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New WPI and CDC XMRV sequences in genbank

Discussion in 'XMRV Research and Replication Studies' started by Bob, May 17, 2011.

  1. barbc56

    barbc56 Senior Member

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    Eco, I missed this. Interesting.

    @Alex. BB, Bob, et. al.

    It appears people are confusing not believing in XMRV in our illness with being negaive, a denialist and also not wanting people to post about XMRV when nothing could be further from the truth.

    Barb. C. :>)
  2. natasa778

    natasa778 Senior Member

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    When I don't believe something is linked to my illness I don't read those posts or visit those threads, or get in any way involved unless topics crop us somewhere in passing. That is sort of a natural path, no? If you don't believe XMRV or anything similar is involved in 'your' illness why on earth are you reading here and posting same questions and comments over and over and over and over again?
    Bob likes this.
  3. barbc56

    barbc56 Senior Member

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    Just because I don't believe xmrv is involved in my illness, it would be silly to not keep up with what is going on. If someone reading is on the fence or doesn't know all the sides of the story, I hope we can all contribute to show all the different perspectives of this topic.

    I try to read as many topics as possible. I also want to be an informed consumer. I've learned a lot from reading all sorts of threads. Someone with a different opinion might make me pause and think about a subject in more detail.

    No one on this board should be asked why they post. IMHO, it's rather rude and if someone has teh evul intentions, they won't say so. This makes it kind of a moot point.

    But I think we need to get back on topic or make a separate thread.

    Over and out. :>)
  4. barbc56

    barbc56 Senior Member

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    I can see from the blast why you are saying the JHK virus is not related. What does that mean in practical terms in relation to our illnes? I may have missed this as we seem to be off topic so maybe I need to read this thread from the beginning. :rolleyes:

    Thanks.

    Barb. C. :>)
  5. RRM

    RRM

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    It would be pretty simple for you and the others to "solve" the problem I've seen discussed during the past previous pages: you can simply block individual users. The fact that this isn't being done, indicates that it's not just about discussing the matter with like-minded people. Discussing things in an open forum is just as much about spreading your ideas, and in this context (mis)information can, and should be critiqued.

    And critique is a good thing. Consider this recent topic for instance. The exact same "BWG thoughts" were posted on another forum almost two months ago, where only proponents posted. Aside from one poster who made a general comment about coding, nobody really questioned any of the three main arguments. However, when you look at responses to the post on this site, you'll see that of the three arguments, one was factually totally wrong (the non-sequencing of cultures, as Ruscetti opted not to do PCR after culture but WB), one was contradicted by pretty compelling evidence (the sequence data from the two healty controls didn't match the sequence data from the spiked controls), while the remaining argument (about the 30% positivity rate) could be reasonable explained by another mechanism.

    Now, regardless if you agree with all of these counterarguments (I'd say it's pretty hard not to in at least two instances), I would argue that you should be glad that you are visiting a site where not every pro-argument is swallowed hook, line and sinker. Even if you wouldn't agree with (some of) my points in the above example, it would still be a good thing that you have considered my arguments and found them to be worthless - it would make your opinion that the original post was correct more valuable than without considering them.

    I could again argue about this all day, but as nobody has said it better than J.S. Mill (although he used quite a lot of words also ;)):

    Sam Carter and Firestormm like this.
  6. RRM

    RRM

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    Basically, the JHK sequence was seen by some as evidence that XMRV is more diverse than previously thought, and more diverse than could reasonably be explained by its creation in a cell line in the early nineties. The problem with the argument can be illustrated with the following joke:

    Q: How many legs does a dog have if you call the tail a leg?
    A: Four. Calling a tail a leg doesn't make it a leg.

    Although Grossberg called his JHK isolate "XMRV" in its Genbank entry, it wasn't. Another scientist (I presume A.D. Miller) called this to Grossberg's attention and Grossberg subsequently corrected it in Genbank.

    In pratical terms, it means that some thought the JHK finding had something to do with the ME/CFS findings (though, rather indirectly), but it appears that it doesn't.
    Sam Carter and Firestormm like this.
  7. barbc56

    barbc56 Senior Member

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    Thanks.

    Thanks RRM. I went through this thread again and found some posts that helped me understand some of this. I may have left out some of the numbers of the posts but will come back and do that. Thanks to all who contributed these. I am sure there are some that I missed.

    http://phoenixrising.me/?p=5568

    Eco's posts #35.

    TWIV #136

    http://www.ncbi.nlm.nih.gov/nuccore/JF274252.1

    #108-
    Post #108

    JHK-3 BLAST.pdf?

    Now, I will include your above two posts. #145 and 146.

