Talk:Prp8

prp8 Peer Review 1

Is the introductory section accessible for non-experts?

It does well to give a brief look at what prp8 is but I would maybe want to see a little more description just about what role it plays in the spliceosome instead of another over of spliceosome and what it does in the cell. You mention molecular rearrangements and maybe you could expand a little bit on that if possible. However you do a very nice job of explaining the concept of the spliceosome and what it does in a very concise manner which anyone with a very basic understanding of biochemistry can understand.

Do the contents of each section justify its length?

The background section is very statistical and short and I am maybe wondering if that could all just be put into a certain chart like in the top right corner giving a quick description. If you feel that is not possible, then I would just leave it the way it is. I think this deserves its own section though just because it is a certain aspect that people might be looking for when coming to the Wikipedia page, and therefore would not want to combine it with another section. You may also be able to take the section about deficiencies and make it a subsection on mutations just to make it more logical in terms of the setup of the page. I do think that the role in splicing is a very important section and it is covered well by you all, and the length definitely warrants the section there.

Are all the important terms/concepts linked to their respective Wikipedia pages for further reference?

Your Wikipedia page does a great job of linking to different important terms which makes it easy to get a grasp of what you guys are talking about just because I can quickly check a term that you guys might mention. The one other that I might link is the term Pre-MRNA. I’m sure a lot of people have heard about mRNA but might be confused as to what a pre-mRNA is and what function it serves in the whole transcription-translation process.

Are the highlighted examples appropriate?

I’m not sure what Dr. Walters means by highlighted examples, but I do like that you guys link to other pages at the very end that relate to the page you guys are doing and help to give your protein/gene more context. I also do like how you guys showed a real example of what happens when this mutation actually comes about and what consequences are shown from it. I think this is very important to give the reader a better understanding of how important this mutation is and what effects that it could have.

Is the content duplicative of any other content already on Wikipedia?

While searching for prp8 or anything related to it, I could not find it on Wikipedia and therefore I do not think this information is duplicated on Wikipedia making it an excellent source of information for others.

Figures

There were no figures and this is most likely due to the fact that a lot of the structure pictures are copyrighted. I would just recommend putting in a picture of the structure which can be done using a program on your own so you don’t have to worry about copyrighting. I’m sure you guys have already discussed this and were just pushed for time on the rough draft and worried about copyrights.

Are the references complete (≥5)?

There are definitely enough references here and they cover a wide range of topics within prp8. Each section has a link to the reference although I am not seeing it for the deficiencies section. If you have already cited that reference once, you might want to just add it in again at the end of that paragraph as clarification for the reader on where you got that specific chunk of information.

Are the references inclusive of non-journals sources?

While going through your references, they all seem to be from various journals although I may be mistaken. You guys could try to gather a little bit of information from a textbook or even a basic government website that might give a little bit of insight into the prp8 protein/gene. It just seems that most of the information thus far is coming from very technical journals, which may not be the best thing if this is the sole source of your information.

Overall Presentation

I felt that your Wikipedia page’s layout was outstanding. The introduction looks good. I like that you have a small table in the right that can be added to and there is a quick reference for contents. I also think you all chose three good sections or topics that would be a great starting point for this Wikipedia page. Hopefully in the future, people will expand on prp8 and hit other topics that it relates to. The references were not lacking although you might want to expand into other sources of information. I also appreciated all the links from the page making it easy to understand the concept, by just being able to quickly read about something on another page.

The major things that I would make sure that I have is of course a figure which I am sure the group is working on before the final product is due, and then maybe expand a tad more on the introduction. You do a great job of talking about splicing but not really about what role prp8 actually plays in the spliceosome. There is just a quick mention about rearrangement. You could also morph together deficiencies and mutations into one section just to make it more concise. Overall I think this is a well done article, and just needs a few changes like the adding of the figure and possibly adding onto the introduction.

Alexgmo (talk) —Preceding undated comment added 04:38, 19 October 2015 (UTC)

Peer Review 2

Upon reviewing Group 2 Wikipedia page, the introductory section clear and concise. The authors address where Prp8 is found, what its central role is and how involved the protein is with the spliceosome. The introduction is easy to follow for those familiar with transcription/translation. The contents of each section for the most part are justified, with an exception to Phenotype mutations of Prp8 across species. Identifying the species C. elegans Prp8 being linked to reproduction and development is important, it just seems that the authors cited the papers for the viewer to further investigate. Perhaps in this section add more on what the abstract of each of the papers are starting to address, this could better correlate with the Mutation paragraph above.

