Mystery Rays from Outer Space

Meddling with things mankind is not meant to understand. Also, pictures of my kids

February 25th, 2009

On undiscovered viruses

How many viruses infect humans? Have we found them all? If not, how many more are there?

We conclude that it is extremely probable that new human viruses will continue to be discovered in the immediate future; we are not yet close to the end of the virus discovery curve.  …Current trends are consistent with a pool of at least 38 undiscovered species that will be reported at an average rate of at least approximately one per year to 2020. … The upper limit for N is finite but large; we cannot rule out hundreds of novel human viruses to be reported in the future. 1

New human viruses
The discovery curve for human virus species. Cumulative number of species reported to infect humans (black circles and line). Statistically significant upward breakpoints are shown (vertical lines). Best-fit curve (solid line) and lower and upper 95% posterior prediction intervals (dashed lines) for extrapolation to 2020. 1

The article is free full-text; it includes a list of nearly 200  human viruses discovered from 1901 (Yellow Fever) through 2005 (Human T-lymphotrophic virus 4).

  1. Mark E.J. Woolhouse, Richard Howey, Eleanor Gaunt, Liam Reilly, Margo Chase-Topping, Nick Savill (2008). Temporal trends in the discovery of human viruses Proceedings of the Royal Society B: Biological Sciences, 275 (1647), 2111-2115 DOI: 10.1098/rspb.2008.0294[][]
February 24th, 2009

More chemotherapy and tumor immunity

U-118 glioma cells (Nikon Microscopy Gallery)
U-118 Glioma cells 

In one of the earliest posts I made to Mystery Rays,  I commented on an exciting anti-tumor finding. 1  Basically, the suggestion was that when chemotherapy of tumors works, it doesn’t actually work by killing all the tumor cells; or at least not directly.  Instead, the authors said, chemo works because the dying tumor cells release adjuvants (immune stimulants),2 and what actually eliminates the tumor is the specific immune response to the tumor, driven and enhanced by the immune stimulants.   In other words, the chemotherapy is actually acting like the adjuvant in an anti-cancer vaccine. 

Presumably the reason this form of adjuvant is effective, whereas just giving an adjuvant to a cancer patient is not, is that it’s so tightly linked to the tumor you want the immune system to target.   

In the subsequent year and a half there have been a handful of papers looking more at this phenomenon (not counting the review papers, which have churned out at a great rate). For example, it’s been shown that dying tumor cells are cross-presented efficiently due to HMGB1 and similar immune stimulators.3    Now, there’s a more specific support of the concept. 4 

I don’t know if the Apetoh et al paper was the initial impetus for the latest one, or (more likely) if it was already in progress, but a any rate, unless I’ve missed one, this is the second study that directly looks at HMGB1 effects on tumor regression following tumor cell death, and it reaches basically the same conclusion as the first paper.  This was strictly a mouse study, but they used a highly aggressive brain tumor (glioblastoma multiforme).  As well as chemotherapy they used a gene therapy approach, thus managing to hit four of my Mystery Rays buzzwords (tumor immunity, immunity to viruses, innate adjuvants, and if you’re generous oncolytic viruses as well) all at once.  (What would a Mystery Rays Bingo Card look like?)


If the model is correct, then what you really want to do when treating tumors is a double whammy — kill tumor cells, and simultaneously attract in immune cells.  Curtin et al did this by injecting two recombinant adenoviruses directly into the tumor; one rendered the infected cells sensitive to chemotherapy, and the other attracted dendritic cells (DC are important cells for initiating immune responses). Following chemo, the tumors regressed dramatically (about half the mice survived, compared to 100% death without treatment).  And both of the viruses were necessary; without the immune system, killing the cells wasn’t enough, and without tumor cell death, the immune system couldn’t do enough. 

