User:Jfitz1974/sandbox

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Page Description[edit]

This is my edited sandbox page describing the 5 pillars of Wikipedia as part of the assignment for Dr. Ogg's Molecular Biology course for the Fall 2013 semester.[edit]

The 5 Pillars of Wikipedia[edit]

Wikipedia is an online encyclopedia.[edit]

Wikipedia is a source for verifiable information on variety of topics from a wide range of sources.

Wikipedia has a neutral point of view.[edit]

The information contained withing Wikipedia pages should be unbiased and neutral. If the information pertains to a topic that has multiple viewpoints associated with, all viewpoints should be acknowledged in the page. An editor should refrain from including his or her bias or preference for or opinion about one side or another.

Wikipedia is free content that anyone can access, edit and use.[edit]

The information contained within Wikipedia pages should not be plagiarized or violate copyright laws. The content should come from free sources, but if non-free content must be used, then the use must adhere to fair use policies. The content included in the article is not the property of any editor and is subject to any and all edits deemed necessary by another editor to improve the Wikipedia article.

Editors should interact with each other in a respectful and civil manner.[edit]

When interacting with other editors of Wikipedia pages, one should be polite, cordial and behave in a professional, adult manner. Do not make multiple edits simply because another person edits a page to which you were contributing. Should a conflict, disagreement or dispute arise between you and another contributor, try to resolve the situation via the talk pages or the dispute resolution process.

Wikipedia does not have firm rules.[edit]

When adding content to Wikipedia pages, adhere to the current rules for contributing but understand that those rules may change over time. Also note that in the interest in making a page that best that it can be, exceptions to the rules may be made on occasion. Be diligent in making edits and do so without the fear of making mistakes since previous versions of the page are saved and can be retrieved.


Summary of Characteristics of Target Article.[edit]

  • B Quality Article
    • Much work has been done on the article and the article is mostly complete.
    • The article contains a lot of information, graphics and many referenced sources.
    • The article still needs some work to be considered a good article.
  • GA (Good Article) Quality Article
    • The article is of near-professional quality.
    • There are no obvious problems detected within the article.
    • The article contains an abundance of information with several graphics and many sources cited.
    • The article is appropriate for a wide variety of users.


References[edit]

Wikipedia Training for Students.[edit]

Wikipedia: Training / For Students / Five Pillars

Article Assessment Video[edit]

[[1]]


Extrachromosomal DNA Article Work Area[edit]

Extrachromosomal DNA is any DNA that is found outside of the nucleus of a cell. It is also referred to as extranuclear DNA or cytoplasmic DNA.[1] Most DNA in an individual genome is found in chromosomes but DNA found outside of the chromosomes also serve important biological functions.[2]

In prokaryotes, nonviral extrachromosomal DNA is primarily found in plasmids whereas in eukaryotes extrachromosomal DNA is primarily found in organelles. [3] Mitochondrial DNA is a main source of extrachromosomal DNA.[2] Extrachromosomal DNA is often used in research of replication because it is easy to identify and isolate. [3]

Extrachromosomal DNA in Viruses[edit]

Viral DNA is an example of extrachromosomal DNA. Understanding viral genomes is very important for understanding the evolution and mutation of the virus.[4] Viruses are made up of a nucleic acid core surrounded by a protein coat. They are parasitic and require a host to replicate. Viruses utilize the host cells resources to replicate. Some viruses, such as HIV and oncogenetic viruses, incorporate their own DNA into the genome of the host cell. [5] Viral genomes can be made up of ssDNA, dsDNA, ssRNA, or dsRNA. Viruses can also be found in both linear and circular form [6]

Influenza is a well-known virus. There are three main types of Influenze differentiated by proteins, Influenza A, B, and C. The viral genomes of A and B consist of ssRNA. The high mutation rates, caused by high error rates in ssRNA replication, is one reason these viruses have high evolutionary success. [7]

Extrachromosomal DNA in Prokaryotes[edit]

Extrachromosomal DNA exists in prokaryotes as circular or linear plasmids. Bacterial plasmids are typically short sequences, consisting of 1 kb to a few hundred kb segments, and contain an origin of replication which allows the plasmid to replicate independently of the bacterial chromosome.[8] The total number of a particular plasmid within a cell is referred to as the copy number and can be as few as two copies per cell up to several hundred copies per cell.[9] Circular bacterial plasmids are classified according to the special functions that the genes encoded on the plasmid provide. Fertility plasmids allow for conjugation to occur, resistance plasmids contain genes that convey resistance to a variety of different antibiotics such as ampicillin and tetracycline, virulence plasmids contain the genetic elements necessary for the bacterium to become pathogenic, and degradative plasmids harbor the genes that allow the bacterium to degrade a variety of substances such as aromatic compounds and xenobiotics.[10] Bacterial plasmids can also function in pigment production, nitrogen fixation and the resistance to heavy metals in those bacteria that possess them.[11]

Naturally occurring spherical plasmids can be modified to contain multiple resistance genes and several unique restriction sites, making them valuable tools as cloning vectors in biotechnology applications.[8]

pBR32 Plasmid of E. coli.

