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Retrovirology Publishes Five Papers on XMRV and Contamination

Discussion in 'XMRV Research and Replication Studies' started by Countrygirl, Dec 20, 2010.

  1. WillowJ

    WillowJ Senior Member

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    I think it goes like this:

    PCR is polymerase chain reaction. You can start with a small amount of genetic material (DNA or RNA) and keep multiplying copies so you get an amount large enough to do testing with. This is the point of PCR amplification. You put the genetic material and enzymes in a machine that cycles through stages with appropriate conditions for various stages of replication (copying).

    You have a primer which will have a sequence of nucleotides matching the a unique (or relatively unique, and unique in your sample) sequence in a specific thing you're looking for (XMRV, mouse mitochondria, a criminal suspect, pGLO, a particular genetic defect, whatever). You can make any sequence you desire, synthetically. You usually have another primer for the other end of whatever you're interested in.

    You put copies of the primer in with the double-stranded (or usually with doubled-over, depending on the virus) RNA (we'll say it's RNA because most viruses are RNA), enzymes, etc. You have a commercial kit which supplies the enzymes and such. The machine heats the RNA so that the parts where two strands (or two parts of the same strand) are bonded together, break apart (it's normally held together with non-covalent bonds, in this case hydrogen bonds). Then returns to a state where H-bonds are again allowed (and I think not too strongly). Now your primer can find a matching sequence on your target RNA and bind.

    An enzyme called RNA Polymerase (RNA Pol for short; DNA Pol if it's copying DNA) is what copies the RNA but it can't start from scratch; it needs something to grab hold of (as it would have in a live cell situation). This is another reason the primers are useful. So it starts copying from the edge of the primer and goes until it falls off the end of the molecule.

    Say unwanted parts of molecule are O, primer are P, desired portion D. (In real genetic material, you would see the sequence represented by the letters C,G,A, and T in DNA or C,G,A, and U in RNA), and matches would look like this:

    3'CGCUCGA5'
    5'GCGAGCU3'

    For simplicity, I'm going to match like this:

    OOOPPDDDPPO
    OOOPPDDDPPO

    please ignore the dashes (leading spaces aren't working) and spaces (not sure what makes those) and not-quite-matches

    Starting DNA:

    OOOOOOOOOPPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPPOOOOOOOOOOOOOOOOOOO
    OOOOOOOOOPPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPPOOOOOOOOOOOOOOOOOOO

    First cycle: (green is the copy)

    OOOOOOOOOPPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPPOOOOOOOOOOOOOOOOOOO
    -------------PPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPPOOOOOOOOOOOOOOOOOOO


    OOOOOOOOOPPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
    PPPPP
    OOOOOOOOOPPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPPOOOOOOOOOOOOOOOOOOO

    Second cycle: (purple is the new copy)

    OOOOOOOOOPPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPPOOOOOOOOOOOOOOOOOOO
    -------------PPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPPOOOOOOOOOOOOOOOOOOOO

    -------------PPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPP -------------PPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPPOOOOOOOOOOOOOOOOOO



    -------------PPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPPP
    OOOOOOOOOPPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPP

    OOOOOOOOOPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPP
    OOOOOOOOOPPPPPPDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDPPPPPOOOOOOOOOOOOOOOOOOO

    With all these loose ends, you can get strands stuck together that you didn't intend. Maybe if you didn't select your primers carefully, you could end up with fragments, or maybe there's recombining RNA/DNA, and thus the variations?
  2. oceanblue

    oceanblue Senior Member

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    Thanks, WillowJ; that's possible but how likely is it and how big an effect. And wouldn't it apply to everything sequenced after amplification by PCR, in which case it might apply equally to everything on the phylogenetic tree?
  3. Bob

    Bob

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    lol

    But this time there has been a mutiny against the British generals... The British footsoldiers have defected to the other side, leaving a small isolated group of desperate British generals standing alone against vast, and growing, American and British forces... I'm following the Yanks, led by General Mikovits!
  4. garcia

    garcia Aristocrat Extraordinaire

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    Try telling that to the Vietnamese and Afghans. :D:D:D

    Agree with you about the "silly brits" though.
  5. Snow Leopard

    Snow Leopard Senior Member

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    The other side of the contamination coin is the potential for cell cultures used for producing vaccines may also be contaminated.
  6. roma

    roma

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    when they found XMRV in prostate cancer the news were generally well accepted, but when they linked XMRV to ME/CFS is when the problems started, what I'm wondering is, did these people with prostate cancer have other health issues that haven't been mentioned? it would be interesting to know. Maybe some of them were ME/CFS patients to begin with..
  7. free at last

    free at last Senior Member

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    Lol Bob, general Mikovits, colonel Alter, captain Klein.

