194 posts · 84,727 views
Immunology, virology, baseball, and pictures of my kids
iayork
194 posts
Sort by: Latest Post, Most Popular
View by: Condensed, Full
- September 2, 2010
- 09:47 AM
- 18 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
- 44 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
- 41 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
- 46 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
- 79 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
- 66 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
- 70 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
- 68 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
- July 26, 2010
- 06:15 AM
- 74 views
Quasispecies thoughts
by iayork in Mystery Rays from Outer Space
Quasispecies theory predicts that slower replicators will be favored if they give rise to progeny that are on average more fit; these populations occupy short, flat regions of the fitness landscape … Flat quasispecies accept mutation without a corresponding effect on fitness … A flat quasispecies with an expansive mutant repertoire can explore vast regions of [...]... Read more »
Lauring, A., & Andino, R. (2010) Quasispecies Theory and the Behavior of RNA Viruses. PLoS Pathogens, 6(7). DOI: 10.1371/journal.ppat.1001005
- July 12, 2010
- 06:14 AM
- 105 views
Short takes: Deep sequencing and HIV drug resistance
by iayork in Mystery Rays from Outer Space
Short comments about what I’ve been reading (besides several hundred influenza articles): Hedskog, C., Mild, M., Jernberg, J., Sherwood, E., Bratt, G., Leitner, T., Lundeberg, J., Andersson, B., & Albert, J. (2010). Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing PLoS ONE, 5 (7) DOI: 10.1371/journal.pone.0011345 The whole deep sequencing thing is [...]... Read more »
Hedskog, C., Mild, M., Jernberg, J., Sherwood, E., Bratt, G., Leitner, T., Lundeberg, J., Andersson, B., & Albert, J. (2010) Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing. PLoS ONE, 5(7). DOI: 10.1371/journal.pone.0011345
- June 22, 2010
- 06:14 AM
- 128 views
Dual-specificity T cells and autoimmunity
by iayork in Mystery Rays from Outer Space
TcR interacting with artificial membrane1
Why does autoimmune disease (sometimes) follow viral infection?2
It’s a pretty well-known phenomenon, but a definite answer isn’t yet known — and of course there may not be a single answer, there may be multiple causes. We know that many autoimmune diseases seem to be triggered by some sort of infection [...]... Read more »
Fujinami, R. (2001) Can Virus Infections Trigger Autoimmune Disease?. Journal of Autoimmunity, 16(3), 229-234. DOI: 10.1006/jaut.2000.0484
McGargill MA, Mayerova D, Stefanski HE, Koehn B, Parke EA, Jameson SC, Panoskaltsis-Mortari A, & Hogquist KA. (2002) A spontaneous CD8 T cell-dependent autoimmune disease to an antigen expressed under the human keratin 14 promoter. Journal of immunology (Baltimore, Md. : 1950), 169(4), 2141-7. PMID: 12165543
Ji, Q., Perchellet, A., & Goverman, J. (2010) Viral infection triggers central nervous system autoimmunity via activation of CD8 T cells expressing dual TCRs. Nature Immunology, 11(7), 628-634. DOI: 10.1038/ni.1888
- June 17, 2010
- 07:29 AM
- 127 views
Dendritic cells that don’t prime
by iayork in Mystery Rays from Outer Space
Dendritic cells in the skin (Langerhans cells) form a dense network of “sentinels” that act as first line of defense of the immune system.1
There’s a lot of interest in using dendritic cells as vaccines these days. A paper in PLoS One2 offers a cautionary note.
Dendritic cells (DC) are the main cell type that drive T [...]... Read more »
Yewdall, A., Drutman, S., Jinwala, F., Bahjat, K., & Bhardwaj, N. (2010) CD8 T Cell Priming by Dendritic Cell Vaccines Requires Antigen Transfer to Endogenous Antigen Presenting Cells. PLoS ONE, 5(6). DOI: 10.1371/journal.pone.0011144
- May 20, 2010
- 07:38 AM
- 139 views
Cross-protection and flu vaccines
by iayork in Mystery Rays from Outer Space
We know that we need to make new vaccines against influenza each year, because new flu strains arise and spread each year and the previous year’s vaccines don’t give protection against the new strains. Of course, there’s intense research toward developing cross-protective vaccines. Ideally, flu vaccines would work like measles vaccines — get a shot [...]... Read more »
Skowronski, D., De Serres, G., Crowcroft, N., Janjua, N., Boulianne, N., Hottes, T., Rosella, L., Dickinson, J., Gilca, R., Sethi, P.... (2010) Association between the 2008–09 Seasonal Influenza Vaccine and Pandemic H1N1 Illness during Spring–Summer 2009: Four Observational Studies from Canada. PLoS Medicine, 7(4). DOI: 10.1371/journal.pmed.1000258
Viboud, C., & Simonsen, L. (2010) Does Seasonal Influenza Vaccination Increase the Risk of Illness with the 2009 A/H1N1 Pandemic Virus?. PLoS Medicine, 7(4). DOI: 10.1371/journal.pmed.1000259
Johns, M., Eick, A., Blazes, D., Lee, S., Perdue, C., Lipnick, R., Vest, K., Russell, K., DeFraites, R., & Sanchez, J. (2010) Seasonal Influenza Vaccine and Protection against Pandemic (H1N1) 2009-Associated Illness among US Military Personnel. PLoS ONE, 5(5). DOI: 10.1371/journal.pone.0010722
- May 5, 2010
- 09:27 AM
- 131 views
Pandemics and publishing (and blogs?)
