Talk:Dicer

Comment

That picture doesn't look like Dicer... it looks like a crystal structure composed of _four_ dicers.—Preceding unsigned comment added by 129.100.18.193 (talk • contribs) 15:22, 4 July 2006

That's exactly what it was. It's now one dicer. Opabinia regalis 05:06, 7 October 2006 (UTC)

Improvements

Hi Everyone,

As part of a group project for a graduate molecular biology class for Johns Hopkins University, my partner and I will be attempting to improve upon this article. We need to raise it's classification to B or higher. We'll be rewriting the article in a sandbox and then adding the information all at once as opposed to constantly changing the posted article. Here are some thoughts about potential changes.

- Adding a protein box linking to database information.
- Include pictures to better explain the mechanism of action.
- Discuss the catalytic site of the protein and biochemical reactions that occur with sRNA.
- Add additional functional information in regards to siRNA.
- Discuss specific roles of dicer in immunity, reproduction, etc.
- Discuss roles of dicer in a selection of model organisms.

We're very open to criticism and suggestions, so please tell us what you think. Rmiller587 (talk) 14:15, 11 March 2014 (UTC)

Also, the article will most likely start changing with the organization of the whole article. We based our model off of other GA level articles, and we will inch more and more towards that level article as we progress throughout the weeks. Thanks for any feedback in advance! Martinhyou (talk) 16:06, 11 March 2014 (UTC)

As an amendment to my previous comment...we will be making periodic changes to the article instead of changing it all at once as I previously suggested. Rmiller587 (talk) 03:42, 12 March 2014 (UTC)

I've created a protein box with relevant links to important databases. Rmiller587 (talk) 17:09, 25 March 2014 (UTC)

Review from Graeme Bartlett

This has undergone a good expansion, at least a C class now. To get to B class it will have to have a pretty complete coverage of the topic, and at this point I don't know enough to see if this is true.

What does "tumors are available" mean? If "dicer can be used for treating patients", how and when is this done? do they get a dicer injection?

In references I would encourage you to use more doi's for the modern references. Also the data format yyyy mmm dd looks a bit dubious in the references. If you know first names for authors put these in too.

There is a paucity of wikilinks. Many of the terms used could be linked to other articles on the topic using for example: [[RNA interference]] giving RNA interference.

In one picture at File:MiRNA-biogenesis.jpg there is a weird green line above the pri-miRNA loop. Also this in .jpg format which tends to have compression artifacts, much better is .svg, and second best is .png format. Graeme Bartlett (talk) 10:27, 30 March 2014 (UTC)

Hi Graeme! Thanks very much for taking the time to review our article. We'll be improving more on the article in the next two weeks to get closer to a B-class and add a more complete picture.

As far as the therapeutic uses paragraph is concerned, I'll let Martin answer those questions since he wrote that part.

The references were generated automatically by wikipedia using the PMID search tool and journal template. Because of this, I'm not sure how to improve upon them in the manner you suggested.

You're definitely correct about wikilinks. I forgot all about them. I'll go back through the article to add more and make sure we continue wikilinking throughout other improvements.

I see the artifacts you mentioned in the picture. We used that picture because it had been previously uploaded. We'll work on that.

Thanks again!Rmiller587 (talk) 19:06, 30 March 2014 (UTC)

Hi Graeme. Thanks a lot for the feedback! I'll work on editing that paragraph as it is a bit vague still at the moment. I'll probably have to use another source to identify how exactly dicer is used to treat the patient as the article I used only briefly went over the specifics. Thanks for the other comments as well and we'll be sure to consider the other points you had. Martinhyou (talk) 16:18, 31 March 2014 (UTC)

Comments from Jocelyn Munson

Good job on the article so far! My comments are below:

In the lead section you wrote Dicer “cleaves double-stranded RNA (dsRNA) and pri-microRNA (pri-miRNA) into short double-stranded RNA fragments”. Instead of writing “double-stranded RNA fragments,” you could be more specific and write “siRNA” and “mature miRNA”. You might also briefly mention the functions of siRNA and miRNA. Is Dicer called by any other names?

“Dicer facilitates the formation of the RNA-induced silencing complex (RISC)” No, it doesn't. It facilitates the activation of RISC, but not the formation.

