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Mystery Rays from Outer Space
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- July 29, 2010
- 06:12 AM
- 3 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
- 06:11 AM
- 3 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
- 2 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
- 4 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
- 2 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
- 5 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
- 4 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
- 3 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
- 4 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
- 8 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
- 6 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
- 5 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
- 4 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
- April 10, 2010
- 10:23 AM
- 4 views
Immune databases and hypotheses
by iayork in Mystery Rays from Outer Space
The folks associated with the IEDB (Immune Epitope Database) have published a very nice and useful guide to all the serious contenders in the immune database field. 1 If you have a particular need, this is an excellent starting point for choosing the appropriate starting point. (It’s an open access article, too.)
They’ve obviously looked [...]... Read more »
Salimi, N., Fleri, W., Peters, B., & Sette, A. (2010) Design and utilization of epitope-based databases and predictive tools. Immunogenetics, 62(4), 185-196. DOI: 10.1007/s00251-010-0435-2
Hearn, A., York, I., & Rock, K. (2009) The Specificity of Trimming of MHC Class I-Presented Peptides in the Endoplasmic Reticulum. The Journal of Immunology, 183(9), 5526-5536. DOI: 10.4049/jimmunol.0803663
Schatz MM, Peters B, Akkad N, Ullrich N, Martinez AN, Carroll O, Bulik S, Rammensee HG, van Endert P, Holzhütter HG.... (2008) Characterizing the N-terminal processing motif of MHC class I ligands. Journal of immunology (Baltimore, Md. : 1950), 180(5), 3210-7. PMID: 18292545
- April 9, 2010
- 10:19 AM
- 4 views
Immune evasion versus superinfection
by iayork in Mystery Rays from Outer Space
Human cytomegalovirus-infected cell
A number of viruses, especially herpesviruses, block the MHC class I antigen presentation system. It’s been widely assumed that this is for the obvious reason and that it allows the virus to avoid T cell recognition and elimination. But there’s been an awkward lack of experimental support for that assumption, to [...]... Read more »
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
- April 1, 2010
- 05:30 PM
- 5 views
Short snorts: Norovirus mutation and evolution
by iayork in Mystery Rays from Outer Space
Norovirus (from J Virol. 82:2079-2088 (2008))
P.G. Wodehouse described his “Blandings Castle” short stories as “the short snorts between the solid orgies”. I usually go for at least one of the solid orgies per week,1 but it’s spring break and I’m hanging out with my kids for the next while.2 So this week and likely next, [...]... Read more »
Bull, R., Eden, J., Rawlinson, W., & White, P. (2010) Rapid Evolution of Pandemic Noroviruses of the GII.4 Lineage. PLoS Pathogens, 6(3). DOI: 10.1371/journal.ppat.1000831
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
- March 26, 2010
- 06:13 AM
- 7 views
Wrapping up
by iayork in Mystery Rays from Outer Space
How does a viral genome get into a viral capsid?
There are several strategies, but often the viral capsid is built first, leaving a pore open at one corner; and then the viral genome is fed into that pore, getting neatly wrapped up around scaffolding proteins like a spool of thread.
Herpesviruses follow that strategy, and here’s [...]... Read more »
Peng, L., Ryazantsev, S., Sun, R., & Zhou, Z. (2010) Three-Dimensional Visualization of Gammaherpesvirus Life Cycle in Host Cells by Electron Tomography. Structure, 18(1), 47-58. DOI: 10.1016/j.str.2009.10.017
- March 24, 2010
- 06:15 AM
- 5 views
DAMPs and PAMPs: The enemy within
by iayork in Mystery Rays from Outer Space
The immune system is, by its nature, destructive. Its function is to eliminate problems. Because it’s so destructive, there are many layers on control that constantly check and limit the response. Equally, there are controls that try to ensure that the response doesn’t start until it’s needed.
How does the immune response know when [...]... Read more »
Zhang, Q., Raoof, M., Chen, Y., Sumi, Y., Sursal, T., Junger, W., Brohi, K., Itagaki, K., & Hauser, C. (2010) Circulating mitochondrial DAMPs cause inflammatory responses to injury. Nature, 464(7285), 104-107. DOI: 10.1038/nature08780
- March 19, 2010
- 06:14 AM
- 6 views
Measles week, Part V: What about the vaccine?
by iayork in Mystery Rays from Outer Space
Measles infection in a brain cell nucleus
Having gone through Parts I, II, III, and IV of Measles week, let’s finish up by asking what this means for measles vaccine.
We know that measles death rates dropped spectacularly well before the vaccine was introduced in 1963 (the first version; a more effective version was released later). [...]... Read more »
MUSCAT, M., BANG, H., WOHLFAHRT, J., GLISMANN, S., & MOLBAK, K. (2009) Measles in Europe: an epidemiological assessment. The Lancet, 373(9661), 383-389. DOI: 10.1016/S0140-6736(08)61849-8
Filia, A., Brenna, A., Panà, A., Maggio Cavallaro, G., Massari, M., & Ciofi degli Atti, M. (2007) Health burden and economic impact of measles-related hospitalizations in Italy in 2002–2003. BMC Public Health, 7(1), 169. DOI: 10.1186/1471-2458-7-169
- March 18, 2010
- 06:14 AM
- 5 views
Measles week, part IV: Some of the answers
by iayork in Mystery Rays from Outer Space
Various workers affected by measles punish a god of measles, while a doctor and drugstore keeper try to protect the god from them. (1862
Well, here we are already at Part IV of Measles Week. Doesn’t time fly? Remember how young we all were, back at Part I, when I raised the question I’m trying [...]... Read more »
Aaby, P. (1985) Severe measles: A reappraisal of the role of nutrition, overcrowding and virus dose. Medical Hypotheses, 18(2), 93-112. DOI: 10.1016/0306-9877(85)90042-8
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