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This is an old revision of this page, as edited by Adrian J. Hunter (talk | contribs) at 11:58, 1 March 2017 (→mouse code: response - not seeing any problem). The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

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I have copied part of this into genetic code so this atm is repeated. but I will expand on it soon. so plz do not delete. --Squidonius (talk) 21:14, 13 October 2009 (UTC)[reply]

expanded (forgot to log in though)--Squidonius (talk) 12:50, 16 October 2009 (UTC)[reply]


Removed for lack of clarity

Removed "from the existing 20 to a theoretically possible 172," because it is not clear what the 20 refers to (though it probably means the 20 amino acids expressed by the standard code) or where the theoretically possible 172 comes from. If the same redundancy as the current codes were used an expansion of about a factor of four might be expected, for example. It is probable that the 172 is based on expanding the existing 64 codes to 216 giving an additional 152 codes, which if they were mapped uniquely to new AAs would yield a total of 172 AAs. It is not clear, however, with the massive re-engineering of the transcription machinery required, why the redundancy in the existing code need be preserved, nor indeed the coding length of 3. All the best: Rich Farmbrough, 01:31, 28 August 2014 (UTC).

Query

First, a thanks. I created this page over five years ago, but I haven't touched it since. I am glad it is in a good shape and bold edits are contested. Today, I was hoping to give it focus and update it with recent literature (in procrastination from writing a grant), but got stopped midway. I promise I'll do it soon. I was partially surprised that my edit got reverted. In it's current form it has a repetition (there are 20 amino acids) and lacks a summary of the how it is done conceptually and what the articles covers, so I will fix it. I will add reference, but I was hoping to build on my previous edit. I assume it wasn't a needs references issue, right? Two issues I see that are problematic are (i) choice of the usage of terms standard and nonstandard, and (ii) the claim that UAG recoding is the most prominent. --Squidonius (talk) 05:12, 2 February 2015 (UTC)[reply]

lead

Squidonius please stop adding content to the lead that is not in the body. please see WP:LEAD. Please improve the body first, and if what you add is important enough to add to the lead, then do it afterwards, after reviewing the whole article. thanks. Jytdog (talk) 00:17, 3 February 2015 (UTC)[reply]

Thank you for your concerns. I was planning on editing the body accordingly —I was just starting from the top as one does.
The article needs structure (hence the lead), focus and a more rounded coverage: at its current state it has as much focus as an undergraduate essay —I'll admit I am partly to be blamed (it is a partial transplant of a lit review).
Parenthetically, I would like to stress that I know what I am doing: I haven't been active for a long while on wikipedia, but I am not a new user, in fact I have done many bold edits (e.g. I untangled the mess that used to E. coli and split it into three articles) and, in real life, I have authored several peer-reviewed papers, so I know how to make a story coherent.
Therefore, in conclusion, I would like to know if you are okay with my editing this article and would really appreciate any suggestion or help.
really, please actually read WP:LEAD. it is not logical to start with the lead. The lead should be the last thing you do if you want to update an article. The lead just summarizes the body, and you cannot summarize something from the body if it isn't there yet. Right? And weight in the lead, should reflect weight in the body. And you cannot know the weight something has in the body if it isn't there yet, either. Jytdog (talk) 02:42, 3 February 2015 (UTC)[reply]
but of course!!! please be bold. please also use secondary sources, not primary ones. WP is not a scientific review article. Thanks! Jytdog (talk) 02:43, 3 February 2015 (UTC)[reply]

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mouse code

In this section

Orthogonal sets in mammalian cells
   tRNATyr-TyrRS pair from Bacillus stearothermophilus[41]
   modified tRNATrp-TrpRS pair from Bacillus subtilis trp[42]
   tRNALeu–LeuRS pair from Escherichia coli[43]
   tRNAAmber-PylRS pair from the archaeon Methanosarcina barkeri and Methanosarcina mazei

41, 42 and 43 are primary sources. The last one is unsourced. I added an important primary source. @Jytdog: reverted it. I am going to insert it again. I was thanked by one experienced user for the original edit. I would like to hear comments fom the community about this brewing edit conflict. @Adrian J. Hunter: Thanks, DennisPietras (talk) 16:04, 24 February 2017 (UTC)[reply]

