Invest in ME Conference 12: First Class in Every Way
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"complex" post-transcriptional element of "simple" retrovirus

Discussion in 'Other Health News and Research' started by anciendaze, Mar 26, 2015.

  1. anciendaze

    anciendaze Senior Member

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    The “complex” RNA post-transcriptional element of a “simple” retrovirus

    DOI:10.1080/2159256X.2015.1017085 Katarzyna J. Purzyckaa, Guy R. Pilkingtonb, Barbara K. Felberb* & Stuart F.J. Le Gricec* Publishing models and article dates explained
    • Received: 23 Dec 2014
    • Accepted: 3 Feb 2015
    • Accepted author version posted online: 16 Mar 2015


    Abstract

    Replication of retroviruses and transposition of endogenous retroelements exploits a unique mechanism of post-transcriptional regulation as a means of exporting their incompletely-spliced mRNAs (which serve as both the genomic RNA and the template for protein synthesis). Following discovery of the Rev response element (RRE) that mediates nucleocytoplasmic export of the full-length and singly-spliced human immunodeficiency virus type 1 (HIV-1) genome, equivalent cis-acting regulatory elements have been characterized for both complex and simple retroviruses and retroelements, together with the obligate viral and host proteins with which they interact. The exception to this is the gammaretrovirus family of simple retroviruses, exemplified by reticuloendotheliosis virus (REV), murine leukemia virus (MLV) and xenotropic MLV-related retrovirus (XMRV). In this commentary, we discuss our recent data that reported structural and functional data on the MLV/XMRV post-transcriptional regulatory element (designated the PTE). The PTE was characterized by a highly-structured region of multiple stem-loops (SL1 – SL7) overlapping the pro and 5’ portion of the pol open reading frames, comprising a bipartite export signal whose structures are separated by ˜1400 nt. In addition, structural probing suggested that SL3 nucleotides were involved in pseudoknot formation. These data, when compared with RNA transport elements of complex retroviruses (HIV) and simple murine retrotransposons (musD), collectively present an emerging picture that long-range tertiary interactions are critical mediators of their biological function.

     
  2. anciendaze

    anciendaze Senior Member

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    Elsewhere, I was asked to explain what the abstract means (I have not had time to read the whole paper). This question of the XMRV controversy came up, and I felt obligated to give an opinion on that. I am sure this will not please many people, but I have been asked to say something here. If necessary I will produce a blog post, since I am giving personal opinions on a topic about which there is more heat than light.

    I'll try to explain some of the language, though I'm not sure this will translate into what I was asked to explain. As always, these are my own opinions, not supported by experts worried about hanging onto their funding.

    Genes inserted as DNA by retroviruses are transcribed into RNA before they are translated into proteins. Life would be simple if this were the kind of process engineers design, with a long string of DNA being turned into a single long string of RNA, which then gets fed into an organelle which turns this into the precursor for a protein. Nature does things differently. Those long DNA sequences are turned into multiple shorter sequences of mRNA which then need to be spliced together to form the complete blueprint for a particular protein.

    This is the level at which RNA interference takes place. Host cell enzymes can cut viral RNA into pieces called microRNA or short-interfering RNA. These pair up with longer sequences of mRNA, but essentially jam the machinery of cellular transcription. This can "knock-down" entire genes for particular proteins, or cause deletions by "knocking-out" one kind of mRNA before it is spliced in. Another source of large deletions is caused by "pseudoknots" in RNA which break off during this stage.

    What this paper is describing as "long-range tertiary mediators" are interactions between complicated structures in RNA and proteins which have previously been ignored. Retroviral sequences are actively manipulating post-transcriptional (DNA to RNA) transformations. They are also quite active in such things as the export of RNA sequences out of the nucleus and into the cytoplasm of the cell. (This not only affects protein synthesis in host cells, it can also influence sequences transported to mitochondria. Human mitochondria are especially dependent on genes held in the nucleus, compared to other organisms. They are not even close to being independent organisms.)

    This is a particular problem when deletions show up in practice, like a notorious one which characterized XMRV. Standard statistical assumptions of independent point mutations would suggest this would never appear twice by chance in the history of the human race. While the process I'm describing mainly concerns translation into proteins, retroviruses possess a unique ability to directly exploit changes in RNA by reverse transcription into DNA inserted in genes, which profoundly undermines those arguments about probabilities.

