Talk:Poly(A)-binding protein

Peer review and responses during the educational assignment in Fall 2015
Changes to this wikipedia article were made as a project for a biochemistry class at the University of Michigan-Ann Arbor. Many editing steps were taken including peer reviews shown here for our sandbox/article. — Preceding unsigned comment added by Alexgmo (talk • contribs) 17:25, 17 November 2015 (UTC)

Poly(A) Binding Protein Peer Review 1
When first viewed your Wikipedia draft on sandbox, it was difficult to navigate through the page, as there are no visuals and introduction of the protein to capture the eyes and support the content. Thus, it needs a short introductory section before the first heading along with a 3-D figure of the Poly(A) Binding Protein to make it more visually accessible for non-experts (current Wikipedia site has it but the draft on sandbox doesn’t). Introduction may include, but not limited to, the function and the localization in an organism, and specificity of the Poly(A) Binding Protein interactions. Format-wise, the length of each section is appropriate but it would be helpful if there were more headings under contents and subcategories within (e.g. expression and inhibition of the PABP, functions of PABP in different organisms like yeast). As of right now, there are no figures added to sandbox. My suggestions on apposite figures are 3-D protein structure, a feedback mechanism of how it binds and regulates, possible mutations and its effects. High quality images with corresponding caption will make your Wikipedia page visually appealing and non-expert-friendly. First heading that details the structure of the protein seems rather technical; it may be due to absence of figures and direct reference links but I think it would only be beneficial to use slightly less technical words, but formal, for easy understandings of the readers. For example, a phrase “…binding affinities to be on the order of 2-7nM…” can be explained further. Moreover, I have noticed the use of first person word (we) in the “Rotavirus NSP3” paragraph but it is unnecessary to incorporate yourself when describing the differences in protein activity during rotavirus infection. Along the same line, the tone of voice for “Mutations” section is a concern to readers, as it sounds informal; for instance, “what makes the PABPN1 protein so different that all other genes …” should be rephrased. The content is partially duplicative of current Wikipedia page but they have expanded more and replaced “Expression and binding” with “Mutations” section. Speaking of the references, although there are at least five, I would consider them incomplete since those need to be in a correct format incorporating the author, title, etc. instead of a link. The references section can be elaborated and developed upon utilizing variety of sources other than journals. In addition, the entire draft on sandbox lacks links to respective Wikipedia pages or to external sources. Since the concepts and terms used in this page may not be familiar to all audience, this change is critical (you can do it by putting Anneskim (talk) 19:04, 20 October 2015 (UTC)

Poly(A)Binding-Protein Peer Review 2
When first reading the sandbox version of the article, it seems as if it jumps straight into the technical content of the article really quickly. Therefore, a good idea is to add a short introductory section breaking down the major specifics of Poly(A)Binding-Proteins. This section should not be technical and should be accessible to all readers. It could summarize the structure of Poly(A)Binding Protein in easy-to-understand language and also include a brief overview of Poly(A)Binding Protein function. It may also be advisable to include a graphic or image of the protein itself, whether this be a 3D image or a stick figure. The first section includes important information that is written in a concise and clear to understand manner. However, I would suggest including a graphic to go along with the words as it very descriptive and would do well when paired with a visual representation. Beyond that particular example, it would be prudent to add graphics and/or figures to the article to break up the text and make the article more interesting. Graphics and images also provide an added depth of understanding to the article for the reader. In terms of citations, most paragraph chunks have been linked to an outside primary literature source; however, there is some information that has not been cited in the first section. The article also does not link any content back to their original Wikipedia pages for further reference and more in-depth information. However, the references that are used are all primary journal sources from PubMed and contain good information. There are at least five sources, meeting the requirements of the assignment. There are no references that are non-journal sources. The lack of non-journal sources could contribute to the overall highly academic tone of the article. Overall, the article contains a plethora of good information. The authors could potentially create the 'Rotavirus NSP3' section into a subsection, as it discusses a particular function of Poly(A)Binding-Proteins. The 'Mutations' section is very interesting, and it would be nice to link the particular diagnosis that is discussed to it's particular Wikipedia page for further reference. It is slightly lacking in organization, and the paragraphs do not have an easy flow yet. The lack of images and graphics also contribute to the dry tone of the article. While the information itself is not necessarily the most exciting piece of fiction, a graphic here and there breaks up the robotic nature of the article and makes the information easier to digest. However, it provides a very good base with which to build off of and is a major improvement from the original article. Aruesch (talk) —Preceding undated comment added 23:22, 21 October 2015 (UTC)