The first source in the “History” section doesn't have specific information on the discovery of Dicer. Different sources are needed. Also, how did Bernstein observe Dicer’s “dicing” activity?

In the “History” section, the last two sentences are confusing. According to the cited source (10.1016/j.cell.2009.12.023), epigenetic silencing is caused by methylation of target miRNAs. Also, the other cited source does not link to anything.

In the figure caption, you wrote: “The distance between the RNase III and PAZ domains, determined by the length and angle of the connector helix, has been suggested as the determinant for the length of siRNA molecules produced by a given Dicer variant”. And then in the “functional domains” section, you wrote, “The distance between the PAZ and RNaseIII domains is determined by the angle of the connector helix and influences the length of the micro RNA product”. Which is it? According to your cited source (PMID 16410517), both siRNA and miRNA (small RNAs) are influenced by the angle between the two domains.

A simple diagram illustrating the Dicer domains would be helpful (similar to Figure 1 in PMID 16214139)

In my opinion, the RNA-induced silencing complex (RISC) needs its own section. Describing its mechanism would be especially helpful.

Regarding the “role in RNA interference” section, DGCR8 is not mentioned in this source (PMID 20179193). SiRNAs should be written about in this section, since they also take part in RNA interference.

In my opinion, the “role in cancer” and “role in tumorigenesis” sections should be combined.

Which “double strand break repair mechanisms” is Dicer involved in?

How does Dicer “silence transposons”?

How does Dicer “direct chromatin modifications”?

Instead of “oncogenic,” write “cancerous” instead

This sentence is confusing: “Although it is known that miRNA is important in relation to human cancer and RNA, their specific functions are relatively unknown”.

PMID 16214139 is cited twice (5 and 7)

More Wikilinks are needed (transposons, chromatin, etc)

Add an “external links” and “see also” section

The figure with the mechanism is too small

In most cases (see above), your sources are cited correctly. In my opinion, you didn't plagiarize, but the way the article is currently written is too complicated. This is especially true for the “functional domains” section. Be as clear and straightforward as possible.

I hope you find my comments helpful! --Jocelyn Munson (talk) 22:01, 31 March 2014 (UTC)

Hi Jocelyn. Thanks for the thorough review! I'll try my best to address your comments. Some of them are about parts we haven't written and were in the stub when we started working on it. I recognize there's no way for you to know that though.

We haven't actually worked on the beginning paragraph yet. I think leaving short double stranded RNA is fine since that sentence shows up when you first google dicer. If you don't know what siRNA or miRNA is, you then have to google those to figure out what dicer does. Short double stranded RNA is more descriptive for a basic overview paragraph. Mentioning what siRNA and miRNA are is a great idea though!

Dicer's other aliases are listed in the "identifier" portion of the protein box on the right.

We definitely know the history paragraph needs work. Thanks for noticing! I think your idea about adding info about the specific experiments that led to the discovery of dicer are a great idea.

The picture you referred to was also in the article (along with the description) when we started working. I'm not sure if we'll end up keeping it or not. Just in case, I left it in there for now. Before we're finished though, we'll need to resolve that discrepancy, one way or another.

There's a picture of domains in the protein box on the right that will expand to a larger size when clicked on.

I think you're right about RISC. I'll work on dedicating a section just to RISC. Thanks for the idea!

Thanks for adding a list of questions! I'll make sure to add that info by the next article due date.

I don't think cancerous and oncogenic are synonymous, especially in a scientifically orientated article.

Again, I think you're right. I'll work on the weird sentence. I think it sounded better in my head before I typed it out. Re-reading it now I totally agree.

We did have some issues with articles showing up multiple times in the sources. I'm not sure what's going on with it yet but we'll make sure to have it fixed before the end. Thanks!

I definitely dropped the ball on wikilinks in sections I wrote. I'll make sure to fix that by next week as well.

A see also and external links section is a great idea. Thanks!