    Those arguments served polemical purposes by allowing the assertion that all such had to be the result of laboratory contamination, despite a real problem connecting some of those sequences with the ones generated in a particular recombination event in a single laboratory. Some wild mice appeared to have a virus with the same characteristic deletion, but acknowledging that would have had very serious implications for the political problem of containing the public relations consequences of the XMRV episode. Instead of chasing down each source of contamination, the consensus opinion of experts was that they had to be laboratory contamination. This was then used to deny funding for investigation of these anomalies, neatly eliminating the possibility of falsifying the consensus opinion.

    One thread leading into the search for XMRV was the discovery of variants of human RNAse-L which had an enormous deletion reducing their size from 85 to 37 kilodaltons. RNAse-L plays an important role in defenses against human viral infections. Silverman should have suspected something wrong in his research at the point where the evidence of XMRV and the evidence of the RNAse-L variant parted company. It was always unlikely that every adult with the variant RNAse-L had possessed defective RNAse-L from birth. There are simply too many childhood viral diseases which could kill. This suggested some post-transcriptional process initiated by something like a virus was causing a major deletion in a host protein active in defense against viral infections.

    This paper suggests there is a great deal more going on than previously admitted. Beyond knocking down host sequences, retroviruses are actively exploiting mechanisms which precede translation into proteins to further their own interests.
     
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  3. anciendaze

    anciendaze Senior Member

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    The previous post led to arguments about contamination, which prompted me to produce another post:

    There was real contamination with a recombinant which took place in research by Silverman and Jaydip Dasgupta. Important questions about the origin of that recombinant have not been answered.

    It speaks volumes about the politics of biomedical research that there was no concern at all about possible contamination of cell lines, or about shipping contaminated cell lines around the world for about 20 years. This would not serve any political purpose. When such a purpose appeared, it did not serve research funding interests to attack Cleveland Clinic, which is a real powerhouse in medical research. Instead critics went after the weakest member of the herd, like wolves attacking caribou.

    Mikovits had already found that strict adherence to sequences provided by Silverman did not distinguish patients from controls, so she relaxed stringency. At this point they did not know exactly what they were looking for, and still don't. It is entirely possible that patients were expressing HERVs more frequently than controls. This would explain similar dramatic differences in DeFreitas' results as well as those by Lo and Alter. Insistence on strict sequences, and ignoring HERVs, guaranteed failure to detect XMRV.

    The decision to ignore sequences resembling HERVs or "mouse viruses" dates back to the 1980s. It is basically a social convention which serves to keep attention on HIV, while ignoring any retroviruses which are less lethal and more widespread. Rapid replication is the key to this kind of distinction, both to make laboratory experiments possible in a short time, and to have replication of pathological sequences dominate sequences originating from recombination inside a host. Unfortunately, this narrow focus has failed to deal with HIV, which can lie low for a couple of years, and does a great job of stimulating expression of HERV sequences.

    When the experiment on recombination of pre-XMRV1 and pre-XMRV2 took place, nobody was too worried about the fact that these fragments of old retroviruses were too highly defective to initiate a retroviral infection. If need be they could always invoke the fact that "everyone knows" mice are just lousy with competent retroviruses, which can be invoked to explain whatever you want. The fact that nobody knows if any given research animal harbors latent retroviruses which can activated at the drop of a hat doesn't translate into questions about humans harboring latent retroviral infections; mice do not vote or draw disability payments. Applying the same reasoning to humans is Verboten. There are too many HERVs with genes having complete open reading frames that might either act together to reconstitute an active retrovirus, or become active as a result of a negligible infection by an active retrovirus which recombination converts into an active infection by HERVs. A single infected cell on mucous membranes could churn out significant numbers of fully competent retroviruses, and still remain below current thresholds for detection.

    If we were talking about any other species, existing evidence of recent activity in HERVs and transposable elements would lead to the assumption that the human species also harbors endemic slow retroviral infections which most individuals are able to control, most of the time. For political reasons this obvious inference must never even be considered in research publications.

    During the circus over XMRV we heard such pronouncements as "every gibbon ape in U.S. zoos is infected with GALV, and it doesn't do them any harm." (Except when it causes a particular kind of myeloid leukemia in which it was discovered. Are you saying the corresponding human chronic myeloid leukemia is an insignificant problem?) We also heard "if it only infects one cell in a thousand it can't cause significant disease." (How many cells out of a trillion or so are needed to start cancer growing? What percentage of cells in peripheral blood are infected before we reach the threshold of detection for HIV-1?)

