User talk:Chemkoach1/Nonsense mutation

Olivia's Peer Feedback

Content

Is the introductory section accessible for non-experts?

Yes, the introduction paragraph is pretty good for non-experts. For starters, many of the vocabulary words are linked in order for readers to help readers go to these pages if needed. The group only edited the last part of the introduction paragraph in order to include how nonsense mutations may lead to mutations. I think in order to make this information more accessible for all levels of readers, there should be some basic info explaining mRNA/coding strands and how bases are inserted to begin with before explaining a mutation.

Do the contents of each section justify its length? For the “suppressing nonsense mutations” paragraph, there are a few different ideas talked about within the same paragraph. This section could be divided into different paragraphs, and the content could be expanded on, maybe adding a visual to increase reader clarity. The genes and diseases portion is good and adequate in length. It is not the main focus of the page, however it is important content to include for readers to fully understand the impact nonsense mutations may have.

Are all the important terms/concepts linked to their respective Wikipedia pages for further reference? They did a good job at linking the important terms for this page, but there are a few more terms that could be linked. Some examples are “toxin” “fitness” “tRNA” and “anticodon”.

Are the highlighted examples appropriate? The example showing a nonsense mutation is both visually appealing and easy to understand. The associated amino acid sequence for the protein coded is also displayed, so it is visible how the nonsense mutation impacts the protein. However, there is room to add another example later on when the types of nonsense mutations are being discussed. For example, there is a paragraph explaining how a mutation at close proximity to the last amino acid is likely to be neutral. It would be beneficial for readers if there was a corresponding visual for this example.

Is the content duplicative of any other content already on Wikipedia? This article has similar content to DNA, sequence, and other mutation pages, but this is primarily because much of the information overlaps. However, all of the newly added diseases caused from nonsense mutations are pretty specific to this exact error, so this content is new. The possible outcomes of nonsense mutations part is also specific to nonsense mutations, and this information doesn’t exist on any other pages.

Figures Are the figures original and of high quality? There aren’t any figures on this page. The one example of nonsense mutation shows a sequence of DNA and how the mRNA error looks for a nonsense mutation, but this is the extent of any images. I think there should be figures added in order to help the reader with clarity on the content. One area that could really benefit from figures is the genes and diseases section. The descriptions of signaling pathways are very difficult to follow without a figure associated.

Are the figures informative and added to the text? N/A

Are the Chemdraw structures chemically accurate, aligned, and easy to read? N/A

References Are the references complete (≥ 10)? This group added six references to the original page. If they need 10 additional references in total, this means they need to add 4 more on top of these 6.

Are the references inclusive of non-journal sources? Yes, this group’s references are inclusive of non-journal sources. On top of sources from journals, they also included sources from the National Library of Medicine. The link for their 10th source doesn’t work, but besides this all of their other references look good and reliable!

Overall Presentation

Provide a short summary of the entire content/figures/references, highlighting both what the group did well and well as what still needs to be improved.

Overall, the group did a great job establishing the strengths and weaknesses of the previously existing pages. They greatly improved on the effects and genetic diseases caused by nonsense mutations, both in the introduction and by including an additional section to expand on specific diseases. They added an entire section explaining the three possible outcomes of nonsense mutations, which wasn’t included previously. They added a section on suppressing nonsense mutations as well, but this section is a bit hard to follow and could use some figures. Overall, the page would benefit from any figures; especially when specific mechanisms are being mentioned such as the TGF-b/BMP signaling pathway in the SMAD8 section. I really enjoyed reading the specific diseases caused by nonsense mutations, but more words in these sections could be linked to other wikipedia pages in order to add clarity. Overall, this group added a lot of useful additional information the page was previously lacking. Good job! 2601:400:C201:15D0:3020:71C4:8881:41EB (talk) 20:32, 13 October 2022 (UTC)

PR of Group 5 - Myron Shaba

Read the current Wikipedia site on the topic (if there is one). Read at least one review or reference article related to the topic.

Consider each of the following general questions and write a response in paragraph form.

■ Is the introductory section accessible for non-experts?

