Talk:Nucleoid

A fact from Nucleoid appeared on Wikipedia's Main Page in the Did you know column on 11 March 2020 (check views). The text of the entry was as follows:

Did you know... that the nucleoid keeps the bulk of a bacterium's DNA both compact and well organized?

A record of the entry may be seen at Wikipedia:Recent additions/2020/March. The nomination discussion and review may be seen at Template:Did you know nominations/Nucleoid.

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Molecular Biology: Genetics / MCB

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This article was adapted from Subhash Verma; Zhong Qian; Sankar L Adhya (December 2019). "Architecture of the Escherichia coli nucleoid". PLOS Genetics. 15 (12): e1008456. doi:10.1371/JOURNAL.PGEN.1008456. ISSN 1553-7390. PMC 6907758. PMID 31830036. Wikidata Q84825966.{{cite journal}}: CS1 maint: unflagged free DOI (link) after peer review (reviewer reports) under a CC BY 4.0 license (2019).

Proposed merge

I'm proposing to merge genophore into this article. They seem to cover the same subject and nucleoid appears to be much more frequently used. I found 1329 articles on PubMed using the term nucleoid versus 14 using the term genophore. - tameeria 21:36, 29 April 2007 (UTC)[reply]

Use of Genphore vs Chromosome

The article states the term is misleading, given the source I believe that may have been correct, but modern parlance has come to use bacterial/prokaryotic chromosome as opposed to the more concise genophore. I suggest that it is 1) removed from the article 2) represented with more recent citation(s). A cursory search of "genophore" and "prokaryotic chromosome" on EBSCO ASC returns a number of results greater by a little more than a hundred papers. Specifically:

Egan, Elizabeth S., Michael A. Fogel, and Matthew K. Waldor. "Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes." Molecular Microbiology 56.5 (June 2005): 1129-1138. Academic Search Complete. EBSCO. Washington State University Vancouver, Vancouver, WA. 28 Aug. 2009 <http://www.systems.wsu.edu/scripts/wsuall.pl?url=http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=16975437&site=ehost-live>.

Volkov, A., et al. "A Prokaryotic Condensin/Cohesin-Like Complex Can Actively Compact Chromosomes from a Single Position on the Nucleoid and Binds to DNA as a Ring-Like Structure." Molecular & Cellular Biology 23.16 (15 Aug. 2003): 5638. Academic Search Complete. EBSCO. Washington State University Vancouver, Vancouver, WA. 28 Aug. 2009 <http://www.systems.wsu.edu/scripts/wsuall.pl?url=http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=11091191&site=ehost-live>.

Worning, Peder, et al. "Origin of replication in circular prokaryotic chromosomes." Environmental Microbiology 8.2 (Feb. 2006): 353-361. Academic Search Complete. EBSCO. Washington State University Vancouver, Vancouver, WA. 28 Aug. 2009 <http://www.systems.wsu.edu/scripts/wsuall.pl?url=http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=19411445&site=ehost-live>.

All of which it is worth noting are from recent journals on microbiology. Genophore still does have modern usage as well (as seen in several recent phycology journals). Therefore, the usage of genophore is archaic and concedes no more validity than chromosome in reference to prokaryotes. Septicmadman (talk) 19:39, 28 August 2009 (UTC)[reply]

I am removing the section referring to the genophore for two reasons:

Although papers using the term genophore can be found by searching PubMed and PubMed Central, few of them are from scientists who work on organisms with nucleioids, i.e. bacteria. The usage of chromosome for bacteria dates back to at least the 1960s. In her obituary (pdf) for Hans Ris^[1], Lynn Margulis wrote:

Ris was very disappointed when his appropriate name for the “bacterial chromosome, the “genophore ”, a term he coined, was not generally known or, if known, not accepted by important microbiologists.

This is consistent with the term not being the standard in microbiology (consistent with my own experience as a bacterial molecular biologist).

Second, whether you come down on the side of Ris or not, the section on genophore/chromosome at the beginning of this article ranges into material that is off-topic with respect to the focus of this article, which is nucleioids.

JimHu (talk) 20:58, 12 November 2013 (UTC)[reply]

References

^ Margulis, L (2005) Hans Ris (1914-2004). Genophore, chromosomes and the bacterial origin of chloroplasts. Int Microbiol. 8(2):145-8.

Nucleoid-associated proteins or histone-like proteins

Integration host factor (IHF), factor for inversion stimulation (Fis), Heat-unstable protein (HU), heat-stable nucleoid structuring (HNS) and structural maintanance of chromosomes (SMC) are some recognized proteins involved for the condensation package of DNA in bacteria. I haven't found any information about these proteins on wikipedia and at least it may be good to just mention them in this article.

U1012738 (talk) 13:50, 29 December 2012 (UTC)[reply]

Dawkins Styled Word Creation

"Condensation" does not describe any cellular stage in preparation for division or any other cellular, if you don't have a firm grasp on cellular biology, it may be deleterious to write or edit on such topics. Not a hard and fast rule by any means, as doing so isn't even in the same ball park as what some of the once "reputable" scientific journals (they lose their status as "reputable" among the scientific community) are doing which is going from academically peer reviewed to private publications, which inevitably leads to bogus content. The strange thing is that way back when it was this misguided work of the church, and now the work of a small subset of Atheists. Either way, it only delays the truth that science is able to report. The term "genaphore" itself is a term I strongly suspect to be right up there with condensing of DNA, it's a Dawkinsian styled word. Shakespeare may have been a great writer, but he sure would have made a mess of science if he was given any scientific credibilityDirtclustit (talk) —Preceding undated comment added 04:07, 20 September 2013 (UTC)[reply]

Update from PLOS Genetics Topic page

This article has been expanded with content from under a CC BY license from doi:10.1371/journal.pgen.1008456(earlier drafts provenance) so should be compatible with Wikipedia's licenses. T.Shafee(Evo&Evo)^talk 00:15, 18 December 2019 (UTC)[reply]

(Copied from WT:MOLBIO#Topic_Page_on_Nucleoid) The article in PLOS Genetics is titled "Architecture of the Escherichia coli nucleoid" as one of the reviewers pointed out that all of the information presented was specific to E. coli. However since the previous Nucleoid article in Wikipedia almost all that is known about nucleoids comes from E. coli. My inclination is that it is still most logical to integrate the info into Nucleoid, since 1) pretty much everything that's known about nucleoids comes from E. coli and 2) the previous start-class article also only discussed E. coli so would be odd for that to be the general Wikipedia page, with separate page on "E. coli nucleoid". However I'd be interested in others' thoughts on this. Some of the figure captions are also pretty long, so could do with a significant trim. T.Shafee(Evo&Evo)^talk 00:47, 18 December 2019 (UTC)[reply]

[1] Margulis, L (2005) Hans Ris (1914-2004). Genophore, chromosomes and the bacterial origin of chloroplasts. Int Microbiol. 8(2):145-8.

[1]