Poly(A)Binding Protein Peer Review 3
Group 1’s sandbox seems to be on a great start for excellent Wikipedia entry. However, I think this group can focus little more on its content. First, there’s no introduction section for readers to get a basic idea of what Poly A Binding Protein is. The introduction from the original entry seems concise but vague, so if Group 1 could expand from the original introduction and make it easy enough for non-experts to understand it would great. Perhaps giving a brief description about its main functions and where they commonly found would lead to a good introduction. I like how this group included a section about the structure of the Poly A binding protein since the original entry didn’t include it. I also like how the three different components of PABPC is discussed in different paragraphs, but the content seems too technical and may be difficult for non-experts to understand. Therefore, adding pictures of the PABPC structure and links to terms that might be difficult for non-experts to understand, it would make this section more accessible. Other sections seem clear enough to understand, but I’m not getting clear of understanding of what this protein’s functions are. There’s one sentence on PABPN1’s ability to do polyadenylation of mRNA precursors in the mutations section, so perhaps adding a section for its functions and its chemical mechanisms would be ideal. In addition, in Rotavirus NSP3 section, "we" is used in couple sentences. Try to avoid using pronouns since this is an Wikipedia entry, not a research paper or a story. Otherwise, the sections that the sandbox has seem relevant and interesting. Also, the content doesn’t overlap with the original Wikipedia entry, which suggests that this group put extra efforts to discuss about different aspects about Poly A binding proteins.

As mentioned, a picture of different parts of PABPC (RRMS and PABC domain) would be helpful to understand what each components look like; for example, a picture of β sheets and α-helices of RRMs’ globular domain would be helpful. Also, pictures of symptoms and patients with PABPN mutation would give a clearer idea and dangers of these diseases.

Overall, the presentation is off to a great start with interesting headings about the Poly A Protein. I like how you guys included about the structure of the protein and the diseases that might occur with mutation of this protein. However, I think if you included the functions section to talk about its general functions and the chemical mechanisms involved in their functions, it would make the entry more interesting. Also, adding a brief introduction about the protein in the beginning of the entry would allow the readers to preview what the entry is going to be out and quickly learn the general concept before reading the rest of the entry. Finally, as mentioned in the previous paragraph, adding figures for the Poly(A) Binding Protein Structure and mutations would be helpful. Otherwise, the entry looks good so far as explanation seems pretty clear and most of the paragraphs include a reference, which makes this entry more reliable. Augus0224 (talk) 18:23, 22 October 2015 (UTC) — Preceding unsigned comment added by Augus0224 (talk • contribs) 17:21, 22 October 2015 (UTC)

Poly(A)Binding Protein Peer Review 4
Unlike the original Wikipedia page, I see that the sandbox lacks an introductory section that explains about the PAB. Although the original page lacked a lot of details, I personally think the introduction would still help a lot for the understanding of the audience. If to add the introduction section, it could just expand on the original Wikipedia page. As the original page explains what PAB is and where it is located, an information related to how significant PAB is could be helpful. For instance, it could talk about why PAB is necessary and how the regulation of such protein is influential very briefly which could definitely help the readers obtain more information and encourage them to read more throughout the page. I personally think lack of information in the introduction already loses more than half of the audience’s interest and people will move on quickly to find another site that contains more information that they desire. Also, it would be important to mention the subtitles or categories that would be discussed later on. It should briefly talk about the contents in the introductory paragraph so that the audience could expect what to read and see the correlation between PAB and the contents. For instance, a short explanation about the rotavirus NSP3 and mutation in the introduction would decrease the confusion of why such categories are important for PAB. Similar to the original page, it was confusing to read about the rotavirus without any explanation before hand. Also, including small categories in the subtitles would help to organize what is important in each categories. For instance, mutation could be divided into two categories where first one explains about the OMPD while the second one could talk about the known inhibition of mechanisms or therapeutic targets that could cure such disease. In addition, although the references were cited, it wasn't really helpful because there were no links for each citation. It would be helpful to make a link for information that was brought from a specific literature. Also, some kind of figures that relates to PAB would be helpful. Unlike the original page, I couldn't find any figures in the sandbox and I would recommend to put some figures that could help the audience to understand the PAB more easily. For instance, it could be the protein structure or the mechanism of how PAB works. Such image would make it easier for the audience to grasp the idea of how PAB works or looks while they are reading the information given. On the other hand, I thought the whole organization of the draft looked good. I really liked how the mutation section was added that talked how PAB could influence humans. Similarly, our group added how a specific enzyme could influence the human cancer by making a separate sub-section under the explanation of eukaryotic systems. I think relating these topics with human related disease definitely helps to grab the attention of people. Therefore, focusing on putting more details for each section while dividing into smaller categories would look better. Adding figures that relate to each section would definitely be a plus to the readers. Junbump (talk) 17:59, 22 October 2015 (UTC)

