New WPI and CDC XMRV sequences in genbank

[Sam Carter]

It would be good if the NCF put dates to it's articles, i have no idea when this was written, probably some years ago.

The article is from the Winter 1999-2000 newsletter, Eric.

http://www.ncf-net.org/archive.htm

 

[eric_s]

Thanks, Sam. It looks like many interesting leads (also quite shocking stuff), but we don't know what happened in the meantime. Probably even for scientists it's hard to make sense of these things.

 

[bullybeef]

Just been checking Genbank and looks like JHK-3 is now defined as a XMRV variant. This entry was only modified on December 14, 2011!!

 

[currer]

How/who decides on these classifications bullybeef? Is it the researcher?
The JHK virus - thats the one from 1992 discovered by Grossberg. Predates xmrv and Paprotka then.

 

[bullybeef]

How/who decides on these classifications bullybeef? Is it the researcher?
The JHK virus - thats the one fron 1992. predates xmrv and paprotka then.

I wish I knew whom decides on the classification, currer, but I've looked at JHK before and there wasn't any reference to it being a human gamma retrovirus. I guess, with it only being modified last month, something has changed very recently.


And this is the problem we're going to have, any new HGRV realisation or discovery won't be published, it will just be modified to keep it from the media.

 

[currer]

Does this association with XMRV mean that the JHK virus is accepted as being a human retrovirus - not a mouse XMRV?

 

[bullybeef]

The following was published in 1997: http://www.ncbi.nlm.nih.gov/pubmed/9201810

Res Virol. 1997 May-Jun;148(3):191-206.

A human B-lymphoblastoid cell line constitutively producing Epstein-Barr herpesvirus and JHK retrovirus.

Grossberg SE, Kushnaryov VM, Cashdollar LW, Raisch KP, Miller G, Sun HY.

Source
Department of Microbiology, Medical College of Wisconsin, Milwaukee 53226, USA.

Abstract

The human B-lymphoblastoid cell line, designated JHK-3, with pre-B-cell characteristics, chronically produces two viruses, Epstein-Barr virus (EBV) and JHK virus, an apparently novel retrovirus. The JHK-3 cells are much more productive of extracellular EBV than the high-producer marmoset line B95-8. The extracellular virus of the JHK-3 EBV strain is relatively fragile, more broadly dispersed in an ultracentrifuged sucrose gradient than the B95-8 EBV and more susceptible to disruption by combined treatment with urea and dithiothreitol. By restriction fragment length polymorphism analysis, the JHK-3 EBV strain resembles the EBV strain FF-41. The JHK-3 cells also produce an incompletely characterized, relatively fragile, enveloped, icosahedral RNA virus that contains Mn(++)-dependent reverse transcriptase. JHK virions measure 85 nm in ultrathin sections, much smaller than other Retroviridae. The JHK virus exhibits a distinctive morphogenesis, most nearly resembling C-type retroviruses. The JHK-3 cell line provides a human cell model for investigating virus/virus interactions and their pathogenetic affects on host cells which chronically and simultaneously produce DNA and RNA viruses.

It does seem since this was published , it has been decided JHK was always a new human gamma retrovirus and one of many XMRV variants, including VP42 (Silverman's prostate clone), and Judy's and Alter/Lo's pMRV. But I have read evidence (can't find it now) that JHK was first isolated in 1989.


That date was one year after ME became known as "CFS".


So based on the JHK cell line producing two viruses, JHK-3 and EBV, could it be conceivable that gamma retroviruses work in tandem, or use regular viruses to move from person to person. This would explain why outbreaks were short, and yet people whom caught a regular virus like glandular fever/mono, they never got better because JHK was using the treatable virus as a trojan horse! And the infectiousness only lasted once the regular virus finished it's incubation period. It is an ideal way for a virus to complete it's live cycle.

Makes perfect sense to me, and this would be one of many explanations why governments would be scared to death of HGRVs.


Also see: http://www.ncf-net.org/forum/ncftruths.html?forumid=331851&forumid=331851&forumid=331851

The basic thing you should know is that nearly all ME/CFIDS patients have a virus called HHV-6A and inside that is a retrovirus that one researcher has named the JHK virus.

 

[Ecoclimber]

JHK-3 is not a variant of XMRV. As you can see from the blast; its closest relative is the retrovirus isolated from VCaP cells. Bona fide XMRV isolates are pretty far down this list. I assume this will be corrected in the GenBank entry by the author.


Eco

 

[bullybeef]

Partial molecular cloning with novel consensus PCR primers of the murine JHK retrovirus of human origin, a variant of the Xenotropic murine leukemia virus-related virus (XMRV)

http://www.uniprot.org/uniprot/G0WKJ6

http://www.ncbi.nlm.nih.gov/nuccore/HM119591.1

http://www.mcw.edu/microbiology/SidneyGrossberg.htm


The JHK virus Genbank entry was only modified on Dec 14 2011.

