| [1] | Zwirner NW, Domaica CI (2010) Cytokine regulation of natural killer cell effector functions. Biofactors 36: 274-288. doi:10.1002/biof.107. PubMed: 20623510.
|
| [2] | Trowsdale J, Barten R, Haude A, Stewart CA, Beck S et al. (2001) The genomic context of natural killer receptor extended gene families. Immunol Rev 181: 20-38. doi:10.1034/j.1600-065X.2001.1810102.x. PubMed: 11513141.
|
| [3] | Natarajan K, Dimasi N, Wang J, Mariuzza RA, Margulies DH (2002) Structure and function of natural killer cell receptors: multiple molecular solutions to self, nonself discrimination. Annu Rev Immunol 20: 853-885. doi:10.1146/annurev.immunol.20.100301.064812. PubMed: 11861620.
|
| [4] | Long EO (1999) Regulation of immune responses through inhibitory receptors. Annu Rev Immunol 17: 875-904. doi:10.1146/annurev.immunol.17.1.875. PubMed: 10358776.
|
| [5] | Isakov N (1997) Immunoreceptor tyrosine-based activation motif (ITAM), a unique module linking antigen and Fc receptors to their signaling cascades. J Leukoc Biol 61: 6-16. PubMed: 9000531.
|
| [6] | Khakoo SI, Rajalingam R, Shum BP, Weidenbach K, Flodin L et al. (2000) Rapid evolution of NK cell receptor systems demonstrated by comparison of chimpanzees and humans. Immunity 12: 687-698. doi:10.1016/S1074-7613(00)80219-8. PubMed: 10894168.
|
| [7] | Sambrook JG, Bashirova A, Palmer S, Sims S, Trowsdale J et al. (2005) Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates. Genome Res 15: 25-35. doi:10.1101/gr.2381205. PubMed: 15632087.
|
| [8] | Rajalingam R, Parham P, Abi-Rached L (2004) Domain shuffling has been the main mechanism forming new hominoid killer cell Ig-like receptors. J Immunol 172: 356-369. PubMed: 14688344.
|
| [9] | Guethlein LA, Flodin LR, Adams EJ, Parham P (2002) NK cell receptors of the orangutan (Pongo pygmaeus): a pivotal species for tracking the coevolution of killer cell Ig-like receptors with MHC-C. J Immunol 169: 220-229. PubMed: 12077248.
|
| [10] | Hershberger KL, Shyam R, Miura A, Letvin NL (2001) Diversity of the killer cell Ig-like receptors of rhesus monkeys. J Immunol 166: 4380-4390. PubMed: 11254692.
|
| [11] | Bimber BN, Moreland AJ, Wiseman RW, Hughes AL, O'Connor DH (2008) Complete characterization of killer Ig-like receptor (KIR) haplotypes in Mauritian cynomolgus macaques: novel insights into nonhuman primate KIR gene content and organization. J Immunol 181: 6301-6308. PubMed: 18941221.
|
| [12] | Mager DL, McQueen KL, Wee V, Freeman JD (2001) Evolution of natural killer cell receptors: coexistence of functional Ly49 and KIR genes in baboons. Curr Biol 11: 626-630. doi:10.1016/S0960-9822(01)00148-8. PubMed: 11369209.
|
| [13] | Hershberger KL, Kurian J, Korber BT, Letvin NL (2005) Killer cell immunoglobulin-like receptors (KIR) of the African-origin sabaeus monkey: evidence for recombination events in the evolution of KIR. Eur J Immunol 35: 922-935. doi:10.1002/eji.200425408. PubMed: 15714591.
|
| [14] | Palacios C, Cuervo LC, Cadavid LF (2011) Evolutionary patterns of killer cell Ig-like receptor genes in Old World monkeys. Gene 474: 39-51. doi:10.1016/j.gene.2010.12.006. PubMed: 21185924.
|
| [15] | Cadavid LF, Lun CM (2009) Lineage-specific diversification of killer cell Ig-like receptors in the owl monkey, a New World primate. Immunogenetics 61: 27-41. doi:10.1007/s00251-008-0342-y. PubMed: 19009288.
|
| [16] | Guethlein LA, Older Aguilar AM, Abi-Rached L, Parham P (2007) Evolution of killer cell Ig-like receptor (KIR) genes: definition of an orangutan KIR haplotype reveals expansion of lineage III KIR associated with the emergence of MHC-C. J Immunol 179: 491-504. PubMed: 17579070.
|
| [17] | Menezes AN, Bonvicino CR, Seuánez HN (2010) Identification, classification and evolution of owl monkeys (Aotus, Illiger 1811). BMC Evol Biol 10: 248. doi:10.1186/1471-2148-10-248. PubMed: 20704725.
|
| [18] | Robinson J, Mistry K, McWilliam H, Lopez R, Marsh SG (2010) IPD--the Immuno Polymorphism Database. Nucleic Acids Res 38: D863-D869. doi:10.1093/nar/gkp879. PubMed: 19875415.
|
| [19] | K？ll L, Krogh A, Sonnhammer EL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338: 1027-1036. doi:10.1016/j.jmb.2004.03.016. PubMed: 15111065.
|
| [20] | Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-580. doi:10.1006/jmbi.2000.4315. PubMed: 11152613.
