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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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Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.
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A Natural Mechanism Can Turbocharge Viral Evolution
A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.
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Our Projects
Polar Phytoplankton Need Zinc to Cope with the Cold
As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.
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When “The Blob” Made It Hotter Under the Water
Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.
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Genome Insider podcast: THE Bioenergy Tree
The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.
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Data & Tools
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JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”
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A User-Centered Approach to Accessing JGI Data
Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.
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A More Intuitive Phytozome Interface
Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.
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User Programs
Digging into Microbial Ecosystems Deep Underground
JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.
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Boosting Small Molecule Production in Super “Soup”
Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.
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A Powerful Technique to Study Microbes, Now Easier
In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.
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Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.
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Monitoring Inter-Organism Interactions Within Ecosystems
Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.
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Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.
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August 12, 2014

Detecting genome-wide DNA methylation patterns in Shewanella oneidensis MR-1

Detecting genome-wide DNA methylation patterns in Shewanella oneidensis MR-1

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