Wikipedia:USEP/Courses/JHU MolBio Ogg SP14/Group 81E

AP-1 Binding Site Assessment
The AP-1 binding site article is a very small article (2 sentences). There are no inline references and the only external link directs to nowhere. The talk page shows no new work since it was started in 2006. However, the importance scale is ranked low. There is a Wikipedia article for AP-1 transcription factor which is also a stub and ranked as mid-important. We could possibly provide info that would benefit both articles.

Bibliography:
 * 1) Erwin F Wagner, AP-1  Introductory remark, Oncogene,  30 April 2001, Volume 20, Number 19, Pages 2334-2335, http://www.nature.com/onc/journal/v20/n19/pdf/1204416a.pdf
 * 2) Huamin Zhou, Tyler Zarubin, Zhiliang Ji, Zheng Min, Wei Zhu, Jocelyn S. Downey, Shengcai Lin, and Jiahuai Han, Frequency and Distribution of AP-1 Sites in the Human Genome,  DNA Research 12, 139–150, 2005  http://dnaresearch.oxfordjournals.org/content/12/2/139.full.pdf
 * 3) G Risse, K Jooss, M Neuberg, H J Brüller, and R Müller, Asymmetrical recognition of the palindromic AP1 binding site (TRE) by Fos protein complexes, EMBO J. 1989 December 1; 8(12): 3825–3832.
 * 4) Chung KY, Agarwal A, Uitto J, Mauviel A.  An AP-1 binding sequence is essential for regulation of the human alpha2(I) collagen (COL1A2) promoter activity by transforming growth factor-beta. J Biol Chem. 1996 Feb 9;271(6):3272-8.

Nondisjunction Article Assessment
The nondisjunction article is short. It provides a definition of the term and some basic information about it, but it provides no inline citations. There is one reference, a textbook that has no online presence. There is only one figure. It is ranked as high-importance in both the Genetics and Molecular and Cellular Biology WikiProjects. There is another paragraph on the talk page that provides 2 additional references; one is the definition and the other is a classroom laboratory exercise. This article can be expanded to provide more information about this disorder, including a discussion about how it works, why it occurs, when it occurs in mitosis and meiosis (including pictures) and what disorders arise from nondisjunction.

Bibiography:
 * 1) Griffiths AJF, Miller JH, Suzuki DT, et al., An Introduction to Genetic Analysis. 7th edition. New York: W. H. Freeman; 2000. http://www.ncbi.nlm.nih.gov/books/NBK21870/
 * 2) Disorders in Chromosome Number, https://www.boundless.com/biology/modern-understandings-of-inheritance/chromosomal-basis-of-inherited-disorders/disorders-in-chromosome-number/
 * 3) OpenStax College. Chromosomal Basis of Inherited Disorders [Connexions Web site]. June 26, 2013. Available at: http://cnx.org/content/m44483/1.6/.
 * 4) T. Dailey, B. Dale, J. Cohen, and S. Munné, Association between nondisjunction and maternal age in meiosis-II human oocytes. Am J Hum Genet. 1996 July; 59(1): 176–184.
 * 5) A Chakravarti, The probability of detecting the origin of nondisjunction of autosomal trisomies., Am J Hum Genet. 1989 May; 44(5): 639–645.,
 * 6) Kara E. Koehler, R. Scott Hawley, Stephanie Sherman, and Terry Hassold Recombination and nondisjunction in humans and flies Hum. Mol. Genet. 1996 5: 1495-1504.  http://hmg.oxfordjournals.org/content/5/Supplement_1/1495.full.pdf+html

Base Flipping
At the current time, there are no articles or stubs on Wikipedia about base flipping. Because this mechanism is very important for DNA repair, for example, I believe there is a need for this information to be added as a quality article. There are many scholarly articles available on this topic and since there is nothing on Wikipedia about it, makes it a great target to approach with a vast amount of editing possibilities for future improvement. The article will need to contain, the definition of base flipping, the history behind its discovery, what it consists of, what are the mechanisms involved, what studies have been done to this point, just to name a few areas to be targeted.

