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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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    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
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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)
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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)
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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)
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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)
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Home › CSP Plans › Why sequence four Labyrinthulomycete species?

Approved Proposals FY10

Why sequence four Labyrinthulomycete species?

These common marine microorganisms with the tongue-twisting name behave like fungi in the ocean ecosystem but are actually protists. Their abundance in the ocean varies with the changing seasons. They feed on non-living organic matter such as decaying algae, plants such as mangrove leaves and salt marsh grass or even animal tissues. Species that belong to the Labyrinthulomycete category all fall under a larger category of protists that also includes diatoms and brown algae.

Labyrinthulomycetes help break down organic matter in the waters, and some species can also break down crude oil and tarballs. Researchers believe they also “upgrade” the quality of the debris that feed other marine organisms by adding nutrients. Long chain fatty acids produced by Labyrinthulomycetes have already been included in human food supplements.

Sequencing the genomes of several Labyrinthulomycete species is expected to give ocean scientists and microbiologists more information about the microorganisms’ roles in the carbon cycle and other biogeochemical cycles. The genomes to be sequenced in this project fall into three different categories: thraustochytrids, which are very important to decomposing terrestrial plant debris, aplanochytrids, which were recently recognized as a major group in marine systems and labyrinthulids, which are usually associated with living plants and algae since they seem to have a higher tolerance for antimicrobial compounds than other Labyrinthulomycete species.

Composite of the same Aurantiochytrium limacinum cell seen through Nomarski view (left) and fluorescence view (left) Aurantiochytrium limacinum photo courtesy Daisuke Honda, Konan University

Composite of the same Aurantiochytrium limacinum cell seen through Nomarski view (left) and fluorescence view (left)
Aurantiochytrium limacinum photo courtesy Daisuke Honda, Konan University

Principal Investigators: Jackie Collier, Stony Brook University

Program: CSP 2010

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