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Wikipedia:USEP/Courses/JHU MolBio Ogg FA13/Group 81H

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Group 81H

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This is a group page for the Johns Hopkins Molecular Biology 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 grabriggs

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Extrachromosomal DNA

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This article is categorized as a stub and has high importance. It lacks references completely and gives only a very general overview of this topic. It would require significant work in expanding on the topic, providing references, inserting pictures, and manipulating the article to a level of higher literary quality. There has been no discussion among editors on the talk page for this topic.

Extrachromosomal DNA [1] [1]

Mitochondrial Genes [2] [2]

Extrachromosomal circular DNAs and genomic sequence plasticity in eukaryotic cells [3] [3]

Extra-chromosomal elements and the evolution of cellular DNA replication machineries [4] [4]

Restriction Site

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The page for restriction site is also a stub class and is classified as high importance. This page does have a decent, but basic description of how a restriction enzyme works. On the talk page there is an open question about whether this page and the "restriction enzyme" page should be combined. There is also a question about how to link the term palindrome. There are four references from two sources. This article could use expansion of how a restriction site works, information on restriction enzymes, and illustrations to help explain the topic.

Restriction Endonucleases [5] [5]

Molecular Biology of the Gene [6] [6]

Molecular Cloning: A Laboratory Manual [7] [7]

Initial article assessments from Seanmcaruthers

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Polysomy

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Polysomy is a stub-class article listed with high importance for WikiProject Molecular and Cellular Biology and mid importance for WikiProject Medicine. It is currently a 3 sentence description of polysomy and contains just one reference. It was began on 11 October 2005 and has only had minor edits since that time. It lacks organization and other than a mention of Down’s syndrome, its relevance is not clear. It will require extensive addition from expert resources to develop this topic. There is no activity on the talk page.

A review of trisomy X (47,XXX)[8]

Chromosomal duplication is a transient evolutionary solution to stress[9]

Neutral mutation

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Neutral mutation is graded as a stub class article in WikiProject Genetics with no importance yet given. It is stub-class with high importance in WikiProject Molecular and Cellular Biology. The article contains no citations. It contains a mutation info box with relatively no information. The body of the article provides a summation in a few sentences, but the usefulness and relevance is vague and needs more development. Due primarily to the brevity, the article is unstructured. The talk page only contains one brief conversation about one edit. Extensive referenced additions will be required to improve this article to our desired grade level.

Weak Selection and Protein Evolution[10]

Population Growth Enhances the Mean Fixation Time of Neutral Mutations and the Persistence of Neutral Variation[11]

Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster[12]

Article selection rationale

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Neutral mutation - The first and foremost justification for our selection is the lack of an informative and referenced article currently on Wikipedia. The current article consists of a simple short summary with absolutely no references. The article is considered High-importance under WikiProject Molecular and Cellular Biology and of unclassified importance for the WikiProject Genetics. This classification along with the importance of understanding and documenting the mechanisms of molecular evolution for both academic and casual researchers make this an article of prime note for upgrading. Through our discussions and preliminary literature searches, we decided this would be an article that we would find both exciting to enhance as well as contribute to the overall information on molecular biology in Wikipedia. Under PubMed as of October 13, 2013, there are 5176 articles that return when “neutral mutation” is queried. As more and more sequence data is generated and as new and unique synthetic biology experiments test and demonstrate the roles of mutations in evolution, the role of neutral mutation will be of great interest to those adding new tenets to evolutionary theory. Neutral mutation is supposed to be separate from natural selection and occur truly randomly since it is not affected by traditional Darwinian selective pressure. The idea of random and neutral mutation being involved in the evolution of a species seems very interesting, particularly since when thinking about evolution selective pressure generally seems to be the key driving force considered. Because of the unique qualities of neutral mutation it is an important topic in the discussion of evolution and could serve as a valuable tool in describing the overall process of genetic change over time. Since our knowledge of this subject is limited it allows us to not only develop a wikipedia page but learn more about this topic in the process.

Unit 10 Progress Update

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  • Added to and improved prose for each section
  • Added picture of Darwin, changed table for codons
  • Split types of neutral mutations into subsections

Grabriggs (talk) 02:36, 12 November 2013 (UTC)[reply]

  • Refined lead per suggestions
  • Added prose to Identification and measurement section, eliminated confusing section
  • Added molecular clocks section

Seanmcaruthers (talk) 04:13, 12 November 2013 (UTC)[reply]

Week 12 Progress Update

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  • Added prose to multiple sections
  • Added additional links
  • Updated references with DOI information

Grabriggs (talk) 02:03, 26 November 2013 (UTC)[reply]

  • Reworked the lead and eliminated citations
  • Added more explanation to equations
  • Expanded molecular clocks section
  • Added external links section

Seanmcaruthers (talk) 07:41, 28 November 2013 (UTC)[reply]

Week 14 Final Progress Update

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  • Updated the codon table again, multiple editors have commented on the couple different images we've added throughout the semester; finally found a simple, clear image to add
  • After comments from Klortho updated the codon chart one more time, Birdy0124 suggested and linked to a good quality chart which I ended up inserting
  • Added minor edits to prose in multiple sections to reflect ideas from commenting editors

