User talk:Oliviasw/Deoxyribonuclease

Deoxyribonuclease Peer Review 1

The “Structure” section requires better explanation and contextualization of terms. Currently, the three bullet points do not make sense to an audience who lacks prior knowledge of BthDNase II and PLD family members. This section contrasts the structures of different DNases, but it never provides an actual structural description. I suggest describing a generic or reference structure. I would also suggest adding an image to help visualize the the structure. You could use the PDB and PyMol to create the image.

The headers “Modes of action” and “Mechanism” seem confusingly similar because a mechanism is a mode of action. Furthermore, the “Modes of action” section does not actually talk about modes of action, but instead discusses different types and a therapeutic use in cystic fibrosis. I suggest moving this information to the sections “Uses” and “Types.” Also, do you have a citation for the cystic fibrosis information?

The “Mechanism” section begins by mentioning the “PLD family members,” which is a term that the article still needs to explain. As the section continues, the information is highly specialized and citations must be provided. I worry about potential plagiarism issues here. For example, the word “our” in the phrase “comparison of our BthDNase II crystal structure” hints to that phrase being copied directly from a journal article. I would also suggest writing this section in prose rather than in bullet points to better match the style of wikipedia. Providing an image would help the reader visualize how the different residues are contributing to hydrolysis.

I would suggest converting the “Types” section to prose rather than bullet points.

In the “Assay” section, there is a note for “citation needed” which needs to be filled in with a citation.

Raspberry Neuron (talk)Raspberry Neuron

Deoxyribonuclease Peer Review

Looking at the introductory section I believe that is general enough and accessible for people who aren’t experts. I like the idea of adding a section for the structure of Dnase. However, it could be beneficial to expand it a bit more because currently, I think it would be difficult for a non-expert to understand it. I also think the structure might be a little too specific without further contextualization. A way to maybe provide some context is to expand more generally on what the secondary structure is (alpha helix etc). There also don’t seem to be citations for the structure section so that is important to add.

In the "modes of action" section it doesn’t seem to connect well between the points listed which could also be changed to a paragraph format. The general use of the word “some” in this section is too vague and could be more specific. On the other hand, you might be able to place some of this information under types or mechanisms as it talks about cleavage. At the end of the “modes of action” section there is an example given of cystic fibrosis treatment. This placement doesn't make sense and should be moved to "Uses" or its own section. The "Uses" section could also use some introductory sentences.

In the mechanism section, there don’t appear to be any citations and it also appears to be coming from a specific paper so adding those to the corresponding sentences is important. In general, this section is very specific, however, that gets a little confusing for non-experts so it might be worth it to rephrase this section to be more general.

I like the expansion of the “Types” section and the in-depth characterization. The bullet points are a little disjointed and either could be connected better or simply put into paragraph formatting. In paragraph formatting, it might be worth it to use the headers and subheaders to separate the various types. Once again, for this section citations need to be added.

Figures could be added as well since the original page only has one at the beginning. A potential location for a figure is at “Types” with the structure of Dnase1. You could even do a ChemDraw for part of the reaction mechanism or provide a structure for the section “Structure” using ChemDraw or Pymol if you want to show secondary structure components. Chem455umich (talk) 02:53, 14 October 2022 (UTC)

Deoxyribonuclease Peer Review 3

The "Structure" section of the article would be easier to understand if it was written in sentences instead of the bullets points. Additionally, more information should be added because as a reader it is very difficult to understand with the information currently available. The content currently in this section appears to be relevant and important but just needs more context to be better understood. This section also lacks any citations at all which should be added to make the information credible.

The "Mechanism" section of the article is more detailed but is still written in bullet points when it would benefit from being written in cohesive sentences. There are many terms such as "covalent intermediate", "PLD family members", and "H279" that all need a definition and/or explanation. Readers without background in this knowledge do not already know what these terms mean which makes the material too technically different to understand. Again this section is also lacking any citations at all. This is important to make information credible and avoid plagiarism. I also think there could still be more details added to improve the section overall.

The "Uses" section of the article has an intriguing topic sentence but it lacks any citation. Following this, the paragraphs in this section do not follow what was introduced in the topic sentence. While health-related, they are not the same ideas presented in the beginning. This section could also use further detail and explanation.

The "Types" section of the article contains much more information but also lacks any citations. It is also in bullet point form and should be changed to full sentence structure which is how most wikipedia articles are written. By writing this section in full sentences it will also help provided the context and explanations that are needed.

The "Assay" section of the article needs a bit more explanation on what an assay is and why it is important. This would provide context and help the rest of the section make more sense. This section also does not have any citations.

Overall this article has a good start but needs substantial changes. There is hardly any citations within the article which makes most of the information irrelevant because none of it is credited. There are also only four references listed for the entire article which is not enough for the amount of information written. The whole article needs refinement including more details, examples, definitions, and explanations.

Izcabral (talk) izcabral Izcabral (talk) 03:28, 14 October 2022 (UTC)

Deoxyribonuclease Peer Review 4

The introductory paragraph is clear and understandable for non-experts. Group 4 added a section named Structure which can help the audience grasp a basic idea about the chemical complexity of this enzyme. I suggest group 4 to use images of DNase structures. This section will be easier to follow with visuals.

The Modes of Action section is a bit vague in my opinion. This section can be combined into Types when specifying how different DNase functions. It could also be improved by providing more information on how the DNase specifically acts on the target.

The Mechanism section could also use some images to illustrate each step of the process. I think this new section is a great way to help the audience learn more about DNase; however, Group 4 needs to add more references to back up their statements.

The Uses section remains unchanged. I suggest group 4 rename this section to protocol and move it after the assays section. It is a bit abrupt to have a section on DNase’ usage in wet labs in between explaining their chemical and molecular properties.

The Types sections are expanded with a lot of useful information compared to the original Wikipedia page; however, the bullet point format seems really disorganized. It is really difficult to follow some of the points such as Normal pH and Nonspecific except for at AP site. There are also typos in spelling. This section would be better if written in paragraphs.

The assays section needs more references and content. Group 4 made some changes that explained the mechanism of DNase assays. This section can be improved by addressing the protocol of the assays at the end.

Overall, I think Group 4 did a great job organizing and expanding the content. It would be a lot better if they can provide some visuals and cite their references. Lmc2001 (talk) — Preceding undated comment added 05:40, 15 October 2022 (UTC)

MLibrarian Feedback

Generally speaking, this article needs more work, it needs to convey a story and the formatting shall be appropriate. 1) Article draft seems to be a section heading now, I hope you are planning to change that. The introductory definition shall belong to no section, just as it is in the original Wiki article; 2) Are you planning to have a figure for structure? If not, these couple of sentences could go without any special sub-section and be combined with existing sections. 3) As Wiki article is for general public, you cannot expect that people will know the jargon. Therefore, please spell out all the abbreviations and/or link them to existing Wiki articles. For example, Phospholipase D (PLD) and a link to https://wiki.riteme.site/wiki/Phospholipase_D 4) Provide as many links as possible to existing Wiki pages. For example, M. Kunitz to https://wiki.riteme.site/wiki/Moses_Kunitz 4) Mechanism section would benefit from a picture 5) I do not think that section "Types" shall be here. The first sentence where you link to existing wiki pages could easily go to the top paragraph. You can in turn add information to existing Wiki pages on deoxyribonuclease I and deoxyribonuclease II but I would not write much about them here. MLibrarian (talk) 20:57, 19 October 2022 (UTC)