Pertaining to the important terms/concepts of the Wikipedia page correlate well with the content provided. Prp8 resides in the catalytic core of the spliceosome, the authors link spliceosome, introns, exons, and PTMs. All of these links are appropriate ranging from the experienced reader to the inexperienced reader. Another important link the authors included was the RRM, this was helpful in analyzing the structure of Prp8 and understanding the chemical properties. The highlighted examples as mentioned earlier are appropriate, the authors should add links to co-immunoprecipitation and western blot techniques when talking about Prp8’s role in splicing to satisfy all types of readers. The authors did their best in terms of not duplicating any other content on Wikipedia. Any data attempted to search came right to the sandbox, maintaining the integrity of the page.

The figures of Prp8 are of good resolution. When following the links to the images, they’re from RCSB PDB, where many crystal structures of Prp8 range from 2.00 angstroms to 3.60 angstroms. The crystal structures/Cryo-EM structure of Prp8 were detailed, from what can be analyzed no discrepancy in R factors. When describing Prp8, it would have been helpful to have a figure specifically pointing out where RRM, MPN/JAB ubiquitin binding domain, and NLS are on the protein. Overall, the pictures have great resolution, R factors correlated. The crystal structures appeared to be accurately refined.

The author’s Wikipedia page contains an adequate amount of references. However, five out of the eight references pertain to the Phenotype mutations of Prp8 across species. If the author were to add more references on the Background of Prp8, this could help further validate their data researched. The references are all from journals published by other authors on subject material pertaining to Prp8. These are reliable references, as some of the references are recognized by Nature.

Overall, the Wikipedia page on Prp8 is off to a great start. The authors focused on the core data of Prp8. Data such as background, Prp8’s role in splicing, what Prp8 is composed of, and diseases associated with the mutation of Prp8. The organization of the Wikipedia page is easy to navigate and flows well. The authors need to link co-immunoprecipitation and western blot when referring to common research methods of Prp8. Further background research on Prp8 with additional references would further validate their Wikipedia page. Specific identification of RRM, MPN/JAB ubiquitin binding domain, and NLS on Prp8 would be helpful, along with having at least one of those available protein structures on the Wikipedia page.

Dwcolli (talk) 22:13, 21 October 2015 (UTC)

Peer Review #3

Content

• Is the introductory section accessible for non-experts? I believe that the introductory section is satisfactory for someone that is not an expert in the field. This is because most everything is hyper linked to some other page that describes important concepts and what the Prp8 protein function is. An additional link that could be added is on for mRNA, and also expand more on the molecular rearrangements that occur.

• Do the contents of each section justify its length? I believe that this page length and description are meeting the rules and guidelines for how far they are in the editing process. I believe as time continues the length, description, and quality of the page will be increased. The only section that I think could be lengthened for where they are at in the page so far is the location and Genomic sequence.

• Are all the important terms/concepts linked to their respective Wikipedia pages for further reference? Most everything that needs to be linked is. In the Mutation section, it seems beneficial to link what exactly a missense mutation could be given that there are multiple types of mutations.

• Are the highlighted examples appropriate? If by highlighted you mean linked then yes, however if you mean the highlighted topic example such as the structure of Prp8, or others then again I think that the location and genomic sequence can be more in depth.

• Is the content duplicative of any other content already on Wikipedia? No, not that I could find.

Figures

• Are the figures original and of high quality? The page uses links to the figures, which is fine except I think that there is actually supposed to be a figure on the page. Since they do not have any on the page, they could include a .pdb image screenshot or something of that nature that does not violate copyrights laws. Also if it is possible a 3d image would be nice or multiple 2d images to show active sites and pockets.

• Are the figures informative and add to the text? The links to the figure are very good and are credible. I believe that the link showing the Pdp8 structure PDP 4I43 is great , but like I said before above, and also taking into consideration that maybe the user does not have PyMOL, integrating a rotational view is desired if possible.

• Are the substance and/or protein structures chemically accurate, aligned, and easy to read? Again, it seems so, however a figure or representation of the file instead of just a link may be a good idea if it does not violate any laws. The resolution when following the links is very good.

References

• Are the references complete (≥5)? They are of good quality, numerous (8), and from credible sources.

• Are the references inclusive of non-journals sources? Yes. The references are of good quality but I don’t know if I am being picky here, I would like to an encyclopedia or textbook reference available.

Overall Presentation

• Provide a short summary of the entire content/figures/references, highlighting both what the group did well and well as what still needs to be improved.