The same treatment in mice without TLR2 did nothing.  TLR2 is an innate immune recognition molecule that triggers inflammation in the presence of (among other things) HMGB1, which is released from dying cells.  This is similar to the Apetoh et al paper, and Curtin et al took the studies a little further by showing that TLR2 had to be on dendritic cells (as opposed to the tumor itself). What’s more, when all the parts were in place (tumor cell death, DC  present, DC expressing TLR2) there was a strong specific anti-tumor cytotoxic T lymphocyte response, while without the TLR2 stimulation there was little such response.

In other words, they’ve firmed up the probable pathway by which chemotherapy eliminated these tumors. The chemotherapy killed cells directly, and the dying cells released HMGB1; the HMGB1 activated dendritic cells in the tumor, by triggering their TLR2 receptor; the activated DC then in turn activated CTL specific for the tumor; and the CTL then completely eliminated the tumor and prevented the remains from regrowing.  (Some of the steps in this pathway remain formally unproven, but the data are consistent with this model.) 

It’s not clear, yet, if this is the universal explanation for successful chemotherapy, or whether chemo sometimes or often works by killing the tumor directly with no requirement for immunity. The authors here looked at several different tumors, expanding on the more correlative data from Apetoh et al., and so far all the cancers that have been checked fall into the immune clearance category.  So, while it’s a long, long way from the bedside, it’s certainly encouraging. 

In conclusion, the results reported provide compelling evidence for the role played by HMGB1 in mediating the efficacy of antiglioma therapeutic regimes that are based on tumor cell killing strategies … [C]ancer immunotherapies coupled with effective cell killing modalities may be necessary to achieve therapeutically relevant antitumor efficacy. 4

  1. Toll-like receptor 4-dependent contribution of the immune system to anticancer chemotherapy and radiotherapy. Apetoh et al. Nature Medicine 13, 1050 – 1059 (2007)  doi:10.1038/nm1622

    Also this review:

    Apetoh, L., F. Ghiringhelli, A. Tesniere, A. Criollo, C. Ortiz, R. Lidereau, C. Mariette, N. Chaput, J. P. Mira, S. Delaloge, F. Andre, T. Tursz, G. Kroemer, and L. Zitvogel. 2007. The interaction between HMGB1 and TLR4 dictates the outcome of anticancer chemotherapy and radiotherapy. Immunol. Rev. 220:47-59.

    and this one:

    Apetoh, L., A. Tesniere, F. Ghiringhelli, G. Kroemer, and L. Zitvogel. 2008. Molecular interactions between dying tumor cells and the innate immune system determine the efficacy of conventional anticancer therapies. Cancer Res. 68:4026-4030.

    and this review from a different group:

    Campana, L., L. Bosurgi, and P. Rovere-Querini. 2008. HMGB1: a two-headed signal regulating tumor progression and immunity. Curr. Opin. Immunol. 20:518-523.[]

  2. Specifically, the dying cells release a protein called HMGB1, which has been shown to be an endogenous adjuvant[]
  3. Brusa, D., S. Garetto, G. Chiorino, M. Scatolini, E. Migliore, G. Camussi, and L. Matera. 2008. Post-apoptotic tumors are more palatable to dendritic cells and enhance their antigen cross-presentation activity. Vaccine 26:6422-6432.[]
  4. James F. Curtin, Naiyou Liu, Marianela Candolfi, Weidong Xiong, Hikmat Assi, Kader Yagiz, Matthew R. Edwards, Kathrin S. Michelsen, Kurt M. Kroeger, Chunyan Liu, A. K. M. Ghulam Muhammad, Mary C. Clark, Moshe Arditi, Begonya Comin-Anduix, Antoni Ribas, Pedro R. Lowenstein, Maria G. Castro (2009). HMGB1 Mediates Endogenous TLR2 Activation and Brain Tumor Regression PLoS Medicine, 6 (1) DOI: 10.1371/journal.pmed.1000010[][]
February 21st, 2009

Life & Death, pre-vaccination

Philosophy of Death
The Philosophy of Death
John Reid (MDCCCXLL) 

What did people die of, before vaccination?

