Talk:Transferase

message: Addition of a longer introductory section, with more information and sources might be nice.  Have also discussed the addition of a section expanding explanation of the various types of transferases.  Other sections we have discussed as possible targets for expansion include: structural considerations, cofactors/coenzymes, regulation/inhibition, kinetics, disease importance, and applications to biotechnology/medicine.  Also, a good diagram is likely necessary to better illustrate the action of a transferase. --WillPugarth (talk) 23:49, 22 October 2013 (UTC)
thread_title: Possible Revisions

message: I have been working on the diseases section from the outline. Covered three so far, galactosemia, SCOT deficiency, and carnitine palmitoyltransferase II deficiency, with references.Adimart1 (talk) 06:09, 29 October 2013 (UTC)
replies: text: Excellent! If you don't mind, I thought I might start work on the introduction section (that you already found citations for).--WillPugarth (talk) 22:56, 29 October 2013 (UTC)
replies: text: I have adjusted some of the sub headings and added a section on the history of transferases, crosslinking to other wikipedia sites is necessary in history section.--WillPugarth (talk) 01:26, 30 October 2013 (UTC)
replies: text: I have added some in text links to other Wikipedia articles by keyword--WillPugarth (talk) 02:15, 30 October 2013 (UTC)
thread_title: Unit 8 Article Revsions

message: Great job getting started on the article! The outline of the article looks very good. I particularly like that you included the history of the enzyme so that readers can get some additional information as to how transferases were discovered. I would also suggest adding information on the scientists involved in the discovery of transferases, if available, and the techniques that they used to discover them. This would allow the reader to read more on the scientists if they are interested; hopefully, there are wiki links for them as well! 
Overall, the writing flows very well and the sections that have been edited are well cited. However, the “Nomenclature” section is still in need of citations. Also, the in-line citations should generally be located after the period. So, for the “Transferase reactions” section, the citations should be moved to after the period. In addition, the last sentence in the “Transferase reactions” section is missing a period.  
Also, I would suggest reorganizing the structure of the article just a bit and discussing the transferase reactions before transferase deficiencies. This would allow readers to get a complete background on transferases prior to learning about how transferase deficiencies are involved in disorders. Let me know what you guys think! Great start on the article. I am very excited to see how it turns out! -Agulati4 (talk) 23:58, 4 November 2013 (UTC)
replies: text: Thank you very much for the informative feedback!  I will definitely look into these issues as soon as I can.  I actually was in the process of revising the "Nomenclature" section when you posted, so hopefully I added some appropriate citations.  Additionally, I just added some information on a Nobel Prize related to a specific transferase.  Again, thanks for the feedback! --WillPugarth (talk) 00:05, 5 November 2013 (UTC)
