Group 81G
editThis is a group page for the Johns Hopkins Molecular Biology course. This group will be working on the article TBD.
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 (as specified in the milestone summary chart.
Please create a new section here for each of those assignments.
Initial article assessments from KevinBrownJHU
editComplementarity This article is a bit short and could use some added information related to complementarity. Maybe add information related to what it can help with, such as transcript regulation caused by Antisense Transcripts[1] or even in the presence of kissing hairpins [2]. The page seems to be started about how things line up, but light on a lot of real details. Such as the fact that A pairs with T, but there are plenty of cases where it isn't always so, such as in extremophiles.
Neutral Mutation This stub of an article needs to be expanded on to include more details of how and why some mutations are silent. SNPs show this to some degree as does the standard codon table for translation. SNPs are also part of population studies, that this stub links to. Not sure if this fits with the main stub about neutral mutations, but the conversion of one pathway to another[3] via mutation would seem to fit as a neutral change. A study was done on mtDNA with gene variants to determine if the variants were just polymorphisms or deleterious to a human [4]
Initial article assessments from AjoneWiki
editExtrachromosomal DNA
edit- The article Extrachromosomal DNA is a stub. It contains no citations or other references, is very short (two short paragraphs), contains a brief definition and has minimal information covering the occurrence of extra chromosomal DNA, "normal" vs. cancerous. The talk page contains no discussion but shows that the article is part of two WikiProjects:
- Wikipedia:WikiProject_Molecular_and_Cellular_Biology, which classifies the article as a stub and as highly important
- Wikipedia:WikiProject_Genetics which hasn't accessed the article yet.
Possible Resources/References:
editHistone octamer
edit- The article Histone octamer is a stub. The article consists of a single paragraph giving a very brief definition and listing the sub units of the histone octamer. It contains no citation or inline references, but merely redirects the reader to a few other wiki articles Nucleosome, Histone and Chromatin, respectively. The talk page is very limited as it has only one user comment. The article is also accessed by the Wikipedia:WikiProject_Molecular_and_Cellular_Biology, which classifies it as a stub and as highly important.
Possible Resources/References:
editArticle selection rationale
editComplementarity is a good choice as the current information is barely past the level of a stub article. A lot of new information and organization will be needed as the article as it currently exists seems to contain information already present in the base pair section. Some possible expansions include self-complementary sequences (like the folding of RNA strands into functional units of tRNA). While the current article limits itself to just touching on DNA complementarity, amino acids also show a form of complementarity which leads to how a protein folds or how they bind to each other.[10] Another Wiki-article, which may overlap with Complementary is Complementary DNA. It will be important to refer to the other Wiki article to avoid information overlap or in alternative to merge the articles if possible to ease user access. The article complementary was also assessed by the Wikipedia:WikiProject_Molecular_and_Cellular_Biology. It classified the article as a stub and as highly important. Another reason for selecting the article is that nobody appears to be working on it. One of the few edits to the talk page was made in 2010 when information on tRNA and wobble were removed. It also appears as if in 2005 parts of the article were removed to create new sub article - leaving the "bare bones" without editing the main article.
Unit 8 progress report
edit- Contributions consisted mainly of prose
- Created table to visualize base pairing
Unit 10 progress report
edit- Reviewed and implemented several suggestions from peer review
- Added context to the lead section as well as links
- Added prose to individual sections
- Updated table on base pairing
Unit 12 progress report
edit- Added more citations throughout article
- Added more visuals
- Added some prose such as cDNA
- Improved language to make text more accessible
Unit 14 Final progress report
edit- Revised wording throughout article based on suggestions
- Edited overall article flow following JFitz1974's advise
- Added illustration and citation in Ambigrams section
- Edited for typos throughout
- Added prose such as a definition of Antisense transcript (suggested by Klortho)
- Added brief introduction to the regulatory section (suggested by Donbinincom)
- Added more visuals
References
edit- ^ Xie, ZH (Feb 2010). "Natural antisense transcript and its mechanism of gene regulation". Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji. 32 (2): 122–8. PMID 20176555.
- ^ Salim, N; Lamichhane, R; Zhao, R; Banerjee, T; Philip, J; Rueda, D; Feig, AL (Mar 7, 2012). "Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex". Biophysical journal. 102 (5): 1097–107. PMID 22404932.
- ^ Smith, WS; Hale, JR; Neylon, C (May 6, 2011). "Applying neutral drift to the directed molecular evolution of a β-glucuronidase into a β-galactosidase: Two different evolutionary pathways lead to the same variant". BMC research notes. 4: 138. PMID 21548964.
- ^ Mitchell, AL; Elson, JL; Howell, N; Taylor, RW; Turnbull, DM (Feb 2, 2006). "Sequence variation in mitochondrial complex I genes: mutation or polymorphism?". Journal of medical genetics. 43 (2): 175–9. PMID 15972314.
- ^ Boyer, Rodney F. (2006). Concepts in biochemistry (3rd ed.). Hoboken, NJ: Wiley. ISBN 0471661791.
- ^ a b James D. Watson; Tania A. Baker; Stephen P. Bell; Alexander Gann; Michael Levine; Richard Losik; Stephen C. Harrison. Molecular biology of the gene (7th ed.). Boston: Benjamin-Cummings Publishing Company. ISBN 0321762436.
- ^ Cohen, S; Segal, D (2009). "Extrachromosomal circular DNA in eukaryotes: possible involvement in the plasticity of tandem repeats". Cytogenetic and genome research. 124 (3–4): 327–38. PMID 19556784.
- ^ Skene, PJ; Henikoff, S (Jun 2013). "Histone variants in pluripotency and disease". Development. 140 (12): 2513–24. PMID 23715545.
- ^ Munshi, A; Shafi, G; Aliya, N; Jyothy, A (Feb 2009). "Histone modifications dictate specific biological readouts". Journal of genetics and genomics = Yi chuan xue bao. 36 (2): 75–88. PMID 19232306.
- ^ Siemion, IZ; Cebrat, M; Kluczyk, A (Dec 2004). "The problem of amino acid complementarity and antisense peptides". Current protein & peptide science. 5 (6): 507–27. PMID 15581420.