Talk:Major urinary proteins

GA Review

This review is transcluded from Talk:Major urinary proteins/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Sasata (talk) 16:45, 25 January 2010 (UTC)

Hi, I've signed up for this review. Comments to follow in a day or three. Sasata (talk) 16:45, 25 January 2010 (UTC)

Wow! Very good article, I enjoyed reading it. Are you a scientist by profession? Just a few minor nitpicks below. I'll read it through again in a couple of days to check references, and make sure that any biochem jargon which I understood is adequately explained for the average reader. Sasata (talk) 17:07, 26 January 2010 (UTC)

• who discovered the mups? How about a cite to the original paper(s)?
• "The central Class B Mup gene cluster formed by number of sequential duplications from one of the Class A Mups." missing a word somewhere
• "It is currently unknown if reptiles have Mup genes." Can this be sourced or is it your own observation?
• suggest removing several uses of "recently", and replacing with years

Thank you for the review (and also for the copy edit). Your suggestions are excellent, I'll incorporate them a little later today. Yes, I am a scientist. In fact my colleagues and I and been looking at these proteins for a while and we have found a cool new function for them. I'll have to wait until that is published before I can add it to the article, of course, but I hope once that happens the it should be comprehensive enough to try for FA status. Rockpocket 21:20, 26 January 2010 (UTC)

I have (hopefully) addressed your helpful suggestions. Your question about who discovered Mups directed me to some very old, and quite fascinating, literature. From that I learned a remarkable bit of trivia: Mups were first discovered by Gavin Newsom's great-grandfather! Rockpocket 08:19, 27 January 2010 (UTC)

Excellent! I'm happy to promote this article to GA status, and look forward to its appearance at FAC. Please write more biochem articles! Sasata (talk) 15:29, 27 January 2010 (UTC)

GA review (see here for criteria)

1. It is reasonably well written.

   a (prose): b (MoS):

   Very well written, complies with MoS.

2. It is factually accurate and verifiable.

   a (references): b (citations to reliable sources): c(OR):

   Article is richly cited, and all are to reliable sources. A spot check of several citations turned up nothing amiss.

3. It is broad in its coverage.

   a (major aspects): b (focused):

   Thoroughly covers the topic.

4. It follows the neutral point of view policy.

   Fair representation without bias:

5. It is stable.

   No edit wars etc.:

6. It is illustrated by images, where possible and appropriate.

   a (images are tagged and non-free images have fair use rationales): b (appropriate use with suitable captions):

   All images have appropriate free-use licenses or are PD.

7. Overall:

   Pass/Fail:

Post FA suggestions

I'm not sure where this text should go, but I submit that there are some issues of factual correctness and also, attribution and POV issues in this article. I shall endeavour to become adept at editing pages before correcting them. For example, the gel image shown would likely be misinterpreted as an SDS-PAGE gel (it is native gel, and the proteins migrate very differently) and the arrow emphatically does not point to darcin - it points to a completely different MUP. Rather than enumerate the issues here, I will seek to update this page as soon as I have the confidence to do so. To avoid issues of CoI, I am a protein chemist who has worked on MUPs for the last 18 years and who is cited frequently in this article. —Preceding unsigned comment added by Rbeynon (talk • contribs) 22:42, 21 June 2010 (UTC)

I've been thinking about this some more. It's not clear to me that several of the proteins here are truly MUPs. Proteins such as the pig salivary lipocalin match to other large mammal allergens, but the MUPs are a group apart. Given the specific roles of rodent MUPs in chemical communication, largely mediated through urine, it might be prudent to open a discussion as to whether the other lipcalins should be split off, possibl? as 'lipocalin allergens' Rbeynon (talk) 16:15, 24 June 2010 (UTC)

Hello Rob, this is Darren (Logan). I've been working on this with some other editors as part of our public understanding of science drive. Thanks for your edits clarifying the gel image - the mis-identification of the band as darcin was my fault - an fixing other issues. I've partially reverted only your most recent significant edit, however, for the following reasons.

