Wikipedia talk:WikiProject Molecular Biology/Molecular and Cell Biology/Archive 6

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Molecular and Cell Biology
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Preparing for WikiData in gene/protein infoboxes

It is now possible to use content from WikiData to drive infoboxes in English Wikipedia. This will greatly improve our ability to keep trusted, structured content cleanly presented and up to date in the context of Wikipedia. Members of the

Gene Wiki project are now deploying bots for populating wikidata with infobox-relevant content. As an example, I temporarily altered the article on the RREB1 gene to make use of a new 'gene' infobox built using wikidata. Doing this brought up the fundamental issue of what these articles are about: genes, gene products or both? In wikidata, the community has decided that genes, proteins, and other products (e.g. RNA) should all have distinct entries ('items') in wikidata. In order for that infobox to work, the sitelink needs to exist between the Wikipedia article and the WikiData item about the gene. Right now, a lot of these sitelinks connect such articles to entries about proteins. For example, click on the 'wikidata item' link in the navigation panel on the left of the VIPR1 article and you end up on a protein item (that, confusingly, has an RNA expression image attached to it). In the next phase of WikiData technology release (already available on many non-english Wikipedias) it will be possible to build infobox content from multiple wikidata items. This means that we can attach images, gene ontology annotations etc. to the appropriate protein items and then render that information on a unifying gene article. But, for everything to work, we need a consistent policy for linking gene articles to gene items in wikidata. I've started a discussion on wikidata about this issue and hope that you can join in. --Benjamin Good (talk
) 17:50, 1 July 2015 (UTC)

Copyright Violation Detection - EranBot Project

A new copy-paste detection bot is now in general use on English Wikipedia. Come check it out at the EranBot reporting page. This bot utilizes the Turnitin software (ithenticate), unlike User:CorenSearchBot that relies on a web search API from Yahoo. It checks individual edits rather than just new articles. Please take 15 seconds to visit the EranBot reporting page and check a few of the flagged concerns. Comments welcome regarding potential improvements. These likely copyright violations can be searched by WikiProject categories. Use "control-f" to jump to your area of interest (if such a copyvio is present).--Lucas559 (talk) 16:17, 2 July 2015 (UTC)

Protein articles without symbol

I have created Category:Protein articles without symbol. It is populated by the templates {{Infobox protein}}, {{Infobox protein family}} or {{Infobox nonhuman protein}}, when an article has no symbol (|Symbol=).

In general, it is bad practice to have a "?" shown in mainspace to say "to be edited". The reader does not know what it means. A maintenance task could be to either find the symbol, or to enter a text on why there is no symbol. (At this moment, minutes after the template edits, 35 articles are listed).

I myself was looking for a wikilink to that "Symbol" definition for proteins, but could not find one. Is there an institute or system to generate these? Can it be linked to by Symbol? -DePiep (talk) 17:17, 8 July 2015 (UTC)

@DePiep: Useful! The {{Infobox protein}} template documentation states the the |Symbol= is from HUGO, so I guess they only exist for human genes? If that's the case, perhaps the "Symbol" text in the infobox should link out to HUGO. T.Shafee(Evo﹠Evo)talk 23:48, 8 July 2015 (UTC)
I could be bold doing this because showing "?" in mainspace is bad. Full stop. If "Symbol" does have a target wikilink, then please say or add. -DePiep (talk) 00:05, 9 July 2015 (UTC)
There is no one single way to find these symbols and I am afraid this will require manual searching and editing to fix. If the {{Infobox protein family}} is missing the pfam symbol, just follow the pfam link, and that page will provide you with the symbol. Several of the {{Infobox nonhuman protein}} because the gene has never been cloned, just the protein. A few were inappropriate uses of the infobox (e.g., just a place holder for the graphic). I have been going through the list of missing symbols and have fixed a bunch of these. The number of articles in these category is now less than 40. Boghog (talk) 04:28, 9 July 2015 (UTC)
The max number was 52 articles, now just one left (out of ~11,000 articles, nice work already you protein editors!). All fine then. I suggest to keep this category, to catch new protein articles. Or maybe: 'very unlikely, so lets remove this check'. -DePiep (talk) 20:02, 9 July 2015 (UTC)

Warnowiaceae

I'm not sure how this fits into this class or species, but shouldn't this article include information on the ocelloid bearing dinoflagellates (warnowiids?) - quite unique in being a very complex single-cell organism which simulates a relatively complex 'eye' called an ocelloid that has structures in it similar to parts of mammalian eyes?

The photosensitive ocelloid probably forms from a chloroplast and might be used to hunt or evade. The ocelloid can also be directed within the cell. The erythropsidinium ocelloid dinoflagellates are also apparently unique in that they have a piston-like structure which they can use to move. --24.88.64.22 (talk) 05:28, 4 July 2015 (UTC)

I completely missed this when it was posted, but someone prodded me about it - there was a widely reported Nature paper a couple of weeks ago on these guys. Warnowiaceae and ocelloid exist now if anyone has more to add! Opabinia regalis (talk) 06:17, 24 July 2015 (UTC)

WP:Lead sentence at the Estrogen
article

Opinions are needed on the following matter:

talk
) 13:25, 25 July 2015 (UTC)

Creating an infobox template for cell lines

Reading several articles about different cell lines, I noticed that they are mostly very different in regard to style and scope. I was thinking that an infobox that summarises facts that are relevant to all cells lines could be useful in giving them a common appearance and in making key facts more accessible. For example, it could comprise facts such as the tissue and species of origin (epithelial / lymphoid..., human / mouse...), growth type (adherent / suspension) and maybe shortcut links to databases such as ATCC, ECACC or DSMZ using the respective identifiers. Do you think such an infobox could be useful?