It is great that you want to improve the article. Rather than arguing in favor of a low quality edit by pointing out the results of other low quality edits, why not improve the article by adding better refs? The specific issue as I noted in my edit notes was WP:NOTNEWS and the primary source. Adding content about hot off the presses science is unwise in an encyclopedia; we have no deadline here, and papers are sometimes retracted and often just ignored. As an example, remember that scientist who published work showing that if you shake cells (really!) you could turn them into stem cells? There was huge media hype around that. And yep, people rushed to add content based on the hyped primary source to WP. (Note the edit date, and the date the paper came out) only to delete it later when the paper was retracted. (We actually have a whole article on that mess Stimulus-triggered acquisition of pluripotency) We should not be jerking the public around like that. There is no reason to do that - we have no deadline here. Jytdog (talk) 16:08, 24 February 2017 (UTC)[reply]
@Jytdog: et al. I am going to wait for other comments about this debate before I act further. However, to make it easier for people to see the text in question, here it is...
Sorry to keep you waiting, DennisPietras.
I don't see any material difference between the line DennisPietras added and the other content in nearby sections, so I don't see any point discussing that edit specifically – either we want everything in those sections (including DennisPietras' addition), or we want to get rid of the entire sections. Here are the sections I'm referring to:
Extended content

Orthogonal sets in E. coli

The orthogonal pairs of synthetase and tRNA that work for one organism may not work for another, as the synthetase may mis-aminoacylate endogenous tRNAs or the tRNA be mis-aminoacylated itself by an endogenous synthetase. As a result, the sets created to date differ between organisms.

  • tRNATyr-TyrRS pair from the archaeon Methanococcus jannaschii
  • tRNALys–LysRS pair from the archaeon Pyrococcus horikoshii[2]
  • tRNAGlu–GluRS pair from Methanosarcina mazei[3]
  • leucyl-tRNA synthetase from Methanobacterium thermoautotrophicum and a mutant leucyl tRNA derived from Halobacterium sp[4]
  • tRNAAmber-PylRS pair from the archaeon Methanosarcina barkeri and Methanosarcina mazei
  • tRNAAmber-3-Iodotyrosyl-tRNA synthetase (variant of aminoacyl-tRNA synthetase from Methanocaldococcus jannaschii)[5]

Orthogonal sets in yeast

  • tRNATyr-TyrRS pair from Escherichia coli[6]
  • tRNALeu–LeuRS pair from Escherichia coli[7]
  • tRNAiMet from human and GlnRS from Escherichia coli[8]
  • tRNAAmber-PylRS pair from the archaeon Methanosarcina barkeri and Methanosarcina mazei[9]
  • tRNAAmber-4,5-dimethoxy-2-nitrobenzyl-cysteinyl-tRNA synthetase[10]

Orthogonal sets in mammalian cells

  • tRNATyr-TyrRS pair from Bacillus stearothermophilus[11]
  • modified tRNATrp-TrpRS pair from Bacillus subtilis trp[12]
  • tRNALeu–LeuRS pair from Escherichia coli[13]
  • tRNAAmber-PylRS pair from the archaeon Methanosarcina barkeri and Methanosarcina mazei
  • In 2017 a mouse engineered with an extended genetic code that can produce proteins with unnatural amino acids was reported.[14]