    The quote you have above by Abraham Lincoln was my signature on another forum, LOL!! ;)

    I like the other quote. It would be a good one to put on my office wall. (read desk at home with a bulleting board next to it.):D

    Barb C.:>)
    Firestormm likes this.
  8. Firestormm

    Firestormm Senior Member

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    Is there a link to this naming/renaming of JHK development at all? Just wondering how one has come by the information. Not doubting it but would like a look-e-loo if I may :D

    Not that I understand sequencing!
  9. bullybeef

    bullybeef Senior Member

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    But the JHK virus was isolated from a patient with ME in 1989:

    See: http://www.patentstorm.us/patents/5827750/description.html?forumid=331851



    Obviously JHK isn't VP62 which seems to mean XMRV when it is used in negative publications, so Grossberg probably means JHK is a human gamma retroviral variant. His Genbank entry still clearly states the organism is "XMRV", but it is of the JHK-3 strain: http://www.uniprot.org/uniprot/G0WKJ6


    And regardless of whether it is a XMRV, it is still a retrovirus that was isolated from a patient with ME over 20 years ago, yet only added to Genbank in Oct 2011. Based upon this, the US government have been quite happy to allow this discovery to remain without the need of "replication" (or rather another scientist loosely attempting to validate the discovery) or retraction. In other words, they have been aware for sometime people with ME are carrying a retrovirus, something that also ties in with EBV.


    And knowing that ME was first coined Chronic EBV in the US in the 1980s, that has too much of a coincidence.
  10. Jemal

    Jemal Senior Member

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    And JHK is still a MLV, right?
  11. Bob

    Bob

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    Hopefully this sort of pathogen would pop up in Lipkin's non-XMRV study, if it's in many ME patients.
  12. bullybeef

    bullybeef Senior Member

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  13. Jemal

    Jemal Senior Member

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    Yeah, thanks. I noticed that title in Genbank as well. I was checking to see if there's still discussion if this virus is even MLV related or not (checking to see if there's agreement/disagreement).
  14. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

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    The problem with the RRM's argument can be illustrated with the following:

    Q: How many XMRVs does a me/cfs patient have?
    A: One, if we call all MLVs/MRVs XMRV, hundreds if we call them JHK-3, VP42, S-162, etc
    A2: None, if we look only for VP-62, and don't bother looking in tissue for any MLVs




    This quote is unchanged from 2009, and most likely paraphrased from his 1997 paper, which is pre the XMRV Science paper, or at least the very early days. He changed the genbank entry to XMRV late last year, so he at least thought it was XMRV for quite a long time. The reasons for his turnabout in the last few weeks are unknown.

    Note sure who made this statement, but it doesn't necessary follow from the Grossberg quote.

    All other information on the patent remains the same, so most probably a problem with nomenclature.

    JHK-3 is a gammaretrovirus. It was found only in the blood of a me/cfs patient, not in the blood of a normal control, nor to my knowledge in cell lines as a contaminant as yet.

    Sorry, while I was compiling, other posts came in... some repetition.
  15. RRM

    RRM

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    No. That is not a genuine Genbank link. Your link, which gets its information from Genbank, has apparently not been updated to reflect the January 18th change. This is the correct Genbank link (also for Firestormm):

    http://www.ncbi.nlm.nih.gov/nuccore/330687872
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  16. bullybeef

    bullybeef Senior Member

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    It does look like Grossberg has modified his entry on Jan 19th 2012 to remove "XMRV" (which is fine because when they use "XMRV" they really mean VP62, and in that sense "XMRV" is dead, in fact it has never been alive in nature), and replaced it with MLV-related JHK human retrovirus.
    See: http://www.ebi.ac.uk/cgi-bin/sva/sv...ION28813-1327317397-1&index=0&view=1409200631


    So little change there then. ;) Still looks like a HGRV to me. :D
    RL_sparky likes this.
  17. Bob

    Bob

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    I thought JHK has been found in a cell line bullybeef? Are you saying that the specific strain JHK-3 hasn't been found in a cell line yet?
  18. RRM

    RRM

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    A classic strawman. I have never said that XMRV is defined by VP62 or any other single sequence. I have never said that people should only look for VP62 (or only in tissue, but I don't see what that has to do with the discussion anyway).

    Calling something XMRV just doesn't make it so. That is a simple fact.

    This is not XMRV, not because I don't want it to be, or not because Grossberg decided not to call it XMRV, but because known XMRV sequences cluster together and this sequence clusters somewhere else on a phylogenetic tree. It means they are distinct findings. It's basically the same as with Lo's sequences. Although they were similar to XMRV, one could not have reasonably evolved into the other into a relatively short period of time, and therefore they are disctinct. And therefore they reflect, if true at all, different infections.
    Sam Carter and Firestormm like this.
  19. bullybeef

    bullybeef Senior Member

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    According to the study, the JHK-3 strain is from the human B-lymphoblastoid cell line, Bob: http://www.ncbi.nlm.nih.gov/pubmed?term=Grossberg SE jhk


    Also see: http://www.patentstorm.us/patents/5827750/description.html?forumid=331851

    RL_sparky likes this.
  20. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

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    The operative word is 'contaminant'. As far as I know Raisch found a C virus in a cell line which may be the same. Grossberg later claims it came from an me/cfs patient.

    At the moment, the contamination folk are pinning their argument on the fact that because they haven't found the virus in us, it must either be a lab artifact or in mice. As far as I know, none of the strains referred to in the prior posts have been found in mice. Yet it is pseudotyping like crazy in cell lines in labs.

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