User talk:Raspberry Neuron/sandbox

Repeated Sequences Peer Review 1
Introduction

I think the introduction is clear to read for someone of any background. I do think the introduction could better set-up the information deeper in the article. For example, tandem repeats are mentioned, but not interspersed repeats; and transposable elements are mentioned but they do not have their own main heading. Additionally, it may be beneficial to give a little more detail on the disease aspect here, perhaps a short explanation that many result from trinucleotide repeats like Huntington's, etc. History

I think the history section contains information that doesn't belong in "History." To be specific, the information after the sentence on Barbara McClintock is not based in a historical context that adds to the history of discovery. While it is not bad information, I don't think its "history." Additionally, the last piece of information here is preceded by "only supported by a limited set..." Given Wikipedia guidelines, it may be good to exclude this as only largely established information should be put onto Wikipedia. The section on sequencing I think can be made more succinct for clarity, as the current version may be overly-complex.

Tandem Repeats

This section contains some really good information. I think the part explaining recombination could be left out though, and could just be linked the the "Genetic Recombination" Wikipedia page.

Interspersed Repeats

This section is really well written and organized, very informative!

I am slightly confused on the types of repeats you've written about in the article. In the "history" section it says there are 3 major types (transposable elements, tandem repeats, and high copy number genes) but you discuss tandem repeats and interspersed elements. Either an explanation, change to this part in "History," or a few additions to the "types" section I think would be beneficial. Human Disease

I like these and like that you included the specific ties to repeated sequences and didn't get bogged down trying to detail the diseases. Figures

The figures are nice and are CC licensed. I would recommend putting a description for these figures though, because alone they don't provide much information. I'm also not sure if the second figure is well related to the topic, and think it may be a good idea to seek a better-fitting figure. References You have a good list of references here. A few of these though require some attention, as denoted by the red text in the citation. Additionally (and my group was at fault with this too), try to include some non-journal sources to diversify your references list.

General Comments

I think overall the article does a nice job explaining the important pieces of information for repeated sequences. As a general comment, I would recommend reading through the article closely and fixing some grammatical mistakes in the early half of the article.

Charkner (talk)

Repeated Sequences Peer Review 2
I believe this article is a great development from the original one, so great job with the first draft! The introduction was accessible for non-experts, as I, a non-expert, was able to understand it. The lengths of each section seem appropriate. I would suggest linking more Wikipedia pages to important terms and concepts (for example, tandem repeats and interspersed repeats). The examples of the repeated sequences are appropriate, highlighting their roles in disease. Tandem repeats and interspersed repeats seem to already have Wikipedia pages, but I understand why they are relevant as examples of repeated sequences. The figures seem good too, but I would add some text under each one and reference them in the text. I believe the references are appropriate for the assignment, with more than 10 references and some coming from non-journal resources. However, some references have some warnings to check date values (red text at the end). Therefore, the article is an overall well-written one. Some refinements in linking a couple of relevant Wikipedia articles, adding texts under the figures and referencing them in the text, and double-checking the date values errors in the references, for example, can improve the article. Also, here are some typos (in my opinion) that you might want to double-check:

- "The disposition of repetitive elements consists either in arrays of tandem repeated sequences (satellite DNA), or in repeats dispersed throughout the genome called interspersed repeats (see below)" to "The disposition of repetitive elements consists either in arrays of tandem repeated sequences (satellite DNA) or in repeats dispersed throughout the genome called interspersed repeats (see below)".

- " For instance in human, mouse and fly, several classes of repetitive elements present a high tendency for co-localization within the nuclear space, suggesting that DNA repeats positions can be used by the cell as a genome folding map" to "For instance, in humans, mice, and flies, several classes of repetitive elements present a high tendency for co-localization within the nuclear space, suggesting that DNA repeats positions can be used by the cell as a genome folding map."

- "Although it is difficult to be sequenced, these short repeats have great value in DNA fingerprinting and evolutionary studies" to "Although they are difficult to be sequenced, these short repeats have great value in DNA fingerprinting and evolutionary studies."

- "Bustos. et al proposes one method of sequencing long stretches of repetitive DNA" to "Bustos. et al propose one method of sequencing long stretches of repetitive DNA."

- "Finally, this product which has deleted fragments is multiplied and analyzed with toothpick plasmid assay" to "Finally, this product, which has deleted fragments, is multiplied and analyzed with toothpick plasmid assay."

