Talk:Missense mutation

message: compare: "A special type of missense mutation that results in truncation of code is the nonsense mutation"
with: "mutations that change an amino acid to a stop codon are considered nonsense mutations, rather than missense mutations"
Which one is true? Hauberg (talk) 14:33, 18 November 2013 (UTC)
thread_title:  Oxymoron 

message: The sentence:
:"For example, in sickle-cell disease, the 20th nucleotide of the gene for the beta chain of hemoglobin found on chromosome 11 is erroneously changed from the codon GAG (for glutamic acid) to GUG (which codes valine), so the 6th amino acid is incorrectly substituted (after the initial methionine amino acid is removed)."
is very unclear without a picture or an example sequence illustrating what is happening. Another interesting reference to this is: http://www.cell.com/AJHG/abstract/S0002-9297%2807%2961104-5# with DOI: 10.1086/513473 .
Jahibadkaret (talk) 12:18, 30 September 2010 (UTC)
thread_title:  Need of clarification 

message: Why is the base change labeled erroneous? Although sickle-cell is a disease, it also confers heterozygous advantage in the presence of malaria, so the label of 'erroneous' seems biased.
"For example, in sickle-cell disease, the 20th nucleotide of the gene for the beta chain of hemoglobin found on chromosome 11 is erroneously changed from the codon GAG (for glutamic acid) to GUG (which codes valine), so the 6th amino acid is incorrectly substituted (after the initial methionine amino acid is removed)."  —Preceding unsigned comment added by 128.97.41.120 (talk) 19:35, 28 March 2011 (UTC)
thread_title:  Bias? 

message: A classmate and I are looking to improve this article for our Molecular Cell Biology course. Does anyone have any suggestions or ideas for improving this page? My classmate and I were considering adding:
*History and possibly discovery
*Other examples of illnesses that result from missense mutations
*Relevant mechanisms
*Good images
Our ideas are still tentative and we are still in the process of finding appropriate secondary sources like textbook references, review articles, and etc. for this page. If there are any images or references you would like used, please let us know. Thank you and we will do our best to improve the page! Bcheon1 (talk) 22:06, 13 March 2013 (UTC)
thread_title:  Ideas for improvement – Ambassador Program - JHU Group 82D 

message: Here are some suggestions to improve your article on missense mutations:
• The first paragraph needs clarification and needs to flow better.  In the very first sentence of the article, for example, the parenthetical phrase “(a type of nonsynonymous mutation)” should be moved to some later point in the article where you can explain what this means.  The first sentence should be an opportunity to introduce your topic in a clear, simple fashion -- without immediately confronting the reader with a confusing term like “nonsynonymous”.  
• In the second sentence, I would replace the indefinite article “This” with “Missense mutations . . . “ –- just for clarity’s sake.
• The third paragraph (which currently consists of the single sentence “A special type of missense mutation that results in truncation of code is the nonsense mutation”) needs to be clarified and expanded (or else merge it into the 2nd paragraph).
• The four paragraphs in the “Specific Diseases” section of the article are generally well written, but many of the other paragraphs in the article are still somewhat choppy and need to be improved stylistically.  It may be that these paragraphs are still more or less in “outline” form and simply need to be rewritten so that they flow better and have good transitions from one sentence to another.
• The “Experimental analysis” section needs to be reworked and expanded.  
• Footnote 18 is a 1997 article specific to p53, a tumor suppressor that has a rather unique standing in the oncology field (in fact, I don't know of a tumor supressor that has a higher linkage between mutation rate and cancer susceptibility).  While I agree that this citation is supportive of the sentence to which it's attached, this sentence stands for a much broader concept (the linkage between mutations and cancer susceptibility generally); and therefore, I was thinking that this sentence could represent a great launching point for a whole section on this topic, and thus this sentence would be a good place to cite to a broader "review article" on this topic.      — Preceding unsigned comment added by Jgould1400 (talk • contribs) 10:37, 12 April 2013 (UTC)
replies: text: Thanks for your thoughtful feedback. I read a very similar feedback for paragraphs where the Bedwell’s lecture is used. Yes, they need to be updated by adding the original article. During Unit 11-12, 82D team would update article accordingly. 82D team welcomes your opinion and other bright idea. Best Regards. /Mhk5600 (talk) 06:59, 13 April 2013 (UTC)
replies: text: Hello Jim. Have you read our article page, missense_mutation, recently? We have updated missense_mutation page with a lot of effort and discussion. While this article is being updated, your comments have been fully considered, of course. First, the 1st paragraph has been rewritten and re-organized. A term, “nonsynonymous”, and the original 3rd paragraph in the lead section have been relocated to the section 2 for a balance. Repeated citations from Bedwell’s lecture have been corrected. The original references have been located and cited accordingly. Citations are now well-balanced throughout the section 2. With all due respect, some of your comments could not be integrated as we think that the current way would be better for now. When Unit 14 week comes, your other comments could be considered, again. I hope you learned something about missense mutation from this article. Happy editing. /Mhk5600 (talk) 04:04, 28 April 2013 (UTC)