I think that the introduction section is somewhat accessible for non-experts, but could be improved. For example, when discussing the effects of a missense mutation on codons and protein synthesis, it may be useful to provide additional information or context on the molecular biology behind this process for those who may not be familiar with it. The first sentence of the introduction contains vocabulary like “Transcribed mRNA” that may be foreign to some readers. I would rephrase this sentence to say, “ A nonsense mutation is a point mutation in a sequence of DNA that results in a truncated protein,” followed by a detailed explanation of how and why this occurs. I think this change would make the introduction easier to follow for readers outside of the molecular biology space.

■ Do the contents of each section justify its length?

Yes. I believe the group does a good job of ensuring that the sections are not too long or too short. I do believe that more information could be added to the associated disease section since only two examples are provided. I also think the length of the introduction will improve with the necessary adjustments mentioned above.

■ Are all the important terms/concepts linked to their respective Wikipedia pages for further reference?

I think that the group does a strong job in the beginning of linking important concepts to their respective Wikipedia articles. I would recommend doing so in the rest of the paper as well. For example, in the “Suppressing Nonsense Mutations” section, you could link the word “eukaryotes” to its wiki page.

■ Are the highlighted examples appropriate?

For the example section, I would change the title to “Example.” I would also add some additional information here about what it is the diagram shows. For example, The first sentence could be, “Pictured above is...” followed by your explanation. Otherwise, this is a good example of what a nonsense mutation looks like from a base-pair perspective.

■ Is the content duplicative of any other content already on Wikipedia?

I could not find any related content on Wikipedia that was duplicative of the group’s article. I believe that the page is original and unique.

Figures

The Wikipedia article is missing figures, which I think would be tremendously helpful in making it a bit more visually appealing and informative for readers. Maybe add a figure showing a ribosome translating mRNA with a nonsense mutation? This would make it easier for non-experts to grasp the concept.

References

■ Are the references complete (≥ 10)?

The number of references is sufficient, but some of the references appear to be missing crucial information (written in red) such as dates and journal names. I also noticed that one of the references is linked to a web archive, “Wayback Machine” which I believe needs to be changed to the official website where the information is coming from.

■ Are the references inclusive of non-journal sources?

Yes, the group cites references from the National Library of Medicine outside of their journal sources.

Overall

■ Provide a short summary of the entire content/figures/references, highlighting both what the group did well and well as what still needs to be improved.

I think this is a very good start to a strong wiki article. The group starts by introducing the concept of a DNA mutation and goes on to mention how it affects protein structure as well as the diseases it may cause. I think the group did well in linking important concepts to their respective wiki pages in the beginning. For the introduction, I believe it can be reworked to add in some necessary contextual information and make some adjustments to the sentence structure. I would also add an independent clause to the second-to-last sentence of the first paragraph, “As nonsense mutations…”  to make it a complete sentence. I would also recommend adding at least one figure to make the page more explanative and complete. The group does a good job ensuring that section lengths are appropriate for the most part. I would recommend adding additional information to the example section to make it more descriptive, otherwise the example provided is good. Additionally, the “Genes & Diseases Associated with Nonsense Mutations” section needs to be revised as it is currently a direct copy/paste from the referenced articles for both paragraphs. Lastly, the references are mostly good with some of them just needing a few details added in. Overall this is a very good draft with much potential for improvement. Shabam111 (talk) 03:33, 14 October 2022 (UTC)

Chem 455 Wikipedia Project Peer Review: Mary Show

Content

Is the introductory section accessible for non-experts? The revised introduction section is a good start to explaining what a nonsense mutation is and its basic attributes. I think the group only revised the last paragraph of the introduction where it discusses nonsense mutations pertaining to diseases. The group can expand the first paragraph of the introduction to make it more accessible for non-experts. The first paragraph jumps into genetics which many people have a limited understanding of. The second paragraph of the introduction implements a wise way to differentiate nonsense mutations from other mutations that non-experts could get confused which I think is a good idea! The third paragraph about the disease may be better suited in a separate category on the Wiki page and can be more briefly mentioned in the introduction.

Do the contents of each section justify its length? The contents of each section somewhat justified its length. As mentioned in the previous paragraph, the last paragraph of the introduction could have been divided and organized into its own section. I know there is a “genes and diseases associated with nonsense mutations” section, but the group may consider adding the diseases from the introduction to that section and elaborating more on them.