Poly(A) Binding Protein Peer Review 5
As I skimmed through the page, there was a general outline of the binding structure, but it seemed to lack the sufficient amount of information. The length of the page should definitely be lengthened. However, this can be done easily as the group already has the general outline completed. The introduction should be more narrowed down and explain the protein in detail. As a non-expert, I had no idea what this poly (A) protein was about and the group dove right into the subject without a clear introduction. Why is this binding protein structure important for the understanding of cellular biology? And there seems to be an important factor RRM, which is also lightly dealt with. What are these motifs really for and how do these relate back to the function as a whole? I liked how you talked about the studies, but again, they are explained in little detail. Moreover, there should be lots of figures as the page looks so much cooler with pictures and graphs! You also talked about the PAIP 1 and eRF3 and other motifs. They should be explained with pictures to allow the readers to understand where the localization occurs. Perhaps you could explain the relationship between the structure of the protein and its function. You also should talk about the regulation of this protein to enhance the quality of this page. I liked the examples of Rotavirus and mutations like OPMD, but these should be explained in details. They seemed a little vague because they sound more like an abstract instead of a full explanation. For example, you mentioned that PABPN1 mutation causes OPMD, but what this protein is should be with more detail. You can also add subsections under big three categories to organize your page better. Also, you should have direct hyperlinks, so we can refer back to already existing pages to have more background information. The Mutation section has some repetition, which can easily be fixed later. Finally, you have 5 references, including non-journal articles. They should be in the right reference format. Overall, you guys are in the right track, and just continue to work on it!

limjiho18Limjiho18 (talk) 18:38, 22 October 2015 (UTC)

Review from GSI
1. The group has done a good job in modifying and adding information to the existing page of wikipedia. However, I feel that they could have add few more sentences to the introduction. A brief overview on the significance of PABP and its activity would complete the picture about this protein at the introductory level.

2. There are couple of different terms in this sandbox which need to be connected to the associated wikipedia pages already existing (e.g. RNA recognition motifs/RRM, eRF3, eIF4F, 5′ cap, 3′ poly A etc.).

3. Technical terms and phrases like "co-immunoprecipitation", " CV1 cell cDNA library" can be too hard to digest for the general readers. Try to explain the term briefly and connect them to the wikipedia pages if existing.

4. The heading "Mutations" would be better if changed to the heading as "Diseases associated with PABP". This would simplify the approach of the section to general readers as it is giving a broader impact regarding this protein.

5. Under the " Mutation" section, the flow of the story does not seem fluent. It would be better, if the general information (e.g. symptoms and age of occurrence) are mentioned first followed by the detailed molecular insights of the mutation (i.e, if the second paragraph can come before the first one).

— Preceding unsigned comment added by Soumigchem (talk • contribs) 00:14, 23 October 2015 (UTC)

Suggestions from ChemLibrarian
Good job with adding three sections to the original article. Here are my suggestions for improvement.


 * 1) As pointed out by other reviewers, you need to have a introduction section ( a lead section in Wikipedia term). I understand that you may be thinking about using the lead section in the original article Poly(A)-binding protein. Please move it here and improve that lead section.
 * 2) Your section, Rotavirus NSP3, also exists in the original article Poly(A)-binding protein. I see that you did not use any of the existing content in the original article. It's not a good practice. Imagine that 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.
 * 3) In fact, when you move your article to the formal space, please do not just overwrite the current content with yours. Instead, incorporate your sections into the current version.
 * 4) I see that you have not added any images to the article yet. Please check out slide 21 and 37 of the Slides for Wikipedia Editing Basics I posted on the CTools site for link to video tutorials and notices about copyright issues.   — Preceding unsigned comment added by ChemLibrarian (talk • contribs) 13:29, 23 October 2015 (UTC)
 * 5) The references you added are not in the right format. Please watch the two video tutorials linked below and revise your references. Your peers also have pointed out that you may need to use some references besides journal articles. Here is one suggestion to diverse your references. If you rename the section Mutations to Diseases associated with PABP as suggested by your GSI, you may be able to find some news articles or webpages from Mayo clinics etc. about relevant diseases.

ChemLibrarian (talk) 13:23, 23 October 2015 (UTC)

Responses
We plan to incorporate images for the article, improve on the introduction, incorporate original content from Rotavirus NSP3, ensure references are in the correct format, change mutations section to "diseases associated with PABP", improve general flow of material, and also connect terms such as "RoXan".

For the structure section, we plan on adding in a figure correlating to the specific RRM motifs talked about. We will also add in more references so people can go look into more detail if they want.

For the Rotavirus section, Rotavirus NSP3 could be developed as a subsection. Need to Address how it is involved with Poly(A)-Binding Protein. Can Chang the title to “Rotavirus NSP3’s Involvement with Poly(A)-Binding Protein” Also can expand on original content of how it evicts the Poly(A)-Binding Protein from eIF4F.

For the mutations section, we plan on changing the name to diseases associated with and making sure to link terms to other wikipedia articles. We also need in a short section on future research where someone can go learn more.

Overall, we need to make sure to incorporate previous information from the wikipedia article into ours without deleting any of it. — Preceding unsigned comment added by Alexgmo (talk • contribs) 19:07, 17 November 2015 (UTC)