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DOE Joint Genome Institute
Enabling advances in bioenergy and environmental research
Enabling advances in bioenergy and environmental research
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Registration is now open for the 14th Annual JGI Genomics of Energy & Environment Meeting, set for April 2-5, 2019 at the Hilton San FranciscoUnion Square. The meeting will be preceded by the New Lineages of Life (NeLLi) Symposium. See the agenda and confirmed speakers at usermeeting.jgi.doe.gov. #JGI2019

#genomics #energy #environment #plants #fungi #microbes #metagenomics #bioinformatics #technology #datascience #microbiome

cc: +Berkeley Lab +U.S. Department of Energy
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Avail of early-bird registration rates till the end of December for our 14th Annual JGI Genomics of Energy & Environment Meeting!

The annual Meeting will take place April 2-5, 2019 at the Hilton San Francisco Union Square, and will be preceded by the New Lineages of Life (NeLLi) Symposium. See the agenda and confirmed speakers at usermeeting.jgi.doe.gov. #JGI2019

#genomics #energy #environment #plants #fungi #microbes #metagenomics #bioinformatics #technology #datascience #microbiome
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“Most of the phylogenetic diversity represents early diverging fungi. We know from environmental DNA surveys that they’re common in many habitats, but they’re presumably microscopic so you really have to look for them. We would love to be able to look at a given sample and identify what the cells might look like, but we also want to look at the genomes of the organisms and infer what they’re like. That’s where single-cell genomics comes in.” -Tim James, +Michigan State University

Reported today in the journal Nature Microbiology, JGI researchers partnered with James and others to develop a pipeline to generate genomes from single cells of uncultivated fungi. The approach was tested on several uncultivated fungal species representing early diverging fungi, the earliest evolutionary branches in the fungal genealogy that provide a repertoire of important and valuable gene products. More: jgi.doe.gov/expanding-fungal-diversity-one-cell.

#genomics #energy #environment #fungi #science

cc: +Berkeley Lab
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"These new [Community Science Program] projects not only expand on and improve our collection of reference genomes, but deeply explore the structure and regulation of their genes. They leverage new capabilities and higher throughput in DNA sequencing, synthesis and metabolomics to advance DOE mission science." -Susannah Green Tringe, JGI User Programs Deputy.

Learn more about the 23 approved CSP 2019 proposals, just over half of which come from primary investigators who have never led any previously accepted JGI proposal. Read: jgi.doe.gov/preparing-for-sequence-data-deluge

cc: +U.S. Department of Energy +Berkeley Lab

#genomics #energy #environment #plants #fungi #microbiology #metagenomics #viruses #science
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In our Science Highlights: Sugarcane is a cultivated crop that very efficiently converts solar energy into plant biomass, which can then be crushed to extract the sugar-laden juice that can be further purified to produce alternative biofuels. The JGI was part of an international team that successfully assembled a first monoploid reference sequence of sugarcane using a targeted approach. The reference sequence is useful for mapping the genes involved in sugar production and for identifying different variants on different chromosomes, information that can be used to assemble a more complex and more realistic polyploid sugarcane genome, work already underway through JGI's Community Science Program. Learn more at jgi.doe.gov/first-monoploid-reference-sequence-sugarcane.

#genomics #energy #environment #sugarcane #biofuels #biomass #science

cc: +Berkeley Lab
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Sixty percent of U.S. natural gas comes from hydraulically fractured shales located primarily in Ohio, West Virginia, and Pennsylvania. As engineers inject water and chemical additives into the ground, microbes hitch a ride. Reported earlier this year in the journal PNAS, researchers at +The Ohio State University +University of New Hampshire and +West Virginia University recreated a shale microbial community in the laboratory. The work was enabled by the FICUS collaborative science initiative between 2 +U.S. Department of Energy national user facilities: JGI at +Berkeley Lab and the Environmental Molecular Sciences Laboratory at +Pacific Northwest National Laboratory (PNNL). More on this joint science highlight: https://bit.ly/2x0JQ0O

#genomics #energy #environment #metagenomics #microbes #fracking
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We typically think of the universal genetic code as being stable, where mRNA is translated into protein as codons are assigned to either a stop codon or one of the 20 unquestioned amino acids. Occasionally, scientists see departures from this standard code. Until a 2016 study led by the JGI, the only such example in eukaryotes was the reassignment of CUG from leucine (its usual meaning) to serine in budding yeasts.

In work reported earlier this year in the journal Nature Communications, an international team of researchers from institutions including +UCD - University College Dublin +Vanderbilt University and the +University of Wisconsin-Madison found multiple CUG reassignments in a data set of 52 yeast genome species. Scientists are not sure why or how the change came about, but knowing if yeasts’ genetic codes are the same is important for gene expression experiments. Read on: https://jgi.doe.gov/evolutionary-changes-genetic-code-of-yeasts/


#fungi #genomics #genetics #energy #environment #biotechnology #innovation #science
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Conditions such as extreme cold, high levels of salinity and the sheer distance from other parts of the world have kept microbial populations on Antarctica distinct and unique. In our Science Highlight: we collaborated with Rick Cavicchioli of +UNSW Sydney to better understand how Antarctic archaea adapted to these conditions, information that could have biotechnological applications.

Learn more: jgi.doe.gov/defining-a-pan-genome-for-antarctic-archaea

#genomics #energy #environment #antarctic #microbiology
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“One of the hallmarks of JGI is our diverse workforce and our diverse collaborators around the world. That said, we recognize that workforce in genomics, including JGI, is not representative of the diversity in the population, especially here in California. The opportunity to tap into the diverse talent that UC Merced has is tremendous for us, and we are very grateful for this opportunity.”

On July 26, 2018, the JGI celebrated the culmination of the fifth summer of its flagship education program, the JGI-UC Merced Genomics Internship, with UC Merced. Read the full story and watch the video at jgi.doe.gov/high-five-celebrating-the-jgi-uc-merced-genomics-internship-program.

#genomics #energy #environment #internship #merced #training #diversitymatters #STEMcareers #science #technology #engineering #computing

cc: +Berkeley Lab +U.S. Department of Energy +UCMerced +National Science Foundation
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Proposals are now due September 24, 2018 for our joint Biological Data Science Call, which enables researchers to tap a diverse portfolio of advanced computational resources – at no cost – to translate the wealth of genomic and metagenomic data generated worldwide into biological discovery.. Details: http://bit.ly/FY19-BDS-FICUS.

Successful applicants of the FICUS Biological Data Science Call will access capabilities through two +U.S. Department of Energy Office of Science User Facilities: the Joint Genome Institute (JGI) and National Energy Research Scientific Computing Center +NERSC, as well as the DOE Systems Biology Knowledgebase (KBase).


cc: +Berkeley Lab


#genomics #energy #environment #bidata #hpc #computing #systemsbiology #informatics #science
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