Wikipedia:United States Education Program/Courses/JHU MolBio Ogg 2013/Group 81H

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Unit 14 RNA Silencing Wikipedia Article Progress Report

Our topic of RNA Silencing did come together well at the end, but we did encounter a little synchronization problem since we were editing a same part at the same time, which is not hard to do, especially when you are trying to manage citations. I think it's a small reminder that you should always write your text on another support than the Wikipedia page, because anything can happen, like an electrical break.

Anyway, based on the great commentaries from our classmates, we rearranged our article so that it flows better. I believe that we now have a solid article, still a little conflicted about the relationship with the RNAi article, but I think that we have a shorter synopsis of the whole domain and we are looking at it differently, so that maybe for some, it might be easier to grasp.

Later, maybe, we might be asked to merge both articles, but I do believe we brought in a lot of new info, since their article had not really been updated in a while. Those editors haven't yet tried to correct ours. (That was one thing that surprised us both, that no one, outside of our class, has said something about our article.)

This experience was one of a kind, and I think we both enjoyed it. MartinLubell (talk) 07:55, 10 May 2013 (UTC)

Agreed. To add to Martin's assessment, towards the very end is where I felt the structure/content came together. Until a somewhat finalized article has been put together, there is only flux and whatever accretion of information you have started to flesh out. To conclude our work on this project, the following work has been recently done on the page:

• Addressed comments posted by our reviewers
• Added a significant amount of explanation
• Added an explanatory table to illustrate
• Proof read, consolidated repeated citations
• Polished phrasing and corrected grammar etc.
• Reorganized two of the last section heads

To reflect on this experience, the feedback from our classmates was invaluable. The more time you spend writing something the more you lose sight of big picture things like organization, ease of comprehension, flow, clarity. On the other hand, you spend time obsessing about other important things like citations, accuracy, and articulating ideas. So, ideally you get both through this exercise and hopefully the public benefits. Going from the phase of not understanding anything, to a literature search, to an outline, to a first draft, to a second draft, and now to finalizing the content and organization has been a challenging, time-consuming, but altogether very rewarding experience. As I indicated in my reflection piece on the discussion board, I am a huge fan of this part of the curriculum. Ppelletier (talk) 07:52, 10 May 2013 (UTC)

Unit 9 Progress Report

1. Created a section entitled "Overview" the object of which is to situate the topic in a broader scheme than related topics such as RNA interference.
   1. Address RNA silencing and how it has evolved over the years, whether there are any other types of RNA silencing in addition to miRNA and siRNA, and begin to craft some distinctions, to the extent this is helpful in understanding RNA silencing as a broad topic covering a variety of mechanistically related pathways.
   2. One justification is, not only is this broader construction consistent with summary articles and introductory material, but there are technical reasons--e.g., despite early focus in the literature on RNAi as a core mechanism which occurs at the level of mRNA translation, others have since been identified in the broader family of conserved RNA silencing pathways acting at the DNA and chromatin level.
2. Identified the following key references for situating this topic (as distinct from more pointed citations which support specific statements of fact), these are great comprehensive overviews with solid introductory text:
   1. Moazed, D (2009 Jan 22). "Small RNAs in transcriptional gene silencing and genome defence.". Nature 457 (7228): 413–20. PMID 19158787
   2. MEISTER, G. (1 March 2004). "Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing". RNA 10 (3): 544–550. doi:10.1261/rna.5235104.
   3. Tijsterman, M; Ketting, RF; Plasterk, RH (2002). "The genetics of RNA silencing.". Annual Review of Genetics 36: 489–519. PMID 12429701.
3. Organized the talk page for the article to seek community feedback on approach and preliminary outline which will be used to develop concepts. Specifically, to seek feedback on the choice to construe RNA silencing as a broader topic than RNA interference. It will be important to clear this up early.
4. Note as follow up items
   1. Create original images/illustrations (found some good sources from which to draw inspiration)
   2. Develop therapeutic application section, lots of really interesting articles available
5. Added a section on the associated mechanisms as well as a summary of the distinctions between miRNA, siRNA, and piwiRNA. Looking to generate original illustrations to help conceptualize the distinctions.

Ppelletier (talk) 17:49, 5 April 2013 (UTC)

Article Editing Notes and Observations

Preliminary Outline

1. General Overview
   1. Definitions (PP-Unit 9)
      1. RNA silencing
      2. RNAi
      3. miRNA
      4. siRNA
      5. rasiRNA
   2. Summary (PP-Unit 9)
      1. family of gene silencing effects
      2. post-transcriptional gene silencing (PTGS)
      3. general overview of RNA silencing
2. Molecular mechanisms (ML-Unit 9)
   1. Key players
   2. Mechanistic description
3. Biological functions (ML-Unit 9)
   1. Processes affected
   2. Manifestations
4. In-depth
   1. Recent discoveries
   2. Laboratory techniques
   3. Medical implications
   4. Technological applications
5. History and Discovery
6. Open ended questions

