Wikipedia:USEP/Courses/JHU MolBio Ogg FA13/Group 84F

Group 84F
This is a group page for the 410.602 Johns Hopkins Molecular Biology, section 84 course. This group will be working on the article TBD.

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 (as specified in the milestone summary chart.

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

Initial article assessments from Agulati4
The following are initial assessments of the Gene Silencing and Leucine Zipper articles.

Assessment of Gene Silencing Article
I will assess the article using the following categories listed under Wikipedia’s good article criteria:

1. Well-written:
 * The article is not very well-written. There are some minor grammar errors that need to be fixed. The article also does not flow well. The information is not presented in an organized manner, but rather jumps from one topic in gene silencing to another.

2. Verifiable:
 * The article does contain a section for external links, but does not have a list of references nor any in-line citations that can be used to validate the information presented.

3. Broad coverage:
 * The article does not explain all aspects of gene silencing. Although it does provide some information on gene silencing at the transcriptional and post-transcriptional level, it merely provides links to other Wiki pages (if available) for the other types of gene silencing.

4. Neutral:
 * The article is neutral. The editors have not added any of their personal opinions to the information presented.

5. Stable:
 * The article seems stable and does not seem to have changed many times.

6. Illustrated:
 * There are no images to illustrate how gene silencing works or the mechanism behind it.

Wikipedia Editors Discussion on Improvement: On the Talk page for the article, there has been talk of how transposons are related to gene silencing and the hyperlink for post-transcriptional processes taking you to translation instead. However, there has been no talk of how to improve the article, beyond providing the correct links and explaining how what you write is associated with gene silencing.

My Thoughts on Improvement: The article needs more references and the information in the article needs to be properly cited. Furthermore, the article should further discuss topics involved in gene silencing in addition to providing a definition. Other than a brief sentence regarding the gene silencing mechanisms used in experimental studies, the article does not elaborate on the how gene silencing is used in research. The article could also delve deeper in how gene silencing occurs in different organisms.

References:
 * 1) Wilson, RC and Doudna, JA. Molecular mechanisms of RNA interference. Annual review of biophysics. 2013. 42: 217-39. PMID 23654304
 * 2) Fukushige, S. and Horii, A. DNA methylation in cancer: a gene silencing mechanism and the clinical potential of its biomarkers. The Tohoku journal of experimental medicine. 2013. 229(3): 173-85. PMID 23419314
 * 3) Lee, HJ. Exceptional stories of microRNAs. Experimental biology and medicine (Maywood, N.J.). 2013 Apr. 238(4): 339-43. PMID 23759998

Assessment of Leucine Zipper Article
I will assess the article using the following categories listed under Wikipedia’s good article criteria:

1. Well-written:
 * The article is well-written with no apparent spelling or grammar errors.

2. Verifiable:
 * The article contains a reference list of only two references and only two inline citations. The rest of the information cannot be verified.

3. Broad coverage:
 * The article explains the structure of the leucine zipper well, but does not provide any in-line citations. In addition, though it mentions that they are involved in regulation gene expression, it does not elaborate on the topic.

4. Neutral:
 * The article is neutral. The editors have not added any of their personal opinions to the information presented.

5. Stable:
 * The article seems stable and does not seem to have changed many times.

6. Illustrated:
 * There are only two images: one illustrating the leucine zipper and the other showing how the leucine zipper interacts with DNA.

Wikipedia Editors Discussion on Improvement: On the Talk page for the article, there has only been discussion on why the image depicting the leucine zipper binding to DNA was chosen for the article.

My Thoughts on Improvement: The article explains the structure of the leucine zipper well, but it does not adequately explain how and why the leucine zipper is utilized inside the cell and how it can be used in research studies.

References:
 * 1) Ryadnov, MG, Papapostolou, D., Woolfson, DN. The leucine zipper as a building block for self-assembled protein fibers. Methods in molecular biology (Clifton, N.J.). 2008. 474: 35-51. PMID 19031059
 * 2) Miller, M. The importance of being flexible: the case of basic region leucine zipper transcriptional regulators. Current protein & peptide science. 2009 Jun. 10(3): 244-69. PMID 19519454
 * 3) Elhiti, M. and Stasolla, C. Structure and function of homodomain-leucine zipper (HD-Zip) proteins. Plant Signaling & Behavior. 2009 Feb. 4(2): 86-8. PMID 19649178
 * 4) Zhou, GP. The structural determinations of the leucine zipper coiled-coil domains of the cGMP-dependent protein kinase Iα and its interaction with the myosin binding subunit of the myosin light chains phosphase. Protein and peptide letters. 2011 Oct. 18(10): 966-78. PMID 21592084

Initial Article Assessments from Opalite3579
The following article assessments will pertain to Exoenzyme and Ubiquitin-conjugating enzyme articles. I will be basing my assessments on Wikipedia's Good Article criteria.