Linear bacterial plasmids were first identified in Streptomyces bacteria, but have since been identified in a number of other bacterial species. Antibiotic resistance genes have been found on linear plasmids as well as on circular plasmids.[10]

Extrachromosomal DNA in Eukaryotes[edit]

Mitochondrial DNA[edit]

Chloroplast DNA[edit]

Extrachromosomal Circular DNA[edit]

Extrachromosomal circular DNA (eccDNA) is present in all eukaryotic cells, is usually derived from genomic DNA, and consists of repetitive sequences of DNA found in both coding and non-coding regions of chromosomes. EccDNA can vary in size from less than 2000 base pairs to more than 20,000 base pairs.[12] In plants, eccDNA contains repeated sequences similar to those that are found in the centromeric regions of the chromosomes and in repetitive satellite DNA.[13] In animals, eccDNA molecules have been shown to contain repetitive sequences that are seen in satellite DNA, 5S ribosomal DNA and telomere DNA.[12] Certain organisms, such as yeast, rely on DNA replication to produce eccDNA[13] whereas eccDNA formation can occur in other organisms, such as mammals, independently of the replication process.[14] The function of eccDNA has not been widely studied, but it has been proposede that the production of eccDNA elements from genomic DNA sequences adds to the plasticity of the eukaryotic genome and can influence genome stability, cell aging and the evolution of chromosomes.[15]

Extrachromosomal DNA and Biotechnology[edit]

Extrachromosomal DNA in Medicine and Disease[edit]

Sometimes called EEs, extrachromosomal elements, has been associated with genomic instability in eukaryotes. Small polydispersed DNAs (spcDNAs) are commonly found in conjunction with genome instability. SpcDNAs are derived from repetitive sequences sucah as satellite DNA, retrovirus-like DNA elements, and transposable elements in the genome. They are thought to be the products of gene rearrangements. Double Minute Chromosomes (DMs) are also extrachromosomal elements that are associated with genome instability.[2] DMs are commonly seen in cancer cells. [16] DMs are thought to be produced through breakages in chromosomes or overreplication of DNA in an organism. Studies show that in cases of cancer and other genomic instability, higher levels of EEs can be observed.[2]

Relevant Research[edit]

