Talk:Homologous recombination

message: The introduction does not actually say what HR is.  ie. no summary explanation.  —Preceding unsigned comment added by 99.234.154.88 (talk) 19:33, 20 April 2009 (UTC)
replies: text: Could you be more specific on how you think the introduction could be improved?  The first sentence notes that HR "is a type of genetic recombination in which genetic material is exchanged between two similar or identical strands of DNA", which is a high-level definition of what HR actually is. Thanks, Emw2012 (talk) 19:43, 20 April 2009 (UTC)
thread_title: Introduction

message: I do not know how to add a reference, but would add "Molecular Biology of the Gene, Fifth Edition" by James D. Watson, et al. I started to add it, but it seemed like a mess, so I left it out. 
I would add this article also: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18022364
It discusses how RecD appears only to be inactivated, not lost from the complex. It has some important information for the RecBCD articles, as well. —Preceding unsigned comment added by RegiG (talk • contribs) 02:01, 1 July 2008 (UTC)
thread_title: Reference to Add

message: Hello, I have a few suggestions to help improve this article.  First, though, big thanks to Emw2012 for all his recent work on this article.  I've been watching these edits and the improvement is really remarkable!  Here are my suggestions:
*More detailed information on the roles of the eukaryotic recombination proteins, similar to the discussion of the bacterial proteins in the article.  A good place to start could be the biochemical roles of the Rad52 epistasis group in yeast, and then move on to mammalian proteins.
*The mechanism of 5' end resection has recently been elucidated and should be in this article.  Here is a good review.  I think this would also be a good place to talk about regulation of the choice between recombination and non-homologous end joining for double-strand break repair.
*A section on the single-strand annealing pathway should be added.
*Holliday junction resolvases should be discussed, in particular the recent series of papers on Slx1-Slx4 that came out in Cell and Molecular Cell in July.
I will help with some of this if I get a chance.  Amazinglarry (talk) 02:29, 24 August 2009 (UTC)
replies: text: * Thanks for your suggestions, and your compliment.  I agree that the 'In eukaryotes' section would benefit from giving more attention to specific proteins and their role.  I've also had an explanation of post-synapsis steps of bacterial and eukaryotic recombination on the backburner; I will give that attention along with your other suggestions.  I'm very appreciative to have someone with significant experience in DNA repair research giving feedback on the article.  Emw2012 (talk) 04:14, 24 August 2009 (UTC)
thread_title: Suggestions

message: "The World of the Cell", introductory book on Cell biology, , Pearson/BenjaminCummings, mentions on page 627 five different situations in which hom. rec. occurs: 1) Two different phages infect the same bacterium 2) Uptake of raw DNA in bacteria (transformation) 3) Systematic transfer of genetic material (plasmids) between bacteria (conjugation) 4) Prophase I 5) Transfer of bacterial genes between bacteria by incorporation in virus (phage) (transduction). The present article mentions meiosis and mitosis. This seems rather incomplete. --Ettrig (talk) 07:19, 7 September 2009 (UTC)
replies: text: Transformation is pretty much covered in the gene targeting section, and the other 3 (conjugation, transduction, 2 phages) could be added in a couple sentences in the "In bacteria" section.  They're probably worth a mention for historical reference, but maybe try to keep it short since phage is not used as a model system for genetics much any more.  I don't think many people are going to come to this article looking for phage stuff.  Amazinglarry (talk) 12:15, 7 September 2009 (UTC)
replies: text: Outdated research. Interesting. The book is copyrighted 2009. But aren't transfer by virus and recombination of viruses important for evolution and humankind, e.g. in creating new influenzae strains? --Ettrig (talk) 12:52, 7 September 2009 (UTC)
replies: text: Regarding transformation, conjugation etc., I've tried to address these with the "Horizontal gene transfer" subsection of "In bacteria".  I'll augment the section and mentioned the particular types of HGT since the target audience may not take note of HR's role in them otherwise.  I think it would also be good to at least briefly discuss the relationship between HR and viral reassortment, which you've alluded to. Emw2012 (talk) 13:45, 7 September 2009 (UTC)
replies: text: But when reading reassortment I get the impression that this is not HR, so there is no relation? --Ettrig (talk) 14:15, 7 September 2009 (UTC)
replies: text:  You're right -- I had a misunderstanding about reassortment that was cleared up by the explanation here.  Homologous recombination in viruses seems to be the subject of at least a few papers (e.g. this paper and several articles citing it).  I agree that viral HR should be discussed in the article. Emw2012 (talk) 17:20, 10 September 2009 (UTC)
thread_title: Context of ocurrence

