links from this episode

Genome Insider is a production of the Joint Genome Institute.

]]> JGI Buzzsprout-11110992 Thu, 11 Aug 2022 09:00:00 -0700 365 3 2 full false Chomping Toward Better Plastic Recycling Chomping Toward Better Plastic Recycling We know all kinds of things about plastic – except, how to break it down for recycling. But some hungry insects can digest plastic. So researchers are taking a look at how these critters process plastic, to improve plastic recycling by following their lead.

Episode Transcript

Links from this episode:

Sequencing the Amazonian Stinkbird’s Microbiome

Acronym Action: EPICON project

Submit a proposal to work with the JGI!

Find out more about the FICUS program between JGI and EMSL

Genome Insider is a production of the Joint Genome Institute.

--

Sound Effects Credits:

"Splash, Small, A.wav" by InspectorJ (www.jshaw.co.uk) of Freesound.org

“Water movements big splashes and waves” by KyleS of Freesound.org

“Fishing-rod” by KirstenBrooks3232 of Freesound.org

“By a Pond Ambience” by Cueckermann of Freesound.org

“Splash, edited” by MRicken1 of Freesound.org

“Fishing Rod Whip” by TyroneW of Freesound.org

]]> We know all kinds of things about plastic – except, how to break it down for recycling. But some hungry insects can digest plastic. So researchers are taking a look at how these critters process plastic, to improve plastic recycling by following their lead.

Episode Transcript

Links from this episode:

Sequencing the Amazonian Stinkbird’s Microbiome

Acronym Action: EPICON project

Submit a proposal to work with the JGI!

Find out more about the FICUS program between JGI and EMSL

Genome Insider is a production of the Joint Genome Institute.

--

Sound Effects Credits:

"Splash, Small, A.wav" by InspectorJ (www.jshaw.co.uk) of Freesound.org

“Water movements big splashes and waves” by KyleS of Freesound.org

“Fishing-rod” by KirstenBrooks3232 of Freesound.org

“By a Pond Ambience” by Cueckermann of Freesound.org

“Splash, edited” by MRicken1 of Freesound.org

“Fishing Rod Whip” by TyroneW of Freesound.org

]]> JGI Buzzsprout-10967879 Thu, 28 Jul 2022 09:00:00 -0700 1270 3 1 full false Filling in the Plant Tree of Life Filling in the Plant Tree of Life What if we understood plants and how they adapt to their ever-changing environments better? We could unlock new innovations to drive more productive food, medicine, and bioenergy crops. But most available genomes are from narrow swaths of the plant tree of life. One project aims to change that. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-episode-10-filling-in-the-plant-tree-of-life/.

]]>

What if we understood plants and how they adapt to their ever-changing environments better? We could unlock new innovations to drive more productive food, medicine, and bioenergy crops. But most available genomes are from narrow swaths of the plant tree of life. One project aims to change that. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-episode-10-filling-in-the-plant-tree-of-life/.