I am currently building an experimental template on my userpage, you can access it at User:Shinryuu/Template:Infobox cell line. In my sandbox I created a test infobox based on the widely used HEK 293 cells to test the template. However, it is the first template I ever built, and it is still fairly rudimentary. If you think this could be a useful contribution, any advice or contribution would be very welcome. Shinryuu (talk) 18:33, 3 August 2015 (UTC)

These articles truly need more love, including templates and sourcing. I approve of this idea. I'll also stick some of these articles on my create/expand to-do list. Jo-Jo Eumerus (talk, contributions) 18:37, 3 August 2015 (UTC)
If the idea is generally approved, I would say the template is almost good to go. I'm not sure if I've included all major cell line databases though. Currently, the template has shortcuts to the
ICMP, BCCM/LMG, NCPPB and CDBP (Collection Française de Bactéries associées aux Plantes), have bacteria or other organisms, but no cell lines as far as I know. Is that correct? Shinryuu (talk
) 20:12, 5 August 2015 (UTC)

"Radical"

The naming of Radical (chemistry) is under discussion, see Talk:Radical (chemistry) -- 67.70.32.190 (talk) 04:58, 6 August 2015 (UTC)

Proposed major overhaul of Cell (biology)

I am planning a major overhaul of Cell (biology) in the next couple of months. Please see my full proposal at Talk:Cell (biology)#Proposed major overhaul and leave any suggestions or comments you have for me there; I would like to keep the discussion all in one place if it's at all possible. Thank you. AmericanLemming (talk) 00:13, 22 August 2015 (UTC)

Good plan. I'll help out where I can. Luckily there are already some good images about the place by
user:Kelvinsong. It might also be worthwhile having a look at the Gene article for a possible way to reference MBOC. T.Shafee(Evo﹠Evo)talk
01:22, 22 August 2015 (UTC)

New article

(talk)
18:56, 13 August 2015 (UTC)

My suggestion is: not merge but to delete
talk
) 21:33, 28 August 2015 (UTC)

Juvenile hormone epoxide hydrolase

I created a new article by this name about a a week ato, submitted for checking. How long until it apprears> Graybeard biochemist.

User:GraybeardBiochemist/sandbox? That needs a bit of structure and wikifying. Also, there is a huge block of italicized text in the middle. Jo-Jo Eumerus (talk, contributions
) 09:51, 28 August 2015 (UTC)
@GraybeardBiochemist: You didn't actually submit the article for submission. There is a button at the top of your sandbox which needs to be pressed before in order to submit it. In any case, I have wikified it and moved it into mainspace (see Juvenile hormone epoxide hydrolase). Boghog (talk) 11:03, 29 August 2015 (UTC)

-ome/-omics articles

A recent AfD for

channelomics ended in a decision to merge with channelome, but nobody has strong opinions on which way the merge should go. Thoughts at Talk:Channelomics#Merge_discussion? We have a number of similar pairs of articles - glycome/glycomics, lipidome/lipidomics, etc. - for which this might be relevant. Opabinia regalis (talk
) 04:45, 30 August 2015 (UTC)

The term "beta cullularis"

Per this section on my talk page, there is concern that the term beta cullularis, which was added to the

talk
) 04:15, 5 September 2015 (UTC)

Based on Google, it looks like a mis-definition of the actual concept of
B-cell, which actually fits in there - B cells are the core of the humoral immune system.Jo-Jo Eumerus (talk, contributions
) 08:11, 5 September 2015 (UTC)

m
TAAR4 and hTAAR3

Mouse TAAR4 has been identified as a (the first?)

pheromone receptor for sex pheromones
in mice; should that be kept/deleted?

Seppi333 (Insert 2¢) 04:40, 11 September 2015 (UTC)

Are there other sources that confirm this claim? I am always uneasy about using a single source for a major claim as they tend to be unreplicatable so frequently. Unless this finding has already been replicated, that is.Jo-Jo Eumerus (talk, contributions) 07:20, 11 September 2015 (UTC)
There's a few reviews and 2 primary sources on TAAR4 in mice (PMID 23624375 + PMID 23407976) that I know of which cover this. The PMID linked above is a review. Seppi333 (Insert 2¢) 07:28, 11 September 2015 (UTC)

Chlorophyllase

Hi

Can someone with a little more knowledge of plant metabolism please take a look at the article.

"Of high importance to all photogenic organisms is chlorophyll, and so, its synthesis and breakdown"

I believe that all plants look good in a photo, and that chlorophyll could probably be promoted from "high importance" to "necessity".

There are a few others I noted, but if it is full of these, I would prefer someone else to check the accuracy of the chemistry and biological processes mentioned.

"chlorophyllase initiates the catabolism of chlorophyll to from chlorophyllide" - is it really both ways? "Chlorophyll degradation occurs in the turnover of chlorophyll" - unexplained "After Pheophorbide a is formed, the poryphin ring is cleaved by Pheophorbide an oxide to form RCC causing the plant to lose its green color. RCC is then broken down into pFCC." - should that be "an" or just "a" or do they mean "an oxide" & meaningless acronyms unless accompanied by a first use explanation.

