Talk:Cyclic nucleotide

Update by JHU program

Hi there, I'm a member of the group that will be working on this article for the JHU program. We've got an initial outline for the flow of the article:

1. Chemistry of cNMPs
   1. structure, what makes it cyclical (this is already present to some extent in the article)
   2. the basic components of the structure (maybe this goes first?)
2. Biochemistry
   1. synthesis in regards to biological pathways
   2. locations where cNMPs can generally be found in the cell or certain tissues
3. Biology
   1. examples of biological significance like their role in gated ion channels (there's a lot there!)
   2. examples of disruptions of cNMP pathways

We are also planning on including some historical milestones as part of the overall narrative. This will definitely be an evolving structure... Dugalmaguire (talk) 20:26, 13 March 2013 (UTC)

Along with Dugalmaguire, we have just posted a first draft of a re-write to this article. Please contact either of us via the article Talk page or directly with questions, suggestions, or concerns regarding improvements to this article. Thanks in advance for your help. Davidwhanks (talk) 02:32, 4 April 2013 (UTC)

Comments from Ppelletier

Does the lead section follow Style Guidelines?

I think this is a fantastic article, very well written and organized, so my comments are limited to one very minor highlight as far as the style guidelines go. The statement "it is varied and in some cases, still tenuous" may be construed as an opinion. To the extent it is true, maybe consider citing to an article that says so.

Hi Ppelletier, thanks much for pointing us to this sentence. After re-checking the references, you're right that this is a statement of opinion. It's been restructured to remove "tenuous".

Does the content accurately represent the cited sources?

Based on a high level review of the citations, I believe there is support for all the main assertions. The technical description appears accurate.

Is the writing clear, comprehensible, and doesn't use too much jargon?

The authors have done a good job of keeping the description straight forward, however, I think you would need to feel comfortable with the basics of biochemistry to appreciate the excellent summary of the literature reflected in what has been posted. This is not a criticism, but more of a suggestion, that having a very high level one or two sentence explanation at the beginning may go a long way for a layman.

Do the contents of each section belong in that section?

Yes, I think the organization is accurate and straight-forward.

Are there gaps in the content?

One of the great things about Wikipedia is that from this framework others will be able to build out more nuanced subject matter. For the improvements made the stub, I think this is an excellent presentation of the fundamentals. I have not specifically identified any gaps.

Is there ambiguity or inaccuracy over sources?

Not that I have observed. The sources are used consistently and their teachings are straight forwardly associated with the propositions they are cited to support.

Could the content be structured differently?

While there are obviously many ways to structure the article, the authors have done a very good job of keeping the organization straight forward while also comprehensive.

Are there parts of the article that are not clearly explained

Aside from a one or two sentence overview that makes the topic immediately accessible to a layman, the article clearly explains the most important concepts.

Is the content within Wikipedia's guidelines

Yes! Great job so far. Keep up the good work.

Ppelletier (talk) 02:24, 3 May 2013 (UTC)

Thanks very much Ppelletier, I'm glad you've been assigned to our article. Your comments for the fluorescent tag page were great. The summary sentences are a good suggestion, and a good direction to go. thanks! Dugalmaguire (talk) 13:20, 3 May 2013 (UTC)

Of course! And my compliments again on the quality of the writing and content coverage. This is a really strong post. Ppelletier (talk) 02:27, 7 May 2013 (UTC)

Comments from Jbmontgomery24

First and foremost, Dugalmaguire and Davidwhanks, you both have done an excellent job by incorporating a substantial amount of information to the Cyclic nucleotide article for the first contributions. I look forward to learning more about the content as more contributions are added to this article. Below I have listed the positive aspects of the current article as well as some possible suggestions to consider during the revision process.

Positive Aspects:

• A strong lead section that follows the Style Guidelines of Wikipedia with appropriate and accurate references. The images fit well to give the reader some information on the biochemical structure of the article’s topic.
• Overall, the article was well-written, accurate, and had an easy flow throughout. The concepts of the lead section and supporting content were straightforward and not ambiguous.
• The article has a neutral point of view throughout the whole article, which are supported well by references.
• Avoided plagiarism and paraphrasing in regards to the references.
• A great source of references was used to support the article.
• The grammar looked wonderful. I only tweaked a minor edit of a comma after “however” and added the word "and" in between cAMP and cGMP (original said cAMP an cGMP) in the “Synthesis and Degradation” section. Now the sentence reads: "However, the cAMP and cGMP degradation pathways are much more understood than those for either cCMP or cUMP.[7]"

Suggestions:

