User talk:Ssh514/sandbox

Bacterial DNA binding protein Peer Review 1

I thought your page is very informative. I thought the way it was broken into sections was good and easy to understand. I thought the introduction was fine, but make sure to define some abbreviations. For example, HU and IHF. Also consider linking those to their own wiki pages to make it more accessible to someone who isn't an expert in the field. I broke up the wiki page by section to comment on them specifically: -History- Good start, but add more about the specific research that was done that lead to its discovery/further research. -Role in DNA Replication- Question: You talk about SSB here, is that similar to Bacterial DNA binding protein? Make this clearer, or just don't mention it. Also, I think SSB has its own wiki page, so you could link it! -Examples- I really liked how specific and detailed the examples are; however, I think it might be a better layout to have a "function" heading and then add the examples as a subsection of the function heading. I think this would be more useful for a user trying to learn more about the binding protein- rather than making them read more to find the information they are probably looking for. -References- I think we are supposed to have at least 5 resources for this assignment. I think if you could find a couple of more papers, you could expand more on both the introduction and the function of the Bacterial DNA binding protein. I thought the overall look of the page was great. The order of the sections made complete sense and it was easy to follow. As I mentioned earlier, I think you should consider making function its own section, rather than examples. Definitely keep the examples in the page though! I thought they were well though through and could work as a subsection of a function heading. Good job! Kvbayne (talk) 01:18, 21 October 2015 (UTC)[reply]

Bacterial DNA binding protein Peer Review 2

Devon Pendlebury 23242030 Content: The content has been improved from the original page. If there are any other functions of DNA binding proteins this might improve the page. Another interesting topic to talk about is whether any DNA binding proteins are being targeted in antibiotics or disease treatment? E.g. http://www.nature.com/ncomms/2014/140611/ncomms5124/full/ncomms5124.html I think the introduction is good and could be mostly understood by the general public. The history section is only 2 lines long so maybe could be omitted or extended. The examples given are good and seem relevant to the field. I think it would be helpful to explain what HU and IHF abbreviations are straight away when they are mentioned. You explain IHF but not where HU protein gets its name from. Figures: A figure would be helpful to add. Perhaps a crystal structure of one of the proteins if these are available or some kind of schematic of them interacting with DNA. References: Good job at updating the references so that they are newer and more relevant but an increase in the number of references might improve the page. All of the references are from journal publications so more variety could be included although I understand this might be hard to find. Overall Presentation A figure would improve the overall presentation. The group did well on improving the content and length of the page and gave specific examples to help improve their explanation of function. I was a bit confused by the DNA replication section. Are all DNA binding proteins involved in this or just the SSB protein? If just the SSB protein then maybe this should have it’s own section in the examples area. I like the order and flow of the sections overall. Devon286 (talk) 14:42, 22 October 2015 (UTC)[reply]

Bacterial DNA binding protein Peer Review 3

Content: I like that you have simplified the introduction to make it more accessible to read but I still think that this can be improved upon by stating full names to things before introducing the abbreviation. I think that instead of stating that it has a variety of functions you can include examples of it because saying variety is too vague. links to other wiki pages on HU or IHF would be helpful.

In the second paragraph i think it wold be useful to give the size of HU so that the reader can have a relative idea as well as a what abundance of residues contribute to it being chemically basic. The sentence that includes “protein in high abundance coming out from DNA cellulose under high salt concentrations." is confusing and could be elaborated on to make what you're trying to state more clear.

In the third paragraph, you introduce RNA polymerase and then SSB and then in the next paragraph you talk about why they are important to the topic. This is a bit choppy, I think it would be more impactful if you introduced one and then discussed the importance of it and then do the same for the next and at the end tie the two together at the end. You cite an authors experiment in this paragraph but this is the first time this person has been introduced so you should sing it Name et al. then you can refer to it as the authors later.

In the fourth paragraph what do you mean by intrinsic curvature, you should either explain it or link to another page that does. Please also include links to the site on rRNA, P1 promoter, and RNA polymerase.

In the last paragraph, again i think you should state the group you are referring to by name and have links to the wiki site for mRNA, rpoS, and DsrA.

Figures: I think figures would make a huge difference in the clarity of the article. Perhaps crystal structures or figures of how it is interacting with DNA.

References: I like that the references are much more up to date than the current wiki article, but I think you could use more to strengthen the argument.

Overall There is a lot of improvement from the current wiki page and the break up of the topics makes sense. I think if you made specific functions their own section then it might help with the flow and clarity of the article but if not it still makes sense the way it is currently. I do think that reading a few more papers might help to expand on some topics but overall good job! Sjocox (talk) 18:25, 22 October 2015 (UTC) — Preceding unsigned comment added by Sjocox (talk • contribs) 18:08, 22 October 2015 (UTC)[reply]

Bacterial DNA binding protein Peer Review 4

I completed a peer review of the Bacterial DNA-Binding Protein Wikipedia page. To begin, I read a scientific article about the protein entitled, “The Bacterial DNA-binding Protein H-NS Represses Ribosomal RNA Transcription by Trapping RNA Polymerase in the Initiation Complex.” This article gave me a strong overview of the protein, allowing me to critically analyze and review this wikipedia page. I next reviewed the current wikipedia page. This page contained little information and was not written in a clear and concise manner. Additionally, the only section present was the introduction, leaving plenty of room for edits.