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  1. ^ "Encyclopedia Britannica: Extrachromosomal DNA".
  2. ^ a b c d e Kuttler, Fabien; Mai, Sabine (2007). "Formation of non-random extrachromosomal elements during development, differentiation and oncogenesis". Seminars in Cancer Biology. 17: 56–64. doi:10.1016/j.semcancer.2006.10.007. PMID 17116402.{{cite journal}}: CS1 maint: date and year (link)
  3. ^ a b c Rush, Mark G.; Misra, Ravi (November 1985). "Extrachromosomal DNA in eukaryotes". Plasmid. 14 (3): 177–191. doi:10.1016/0147-619X(85)90001-0. PMID 3912782.{{cite journal}}: CS1 maint: date and year (link)
  4. ^ Sanjuán, R.; Nebot, M. R.; Chirico, N.; Mansky, L. M.; Belshaw, R. (2010 Oct). "Viral mutation rates". Journal of Virology. 84 (19): 9733–48. doi:10.1128/JVI.00694-10. PMC 2937809. PMID 20660197. {{cite journal}}: Check date values in: |date= (help)
  5. ^ Silverthorn, Dee Unglaub (2007). Human Physiology. Peason/Benjamin Cummings.
  6. ^ "Viral Genomes".
  7. ^ Hampson, A. W.; MacKenzie, J. S. (2006 Nov 20). "The influenza viruses". The Medical Journal of Australia. 185 (10 Suppl): S39-43. doi:10.5694/j.1326-5377.2006.tb00705.x. PMID 17115950. S2CID 17069567. {{cite journal}}: Check date values in: |date= (help)
  8. ^ a b c Nelson, David (2008). Lehninger Principles of Biochemistry. New York: W. H. Freeman and Company. pp. 307–308. ISBN 978-0-7167-7108-1.
  9. ^ a b Watson, James (2007). Recombinant RNA: Genes and Genomes- A Short Course. New York: W. H. Freeman and Company. p. 81. ISBN 978-0-7167-2866-5.
  10. ^ a b c Dib, Julián Rafael; Liebl, Wolfgang; Wagenknecht, Martin; Farías, María Eugenia; Meinhardt, Friedhelm (2013). "Extrachromosomal genetic elements in Micrococcus". Applied Microbiology and Biotechnology. 97: 63–75. doi:10.1007/s00253-012-4539-5. PMID 23138713. S2CID 253773706. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: date and year (link)
  11. ^ a b Barnum, Susan (2005). Biotechnology- An Introduction. California: Brooks / Cole. pp. 62–63. ISBN 978-0-495-11205-1.
  12. ^ a b c Cohen, Sarit; Agmon, Neta; Sobol, Olga; Segal, Daniel (2010). "Extrachromosomal circles of satellite repeats and 5S ribosomal DNA in human cells". Mobile DNA. 1 (1): 11. doi:10.1186/1759-8753-1-11. PMC 3225859. PMID 20226008.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: unflagged free DOI (link)
  13. ^ a b c Navrátilová, Alice; Koblížková, Andrea; Macas, Jiří (2008). "Survey of extrachromosomal circular DNA derived from plant satellite repeats". BMC Plant Biology. 8 (90): 90. doi:10.1186/1471-2229-8-90. PMC 2543021. PMID 18721471.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: unflagged free DOI (link)
  14. ^ a b Cohen, Zoya; Lavi, Sara (2009). "Replication of Independent Formation of Extrachromosomal Circular DNA in Mammalian Cell-Free System". PLOS ONE. 4 (7): e6126. doi:10.1371/journal.pone.0006126. PMC 2699479. PMID 19568438.{{cite journal}}: CS1 maint: date and year (link)
  15. ^ a b Cohen, Sarit (2002). "Formation of extrachromosomal circles from telomeric DNA in Xenopus laevis". EMBO Reports. 3 (12): 1168–1174. doi:10.1093/embo-reports/kvf240. PMC 1308322. PMID 12446568. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  16. ^ a b Shimizu, Noriaki (2011). "Molecular mechanisms of the origin of micronuclei from extrachromosomal elements". Mutagenesis. 26 (1): 119–123. doi:10.1093/mutage/geq053. PMID 21164192.{{cite journal}}: CS1 maint: date and year (link)
  17. ^ Shibata, Yoshiyuki; Kumar, Pankaj; Layer, Ryan; Willcox, Smaranda; Gagan, Jeffrey R.; Griffith, Jack D.; Dutta, Anindya (April 6, 2012). "Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues". Science. 336 (6077): 82–86. doi:10.1126/science.1213307. PMC 3703515. PMID 22403181.{{cite journal}}: CS1 maint: date and year (link)
  18. ^ Goebel, Werner (1970). "Studies on Extrachromosomal DNA Elements". European Journal of Biochemistry. 15 (2): 311–320. doi:10.1111/j.1432-1033.1970.tb01009.x. PMID 4926129.
  19. ^ Cummings, Donald (1979). Extrachromosomal DNA. New York: Academic Press Inc.
  20. ^ Colosimo, A. (2002). "Extrachromosomal genes: a powerful tool in gene targeting approaches". Gene Therapy. 9 (11): 679–682. doi:10.1038/sj.gt.3301749. PMID 12032686. S2CID 2170777. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)CS1 maint: date and year (link)
  21. ^ Cara, A (1997). "New insight on the role of extrachromosomal retroviral DNA". Leukemia. 11 (9): 1395–1399. doi:10.1038/sj.leu.2400776. PMID 9305590. S2CID 12624364. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)CS1 maint: date and year (link)
  22. ^ Preer Jr., John R. (1971). "Extrachromosomal inheritance: Hereditary symbionts, mitochondria, chloroplasts". Annual Review of Genetics: 5361–5406.{{cite journal}}: CS1 maint: date and year (link)
  23. ^ Cohen, Sarit; Houben, Andreas; Segal, Daniel (2008). "Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants". The Plant Journal. 53 (6): 1027–1034. doi:10.1111/j.1365-313X.2007.03394.x. PMID 18088310.{{cite journal}}: CS1 maint: date and year (link)
  24. ^ Jabaji-Hare, S.H. (1994). "Extrachromosomal plasmids in the plant pathogenic fungus Rhizocontia solani". Current Genetics. 25 (5): 432–431. doi:10.1007/BF00351781. PMID 8082188. S2CID 20902405. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)CS1 maint: date and year (link)
  25. ^ Cohen, S.; Yacobi, K.; Segal, D. (2003). ""Extrachromosomal circular DNA of tandemly repeated genomic sequences in Drosophila."". Genome Research. 13 (6A): 1133–1145. doi:10.1101/gr.907603. PMC 403641. PMID 12799349.{{cite journal}}: CS1 maint: date and year (link)
  26. ^ Shibata, Yoshiyuki (2012). ""Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues."". Science. 336 (6077): 82–86. doi:10.1126/science.1213307. PMC 3703515. PMID 22403181. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  27. ^ Goebel, Werner (1970). "Studies on extrachromosomal DNA elements". European Journal of Biochemistry. 15 (2): 311–320. doi:10.1111/j.1432-1033.1970.tb01009.x. PMID 4926129.

Potential Images to Use[edit]

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