• Consider moving the “History” section directly after the lead section instead of at the end. This would give the reader some background information before proceeding to specific supporting information. Also, it will give the reader a sense of chronological order throughout the article.
• When referencing one paragraph from the same source, the citation only needs to be after the last sentence of the paragraph, not after ever sentence in the paragraph. I noticed this under the “Chemistry of cNMPs – Structure”, “Additional Chemical Information”, and “Biology” sections. I asked this question earlier on to one of the OAs since I wasn’t too sure since Wikipedia is particular. It is an easy fix!
• Continue to add more supporting information (of course first contributions have only been made so plenty of time for more additions).
• Reference #3 from “answers.com” is probably not deemed as a reliable source. Although it has useful information, Wikipedia prefers publications from journals and books.

I have attached a few articles that I thought seemed useful as you continue your project on this article. Please feel free to use them, but don’t feel obligated to do so either. Please view them in the References section. If you have any other additional questions and/or comments, don’t hesitate to ask. I would be more than willing to help you both in any way I can. I look forward to seeing this article continue to evolve, and I will continue to be in touch with additional feedback if needed. Keep up the superb work! Good luck! Jbmontgomery24 (talk) 16:55, 10 April 2013 (UTC)

Thank you very much Jbmontgomery24 for a very thorough evaluation of our posting. After going back over, I definitely agree about the 'answers.com' reference. It should be replaced, and probably can be without much trouble. We'll keep an eye on the inline citations and look your references over. Awesome, thanks! Dugalmaguire (talk) 18:56, 11 April 2013 (UTC)

Not a problem, Dugalmaguire! If you need another set of eyes to review anything else as more contributions are added, feel free to let me know. I look forward to seeing the evolution of the article over the next few weeks! Jbmontgomery24 (talk) 19:16, 11 April 2013 (UTC)

Thanks for the ref on differential activation Jbmontgomery24, that fit in nicely with the biochemistry section. Dugalmaguire (talk) 22:10, 23 April 2013 (UTC)

I'm glad to see that you found that reference useful for your article. The Hardman reference was a nice 'review' of your article; however, I know you both have already added substantial references on the overall topic. Nice job on editing out the 'answers.com' reference! I thought it may be an easy fix, and I'm glad to see it was.

The images throughout the whole article give it an easier understanding on this topic. I like how you both moved the cGMP image from the lead section to the 'Chemistry of cNMPs' section; it makes the article proportional. Also, the 'Generic Cyclic Nucleotide Biosynthesis Reaction' image fits very well in the 'Biochemistry' section. Well done!

I look forward to reading through your article as more edits/additions are made. I will keep in mind if I come across anymore insightful papers that may suit your article well, I will link it to this page. I understand this project will be coming to an end soon, but I may find useful sources before the final deadline, which could even add more to the article. Best of luck to you both! Again, it looks wonderful thus far, and keep up the excellent work! Jbmontgomery24 (talk) 19:34, 24 April 2013 (UTC)

I noticed there were some further edits done based on the recommendations given by Klortho. Just an FYI - there are a few linked words that are shown in red since they aren't actually linked to any particular page. You may want to unlink those few words. Looks great! Jbmontgomery24 (talk) 16:25, 25 April 2013 (UTC)

Thanks for the heads up Jbmontgomery24, as well as the continued input! Dugalmaguire (talk) 14:16, 27 April 2013 (UTC)

Not a problem! You both have done a great job on unlinking the few words that were in red within the main body of your article; however, there are a still a few words that are in red under the 'Nucleic Acid Constituents' table. Perhaps, these may need to be unlinked? In addition, I like how you both added another image under 'Synthesis and Degradation', which fits quite nicely here. I have enjoyed reading and learning about your article throughout this whole review process. If anything else comes up before the deadline, please feel free to ask. Excellent job! Jbmontgomery24 (talk) 13:17, 6 May 2013 (UTC)

That table is a template thing, unfortunately we don't have a whole lot of control over the content. Thanks for checking in! Dugalmaguire (talk) 01:55, 7 May 2013 (UTC)

Thanks for the update! I wasn't too sure if it was possible, but I thought it was worth double-checking. Looks great! Jbmontgomery24 (talk) 11:43, 8 May 2013 (UTC)

Comments from aaron.aude

Like Jbmontgomery24, I would echo that both of you have started to refine this article with interesting topics, content and structure. I'm looking forward to more content and frankly learning more along the way.

My comments are related to the sections currently in the article. I tend to focus more on tone, structure and readability.