- Here I would use the words "challenging" or "difficult" instead of "hard" and use "small" instead of "tiny": "Repetitive DNA is hard to sequence using next-generation sequencing techniques: sequence assembly from short reads simply cannot determine the length of a repetitive part. This issue is particularly serious for microsatellites, which are made of tiny 1-6bp repeat units."

Coolbiochem Coolbiochem (talk) 00:56, 14 October 2022 (UTC)

Repeated Sequences Peer Review 3
I think this is a very successful first draft and a well-constructed update to the current page. As someone who is not familiar with this topic at all, I believe the introductory section immediately gives me a brief overview of what repetitive sequences are. I think it might be more attractive to the audience if you can name and link some of the related diseases (that you mentioned below) to the third paragraph of your introduction.

I agree with my fellow reviewers that the figures are good but not helpful for the content. Descriptions or figure legends can associate the figures with your content, and in this way, they create a better visualization of what you are trying to present.

I like that you listed tandem and interspersed repeats as in-depth examples of repeated sequences. In addition, the examples for repeated sequence related diseases are attractive to non-experts, and they are kept concise so that the audiences do not get distracted from the main topic. The references associated with the examples are all peer-reviewed journal articles, so some non-journal/introductory sources can also be something you want to look into. There are some citation errors from the system, and you can simply fix that by deleting the month but keeping the year in your date section of the citation.

There are some minor mistakes in the subject-verb agreement. Please go through the text and check the singular/plural problems. Eynivek (talk) 01:34, 14 October 2022 (UTC)

Repeated Sequences Peer Review 4
Content

I like the introductory section part because I think the definitions are very clear to readers that are not experts in the field. However, it may be nice to provide a few examples like GGGCCC in the front so that people can immediately realize this is what a repeated sequence is. The contents of each section do justify its length. I was confused when reading the discovery repeats because the authors started by saying the function of repeated sequence. I hope they can focus on the discovery first and then talk about the function. I also think the sequencing method probably does not fit into the history part. It can be a separate section. The examples are appropriate. I like the part when they talk about the disease. It is what people are interested to learn these days, like the GGGCCC in ALS. I think the content already on Wikipedia is a backbone of a minimal amount of knowledge, but Group 3 did a good job of expanding it.

Figures

I appreciate the authors try citing some figures of the disease, but from my point of view, they are not explained well enough or are direct for the readers to read. There are many diseases there, and I hope they can add captions to the figures and add them to the text. They can explain why these figures are important to the topic and which aspect they want to focus on in the figure. Another thing is I hope the authors can provide more figures in the introduction. Biology is abstract to most people. For repeated sequences, simply a structure on DNA can help a lot. For the sequencing methods part, a workflow figure may help the readers understand better.

References

I appreciate the effort that the authors search many journals (>10) and reference them here. However, I think they need to cite the original papers but not cite the review all the time in the introduction part.

Summary on Peer Review

I think Group 3 found the proper review and did an extensive search of the journals, which is very well. I like the introduction because it clearly defines the topic and has good logic. I also like how they include so many diseases. The repeated sequence is highly implied in many neurodegenerative disorders, which is something the scientific community and the general audience are interested in. However, I think the authors should work on conveying the information by citing more figures and better references to the content. Another thing is I hope they can start by talking about Barbara McClintock and then go to the functions. Moreover, adding one more section for the sequencing method may be better since it doesn't seem to fit in the history part.

Jingxtang Jingxtang (talk) 02:52, 14 October 2022 (UTC)

MLibrarian Feedback
1) Section history does not contain any single date, which in my mind is usually associated with historical facts. Could you add the dates to when discovery was first made? When it was confirmed? And when it was fully recognized?

2) In my opinion, subsection Sequencing Methods does not belong to History section. History section thus shall only contain 1 subsection, which heading "Discovery..." shall be removed. Sequencing Methods seem to better fit the section with Repeated Sequences in Human Disease. Perhaps, as in current Wiki version, you could call that section "Biotechnology" or generally speaking "Sequencing Methods"

3) Make sure to link to existing Wiki pages. For example, Friedreich's ataxia: https://en.wikipedia.org/wiki/Friedreich%27s_ataxia, which in your text is Friedreich Ataxia, so make sure that the name is spelled uniformly, Myotonic dystrophy - https://en.wikipedia.org/wiki/Myotonic_dystrophy, etc.

4) In Types and Functions, the current version Wiki page also mentions Direct and Inverted repeats, which do not seem to be even mentioned in your version. Are you planning to include this information? I would not recommend just deleting the information, unless it is incorrect. It would be fine to briefly mention if you do not plan to expand on it. MLibrarian (talk) 02:48, 19 October 2022 (UTC)