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This is an old revision of this page, as edited by CodeSwitch (talk | contribs) at 16:05, 27 September 2017 (→Assignment 2 - Methyltroph). 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 a notable subject because they have a unique metabolism that has been well documented since 1892.[24] Methylotrophs have been found in wetlands[25], oceans[26][27], soil[28][29][30], plants[31][32], deserts[33], lake sediment[34][35][36], soda lakes[37][38], volcanic mud pots[39], the human body[40][41] and even Antarctica[42][43], highlighting their global significance. Based on keyword search in literature databases[44], there are over 500 publications on methylotrophs and almost 800 publications based on methanotrophs (a subset of methylotrophs), exemplifying the importance of this unique metabolic ability in ecological[45][46][47][48][49][50], commercial[51][52][53][54][55][56][57] and bio-remedial[58][59] activities.

Despite the available information, the current Methylotroph page contains scant information which is often misconstrued and uncited. My focus will be on the “General Microbiology” section because it is almost entirely composed of contradictory, false or irrelevant statements, potentially due to relying heavily on one source. The manifests in the careless suggestion that methylotrophy is limited to bacteria, omitting methylotrophic yeasts[60][61][62] and Archaea[63][64]. Then a faulty generalization is made regarding cellular structure, simultaneously suggesting that methanotrophs are not methylotrophs despite the two not being mutually exclusive[65]. This leads to another incorrect statement suggesting that there is “a single obligate methylotroph” despite overwhelming evidence of many obligate C1 organisms[66][67][68][69][70][71][72][73], many of which are methanotrophs[74][75][76][77] (and hence also methylotrophs).

The rest of this section continues with generalizations on structure that do not apply to a significant amount of methylotrophs. By focusing on structure, which varies between methylotrophs[78], the article fails to discuss the one thing all methylotrophs share- the ability to shunt single carbon units into metabolic pathways[79][80]. Further subdivisions such as Obligate/Facultative, Methanotrophic/Non-Methanotrophic and Bacteria/Archaea/Fungi can, and should be made in subsequent edits, because there are certainly within-group structural similarities[81][82].

However, my focus will be on the general theme of producing and oxidizing formaldehyde, a central intermediate used in the assimilatory and dissimilatory processes of all methylotrophs[83][84][85]. A common dissimilatory pathway[86][87][88] and the main assimilatory pathways (RuBP[89], RuMP[90], Serine[91][92], CBB[93][94], and XuMP[95][96][97]) that use formaldehyde will be discussed in detail along with important intermediates and products. However, enzymes and structures used for these pathways differ[98] and only the most common will be addressed for the reader’s sake.

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