Talk:Extrachromosomal DNA

message: Updating Article Information
:I along with Jfitz1974 will be updating this article for the next few weeks through a graduate class at Johns Hopkins University.  We aim to give more comprehensive reference information about extrachromosomal dna.  Rebeccachappel (talk) 21:25, 22 October 2013 (UTC)
replies: text: Thank you for your suggestions.  We will make the necessary changes to improve the article. Jfitz1974 (talk) 00:46, 4 November 2013 (UTC)

text: I have moved the introductory paragraph to the top of the page, above the table of contents as you suggested and I think it looks a lot better as a result; thank you.  There were several issues with the relevant research section and one of the wiki ambassadors was generous enough to help rectify some of the major issues. I, too,  believe though, as you mentioned,that the section needs some refinement.  I would like to wait until the page is a little further along, and then will go in and make those necessary refinements.  I completely understand your suggestion to combine the biotech and medicine/disease sections under one heading but that wasn't quite the route I was envisioning when I proposed the medicine/disease section.  I think that a name change from medicine/disease to just "disease" would better convey my intentions.  I would like to show how defects in extrachromosomal DNA can lead to various diseases.  The use of extrachromosomal DNA to treat diseases can easily fit under the biotech heading.  Do you have any suggestions as to what types of external links you would like to see in an external links section?  I would be happy to look into it.  Thanks again for all of your suggestions. Jfitz1974 (talk) 21:17, 10 November 2013 (UTC)
replies: text:  Thanks for the review! Jason seems to have taken care of a lot of the suggestions.  I am going to address the ones that I can as well.  It's also great to have some new eyes on it.  I agree with Jason about the categories but we will keep everything in mind as we complete the article.  I have a small list of external links that I will add - that's a great suggestion! Thanks again! Rebeccachappel (talk) 13:25, 11 November 2013 (UTC)
thread_title: Untitled

message: The article appears to be coming along nicely compared to the previous version last updated in March 2013. Some structure has been added to the article with the addition of a table of contents and several subsections. The prose has been moved from a brief unreferenced introductory paragraph to several different topics with in-line citations along with a potential embedded image. Many links to relevant research has been appended to the end of the page.
Some suggestions that I can make are:
# The introductory paragraph can be moved above the table of contents to match the format of more developed articles (see Genetics)
# The long list of relevant research seems more unrefined and is probably better suited for the talk page or a sandbox
# The image can be embedded with a subtitle
# Hierarchical grouping of the subtopics could improve the structure of the article e.g. grouping Extrachromosomal DNA and Biotechnology and Extrachromosomal DNA in Medicine and Disease under as common section named Research and Technology might be less redundant
# See also and External Links sections may be useful for readers
# "Extrachromosomal DNA is any DNA that is found outside of the nucleus (chromosomal DNA) of a cell"
Oalnafo1 (talk) 20:51, 2 November 2013 (UTC)
replies: text: Thank you for your suggestions.  We will make the necessary changes to improve the article. Jfitz1974 (talk) 00:46, 4 November 2013 (UTC)

text: I have moved the introductory paragraph to the top of the page, above the table of contents as you suggested and I think it looks a lot better as a result; thank you.  There were several issues with the relevant research section and one of the wiki ambassadors was generous enough to help rectify some of the major issues. I, too,  believe though, as you mentioned,that the section needs some refinement.  I would like to wait until the page is a little further along, and then will go in and make those necessary refinements.  I completely understand your suggestion to combine the biotech and medicine/disease sections under one heading but that wasn't quite the route I was envisioning when I proposed the medicine/disease section.  I think that a name change from medicine/disease to just "disease" would better convey my intentions.  I would like to show how defects in extrachromosomal DNA can lead to various diseases.  The use of extrachromosomal DNA to treat diseases can easily fit under the biotech heading.  Do you have any suggestions as to what types of external links you would like to see in an external links section?  I would be happy to look into it.  Thanks again for all of your suggestions. Jfitz1974 (talk) 21:17, 10 November 2013 (UTC)
replies: text:  Thanks for the review! Jason seems to have taken care of a lot of the suggestions.  I am going to address the ones that I can as well.  It's also great to have some new eyes on it.  I agree with Jason about the categories but we will keep everything in mind as we complete the article.  I have a small list of external links that I will add - that's a great suggestion! Thanks again! Rebeccachappel (talk) 13:25, 11 November 2013 (UTC)
thread_title: Comments from Oalnafo1