Thanks for all of your suggestions! I think these will help a lot!Rmiller587 (talk) 01:57, 1 April 2014 (UTC)

I think Dicer is known for cleaving pre-miRNA and not pri-miRNA, which is cleaved by Drosha to generate pre-miRNA. I did not do a very extensive literature search though, so I am not 100% sure. Please check this again.129.206.70.143 (talk) 12:23, 1 April 2014 (UTC)

You're right! I didn't even notice that. I changed it right away. The paragraph Martin wrote about RNAi has it correct but the first paragraph was wrong. Thanks!Rmiller587 (talk) 14:14, 1 April 2014 (UTC)

Thanks for all of that! The suggestions from both you and Graeme are great and we'll be working on the article overall to make it better! We will focus a bit more on the introduction and history sections to make it more suitable for a GA/B level article. Martinhyou (talk) 22:34, 1 April 2014 (UTC)

PEER REVEIW FROM KATHERINE BARNHILL

The article looks great, so far!

The lead section is extremely technical (which, it should be, to some extent), I think you would benefit from decreasing the scientific jargon and definitely including some more wikilinks to assist the readers in understanding.

The images are all great and well placed, I like that the 3D picture is arranged right next to the FUNCTIONAL DOMAINS (so that I can visualize where the domains are actually located) and the RNA INTERFACE (so that I can visualize where the RNA fits in to produce said interface) sections. Upon a second review, I did have some trouble deciphering all that was going on in the mechanism image, so I suggest getting a larger one.

I agree that the RISC should have it's own section, the information provided here will provide a more thorough understanding of the role that Dicer plays.

The references are well cited and well picked, and are cited appropriately.

The overall tone of the presented information remains neutral throughout the duration of the article, very concise. The jargon can be quite cumbersome, so I would suggest including more wikilinks in the entire article (especially in the functional domains and RNA interface sections).

Expound on how this molecule can be used in cancer treatment, since this subject is of high importance and interest. Klbarnhill (talk) 23:44, 1 April 2014 (UTC)

Thanks Katherine! Great suggestions :) The mechanism picture will expand when clicked on. You don't have to look at it in the smaller format. The protein domains picture in the protein box also gets larger. Rmiller587 (talk) 13:38, 3 April 2014 (UTC)

You can resize images. See Wikipedia's picture tutorial. Hope that helps! --Jocelyn Munson (talk) 23:56, 7 April 2014 (UTC)

Thanks! Do you think this size is better? Rmiller587 (talk) 17:28, 8 April 2014 (UTC)

Yes, I do think that this size is better. --Jocelyn Munson (talk) 01:23, 9 April 2014 (UTC)

I agree, the size is much better and fits in well with the page! Klbarnhill (talk) 19:47, 15 April 2014 (UTC)

New Improvements 4.8.2014

Hey All,

Here are the following contributions we have made in the last two weeks:

• Edited the introduction to be easier for the general public
• Added and reformatted the History section to "Discovery" and added more relevant, scientific information
• Added more detail into RNA interference while elaborating differences between microRNA and siRNA.
• Added a new photo with siRNA and miRNA diagram
• Added a new section called "Viral Pathogenesis"
• Elaborated on "Diagnostic/Therapeutic Tool" section of how injections of siRNA take place.
• Added a few more citations relevant to the new information and data added.
• Took into consideration the remarks made by peer reviewers and changed areas accordingly.

Thanks! Martinhyou (talk) 03:16, 9 April 2014 (UTC)

I think the article has made some great improvements since I last looked over it. I did notice one small thing. In the "see also" section, RISC links to the "reduced instruction set computing" page. This is the correct link. --Jocelyn Munson (talk) 22:55, 9 April 2014 (UTC)

Thanks for catching that! I made the changes accordingly. Martinhyou (talk) 15:13, 10 April 2014 (UTC)

Review by Neelix

I like the direction in which this article is going. Here are some tips for further improvement:

1. Pay attention to punctuation; the first word of the lead should be followed by a comma, "Dicers ability" should read "Dicer's ability", etc.
2. Be careful not to squash text between images; either space the images throughout the article or decrease the number of images until there is enough paragraphical text for there to be room.
3. Sections should contain more than one paragraph each, and paragraphs should consist of more than one sentence each.
4. There should be no unsourced information in the article; paragraphs that do not conclude with a citation thereby leave their concluding sentence unsourced.
5. Add more wikilinks; the final section of the body currently has none.
6. Be sure to contextualize the information you present. The "Discovery" section provides very interesting background information, but it currently makes no indication of whether Dicer was discovered in the 1800s or in 2014.
7. There should be no self-links in the article; a link to Dicer on the Dicer article will cause the word to be bolded when it should not be bolded.

