Mystery Rays from Outer Space

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Immunology, virology, baseball, and pictures of my kids

iayork
206 posts

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  • February 27, 2011
  • 07:43 AM
  • 744 views

Patients, pathogens, ecosystems

by iayork in Mystery Rays from Outer Space

“A terrified man realizing he has just contracted the plague, surrounded by a group of people.” By E.M. Ward, 1848. Even the most lethal pathogens we know of don’t kill every single infected individual.1. Sometimes this is because the pathogen that infects the person is relatively weak. Sometimes it’s because the dose was low. And [...]... Read more »

  • December 8, 2010
  • 06:14 AM
  • 643 views

Do TRegs discriminate?

by iayork in Mystery Rays from Outer Space

As I’ve noted several times before, regulatory T cells are important reasons for the poor immune response to tumors. TRegs are normal components of an immune response, “designed” to keep inflammation from running riot in general and to prevent responses to self-antigens in particular. Whether it’s because tumors are mostly (though not solely) self antigens, [...]... Read more »

James, E., Yeh, A., King, C., Korangy, F., Bailey, I., Boulanger, D., Van den Eynde, B., Murray, N., & Elliott, T. (2010) Differential Suppression of Tumor-Specific CD8 T Cells by Regulatory T Cells. The Journal of Immunology, 185(9), 5048-5055. DOI: 10.4049/jimmunol.1000134  

  • November 30, 2010
  • 06:14 AM
  • 838 views

HIV evolution: individual vs. population

by iayork in Mystery Rays from Outer Space

Worldwide HIV/AIDs Epidemic Statistics (We are in the process of selling one home and buying another, while at work I just finished organizing a course on biosecurity for an international group. In the upcoming week I’m traveling to a conference in Washington. To say nothing of the Thanksgiving holiday. All this means short and scarce [...]... Read more »

Fryer, H., Frater, J., Duda, A., Roberts, M., , ., Phillips, R., & McLean, A. (2010) Modelling the Evolution and Spread of HIV Immune Escape Mutants. PLoS Pathogens, 6(11). DOI: 10.1371/journal.ppat.1001196  

  • November 4, 2010
  • 06:41 AM
  • 722 views

Mutation rates in man and virus

by iayork in Mystery Rays from Outer Space

John Hawks1 has a long and very interesting post on the human mutation rate — not just the actual number (which turns out to be less well documented and much more slippery than I had realized), but the techniques used to calculate the rate, and difficulties therein. So much of the literature in this area [...]... Read more »

  • November 3, 2010
  • 06:14 AM
  • 601 views

Shield or target? A downside of immune evasion

by iayork in Mystery Rays from Outer Space

T cells (green) and herpesvirus-infected cells (red) (from Akiko Iwasaki) We know that lots of viruses, especially herpesviruses, block antigen presentation. The assumption has been that they are thereby preventing T cells from recognizing infected cells, though long-term readers of this blog1 will know that I’ve been puzzled about the details of this for quite [...]... Read more »

  • October 28, 2010
  • 06:14 AM
  • 857 views

Immunological standoff

by iayork in Mystery Rays from Outer Space

TRegs infiltrate into a tumor There’s increasing evidence supporting the notion that tumors are often not rejected by the immune system because regulatory T cells actively block the immune response to the tumor cells. 1 That means that within the tumor, two branches of the immune response are fighting it out. If the TRegs win, [...]... Read more »

  • October 22, 2010
  • 06:14 AM
  • 700 views

Mosquitos: Blaming the victim?

by iayork in Mystery Rays from Outer Space

Malaria parasite in mosquito midgut We often think of mosquitoes as willing co-conspirators in spreading human1 pathogens. But of course, in most cases the mosquito would be just as happy to get rid of the pathogen themselves; even if it doesn’t cause as severe as disease in the mosquito as in humans, it’s not doing [...]... Read more »