    Nobody gets too upset if a percentage of gibbon apes are put down because it would be inhumane to subject them to the treatments humans with myeloid leukemia endure. Nobody is surprised if chimpanzees, our closest natural relatives, show abundant evidence of recent active gamma retroviral infections, or if rhesus monkeys suffer mammary tumors caused by Mason-Pfizer Monkey Virus. From a certain standpoint this has nothing to do with human health, despite clear evidence that retroviruses can leap much larger gaps between species, genera, families, orders and even classes. (And, have done so quite recently.)

    I could point out that contamination would explain those results of the recombination experiment. I am not suggesting it, though I'm not impressed by efforts to avoid this. What I am suggesting is that pursuit of contamination as an explanation is highly selective for reasons that have nothing to do with biological reality and a great deal to do with turf battles among researchers.

    I don't know what is out there in the wild, and I don't know if any threat to human health should be called XMRV. What I do know is that research on beta and gamma retroviral sequences in humans has been systematically neglected and disparaged. Rather than having various challengers promote a particular sequence as the cause of any particular human disease, which competing researchers can then attack, it is past time to use current technology to find out whatever is out there in humans, and then find the connection with diseases, known and unknown.
     
    Last edited: Mar 26, 2015
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  4. anciendaze

    anciendaze Senior Member

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    That last post led to more misunderstanding, so I made another attempt to state my position, and avoid return bouts of previous arguments. You can decide if this helped:

    Just to avoid another bout in which opponents make "straw-man" arguments against the wrong questions, I'm going to state my position again.

    I do not believe there is an entirely new gamma retrovirus causing a new disease in humans, (except in the same sense that each year's flu is likely to be a somewhat different disease.) I do not believe humans are uniquely immune to retroviruses which affect all primates which have been carefully studied.

    What I do believe is that humans have been exposed to a wide variety of retroviruses during the period in which they have domesticated other animals and lived in permanent dwellings. Those people who were especially vulnerable to these died without leaving descendents. The survivors acquired new HERVs which are rare or nonexistent in chimpanzees. Some of these are much closer to being fully replication-competent than those fragments blamed for creating XMRV. The result is that all modern humans carry active retroviral infections which are simply slow enough to allow them to reproduce before their immune systems become senescent, and degenerative diseases kill them.

    This is not something which has persisted for "millions of years", though there have certainly been other retroviruses around that long. This is not even ancient history on the scale of human history. When Europeans spread to other parts of the world they carried two things with them: domesticated animals other cultures lacked, and infectious diseases characteristic of Eurasian civilization. In populations which had already been exposed to both the animals and many diseases there might be terrible conflicts, but without the population collapse which took place in those populations without prior exposure. For all practical purposes we can prove that one human retrovirus was carried from Africa to as far away as Japan by European explorers and African slaves. It is pure hubris to claim there were no other retroviruses, when the populations most affected by them are extinct. Along with deliberately domesticated animals, Europeans also carried such creatures as mice, fleas and lice, completely changing the threat picture for infectious diseases.

    By my reckoning, based on estimates of populations prior to contact, I would estimate that this process generally eliminated 85% of precontact populations over several generations, which fits the idea of slow infectious diseases. The particular known diseases involved varied according to historical contingency, climate, etc. This suggests to me that there were other factors affecting immune competence, and retroviruses are high on the list of suspects for immune impairment. Europeans naturally viewed this process as evidence of innate superiority of either race or culture, not a kind of biological warfare caused by appalling hygiene.

    Modern medicine didn't really begin to control infectious diseases in any systematic way until the 20th century. Prior to that every large city was a population sink in which deaths outnumbered births. It is hard even to estimate the impact since reliable statistics were seldom up to current standards. One estimate I've used is similar to typical third-world mortality rates where hygiene is poor today: 25% of live births died before age 5. On top of this you have to consider the fact that about 1/3 of those who lived to adulthood left no descendents. Human genetics have been modified extensively as the result of constant culling by infectious diseases.

    If we want a world in which this process of culling does not continue, with associated suffering, we have to expect that random variation will again produce genetic variants of humans which are not innately immune to such things as smallpox, polio, measles, etc. This also applies to that 85% figure of native populations which succumbed to slow human diseases we have probably not even identified. Left unchecked, HIV would eliminate about 99% of humans. Even with current treatments HIV may still eliminate everyone without some very special genes over a century or two. Current treatments solve a political problem, but may not change the long-term biological outcome in the slightest.