Below is a page from the Journal of the Statistical Society of London, from 1850, showing causes of death in the Metropolis from 1848-1850. For your convenience, I’ve made a chart of the infectious causes.   Some of these diseases (cholera, typhus) have been mainly eliminated by hygiene; a few (scarlatina – Scarlet Fever) by antibiotics; some (influenza) are still scourges, though not nearly as serious; and many, including most of the major killers of 1850, are history — or would have been history, if not for the valiant efforts of the anti-vaccine loons, who are trying to bring us back to the good old days when children routinely died of whooping cough, measles, and smallpox.  

For other exciting charts:

Here’s the images (click for larger versions):

Mortality of the Metropolis Mortality in the Metropolis - chart
Journal of the Statistical Society of Landon, Vol. XII
London: John William Parker, 445, West Strand 1850
Selected infectious Diseases, 1848-1850 





February 19th, 2009

Google vs. influenza

It seems that influenza is a popular target for internet-based research; perhaps because it’s so common and well-known that population trends can be picked up accurately this way.

Five scientists, and one from the CDC, have published evidence in Nature1 that Google search terms are accurate ways of measuring influenza epidemics.  Their influenza tool is available at (and has an explanation of the techniques involved).  Their accuracy seems pretty decent, as the figure below shows — red traces are CDC-recorded cases, black is the cases as predicted from Google searches.  

Google influenza searches
A comparison of model estimates for the mid-Atlantic region (black) against CDC-reported ILI percentages (red)1

There are a surprising number of on-line maps for influenza and avian influenza, although as though far as I know they’re all much more descriptive (all based on reported cases) than Google’s version, which is (sort of) predictive.  For example, there’s the avian influenza outbreak map, various maps from the WHO , and the CDC’s set of maps.  (There’s also Bird Flu Breaking Newswhich occasionally links to my posts, but the site seems to be broken; too bad, because if I remember correctly, it had an interesting variant on maps that was conceptually related to Google’s — showing where new discussion on avian flu was located.)  

  1. Jeremy Ginsberg, Matthew H. Mohebbi, Rajan S. Patel, Lynnette Brammer, Mark S. Smolinski, Larry Brilliant (2009). Detecting influenza epidemics using search engine query data Nature, 457 (7232), 1012-1014 DOI: 10.1038/nature07634[][]
February 16th, 2009

Not merely bioweaponized, but mutualistic bioweaponized wasps

Parasitic waspA while ago I mentioned the truly spectacular symbiosis between some parasitic wasps and their weaponized internal viruses.   These wasps parasitize caterpillars and the like; and to subdue their prey, the wasps inject viruses into their prey, along with their own eggs. The viral immune evasion functions then block the caterpillar’s defenses, allowing the wasp’s eggs to replicate.  The viruses, in turn, get free replication, because they’re actually part of the wasp genome – wasp genes, that assemble to look like viruses and act like viruses.

Back in the prehistoric days when I first talked about it (December ’07), it wasn’t clear whether these were all actually viruses that had become symbiotic and moved into the wasp genome, or whether they started out as wasp genes that became more and more virus-like:

A more parsimonious hypothesis would be that bracoviruses do not originate from any of the large genome viruses characterized to date. They may have been built up from a simple system producing circular DNA intermediates, such as mobile elements, within the wasp genome. The acquisition of a capsid protein, possibly of viral origin, around the circular DNA intermediates would have allowed infection of lepidopteran cells. Finally, virulence genes could have been acquired from the wasp genome at different times during evolution of bracovirus-bearing wasp lineages, thus explaining why CcBV genes encoding proteins with a predicted function resemble cellular genes. 1

Because I know my dedicated readers2 have been fretting about this since I mentioned it, I now am happy to report that the question is apparently settled:3  Bézier et al. searched through various wasp genomes and found the genes associated with the virus-like particles, and were able to show that in fact they were originally viruses — specifically, members of the nudivirus family — that moved into the wasps’ genomes.  Nudiviruses are known (though not well-studied) insect viruses, but apparently they’ve not been known to infect Hymenoptera.  