Bibliography:
 * 1) Huang, Niu, Nilesh K. Banavali, and Alexander D. MacKerell Jr.. "Protein-facilitated Base Flipping in DNA by Cytosin-5-methyltransferase." PNAS 100.1 (2003): 68-73. Web. 29 Jan. 2014. .
 * 2) University, James D. Watson, Cold Spring Harbor Laboratory, Tania A. Baker, Massachusetts Institute of Technology, Alexander Gann, Cold Spring Harbor Laboratory, Michael Levine, University of California, Berkeley, Richard Losik, Harvard (2014). Molecular biology of the gene (Seventh edition ed.). Boston: Pearson/CSH Press., ISBN 978-0-321-76243-6.
 * 3)  B. Bouvier and H. Grubmüller. A Molecular Dynamics Study of Slow Base Flipping in DNA using Conformational Flooding. Biophys. J. 93: 770-786 (2007), ,

Spermatocyte
The Spermatocyte article is very small where there is only one line written that contains the definition. The article does not cite any references, but it contains wikis that directs you to other definitions. Out of the five wikis present, only one contains a great article (between A and FA quality), all others are ranging from a stub to a start article. It contains two images but no major explanations around them. This article also provides a vast amount of editing possibilities and a variety of scholarly journals are also readily available. Finally, the spermatocyte article has been rated as high-importance on the Molecular and Cellular biology Wikiproject.

Bibliography:
 * 1) Raverdeau, Mathilde, Aurore Gely-Pernot, Betty Feret, Christine Dennefeld, Gerard Benoit, Irwin Davidson, Pierre Chambon, Manoel Mark, and Norbert Ghyselinck. "Retinoic Acid Induces Sertoli Cell Paracrine Signals for Spermatogonia Differentiation but Cell Automonously Drives Spermatocyte Meiosis." PNAS 109.41 (2012): 16582-16587. Web. 22 Feb. 2014..
 * 2) Hogarth, Cathryn, and Michael Griswold. "The Key Role of Vitamin A in Spermatogenesis." Journal of Clinical Investigation 120.4 (2010): 956-962. Web. 22 Feb. 2014..
 * 3)  IP, A Rohrwasser, DA Terreros, RF Gesteland, and JF Atkins. "Discovery of Spermatogenesis Stage-specific Ornithine Decarboxylase Antizyme: Antizyme 3." PNAS 97.9 (2000): 4808-4813. Web. 22 Feb. 2014..

Article selection rationale
DNA base flipping is a mechanism in which a single nucleotide base in the DNA structure is rotated out from the DNA backbone by 180 degrees so that an enzyme can perform work on it. Discovered in 1994, it has shown to be used in many biological processes. Studies have shown that DNA methylation, various DNA repair mechanisms, and events required for transcription and DNA replication are initiated by flipping of a DNA base out of the double helix. . As this will be our very first time working on Wikipedia, we are excited to make a substantial contribution on a topic that is non-existent today. Therefore, the fact that there is no information currently available on Wikipedia created a layer of interest and motivation for both of us. We also believe that adding DNA base flipping information on Wikipedia as a quality article would be beneficial to many science students as quick reference guide during their studies. Furthermore, there are many scholarly articles available on base flipping, and it will give us the opportunity to elaborate on many aspects of it. This is a significant topic to develop with a vast amount of editing possibilities as new research unfolds and new discoveries are made in the future.

The following list is a preliminary outline of the article. As we do additional research into this topic, this list may change and expand.
 * 1) Definition
 * 2) History behind its discovery
 * 3) Biochemistry
 * 4) Mechanisms involved
 * 5) Studies done to this point
 * 6) Base flipping mutations
 * 7) Additional topics as needed

Unit 8 progress report

 * Writing contributions
 * Article did not exist
 * Created all new draft article with citations
 * Figures
 * Used Inkscape to create base flipping figure by modifying a free access figure in Wikimedia Commons library
 * Created account and uploaded to Wikimedia Commons
 * Found other figures in Wikimedia Commons to include

Unit 10 progress report

 * Suggested edits from first peer review
 * Updated lead section with wiki-links and additional prose
 * Mechanism section updated for clarity
 * Discovery section updated for clarity
 * Second contribution
 * Updated several section headings for clarity
 * Added new information about restriction endonucleases including appropriate citations and wiki-links

Unit 12 progress report

 * Suggested edits from second peer review
 * Fixed wording in several sections
 * NMR section
 * DNA methylation
 * Restriction endonucleases
 * Added additional wiki-links to all sections
 * Added new material
 * NMR technique expanded to include what has been revealed about base flipping
 * Added "See also" section
 * Added additional citations

Final progress report

 * Suggested edits from final peer review
 * Lead image was move to the top of the article so that the image and text of the lead were side-by-side
 * Re-wording and re-phrasing edits to various sections was done as suggested
 * Citations in the lead paragraph was deleted
 * Added new material
 * New image added to Wikimedia Commons and then added to the mechanism section
 * New image added to hybridization probe section
 * Alternative text to all images for visual impaired