    HIV also does a fantastic job of stimulating expression of HERVs. These have been treated as a kind of smokescreen which needed to be cleared away in order to come to grips with the real infectious agent. What is more, HIV has a tremendous ability to recombine, even in individual patients. The most distant branches of phylogenetic trees of sequences constructed by computers, based on available sequence information, scarcely have 50% homology. Nothing stops it from picking up and exploiting useful sequences from HERVs.

    My contention that the entire human race was already infected with multiple slow retroviral infections responsible for diseases as well known as breast cancer exposes the extent to which ignoring HERVs (and transposable elements) as inactive evolutionary fossils has resulted in serious failures in many branches of medicine into which many billions of dollars of research money have been poured without reducing incidence of many targeted diseases at all. Good public health policies reduce incidence of disease, which is quite different from increasing rates of treatment.
     
  5. duncan

    duncan Senior Member

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    This is a lot of very good explanatory writing. Thank you for taking the time and expending the effort.
     
  6. ukxmrv

    ukxmrv Senior Member

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    You do a fantastic job of explaining this @anciendaze.
     
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  7. anciendaze

    anciendaze Senior Member

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    I've had some other feedback arguing that I am ignoring clusters of cancers, etc. What I see are not clusters of cancers directly caused by a single infectious agent, but clusters of immune impairment leading to a variety of diseases, including rare cancers. I want to warn people that arguing the wrong infectious cause will result in controversy causing longer delays before problems are dealt with.

    Here are links which will take you to two papers arguing different sides of the debate about thyroid cancer in ME/CFS patients: Teitelbaum, Hyde.

    Here's what I commented:

    I have consistently said that immune dysfunction is a fundamental problem in ME/CFS and many other diseases, including a number of cancers. When I have asked oncologists to estimate the rate at which cancerous cells arise in healthy people, and are eliminated by a healthy immune response, I get either blank looks or the statement that a single cell is not cancer. Cancer is such an emotionally-loaded word that doctors do their best to avoid saying it until there is overwhelming evidence of life-threatening disease. Cheney's comment about 100% of people over 50 having thyroid cancer could probably be extended to males and prostate cancer. There are "pre-cancerous" cells present in everyone that age. I've also been through arguments about such cells in women not being evidence of uterine cervical cancer.

    For those who don't know, here is the article by Robert Good Cheney mentions in that letter. Check the date. This was the point at which my question about immune response eliminating cancer cells should have been addressed. What happened instead was creation of an institutional "war on cancer" which has totally failed to reduce incidence.

    This evidence is entirely consistent with my assertion that the entire human race is infected with slow retroviruses which are sufficiently well adapted to the species so that most of the time they don't kill people before they have time to reproduce. Prior to 20th century advances in medicine few people lived to advanced ages. Even when Social Security was introduced about 90% of those contributing did not live to age 65.

    I want to remind readers that in the case of MS even finding actual retroviral virions in some patients has not changed the perception of the medical profession that this is not an infectious disease. Unless you understand the reasons this situation persists, you don't have a chance of making a case for retroviral etiology of ME.

    Added: I am not downplaying the significance of these cancers, in fact, I am arguing that you won't find big differences from the general population because the HERVs responsible are widespread, but most of the time, in most people, they are held latent.

    I have also argued that expression of immunosuppressive domains in env genes of known HERVs could have some of the effects we see in ME/CFS without the presence of very active retroviral infections.
     
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  8. natasa778

    natasa778 Senior Member

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    This. And why I have no faith in Lipkin's big project.
     
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  9. natasa778

    natasa778 Senior Member

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    Those effects happen in animals, including primates. BUT you surely cannot be suggesting something as heretical as humans being some kind of animal ;-)
     
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  10. anciendaze

    anciendaze Senior Member

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    Humans are large mammals with several times the delay between nursing and reproduction you find in cattle or horses, where we find BLV and EIAV, just for example. We should expect well-adapted retroviruses to be slow and "mostly harmless", except when they cause disabling or life-threatening conditions in a modest percentage of the population. These might well place limits on human longevity which would affect everyone, not just those who die before reproducing.

