MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'RRResearch' source. Mon, 17 Nov 2008 22:53:55 +0100 http://rrresearch.blogspot.com/2008/11/outline-for-why-do-bacteria-take-up-dna.html As I said in the previous post, this will be a review article emphasizing how we can decide why bacteria take up DNA, rather than claiming we have enough evidence to decide.It will begin with an overview about why this question is so important. To make the writing easier I can probably modify text from my grant proposals and from Do bacteria have sex, but this new introduction should be a lot shorter than the coverage of this issue in that article. The basic things to say are:Recombination between bacteria has been enormously important in their evolution, so we really should try to understand why it happens.It's usually been assumed that the processes that cause recombination exist because the recombination they cause is selectively advantageous. (This might be viewed as meta-selection - s... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1960791 Thu, 13 Nov 2008 18:15:00 +0100 1960791 http://rrresearch.blogspot.com/2008/11/review-articles-to-be-written.html Two, in fact. I really really need to publish a review about the evolution of competence (=DNA uptake). Something like my Do bacteria have sex review, but updated and focusing much more on the competence and uptake issues. And I've also promised to write a chapter on competence and transformation for a book celebrating a wonderful colleague. The model for this book is Phage and the Origins of Molecular Biology, written as a feitschrift for Max Delbruck. Ideally I'd love to produce something as charming as Andre Lwoff's The Prophage and I in that book, but I think I'd better lower my standards and get the job done.Starting now.OK, the first things I need are outlines.For the book chapter, I was thinking about writing it as several levels of history, maybe interleaved (?): my personal histor... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1955285 Wed, 12 Nov 2008 17:34:00 +0100 1955285 http://rrresearch.blogspot.com/2008/10/why-do-bacteria-take-up-only-one-dna.html People who disagree with us about the nutritional importance of DNA for bacteria very often cite the degradation of one DNA strand at the cell surface. Like almost all (maybe all) other competent bacteria, H. influenzae initially binds double-stranded DNA, but brings only one of the two strands across the inner membrane into the cytoplasm. The other strand is degraded to nucleotides in the periplasm. In Gram-positive bacteria the degradation also occurs at the surface, before the remaining DNA strand is transported into the cytoplasm, and the released nucleotides are found in the culture medium.(Hmm, aside, I must go back and check the old literature, to see if it's the nucleotides or only the phosphates that are found in the medium. This is significant because we know that the phosphate m... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1914695 Tue, 28 Oct 2008 23:49:00 +0100 1914695 http://rrresearch.blogspot.com/2008/10/super-ultra-high-throughput-sequencing.html A potential collaborator/coworker has suggested what I think would be a great experiment, if we can find a way to do it economically.  But it would require sequencing to very high coverage, something I know almost nothing about the current economics of.Basically, we would want to sequence a pool of Haemophilus influenzae DNA from a transformation experiment between a donor and a recipient whose (fully sequenced) genomes differ at about 3% of positions, as well as by larger insertions, deletions and rearrangements.  The genomes are about 2 mb in length. The DNA fragments could have any desired length distribution, and the amount of DNA is not limiting.  Ideally we would want to determine the frequencies of all the donor-specific sequences in this DNA.  For now I'll limit the problem to ... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1907699 Sat, 25 Oct 2008 14:11:00 +0100 1907699 http://rrresearch.blogspot.com/2008/10/more-from-elsevier-names-removed.html Email from an Elsevier Publisher:Dear Rosie,I'm so sorry this process has been difficult. As you say below, you can pay by credit card (personal or institutional). We don't have an agreement with CIHR, but they may indeed refund the cost of the sponsored access. That's something CIHR will have to advise you on. The journal manager for JMB; jmb@elsevier.com (name removed) is working with her colleagues to make your article available should you wish. If you haven't completed the paperwork for payment, the link is here:http://www.elsevier.com/framework_authors/Sponsoredarticles/sponsoredarticleoption.pdf I see on your blog, however, that you've given up due to frustration with the process and the inability of the service group to respond to your questions. I know they did the best they could.... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1859584 Tue, 07 Oct 2008 14:03:00 +0100 1859584 http://rrresearch.blogspot.com/2008/09/i-give-up.html I give up. No, Elsevier, I am not going to give you $3000. Principles be damned.Dear Dr Redfield,Thank you for your reply.A purchase order is for your benefit only, Elsevier do not require one, please see below link:http://epsupport.elsevier.com/article.aspx?article=1296&p=3Elsevier accept 3 methods of payment, please see below link:http://epsupport.elsevier.com/article.aspx?article=1718&p=3As previously advised your article can be made available via open access, however you must cover the cost of USD$3,000.Please confirm if you wish to proceed, I will update our system and send the forms for invoicing.Elsevier Support Person (Source: RRResearch) RRResearch blogs http://www.medworm.com/rss/comments.php?id=1837260 Mon, 29 Sep 2008 