Jump to content

User talk:CodeSwitch/sandbox

Page contents not supported in other languages.
From Wikipedia, the free encyclopedia
< User talk:CodeSwitch
This is an old revision of this page, as edited by CodeSwitch (talk | contribs) at 19:18, 21 September 2017 (→Assignment 2 - Methyltroph: new section). The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

Bacterial Circadian Rhythms

This article needs a section after the lead that better explains what circadian rhythms are and their general role in organisms[1][2]. A section discussing why bacterial circadian rhythms need to synchronize with the environment should be created and updated with current understanding[3][4].

The section “Relationship to Cell Division” should discuss how bacterial circadian rhythms gate-keep for cell division[5][6]. The section “Global regulation… chromosome topology” should explain the choice of using cyanobacteria for elucidating circadian rhythms instead of eukaryotes[7][8] and elaborate on chromosomal compaction due to circadian rhythms[9]. The “molecular mechanism” section regarding KaiABC proteins needs updating as it doesn’t discuss the reciprocal interplay between the Kai proteins[10][11][12][13] and doesn’t explain the post-translational regulation mechanism adequately[14].

Other significant proteins in bacterial circadian rhythms such as SasA[15][16], CikA[17][18] and RpaA[19][20] should also be discussed. New research such as the successful transplantation of KaiABC proteins in prokaryotes other than cyanobacteria[21] and how diurnal variation of gut bacteria influence mouse circadian rhythms[22][23] should be added.

Some general improvements might include simplifying diction and shortening section headings. The section “Adaptive Significance” shouldn’t begin with a question and the extrapolation to “all organisms” is suspect and should be cited or removed, along with phrases such as “seemed reasonable”, exquisitely precise”, “while intuitive”, “persuasive evidence… is lacking”, and “Cyanobacteria are… of the few organisms…”. All references are from peer-reviewed journals with no obvious bias towards any single source, however, proper hyperlinks need to be added. CodeSwitch (talk) 19:09, 16 September 2017 (UTC) CodeSwitch (talk) 19:06, 16 September 2017 (UTC) CodeSwitch (talk) 20:18, 17 September 2017 (UTC)[reply]

Reflection

I learned during my evaluation of this article that it is difficult to write a quality Wikipedia entry. Finding current/updated research for my critique was very easy, likely because there has been little activity on this page. The word count was difficult so I primarily focused on content. In the future, it may be beneficial to assign 250 characters for content improvement (new/updated research) and 250 characters for some of the probing questions. CodeSwitch (talk) 02:39, 18 September 2017 (UTC)[reply]

Assignment 2 - Methyltroph

Methylotrophs are important[24]

