Talk:Protein inhibitor of activated STAT

message: I checked the DOI for reference #9, and that is the correct number listed in the article. However, when I click on the DOI link, it takes me to an error page. I am not sure how to resolve this one. Perhaps we should just remove the DOI number/ link but keep the rest of the reference?
:The DOI link for reference 9 should take you to the correct page. --Jocelyn Munson (talk) 20:59, 28 April 2014 (UTC)
thread_title: References

message: I found an image of PIAS3, but I think we need permission to use it. What do you think? --Jocelyn Munson (talk) 20:56, 16 April 2014 (UTC)
replies: text: I agree- I think that we would need permission. As I understand it, papers may be open access, but the content and images are copyrighted, and permission would need to be obtained.--Catwell99 (talk) 02:37, 23 April 2014 (UTC)
replies: text: Since this image has not yet been published in any scientific journal, and it hasn't been released into the public domain by its creator, I doubt we'll obtain permission to use it.--Jocelyn Munson (talk) 21:49, 28 April 2014 (UTC)
thread_title:  Images 

message: I added a few sentences to the lead section. I also plan on creating an image illustrating the conserved domains of PIAS, which will be uploaded soon. --Jocelyn Munson (talk) 23:17, 20 March 2014 (UTC)
replies: text: I added a preliminary summary of the PIAS protein function. I'll start work on the related disease area soon. --Catwell99 (talk) 03:47, 26 March 2014 (UTC)
replies: text: I think we should get rid of the mechanisms section. It can be a subsection within the functions section as needed. What do you think? --Jocelyn Munson (talk) 23:45, 7 April 2014 (UTC)
replies: text: Makes sense. I was struggling with having both the functions and mechanisms section. It does seem redundant. I'll remove the mechanisms section.--Catwell99 (talk) 00:24, 9 April 2014 (UTC)
replies: text: Are you going to add to the "applications in disease treatment" section? I don't think I'll have time to start it tonight. --Jocelyn Munson (talk) 01:18, 9 April 2014 (UTC)
replies: text: Yes. I'm working on the application in oncology currently (offline). I'll post it soon. --Catwell99 (talk) 02:11, 9 April 2014 (UTC)
replies: text: I started the structure subsections. They're not finished (obviously) but I didn't want to leave them blank. I'm done for tonight, but feel free to edit any subsections I've worked on. By the way, I added the progress report to our group page. Have a good night! --Jocelyn Munson (talk) 03:06, 9 April 2014 (UTC)
replies: text: Thanks Jocelyn! BTW- I came across a reference which mentions 5 mammalian PIAS proteins instead of 4. Should we update the Wiki article accordingly? The article that I came across lists the following as members of the mammalian PIAS family: PIAS1, PIAS3, PIASxα, PIASxβ, and PIASy. PMID for this article is: 12773095  --Catwell99 (talk) 04:17, 9 April 2014 (UTC)
replies: text: PIASxα and PIASxβ are isoforms of PIAS2 (also known as PIASx). I didn't want to get too technical in the lead by listing all seven known PIAS proteins. So I just listed the main four, and wrote "apart from PIAS1, each PIAS protein has two isoforms." But feel free to edit it if you want to. Also, SabFernMB suggested making a table highlighting the structural differences between each protein. What do you think of this idea? --Jocelyn Munson (talk) 19:24, 9 April 2014 (UTC)
replies: text: Sounds good. I think that we should also incorporate a picture regarding the function as JHayes suggested. --Catwell99 (talk) 01:56, 16 April 2014 (UTC)
replies: text: In addition to more pictures, I think that we may be able to make some of the language a bit more accessible to the general public on the next review and contribution. What do you think?--Catwell99 (talk) 02:04, 16 April 2014 (UTC)
replies: text: I agree, we should make the language more accessible. --Jocelyn Munson (talk) 18:58, 16 April 2014 (UTC)

text: Reference 29 needs to be fixed because it was never defined.--Jocelyn Munson (talk) 21:01, 28 April 2014 (UTC)

text: This should be fixed now. (It is now reference 36.)--Catwell99 (talk) 00:08, 7 May 2014 (UTC)
thread_title:  Progress 