Thanks Chaosdruid (talk) 11:34, 16 September 2015 (UTC)

Circular DNA

Circular DNA was redirected earlier this year. Could someone check that and make sure it was a desirable change? WhatamIdoing (talk) 19:52, 16 September 2015 (UTC)

Rather dubious on this redirect: "Circular" does generally refer to ring-shaped things, not helical ones. A
Circular bacterial chromosome (or a circular chromosome that is, if there is material for a non-bacterial chromosome article) that is, not a DNA supercoil.Jo-Jo Eumerus (talk, contributions
) 19:59, 16 September 2015 (UTC)
Supercoiling can happen on linear or on circular DNA. The redirect is incorrect.
talk
) 20:18, 16 September 2015 (UTC)
Awkward. It would be great for Wikipedia to have something for anyone who types "circular DNA" into the search box, but I agree that there's not enough for an ordinary article. Perhaps something like a disambiguation page, linking to
Inverse PCR, plus anything else I haven't thought of? Adrian J. Hunter(talk•contribs
) 09:11, 17 September 2015 (UTC)
I'd second Adrian J. Hunter's suggestion. That way people can decide what they really meant when prompted with a few alternatives. I suspect that most people when they search circular DNA have a particular instance something in mind. T.Shafee(Evo﹠Evo)talk 23:35, 17 September 2015 (UTC)
I too support the creation of a disambiguation page listing all known circular DNA molecules.
talk
) 00:46, 18 September 2015 (UTC)
+1. Would be interesting to see the traffic through each of the links on that page... Opabinia regalis (talk) 02:13, 18 September 2015 (UTC)

Aye, disambiguate this. If it turns out that "circular DNA" is article-worthy we can simply move the disambiguation to Circular DNA (disambiguation).Jo-Jo Eumerus (talk, contributions) 07:08, 18 September 2015 (UTC)

Thanks all. Done! I was surprised by how many plausible intended targets there are. Adrian J. Hunter(talk•contribs) 13:47, 18 September 2015 (UTC)

Requested move 12 September 2015 (Semantics!)

The following is a closed discussion of a requested move. Please do not modify it. Subsequent comments should be made in a new section on the talk page. Editors desiring to contest the closing decision should consider a move review. No further edits should be made to this section.

The result of the move request was: moved. Pretty clear consensus that the proposed title is more common in reliable sources and more correct. I'll move the project and the subpages, project members should probably do the rest about updating templates, categories, etc. Drop me a note if there's anything that requires admin assistance, though. Jenks24 (talk) 16:00, 29 September 2015 (UTC)


common parlance. I'm happy to be voted down if people think it'd be too much of a hassle, but I thought it should at least be discussed (I'm not even certain that Wikiprojects can be renamed). T.Shafee(Evo﹠Evo)talk 12:28, 12 September 2015 (UTC) Relisted. Jenks24 (talk
) 11:30, 21 September 2015 (UTC)

Valid point, although I am still not 100% sure about its application. A noun-used-as-adjective is called a noun adjunct. Hence you are correct that strictly speaking "cell" in "cell biology" is not a adjective. On the other hand, it is used like an adjective. So does "molecular and cell biology" biology follow the recommended repetition in grammatical form or not? I am now coming to the conclusion that it does not. Regardless of grammatical rules, at least to my ear, "molecular and cellular biology" sounds better. Boghog (talk) 12:50, 20 September 2015 (UTC)
The above discussion is preserved as an archive of a requested move. Please do not modify it. Subsequent comments should be made in a new section on this talk page or in a move review. No further edits should be made to this section.

Robert Lustig

Could someone please take a look here and see what you think?

Cheers, Anna Frodesiak (talk) 15:34, 6 October 2015 (UTC)

Please folks, zip over there and have a look. Anna Frodesiak (talk) 13:13, 7 October 2015 (UTC)

Amino Acid Representations

I have noticed that many, if not all, the amino acids on their individual pages and on the amino acid page are represented in their non-ionic form. I feel this is misleading, or misinforming, as it is the form least likely found in nature. The Zwitterionic form would be the best form to include, in my opinion. How does anyone else feel? I would be happy to change the structures if the community doesn't mind. I have noticed there has been some discussion on the amino acid talk page, and on some of the individual pages, but nothing has been changed. There also seems to be some discussion in the WikiProject:Chemistry, so I will ask there as well.Htienson (talk) 21:52, 20 October 2015 (UTC)

Human Alkyladenine DNA Glycosylase

I found an article titled

Human Alkyladenine DNA Glycosylase which is very good created by University of Barcelona biochemistry students. The problem is the article orphaned. What is the proper title so it is not orphan anymore? MRFazry (talk
) 12:13, 28 October 2015 (UTC)

Hi
orphan
if it's not wikilinked from any other articles. It's not really a problem with the article title. It can be de-orphaned by introducing links to it from other articles.
But before we look at introducing new links, do you (or does anyone else) think
MPG (gene) should be merged? Adrian J. Hunter(talk•contribs
) 12:33, 28 October 2015 (UTC)
 Done Yes, these two articles should as well as a third article, DNA-3-methyladenine glycosylase II, should also be merged. I have been bold and merged all three into DNA-3-methyladenine glycosylase. Boghog (talk) 20:44, 28 October 2015 (UTC)

Talk:APAF1

Would somebody check if there's references availble for these statements. " APAF-1 and CED-4 homologs have been found in all currently sequenced animal genomes." Also, do you guys think the statement "The Apaf-1 protein was identified by Xiaodong Wang.[3]" should be part of the introduction of should it have its own section?

Mostafa Elbery (talk) 00:57, 28 October 2015 (UTC)

 Done Both unsourced statements and unnecessary hype now removed. Boghog (talk) 20:57, 28 October 2015 (UTC)

Help with ASCB edit-a-thon?

The American Society for Cell Biology is running a Wikipedia edit-a-thon at the annual meeting in San Diego, CA this year from 8am-12noon on Sunday, December 13. However, we’re lacking experienced editors to help facilitate. We’re hoping to recruit 10 facilitators (who’ll get complimentary meeting registration) to assist a maximum of 100 participants.

