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

Group 84C

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 hnagy2

Following are my initial assessments for two Wikipedia articles.

Article 1: Homoplasmy

This article, Homoplasmy, is found on the Wikipedia listing for molecular and cellular biology stubs. The article is very sparse, consisting of four sentences. Two of the three references are published scientific articles. The other reference is a tertiary reference, an online slide for a medical course. This reference is cited the most. There is an unsupported closing claim with a "citation needed" tag. There are no accompanying illustrations. No contextual information is provided. Abbreviations are used with no initial clarification. The tone is neutral with general information but much is left unexplained. The talk page is inactive. The review history shows that the article was created in 2008 and edited twice in 2011. The article has remained unchanged since. More background information with proper context could be added. Relevant sub-topics, such as the role of homoplasmy maintainence in cancer and mitochondrial disease, would be appropriate if kept brief though not necessary.

References:

1) Bianchi, NO; Bianchi MS, Richard SM (Mar 2001). "Mitochondrial genome instability in human cancers". Mutation Research 488 (1): 9–23. PMID 11223402.

2) Chatterjee, A; Mambo E, Sidransky D (7). "Mitochondrial DNA mutations in human cancer". Oncogene 25 (34): 4663–74. PMID 16892080.

3) Ling, Feng; Mikawa T, Shibata T (2011). "Enlightenment of Yeast Mitochondrial Homoplasmy: Diversified Roles of Gene Conversion". Genes 2 (1): 169–190. doi:10.3390/genes2010169.

4) Shibata, T; Ling F (Feb-Apr 2007). "DNA recombination protein-dependent mechanism of homoplasmy and its proposed functions". Mitochondrion 7 (1-2): 17–23. PMID 17280877.

Article 2: Kataegis

This article, Kataegis, is found on the Wikipedia listing for molecular and cellular biology stubs.This article describes a term coined in a 2012 published Cell article, which has been gaining modestly in popularity in scientific journals and online in the context of cancer genomics. This stub article is very short with six sentences and two inline references. Both references lead to the correct supporting articles. The review history shows that this article was modified several times in 2012 and once in August of 2013. The article is relatively stable but little information has been added over time. There is no activity on the talk page and it is ranked as a low-importance stub article. Given its brevity, the article is broad but gives only the most cursory explanation of the term and little contextual information. The addition of more contextual information with appropriate categorization would be beneficial, as well as its relationship to the linked terms.

References:

1) Alexandrov, LB; Nik-Zainel S, et al. (22). "Nature | Article Print Email Share/bookmark Signatures of mutational processes in human cancer". Nature 500 (7463): 415–421. PMID 23945592.

2) Donley, N; Thayer MJ (Apr 2013). "DNA replication timing, genome stability and cancer: late and/or delayed DNA replication timing is associated with increased genomic instability". Seminars in Cancer Biology 23 (2): 80–89. PMID 23327985.

3) Setlur, SR; Lee C (25). "Tumor archaeology reveals that mutations love company". Cell 149 (5): 959–961. PMID 22632962.

4) Taylor, BJ; Nik-Zainal S, Wu YL, Stebbings LA, Raine K, Campbell PJ, Rada C, Stratton MR, Neuberger MS (16). "DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer". Elife 2 (e00534). PMID 23599896.

Initial Article Assessment from Juanquina Thomas

Article 1 Lipotropin

Lipotropin was selected from the stub list on the Molecular and Cellular Biology page. This article is a stub article for several reasons. It does not have a clear and concise point. There is a single sentence used to define the topic-at-hand, and then the subject automatically switches to another topic. The verifiability is lacking as well. One of the sources is not a secondary source. It is an allegation report of players said to have used enhancement drugs while playing for the AFL. It is not broad in its coverage, as it does not address the main topic, nor does it stay focused on the topic. The report of players using drugs in the AFL makes this article biased. There are also no images related to this article. There has been discussion on the talk page amongst authors. It seems that there has been a lot of redundancy removed from the article. Maybe this contributes to its skeleton structure.

References:

1. beta-Lipotropin. (2013). The Harvard Clinical and Translational Science Center .

2. Matsuoka, Hiroaki; Mulrow, Patrick J.; Franco-Saenz, Roberto; Li, Choh Hao (NaN undefined NaN). "Effects of β-Lipotropin and β-Lipotropin-derived Peptides on Aldosterone Production in the Rat Adrenal Gland". Journal of Clinical Investigation 68 (3): 752–759. doi:10.1172/JCI110311.

Article 2 Zoo Blot

The Zoo Blot article was also found on the Molecular Biology page stub list. This article is not well written as it does not have a clear and concise point. In the introduction sentence, zoo blot is referred to as the same thing as a garden blot, and then they are later defined as two different blots. No verifiability exists as there is no citations or references listed on the page. It is lacking in its coverage because of the change of topic in the beginning statement. By the looks of the talk page, there has been discussions involving a few grammatical and spelling changes. There are no images related to this article either.