Are all the essential terms/concepts linked to their respective Wikipedia pages for further reference? The group does an adequate job linking their page for further reference, but there are many words on the page that may benefit from a link. Some of these include mutation in general, the diseases they mention in the last paragraph of the introduction (since they don’t elaborate on them), gene silencing, DNA sequence, transcript, etc.

Are the highlighted examples appropriate? The highlighted example that shows the nonsense mutation is easily understandable and the nonsense mechanism is described simply. However, this was already found on the page prior to the group’s edits. The group could improve on this aspect of their revision by providing another example of the mechanism with a disease they mention in the introduction or in the “genes and diseases associated with nonsense mutations” section.

Is the content duplicative of any other content already on Wikipedia? The content is a bit duplicative of the mutation wiki page but that is understandable because nonsense mutations are a type of mutation. Furthermore, the diseases and disorders described on the page are a little duplicative of the Wikipedia page “List of genetic disorders”. The group does a good job of describing the content in a way that is not too repetitive of the existing content on Wikipedia but should be cognizant of this repetitive risk when adding more content for their revised draft.

Figures

Are the figures original and of high quality? Are the figures informative and added to the text? Are the Chemdraw structures chemically accurate, aligned, and easy to read? The group does not include any new figures in the first draft. They should highly reconsider adding figures to the revised version to further emphasize the concept of nonsense mutations. These figures should be high-quality originals. The figures that are currently on the page are informative and high quality. The group should find more figures like that to implement on the page. One suggestion of the type of figures the group should include could be mechanisms to which specific diseases are activated based on a nonsense mutation. The group should also include one or two ChemDraw structures. These can be replicated nucleotide sequences of the genetic code showing the three types of stop codons that could result in a nonsense mutation.

References

Are the references complete (≥ 10)? This group has added just six references to the original page of nonsense mutations. They should include at least four more references to their draft based on the additional information they will include in their final revision. These should be inclusive of non-journal sources and references that add validity and reliability to the original page.

Are the references inclusive of non-journal sources? The group’s references are inclusive of non-journal sources. They have reliable sources from non-journal websites including the source from the National Library of Medicine website about LGR4. There is a good balance between references from journals and non-journal sources. When the group adds more references to their final draft, they should continue to add sources from both categories. Great start though!

Overall Presentation

Provide a short summary of the entire content/figures/references, highlighting what the group did well and what still needs improvement. Overall, this was a great start! It is obvious that the group put in the time and effort in attempting to make the nonsense mutation Wikipedia page better based on the first draft. There are definitely ways they could further improve the page. These include expanding more on the content they presented, such as the disease they presented in the introduction. Furthermore, the group should include more references to the revised version. They need at least four more reliable sources due to there only being six new references in the first draft. It would be ideal to have more than 10 sources in the final draft. Also, the group should definitely include figures in the final draft. This would be essential to construct an effective finalized draft that improves the understanding of nonsense mutations. It would be beneficial to include the figures so readers can find the page an easier, more appealing read. The first draft did a great job introducing new sections such as possible outcomes of nonsense mutations, suppressing nonsense mutations, and genes & diseases associated with nonsense mutations. With the suggestions stated throughout this peer review, the group can further improve the page! — Preceding unsigned comment added by Maryshow (talk • contribs) 03:40, 14 October 2022 (UTC)

Isabel's Nonsense Mutation Peer Review 1

Content

1. Is the introductory section accessible for non-experts?

The introductory section could definitely be elaborated upon to ensure that all readers are able to understand the literature. Further elaboration on exactly what a point mutation is might help the reader better understand its relation to nonsense mutations, not just because it was said to be related. They do a great job at differentiating the nonsense from other DNA mutations, however, the addition of information on what a point mutation is will better help the reader. Application of the mutation to diseases is a great way to help non-experts understand the importance and increase interest as they might learn why this is a relevant article.

1. Do the contents of each section justify its length?

Yes, for the majority of the article, the contents do justify its length. However, the content specifically in the Suppressing Nonsense Mutations section could benefit from subsections such as done in Genes & Diseases Associated with Nonsense Mutations and Possible Outcomes… sections. This might help clarify and separate the content in a way that can make the reading more digestible. Another suggestion might be to follow the structure and length of the Pathology Associated with Nonsense Mutations section as it is a perfect length and includes a graphic that only allows for better understanding.

