User talk:Cherrysu/sandbox

Welcome to my talk page!

The article in sandbox is still in progress. We will add more contents in section 'Structure' later. Feel free to leave suggestions and comments here.

Cherrysu (talk)

Structure and function” section
-Perhaps you can include a schematic diagram of how this riboswitch works? I didn’t see any diagram in the Wikipedia page for Riboswitch. Visualization is very useful to make your explanation more comprehensible.

-Explicate what “docking” and “undocking” state is in biochemical term (e.g. x part of mRNA is exposed in docking state) for clarity

Transcriptional Regulation” section
-Fix the reference after the first sentence

-Maybe you can provide a link leading to another Wikipedia for your last phrase, “Off-regulation of genetic expression”? I’m not sure if that’s what it’s technically called. Are you referring to transcriptional termination?

Translation regulation” section
-How does the concentration of Mg salt affect the docking/undocking equilibrium? Does higher [Mg] favor docking equilibrium? What is the biochemical mechanism behind that?

Physiological relevance in bacterial gene regulation” section
-First paragraph of this section should be revised for grammar to make it more coherent.

-In the last paragraph, there is redundant information, namely the inputting of queuine into the first anticodon position of tRNA

-Are there specific species of eukaryotes more susceptible this queuine deficiency? Going beyond biochemical implication, what are other complications that could arise from queuine deficiency that affects the eukaryote’s survival capability?

Matt Chadwick Peer Review
Matt Chadwick Peer Review

Introduction - Great introduction here. You succinctly described what preQ1 riboswitch is within the first sentence. However, in the very next sentence; I wasn't sure what the queuosine pathway is, so maybe provide a link to a wikipedia article or end that sentence with a source so I know where to go find more information about it. The wording of this sentence could also be better phrased. Although I think I know what the sentence is trying to say, it could be made more clear. Also be sure to double check grammar throughout the article while your editing it. In the last sentence "an" should be taken out as the sentence is referring to two riboswitches not a singular one. I don't know if the wikipedia editors are sticklers for grammar or not.

History Good background here, perhaps give credit to the lab that found the preQ1 riboswitch even though you gave references.

Structure and Function I also agree with Monica about providing an additional image regarding the mechanism of the riboswitch, as it's one thing to read about it, but another to actual get a visual representation of what is actually happening. Again check spelling and grammar in this paragraph, you meant "from" but said "for" in the second sentence. Also provide links to the other wikipedia sites when you mention technical terms such as "intercalation", "heteroatom', "ligand" and etc. Overall though, this paragraph was highly informative.

Transcriptional regulation Here, the first sentence needs to have a proper reference. This paragraph was fairly technical and verbose in my opinion. If we are trying to share the science of pre Q1 riboswitches to a larger audience I think the paragraph needs work to make it more understandable. For example, instead of saying pre Q1 riboswitch mediates transcriptional attenuation, you could say pre Q1 riboswitch causes early termination of transcription. Both phrases are correct I believe, but one is more readable. Furthermore, the mention of terminator and anti-terminator was hard to follow as each word is mentioned several times within a short period of one or two sentences. Likewise, it's not immediately apparent of what you mean when you say the anti-terminator or terminator hairpin so the reader might get lost in the technicalities of the topic.

Translation regulation It might be my own bias coming into play since this made direct references to the news and views article we wrote about, but I found this paragraph more fluid and understandable. Of course, provide links to the wikipedia articles again such as when you mention the Shine-Dalgarno sequence. I also notice you've mentioned docking and undocking in almost every paragraph. It might be worthwhile to take a few sentences to explain that concept if you can't just provide a wikipedia link to another article explaining it.

Physiological relevance in bacterial gene regulation Good paragraphs here. Very informative. "its output impacts the amount of two proteins that are in the coding region of the Tte mRNA, which are TTE1564 and TTE1563." This sentence needs to be re-worded. It should probably be split up into two sentences to make more clear the connection between Tte bacteria and the two different proteins preQ1 riboswitch interferes. I also thought there was some redundancy in the last paragraph. Additionally, I think you can go even further here, and that this section warrants more information, or could even be cut down. I think this paragraph lacks a clear main idea and is juggling multiple ideas at the same time. — Preceding unsigned comment added by Chaddy1080 (talk • contribs) 22:46, 19 October 2016 (UTC)

