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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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    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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    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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    A plantation of poplar trees. (David Gilbert)
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    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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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
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    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)
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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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Archived Educator Resources
Home › Archived Educator Resources › Assembly Exercise › Computer Demo

Computer Demo

Point your browser to the National Center for Biotechnology Information’s nucleotide BLAST page. (You can get there by going to http://www.ncbi.nlm.nih.gov/ and clicking BLAST in the top navigation bar, then going to the Basic BLAST area and selecting “nucleotide blast”.) You may want to keep a window with these instructions open and open the nucleotide BLAST page directly in a new window.

Below is a list of things to do:

  1. Have the class read the longest continuous sequence located in group 1’s contig. Enter that into the “Enter accession number, gi, or FASTA sequence” textfield on the form. Alternatively you can copy the sequence from below and paste it into that window. The sequence is : CATATTGGCTGAAGACCAAGAGGGAAGAAGCAC
  2. Make sure the Database drop-down menu is set to “nucleotide collection (nr/nt).”
  3. Click the BLAST button. BLAST starts looking in GenBank (a database of genetic sequences) for sequences that match the query sequence that you entered. Not only does it look for the query sequence, but it also looks for the reverse complement.
  4. Wait about ten seconds until the results are ready.
  5. Once the results are up, scroll down the page past the alignment image and click the first link AC026748.7. This opens up a GenBank page. Note in this GenBank record that this is the sequence for Homo sapiens chromosome 5 clone RP11-325I22. In the reference portion note that the JGI did this sequence.
  6. Go back to the BLAST results page by hitting your browser’s Back button. You may have to refresh the page. On the results page go and click the next link AF119117.1. This again opens up a GenBank page that shows a GenBank record that is specific for the gene that this sequence belongs to. Copy the gene identifier SLC6A3 from the Definition section.
  7. Click the OMIM link on the top menu or go to http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM.
  8. Paste SLC6A3 into the search textfield at the top of the page and click “Go”.
  9. The results of the OMIM search show entries associated with behavior-related issues. Also point out that one of the entries shows that this gene is associated with ADHD, or attention-deficit hyperactivity disorder. If you want to find out more about ADHD, click the numeric link.
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