message: Hi guys, here are my comments on your work so far. Let me know if you have any questions! I'm happy to help you with anything.
* The introduction should be a lead section instead. Start it the same way and bold "Extrachromosomal DNA". 
* Your sections are all too small of a subheading. Use two equals signs for a regular heading and three for a subheading.
* In general, you need a lot more wikilinks. Think about what the average reader knows and link terms they may find helpful.
* Your first citation is the Encyclopedia Britannica - this is a general reference work and shouldn't be cited here.
* Rush and Misra needs a PMID as it currently links to an internal JHU site that no one else can access.
* The NCBI viral genome reference needs to be more than just a bare link. Use the cite menu and the "cite web" pull down option to fill in the citation, or use the  template from scratch.
* It would help if you glossed terms like dsDNA the first time they appear by writing something like "double stranded DNA (dsDNA)".
* You should explain for the lay reader why a high mutation rate correlates to evolutionary success. I know it's common sense to you but the average reader probably doesn't have that background.
* Gloss kb the same way.
* Something went wrong with your attempt to display the restriction site picture - try removing the colon before "File" and add a caption.
* The Micrococcus source is a good start for the discussion of different types of plasmid but that source only supports the existence of those types of plasmids in this single genus. It would be helpful if you could find a source that discussed these types of plasmids in general.
* The Relevant Research section should not have surrounding <ref> tags - it should just be a list of sources. If you need help formatting let me know.
* Clarify that in yeast, chromosomal DNA replication is needed for eccDNA to form.
* A PMID for Cohen et al. would be fantastic.
* There's a weird bit of text after the reference list, is that missing from somewhere else in the article?
All the best, Keilana|Parlez ici 19:10, 3 November 2013 (UTC)
replies: text: Thank you Keilana for your suggestions.  I do have a little trouble with reference lists, so if you could please give me some suggestions on how to fix the Relevant Research section, I would greatly appreciate it.  Thanks! Jfitz1974 (talk) 00:49, 4 November 2013 (UTC)

text: For which Cohen article would you like to see a PMID?  Thank you for the suggested fix for the image, I've gotten that to display correctly now and also thank you so much for cleaning up the reference list for us.  Per your suggestion, I have found some more relevant articles that discuss linear bacterial plasmids and will be updating that section accordingly.  Thank you as well for the suggestions to gloss certain terms, it is often easy to forget that not everyone knows the lingo as well as others.  Formatting changes have been made per your suggestion as well. Jfitz1974 (talk) 21:08, 10 November 2013 (UTC)
replies: text: Thanks Keilana! The general reference work was my reference and I will change that.  I appreciate you catching that.  I will also make sure I don't have any abbreviations without having the full name first (as with your dsDNA example).  Thanks for the review!  — Preceding unsigned comment added by Rebeccachappel (talk • contribs) 13:28, 11 November 2013 (UTC)
thread_title:  Review by Keilana 

message: Overall I would say the article is coming along nicely. While I enjoy that you have set a clear outline for where you intend to go, I don’t feel that entering your unfinished ideas into the main article before you have something to say is the right way of handling things. If someone were to come across this article today they would be very confused why several pieces of information are missing and might be thrown off. That being said you are off to a great start in terms of references. You are well exceeding the minimum one source per paragraph and have a ton of references already set up in your article. While this is great, you do tend to lack prose to make your factual claims and citations flow together. Touching up the sections to read more fluidly would greatly benefit the reader. I always like to keep the big picture in mind when writing so if you stop at a random location you should be able to remember how you got there and why what you are reading/writing is important to the subject. Nevertheless, what you have so far is a good chunk and I feel like you are heading in the right direction. 
Suggestions:
#Keep your outline in your sandbox. It shouldn't be out there for everyone to see.
#The relevant research section seems kind of superfluous considering that it’s mostly just a re-citation of articles already included in the article. Perhaps keep this in your sandbox as well.
#You might want to link your articles to their online pages. There is an option in the ref creator to do so.
#Add prose to make your paragraphs come together and easier to read.
Dmille96 (talk) 00:16, 6 November 2013 (UTC)
replies: text: Thank you for your suggestions; will review and make necessary improvements. Jfitz1974 (talk) 20:16, 6 November 2013 (UTC)