 

[Ecoclimber]

Partial molecular cloning with novel consensus PCR primers of the murine JHK retrovirus of human origin, is NOT, repeat NOT a variant of the Xenotropic murine leukemia virus-related virus (XMRV.) Its closest relative is the retrovirus isolated from VCaP cells as shown in the Blast report as mentioned in my post 108. It will updated by Grossberg to reflect this change. Just look at the Blast report. No need to state erroneous information to confuse people.

Eco

 

[bullybeef]

Not stating anything, just posting a recently modified Genbank entry. The JHK sequence was only added to Genbank as a XMRV on October 19, 2011. Could I ask, if the change is necessary, why wouldn't Grossberg add this change last month (December 14, 2011) when the entry was modified?

 

[Ecoclimber]

You would have to ask Grossberg that question. I suggest you could perhaps write to him and ask him that question. What I do know is that a very prominent scientist in the field of retrovirology research who wishes to maintain his privacy has contacted him and has also contacted GenBank to remove it as a XMRV variant.

Eco

 

[Tony Mach]

And this is the problem we're going to have, any new HGRV realisation or discovery won't be published, it will just be modified to keep it from the media.

So why do you still bother looking into this, if you think that some sort of conspiracy is going to keep all evidence for your thesis from ever being published?

 

[bullybeef]

Hold on....whoops, I made a cock up...this is the denialist site isn't it, sorry, my bad. Please move along, nothing to see here.

 

[Mark]

Hold on....whoops, I made a cock up...this is the denialist site isn't it, sorry, my bad. Please move along, nothing to see here.

How disappointing that this post was liked by several members. I really don't appreciate posts insulting the forum as a whole.

No, this is not 'the denialist site'. This is a site where members hold diverse opinions, and where you can expect to see both sides of the argument represented. People on both sides of this argument are welcome to post here if they do so respectfully and stick to the arguments and the science and refrain from rudeness and personal attacks. And plenty of our members have been supportive of Dr Mikovits and are still open-minded on HGRV research. We simply present this forum as a place where the issues can be discussed respectfully.

If people who support the HGRV/XMRV theories have an answer to the points made above, and elsewhere, regarding XMRV and HGRV research, then they are welcome to post that answer here. If such people prefer not to post a reasoned answer because they would prefer a forum where everyone agrees with them, then they are just running away from the argument.

 

[Bob]

Hi Mark, I was one of the people who 'liked' bullybeef's post, and I did it out of immense frustration because of the preceding post to bullybeef's post, by Tony Mach.

It's one thing to constructively express an opinion about XMRV, but on this forum we can't share information about XMRV and discuss specific aspects of XMRV in a constructive and positive manner without being shouted down, or without argumentative comments, as has happened above.

This particular thread has always been an extremelly constructive and informative thread, and bullybeef has a particular line of thought/inquiry about XMRV which he seems to be pursuing in a constructive manner (unless i've missed something). But it seems that any line of conversation about XMRV on this forum is now challenged by a minority of very vocal and energetic members. OK, fair enough, it's an open forum, but some of the persistent negative challenging in the XMRV threads does lead to immense frustration for those of us who are interested in exploring all the avenues that XMRV research leads us, whether XMRV is related to ME or not. It has come to the point where we cannot now explore the subject constructively without our interest in the subject being persistently challenged in what seems to me as a very petty, point-scoring, argumentative way.

The post preceding Bullybeef's was not constructive and it was one of those frustrating negative posts which do not help to either further our understanding about XMRV, or to share information about XMRV. It was because it was placed in this, hitherto, very constructive thread that it was so upsetting. I can only speak for myself, but i imagine that other people were equally as frustrated as I was to read it, hence the unexpected number of 'likes' for bullybeef's post.

I don't post about XMRV on this forum any longer, because it has become such a hostile environment to the subject. We can't share or discuss information about XMRV without being shouted down. I know that the forum has to incorporate all points of view, but this means that those of us who are interested in exploring the subject in a positive, constructive and informative way, can't do so. We can't share information without being constantly and persistently challenged in a way that feels unsupportive, negative, petty and not at all constructive. I've been a very loyal member of this forum for at least a couple of years, but I've now had to withdraw from it, partly because of the way the discussions about XMRV now take such a negative turn.

So, for me, it's not simply a case of people expressing their views and opinions, but it's a case of discussion being inhibited, information sharing being made difficult, and the general atmosphere being made unpleasant, because some members do not wish to see any discussion about XMRV when it relates to an association with ME. If people are not interested in the XMRV-ME connection then they have the option of simply not discussing it, but some members seem particularly motivated to disrupt discussion about XMRV for their own reasons.