The work done completed so far is excellent. The web page is well laid out regarding the format. The table of the Crystal Structure of Prp8 is in a good position, but more could be added to preview the structure. The topics covered such as the introduction, background, location and genomic sequence, role in splicing, mutation, phenotype mutations of Prp8 across species, Deficiencies, and the references were thought out carefully and only minor modifications are needed. As mentioned previously, the missense mutation, structure, and mRNA, can use some more detail. Another thing that could be expanded on for a more complete idea is the molecular rearrangements that occur I like the detail of the disease that is caused by the mutation in the protein is mentioned because it gives a more practical sense to what why this protein research is important. Your references seem well documented and credible, but as I mentioned before I would personally like to see an actual book being referenced.

Formulev (talk) 19:12, 22 October 2015 (UTC)

 — Preceding unsigned comment added by Formulev (talk • contribs) 18:21, 22 October 2015 (UTC) 

Suggestions from ChemLibrarian

Good job with creating a new article. Here are my suggestions.

1. Please consider combine the Background section with the lead section. If you make the background section a little more concise, I don't see a reason why it has to be a separate section from the lead section.
2. It's great that you start to use a Info Box template for protein. If you haven't found it, please follow the directions on this page Template:Infobox protein to fill in the template.
3. Your references appears to right. But I don't think you have formatted it correctly. Please watch the following video tutorial and revise the reference formatting. Let me know if you need additional help.

ChemLibrarian (talk) 15:00, 23 October 2015 (UTC)

Review from GSI

Soumigchem (talk) 21:39, 23 October 2015 (UTC)

The page is well written and the development of the topic is reasonable. I think it only needs a few minor changes.

1. In the introduction part, it would be better to introduce the Prp8 protein first, as a large, conserved and unique protein and then talk about Prp8 gene.

2. While talking about background, it would be easier for the readers if they can get the acronyms of USA2, DBF3 and SLT21.

3. A schematic diagram of the splicing process, highlighting the step involving Prp8 protein, can give a better and more clear picture of the activity of Prp8 protein.

4. The location of Prp8 gene is mentioned twice, one in the Background and other under the subsection Location and genomic sequences. I think it should be good enough to mention it once, may be under the subsection 'Location and genomic sequences'. Besides, I think the coordinate numbers of Prp8 gene on chromosome is unnecessarily complicating the content.

5. Lastly, to maintain the proper categorization of different subtopics, I would prefer to put Mutation and Deficiencies as subsections under a general heading Diseases associated with Prp8.

How we addressed peer critiques

Our peer critiques offered helpful suggestions that helped us edit our Wikipedia draft and produce the version you see here. Most of the suggestions were minor edits that we quickly implemented. Major areas of feedback were about the lack of original figures, organization and redundancy of sections, and the limited amount of non-journal references used. We tried to address some of these concerns with our edits, summarized below.

Introduction We received feedback that some of the information in our History and lead section was statistical and could be moved to a table, so we inserted an Infobox at the top of the page to incorporate some of the information in an easier to read format. We were unable to track down the organisms or the meanings of the abbreviations that the aliases came from, so we incorporated them into the Infobox as well and this is an area that future Wikipedia editors could continue exploring. We also originally had a very brief section on the location of Prp8 and one of our critiques pointed out that this information was redundant elsewhere in the article, so we deleted this section and incorporated the information into the Introduction and History sections. We also chose to slightly expand the History section to justify it being separate from the lead section.

Mutation Section Based on the feedback, we reorganized this section to be clearer. We changed the header titles and made "Deficiencies" and "Phenotype mutations of Prp8 across species" subsections underneath the broader "Mutations" header.

Variety of Sources Our peers acknowledged that we only cited primarily journal articles. To address this lack of variety in our sources, we incorporated information from a biochemistry textbook as well as an internal WikiGenes website page in the "Role in Splicing" section.

Figures Our original figure was pulled down for copyright reasons. After discussing with our peers, we decided the most helpful figures would be of the crystal structure (highlighting some of the important domains) and a splicing mechanism diagram. We generated original crystal structures through PyMOL (highlighting important structural domains and binding regions) and created a mechanism diagram that highlighted Prp8's specific role in splicing. We included this diagram to address some of the questions our peers had about what molecular rearrangements occurred within Prp8 and the spliceosome during the splicing process.

Minor Edits There were basic changes that others pointed out in the peer reviews that were simple to correct. We reformatted some of the references to match Wikipedia guidelines. We renamed the "Background" section as "History" to better match Wikipedia's common formats. We linked additional terms to existing Wikipedia pages, like pre-mRNA, immunoprecipitation, missense mutation, and Western blot. We rephrased the lead section so that Prp8 gene was introduced before Prp8 protein.

Duplicate?

It seems this article is a duplicate of PRPF8.

--~~~~ SleepyWaterHog (talk) 20:33, 6 May 2023 (UTC)