    private Wessley, private sharp, private white, Striped there ranks due to misconduct.
    Myra mclure the prison officer shouts no freedom for these renegades. General Mikovits orders her capure first, through interrogation, she spills the beans,and proceeds to admit, they was never trying to find xmrv from the beggining, it was a dog and pony show, weres George, he might want to interrogate further.
  8. free at last

    free at last Senior Member

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    Maybe Sophia Mirza contracted XMRV after the vaccinations, and the variouse viruses she was exposed to then let all hell break loose,Or maybe she already had it, but the vaccines triggered it into activation ? I WISH HER SPINAL FLUID COULD BE TESTED BY jUDY AND Alter
  9. Cloud

    Cloud Guest

    This has been my view all along. Looking at risk factors, transmission possibilities, the different modes of disease onset, and my own experience, I believe contaminated vaccine is the most likely source.

    My thoughts: Overachiever (chronic stress) is our dominant personality trait and supposedly xmrv loves cortisol. We have both clusters and isolated cases. Onset almost always follows Immune stress and trauma, but not always as an infection. And, we have government health agencies strongly resisting discovery of the cause of this illness. I did not have an infectious onset....it was triggered by stress and the Hep B vaccine. Since I had 25 years of excellent health prior to onset, whatever was triggered had most likely been there (latent) for many years. I believe I contracted xmrv one of 2 ways....vertically, or via contaminated vaccine in childhood. I lean heavily to the latter.



    Dr Judy has suggested vaccine as a trigger:

    "On that note, if I might speculate a little bit," she said, "This might even explain why vaccines would lead to autism in some children, because these viruses live and divide and grow in lymphocytes -- the immune response cells, the B and the T cells. So when you give a vaccine, you send your B and T cells in your immune system into overdrive. That's its job. Well, if you are harboring one virus, and you replicate it a whole bunch, you've now broken the balance between the immune response and the virus. So you have had the underlying virus, and then amplified it with that vaccine, and then set off the disease, such that your immune system could no longer control other infections, and created an immune deficiency."

  10. Dx Revision Watch

    Dx Revision Watch Suzy Chapman dxrevisionwatch.com

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    As published by the ME Association, today:

    http://www.meassociation.org.uk/?p=3628

    Retrovirology summary of the first international workshop on XMRV

    December 23, 2010

    The open access journal Retrovirology has published a 23-page summary of the first international workshop on XMRV which was held at Bethesda, Maryland , in September. The authors of the summary are Jonathan P Stoye, Robert H Silverman, Charles A Boucher and Stuart F J Le Grice, and the event was co-sponsored by the National Institutes of Health, the Department of Health and Human Services and Abbott Diagnostics.

    The abstract appears below:

    Review

    The Xenotropic Murine Leukemia Virus-Related Retrovirus Debate Continues at First International Workshop

    Jonathan P Stoye , Robert H Silverman , Charles A Boucher and Stuart FJ Le Grice

    Retrovirology 2010, 7:113doi:10.1186/1742-4690-7-113

    Published: 22 December 2010

    Abstract (provisional)

    The 1st International Workshop on Xenotropic Murine Leukemia Virus-Related Retrovirus (XMRV), co-sponsored by the National Institutes of Health, The Department of Health and Human Services and Abbott Diagnostics, was convened on September 7/8 on the NIH campus, Bethesda, MD. Attracting an international audience of over 200 participants, the 2-day event combined a series of plenary talks with updates on different aspects of XMRV research, addressing basic gammaretrovirus biology, host response, association of XMRV with chronic fatigue syndrome and prostate cancer, assay development and epidemiology. The current status of XMRV research, concerns among the scientific community and suggestions for future actions are summarized in this meeting report.

    The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.

    http://www.retrovirology.com/content/pdf/1742-4690-7-113.pdf
  11. Dx Revision Watch

    Dx Revision Watch Suzy Chapman dxrevisionwatch.com

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    Woah, Cloud. I'm not comfortable with statements like this that make sweeping generalizations about "personality traits" and alleged association with, or predictor of CFS and ME.

    Suzy
  12. WillowJ

    WillowJ Senior Member

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    Actually, I spoke too soon (good thing I wasn't talking to a newspaper :grin: ); I think the problem is more likely to be that while the Polymerase complex has a proofreading mechanism, in PCR you're in a cell-free system. But in the cell there are more proofreading mechanisms. So if a mistake gets past the proofreading, it won't be corrected like it would in a real situation.

    Yes, I have limited knowledge of various viruses and am going only off my general knowledge of PCR. Why it would affect one thing more than another I don't know. What he said was that it would arise from PCR, which was a general statement.

    Not sure where a phylogenetic tree comes in? PCR is an artificial system. We run PCR, do some lab tests, and then when we're through put the materials in an autoclave (complete sterilization via heat and pressure), freeze for later testing, or otherwise safely and carefully dispose of them. We don't return amplified material to a live system.
  13. Bob

    Bob

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    lol

    And don't forget private Reeves who has already been stripped of his rank and posted to do menial work due to associating with the enemy and general untrustworthiness...