message: Over the next several weeks, Catwell99 and I plan on improving this article. Sections to be added include: history, structure, mechanisms, functions, application in disease treatment, and current research.  We also plan on expanding the lead section, and adding relevant images and tables.  This is the first time either of us have edited a Wikipedia article, so any feedback is welcome! Jocelyn Munson (talk) 23:37, 11 March 2014 (UTC)
thread_title:  Improvements 

message: It looks like you've researched this topic thoroughly! Here are some suggestions about how you might further improve the article:
#Empty sections should be either removed or populated.
#All information in the lead should also be present in other sections of the article; the lead acts as a summary of the article, and therefore does not require citations.
#When citing specific information from multi-page sources, page numbers should be specified.
#A "Further reading" section listing books on the subject would be beneficial.
#It would be helpful to add more wikilinks to other relevant articles, particularly in the "Functions" section.
#Be sure to write the article in such a way that members of the general public will be able to follow; terms like "homologues" should either be wikilinked or explained.
#If the section is called "External links", then there should be more than one link.
You've done a good job to start off. Let me know if you have any questions on the above. Neelix (talk) 04:39, 31 March 2014 (UTC)
replies: text: Thank you for the feedback Neelix! We've worked on the wikilinks, but could probably improve the language to make it a bit more understandable to the general public. Also, we'll work on the references to make sure that we reference the pages from books. --Catwell99 (talk) 02:02, 16 April 2014 (UTC)
thread_title:  Review by Neelix 

message: # A good start to the lead section as it contains information on function and applications.  You may want to include information on history, mechanisms and structure to provide the reader with an overview of the main points of the article, as outlined in the table of contents. 
#The table of contents clearly outlines the main points of the article, and direction in which the article is going.  
# Each section is coherent, in accordance with the section headings.   
# History Section: you may want to add information on who made the discovery, and how the discovery was made.
# Structure: you may want to include a table summarizing the differences/similarities in protein structure for each of the seven known proteins. 
# Good start on wikilinking, and reference section.
# Reference 1: looked up the link provided and it only provides the abstract, which does not clearly indicate the source of the information provided in article. For example, the first sentence indicates that PIAS interacts with at least 60 different proteins.  Could not find this information from the abstract. You may want to replace the reference link with one where the whole article is easily accessible, and clearly supports the information provided.SabFernMB (talk) 00:48, 2 April 2014 (UTC)
replies: text: Great comments! Regarding the closed-access article, it's such a great source that I'll probably keep referencing it.  But I'll try to reference open access articles that support the same information. Also, the lead section probably won't be completed until the article is close to being finished. --Jocelyn Munson (talk) 23:34, 7 April 2014 (UTC)

text: Forgot to mention this earlier, but making a table sounds like a good idea. As we gather more information on each protein, we'll probably end up making one. --Jocelyn Munson (talk) 19:28, 9 April 2014 (UTC)

text: I made three tables! Let me know if you find them helpful.--Jocelyn Munson (talk) 00:13, 23 April 2014 (UTC)

text: The tables are informative and easily to understand. Great job!01:17, 23 April 2014 (UTC)
thread_title:  Comments from SabFernMB 