• The article has recently been promoted to Featured status, and as such underwent a peer review process. Part of that process involved the systematic simplification of the the lead, per WP:LEAD, to its current version. I don't think it is advisable to significantly rework a featured article so soon after promotion, especially not with the re-addition of technical language. Something that is becoming clear to me is that technical experts don't usually write the best Wikipedia articles (on their subject of expertise), mainly because they are so knowledgable that the language and details they contribute leaves the average Wikipedian completely mystefied. After all the info is down, it usually takes non-experts to make it accessible to Wikipedia's audience. This is the huge benefit from the FA review process.
• I've removed the new nomenclature section. While I, personally, agree with the sentiments, it was written in a prescriptive, rather than a descriptive manner (e.g. A formal nomenclature of the rodent MUPs is needed and When it is possible to ascribe specific function to particular Mups, a trivial name can be helpful.). Unfortunately these types of statements fall under opinion and require sourcing and attribution (FA reviewers would ask, "who says a formal nomenclature is needed?" and "helpful...according to what criteria?"). As far as I am aware, there are no reliable sources out there that specifically expresses this opinion and because this is a FA, its imperative everything is impeccably sourced. That said, perhaps we should have a section on the different nomenclatures used. The reason we didn't include the Mudge et al gene nomenclature is because (again as far as I am aware) it was never submitted to any of the public databases and/or went through the nomenclature committees so we've been unable to verify them against each other. Do you happen to know if it was submitted anywhere?
• There was some discussion over the inclusion of things like SAL and Feld4 in the article. Ultimately, I think, I comes down to asking "what is in a name?" On one hand you are right, of course, it is somewhat ridiculous to describe these proteins as "major urinary proteins", when they are not expressed in urine in their species. But such anomalies are not rare. Consider Melanin concentrating hormone, which doesn't concentrate melanin in any mammal, but is so named because it is the orthologue of the fish protein that does just that. Similarly, SAL and Feld4 most certainly are the orthologous protein products of Major urinary protein genes in their respective species, that just happen to have restricted expression patterns. There is no doubt that SAL and Feld4 are the pig and cat version of rodent Mups (verifiable, published syntenic and phylogenetic analyses affirm this). From a genetic nomenclature perspective, consistency within and between species is desirable (according to the nomenclature committee guidelines: "Sequencing can identify genes that are clearly members of a family (paralogs). Where possible, members of the family should be named and symbolized using the same stem followed by a serial number. The same family members in different mammalian species (orthologs) should, wherever possible, be given the same name and symbol. [my bold] Pseudogenes should be suffixed by -ps and a serial number if there are multiple pseudogenes. Note that the numbering of pseudogenes among species is independent and no relationship should be implied among mouse, rat, or human pseudogenes based on their serial numbering.") We've tried to adhere to this when referring to genes in the article, while being as clear as possible to minimize confusion (e.g. "Fel d 4 (Felis domesticus allergen 4), the product of the cat Mup gene, and Rat n 1 (Rattus norvegicus allergen 1), the product of the rat Mup13 gene"). In the absence of any formal consensus, my understanding of the literature is that Major urinary protein is probably the most commonly used term for the protein products, and therefore that should probably be the base name of the genes as they are characterized, followed by a serial number per the guidelines. This was accepted by NCBI when we submitted it to their TPA database, so that is the basis we've moved forward on. Of course, matters are significantly complicated when referring to specific Mups from wild animal. I don't honestly know what the nomenclature committee's position on this is.
• If I understand correctly, you are proposing we split up the article based on functional significance? I'm not sure the functional differences between the Mup genes from rodent and non-rodent species are as clearly defined as you suggest, though. The rodent Mups also encode potent lipocalin allergens so that function is not a basis distinguishing them; SAL also binds small molecule pheromones and Feld4 also functions as a kairomone, so a role in chemical communication is not a good delineator either. There is always a case that daughter articles could be made for any individual gene/protein, or groups of them from individual species. I think that would ultimately be desirable, but it does not preclude a "parent" article on the entire gene family as this was conceived. As daughter articles are written (and please do write them!), that can certainly be accommodated in the text of this article using {{see also}}.

This all said, I'm not suggesting the article shouldn't be improved - it certainly can (in fact, I think it needs a section on the effect of sequence and structure on ligand binding) - and your expertise would be most welcome. Its just that FA articles are required to be stable, so we should probably thrash out any significant changes here, on the talk page, first. Rockpocket 23:48, 24 June 2010 (UTC)

Hi Darren, I'll think about the issues you raise, and keep my edits away from the article. I'd go as far as to say that the mouse MUPs are the only ones for which there is any understanding of function, and for me, a functional perspective makes more sense. The story/article is also tighter and less qualified that way.

I guess I didn't understand that although I was able to edit, I should not attempt to do so - doesn't make sense to me in Wikipedia context, but there we go. However, I would ask you to reinstate the comment about our naming of darcin. It wasn't in honour of anyone. It was a humorous name, and intended to bypass the nomenclature mess by ascribing a name to a protein with a specific function. Thanks. More comments on other things to follow. ATB Rob —Preceding unsigned comment added by Rbeynon (talk • contribs) 16:30, 25 June 2010 (UTC)

Hello. If you have an alternative suggestion for organizing the information in Wikipedia, then its certainly something we should consider. How would you propose we go about it?

Perhaps I didn't explain myself very well regarding the editing of the article. I don't wish to imply you or anyone else is restricted from contributing to this article. You can edit it. Its simply that the article in its current state has fulfilled the Featured article criteria. Its generally frowned upon for any one individual to significantly rework standing FAs without talk-page consensus, as there is a significant possibility it could endanger the FA status. Experienced FA editors will sometimes do this, but this is good advice for newer editors who are not familiar with the idiosyncrasies of Wikipedia. Therefore its likely that significant edits without discussion will be reverted. Rather than go through that, I was suggesting it might be a good idea to work through the edits on the talk page first, so they can be discussed. I fully intend to do that myself, so its not something aimed at you specifically. Do feel free to ahead with any minor issues you see, though. I've made the edit re darcin as you asked. Rockpocket 21:31, 25 June 2010 (UTC)

Seriously guys?

THIS got featured? --72.197.35.238 (talk) 02:54, 2 August 2010 (UTC)

Seems it did, which I think is pretty cool, but you may see it differently. __meco (talk) 17:02, 2 August 2010 (UTC)

Vandalism report

Someone "Citation-needed" spammed the beginning of the article.--97.119.246.11 (talk) 14:00, 2 August 2010 (UTC)

Endogeny

I'm not a biologist and I'm I'm having trouble understanding "Their endogenous function within an animal is unknown." I don't know if it is this article or Endogeny or both that need work. --Kvng (talk) 14:24, 2 August 2010 (UTC)

Its known what effect Mups have on other animals. However, they presumably also have some biologically beneficial purpose in the producing animal. Clearly the gene would not be maintained in the cat or rat genome if the only purpose it served was to warn their prey of their presence. This endogenous function is not really understood yet. Rockpocket 17:10, 2 August 2010 (UTC)

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