by iayork in Mystery Rays from Outer Space
A majority of the epidemiological articles on SARS were submitted after the epidemic had ended, although the corresponding studies had relevance to public health authorities during the epidemic. … although the academic response to the SARS epidemic was rapid, most articles on the epidemiology of SARS were published after the epidemic was over even though [...]... Read more »
Xing, W., Hejblum, G., Leung, G., & Valleron, A. (2010) Anatomy of the Epidemiological Literature on the 2003 SARS Outbreaks in Hong Kong and Toronto: A Time-Stratified Review. PLoS Medicine, 7(5). DOI: 10.1371/journal.pmed.1000272
- May 4, 2010
- 06:46 AM
- 142 views
Does immune evasion allow rapid HIV progression?
by iayork in Mystery Rays from Outer Space
I was getting a little concerned and distressed by the lack of evidence for any function of viral MHC class I immune evasion. It’s kind of a relief to see articles demonstrating function coming out.
MHC class I is the target for cytotoxic T lymphocytes (CTL), which are generally believed to be pretty important in [...]... Read more »
Gold MC, Munks MW, Wagner M, McMahon CW, Kelly A, Kavanagh DG, Slifka MK, Koszinowski UH, Raulet DH, & Hill AB. (2004) Murine cytomegalovirus interference with antigen presentation has little effect on the size or the effector memory phenotype of the CD8 T cell response. Journal of immunology (Baltimore, Md. : 1950), 172(11), 6944-53. PMID: 15153514
Lu, X., Pinto, A., Kelly, A., Cho, K., & Hill, A. (2006) Murine Cytomegalovirus Interference with Antigen Presentation Contributes to the Inability of CD8 T Cells To Control Virus in the Salivary Gland. Journal of Virology, 80(8), 4200-4202. DOI: 10.1128/JVI.80.8.4200-4202.2006
Stevenson, P., May, J., Smith, X., Marques, S., Adler, H., Koszinowski, U., Simas, J., & Efstathiou, S. (2002) K3-mediated evasion of CD8 T cells aids amplification of a latent γ-herpesvirus. Nature Immunology. DOI: 10.1038/ni818
Hansen, S., Powers, C., Richards, R., Ventura, A., Ford, J., Siess, D., Axthelm, M., Nelson, J., Jarvis, M., Picker, L.... (2010) Evasion of CD8 T Cells Is Critical for Superinfection by Cytomegalovirus. Science, 328(5974), 102-106. DOI: 10.1126/science.1185350
Friedrich, T., Piaskowski, S., Leon, E., Furlott, J., Maness, N., Weisgrau, K., Mac Nair, C., Weiler, A., Loffredo, J., Reynolds, M.... (2010) High Viremia Is Associated with High Levels of In Vivo Major Histocompatibility Complex Class I Downregulation in Rhesus Macaques Infected with Simian Immunodeficiency Virus SIVmac239. Journal of Virology, 84(10), 5443-5447. DOI: 10.1128/JVI.02452-09
- April 29, 2010
- 06:14 AM
- 144 views
Influenza variations, part II
by iayork in Mystery Rays from Outer Space
About 15 minutes after I wrote my last article on influenza variation, I was reading the Journal of Virology and ran across another paper1 on the same thing, that at least partly addresses some of the missing points in the earlier ones.