replies: text: Hi Will! The article is looking great! You all have made some great progress. I really like how the history is split up according to dates. This makes it a lot easier to read and understand what discoveries happened when. The biotechnology applications involving transferase section is also a very good section to add as most people will want to know not only what transferase is, but how it is used and applied. Great job! - Agulati4 (talk) 23:38, 15 November 2013 (UTC)
replies: text: Hello again Agulati4!  Thanks for the continued feedback.  We are hoping to add much, much more, but it has been difficult to find very much information.  The goal is to add more to the biotechnology section, as that seems to be very interesting.  Additionally, I am currently not sure what else to add as far as new sections are concerned.  If you have any ideas, feel free to add them here! Again, thank you for all the correspondence
--WillPugarth (talk) 06:51, 18 November 2013 (UTC)
replies: text: Hey, Agulati4, Thanks so much for the advice. I have expanded the reactions section, combined the two we accidentally had and moved it to the beginning-ish of the page. Much appreciated. Adimart1 (talk) 06:21, 21 November 2013 (UTC)
replies: text: Hi WillPugarth and Adimart1, I was thinking about new sections or information you could add to the article. I am always very interested in reading about how certain molecules or enzymes affect the development of diseases in humans. So, I was thinking you could add a new section on the involvement of transferases in diseases or just add to the transferase deficiencies section. Here are some articles I found that may help: 1) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1379001/pdf/gut00588-0109.pdf, 2) http://www.ncbi.nlm.nih.gov/pubmed/9802272, and 3) http://www.ncbi.nlm.nih.gov/pubmed/16020876. The first and second articles are about Gluthathione transferase and its involvement in diseases and Parkinson's disease, respectively. The last article is about Gamma-glutamyl transferase and its link to cardiovascular disease. I hope that helps! - Agulati4 (talk) 05:53, 26 November 2013 (UTC)
replies: text: Thanks for the additions! I definitely like where you are going with this.  I also looked into the Glutathionine transferases and found them interesting.  I definitely would like to add some information on this to article, but previously I wasn't sure how I would word it.  Now with a little more Wikipedia editing experience, I feel I might be able to make this addition.  Again, thanks for all the help, as well as the sources!--WillPugarth (talk) 01:53, 2 December 2013 (UTC)
replies: text: I'm glad the suggestions were helpful! I really like how you have expanded on the diseases affected by transferase deficiencies under the "Deficiencies" section. It's really looking great! - Agulati4 (talk) 19:10, 5 December 2013 (UTC)
replies: text: Thanks! It was definitely a group effort! I think this article still needs some clean up time, but otherwise it is looking better and better! Everyone has helped immensely with their suggestions, and for that I am quite appreciative. --WillPugarth (talk) 19:29, 7 December 2013 (UTC)
replies: text: Hi everyone! The article is looking absolutely amazing! Great work! - Agulati4 (talk) 00:31, 13 December 2013 (UTC)
replies: text: Thanks again! We definitely put a lot of time into it.  Hopefully we will be able to improve it some more! --WillPugarth (talk) 03:34, 14 December 2013 (UTC)
thread_title: Peer-review by Agulati4

