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Author Topic:   Quick Questions, Short Answers - No Debate
Wounded King
Member (Idle past 90 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 65 of 653 (454038)
02-05-2008 9:48 AM


What's that you say Dr.A?
Dr.A writes:
What Happens When A Ribosome Translates mRNA Lacking A Stop Codon?
Such transcripts are called 'nonstop' and they are targeted for degradation when they cause the ribosome to hang in the absence of a termination codon.
The mechanisms of degradation are different in prokaryotes and eukaryotes.
TTFN,
WK

Replies to this message:
 Message 67 by Dr Adequate, posted 02-07-2008 9:11 AM Wounded King has replied

  
Wounded King
Member (Idle past 90 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 69 of 653 (454502)
02-07-2008 11:28 AM
Reply to: Message 67 by Dr Adequate
02-07-2008 9:11 AM


Re: What's that you say Dr.A?
Thanks. That seems to conflict with the idea I'd picked up that frameshift mutations are less harmful near the end of the gene. 'Cos the nearer the end of the gene they are, the more likely it is that the frameshift will make the thing nonstop.
Well it wouldn't necessarily make it much more likely to have a 'nonstop' transcript in any case as there is still a high likelihood there will be a new stop site introduced by the frameshift either in the remaining coding sequence or in the 3' untranslated region.
TTFN,
WK

This message is a reply to:
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Wounded King
Member (Idle past 90 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 84 of 653 (456982)
02-21-2008 4:16 AM
Reply to: Message 83 by Dr Adequate
02-20-2008 7:31 PM


Re: More Genetics
1) '5 prime' and '3 prime'
2) Personally I'd pronounce it 'Aims'.
3) As far as I can tell they are homologous to the extent that the spliceosomal introns are thought to be derived from self-splicing group II introns. I don't know to what extent they are homologous in terms of actual sequence similarity however.
TTFN,
WK

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Wounded King
Member (Idle past 90 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 109 of 653 (497662)
02-05-2009 12:08 PM
Reply to: Message 108 by Blue Jay
02-05-2009 10:52 AM


Re: Mutation Rates
We had a quite lengthy thread that had mutation rates as part of one of Mark Kennedy's threads on Genetics and Human Brain Evolution
The ~100 figure I got from a paper by Kondrashov (2003), who says 'the total number of new mutations per diploid human genome per generation is ~100'. There are other methods used to estimate mutation rates than those Kondrashov suggests and they all give slightly different rates.
TTFN,
WK

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Wounded King
Member (Idle past 90 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 145 of 653 (522343)
09-02-2009 4:21 PM
Reply to: Message 141 by Taz
09-02-2009 3:44 PM


Shameless fanboyism
Are you sure you aren't thinking thinking of the plot of the Doctor Who adventure 'State of Decay'?
Totally understandable, that's a great story.
TTFN,
WK

This message is a reply to:
 Message 141 by Taz, posted 09-02-2009 3:44 PM Taz has replied

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Wounded King
Member (Idle past 90 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 149 of 653 (522372)
09-03-2009 3:41 AM
Reply to: Message 148 by Dr Adequate
09-03-2009 2:38 AM


Re: Bacteria Evolving Loss Of Function --- Example Please?
This also isn't exactly what you were looking for ...
Bizzarri et al. 2008 writes:
Four strains of B. thuringiensis, which had been isolated in vegetative form from leaf surfaces, were grown for 500 generations in batch culture in a rich medium. One of the strains, S4g, differed from the parent in the following respects: greater cell width; changed plasmid profile; complete loss of ability to produce delta-endotoxins; loss of ability to produce beta-exotoxin and disruption of vip3 gene; radically different fatty acid composition; and altered metabolic activity. Two of the other evolved strains (S1g and S6g) showed differences in fatty acid profiles compared with the parents. Genetic finger-printing showed that there were also mutations in the cry genes of two of the evolved strains (S1g and S2g). The delta-endotoxins of strain S6g were significantly less toxic to the larvae of Pieris brassica compared with those of the parent and it also differed in the plasmid content.
In this paper (Bizzarri et al, 2008) what the bacteria lose is not metabolic functions associated with vital function as much as those associated with toxicity to insects which eat the bacterias normal hosts.
One of the Lenski lab's long term evolution papers was on this topic (Cooper and Lenski, 2000) and may be more along the lines you were looking for.
Cooper and Lenski writes:
We analysed the decay of unused catabolic functions in 12 lines of Escherichia coli propagated on glucose for 20,000 generations. During that time, several lines evolved high mutation rates11. If mutation accumulation is important, their unused functions should decay more than the other lines, but no significant difference was observed. Moreover, most catabolic losses occurred early in the experiment when beneficial mutations were being rapidly fixed, a pattern predicted by antagonistic pleiotropy. Thus, antagonistic pleiotropy appears more important than mutation accumulation for the decay of unused catabolic functions in these populations.
Unfortunately they don't identify the specific mutations involved in this paper. Another paper however does go into the molecular genetic details of the loss of ribose catabolism (Cooper et al., 2001). Interestingly they find this loss associated with increased fitness.
Cooper et al. writes:
At the molecular level, the loss of ribose catabolic function involved the deletion of part or all of the ribose operon (rbs genes). The physical extent of the deletion varied between mutants, but each deletion was associated with an IS150 element located immediately upstream of the rbs operon. The deletions apparently involved transposition into various locations within the rbs operon; recombination between the new IS150 copy and the one upstream of the rbs operon then led to the deletion of the intervening sequence. To confirm that the beneficial fitness effect was caused by deletion of the rbs operon (and not some undetected mutation elsewhere), we used P1 transduction to restore the functional rbs operon to two Rbs(-) mutants, and we constructed another Rbs(-) strain by gene replacement with a deletion not involving IS150. All three of these new constructs confirmed that Rbs(-) mutants have a competitive advantage relative to their Rbs(+) counterparts in glucose minimal medium.
TTFN,
WK

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 Message 148 by Dr Adequate, posted 09-03-2009 2:38 AM Dr Adequate has not replied

  
Wounded King
Member (Idle past 90 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 159 of 653 (617934)
05-31-2011 4:52 PM
Reply to: Message 156 by New Cat's Eye
05-31-2011 2:08 PM


Re: sweet phylogenic tree
Best place is probably in the Links and Information forum.
TTFN,
WK

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Wounded King
Member (Idle past 90 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 206 of 653 (635869)
10-02-2011 1:53 PM
Reply to: Message 205 by RAZD
10-02-2011 12:51 PM


Re: Chat forum?
The difference is in timing, a live chat session is quite different from an ongoing discussion on a message board. To get the same sort of experience on a normal EVC thread all the participants would need to be clicking on refresh about once a second.
TTFN,
WK

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Wounded King
Member (Idle past 90 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 209 of 653 (635903)
10-02-2011 7:34 PM
Reply to: Message 208 by Larni
10-02-2011 6:08 PM


Re: Chat
Well like Jar says, it wouldn't be hard to arrange an IRC channel somewhere that people could use until there is a formal chat system.
TTFN,
WK

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Wounded King
Member (Idle past 90 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 273 of 653 (655203)
03-08-2012 4:14 PM
Reply to: Message 272 by foreveryoung
03-08-2012 4:09 PM


Re: searching online through the literature
It might help if you specified what the field is you are researching. There are a number of niche resources out there and while I would feel confident giving someone advice on searching the biomedical literature I would be a lot less sure for disciplines such as geography or physics.
TTFN,
WK

This message is a reply to:
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