Talk:SR protein

message: I think it would be a good idea to include a reference to "Recent studies (in 2006) suggest". 130.243.248.239 23:15, 10 February 2007 (UTC)
thread_title: Comments

message: *Fixed a few small errors, mainly spelling
*First two sentence of introduction could be combined, since they are a little repetitive.
*Do you need to cite anything in the last paragraph of the intro?
*I'm not sure if you have to make a reference after every sentence if the whole paragraph is citing the same source. For example, the first paragraph of structure.
*Is there a distinctive purpose of the RRMH domain? Do proteins that have them have a special function?
*The last two sentences of the second paragraph in structure seems a little out of place, perhaps you can alter the sentence so they fit a little better.
*I would combine the first two sentences of location and translocation. I'm also a little confused about what you are trying to say. Are most SR proteins found in nuclear speckles or outside of them in the nucleus.
*In the second sentence of location and translocation, should it be 'remain in the cytoplasm'?
*What are the roles of shuttling and non shuttling SR proteins?
*Do you know what phosphatases and methylases interact with SR proteins?
*One of the functions is translation, but there is no section for it. 
*What is STD in the Alternative splicing section?
*I'm a little confused about what the SR protein binds to, does it bind to the kinase, the RNA Pol II, or the mRNA.
*I don't think you should anthropomorphize the protein, it doesn't 'see' to mRNA.
*An image would be great for the Alternative splicing section to make it a little more understandable.
*Exon independent and dependent roles don't have any sources. 
*A lot of the information in the mRNA export section is repeated earlier.
*In the Genomic Stabilization section, when you refer to SR proteins becoming hypophosphorylated, does that refer specifically to SF2/ASF?
*Are these human proteins? If so then all of the proteins should link to a page or have a red link. 
Good Job so far, keep it up. Maximus155 (talk) 04:14, 26 March 2013 (UTC)
thread_title: Comments from Maximus22

message: *Fixed a few small errors, mainly spelling: Done
*First two sentence of introduction could be combined, since they are a little repetitive: Done
*Do you need to cite anything in the last paragraph of the intro: Done
*I'm not sure if you have to make a reference after every sentence if the whole paragraph is citing the same source. For example, the first paragraph of structure: I tried combining a few things but I really don't want to plagiarize, so some things might be over cited 
*Is there a distinctive purpose of the RRMH domain? Do proteins that have them have a special function?: I haven't found any information about the specifics of RRMH, only that they exist
*The last two sentences of the second paragraph in structure seems a little out of place, perhaps you can alter the sentence so they fit a little better: Done
*I would combine the first two sentences of location and translocation. I'm also a little confused about what you are trying to say. Are most SR proteins found in nuclear speckles or outside of them in the nucleus: Done
*In the second sentence of location and translocation, should it be 'remain in the cytoplasm'?: Done
*What are the roles of shuttling and non shuttling SR proteins?: Done
*Do you know what phosphatases and methylases interact with SR proteins?: Haven't found any yet but still looking for papers about this
*One of the functions is translation, but there is no section for it.: Done 
*What is STD in the Alternative splicing section?: Typo, supposed to be CTD, Done
*I'm a little confused about what the SR protein binds to, does it bind to the kinase, the RNA Pol II, or the mRNA.: Tried to clear that up as much as possible, Done
*I don't think you should anthropomorphize the protein, it doesn't 'see' to mRNA.: Done, thats how the review paper describes it 
*An image would be great for the Alternative splicing section to make it a little more understandable.: Will look for one
*Exon independent and dependent roles don't have any sources.: Done 
*A lot of the information in the mRNA export section is repeated earlier.: Tried to make it more clear and more separate about the localization and how SR proteins export mRNA, Done
*In the Genomic Stabilization section, when you refer to SR proteins becoming hypophosphorylated, does that refer specifically to SF2/ASF?: Done, assuming all SR proteins go through phosphorylation events as any other as long as they have the same sort of function regardless of species 
*Are these human proteins? If so then all of the proteins should link to a page or have a red link.: Done  — Preceding unsigned comment added by BreCaitlin (talk • contribs) 19:52, 15 April 2013 (UTC)
thread_title: Reply to Peer Review

