User talk:Uh0hN0/sandbox

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"Bacterial circadian rhythms" Article Critique 

    The article mentions the refuting of the belief that circadian rhythms didn't exist in prokaryotes multiple times, such as in the lead, "History" (twice mentioned) and "Adaptive Significance" sections, to the point of redundancy, overrepresentation and irrelevance with respect to the last section. The article also exhibits problems in citing some of the claims made. In the "Regulation of gene expression and chromosomal topology" section, the article states in "eukaryotes, about 10-20% of the genes are rhythmically expressed," however no citation is given for this specific fact. The next following citation, #14, fails to mention those specific numbers[1] (reference #1 suggests a figure of 5-15%,[2] but even this is uncited by the article), but does report that prokaryotes seem to have more extensive rhythmic expression of their genes than eukaryotes. However, the paper then proposes some alternative explanations for this observation[1] (p. 1474) which the article doesn't mention, failing to accurately portray the subtopic. Another instance is when the article claims that the cyanobacterial circadian system is "the only circadian system in which the structures of full-length clock proteins have been solved," again without providing a citation. The closest reference, #17, doesn't reinforce this claim.[3] While these claims may be accurate, they are at best not properly cited. Lastly, the article might be updated to note that some research suggests that Enterobacter aerogenes is the first non-cyanobacteria bacteria to exhibit a circadian rhythm[4] and mention the potential relevance of bacterial circadian rhythms in relationships with their hosts.[5]

Uh0hN0 (talk) 05:46, 18 September 2017 (UTC)[reply]

Notes

  1. ^ a b Liu, Y., Tsinoremas, N.F., Johnson, C.H., Lebedeva, N.V., Golden, S.S., Ishiura, M., and Kondo, T. (1995). Circadian orchestration of gene expression in cyanobacteria. Genes Dev. 9, 1469–1478.
  2. ^ Johnson, C.H., S.S. Golden, M. Ishiura, and T. Kondo (1996) Circadian clocks in prokaryotes. Mole. Microbiol. 21: 5–11.
  3. ^ Kondo, T., N.F. Tsinoremas, S.S. Golden, C.H. Johnson, S. Kutsuna, and M. Ishiura (1994) Circadian clock mutants of cyanobacteria. Science 266: 1233–1236.
  4. ^ Paulose, J. K., & Cassone, V. M. (2016). The melatonin-sensitive circadian clock of the enteric bacterium Enterobacter aerogenes. Gut Microbes, 7(5), 424–427. http://doi.org/10.1080/19490976.2016.1208892
  5. ^ Johnson, C. H., Zhao, C., Xu, Y., & Mori, T. (2017). Timing the day: what makes bacterial clocks tick? Nature reviews. Microbiology , 15(4), 232-242. doi:10.1038/nrmicro.2016.196

Wikipedia Assignment #2: Ultramicrobacteria Article Proposal

The article on ultramicrobacteria is fairly short; the first paragraph gives an overview of the subject, while the other two paragraphs add minor context to the article. However, the first paragraph makes incorrect assertions, creating a significant knowledge gap on the topic. The article incorrectly states that "[m]any, if not all, of these small bacteria are dormant forms of larger cells that allow survival under starvation conditions" even when the cited source and others make a distinction between starvation forms of bacteria and ultramicrobacteria.[1][2] Having made this false equivalence, the article then describes ultramicrobacteria as having the common physiological traits of starvation form bacteria, ignoring actual features of ultramicrobacteria such as occasional parasitism of other prokaryotes, their high surface area:volume ratio or small genomes.[3] The article also makes no mention of the considerable ambiguity in classifying organisms < 0.1 µm^3, an issue which has plagued this article and even research.[3] For instance, "nanobacteria" has been used synonymously with ultramicrobacteria in academic papers, despite being different.[3] While the second paragraph acknowledges a difference, it attributes the confusion to the reader instead of the literature. And again, the article fails to distinguish ultramicrobacteria from ultramicrocells[4] or small bacterial forms,[5] terms which encapsulate starvation form bacteria, ultramicrobacteria etc.. The last paragraph describes a 2015 Nature Communications study which only holds significance in reporting seemingly contradictory results to the false claims in the first paragraph (ie. cell division despite dormancy), which warrants its removal. I intend to improve this article by mentioning some of the actual common and/or interesting physiological characteristics of ultramicrobacteria,[3] the ambiguous terminology surrounding ultramicrobacteria,[3][4] their diversity[4] and difficulties in studying ultramicrobacteria.[6][7] I will also correct or remove false information. Ultramicrobacteria are a topic of growing notability, having been the subject of multiple comprehensive literature reviews and topic summaries[1][3][4] and numerous research papers examining specific ultramicrobacterial phenomenon such as their predation,[8] better methods to enrich them[9] and the various environments in which they are found.[10][11] There is enough literature to constitute a Wikipedia article on ultramicrobacteria.