1. Are all the important terms/concepts linked to their respective Wikipedia pages for further reference?

For the most part, the editors did a good job linking the important concepts. However, links to words such as chain termination mutations, tRNA, mRNA, translation, transcription, nonfunctional polypeptides, etc. might help significantly clear up any confusion for non-expert readers.

1. Are the highlighted examples appropriate?

Yes, the highlighted examples are strong and appropriate in demonstrating a non-sense mutation. To take this a step forward, the incorporation of images with each example that is included of each of the types of non-sense mutation might better help and be helpful for the reader. However, even in the introduction, the editors do a great job of incorporating several examples to further simplify the subject matter.

1. Is the content duplicative of any other content already on Wikipedia?

It has a lot of overlap with the nonsense suppressor and the Suppressing Nonsense Mutation, however, this is highly understandable as the Wikipedia page of the nonsense suppressor should provide more detail on the subject than provided in this paper. However, this is to be fully understood and expected as they are covering the same material. Overall, this Wikipedia article is not duplicative of other content and does a great job of introducing readers to nonsense mutations in detail.

Figures

1. Are the figures original and of high quality?

No new figures were added by this group.

The first two figures included for the example are great in showing a nonsense mutation in high quality and very clear. They are original in composition however, not original in content which is a quality that makes the content more understandable so that the reader can directly understand it.

There is only one other figure included on the page and it was added by the previous author. Additionally, the figure included is not very specific to nonsense mutation and does not relate the diseases highlighted in red back to the Wikipedia page. It is highly recommended that they include figures that can better support their explanations. They could take inspiration from the previous author and do a similar figure however relating it back to the diseases that are mentioned by them in the article. They could also create figures for the types of mutations to clearly demonstrate them.

1. Are the figures informative and added to the text?

No new figures were added by this group.

The first two example figures are great in informing and directly showing the reader an example of the nonsense mutation. However, the second figure does not have any relation back to the disease mentioned in the article. Suggestions are mentioned in question 1 of the figure section.

1. Are the Chemdraw structures chemically accurate, aligned, and easy to read?

There are no Chemdraw structures included. Suggestions are mentioned in question 1 of the figure section.

References

1. Are the references complete (≥ 10)?

The group only added 6 new sources to combine with the original 8 already provided by the previous author. They should include more of both non-journal and journal sources to complete the requirement.

Additionally, they should make sure that all their sources are still accessible. For example, their  "PTC Therapeutics | ataluren". PTC Therapeutics. Retrieved 2017-10-05 is no longer available.

1. Are the references inclusive of non-journal sources?

Yes, they do include a non-journal source, however, they should definitely include more to add to their sources. That seems to be the only non-journal source included.

Overall Presentation

1. Provide a short summary of the entire content/figures/references, highlighting both what the group did well and well as what still needs to be improved.

Overall, the group has a very strong start to fine tuning their Wikipedia page. The edits they have made have only provided a greater understanding and have made the content far more digestible for the reader who might not be familiar with the content. The examples that are introduced throughout the page are pivotal to this. Furthermore, the inclusion of the prevalence of diseases that result and the types of the nonsense mutation have only strengthened their paper. Their overall organization and clarity in structure and explanation make this page user friendly.  However, I would highly recommend they review their links, making sure that keywords such as chain termination mutations are linked so readers (apart from getting a general understanding from the page) can explore more about such topics linked to nonsense mutations. Additionally, there should be an introduction of figures, whether they be concerning the diseases discussed or on the types. This will only strengthen their page and allow readers to have a better understanding. Finally, the addition of more sources, specifically non-journal sources, will also diversify the sources available and only allow for greater understanding. Overall, great job!

~~~Isabel Sanchez-Tembleque Wood Isabelstw (talk) 03:42, 14 October 2022 (UTC)

MLibrarian Feedback

I like how article was expanded and structured. I just want to suggest finding a way to combine sections on "Genes & Diseases Associated...." with "Pathology Associated...". Those are similar concepts and if you could structure them into one section it would be more logical, I believe. Also, please add links to other Wiki articles (you linked many but not all). Another important thing - please spell out all abbreviations (ENDOGLIN, SMADF, TGF-b/BMP) as Wiki articles are for everyone including people who are not familiar with the specific jargon. First time something is mentioned, it is important to spell it out.MLibrarian (talk) 19:17, 20 October 2022 (UTC)