If you can’t make the meeting in person, we’d also love remote admin help (in case we run into issues with with account creation, though we’re requesting participants do this ahead of time) or simply any advice on how to run the event! Please don’t hesitate to contact me. Thanks in advance! Jessica Polka (talk) 21:15, 22 November 2015 (UTC)

@Jessica Polka: I'd love to help out, but I'm in Melbourne so even helping online is a bit tricky! However I've taught workshops on Wikipedia editing for scientists before, so I've a few resources that could be helpful for you.
Hope any of that helps. T.Shafee(Evo﹠Evo)talk 03:39, 23 November 2015 (UTC)
@Evolution and evolvability: Thank you so much for this, Thomas. This is all extremely helpful! I'm emailing you now as well. Jessica Polka (talk) 20:29, 23 November 2015 (UTC)

Seeking advice for nullomer article

I recently looked at the article for nullomers and found that the first sentence was not coherent with the cited sources, so I corrected it. I would appreciate it if someone could look over my edit and confirm that it is technically correct. The second sentence poses me a greater problem, because it seems to me that one of the sources contradicts it – see Talk:Nullomers. However, I feel that my (very limited) knowledge of natural selection does not allow me to judge whether it is, indeed, false. Again, I would appreciate a sufficiently knowledgeable person helping me out here. Thanks! 5mv2 (talk) 16:40, 1 December 2015 (UTC)

Wikidata pilot

I remember recently some biological topic was very advanced in using and updating Wikidata. Can someone give a link? -DePiep (talk) 09:28, 8 December 2015 (UTC)

@DePiep: perhaps you are thinking of https://www.wikidata.org/wiki/User:ProteinBoxBot or https://www.wikidata.org/wiki/Wikidata:WikiProject_Molecular_biology? Best, Andrew Su (talk) 19:05, 8 December 2015 (UTC)

Volunteers for edit-a-thon

The Experimental Biology 2016 conference (San Diego, April 2-6 2016) is looking for volunteers to help with a Wikipedia edit-a-thon on articles related to biochemistry and molecular biology. Volunteers get free conference registration. For more details, see http://www.asbmb.org/meetings/AM2016/publicengagement/Wikipedia/. Best, Andrew Su (talk) 16:30, 10 December 2015 (UTC)

"Periodic table of proteins"

Editors here may be interested in a new paper in Science that advances an regular organizational principle for proteins on patterns of their structures (dimers, cycles, etc.) A simplified explanation here and a searchable interactive website is here. This might be linkable with some of the wikidata work going on. LeadSongDog come howl! 18:53, 11 December 2015 (UTC)

Cool. Thanks for the heads up. The title is a bit misleading however. This periodic table organizes
protein folds. Boghog (talk
) 18:57, 11 December 2015 (UTC)
I've remember seeing Teichmann present on this a couple of years back so I'm very glad it's now published and citable. It should certainly be mentioned in protein complexes / Protein_quaternary_structure sections. Depending on how well cited it is in a few years time, we could think about using its organisation nomenclature and/or organisation for e.g. Protein_quaternary_structure#Nomenclature_of_quaternary_structures. T.Shafee(Evo﹠Evo)talk 23:36, 11 December 2015 (UTC)

Featured pictures of proteins

Hi all - I recently stumbled across this image (which I originally created back in 2006) in an article and was reminded that it is currently a

featured picture. I nominated it for delisting here, but the discussion there is more interesting than I expected and more input would be appreciated. Thanks! Opabinia regalis (talk
) 21:17, 14 December 2015 (UTC)

Serpin article

Hi all, I've been doing some updates on the

Featured article at the end of the year. T.Shafee(Evo﹠Evo)talk
11:48, 24 December 2015 (UTC)

I am seeing a few maintenance tags as well as some paragraphs that look unsourced to me.Jo-Jo Eumerus (talk, contributions) 12:25, 24 December 2015 (UTC)
Hah. I'd even been the one to add them in, but completely failed to spot they were still there. Fixed now. T.Shafee(Evo﹠Evo)talk 02:09, 2 January 2016 (UTC)

Seeking help to review miRNA page

I am trying to get your opinion if the information gathered for micro-RNAs from text mining sources is relevant and of enough quality to include in wiki talk pages for potential use in wiki articles. As an example, I have prepared the one for mir-194 I would appreciate if you could take a look at the page and provide your feedback on the content. Carighi (talk) 13:51, 5 January 2016 (UTC)

No problem placing this on the talk page of
paraphrased, (2) the external links are removed, and (3) in line citations are included (e.g., [1] using for example this tool). A complete list citations for this gene may be found here. I hope this helps. Cheers. Boghog (talk
) 15:21, 5 January 2016 (UTC)

References

  1. PMID 25096247
    .
Better yet, this material is probably more appropriate for the MIR194-1 article. Perhaps mir-194 microRNA precursor family and MIR194-1 should be merged. Boghog (talk) 15:41, 5 January 2016 (UTC)
I think the MIR194-1 article needs deleting or substantially editing. Its an RNA not a protein as stated in the article. I think it would be great that the Gene Wiki effort included all human non-coding RNAs as well, but I thought it was protein only. Getting back to the topic in hand. I think the text mined data will be super useful for people who are editing these miRNA articles. The talk page would be the best place for this information, which editors could migrate into the main article. However, I'm not sure also about the copyright issues of including the text mined sentence. Probably best not to include that in Wikipedia unfortunately and just link off to the external site for that. Alexbateman (talk) 14:51, 6 January 2016 (UTC)
parameter. I have edited the bot generated lead sentence in MIR194-1 so that it is now clear that this is a non-coding RNA. I have also made a few adjustments to the "protein" infobox. The rest of the article should be fine. Boghog (talk
) 17:07, 6 January 2016 (UTC)
There are currently 46 Gene Wiki non-coding RNA articles that contain a {{
GNF Protein box}}. This list could be expanded significantly (see Category:Non-coding RNA). Boghog (talk
) 20:21, 6 January 2016 (UTC)
Alexbateman may also be able to advise on this, since he has extensive experience in moving information between Wikipedia and other scientific database sites. T.Shafee(Evo﹠Evo)talk 22:40, 5 January 2016 (UTC)

Chondronectin = ?