    Variations in BLV sequences already mean we miss most provirus in cattle. People who drink unpasteurized milk do show antibodies to BLV. If this is completely unable to replicate in humans there must be a high viral load in that milk. (Anyone want to handle a press release which will settle this question one way or the other without causing panic?) What I'm imagining is an exaggeration of these characteristics proportional to the time a virus must lie latent.

    I note that chimpanzee infants fed unpasteurized milk from cows with BLV had a strong tendency to die rapidly. Their ancestors had not been selected for immunity to BLV.
     
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  11. barbc56

    barbc56 Senior Member

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    At least Silverman was willing to explore what happened as well as being flexible in his thinking as the science changed.

    The credibility and professionalism of Silverman and Lipkin, suggests, at least to me, that they would be open to considering other hypotheses IF there was credible science behind it.
    http://news.sciencemag.org/2012/09/retraction-first-paper-xmrv-takes-authors-surprise
     
    Last edited: Mar 27, 2015
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  12. anciendaze

    anciendaze Senior Member

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    @barbc56,

    We could spend a great deal of fruitless discussion on "he said, she said". This is not my purpose. The controversy exposed defects in current research models, and powerful political forces within research communities. I can't do much about politics or personalities.

    At the time the controversy erupted I genuinely expected that, whatever the outcome, we would gain new science as a result. This has not happened. We still don't know how to prevent a similar mess, except to avoid doing research on certain subjects. We never did find out how contamination ended up affecting patient samples far more than controls, and not just in a single laboratory. The lopsided percentages show a striking resemblance to those reported many years ago by DeFreitas, in claims about a different retrovirus which was never identified. At the end of this tunnel we still have retroviral sequences in 85% of samples collected with extraordinary care, though these affect controls as well as patients. It appears there is a serious unidentified problem with common research techniques.

    What I am saying in this series of posts is that I would not expect a controversy like the one over XMRV to reach any conclusion except contamination, given current ground rules. You can't apply Koch's postulates unless it is possible to find uninfected individuals and a single, clearly identifiable pathogen which behaves well in laboratory practice. This does not appear to be possible in quite a range of diseases which may still have more complicated infectious etiology. (My favorite example here is shingles, which we now know appears long after acute infection by VZV. Finding the cause during the years when the virus lies latent is a real challenge.)

    We tend to forget that Koch developed his postulates for infectious disease at a time when there was powerful opposition to the germ theory -- even in the cases of cholera or TB. One leading medical researcher even led a walkout of doctors when Koch presented his findings on TB at a conference. Why he did this is harder to explain than the textbook cardboard descriptions of the incident allow. Suffice it to say he felt he had excellent scientific and political reasons for this opposition. He was actually considered a progressive intellectual, and he also opposed vaccination for smallpox. Since incidence of smallpox now appears to be zero, I don't expect many people to agree today.

    Another professor was so certain that Koch was wrong about cholera that he actually drank water containing vibrio cholerae in front of a class of medical students to discredit the idea. What he proved by this was that he had acquired immunity. Fortunately, cities began cleaning up water supplies to eliminate odors before the medical profession reached any consensus on germ theory.

    Had there been a pathogen with the characteristics I expect it would not have been easy to culture it in laboratories, or to find consistent sequences in an environment dominated by multiple HERVs. It would have replicated too slowly, and recombined too frequently. This is not to say it would be harmless. Any pathogens which only killed people after about age 35 would have been hard to detect when most people died at earlier ages. Today the diseases they cause would be turning up at increased incidence. This is something I perceive happening.

    I don't say that XMRV or any particular pathogen is behind ME/CFS/SEID/WTF. I don't claim to know that any particular disease of unknown etiology is entirely caused by any specific pathogen. What I am saying is that the social conventions adopted during the 19th century battle over the germ theory of disease are not appropriate for a wide range of unsolved medical problems. I am also unimpressed by the extent to which conventional thinking and treatment has failed to reduce incidence of, for example, cancer or mental illness, despite really substantial expenditures.

    Instead of people proposing single causes defined by a specific sequence of nucleotides, which others will knock down without advancing the state of the art at all, it is time to use existing new tools which will let us determine what is actually going on in people, both when they are sick and when they appear healthy. At least half of this (the control arm) is fundamental biology which should not be charged to the account of any particular patient group disadvantaged by illness.
     
    Last edited: Mar 29, 2015
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  13. barbc56

    barbc56 Senior Member

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    I agree. However, I brought this up as disparaging remarks were made about Silverman. That's fair game in the world of debate.

