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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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    (PXFuel)
    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 genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    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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    Photograph of a stream of diatoms beneath Arctic sea ice.
    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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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    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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    A plantation of poplar trees. (David Gilbert)
    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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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    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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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    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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    Phytozome portal collage
    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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    screencap from Amundson and Wilkins subsurface microbiome video
    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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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    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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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    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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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    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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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    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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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    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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Home › Items tagged with: IMG

Content Tagged "IMG"

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October 21, 2013

Combining profiling and genomics yields novel metabolites

Cyanobacteria’s ability to capture solar energy and fix CO2 holds promise for biotech applications The Science Researchers studied 10 different cyanobacteria to identify their secondary metabolites (compounds produced during normal cellular metabolism not directly involved in cell growth, that may play an important role in interactions outside the cell) and the genes linked to those… [Read More]

February 8, 2013

Student tools for hands-on genomics and bioinformatics lessons

Driven in part by the increased emphasis to give life sciences students hands-on experience in “real research,” the DOE Joint Genome Institute’s Genomics and Bioinformatics Education Program developed a series of educational modules for undergraduate programs to explore and annotate publicly available microbial genome datasets. Known collectively as the Integrated Microbial Genomes Annotation Collaboration Toolkit… [Read More]

December 3, 2012

Cheryl Kerfeld on IMG-ACT in The Scientist

  “Bioinformatics has become such an integral part of research. And being able to do this, to use these tools in an informed way and in a way that’s somewhat discerning . . . is really important,” explains Cheryl Kerfeld, director of the Genomics and Bioinformatics Education Program at the Department of Energy’s Joint Genome… [Read More]

October 26, 2012

IMG v4 announcement in GenomeWeb

The Department of Energy’s Joint Genome Institute has released a fourth version of the Integrated Microbial Genomes system, which serves as a community resource for analyzing and annotating genome and metagenome datasets….IMG currently contains 11,753 total genomes, plasmids and genome fragments; 2,075 metagenome samples; and 2,372 genomes and 804 metagenome samples in IMG/ER and IMG/M-ER,… [Read More]

July 6, 2012

GEBA Gets More Cellulase

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June 13, 2012

DOE JGI’s IMG/M data system in Berkeley Lab’s release on the Human Microbiome Project

Berkeley Lab’s role in mapping the human microbiome revolves around big data, both analyzing it and making it available for scientists to use worldwide…. Berkeley Lab scientists developed and maintain a comparative analysis system called the Integrated Microbial Genomes and Metagenomes for the Human Microbiome Project (IMG/M HMP). It allows scientists to study the human microbiome… [Read More]

June 1, 2012

Comparative genomics method to tag novel nitrogen-fixation genes

Nitrogen is crucial for plant growth but plants cannot harness it directly from the atmosphere. In the United States, legume crops such as soybeans and peas rely on nitrogen fertilizers to boost yields; in 2007, 13 million tons of industrially-produced fertilizers were applied. Soil bacteria such as Sinorhizobiummeliloti have a symbiotic relationship with plant hosts… [Read More]

March 9, 2012

Bioinformatics challenges for metagenomic analyses

There are more microbes in, on and around the planet than there are stars in the sky. However, the vast majority of these microorganisms have not yet been studied, in part because many of them do not thrive when moved out of their natural environment. A spoonful of soil contains a complex and diverse microbial… [Read More]

November 18, 2011

New tools for the IMG/M analysis system

Since the initial release of the Integrated Microbial Genomes with Microbiome samples (IMG/M) system in 2007 to support the comparative analysis of metagenomic data sets, DOE JGI researchers have made several updates in order to keep pace with the rapid increase in data set generation due to advances in sequencing technologies. As reported by researchers… [Read More]

November 4, 2011

A metagenomic approach to analyzing rice endophytes

During the call for 2012 proposals for the DOE JGI’s Community Sequencing Program, one of the areas of focus researchers were asked to consider was that of plant-microbe interactions. Microbes that live in plants or in the rhizosphere where plant roots and soil interact can play crucial roles in plant health. This is of particular… [Read More]
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