*A CALL FOR ACTION!* We need the isolates sequenced!

[omerbasket]

It would be good to get clear on what's going on.

Good, than you can contact Dr. Mikovits and ask her. I'm sure you know her email address.

It was said on the ME/CFS forums that Dr. Mikovits says it costs 2,500$ to sequence one isolate. This is a rumor, and I don't know if that's accurate. It could be that it is accurate and that Racaniello is talking about another sequencing method which costs much less (but the techniques that he supported so far seem to not be able to find XMRV, for some reason, so perhaps this is also why you need a more expensive technique). Also, Dr. Mikovits talks sometimes about "bulk cloning" against "indivudually cloning" - the latter is much better, and perhaps that's also what happens in sequencing - I don't know.

But again, if Dr. Mikovits says that it costs 2,500$ for each, than that's what it costs (and she can probably explain why Racaniello talks about 81$...), and therefore, I WOULD URGE YOU AGAIN, CORT, TO ASK HER - SO THAT WE CAN KNOW WHAT SHE REALLY SAYS AND WE CAN GIVE HER THE OPPORTUNITY TO EXPLAIN, BEFORE PEOPLE START TO DOUBT HER WITH NO FACTS IN THEIR HANDS.

 

[Bob]

omerbasket, I don't think anyone on this thread has been 'doubting' Judy or the WPI... That's not the way I read the discussion... It was more about discussing the possibilities, without having any answers... I hope I didn't give the impression of doubting Judy's integrity... That wasn't my intention... I suppose it's not really helpful having this sort of speculative discussion, but it would be nice to know what's going on! I suppose we'll just have to be patient!

 

[omerbasket]

omerbasket, I don't think anyone on this thread has been 'doubting' Judy or the WPI... That's not the way I read the discussion... It was more about discussing the possibilities, without having any answers... I hope I didn't give the impression of doubting Judy's integrity... That wasn't my intention... I suppose it's not really helpful having this sort of speculative discussion, but it would be nice to know what's going on! I suppose we'll just have to be patient!

With certain people here, I don't need them to say much in order to feel that they doubt her integrity. Anyway, this does not matter - as it would be much more fair to contact her and recieve her answer, before starting to speculate. She is much more than fair in regard to answering her mails - she answers them, and she does that, most of the times, quickly.

 

[jace]

From the transcript I made of the discussion after Alter's summing up re Mikovits and Coffin:

Judy Mikovits

I'm just saying when the Lipkin study's done - two years from now - the way it's set up there's 1300 samples, and I've got to do what I do and it takes two months on every one of them

I imagine that this work is what the NIH grant mentioned earlier was given for. I too remember that Judy said it was more like $2,500 to sequence the virus, and let's face it, she should know.

 

[insearchof]

From the transcript I made of the discussion after Alter's summing up re Mikovits and Coffin:

Judy Mikovits


I imagine that this work is what the NIH grant mentioned earlier was given for. I too remember that Judy said it was more like $2,500 to sequence the virus, and let's face it, she should know.

So, the inference is....that there will be short cuts to produce results within that time frame?

 

[Cort]

Omerbasket - I'm not bashing Judy. If its 2,500 to do one isolate that seems well worth it. If you consider that you only need 4 o5 isolates with high genetic variability to overturn the contamination theories I think $10,000 or even more an isolate would be well worth it. Its the contamination stuff, after all, that may be inhibiting the WPI from publishing papers or for getting more funding or from convincing drug companies to start on treatment trials. To me, sitting on the outside, a laymen, it seems like a great idea to get that data out

 

[currer]

QUOTE...THe low gene variability data is also what has prevented much of the research establishment from accepting that the Lo/ALter MLV sequences are part ofthe XMRV family.....right now there is too much of a gap between XMRV and the MLV sequences genetically for them to appear that they come from the same source. If that was true then there should be a gradation of sequences that are intermediate between the two. Instead in the analyses there's XMRV on one side and the MLV's on the other. If the WPI could fill in those spaces then they would get alot more agreement that these two findings are related.....QUOTE CORT.


Cort, the sequence gap between MLVs and XMRV is not a problem as far as I can see as they are not one virus.

XMRV is the virus you find if you do PCR specifically or it. There are other MLVs also present in about a third of patients.
XMRV does not need to mutate in the human population much if it is spreading not from human to human but from cell line to human. http://www.thelancet.com/journals/laninf/article/PIIS147 (This link is from the PR thread on Gkikias Magiorkinis article in the Lancet of April 2011)
XMRV itself is only one type of MLV.