To brutally truncate my earlier comments: influenza should generate a huge number of mutants [...]... Read more »
Hoelzer, K., Murcia, P., Baillie, G., Wood, J., Metzger, S., Osterrieder, N., Dubovi, E., Holmes, E., & Parrish, C. (2010) Intrahost Evolutionary Dynamics of Canine Influenza Virus in Naive and Partially Immune Dogs. Journal of Virology, 84(10), 5329-5335. DOI: 10.1128/JVI.02469-09
Kuroda, M., Katano, H., Nakajima, N., Tobiume, M., Ainai, A., Sekizuka, T., Hasegawa, H., Tashiro, M., Sasaki, Y., Arakawa, Y.... (2010) Characterization of Quasispecies of Pandemic 2009 Influenza A Virus (A/H1N1/2009) by De Novo Sequencing Using a Next-Generation DNA Sequencer. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010256
Novella, I., Presloid, J., Zhou, T., Smith-Tsurkan, S., Ebendick-Corpus, B., Dutta, R., Lust, K., & Wilke, C. (2010) Genomic Evolution of Vesicular Stomatitis Virus Strains with Differences in Adaptability. Journal of Virology, 84(10), 4960-4968. DOI: 10.1128/JVI.00710-09
- April 27, 2010
- 06:14 AM
- 176 views
Influenza variations
by iayork in Mystery Rays from Outer Space
Indeed, the amount of HIV diversity within a single infected individual can exceed the variability generated over the course of a global influenza epidemic, the latter of which results in the need for a new vaccine each year. 1
That was said as part of a discussion on HIV vaccines, but let’s think about it from [...]... Read more »
Walker, B., & Burton, D. (2008) Toward an AIDS Vaccine. Science, 320(5877), 760-764. DOI: 10.1126/science.1152622
Ramakrishnan, M., Tu, Z., Singh, S., Chockalingam, A., Gramer, M., Wang, P., Goyal, S., Yang, M., Halvorson, D., & Sreevatsan, S. (2009) The Feasibility of Using High Resolution Genome Sequencing of Influenza A Viruses to Detect Mixed Infections and Quasispecies. PLoS ONE, 4(9). DOI: 10.1371/journal.pone.0007105
Kuroda, M., Katano, H., Nakajima, N., Tobiume, M., Ainai, A., Sekizuka, T., Hasegawa, H., Tashiro, M., Sasaki, Y., Arakawa, Y.... (2010) Characterization of Quasispecies of Pandemic 2009 Influenza A Virus (A/H1N1/2009) by De Novo Sequencing Using a Next-Generation DNA Sequencer. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010256
- April 22, 2010
- 11:08 AM
- 175 views
Modeling disease and epidemics
by iayork in Mystery Rays from Outer Space
Fig. 5. Boundary of the Hopf bifurcation of the endemic steady state … 1
I don’t pretend to be a mathematician or to understand the more complex disease models that are out there, but I do think modeling is an essential way of understanding how to effectively deal with diseases. A recent paper1 looks at epidemic [...]... Read more »
Blyuss, K., & Kyrychko, Y. (2009) Stability and Bifurcations in an Epidemic Model with Varying Immunity Period. Bulletin of Mathematical Biology, 72(2), 490-505. DOI: 10.1007/s11538-009-9458-y
- April 20, 2010
- 09:44 AM
- 159 views
Rotavirus vaccine and herd immunity
by iayork in Mystery Rays from Outer Space
Rotaviruses are one of the most common causes of gastroenteritis in children. A new rotavirus vaccine was introduced a few years ago; what impact has it had on disease?
This study confirms on a national scale that the 2008 rotavirus season among children aged <5 years was dramatically reduced compared to pre-RV5 seasons. … [...]... Read more »
Curns, A., Steiner, C., Barrett, M., Hunter, K., Wilson, E., & Parashar, U. (2010) Reduction in Acute Gastroenteritis Hospitalizations among US Children After Introduction of Rotavirus Vaccine: Analysis of Hospital Discharge Data from 18 US States. The Journal of Infectious Diseases, 2147483647. DOI: 10.1086/652403
Weinberg, G., & Szilagyi, P. (2010) Vaccine Epidemiology: Efficacy, Effectiveness, and the Translational Research Roadmap. The Journal of Infectious Diseases, 2147483647. DOI: 10.1086/652404
- April 15, 2010
- 06:15 AM
- 146 views
Living in the future: Mouse TcR clones
by iayork in Mystery Rays from Outer Space
T cell receptor (top) interacting with MHC
It would be nice if I could claim that advances in biology are driven by pure intellectual processes, by hermits on mountaintops achieving new theories through mediation and deep, pure thoughts. Of course, that’s not the case. I think its fair to say that many, if not most, of [...]... Read more »
Kirak O, Frickel EM, Grotenbreg GM, Suh H, Jaenisch R, & Ploegh HL. (2010) Transnuclear mice with predefined T cell receptor specificities against Toxoplasma gondii obtained via SCNT. Science (New York, N.Y.), 328(5975), 243-8. PMID: 20378817
Kisielow P, Blüthmann H, Staerz UD, Steinmetz M, & von Boehmer H. (1988) Tolerance in T-cell-receptor transgenic mice involves deletion of nonmature CD4 8 thymocytes. Nature, 333(6175), 742-6. PMID: 3260350
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.
