Author Topic: New sequences published  (Read 8194 times)

bakercape

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Re: New sequences published
« Reply #30 on: May 18, 2011, 01:26:09 AM »
Didn't Coffin just try to say the new genbank sequences variation could be blown of as just the variation you would see through multiple culture runs or something like that. I thought I heard that somewhere.  Does this ring a bell and is that even possible?

It seems they are running out of stuff to throw at the wall and it's getting close to checkmate.  Is the vice tightening on these denialists or am I getting overly optimistic?
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Tango

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Re: New sequences published
« Reply #31 on: May 18, 2011, 01:27:19 AM »
Didn't Coffin just try to say the new genbank sequences variation could be blown of as just the variation you would see through multiple culture runs or something like that. I thought I heard that somewhere.  Does this ring a bell and is that even possible?

It seems they are running out of stuff to throw at the wall and it's getting close to checkmate.  Is the vice tightening on these denialists or am I getting overly optimistic?

He said the ones in there before.

Coffin has nothing but a grave being dug out for him by him.
« Last Edit: May 18, 2011, 01:29:23 AM by v99 »
"I suspect there have been a number of conspiracies that never were described or leaked out. But I suspect none of the magnitude and sweep of Watergate." Woodward

"I would favor any name that does not impose (or give the appearance of imposing) taxonomic preconceptions on the nomenclature." Coffin

cassea

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Re: New sequences published
« Reply #32 on: May 18, 2011, 01:28:15 AM »
I have only heard Virology blog say that they are different viruses.

and Coffin maybe? You know, the "it might be another retrovirus you've found, just not XMRV"

Tango

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Re: New sequences published
« Reply #33 on: May 18, 2011, 01:29:57 AM »
and Coffin maybe? You know, the "it might be another retrovirus you've found, just not XMRV"

That was only about XMRV.  There are no ideas around the Lo/Alter study.
"I suspect there have been a number of conspiracies that never were described or leaked out. But I suspect none of the magnitude and sweep of Watergate." Woodward

"I would favor any name that does not impose (or give the appearance of imposing) taxonomic preconceptions on the nomenclature." Coffin

Gerwyn

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Re: New sequences published
« Reply #34 on: May 18, 2011, 07:41:18 AM »
 i did not expect the sequences to demonstrate such a high level of variation

Daisymay

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Re: New sequences published
« Reply #35 on: May 18, 2011, 09:39:13 AM »
So.............. this high level of variation which can't be explained by Coffin's multiple culture runs I take it(?) seriously dents the contamination theory, i would have thought irrevocably or am I wrong, is that just my ignorance and wishful thnking!


Plus of course the immune profile paper

Tango

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Re: New sequences published
« Reply #36 on: May 18, 2011, 10:35:57 AM »
Yes.  I'm surprised too. 

Now we need to start getting clinical trials.
"I suspect there have been a number of conspiracies that never were described or leaked out. But I suspect none of the magnitude and sweep of Watergate." Woodward

"I would favor any name that does not impose (or give the appearance of imposing) taxonomic preconceptions on the nomenclature." Coffin

Daisymay

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Re: New sequences published
« Reply #37 on: May 18, 2011, 11:29:18 AM »
i did not expect the sequences to demonstrate such a high level of variation

Why Gerwyn and V99, because XMRV replicates slowly? because we've been led to belief it is a comparatively new  human retrovirus ?

Why do you say that Gerwyn and V, not questioning you, just wanting to know why......

Gerwyn

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Re: New sequences published
« Reply #38 on: May 18, 2011, 11:40:01 AM »
Why Gerwyn and V99, because XMRV replicates slowly? because we've been led to belief it is a comparatively new  human retrovirus ?

Why do you say that Gerwyn and V, not questioning you, just wanting to know why......

it looks like they are different strains but have not looked really closely. It just took me by surprise .I was looking for evidence why optimising a PCR assay using a clone is such an assenine thing to do when RNA viruses replicate using a low fidelity enzyme. I found a lot more variation than I expected because gammaretroviral reverse transcriptases are supposed to result in less mutations than HIV reverse transcriptase.