Uh0hN0 (talk) 08:33, 27 September 2017 (UTC)[reply]

Notes

  1. ^ a b Velimirov, B. (2001). "Nanobacteria, Ultramicrobacteria and Starvation Forms: A Search for the Smallest Metabolizing Bacterium". Microbes and Environments. 16 (2): 67–77. doi:10.1264/jsme2.2001.67. Retrieved 2008-06-23.
  2. PMID 8561477
    . doi:10.1146/annurev.mi.49.100195.003431
  3. ^ a b c d e f Duda, V; Suzina, N; Polivtseva, V; Boronin, A (2012). "Ultramicrobacteria: Formation of the Concept and Contribution of Ultramicrobacteria to Biology". Microbiology. 81 (4): 379–390.
  4. ^
    ISBN 9780470015902
    . Retrieved September 26, 2017.
  5. ^ Lysak, L. V., Lapygina, E. V., Kadulin, M. S., & Konova, I. A. (2014). Number, viability, and diversity of the filterable forms of prokaryotes in sphagnous high-moor peat. Biology Bulletin, 41(3), 228-232. doi:10.1134/S1062359014030066
  6. ^ Janssen, P. H., Schuhmann, A., Mörschel, E., & Rainey, F. A. (1997). Novel anaerobic ultramicrobacteria belonging to the verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil. Applied and Environmental Microbiology, 63(4), 1382-1388.
  7. ^ Lysak, L. V., Lapygina, E. V., Konova, I. A., & Zvyagintsev, D. G. (2010). Population density and taxonomic composition of bacterial nanoforms in soils of russia. Eurasian Soil Science, 43(7), 765-770. doi:10.1134/S1064229310070069
  8. ^ Boenigk, J., Stadler, P., Wiedlroither, A., & Hahn, M. W. (2004). Strain-specific differences in the grazing sensitivities of closely related ultramicrobacteria affiliated with the polynucleobacter cluster. Applied and Environmental Microbiology, 70(10), 5787-5793. doi:10.1128/AEM.70.10.5787-5793.2004
  9. ^ Neuenschwander, S. M., Salcher, M. M., & Pernthaler, J. (2015). Fluorescence in situ hybridization and sequential catalyzed reporter deposition (2C-FISH) for the flow cytometric sorting of freshwater ultramicrobacteria. Frontiers in Microbiology, 6, 247. doi:10.3389/fmicb.2015.00247
  10. ^ Hahn, M. W., Lünsdorf, H., Wu, Q., Schauer, M., Höfle, M. G., Boenigk, J., & Stadler, P. (2003). Isolation of novel ultramicrobacteria classified as actinobacteria from five freshwater habitats in europe and asia. Applied and Environmental Microbiology, 69(3), 1442-1451. doi:10.1128/AEM.69.3.1442-1451.2003
  11. ^ Sahin, N., Gonzalez, J. M., Iizuka, T., & Hill, J. E. (2010). Characterization of two aerobic ultramicrobacteria isolated from urban soil and a description of oxalicibacterium solurbis sp. nov. FEMS Microbiology Letters, 307(1), 25-29. doi:10.1111/j.1574-6968.2010.01954.x

UhohNo's Peer Review

Positive Feedback

Writing is concise and easy to understand (no run-on sentences, grammar or spelling errors). The writing is neutral – no persuasive statements. For example, the genome content of P. ubique is described but it is also stated that genomic data is lacking (balanced coverage). Ideas are supported by numerous references from peer-reviewed journals and textbooks.