Jeremy Lynn Peer Review
Content: The modifications made to the existing PreQ1 riboswitch paragraph successfully improve the accessibility of the topic by simplifying the language and clarifying the terms. The opening paragraph of your updated page therefore serves as a strong introductory paragraph for the rest of the content. Generally, the content length of each section is justified by richness of information presented. The “history” section of your page is well written and provides a sufficient chronological account of the topic. In the “structure and function” section, perhaps consider relocating the last two sentences to their respective sub-sections. Mentioning that the transcriptional and translation regulation methods are the two most common types of gene regulation mediated by PreQ1 is sufficient here. Readers interested in learning more about either of these specific topics will likely read the subsection written specifically on the topic, so it is not necessary to state that information preemptively here. Instead, consider placing these two sentences as introductory sentences in their respective sections. Furthermore, there are several instances in the “structure and function” section and the three proceeding sections where words are not linked to their respective Wikipedia page. For example, messenger RNA (mRNA), pseudo knot, and RNA polymerase are all examples of terms with existing Wikipedia pages to which these terms should be linked. Finally, I found the “physiological relevance in bacterial gene regulation” section to be very dense and technical. While this section effectively puts forth factual information, perhaps try adding explanatory statements to this section to open the topic to a broader range of readers. Overall, the page does a good job of presenting new information that is not currently present on Wikipedia, and successfully adds to the existing content on riboswitches.

Figures: The PyMol figure added to the page is both professional and original. The substance of the figure appears to be accurate as well. Proper citation is given to the original crystal structure. To add importance and meaning to this figure, perhaps consider adding a sentence referencing and explaining the figure in the actual body of text.

References: The addition of 13 new primary research articles to this page is sufficient. However, it appears as though you need to add references to the translation regulation section. The paper we read for the first news and views article definitely needs to be added when you talk about the translational riboswitch from bacteria Thermoanaerobacter tengcongensis (Tte). Otherwise, all information seems to be sufficiently cited.

Overall Presentation: The page is professional, well organized, and easy to maneuver. The layout facilitates fast retrieval of specific information. Very well done. — Preceding unsigned comment added by Jerlynn5 (talk • contribs) 00:24, 20 October 2016 (UTC)

Brady Reeves Peer Review
Content: The deletions you made to the existing introduction/page were helpful in the sense that detailed information was moved into later sections. This left the basic information, which gives the reader an idea of what the preQ1 riboswitch is. I might suggest switching the usage of “cis acting element” with transcription and translation regulator, or something a little more basic for use in the introduction. Also, I don’t see the importance of the atomic-resolution 3D image in the intro, especially when you have an entire section for structure and function. I would also try to highlight more key terms in the intro such as aptamer, as these terms have pages and are not trivial. As for the history section, I am impressed with how much was researched regarding this topic because there was no history on the previous page. However, I would try to add concrete dates in the areas where “later on” and “recognized even later” were used. Unless the specifics are not known, I would add a date or change the wording because it kind of sounds like a guess the way it is written. Under structure and function, I thought the entire section was well thought out, and the information is present. The headings neatly encapsulate each section, which gives the reader landmarks to guide their reading. I would definitely link many words to their respective pages and reference more frequently. There are quite a few sentences that feel like common knowledge since we just wrote a News and Views on the topic, but I think that due to the youth of this topic, basically everything regarding the riboswitch should be cited. The physiological relevance section was kind of confusing to me. The first paragraph is informative about the riboswitch and its relevance, but it is kind of “choppy” and should be revised to flow better. The second paragraph doesn’t really seem like it belongs on this page. I understand that these effects are the result of the activity of the riboswitch, but I think the level of depth involved with this process should be on the page of the enzyme rather than the riboswitch. I suggest being a bit more broad with the physiological relevance section, but I may be missing the point you are trying to make.

Figures: The figure is both easy to interpret and located appropriately on the page. The only suggestion I have regarding the figure is a better explanation to what the bound state and free state mean. I know it may seem self-explanatory, but simply stating that the RNA is bound to preQ1 in the bound state and noting the differences in the two figures would allow the figure to be interpreted without reading the entire page.

References: The page seems to be well researched, but I would just add the sources to the text as stated earlier in the critique. Also, the rubric suggests adding non-journal sources, and as far as I could tell, all of your sources were from primary sources. It may be useful to reference a well-known biochemistry textbook for small bits of information in the structure and function section, such as the first sentence of translation regulation.

Overall Presentation: It is apparent that the topic was thoroughly researched, and the page passes the eye test, meaning that when I visited your sandbox, the page felt like an existing page rather than a draft. As mentioned earlier, I would focus on linking key terms, properly referencing throughout the text, and placing sentences under the appropriate heading. Also, since the paper we read for the news and views explained how the riboswitch could have many different degrees of regulation based on preQ1 concentration, information beyond just the ON/OFF switch could be added. Looking forward to seeing the final product of this page! — Preceding unsigned comment added by Reevesbl (talk • contribs) 01:20, 20 October 2016 (UTC)

Additional comments from the librarians
Overall, a well-structured rewrite, as your peers have already mentioned. My main suggestion is that you be more thorough in linking the technical terms in the article to their existing Wikipedia pages - it appears that most of the links included in the text are the ones that were inherited from the previous version of the article. ScottMLibrary (talk) 19:05, 20 October 2016 (UTC)