As the commentary 4  on this paper observes:

Whereas viruses have been typically seen as either parasites or commensals, we must now recognize a potential for obligatory mutualism. … We would suggest that the more interesting lesson here for virologists and for evolutionary biologists may be that there is now reason to start thinking about virus-host relationships in much broader terms, so as to include not only mutualism, which may be a lot more common than previously contemplated, but also obligatory mutualism, as exemplified by the wasp-nudivirus story. 4

  1. Espagne, E. et al. Genome sequence of a polydnavirus: insights into symbiotic virus evolution. Science 306, 286-289 (2004[]
  2. Hi, Mom![]
  3. A. Bezier, M. Annaheim, J. Herbiniere, C. Wetterwald, G. Gyapay, S. Bernard-Samain, P. Wincker, I. Roditi, M. Heller, M. Belghazi, R. Pfister-Wilhem, G. Periquet, C. Dupuy, E. Huguet, A.-N. Volkoff, B. Lanzrein, J.-M. Drezen (2009). Polydnaviruses of Braconid Wasps Derive from an Ancestral Nudivirus Science, 323 (5916), 926-930 DOI: 10.1126/science.1166788[]
  4. Stoltz, D. B., and J. B. Whitfield. 2009. VIROLOGY: Making Nice with Viruses. Science 323:884-885[][]
February 14th, 2009

Darwin Day

Yeah, I know I’m late for Darwin Day. It took me a bit to find the picture I remembered.  This is by Carl Buell, and it imagines a young Darwin on the Galapagos.  As Buell pointed out, the iconic images of Darwin — check out any of the scores or hundreds that were posted on Darwin’s 200th — is of the elderly, bearded, solemn sage, after Origin was published.   Think instead of the young Darwin, playful and imaginative, the man who sailed around the world, roared up mountains, who rode horses through Brazil and tortoises through the Galapagos.

Young Darwin (by Carl Buell)

February 12th, 2009

On peer review and fraud

Fraud Squad

Following the Wakefield fraud story, I’ve seen several blogs and blog commenters suggesting that The Lancet was at fault for failing to catch the fraud in the peer review process.  I (and I think most practicing scientists) don’t agree with that condemnation, which I think shows that many people outside the field don’t really understand what peer review is supposed to do.  I’m just going to together a couple of comments I’ve made on other blogs …

At Hoyden About Town, I said (in part):

There’s been lots of criticism of The Lancet for publishing this study (they’ve since caused it to be retracted) — but I don’t agree with most of that criticism. Scientific journals should try to catch fraud, but this kind of fraud, wholesale fakery, is ironically hard to catch than the simpler forms where, say, a single part of one figure is changed. It’s not possible for a journal to go back and re-scrutinize all the primary data in all the papers it publishes, for example. It’s necessary to rely on the scientific process as a self-correcting mechanism. Of course, that’s pretty much what happened in this case — Wakefield’s work was rapidly and thoroughly refuted in the scientific literature — but the mainstream press has lagged far behind the scientific consensus. If it wasn’t for ambulance chasers, scandal-seeking newspapers, ignorant and naive reporters, and greedy lawyers, this would have diappeared within a year of Wakefield’s first article, as happens with almost all the mistaken, careless, and misinterpreted scientific papers that are published by the dozen every day.

Here I’ve bolded a sentence that’s worth re-emphasizing: This was fraud, but it didn’t directly set science back very far, because good science refuted it quickly and rapidly.  It was the non-science world that set back research on autism, by accepting what scientists already knew was wrong.

Effect Measure made a similar point about peer review:

Wakefield provided the case summaries (which we now know were doctored) and a reviewer would not have had access to or had the time to look at the original medical records. The same is true for the journal. Accurate representation of raw data is taken on trust. I don’t think The Lancet can be taken to task for not catching this. This kind of scientific misconduct is only found after the fact.

In the comments on the Effect Measure article, Sam C made an interesting suggestion:

Review is fine for good science and for research where errors will not have far-reaching impact (so the normal process of correction and extension by future workers is appropriate).

