User:Kneal0627/sandbox

The Five Pillars

1. Wikipedia is an online encyclopedia.

Information found on Wikipedia contains various elements of the following:

• general encyclopedias,
• specialized encyclopedias,
• almanacs, and
• gazettes.

It is not intended to serve and should not be interpreted as any of the following:

• a dictionary,
• a book,
• a newspaper, or
• a collection of source documents.

It should NOT be used as a soapbox or advertising platform.

2. Wikipedia has a neutral point of view.

• Articles should aim to document and explain major points of view in an impartial, unbiased manner. One or more points of view may be discussed within the same article; however, each should be represented fairly based on information gathered. The editor should never portray one particular point of view as the "correct" point of view.
• Advocacy should be avoided. Issues should be characterized rather than debated.
• Editors should refrain from inserting personal opinions or personal observations. Contributed edits should be from an objective rather than subjective point of view.
• Editors should use reliable sources to ensure verifiable accuracy. This is critical to any article found on Wikipedia. Articles may be further edited and/or removed if the contributed editions do not exhibit verifiable accuracy.

3. Wikipedia is free content.

• Any person may use, edit, and distribute content found on Wikipedia. As a result, no editor owns a particular article, and any article posted or contributed edits may be continually edited and/or removed.
• Copyright laws should be respected. Plagiarism should also be avoided by citing references.

4. Any editor of Wikipedia, commonly referred to as Wikipedians, should interact with others in a respectful, civil manner.

• Despite disagreements on an article, Wikipedians should be polite and respectful toward one another. Avoid personal attacks and edit wars. In the event of a conflict, use the talk page or follow the dispute resolution process.
• Act in good faith.
• Remember you are not the only editor on Wikipedia. New Wikipedians should be well-received to current editors.

5. Wikipedia does not have firm rules.

• The principles, rather than literal wording, of Wikipedia's rules are most important. The rules are not set in stone, thus exceptions may be made. Rules are also likely to change over time.
• Do not be reckless in making edits; however, do be bold. Prior versions of articles are saved, and mistakes are easily corrected.

Multiple Sclerosis

Multiple Sclerosis (MS) is an autoimmune disease characterized by the deterioration of the myelin sheaths which protect neurons. While several treatment options are available, researchers continue to investigate further treatment options as they search for a cure to MS. Vitamin A has recently been suggested to be added to current treatment options. Vitamin A plays a pivotal role in immunological response as well as brain development. Retinoic acid (RA), the metabolite of Vitamin A, is known to associate with nuclear receptor-mediated signaling pathways in the brain. Due to its metabolite RA, Vitamin A also plays a key role in regeneration, cognition, behavior, and plasticity. Due to its various functions, it is speculated that Vitamin A had dual functions but may also provide brain function. Although magnetic resonance imaging (MRI) provides the optimal way to monitor the progression of MS, new developments in position emission tomography (PET) may offer a way to investigate underlying MS pathophysiology, such as demyelination and remyelination. Vitamin A trials could potentially be monitored using PET as well as MRI.

Preliminary Outline

I. Gene Cluster defined

a. Creation of gene clusters

i. Gene Duplication

ii. Tandem arrays vs. Gene Clusters

b. Examples

II. Bioinformatics

a. Cluster trees

b. Maps

III. Research

References

1. Sherwood EJ, Hesketh AR, Bibb MJ. Cloning and analysis of the planosporicin lantibiotic biosynthetic gene cluster of Planomonospora alba. J Bacteriol. 2013;195(10):2309-21. http://www.ncbi.nlm.nih.gov/pubmed/23475977
2. Higgs DR, Vickers MA, Wilkie AO, Pretorius IM, Jarman AP, Weatherall DJ. A review of the molecular genetics of the human alpha-globin gene cluster. Blood. 1989;73(5):1081-104. http://www.ncbi.nlm.nih.gov/pubmed/2649166
3. Hardison R, Miller W. Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters. Mol Biol Evol. 1993;10(1):73-102. http://www.ncbi.nlm.nih.gov/pubmed/8383794
4. Graham, G. (1995). Tandem genes and clustered genes. Journal of Theoretical Biology, 175(1), 71-87. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/7564393 (This is a great article about the difference between tandem arrays and gene clusters and how they can turn into each.)
5. Caron, H. et al. (2001). The human transcriptome: clustering of highly expressed genes in chromosomal domains. Science, 291, Retrieved from http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.169.4274&rep=rep1&type=pdf (This article contains great figures and elaborates on human gene clusters.)
6. I’m not sure we can actually use this as a reference since it is technically a lecture; however, it does present some great figures and information. Perhaps we can look for something similar. http://www.discoveryandinnovation.com/BIOL202/notes/lecture26.html
7. Garcia-Fernàndez, J. (2005). Genesis and evolution of homeobox gene clusters. Nature Reviews Genetics, 6, 881-892. doi: 10.1038/nrg1723. http://www.nature.com/nrg/journal/v6/n12/box/nrg1723_BX2.html (Excellent specific example)
8. Haselkorn, R. (1998). The use of gene clusters to infer functional coupling. Proceedings of the National Academy of Sciences, 96(6), 2896-2901. doi: 10.1073/pnas.96.6.2896 http://www.pnas.org/content/96/6/2896.short (Research)
9. Blanco, E., Pignatelli, M., Beltran, S., Punset, A., Pérez-Lluch, S., Serras, F., Guigó, R., & Corominas, M. (2008). Conserved chromosomal clustering of genes governed by chromatin regulators in drosophila. Genome Biology, 9(R134), doi: 10.1186/gb-2008-9-9-r134 http://genomebiology.com/2008/9/9/R134 (Research)
10. http://david.abcc.ncifcrf.gov/gene2gene.jsp (Bioinformatics)
11. http://segmine.ijs.si/use_cases/ (Bioinformatics)
12. Yi G, Sze SH, Thon MR. Identifying clusters of functionally related genes in genomes. Bioinformatics. 2007;23(9):1053-60. http://bioinformatics.oxfordjournals.org/content/23/9/1053.long (Bioinformatics, general info) This is a really good article about bioinformatics approaches to finding gene clusters. It also gives a good background on gene clusters in general. It also references to other quality articles related to gene clusters
13. Michalak P. Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics. 2008;91(3):243-8. http://www.ncbi.nlm.nih.gov/pubmed/18082363 This article discusses some of the possible mechanisms for how gene clusters could form

Possible Figures/Images to Use

• Here is one possibility. It shows a olfactory receptor gene clusters: http://www.nature.com/nature/journal/v440/n7083/fig_tab/nature04632_F2.html
• This is a figure displaying the Hox gene clusters among several species. This image is taken from another Wikipedia article about the Hox gene, so it would be suitable to use in this article. It is also a really good example to discuss in the article. https://en.wikipedia.org/wiki/File:Genes_hox.jpg