]]>

JGI Buzzsprout-9804357 Tue, 08 Feb 2022 09:00:00 -0800 1362 plants, genomes, biology, tree of life, evolution, ecosystems, diversity, genetics, adaptations, data, DNA, bioenergy, food, medicine, wood, chemicals, environment, team science, logistics, cacao, C-fern, fern, Arabidopsis, moss, scientists 2 10 full false Creating an Energy Market for Miscanthus Creating an Energy Market for Miscanthus What grass is a prized ornamental and a bioenergy plant? Meet Miscanthus, an attractive addition to your garden and a potential fuel for the future. But, to be competitive in the market, both energy policy and Miscanthus will need some upgrades. In this episode, hear from scientists working on understanding Miscanthus biology and the economic terrain to help make the plant a viable alternative to fossil fuels. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-episode-9-creating-an-energy-market-for-miscanthus/.\]\]> What grass is a prized ornamental and a bioenergy plant? Meet Miscanthus, an attractive addition to your garden and a potential fuel for the future. But, to be competitive in the market, both energy policy and Miscanthus will need some upgrades. In this episode, hear from scientists working on understanding Miscanthus biology and the economic terrain to help make the plant a viable alternative to fossil fuels. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-episode-9-creating-an-energy-market-for-miscanthus/.\]\]> JGI Buzzsprout-9486651 Tue, 23 Nov 2021 09:00:00 -0800 1343 bioenergy, policy, economics, history, farmers, biology, carbon, climate change, chemicals, biology, plants, traits, breeding, CRISPR, genetics, team science, research, genome, ornamental, garden, marketing, incentives, Renewable Fuel Standard 2 9 full false Dispatches From JGI Interns Dispatches From JGI Interns Every summer, the JGI invites undergraduate and graduate students from the University of California, Merced to participate in the flagship JGI-UC Merced Internship Program and engage in real, impactful research projects with JGI mentors. In this episode, hear two interns from the 2021 cohort describe their deep dives into genomics, computational tools, and big data. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-episode-8-uc-merced-intern-dispatches/.\]\]> Every summer, the JGI invites undergraduate and graduate students from the University of California, Merced to participate in the flagship JGI-UC Merced Internship Program and engage in real, impactful research projects with JGI mentors. In this episode, hear two interns from the 2021 cohort describe their deep dives into genomics, computational tools, and big data. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-episode-8-uc-merced-intern-dispatches/.\]\]> JGI Buzzsprout-9389302 Tue, 19 Oct 2021 09:00:00 -0700 1410 Biology, genomics, genomes, internship, mentors, national lab, viruses, RNA, DNA, protein, photosynthesis, models, graphs, networks, genome comparison, data visualization, bioinformatics, coding, diversity, big data, terabyte 2 8 full false THE Bioenergy Tree THE Bioenergy Tree The US Department of Energy’s favorite tree is poplar. They’re the fastest growing trees in the Northern Hemisphere, making them tantalizing plants to harness for bioenergy. In this episode, hear from Oak Ridge National Laboratory scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-ep-7-the-bioenergy-tree/.\]\]> The US Department of Energy’s favorite tree is poplar. They’re the fastest growing trees in the Northern Hemisphere, making them tantalizing plants to harness for bioenergy. In this episode, hear from Oak Ridge National Laboratory scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-ep-7-the-bioenergy-tree/.\]\]> JGI Buzzsprout-9190596 Tue, 14 Sep 2021 08:00:00 -0700 1509 Bioenergy, biology, bioeconomy, biofuel, bioproducts, biomass, plants, carbon sequestration, climate change, genome sequencing, poplar, fungus, genes, breeding, lignin, shipping, aviation, solution 2 7 full false Back to the Future! A Sorghum Story Back to the Future! A Sorghum Story You might know sorghum as an edible grain. But there are some sorghum varieties, grown on marginal land with little water, which were developed specifically to turn their biomass into sustainable biofuel and bioproducts. John Mullet, a biologist at Texas A&M University, tells us how sorghum’s historical — and literal — roots could play a big role in our energy future.

Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-ep-6-back-to-the-future-a-sorghum-story.

]]> You might know sorghum as an edible grain. But there are some sorghum varieties, grown on marginal land with little water, which were developed specifically to turn their biomass into sustainable biofuel and bioproducts. John Mullet, a biologist at Texas A&M University, tells us how sorghum’s historical — and literal — roots could play a big role in our energy future.

Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-ep-6-back-to-the-future-a-sorghum-story.

]]> JGI Buzzsprout-9000013 Tue, 10 Aug 2021 09:00:00 -0700 1343 Bioenergy, biology, bioeconomy, sorghum, biofuel, bioproducts, plants, carbon, sequestration, climate change, drought, genome, sequencing, economic development, greenhouse gas emissions, biorefineries 2 6 full false A Powerful Technique to Study Microbes, Now Easier A Powerful Technique to Study Microbes, Now Easier Lawrence Livermore National Lab biologist Jennifer Pett-Ridge collaborated with JGI scientists on an ambitious project: to bring in robots to help process experiments that measure microbial activity in soil. Now, the researchers and robots have made these experiments easier for scientists everywhere.

Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-ep5-a-powerful-technique-to-study-microbes-now-easier

]]> Lawrence Livermore National Lab biologist Jennifer Pett-Ridge collaborated with JGI scientists on an ambitious project: to bring in robots to help process experiments that measure microbial activity in soil. Now, the researchers and robots have made these experiments easier for scientists everywhere.

Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-ep5-a-powerful-technique-to-study-microbes-now-easier

]]> JGI Buzzsprout-8662805 Tue, 08 Jun 2021 08:00:00 -0700 554 Soil, plants, roots, microbes, DNA, genomics, isotopes, stable isotope probing, experiments, molecular biology, biology, microbiology, ecology, automation, robots, science, research 2 5 full false Party in the Rhizosphere Party in the Rhizosphere There’s a party in the soil, and microbes are the VIPs. They’re feasting on the compounds that plants secrete through their roots, creating a lively zone called the rhizosphere. In this episode, biologist Jennifer Pett-Ridge of Lawrence Livermore National Laboratory has your backstage pass.

Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep4-party-in-the-rhizosphere

]]> There’s a party in the soil, and microbes are the VIPs. They’re feasting on the compounds that plants secrete through their roots, creating a lively zone called the rhizosphere. In this episode, biologist Jennifer Pett-Ridge of Lawrence Livermore National Laboratory has your backstage pass.

Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep4-party-in-the-rhizosphere

]]> JGI Buzzsprout-8522616 Tue, 18 May 2021 09:00:00 -0700 1551 Soil, plants, roots, microbes, carbon cycling, rhizosphere, fungi, bacteria, archaea, viruses, DNA, genomics, isotopes, stable isotope probing, biology, microbiology, ecology, guilds, science, research 2 4 full false Better Living Through Bioenergy Better Living Through Bioenergy Biofuels and bioproducts are a way to kick our addiction to fossil fuels. In this episode, we get a peek into how scientists Aindrila Mukhopadhyay and Steve Singer are harnessing the versatile bacterium Pseudomonas putida to break down biomass and help bring about a more sustainable, bio-based economy. They conduct research at the Joint BioEnergy Institute (JBEI), a JGI partner and one of the four US Department of Energy Bioenergy Research Centers.

Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep3-better-living-through-bioenergy/

]]> Biofuels and bioproducts are a way to kick our addiction to fossil fuels. In this episode, we get a peek into how scientists Aindrila Mukhopadhyay and Steve Singer are harnessing the versatile bacterium Pseudomonas putida to break down biomass and help bring about a more sustainable, bio-based economy. They conduct research at the Joint BioEnergy Institute (JBEI), a JGI partner and one of the four US Department of Energy Bioenergy Research Centers.

Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep3-better-living-through-bioenergy/

]]> JGI Buzzsprout-8322153 Tue, 13 Apr 2021 09:00:00 -0700 1700 Bioenergy, biofuel, bioproducts, DNA synthesis, synthetic biology, genetic engineering, metabolic engineering, biology, sustainability, bioeconomy, fossil fuels, climate change, climate refugees, functional genomics, CRISPR, bacteria, microbes 2 3 full false Cracking the Secrets of the Diatom’s Shell Cracking the Secrets of the Diatom’s Shell Diatoms, a group of tiny algae, are also known as “living opals” because of the strange, beautiful properties of their silica shells. But what genes are responsible for such mesmerizing exteriors? Setsuko Wakao and Kris Niyogi, biologists at UC Berkeley and Lawrence Berkeley National Laboratory, aim to find out.

Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep2-cracking-the-secrets-of-the-diatoms-shell/.

]]> Diatoms, a group of tiny algae, are also known as “living opals” because of the strange, beautiful properties of their silica shells. But what genes are responsible for such mesmerizing exteriors? Setsuko Wakao and Kris Niyogi, biologists at UC Berkeley and Lawrence Berkeley National Laboratory, aim to find out.

Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep2-cracking-the-secrets-of-the-diatoms-shell/.

]]> JGI Buzzsprout-8076824 Tue, 09 Mar 2021 09:00:00 -0800 1050 Diatoms, photosynthesis, silica, shell, cell wall, biomaterials, nanoscale, opal, carbon cycle, carbon sequestration, CRISPR, RNA, synurophytes, algae, genes, genome, genetics, biomineralization 2 2 full false Exploring the Diversity of the American Prairie’s Switchgrass Exploring the Diversity of the American Prairie’s Switchgrass A tall native plant of the North American prairie, switchgrass (Panicum virgatum) has long been a tantalizing potential biofuel feedstock. But switchgrass has a complex genome and, as a species, encompasses dizzying diversity. So, a team of scientists made an ambitious plan to link the plant’s diverse traits — height, biomass, hardiness to cold, etc. — to its genes. The undertaking took shovels, trucks — and more than a decade.

