Talk:Histamine N-methyltransferase/GA2

GA Review
The edit link for this section can be used to add comments to the review.''

Nominator:

Reviewer: Sammi Brie (talk · contribs) 22:25, 23 March 2024 (UTC)

Some reference issues. Britannica needs to be excised, and I need some explanation on the blood serum line. I also want to see Esculenta's comments if they materialize soon. Ping me when done; I may still hold for Esculenta to determine if the issues from GA1 still linger. Sammi Brie (she/her • t • c) 02:26, 24 March 2024 (UTC)


 * I removed the reference to Britannica and put different sources for the sentence "DAO is primarily responsible for metabolizing histamine in extracellular (outside cells) fluids, which include interstitial fluid (fluid surrounding cells) and blood plasma". If you still find these sources problematic, we can support particular parts of this sentence or remove it at all, as this sentence is about a different enzyme, other than what is covered in this article, so this sentence is not essential in this article. I will reply to your other issues soon. Maxim Masiutin (talk) 13:45, 24 March 2024 (UTC)

I also saw that was previously requested to provide feedback on this article at some point. Feel free to join in. Sammi Brie (she/her • t • c) 01:53, 24 March 2024 (UTC)

Lead

 * Research on knockout mice lacking the Hnmt gene Is this styling appropriate for the gene in mice?
 * Genetic variants affecting HNMT activity have also been implicated in various neurological disorders like Parkinson's disease and attention deficit disorder, still, as of 2024, it remains unclear whether alterations in HNMT are primary causes or secondary effects of these conditions. The first comma should be a semicolon. WP:CINS

Protein

 * 33kDa Link this unit and add a space after "33".
 * It has a classic fold found in many other methyltransferases, and consists of a seven-stranded beta-sheet surrounded by three helices on each side. Remove comma after "methyltransferases" (CinS)

Species

 * Consider consolidating into fewer, longer paragraphs.
 * Italicize or don't italicize the gene acronym consistently.

Function

 * Reintroduce "diamine oxidase (DAO)" on first mention in the body of the article.
 * DAO is predominantly expressed in the cells of the intestinal epithelium and placenta, but not in the central nervous system (CNS). Remove comma (CinS)
 * Link "central nervous system" on first mention and de-link it later.

Clinical significance

 * It is presumed by some scholars that in the case of flawed HNMT activity, the most affected organs are the brain, liver, and mucous membrane of the bronchus, consequently, flawed HNMT activity can lead to chronic forms of HIT Another comma splice; the comma after "bronchus" should be a semicolon.
 * The exact mechanisms by which deficiency or impaired activity of HNMT causes HIT are not fully understood but are hypothesized to involve genetic factors: variations in genes encoding for HNMT have been presumed as potential contributors to increased susceptibility to allergic diseases and more severe courses of conditions like atopic dermatitis and allergic rhinitis: while deficiencies in DAO may be considered the primary cause of HIT, variations in both DAO and HNMT genes could play a role in its development; the interplay between these enzymes may influence effectively histamine is broken down and cleared from the body, but the reliable studies to confirm these hypothesis are lacking. Split this very, very long sentence, possibly in three.
 * cause of aggravate should be "cause or aggravate"
 * Studies predict that one such inhibitor can be metoprine, which crosses the blood-brain barrier and can potentially increase brain histamine levels by inhibiting HNMT, still, as of 2024, treatment of methamphetamine overdose by HNMT inhibitors is still an area of research. Semicolon, not comma before "still"
 * It can bind to histamine receptors, still, NMH has a lower affinity and efficacy than histamine for these receptors maybe It can bind to histamine receptors, but NMH has a lower affinity and efficacy than histamine for these receptors
 * Still, NMT, being a produce in a reaction catalyzed "product"