You've been doing a great job in developing this article. I hope you'll contact me if you have any questions about my suggestions. Neelix (talk) 03:59, 14 April 2014 (UTC)

Thanks for the review! We'll be sure to make the changes with punctuation, increasing paragraph lengths, adding citations, and adding more wikilinks for the next contribution. We are covering the overall picture at the moment and will fill in the gaps as the weeks go on. Thanks for the tip with the Dicer part! Didn't know it did that. Martinhyou (talk) 15:39, 14 April 2014 (UTC)

Thanks Neelix! We'll be adding more text and probably not too many more images so the images should be spaced more appropriately soon. As for Dicer's discovery, I cited the original article that named and characterized Dicer. It was published in 2001 so that time should coincide with Dicer's discovery. I'll add in a date though so it's more obvious and a viewer doesn't have to scroll down to find the date. Thanks again for your help! We'll make sure to address all of your points before our next submission date. Rmiller587 (talk) 03:07, 16 April 2014 (UTC)

Review by Alpha Centauri b

It looks like you've done a lot of work on this article already and I think it is looking pretty good.

• the interactions section needs to be expanded. Could you define the interactions with EIF2C2 and TARBP2 further?
• The macular degeneration section could also be expanded more. What does that sentence mean?
• In the section on "As a diagnostic and therapeutic tool", I think it would sound better if you mention which study showed the result instead of saying "A study showed...".

Alpha centauri b (talk) 20:26, 14 April 2014 (UTC)

Thanks acb! I agree with all of your comments. We'll be addressing those, by adding more information and explanations of interactions. Thanks for the ideas! Rmiller587 (talk) 03:07, 16 April 2014 (UTC)

Thanks for the comment! I think it's a great idea to add some more studies, but I think wikipedia policy asks to not put original experiments if possible. We'll try to add more info though as we go along. Martinhyou (talk) 23:48, 22 April 2014 (UTC)

Comments from msmrugby - 4/15/14

Overall impression is that this article is well on its way to being very good. My comments are not major issues, just minor tweaks to help move things forward. Great references, citations and the organization is logical. Consider a separate mechanism section to clearly point the reader to the section that explains how the enzyme works. Section specific suggestions are below.

Intro Section

• Sentence with Ortholog needs to be introduced. The connection between Dicer and Ortholog is not made, and the second sentence immediately states that Orthologs are found in many organisms.
• Could use some additional citations in the lead paragraph. After the 2nd sentence there are no citations.

Discovery

• 2nd Sentence – Clearly state that Emily conducted an experiment with Dicer by separating it from the RISC enzyme complex after initiating the RNAi pathway with dsRNA transfection. In its current state, you figure out it’s an experiment in the next sentence where you indicate that the experiment showed that RISC…
• When was Dicer discovered?
• The picture to the left is very useful; however, it mentions a platform domain that is not mentioned in the verbiage to the right. Suggest making the two consistent.

Role of RNA Interference

• siRNA could be introduced further. How are they produced? The initial paragraph speaks of pri-RNA and pre-RNA, but then goes right into siRNA. Could use a slight introduction at the beginning of the 2nd paragraph to explain the relevance to the other RNAs.
• Last sentence could use a citation.

Interactions

• Needs expansion. Explain the relevant interactions if possible.

Clinical Significance

• Provide more information on macular degeneration. How does it induce toxicity?
• sRNA is mentioned in this section and the Functional Domains section, but is not defined like the other RNAs are. (i.e. Small RNA)

As a Diagnostic and Therapeutic Tool

• Suggest changing the heading to Applications or Diagnostic and Therapeutic Applications.

See Also

• List could be expanded to include other relevant items listed in the article.

Msmrugby (talk) 03:28, 16 April 2014 (UTC)

Thanks for the comments!

• We actually need to remove all citations from the lead paragraph as the lead section should not have citations. We'll moving those citations and repeating original info in the lead in another body paragraph. Ortholog is not a protein, it's a term. Click the wikilink to learn more.
• I mentioned Dicer was separated by RISC "...was discovered by separating it from the RISC enzyme complex after initiating the RNAi pathway with dsRNA transfection." Do you think I should write more about her experiments? Her paper was published in 2001 so we'll be adding that info in like you and Neelix have suggested.
• We've been trying to stay away from getting into siRNA too much. There's a huge wiki about RNAi so we thought it best to only explain it a little. I'll go back through it and see if we can expand it more without repeating information in other wikis too much.
• We'll address the rest before next week.

