Talk:Minigene

Review by Neelix
It looks like you've made a great start to this article! Here are some recommendations for further improvement:


 * 1) I would recommend summarizing the initial quotation in your own words rather than providing it verbatim; Wikipedia articles tend to start with a sentence such as "A minigene is...".
 * 2) There should be no bolding in the article apart from the title of the article in the first sentence of the lead.
 * 3) The "External links" section should be at the end of the article.
 * 4) The "Types of Minigenes" section could use expanding and sourcing.
 * 5) There is no need to repeat the title of the article in each of the article's section titles; "Construction of a Minigene" can be simplified to "Construction", etc.
 * 6) Is the Gene Ontology Project so notable and unique that it deserves its own section in this article? If so, the section should be dominated by secondary sources rather than primary ones.
 * 7) If the "Books on minigenes" section is intended to list books that are not used to source content in the article, then it should be entitled "Further reading" and should be expanded to include more than one book.

I hope you find these recommendations helpful. Let me know if you have any questions. Neelix (talk) 03:57, 31 March 2014 (UTC)

Review by martinhyou
Hello. I am one of your peer reviewers. Here are my thoughts to improve the article:

Introduction

 * Paraphrase the first sentence instead of using quotes. Also, use simpler language so that anyone who is first reading this article can understand what a minigene does.
 * Shouldn’t say “This article” in the 3rd sentence. Everything in Wikipedia is paraphrased from other articles so it is a given that anything is from other articles or readings.
 * The last sentence is a run-on. Reword it if you can.

Construction of a Minigene

 * You don’t have to mention where the source/protocol is from.
 * Last sentence “to evaluate expression.” For what exact type of expression though? Why do you want to evaluate expression? The protocol name itself explains what the minigene is for, but it’s not really elaborated upon the rest of the paragraph except indirectly with how the minigene is co-transfected into different cell types with various splicing factors… etc.

Types of Minigenes

 * Go into examples of different minigenes. Their different roles (if any), their different structures, etc.

Use of Minigenes

 * Maybe switch the first and second sentence. The second sentence seems like a better intro and then the first seems closer to the exact method of using that to figure out pathogenesis.
 * “Minigenes provide the opportunity to do just that” may be an unnecessary sentence since it is somewhat implied.
 * There is good info in this paragraph but it doesn’t really flow together.

Endocrine Diseases/Neurodegenerative Diseases

 * Nice paragraphs! I like the explanation in these paragraphs and how minigenes tie into the diseases. Possibly may need some citations though with a few sentences because there is a lot of information that isn’t cited in the paragraph.

Overall Article
Martinhyou (talk) 17:42, 1 April 2014 (UTC)
 * There’s quite a few spelling mistakes so please look over it again. I’ve changed a few of them that I caught.
 * May be best to start with the background of Minigenes as the first paragraph instead of about the construction of it. You could use the “construction of a minigene” work, but you would have to re-word it to explain the relevance the production of a minigene has to its function.
 * A few pictures would be great with this article. A good one would be a diagram of what a minigene looks like, possibly pictures involving the construction of a minigene protocol, different types of minigenes, and minigene pathway/role in the diseases mentioned.
 * It would be good to expand upon the subject in other ways. A structure paragraph may be good along with other ways minigenes tie into normal functions besides just understanding different diseases.
 * The introduction probably needs the most work out of all the paragraphs to help ease the reader into the article.
 * Overall, nice job! Looks like it’s going in the right direction!

Response: Thank you for your review. Yes, several of the changes you suggested are in the works, including diagrams and an infobox. I am also trying to tie naming of minigenes to gene ontology in general.
 * ♠ Deacon C (talk) 03:39, 3 April 2014 (UTC)

Comments from msmrugby
General Comments Overall, very good start to the article. Plenty of initial content. Nice citations and good reference list. Watch the coversational tone in some sections. The transition words (thus, specifically, therefore) make it seem conversational in some places.

Specifics
 * Structure could be revised slightly. Under uses, I suggest not having individual subsections per disease, but rather, having one subsection labled therapeutic targets to align with text in uses section.
 * There are opportunities for additional internal links ( IGHD, GH-1, HGH, etc.).
 * The first sentence could be stronger. Suggest getting rid of long quote, and replacing with a more direct statement.  Instead of "A minigene contains...", replace with "A minigene is...".
 * Add an image if possible. A process flow would be nice.
 * Add content to types section.
 * Construction section - First sentence is too wordy. Suggest making it more concise.
 * Opportunity to add additional citations for many technical statements.
 * Neurodegenerative Dieseases section - Discussing tau protein. How is tau protein related to minigene article.  Is it a minigene?  Explain quickly in beginning.
 * Fix spelling and grammer mistakes.
 * Again, very nice start!