I have been searching unsuccessfully for the contemporary name of the protein chondronectin, which I hope will lead me to the gene encoding it. "Chondronectin" does not appear in any contemporary protein databases that I could find. Can anyone help?

הסרפד (call me Hasirpad) 19:08, 11 January 2016 (UTC)

Thanks for the heads up. Chondronectin is a protein that was characterized in the early 1980s but has never been cloned (see for example
PMID 3196081). Chondronectin apparently is a dead end. Boghog (talk
) 20:24, 11 January 2016 (UTC)

Swati Patankar

Is this person notable? --Dweller (talk) 14:00, 14 January 2016 (UTC)

I Googled her name and although she seems very competent (molecular biologist and has published papers), but she is not notable to Wikipedia guidelines.
talk
) 14:52, 14 January 2016 (UTC)
Thanks. It's at AfD now. --Dweller (talk) 09:34, 15 January 2016 (UTC)

Most viewed page: xDNA???

According to the popular pages stats, xDNA is listed as the most viewed MCB article in the last month. This is a rather remarkable result for such an obscure topic. I suspect it may have an alternative meaning that is driving traffic to xDNA, perhaps:

Any ideas? Boghog (talk) 17:58, 17 January 2016 (UTC)

Those stats and the stats.grok.se ones never quite match up, but there you see two days of high traffic, Dec 2-3. Linked from somewhere popular, I guess? Opabinia regalis (talk) 18:31, 17 January 2016 (UTC)
Hmm, #2 on the list,
carrier protein, also has one day of high traffic, Dec 22. The rest of the list looks like reasonable, real traffic. Popular link or stats aggregation error? Opabinia regalis (talk
) 18:36, 17 January 2016 (UTC)
Thanks! Looks suspiciously like an aggregation error. These stats are not unique visits hence these stats could also have been the result of some sort of malfunctioning web crawler. Boghog (talk) 19:06, 17 January 2016 (UTC)

New project on here

Hello all! As a spare time project, I’m looking to do spend some time in the next few months messing around with R, its graphics packages in particular. I’d be interested in combining this with my contributions to Wikipedia (do two obsessions together!) - does anyone have suggestions for any publicly available biosciences data that might be interesting to do something with? Blythwood (talk) 12:37, 19 January 2016 (UTC)

Help on AfC

Can someone please take a look at Draft:Meso-zeaxanthin. I'm also posting at Wikipedia:WikiProject Chemistry, since I think it could be evaluated by someone from either group. Thanks in advance. Onel5969 TT me 13:07, 4 February 2016 (UTC)

RNA expression images in protein infoboxes

This has kind of mildly annoyed me for a while now - the PBB infoboxes are often populated by RNA expression by tissue graphs like this one, which is a good idea in principle, but they're tiny and unreadable and unlabeled, and the data is from 2007. I don't think these are adding anything to the articles they appear in at this point. Any interest in/objections to removing these? Legible re-renderings of current data could be added later if available, though I'd be more inclined to use text aggregated at the organ level ("brain", "kidney", etc., preferably supplied by bot), with links to sources of finer-resolution data. Opabinia regalis (talk) 07:56, 7 February 2016 (UTC)

The person to ask about this
discussion). Perhaps it would be better to replace these figures with an external link to a database such as the Human Protein Atlas which contains both mRNA and protein expression data (e.g., QARS). Boghog (talk
) 08:51, 7 February 2016 (UTC)
That's a good idea. The existing BioGPS link is handy for the interactive figure, but since it has a different orientation and different colors than the static versions on-wiki, it doesn't really help calibrate expectations for what the local ones mean. Opabinia regalis (talk) 20:07, 7 February 2016 (UTC)
  • As a reader, I like images like that even if they are outdated. They can be labelled as from 2007. I would rather the images kept, a note made on the talk page, and call like here for improvement rather than removing them entirely. Any other information that is confusing about the image could be added tot he image to make it clearer what it is about. --David Tornheim (talk) 01:27, 14 February 2016 (UTC)

Suggestions welcome on article-writing handbook for university students writing about genes and proteins

Hello all! The Wiki Education Foundation is creating a guidebook for higher ed students in the USA and Canada who are assigned to write articles about genes and proteins. If anyone has good advice for students, or would like to review the contents of the handbook to suggest changes, we'd love to hear from you! You can find the proposed draft here. This guide is intended to serve as a complement to a series of guidebooks on editing basics and participating in the community. The core of the brochure is therefore focused exclusively on writing these kinds of articles. Thanks in advance! Eryk (Wiki Ed) (talk) 17:43, 16 December 2015 (UTC)

Hi @Eryk (Wiki Ed): My advice is that articles need to be written so lay persons can read them. Please see my comment below at [1] about this problem. I will take a look where you said and possibly comment, but I do not know if I want to get too involved in the manual of style discussions except to make this one point. --David Tornheim (talk) 02:05, 14 February 2016 (UTC)

Hybridoma technology article

I came to

Genetic Engineering -> Genetic_engineering#Manufacturing -> Monoclonal antibody -> Monoclonal antibody#Production
. A couple of points:

(1) The article's writing is way too technical for a general purpose encyclopedia. The starting sentence is:

Hybridoma technology is a technology of forming hybrid
myeloma (B cell cancer) cell that is selected for its ability to grow in tissue culture
and for an absence of antibody chain synthesis.

Despite having a considerable amount of upper level education and a Masters degree in science, I read that sentence and feel like I have no clue what Hybridoma technology is or why it is important. Further reading in that article and

monoclonal antibodies
did not help much for the same reason. Imagine the frustration of the lay person with no background in science.

