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

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Group 84D[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.



NOTE: Please see the bottom of this page for: Unit 14 Final Progress Report



Initial article assessments from Jim Perry and Godwin Ifere[edit]

Article 1: Isomerase[edit]

Here is Jim Perry's assessment of the article using the 6 criteria in Wikipedia:Good_article_criteria.

Well-written Verifiable Broad Neutral Stable Illustrated
No. Almost nothing there. Limited references. No. Ok for what is there. No. Not at all.

This article has only 2 sentences so it is a very "stubby" stub. It has no references for any statements in the text sections. EC classifications are listed, so that provides something to be expanded upon. There is nothing in the talk page. "Isomerase" is a very broad topic so I would envision several sub-sections for this article. Here are possible future references. [1] [2] [3] [4]

Possible Future References:

  1. ^ Rivière, Andrzej Galat, Sylvie (1998). Peptidyl-prolyl cis/trans isomerases. Oxford: Oxford University Press. ISBN 9780198502883.{{cite book}}: CS1 maint: multiple names: authors list (link)
  2. ^ Andreu, CI; Woehlbier, U; Torres, M; Hetz, C (31 August 2012). "Protein disulfide isomerases in neurodegeneration: from disease mechanisms to biomedical applications". FEBS Letters. 586 (18): 2826–34. PMID 22828277.
  3. ^ Ferreira, PA; Orry, A (June 2012). "From Drosophila to humans: reflections on the roles of the prolyl isomerases and chaperones, cyclophilins, in cell function and disease". Journal of neurogenetics. 26 (2): 132–43. PMID 22332926.
  4. ^ Dilworth, D; Gudavicius, G; Leung, A; Nelson, CJ (February 2012). "The roles of peptidyl-proline isomerases in gene regulation". Biochemistry and cell biology = Biochimie et biologie cellulaire. 90 (1): 55–69. PMID 21999350.

 --------End of first article assessment from Jim Perry -----------------------------------------------------------------------------------------------------------------


Godwin Ifere
First article: Isomerase
The following is a summary of assessment of this article in accordance with “Wikipedia: Good_article_criteria”
Good Article Criteria Comments

1. Well written: Does not comply with style of Wikipedia; article to concise. 2. Verifiable: List of references not in accordance with style. Original research, no in-line citation from reliable sources. 3. Broad in its coverage: Not broad in coverage. 4. Neutral: Neutral, but no due weight to each item. 5. Stable: Not stable as it is subject to edit war. 6. Illustrated if possible: No illustrations whatsoever.

Summary: This article is thought by other editors in the “Talk” page to be within the scope of WikiProject Molecular and Cellular Biology group. It has however been rated as a stub-Class on the projects quality page and is also believed to be on its mid importance rating. Isomerases are a broad category of enzymes and within these various classes I would use the following reference sources to describe the activities of some members of these subclasses.[1] [2] [3] [4] [5]

Relevant References

  1. ^ Aguirre, Y; Cabrera, N; Aguirre, B; Pérez-Montfort, R; Hernandez-Santoyo, A; Reyes-Vivas, H; Enríquez-Flores, S; de Gómez-Puyou, MT; Gómez-Puyou, A; Sanchez-Ruiz, JM; Costas, M (22 August 2013). "Different contribution of conserved amino acids to the global properties of Triosephosphate isomerases". Proteins. PMID 23966267.
  2. ^ Luo, X; Zhang, L; Li, H; Zhang, S; Jiao, Y; Wang, S; Xue, C; Fan, R (24 September 2013). "Comparison of enzymatic activity of two linoleic acid isomerases expressed in E. coli". Molecular biology reports. PMID 24062071.
  3. ^ Abdel-Mawgoud, AM; Lépine, F; Déziel, E (6 September 2013). "A chiral high-performance liquid chromatography-tandem mass spectrometry method for the stereospecific analysis of enoyl-coenzyme A hydratases/isomerases". Journal of Chromatography A. 1306: 37–43. PMID 23906801.
  4. ^ Reinstein, J (30 July 2013). "Proximity Effects on the Protein Domain Level: Engineering Prolyl Isomerases through Combinatorial Biochemistry". Journal of Molecular Biology. PMID 23911550.
  5. ^ Lara-González, S; Estrella-Hernández, P; Ochoa-Leyva, A; Del Carmen Portillo-Téllez, M; Caro-Gómez, LA; Figueroa-Angulo, EE; Salgado-Lugo, H; Miranda Ozuna, JF; Ortega-López, J; Arroyo, R; Brieba, LG; Benítez-Cardoza, CG (4 June 2013). "Structural and thermodynamic folding characterization of triosephosphate isomerases from Trichomonas vaginalis reveals the role of destabilizing mutations following gene duplication". Proteins. PMID 23733417.