Thanks again for the comments! Rmiller587 (talk) 16:59, 16 April 2014 (UTC)

Very good. Just to clarify the ortholog comment. Right now, your first sentence introduces Dicer, then your next sentence immediately speaks of Orthologs. There is no connection statement that links the two, so it reads a little choppy right now. I'm assuming Dicer is considered an ortholog, so perhaps adding that to the first statement will provide the transition I'm speaking of. Regarding the experiment comment, I'm not suggesting anything major. Just suggesting that you indicate in the 2nd sentence that an experiment was conducted. In the current state, the third sentence mentions the experiment, yet the second sentence is talking about it. Lastly, the comment re: siRNA is to provide a little more information to be consistent with how you speak of the other RNAs pre, pri, etc. Hope this helps. Msmrugby (talk) 19:57, 16 April 2014 (UTC)

Great work on the article. You've made a lot of improvements and it looks to be in great shape!Msmrugby (talk) 03:50, 30 April 2014 (UTC)

New Improvements for 4.22.2014

Here are the improvements we've made these last weeks:

• Introduced more wikilinks
• Added citations in the correct locations
• Made changes to sentences grammatically and contextually.
• Added an extra paragraph under "Applications" based on how siRNA is injected.
• Added an extra paragraph under "Applications" explaining more in-depth advantages/disadvantages of siRNA/miRNA/antibodies/small molecular inhibitors.
• Changed picture size to 250 pixels for the one about miRNA production.
• Added insect paragraph
• Expanded macular degeneration paragraph
• Removed Interactions section
• Addressed previous comments

Martinhyou (talk) 00:39, 23 April 2014 (UTC)Rmiller587 (talk) 02:11, 23 April 2014 (UTC)

Again, great job on improving the article! I would expand the interactions section a little more. --Jocelyn Munson (talk) 01:00, 23 April 2014 (UTC)

Thanks Jocelyn! I think we'll ditch the interactions paragraph for now. I'm not sure it really adds much at the moment. Rmiller587 (talk) 02:11, 23 April 2014 (UTC)

The improvements look great. The article has certainly come a long way. I like the insect paragraph that you added! It looks as though you have addressed a lot of the previous suggestions. nice job. Alpha centauri b (talk) 02:46, 23 April 2014 (UTC)

I have a few minor suggestions after re-reading the article:

• The "In Insects" section should be renamed to "Dicer In Insects"
• Dicer should be capitalized everywhere in the article
• "West Nile Virus, Dengue Fever and Yellow Fever" should be "West Nile virus, dengue fever and yellow fever"
• Drosha and Pasha need to be wikilinked --Jocelyn Munson (talk) 20:31, 28 April 2014 (UTC)

Review by Deacon C, 24 April

This is a great article, you have done a very nice job on it. It incorporates some of the same features that I wanted to put in our article. I wonder, though if there is too much information on the page. I don't mean the written format, but the info box. This is not a critiscism but actually a question. I know that for suggested categories, the infobox needs to have certain elements in its template; I think that proteins falls under this category. Maybe you could let me know as this would help me also.

One of the things I noticed is that the pictures go across lines in the article (drop into different sections) and I think this can be corrected. One of the documents that I found useful in image formatting can be found at: https://wiki.riteme.site/wiki/Wikipedia:Extended_image_syntax. I actually have to correct this problem myself. This would make the page look not quite so crowded.

Because Dicer is involved in a series of steps in RNA silencing, one always has to describe additional steps in the process which makes for the possibility that the article might drift away from the main subject when going into this explanatory detail. I mentally removed various descriptive diagrams and then re-read the sections, to me the medical sections would not be understandable without them. I think you have struck the correct balance here. Congratulations on a difficult topic.

♠ Deacon C (talk) 00:08, 30 April 2014 (UTC)

Thanks for the review! I'm really glad you liked the article.