message: Overall you have a really good start, just need to expand and explain more. Here are my comments: 
In the lead section, the portion about the specific PIAS genes and proteins might be too specific/technical for the lead. Maybe make a new section to overview the different members of the PIAS family?
The history section needs to be expanded on; as it stands I don't think there's enough information to warrant its own section. The last two sentences sound a bit fragmented, you might want to combine them.
The structure section needs to be clarified, there's too much unexplained jargon as it is. Links or brief descriptions of the domains/motifs would be helpful. If possible, explanations of what the different domains/motifs do for the protein, like the one you have for SAP, would be useful. The image you have is good; if you can find an image of a 3D structure it would help further visualize what these proteins look like.
The functions section could use some wikilinking. Gene expression, transcriptional co-regulator, ubiquitin, and DNA repair could all use wikilinks. Further explaining how PIAS proteins are involved in gene expression and DNA repair is also needed.
I'm sure you know that you need to put information in the mechanisms and applications sections. However, it might be unnecessary to make mechanisms and functions different sections. It might be easier to understand and follow with a structure like "this mechanism performs this function" all in one section. Just something to consider, it's hard to say if it's better without having any information in the mechanism section to go off of. The applications section is really important, it'll most likely be what someone wants to know, so definitely keep that section and go into detail.
The see also link to the JAK-STAT pathway is good, but there should be at least some mention of it in the article itself, so a reader might have some idea of why it's related.
There are plenty of references, and many of them are used more than once, which is good. Try to use as many open access articles as possible; the first reference is closed access and the one you've cited the most, which makes it hard to verify or get more in depth information. The inline citations are good, there's no ambiguity about which article supports which statement.
Hope you find my comments helpful! Lisawisa (talk) 01:27, 2 April 2014 (UTC)
replies: text: They are helpful! I definitely agree about combining the mechanism and function sections. That's a good idea. The way the structure section was written was too complicated. I'm going to break down this section into subsections. And you're right, I should mention the JAK-STAT pathway somewhere in the article.  My partner began the functions section, but I'll add in wikilinks. --Jocelyn Munson (talk) 23:41, 7 April 2014 (UTC)
replies: text: Really impressed with the changes you've made to the structure section. It's a lot clearer now, and I like how you explained the purpose of the domains/motifs. In the discovery section, you might want to give a general date when they were discovered, so people can get a general idea of how long we've known about these proteins. In the functions section, can you further explain how they're involved in gene expression? Overall, you guys have really made a lot of improvements, keep it up! Lisawisa (talk) 02:13, 16 April 2014 (UTC)
replies: text: I added dates to the discovery section. --Jocelyn Munson (talk) 00:10, 23 April 2014 (UTC)
replies: text: Everything's looking really good! The tables are a great way to display the structural differences. FYI, there's an error with reference 29, it's not showing up right. Lisawisa (talk) 20:47, 29 April 2014 (UTC)
thread_title:  Comments from Lisawisa 

message: The leading section was great. The subject was defined in the first sentence, bolding was done well, it explained the notability with the last paragraph of the leading section and there are a good amount of links to other articles. The leading section was put in general terms which is great for readers. There is a slight redundancy in the second and third sentences of the first paragraph and the last two sentences of the first paragraph could be combined to make them slightly more effective. A picture next to the leading section would be a great addition and really draw positive attention to the article. 
Great job with the sources! A vast majority of your sources were free to the public which is great for people that need to read more into the information they find in the article. There is a great population of articles from different years which is great for representing the history of the research while still including some very recent articles from the past few years. It might be important to point out that the first and 17th source are the same source, so it might be beneficial to combine them. Otherwise, the sources look good. 
The writing overall is pretty well done. There are a few places where some further explanations could be beneficial. I made two suggestions for the leading section. A bit more in-depth history of the discovery of proteins would be nice. How was the discovery made? How soon was "soon followed"? Also, the second paragraph is a run on sentence. For the structure paragraph, is it possible to find the sizes of PIAS proteins 2 and 3? It would be nice to see a comparison between the proteins and their isoforms, such as an explanation of what each one does and how they differ. A bit more description of the RING domain, AD and SIM, and S/T region sections would be great as well. The Functions and disease treatment sections are well written! There isn't too much jargon in your article which is really great and the information provided in each section seemed to fit well. There aren't many gaps, but a few more in-depth facts in the previously mentioned sections would really help out. I think the construction of the article is well done. The sections seem to be in a good order for comprehension, but i do suggest putting in a few more facts about the proteins and their respective isoforms in the structures section. It would give a lot of great information and would even help in explanations for other sections. In terms of perspective, the article does well with sticking to a neutral point of view. It presents the facts in an easy to understand construction and does so well. Great job on the article so far!BigA726 (talk) 00:30, 14 April 2014 (UTC)
replies: text: Thanks for reviewing the article! I agree; the Structure section definitely needs more work.  Comparing each isoform is a good idea, and we plan on doing that.  More details will be added to the Discovery section as well.  We will clean up the redundant writing when the article is close to completion. By the way, I combined the 1st and 17th source.  Thanks for pointing that out! --Jocelyn Munson (talk) 21:21, 14 April 2014 (UTC)
thread_title:  Review by BigA726 

