Wikipedia:United States Education Program/Courses/JHU MolBio Ogg 2012/Section 81/Group 81C
Group 81C
[edit]This is the Wikipedia page for 410.602 Molecular Biology, 2012, group 81C. This group will be editing the Reverse transcription polymerase chain reaction 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
[edit]Reverse transcription polymerase chain reaction
[edit]Group 81C elected to enhance the reverse transcription polymerase chain reaction (RT-PCR) article out of Wikipedia: WikiProject Molecular and Cellular Biology (MCB). The selection was based primarily on three factors: 1) importance of RT-PCR, 2) opportunity for significant improvement on the existing article, and 3) availability of sufficient resources for article enhancement.
Since its introduction in 1977, Northern blot had been used extensively for RNA quantification despite several shortcomings.[1][2] However, the discovery of reverse transcriptase during the study of viral replication of genetic material led to the development of RT-PCR which has since displaced Northern blot as the method of choice for RNA detection and quantification.[3] Due to its simplicity, specificity and sensitivity, RT-PCR is used in a wide range of applications from experiments as simple as quantification of yeast cells in wine to more complex uses as diagnostic tools for detecting infectious agents such as the avian flu virus.[4][5] With such widespread use leading to high awareness and likelihood of internet queries, it is not surprising that RT-PCR article garnered a “High” rating on WikiProject MCB article importance scale.
Despite the major importance of RT-PCR to science, industries, and the wiki communities alike, the article is lacking and mildly educational at best. The system used to designate the quality of WikiProject MCB articles is consistent with the generally accepted guideline developed by Wikipedia: Version 1.0 Editorial Team. This particular article with a “Start” rating is significantly under-developed. It is our goal to expand on the history, protocol, mechanism, and the application of RT-PCR. As well, we wish to greatly expand the article on the uses of RT-PCR in the diagnosis of genetic diseases. An example would be the diagnosis of genetic diseases such as Lesch–Nyhan syndrome that causes the malfunction in the HPRT1 gene, which clinically leads to the fatal uric acid urinary stone and symptoms similar to gout.[6]
With our contribution to the article, one major issue that we will address is the confusion in the nomenclature we face when describing the various branches of PCR. Although the abbreviation RT-PCR should be used to refer to reverse transcription PCR, not all authors adhere to the convention and use the acronym to denote real-time PCR (qPCR).[7] To further add to the confusion, qRT-PCR and RT-qPCR are both used to describe quantitative real-time RT-PCR depending on the author.[8][9] We hope to prevent future inconsistencies by outlining the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines for the standardization of PCR-related nomenclature.[7] Furthermore, the article currently has no listed resources. We aim to add reliable references to the article. This not only will give the article more credibility, but will provide links to additional resources in case readers want to further expand their knowledge. A number of potential resources were identified in our preliminary screening. With insights from these additional sources, we look forward to significantly enhancing this under-developed, important article.
References:
- ^ Alwine JC, Kemp DJ, Stark GR (December 1977). "Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes". Proc. Natl. Acad. Sci. U.S.A. 74 (12): 5350–4. PMC 431715. PMID 414220.
- ^ Streit S, Michalski CW, Erkan M, Kleeff J, Friess H (2009). "Northern blot analysis for detection and quantification of RNA in pancreatic cancer cells and tissues". Nat Protoc. 4 (1): 37–43. doi:10.1038/nprot.2008.216. PMID 19131955.
- ^ Bustin SA (October 2000). "Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays". J. Mol. Endocrinol. 25 (2): 169–93. PMID 11013345.
- ^ Hierro N, Esteve-Zarzoso B, González A, Mas A, Guillamón JM (November 2006). "Real-time quantitative PCR (QPCR) and reverse transcription-QPCR for detection and enumeration of total yeasts in wine". Appl. Environ. Microbiol. 72 (11): 7148–55. doi:10.1128/AEM.00388-06. PMC 1636171. PMID 17088381.