18:33:00 +0100 1837260 http://rrresearch.blogspot.com/2008/09/saga-continues.html Reply from the Elsevier Support Person:Dear Dr Redfield,Thank you for your reply and apologies for any confusion caused.Elsevier has established agreements and developed policies to allow Authors who publish in Elsevier journals to comply with the manuscript archiving requirements of funding bodies, as specified as conditions of researcher grant awards, the below is a list of these:Arthritis Research Campaign (UK)British Heart Foundation (UK)Cancer Research (UK)Chief Scientist OfficeDepartment of Health (UK)Howard Hughes Medical Institute (US)Medical Research Council (UK)National Institute of Health (US)Wellcome Trust (UK)As mentioned on the below link:http://www.elsevier.com/wps/find/authorsview.authors/sponsoredarticlesMore than 40 journals published by Elsevier offer authors the option ... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1833250 Fri, 26 Sep 2008 14:51:00 +0100 1833250 http://rrresearch.blogspot.com/2008/09/more-elsevier-hassles-about-open-access.html Recent correspondence, beginning with the last of a series of emails about a form that had gone astray:Hi Elsevier Support Person (I'll won't use this person's name),I've attached pdfs of the signed sponsorship form and the purchaseorder to this email. I'm also cc'ing the email to the Sponsoredarticles address,Thanks,Rosie--------------------------------------------------Dear Dr Redfield,Thank you for your reply.The funding body listed on your sponsorship article form is not abody Elsevier currently has a policy with, therefore we cannotprocess this.For more information and a full list of our Funding Bodies, pleasesee below link:http://epsupport.elsevier.com/article.aspx?article=1261&p=3Yours sincerely,Elsevier Support Person--------------------------------------------------Dear Elsevi... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1833251 Fri, 26 Sep 2008 13:51:00 +0100 1833251 http://rrresearch.blogspot.com/2008/09/other-nucleases-that-might-act-on.html I just discovered a 2008 paper in Mutation Research, about the phenotypes of H. influenzae exonuclease mutants, and I've emailed the senior author asking if they would be willing to send us chromosomal DNA of these mutants, so we could test a pet hypothesis of mine.The hypothesis concerns the functions of the competence-induced genes comM and dprA. Phenotypes of mutants in other bacteria suggest that the products of these genes protect incoming DNA from nuclease degradation. But what nuclease? By testing the competence phenotypes of double mutants we've ruled out ExoV (recBCD). Using the new mutants would let us test the involvement of other nucleases. (The hypothesis is described more thoroughly in this blog post.)A 2002 paper about Snyechocystis shows that knocking out recJ increases tra... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1825793 Tue, 23 Sep 2008 18:08:00 +0100 1825793 http://rrresearch.blogspot.com/2008/09/open-access-and-other-sliminess-at.html Our latest paper on CRP sites has been accepted by the Journal of Molecular Biology. This is great, but now I'm dealing with the messy post-acceptance issues.First, our page proofs have gone astray. The Elsevier manuscript-tracking page (yes, JMB is part of the evil empire of scientific publishing) says that page proofs were sent out on Aug. 27. They should have been sent by email, but I've seen no sign of them so far. Usually page proofs are supposed to be corrected and returned within 48 hrs; I've just emailed a person at JMB about them.While looking for the proof email I discovered that I'd ignored other bureaucratic requirements. I needed to complete an on-line document assigning all copyright to Elsevier. This document made no mention of an open-access option, but I accepted it anyway... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1754752 Tue, 02 Sep 2008 19:47:00 +0100 1754752 http://rrresearch.blogspot.com/2008/08/searching-for-motifs.html Well, I don't know why my first attempt at running a Gibbs motif search with the Gallibacterium genome returned errors. The errors it described were ones I hadn't made (as far as I could tell), so I resubmitted the runs and they were fine.But the grid-computer system was slow to get around to my runs (probably those physicists and meteorologists hogging the system), so I poked around and rediscovered that the Gibbs motif searcher program now also runs on Macs. Luckily one of the post-docs had just come back from a two-week course that required intensive use of Unix, so she was able to dive in and sort out the permissions etc. for me. So now I can run the Gibbs searches on my newish MacBook Pro and on our other fast Mac. And I can also still run them on the grid system too.Results: I can't ... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1709226 Sat, 16 Aug 2008 00:56:00 +0100 1709226 http://rrresearch.blogspot.com/2008/08/can-i-remember-how-to-run-gibbs-motif.html Our visiting grad student is working with Gallibacterium, a Pasteurellacean relative of Haemophilus. To help her optimize transformation we would like to find out about its uptake bias. As a first step, we'd like to find out whether it has repeats in its genome that resemble the known Pastuerellacean uptake signal sequences (USS) - fortunately a Gallibacterium genome sequence is available. I've done this analysis for all the other sequenced Pasteurellacean genomes, so I said I'd do this one too. Should be easy...My first approach was to give the genome sequence to our Perl program that simulates USS, not because I want to do that, but because the program's first step is to count the numbers of full and partial USS matches in the starting sequence. The program was set up to do that for the ... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1709227 Thu, 14 Aug 2008 15:39:00 +0100 1709227 http://rrresearch.blogspot.com/2008/08/crp-maniscript-revisions-submitted-on.html As usual, it took me about 3 tries to get the manuscript resubmitted with all the files in their correct forms. But it's done.I'm going to try to get back to the bench next week, doing some competence-induction experiments with Gallibacterium, brought to the lab by our visiting grad student. Oh boy! (Source: RRResearch) RRResearch blogs http://www.medworm.com/rss/comments.php?id=1696243 Tue, 12 Aug 2008 02:49:00 +0100 1696243 http://rrresearch.blogspot.com/2008/08/manuscript-almost-ready-to-go-back.html Our manuscript about how the CRP proteins of E. coli and H. influenzae differ in their sequence specificity has been provisionally accepted, and the revised version is almost ready to send back to the journal. We weren't able to do the one experiment requested by the editor, but we make what we think is a pretty good argument about why it isn't needed.The only remaining problem is that some of the figures look a bit weird, I think due to being shuffled between different formats. The dark grey shading in some of the bar-graph bars has turned into a dark grey check pattern. My former-postdoc-coauthor converted the figures into high-resolution PDFs so he could email them to me, but maybe he should instead post them to one of those file-sharing sites where I can download them. I know Google Gr... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1693712 Sat, 09 Aug 2008 22:25:00 +0100 1693712 http://rrresearch.blogspot.com/2008/08/where-are-they-now-part-2.html Two more lines of research that we're no longer working on:3. When did eukaryote sexual reproduction begin? During the first 10 years that I was working on competence, I fully intended to switch to studying the origins of meiosis in eukaryotes. The plan, and the reasons I set it aside, are explained in this post from last summer. (Fortunately John Logsdon has taken up the torch.)As the first steps in this project Joel Dacks, then a M.Sc. student in my lab, and I published two papers on the phylogeny of early-diverging eukaryotes. These results have been since confirmed by more detailed analyses, although the deep phylogeny of eukaryotes is still rather obscure.4. Quorum sensing and/or diffusion sensing: Most bacteria secrete small more-or-less inert molecules into their micro-environments ... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1679423 Mon, 04 Aug 2008 21:53:00 +0100 1679423 http://rrresearch.blogspot.com/2008/08/where-are-they-now.html In the course of updating my CV I've been checking what's become of hypotheses and projects we initiated but are no longer working on. The good news is that all of them are still active areas of research, and the ones I consider most important are getting increasing attention. Here's a quick overview of two of them.1. Mutation rates in males vs females: In response to a paper reporting that point mutation rates are much higher in males than females (because sequences on X chromosomes evolve slower than sequences on Y chromosomes), I used a computer simulation model to show that the excess mutations in male lineages usually canceled out the benefits of sexual recombination for females (Redfield Nature 1994). This paper made a big media splash when it came out; Natalie Angier wrote it up for... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1677204 Sun, 03 Aug 2008 21:07:00 +0100 1677204 http://rrresearch.blogspot.com/2008/07/test-post-from-iphone.html The culture media problems we were having last fall are back. This time the postdocs suspect the medium, so they've ordered a new stock of the Bacto stuff.I think I won't try to post any more from my phone until my iPhone typing speed improves.Sent from my iPhone (by email to Blogger, because the iPhone doesn't support MMS messaging). (Source: RRResearch) RRResearch blogs http://www.medworm.com/rss/comments.php?id=1655511 Fri, 25 Jul 2008 20:55:00 +0100 1655511 http://rrresearch.blogspot.com/2008/07/how-arbitrary-is-position-weight-matrix.html Recently I've run some USS-evolution simulations that started with a 50 kb segment of the H. influenzae genome rather than with a random sequence of base pairs. I used the position weight matrix derived by Gibbs analysis of the whole genome, thinking that this would be a non-arbitrary measure of the over-representation of the uptake sequence pattern. I was hoping that this bias would be strong enough to maintain the uptake sequences already in the genome, but the genome score fell to about half (or less) of its original value after 50,000 or 100,000 cycles.That started me wondering whether the position weight matrix should be treated as a fixed set of values, or just as telling us the relative value that should be applied to each base at each position. Said another way, could different set... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1652375 Thu, 24 Jul 2008 19:14:00 +0100 1652375 http://rrresearch.blogspot.com/2008/07/sent-from-my-new-iphone-unfortunately-i.html (Source: RRResearch) RRResearch blogs http://www.medworm.com/rss/comments.php?id=1640297 Sun, 20 Jul 2008 14:59:00 +0100 1640297 http://rrresearch.blogspot.com/2008/07/some-calculations-and-implications.html In playing around with our Perl model of uptake sequence evolution, I've been surprised by how weak the effect of molecular drive seemed to be.  But I just did some back-of-the envelope approximations and realized that our settings may have been unreasonable.We can use the relationship between the genomic mutation rate the model is assuming and known real mutation rates for a rough calibration.   Real mutation rates are on the order of 10^-9 per base pair per generation.  