Grabriggs (talk) 20:03, 7 December 2013 (UTC) Grabriggs (talk) 05:28, 11 December 2013 (UTC) Grabriggs (talk) 00:38, 13 December 2013 (UTC)[reply]

  • made modifications for clarity and coherence to lead and clocks section based on review comments

Seanmcaruthers (talk) 07:55, 12 December 2013 (UTC)[reply]

Final progress report

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  • Over the course of the project, added the Identification and measurement of neutrality and Molecular clocks section
  • All of the reviewers provided helpful advice and constructive criticism. For the most part I took their advice and changed to reflect what things they felt were confusing/unnecessary/redundant. I am particularly grateful for the reviews by the ambassadors.
  • Took over reworking the lead many times to reflect what we were covering in the article and to address comments.
  • This was a few sentence stub article with no citations when we began. I think we have put together a well written and informative improvement

Seanmcaruthers (talk) 08:05, 12 December 2013 (UTC)[reply]


  • Started working on this page by writing a lead, history, impact on theory, and types of neutral mutations sections. My partner was able to rework the lead after comments from editors and did an outstanding job keeping it updated to reflect our evolving page.
  • Continued to add prose and edit the other sections originated by me while partner focused on the sections he originated
  • Added picture and table which was eventually updated 4 times as editors left comments
  • Added numerous wikilinks
  • Utilized multiple ideas and suggestions from most if not all classmates and ambassadors that left comments. Additionally used comments from an outside editor not associated with our class.
  • As my partner states above, this was a stub of an article with no references when we started and I believe that as a team we have greatly improved it. It will be interesting to see it continue to evolve.

Grabriggs (talk) 00:47, 13 December 2013 (UTC)[reply]

Bibliography

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  1. ^ Donald J. Cummings; et al., eds. (1979). Extrachromosomal DNA. New York: Academic Press. ISBN 9780323145350.
  2. ^ Piotr Slonimski, ed. (1982). Mitochondrial genes. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory. ISBN 087969145X.
  3. ^ Gaubatz, JW (September–November 1990). "Extrachromosomal circular DNAs and genomic sequence plasticity in eukaryotic cells". Mutation Research. 237 (5–6): 271–92. doi:10.1016/0921-8734(90)90009-G. PMID 2079966.
  4. ^ McGeoch, AT; Bell, SD (July 2008). "Extra-chromosomal elements and the evolution of cellular DNA replication machineries". Nature Reviews. Molecular Cell Biology. 9 (7): 569–74. doi:10.1038/nrm2426. PMID 18523437. S2CID 1501317.
  5. ^ Alfred M. Pingoud, ed. (2004). Restriction endonucleases. Berlin [u.a.]: Springer. ISBN 3540205020.
  6. ^ James D. Watson; Tania A. Baker; Stephen P. Bell; Alexander Gann; Michael Levine; Richard Losik; Stephen C. Harrison (2014). Molecular biology of the gene (7th ed.). Boston: Benjamin-Cummings Publishing Company. ISBN 9780321762436.
  7. ^ Sambrook, Michael R. Green, Joseph. Molecular cloning : a laboratory manual (4th ed.). Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press. ISBN 9781936113415.{{cite book}}: CS1 maint: multiple names: authors list (link)
  8. ^ Tartaglia, Nicole R; Howell, Susan; Sutherland, Ashley; Wilson, Rebecca; Wilson, Lennie (1 January 2010). "A review of trisomy X (47,XXX)". Orphanet Journal of Rare Diseases. 5 (1): 8. doi:10.1186/1750-1172-5-8. PMC 2883963. PMID 20459843.
  9. ^ Yona, A. H.; Manor, Y. S.; Herbst, R. H.; Romano, G. H.; Mitchell, A.; Kupiec, M.; Pilpel, Y.; Dahan, O. (29 November 2012). "Chromosomal duplication is a transient evolutionary solution to stress". Proceedings of the National Academy of Sciences. 109 (51): 21010–21015. Bibcode:2012PNAS..10921010Y. doi:10.1073/pnas.1211150109. PMC 3529009. PMID 23197825.
  10. ^ Akashi, H; Osada, N; Ohta, T (September 2012). "Weak selection and protein evolution". Genetics. 192 (1): 15–31. doi:10.1534/genetics.112.140178. PMC 3430532. PMID 22964835.
  11. ^ Waxman, D. (16 March 2012). "Population Growth Enhances the Mean Fixation Time of Neutral Mutations and the Persistence of Neutral Variation". Genetics. 191 (2): 561–577. doi:10.1534/genetics.112.139220. PMC 3374318. PMID 22426878.
  12. ^ Schrider, D. R.; Houle, D.; Lynch, M.; Hahn, M. W. (3 June 2013). "Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster". Genetics. 194 (4): 937–954. doi:10.1534/genetics.113.151670. PMC 3730921. PMID 23733788. Retrieved 7 October 2013.
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