message: The article currently says "Studies in several model bacteria ...". Is "model" valuable here? I think the normal use of "model" in contexts like these is used to signal that one really is interested in studying a mechanism in the human body, but studying the corresponding mechanism in another organism instead, in the hope that the mechanism in the other organism is sufficiently similar to the human one. This article is not specifically about human HR. --Ettrig (talk) 16:13, 10 September 2009 (UTC)
replies: text: While the article isn't exclusively about human HR, I don't think the use of "model" throughout is unwarranted.  Research in bacterial HR is often done with the assumption that findings there will at least somewhat transfer to understanding of human HR -- this is evidenced by various societies for eliminating cancer funding research in bacterial HR, for example.  Since they can reveal how many aspects of HR mechanisms work in other organisms, including us, bacteria can indeed be model organisms.  With regard to a distinction between "workings" and "mechanisms", I don't see how there's much of a difference, if any.  Consider the list of bacteria in the article on model organisms.  It is precisely because they reveal information about low-level biological phenomena (e.g., HR) applicable to other organisms that those bacteria are considered model organisms.  The listing for E. coli contains more or less the wording you removed.  Looking at RNAi, another featured article on a mechanism in molecular biology, I don't see how this article differs in appending "model" to various organisms. Emw2012 (talk) 17:04, 10 September 2009 (UTC)
replies: text: I think you're reading a little too much into the phrase, Ettrig.  Pretty much any organism used frequently in research is called a "model organism" or referred to as a "model system."  It's just a phrase, it's not meant to imply that studying a non-human organism for reasons other than gaining insight into human biology is somehow unimportant.  Amazinglarry (talk) 00:36, 11 September 2009 (UTC)

text: I agree, if for example we are studying HR in E. coli, then it is a model organism for (from least to greatest specificity) HR in general, HR in bacteria, HR in gram negative bacteria, HR in Enterobacteriaceae, and the strain your studying is a model for other E. coli strains. Gobbits (talk) 06:56, 18 May 2015 (UTC)
thread_title: Model bacteria

message: I think that the section needs to be significantly streamlined, it has a lot of unnecessary information, and it doesn't have any sources for half the things it says. Gobbits (talk) 07:02, 18 May 2015 (UTC)
thread_title:  Bacterial Transformation 

message: For starters, this is a nice article! In the Protein Engineering section, we might consider adding links to DNA shuffling, RACHITT and other similar articles. However, those two articles I mentioned are in need of attention. Pdcook (talk) 17:03, 18 September 2009 (UTC)
thread_title: Protein engineering

message: the intro says These new combinations of DNA produce genetic variation. This is grammatically wrong. The process of recombination produces genetic variation. The combinations themselves ARE the genetic variation. The article is so well formulated in general, that I dare not make the corrections myself. In my opinion it is overdue for the GA stamp. --Ettrig (talk) 16:00, 21 September 2009 (UTC)
replies: text: * Good point. I've changed 'produce' to 'represent', and tweaked the rest of the sentence for flow. Emw2012 (talk) 17:28, 21 September 2009 (UTC)
thread_title: Editorial

