tag:blogger.com,1999:blog-32079676.post9209167107674602861..comments2024-02-13T21:22:02.522-08:00Comments on RRResearch: A terminology problemRosie Redfieldhttp://www.blogger.com/profile/06807912674127645263noreply@blogger.comBlogger1125tag:blogger.com,1999:blog-32079676.post-30478404552469529752009-09-03T13:07:40.054-07:002009-09-03T13:07:40.054-07:00I like defining briefly the history of USS, admitt...I like defining briefly the history of USS, admitting the term is flawed, and using the two terms you brought up without reference to USS.<br /><br />(1) Genomic motif (or even "genomic Gibbs motif", since it was defined without any information about uptake)--well characterized<br />(2) Uptake motif (or even simply "uptake bias")--barely characterized<br />(3) Core USS... the original 9mer known to be sufficient for uptake. Just for purposes of introduction, and indeed it is clearly an uptake signal.<br /><br />This way, you can say that Gibbs sampling reveals an abundant genomic motif, which contains strong consensus positions that match the known core USS. This suggested that the genomic motif has arisen by molecular drive due to biased uptake. Cite references to bioinformatics work that build up this model, and preliminary data that partially refutes it.<br /><br />Then the proposed work is to measure the actual uptake bias of the outer membrane and evaluate the extent to which the genomic Gibbs motif reflects biased uptake.<br /><br />This way, USS only comes up in the introduction; thereafter it is a comparison between Gibbs sampling of the genome sequence and actual uptake biases. Then the uptake bias measurements would be done with two pools: fragmented genomic DNA and a degenerate genomic motif.<br /><br />When discussing individual genomic positions that are efficiently taken up, I like the term "uptake signal", rather than USS, since it doesn't have any baggage...Changhttps://www.blogger.com/profile/12291718994939895064noreply@blogger.com