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

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Group 84G[edit]

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 Madscientist2007[edit]

Capping enzyme[edit]

Article Assessment[edit]

The article is undoubtedly still a Stub-Class article as it is not much more than a definition. This status is also verified on the article’s talk page. While it is straight and to the point, as it is, the “article” is more suited for an entry in a dictionary or in a one volume science related encyclopedia. For what it is worth, the author(s) obviously put thought into what they wrote, even though it is presented in a bare bones or “just the facts, ma’am” manner. There are also quite a few links to other Wikipedia pages for key terms and related topics or explanations. In addition, it would be helpful to have at least one illustration depicting the activity of the enzyme.

While there is a section for references, there are no inline citations. As such, it is hard to say as to where each piece of information comes from unless one takes the time to backtrack it themselves. Furthermore, there are only two sources list in the reference section. On the other hand, the information does come from a textbook and an established scientific journal.

As of yet, there is no discussion on the article’s talk page. In some respects, this is surprising, as the article clearly needs additional work to improve it even to Start-Class.

Suggested Bibliography of Relevant Research[edit]

1) Schoenberg, D. R., & Maquat, L. E. (2009 September 9). Re-capping The Message. Trends in Biochemical Sciences, 34(9), 435-442. PMID 19729311

2) Shuman, S. (1997 November 25). Origins of mRNA identity: Capping enzymes bind to the phosphorylated C-terminal domain of RNA polymerase II. PNAS, 94(24), 12758–12760. PMC 34174

3) Shuman, S., & Schwer, B. (1995). Molecular Microbiology (1995) 17(3), 40 RNA capping enzyme and DNA ligase: a superfamily of covalent nucleotidyl transferases . Molecular Microbiology, 17(3), 405-410. doi:10.1111/j.1365-2958.1995.mmi_17030405.x

4) Our textbook: Watson, J. D., Baker, T. A., Bell, S. P., Gann, A., Levine, M., Losick, R., et al. (2013). Mechanisms of Transcription. Molecular biology of the gene (Seventh ed., pp. 458-459). Cold Spring Harbor: Cold Spring Harbor Laboratory Press.

Isomerases[edit]

Article Assessment[edit]

The article is undoubtedly still a Stub-Class piece, as is verified on the article’s talk page. There are no diagrams or pictures to illustrate the topic. Also, unlike some of the other articles, this topic has been broken down into several sections, albeit short ones. For example, the introductory or opening section is in essence is a definition.

The section on nomenclature is to the point and in all honesty, may not be able to be expanded much more. However, a final decision on this would have to be reached only after more extensive research is done. For instance, there may be some history behind this naming scheme, or there may be exceptions to the rule. In terms of the former, the scope of the history, if available, may even be such that it warrants a separate section.

The section on classification is essentially a list of the classes of isomerases. While there are several links to other Wikipedia pages on each line of the list, the class designations (i.e. EC 5.1) serve only as links to other links with no cohesiveness to the bigger picture. Only the key terms lead to other articles, all of which are either Stub-Class or Start-Class. However, this list is not a horrendous start, especially since the list lends itself well to subheadings and subsections under the main heading “Classification.”

While there is a section for references, there are no inline citations. As such, it is hard to say as to where each piece of information comes from unless one takes the time to backtrack it themselves. Furthermore, two of the three sources listed are dictionaries. The third source provides more information, especially when you navigate through the links embedded within the text.

As of yet, there is no discussion on the article’s talk page.

Suggested Bibliography of Relevant Research[edit]

1) Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (2010 September). The Enzyme List:: Class 5 - Isomerases. Retrieved from ExplorEnz - The Enzyme Database. http://www.enzyme-database.org/downloads/ec5.pdf

2) Bugg, T. (2004). Isomerases. Introduction to enzyme and coenzyme chemistry (2nd ed., pp. 227-238). Oxford, UK: Blackwell Pub.