(2) According to the

Genetic Engineering
article:

Genetic engineering is used to mass-produce insulin, human growth hormones,
antihemophilic factors, vaccines and many other drugs.[1][2]
[emphasis added.]
  1. ISBN 978-0-19-516950-8
    .
  2. ^ "Engineering algae to make complex anti-cancer 'designer' drug". PhysOrg. 10 December 2012. Retrieved 15 April 2013. {{cite journal}}: Cite journal requires |journal= (help)

The material in

monoclonal antibodies#Production and Hybridoma technology
to be able to correct them at this time.

--David Tornheim (talk) 02:01, 14 February 2016 (UTC)

Thanks for the heads up. I took a stab at simplifying the lead and hopefully it is now more accessible. The sentence from the Genetic Engineering article is a bit misleading. Not all monoclonal antibodies are drugs. In fact, the majority monoclonal antibodies are used for other purposes such as diagnostics or research tools. Furthermore genetic engineering usually implies isolation and cloning of DNA. Hybridomas can be produced without isolation of DNA hence these hybridomas are not the product of direct genetic engineering. Genetic engineering can be combined with hybridoma technology, but it is not required. Boghog (talk) 08:39, 14 February 2016 (UTC)
Thank you! --David Tornheim (talk) 10:48, 14 February 2016 (UTC)

Maint cat

Maintenance: shouldn't his one be empty?: Category:Protein articles without symbol -DePiep (talk) 02:23, 9 February 2016 (UTC)

 Fixed Boghog (talk) 13:20, 15 February 2016 (UTC)

Duplicate pages (LNA/BNA)

Locked nucleic acid and Bridged nucleic acid describe the same concept: synthetic nucleotides with sugar rings locked in pucker formations to favor one helical form over the other. They are clearly talking about the same thing, and the terms have been used interchangeably in the literature (e.g. Kuwahara & Obika, "In vitro selection of BNA (LNA) aptamers", Artificial DNA: PNA & XNA (2013) 4:39-48 PMID: 24044051). They should probably be merged. Both articles solely reference locking the sugar in the 3'-endo pucker (there are also 2'-endo-locked versions - see Vesper & Wingel, Biochemistry (2004) 43:13233–13241 PMID: 15491130), so their is room for expansion as well. 134.121.126.47 (talk) 01:40, 20 February 2016 (UTC)

Immunoglobulin E

An IP editor is changing an entire paragraph in the lead, apparently in disagreement with who discovered IgE. Could some knowledgeable project members from here take a look? Thanks -

theWOLFchild
23:30, 25 February 2016 (UTC)

Hello. The changes made by the IP user are correct, according to his references cited and this additional [and powerful] Review article: The discovery of IgE, Stanworth DR. Allergy 1993: 48: 67-71.]. The literature is in agreement in that the two teams that independently discovered IgE were: Johansson & Bennich (mostly), and Ishizaka's team. And it is evident that Lichtenstein and Norman made a subsequesnt discovery on myeloma using the already discovered IgE. Cheers,
talk
) 04:47, 26 February 2016 (UTC)

please help protect gene articles from deletion

A user with the handle User:Winterysteppe has proposed the article NFE2L1 for deletion. As the articles on human genes go, this one is pretty good: citing 38 different peer-reviewed journal articles and providing quite a bit of useful text. If it gets deleted on the grounds of 'no original research', basically all the articles on Wikipedia that cite research indexed in PubMed (meaning nearly every article of interest to the MCB project) would stand to be deleted. Please help me protect this article along with the rest of science... (I'm not sure exactly how to do that.) --Benjamin Good (talk) 22:26, 26 February 2016 (UTC)

That was a "proposed deletion" (see
WP:PROD), which can be done by any editor and undone by any editor, including you. This one was particularly clueless, and the "prod" has already been removed by another editor. It certainly doesn't have any implications for our broad array of gene articles. Thanks for pointing this out, though. Looie496 (talk
) 22:46, 26 February 2016 (UTC)
Thanks for calling me clueless Looie496. Make sure next time you don't say it publicly. Also, it heavily relies on original research but Wikipedia says its not a host for original research. Winterysteppe (talk) 23:11, 26 February 2016 (UTC)
@Winterysteppe: "Original research", as in how science defines it, you mean? Jo-Jo Eumerus (talk, contributions) 23:21, 26 February 2016 (UTC)
I'm sorry, but "prod"ing an article with so many sources in reputable academic journals is clueless. Asking for sources that are review articles (per
WP:MEDRS) would have been reasonable. And by the way, "Research Gate" has no connotation of OR. ResearchGate is a site that allows scientists to supply freely accessible pdf versions of published papers, so that they can be read by people who can't access the journals they were published in. Looie496 (talk
) 22:22, 27 February 2016 (UTC)

Protein Expression and Purification

The article

Pichia pastoris? Uanfala (talk
) 10:37, 9 March 2016 (UTC)

I've done a bit of re-organisation using renaming and redirects to disambiguate and cross-reference:
Hopefully it's at least helped a bit. T.Shafee(Evo﹠Evo)talk 13:13, 9 March 2016 (UTC)
That looks good! Thank you for sorting it all out! Uanfala (talk) 19:33, 9 March 2016 (UTC)

Clarification Needed at Anoxygenic photosynthesis

Hey all! I recently stumbled upon a couple of clarification-needed tags at Anoxygenic photosynthesis. Unfortunately, I don't really understand the paragraph in question (at the bottom, about the electron transport chain in Green Sulfur Bacteria). Any chance anyone here with a bit more experience in biochemistry could make sense of the paragraph, clean it up, add a citation, and save the day? Thanks a bunch!! Ajpolino (talk) 03:53, 12 March 2016 (UTC)

Remove CD45 for thrombocytes in this image: File:Cluster_of_differentiation.svg

Hello all, would someone with editing image experience remove the CD45 marker for thrombocytes in this image: [2]. Correct me if I am wrong but CD45 is not present in thrombocytes (and neither in red blood cells but they are not in this image but I digress). I got this info from the following source: [3], although not sure if things have changed since then. Happy to be corrected. I also made a similar request for this image: [4], see: [5] Thank you for your assistance.Calaka (talk) 05:47, 17 March 2016 (UTC)

If memory serves, CD45 is absent only on red blood cells and plasma cells, so we'd have to check before doing this.Jo-Jo Eumerus (talk, contributions) 06:34, 17 March 2016 (UTC)

"Basophil"

The usage of

talk:Basophil granulocyte -- 70.51.46.39 (talk
) 04:54, 19 March 2016 (UTC)

Genome engineering - COI - Review required

COI concerns have been raised w.r.t.