Sourcing and spot checks

 * 4: PubMed search for mouse in the infobox, not a typical reference. Instead doing
 * 6: List of isoforms in UniProt. One mentions that it has no histamine-methylating activity. Your article says that only one has it. Which is correct?
 * 16: Trends in Biomedical Sciences article. The 230 figure is in [15]. This article is about convergence of different types of MTases. ✅
 * 26: Find a new reference that meets RSMED for the definition of extracellular fluid.
 * 28: The DAO protein is stored in plasma membrane-associated vesicular structures in epithelial cells of kidney and intestine and is secreted into the circulation upon stimulation ... The highest expression of DAO has been observed in the intestine, kidney and placenta ✅
 * 45, 47: Can you help me find the claim in these references? I don't see "blood serum" anywhere.
 * 61: p534 Since the key metaboliteNτ-methylhistamine, like all other metabolites, is inactive at the different  members  of  the  histamine  receptor family ✅

Images
The visualization is published under CC-BY license, as is the methylation diagram. Encouragement: Consider alt text, probably "Refer to caption", for the latter.

Gene name capitalization
User:Sammi Brie, there is a convention for the molecular biology articles (WikiProject_Molecular_Biology/Style_guide_(gene_and_protein_articles)) that human genes should have all characters capitalized whereas other species genes should only have the first letter capitalized, referring to gene nomenclature that is followed by peer-reviewed articles. Maxim Masiutin (talk) 14:04, 24 March 2024 (UTC)


 * @Maxim Masiutin I kind of thought this was the case but was not immediately sure. The italicization was still inconsistent, though. Sammi Brie  (she/her • t • c) 15:41, 24 March 2024 (UTC)
 * @Sammi Brie I was very careful to italicization. Italicized word means gene name whereas non-italicized means protein name, according to the same convention. Maxim Masiutin (talk) 16:53, 24 March 2024 (UTC)
 * Thank you for explaining. Sammi Brie  (she/her • t • c) 17:05, 24 March 2024 (UTC)
 * I also tried to write sentences in a specific way to use terms for which wikipedia articles exist with that name, to avoid using pipe characters in wikilinks, as suggested by MOS:PIPE. Maxim Masiutin (talk) 22:41, 24 March 2024 (UTC)

Earlier review
User:Sammi Brie, on December 1st, 2023, I asked User:Esculenta to review the article again, just for your information. Maxim Masiutin (talk) 17:56, 24 March 2024 (UTC)

Lead section
Maxim Masiutin (talk) 17:56, 24 March 2024 (UTC)
 * 1) On gene name capitalization and italicization, that particular instance was correct, but you were right that there were some places of inconsistency, that I fixed today, overall, I hope that I addressed this issued in the  subsection of this talk page.
 * 2) Replaced comma to semicolon on the sentence that had ", still, ". I also did this replacement in two other places in the article.

Protein section
Maxim Masiutin (talk) 17:56, 24 March 2024 (UTC)
 * 1) On 33kDa, I slightly reworded the sentence so that removed abbreviation from the unit, added wikilink to it and made it explicit that it was a unit of mass, so that the new sentence is friendlier to a reader who is not a specialist in the domain.
 * 2) Removed the comma before "and consists of".

Gene section
Maxim Masiutin (talk) 17:56, 24 March 2024 (UTC)
 * 1) Consolidated into fewer longer paragraphs, by topic.
 * 2) Checked the case/italic appropriateness.

Function section
User:Sammi Brie, Maxim Masiutin (talk) 17:56, 24 March 2024 (UTC)
 * 1) On sourcing: I removed the reference to Britannica and put different sources for the sentence "DAO is primarily responsible for metabolizing histamine in extracellular (outside cells) fluids, which include interstitial fluid (fluid surrounding cells) and blood plasma". If you still find these sources problematic, we can support particular parts of this sentence or remove it at all, as this sentence is about a different enzyme, other than what is covered in this article, so this sentence is not essential in this article.
 * 2) Reintroduced full "diamine oxidase" on first mention.
 * 3) Removed the comma in the sentence "DAO is predominantly expressed in the cells of the intestinal epithelium and placenta but not in the central nervous system (CNS)."
 * 4) Linked "central nervous system" on first mention and de-linked it later in this section, however, I added one wikilink to CNS in one of subsequent sections to "remind" the reader on the abbreviation.