    I am well aware of Koch's postulates.

    My personal take on this issue, is that most of the above points were credibly discounted several years ago.

    Enough said on my part so I will move on to other matters.

    Barb
     
  14. nandixon

    nandixon Senior Member

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  15. anciendaze

    anciendaze Senior Member

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    Excuse me, Barb, but I was not simply bad mouthing Silverman. I specifically said that he should have suspected a problem when he lost the connection with RNAse-L. If I were going to attack him I'd point out that the offending cell line was in his laboratory, and the contamination with plasmids used to multiply XMRV sequences took place far outside of Mikovits control. He didn't even inform collaborators that he had handled the contaminated cell line until long after they were embroiled in a vicious debate. No evidence of plasmid contamination, which shows deliberately inserted markers, was ever found in her laboratory, and they specifically tested for those markers. Arguments that all positive results must be the result of contamination were generally made by innuendo, even though the obviously sloppy work was done elsewhere. To this day, we still don't know why several attempts showed a high percentage in patient samples rather than controls, and the only explanation I've heard is literally "maybe you handled them more."

    (I will not defend various personalities involved. In my experience, innovative scientists can be extremely abrasive, and I can say this without ever having met Robert Gallo.)
    I really don't intend to get into a rematch, but there is a problem with the internal logic of that argument.

    The precursors to XMRV used in the experiment which produced "multiple replication-competent retroviruses" were mere fragments. They were much farther from being competent than HERV-Fc1, and present in fewer copies than HERV-K111. To reason from an experiment which demonstrates recombination in mice to the conclusion that no such replication-competent gamma or beta retroviruses can arise in humans is to turn the statement "we don't know any such retroviruses exist in humans" into "we know no such retroviruses exist in humans", a serious logical fallacy. Even if such a conclusion were true at the time of the dispute, that experiment provided excellent evidence that novel gamma retroviruses are constantly being generated through common biological processes. Nothing limits these processes to laboratories. For convenience, laboratory experiments accelerate natural processes. This has to be compared with populations of both humans and other mammals randomly performing unplanned experiments in parallel in billions of individuals. (Even there, I'm ignoring gamma retroviruses in fowl, but who ever heard of a virus jumping from chickens to humans?)

    This leads me to ask about efforts to monitor the emergence of new human gamma or beta retroviruses. Basically, it appears that these tasks are either based on wishful thinking, or reliance on a new virus generating a really impressive body count.
     
    Last edited: Mar 28, 2015
  16. MeSci

    MeSci ME/CFS since 1995; activity level 6?

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    @anciendaze

    Due to foggy-brain syndrome I am unable to absorb much of this thread at present, but I wonder whether this is relevant.

    I have long been astonished at the extraordinary mixtures of materials from different species that are used in in vitro research, and to some extent also in disease testing methods. It has occurred to me whenever I see such in vitro 'menageries' that they must greatly reduce the likelihood of obtaining accurate, reliable or meaningful findings/results.

    For example, an in vitro study will commonly use bovine serum as a medium, and may add into the mix something bizarre like goat anti-rabbit antibodies, ovine enzymes and immortalised human cancer cells.

    Does this kind of mixing not create an extremely-unnatural environment, perhaps one unlikely to occur naturally in the human body or to produce results that tell us much about the human condition?

    I think I have gathered from roughly scanning some of your text that some such mixing will occur naturally (through diet, for example?) but do you think it has other implications?

    Sorry if I am talking rubbish but as I say, my brain is not functioning well.
     
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  17. anciendaze

    anciendaze Senior Member

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    @MeSci

    As I've suggested above, laboratory experiments are done in a way that makes it possible to obtain results in one human lifetime or less. Even things we regard as extremely unnatural, like placing infected cells from one species inside another, do happen, for example, when parasites feeding on blood move from one host to another. (Really appalling things can come out of people living in regions with poor hygiene, and I'd like to forget some images connected with things I have learned about human parasites.) We generally look for infections capable of surviving in the parasite (host to the virus, while another species is host to the parasite), as happens with a flavivirus in yellow fever surviving in mosquitoes, but this is not necessary.

