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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

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    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    • MycoCosm
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    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

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    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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About Us
Home › About Us › Workforce Development & Education Outreach › Partnering with CalTeach – Training the Next Generation STEM Workforce
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Partnering with CalTeach – Training the Next Generation STEM Workforce

As set out in the JGI Five-Year Strategic Plan – “Beyond Basepairs, A Vision for Integrative and  Collaborative Genome Science” – through early introduction to the resources and disciplines advanced by the JGI, we seek to inspire more students to enter the science, technology, engineering, and mathematics (STEM) workforce. In doing so, it is our ambition to further develop a more diverse and inclusive pool of talent for career opportunities at JGI and Berkeley Lab.

We seek to inspire more students to enter the science, technology, engineering, and mathematics (STEM) workforce. In doing so, it is our ambition to further develop a more diverse and inclusive pool of talent for career opportunities at JGI and Berkeley Lab. As set out in the JGI Five-Year Strategic Plan, it is our goal to bring forth the resources and disciplines advanced by the JGI to the next generation of scientists.

In 2021, the JGI began partnering with CalTeach to explore opportunities for highlighting JGI data portals as potentially teachable assets with participating undergraduate STEM majors interested in exploring a career in education. That summer, JGI mentors welcomed four CalTeach Summer Research Institute (SRI) participants who immersed themselves in the JGI Integrated Microbial Genomes & Microbiomes (IMG/M) data management system and the JGI fungal genomics comparative analysis portal MycoCosm. For Summer 2022, the JGI hosted CalTeach interns to develop tutorials for the JGI comparative genomics platform for algae, PhycoCosm.

The results were these video tutorials.

 

IMG/M Case Studies

  • Erone Cao, “A Genomic Approach to Oil & Sustainability” – watch Erone’s video
  • Jia Xin Sun, “Exploring Hydrothermal Vents Using Metagenomic Analysis” – watch Jia’s video
  • JGI Mentors: Natalia Ivanova and Rekha Seshadri

More information about how IMG/M can be used may be found in this short video and in these webinars. 

MycoCosm Case Studies

  • Amanda Gonzaga, “MycoCosm KEGG Browser Tutorial” – watch Amanda’s video
  • Arthi Inagandla, “MycoCosm Tutorial” – watch Arthi’s video
  • JGI Mentors: Sajeet Haridas and Stephen Mondo

PhycoCosm Case Studies

CalTeach intern Emily Chase next to her poster2022 intern Emily Chase CalTeach intern Cynthia Shi next to her poster2022 intern Cynthia Shi CalTeach intern Valerie Tran next to her poster2022 intern Valerie Tran
  • Cynthia Shi, “Endosymbiotic Gene Transfer discovered with PhycoCosm” – watch Cynthia’s video
  • Valerie Tran, “Understanding gene regulation in Scenedesmus algae” – watch Valerie’s video
  • JGI Mentors: Sara Calhoun, Bishoy Kamel and Alan Kuo

Phytozome

San Francisco high school teacher Jeffrey Kim worked with the JGI’s Patrick Davidson on a module harnessing the plant data portal Phytozome.

Jeffrey Kim's poster summarizing his Summer 2022 work on developing an educational module using Phytozome

More Information About this Program

For more information about MycoCosm, additional resources including a more extensive webinar may be found here.

For debrief about how to work with CalTeach and the JGI, check out this video.

Those interested in partnering with the JGI through CalTeach, please contact: jgi-comms@lbl.gov.

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