Using such a low rate per simulation cycle would make our simulations take forever, so we've been using much higher rates (usually 10^-4 or higher) and treating each simulation cycle as collapsing the effects of many generations.  But we didn't take the implications of this seriously.  If we do, we have each simulati... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1637813 Sat, 19 Jul 2008 02:21:00 +0100 1637813 http://rrresearch.blogspot.com/2008/07/uss-perl-project-becomes-uss-drive.html I think I'm going to start using the label "USS-drive" for the manuscript that describes our "USS-Perl" computer simulation model.  That's because the focus of the manuscript will be on understanding the nature of the molecular drive process that we think is responsible for the accumulation of uptake sequences in genomes.The plan is to combine the modeling analysis with our unpublished results on the bias of the uptake machinery and on the nature of the motif that has accumulated in the genome.The broad outline will be as follows:We want to understand how the bias of the uptake machinery can affect evolution of sequences in the genome, assuming that cells sometimes take up and recombine homologous sequences from closely related cells.  And we want to examine this in the context of what i... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1631125 Thu, 17 Jul 2008 00:59:00 +0100 1631125 http://rrresearch.blogspot.com/2008/07/on-to-other-manuscripts.html Discussion.  It's not nearly as far along as I'd hoped, but it's a much better piece of science than it was shaping up to be a week ago.  One key step was switching the axes of a couple of the figures.  Seems like a minor thing, but putting "% sequence identity" on the X-axis rather than the Y-axis transformed the data from meaningless to crystal clear.  The only big piece of analysis we still need is an examination of which of the H. influenzae genes that don't have BLAST hits in our three standard gamma-proteobacterial genomes also don't have hits in the more closely related A. pleuropneumoniae genome.  Those that don't are stronger candidates for having entered the H. influenzae genome by horizontal gene transfer, and we predict they will also have relatively few uptake sequences.S... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1625654 Tue, 15 Jul 2008 14:22:00 +0100 1625654 http://rrresearch.blogspot.com/2008/07/divergence-of-genes-in-different-cog.html The bioinformatics manuscript is coming along nicely (though of course a lot more slowly than I had hoped).One of the things it does is show that the densities of uptake sequences in genes does not correlate well with the 18 'COG functional categories' that genes have been assigned to.  This is a significant result because a previous paper claimed a strong correlation between high uptake sequence density and assignment to a modified COG functional category containing 'genome maintenance genes'.  This result was considered to provide strong support for the hypothesis that uptake sequences exist to help bacteria get useful new genes, a hypothesis I think is dead wrong.Our hypothesis is that the distribution of uptake sequences among different types of genes (with different functions) shoul... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1616148 Sun, 13 Jul 2008 00:54:00 +0100 1616148 http://rrresearch.blogspot.com/2008/07/base-composition-analysis-supports-gene.html Both our results and those recently published by another group suggest that uptake sequences are less common in genes that don't have homologs in related genomes.  I'm using 'related' loosely here, as our analysis searched for homologs in genes from other families of bacteria whereas the other group searched in members of the same genus.  But both results are best explained by the hypothesis that genes lacking uptake sequences are often those that a genome has recently acquired by lateral transfer from genomes that don't share that species' uptake sequence. To test this, we looked at gene properties that might give evidence of lateral transfer.  The simplest such property is base composition (%G+C), a property that differs widely between different bacterial groups and changes only slow... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1582038 Sat, 05 Jul 2008 13:26:00 +0100 1582038 http://rrresearch.blogspot.com/2008/07/order-of-results.html We're still working out the order in which we present the different results in our draft manuscript.  The first parts of the Results are now the analysis of how uptake sequence accumulation has changed the frequencies of different tripeptides in the the proteome, and of why some reading frames are preferred.  The next decision is how we present the results that use alignments of uptake-sequence-encoded proteins with homologs from three 'control'  genomes that do not have uptake sequences.  We had tentatively planned to first describe the finding that genes that don't have uptake sequences are less likely to have homologs in the control genomes (call this analysis A), then move to the genes that do have homologs in all three control genomes, first considering the overall degree of simil... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1582039 Sat, 05 Jul 2008 13:02:00 +0100 1582039 http://rrresearch.blogspot.com/2008/07/organization-of-results.html My bioinformatics collaborator and I are making good progress on both the writing of our manuscript and on improving the data that's going into it.  One of the latter came when I redid an analysis I first did about a year ago, this time being more meticulous about the input data and more thoughtful about how I used it.The question the data address is why uptake sequences in coding regions are preferentially located in particular reading frames, specifically the effect of the codons they use on how efficiently the mRNA can be translated.  