message: Great Job! couple of comments...
# Lead/Style: Your intro, headings, and style are all well done.  The writing is certainly very clear and concise, yet very informative.  You all have done a great job on the linking. My main suggestion here would be a picture. The first impression when you see the article is there is a lot of text (obviously until you scroll down and see the pictures) Perhaps a simple picture close to the heading?
# For the Discovery, a brief summary of the experiment that served to discover, or if not easily done, perhaps an example of "typical" experiment done. I feel this would go a long way in helping the reader to envision what is going on and what steps were taken to discover this critical step. Another idea would be to incorporate data or figures from the initial experiments that lead the scientists to discover/draw the conclusions they did. 
# Structure: The simplicity and sectioning down here I would not change. It does a great job taking technical concepts and highlighting important points. The biggest contribution here would be simple pictures, the ones you have are great. For instance a pictures that I think would help to describe would be a membrane diagram of PIAS proteins moving in nucleus. Perhaps a simpler one like this highlighting PIAS - http://www.nature.com/nrm/journal/v4/n9/fig_tab/nrm1200_F3.html 
# Function: Again, flow chart-like image to help? Perhaps something like this http://www.nature.com/cr/journal/v16/n2/fig_tab/7310027f3.html#figure-title
# Your references look great.  the sources and dates are well varied, and the majority are public - again, great.  
#  Your topic is very "connected" as such, has been well described in the article - I would expand on the "see also" to include more of these connections.  Things like NF-κB and p53 are first ideas that come to mind.
Overall, this looks great!.  One last thing is I think you all have done a wonderful job on interacting with the talk pages and incorporating the suggestions into the article thus far - this certainly made it hard for me to find even more suggestions :) Jhayes21 (talk) 15:13, 15 April 2014 (UTC)
replies: text: All great suggestions. The external links are very helpful, thanks! We definitely plan on adding more images.  As we make these changes to the article, let us know what you think. --Jocelyn Munson (talk) 20:36, 15 April 2014 (UTC)

text: Thanks for the feedback! I agreed that we should add some pictures in regarding the function. I like the picture that you provided through the link. We'll have to incorporate something along those lines. --Catwell99 (talk) 01:54, 16 April 2014 (UTC)

text: Unfortunately, I didn't have a chance to create any images before the third contribution deadline. But I definitely plan on creating at least one before the semester ends. Regarding the Discovery section, I think writing about the experiments they did would be too complicated, but I included a wikilink. Also, finding an image for the lead section is proving to be difficult. --Jocelyn Munson (talk) 00:26, 23 April 2014 (UTC)
replies: text:  Looks awesome! the pictures and rearrangement you all have done looks great!  The wikilinks for experiment was a good idea instead.  Nice job again! Jhayes21 (talk) 21:38, 6 May 2014 (UTC)
replies: text: Thanks! Paraptosis looks great too! :) --Jocelyn Munson (talk) 01:49, 7 May 2014 (UTC)
thread_title:  Comments from Jhayes21 

message: Hi guys, great job so far! Here are some suggestions and other comments for you as you finish out the semester.
* Nice job linking important terms! That is very helpful for glossing difficult language.
* That said, you could maybe do a little more glossing in the lead of the article - it's a little short in comparison to the body so you have some wiggle room to explain in a little more detail. It's much better though!
* One guideline I want you to be aware of is on medical reliable sources. We have stricter regulations for referencing articles that cover medicine; the one that's relevant here is that you need to have articles from the last 5 years, preferably review articles. Ogata et al and Brantley et al are a little old. 
* I ran a plagiarism check and only found one instance of sorta-close paraphrasing, which is super easy to fix - the sentence "Furthermore, in a retrospective study of advanced gastric cancer patients who had received second-line docetaxel-based chemotherapy, patients who had high or intermediate levels of BRCA1, PIAS1, and PIAS4 showed longer survival." just needs a little bit of rewording.
* With regards to the review requirement of MEDRS, none of the papers you cited in the medical applications section is a review paper. If you could hunt through the articles that reference those and look for review articles that include the same information, that would be the best way to go about it. If that doesn't work, try to find different review articles that have similar/the same information and incorporate those instead.
Good luck, and let me know if you have any questions! Best, Keilana|Parlez ici 00:18, 17 April 2014 (UTC)
replies: text: Thanks for your review! I agree, the lead could be expanded further. We'll do that on our final contribution. I'll let Catwell99 make the necessary changes to "Potential applications in disease treatment" section since she wrote it. --Jocelyn Munson (talk) 00:39, 23 April 2014 (UTC)