Initial article assessments from Pozmi[edit]

Article Assessment of Exogenous DNA[edit]

The article on exogenous DNA is currently considered a stub. In terms of a GA, it is completely lacking illustrations, and references of any kind (not to mention inline citations). The article coverage is not sufficiently broad or detailed, but it does link to a number of biological concepts that can be built upon, such as transfection and transformation. However, the material of this article requires formatting into different sections, such as the role of exogenous DNA in different organisms and exogenous DNA versus endogenous DNA. In short, there are many areas to improve, although the article has provided guidelines in terms of material.

Discussion on the talk page covers sentence phrasing, and the inclusion of plasmids in the article. Indeed, plasmids are a relevant concept that should be covered in an article on exogenous DNA.

Possible Bibliography[edit]

1. [1] 2. [2] 3. [3] 4. [4] 5. [5]

  1. ^ Friedberg, EC; McDaniel, LD; Schultz, RA (February 2004). "The role of endogenous and exogenous DNA damage and mutagenesis". Current opinion in genetics & development. 14 (1): 5–10. PMID 15108798.
  2. ^ Anzar, M; Buhr, MM (1 March 2006). "Spontaneous uptake of exogenous DNA by bull spermatozoa". Theriogenology. 65 (4): 683–90. PMID 16054207.
  3. ^ Magaña-Schwencke, N; Averbeck, D (November 1991). "Repair of exogenous (plasmid) DNA damaged by photoaddition of 8-methoxypsoralen in the yeast Saccharomyces cerevisiae". Mutation research. 251 (1): 123–31. PMID 1944369.
  4. ^ Igoucheva, O; Alexeev, V; Yoon, K (February 2006). "Differential cellular responses to exogenous DNA in mammalian cells and its effect on oligonucleotide-directed gene modification". Gene Therapy. 13 (3): 266–75. PMID 16177821.
  5. ^ Alberts, Bruce (2008). Molecular biology of the cell (5th ed.). New York: Garland Science. p. 556. ISBN 9780815341062.

Article Assessment of Inverted Repeats[edit]

The article on inverted repeats currently has a single reference and inline citation. The source is a textbook and it is likely that more information can be cited from it in the body of the article. It will, of course, require many more references to bring this stub closer to a GA. This article also lacks images, which can be used to clarify points. The scope of the article does mention varied relevant topics under "see also" but there is a general lack of detail and explanations. As well, it would be more apt to link to DNA palindromes rather than the current palindrome link. As more information is added to the article, it can be further formatted into sections. As well, the current section for "examples" can be revised for clarity and expanded upon. All in all, the article provides a base from which images, references, and depth can be added. Most importantly, points of the current article should be reviewed for accuracy.

Discussion of the talk page contains a dispute about one of the lines currently in the article, claiming it to be false. Although first posted two years ago, this issue remains unresolved and the sentence is unchanged in the article.

Possible Bibliography[edit]

1. [1] 2. [2] 3. [3] 4. [4] 5. [5]

  1. ^ Watson, James D. (2014). Molecular biology of the gene (7th ed.). Boston: Benjamin-Cummings Publishing Company. pp. 379, 395–396. ISBN 978-0-321-76243-6.
  2. ^ Fattash, Isam; Rooke, Rebecca; Wong, Amy; Hui, Caleb; Luu, Tina; Bhardwaj, Priyanka; Yang, Guojun; Bainard, Jillian (8 March 2013). "Miniature inverted-repeat transposable elements: discovery, distribution, and activity". Genome: 1–12. doi:10.1139/gen-2012-0174. Retrieved 8 October 2013.
  3. ^ Pray, Leslie A. (2008). "Transposons: The jumping genes". Nature Education. 1 (1). Retrieved 8 October 2013.
  4. ^ Pistón, F; Gil-Humanes, J; Barro, F (17 September 2013). "Integration of promoters, inverted repeat sequences and proteomic data into a model for high silencing efficiency of coeliac disease related gliadins in bread wheat". BMC plant biology. 13 (1): 136. PMID 24044767.
  5. ^ Hu, L; Kim, TM; Son, MY; Kim, SA; Holland, CL; Tateishi, S; Kim, DH; Yew, PR; Montagna, C; Dumitrache, LC; Hasty, P (26 September 2013). "Two replication fork maintenance pathways fuse inverted repeats to rearrange chromosomes". Nature. 501 (7468): 569–72. PMID 24013173.