text: Adding  to what Mhk5600 said, thank you again for reviewing in such detail. You are completely right about introducing the concept of nonsynonymous mutation later on in the article instead of in the lead paragraph. We currently don’t see an exceptionally good place to move it so we’ll keep it there for now but we plan to move it later when it’s more appropriate. I have implemented your suggestion on replacing the indefinite article in the second sentence. For the third paragraph, we agree with you and we’re currently looking into the best way to do it. For the diseases section, we agree that the writing can be improved but we’re going to put that off for now since it isn’t that bad and probably takes lower priority. We are actually currently working on the Experimental Analysis section to be more substantial. Bcheon1 (talk) 04:14, 25 April 2013 (UTC)
replies: text:   Very nice revision!  The first paragraph is now nice and clean and reads well.  Jgould1400 (talk) 03:59, 3 May 2013 (UTC)
thread_title:  Comments from Jgould1400 

message: Good job guys! The article looks good. I have a few suggestions though:
- In the first paragraph of the lead section, some of the writing is unclear (two ellipses in the same sentence) and inconsistent citation is used. The second paragraph of the lead has no citations. 
- I'm not sure the lead acts as a summary of the article as the manual of style recommends. The manual of style states "The emphasis given to material in the lead should roughly reflect its importance to the topic"
- The "causes of missense mutations" section has very specific references to some topics and no reference at all for other. A more broad reference (such as a textbook) might work well here. 
- The DNA replication part of the "causes of missense mutations" is worded oddly and could easily have a reference
- You guys rely heavily on the slides from the Bedwell lecture. It would be better to find out where those notes were sourced from, and cite the original material. 
- It would be nice to get a slightly expanded explanation of  fastpp WeberOwl (talk) 03:16, 12 April 2013 (UTC)
replies: text: Thanks for your thoughtful feedback. I mainly contribute paragraphs where heavily reply on the slides from the Bedwell’s lecture. I would find out the original article for each note where the Bedwell’s lecture is cited. When you find a better or alternative topic to add from our update in Unit 11-12, please add your comment in this talk page. I also welcome to hear your additional feedback. Happy editing. /Mhk5600 (talk) 06:45, 13 April 2013 (UTC)
replies: text: How's it going in finding those primary sources? I still think this could add a lot to the quality of the article. WeberOwl (talk) 01:30, 25 April 2013 (UTC)
replies: text: I only can say I am working to meet that review and suggestion. The bedwell's lecture note does not have much of citation I can use. I need to find primary sources myself for some. If I could not find sources, I may need to change few paragraphs slightly. Only a little over day left. I am keep googling and reading, whenever I have time to find sources. /Mhk5600 (talk) 01:53, 25 April 2013 (UTC)
replies: text:  I have done quick skims through the appropriate secionts of the textbooks by Watson et al. and Lodish et al. and it seems like there isn't a lot of significantly new information over the Bedwell lecture. Despite this, I think it may be wise incorporate other textbooks so that the information come from multiple sources. This would help with the credibility of the writing. Bcheon1 (talk) 04:42, 25 April 2013 (UTC)

