Genome Insider (original) (raw)

SIPs with Standards 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:

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:

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:

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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Links from this episode:

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:

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.

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.

Links from this episode:

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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:

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:

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.

Links from this episode:

Genome Insider is a production of the Joint Genome Institute.

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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.

Links from this episode:

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.

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

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

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

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

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

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

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

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

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

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