Assessment of Exoenzyme article

 * 1) Well-written The article has great sentence structure. It is clear and concise, albeit very basic in the information that is presented.
 * 2) Verifiable This article does not have in-line citations and does not include a list of references.
 * 3) Broad in its coverage This article defines what an exoenzyme is, but does not elaborate into any of the listed examples of extracellular enzymes.
 * 4) Neutral This article does not have a bias.
 * 5) Stable This article has been very quiet, and is in a good condition to be worked upon as there are no content disputes.
 * 6) Illustrated This article does not contain any illustrations, diagrams, or visual depictions of what an exoenzyme is.

References
 * 1) Vogelsgesang, M, Pautsch A, Aktories, K. "C3 exoenzymes, novel insights into structure and action of Rho-ADP-ribosylating toxins." Neunyn-Schmiedeberg's Archives of Pharmacology. 2007. 374(5-6): 347-60. PMID 17146673
 * 2) Just, I, Rohrbeck, A, Huelsenbeck, SC, and Hoeltje, M. "Therapeutic effects of Clostridium botulinum C3 exoenzyme." Neunyn-Schmiedeberg's Archives of Pharmacology. 2011. 383(3): 247-52. PMID 21193903
 * 3) Braun, PG. "Microbial exoenzyme production in food." Advances in Applied Microbiology. 2007. 61:59-87. PMID 17448788

Assessment of Ubiquitin-conjugating enzyme article

 * 1) Well-written The article has great sentence structure. It is clear, concise, and has a good flow.
 * 2) Verifiable This article has few in-line citations and includes a very short list of references.
 * 3) Broad in its coverage This article presents very basic knowledge of E2 enzymes, but is lacking detailed descriptions of the biochemistry behind ubiquitination.
 * 4) Neutral This article does not have a bias.
 * 5) Stable This article has been calm and there is no evidence of content disputes.
 * 6) Illustrated This article contains only 1 illustration, and would benefit from the inclusion of more.

References
 * 1) Neutzner, M, and Neutzner A. "Enzymes of ubiquitination and deubiquitination." Essays in Biochemistry. 2012. 52:37-50. PMID 22708562
 * Liu, J, and Nussinov, R. "The role of allostery in the ubiquitin-proteasome system." Critical Reviews in Biochemistry and Molecular Biology. 2013. 48(2):89-97. PMID 23234564

Article selection rationale
We chose gene silencing as our article for the Wikipedia project since we believe we can greatly improve and enhance the current article. There are a lot of topics that we can expand upon under gene silencing. First, we can further discuss the background and discovery of gene silencing, why it is vital for the function of the cell, and the regulatory mechanisms used to silence genes. There are several mechanisms used to silence genes in the cell. These mechanisms generally involve the use of siRNA, antisense oligonucleotides, and ribozymes. We can expand upon each of these mechanisms by describing the important cellular machinery that comes into play and by discussing how these mechanisms occur in eukaryotes and prokaryotes. We can also add to the topics listed in the original article, such as transcriptional gene silencing, post-transcriptional gene silencing, and meiotic gene silencing. In addition, we can explore how and why gene silencing is utilized in research experiments and discuss its potential in gene therapy. Currently, the article only contains a brief sentence regarding the use of gene silencing mechanisms in experimental studies, but it does not elaborate on its usage in research.

Other than detailed information, there are also other things lacking in the current article. In-line citations and references need to be added to provide proper validation for the information presented. In addition, illustrations and drawings should be added to depict the core concepts of gene silencing. We also need to implement a flow to the article so that these different topics make sense together and don't come across as disjointed. It will make a difference to the reader. We really look forward to working on the gene silencing article!

Unit 8 progress report

 * Added prose to the article
 * Created image using Inkscape to depict the general mechanism utilized by ribozymes and uploaded it to the article page

Unit 10 progress report

 * Added prose to the article
 * Edited and made changes to prose written in Unit 8 based upon comments from reviewers

Unit 12 progress report

 * Added prose to sections in the article
 * Added image from Wikipedia Commons
 * Edited and made changes to prose based upon suggestions from reviewers

Final progress report

 * Added prose to new sections in the article
 * Added images from Wikipedia commons
 * Added and edited wikilinks
 * Edited and made changes to prose according to suggestions from reviewers