message: *"SDSA is completed with the removal of 3' flaps" What does "flap" refer to in this context? I would be satisfied with a wikilink, but I didn't see any helpful articles at flap.
:* I don't think 3' flaps are notable enough to warrant a separate article.  I've added some explanation. (If the reader understandably struggles to visualize this concept, 3' flaps are shown in Step 4 of the animation in Figure 5.) Emw (talk) 02:39, 9 July 2010 (UTC)
replies: text: *Hrm, the animation doesn't seem to be working. Are you certain that you uploaded the file correctly? --Cryptic C62 · Talk 20:06, 12 July 2010 (UTC)
replies: text: * Yes, the file was uploaded correctly.  MediaWiki's support for SVG isn't good, and its support for animated SVG is worse. The user must click once to access to the 'File page' -- which has a PNG rendering of the static SVG -- then click that rendering to access the underlying SVG file.  That SVG file only renders as an animation in browsers that support animated SVG, or SMIL; this is indicated in the caption of Figure 5.  The static PNG rendering of the animated SVG is a tolerable substitute for browsers that don't support the format -- Firefox and IE.  For browsers that do support animated SVG -- Chrome, Opera and Safari -- using the format is a substantial aid in visualization.  Firefox 4 beta natively supports animated SVG, and upon its public release in Q4 2010 will significantly increase the share of users with easy access to this animation.  I believe the current IE9 beta also supports animated SVG, although not flawlessly. Emw (talk) 02:56, 14 July 2010 (UTC)
replies: text: * More than 80% use Internet Explorer or Firefox, meaning the vast majority of our readers won't be able to see the animation. Perhaps Animated PNG or Animated GIF would be a better choice in terms of WP:ACCESSIBILITY. --Cryptic C62 · Talk 16:36, 15 July 2010 (UTC)
replies: text: * I don't think an animated PNG and or GIF would be an adequate substitute for the SVG animation in question.  The length of the animation would make the file size of an animated PNG/GIF version much larger than the current SVG version.  Also, infinite loops of animated PNG/GIFs can be quite distracting.  While the animation won't be accessible to everyone, and this is unfortunate, I don't see anything in WP:ACCESSIBILITY particularly relevant to this issue.  While about 80% of users don't have native support for animated SVG, over 50% don't use browsers with  native support for Ogg Theora, MediaWiki's only supported video format.  If I were to change the format (or make new animations), I would consider Ogg Theora if not SVG.  Because the animation is informative even as a still frame, I think the use of animated SVG can be considered a progressive enhancement for users with support. Emw (talk) 23:20, 17 July 2010 (UTC)
replies: text: * I strongly disagree that the animation is informative as a still frame. As someone who knows very little about cell bio and as someone who has never seen the animation and can't imagine what it might look like, the still frame provides no new information of any kind. Why not simply employ a step-by-step diagram like in Figure 7? --Cryptic C62 · Talk 12:12, 20 July 2010 (UTC)
replies: text: * The still frame has a list of steps which reinforce the pathway's description in the text, and also shows the positioning of repeat elements in DNA.  Given that, I think the still frame is somewhat informative, although not as informative as the animation, thus making the animation a progressive enhancement.  If I have time, I may create an animated SVG which shows a more comprehensive still-frame after being processed by MediaWiki. Emw (talk) 11:54, 23 July 2010 (UTC)

text: * Branch migration can be toward the 3' end or the 5' end, so the phrase 'in one direction' is not extraneous.  In my opinion it is also not useless detail for the lay person; it helps somewhat to visualize the process.  A diagram here would be especially helpful. Emw (talk) 11:54, 23 July 2010 (UTC)
replies: text: * Perhaps the 3'/5' bit can be stated explicitly: "The pathways are also similar in their phases of branch migration, in which the Holliday junction slides towards the 3 end or the 5' end" --Cryptic C62 · Talk 14:17, 27 July 2010 (UTC)