message: *The leading section is too long and informative. I think that you can do in deleting the last three paragraphs. For example, you don't need to provide a section on history or on experiments explaining redundancy. The leading section should be a quick, general summary of what SR proteins are and what they do. If someone wants to read about the history or experiments, they can do that in the main body of the article.
**Done, thanks
*How about taking the last paragraph of the leading section: "Experiments have shown that knocking down SR proteins. . ." and making that its own section in the article entitled something like "Experimental evidence of SR proteins"? I think this information belongs in its own section. As I stated above, it seems a bit too specific for the leading section. 
**Done, moved it to splicing
*I don't think you need to have so many citations in the leading section. Generally the leading section does not contain citations but instead provides an overview of the article.
**Done
*I went through and corrected grammar and citation placement for a couple of the sources.
**Thanks
*Only the first word of each section title should be capitalized. I went through and changed this for you.
**Thanks
*In the section entitled "Splicing," you have two subcategories entitled "exon dependent roles (splicing)" and "exon independent roles (splicing)." I deleted the "(splicing)" from both of these because it seems redundant to me. Since these are already a subcategory of the Splicing section, I don't think you need to say again that it refers to splicing. Given its placement in the article, this should be understood.
**Thanks
*Went through and added more wiki-links for you.
**Thanks
*Sources look good.
*Is there any research you have found on clinical trials or implications involving SR proteins? It may be good to add a section to the end of the article. You do a nice job outlining the SR mechanisms and their functions, but then it leaves me wondering why this is important and curious to know if this can help contribute to medicine or diseases in anyway.
**Done
*Do you think it would be a good idea to give a summary box or figure showing all the proteins used in the "Splicing" section? There is a lot of information provided there, so if you could present it in an organized manner and give a visualization, it may help the reader.
**Done, not sure how it got there, thanks if you did it
MChapman5 (talk) 22:41, 19 April 2013 (UTC)
thread_title:  Peer Review comments from MChapman5 

message: Overall, an impressive contribution.
This is a technical article, however per WP:LEAD, at least the first paragraph of the article should be kept dead simple so that it can be understood by a wide audience. Furthermore the lead paragraph should quickly define the scope of the article and explain why the subject is important.  The remaining paragraphs of the lead should briefly summarize the contents of the entire article and in roughly the same order as they are presented in the article (e.g., discovery, subcellular location, and function).
I may add more comments later.  Boghog (talk) 08:49, 21 April 2013 (UTC)
thread_title:  External review 

message: * The leading section seems to be too short/brief.  I think that it should be treated like a journal article abstract, which means that it should summarize each of your sections so that the readers understand the scope of the information that this Wiki article contains.  I would suggest using the proteasome article as a reference since it achieved feature article status.
**Redone
* The section title Examples seems a little to vague to me.  Perhaps SR genes would be more appropriate.  However, I do really like the table.  It brings excellent structure; however, it might be beneficial to list some genes and subsequent proteins found in other organisms.  This can demonstrate that SR proteins are found in more than just humans.  I would suggest using organisms that come from different classifications, such as an invertebrate, fish, reptile, etc.
**I didnt do this so i'm not 100% about what to do with it 
* This article is a technical article, which means it can appear rather dense.  I suggest adding either more wiki links or short in-text explanations of complicated terms to avoid confusion from technical jargon and the so-called scientific "alphabetic soup".
**Done
* Are mRNA export, genome stabilization, non-sense mediated decay, and translation all a result of splicing?  If so, I would suggest moving them out of the function section and putting them under SR-induced responses.  This would establish that while the main function of SR proteins is splicing, these are the effects of said splicing.
**They are all functions, so i left them in functions
* You mentioned plants and Drosophila in your class presentation, perhaps you could discuss them in this article.  
**going to add it later when ive got more time  — Preceding unsigned comment added by BreCaitlin (talk • contribs) 03:43, 12 May 2013 (UTC)
thread_title: Comments from Gpruett2

message: *The first thing I noticed was the overall format that was used. That was great.
*I noticed with this article in particular that the citations were all at the end of the paragraph. I've usually seen it where the citations come right after the sentence that used the source, but if the paragraph is a hybrid of all of the sources listed at the end, that is most likely more than okay.
*There were some red words in the article, that could use fixing with the linkage.
*I liked the clarity that was used when describing the location and translocation of the SR proteins.
*Serine was misspelled in the third paragraph.
**Good catch
*I thought all of the ways you used our sources were great. I checked a lot of the sources and they all seemed to be in your own words. The wording was very clear and relatively easy to understand.
*For the source of SR-related proteins and the processing of messenger RNA precursors, I was unable to get to the actual paper, just the abstract, from the source at the bottom of the Wikipedia page. I found it at another source. This might not be the optimal citation, but honestly would be of least priority.
**Thanks
*The second paragraph under genomic stabilization was really well done with using that source. It is hard to visualize this actually happening, and visuals would always be nice, but that is most likely beyond the scope right now.
*SR proteins SF2/ASF alternatively splice* the transcript of MNK2.
*It appears there is a lot of cross talk between the SR proteins and mTOR. Halfway through the paragraph you mention the mTOR pathway, but literally everything within that paragraph has to do with the mTOR pathway.
*It appears that SF2/ASF interacts directly with mTOR. This is most likely mTORC1, as most papers when referring to mTOR refer to mTORC1. Probably making the link go to that page would be better. It seems that it binds to and activates mTOR. When mTOR is activated, it will phosphorylate 4EBP, which causes it to leave eIF4E, activating the eIF4E. mTOR will also activate S6K, which will phosphorylate eiF4B and S6 on the small ribosomal subunit. There is a picture of this occurring on the mTORC1 page. This might help clarify what is going on in your page.
**Will do
Flemingrjf (talk) 08:37, 7 May 2013 (UTC)
thread_title: Comments from Flemingrjf

