User talk:Tanxt/sandbox

This group did greatly enhanced a page, rolling circle replication, that previously existed but was lacking completeness. In regards to the introductory paragraph, I think that it starts off very strong as you explain the importance of understanding this mechanism as it has applications in numerous organisms and in research. You also did a good job linking topics to their respective Wikipedia pages. However, I think the wording of the final sentence can be improved and made more clear perhaps by splitting it into more sentences and offering more detail on why these techniques employ this type of replication. I realize this is taken from the original page but I would get rid of the word “basically” it when speaking of the five steps of rolling circle replication and avoid it in this type of writing. Here I would also add replication after rolling circle when listing the steps.

I think that you have a good amount of information in each section without being overly detailed or overly simplified and your contributions to a new section on rolling circle replication, immuno-RCA, and part of the virology section really improve the content and quality of this article. Overall, the article is enhanced by the fact that you were able to find figures that match your topic. References meet the criteria of having more than 5 sources as well as including both reviews and journal articles.

This page was improved by your description of the process of rolling circle amplification, the process of immuno-RCA and diagram, and the additional example added to the virology section. It looks like some of the original minor mistakes I saw have been cleared up but I would suggest another run through as I initially noticed issues with spacing, grammar, and tense used. I also think that the procedure for immuno-RCA can be made clearer, perhaps add a link to an immunoassay/immunohistochemistry typical protocol to make it easier for readers to follow or give a brief overview of it in your own words. I would also be careful about citations since it seems there are very few in the rolling circle amplification section yet a lot of information that is not what you would consider "general knowledge". The section titled Rolling Circle Amplification can also be improved with the insertion of appropriate links to other Wikipedia pages that would help readers understand some of the jargon better. Other small edits I would suggest would be to only link concatemer once to its respective Wikipedia article (here it is done twice) and link ELISA in the Immuno-RCA section to its Wikipedia page.

In conclusion, this group has added important details and information to this page on Rolling Circle Replication which as they have pointed out is very important in both DNA and RNA, bacteriophages and viroids, and in many research techniques. The figures enhance the understanding of these processes and the references are complete. The information they added was well thought out and improves the reader's understanding of the wide applications this process is a part of. Some clarity in the writing and steps will help better this article as well as more links to corresponding Wikipedia pages in case readers have further questions.

Remerl (talk) 03:12, 24 October 2017 (UTC)

Rolling Circle Replication Peer Review- Julia

This Wikipedia page addressed the topic of “rolling circle replication.” The group substantially improved a Wikipedia site already made. Students and non-experts on the topic can feasibly read the Wikipedia page, and this group expanded upon important topics that the current Wikipedia page does not have. I would, however, suggest including why Rolling Circle Replication is so widely utilized by living organisms; you should emphasize the value that this process offers by allowing the circumvention of the synthesis of an RNA primer.

Additionally, when writing potentially challenging topics such as this one, beware of run on sentences. For example, the first sentence in the “Rolling Circle Amplification” section should be broken up. Here, I would also suggest including a sentence or two that recognizes the applicability of this method over nucleic acid amplification techniques. You noted that this method is isothermal, which evades the need for thermal cyclers, and that it can be conducted in both a free solution and on immobilized targets, but you should also note why this particular aspect is beneficial. RCA is a more sensitive, faster, and cost effective method of nucleic acid amplification.

A few important terms still need to be linked to their corresponding Wikipedia pages. Hyperlink PcrA, the host-encoded helicase, to its respective Wikipedia page. Phi29 DNA polymerase, T4 DNA ligase (found in the Wiki page DNA ligase), and ELISA should also all be given a hyperlink. The polymerases used in RCA should also be referenced to their appropriate source.

I think you touched upon the three steps of the DNA RCA reaction very nicely, but they should be expanded upon and clarified. For example, how does restriction enzyme digestion function in this RCA technique? This should also have a source. Furthermore, the third step involved in the DNA RCA reaction is a little bit hard to understand. How is the fluorescence detected? Is it fluorescence microscopy? Flow cytometry? FRET? You should also include a source here.

In the Immuno-RCA section, the procedure should be given a source. Additionally, the numbering on the two different protocols is slightly confusing. If there is a way to make the differentiation between the two different techniques more obvious, it could help elucidate the section.

This Wikipedia page is very well done. The additions are pertinent to the topic and clarify some very important points that the published page does not have. The figures are helpful and easy to understand, and the new addition of the illustrations in the “Rolling Circle Amplification” section and the “immuno-RCA” section are useful visual tools. The figures are high quality, informative, and accurate.

There are many references listed below. It appears as though your sources meet the criteria for the assignment; there are more than five and include both reviews and journal articles.