Article 2: Inverted Repeat[edit]

Here is Jim Perry's assessment of the article using the 6 criteria in Wikipedia:Good_article_criteria.

Well-written Verifiable Broad Neutral Stable Illustrated
No. Yes, but only 1 reference. No. Ok for what is there. No. No illustrations.

This stub has only a few sentences and a grand total of one reference. Examples are limited but external links may help give some insights for future work on this article. The talk page has only one comment from a writer (that did not sign their post) claiming that information in the text is incorrect. Bottom line is that this article needs major work. "Inverted repeat" is a very broad topic. MeSH uses "Inverted Repeat Sequence" as preferred term for a major heading, so it might make sense to modify the page to that term. Here are possible future references. [1] [2] [3] [4]

Possible Future References:

  1. ^ Richter, C; Chang, JT; Fineran, PC (19 October 2012). "Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR associated (Cas) systems". Viruses. 4 (10): 2291–311. PMID 23202464.
  2. ^ Kato, T; Kurahashi, H; Emanuel, BS (June 2012). "Chromosomal translocations and palindromic AT-rich repeats". Current opinion in genetics & development. 22 (3): 221–8. PMID 22402448.
  3. ^ Tanaka, H; Yao, MC (March 2009). "Palindromic gene amplification--an evolutionarily conserved role for DNA inverted repeats in the genome". Nature Reviews. Cancer. 9 (3): 216–24. PMID 19212324.
  4. ^ Bikard, D; Loot, C; Baharoglu, Z; Mazel, D (December 2010). "Folded DNA in action: hairpin formation and biological functions in prokaryotes". Microbiology and molecular biology reviews : MMBR. 74 (4): 570–88. PMID 21119018.

 ----------------------------- End second assessment from Jim Perry --------------------------------


Godwin Ifere
Second Article: Inverted Repeats
The following is a summary of assessment of this article in accordance with “Wikipedia: Good_article_criteria”

Good Article Criteria Comments 1. Well written: Does not comply with style of Wikipedia; article to concise. 2. Verifiable: List of references not in accordance with style. Original research, only one in-line citation from a reliable sources. 3. Broad in its coverage: Not broad in coverage. 4. Neutral: Neutral, but no due weight to each item. 5. Stable: Not stable as it is subject to edit war. 6. Illustrated if possible: No illustrations whatsoever.

Summary: This article is similar in content and style to the first article and is again thought by other editors in the “Talk” page to be within the scope of WikiProject Molecular and Cellular Biology group. It has however been rated as a stub-Class on the projects quality page and is also believed to be on its mid importance rating. References are provided for additional inverted repeats to illustrate the different examples and their effects.[1][2] [3] [4] [5]

Possible Future References

  1. ^ Hallast, P; Balaresque, P; Bowden, GR; Ballereau, S; Jobling, MA (July 2013). "Recombination Dynamics of a Human Y-Chromosomal Palindrome: Rapid GC-Biased Gene Conversion, Multi-kilobase Conversion Tracts, and Rare Inversions". PLOS Genetics. 9 (7): e1003666. PMID 23935520.
  2. ^ Chen, X; Xiao, F; Guo, J (May 2013). "[The mechanisms of palindrome-stimulated mutation and related human diseases]". Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji. 35 (5): 571–7. PMID 23732662.
  3. ^ Inagaki, H; Ohye, T; Kogo, H; Tsutsumi, M; Kato, T; Tong, M; Emanuel, BS; Kurahashi, H (2013). "Two sequential cleavage reactions on cruciform DNA structures cause palindrome-mediated chromosomal translocations". Nature Communications. 4: 1592. PMID 23481400.
  4. ^ Zhao, Q; Hu, X (September 2013). "Postoperative pulmonary hypertensive crisis caused by inverted left atrial appendage after cardiopulmonary bypass surgery for congenital heart disease in a neonate". Heart, lung & circulation. 22 (9): 781–3. PMID 24054493.
  5. ^ Västermark, A; Saier MH Jr (28 August 2013). "Evolutionary relationship between 5+5 and 7+7 inverted repeat folds within the amino acid-polyamine-organocation superfamily". Proteins. PMID 24038584.