But cases like this need audit. An audit can not always detect deliberate fraud (just as in financial auditing), but it might pick up errors of protocol (like the O’Leary lab’s inadequate controls in their DNA/RNA work) or substandard or imperfect work (inappropriate statistical techniques, equipment whose limitations are not understood, results transferred incorrectly, etc.).

Engineering organisations use ISO standard QA systems, but these only work if applied correctly and conscientiously.

Perhaps any grant award should require that some percentage of the award be allocated to an independent audit of techniques, results and conclusions?

I replied to his comment as follows:

Sam, this is an interesting idea I haven’t heard floated before. I think it’s not doable as a portion of every grant, but I wonder if there could be a separate fund set aside specifically for audits. I’m not sure how it could work, and it would be a real problem to get it balanced properly, though — if there were a standing committee or organization, I could see it getting bogged down in bureaucracy, dinging every paper they come across for trivial procedural errors (“Patient #214 signed the form but failed to initial the 17th page”) so that genuine problems would be hidden anyway.

I don’t know much about formal audit procedures.  Is there a precedent for a useful type of audit that would focus on fraud detection and completely broken research, without getting bogged down in trivia?

I want to make a mention of the Journal of Experimental Medicine and the Journal of Cell Biology, which seem to me to be taking a much more proactive attitude toward fraud than most other scientific journals:

“The issue of data integrity should not be left to chance and probability. This is scholarly publishing, not blackjack.”

M. Rossner (2008). A false sense of security The Journal of Cell Biology, 183 (4), 573-574 DOI: 10.1083/jcb.200810172

February 10th, 2009

Immune control of Hepatitis C virus and HIV: coincidence or plan?

HCV and lipid droplets, by Torsten Schaller
HCV protein associated with lipid droplets
Torsten Schaller, Research As Art)

Although there are quite a few viruses that infect and then persist in the infected animal for a long time, most of these viruses don’t cause a lot of problems during the persistent state. Herpesviruses, adenoviruses, and several other families can stick around for a long time (life-long, in the case of most herpesviruses) and although you’ll sometimes see occasional recurrence, and occasionally there can be serious disease from the reactivation (examples being shingles, from recurrent varicella-zoster virus, or the very rare cancers associated with Epstein-Barr virus) — for the most part these are really unusual outcomes. Mostly we can stroll around with our complement of viral passengers and we’re perfectly fine with it.

There are a handful of exceptions, in humans and in other animals, where viruses that cause chronic infection also cause chronic, severe disease. With these viruses we’d like to know why they become chronic in the first place (why doesn’t the immune system eliminate them?), and we’d like to know why they cause disease (why aren’t they like our friendly neighborhood herpesvirus)? We don’t have good answers for either of these questions. In fact, I don’t think we even have a good sense if the answers are the same for different viruses, or whether each of them manages to persist and cause chronic disease through their own unique factors.

Two of the most prominent chronic virus diseases in humans are HIV and HCV (hepatitis C virus). A recent paper1 suggests that these guys may have at least something in common in the way they escape immune control, and in the way the immune system controls them.

HCV protein distribution in cells
HCV protein distribution in infected hepatoma cells
(Mark Harris lab)

It’s pretty well known that one way HIV escapes immune control is that it mutates so fast, the immune system can’t get a grip on it. In particular, the cytotoxic T lymphocytes (CTL) that are specialized to control virus infections need to recognize a stretch of about 9 amino acids (a peptide, in other words), and if that sequence changes the CTL may no longer recognize the virus. (I’ve talked about that here and here.) It’s also become clear that HCV does the same thing, although perhaps less dramatically than does HIV, and that this mutational immune escape is one reason HCV can persist and continue to cause disease (see here for more).

With HIV, there are a number of “elite controllers” who seem to be resistant to the virus’s ability to mutate away from immune control. In many cases this seems to be because the CTL in those individuals are focused on a particular critical stretch of amino acids that simply can’t mutate without severely damaging the virus (reducing HIV’s replicative fitness). The reason these elite controllers select that critical peptide is that they have a MHC class I allele that specifically binds to that peptide sequence. The HLA-B27 and HLA-B57 alleles seem to be particularly likely to find critical peptides, and people with those MHC alleles are more likely to be elite controllers.