message: * History section, first sentence: proteins are discovered by people, maybe by using antibodies.  — Preceding unsigned comment added by Biolprof (talk • contribs) 16:05, 8 May 2013 (UTC)
thread_title:  Comments from Biolprof 

message: Great job with your project! Let's start with the things I particularly enjoyed/appreciated:
====Good stuff====
*Lots of informative content
*Good organization
And here are some suggestions for improvement:
====Suggested improvments====
History
*These sentences need rewording so it doesn't sound like the antibodies discovered the SR proteins: "SR proteins were discovered independently by two different monoclonal antibodies. The first antibody, mAb104 found SR proteins in the nucleus of amphibian oocytes."
**Done
*Likewise, this wording is confusing; are you talking about two proteins here, or four?: "Tra and Tra-2, transformer and transformer-2 (TRA2A and TRA2B)"
**I think someone else fixed this
Examples
*This section title should maybe be changed to something like "Genes."
**Done
Structure
*An image of the protein structure would be a nice addition.
**An image would have been nice, but i wasnt sure about where to get a copy right free one
Location and translocation
*These two sentences seem to contradict each other, and should be linked together to remove the confusion: "SR proteins are located in both the cytosol and in nuclear speckles in the nucleus. SR proteins are mostly found in the nucleus."
**Done
*This sentence could use rewording to make it less confusing (which proteins enter and which leave?), and the sentence that follows it adds to the confusion: "Phosphorylation of the RS domain causes the SR proteins to either remain in the nucleus or enter the nucleus. Partial dephosphorylation of the RS domain causes the SR proteins to leave the nucleus and SR proteins with unphosphorylated RS domains are found in the cytosol."
**Done
Function
*I would change the wording of the following sentence: "SR proteins have been shown to have roles in alternative and constitutive splicing resulting in differential gene expression in addition to roles in mRNA export, genome stabilization, non-sense mediated decay, and translation."
**Suggestion: "SR proteins have roles in alternative and constitutive splicing, resulting in differential gene expression, and also play a part in mRNA export, genome stabilization, nonsense-mediated decay, and translation."
***Done
*I would also change the wording of this sentence: "Before initiation of transcription the CTD has low levels of phosphorylation. CTD has high phosphorylation levels, hyperphosphorylated, during initiation and elongation."
**Suggestion: "Before initiation of transcription, the CTD has low levels of phosphorylation, but it is subsequently hyperphosphorylated during initiation and elongation."
***Done
*More in-text links would be helpful, especially for proteins.
**Done
Best of luck! Jnims (talk) 19:53, 8 May 2013 (UTC)
thread_title:  Comments from Jnims 

message: History
*These sentences need rewording so it doesn't sound like the antibodies discovered the SR proteins: "SR proteins were discovered independently by two different monoclonal antibodies. The first antibody, mAb104 found SR proteins in the nucleus of amphibian oocytes."
**Done
*Likewise, this wording is confusing; are you talking about two proteins here, or four?: "Tra and Tra-2, transformer and transformer-2 (TRA2A and TRA2B)"
**I think someone else fixed this
Examples
*This section title should maybe be changed to something like "Genes."
**Done
Structure
*An image of the protein structure would be a nice addition.
**An image would have been nice, but i wasnt sure about where to get a copy right free one
Location and translocation
*These two sentences seem to contradict each other, and should be linked together to remove the confusion: "SR proteins are located in both the cytosol and in nuclear speckles in the nucleus. SR proteins are mostly found in the nucleus."
**Done
*This sentence could use rewording to make it less confusing (which proteins enter and which leave?), and the sentence that follows it adds to the confusion: "Phosphorylation of the RS domain causes the SR proteins to either remain in the nucleus or enter the nucleus. Partial dephosphorylation of the RS domain causes the SR proteins to leave the nucleus and SR proteins with unphosphorylated RS domains are found in the cytosol."
**Done
Function
*I would change the wording of the following sentence: "SR proteins have been shown to have roles in alternative and constitutive splicing resulting in differential gene expression in addition to roles in mRNA export, genome stabilization, non-sense mediated decay, and translation."
**Suggestion: "SR proteins have roles in alternative and constitutive splicing, resulting in differential gene expression, and also play a part in mRNA export, genome stabilization, nonsense-mediated decay, and translation."
***Done
*I would also change the wording of this sentence: "Before initiation of transcription the CTD has low levels of phosphorylation. CTD has high phosphorylation levels, hyperphosphorylated, during initiation and elongation."
**Suggestion: "Before initiation of transcription, the CTD has low levels of phosphorylation, but it is subsequently hyperphosphorylated during initiation and elongation."
***Done
*More in-text links would be helpful, especially for proteins.
**Done
Best of luck! Jnims (talk) 19:53, 8 May 2013 (UTC)
thread_title: Suggested improvments