Bartholomay, L., Waterhouse, R., Mayhew, G., Campbell, C., Michel, K., Zou, Z., Ramirez, J., Das, S., Alvarez, K., Arensburger, P.... (2010) Pathogenomics of Culex quinquefasciatus and Meta-Analysis of Infection Responses to Diverse Pathogens. Science, 330(6000), 88-90. DOI: 10.1126/science.1193162  

  • October 20, 2010
  • 07:04 PM
  • 1,591 views

It takes a village

by iayork in Mystery Rays from Outer Space

Our results suggest that, for typical connection strengths between communities, spatial heterogeneity has only a weak effect on outbreak size distributions, and on the risk of emergence per introduction. For example, if R0=1.4 or larger, any village connected to a large city by just ten commuters a day is, effectively, just a part of the [...]... Read more »

  • October 7, 2010
  • 06:14 AM
  • 668 views

MHC vs pathogens: Evolution showdown

by iayork in Mystery Rays from Outer Space

I’m not finding time to give these papers a full post each, so let me pool together several in the same theme: MHC alleles and protection against pathogens. It’s generally accepted that the reason there are so many MHC alleles is related to their ability to protect against pathogens.1 The version is probably the frequency-dependent [...]... Read more »

Koehler, R., Walsh, A., Saathoff, E., Tovanabutra, S., Arroyo, M., Currier, J., Maboko, L., Hoelsher, M., Robb, M., Michael, N.... (2010) Class I HLA‐A*7401 Is Associated with Protection from HIV‐1 Acquisition and Disease Progression in Mbeya, Tanzania. The Journal of Infectious Diseases. DOI: 10.1086/656913  

MacNamara, A., Rowan, A., Hilburn, S., Kadolsky, U., Fujiwara, H., Suemori, K., Yasukawa, M., Taylor, G., Bangham, C., & Asquith, B. (2010) HLA Class I Binding of HBZ Determines Outcome in HTLV-1 Infection. PLoS Pathogens, 6(9). DOI: 10.1371/journal.ppat.1001117  

  • September 23, 2010
  • 06:14 AM
  • 1,023 views

Monkeypox, smallpox

by iayork in Mystery Rays from Outer Space

Confluent smallpox1 Vaccination against smallpox ended some 40 years ago. As the vaccinated population gets smaller and the susceptible population gets larger, at least one poxvirus is re-exploring the human population. Not smallpox, of course, but monkeypox, which is becoming dramatically more common in humans than it used to be.2 Monkeypox (which is actually primarily [...]... Read more »

Rimoin, A., Mulembakani, P., Johnston, S., Lloyd Smith, J., Kisalu, N., Kinkela, T., Blumberg, S., Thomassen, H., Pike, B., Fair, J.... (2010) Major increase in human monkeypox incidence 30 years after smallpox vaccination campaigns cease in the Democratic Republic of Congo. Proceedings of the National Academy of Sciences, 107(37), 16262-16267. DOI: 10.1073/pnas.1005769107  

Pierre Formenty, Mohammed O. Muntasir, Inger Damon, Vipul Chowdhary, Martin L. Opoka, Charlotte Monimart, Elmangory M. Mutasim, Jean-Claude Manuguerra, Whitni B. Davidson, Kevin L. Karem.... (2010) Human Monkeypox Outbreak Caused by Novel Virus Belonging to Congo Basin Clade, Sudan, 2005. Emerging Infectious Diseases, 16(10). info:/10.3201/eid1610.100713

Hutson CL, Lee KN, Abel J, Carroll DS, Montgomery JM, Olson VA, Li Y, Davidson W, Hughes C, Dillon M.... (2007) Monkeypox zoonotic associations: insights from laboratory evaluation of animals associated with the multi-state US outbreak. The American journal of tropical medicine and hygiene, 76(4), 757-68. PMID: 17426184  

  • September 20, 2010
  • 06:14 AM
  • 672 views

MHC on the brain

by iayork in Mystery Rays from Outer Space

Needleman et al, 1 Fig 1: Section of rat vidual cortext stained for MHC class I (green) and nuclei (red) Needleman et al, 1 Fig 1: Section of rat vidual cortext stained for MHC class I (green) and nuclei (red) I said the other day that not all MHC class I molecules are involved in immunity, and [...]... Read more »