It's an open forum, so I don't blame anyone for any of this (except perhaps the minority of non-patient members who are here to just point-score in a 'bad science' type of way, rather than having a genuine interest in CFS/ME), and I acknowledge that people on the 'other side of the argument', in relation to XMRV, have felt equally uncomfortable expressing their points of view in the past, because they would be constantly attacked when challenging the view that XMRV was a possible cause of ME.

I am still open minded about gamma-retroviruses in relation to various diseases, and I'm looking forward to seeing the Lipkin results, whether they are positive or negative.
But I am interested in the subject of XMRV, whether it's related to ME or not, so I need to have a forum where I can discuss it safely without being persistently challenged by people who aren't really interesting in my welfare, or who aren't interested in the wider science of retrovirology, or who aren't interested in ME, but who are only interested in point-scoring in a very narrow-minded way.

Anyway, I just thought I'd share my recent experiences of the forum and to hopefully help you understand the possible reason why bullybeef's post got so many 'likes'. (I'm assuming that I haven't missed something on this thread, and that posts haven't been deleted by mods.)

This post does not add anything useful to this thread, so I will probably delete it in a few hours.

 

[RustyJ]

How disappointing that this post was liked by several members. I really don't appreciate posts insulting the forum as a whole.

No, this is not 'the denialist site'. This is a site where members hold diverse opinions, and where you can expect to see both sides of the argument represented. People on both sides of this argument are welcome to post here if they do so respectfully and stick to the arguments and the science and refrain from rudeness and personal attacks. And plenty of our members have been supportive of Dr Mikovits and are still open-minded on HGRV research. We simply present this forum as a place where the issues can be discussed respectfully.

If people who support the HGRV/XMRV theories have an answer to the points made above, and elsewhere, regarding XMRV and HGRV research, then they are welcome to post that answer here. If such people prefer not to post a reasoned answer because they would prefer a forum where everyone agrees with them, then they are just running away from the argument.

To your credit Mark, you left the comment stand. Your response, for mine, was a little over the top. I am posting on the premise that you may have been trying to open up some sort of debate on this issue. So here are my thoughts.

I strongly support Bob's statements above and have found him to be one of the most helpful, patient and long suffering members of this forum. When members like Bob, who have made valuable contributions to the site, for the benefit of me/cfs patients, say something is wrong here, maybe it is time to listen.

Ordinarily Mark what you say might be considered fair, if it were a level playing field. However when one side of the debate has severe cognitive, memory and energy limitations, and the other side is invariably healthy, indifferent to me/cfs and with self interests other than our illness, then you can hardly say it's a level playing field. It would only be a level playing field if patients were represented by retrovirus researchers.

I also think the question of motive is very important, as it colors how these people (the so-called denialists) are perceived. I have yet to hear a valid reason for these people to spend so much time on this forum spreading their message, other than they want to get the science right - such altruism, I think not. Why are they so concerned about what patients think, when they have so little regard for our illness? I have suffered people of this ilk for decades. They are the same people who labelled me neurotic, malingering, forced me into cleaning toilets to get by and have deliberately set back research into biological causes for decades. I have a deep anger for them. And so does every member of this forum who has had to suffer the indignities and ridicule of a lifetime.

Most sites would label these people trolls, not because they are rude and abrasive (most are obsequiously polite, which is how you can tell they don't have me/cfs) but because they are usually shills from the Bad Science forum, invariably pushing an anti me/cfs message. Their presence is usually misrepresented, co-ordinated both within this forum and across other forums whenever an issue is to be countered, and is suggestive of a commercial or other self-interest purpose. This is not suggestive of an intent to help us out, but to indoctrinate. This is not in the spirit of what the forum is supposed to be.

There is barely a handful of patients with the scientific cred to debate the denialists. And not one has the energy to come back time and time again to argue against the same old denialst party line. And yes, plenty of the site's members are stlll open-minded about HGRVs, but not, apparently the denialists. Invariably their stance is one of completely denying the existence of HGRVs. Where is the middle ground?

It's not as if what BB said was news to most of us either. And should not be to you, if you were being honest. I bet if you took a poll, BB's opinion would be widely supported, particularly by the silent majority of patients who do not have the strength to debate the HGRV issue. The result would be somewhat along the lines of the poll the admin ran on support for the CAA. That the admin got that one so wrong could be interpreted as an example of an administration out of touch with its membership. I think you are out of touch on this one too. The interesting question is why?

