tag:blogger.com,1999:blog-32079676.post1135829767467716529..comments2024-02-13T21:22:02.522-08:00Comments on RRResearch: And a possible NSERC proposalRosie Redfieldhttp://www.blogger.com/profile/06807912674127645263noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-32079676.post-7066194535727525782012-07-20T12:10:25.441-07:002012-07-20T12:10:25.441-07:00I really don't know what to make of them. I s...I really don't know what to make of them. I suspect they're selected on because they have direct effects on the cells, independent of the gene transfer they cause. Being a donor apparently requires cell death, which makes selection for transfer effects particularly unlikely.Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-45867445741642050972012-07-20T11:29:30.041-07:002012-07-20T11:29:30.041-07:00What do you think about gene transfer agents? They...What do you think about gene transfer agents? They don't appear to me to have any obvious function besides transferring bacterial DNA. Clearly they evolved from phages that didn't care one bit about transferring anything but their genome, but they don't do that any more. And they seem to be under purifying selection.zmilhttps://www.blogger.com/profile/07235676056579625819noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-56820649456587338692012-07-19T21:42:11.338-07:002012-07-19T21:42:11.338-07:00Good retort! Very effective and to the point! A mi...Good retort! Very effective and to the point! A minor thing remains - tell the actual mechanisms then...<br /><br />But, just so you may understand my point a little better, another analogy: There is no doubt that proteins play a crucial role in membrane fusion. At the same time, by now it is 100% clear that all they do is promote the basic sequence of events that are observed without any proteins in many "artificial" membrane fusions (PEG-, osmotic shock-, peptite-mediated, etc).DKnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-78803194182507382502012-07-19T21:20:57.788-07:002012-07-19T21:20:57.788-07:00I'm not wasting any more courtesy on an ignora...I'm not wasting any more courtesy on an ignorant troll...Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-85842477881520508012012-07-19T21:15:50.627-07:002012-07-19T21:15:50.627-07:00But in the case of DNA uptake, the proteins ARE wh...<i>But in the case of DNA uptake, the proteins ARE what's doing the work. This is active uptake, not passive permeation as in the E. coli 'heat shock' transformation you referred to.</i><br /><br />Since I don't think you know the mechanism of either, I don't see what makes you so confident making such statements. Personally, I'd bet that you are wrong and that the "active uptake" is merely a protein-assisted version of the more general phenomenon.DKnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-70307062307623155592012-07-19T19:26:31.883-07:002012-07-19T19:26:31.883-07:00But in the case of DNA uptake, the proteins ARE wh...But in the case of DNA uptake, the proteins ARE what's doing the work. This is active uptake, not passive permeation as in the <i>E. coli</i> 'heat shock' transformation you referred to.<br /><br />You're right that the DNA properties do matter. We're also analyzing the physical properties of the DNA fragments that are preferentially taken up, as we hypothesize that these properties play a big role in the initiation of uptake. And we're also going to look for sequence effects in the post-initiation progression of uptake.Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-7469176656851036312012-07-19T19:08:13.604-07:002012-07-19T19:08:13.604-07:00I looked at it (obviously, not detailed enough to ...I looked at it (obviously, not detailed enough to check out refs and all that but enough to get a sense of what's there). Just IMO: I find the emphasis on proteins really annoying and misguided. There is a fundamental physical problem and you are trying to reduce it to what seems to be a small and not particularly representative subset of related phenomena. To illustrate with analogy: to understand how ribosome works, one needs to figure that it's RNA doing most of the work. Focusing on its proteins may get you funded but won't get you very far with regard to understanding of the what's going on. <br /><br />P.S. Interesting to see that not much has changed in 20 years.DKnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-88704806186418357142012-07-19T16:53:24.599-07:002012-07-19T16:53:24.599-07:00Hi DK: If you'd like to bring your knowledge ...Hi DK: If you'd like to bring your knowledge up to date you could read our latest grant proposal. It's <a href="http://www.zoology.ubc.ca/~redfield/proposals/Uptake%20proposal.pdf" rel="nofollow">here</a>.Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-85851852254220810482012-07-19T16:48:04.867-07:002012-07-19T16:48:04.867-07:00Last time I checked, no one knows even how heat-sh...Last time I checked, no one knows even how heat-shock transformation of E.coli works. Seems like there was an active research on the subject in the 1970s and 1980s but it proved too difficult, and so it fizzled as not worthy of attention. <br /><br />I haven't actually followed the literature for something like 20 years but back then the field that studies bacterial natural transformation competence and mechanisms of DNA uptake was in embryonic state with hardly anything understood. Whether there is DNA sequence bias is, IMO, not even a particularly interesting question on the background of the question of how a highly hydrophilic molecule gets of a size comparable with cell size gets through the cell wall and hydrophobic plasma membrane.DKnoreply@blogger.com