Goddard, C., Butts, D., & Shatz, C. (2007) Regulation of CNS synapses by neuronal MHC class I. Proceedings of the National Academy of Sciences, 104(16), 6828-6833. DOI: 10.1073/pnas.0702023104  

Zohar O, Reiter Y, Bennink JR, Lev A, Cavallaro S, Paratore S, Pick CG, Brooker G, & Yewdell JW. (2008) Cutting edge: MHC class I-Ly49 interaction regulates neuronal function. Journal of immunology (Baltimore, Md. : 1950), 180(10), 6447-51. PMID: 18453559  

Goddard CA, Butts DA, & Shatz CJ. (2007) Regulation of CNS synapses by neuronal MHC class I. Proceedings of the National Academy of Sciences of the United States of America, 104(16), 6828-33. PMID: 17420446  

  • September 7, 2010
  • 06:14 AM
  • 668 views

Assassination or accident?

by iayork in Mystery Rays from Outer Space

I have as much respect for viruses’ ability to manipulate their host as the next guy, and I’m probably more of a fan of viral immune evasion than that next guy. But I still do think that coincidences do happen. A paper from John Trowsdale and colleagues1 shows that Kaposi’s Sarcoma Herpesvirus (KSHV) destroys HFE, [...]... Read more »

Rohrlich PS, Fazilleau N, Ginhoux F, Firat H, Michel F, Cochet M, Laham N, Roth MP, Pascolo S, Nato F.... (2005) Direct recognition by alphabeta cytolytic T cells of Hfe, a MHC class Ib molecule without antigen-presenting function. Proceedings of the National Academy of Sciences of the United States of America, 102(36), 12855-60. PMID: 16123136  

Drakesmith H, Chen N, Ledermann H, Screaton G, Townsend A, & Xu XN. (2005) HIV-1 Nef down-regulates the hemochromatosis protein HFE, manipulating cellular iron homeostasis. Proceedings of the National Academy of Sciences of the United States of America, 102(31), 11017-22. PMID: 16043695  

  • September 2, 2010
  • 09:47 AM
  • 1,379 views

Immunity under natural selection

by iayork in Mystery Rays from Outer Space

HapMap 3, officially announced in today’s issue of Nature,1 is an “integrated data set of common and rare alleles” in human populations, built from “1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations“.  As well as being a resource for genome-wide studies, there are a number of things that can [...]... Read more »

Douroudis K, Kingo K, Silm H, Reimann E, Traks T, Vasar E, & Kõks S. (2010) The CD226 Gly307Ser gene polymorphism is associated with severity of psoriasis. Journal of dermatological science, 58(2), 160-1. PMID: 20399620  

Maiti AK, Kim-Howard X, Viswanathan P, Guillén L, Qian X, Rojas-Villarraga A, Sun C, Cañas C, Tobón GJ, Matsuda K.... (2010) Non-synonymous variant (Gly307Ser) in CD226 is associated with susceptibility to multiple autoimmune diseases. Rheumatology (Oxford, England), 49(7), 1239-44. PMID: 20338887  

Heron M, Grutters JC, Van Moorsel CH, Ruven HJ, Kazemier KM, Claessen AM, & Van den Bosch JM. (2009) Effect of variation in ITGAE on risk of sarcoidosis, CD103 expression, and chest radiography. Clinical immunology (Orlando, Fla.), 133(1), 117-25. PMID: 19604725  

Luke MM, O'Meara ES, Rowland CM, Shiffman D, Bare LA, Arellano AR, Longstreth WT Jr, Lumley T, Rice K, Tracy RP.... (2009) Gene variants associated with ischemic stroke: the cardiovascular health study. Stroke; a journal of cerebral circulation, 40(2), 363-8. PMID: 19023099  

