Talk:ADAR

Mislabeling?

Correct me if I'm wrong, but isn't the ADAR an enzyme and not a gene? Kehrbykid (talk) 01:14, 20 March 2009 (UTC)

As for most proteins whose gene has the same name as the protein, ADARs are proteins encoded by the adar genes. --Astrowob (talk) 11:07, 4 April 2011 (UTC)

==Peer review and responses during the educational assignment in Fall 2015==

ADAR Peer Review 1[edit source] - Intro: Question: In the first paragraph, ADAR is introduced as mutating RNA. In the last sentence of the paragraph, it mentions that I functions the same as G in both TRANSLATION and REPLICATION. What does this have to do with the ADAR (considering both translation and replication occur before ADAR acts?)

- Types of ADAR: "ADAR1 has two known isoforms known as ADAR1p150 and ADAR1p110 3 (insert period to end sentence) ADAR1p110 is only found in the nucleus and ADAR1p150 goes from the nucleus to the cytoplasm[5]." (also check the periods at the ends of the other sentences because some have too many spaces between the ends of the sentences)

- Biochemical Reaction: Awesome. Very simple and to the point, yet informative. If possible, include a step by step description of the attack or a picture.

- Active Site: Great, but check sentence flow and grammar. (ex. In humans, the enzyme’s active site has …) Consider making the crystal structure discussion its own paragraph.

- Model organisms: Very interesting paragraph, I’m happy you included it. Clarification: “none survived until weaning” could be worded better… maybe “none survived past weaning” or just “none survived weaning.” Question: Do you know what the two “significant” abnormalities were that appeared?

- Aicardi-Goutieres Syndrome: Question: Are further studies being carried out to investigate this disease? If yes, I would mention scientists are still trying to solve what causes this syndrome and that we do not totally understand the disease today. Otherwise, the phrase “the body most likely..” makes me lose confidence in the Wiki articles authors depth of knowledge, when in actuality, the entire scientific community is still speculating about the disease.

- Hepatocellular carcinoma: “The imbalance of ADAR expression could change the frequency of A to I transitions in the protein coding region of genes, resulting in mutated proteins which drive the disease” … back to my first question, does ADAR mutate RNA (i.e.after translation and replication) or before?

- Melanoma: great paragraph

- DSH: Clarification: “and may occur in Japanese” … does it only occur in these families OR is it just most prevalent in these families

- Overall order of page: After the introduction paragraph, I would move the discovery and function/ origin of ADAR to the beginning of the document. They both have great introductory information that would be helpful to understanding ADARs catalytic ability, role in disease, etc. RLLombardi (talk) 20:27, 20 October 2015 (UTC)Rachel Lombardi

Review ADAR[edit source] -Content: To start, the introduction is a good general overview of what ADAR does as an enzyme inside of the cell with dsRNA. It is easy to follow for anyone with general science knowledge. Going to the more content area, maybe move the Discovery and Function and Origin sections up to the first two section. This is a minor fix that could help the information on the page flow a little better. Then follow those sections up with the types of ADAR. In the Types of ADAR section, when introducing the three types of ADAR, something about it just doesn't flow. Try saying each ADAR1, ADAR2, and ADAR3 when introducing them. In the Biochemical Reaction section, maybe this would be a great place to make a figure of how deamination happens with molecular structures of how water is added to carbon-6 etc. using ChemDraw. Nice job linking subjects to different terms in the article that help with following along with the content.

-Figures: Obviously you will be placing more images in this article, but a few noted places on where images would help in my opinion. Like I said above, an image with what happens in assisting in the biochemical reaction. Another helpful image would be the Model Organism section.

-References: Great amount of sources. Just make sure there are non-journal sources in there as well.

-Overall Presentation: Great addition to this page of ADAR. Gives some nice content of how it functions and how it is involved with different diseases. Disease section gives nice detail of how ADAR plays a promenant role in each case. Just a few formatting critiques. First, bold ADAR in the introduction section to help show that it is the key word of the page and what the reader should pay attention to. Second, when saying ADAR1, ADAR2, or ADAR3, use the full name and not just 1, 2, or 3; it will help with just formality in the article. And lastly, like I said before, maybe move the more general informative sections up to the beginning to help give the enzyme a little more background information before jumping into the more extensive details.

(Bsgregg (talk) 01:02, 22 October 2015 (UTC))

ADAR Peer Review 3[edit source] Content

Intro: " Inosine is structurally similar to that of guanine (G);" remove "that of"

"In mammals there are three types of ADARs, 1, 2 and 3..." add a colon before 1, 2, and 3, rather than a comma.

Link to the protein isoform wikipedia article when isoforms are mentioned.

The active site and dimerization sections looked really great, good work!

I would expand on the "model organisms" paragraph, perhaps include the link to the model organism wiki.

Try to polish up grammar and logical flow of sentences. Check punctuation and the proper case/tense of your writing. Make sure you are consistent!

Figures

Suggestions for figures: a picture of the protein or Inosine from pymol (or something similar) could be useful, as would a diagram of the reaction or the reaction mechanism of the deamination mentioned in "Biochemical Activity." I think model organisms could use a picture as well.

References

Lots of great sources and citations!

Overall Presentation

Definitely move the discovery and the origin sections to the beginning of the article. You could split up "origin" and "function" if you feel you have enough content to add to both of them to make them separate sections.

I think that this is an excellent addition to the existing wiki page for ADAR. Most of my concerns were with grammar and phrasing, so I encourage you to proofread the article extensively to produce a more polished wiki page. I think you can also add a few more internal wiki links (such as those for isoforms and model organisms). I think you could expand on model organisms and the origin and function of ADAR (which shouldn't be an issue since it seems you have lots of great sources!) and re-order some of the sections on the page for clarity.