Overall, this was a very well thought out addition to an already existing Wikipedia page. The original Wikipedia page was sparse and incomplete and I felt that this group did a wonderful job discussing the merits of rolling circle replication and amplification. The figures are clear and lend support to the claims made in each individual section. I think, however, more hyperlinks need to be added to clarify potentially complicated topics and to appeal to a wider demographic that includes non-experts on the subject. Likewise, sources should be added to back up your claims. You should also discuss the relevance of this topic; how these techniques can further scientific advancement and biochemical research and why we might be interested in pursuing them.

Very minor grammar checks: the first step of the DNA RCA reaction- both examples should be e.g., not i.e. Second step of DNA RCA reaction- take out “Please” before “please note.” First sentence of the last paragraph of the Rolling circle Amplification introductory section- missing a word after “ultra-low [null abundance].” In the “Virology” section, the sentence “[…] but in HPV-16 it is believed that the E1 hexamer [..]” and the last sentence “it is believed […]” should be changed so that they are written in the active voice. Juliaeisenberg (talk) 12:58, 24 October 2017 (UTC)

Wikipedia Peer Review – Jessica Fratzke

The Wikipedia article to be published, “Rolling Circle Replication,” has a great foundation. To start, the authors introduce the topic in a manner that is both concise and clear. Additionally, the information is presented in a manner that could be almost entirely understood by non-experts. To improve the introduction, I would suggest editing the segment that begins with “Rolling circle has basically five steps:”. First, statements should be concrete and confident, as well as cited whenever necessary: “Rolling circle has basically five principal steps:[1]” Of course, you can decide where you choose to put the citation, but I recommend adding it to the end of this initial opener since it encompasses all of the numbered steps. In addition, the statement “DNA is ‘nicked…”’ may be too general for a non-expert. Maybe state, “DNA will be is ‘nicked,’ or cut at a specific recognition nucleotide.” Lastly, there are some necessary syntax adjustments to be made in the introduction, found below.

“the mechanism is also widely used in molecular biology, biomedical engineering research, and nanotechnology.”

“Replication of both "unnicked" and displaced DNA completes .”

Moving forward, I would like to comment on the contents of this Wikipedia article. First and foremost, the content is original or new to Wikipedia, thereby providing a valuable contribution to the online encyclopedia. In addition, the contents of each section justify its length. The opening segment is an appropriate length for an introduction, and the supporting body sections are appropriate based on content: the detailed description of the topic and its application are extended, and the section on virology is enough to get the point across, while also providing a practical example. In addition to this, the authors need to consider linking more key terms to their corresponding Wikipedia pages for reference. I would suggest linking (in order of the article) “PcrA,” “tandem repeats,” “dNTPs” (doesn’t have a Wiki page, but the page “nucleoside triphosphate” covers them in detail and could be helpful to the reader if linked), “Phi29” (found on Wiki as Φ29 DNA polymerase), “Bst” (doesn’t have a Wiki page, but the page Geobacillus stearothermophilus details its polymerase), “Vent exo- DNA polymerase” (listed as “Vent DNA polymerase”), “polymerase chain reaction,” “fluorescent detection” (as “fluorescence spectroscopy”), “gel electrophoresis,” “ELISA,” “immunoassay,” “immunohistochemistry,” “oligonucleotide,” “fragment antigen-binding,” “HPV,” and “cervical cancer.” I would also like to take a second to note that the body of the article seems to be missing necessary placement of citations. In fact, there is only one in the section entitled “Rolling Circle Amplification.” Lastly, I would like to note that the “Circular DNA replication” section should amplify the five steps in the introduction. When some pieces are lost or there are missing pieces, the reader has gaps in their learning of the information. For example, in the five steps it mentions Okazaki fragments, but this is not mentioned at all in the in-depth explanation of the process in the proceeding section. Try your best to paint a complete picture for the reader.

Minor edits in content text:

Step two under "There are typically three steps in involved in a DNA RCA reaction":  Please note that Multiple primers can be employed to hybridize with the same circle.

Step three under same section missing comma and hyphen: fluorophore-conjugated dNTP, fluorophore-tethered complementary, or fluorescently-labeled molecular beacons.

The paragraph under step 3 of the same section the sentence seems to end abruptly with missing information: making it particularly useful for detecting targets with ultra-low [null abundance].

Under Immuno-assay: As a result, immuno-RCA gives a specifically amplified signal (high signal-to-noise ratio). So it is commonly used for detecting, quantifying and visualizing low abundance proteic markers in liquid-phase immunoassays[3] [4]and immunohistochemistry. Edit: As a result, immuno-RCA gives a specifically amplified signal (high signal-to-noise ratio), making it suitable for detecting, quantifying, and visualizing low abundance proteic markers in liquid-phase immunoassays[3] [4]and immunohistochemistry.