Article selection rationale[edit]

Our group decided to select the “Inverted repeat” article. The basic rationale for this choice is that the article is desperately in need of help! The article is currently a stub with only a few sentences and one reference. There is also an issue on the article’s talk page concerning inverted repeats and palindromes that definitely needs to be resolved.

A good connection with personal interests is another reason for this choice. Both members of this group (Jim Perry and Godwin Ifere) are studying bioinformatics and “sequences” are a topic of personal interest to them. Additionally, this article provides the opportunity to use lots of illustrations because inverted repeats explanations benefit from "visual aids". We believe that the gathering of illustrations will be enjoyable and plan to have a very “colorful” article when we are complete.

Another reason for this choice is that the topic is quite broad and we can focus on a number of areas. Inverted repeats play a significant role in determining specific traits in humans, including its heavy presence in the Y chromosomes, within genes important for male fertility. Above all, terminal inverted repeats flank the ends of many transposable elements, signifying their importance in various mutations. Because inverted repeats play a role in both DNA and RNA, we will discuss the effects under two major divisions for the article. We anticipate very rich information sources to populate our references. Our hardest task may be determining how best to organize all that is available. There are existing database of Inverted Repeats and some are listed in the current article as external links. We will likely investigate these and document there general areas of coverage in the article. They may also provide other paths for us to follow as we investigate what should be included in the final article.

One additional item is “terminology”. MeSH indicates that “Inverted Repeat Sequence” is the preferred term for a major heading, so we may consider changing the article title to match up with this preferred term.

Godwin Ifere 22:49, 15 October 2013 (UTC) and Jim Perry (Jim892) 23:08, 15 October 2013 (UTC)[reply]


Unit 8 Progress Report[edit]

Our "Unit 8" group contributions to the inverted repeat article are as follows:

  • The outline structure developed in Unit 7 has been implemented on the main article page.
  • Contributions in the form of "prose" were developed, checked with "www.turnitin.com" and the posted in the introduction, examples, and biological features/functions sections.
  • Illustrations of inverted repeats were made with a graphics software program, uploaded to Wikipedia (with the appropriate "wide open" license for graphics that we create ourselves) and posted in the article.

Unit 10 Progress Report[edit]

  • Additional contributions in the form of prose have been added and several references have been added or updated.
  • A section on programs and databases has been enhanced with new items, detailed descriptions and links.
  • There has been extensive discussion between group members and with the reviewers (reviews from Unit 9).
  • Based on reviewer's comments and on Unit 8 feedback, we added a healthy quantity of Wiki-links.
  • New section on mutations and disease was added with illustration from Wikimedia Commons.
  • Illustration developed in Unit 8 was moved to Wikimedia Commons. Contacted administrator to remove old image from English Wikipedia.

Unit 12 Progress Report[edit]

  • Prose updates were made to the introduction per suggestions from reviewers, along with references and wiki-links.
  • Sub-sections under Inverted Repeats, Mutations and Disease were developed and added.
  • Illustrations for the two sub-sections were created with Excel and a graphics package. These are adaptations of figures from the original reference (original figures appear to have been done on a manual typewriter!) Contacted the publisher and received permission to use the figures from the original article and loaded the illustrations and documentation into Wikimedia Commons for use on this article. Whew! This turned out to be very time consuming!
  • There has been good discussion between group members and with the reviewers (reviews from Unit 11).
  • Consulted with Online Adviser regarding an issue in the introduction (see talk page).
  • Discussed the use of Citation-Bot with a Wikipedia volunteer who found our page and made suggestions.

Unit 14 Final Progress Report[edit]

  • Upgraded subsection on direct repeat versus inverted repeat
  • Used illustrations in color to emphasize the different types of repeat
  • Added new section on Inverted Repeats in Riboswitches. Illustration was done manually after we received a rejection of a request to use a figure from Proceedings of the National Academy of Sciences. They would not agree to Wikipedia's terms that require the material be available for "all purposes" including commercial use.
  • Added new section on Inverted Repeats in Pseudoknots. Adapted an illustration already in Wikimedia commons to identify the inverted repeat sections.
  • Added material to subtitle sections on Biological features and functionality
  • Removed some subheadings that seem redundant
  • Expanded prose in section on inverted repeat, mutations and disease.
  • Added figures on the preceding section for illustrative purposes
  • Adjusted capitalization and length of headings to meet Wikipedia conventions based on reviewer's comment.
  • Added a "sidebar" with related links per suggestion from one of our reviewers.
  • Added "categories" at the bottom of the page per suggestion from a reviewer.
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