• The template I followed is here https://wiki.riteme.site/wiki/Template:GNF_Protein_box. I filled in as much information as I could. Really, it's just a box filled with links to database information. It's useful to have this all in one place if you're really interested in all that is Dicer but for the average user, I suspect it will go unnoticed. Most probably don't care to know the chromosome position of the dicer gene in humans and mice.
• Fixing the pictures may or may not work. My concern is that making them smaller so they fit into sections will lead to a repeat of above comments to make them bigger. If we just make it so they don't spread into other sections but leave them the size they are, then we might have unnecessary blank space in our article. Is there a specific picture you'd like to see confined to a section? I could mess around with sizes to figure out how to make it work if you think it will improve the article.

Thanks again for the compliments! If you think of anything else, let us know!Rmiller587 (talk) 02:18, 30 April 2014 (UTC)

Yeah we've had a bit of trouble with the pictures. It seems like it's okay when the browser is smaller or the resolution on the computer is smaller, but when those get altered, the wikipedia page seems to look a bit off. We'll work on smoothening it out if possible. Thanks for all the great comments, and glad you liked it! Martinhyou (talk) 16:51, 30 April 2014 (UTC)

Comments from Catwell99

Great job! I really like the pictures and tables as well as the placement of the pictures and tables along the right hand side of the article. Additionally, the article is well-organized and easy to read. The lead section is also well-done. Also, great job on wikilinking the more technical terms.

You may want to consider moving some of the text from the "Disease" section under Macular Degeneration and Cancer to Applications section. For example, the initial sentence in the Macular Degeneration section describes the issue of macular degeneration in developed countries. In my view, this sentence implies that you'll start to discuss potential therapeutics within the next paragraph.

Overall, a really nice job though. It was hard to find anything to suggest revising! --Catwell99 (talk) 03:30, 30 April 2014 (UTC)

Thanks Cat! For the Macular Degeneration and Cancer section, that may be an idea that we take into consideration as we try to piece it all together by the end. We have been wanting to expand the Applications section more and that's a good idea. Thanks for all the nice comments too! Martinhyou (talk) 16:49, 30 April 2014 (UTC)

Review from Keilana

Hi guys, great job so far. Here are my comments for you as you finish things up - let me know if you have any questions or need help with anything!

• You should go through and do a thorough copyedit, I noticed a few grammar/spelling errors here and there you could take care of.
• In general, we don't put citations in the lead, because theoretically everything in there should be cited and talked about later in the article, since it's meant to be a summary.
• Great job giving relevant, good explanations in your captions.
• Overall great job. I honestly don't have much more to tell you. This is a really detailed, well-sourced article. Nice job!

All the best, Keilana|^{Parlez ici} 16:38, 3 May 2014 (UTC)

Thanks Keilana! We'll go through the article thoroughly and make sure there are no errors. I've been meaning to remove the citations from the lead but I end up overlooking that paragraph. Thanks for picking up on that. I'm glad you liked the article! If you think of anything else, let us know. Rmiller587 (talk) 21:03, 3 May 2014 (UTC)

Thanks for the comments, Keilana! We'll be tidying up and making our finishing touches to the article with your review along with the other two. We wanted to make sure all the articles and information was there and we'll probably add a bit more information, and then fix up the article to look nice grammatically and picture-size wise. Martinhyou (talk) 20:11, 5 May 2014 (UTC)

New Improvements 5.5.2014

Here are the final improvements made for this article:

• Fixed multiple grammatical errors related with sentence structure, transitions, and spelling.
• Introduction was restructured and edited to have no citations. Ortholog sentence was placed in the "Discovery" section.
• New paragraph added in Discovery with the relevance of first structure discovery in Giardia and comparison with Human Dicer. Allows for better transitioning between the paragraphs.
• Found newer research that shows the functioning of DUF283 in Human Dicer. Added corrections in the appropriate location.

Martinhyou (talk) 22:02, 5 May 2014 (UTC)

We also added a section about dicer like proteins in plants. Rmiller587 (talk) 01:21, 7 May 2014 (UTC)

Outstanding job!

Just wanted to say that I think you guys did a really good job on this article. You made my day! Klortho (talk) 01:44, 7 May 2014 (UTC)

Thanks Klortho! Glad we could contribute to the Wiki community and also make your day! Martinhyou (talk) 03:12, 7 May 2014 (UTC)

Thanks very much! I'm really glad you liked our article. Like Martin said, it was great to have the opportunity to contribute to the Wikipedia community. Rmiller587 (talk) 21:21, 7 May 2014 (UTC)