text: Thank you for the continued input!  What are your thoughts on moving these comments into the FAC review?  I see two benefits: 1) it would make it easier in the future to find the reviews for this FAC, and 2) it would inform potential FAC reviewers and the FAC delegates that reviews are still ongoing. Emw (talk) 06:07, 8 July 2010 (UTC)
replies: text:  I used to leave all of my comments on the FAC page, but doing so created two problems which were easily solved by leaving them on the talk page instead: the first is that leaving so many comments can clutter up the FAC page and also bog down the main listing at WP:FAC. The second is that if the FAC closes (successful or not) before I finish my review, I can continue working with the author without having to edit an archived page. The other reason that I personally prefer leaving comments on talk pages is that it opens up the discussion to other interested editors who may not be familiar with the FAC process. As for your concern about keeping the FAC delegates informed, don't worry about it. User:Karanacs and I have been through this song and dance many times before. As long as it's clear that the author (you) is committed to addressing my nitpicks (which is obviously the case here), she won't close the FAC as unsuccessful just because I go through articles like a snail through molasses. --Cryptic C62 · Talk 18:29, 8 July 2010 (UTC)
thread_title:  Unresolved issues 

message: This article has a dead link (ref 2) MacDaid (talk) 18:28, 26 June 2010 (UTC)
replies: text: Thanks, fixed. Emw (talk) 00:55, 27 June 2010 (UTC)
thread_title:  dead link 

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replies: text: I nominated this image for deletion because it seems to have been a screenshot of Figure 1B from Genes Dev. 2007 December 15; 21(24): 3296–3307. The image is Copyright © 2007, Cold Spring Harbor Laboratory Press. Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2113030/figure/F1/.  I've removed the figure (Figure 7A) and its caption from this article.  This shouldn't affect the article much, since the figure was largely redundant with Figure 7B (now Figure 7). Emw (talk) 16:15, 27 March 2012 (UTC)
thread_title: File:RecBCD recomb model.tif Nominated for speedy Deletion

message: I have tried multiple times to insert a reference correctly at the end of the section on viruses.  My reference works perfectly in my sandbox.  I have tried using Wikipedia template filling to make sure I did it correctly, but I get the same error each time, Cite error: A  tag is missing the closing  (see the help page).Chaya5260 (talk) 23:39, 8 December 2013 (UTC)
thread_title: difficulty with </ref>

message: This is a big topic now in ovarian cancer, and as a target of PARP inhibitor drugs. - Rod57 (talk) 13:10, 30 December 2016 (UTC)
replies: text: No response for a few years and the section is small and fits here. I would suggest that if you are interested and there is enough notability then you can create the article yourself. AIRcorn (talk) 03:46, 31 March 2018 (UTC)
thread_title:  Proposed split out of Effects of dysfunction section to Homologous recombination deficiency 

message: One big issue is if the fragmentation places exhibit some bias (not necessarily absolute but regional), and that opens the path to more questions (if epigenetic changes have an impact on the patterns of recombinant fragmentation).
It doesn't have to happen all the time and at exact places; even small biases play a huge role in millions of years of evolution.
We need more data.  — Preceding unsigned comment added by 2A02:587:4104:99BE:B1CD:5E5B:5D0B:33E4 (talk) 01:37, 22 October 2020 (UTC)
thread_title:  Recombination: biased or not fragmentation segments/fragments 

message: Ref 102 (Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine) was the correct reference for what was being claimed, with correct name and authorship, but all links went to the subsequent paper from the same journal (Specifically a paper about use of an alcohol screening tool in Russia)
While it was an easy fix, other uses of the same source on different pages, probably should be checked, to see if this is a systemic issue due to the journal readdressing or incorrectly addressing their DOIs initially, or if this is a one time issue.  — Preceding unsigned comment added by PewterPenguin (talk • contribs) 04:41, 27 December 2021 (UTC)
thread_title:  Reference links to WHO Bulletin: 1 July 2021