text: There were several issues associated with the relevant research section as noted by you and the other reviewers. With the assistance of one of the ambassadors, I believe the major issues have been addressed and rectified.  I would like to keep the section on the page to include several articles that were found during the course of the research that provide interesting insights on the topic but weren't directly referenced in the writings of the page. As the article progresses and more content is added, we will go through and add / adjust prose to ensure that the entire page flows to the best of its ability.  After the second round of contributions, hopefully no sections will be without content. Jfitz1974 (talk) 21:25, 10 November 2013 (UTC)
replies: text: Thanks for the review! I agree with you about the outline on the main page (which has been fixed).  I am working on my sections to make the prose flow in a better manner - some of my prose does feel like facts clumped together.  Thanks! Rebeccachappel (talk) 13:30, 11 November 2013 (UTC)
thread_title:  Comments by Dmille96 

message: Hey guys, you have a really great start to this page.  I especially like the Relevant Research section.  You only have a couple of visuals in there though and I know you don't want to distract readers from the info with unnecessary pictures but I think at least one more perhaps within the Extrachromosomal DNA in eukaryotes would be good.  Also, in the section under Extrachromosomal DNA in prokaryotes there is a huge sentence that is hard to read.  It starts with Fertility plasmids.  Maybe you can find a way to reword this or break it into two sentences since its so long.  Besides that I only found one grammatical error and its under Extrachromosomal DNA in medicine and disease.  The second sentence of the second section under this title needs its first letter (point needs to be Point) capitalized. Good job. Sridenour (talk) 13:13, 19 November 2013 (UTC)
replies: text: Hi Sonya, thank you for the review! We are continually on the look out for more visuals; we both agree with you on that point.  I like the idea of trying to find one in the eukaryotes section - it would make it more engaging I think.  I will fix the grammatical error in the DNA in medicine and disease section now.  I'll take a look at the sentence in the Prokaryotes section (once my partner can see it also -I don't want to make any change too major until all the reviews are in).  Thanks again! Rebeccachappel (talk) 20:44, 19 November 2013 (UTC)
replies: text: Thank you for the input Sonya. I do see what you mean about the long sentence in the prokaryote section.  I was attempting to explain the different typed of plasmids and didn't quite realize how long the sentence actually was. I will fix it. I too would love to have more graphics in the article, but they truly are difficult to find without plagiarizing.  We are continuing to search for graphics, and I will create them as I can.  Thanks so much for your suggestions! Jfitz1974 (talk) 05:07, 20 November 2013 (UTC)
replies: text: I've edited that extremely long sentence in the prokaryotes section and found a graphic of mtDNA on Wikipedia commons to include.  Thanks for the suggestions! Jfitz1974 (talk) 02:04, 26 November 2013 (UTC)
replies: text: Hey just looked at this and it reads a lot smoother.  Good job. Sridenour (talk) 19:57, 26 November 2013 (UTC)
thread_title: Review by Sonya Ridenour