Summary Section

• This text could be more succinct - exactly what it is, structure and leave the details to the sections below.
• Removal of 'our' in this section.
• Reference to answers.com for definition is okay, but it may be better to have a more scientific reference for the definition.
• I believe the tone of this section could be improved to keep a reader interested

• Reference to the images on the article - how do these relate? Perhaps create a verbal tie between the two?

Structure Section

• Is there anything novel or interesting about the structure of these molecules? Any interesting variations or inter species variations? If I were coming to this article, this would pique my interest.
• Perhaps combine the structure with additional chemical information section? These seem to be complimentary?

BioChemsitry, Cellular distribution Section

• Suggest linking to the types of eukaryotic cells - like smooth muscle, liver cells, etc. - to content within Wikipedia.
• Minor spelling/capitalization issue with the word "Many"
• Recommend linking to beta sandwich. Not sure many readers would know what this is.
• Section varies in assumed reader's knowledge of biochemistry. Perhaps a basic primer on some of the biochem involved?
• I really like the table

Biology Section

• Would recommend tying back what the signals are - the first two paragraphs in this section are confusing and don't follow the flow from previous sections.
• I like the biological significance area. Had you thought about a map of the body to highlight where these areas are? This could be an interesting hot spot map of regions of the body and cNMPs

I will take some time this week to seek out reference articles to the areas I mentioned above. Great article, and enjoy working with you to collaborate on its content.

Aaron.aude (talk) 02:59, 12 April 2013 (UTC)

Thanks Aaron.aude, you have both given very in depth reviews. I've started on some of your smaller suggestions, I liked the idea of referencing images in the text. As both you and Jbmontgomery24 are in agreement of the 'answers.com' reference, that should definitely be a priority. I've added some more information and an image in response to the biochem section, but it will continue to be a target for improvement. Thanks. Dugalmaguire (talk) 15:46, 14 April 2013 (UTC)

Hi Aaron.aude. We didn't get a chance to expand on your idea of a highlight map for biological significance. That's a good idea and I think an area we can really focus on. Thanks! Dugalmaguire (talk) 14:19, 27 April 2013 (UTC)

Comments from Klortho

• Remove "To date" -- it doesn't make any sense here.
• Ligand should link to Ligand (biochemistry), not Ligand.
• Does "the role of cyclic nucleotides in cellular pathways continues to expand", or is it that our knowledge of that role is expanding?
• The lead is very well linked, but you could use more links in the main article body. For example, Glycogen, Gerty Cori, Carl_Ferdinand_Cori. Some sections are completely lacking in links, and they would really benefit the article, I think.
• Several of your sections are written as bulletted lists. This style is somewhat discouraged. Where appropriate, could you rewrite them as prose?
• In general, a good job!

Klortho (talk) 01:59, 25 April 2013 (UTC)

Hi Klortho, thanks very much for the suggestions. They all make perfect sense and I'll start to work these in today. Davidwhanks (talk) 13:34, 25 April 2013 (UTC)

Hi Klortho, thanks for the 'role' sentence advice, is was awkward. Will continue to make adjustments. thanks. Dugalmaguire (talk) 19:44, 25 April 2013 (UTC)

Close Paraphrasing

Hey guys, I'm almost done with a full review, but I found an instance of too-close paraphrasing, in the sentence beginning "Even though many of the proteins have very different biological functions...". Please rewrite it as soon as possible, close paraphrasing is unacceptable and counts as plagiarism. Thanks - I'll have the review for you in a little bit. Keilana|^{Parlez ici} 18:58, 26 April 2013 (UTC)

Hi Keilana, i've changed that sentence, sorry about that! Dugalmaguire (talk) 19:27, 26 April 2013 (UTC)

Please review the rest of your article for instances of that kind of close paraphrasing. It is a very serious matter, and we'll be reviewing all the articles for plagiarism after the final version is done. It would be terrible for you to lose points (and, technically, you could get a zero) after all the hard work you have done. Thanks! Klortho (talk) 02:19, 28 April 2013 (UTC)

I will for sure! Dugalmaguire (talk) 03:42, 28 April 2013 (UTC)

Awesome, thanks for taking care of it! You've done really well with the paraphrasing, especially for such a long article. I'm just gonna post the rest of my review below - they're just suggestions, I know it's a lot. However, most of them are pretty small things, so try to do as much as you can. Let me know if you have questions!