message: This is a great article. I enjoyed reading It.  You guys are in the right direction.  I suggest the following improvements for this article.  
 
*The first thing I noticed is that the references are not in proper format.  Wikipedia has a cite function that makes it easy for citing books and journals. I’ve actually changed one of the references within the reaction section.  I used Pub med ID and wiki generated the format.  In most cases it is possible to find a Pub Med ID for an article.  
*In the lead section the word “Biochemistry ..” could be omitted.  I think it is obvious from the definition of the word that the topic falls under this subject. According to Wikipedia lead guideline there is no need to add inline citation in the lead section. 
*You were editing the article when I was reviewing it.  I think the reaction example should stay in the lead section.  It shows what transferases do.  However, you have to clearly explain the part that transferases play in your example. 
*I think the organization is great for the article.  It would improve to place the reaction section under nomenclature.  This way the reader knows the function of these groups of enzymes.  Afterward it would make sense to read the deficiencies.  
*In the History section the reference you cite are about the actual discoveries.  I think it would be better to cite a historic source.  It would be better Wikipedia article when you cite conclusions made by others. 
*The Nomenclature section needs additional citation.  I think it would also improve article to add example for the formal names and the common names. 
*I like the list of classifications, and the wikilinks for each classifications.  It may improve article if you clarify what EC stands for.   
*The transferase reaction section is very important for this article.  You have started mentioning some key enzymes.  I think you should include at least one example from each classification.  It would make a better article to explain reaction mechanism.  
*The article also needs images.
Happy editing.  Galemu2 (talk) 03:36, 5 November 2013 (UTC)
replies: text: Thanks Galemu! I actually had thought I had responded to your post, but I must have forgotten, or accidently cancelled my response.  Either way, I am working on the citations right now and I just found a historical type source to use for the history section.  I am also planning on adding examples to the nomenclature section as suggested. Thanks for all the feedback!--WillPugarth (talk) 02:13, 13 November 2013 (UTC)
replies: text: Hello again Galemu! We have tried to incorporate as many of your suggestions as possible.  Sadly, I haven't been able to find historical source (like a textbook) for the history section other than the sources I have found.  The oldest source so far is from 1941, but it references transferases as if they are commonly known.  I'd ideally like to have a source that says what the first transferase discovered was, or how they came up with the name (like when the EC system was created), but that information seems to be difficult to obtain.  Additionally, I am still updating the reactions section to include examples, as per your suggestion.--WillPugarth (talk) 06:56, 18 November 2013 (UTC)
replies: text: Hello WillPugarth.  Keep up the good work.  The article is improving very well.  I understand you are still updating the recommended improvements.  I just wanted to throw this out.  We just finished class discussed on translation.  We learned that the enzyme amino aceyl tRNA synthetase charges tRNAs with their corresponding amino acids.  I mention this because I think this enzyme is a well-noted transferase enzyme and might be a great image for lead section.  Good luck with the edits.  Galemu2 (talk) 05:38, 19 November 2013 (UTC)
replies: text: Hey Galemu, you clearly put a lot into your review. We have been reworking and expanding several sections. Our plan is to try to have one at least from each classification and our text is actually a huge help here. Thanks, Adimart1 (talk) 06:24, 21 November 2013 (UTC)
replies: text: Helo Adimart1 and WillPugarth.  Great job on improving this article.  I can see you guys have really put in some time into this article.  You have used lots of references.  I really like that you put in examples for each category of transferase enzymes.  Keep up the good work.  Galemu2 (talk) 06:18, 7 December 2013 (UTC)
replies: text: Hello again Galemu!  Thank you for all your support and recommendations so far!  We are still working on quite a bit of the suggestions that we have been given, trying to figure out what works and what doesn't.  We are hoping to still add some more information as well as clean up quite a bit of the syntax, as well.  Again, thank you or all your help!--WillPugarth (talk) 20:33, 7 December 2013 (UTC)
replies: text: Hello WillPugarth.  Hope all is well.  Great job on improving this article.  I like seeing the reaction images.  Its a great way of showing what the enzymes are doing.  One small subbestion i have is that the navigation box should be placed below the “see also” section and above the references.  Other than that great job.  Galemu2 (talk) 04:18, 14 December 2013 (UTC)
replies: text: Hi again! Thanks for the support throughout the term.  I double checked what you were saying about the navbox.  It seems there are some conflicting ideas about where it is supposed to be located.  I followed the link you included, but didn't find any information on where navboxes were supposed to be.  So I went over to navboxes and that said that navboxes go under the article's appendix.  But then I read somewhere else that it goes under the "See also" section, as well. So I think I will leave it for now, pending clarification.  Thanks for noticing that, until now I didn't even realize that there was a set place for it (although someone else came through a couple of weeks ago and moved the navbox to where it is now)! --WillPugarth (talk) 20:24, 14 December 2013 (UTC)
thread_title: Comments from Galemu2

message: * We have added two new sections to the article: "Transferase Deficiencies" and "History."
* Added new Wikipedia cross reference links to other articles
* Added prose
* Added/Revised "See also" heading
* Added/Revised "References" heading  
--WillPugarth (talk) 00:49, 14 November 2013 (UTC)
thread_title: Progress Report from 10/29/2013

message: Completed (since last report):
* Added new sections with new content
* Improved wikilinking, improved syntax, content edits, new citations
* Added images and equations
* Expanded EC terminology section into short descriptions of each class
In progress (before next report):
* Add section on Terminal transferase
* Add section on Medicines/therapies that use transferases  — Preceding unsigned comment added by WillPugarth (talk • contribs) 07:08, 18 November 2013 (UTC)
thread_title:  Progress Report for 11/15/2013 (Unit 10) 

