206 posts · 144,046 views
Immunology, virology, baseball, and pictures of my kids
iayork
206 posts
Sort by: Latest Post, Most Popular
View by: Condensed, Full
- February 27, 2011
- 07:43 AM
- 313 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 »
Centers for Disease Control and Prevention (CDC). (2011) Fatal Laboratory-Acquired Infection with an Attenuated Yersinia pestis Strain --- Chicago, Illinois, 2009. MMWR. Morbidity and mortality weekly report, 60(7), 201-5. PMID: 21346706
- December 8, 2010
- 06:14 AM
- 271 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
- 257 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
- 292 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 »
CASTRO, C., ARNOLD, J., & CAMERON, C. (2005) Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective. Virus Research, 107(2), 141-149. DOI: 10.1016/j.virusres.2004.11.004
- November 3, 2010
- 06:14 AM
- 299 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 »
Lampen, M., Verweij, M., Querido, B., van der Burg, S., Wiertz, E., & van Hall, T. (2010) CD8 T Cell Responses against TAP-Inhibited Cells Are Readily Detected in the Human Population. The Journal of Immunology. DOI: 10.4049/jimmunol.1001774
- October 28, 2010
- 06:14 AM
- 296 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 »
Kuczma, M., Kopij, M., Pawlikowska, I., Wang, C., Rempala, G., & Kraj, P. (2010) Intratumoral Convergence of the TCR Repertoires of Effector and Foxp3 CD4 T cells. PLoS ONE, 5(10). DOI: 10.1371/journal.pone.0013623
- October 22, 2010
- 06:14 AM
- 334 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
- 1,316 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 »
Kubiak, R., Arinaminpathy, N., & McLean, A. (2010) Insights into the Evolution and Emergence of a Novel Infectious Disease. PLoS Computational Biology, 6(9). DOI: 10.1371/journal.pcbi.1000947
- October 7, 2010
- 06:14 AM
- 300 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
Appanna, R., Ponnampalavanar, S., Lum Chai See, L., & Sekaran, S. (2010) Susceptible and Protective HLA Class 1 Alleles against Dengue Fever and Dengue Hemorrhagic Fever Patients in a Malaysian Population. PLoS ONE, 5(9). DOI: 10.1371/journal.pone.0013029
Guivier, E., Galan, M., Male, P., Kallio, E., Voutilainen, L., Henttonen, H., Olsson, G., Lundkvist, A., Tersago, K., Augot, D.... (2010) Associations between MHC genes and Puumala virus infection in Myodes glareolus are detected in wild populations, but not from experimental infection data. Journal of General Virology, 91(10), 2507-2512. DOI: 10.1099/vir.0.021600-0
- September 23, 2010
- 06:14 AM
- 290 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
Nalca, A., Livingston, V., Garza, N., Zumbrun, E., Frick, O., Chapman, J., & Hartings, J. (2010) Experimental Infection of Cynomolgus Macaques (Macaca fascicularis) with Aerosolized Monkeypox Virus. PLoS ONE, 5(9). DOI: 10.1371/journal.pone.0012880
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
- 334 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 »
Needleman, L., Liu, X., El-Sabeawy, F., Jones, E., & McAllister, A. (2010) MHC class I molecules are present both pre- and postsynaptically in the visual cortex during postnatal development and in adulthood. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1006087107
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
Huh, G. (2000) Functional Requirement for Class I MHC in CNS Development and Plasticity. Science, 290(5499), 2155-2159. DOI: 10.1126/science.290.5499.2155
- September 7, 2010
- 06:14 AM
- 313 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 »
Rhodes DA, Boyle LH, Boname JM, Lehner PJ, & Trowsdale J. (2010) Ubiquitination of lysine-331 by Kaposi's sarcoma-associated herpesvirus protein K5 targets HFE for lysosomal degradation. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20805500
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
- 1,034 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 »
The International HapMap 3 Consortium. (2010) Integrating common and rare genetic variation in diverse human populations. Nature, 52-58. DOI: 10.1038/nature09298
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
- 338 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
- 332 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 »
Oliver KM, Degnan PH, Hunter MS, & Moran NA. (2009) Bacteriophages encode factors required for protection in a symbiotic mutualism. Science (New York, N.Y.), 325(5943), 992-4. PMID: 19696350
Degnan PH, Yu Y, Sisneros N, Wing RA, & Moran NA. (2009) Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors. Proceedings of the National Academy of Sciences of the United States of America, 106(22), 9063-8. PMID: 19451630
Degnan PH, & Moran NA. (2008) Evolutionary genetics of a defensive facultative symbiont of insects: exchange of toxin-encoding bacteriophage. Molecular ecology, 17(3), 916-29. PMID: 18179430
Degnan PH, & Moran NA. (2008) Diverse phage-encoded toxins in a protective insect endosymbiont. Applied and environmental microbiology, 74(21), 6782-91. PMID: 18791000
- August 17, 2010
- 06:15 AM
- 299 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 »
Shi, M., Lam, T., Hon, C., Murtaugh, M., Davies, P., Hui, R., Li, J., Wong, L., Yip, C., Jiang, J.... (2010) Phylogeny-Based Evolutionary, Demographical, and Geographical Dissection of North American Type 2 Porcine Reproductive and Respiratory Syndrome Viruses. Journal of Virology, 84(17), 8700-8711. DOI: 10.1128/JVI.02551-09
- August 10, 2010
- 06:14 AM
- 398 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
- 1,390 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
- 351 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
- 271 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 »
Sanville, B., Dolan, M., Wollenberg, K., Yan, Y., Martin, C., Yeung, M., Strebel, K., Buckler-White, A., & Kozak, C. (2010) Adaptive Evolution of Mus Apobec3 Includes Retroviral Insertion and Positive Selection at Two Clusters of Residues Flanking the Substrate Groove. PLoS Pathogens, 6(7). DOI: 10.1371/journal.ppat.1000974
topics
join us!
Do you write about peer-reviewed research in your blog? Use ResearchBlogging.org to make it easy for your readers — and others from around the world — to find your serious posts about academic research.
If you don't have a blog, you can still use our site to learn about fascinating developments in cutting-edge research from around the world.