References

  1. ^ Han, S.; et al. "Expanding the genetic code of Mus musculus". Nat. Commun. 8. doi:10.1038/ncomms14568. {{cite journal}}: Explicit use of et al. in: |last1= (help)
  2. ^ Anderson, J.C.; Wu, N.; Santoro, S.W.; Lakshman, V.; King, D.S.; Schultz, P.G. (2004). "An expanded genetic code with a functional quadruplet codon". Proc Natl Acad Sci USA. 101 (20): 7566–7571. Bibcode:2004PNAS..101.7566A. doi:10.1073/pnas.0401517101. PMC 419646. PMID 15138302.
  3. ^ Santoro, S.W.; Anderson, J.C.; Lakshman, V.; Schultz, P.G. (2003). "An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli". Nucleic Acids Res. 31 (23): 6700–6709. doi:10.1093/nar/gkg903. PMC 290271. PMID 14627803.
  4. ^ Anderson, J.C.; Schultz, P.G. (2003). "Adaptation of an orthogonal archaeal leucyl-tRNA and synthetase pair for four-base, amber, and opal suppression". Biochemistry. 42 (32): 9598–9608. doi:10.1021/bi034550w. PMID 12911301.
  5. ^ Minaba, Masaomi; Kato, Yusuke (2013). "High-Yield, Zero-Leakage Expression System with a Translational Switch Using Site-Specific Unnatural Amino Acid Incorporation". Applied and Environmental Microbiology. 80 (5): 1718–1725. doi:10.1128/AEM.03417-13.
  6. ^ Chin, J.W.; Cropp, T.A.; Anderson, J.C.; Mukherji, M.; Zhang, Z.; Schultz, P.G. (2003). "An expanded eukaryotic genetic code". Science. 301 (5635): 964–967. Bibcode:2003Sci...301..964C. doi:10.1126/science.1084772. PMID 12920298.
  7. ^ Wu, N.; Deiters, A.; Cropp, T.A.; King, D.; Schultz, P.G. (2004). "A genetically encoded photocaged amino Acid". J Am Chem Soc. 126 (44): 14306–14307. doi:10.1021/ja040175z. PMID 15521721.
  8. ^ Kowal, A.K.; Kohrer, C.; RajBhandary, U.L. (2001). "Twenty-first aminoacyl-tRNA synthetase–suppressor tRNA pairs for possible use in site-specific incorporation of amino acid analogues into proteins in eukaryotes and in eubacteria". Proc Natl Acad Sci USA. 98 (5): 2268–2273. Bibcode:2001PNAS...98.2268K. doi:10.1073/pnas.031488298. PMC 30127. PMID 11226228.
  9. ^ Hancock, S. M.; Uprety, R; Deiters, A; Chin, J. W. (2010). "Expanding the genetic code of yeast for incorporation of diverse unnatural amino acids via a pyrrolysyl-tRNA synthetase/tRNA pair". Journal of the American Chemical Society. 132 (42): 14819–24. doi:10.1021/ja104609m. PMC 2956376. PMID 20925334.
  10. ^ Kang, Ji-Yong (2013). "In vivo Expression of a Light-activatable Potassium Channel Using Unnatural Amino Acids". Neuron. 80: 358–370. doi:10.1016/j.neuron.2013.08.016.
  11. ^ Sakamoto, K.; Hayashi, A.; Sakamoto, A.; Kiga, D.; Nakayama, H.; Soma, A.; Kobayashi, T.; Kitabatake, M.; et al. (2002). "Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells". Nucleic Acids Res. 30 (21): 4692–4699. doi:10.1093/nar/gkf589. PMC 135798. PMID 12409460. {{cite journal}}: Explicit use of et al. in: |first9= (help)
  12. ^ Zhang, Z.; Alfonta, L.; Tian, F.; Bursulaya, B.; Uryu, S.; King, D.S.; Schultz, P.G. (2004). "Selective incorporation of 5-hydroxytryptophan into proteins in mammalian cells". Proc. Natl. Acad. Sci. USA. 101 (24): 8882–8887. Bibcode:2004PNAS..101.8882Z. doi:10.1073/pnas.0307029101. PMC 428441. PMID 15187228.
  13. ^ Wang, W.; Takimoto, J.; Louie, G.V.; Baiga, T.J.; Noel, J.P.; Lee, K.F.; Slesinger, P.A.; Wang, L. (2007). "Genetically encoding unnatural amino acids for cellular and neuronal studies". Nat. Neurosci. 10 (8): 1063–1072. doi:10.1038/nn1932. PMC 2692200. PMID 17603477.
  14. ^ Han, S.; et al. "Expanding the genetic code of Mus musculus". Nat. Commun. 8. doi:10.1038/ncomms14568. {{cite journal}}: Explicit use of et al. in: |last1= (help)
Rarely do I find myself in disagreement with Jytdog, whose work in purging dreck from Wikipedia I respect tremendously, but I'm not seeing any problem with this section. I don't think the intention behind WP:NOTNEWS is to prevent primary sources being used until some amount of time has passed; that part of policy even says "editors are encouraged to include current and up-to-date information within [Wikipedia's] coverage." Rather, I think the salient policy is WP:PRIMARY. Said policy explicitly permits the use of primary sources with care, subject to several caveats, none of which I can see apply here. Use of primary sources to support individual lines in list-content is common in featured lists such as List of ant subfamilies, List of Armillaria species, and List of parasites of the marsh rice rat.
Regarding the Stimulus-triggered acquisition of pluripotency saga, I think it's problematic to let a single extraordinary event strongly influence the way we do day-to-day editing – hard cases make bad law. In any case, a reliance on secondary sources would not have kept all that out of Wikipedia, as the original Nature paper was rapidly (and with disappointing credulity) reported on by numerous reputable secondary sources, eg New Scientist, BBC, The Guardian. Adrian J. Hunter(talk•contribs) 11:57, 1 March 2017 (UTC)[reply]
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