    Anyone with much experience around horses will be aware that tabanid flies can do a remarkable job of removing blood from individual animals. (This can amount to some hundreds of ml/day.) Fresh blood carried in mouth parts of these flies can be directly injected into other individuals. This is the way equine infectious anemia is often transmitted between horses, and people who have imported horses will be aware that special quarantine procedures are required to prevent such transmission until it is clear a particular horse is uninfected.

    All modern humans appear to have defenses against equine infectious anemia virus, a lentivirus. This could be because all who were not immune died out within a dozen generations or so after horses were introduced to their environment. It is virtually impossible to find humans today who have never been exposed to such means of transmission.

    When we find that a virus can infect human cells in vitro, as happens with a number of gamma retroviruses, this is usually said to be no indication that the virus represents a threat to human health, since laboratory cell lines lack the immune systems of intact humans. Unfortunately, the environment of mucous membranes like those in lungs, sinuses and gut, is remarkably similar to a culture plate, and supports a diversity of microbes we have still not fully inventoried. Human immune cells do move among these, attacking particular human pathogens, but that opens a new route for infection if those immune cells are themselves vulnerable to infections which will not be immediately detected when they return to other physiological compartments. Latent provirus may very well be carried into the body, and into immunologically-privileged sites, as a result.

    Transmission to sites like the lungs via dust particles is one common means of transmitting hantavirus from droppings of wild mice which invade human habitation during a mouse population collapse. Gamma retroviruses can also be found in mouse droppings. This is only one possible source, and at least is confined to situations where you might expect to stir up dust by sweeping. There are other possible sources of such retroviruses you may not want to think about: bat guano, dust storms. There is absolutely no question that bats carry a wide range of viruses, including gamma retroviruses. They also feed on insects while flying unobserved at night, and crap not just "in the woods", but wherever they feel moved. (Dust clouds from the Sahara can cross the Atlantic, and I've had a car paint job ruined by such dust particles in Florida.) Such sources are hard to avoid.

    We don't know nearly as much about the biota of human mucous membranes as we thought we did some time ago. This takes me back to a much earlier paper. The study was aimed at finding DNA viruses characterizing the altered environment of lungs of cystic fibrosis patients. (Retroviruses could only be inferred indirectly.) The surprise was what the control arm revealed about unknown viruses in healthy humans. Most of these are, no doubt, harmless, or even beneficial. (Viral phages, including retroviruses, help to control bacterial or fungal infections.) What I find indisputable is that there was a great deal in there nobody had predicted. Later papers have warned about false discovery of viruses on mucous membranes, but the flood of information I expected on human viral biota has been slow to materialize. I strongly suspect this is being deliberately downplayed to avoid letting the public know just how ignorant we are, and how far the medical research community is from coping.

    When we encounter viruses which can infect human immune cells in vitro, they may well infect immune cells on the surface of the lungs. We need to ask if these can cross back into other physiological compartments without being eliminated by immune response. Latent provirus probably can. If infected, but asymptomatic, cells cross into immunologically privileged environments like the brain, we have a whole new can of worms to deal with, and not just in the case of HIV.

    Arguments that this doesn't affect the majority of human beings are basically political arguments which would not be applied to infectious diseases like poliomyelitis, to which some 95% of humans have generally been immune because of thousands of years of natural selection. It is not that this could not produce disease, but that there are more pressing infectious diseases to deal with first. The difference is that polio produces obvious cripples and horrifying child deaths in those exceptional cases lacking immunity. In the case of retroviral diseases, we have clear evidence genetic variation in the TRIM5 alpha gene is connected with susceptibility. Variations in this same gene appear to correlate with incidence of MS.

    MS has a suspected association with a gamma retrovirus and HERV-Fc1. The defects in HERV-Fc1 amount to only a misplaced stop codon and a frameshift in the pol gene. For comparison, I'll mention that MMTV in mice has two frameshift defects, yet is responsible for about 95% of mammary tumors in mice. Beyond the possibility that another HERV might supply a short "patch" sequence to fix the defect, or a possible role for an exogenous "helper virus", I'd point out that changing a single codon consisting of three base pairs is not a wildly improbable event. This could make HERV-Fc1 about as functional as MMTV.

    Even without becoming fully replication-competent, there is no question that envelopes of type-C and type-D virions do often contain immunosuppressive domains which might promote infection by unrelated viruses if such env genes were expressed.

    I don't know that this kind of suggested pathology takes place in any clearly identified disease. I do know that most medical researchers are not doing much about it, other than arguing that it can't happen. This is clearly of benefit for the existential problem of research: obtaining and protecting your own funding.