message: Hi, I can see you've put a lot of work into this article, and it is really shaping up to be pretty good.  Here are some random comments/suggestions.
* "methylated" could be wikilinked
* Clean up the "Relevant research" section
** Is there a need for this section at all?  I didn't do an exhaustive check, but it seems redundant with the references.  Anything that is a reference doesn't need to be here.
** Textbooks and general references shouldn't be here -- they are too broad.
* Headings:  I don't think you should have "Extrachromosomal DNA" in all of the headings.  Maybe not in any of them -- it is redundant.
* The section "Extrachromosomal DNA in viruses" is very confusing.  
** I am not sure what you are talking about here.  There is a fundamental symmetry problem here:  you have other sections, "in prokaryotes" and "in eukaryotes", where you are talking about the DNA of those types of organisms.  But in this section, I think you are talking about viral DNA qua extrachromosal DNA in other organisms.  Is that right?
** Way too much detail about what a virus is.  Most of this detail is irrelevant to your specific topic.  Only include a brief phrase saying what a virus is, and then only as much other detail as is directly relevant to when viruses become extrachromosomal DNA in other organisms
** Another example of irrelevant detail:  why is the paragraph about the influenza virus in at all?  I can't see how it ties in to the topic (maybe it does, but I don't think you've explained it.)
** Ditto for all the stuff about p53.  Why is this relevant?
* "Cells have sensors that can specifically recognize viral RNA".  Again -- why is this in this article?  This article is about DNA, not RNA.
* The rest of the article looks really very good.  Lots of good content, the writing is good, and lots of wikilinks.  The references are plentiful and well formatted (PMIDs would be nice, but you have DOIs, so it's okay).  I think, if you can fix the "Extrachromosomal DNA in viruses" section, this will be a good article indeed!
Klortho (talk) 04:47, 20 November 2013 (UTC)
replies: text: Thanks for your input and advice.  Cleaning up the relevant research section is at the top of the priority list for my next edit.  I did realize that there was a textbook in there and will definitely remove it. Would it be appropriate it have a "For Further Reading" section to list some of the relevant articles that weren't used as resources?  I definitely see your point about redundancy by using "extrachromosomal DNA in each heading; do you think that just saying "in prokaryotes" or "in eukaryotes" is good enough for the headings?  Thanks again for the suggestions and words of encouragement! Jfitz1974 (talk) 05:14, 20 November 2013 (UTC)
replies: text: I will definitely focus on cleaning up the viruses section in the next update.  Thanks for the comments! I will try to link everything back to the main topic in a more concise manner.  I appreciate the feedback! Rebeccachappel (talk) 14:33, 20 November 2013 (UTC)
replies: text: I've cleaned up the relevant research section and simplified the headings.  Thanks again for your suggestions! Jfitz1974 (talk) 02:07, 26 November 2013 (UTC)
thread_title:  Comments from Klortho 

message: Overall the article has seen a lot of information added. That is good for the article, but I'm not sure how much of it really fits the subject. The definition given in the lead-in section doesn't work for either viruses or bacteria as they don't keep chromosomes/plasmids in a nucleus, so everything they have would fit as "Extrachromosomal DNA". In the case of viruses, most transport RNA, like the mentioned influenza viruses.
*The technical terms interspersed throughout the article should be linked to appropriate Wiki pages to help break down the language barrier. E.g. anogenital tract.
*When prepping to use a shorthand, it is best if the first time the full thing is used with the shorthand next to it.
**e.g. Mitochondrial DNA (mtDNA). This was done late in the section, but mtDNA was used several times before this was done.
KevinBrownJHU (talk) 02:32, 21 November 2013 (UTC)
replies: text: Thank you for your input Kevin. With regard to using the mtDNA shorthand, please note that the first time the shorthand is used is in the section titled Mitochondrial DNA and that in the first sentence we state that "The mitochondria present in eukaryotic cells contain multiple copies of mitochondrial DNA referred to as mtDNA..." It is after that statement when we start to use the shorthand almost exclusively. Are there any other instances where you feel we've used the shorthand before stating what it means?  If so, we will gladly fix them.  Although bacteria lack a distinct nucleus, they do have a nucleoid region in which the main chromosome is found.  The extrachromosomal DNA in the form of plasmids is found outside of this nuceloid region.  I see how that can be misleading, so I will take the necessary actions to clarify that.  Are there other terms you feel should be wikilinked in addition to anogenital tract?  Thanks! Jfitz1974 (talk) 03:40, 21 November 2013 (UTC)
replies: text: Thanks for the review Kevin.  Some of the other reviewers also mentioned that some of the material might be out of scope.  That is definitely something I will try to edit in this next contribution.  I think Jason has commented on the Wiki links and we will both try to find any additional ones that need to be linked.  Thanks! Rebeccachappel (talk) 18:17, 22 November 2013 (UTC)
thread_title:  Comments from KevinBrownJHU 