See Dr Deckoff-Jones latest blog. http://treatingxmrv.blogspot.com
She has put up links to research published in the 1970s showing MLVs in human lymphomas. The papers concluded that these MLVs had been acquired during life somehow as they were not in the germline.

 

[Bob]

There are other MLVs present in about a third of patients.

I don't think that I've seen this info anywhere before...
Are you referring to any specific research, currer?
Would you mind pointing to where you read or heard about this please?

 

[Bob]

See Dr Deckoff-Jones latest blog. http://treatingxmrv.blogspot.com
She has put up links to research published in the 1970s showing MLVs in human lymphomas. The papers concluded that these MLVs had been acquired during life somehow as they were not in the germline.

Here's a direct link to the specific blog entry that you are referring to, in case it's helpful to anyone.
http://treatingxmrv.blogspot.com/2011/05/aloha.html

 

[currer]

Hi, Bob,
I remember you made a similar request of me some time ago!
My memory is that Judy Mikovits stated this in her talk at the New York Academy of Sciences "Pathogens and the Blood Supply" webinar on March 29 2011.

If you can find this talk up on the web, I'd be grateful as I'd like to hear it again. Last I heard it had been taken down.
PS. Do you take notes? You often want references.

 

[Bob]

Hi, Bob,
I remember you made a similar request of me some time ago!
My memory is that Judy Mikovits stated this in her talk at the New York Academy of Sciences "Pathogens and the Blood Supply" webinar on March 29 2011.

If you can find this talk up on the web, I'd be grateful as I'd like to hear it again. Last I heard it had been taken down.
PS. Do you take notes? You often want references.

Hi currer,
Thanks very much for the info.
Yes, I thought I'd asked you for some details before... But i couldn't remember what details I'd asked you for (I've got an appalling memory!)... I thought you couldn't remember your source of info last time? So thanks for this info.
You do post interesting titbits of information! And I follow the XMRV developments extremely closely.
I don't always make notes, but I do make mental notes about significant news, and sometimes I make a list of links to the news sources.
It's strange, but I seem to have an excellent memory for XMRV news but nothing else! But I think my memory was a bit like that before I was ill anyway. (Able to remember certain types of info but not others.)
I'll have a look for that video, and if I find it, I'll be sure to let you know.
Thanks,
Bob

 

[Bob]

hi currer, do you think that you are you referring to the info in the post below, that i've bolded?

New York Academy of Sciences Webinar
29 March 2011

Both Judy Mikovits and Ian Lipkin presented at this webinar. Lipkin's slides were not available, so there was no visual aid - but his presentation was on hunting pathogens, not XMRV specific. Judy was talking about XMRV detection and disease association.

These are taken from my hastily typed notes. Any errors are mine, and I cannot guarantee 100% accuracy. I have also had to interpret some of it, so I may have introduce bias - I hope not, but there is no substitute for listening to it or a word for word transcript.


Lipkin

Lipkin reported on intestinal biopsies in autism spectrum distorder, and they are finding a deficiency in enzymes for the metabolism and transport of sugars. Because of sugar alterations this may result in the dysbiosis that is frequently seen.

Lipkin was asked something like five questions, four were directly or indirectly about XMRV. He did not give answers that are very relevant to us, except for the upcoming study on XMRV. Three labs have been met with and had an agreed plan, the same for six clinicians. The hold up has been getting approvals, especially from Stanford and Harvard - but they should be ready to go soon.


Mikovits

Mikovits covered a lot of ground. Much of it is well known and I shall not report it again. I will however touch on the high points of the anti-contamination findings, even if is already well known.

1. They have measured high levels viral proteins from patients.

2. 30% of ME/CFS patients have two strains of viruses.

3. APOBEC3G induces G to A hypermutation, but while this mutates the viral RNA, the resulting amino acid sequence is frequently unaltered, and the virus can still be transmitted. APOBEC3G just reduces the viral load.

4. Diseases associated with XMRV -
mcl
thymoma (a thymus cancer)
melodysplasia
lymphoma
itp ( ideopathic thrombocytopenia, 50% in one study had XMRV)
cll
itp

5. All 60 cell lines at the WPI have been tested for XMRV and are not contaminated.

6. Something Lipkin had also noticed, copathogens can increase severity.

7. Patient contacts including caretakers have higher risk of XMRV so this might be considered as a screening criteria for blood donations.

8. A question about XMRV transmission noted that an implication of CROI is that XMRV might be airborne. This is being investigated, but is not proven.

9. Mikovits is talking to Dr. Lerner about XMRV and herpes virus interactions.

10. Mikovits describes ME/CFS as an Aquired Immune Deficiency.

11. A new high security lab may enable research they have not been able to do so far.

12. It was confirmed that Chronix have indeed claimed to have found fully integrated XMRV in ME/CFS, including flanking DNA on both sides of the virus.