I had used the overall frequencies of different codons in the proteome (all the proteins the genome encodes) to estimate codon 'quality', by summing the frequencies of the three codons specified by the uptake sequence in a specific reading frame, and div... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1582040 Sat, 05 Jul 2008 12:40:00 +0100 1582040 http://rrresearch.blogspot.com/2008/07/my-bioinformatics-collaborator-is-in.html My bioinformatics collaborator is in town till next Friday, so we can work together to finish up our uptake sequence manuscript.  We have done (she has done) a lot of different analyses addressing various questions about how uptake sequence accumulation has affected protein evolution and vice versa, and I'm having a hard time keeping them all straight (partly because I haven't been thinking about this project for a while).  The manuscript is mostly written already; but some parts of the Results are still up in the air because they were waiting for some final data.  It also needs polishing and some revising to incorporate results from a Neisseria uptake sequence paper that came out a few months ago.To cope with all the data we've been occasionally creating 'Flow of Results' pages that s... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1575468 Thu, 03 Jul 2008 13:32:00 +0100 1575468 http://rrresearch.blogspot.com/2008/06/speedy-simulations.html Our programming assistant has finished his work for us.  At least, he's finished the period when he's employed by us, but now he's gotten the research bug and wants to stay involved to see how the program he's developed for us works out.At present it works great - MUCH faster than before.  One of the reasons is that it no longer scores the genome in every cycle.  I'm doing a run now with a big genome (100 kb) and I can see it pause at every 100th cycle, as it takes the time to score the genome.  This is a sensible improvement, as the genome score isn't needed for the progress of the simulation - it just lets us the user monitor what's happening, and provides information used if the run needs to decide whether it has reached equilibrium.I'm using this run to test whether the final accum... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1518720 Sat, 14 Jun 2008 02:29:00 +0100 1518720 http://rrresearch.blogspot.com/2008/06/sex-and-recombination-in-minneaopolis.html The meeting on Sex and Recombination that was to be held in Iowa City next week has been canceled because of severe flooding! (And just when I was getting my talk pulled into shape too...) I suspect I'm not the only one who planned to combine that meeting with the big Evolution meetings in Minneapolis, June 20-24. I'm flying into Minneapolis on June 15. If you'd like to get together with me or other sex-refugees, post a comment below and we'll see what we can organize. (Source: RRResearch) RRResearch blogs http://www.medworm.com/rss/comments.php?id=1516567 Thu, 12 Jun 2008 22:35:00 +0100 1516567 http://rrresearch.blogspot.com/2008/06/preparing-talks.html I've been struggling to pull together ideas and data for the two talks I'm giving (next week and the week after) at evolution meetings.  Yesterday was my turn to give lab meeting, and I used it to get help from the post-docs.  My draft talks were a mess, but the post-docs had lots of excellent suggestions.  Both talks will use the same introduction to the evolutionary significance of bacterial DNA uptake, and will then diverge. On the USS-evolution simulation front, the model is running nicely and I'm using it to quickly collect data for my first talk (20 minutes, for the Sex and Recombination meeting).  But I have to compromise statistical significance with run time, as the large genomes needed to get lots of sequence data take a long time to simulate.  On the proteome-evolution fro... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1508481 Tue, 10 Jun 2008 12:53:00 +0100 1508481 http://rrresearch.blogspot.com/2008/06/creeping-up-to-equilibrium.html One other issue about equilibrium:In our previous (unrealistic model) we found that USS initially accumulated very quickly, as singly and doubly mismatched sites were converted to perfectly matched sites. But this happened at the expense of depleting the genome of those mismatched sites, and further accumulation of perfect sites required waiting a long time for mutation of worse sites to regenerate the singly and doubly mismatched ones, which would then slowly allow further increase in the number of perfect matches. So achieving true equilibrium took a long time.I expect this phenomenon to also apply in this new model. So I'm not at all confident that an early leveling-off of the rate of increase indicates closeness to the true equilibrium.In the graphs to the left, the upper simulation pr... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1499969 Fri, 06 Jun 2008 19:14:00 +0100 1499969 http://rrresearch.blogspot.com/2008/06/simulating-uss-evolution.html Yes, the Perl model has progressed to the point where it's now a research tool. But I now need to focus my use of it, to get useful data rather than just noodling around to see what happens.One remaining uncertainty is the decision that a simulation has reached an equilibrium, where forces increasing the frequency of USS-like sequences are balanced by forces decreasing it. So far I've been running simulations for a specified number of cycles instead of 'to equilibrium', because I'm not confident that they will indeed correctly identify equilibrium conditions. Now I guess I should take the settings I used for runs that did reach what I consider to be equilibrium, and rerun them 'to equilibrium' instead of to the specified number of cycles.A problem is that the runs still take quite a long t... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1499970 Fri, 06 Jun 2008 17:22:00 +0100 1499970 http://rrresearch.blogspot.com/2008/06/means-arithmetic-and-geometric-additive.html Now that we've replaced our old additive scoring algorithm with a multiplicative one (see this post), the algorithm that decides whether the simulation has reached its equilibrium isn't working well. The post-doc suggests that this is because we need to track the changing score of the genome using a multiplicative mean rather than an additive mean.The test for equilibrium works as follows: The USS-score of the genome is calculated each generation, and is used to calculate both a "recent" mean score (over the interval between status updates, usually specified as a percent of the elapsed cycles) and a "grand" mean score (over the entire run). Both means are calculated as simple averages (sum of the scores divided by the number of scores). Early in the run the grand mean is much smaller than ... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1488290 Mon, 02 Jun 2008 17:11:00 +0100 1488290 http://rrresearch.blogspot.com/2008/06/thank-you-for-comments.html The profiling I did yesterday, using DProf as suggested in a comment from Keith, showed that most of the runtime was spent in the switch statements that are the heart of the sliding-window scoring algorithm. In new comments, Keith and Conrad explained that 'switch' is not the fastest way to do the scoring, and that replacing it with a cascade of if/else statements could be a lot faster. So I've just replaced all three of the switch scoring steps with if/else cascades, and here's the spectacular results. Thanks, guys! (Source: RRResearch) RRResearch blogs http://www.medworm.com/rss/comments.php?id=1484928 Sun, 01 Jun 2008 18:11:00 +0100 1484928 http://rrresearch.blogspot.com/2008/05/benchmarking-uss-model.html (I don't think 'benchmarking' is actually the right term for what I've been doing...)The comments on my last post recommended using the Perl profiling function to find out which parts of our simulation are indeed responsible for its slow runtime. So I Googled "DProf" and ran it on the simulation, and then poked around to find out how to use 'dprofpp' to turn the DProf output into a table listing where most of the time was being spent. Pretty soon I discovered that I just needed to type 'dprofpp' at the usual prompt. (duh).Then I spent quite a while trying to figure out what the profile entries meant. Here's an example of the output.Total Elapsed Time = 65.63472 Seconds User+System Time = 63.53472 SecondsExclusive Times%Time ExclSec CumulS #Calls sec/call Csec/c Name 41.6 26.44 37.689 5438... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1482087 Sun, 01 Jun 2008 01:35:00 +0100 1482087 http://rrresearch.blogspot.com/2008/05/speeding-up-simulation-of-uss-evolution.html Our Perl model of USS evolution now runs fine and does just about everything we want it to. Unfortunately it takes a long time to do this. To date we haven't bothered much about speed, being more concerned with just being able to do the job. But now it's time to improve its efficiency. I see several points where big improvements can be made, but first I should describe the steps the simulation presently takes.1. Create genome sequence. This is done only once per run so speed isn't important.In each cycle: (Efficiency is much more important for steps done every cycle.)2. Mutate the genome, and choose and mutate a specified number of fragments of the genome. I think the mutation step is already quite efficient. The number of fragments that need to be processed each cycle can probably be redu... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1475222 Wed, 28 May 2008 16:37:00 +0100 1475222 http://rrresearch.blogspot.com/2008/05/why-wont-usss-accumulate-in-our-model.html Our Perl model of USS evolution in a genome runs well, but USS-like sequences accumulate only slightly. I've been playing around with various factors that might be responsible but haven't really gotten anywhere. I need to get these factors clear in my mind, so it's time for a blog post about them.What the model does (before I started fiddling with it on Friday): (I should clarify that this version (USSv5.pl) doesn't yet have all the formatting bells and whistles that would make it graceful to use, but it does have the basic functionality we think we want.) It first creates a random 'genome' sequence of specified length and base composition, whose evolution the model is going to simulate. In each evolutionary cycle it first takes random segments of this genome, mutates them according to a s... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1458584 Tue, 20 May 2008 15:49:00 +0100 1458584 http://rrresearch.blogspot.com/2008/05/progress-on-uss-bioinformatics.html Yesterday my bioinformatics collaborator came by for a collaborational visit - she's in town for a few days. I've been quite frustrated by our slow sporadic email correspondence so it was great to discuss the work face-to-face.We clarified a number of issues about the data - because she's generating it and I'm doing the writing about it, this is where all our problems lie. There's only one data set still to generate, a comparison of the peptides encoded by uptake sequences with their homologs in species that don't have uptake sequences. But there's still lots of writing to be done. I'm hoping she'll be able to come work with us for a couple of weeks early in the summer, so we can work on the writing together. (Source: RRResearch) RRResearch blogs http://www.medworm.com/rss/comments.php?id=1446132 Fri, 16 May 2008 00:19:00 +0100 1446132 http://rrresearch.blogspot.com/2008/05/biological-relevance-of-uss-scoring.html In response to a recent post about how our USS-evolution model will score USS-like sequences, a commenter (Neil) says "I see ROC curves and cross-validation in your future." Google tells me that ROC (receiver operating characteristics) curves are graphs representing the relationship between a signal receiver's sensitivity and its specificity.  