I next moved on to review the Sandbox version of this page. The first thing that struck in a positive light was the simple and clear writing of the introduction. Unlike the dense and difficult to read version of the original page, this version was clear and concise. However, I do think there is room for improvement in this section. First off, I would change the wording of the second sentence to say, “They are commonly referred to as histone-like, as they share many similarities with eukaryotic histone proteins, including the ability to bind directly to DNA.” I would also change the wording of the second paragraph’s first sentence to, “An example of a Bacterial DNA Binding Protein is the HU protein in E. Coli…” Additionally, I would change the next sentence to say, “Another example is the Integration Host Factor (IHF) protein, which can wrap DNA…” as it is unnecessary to state what IHF stands for a separate sentence. Next, while I think the original page’s intro was too dense and poorly worded, I think the new page should have a meatier introduction with a little more information. In other words, this page does a good job of cleaning up the original intro, but I think there is room to add more information and to give a stronger overview of what this family of proteins is all about; give me some more information so I don’t have to read the entire article to have a solid understanding. That being said, the article is definitely friendly for non-experts to read right now and the examples are appropriate. Additionally, this content is duplicative of the intro on wikipedia right now, so that material must be deleted when you post this content. Also, the intro section is lacking citations, which is a big no-no. If you are going to take information from the original page, be sure to keep the citations. Finally, terms in the first paragraph missing links to other wiki articles include: proteins, DNA, eukaryote, amino acid, dimer, and genetic recombination.

Next, I read the “History section. I felt this section was lacking content. The first sentence has no backing and the material in the second sentence could definitely be expanded upon. Tell me who led these first investigations and what else they found. Were there further experiments done? Again, this section is lacking citations. Finally, terms missing links in this section include: eubacteria, cyanobacteria, archaebacteria, transcription, cellulose, concentration.

The “Role in DNA Replication” section is much more detailed than the previous section. My first minor suggestion is separating the “Research suggests” and “The protein is involved” into two separate sentences. My second suggestion is to provide context for the SSB protein. IS that an example of a Bacterial DNA Binding Protein? If so, this is not stated. Additionally, rather than ending the paragraph with ‘the role of SSB protein during DNA Replication has been studied,’ continue on to tell me about these studies in the same paragraph. Finally, terms missing a link in this section include: lagging strand, nucleotides and replication fork.

The H-NS section is very well written! My only notes are about missing links, including Histone-like nucleoid-structuring protein and rRNA. Otherwise this section is great and has appears to have all necessary citations! The HU sections is also very written. It is missing links for translation, transcription, alpha helix, beta-sheet, DsrA RNA and rpoS. This section is also missing a citation for the second paragraph. Otherwise, it is once again very well written! Nice job. Finally, the page is missing a figure, which is required for the project. Be sure to add one before turning in the project!

Overall, the article is very good. The last two sections were written very well and contained very detailed information. The first two sections could use some work, and appear to be missing all necessary citations. Additionally, the “Role in DNA Replication” sections could use a little, work, but is definitely on its way to perfection. Great job and I can’t wait to see the final product!

Suggestions from ChemLibrarian

Good job with structuring your article. Here are my suggestions.

It's great that you revised the lead section into a more concise version. However, I see that you did not use any of the existing content in the original article Bacterial DNA binding protein. It's not a good practice. Imagine how you feel if editors come in later remove your contributions completely. So, please do try to incorporate the sentences in the original article into your paragraph, especially keep all the reference cited there.

The History section needs more work. Starting the sentence with HU-type of protein makes it confusing since it's only one example of Bacterial DNA binding protein. Adding a citation is necessary when you are talking about history.

As pointed out by your peers, there are many terms need to be linked to other Wikipedia articles. Please use the "[[]]" to do so.

I see that you have not added any images to the article yet. Please check out slide 21 and 37 of the Slides for Wikipedia Editing Basics I posted on the CTools site for link to video tutorials and notices about copyright issues.

In general, you need more references.

ChemLibrarian (talk) 15:33, 23 October 2015 (UTC)[reply]

Review from GSI

Good job done in editing and adding new information to the page. Few minor changes or clarifications can improve the draft.

1. In the introduction, the group has used the phrase 'variety of functions' in the first sentence. However, it seems arbitrary and too general and needs more explanations. It would be better if they can name a few functions.

2. I would suggest to keep consistency in the information provided about different DNA binding proteins, in the introduction part. For example, the location of HU is mentioned but not the acronym or structure. On the other hand, for IHF, the acronym and the structure are written, but not the location. Also, I think it is better to list all the examples, which they have discussed separately latter, in the beginning; i.e. mention H-NS in the Introduction with HU and IHF as well as include and discuss about IHF as an example under the heading Examples. Moreover, showing all the examples in a table form and comparing different aspects of them can make the topic more interesting.

3. A diagram depicting the binding of Bacterial-DNA-binding protein to lagging strand would be more user-friendly to lead the readers through the subtopic Role in DNA replication.

4. A comparative study between bacterial and eukaryotic DNA binding proteins can point out the evolutionary importance of such proteins.

Soumigchem (talk) 22:46, 23 October 2015 (UTC)[reply]