With the results just published in the journal Nature, listen to the episode for a romp through their switchgrass story. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep1-exploring-diversity-of-american-prairie-switchgrass/.

]]> A tall native plant of the North American prairie, switchgrass (Panicum virgatum) has long been a tantalizing potential biofuel feedstock. But switchgrass has a complex genome and, as a species, encompasses dizzying diversity. So, a team of scientists made an ambitious plan to link the plant’s diverse traits — height, biomass, hardiness to cold, etc. — to its genes. The undertaking took shovels, trucks — and more than a decade.

With the results just published in the journal Nature, listen to the episode for a romp through their switchgrass story. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep1-exploring-diversity-of-american-prairie-switchgrass/.

]]> JGI Buzzsprout-7662985 Thu, 04 Feb 2021 10:00:00 -0800 1114 Biofuel, switchgrass, prairie, genome, genomics, genes, adaptations, research, sequencing, plants, drought, evolution, gardens, bison, grazing, bioenergy, diversity, variety, traits, drought, winter, plant breeding, biomass, yield 2 1 full false The Soil Blooms Green The Soil Blooms Green Every fall, a mysterious green growth appears on farmers’ fields: a microbial community that might be quietly improving the soil. Penn State researchers Mary Ann Bruns and Terry Bell are digging in to understand how. Find more info on this episode, including the transcript, here.

We hope you enjoy this last episode of Season 1! Stay tuned for Season 2, coming in 2021.

]]> Every fall, a mysterious green growth appears on farmers’ fields: a microbial community that might be quietly improving the soil. Penn State researchers Mary Ann Bruns and Terry Bell are digging in to understand how. Find more info on this episode, including the transcript, here.

We hope you enjoy this last episode of Season 1! Stay tuned for Season 2, coming in 2021.

]]> JGI Buzzsprout-6327955 Wed, 11 Nov 2020 09:00:00 -0800 990 Cyanobacteria, soil, biofilm, ecosystem, pollution, agriculture, organic, fertilizer, microbial additives, microbes, synthetic, natural, Department of Energy, farming, sustainable, US Department of Agriculture, nitrogen fixation, photosynthesis, corn maze 1 9 full false A Plantiful Future: Xiaohan Yang A Plantiful Future: Xiaohan Yang Can plants help humans attain a renewable energy future? Can they help lock away more carbon? Xiaohan Yang, a scientist at Oakridge National Laboratory, believes they can. And, what’s more, that using gene editing technology to conscientiously mix traits of different plant species will help us get there. Find more info on this episode, including the transcript, here.]]> Can plants help humans attain a renewable energy future? Can they help lock away more carbon? Xiaohan Yang, a scientist at Oakridge National Laboratory, believes they can. And, what’s more, that using gene editing technology to conscientiously mix traits of different plant species will help us get there. Find more info on this episode, including the transcript, here.]]> JGI Buzzsprout-5821192 Tue, 13 Oct 2020 10:00:00 -0700 1216 Plants, future, biology, gene editing, genetic engineering, CRISPR, biotechnology, synthetic biology, applied science, Department of Energy, renewable energy, biofuel, carbon, photosynthesis, genome, ecosystem, artificial intelligence, AI, technology 1 8 full false Decoding Yellowstone’s Microbial Mats Decoding Yellowstone’s Microbial Mats Life as we know it wouldn’t exist without cyanobacteria; they began oxygenating Earth over two billion years ago. A team of researchers set out to Yellowstone National Park to study how cyanobacteria are living, communally, in microbial mats. Along the way, they’ve encountered surprises, adopted new technologies, and made a few discoveries about the microbial mat denizens.

Find more info on the episode, including the transcript, here: https://jgi.doe.gov/genome-insider-episode-7-decoding-yellowstone-microbial-mats/

]]> Life as we know it wouldn’t exist without cyanobacteria; they began oxygenating Earth over two billion years ago. A team of researchers set out to Yellowstone National Park to study how cyanobacteria are living, communally, in microbial mats. Along the way, they’ve encountered surprises, adopted new technologies, and made a few discoveries about the microbial mat denizens.