Consider your repetitive use of "So," which if changed in the text, would provide a more professional article: "So the Fab (Fragment, antigen binding) section on the detection antibody can still bind to specific antigens and the oligonucleotide can serve as a primer of the RCA reaction."

Finally, take out second part in this. We understand this is what is given based on context:

The procedure is as follows:

-Regular Immunoassay/immunohistochemistry protocol.

Next, I would like to encourage the authors to use interesting research involving the use of rolling circle replication as examples to provide depth to their article. For example, the authors state “Rolling circle replication has found wide uses in academic research and biotechnology, and has been successfully used for amplification of DNA from very small amounts of starting material,[1]” under the detailed description of the method, but do not provide any concrete examples. It would be interesting if the authors provided an example where rolling circle replication proved useful in providing groundbreaking results in research. It would be equally beneficial to consider an addition of a noteworthy example(s) to the Rolling Circle Amplification and Immuno-RCA sections. Perhaps the authors can make a section entitled “Application” to address this all in one section. Looking into the topic myself, I found some interesting articles, I will provide a few here to give you an idea of how you can implement application in your article: multiple discussing its clinical application for detection of tuberculosis (https://www.ncbi.nlm.nih.gov/pubmed/23750210 and http://jcm.asm.org/content/52/5/1540.full), application in nanotechnology (http://pubs.acs.org/doi/abs/10.1021/am504035a). In addition, the authors use the article "Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine," but should take advantage of the fact that it goes into more detail about different detection techniques using RCA and discusses nanotechnology and materials science for a variety of applications: drug delivery, detecting parasites in biological samples, construction of different kinds of DNA structures, monitoring enzymatic activity…really interesting stuff! This is another review that addresses the advantages and limitations of rolling circle in comparison to similar techniques—might be worthwhile to include in the section that details Circular DNA Replication: http://onlinelibrary.wiley.com.proxy.lib.umich.edu/doi/10.1002/anie.200705982/full Examples under Virology section are appropriate.

Now, I will address the authors use of figures, which I believe is well done. There are figures for four of the main sections, and each one is original, high quality, accurate, aligned appropriately, easy to read, and adds to the text by providing an essential visualization of the process described in that section. As the reader, these images strengthened my understanding of the material as they show the status of the DNA throughout the process. My only critique would be that the figure for Circular DNA Replication reveals four steps while the description in the introduction details five. I personally followed the figure well with the description in the Circular DNA replication. My suggestion would be to take out step 3 in the five steps and make it four steps, since step 3 actually just provides information related to step 4. This information, then, can be briefly mentioned when discussing the replication step in the Circular DNA Replication section. There is no figure for the Virology segment, which is appropriate.

To briefly comment on the references in this article, the authors use greater than five (a complete list of references), and use different sources, including journal articles that present original research and review articles. If the authors would like to include an additional source category to further strengthen their page, they could choose to include information from books, such as this "Rolling Circle Amplification (RCA)", which covers a lot of information related to RCA: http://www.springer.com/us/book/9783319422244. Finally, references 1 and 2 are duplicates, and reference 8 is incomplete at the end of the Wikipedia page under References.

To sum, the authors overall did a great job in providing original content to Wikipedia and presenting it in a concise and clear way. They presented figures that were both appropriate to the content, and added to the text by providing a great visualization of the processes occurring. However, there remain some areas in the text that can be improved. The authors should look over the entire article in order to make the syntax more concrete and concise, link more key terms to their corresponding Wikipedia pages, and provide citations where necessary. In addition to these details, the authors should consider adding interesting research as examples of the application of their topic, and possibly adding one more source type to strengthen their page. Overall, fine work thus far by the authors, and I look forward to reading the final product.

Jfratzke (talk) 14:56, 24 October 2017 (UTC)

MLibrarian's Topic Review
Excellent job on expanding this article and use of figures! I have only minor suggestions on hyperlinking: "DNA polymerase", "DNA", "RNA", "Human Papillomavirus", "circular DNA", "ELISA" Also the caption for the last figure - please start from capital letter and finish with the period. And since the article has many subheadings now - consider making a Content, see RNA interference Featured article for example. MLibrarian (talk) 16:52, 27 October 2017 (UTC)

Nils' Comments
Nice job - keep going by perhaps adding some more applications of the RCR in analytical sensing.

Gillian's Comments
Great Job! I might try to connect it to the bigger picture in terms of where RCA fits into general amplification techniques in the introduction, such as its use in signal or target amplification techniques.