They thus represent the receiver's ability to detect true positive signals and its tendency to falsely report events that aren't true signals.Does this apply to USS?  That's actually a scientific question about the nature of USS - are they really signals?  USS stands for 'uptake signal sequence', a name chosen because they were assumed to have evolved so competent bacteria could distinguish closely related 'self' DNA fragments from 'foreign' DNA. ... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1446133 Thu, 15 May 2008 13:42:00 +0100 1446133 http://rrresearch.blogspot.com/2008/05/testing-new-scoring-system.html The undergrad is creating a new version of the USS model program with the scoring done multiplicatively rather than additively (see previous post). I was originally thinking we'd start by just playing around with it, to see what happens. But after a conversation with the post-doc I realize that we should start out being more systematic.What we need to do first is just find out what scores are produced by different sequences using this system:What score does a random sequence of a specified length (and base composition) produce? We'll test 100, 1000 and 10000bp.What score does a sequence produce that differs only in containing one USS perfectly matched to the matrix consensus?And we'll do the same tests with differently weighted matrices, using both additive and multiplicative scoring:Addit... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1442934 Wed, 14 May 2008 23:52:00 +0100 1442934 http://rrresearch.blogspot.com/2008/05/scoring-uss-like-sequences-in-our-model.html Months ago (last fall?) a post-doc and I spent what seemed like a lot of time at the whiteboard in the hall, considering different ways our planned USS model might score the sequences it was considering for their similarity to a USS motif.We eventually settled on the crude system shown on the left (yellow table). It evaluates how well the DNA sequence in a 10-base window matches the USS core consensus. Each match to the consensus earns a point, with the total score for the sequence being the sum of the points it's earned. At the time, we realized that this way of scoring had two (or three?) big problems, but we needed something simple to get the model working so we settled for this.The first problem is that the score is not very sensitive to how good the match is. The yellow numbers beside... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1439637 Tue, 13 May 2008 22:47:00 +0100 1439637 http://rrresearch.blogspot.com/2008/05/perl-code-had-bug-but-i-found-it.html The bells-and-whistles version of the Perl model of USS evolution still had a bug, which became apparent once I fiddled the fragment scoring system to strongly favour good matches, and turned off mutation of the genome sequence (so only the fragments mutated). The bug manifested itself in the program cycles stopping, at fairly random points in the run (never stopping twice at the same cycle number or genome score, as far as I could tell).After a LOT of careful detective work on my part, entirely unencumbered by knowledge of any Perl debugging tools, I found that a 'while' counter was being incremented at the wrong place (inside an 'if' instruction that was inside its 'while' loop, instead of just inside its 'while' loop). I still don't understand why this would cause the runs to stick at r... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1439638 Tue, 13 May 2008 01:05:00 +0100 1439638 http://rrresearch.blogspot.com/2008/05/as-usual-perl-problem-was-line-feeds.html Somehow, in being emailed to me, the USSv4a.pl and settings.txt files both acquired nasty Mac carriage returns instead of nice well-behaved Unix line feeds. This kind of problem has arisen often enough in the past that I knew to suspect it, but I had to figure out how Komodo deals with line feed issues before I could confirm that this was the problem and correct it.Now the program runs fine, but it prints some reporting lines probably created by the undergrad while he was debugging the new bells and whistles.......Three hours later.... I've found, understood and removed the unwanted reporting lines, and found and fixed a big mistake in how the program decided whether it was time to print out a report. And found and fixed several minor problems.... (Source: RRResearch) RRResearch blogs http://www.medworm.com/rss/comments.php?id=1434525 Sun, 11 May 2008 17:40:00 +0100 1434525 http://rrresearch.blogspot.com/2008/05/not-as-simple-task-as-it-should-have.html Before he left last night the undergrad sent me what should be a fully functional version of our USS model, with the desired new features all working (they're described here).  But I just tried to run it on my home computer and absolutely nothing happens.  I enter "perl USSv4a.pl" at the Terminal prompt, and I just get another terminal prompt.The problem is likely with the computer, not the program.  This is the first program I've tried to run on it since I replaced the hard drive a few months ago - as everything on the old drive was lost I was effectively starting from scratch.  I don't think I need to install perl - I've never had to do that before.  The USSv4a.pl file is in the Rosie directory, as is the settings.txt file it calls.  I could create a 'Hello World' perl file to test... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1433777 Sat, 10 May 2008 14:35:00 +0100 1433777 http://rrresearch.blogspot.com/2008/05/time-to-start-preparing-some-talks.html I have three talks to give in the next month and a half, so I need to start preparing them now.First a 20- or 25-minute one at the annual workshop of the new CIfAR Program in Integrated Microbial Diversity, held somewhere not far from here, sometime close to the end of May. The guy in the next office invited me but he's out of town so I can't recheck the details. This talk will describe what we know about how natural selection has acted on the genes that cause bacterial genetic exchange. I think I can probably do this with slides I already have prepared.Next, a 20-minute talk at a conference titled "Sex and Recombination: In Theory and In Practice", at the University of Iowa in mid-June. This talk will begin by introducing everything that the above talk will take 20 minutes to cover, and w... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1432536 Fri, 09 May 2008 00:27:00 +0100 1432536 http://rrresearch.blogspot.com/2008/05/my-very-old-analytical-uss-evolution.html I found my old USS evolution model in the files with my 1999 NIH grant proposal. It's not a computer simulation of evolution but analysis of equations describing an equilibrium. It uses only very simple algebra, so calling it an 'analytical' model is probably giving it more credit than it deserves. The introductory text gives an excellent description of the background, so here it is:This model starts with the following assumptions:H. influenzae cells have a preexisting DNA uptake system that preferentially transports fragments containing a USS0 (the 9bp core: 5'AAGTGCGGT). Fragments with imperfect (USS1) sites are not favoured. Fragments of H. influenzae DNA are frequently brought into cells by this system. Once inside the cell these fragments recombine with and replace homologous regions ... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1426496 Wed, 07 May 2008 02:12:00 +0100 1426496 http://rrresearch.blogspot.com/2008/05/gene-transfer-agent-evolution.html My GTA colleague suggests that GTA may persist because of species-level selection. 'Species' is a tricky concept because these are bacteria, but we can simplify this to consider selection of lineages.The basic idea is like that proposed to explain the surprisingly high frequency of bacterial lineages with defective mismatch-repair genes. Like most mutations, most GTA-mediated recombinational events will probably be deleterious. But some will be beneficial. Each time a beneficial recombination event occurs the lineage of cells descending from it will all contain GTA as well as the new combination. Provided the short-term and long-term costs of GTA don't cause the new lineage to go extinct or lose its GTA genes before the GTA-mediated beneficial change, lineages with GTA could take over.Evol... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1423257 Mon, 05 May 2008 21:03:00 +0100 1423257 http://rrresearch.blogspot.com/2008/05/uss-dont-accumulate-because-bias-is.html In our very-preliminary version of the USS evolution model, we've been using a very simple scheme to score the similarity of DNA sequences to the USS motif. We just count the number of matches to the 10bp core USS sequence. Right now I'm keeping everything simple by running the model with DNA fragments that are only 13 bp long (and a genome that's 200-1000 bp long).So a fragment with a perfect 10 bp match to the motif is only twice as likely to recombine back into the genome as a fragment with only 5 bp matching. We know from our earlier model, and from a calculation I did years ago, that the bias favouring USS needs to be much stronger than this if it is to overcome the randomizing effects of mutation. For example, (ignoring the effects of base composition) a sequence that matches the mot... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1419099 Sun, 04 May 2008 01:58:00 +0100 1419099 http://rrresearch.blogspot.com/2008/05/why-dont-uss-accumulate-in-our-model.html The undergraduate is working at home, making improvements to the use-ability of our Perl model of USS evolution, while I'm here doing some test runs with the slightly unwieldy version we have now.This is the version that incorporates the first major improvement. Instead of a single "best-score" fragment recombining with the genome in each cycle, each of the scored fragments can recombine with the genome, with a probability proportional to its score. In principle this should allow the recombination to introduce new USS-like sequences faster than they are lost from the genome by mutation. But in practice the USS-score of the genome drifts up and down but doesn't consistently increase."When in doubt, run more controls."So I've made a modified version of this program that has the same feature ... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1417880 Fri, 02 May 2008 21:23:00 +0100 1417880 http://rrresearch.blogspot.com/2008/04/komodo-rocks.html Today we started using Komodo Edit as our editor for Perl.  It's much better than Mi:  better colouring (the numbers are all in red), more reliable indentation, and it catches syntax errors on the fly.  And, very cute, when I typed "if (" , it automatically added the second bracket ")" on the far side of my cursor, to make sure I remembered that I needed to close the (if condition) brackets.Our most immediate goal is to transfer some of the features of our old/abandoned program into this new one.  This includes some basic/sensible features: reading the parameter settings for each run from a separate file, rather than changing the code of the program, and having a mechanism to neatly end the program and save the interim work when it's interrupted with a control-C.There are also a couple... RRResearch blogs http://www.medworm.com/rss/comments.php?id=1411782 Thu, 01 May 2008 04:55:00 +0100 1411782