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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: termite

Content Tagged "termite"

Page 1 of 212»

April 19, 2013

Termite diets dictate microbes in their guts

Realtors and homeowners cringe at the thought of termites on their properties, but for bioenergy researchers, these insects are rich harbors of microbial communities that can break down woody lignocellulose. In 2007, the DOE Joint Genome Institute sequenced the microbes in the hindgut of termites from Costa Rica (from the Nasutitermesgenus) to identify the genes… [Read More]

July 27, 2012

Revisiting the importance of studying the microbes in termite guts

According to Leadbetter, the termite holds the key to unlocking all of this potential. But understanding how to do it won’t be easy.People have enlisted the help of microbes before, but never with this degree of complexity. “For 6,000 years,” he said, “we’ve been making beer, wine and bread using yeast,” which is a single-cell… [Read More]

May 6, 2012

Mount Marty College students wrap first project with DOE JGI’s “Interpret a Genome” program

“Annotating genes is a lot of work, and you have to pay a lot of attention to detail,” said April Knapp, one of seven students who presented findings from the class’s research Friday. “But it’s also very interesting because bioenergy and biofuel is such a high-needs fields. To know that the research we did here… [Read More]

February 18, 2012

Dietary impacts on hoatzin crop microbial communities

Many DOE JGI metagenomic projects focus on microbial communities in the guts of the cow, termite and even the desert locust, all known to break down plant biomass for energy. In studying these and other gut microbial communities, researchers hope to identify and isolate genes involved in plant biomass degradation, and apply them to biofuel… [Read More]

September 30, 2011

Structural Analysis of Cow and Hoatzin Microbial Communities

Inside the guts of many animals, microbes break down the plant fibers ingested as part of their diet. These microbes are of interest to bioenergy researchers who want to learn from nature and apply these cellulosic degradation capabilities toward biofuel production. To this end, at the JGI, several sequencing projects have focused on the microbial… [Read More]

March 13, 2011

Phil Hugenholtz on metagenomics and ecogenomics in Australian Life Scientist

In research published in Nature in 2007, Hugenholtz, along with collaborators from the California Institute of Technology and Diversa (now Verenium) Corporation, used metagenomics to detail the process by which a dry wood feeding termite, a Nasutitermes species, breaks down cellulose.  They generated 62 million base pairs – a “drop in the ocean by today’s… [Read More]

January 28, 2011

Cow rumen metagenome study in Technology Review

The first step in cellulosic biofuels is converting tough plant materials made of cellulose and lignin into sugars that can then be fermented to make fuels. But this is expensive and currently requires a large quantity of enzymes to break down cellulose. “We’re talking truckloads,” says Frances Arnold, a professor of chemical engineering at Caltech… [Read More]

January 27, 2011

Cow rumen metagenome study on EurekAlert

“Microbes have evolved over millions of years to efficiently degrade recalcitrant biomass,” said Eddy Rubin, Director of the JGI and a lead on this study. “Communities of these organisms can be found in diverse ecosystems, such as in the rumen of cows, the guts of termites, in compost piles, as well as covering the forest… [Read More]

December 1, 2010

Unpredictable MDA biases in metagenomic analyses

Genomic studies of low-biomass environments is often limited by the amount of DNA available, and one solution has been to use a whole genome amplification technique that uses phi29 DNA polymerase known as multiple displacement amplification (MDA). When used in single cell genomic studies, one noted drawback of the procedure has been amplification bias that… [Read More]

July 30, 2010

Tammar wallaby foregut microbiome

Australia and New Zealand were separated from other land masses for millennia, and the unique marsupials found there such as kangaroos and wallabies have forestomachs adapted to efficiently break down lignocellulosic plant mass to extract nutrients. Australian marsupials such as the Tammar wallaby (above) contain unique, uncultured bacteria that could be useful in breaking down… [Read More]
Page 1 of 212»

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