message: Great work so far everyone.  You have added an impressive amount of information that is well sourced, fluent, and informational.  Initially there appeared to be some information that I questioned its inclusion.  For the most part you explain the relevance and it is clear why you explain topics in detail. Along with Klortho though, some of the detail in the virus section seems out of place.  It is useful information, but mechanisms and life cycle details just seem more appropriate for different articles.  You incorporated the suggestions from the first round of reviewing very well.  Your in text links all appear appropriate.  I would add one for long terminal repeats (LTRs) in the first paragraph of the “Extrachromosomal DNA in viruses” section.
Considerations
* 5th sentence in “Extrachromosomal DNA in prokaryotes” is a bit hard to process due to its length and amount of information.  I believe Sonya had the same concern.
* In the following paragraph where it says “Naturally occurring spherical plasmids” should probably be circular plasmids.
* I was left wondering why the genetic code differs in mitochondria and what all this means.
* I see the relevant research section is addressed a lot on this page.  I question its necessity and would remove items that appear in your references, but would not suggest taking the section out at this time.  Sounds like you are working on it.  I suggest at least putting it in alphabetical order by author.
* Several sentences start with “Studies show” or variants of this.  It’s great you are putting up to date information in.  However, if the material is not generally accepted fact in the literature, maybe it should not be included or if it is accepted, it can be stated a little more definitively.
Keep up the good work.  You've put a lot of effort into this and it shows.Seanmcaruthers (talk) 06:46, 21 November 2013 (UTC)
replies: text: Thank you Sean for the suggestions.  I will definitely work on getting that lengthy prokaryote sentence down to a more manageable format.  I will also work on elaborating on the point about the mitochondrial genetic code so that it seems more relevant to include.  I really like the idea about alphabetizing the relevant research section, thanks! Jfitz1974 (talk) 14:15, 21 November 2013 (UTC)
replies: text:  Thanks Sean for the review! We have relied a lot on relatively recent studies and papers.  I agree with you that some of the language we used did not evoke as much confidence in the data as it should have.  We definitely are confident in the information used in the article so I will change some of the language to reflect that. Thanks again! Rebeccachappel (talk) 18:22, 22 November 2013 (UTC)
replies: text: I've cleaned up and alphabetized the relevant research section and worked on simplifying that long prokaryote sentence.  I've also added some more information regarding the mitochondrial genetic code in hopes of trying to clarify it more. Thanks again for your suggestions Sean! Jfitz1974 (talk) 02:10, 26 November 2013 (UTC)
replies: text: Hey all.  You've done a great job addressing everyone's points.  You've provided a lot of new additional relevant information as well.  I'm a little confused about the last paragraph in the Medicine and Disease section.  I thought that the presence of mtDNA was the norm in most protozoa, so the relevance of its presence in the malaria parasite is unclear to me.  Watch for proper italics use in organism names such as Sequoia sempervirens.  I know it's getting to the end of the project, but information on circulating DNA in plasma and serum could be interesting to include and is a pretty hot topic.  Good job.Seanmcaruthers (talk) 06:06, 4 December 2013 (UTC)
replies: text: Thanks for the follow up Sean! I will definitely try to make that section more clear.  The addition of some information on circulating DNA in plasma does sound like a good addition - I'll look into that for the next contribution! Thanks Rebeccachappel (talk) 14:24, 4 December 2013 (UTC)
thread_title:  Comments from Seanmcaruthers 