Msmrugby (talk) 04:57, 2 April 2014 (UTC)

Response: Thank you for your review. Yes, I also think the disease section could be reorganized. I have made changes to the introduction based on your suggestions. We are adding diagrams and an infobox (see above response). About the additional internal links...Hmm, well there could always be more links with a general subject like minigenes, let me think about it. The construction section will probably be entirely re-written as I don't like it either ! The different types of minigenes section is obviously still under construction.
 * ♠ Deacon C (talk) 03:47, 3 April 2014 (UTC)


 * I see you've made some changes. Looking good!!  Incorporating an image would add value if you can find one. Msmrugby (talk) 03:38, 16 April 2014 (UTC)

Review by tmckenne
Hello, I am one of your peer reviewers for this article. I think you've got a great article going here and with continued work and additions it will be really good.


 * Try finding an image or diagram for the article. It can be hard to find images for things like this but keep looking, you'll find something and I'm sure you're working on it.
 * Elaborate on the types section more. Try to get it to be paragraph length.
 * Very good uses section. I really like the different types of uses that you explain.  There is good information here and I like how you've broken it out.
 * Reference a couple more further reading options.
 * It would be interesting if you have time to add a history/discovery section to talk about who discovered the minigene.
 * There are some punctuation mistakes throughout the article. Especially look at the last sentence of the cancer section and many times when you list multiple items and don't have the correct number of commas.
 * Consider working on the introduction paragraph. It doesn't seem to flow very well.  The sentence that says 'This article address...' seems out of place.

Let me know if you have any questions or thoughts! Overall very good job! Tmckenne (talk) 19:40, 12 April 2014 (UTC)


 * Thank you Tmckenne. I missed the crazy commas at the end of the cancer sub-section. I think they were intended to go between the references, but that didn't work out somehow. I fixed that and appreciate you pointing it out. We'll work on the history/discovery section and adding images. Thanks again for your review. Tmo32 (talk) 02:44, 15 April 2014 (UTC)

Reply Deacon C
Yes, well you would think there would be plenty of public images, but none quite fit the bill. I will have to hand draw them with inkscape and so I guess I have been dragging my feet a bit; however, I hope to finish this tomorrow. Yes, the introductory paragraph is rough: I changed it from a quoted expression to a description, but now I think I will just junk the whole thing and start over. Thanks for your review, it was the most helpful so far.


 * ♠ Deacon C (talk) 20:33, 12 April 2014 (UTC)

Review by Crandel5425
Good work so far, here are some of my comments: Can't wait to fully read when you're finished! Crandel5425 (talk) 02:29, 14 April 2014 (UTC)
 * An image always makes articles better. I saw in your sandbox placeholders, but no real image. Wiki says to "Be Bold' I would suggest attempting to insert images and go from there. If you're unsure whether or not they infringe on copyright, wiki editors are always there to help.
 * adding history into its discovery would be useful
 * expansion of "types" of minigenes would be useful - either in a list or detailed format would work.
 * I like that you separated the bibliography (we'll have to do the same).
 * finding more references to include history and details on the types of minigenes should be included.
 * I like the overall format
 * some punctuation and sentence flow in some paragraphs like the lead would help the article flow better.
 * Maybe simplifying some ideas, like in "construction" make it difficult for me to follow


 * Thanks for the review Crandel! Maybe we should just be bold with the images and see what happens? It is in desperate need of an image. I agree on your suggestion for a discovery/history section and will try to add some related content next week. Thanks again! Tmo32 (talk) 02:41, 15 April 2014 (UTC)

Reply by Deacon C
Thanks for the great review. Like life, this page is a work in progress. Yes, I have thought of all the things you have mentioned; time and not ambition is the enemy here. You should have seen the number of subject headings we had earlier...though they got deleted. I have more free time this week, so I hope the page will take a sharp turn towards finished product.
 * ♠ Deacon C (talk) 03:23, 14 April 2014 (UTC)
 * I know the feeling. Good work so far Crandel5425 (talk) 13:57, 14 April 2014 (UTC)

Review from Keilana
Here are some suggestions and comments for you going forward. Let me know if you have any questions or concerns.