References:

1. Redei, G. P. (2013). Zoo Blot. Springer Reference .

2. Watch Zoo Blot Video. (2013). Retrieved Oct 8, 2013, from VGuide: http://www.ovguide.com/zoo-blot-9202a8c04000641f80000000047d979f#

3. What-when-how In Depth Tutorials and Information. (2013). Retrieved October 8, 2013, from Zoo Blot (Molecular Biology): http://what-when-how.com/molecular-biology/zoo-blot-molecular-biology/

Article Selection Rationale

We chose the article Isomerase for review. This article is a stub-class article, and requires a lot of work to be considered a good article. There is little to no content concerning the topic-at-hand. Isomerase is defined by an equation that is not written very well. This article lists one function of isomerase stating that "converts sugar syrup into fructose syrup." That statement does very little to add to what an isomerase is and how it acts.

This article is a great candidate for review due to it being poorly written, stating very few facts. It also contains very few resources, which is probably why there is very little information. The article can not really be judged on its coverage, neutrality, or stability seeing as there is not much content to assess. The view history page indicates that there has not been many efforts in editing or reviewing the article. The first edit took place in 2007, and the last edit took place in 2008. This indicates that there has been no current research and edits to this topic.

My partner and I will be able to add to the substance of this article by discussing isomerase more in depth. We will be able to specify different isomerases and their functions, where isomerase can be found, and the major classes of isomerases.

Unit 8 update

All of our contributions were prose and references. Updates included:

• sub-categories of isomerases
• a general explanation of the sub-classes
• specific cases and mechanisms found in some of those sub-classes
• implications for human disorders

Unit 10 update

We implemented all of the suggestions we received on both small edits and overall reorganization. Much of the specific information from the article lead was moved into the body text so that the lead has only cursory information. More references were added as appropriate and wikilinks were added for specialized terminology. Spelling errors were corrected and the article title was bolded in the lead. Category links in the body text and headings were removed as suggested for a more streamlined look, with category links at the end of the article. Suggestions on how to make the body text flow better were taken by rearranging paragraphs containing background information and reshuffling into appropriate subsections. The text is more understandable and has a more intuitive flow. Information of isomerase subcategories were added, i.e. what makes each category unique and what these classes of reactions encompass. Schematics of reaction mechanisms were added as well.Hnagy2 (talk) 01:28, 11 November 2013 (UTC)

In addition to edits hnagy2 mentioned, we also expanded content in the human disease section of the paper. More wikilinks were added throughout the page's content. Awkward sentences and wording were rearranged to produce a better flow of jargon. With the new edits, the article is now expanded, more organized, and reads more easily. Juanquina Thomas (talk) 04:49, 16 November 2013 (UTC)

Unit 12 update

The suggestions we received really helped to give us direction. The biggest contributions for me this time around were images and their formatting. Images were added for the introduction, along with images of isomers and of isomerase reactions by category. Useful tips were given for how to productively search the Wikipedia Commons and I appreciated that. The article is easier to follow now with visual aids, especially for those potential readers who are not familiar with the concept of isomers in general. More wikilinks were added for scientific terminology for ease of look-up as well. Another big change implemented was adding concrete, wikilinked examples of isomerases for each category and sub-category. That section was very brief and vague before but the examples give more context. For the two categories without sub-categories (and few examples overall) I listed every enzyme presently in that category. It is a much more thorough background now. I also added another example of an isomerase mechanism that is a little unusual. Some of my parts may still be choppy but the basic content is there.Hnagy2 (talk) 03:29, 27 November 2013 (UTC)

Edits have been made for the section, "the role of isomerases in human disease". More content has been added, as well as a few more reliable sources as our peers have suggested. There was a suggestion to include more citations in the TPI section. I have included a few more, however, the source that is cited several times is the most reliable one and I have yet to find another that can provide as much pertinent information. I will be continuing my research efforts in hopes of expanded this sections even more. I found a few pictures related to each deficiency. No one suggested it, but I'm wondering if I should add photos in that section? I don't want to crowd the page, seeing as if we have taken suggestions and added images in the intro, and isomerase category section. I am continuing to progress this section and add relevance to the article. Juanquina Thomas (talk) 04:50, 27 November 2013 (UTC)

Final progress report

I took the helpful suggestions from the last review into account. I formatted the individual sub-classes and examples into tables so that the categorization section looks much cleaner. I was uncertain about adding new content to the article so late but the suggestions were for topics I had considered before and regretted not doing, so I added to the article. Under the isomerization section I added some information about isomerase kinetics and how experimentally determining that information for isomerases differs from other enzyme classes. I also added a small section at the very bottom on industrial applications to dovetail my partner's section on medical implications. Aside from those additions I proofread and added clarifications where it seemed necessary to my sections.Hnagy2 (talk) 22:41, 14 December 2013 (UTC)

In the last contributions to the article, I took some of the advice of classmates in making improvements. I added some information and few more citations to the new section (industrial applications) that was added by my partner. Also, in the deficiency sections of the article, I re-worded a few things and found a few more sources to cite. I did that because a few of our peer reviews mentioned repetition of the same sources. There were a total of 3 new sources added to this section. A few of our peer reviews also suggested new topics to add, however, I did not feel entirely comfortable adding such large sections of information upon the last peer review and contributions. I also read through the article and made a few grammatical corrections. I felt like I could keep going on and forever with contributions, but I feel I made the necessary contributions/edits needed. Juanquina Thomas (talk) 02:48, 15 December 2013 (UTC)