message: You have added a lot of information to the article. Very impressive! Overall, the article is not only very informational and fluent, but also interesting written. Good job!  In general, the information you provided is relevant and precise, however,  once in a while it seems to extend the scope of the article by a bit. For example, I am not sure if you need details about how TLRs recognize foreign extra chromosomal DNA, but rather that organism have such systems in place – it might be appropriate to add a Wiki link instead and to refer to the original article.
Other Wiki-links to consider: 
*Nuclear DNA
*Bacteria/bacterial
*Antibiotics
*Gene
*Virus/viral
*Sequoia sempervirens and other organisms you are referring to
Good Job, it’s a great article.AjoneWiki (talk) 20:17, 7 December 2013 (UTC)
replies: text: Thanks for the review! I agree with you that a Wiki link to the TLR section could help to take out some information that strays from the Extrachromosomal DNA subject...I'll try to edit that section for the next submission.  The other Wiki options are great too - thanks! It's great to have another set of eyes review everything.  Rebeccachappel (talk) 20:22, 7 December 2013 (UTC)
replies: text:  Thanks for the feedback! I'll go through once more and make sure we have the appropriate items wikilinked.  Jfitz1974 (talk) 02:39, 8 December 2013 (UTC)
replies: text:  No problem!AjoneWiki (talk) 23:15, 11 December 2013 (UTC)
thread_title:  Comments from AjoneWiki 

message: # This is a great article well written for your average high school student, in terms of language and level of complexity
# You have high quality references and your subheadings/subsections are simple and easy to follow
# I like that you have a section on relevant research studies. However I wondered if this was also not serving the purpose of another reference list
# The images that are on the page have well supplemented the existing prose 
Sincerely Mtee87 (talk) 04:02, 8 December 2013 (UTC)
replies: text: Thank you for the review! I will make sure that the relevant research does not mimic anything in the references - the main point about that section is just further reading available (some with information beyond the scope of our article).  Thanks! Rebeccachappel (talk) 18:41, 8 December 2013 (UTC)
replies: text:  Thank you for your feedback!  As Rebecca pointed out, the relevant research section is to provide resources for more information on the topic.  There should not be any overlap with the actual references section but we will check over it one more time just to make sure.  Thanks!! Jfitz1974 (talk) 01:42, 9 December 2013 (UTC)
thread_title:  Comments from Mtee87 

message: Hi guys! Great job this semester. I have a few more comments for you to think about in the last few days of the semester - let me know if you have any questions about it!
* In general, you don't need to put citations in the lead. Since it's a summary of everything else in the article, everything it contains will be talked about and cited elsewhere.
* The whole article could use a solid copy-edit for grammar issues and clarity.
* The phrase "research showed/shows" is generally unnecessary as it's assumed that everything we write is supported by research. If you want to name a specific notable scientist that's okay though.
* Great job linking important terms!
* Does Laddy and Weiner have a PMID? It covers a medical topic so if it's going to qualify as a reliable source it should.
* The image you have illustrating mitochondrial DNA is okay, but an English image would be preferable.
* You don't need to label things "Table 1", "Table 2", etc. Just explain everything about the image that you need to explain in the caption, then go more in depth in the text.
* The last part of the first paragraph of "Inheritance" needs a citation.
All the best and good luck with the last part of the semester! Keilana|Parlez ici 01:01, 11 December 2013 (UTC)
replies: text: Wow, I totally missed that a non-English version of the photo appeared.  I have since fixed the issue (I hope).  As always, thank you for your comments.  We'll go through and do an overall edit as suggested for errors and flow.  I'll also make adjustments to my table caption and double check for a PMID for the Laddy and Weiner article.  Thanks again for all of your assistance, it has been most appreciated! Jfitz1974 (talk) 01:39, 11 December 2013 (UTC)
replies: text: Thanks Keilana, these are great final review notes.  I can add the Inheritance citation (oops!) and go through and try to clean up the language a little.  I am guilty of the "Research shows..." lingo and can make some changes to that.  Thanks for the review! Rebeccachappel (talk) 20:10, 11 December 2013 (UTC)
thread_title:  More comments from Keilana 

message: In the article there is some confusion between the term ecDNA used as a general term (all DNA found off the chromosomes) and ecDNA as a specific variant of eccDNA found in cancer cells. It is somewhat confusing to use the same term with two meanings. Miguelferig (talk) 17:00, 20 November 2023 (UTC)
thread_title:  Confusing two meanings