• Don't capitalize "cyclic" (or other titles of articles), the links work anyways.
• You don't really need citations in the lead as long as the information is discussed elsewhere in the article, which it all is.
• "Each of these historical milestones" - this sentence should be removed, it's not encyclopedic.
• "Earl Sutherland himself" - why "himself"?
• Explain what glycogen phosphorylase does (for the lay reader).
• Reword "glygoren phosphorylase activity in dog liver and how it is influenced by the hormones adrenaline and glucagon", the paraphrasing is a little close.
• You need space before (ATP) in the second para of History.
• Are phosphorylase A and B glycogen phosphorylases or less specific enzymes?
• "phosphorylase B converts to phosphorylase A requires ATP" is both clunky and too-close paraphrasing, it needs rewording.
• You wrote "actin of adrenaline", did you mean action?
• The "Theodore Rall, Sutherland, and Wosilait" sentence is repetitive/clunky, consider merging it with the previous sentence.
• I think the "in 1958 the 'active factor' that the hormones produced" is not correctly cited because I can't find it in Newton and Smith.
• Fix the specificity link.
• Change "Fesenko et al." to "Fesenko, coauthor, and coauthor".
• The DOI on Kaupp and Seifert is broken. The PMID is fine though.
• Reword "In 1985 Fesenko et al....." as close paraphrasing.
• Ditto with the Beavo and Houslay sentence.
• Can you give first names for some of these scientists? It helps give a little bit more narrative to the history section.
• The sentence structure in History is pretty repetitive, try varying it and merging sentences to help the section flow better.
• Can you explain the 7 transmembrane segment structure a little more?
• The order of cyclase stimulants is the same as the source, switch it up.
• The second paragraph of Structure needs a rewrite (the "1, 2, 3" structure is bad to start) to be in more encyclopedic language.
• Paragraphs 2, 3, and 4 of Structure need expansion and citations.
• More explanatory captions would be awesome on the cAMP and cGMP pictures.
• Footnote 8 ("nucleotide numbering") needs to be a full citation.
• The 2nd paragraph of Additional chemical information needs citations.
• Footnote 9 is bad, you need a more specific link to cite the reaction.
• Spell out NMP, PDE, cCMP, cUMP.
• Do we know the pathways for cUMP?
• Link to smooth muscle, smooth muscle relaxation, glucagon.
• Spell out PKA, cGK1.
• Link molarity in 10^-7.
• Don't capitalize "protein" when you mention protein kinase A.
• cCMP lowers the E50 of cAMP when with cAMP according to the source, this seemed contradicted by the article.
• The first 2 sections of Biology are super awkward and need a rewrite.
• The list of "transmembrane signal transduction, receptor-effector coupling", etc. is in the same order as the source.
• The phrase "causes cAMP to synthesize" is unclear.
• The paraphrasing is a little close on the second paragraph of Biology, that's something really hard to paraphrase right so I suggest you try using two sources.
• The third paragraph of Biology is clunky.
• The first four sentences of the 3rd paragraph of Biology should be cited to source 16 (Bridges et al.)
• Watch the editorializing in the 1st paragraph of Biological significance.
• Citation 17 has 3 authors according to Google books.
• Footnotes should go after punctuation, check throughout.
• You can remove the stub template - it's definitely not a stub anymore! :)

Comments from Jakodak

I would recommend adding an ‘s’ to “interaction“ at the end of the sentence, “Their biological significance includes a broad range of protein-ligand interaction.”

Because the lead section is so good, the weakness of the final sentence stands out for me. Since understanding always improves with time, the final sentence seems a bit redundant. I would recommend rephrasing to something like; “Even after 50 years of their initial discovery, interest in cyclic nucleotides still has not abated.”

In the beginning of the structure section, cAMP and cGMP are described. Since cCMP is important enough to include in the table below it, why not take the opportunity to describe its structure as well. Or place it in a second sentence and note that it is less well understood or just has a more limited biological role.

Under the “Chemistry of cNMPs” section, you have a subsection titled ‘Additional chemical information’, but the material thereunder appears to be continuous with what is in the subsection above it. I recommend removing this subsection and just merge the text.

Overall, this is a very well written and informative article. There seems to be too much compartmentalization, but perhaps that is because the article is still young and more information will justify all the subsections. The tables and pictures are fantastic and I would change nothing in that regard.Jakodak (talk) 14:39, 3 May 2013 (UTC)

Thanks Jakodak for the input. That last sentence in the lead section has been a struggle, will definitely look at rewording. We will also look at what sections can be consolidated. Dugalmaguire (talk) 14:54, 3 May 2013 (UTC)

Cyclic di-nucleotides?

Do cyclic di-nucleotides like cyclic di-GMP fall under the category of Cyclic nucleotides? If yes, then the first sentence of the article is not accurate. --kupirijo (talk) 12:55, 12 June 2022 (UTC)