  • August 24, 2010
  • 06:14 AM
  • 954 views

Adenoviruses and the occupied sign

by iayork in Mystery Rays from Outer Space

“Adenovirus” (by Mapposity) There are two aspects about virology that constantly amaze me: How much we know about viruses, and how little we know about viruses. Adenovirus research offers examples of both. Adenoviruses are probably among the best-studied virus groups.1 We really do know an amazing amount about them. But it was only last year [...]... Read more »

Zhang, Y., Huang, W., Ornelles, D., & Gooding, L. (2010) Modeling Adenovirus Latency in Human Lymphocyte Cell Lines. Journal of Virology, 84(17), 8799-8810. DOI: 10.1128/JVI.00562-10  

  • August 19, 2010
  • 06:14 AM
  • 692 views

And so on, ad infinitum

by iayork in Mystery Rays from Outer Space

Rosy Apple Aphid (Whalon lab, MSU) Normally I don’t talk about research that’s well covered elsewhere, but I like this one so much (and it links back to so many of my earlier posts; check the footnotes for those links) that I’ll make an exception here.  I’d seen bits and pieces of this story, but [...]... Read more »

  • August 17, 2010
  • 06:15 AM
  • 587 views

Pigs (and their viruses) fly

by iayork in Mystery Rays from Outer Space

An emerging disease that I just missed directly seeing emerge is PRRS. PRRS is “porcine reproductive and respiratory syndrome”, which pretty much sums up the disease. It’s caused by — you’ll never guess — Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus that emerged in 1987. That was the year I left large animal [...]... Read more »

  • August 10, 2010
  • 06:14 AM
  • 837 views

DNA virus quasispecies? (Probably not.)

by iayork in Mystery Rays from Outer Space

I’ve talked about quasispecies several times, and emphasized that RNA viruses, with their high replication error rates, are most prone to forming quasispecies. I’ve also pointed out, though, that actually measuring quasispecies is technically difficult, and measuring it for the larger DNA viruses would be even harder. You’d need to run sequences on many viral [...]... Read more »

Cheng, T., Valentine, M., Gao, J., Pingel, J., & Yokoyama, W. (2009) Stability of Murine Cytomegalovirus Genome after In Vitro and In Vivo Passage. Journal of Virology, 84(5), 2623-2628. DOI: 10.1128/JVI.02142-09  

  • August 5, 2010
  • 06:14 AM
  • 1,689 views

The good old days, revisited

by iayork in Mystery Rays from Outer Space

As a general remark, the Measles were mild, while on the contrary, the Mumps were almost invariably severe, and frequently attended with metastasis to the testicles. Some cases of the latter were attended with enormous swelling and high inflammatory excitement, requiring the lancet and other antiphlogistic remedies. … As a local application to the scrotum none appeared to afford [...]... Read more »

Quinlisk, M. (2010) Mumps Control Today. The Journal of Infectious Diseases, 2147483647. DOI: 10.1086/655395  

  • August 3, 2010
  • 06:14 AM
  • 856 views

Lamprey immunity, again

by iayork in Mystery Rays from Outer Space

From A History of British Fish (William Yarrell, 1835) I’ve talked about lamprey immune systems several times (here, here, and here). I find them fascinating because it shows both how our own immune system developed, and also shows alternate routes that can lead to a pretty good, but very different, immune system. Quick background: In [...]... Read more »

Herrin, B., & Cooper, M. (2010) Alternative Adaptive Immunity in Jawless Vertebrates. The Journal of Immunology, 185(3), 1367-1374. DOI: 10.4049/jimmunol.0903128  

  • July 29, 2010
  • 06:13 AM
  • 573 views

Genetic ironies: Retrovirus version

by iayork in Mystery Rays from Outer Space

I’ve mentioned the APOBEC family before (for example, here and here). They’re a group of mammalian genes that (among other things) protect against retrovirus infection. DIfferent strains of mice have different resistance to retrovirus infection. Some strains are highly resistant, others quite susceptible. At least some of this difference in susceptibility comes down to different [...]... Read more »

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