    Pity the poor prisoners if George is let loose on them! I can hear him growling already!
  14. WillowJ

    WillowJ Senior Member

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    That's something that I agree we should look at: can we make our vaccines safer?

    The problem is, the CDC's default "don't panic the populace" mode will never allow them to consider whether vaccines can be made safer (you cannot get safer than "already safe enough! end of story!").

    Maybe the FDA and NIH can do this (check whether vaccines should and could be made safer); they have shown amenability to actual science and reason in recent months.
  15. lancelot

    lancelot Senior Member

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    yes, i am an overachiever, a perfectionist, type A, and i've worked very hard in my career, school, and gym. So are many of my high functioning friends and none of them have CFS. personality traits is not a reason for this disease. There is definitely a physical cause-possibly a smoldering retrovirus that takes 10-20 years to cause disease thereby affecting mainly 30-50yo. It's not like we can mentally or physically fight this disease. this disease is so devastating that it has knocked me to my knees and has broke my will.
  16. Esther12

    Esther12 Senior Member

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    Me neither. I'm a lazy slacker, but I'm still ill!

    I thought all the stuff about 'type A' personalities etc were a result of selection biases: when doctors didn't like to give a diagnose of CFS it was only pushy patients who ended up being referred on to specialists.
  17. Jemal

    Jemal Senior Member

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    Yeah, I think the retrovirus is a large part of the problem. I also have the feeling it takes many years before it results in symptoms. I have had weird health issues for at least a decade and I am now 32. The telltale fatigue I got in december 2009. Before that I "only" had fibromyalgia and some other CFS symptoms. The fibromyalgia was manageable, as it was "just" minor to average pain. The fatigue, the feeling of unwellness, the non-refreshing sleep... that's crushing for me. I used to need only about 6 hours of sleep. Now I can easily sleep 12 hours a day and still feel like a wreck.

    My first health issues manifested itself when I was seeing a woman who suffered from atypical MS. I am wondering if she might have this virus as well...
  18. lancelot

    lancelot Senior Member

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    Sounds sorta like me. I'm 40 now, but was finally disabled by CFS at 37. In the previous year, one day i woke up completely unable to move due to exhaustion with horrendous unrefreshing sleep. this would last for a few days before i came back to normal. then, it repeated again 1x/month then 1X/few weeks and it was lasting longer and longer up to 1 week at a time. i quite work to rest up. i started sleeping +14hours/day(hypersomnia) but the unrefreshing sleep would never go away. After going to the doctor and being put on the poisin pill called cymbalta, i got much much cognitively worse and got insomnia as a result. one thing that didn't change was the horrible unrefreshing sleep whether i had hypersomnia or insomnia. after seeing 5 docs, multiple meds, treatments-accupuncture, TCM herbs, i went downhill fast and never recovered to any point before seeing a doctor. i quite all meds and doctors after 6 months, and i've been slowly getting better after +2years from 10% bedbound functional to 20-30% housebound functional now. I had no previous health problems and was a health nut and gym rat for the last 20 years. friends described me as the "healthiest person i know" now the "sickest".

    What were your weird health issues prior to CFS?
  19. Cloud

    Cloud Guest

    Lol, I knew there was a good possibility of getting jumped over the contaminated vaccine issue...but I didn't consider this one. You guys are completely misunderstanding me...and maybe I could be more clear. I think sometimes my writing is kinda confusing due to brain blur.

    I didn't say anything about being an overachiever and stress causing or pre-determining ME/CFS. What I was trying to convey was that since stress is known to be one of the triggers of this disease, maybe it's activating latent xmrv. I think many would agree with that. Well, how did I get the xmrv? Early childhood contaminated vaccine makes a lot of sense to me. And maybe I had it from an early age but it was suppressed by my immune system until being activated (aka triggered) by stress, acute infection, or some other immune trauma such as another vaccine.

    I've been at this a long time guys....I know the ropes and have a well deserved seat at this table. For 17 years now, I've been involved in real life education on everything ME/CFS and the political Goliath we have been up against for over 1/4 century? I've been side by side on many threads with you guys...but maybe you've still missed my story. Oh hey, lol here it is..... http://forums.aboutmecfs.org/showthread.php?7387-Okey-Dokey-Hokey-Pokey

    as Lily Tomlin would say...And that's the truth
  20. lancelot

    lancelot Senior Member

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    Cloud, don't do it again with your psycobabble! JUST KIDDING!!! HAHA!

    i'm not truly convinced that mental stress is a trigger for this horrendous disease. for sure, a flu, infections, pregnancy, or other physical stressors seem to trigger or initiate this disease. but then again, mine was a gradual 2-3months with no stressors. so what was my trigger? maybe you don't even need a trigger.

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