text: Thanks for the feedback. I'll make the change to the potential applications in disease treatment section that you mentioned. Regarding citing review articles, I haven't seen any review articles on the subject of PIAS proteins when searching pubmed. There are some review articles which mention PIAS (e.g. review of IL-6 pathway), but they aren't specifically focused on PIAS.--Catwell99 (talk) 02:43, 23 April 2014 (UTC)
replies: text: I found a review article that you might find helpful: PMID: 20197240. --Jocelyn Munson (talk) 21:31, 28 April 2014 (UTC)
thread_title:  Review from Keilana 

message: Hi, very nice job on this article!
* Very nice job on the lead. It is written at a comprehensible level, is nicely wikilinked, and flows well.
* One question:  why the "activated" in the acronym?  It is not immediately clear.  Maybe you could mention the reason in the "Discovery" section.
* In "Structure", rather than jumping right to motifs and domains, could you add an introductory sentence or two that describes the state of knowledge about the structure, and/or what the overall structure is?  For example, has it been completely solved for each of the proteins?
* I really like your summary tables.
* I would put "Function" before "Structure".
* (Minor) I'd suggest changing "Potential applications in disease treatment" to just "Potential applications".
* If you have time, you might think about adding .  For a protein family like this, I am not sure how to apply it.  You could first check the template's documentation, or see if there is guidance on the gene and protein article style guide, and failing that, you could ask on the project talk page.
Klortho (talk) 19:40, 27 April 2014 (UTC)
replies: text: Great suggestions, thanks! We will address each of them in this last week. Funnily enough, I never considered why "activated" is in the acronym, but I'll be sure to look it up. Jocelyn Munson (talk) 20:52, 28 April 2014 (UTC)

text: Thanks for the review! I'll update the "Potential applications in disease treatment" to "Potential applications" as you suggested. Regarding your question on "activated" STAT, cytokines interact with a janus kinase receptor (JAK) which in turns promotes phosphorylation of the STAT transcription factors. This phosphorylation is what is meant by "activated" and allows STAT to form a dimer. This phosphorylated dimer is then transported into the nucleus to bind to the promoter of cytokine-inducible genes. The STAT protein Wikipedia article gives a pretty good summary. --Catwell99 (talk) 02:50, 30 April 2014 (UTC)
thread_title:  Comments from Klortho 

message: You really have a great looking article.  I like the pictures you have and the tables help to display the information and make it much easier to follow and less complicated.
* Do you know by whom or where exactly it was discovered?  This could be something to add to the discovery section.  If it is a specific person/group it might be nice to add a picture of them to, if you can find one.
* In the structure section some of them are labeled domain or motif in the subheaders and some are not.  I would standardize this and do it for all of them or none.
* You have a good number of references and seem to link other Wiki articles well too.
* You mention cancer, autoimmune dieseases, and obseity in the introduction as potentials to use to fight against.  However in the potential applications for disease treatment section you only talk about cancer.  Can you find any information on autoimmune dieseases and obseity?
Tmckenne (talk) 00:53, 29 April 2014 (UTC)
replies: text: Thanks for your review!  I do agree with you on the structure subheadings, and they will be fixed. I didn't consider adding a picture to the Discovery section, but if I find one, I'll add it. Information on the other diseases will be added.  If not, I'll reword the lead section. Thanks for pointing that out. --Jocelyn Munson (talk) 00:13, 30 April 2014 (UTC)

text: Thanks for the review! Great idea regarding the discovery section. I am not sure if there is a picture available, but we can look. Regarding the disease potential, we do mention the potential in autoimmune disease but perhaps this needs to be called out more explicitly. The pathways involved (e.g. IL-6 and JAK1) are well-known autoimmune/ inflammatory disease pathways. --Catwell99 (talk) 02:39, 30 April 2014 (UTC)
thread_title:  Review by tmckenne 