Comments and Guidance

On Mar 27, 2013, at 3:31 PM, Sherry Ogg wrote: "Hi Martin, > > RNA silencing is a broader category than RNAi, and RNAi falls into the category of RNA silencing. However, having this distinction does not necessarily mean that everyone considers silencing and interference to be two separate entities. In much of the literature you will hear both terms used interchangeably. After looking at the two articles you linked below, it may be good to give a general overview of RNA silencing and how it has evolved over the years. Are there any other types of RNA silencing, in addition to miRNA and siRNA, which are considered RNAi? Simply making these distinctions would be a good start to the RNA silencing article. If you are confused, I'm sure other Wiki readers have the same confusin. I admit, this will be more of a challenge than expanding on RNAi, but I think it could be substantial. > > I hope this helps in your direction." Ppelletier (talk) 22:38, 4 April 2013 (UTC)

Article Selection Rationale from Group81H

Part of our rationale for deciding to edit the article on RNA silencing was to select a notable topic in need of development, both in terms of substance as well as citations. We also wanted to make sure the topic was narrow enough to develop meaningful and complete definition, while broad enough to have appeal to an audience that is not limited to researchers focused on a topic too specific to be accessible to the general public. RNA silencing is the subject of several recent publications and is a rapidly advancing area of molecular biology, one which is also shaped by the advancing technology available for resolving its complex mechanisms. For example, aside from reducing gene expression, authors are now conceiving of RNA silencing as a mechanism for cellular protection against viruses, transposons, as well as disposing of aberrant or nonfunctional mRNAs. There is a fast growing body of literature that therefore should be read, understood, and written up in a manner that makes these new scientific developments accessible through Wikipedia’s knowledge base. Wikipedia has well developed articles on miRNA and RNAi, so our efforts stand to enrich an already solid foundation. We hope to learn from these well written counterparts and develop a format that is consistent with these models. Both of us initially evaluated the article, indicating we shared an interest in the subject matter, which will undoubtedly start us off on the right foot. It’s easier to write about something you are interested in. Last, the topic is very relevant to our class discussions and will provide us both with an opportunity to explore a fundamental and complex subject in molecular biology.

Initial Article Assessments from Ppelletier

RNA silencing

This article has been rated as Stub-Class on the project's quality scale and of High-importance for improvement. The article is very short. While the content appears to be accurate and supported by citations, the topic is very complex and would benefit from full development. For the same reasons, it is not particularly well rounded. This article would also benefit from illustration. The talk page is not populated with any discussion. In order to make this a more well rounded article, some citations may include:

• An accessible article, discussing the topic as a general concept.

• One regarding a specific RNA silencing mechanism described.

• One with a clinical/therapeutic focus to apply the concepts.

Gene map

While the article has not been formally rated, it is flagged as Stub-Class and of High-importance, as a priority for improvement. Not only is it very short, but it is not particularly coherent or well written. The talk page indicates there were a few general suggestions made in 2006, but nothing appears to have become of them. What is written is not well supported, verifiable, and/or cited to good authorities. This may be because the term “gene map” seems to be somewhat diluted in the scientific literature, so this article would definitely benefit from providing a clear definition that puts the topic in dialogue with gene mapping, which is better defined.

• Defining what a gene map is would be a good start, and the National Human Genome Research Institute has a good page.

• The National Institutes of Health via the National Center for Biotechnology Information also have a great hub for pulling together information on this topic.

• Hopkins Medicine has a decent page defining gene mapping as a discipline, but it may need to be fleshed out and traced to more sources.

Initial Article Assessments from MartinLubell

Basic helix-loop-helix

Link to Wikipedia page: Basic helix-loop-helix

Basic helix-loop-helix Grade: Stub Class
Well-written, but not enough. Seems to be only one author!
Quite a few verifiable references, inline Citations
Maybe not broad enough, well organized though in different sections.
Neutral
Stable (No Editing Wars) Only one line written in Talk page by one author!
Illustrated (With images or graphics)
Some Quickfails
Notes: I think we could get this article to B relatively easily!
A relating article: "Structure and function of helix-loop-helix"

RNA silencing

Link to Wikipedia page: RNA silencing

RNA silencing Grade: Stub Class
Hardly anything written. Competition is fierce with the RNAi page, considered one of the best of Wikipedia!
No references or inline Citations
Not broad enough
Neutral
Stable (No Editing Wars) Not one line written in talk page!
No images or graphics
Most Quickfails
Notes: I think it would be a lot of work to get this article to B status, but it would be very interesting and useful!
An interesting article about RNAi that related to HW#5: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329497/

Group 81H

This is the Wikipedia page for 410.602 Molecular Biology, Spring, 2013, group 81H. This group will be working on the article RNA silencing.

Use the talk page here to collaborate as a group, when learning to use and navigate Wikipedia, assessing articles, or for any other topic.

Use this page (not the talk page) for article assessments; rationale for selecting an article; etc.

Please create a new section here for each of those assignments.