I guess BB's comments were not aimed at 99% of the forum membership of course, but at the administration which allows such an imbalance to occur, and does not acknowledge that patients need more support than the outsiders. In your post you are not defending the forum, because the forum is supposed to support patients, not cause them distress, you are defending the administration.

As an aside, it should send alarm bells ringing when members leave a forum en masse, especially if those members are higher functioning than most, better qualified in research areas than most. But this is what is happening. Those of this caliber still posting on science issues on this site are in the main only do so with reluctance in an attempt to try to stem the tide of denialist info. Otherwise they would not bother. It is too distressing.

You mentioned the number of likes to BB's comment, yet it is blatantly obvious that the like mechanism has been used by both sides of the debate in other threads in an inciteful manner, however this is the first time you have chosen to comment on it. Instead of shooting the messenger perhaps you should be reading the message.

 

[RustyJ]

Anyway, I just thought I'd share my experience of the forum and help you understand why that post got so many 'likes'.

This post does not add anything useful to this thread, so I will probably delete it in a few hours.

Bob, leave it in: All that is necessary for the triumph of ignorance is that good men do nothing.

 

[Bob]

Bob, leave it in: All that is necessary for the triumph of ignorance is that good men do nothing.

Thanks Rusty, I might leave it now that there is a discussion developing. And thanks for your kind words earlier Rusty. I equally hold you in very high regard as well.

But maybe this off-topic discussion should be separated from the thread so as not to ruin this informative thread? Mark, maybe you could do that, if you think it appropriate?


Just for the record, for anyone reading, I totally support Mark in his moderation role... He's the fairest and most thoughtful moderator that i've ever encountered anywhere, and I consider him a friend.

 

[natasa778]

Ordinarily Mark what you say might be considered fair, if it were a level playing field. However when one side of the debate has severe cognitive, memory and energy limitations, and the other side is invariably healthy, indifferent to me/cfs and with self interests other than our illness, then you can hardly say it's a level playing field. It would only be a level playing field if patients were represented by retrovirus researchers.

I also think the question of motive is very important, as it colors how these people (the so-called denialists) are perceived. I have yet to hear a valid reason for these people to spend so much time on this forum spreading their message, other than they want to get the science right - such altruism, I think not. Why are they so concerned about what patients think, when they have so little regard for our illness? I have suffered people of this ilk for decades. They are the same people who labelled me neurotic, malingering, forced me into cleaning toilets to get by and have deliberately set back research into biological causes for decades. I have a deep anger for them. And so does every member of this forum who has had to suffer the indignities and ridicule of a lifetime.

Most sites would label these people trolls, not because they are rude and abrasive (most are obsequiously polite, which is how you can tell they don't have me/cfs) but because they are usually shills from the Bad Science forum, invariably pushing an anti me/cfs message. Their presence is usually misrepresented, co-ordinated both within this forum and across other forums whenever an issue is to be countered, and is suggestive of a commercial or other self-interest purpose. This is not suggestive of an intent to help us out, but to indoctrinate. This is not in the spirit of what the forum is supposed to be.

There is barely a handful of patients with the scientific cred to debate the denialists. And not one has the energy to come back time and time again to argue against the same old denialst party line. And yes, plenty of the site's members are stlll open-minded about HGRVs, but not, apparently the denialists. Invariably their stance is one of completely denying the existence of HGRVs. Where is the middle ground?

It's not as if what BB said was news to most of us either. And should not be to you, if you were being honest. I bet if you took a poll, BB's opinion would be widely supported, particularly by the silent majority of patients who do not have the strength to debate the HGRV issue. The result would be somewhat along the lines of the poll the admin ran on support for the CAA. That the admin got that one so wrong could be interpreted as an example of an administration out of touch with its membership. I think you are out of touch on this one too. The interesting question is why?

I guess BB's comments were not aimed at 99% of the forum membership of course, but at the administration which allows such an imbalance to occur, and does not acknowledge that patients need more support than the outsiders. In your post you are not defending the forum, because the forum is supposed to support patients, not cause them distress, you are defending the administration.

As an aside, it should send alarm bells ringing when members leave a forum en masse, especially if those members are higher functioning than most, better qualified in research areas than most. But this is what is happening. Those of this caliber still posting on science issues on this site are in the main only do so with reluctance in an attempt to try to stem the tide of denialist info. Otherwise they would not bother. It is too distressing.

You mentioned the number of likes to BB's comment, yet it is blatantly obvious that the like mechanism has been used by both sides of the debate in other threads in an inciteful manner, however this is the first time you have chosen to comment on it. Instead of shooting the messenger perhaps you should be reading the message.

Amen bro! Thanks for taking time and energy to express what many feel (it is much easier/quicker to just 'like' bb's post :Retro smile:. What you say has been my experience here 100%