text: Hello WeberOwl. Your consistency about how references need to be cited is greatly appreciated. Please take a moment to read an updated article, missense_mutation, if you have not done already. Within the section 2, 2 of new internal Wiki-link are added for a terminology clarification. 5 of new reference are cited as primary sources. We hope that you are satisfied with our work on finding a primary source. Other sections are updated as well. When you read the lead section, please note that it has been rewritten and re-arranged. We also added  the new section, Computational approaches to predicting missense mutations. If you have a chance to review that, you are very welcomed. Happy Editing. /Mhk5600 (talk) 04:41, 28 April 2013 (UTC)

text: Thanks again for your review. We agree that the lead section needs to be improved and we are still in the process of revising it. This is our top priority at the moment as others have mentioned this as well. We are also still looking for more high quality references as you suggested so we will add those as soon as we can. Bcheon1 (talk) 04:35, 25 April 2013 (UTC)
replies: text: You've done a great job incorporating the suggestions I made, the article is looking good. At this point the only real problem with the article are the boxes that surround your table and chemical formula. You might want to play around with the wiki table function (you'll find it on the tool bar alongside options like bold and citations) to see if it improves things. For the formula, you could write it using a text editor, then snip an image to use within the text on your page.WeberOwl (talk) 00:37, 2 May 2013 (UTC)
replies: text: That sounds great, thank you for following up with us. We're getting ready to make our next round of edits soon so we'll definitely remember to try out your suggested ideas when the time comes.Bcheon1 (talk) 00:52, 2 May 2013 (UTC)
replies: text: It is always good to hear 'a great job'. Thanks. Yes, missense mutation page has been updated substantially throughout Unit 11-12, although there are some aspects that need update. For example, table format is one of them to update. Wiki direction of how to create table format was not clear. To format it better way, we may needs help from the class’s Ambassador. Please check missense mutation page during Unit 14 for table format update. Thanks for your input. /Mhk5600 (talk) 07:42, 2 May 2013 (UTC)
replies: text: Checking in one last time as the semester ends. The table looks good - you're right that it's not obvious/easy to adds tables to wiki pages, so nice job with that. Overall I think you guys did a great job.WeberOwl (talk) 21:03, 9 May 2013 (UTC)
replies: text: Thanks for the last check-up. I know now how to create table a markup language. Have a great summer. /68.116.172.204 (talk) 14:49, 10 May 2013 (UTC)
thread_title:  Comments from WeberOwl 

message: * Echoing a bit on what Jgould1400 said, I would do something with "a type of nonsynonymous mutation".  Rather than removing it altoghter though, maybe you could move it to later, and make it a link?
* Don't link the same thing twice, so close together ("amino acid")
* In the lead, you don't mention DNA anywhere -- I think that's an oversight.  Imagine you're talking to a non-biologist.
* The sentence that begins, "When an amino acid may be encoded by more than one codon " should maybe begin with something like, "In contrast to missense mutations", because it is not immediately clear that you have switched to talking about something else.
* You could link "degenerate coding" to Degenerate_code#Degeneracy
* In general, though, the lead is written in a very clear and understandable way, without too much jargon:  good job!
* In the section "Causes", do not use the bulletted style throughout.  It looks like an outline.  You could keep a few lower-level bulletted lists, but most of it should be rewritten as prose.
* What does "at sub-lethal concentrations" mean?
* I don't understand the text introducing suppressor mutations.  What are the two basic mechanisms?  How can streptomycin, which is a drug, be an example of a mutation?  What does the frequency of errors in codon-anticodon pairing have to do with suppressor mutations?
* Under "intracodon suppression", what are the three intragenic suppression mechansims?  What does "intragenic" even mean?  You introduced it in the paragraph above, but didn't explain it.
* The major section "Relationships with suppressors and other mutations" should be renamed, something more specific to suppression mutation, since that seems to be what each of the subsections is discussing.
* Only capitalize the first word of each section heading.
Klortho (talk) 18:22, 21 April 2013 (UTC)
replies: text: Thanks for your comments on missense mutation article. I see 5 of your comments that I can use from "at sub-lethal concentration" comment to "Only capitalize the first word" comments. I am working on a reference update request as other reviewers point out. I will get back to article again to change based your comments as well. Other parts of your comments would be valuable.82D team will use them in the upcoming update. /Mhk5600 (talk) 18:51, 21 April 2013 (UTC)
replies: text: Hello Chris. Please check missense_mutation article, if the latest update meets with your expectation. All of your comments were very much valuable and considered at best. Some of them are implemented directly. Wordings of “at sub-lethal concentration”, two basic mechanisms, relationship with streptomycin, capitalizing the first word of each section heading were updated. For other comments, we took our best approach to accommodate your review feedback as well as a focus of this article. For instance, as Byron mentioned,  specific wiki’s internal links are added for “intergenic mutation” and “intragenic mutation”, instead of adding a detail explanation of those terminologies. Other sections including the lead section and the section “Causes” were also updated in the same fashion. The current article is much better shape than it was. Happy editing. /Mhk5600 (talk) 05:43, 28 April 2013 (UTC)