  1. ^ Harmer, Stacey L.; Panda, Satchidananda; Kay, Steve A. (November 2001). "Molecular Bases of Circadian Rhythms". Annual Review of Cell and Developmental Biology. 17 (1): 215–253. doi:10.1146/annurev.cellbio.17.1.215.
  2. ^ Ouyang, Y.; Andersson, C. R.; Kondo, T.; Golden, S. S.; Johnson, C. H. (21 July 1998). "Resonating circadian clocks enhance fitness in cyanobacteria". Proceedings of the National Academy of Sciences. 95 (15): 8660–8664. doi:10.1073/pnas.95.15.8660.
  3. ^ Ivleva, Natalia B; Bramlett, Matthew R; Lindahl, Paul A; Golden, Susan S (10 March 2005). "LdpA: a component of the circadian clock senses redox state of the cell". The EMBO Journal. 24 (6): 1202–1210. doi:10.1038/sj.emboj.7600606.
  4. ^ Schmitz, O. (4 August 2000). "CikA, a Bacteriophytochrome That Resets the Cyanobacterial Circadian Clock". Science. 289 (5480): 765–768. doi:10.1126/science.289.5480.765. {{cite journal}}: |access-date= requires |url= (help)
  5. ^ Mori, T.; Binder, B.; Johnson, C. H. (17 September 1996). "Circadian gating of cell division in cyanobacteria growing with average doubling times of less than 24 hours". Proceedings of the National Academy of Sciences. 93 (19): 10183–10188. ISSN 0027-8424. Retrieved 16 September 2017.
  6. ^ Dong, Guogang; Yang, Qiong; Wang, Qiang; Kim, Yong-Ick; Wood, Thammajun L.; Osteryoung, Katherine W.; van Oudenaarden, Alexander; Golden, Susan S. (February 2010). "Elevated ATPase Activity of KaiC Applies a Circadian Checkpoint on Cell Division in Synechococcus elongatus". Cell. 140 (4): 529–539. doi:10.1016/j.cell.2009.12.042.
  7. ^ Cohen, Susan E.; Golden, Susan S. (2 September 2015). "Circadian Rhythms in Cyanobacteria". Microbiology and Molecular Biology Reviews. 79 (4): 373–385. doi:10.1128/MMBR.00036-15.
  8. ^ Kondo, T; Tsinoremas, N.; Golden, S.; Johnson, C.; Kutsuna, S; Ishiura, M (18 November 1994). "Circadian clock mutants of cyanobacteria". Science. 266 (5188): 1233–1236. doi:10.1126/science.7973706.
  9. ^ Smith, R. M.; Williams, S. B. (17 May 2006). "Circadian rhythms in gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus". Proceedings of the National Academy of Sciences. 103 (22): 8564–8569. doi:10.1073/pnas.0508696103.
  10. ^ Tseng, Roger; Goularte, Nicolette F.; Chavan, Archana; Luu, Jansen; Cohen, Susan E.; Chang, Yong-Gang; Heisler, Joel; Li, Sheng; Michael, Alicia K.; Tripathi, Sarvind; Golden, Susan S.; LiWang, Andy; Partch, Carrie L. (17 March 2017). "Structural basis of the day-night transition in a bacterial circadian clock". Science. 355 (6330): 1174–1180. doi:10.1126/science.aag2516.
  11. ^ Kim, Y.-I.; Dong, G.; Carruthers, C. W.; Golden, S. S.; LiWang, A. (26 August 2008). "The day/night switch in KaiC, a central oscillator component of the circadian clock of cyanobacteria". Proceedings of the National Academy of Sciences. 105 (35): 12825–12830. doi:10.1073/pnas.0800526105.
  12. ^ Chang, Y.-G.; Cohen, S. E.; Phong, C.; Myers, W. K.; Kim, Y.-I.; Tseng, R.; Lin, J.; Zhang, L.; Boyd, J. S.; Lee, Y.; Kang, S.; Lee, D.; Li, S.; Britt, R. D.; Rust, M. J.; Golden, S. S.; LiWang, A. (25 June 2015). "A protein fold switch joins the circadian oscillator to clock output in cyanobacteria". Science. 349 (6245): 324–328. doi:10.1126/science.1260031.
  13. ^ Chang, Y.-G.; Cohen, S. E.; Phong, C.; Myers, W. K.; Kim, Y.-I.; Tseng, R.; Lin, J.; Zhang, L.; Boyd, J. S.; Lee, Y.; Kang, S.; Lee, D.; Li, S.; Britt, R. D.; Rust, M. J.; Golden, S. S.; LiWang, A. (25 June 2015). "A protein fold switch joins the circadian oscillator to clock output in cyanobacteria". Science. 349 (6245): 324–328. doi:10.1126/science.1260031.