Thus, the transfected minigenes should contain all RNA-elements necessary to show the same alternative splicing pattern as the corresponding endogenous alternatively spliced gene when compared in a specific cellular environment." They are almost exactly copied from the source. This is unacceptable.
 * You need a full citation for the Stamms lab. Fill in the whole cite web template, which will guide you through it.
 * You absolutely must rewrite these sentences: "A minigene contains a genomic fragment including the alternative exon(s) and the surrounding introns as well as the flanking constitutively spliced cloned in a eukaryotic expression vector.
 * One guideline you should keep in mind is the medical reliable sources guidline, which applies anytime you write about medicine on Wikipedia. The components you should worry about now are the date (must be within the last 5 years) and the review (articles cited should be review articles whenever possible). The citations you should consider taking another look at are: Cooper (date), Stoss (date), Lou (date, review), McCarthy (date, review), Kar (review), Dawson (date, review), Jiang (date, review), Collis (date, review), Ma (date, review), and Acedo (review). (I think I checked them all.)
 * The "Construction" section needs some citations.
 * The citation to Lim et al. is broken, not sure why because it has a PMID. Check this one again and ask me if you need help with it.

All the best, Keilana&#124;Parlez ici 01:23, 17 April 2014 (UTC)


 * Thank you so much for your review, Keilana. Based on your suggestions, we've made some substantial changes to the introduction, so that it is not a direct quote from the source. We also added some references and more information to the construction section and will continue improving here. The broken link in the reference was fixed.


 * I agree with Deacon C's comments below that this article isn't medical. Minigenes are part of life science research, specifically as tools in molecular research. Researchers use minigenes for a variety of applications, only one of which has potential as a therapeutic and this potential has yet to be realized. Most applications are for research only and are focused on helping better understand disease mechanisms. Thanks for the info on medicine articles though - good to know.


 * Thanks again so much for your review. It was very helpful. Tmo32 (talk) 18:06, 18 April 2014 (UTC)

Reply Deacon C
Hi Keilana,


 * The sentences you are concerned about were originally in quotation marks with the cited reference; I thought this provided a nice, official sort of definition to start the article off with. However, my fellow student reviewers didn't like the quotes and just wanted a summary, so I was in the process of changing it.


 * I was unaware of the WP:MEDRS and its guidelines. While minigenes can be used in medical conditions, they also serve as a basic research tool to understand alternative splicing. So I am not sure how to address this: is it only the references which deal with medicine or is it all references in the article ? Also, does this 5 year limit apply to books listed in the further reading section ?


 * I thought I put a full citation in the Stamms web site template, but will double check it.


 * Yes, well, the "construction" section is still under construction and needs work...sorry about the pun.


 * I am not sure about Lim and will have a look at it.


 * Overall, thanks for your review. Our article needed the critical eye your provided (I mean this sincerely) and I will try to start the corrections on 4/17. I will also check all the links to make sure they are operational.


 * ♠ Deacon C (talk) 02:22, 17 April 2014 (UTC)

Review by Misha.S.
Great article! Here are some of the tips I have to offer;

The first sentence, maybe wikilink 'splice reporter vector' or maybe start the sentence with a physical definition of what it is like 'a minigene is a compact version of a gene in which pieces have been removed....' mention a benefit of using them, like' they are easy to insert....'

In the history section maybe start with the second paragraph first then dive into RNA splicing.

In the type seciton, an example of a type of minigene and its part might be easier to visualize.

The cancer section might need some more information,maybe explain how the minigene is useful, technical details

Looking forward to reading the final versionMishasubz (talk) 21:17, 26 April 2014 (UTC)


 * Thanks for the thoughtful review, Misha. I'm rewriting the intro based on other reviewers' suggestions and will work your suggestion to link "splice reporter vector" as well. I agree with your suggestion to change the order of the history section and plan to rewrite this section for better flow. You are right that the cancer section could be elaborated - other reviewers also recommended this, so we will definitely make this happen.
 * Thanks again for your review Tmo32 (talk) 00:49, 30 April 2014 (UTC)