text: Thanks Klortho! We are still deliberating on where to move the part on the nonsynonymous mutations but that is fairly high priority for us since multiple people have mentioned it. The lead section is also undergoing revision with all the suggestions you and others have mentioned. I agree that the causes section should be in prose form so that will be next in the queue. I actually didn't know that only the first word of each section heading should be capitalized but I'll keep that in mind as sections are added in the future. For some of the terms that you mentioned needed explanation, perhaps it might be better to link them since going into detail for those terms may be out of the scope of this article. Bcheon1 (talk) 04:49, 25 April 2013 (UTC)
thread_title:  Comments from Klortho 

message: I took a look at the comments I provided back on April 12th, and I see that you generally agree with my list of suggestions but haven't yet implemented anything yet other than the minor correction of replacing the indefinite article "This" with "missence mutation".  Thus, I won't reiterate my suggestions here -- except to note that the opening three paragraphs are still somewhat confusing and need work.  Among other things, I see that Klortho agrees with me that you should remove phrase “a type of nonsynonymous mutation” from the first sentence of the article (and move this phrase to somewhere later in the article where you can have the opportunity to explain what this means).  I think the opening paragraphs leave one somewhat confused regarding the distinctions between "nonsynonymous mutation" and "synonymous mutation", and I think that this confusion may, in turn, bleed through into the reader's understanding of the definition of "missense".  I also noticed a new "clerical error": It appears that the content of footnote 19 (the citation) has been deleted.  Best of luck in completing your article! Jgould1400 (talk) 06:33, 25 April 2013 (UTC)
replies: text: Hi Jgould1400, thank you for following up with us. We are currently still in the processing of rewriting the lead section. This is a fairly major edit so we decided to work on the draft on a separate document before implementing it here. We agree with your edit suggestions and plan to make sure that all of them are addressed in the next edit. Also, thank you for bringing the footnote error to our attention. It will be fixed soon. Bcheon1 (talk) 13:26, 25 April 2013 (UTC)
replies: text:  As I mentioned above, I really like the improvement to the opening! Jgould1400 (talk) 04:00, 3 May 2013 (UTC)
replies: text: Great! I'm really glad that the improvements we made to the opening were close to what you had in mind. Bcheon1 (talk) 18:21, 10 May 2013 (UTC)
thread_title:  Follow-up comments from Jgould1400 [[User:Jgould1400|Jgould1400]] ([[User talk:Jgould1400|talk]]) 06:33, 25 April 2013 (UTC) 

message: Hi there wiki editors.  I have been assigned your page to do my review on for this unit.  I see a very well formatted page, lots of good information, especially the section linking missense mutations to various diseases, overall very well organized.  The information appears to be clear and not contain too much jargon.  Only a few things I can think of to comment on: some of the wording, sentances, etc is a little choppy and could afford some basic grammatical editing, also I wonder if there might be some additional images you could use to visually show the various types of mutations related to missense, and finally, what kind of equipment or assays are used in the "computational approaches to predicting missense mutations"? PJCollettJHU (talk) 23:11, 29 April 2013 (UTC)
replies: text: Hi PJCollettJHU, thank you very much for reviewing this article. I think you've definitely made some great suggestions. I do agree that many of the sentences and even some entire sections could use some re-writing. This wasn't a priority for us before but now that most of the major sections have been added, we will definitely work on the writing to make it flow better. Now that you mention it, this article is lacking in visuals. I had a little bit of trouble in the past finding additional images that are suitable. However, we will take a another look using your suggestions. Bcheon1 (talk) 22:07, 30 April 2013 (UTC)