    I'll close this post with a question I've asked experts before, after I learned about the bizarre history of avian reticuloendotheliosis virus in fowl. This was transmitted inside a fowlpox virus, and also produced insertions of partial retroviral genomes in Marek's disease virus (MDV), a herpes-type virus of fowl. My question was "suppose there were a retroviral insertion like REV in human herpes-type DNA viruses, what would the corresponding human disease resemble?" When I get any answer at all, it is that the disease would resemble hairy-cell leukemia, for which I still read there is no established etiology.
     
    Last edited: Mar 28, 2015
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  18. MeSci

    MeSci ME/CFS since 1995; activity level 6?

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    Thanks for your detailed reply, @anciendaze. I haven't been able to absorb it fully (yet).

    I was thinking more in terms of research which is not into the kinds of infection that might occur in nature in ways that might relate to the species mix in the research. This type of thing is also done in medical research that is nothing to do with infection.

    The most species-diverse one I have seen so far was a paper on the early development of Cox-2 inhibitors. I think I counted 8 different species from which materials in the in vitro mix had come. Yet at the same time researchers (the same ones) were emphasising how incredibly specific the candidate drugs were, with intricate illustrations of the 3D structure of the human Cox-2 enzyme and the place where the drug bound to it.

    And then they used ovine Cox-2! o_O

    I did not think much of the prospects of that drug. I think it may have been the one that became known as Vioxx.

    Sorry if this is a bit O-T, but my muddled brain is just trying to give examples of how illogical research methods can be.
     
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  19. anciendaze

    anciendaze Senior Member

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    @MeSci

    I was replying to a rather different question about how often natural processes mix-up pathogens from different species, even in ways we consider unique to laboratory research. I am very concerned that people will assume the whole problem of pathogens jumping between species could be prevented by stopping most biological research. What humans explicitly do in laboratories is a still a remarkably small part of the evolution of infectious agents, and it is usually done with far more caution than people exhibit in many other activities outside laboratories.

    The problem you mention is not so much that researchers are illogical as that biology itself was never designed to respect human ideas about how things ought to work. Molecules do not carry labels like clothes saying "Made in Sheep", and a surprising number of them have only insignificant differences when you compare molecules performing the same functions in different species.

    When sequencing proteins was new, and sequencing nucleic acids forming an entire genome almost inconceivable, I remember a conversation about sequencing cytochrome C to determine the differences between chimpanzees and humans. The joke at that time was that they couldn't find any significant differences, so all the differences between humans and chimpanzees must be due to environment and upbringing.

    We now know that cytochrome C is very highly conserved in mammals. We can even find proteins with similar function and strong sequence homology in plants. In fact, the fundamental nature of cytochrome C and B in eukaryotic cells is apparent when we find corresponding genes in the yeast genome. Part of what it takes to make a human can also be used to make Marmite or Vegemite.

    Evolution has used a limited selection of components from available organisms over and over, often in ways which simply defy human logic. A few hundred million years of trial and error can turn up possibilities a sane mind might never imagine, and would probably reject outright if they had been predicted.

    We didn't start out knowing any of this two centuries ago. Biological research has had to work with what was available, since we haven't been able to build any organisms from scratch. A great deal of research has been based on inspired guess. Some successful research has been based on ideas which turned out to be flat wrong. Some episodes in research are downright embarrassing, even before you get to doctors trying to xenograft monkey glands into aging men.

    I have serious reservations about what would have happened to past triumphs of medical research, had they been run by similar organizational structures to the ones we have today. (How would Koch avoid being blacklisted by Virchow's supporters?) This is one reason behind my lack of enthusiasm for the IOM report, separate from my good opinions about individuals involved. My own limited experience tells me that committees are very good at predicting the recent past, an endeavor of questionable utility.
     
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  20. MeSci

    MeSci ME/CFS since 1995; activity level 6?

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    I have to log off now, but just want to answer this part of your message first.

    My brain has recovered enough for me to start to get the gist of this thread better. It is interesting and important, and I will try to read the rest asap.

    Re similarities between species, whilst I respect your knowledge a great deal, I disagree with you here, having specialised in species differences for my freelance work.

    With regard to human and ovine Cox-2, for example, this paper supports my stance:
    (I have not done more than glance at it, btw.) Enzymes are extremely variable between species.
     

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