Comments from Klortho
Hi, here are a few comments.
 * I can't understand the lead. It is written at too high a technical level, and assumes too much prior knowledge of the reader.  E.g. you start out saying "A minigene is a splice reporter vector", which assumes the reader knows what that is (I don't).  You then go on to mention "The gene fragment", and, "... the original and spliced gene".  What gene?  The minigene?  The minigene is the vector, but there's a gene fragment used to create the vector -- it is very confusing.  Could you try to rewrite it in language that a smart high-school student could understand?  Also, a word or two about the etymology would be nice:  why is it called "minigene"?
 * You could use more wikilinks throughout the article.
 * Another thing I don't really understand after skimming this article is whether minigenes are naturally occurring, or only created artificially. I assume that the mention in the "History" section, of the coining of the term in 1977, is a reference to a naturally occurring minigene: the researchers cloned two minigenes, so I assume that the sequences that they cloned were naturally occurring.
 * I like the image that you created, but even there, it is still not completely clear to me what is the minigene. The diagram seems to show a section of mRNA that has been spliced together. So is the minigene a section of mRNA? Or does it comprise a DNA sequence?

I think you have a decent article here, and a lot of good content. My recommendation would be to spend the time you have left trying to improve the readability of the article. Not just the lead, but the whole article, really, is written at too difficult of a technical level. I hope you find this feedback useful. Klortho (talk) 03:04, 27 April 2014 (UTC)


 * Hi Klortho, thanks so much for your review. I appreciate your insight on the intro. I will rewrite it and clear up the confusion as to whether the minigene is naturally occurring or created artificially; it's both actually and I can see how that would be confusing. I'll also try to make the article more readable overall, per your suggestion, and hope that it will be more clear what a minigene is to a wider audience. Tmo32 (talk) 16:57, 27 April 2014 (UTC)

Comments from Jhayes21
Hi All,
 * 1) First impressions - well chosen image :)
 * 2) Lead - I can see from earlier comments that the lead has been the focus of some revisions - I think the work pays off, it is well constructed, simple and informative.  My only suggestion/preference would be to perhaps move the last sentence of the lead "Specifically, mini genes act as a probe to determine which factors are important in splicing outcomes; they can be constructed to test the way both cis-regulatory elements (RNA effects) and trans-regulatory elements (associated proteins/splicing factors) affect gene expression." to the beginning part of the Construction section. I think this change might help with the flow of the article.
 * 3) Types - this section is notably smaller - is there an image that could demonstrate wild type vs mutant?
 * 4) Uses - this section has been well explained, cited, and linked.  The subsections broken down work well with the article.  One thing I did notice was except for one article in 2009, the references for endocrine and neurodegenerative were quite dated.  Has research shifted away from mini genes in these areas? If so, is it worth mentioning and why? Additionally, perhaps elaborating on the cancer section? Perhaps explain a simple experiment where mini genes were used in studying different "splicing in different cancer types, including prostate, lung and breast cancer" or perhaps a simple example of how a mini gene would be used in the "delivery system for cancer immunotherapies" were there any images demonstrating these uses?

Overall, great job! Jhayes21 (talk) 04:29, 29 April 2014 (UTC)

Reply by Deacon C

 * Thanks for your review. Yes, well you hit on quite a few sore points about things to address. Basically, the types section is being re-arranged and will have pictures. The construction section is also being re-arranged and will have pictures. Where the Hell are the pictures ? It is very time consuming to make these images in inkscape: it's not just the drawing, but the planning of what type of information you want to convey and how best to do it. The first image you see went through 3 different modifications, before it looked like it does and I am still not happy. The construction section image has so far taken about 10 hours and is not finished yet, but should be by tomorrow. There is a certain synergy between designing the image and the prose of the article; you think of different things when drawing that would make the article more understandable. So I guess I like to release the finished drawing and revisions at the same time. Yes, I made a list of the medical references and these will be pulled and replaced with newer ones. I was unaware of the Wikipedia medical reference criteria and Keilana spanked us for it on her review, so we will get it taken care of. Thanks for the medical suggestions as well.


 * ♠ Deacon C (talk) 00:23, 30 April 2014 (UTC)


 * Hi Deacon C, the work you all have done looks great! I totally understand your frustration with images, we also had this problem for our article.  I ended up spending many hours trying to create the one that finally appears on our page, but of course, like you, am still frustrated with it. Apologies for the redundancy on medical references, initially when I was first reviewing I was merely making an observation/suggestion and had no idea about the "rules" of medical references. Again, similarly  Keilana was helpful in making us aware of these rules. Glad it seems to have worked out. Jhayes21 (talk) 21:52, 6 May 2014 (UTC)