Genome engineering (and other articles - see Wikipedia:Conflict_of_interest/Noticeboard#Cellectis). It would be well for a neutral and informed editor to review the content of the article, noting that it started as a large dump of text from a user never heard from again, quickly followed by edits from a user with suspected COI. Per the citation thread at the top of the article talk page, it is possible that the company with COI interest, Cellectis, is seeking to promote its interest in Meganuclease
in part by criticising other techniques.

So. If someone who understands the subject could have a read through, especially with a view to the slant of the article being in the direction of Meganuclease or against other techniques. I note that CRISPRs, which I though was all the rage, seems to be described as an also-ran in comparison with Meganuclease. thanks --Tagishsimon (talk) 17:07, 18 March 2016 (UTC)

And this edit on Genome editing should also be studied. Added by a user with declared COI acting on behalf of Cellectis, which has an interest in Meganuclease.
Note that there's a suggested merge between
Genome engineering ... it might be timely to action this as a means of assuring the article quality. --Tagishsimon (talk)
17:14, 18 March 2016 (UTC)
NB: Merge discussion
Peer reviewing these topics is a good idea, given their public impact. I'm happy to help out with reviewing
Genome engineering. T.Shafee(Evo﹠Evo)talk
23:25, 19 March 2016 (UTC)

Track hub

Hi, Can someone help me with this article: Track hub. I used this as the source of information (and a few sentences unfortunately): https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html#Intro

IMHO that page is too complex, and a nice compact WP article covering the basics is useful for all (especially as this is an open standard).

Many thanks, --Dan Bolser (talk) 09:44, 21 March 2016 (UTC)

Dynamic instability

Dynamic instability has been nominated for deletion at RFD -- 70.51.46.39 (talk) 03:29, 29 March 2016 (UTC)

Cubosomes

An article on

Cubosomes was created by a university writing cours, it looks like it is also in the focus in your project. The article needs still a liitle look. Thanks. --Stone (talk
) 07:10, 29 March 2016 (UTC)

A question

Could someone please create a page on

CrmA? It's in the Serpins template, and Serpin is the featured article of the day, so I wouldn't mind :'> 96.237.16.46 (talk
) 00:12, 2 April 2016 (UTC)

Also, could you create this page please? 96.237.16.46 (talk) 00:24, 2 April 2016 (UTC)

Serpin to FA!

For those interested in these things, the

MCB trophy cabinet. T.Shafee(Evo﹠Evo)talk
22:11, 19 March 2016 (UTC)

Congratulations--nice work on bringing a complex topic to FA status! --Mark viking (talk) 23:02, 19 March 2016 (UTC)
Likewise, congratulations. Nice work! Boghog (talk) 23:06, 19 March 2016 (UTC)
Thanks guys! It's currently also
Main page! T.Shafee(Evo﹠Evo)talk
11:45, 2 April 2016 (UTC)

Draft:UNC13A: Are human genes ipso facto notable? Discussion

I reviewed Draft:UNC13A and declined it as not showing the subject’s notability, with only one reference, and that reference cannot be displayed. I also noted that that reference, in its title, refers to ‘’C. elegans’’, which is a worm species, while the article refers to the gene in humans.

User:Biolprof then posted the following:

First, thank you for you amazingly quick response to my submission of Draft:UNC13A as an article for creation. I am a WP Teaching Fellow/University Professor and have a student that would like to expand this article, but I don't want her to be held up by the AfC process. I can have her work further on this stub, but my understanding is that the Wikipedia:WikiProject Molecular and Cell Biology has a project to create a stub for every human gene/protein with the expectation that the stubs will be fleshed out as our knowledge improves. The style guide for these articles is found here. The content of the article I submitted was automatically generated by the GeneWikiGenerator following WP style guidelines. I thought I should be able to automatically send it to WP from the Biogps site, but since I could not, I submitted it as an AfC. Many similar stub articles with just one or two references have been created, some generated by a bot. (For example: ALDH16A1). My response to your specific comments:  my understanding is that WP:MCB has determined that every human gene is notable. Feel free to correct me if I am wrong, but the related genes UNC13B and UNC13D each have a page and neither was created with much more information.  The broken link to the reference has now been repaired. Apologies that I missed this.  Entrez Gene is a definitive reference for all human genes and is cited following the first sentence of all gene/protein articles that I am familiar with.  "(C. elegans)" is included as part of the name for the human protein in Entrez Gene/NCBI web site and was included in the WikiGeneGenerator text, but it is not included in the WP pages for the UNC13B and UNC13D homologs, so I have deleted that. One additional comment: if you still think this article should not be approved, would you consider asking someone from the

WP:MCB
for a second opinion. Thank you for your consideration. Biolprof (talk) 22:14, 9 April 2016 (UTC)

As requested, I am posting to

the Molecular and Cell Biology talk page
. If there has been a decision that every human gene is notable, then that is presumably a notability guideline that establishes ipso facto notability, in that all human genes may be notable if they are properly documented. However, such a guideline must itself be documented as a written guideline, or non-conforming AFC drafts will be declined, and non-conforming articles will be nominated for deletion. I am aware of guidelines that certain people, such as professional athletes in first-tier leagues, and politicians in national or state legislatures, are ‘’ipso facto’’ considered notable; however, references are required to document that they played in those leagues or held those high offices. If the project decides that all human genes are notable, they should publish such a guideline. However, it will not exempt them from the requirement to have references.