text: Thanks for your focused review. A goal from Unit 11-12 Wiki task was to make more improvement, taking inputs and suggestions from first reviewers. What you are pointing out are from sections we worked on mainly during Unit 11-12. Yes, those sections need update. We will work on them during Unit 14. For your last comment about equipments and assays related "computational approaches..", we can describe about it briefly. /Mhk5600 (talk) 07:57, 2 May 2013 (UTC)
replies: text: Hi PJCollettJHU. We have made updates in our article during Unit 14 based on last inputs from peer-reviewers. I hope you like our updates. Have a great summer. /68.116.172.204 (talk) 15:00, 10 May 2013 (UTC)
thread_title:  Unit 13 Review [[User:PJCollettJHU|PJCollettJHU]] ([[User talk:PJCollettJHU|talk]]) 23:11, 29 April 2013 (UTC) 

message: ===Earlier Suggestions===
I think you guys have done an excellent job in adding to this article. It is in a much better state than it was before you started working. I think you would benefit from implementing a number of suggestions that were made by our classmates and others. As Klortho mentioned, DNA is not mentioned at all in the lead.
===Lead===
This is somewhat brief. Again, try to be as broad in your lead as possible-- a sentence that generally explains each of your subtopics will lay the foundation for the in-depth subjects you cover below.
===Causes of missense mutations===
No big issues. Perhaps the organization of this section can be improved. Missense mutations are a type of point mutation. Depurination and deamination are types of spontaneous mutations. Induced mutations and DNA replication are sources of mutagenesis. Start this section with a sentence that clarifies the relation of all of these terms to each other.
Example: "Missense mutations are a type of point mutation caused by spontaneous mutations, induced mutations, or DNA replication and repair errors."
===Relationships with other mutations===
Kudos for following Klortho's suggestion on the structure. It looks much better without the bullets. In my opinion, this section should be at the end and should make up a MUCH smaller proportion of the article than the "Causes" and  "Specific diseases" sections.
===Computational approaches to predicting missense mutations===
No visible problems. I thought this section was done well.
===Specific diseases attributed to missense mutations===
Please take the advice of earlier contributors/comments-- the purportedly biased language is still there in the "Sickle cell disease" subsection. Consider just removing the word "erroneously" altogether and at least mention the advantage the heterozygous phenotype confers against malaria. There were a ton of minor spelling errors ("that" spelled "taht"; "int he" for "in the", which I changed to say "in addition to") that I've changed. Some subject-verb agreement issues were addressed as well. Try to avoid subjective terms like "interestingly" and "surprisingly".
===Experimental analysis===
This is ok if FASTpp is all you could find. Otherwise try to make mention of other analytical methods.
===Overall Impression===
The article is in good shape. You've done an outstanding job in adding to the worth of this article. It is now much more than a dictionary entry, and a substantial contribution to our understanding of mutations. Well done!
-MonopterusAlbus (talk) 20:13, 6 May 2013 (UTC)
replies: text: Thank you so much for your input! I agree that the lead section still needs work, especially in being proportional to the other section in the article. Also, I will be tying in DNA to the lead paragraph soon.  Bcheon1 (talk) 21:32, 8 May 2013 (UTC)
replies: text:  I look forward to seeing your revision.Jgould1400 (talk) 08:52, 9 May 2013 (UTC)
thread_title:  Comments from MonopterusAlbus 

message: The article is in good shape. You've done an outstanding job in adding to the worth of this article. It is now much more than a dictionary entry, and a substantial contribution to our understanding of mutations. Well done!
-MonopterusAlbus (talk) 20:13, 6 May 2013 (UTC)
replies: text: Thank you so much for your input! I agree that the lead section still needs work, especially in being proportional to the other section in the article. Also, I will be tying in DNA to the lead paragraph soon.  Bcheon1 (talk) 21:32, 8 May 2013 (UTC)
replies: text:  I look forward to seeing your revision.Jgould1400 (talk) 08:52, 9 May 2013 (UTC)
thread_title: Overall Impression