message: The general flow of the article is easy to follow and it makes sense. It can be difficult to write on such a broad topic but it went in interesting directions. The lead was kept appropriately general and broad while introducing transferase reactions. The first subsection was succinct and contained good examples without getting bogged down in particulars. I like the idea of touching on the discovery of transferases in general and some of the history behind highlighted breakthroughs. That section is short and simple but it makes the overall concept of this category of enzymes less abstract and more relevant to real life applications. The nomenclature section was straightforward as well with good examples. Highlighting RNA polymerase as an example is a good idea, since so many people probably do not think of them as transferases. 
The organization of the categorization section is clean and streamlined. Using a chart for each category with linked examples is very easy on the eyes. Including sections on uses of transferases in biotechnology and cases of transferase deficiencies is very useful. Expanding a bit on these two subsections would really balance the article and make for an interesting read. Adding subheadings to these sections consistently or not using them at all would be best. The images used were appropriate and strengthen the text. A wide variety of third-party published references were used. They appear to link to the proper papers and are properly formatted. The text in general reads well and seems like a good summary of the included references without overuse of quotes or heavy paraphrasing. The overall structure and compartmentalizing of sub-topics are spot-on. Adding more content to the last few sections will make for a very strong article.Hnagy2 (talk) 05:04, 19 November 2013 (UTC)
replies: text: Hello hnagy2!  Thank you for all your feedback.  I agree with your idea of expanding the section on uses of transferase, as well as the biotechnology coverage. This type of addition will definitely help to improve the interest in transferase. As far as the subheadings are concerned, it is definitely hard to decide whether to use them or not at this point.  If the sections remain so short, it might be best to remove them.  However, if the length of each part becomes rather expansive, then those divisions might be necessary.  We are definitely looking into adding more content to the end sections.  Again, thank you for your review!--WillPugarth (talk) 02:00, 20 November 2013 (UTC)
replies: text: hnagy2, thanks for the review. Several sections do need expansion and we are certainly working on them. The transferase deficiencies sections definitely needs improvement. I hope you'll see more there soon. Adimart1 (talk) 06:35, 21 November 2013 (UTC)
thread_title:  Comments from hnagy2 

message: # expanded glutathione section
# expanded SCOT deficiency section
# expanded CPT-II deficiency section
# expanded Galactosemia section
# added new section: rubber transferases
Adimart1 (talk) 05:55, 23 November 2013 (UTC)
thread_title:  Unit 12 Progress report 

message: Completed:
:1. Further expanded Reactions section
:2. Condensed unnecessary section into introduction
:3. Updated section headings/removed some subheadings
Next:
:1. Finish adding EC divisions to Reactions section
:2. Edit style, grammar, Wikilink corrections, etc.
:3. Add reaction images for Reactions section (or make new diagrams)
:4. Add more academic citations
:5. Kinetics section
--WillPugarth (talk) 01:08, 27 November 2013 (UTC)
thread_title: 11/26/2013 Progress Update

message: Wow!  This article has come a long way!  Really looking nice and very extensive!  I do have a comment/suggestion for the equation in the introduction that concerns X-Group + Y -> X + Y-Group.    No problem with this equation at all.  The larger equation, however, is totally different and so having two different equations is confusing.  My suggestion is to have just one by removing the "small one" (done in normal text) and changing the large equation to be:
 Xgroup + Y \xrightarrow[transferase]{} X + Ygroup 
With this change, the description you have will still work fine.  Once again, nice job on this article!--Jim Perry (Jim892) (talk) 21:33, 4 December 2013 (UTC)
replies: text: Hi Jim. We will definitely consider this suggestion. I don't want to change it without his opinion, but i certainly appreciate the observation. Adimart1 (talk) 04:43, 5 December 2013 (UTC)
replies: text: Hey Jim! I totally didn't catch that discrepancy before.  I will look into changing it as soon as I can.  I will likely use your exampel above, as it looks good.  Thanks again for the assistance throughout the term!--WillPugarth (talk) 20:35, 7 December 2013 (UTC)
thread_title:  Comment on Intro Equation 

