Wikipedia:United States Education Program/Courses/JHU MolBio Ogg 2012/Section 83/Group 83D

Group 83D
This is the Wikipedia page for 410.602 Molecular Biology, 2012, group 83D. This group will be working on the Trans-acting siRNA article.

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 (optional, see Unit 5); rationale for selecting an article (Unit 6); progress reports (Units 9 and 12); and the final report (Unit 14). Please create a new section here for each of those assignments.

Unit 6 - Article Selection Rationale
Trans-acting siRNA

One of the main criteria for our group when it came to choosing an article was finding one with little information and much room for improvement. After reviewing a few of the possible choices, we decided to focus our attention on stub articles because they were the least developed and needed the most amount of work. Another important factor for our group in choosing an article was trying to find something that was relevant to a group member's work. One of our group members has experience with siRNA but never encountered the term trans-acting siRNA. Since a group member has some experience related to this topic, the rest of the group decided it would be a good choice for our article.

The article is designated as a stub and has no associated talk page. It was last modified in December of 2011 and has had a handful of editors. It is only three sentences long and provides minimal information, leaving much room for improvement. The article briefly states that trans-acting siRNA is a type of siRNA and tells how it differs from typical siRNAs. There is no in-depth content or explanation about its mechanism. The article would definitely benefit from the addition of some relevant, appropriately-tagged images to better elucidate how its mechanism differs from that of typical siRNAs. We also thought it would benefit from a paragraph on its discovery, some information about what types of land plants it is found in, and some expansion on its biosynthesis. When the additional information is added, the article can be formatted according to the style guide for protein and gene articles. The article can be broken into appropriate sections, and info boxes can be added. We liked the potential of this article. It is very incomplete and needs a good bit of work, but we were also able to easily find information on it when briefly browsing the internet, and we felt we can learn a lot by researching this topic.

Unit 9 - Progress Report
Following the selection of our article, a to-do list was compiled consisting of items we would like to research and attempt to incorporate into the article. The things we wanted to try to address were providing a mechanism of action, adding images which supplement the content, researching the discovery of trans-acting siRNAs, expanding and elucidating the biosynthesis, and providing examples of plants in which ta-siRNAs were found. We also plan to reformat the article so that it conforms to the styling guide for gene and protein articles. The topics were distributed to group members so that each member could gather data and compile information using their sandbox. These sections will be updated in each sandbox as more information is collected. Instead of making many potentially conflicting edits with each person adding their topics to the article, we decided that it would be best to assess all the accumulated information and then proceed with a large cohesive edit.

To date, research on all topics from our to-do list has begun; these sections are being drafted in each user's sandbox and will be finalized before going live on the article page. So far, several references have been collected and added to each initial draft by utilizing the Wikipedia template filling tool with the Pubmed IDs. Images from the references have been identified as potential updates to the article, but learning how to add images still needs to be researched and practiced. The biggest obstacle with the uploading of images will be ensuring that they have the appropriate copyright status. In order to not have our images removed, they must be our own, freely licensed, public domain, or fair use. Images for ta-siRNAs tend to not fall into these categories, as they are primarily copyrighted images from journals. This issue will be investigated more as our article improvements continue.

As specific areas of improvement, we have found information on the discovery and mechanism of ta-siRNAs. Since much more polished articles exist for siRNAs and miRNAs, one of the things we want to make sure we emphasize in this article is how ta-siRNAs differ from their better known counterparts. The discovery and mechanism both provide unique ways to incorporate this aspect, as they were discovered because of their differences from siRNAs and miRNAs, and their mechanism has been further studied as a result to better understand these differences. We are still compiling more papers and looking for further ways to improve upon the article. A recent paper states that there are currently four known ta-siRNA gene families, TAS1, TAS2, TAS3 and TAS4, and further research on these families might lead to more areas of improvement for this article.

Unit 12 - Progress Report
To date, our group has further expanded on our initial drafts of the sections we identified as improvements to our article. One of the largest expansions is the inclusion of information on the four TAS families in the biosynthesis section. We have uploaded the biosynthesis, mechanism, discovery, and land plants sections to the article and are currently making final edits and adjustments directly on the article page. We are also now using the article talk page to discuss additional improvements so other editors can provide input.

In our peer review of DNA polymerase, Kate suggested that the article include more information on the active site of the polymerase. Potential information to be added would be the interactions, residues, and metal ions that are important for the reaction to proceed. Additionally, we noted that the article would benefit from more sources and citations as there were whole sections which did not have any form of citation for the information. Lauren also pointed out that one of their linked pages did not exist and suggested that they discuss more about how polymerase is used in molecular biology experiments, including which polymerase is used for which type.

Our group also received input from Group 83E. Some of the main suggestions voiced by group members were the inclusion of an image showing the biosynthesis or mechanism of action for ta-siRNA and the present day importance of ta-siRNA. Over the last few weeks, we plan to address the the suggestions attempting to find a suitable image to include in the article. Lauren has uploaded an image for the biosynthesis section, but it needs an expanded copyright rationale before it can be added to the article without being deleted. We are also currently deciding whether or not there is enough information on the TAS families to include subsections on each. Other work will include making sure citations and links to other articles are appropriately incorporated and doing a final edit of the sections.

Final Progress Report
Over the course of the semester, our group made several improvements to our chosen article. Our article was originally designated a stub with little information, and we added sections on the discovery, biosynthesis (including a picture), mechanism, and examples of where ta-siRNAs are found in plants.

We received helpful feedback from our OA Chris and from our peer review posted by Sahar. That feedback encouraged us to expand our article and make it more accessible to a general audience. The Discovery section was reworked to focus more on the initial discovery of ta-siRNA and highlight the differences which set it apart from the previously discovered siRNA and miRNA. Additionally, the section was reworked with the target audience in mind thanks to feedback advising against being to technical and introducing scientific terms under the assumption they are common knowledge. The biosynthesis section was expanded and broken down by TAS families as suggested by John. We also added the ta-siRNA that regulates Auxins as an example of ta-siRNAs found in plants. We replaced our biosynthesis image with one more suitable as suggested by Chris.

The group worked together to make sure the article was formatted well and that the information flowed. We also worked to strengthen the introduction paragraph.