Aialungo (talk) —Preceding undated comment added 14:59, 22 October 2015 (UTC)

ADAR Peer Review 4[edit source] Content

Is the introductory section accessible for non-experts? The brief introduction before the “Types of ADAR” section was clear for anyone who had some knowledge of the DNA replication process. I would maybe go into a little more depth here as to ADAR’s overall importance (i.e. it can change gene expression by changing amino acid sequences, change splice site recognition behavior, and affect RNA stability leading to…) I would also consider either incorporating the “Types of ADAR” section into the introduction or “Viral Activity” section.

Do the contents of each section justify its length? I think each section goes into an appropriate amount of detail for a scientific Wikipedia page. There might be a typo in the “Active Site” section where it says restudies instead of residues. Also, in the “Melanoma” section, both of the “it’s” should be changed to “its”. The “Discovery” and “Function and Origin” sections are both very well explained and provide more context about ADAR for the reader. I would think about reworking the order of the sections and move the “Function and Origin” section first, followed by the “Discovery” section, and so on, closing with the “Disease” section.

Are all of the important terms / concepts linked to their respective Wikipedia pages for further reference? Yes, all of the terms, processes, and molecules that a reader might be confused on were linked throughout the article. The only place they weren’t was in the “Model Organisms” section, but I’m assuming that’s because the current Wikipedia article already has links in that section. I would maybe try to link a page on downregulation when you discuss it in the disease section.

Are the highlighted examples appropriate? Yes, both the specific disease examples and the studies with the mice were helpful.

Is any content duplicative of anything already on Wikipedia? I looked at the existing Wikipedia article and I think this draft does a great job of filling the holes in the article without being redundant. I would consider expanding on the mice studies from the existing article to provide the reader with some overarching conclusions at the end of the section.

Figures There are currently no figures, aside from the protein structure in the existing article. Maybe think about adding an original figure of the mechanism that occurs during the “A-to-I” base switch. Another good place for a figure would be the Discovery section (if there’s any photos or data from the initial study) or the DSH1 section (a picture of the hyperpigmentation). I would also consider cleaning up the existing article’s very long and complex table (if that’s even possible or allowed). There’s obviously copyright issues to consider, but these were just some thoughts.

References The references section is very thorough (32 were listed). There were many credible journal articles listed, but also a book and a PDF study, so there is some variety in sources. Another non-journal one that I found in my search online (http://www.uniprot.org/uniprot/P55265) gave a good, brief overview of ADAR and some more information about its role in the cell, if you find that helpful. It looks like some of the first 10 sources are repeated, so that might be a quick formatting issue to fix. Also, it looks like some of the citations both in this draft and the original are having some formatting issues with Wikipedia (needing date values or having invalid reference tags).

Overall Presentation This is a much improved Wikipedia entry from the existing one on ADAR. This draft offers more background on the discovery and function of ADAR and added content on the mechanism of “A-to-I editing”. It is written in a way that takes what could be complex content and simplifies it for a general public audience. It also points at the larger relevance of ADAR in medicine, which was interesting. I would re-organize the ordering of the content so that the piece flows more logically through the information. I would also try to incorporate some more “big picture” applications (aside from just disease) of ADAR in gene expression or other cellular processes it impacts. Some figures also need to be added for clarity and some editing / formatting needs to be corrected, but this was a well thought out draft.

Kt455 (talk) 15:14, 22 October 2015 (UTC)

Suggestions from ChemLibrarian[edit source] You identified many sources to cite for the article. Good job! Here are my suggestions.

I see that you did not use any of the existing content in the original article ADAR. It's not a good practice. Imagine how you feel if editors come in later remove your contributions completely. So, please do try to incorporate the sentences in the original article into your paragraph, especially keep the reference cited there.Also, those sections in the original article like See Also, Further Readings, External Links, Categories should be kept as is. You have many subsections under the second level headings. I understand this may be making the structure clearer. However, with so many of them having only 2-3 sentences under each subsections. It makes the article appear to be unfinished and too complicated. Please consider removing some of the lower level subheadings or at least making them a 4th or 5th level heading so that they don't appear to be so overwhelming. The logic of the sections may worth re-considering too. For example, the Discovery and Function and Origin sections seem to make better sense to be the first two sections. Many sentences seem to need citations. e.g. "Adenosine Deaminase Acting on RNA (ADAR) and its gene were first discovered accidentally in 1987 as a result of research by Brenda Bass and Harold Weintraub." Since you mentioned the actual time and authors who discovered ADAR, it's natural for people to look for a citation to this 1987 article. Please go through the article to correct similar cases. — Preceding unsigned comment added by ChemLibrarian (talk • contribs) 15:17, 23 October 2015 (UTC) Review from GSI[edit source] Good job done in editing and modifying the wiki-page. I just want to mention few points that can be considered to improve the topic.

1. In the introduction part, the importance of A to I mutation by ADAR is not clear. It would be better if the group can briefly mention the consequences of this mutation (like, re-coding genetic information, therefore changing the translation of a specific gene, so on)

2. I think the systematic development of this article through different sections can be better organized in a different order, such as: Discovery, Origin, Types of ADAR, Function, Viral activity and then Role in diseases.

3. Lastly, the typographical errors in the link numbers under Model Organisms should be checked out.

Soumigchem (talk) 22:12, 23 October 2015 (UTC — Preceding unsigned comment added by Devon286 (talk • contribs)

New article

Hi, there is a new article about ADAR1 and the mechanism of it: [1]. נטע (talk) 07:47, 6 December 2015 (UTC)

Wiki Education assignment: Biochemistry II

This article was the subject of a Wiki Education Foundation-supported course assignment, between 17 January 2022 and 20 May 2022. Further details are available on the course page. Student editor(s): Csully222 (article contribs).

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