message: Overall, you've done a nice job with the article, and there is a lot of useful information within.  I've provide some specific comments below that should help you to refine the article in advance of next week's deliverable.
Specifically
* Would be good to mention the impact on gene expression in the lead section.
* In the lead section, you mention "In addition to regulating activated STAT", but you do not introduce STAT at all before this statement.
* You could probably include some additional Wikilinks in the lead section (SUMO protein, ligase, etc.).
* The flow of content in the Discovery section is a bit choppy and can be revised so that it reads more smoothly.  For instance, you can combine the first and second sentence to say, "The discovery of PIS3 was first published in 1997, and was made while the JAK-STAT pathway was being studied.  
* Under Types of PIAS proteins, suggest revising the second column heading to "Encoded Protein" for clarity.
* Plenty of references/citations.  Nice Job!
* In the Structure section, you mention four domains and two motifs.  This is a great opportunity for a numbered list so that these domains and motifs are easily recognized at the beginning of the section.  I realize you have each described below the main paragraph, however, some as simple as (1) acinus and PIS domain, (2) Pro-Ile-Asn-Ile-Thr (PINIT) motif, etc. would make it clearer to the reader.  I like the table at the end "PIAS protein regions".  Perhaps the table would be better off inserted towards the beginning of the section to address my point.
* The last section "Potential applications in disease treatment" could be cleaned up.  Check grammer, sentence structure, etc.  An example is the second sentence where it should be, "...demonstrated an increased resistance". (not increase).  As with an earlier comment, this sentence could also be combined with the sentence after to read, "In cell cuture, overexpression of PIAS3 demonstrated an increased resistance of HeLa cells to ionizing radiation, indicating a significant role for PIAS3 in DNA repair."
Again, very nice work to date.  There is a lot of great content in place and a long list of references.  Good luck over the next week!Msmrugby (talk) 03:45, 30 April 2014 (UTC)
replies: text: Thanks for your review! I am taking all of your suggestions into consideration. STAT is mentioned before "in addition to regulating activated STAT..." It's in the name of the protein itself: Protein inhibitor of activated STAT. However, I'm definitely planning on changing the wording of the lead section. --Jocelyn Munson (talk) 03:04, 6 May 2014 (UTC)
thread_title:  Review by msmrugby 

message: Overall, you guys have great article! Nice contents, structure, and citations. Few comments for further improvements:
* I know you guys made a wikilink to “STAT” protein, but it would be great for readers if you could you use the unabbreviated name when it first appears or briefly explain what STAT is? 
* It would be better if you can wikilink or briefly explain technical jargons like E3 SUMO-protein ligases.
* Also, maybe re-arranging the middle paragraph would be clearer to readers. Rather than directly stating “The seven proteins that belong to the mammalian PIAS family are encoded by four genes…” maybe place an introductory sentence that PIAS are not only found in mammals and there are seven proteins that belong to the mammalian PIAS family. I’m suggesting this because the very first sentence of the lead section sounds like PIAS regulate transcription specifically in mammals. 
* Discovery section looks good, but it would be better why was significant about these discoveries.
* I like the chart in the Types section. 
* I also like the chart in the structure section. Maybe you can bring the chart up so that it is right below the introductory paragraph.
* For the Function section, I would like to know what kind of gene is transcribed by PIAS (you guys mentioned in the lead section, but not here).
* Under the Application section, shouldn't “an increase” be “increased” or “increased in” in the third sentence? (“In cell culture, overexpression of PIAS3 demonstrated an increase resistance of HeLa cells to ionizing radiation”)
* You guys did great job with citing sources. 
Again, good job guys! Androidhu (talk) 21:43, 1 May 2014 (UTC)
replies: text: Great points, thanks! I fixed the "increase" typo. --Jocelyn Munson (talk) 03:08, 6 May 2014 (UTC)
thread_title:  Comments from androidhu 

message: Reference 36 needs to be fixed. --Jocelyn Munson (talk) 23:34, 6 May 2014 (UTC)
replies: text: It should be fixed now. --Catwell99 (talk) 00:09, 7 May 2014 (UTC)
replies: text: That reference was a duplicate, so I deleted it. It should now refer to the correct article. --Jocelyn Munson (talk) 00:16, 7 May 2014 (UTC)
thread_title:  Reference 36