Good summary of main points from literature – based on all of the references, the unique qualities of ultramicrobacteria (can be isolated from soil, small size, small genome size, and parasitism) are all integrated in the edits. No close paraphrasing evident – great summarization of P. ubique’s genome content from reference 2 (reference had multiple paragraphs about the genome content and you were able to summarize into one sentence).

The organization of paragraphs (description of ultramicrobacteria properties is separated from comparisons to nanobacteria and ultramicrocells) is appropriate. Paragraphs have comprehensive flow of ideas – e.g. smooth transition from P. ubique genome content to how genomic data is lacking due to difficulties cultivating ultramicrobacteria. Cannot comment on placement of edits since the edited section is the lead and only section of the original article. As a lead, it does not go into too much detail in paragraph 1 and provides a good introduction for further discussion in the original article.

Good comparison with ultramicrocells, as information in the original article was reported incorrectly (ultramicrobacteria are not dormant starvation forms of larger cells, according to references 1 and 2).

Great addition of parasitism property of ultramicrobacteria as it was an important section in references 1 and 2 that was not discussed in the original article. This could allow for a new topic in the article.

Suggestions

Minor edit: to also hyperlink gram-negative and write “gram-negative” instead of “-negative” for clarity. “Gram-positive” does not need to be capitalized.

Could elaborate about parasitism as it is an important property not in the original article. E.g. perhaps their small size allows them to be adsorbed by host cells since they are intracellular parasites (reference 2). Should also cite “which is enabled by their small size relative to their hosts” as it was difficult to locate this statement quickly in the sources.

Half of the edits describe ultramicrocells and nanobacteria. Could remove “in their starvation response…. many years”, "calcifying nanoparticles, which were proposed to be living organisms that were 0.1 μm in diameter” and “likely precipitated particles of inorganic material” since it is irrelevant to ultramicrobacteria. Could also clarify that ultramicrobacteria are not dormant in the last sentence of the second paragraph while contrasting them to ultramicrocells.

The first sentence of the edits does not accurately represent the sources. References 2 and 3 say ultramicrobacteria have volumes less than 0.1 μm3, reference 1 says 0.1 mm3, and you reported 0.3 μm3. You might have confused the 0.3 μm diameter with the volume. Since more references say 0.1 μm3 it might be best to change this value to 0.1 μm3.

References 1 and 2 are cited preferentially –it would be more balanced to find the same information in different sources.

Swimminganddogs (talk) 04:06, 9 November 2017 (UTC)[reply]

Peer Review Feedback

Thanks for your feedback swimmingandogs! I just wanted to give my feedback on your points.

1) I’ll change “-negative” to “Gram-negative” to make the sentence a little smoother. However, the Gram in Gram-negative or positive is capitalized since Gram refers to the name of the scientist that developed Gram staining.

2) Great suggestion, I’ll elaborate a little more on what ultramicrobacterial parasitism is and try to more precisely cite the claims I make in those sentences.

3) I think it’s important to briefly describe and distinguish between ultramicrobacteria and other very small microbes since even the scientific literature around these organisms sometimes fails to make a distinction and the reviews I listed devote a significant amount of time to correcting terminology. They also exist in their own distinct paragraphs, meaning the reader can easily avoid them should they judge the information irrelevant. That said, I will try to scale back the info on these other organisms though and/or perhaps integrate them more naturally into the text.

4) Good catch, I forgot that I should be using the accepted definition of smaller than 0.1 micrometers cubed instead of a diameter.

5) References 1 and 2 are review articles on ultramicrobacteria whereas the latter is more focused. I think it would be best not to draw too much on comprehensive sources such that we sacrifice broadness for detail, but your note is still valid.

Uh0hN0 (talk) 05:57, 20 November 2017 (UTC)[reply]

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