message: Impressive work on the article. A couple of small suggestions:
*some evolutionary history cold be included (e.g. relatedness of some transferuses to hydrolases)
*a white background on protein structures is more in line with wikipedia's aesthetic.
Good luck, T. Shafee (Evo&Evo) (talk) 13:34, 7 December 2013 (UTC)
replies: text: Thanks for the post! Honestly, I hadn't even made that connection between transferases and hydrolases myself. From a preliminary search just now, I can see that they are linked mechanistically, so therefore could have a sort of evolutionary past.  I definitely will look into this as it could be included in a future section on kinetics and mechanisms of action for transferases.  I have added two links to my sandbox page to get the process of creating a section on this started.  I agree on the image suggestion as well, but at the time had only found that one enzyme.  Now that I have spent more time working with Wikimedia Commons, I believe I can probably find a better representative molecule.  I will look into it.  Again, thank you for your suggestions!--WillPugarth (talk) 20:50, 7 December 2013 (UTC)
thread_title:  Brief suggestion 

message: Impressive work on the article. A couple of small suggestions:
*some evolutionary history cold be included (e.g. relatedness of some transferuses to hydrolases)
*a white background on protein structures is more in line with wikipedia's aesthetic.
Good luck, T. Shafee (Evo&Evo) (talk) 13:34, 7 December 2013 (UTC)
thread_title:  Brief suggestion 

message: Hey guys, I am assigned to review your article this week. Overall this is a great article. I couldn’t find anything major that needs to be fixed. I just have a few suggestions. I will be using the rubric to critique in this peer review:
===Content coverage===
The article is composed of a lead paragraph and six main sections: History, nomenclature, classification, reactions, role in histo-blood group, deficiencies, and uses in biotechnology.
The lead paragraph is very well done.  It includes the function of tranferase, its involvement in reactions and pathways, and an example of a reaction is provided. This introduction is great in that it is succinct without going into too much detail. My only suggestion is to include a little about transferase deficiencies and how transferases are used in biotechnology. To be in accordance Wikipedia guidelines the lead paragraph should “summarize the body of the article” in equal weight. I think the best way to do this is to include at least one sentence on the main sections of the article.
===Wikilinking===
You guys did a great job adding wikilinks to your article. I only added “translation,” which is location in the lead paragraph. I think it’s relevant enough to be wikilinked. 
===References===
Lots of references are used in the article. They appear to be properly formatted, and the ones I looked at are from research papers and other reliable sources. No suggestions here.
===Writing/spelling/grammar/typos===
No suggestions here either.
===Illustrations===
I really like the use of illustrations in the article especially in the “reactions” section. I also like the chart that you guys used for the classification of tranferases.
76.111.110.6 (talk) 22:52, 7 December 2013 (UTC)
replies: text: Thanks jirwin! We appreciate your review of the article. We will definitely see about adding a little bit to the intro to bring it into line with the wikipedia guidelines. I can't take any credit for the pictures and charts, James is totally responsible for those!!Adimart1 (talk) 20:14, 9 December 2013 (UTC)
replies: text: Thanks for the review! Additionally, thank you for the suggestion about deficiencies needing to be in the intro section, I didn't even think about it at the time! Also thanks for the Wikilink assist, as well. We've been working fairly intensely on the article, so its nice to know that we are on the right path!--WillPugarth (talk) 07:13, 11 December 2013 (UTC)

text: thanks, Juanquina, good luck with your article!!Adimart1 (talk) 20:15, 9 December 2013 (UTC)
replies: text: No worries! Thanks for checking out our article!  Feel free to use anything you think is useful, and don't hesitate to send any suggestions you have our way, we can use all the feedback we can get!--WillPugarth (talk) 07:13, 11 December 2013 (UTC)
replies: text: Hello all, I was just giving your article a final read. I really enjoyed it and think you guys did an awesome job in revamping it. Thanks for your suggestions to our page, it made a world of difference. Good luck to you guys! Juanquina Thomas (talk) 02:52, 15 December 2013 (UTC)
thread_title: Comments from jirwin1097

