Wikipedia:United States Education Program/Courses/JHU MolBio Ogg 2013/Group 82A
Group 82A
[edit]This is the Wikipedia page for 410.602 Molecular Biology, Spring, 2013, group 82A. This group will be working on the article Genomic library.
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.
Please create a new section here for each of those assignments.
Initial Article Assessments From Aluquette
[edit]This article has some good basic information but is not very well written and it does not have much structure or flow. It also lacks references. All three references listed were only cited once in the same sentence. One of the references was from 2001 and may be outdated for this topic. The picture used to demonstrate an insertion is not very useful or informative. The last activity on the talk page was in 2007 so it does not appear that anyone is currently editing it. [1] [2]
This article also has some good basic information but is very brief and incomplete. It only has one reference and no in-line citations. There has not been any activity on the talk page in the past two years and the most recent edits to the page have been minor (grammar, etc.). There is a chart to show the different capacities for vectors used to make libraries, but there are no other charts, figures, pictures, etc. [3] [4] [5]
Initial Article Assessments From Jmudukes88
[edit]Restriction site
[edit]The restriction site article is kind of scattered in its information. It needs to be better structured, have some images, and it has the same reference listed three times (all separate; disjointed). The article should also link some of its possible unknown terms to their respective Wiki page- for example, stick and blunt ends. Overall, some of the grammar needs editing for better flow. The last edits done to the page were done around January 2013, but the last comment on the talk page dates back to December 2011. One of the comments suggested to merge the Restriction site article with the restriction enzyme article. [6] [7]
Nicks
[edit]The nick article needs some updates and revision. It is entirely way too brief and could specifically mention a class of proteins that cause breaks in the DNA, such as topoisomerases. Better yet, include a specific protein such as DNA gyrase. The article is lacking depth, pictures, any references (it assumes we all know what a nick is), and needs to explain it’s relevancy to biology. [8] [9] [10]
Article Selection Rationale
[edit]We believe the Genomic Library article is a great choice for improvement because genomic libraries are an important and widely used tool in molecular biology research. Since Wikipedia has become a very popular source of information for both students and professionals, we expect that this topic is searched for often, and so we feel that this article should be greatly expanded to fully cover the topic of genomic libraries.
We plan to enhance the “lead” section to provide a better overview and also add/expand sections for traditional uses of genomic libraries, current/modern uses, clinical uses, history/discovery[11], and methods of creating a genomic library. The methods section would expose the audience to the procedure of creating a library while also including links to several other Wiki articles. This is also a great section to include some type of diagram or visual aid (like the image in our text) to help explain how to create genomic libraries. We also plan to improve the “Types of vectors” section. We could add information regarding why a particular vector would be used, what size insert it would hold, and how many clones would be needed to create a full genomic library (mathematically).
We hope that our contributions to this article greatly improve its content. Current average ratings of the Genomic library page (through the feedback tool) are 2.4 out of 5 in 67 ratings in completeness; additionally, the trustworthiness of the article is given a 2.9 out of 5 in 67 ratings. By expanding the content and adding appropriate references we hope that these ratings increase.
Unit 9 Progress Report
[edit]- Almost all of the contributions were prose. The headline was modified and content was added to it. The rest of the writing is ours.
- The vector table was updated and content was added to it.
- The image we found through Wikipedia- a user had uploaded this for use. We are trying to learn Inkscape to create a higher resolution image, but it is taking longer than anticipated.
- The mathematical model was too challenging to format in the same way as some math-related Wiki pages. We may format this later on because it would be an ideal modification.
- We created the example for figuring out how many clones are needed in a library based on insert and genome size.
Final Progress Report
[edit]My partner and I are very proud of our improvements to this article. Our biggest contributions came in the form of plenty of added content. We tried to remain as thorough as possible for those looking for specific details (in the subsections) while also keeping simple in each section for those looking for the basics. We took the time to review and discuss every working point made by each of the reviewers whether it was on the talk pages or over the phone/email for lengthier discussion. We then posted annotated changes and reasons for what we did or did not do to that reviewers comment. Below is a list of our specific features added that also took good amounts of time. We’ve included suggestions from reviewers we found very helpful.