- ^ Slomka MJ, Pavlidis T, Coward VJ, et al. (July 2009). "Validated RealTime reverse transcriptase PCR methods for the diagnosis and pathotyping of Eurasian H7 avian influenza viruses". Influenza Other Respi Viruses. 3 (4): 151–64. doi:10.1111/j.1750-2659.2009.00083.x. PMID 19627372.
- ^ Urbach A, Schuldiner M, Benvenisty N (2004). "Modeling for Lesch-Nyhan disease by gene targeting in human embryonic stem cells". Stem Cells. 22 (4): 635–41. doi:10.1634/stemcells.22-4-635. PMID 15277709.
- ^ a b Bustin SA, Benes V, Garson JA, et al. (April 2009). "The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments". Clin. Chem. 55 (4): 611–22. doi:10.1373/clinchem.2008.112797. PMID 19246619.
- ^ Ståhlberg A, Rusnakova V, Forootan A, Anderova M, Kubista M (September 2012). "RT-qPCR work-flow for single-cell data analysis". Methods. doi:10.1016/j.ymeth.2012.09.007. PMID 23021995.
- ^ "Real-Time Quantitative Reverse Transcription PCR".
Unit 9: Progress Report
[edit]This report outlines progress made by Group 81C as of November 6, 2012. Efforts were focused in three main areas: 1) team collaboration framework, 2) overall project planning, and 3) article improvement.
Effective team collaboration framework has been established:
Through the first several weeks of interactions, our group had an opportunity to uncover distinct capabilities of its members to leverage on the project. Jea displayed resourcefulness in information research, as well as expertise in logical organization of contents. Meredith showed keen ability to augment the subject with unique and essential concepts. Kes demonstrated capacity to translate contents into articulate written language that resonates with readers. Upon recognition of these complementary skill sets, the group developed the following framework to collaborate on the project moving forward:
- Jea to take a lead in information research and initial draft of contents
- Meredith to conduct first review and supplement the contents
- Kes to edit contents into a cohesive and fluid document for publication
Project has been planned through completion with target milestones:
Upon selecting the article, the team undertook an assessment of overall improvement needs on the article. The first phase of this evaluation involved exploratory research on the subject to develop a vision for the end product. This was followed by analysis of the current article. Other scientific articles were also reviewed to provide reference points. Based on substantial gap between the desired and current state of the article, the team made the decision to completely reorganize the content into seven (7) relevant sections. Reference materials discovered during evaluation have been categorized under corresponding sections. A target timeline for completion has also been mapped to each section. Team’s plan is summarized below:
| Section | Target Timeline |
|---|---|
| Introduction | Draft during Unit 9, publish by Unit 10 |
| History | Draft and publish by end of Unit 10 |
| Principles | Draft and publish by end of Unit 11 |
| Application | Draft and publish by end of Unit 12 |
| Challenges | Draft and publish by end of Unit 13 |
| Protocol | Draft and publish by end of Unit 14 |
| Publication Guidelines | Draft and publish by end of Unit 14 |
Significant progress has been made on the Introduction and History sections:
An initial draft of the Introduction section has been composed. It is currently undergoing review and edits by group members. By the end of Unit 10, the team plans to complete the final edit and publish the section. Additional revisions will be undertaken through collaborations and interactions with other editors as appropriate. A draft for the History section has also been started ahead of schedule. Search for suitable and appropriate images for the article is also underway. Team will continue to assess one remaining issue of whether qRT-PCR should be included as part of the article.
Based on effective team deployment, comprehensive planning, and progress made on the early sections of the article, the team remains confident that substantial improvement on the article will be delivered by the end of this course.
Unit 12: Progress Report
[edit]This report outlines progress made by Group 81C as of November 30, 2012 in three key areas: 1) article enhancement, 2) peer/external interaction, and 3) project management.