Clinical significance section
Maxim Masiutin (talk) 22:14, 24 March 2024 (UTC)
 * 1) Replaced comma to semicolon after bronchus.
 * 2) Split that long sentence and removed some text that was excessive, combined two paragraphs into one after the deletion.
 * 3) Resolved the "cause of aggravate" issue by keeping only "aggravate".
 * 4) Replaced comma to semicolon before "still"
 * 5) In the sentence that starts with "It can bind to histamine receptors", I analyzed your suggestions and come up with a probably better variant: "NMH can bind to histamine receptors, but has a lower [...]".
 * 6) Fixed a typo in the word "produce"

Sourcing and spot checks reply
Maxim Masiutin (talk) 22:14, 24 March 2024 (UTC)
 * 1) As for the mouse in the gene infobox, I have no control over the data from the article. I only use  template, and it finds the gene from the wikidata and further collects information from databases. What I can do is to remove the infobox at all. Do you think I should remove the infobox?
 * 2) You asked the following: "List of isoforms in UniProt. One mentions that it has no histamine-methylating activity. Your article says that only one has it. Which is correct?". When I went to https://www.uniprot.org/uniprotkb/P50135/entry and scrolled down to "Sequence & Isoforms", I saw three isoforms listed there: P50135-1 This isoform has been chosen as the canonical sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.; P50135-2 Note Has no histamine-methylating activity.; P50135-3 Nothing is mentioned about histamine-methylating activity. My understanding is that only the P50135-1 has histamine-methylating activity, while P50135-2 and P50135-3 have no histamine-methylating activity. UniProt is vague, but at least it does not contradict to the information presented in the article, because UniProt mentions that at least one isoform does not have histamine-methylating activity, while the article mentions that only one isoform has histamine-methylating activity citing a source that explicitly mentions that.
 * 3) On definition of extracellular fluid: I added  that mentions Extracellular fluid is distributed in two major sub-compartments: interstitial fluid and plasma and I also found specific articles that mention that DAO exists in specifically interstitial fluid and specifically in plasma, I added those references.
 * 4) You also asked "45, 47: Can you help me find the claim in these references? I don't see "blood serum" anywhere." -- I added two references after "blood plasma" that should be more explicit.


 * @Maxim Masiutin There is no need to remove anything. The source you have added covers the Britannica replacement. Sammi Brie  (she/her • t • c) 17:57, 25 March 2024 (UTC)
 * @Sammi Brie I didn't know that Britannica is not WP:MEDRS Maxim Masiutin (talk) 18:10, 25 March 2024 (UTC)

Images -- reply
TBD

No issues with images: no need to reply. Sammi Brie (she/her • t • c) 18:27, 24 March 2024 (UTC)


 * Thank you, I didn't know about the MOS:ALT feature, I added the attribute and viewed the page source and there was indeed.
 * I hope I addressed all the issues that you raised. Should there be more issues, please let you know.
 * Thank you very much for your thorough observation, especially on grammar and style. Maxim Masiutin (talk) 22:16, 24 March 2024 (UTC)
 * @Sammi Brie - do you have any further observations or concerns? A couple of days ago I made all the changes that you suggested. Maxim Masiutin (talk) 17:43, 26 March 2024 (UTC)
 * The article has status "On hold: this article is awaiting improvements before it is passed or failed", however, I already implemented all the improvements that you have suggested. Maxim Masiutin (talk) 18:47, 26 March 2024 (UTC)
 * I'm reading through. I think I understand the isoforms and blood serum issues (isoform 3 has the same missing pieces as 2, blood serum is because of where HNMT is found vis-a-vis DAO). This is ready. Sammi Brie  (she/her • t • c) 19:04, 26 March 2024 (UTC)