- Every figure on the page was found by us and uploaded to Wikipedia. The figure in “Genomic library construction” was custom-made for that section and highlights features we had found in a previous, low-resolution image.
- Other figures were modified, “cut”, in order to present relevant information such as the figure in the “Bacterial artificial chromosomes” section
- All figures were modified to achieve the best placement and size in the article. We used other Wikipedia articles to find how they specifically size the image
- Our vector section was created to give a brief detail of the significant vectors used as they are important and relevant to our topic
- Our mathematical example took quite a deal of trial-and-error in order to find what we wanted to present as well as getting the content of the section to make sense
- We’d like to thank everyone that helped below:
- Klortho and Dr. Ogg for recommending LaTeX (with examples) via our talk pages and email communications
- Klortho, again, for specific suggestions on clearing up ambiguities in content as well as any grammatical errors
- Jessicalau90 made a great recommendation of where to include an image in our "Application" section
- Jengel11 proposed to include genetic engineering in the article. It guided us towards other additions of content in our “Applications” section
- Mhk5600 made great comments to address quick-fixes as well as calling out a glaring error within our reflist
- Sharkeyr took the time to find a reference to help explain her specific recommendation of using vectors as controls
Potential references
[edit]- ^ Mullaney JM, Mills RE, Pittard WS, Devine SE (October 2010). "Small insertions and deletions (INDELs) in human genomes". Hum. Mol. Genet. 19 (R2): R131–6. doi:10.1093/hmg/ddq400. PMC 2953750. PMID 20858594.
- ^ Doerfler W (February 2012). "Impact of foreign DNA integration on tumor biology and on evolution via epigenetic alterations". Epigenomics. 4 (1): 41–9. doi:10.2217/epi.11.111. PMID 22332657.
- ^ Choi S, Kim UJ (2001). "Construction of a bacterial artificial chromosome library". Methods Mol. Biol. 175: 57–68. doi:10.1385/1-59259-235-X:057. PMID 11462856.
- ^ Coren JS, Sternberg N (February 2001). "Construction of a PAC vector system for the propagation of genomic DNA in bacterial and mammalian cells and subsequent generation of nested deletions in individual library members". Gene. 264 (1): 11–8. PMID 11245973.
- ^ Hartwell, Leland (2008). Genetics: from genes to genomes. Boston: McGraw-Hill Higher Education. ISBN 0-07-284846-4.
- ^ Szczelkun, MD (April 2011). "Translocation, switching and gating: potential roles for ATP in long-range communication on DNA by Type III restriction endonucleases". Biochemical Society transactions. 39 (2): 589–94. doi:10.1042/BST0390589. PMID 21428945.
- ^ Sisáková, E; van Aelst, K; Diffin, FM; Szczelkun, MD (January 2013). "The Type ISP Restriction-Modification enzymes LlaBIII and LlaGI use a translocation-collision mechanism to cleave non-specific DNA distant from their recognition sites". Nucleic Acids Research. 41 (2): 1071–80. doi:10.1093/nar/gks1209. PMID 23222132.
- ^ Heitman, J; Ivanenko, T; Kiss, A (September 1999). "DNA nicks inflicted by restriction endonucleases are repaired by a RecA- and RecB-dependent pathway in Escherichia coli". Molecular microbiology. 33 (6): 1141–51. PMID 10510229.
- ^ Collin, F; Karkare, S; Maxwell, A (November 2011). "Exploiting bacterial DNA gyrase as a drug target: current state and perspectives". Applied microbiology and biotechnology. 92 (3): 479–97. PMID 21904817.
- ^ Reece, RJ; Maxwell, A (1991). "DNA gyrase: structure and function". Critical reviews in biochemistry and molecular biology. 26 (3–4): 335–75. PMID 1657531.
- ^ Sanger, F; Air, GM; Barrell, BG; Brown, NL; Coulson, AR; Fiddes, CA; Hutchison, CA; Slocombe, PM; Smith, M (24 February 1977). "Nucleotide sequence of bacteriophage phi X174 DNA". Nature. 265 (5596): 687–95. PMID 870828.