Significant amount of contents have been added to the article:
At this point, the Introduction, History, Principles, and Application sections have all been drafted and published on the article page. Confusing nomenclature surrounding PCR has been effectively clarified in the new introduction. Sufficient history has been added to provide proper context for RT-PCR. Substantial overview of principles covering multiple branches of RT-PCR has also been provided. In total, more than 2,000 words have been added to the article in these new sections. A comprehensive list of references consisting of 46 new sources has also been compiled to support the article. Together, these contents represent substantial enhancements to the article that are in line with the team’s goals.
Peers and other editors have been engaged to leverage the Wikipedia environment:
In order to start engaging other Wikipedia editors, the team’s plan for article improvement was made transparent on the talk page of the article. While the article does not appear to have active editors, the team intends to connect and collaborate with any interested editors to further refine the contents.
The group also received peer-review from members of Group 81E. The first set of suggestions were 1) placement of introduction contents, 2) integration of old material with new contents, and 3) minor formatting. Edits made to address the first point was reverted by another editor primarily due to adherence to Wikipedia guidelines. Upon assessing the overall impact, the group decided to keep the introduction section unchanged. Other items were evaluated and addressed. Additional comments received toward the end of Unit 12 will also be assessed moving forward.
In addition to these interactions for the team’s own article, our members have undertaken the following peer-review activities for the stable nucleic acid lipid particle article being edited by Group 81F:
- Jea provided suggestion on the introduction and background content on the article talk page (11/12)
- Kes provided suggestions on project planning and team collaboration framework on the group talk page (11/14)
- Meredith provided suggestions on additional applications to explore on the article talk page (11/29)
Project is being effectively managed against planned milestones:
The team continues to measure and manage its progress against the aggressive milestones. Content development is advancing nicely according to plan as outlined below:
| Section | Target Timeline | Status |
|---|---|---|
| Introduction | Draft during Unit 9, publish by Unit 10 | Published |
| History | Draft and publish by end of Unit 10 | Published |
| Principles | Draft and publish by end of Unit 11 | Published |
| Application | Draft and publish by end of Unit 12 | Published |
| Challenges | Draft and publish by end of Unit 13 | In process |
| Protocol | Draft and publish by end of Unit 14 | In process |
| Publication Guidelines | Draft and publish by end of Unit 14 | In process |
The remaining open items to be addressed are 1) development of last three sections, and 2) identification of suitable image to augment the article, if appropriate. As the semester nears its end, the team looks forward to a strong finish with delivery of the final article.
Unit 14: Final Progress Report
[edit]This final report summarizes the collective contributions made by Group 81C throughout this semester to develop and enhance the reverse transcription polymerase chain reaction article in Wikipedia.
New contents have been fully developed according to project plan:
The article was essentially overhauled from end-to-end. In the process, seven new sections outlined below were added with entirely new contents under each.
| Section | Target Timeline | Status |
|---|---|---|
| Introduction | Draft during Unit 9, publish by Unit 10 | Published |
| History | Draft and publish by end of Unit 10 | Published |
| Principles | Draft and publish by end of Unit 11 | Published |
| Application | Draft and publish by end of Unit 12 | Published |
| Challenges | Draft and publish by end of Unit 13 | Published |
| Protocol | Draft and publish by end of Unit 14 | Published |
| Publication Guidelines | Draft and publish by end of Unit 14 | Published |
More than 3,000 words were added to the article in total. Three images were developed to augment the written contents. Additionally, a comprehensive list of references consisting of 50 new sources was compiled to support the new contents.
Wikipedia environment was successfully utilized to refine the article along the way:
Number of suggestions and comments were received from peers throughout the semester. These feedbacks ranged from grammar corrections to reorganization of contents for better impact. Each input was evaluated fully and addressed appropriately. In addition, interactions with some external Wikipedia editors allowed our team to stay within publication guidelines for Wikipedia.
Overall, our team’s primary objective of significantly enhancing this important yet under-developed article has been successfully met.