User:Hnagy2/sandbox

Here is my sandbox for testing and previewing article content. Fortune favors the bold, after all. Italics aren't so lucky. As an exercise, I will summarize the guidelines of Wikipedia.

Introduction
Wikipedia is open to the public for editing but there are guidelines that must be followed to ensure order and acceptable content. There are five overarching guidelines for the editing process on Wikipedia:


 * 1) Wikipedia is an online encyclopedia
 * 2) Wikipedia has a neutral point of view
 * 3) Wikipedia is free content
 * 4) Editors should interact with each other in a respectful and civil manner
 * 5) Wikipedia does not have firm rules

Wikipedia is an online encyclopedia
Wikipedia follows the format of an encyclopedia or almanac. It should not be treated as a dictionary or repository of linked sources.

Wikipedia has a neutral point of view
Articles should be neutral in tone. Personal views and advocacy are not appropriate. Objective reporting is key. Information should be backed by outside sources.

Wikipedia is free content
Articles on Wikipedia are not copyrighted and any user can edit them. Copyright law must be respected. While short quotes from copyrighted material may be appropriate, free sources are preferable. Plagiarism is not tolerated. Quotes and summarizations must be cited.

Editors should interact with each other in a respectful and civil manner
Respect should be shown to fellow Wikipedia users. Conflict over editing is to be avoided. Feedback should be taken constructively.

Wikipedia does not have firm rules
The spirit of the law is of the most importance. Wikipedia is a fluid community with shifting ideas. Honest mistakes are surmountable.

Verifiability
Using verified sources of information is of the utmost importance as this community is open.

Notability
Only notable topics should be covered. Some criteria to decide if a topic is notable include:


 * significant coverage: the topic in question must be referred to directly and not in a trivial manner.
 * reliable sources: at least two secondary sources from different authors or publishers.
 * independent of the topic: advertising and self-published material does not count for these purposes.

No original research
Wikipedia is a source of tertiary information. Original research is not appropriate. Wikipedia deals with summaries of secondary sources of information.

Copyright and plagiarism
Only short, cited quotations are allowed. Large blocks of text from another source will be removed.

Characteristics of quality articles
Following are some concrete tips for writing high-quality articles on Wikipedia.


 * Quality articles should be well-written. Proper spelling, punctuation and grammar are important. It should stylistically match the community guidelines for formatting and organization.
 * The article should be appropriately broad in scope. In-depth, advanced coverage should be avoided. In-line citations for statistics, direct quotes and controversial statements are expected.
 * A good article is neutral in viewpoint. This is not the place for a soapbox.
 * The article should contain no original research. It must be supported by outside material with listed references.
 * Images, if relevant to the topic, are encouraged.
 * It is expected that the article will remain relatively stable. Daily edits are discouraged.

Unit 5: Article summaries
Carcinogenesis is generally seen as a longterm process involving the accumulation of many somatic mutations over a lifetime. Yet there are patterns of cancer development that are marked by one or a few major mutation events. In contrast to genomic signatures over a large scale, genomic analysis of cancer patients has revealed a pattern of localized clusters of point mutations. This pattern has been termed kataegis, for thunderstorm. This pattern involves the clustering of substitutions at C:G base pairs on the same DNA strand over approximately a kilobase. It has been shown that AID/APOBEC-catalyzed cytidine deamination near DNA breaks contributes to this pattern. These substitution hotspots are often sites of rearrangment as well.

Originally found in a study on breast cancer, this mutation pattern has been found across 30 human cancer types. The introduction of a double-stranded DNA break in yeast increases the likelihood of developing this mutational pattern but a double-stranded break is not sufficient for kataegis development.

Unit 7: Isomerases
Some suitable references:

Adams E. Catalytic aspects of enzymatic racemization. Adv Enzymol. 1976. 44, 69-138.
 * describes racemization at various carbons (methyls, nitrogen-bonded carbons, hydroxyl carbons)

Albery WJ. Evolution of enzyme function and the development of catalytic efficiency. Biochemistry. 1976 Dec 14;15(25):5631-40. .
 * talks about the evolution of some particular isomerases, such as triose phosphate isomerase

Binukumar BK, et al. Topographic regulation of neuronal intermediate filaments by phosphorylation, role of peptidyl-prolyl isomerase 1: significance in neurodegeneration. Histochem Cell Biol. 2013 Jul; 140(1):23-32.

Bugg TDH. "Chapter 10: Isomerases." Introduction to Enzyme and Coenzyme Chemistry, 3rd edition. 2012. Wiley. ISBN 9781118348963
 * A very useful review with mechanisms and categorization

Cho J. Protein disulfide isomerase in thrombosis and vascular inflammation. J Thromb Haemost. 2013 Sep 30.

Enzymes: Types of Enzyme. (2013). Retrieved from Fastbleep: http://www.fastbleep.com/biology-notes/40/116/1159
 * This gives very foundational information on isomerases. It also gives a wonderful schematic on the types of isomerases.

Schomburg D, ed. "Class 3.4–6 Hydrolases, Lyases, Isomerases, Ligases : EC 3.4–6." Springer Handbook of Enzymes, second edition. 2013. Springer: Berlin, Heidelberg. ISBN 9783642362606. doi: 10.1007/978-3-642-36260-6
 * lists particular isomerases

Tajes M. The pathophysiology of triose phosphate isomerase dysfunction in Alzheimer's disease. Histol Histopathol. 2013 Jan;28(1):43-51.
 * human disease etiology

Tanner ME. Understanding nature's strategies for enzyme-catalyzed racemization and epimerization. Acc Chem Res. 2002 Apr;35(4):237-46.
 * goes into isomerases that invert stereochemistry

Triose Phosphate Isomerase. (2013, August 11). Retrieved from Proteopedia: http://www.proteopedia.org/wiki/index.php/Triose_Phosphate_Isomerase
 * This talks about a more specific isomerase, glucose isomerase, yet it gives great detail of the structure.

Walsh C. Enzymatic Reaction Mechanisms. 1979. WH Freeman & Co, Oxford.
 * excerpts show various mechanisms, referenced very often throughout literature

Wilkinson B, et al. Protein disulfide isomerase. Biochim Biophys Acta. 2004 Jun 1;1699(1-2):35-44. .
 * an enzyme that catalyzes disulfide formation, isomerization

Preliminary Outline
A preliminary outline:

I. Overview A. define B. Provide overall use/function C. Note where isomerases can be found

II. Subcategories A. Epimerases B. Racemases C. Allylic isomerases

III. Mechanisms of isomerases A. paraffins to isoparaffins B. ring openings C. transalkylation D. hydrogenation E. hydrocarbon cracking F. cis-trans isomerism G. roles of keto-enol tautomers

IV. Roles in human disease