Find more info on the episode, including the transcript, here: https://jgi.doe.gov/genome-insider-episode-7-decoding-yellowstone-microbial-mats/

]]> JGI Buzzsprout-5282946 Wed, 09 Sep 2020 11:00:00 -0700 1739 Cyanobacteria, microbial mat, field science, Yellowstone National Park, YNP, National Parks, women in science, Wyoming, virus, CRISPR, lysozyme, database, KBase, computer science, hot springs, extremophiles, sharing data, microbes, microbiome, metagenome 1 7 full false How Microbes Can Protect Plants in Drier Straits How Microbes Can Protect Plants in Drier Straits A mini-episode: JGI collaborator Pankaj Trivedi is harnessing microbiome science to make plants more resilient to drought. Find more info on this episode, including the transcript here: jgi.doe.gov/genome-insider-mini-episode-6-how-microbes-can-protect-plants-in-drier-straits/]]> A mini-episode: JGI collaborator Pankaj Trivedi is harnessing microbiome science to make plants more resilient to drought. Find more info on this episode, including the transcript here: jgi.doe.gov/genome-insider-mini-episode-6-how-microbes-can-protect-plants-in-drier-straits/]]> JGI Buzzsprout-4889882 Tue, 11 Aug 2020 09:00:00 -0700 365 Plant, microbes, microbiome, genomics, environment, ecology, ecosystem, earth, climate change, drought, bacteria, agriculture, science, biofilm, boreal forest 1 6 full false Corals in Hot Water Get Help From Their Microbes Corals in Hot Water Get Help From Their Microbes As waters warm due to climate change, corals are in mortal peril. But corals comprise multiple organisms: a coral host, a photosynthetic microalgae, and a little-characterized microbiome. When warm waters stress corals but before they bleach, a coral’s microbes, including its photosynthetic partner, may be what helps them take the heat. Find more info on this episode, including the transcript, here.]]> As waters warm due to climate change, corals are in mortal peril. But corals comprise multiple organisms: a coral host, a photosynthetic microalgae, and a little-characterized microbiome. When warm waters stress corals but before they bleach, a coral’s microbes, including its photosynthetic partner, may be what helps them take the heat. Find more info on this episode, including the transcript, here.]]> JGI Buzzsprout-4540826 Tue, 14 Jul 2020 09:00:00 -0700 1252 Coral, reef, host, bleaching, photosynthesis, microalgae, dinoflagellate, bacteria, genomes, biology, genes, ocean, microbiome, climate change, holobiont, women in science, Mexico, Caribbean 1 5 full false The Big Deal About Short Plants The Big Deal About Short Plants Despite their diminutive stature, “short plants” such as mosses could be uniquely powerful in helping scientists link plant genetic sequences to what they do. But sequencing the genome of one short plant — fire moss — has an unexpected hurdle: ginormous sex chromosomes. Find more info on this episode, including the transcript, here.]]> Despite their diminutive stature, “short plants” such as mosses could be uniquely powerful in helping scientists link plant genetic sequences to what they do. But sequencing the genome of one short plant — fire moss — has an unexpected hurdle: ginormous sex chromosomes. Find more info on this episode, including the transcript, here.]]> JGI Buzzsprout-4097579 Tue, 09 Jun 2020 11:00:00 -0700 1263 Plant, moss, bioenergy, biofuel, energy, genetics, evolution, DNA sequencing, science, fire moss, podcast, environment 1 4 full false River microbiomes from around the world: Kelly Wrighton River microbiomes from around the world: Kelly Wrighton Kelly Wrighton and her group at Colorado State University in Fort Collins have a massive undertaking: sequencing the world’s river microbiomes. And they’re using team science to do it. Find more info on this episode, including the transcript here. ]]> Kelly Wrighton and her group at Colorado State University in Fort Collins have a massive undertaking: sequencing the world’s river microbiomes. And they’re using team science to do it. Find more info on this episode, including the transcript here. ]]> JGI Buzzsprout-3722765 Tue, 12 May 2020 02:00:00 -0700 1433 microbes, microbiome, rivers, genomics, environment, earth, climate change, methane, microorganisms, bacteria, ecology, podcast, ecosystem, carbon cycle, citizen science, women in science 1 3 full false Thawing permafrost, microbes, and viruses: Gary Trubl — Part 2 Thawing permafrost, microbes, and viruses: Gary Trubl — Part 2 Gary Trubl, virologist and postdoc at Lawrence Livermore National Laboratory, has more to share about bacteria-infecting viruses in the arctic. He’s researching how viruses influence the flow of carbon in thawing peatlands — and bioinformatics and isotopes are crucial to the quest. Find more info on this episode, including the transcript here.]]> Gary Trubl, virologist and postdoc at Lawrence Livermore National Laboratory, has more to share about bacteria-infecting viruses in the arctic. He’s researching how viruses influence the flow of carbon in thawing peatlands — and bioinformatics and isotopes are crucial to the quest. Find more info on this episode, including the transcript here.]]> JGI Buzzsprout-3108691 Tue, 14 Apr 2020 02:00:00 -0700 945 viruses, genomics, environment, earth, climate change, permafrost, arctic, microbiome, microorganisms, bacteria, phage, ecology, podcast, ecosystem, bioinformatics, isotopes, carbon cycle 1 2 full false Thawing permafrost, microbes, and viruses: Gary Trubl — Part 1 Thawing permafrost, microbes, and viruses: Gary Trubl — Part 1 Gary Trubl, virologist and postdoc at Lawrence Livermore National Laboratory, has more to share about bacteria-infecting viruses in the arctic. He’s researching how viruses influence the flow of carbon in thawing peatlands — and bioinformatics and isotopes are crucial to the quest. Find more info on this episode, including the transcript here.]]> Gary Trubl, virologist and postdoc at Lawrence Livermore National Laboratory, has more to share about bacteria-infecting viruses in the arctic. He’s researching how viruses influence the flow of carbon in thawing peatlands — and bioinformatics and isotopes are crucial to the quest. Find more info on this episode, including the transcript here.]]> JGI Buzzsprout-2562388 Tue, 10 Mar 2020 02:00:00 -0700 804 viruses, genomics, environment, earth, climate change, permafrost, arctic, microbiome, microorganisms, bacteria, phage, ecology, podcast, ecosystem 1 1 full false Teaser: Ed Hall Teaser: Ed Hall Alison Takemura tells you about the podcast, and Ed Hall, microbiologist at Colorado State University, talks about how this is a unique time in human history.

Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.

]]> Alison Takemura tells you about the podcast, and Ed Hall, microbiologist at Colorado State University, talks about how this is a unique time in human history.

Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.

]]> JGI Buzzsprout-2807500 Sat, 07 Mar 2020 05:00:00 -0800 62 1 bonus false Teaser: Monica Medina Teaser: Monica Medina Alison Takemura tells you about the podcast, and Monica Medina, coral biologist at Penn State, talks about going from tiny critters to magnificent coral reefs.

Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.

]]> Alison Takemura tells you about the podcast, and Monica Medina, coral biologist at Penn State, talks about going from tiny critters to magnificent coral reefs.

Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.

]]> JGI Buzzsprout-2807491 Thu, 05 Mar 2020 05:00:00 -0800 78 1 bonus false Teaser: Kelly Wrighton Teaser: Kelly Wrighton Alison Takemura tells you about the podcast, and Kelly Wrighton, microbiologist at Colorado State University, talks about filters full of microbes.

Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.

]]> Alison Takemura tells you about the podcast, and Kelly Wrighton, microbiologist at Colorado State University, talks about filters full of microbes.

Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.

]]> JGI Buzzsprout-2807488 Mon, 02 Mar 2020 15:00:00 -0800 55 1 bonus false Teaser: Gary Trubl Teaser: Gary Trubl Alison Takemura tells you about the podcast, and Gary Trubl, virologist at Lawrence Livermore National Lab, weighs in on what a peatland sounds like.

Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.

]]> Alison Takemura tells you about the podcast, and Gary Trubl, virologist at Lawrence Livermore National Lab, weighs in on what a peatland sounds like.

Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.

]]> JGI Buzzsprout-2807482 Sat, 22 Feb 2020 13:00:00 -0800 61 1 bonus false