Dr. Yes

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Re: New sequences published
« Reply #39 on: May 18, 2011, 11:44:16 AM »
Haven't checked more than a couple of them - which sequences (accession numbers) are you guys seeing the variation in, and variation relative to what?


 
« Last Edit: May 18, 2011, 11:46:27 AM by Dr. Yes »
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SamIAm

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Re: New sequences published
« Reply #40 on: May 18, 2011, 11:50:11 AM »


WPI sequences -- where is this variation?
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Gerwyn

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Re: New sequences published
« Reply #41 on: May 18, 2011, 12:05:34 PM »


WPI sequences -- where is this variation?


hello samiam I wondered when you would show  up  these are two of them


1 gcagcactgg gggagtgtcc agcgcattgc atccaaccag tctgtggatg tcaagaagag
       61 gcgctgggtt accttctgtt ccgccgaatg gccaactttc aatgtaggat ggcctcagga
      121 tggtactttt aatttaggtg ttatctctca ggtcaagtct agagtgtttt gtcctggtcc
      181 ccacggacac ccggatcagg tcccatatat cgtcacctgg gaggcacttg cctatgaccc

      241 ccctccgtgg gtcaaaccgt ttgtctctcc taaaccccct cctttaccga cagctcccgt
      301 cctcccgccc ggtccttctg cgcaacctcc gtcccgatct gccctttacc ctgcccttac
      361 ccactc
1 agcactgggg agatgtccag cgcattgcat ccaaccagtc tgtggatgtc aagaagaggc
       61 gctgggttac cttctgttcc gccgaatggc caactttcaa tgtaggatgg cctcaggatg
      121 gtacttttaa tttaggtgtt atctctcagg tcaagtctag agtgttttgt cctggtcccc
      181 acggacaccc ggaccaggtc ccatatatcg tcacctggga ggcacttgcc tatgaccccc

      241 ctccgtgggt caaaccgttt gtctctccta aaccccctcc tttaccgaca gctcccgtcc
      301 tcccgcccgg tccttctgcg caacctccgt cccgatctgc cctttaccca aa

this makes it a bit easier to see

181 ccacggacac ccggatcagg tcccatatat cgtcacctgg gaggcacttg cctatgaccc

181 acggacaccc ggaccaggtc ccatatatcg tcacctggga ggcacttgcc tatgaccccc





Tango

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Re: New sequences published
« Reply #42 on: May 18, 2011, 12:15:45 PM »
Isn't it interesting that those letter combinations don't appear in the pretty picture for sequences 1301 and 1302
"I suspect there have been a number of conspiracies that never were described or leaked out. But I suspect none of the magnitude and sweep of Watergate." Woodward

"I would favor any name that does not impose (or give the appearance of imposing) taxonomic preconceptions on the nomenclature." Coffin

fds66

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Re: New sequences published
« Reply #43 on: May 18, 2011, 12:26:00 PM »
any possibility that hypermutation is causing the differences in the ones from the blood samples? Vaguely remember a paper by Patroka (sp?) describing APOBEC3 and Judy Mikovits also mentioned it I think. Haven't looked at the sequences. What differences does hypermutation make - I seem to remember seeing G->A? All vague and possibly irrelevant too. Ignore me if it doesn't help.

Gerwyn

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Re: New sequences published
« Reply #44 on: May 18, 2011, 12:30:57 PM »
any possibility that hypermutation is causing the differences in the ones from the blood samples? Vaguely remember a paper by Patroka (sp?) describing APOBEC3 and Judy Mikovits also mentioned it I think. Haven't looked at the sequences. What differences does hypermutation make - I seem to remember seeing G->A? All vague and possibly irrelevant too. Ignore me if it doesn't help.

sure a possibility  different strains a possibility either way its a replicating retrovirus and not a contaminant of any sort