The new HCV paper1 shows that HLA-B27 is also protective against HCV infection 2, and for the same reason — the HCV peptide that binds to HLA-B27 is a critical sequence that can’t mutate much without severely damaging the virus. (When HCV does mutate away from HLA-B27-mediated control, it’s because it has developed multiple mutations in the peptide, not just one, and it’s exponentially3 harder for the virus to make two mutations vs. one.)

Is it just a coincidence that HLA-B27 is involved in both cases, or is there something specially magical about HLA-B27? I’d be inclined to say it’s just coincidence except that HLA-B27 is such a special molecule4 already. It’s involved in all kinds of disease risks, both reducing the risk of some infectious diseases like HIV and HCV and dramatically increasing the risk of autoimmune diseases like ankylosing spondylitis and many others. And off the top of my head, I think it’s one of the very ancient and highly diversified groups of HLA molecules. So maybe there is something about it that manages to focus on critical viral peptides, or that makes it a particularly strong stimulator of CTL, and that gives it a selective advantage that outweighs its increased risk of autoimmune disease.

  1. Eva Dazert, Christoph Neumann-Haefelin, Stéphane Bressanelli, Karen Fitzmaurice, Julia Kort, Jörg Timm, Susan McKiernan, Dermot Kelleher, Norbert Gruener, John E. Tavis, Hugo R. Rosen, Jaqueline Shaw, Paul Bowness, Hubert E. Blum, Paul Klenerman, Ralf Bartenschlager, Robert Thimme (2009). Loss of viral fitness and cross-recognition by CD8+ T cells limit HCV escape from a protective HLA-B27–restricted human immune response Journal of Clinical Investigation DOI: 10.1172/JCI36587[][]
  2. This part was already known[]
  3. or maybe geometrically, I don’t know[]
  4. Unicorns have HLA-B27! Well-known fact![]
February 8th, 2009

Anti-vaccine child deaths based on lies

Just in case anyone hasn’t heard about this already:

THE doctor who sparked the scare over the safety of the MMR vaccine for children changed and misreported results in his research, creating the appearance of a possible link with autism, a Sunday Times investigation has found. … our investigation, confirmed by evidence presented to the General Medical Council (GMC), reveals that: In most of the 12 cases, the children’s ailments as described in The Lancet were different from their hospital and GP records. Although the research paper claimed that problems came on within days of the jab, in only one case did medical records suggest this was true, and in many of the cases medical concerns had been raised before the children were vaccinated. … Last week official figures showed that 1,348 confirmed cases of measles in England and Wales were reported last year, compared with 56 in 1998. Two children have died of the disease.

–From The Sunday Times.

For more charges against the doctor in question (Andrew Wakefield) see this article in the Times (“The list of allegations against Dr Wakefield took more than an hour to read out“).  In particular, he was paid to find a link between vaccines and illness.

Edit: An excellent roundup of the story and responses is here; a useful timeline of the MMR/autism fraud is here.

February 5th, 2009

Now I really, really like Bill Gates

MosquitoFrom MSNBC:

“Bill Gates just released mosquitos into the audience at TED and said, ‘Not only poor people should experience this.'”

That was the post by Facebook’s Senior Platform Manager Dave Morin on social networking site Twitter.

The event took place at the TED2009 (Technology, Entertainment and Design) conference on Wednesday in Long Beach, Calif., where the Microsoft chairman was delivering a presentation about malaria education and eradication. Malaria is transmitted from person to person via mosquito bites.

The mosquito incident was confirmed by the media office of the Bill and Melinda Gates Foundation, which also noted that the insects released were not carrying malaria. 

Alternate titles:
“It’s a feature, not a bug”
“A patch for Yellow Fever and Dengue will be released with Service Pack 3”

(With thanks to Len Berlind)