13. Pathogenicity is not proven. However, it is suspected that antivirual methylation might be removed by epigenetic factors including those induced by the virus itself.


The rest of the presentation was not of much relevance to ME/CFS, but there was a long presentation on babesia which might be of interest to some. This is still ongoing, but I thought I would post as I doubt much of importance to us will be said in the remainder.

Bye
Alex

 

[currer]

Hi Bob,
Yes I think these notes must relate to the same statement I remember hearing in the talk. But I think I have heard JM say something similar in another talk - was it the one in Norway? This was what you asked me about before and I could only refer you to the video of the talk. I remember that as being findings of even more distant sequences of virus in one patient. This is the problem if the WPI cannot get their research published. We are all dependent on memory or have to hunt through a whole recording of a talk for one bit of info.
However if you look at the abstract on the NYAS site for JM you will see references to other MLVs in there.

I suppose we are drifting off topic for this thread. To get back onto the subject, is it worthwhile to sequence XMRV in such detail if there are many related MLVs in patients, some or all of which may also be pathogenic? (As shown in the 1970s research on lymphoma and MLVs).
Is nailing XMRV just a diversion from the central problem?

 

[Bob]

Hi Bob,
Yes I think these notes must relate to the same statement I remember hearing in the talk. But I think I have heard JM say something similar in another talk - was it the one in Norway? This was what you asked me about before and I could only refer you to the video of the talk. I remember that as being findings of even more distant sequences of virus in one patient. This is the problem if the WPI cannot get their research published. We are all dependent on memory or have to hunt through a whole recording of a talk for one bit of info.
However if you look at the abstract on the NYAS site for JM you will see references to other MLVs in there.

Thanks currer. I'll see if I can find any of the info you've referred to.

I suppose we are drifting off topic for this thread. To get back onto the subject, is it worthwhile to sequence XMRV in such detail if there are many related MLVs in patients, some or all of which may also be pathogenic? (As shown in the 1970s research on lymphoma and MLVs).
Is nailing XMRV just a diversion from the central problem?

Personally, I think that if there are a multitude of MLV's in humans, then the XMRV research will prove to be the first step in investigating all of them properly. Or I'm hoping so anyway.
So I think that XMRV research is the opposite of a diversion... I'm hoping that in the long term it will focus minds on the issue and is a necessary stepping stone to further research development into MLV's in humans.

 

[Bob]

Hi Bob,
Yes I think these notes must relate to the same statement I remember hearing in the talk. But I think I have heard JM say something similar in another talk - was it the one in Norway? This was what you asked me about before and I could only refer you to the video of the talk. I remember that as being findings of even more distant sequences of virus in one patient. This is the problem if the WPI cannot get their research published. We are all dependent on memory or have to hunt through a whole recording of a talk for one bit of info.

I haven't found the video, but none of the synopses of the Norway talk, that I've read, mention her finding more distant variants or sequences. I'll keep my eye out for more info.

However if you look at the abstract on the NYAS site for JM you will see references to other MLVs in there.

I've just had a look and it only refers to XMRVs and PMRVs, unless I've missed something.

Thanks for your help currer.

 

[currer]

Ah, I spot a problem. I think I am using MLV where I should be using MRV. Am I confusing you? I think JM only refers to MRVs in her patients not MLVs.

 

[Bob]

Ah, I spot a problem. I think I am using MLV where I should be using MRV. Am I confusing you? I think JM only refers to MRVs in her patients not MLVs.

It's OK, you're not confusing me (although that isn't difficult)... I knew that you meant 'MRVs'.

 

[KnightofZERO]

I agree, WPI needs $

It would go a long way to put the contamination theories to bed if more sequences were in GenBank showing the genetic diversity you'd expect from a natural infection--or given that there are no human MRV infections besides this one, more genetic diversity than would be found in any cell line.

this is one reason we need to get the WPI money. The sooner we have more sequences the more we know, the sooner we will be helped...

Also I think we should consider asking the NIH to appoint a "Grant Liaison Officer" for ME/CFIDS research of who had some kind of monetary funding power...

We all know that grants take forever to write and forever to get approved. If we can get the NIH to put "an advance on grant funding" for scientists who have done "innovative research" in this field (they should have an idea who these people are after the SOK, but notably WPI)

If this could happen similar the way one gets an advance on some kind of large business payment, until the full grant is approved... it would speed up the science very much at this critical stage.

The low number as documented by Pat Fero to be only about 3.75 ish dollars per each of us per annum--a great deal of which undoubtedly doesn't even go to biomedical research--is disgraceful.