You imply that there is a stub generator to turn out stubs for every human gene without references. Has automatically generating those stubs been approved either by

consensus
or by the WMF? If so, please show the consensus. Otherwise, there is likely to be considerable controversy. I can see that stubs that have been generated without references are, as it stands, likely to be nominated for deletion.

You speak of not wanting to have the AFC process hold up creating the stubs. Once again, please explain what the authorization is for creating these stubs that evidently do not document their own notability.

Robert McClenon (talk) 03:13, 10 April 2016 (UTC)

As far as I know, there is no declaration of inherent notability for human genes. There have been proposals to create stubs for all human genes, but these have been shot down. On the other hand, A quick GScholar search shows 493 hits for gene UNC13A, which makes the gene likely notable. It is associated with
amyotrophic lateral sclerosis (ALS) so has had a bit of work done on it. I agree with the decision to turn down the draft in its current state, but with some work, I think the creators could make a nice little article out of this. One might use, e.g., UNC13B as an example of how to create a solid stub/start class article on a gene. Although the article is short, the references are solid. --Mark viking (talk
) 04:29, 10 April 2016 (UTC)
As stated here, the goal of the Gene Wiki project is to create an article for every notable human gene. Notability generally means that at least one reliable source has documented the function of the gene and/or linkage to a human disease. As Mark mentioned above, UNC13A is associated with ALS and this been covered a number of reliable secondary sources, so this gene clearly is notable. I took the liberty of creating the stub in main space and you can merge your draft into the stub. Sorry for not responding sooner. Boghog (talk) 07:06, 10 April 2016 (UTC)

GeneWikiGenerator - not working for me

I just posted a question

here and then noticed that the last comment on that talk page is quite old, so am posting the link here. Sorry for the redundancy. Biolprof (talk
) 16:46, 8 April 2016 (UTC)

@Biolprof: Hi. Sorry for not responding sooner. The GeneWikiGenerator is working, but the link on the page was out-of-date. The link has been fixed in this edit. Using this tool, I have taken the liberty of creating the UNC13A article. Boghog (talk) 06:54, 10 April 2016 (UTC)
@Boghog: I was able to find the correct link to the GeneWikiGenerator via Google, but when I entered UNC13A and clicked on the "Create" button, I got an error message "Forbidden. CSRF verification failed. Request aborted." When I clicked on the "Toggle Stub Code" button, I could read the code, but not copy it. Maybe permissions are needed that I don't have. But in any case, thank you very much for your help. Biolprof (talk) 15:52, 10 April 2016 (UTC)
I don't think there are any special permissions required other than your browser has to accept cookies. I am pinging (@Andrew Su and I9606:) the developers of BIOGPS to see if they have any suggestions. Cheers. Boghog (talk) 16:11, 10 April 2016 (UTC)
Hi @Biolprof: and @Boghog: ! There are no permissions required. The stub-creation code executes under our PBB_bot account. It sounds like it temporarily failed to login for some reason, so couldn't make the edit. If this happens again, please let us know and we will fix it ASAP -note to @Julialturner:. Thanks! --Benjamin Good (talk) 21:54, 10 April 2016 (UTC)
Hi @
Unc-13 homolog c (c. elegans) instead of UNC13C. I'm not experienced enough to know how to fix this. Sorry for my mistake and thanks for your help. Biolprof (talk
) 18:20, 11 April 2016 (UTC)
Glad to hear that it is now working for you. If you want to rename the article, all you need to do is move it. On the Article/Talk/Read/Edit/View History/¤/More pull down menus, select More and then Move. You can then rename the article to as you intended. Boghog (talk) 20:06, 11 April 2016 (UTC)

GAI (Arabidopsis)

In the article https://en.wikipedia.org/wiki/GAI_%28Arabidopsis_thaliana_gene%29 it is proposed as I read that GAI is similar to a putative transcription factor. in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC316750/ it is mentioned that it could be gene transkripted into a receptor, any suggestions? 2A02:1205:C697:9500:E18B:47F7:11FB:A08D (talk) 20:15, 12 April 2016 (UTC)

Issue with Category:Neurotrophins

Category:Neurotrophins currently contains a number of neurotrophic factors which are not neurotrophins. Should this category be renamed to Category:Neurotrophic factors, or should the articles that aren't about neurotrophins simply be removed from the category? The nav template below lists the 4 neurotrophins + an assortment of other neurotrophic factors (it's not a complete list of factors). Seppi333 (Insert 2¢) 22:08, 12 April 2016 (UTC)

I would be inclined to rename the category as Neurotrophic factors, and leave it populated with the same pages. It seems to me to be a subtle difference anyway, with neurotrophins being a subset of the neurotrophic factors. I suppose one could also have Category:Neurotrophic factors, with a subcategory of Category:Neurotrophins within it, but I think that would be gilding the lily. --Tryptofish (talk) 22:20, 12 April 2016 (UTC)
I've proposed renaming it at WP:CfD - Wikipedia:Categories for discussion/Log/2016 April 13#Category:Neurotrophins. Seppi333 (Insert 2¢) 19:24, 13 April 2016 (UTC)

Selective factor 1

Would it be possible for a knowledgeable person to review this article? There have been some problems with other articles by the same creator.

All the best: Rich Farmbrough, 01:19, 1 May 2016 (UTC).

I've emailed Robert Tjian to see if he might have a quick look over it. T.Shafee(Evo﹠Evo)talk 04:27, 4 May 2016 (UTC)
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