http://www.iayork.com/MysteryRays Meddling with things mankind is not meant to understand. Also, pictures of my kids Thu, 15 May 2008 21:23:03 +0000 http://backend.userland.com/rss092 en I don't know why I read the ScienceDaily newsfeed, because it drives me crazy every single day.  I had naively thought that whoever massages the press releases they receive would have, maybe, a teeny tiny clue about what's gone on in the field before, but they seem to have the ... http://www.iayork.com/MysteryRays/2008/05/15/on-parasitehost-interactions/ We walk a fine line between death due to immune deficiency, smothered under the weight of pathogens and parasites, and death by hyperimmunity, eaten alive by our own defenses. It's amazing that our immune system can be tuned so precisely as to recognize anything foreign, yet ignore the vast ... http://www.iayork.com/MysteryRays/2008/05/14/autoimmunity-and-cd1-part-i/ I'm not so much an antibody guy, but of course I've heard about catalytic antibodies. Catalytic antibodies bind, with the very high affinity that's typical of many antibodies, to transition state molecules, stabilizing the transition state and facilitating the chemical reaction. They've been around for quite a ... http://www.iayork.com/MysteryRays/2008/05/11/a-therapeutic-catalytic-antibody/ 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. --Walker BD, Burton DR (2008) Toward an AIDS vaccine. Science 320:760–764. (See my previous posts ... http://www.iayork.com/MysteryRays/2008/05/10/on-hiv-variation/ The other day I was talking about immune recognition of human endogenous retroviruses (HERVs) in tumors. (HERVs are the husks of ancient retroviruses, now trapped in our genomes. Some of them still express various proteins, either under normal conditions or when stimulated, as in tumors.) One of ... http://www.iayork.com/MysteryRays/2008/05/07/more-hervs/ Human chromosome 5 One of the genes I'm interested in is an aminopeptidase called "ERAP1" ((by us, anyway: York IA, Chang SC, Saric T, Keys JA, Favreau JM, Goldberg AL, Rock KL (2002) The ER aminopeptidase ERAP1 enhances or limits antigen presentation by trimming epitopes to 8-9 residues. Nat Immunol 3:1177–184. ... http://www.iayork.com/MysteryRays/2008/05/07/quick-platypus-note/ I've talked several times about Charlie Janeway's "dirty little secrets", and the insights into fundamental immunity that arose from the concept. I've also mentioned a couple of potential clinical advances arising from it. Here's another one, that I find particularly elegant for its use of the weak to ... http://www.iayork.com/MysteryRays/2008/05/04/the-weak-conquers-the-strong/ After spending a week ((Well, a half-hour every other night for a week)) trying to find a bug in XPlasMap, I just realized that "[-\d]+" should have been "[-\d\.]+" Sheesh. http://www.iayork.com/MysteryRays/2008/05/03/slashdot/ A couple weeks ago I was having a chat with a friend about cancer immunity (as one so often does) and he asked if the Holy Grail of cancer immunity would be to identify tumor antigens. Not at all. There are hundreds of tumor antigens known. (The ... http://www.iayork.com/MysteryRays/2008/04/30/hervs-zombie-target-practice-for-immunity/ We've been promised that as genome sequencing becomes faster and simpler, we'll start seeing practical dividends as well as parlour tricks like sequencing Watson's genome. Some of the dividends are already paying out, as a paper in the latest PLoS Pathogens ((Cottam, E.M., Wadsworth, J., Shaw, A.E., Rowlands, R.J., ... http://www.iayork.com/MysteryRays/2008/04/27/elementary-dr-watson/