  14. ^ Tomita, J. (14 January 2005). "No Transcription-Translation Feedback in Circadian Rhythm of KaiC Phosphorylation". Science. 307 (5707): 251–254. doi:10.1126/science.1102540.
  15. ^ Tseng, Roger; Chang, Yong-Gang; Bravo, Ian; Latham, Robert; Chaudhary, Abdullah; Kuo, Nai-Wei; LiWang, Andy (January 2014). "Cooperative KaiA–KaiB–KaiC Interactions Affect KaiB/SasA Competition in the Circadian Clock of Cyanobacteria". Journal of Molecular Biology. 426 (2): 389–402. doi:10.1016/j.jmb.2013.09.040.
  16. ^ Valencia S., J.; Bitou, Kyouhei; Ishii, Kentaro; Murakami, Reiko; Morishita, Megumi; Onai, Kiyoshi; Furukawa, Yukio; Imada, Katsumi; Namba, Keiichi; Ishiura, Masahiro (May 2012). "Phase-dependent generation and transmission of time information by the KaiABC circadian clock oscillator through SasA-KaiC interaction in cyanobacteria". Genes to Cells. 17 (5): 398–419. doi:10.1111/j.1365-2443.2012.01597.x.
  17. ^ Mutsuda, Michinori; Michel, Klaus-Peter; Zhang, Xiaofan; Montgomery, Beronda L.; Golden, Susan S. (23 May 2003). "Biochemical Properties of CikA, an Unusual Phytochrome-like Histidine Protein Kinase That Resets the Circadian Clock in PCC 7942". Journal of Biological Chemistry. 278 (21): 19102–19110. doi:10.1074/jbc.M213255200. {{cite journal}}: |access-date= requires |url= (help)CS1 maint: unflagged free DOI (link)
  18. ^ Ivleva, N. B.; Gao, T.; LiWang, A. C.; Golden, S. S. (6 November 2006). "Quinone sensing by the circadian input kinase of the cyanobacterial circadian clock". Proceedings of the National Academy of Sciences. 103 (46): 17468–17473. doi:10.1073/pnas.0606639103.
  19. ^ Gutu, Andrian; O’Shea, Erin K. (April 2013). "Two Antagonistic Clock-Regulated Histidine Kinases Time the Activation of Circadian Gene Expression". Molecular Cell. 50 (2): 288–294. doi:10.1016/j.molcel.2013.02.022. {{cite journal}}: no-break space character in |first2= at position 5 (help)
  20. ^ Takai, N.; Nakajima, M.; Oyama, T.; Kito, R.; Sugita, C.; Sugita, M.; Kondo, T.; Iwasaki, H. (1 August 2006). "A KaiC-associating SasA-RpaA two-component regulatory system as a major circadian timing mediator in cyanobacteria". Proceedings of the National Academy of Sciences. 103 (32): 12109–12114. doi:10.1073/pnas.0602955103.
  21. ^ Chen, A. H.; Lubkowicz, D.; Yeong, V.; Chang, R. L.; Silver, P. A. (12 June 2015). "Transplantability of a circadian clock to a noncircadian organism". Science Advances. 1 (5): e1500358 – e1500358. doi:10.1126/sciadv.1500358.
  22. ^ Liang, Xue; FitzGerald, Garret A. (September 2017). "Timing the Microbes: The Circadian Rhythm of the Gut Microbiome". Journal of Biological Rhythms. doi:10.1177/0748730417729066.
  23. ^ Thaiss, Christoph A.; Zeevi, David; Levy, Maayan; Zilberman-Schapira, Gili; Suez, Jotham; Tengeler, Anouk C.; Abramson, Lior; Katz, Meirav N.; Korem, Tal; Zmora, Niv; Kuperman, Yael; Biton, Inbal; Gilad, Shlomit; Harmelin, Alon; Shapiro, Hagit; Halpern, Zamir; Segal, Eran; Elinav, Eran (October 2014). "Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis". Cell. 159 (3): 514–529. doi:10.1016/j.cell.2014.09.048. {{cite journal}}: no-break space character in |first1= at position 10 (help); no-break space character in |first6= at position 6 (help); no-break space character in |first8= at position 7 (help)
  24. ^ Oremland, Ronald S.; Culbertson, Charles W. (2 April 1992). "Importance of methane-oxidizing bacteria in the methane budget as revealed by the use of a specific inhibitor". Nature. 356 (6368): 421–423. doi:10.1038/356421a0. {{cite journal}}: |access-date= requires |url= (help)
Retrieved from "https://en.wikipedia.org/w/index.php?title=User_talk:CodeSwitch/sandbox&oldid=801772693"