Article selection rationale[edit]

For our Wikipedia project, our group decided to work on the molecular-weight size marker article. This article is still at Stub-Class, as is verified by the corresponding talk page. However, it is not without redeeming points, which provide a good foundation to build on.

The article currently provides basic information in the form of an introduction, a DNA markers section, and a protein markers section. From here, there is great potential to expand sections and include sub-sections using ideas we have already discussed. These include history, invention, development, how they work, what they are used for, what they are composed of, types/variants on the market, improvements, problems, and alternatives.

Molecular-weight size markers provide a visual standard against which experimental DNA and protein samples can be compared. With that said, this topic lends itself well to the use of pictures as complements to the text. Additional pictures can be used to illustrate the history and evolution of these markers, the different types in terms of composition, uses, etc., and potential problems and alternatives.

Along with expanding upon these areas, it is clear that the article requires thorough referencing. In considering all the factors in favor of this article, we have not forgotten Wikipedia's guidelines, notably that of neutrality. As these markers are commonly sold by scientific companies, there are many advertisements for different brands. Thus, we will make sure to present the information impartially and use verified resources like textbooks and PubMed.

Overall, one of the biggest draws to this article for our group is the practicality of the topic. Like many others involved in science, each of us in the group has had some experience with DNA and/or protein markers in school and/or work. This is a topic that we believe has a large appeal for those involved in the scientific community. As scientists, we have a responsibility to properly inform our audience on this topic by creating a comprehensive synthesis of the available information.

Unit 8 Progress Report[edit]

  • Added prose contributions.
  • Added references.
  • Included distinguish template.

Madscientist2007 (talk) 00:09, 30 October 2013 (UTC) --Pozmi (talk) 02:19, 30 October 2013 (UTC)[reply]

Unit 10 Progress Report[edit]

  • Added prose contributions.
  • Added a table of some of the proteins commonly used for marker construction.
  • Changed the format of the "Effects of Gel Conditions" section.
  • Added references and corrected problems with inline citations.
  • Added links to other Wikipedia pages.
  • Added image from Wikipedia Commons.

Madscientist2007 (talk) 15:43, 15 November 2013 (UTC) --Pozmi (talk) 01:30, 16 November 2013 (UTC) --Madscientist2007 (talk) 01:47, 16 November 2013 (UTC)[reply]

Unit 12 Progress Report[edit]

  • Changed image sizes to improve visibility.
  • Put references into columns.
  • Added additional wikilinks.
  • Changed paragraph order in the "DNA markers" section.
  • Changed format of article by splitting body into two sections: DNA Markers and Protein Markers.
  • Began changing the terms "ladder" and "standard" to "marker" as appropriate.
  • Added prose contributions
  • Used Upload Wizard to upload nonfree image under Fair Use and added image to article.

--Pozmi (talk) 04:25, 23 November 2013 (UTC)--Madscientist2007 (talk) 15:58, 23 November 2013 (UTC)--Madscientist2007 (talk) 01:37, 26 November 2013 (UTC)--Madscientist2007 (talk) 03:56, 26 November 2013 (UTC)--Pozmi (talk) 06:15, 28 November 2013 (UTC)[reply]

Final progress report[edit]

  • Changed format of several sections (i.e. "Different Uses of Molecular-Weight Size Markers" section, both "Effects of Gel Conditions" sections, and "Choosing the correct protein marker") using description lists.
  • Added prose contributions.
  • Removed prose that was present before this semester.
  • Added Wikilinks.
  • Added images from Wikipedia Commons.
  • Alternated images across left and right side of page.

Jirwin1097 (talk) 02:33, 10 December 2013 (UTC)--Madscientist2007 (talk) 19:38, 14 December 2013 (UTC)--Madscientist2007 (talk) 20:24, 14 December 2013 (UTC)--Madscientist2007 (talk) 22:08, 14 December 2013 (UTC) --Pozmi (talk) 23:50, 14 December 2013 (UTC) --Pozmi (talk) 01:15, 15 December 2013 (UTC)[reply]

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