message: I really like the use of illustrations in the article especially in the “reactions” section. I also like the chart that you guys used for the classification of tranferases.
76.111.110.6 (talk) 22:52, 7 December 2013 (UTC)
replies: text: Thanks jirwin! We appreciate your review of the article. We will definitely see about adding a little bit to the intro to bring it into line with the wikipedia guidelines. I can't take any credit for the pictures and charts, James is totally responsible for those!!Adimart1 (talk) 20:14, 9 December 2013 (UTC)
replies: text: Thanks for the review! Additionally, thank you for the suggestion about deficiencies needing to be in the intro section, I didn't even think about it at the time! Also thanks for the Wikilink assist, as well. We've been working fairly intensely on the article, so its nice to know that we are on the right path!--WillPugarth (talk) 07:13, 11 December 2013 (UTC)
thread_title: Illustrations

message: Hi guys. I wasn't assigned your article for peer review, I was just checking out the structure for ideas for my article (Isomerase). I do like the way you guys put the classifications of transferases in a table. I also noted that guys have several citations! This is great. 76.100.202.179 (talk) 04:58, 9 December 2013 (UTC)
replies: text: thanks, Juanquina, good luck with your article!!Adimart1 (talk) 20:15, 9 December 2013 (UTC)
replies: text: No worries! Thanks for checking out our article!  Feel free to use anything you think is useful, and don't hesitate to send any suggestions you have our way, we can use all the feedback we can get!--WillPugarth (talk) 07:13, 11 December 2013 (UTC)
replies: text: Hello all, I was just giving your article a final read. I really enjoyed it and think you guys did an awesome job in revamping it. Thanks for your suggestions to our page, it made a world of difference. Good luck to you guys! Juanquina Thomas (talk) 02:52, 15 December 2013 (UTC)
thread_title: Comments from Juanquina Thomas

message: Hi All, You article on transferases is very comprehensive and  I must commend you for such an effort. However, please take a look at the introduction and examine the need for the sentence involving PDH and phosphatase. I can under the involvement of a transferase in the PDH complex, but a phosphatase I guess does not belong there. Once the phosphate or phosphoryl group is cleaved, for instance inorganic phosphate, it does not transfer within that reaction to another group. In all, congratulations for your excellent work. Godwin Ifere 04:41, 12 December 2013 (UTC)
replies: text: Thanks for the assistance! I checked what you said, and you were right.  I can't believe I didn't catch the error there with PDH.  I changed the way it was written to remove the phosphate part. Thank you again!--WillPugarth (talk) 03:29, 13 December 2013 (UTC)
replies: text: Hi All, Doing my last visiting rounds to see to the progress of the article. Thanks for doing the little correction. Congratulations to the group for a job well done. Take care Godwin Ifere 04:45, 15 December 2013 (UTC)
thread_title: Comments from Wenwatata

message: Completed since last update:
*Added EC Reactions, Deficiencies, and Histo blood group sections; expanded history section
*Added diagrams and images, equations for each reaction type
*Improved citations
*Made all changes (as far as I can tell) suggested by Neelix in previous review (includes removing duplicate wikilinks, heading fixes, removal of category links, captions added)
*Attempted to address all changes suggested by others
Next/In progress:
*Add section on mechanisms, regulation, and thermodynamics
*Describe cofactors/add cofactors section
*Structure: similarities between Transferases and Hydrolases  — Preceding unsigned comment added by WillPugarth (talk • contribs) 22:56, 14 December 2013 (UTC)
thread_title:  12/14/2013 Progress Update 

message: Overall changes to Transferase Article:
*Extensive content additions
*Improvements to references
*Improved wikilinking
*Addition of images and diagrams.
*Created table for EC classification
*Overall Wikipedia guideline fixes
Special thanks to (in no particular order):
Neelix (main Wikipedia editor), Adimart1 (group partner), Agulati4, Galemu2, Jim892, Pdholak1, Hnagy2, Madscientist2007, T.Shafee (Evo&Evo), jirwin1097, Juanquina Thomas, Wenwatata, and countless others who did quick fixes here and there throughout the project.  Thanks everybody!--WillPugarth (talk) 23:02, 14 December 2013 (UTC)
thread_title:  Final Progress Report