|
| [21] | Vivian JP, Duncan RC, Berry R, O'Connor GM, Reid HH et al. (2011) Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B. Nature 479: 401-405. doi:10.1038/nature10517. PubMed: 22020283.
|
| [22] | Chwae YJ, Cho SE, Kim SJ, Kim J (1999) Diversity of the repertoire of p58 killer cell inhibitory receptors in a single individual. Immunol Lett 68: 267-274. doi:10.1016/S0165-2478(99)00062-0. PubMed: 10424431.
|
| [23] | Goodridge JP, Lathbury LJ, Steiner NK, Shulse CN, Pullikotil P et al. (2007) Three common alleles of KIR2DL4 (CD158d) encode constitutively expressed, inducible and secreted receptors in NK cells. Eur J Immunol 37: 199-211. doi:10.1002/eji.200636316. PubMed: 17171757.
|
| [24] | Maxwell LD, Wallace A, Middleton D, Curran MD (2002) A common KIR2DS4 deletion variant in the human that predicts a soluble KIR molecule analogous to the KIR1D molecule observed in the rhesus monkey. Tissue Antigens 60: 254-258. doi:10.1034/j.1399-0039.2002.600307.x. PubMed: 12445308.
|
| [25] | Campbell KS, Purdy AK (2011) Structure/function of human killer cell immunoglobulin-like receptors: lessons from polymorphisms, evolution, crystal structures and mutations. Immunology 132: 315-325. doi:10.1111/j.1365-2567.2010.03398.x. PubMed: 21214544.
|
| [26] | Feng J, Garrity D, Call ME, Moffett H, Wucherpfennig KW (2005) Convergence on a distinctive assembly mechanism by unrelated families of activating immune receptors. Immunity 22: 427-438. doi:10.1016/j.immuni.2005.02.005. PubMed: 15845448.
|
| [27] | Hao L, Nei M (2005) Rapid expansion of killer cell immunoglobulin-like receptor genes in primates and their coevolution with MHC Class I genes. Gene 347: 149-159. doi:10.1016/j.gene.2004.12.012. PubMed: 15733532.
|
| [28] | Nei M, Rooney AP (2005) Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39: 121-152. doi:10.1146/annurev.genet.39.073003.112240. PubMed: 16285855.
|
| [29] | Hughes AL (2002) Evolution of the human killer cell inhibitory receptor family. Mol Phylogenet Evol 25: 330-340. doi:10.1016/S1055-7903(02)00255-5. PubMed: 12414314.
|
| [30] | Rajalingam R (2011) Human diversity of killer cell immunoglobulin-like receptors and disease. Korean J Hematol 46: 216-228. doi:10.5045/kjh.2011.46.4.216. PubMed: 22259627.
|
| [31] | Boyington JC, Sun PD (2002) A structural perspective on MHC class I recognition by killer cell immunoglobulin-like receptors. Mol Immunol 38: 1007-1021. doi:10.1016/S0161-5890(02)00030-5. PubMed: 11955593.
|
| [32] | Boyington JC, Brooks AG, Sun PD (2001) Structure of killer cell immunoglobulin-like receptors and their recognition of the class I MHC molecules. Immunol Rev 181: 66-78. doi:10.1034/j.1600-065X.2001.1810105.x. PubMed: 11513153.
|
| [33] | Committee for the Update of the Guide for the Care and Use of Laboratory Animals (2011) Guide for the Care and Use of Laboratory Animals. Washington, DC: TNA Press.
|
| [34] | Qiu X, Wu L, Huang H, McDonel PE, Palumbo AV et al. (2001) Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl Environ Microbiol 67: 880-887. doi:10.1128/AEM.67.2.880-887.2001. PubMed: 11157258.
|
| [35] | Lahr DJ, Katz LA (2009) Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase. BioTechniques 47: 857-866. PubMed: 19852769.
|
| [36] | Lenz TL, Becker S (2008) Simple approach to reduce PCR artefact formation leads to reliable genotyping of MHC and other highly polymorphic loci--implications for evolutionary analysis. Gene 427: 117-123. doi:10.1016/j.gene.2008.09.013. PubMed: 18848974.
|
| [37] | Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680. doi:10.1093/nar/22.22.4673. PubMed: 7984417.
|
| [38] | Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739. doi:10.1093/molbev/msr121. PubMed: 21546353.
|
| [39] | Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120. doi:10.1007/BF01731581. PubMed: 7463489.
|
| [40] | Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452. doi:10.1093/bioinformatics/btp187. PubMed: 19346325.
|
| [41] | Zhang J, Rosenberg HF, Nei M (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci U S A 95: 3708-3713. doi:10.1073/pnas.95.7.3708. PubMed: 9520431.
|
| [42] | Kosakovsky Pond SL, Frost SD (2005) Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22: 1208-1222. doi:10.1093/molbev/msi105. PubMed: 15703242.
|
| [43] | Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K et al. (2012) Detecting individual sites subject to episodic diversifying selection. PLOS Genet 8: e1002764. PubMed: 22807683.
|
| [44] | Delport W, Poon AF, Frost SD, Kosakovsky Pond SL (2010) Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26: 2455-2457. doi:10.1093/bioinformatics/btq429. PubMed: 20671151.
|
| [45] | Murrell B, Moola S, Mabona A, Weighill T, Sheward D et al. (2013) FUBAR : A Fast, Unconstrained Bayesian AppRoximation for inferring selection. Mol Biol Evol. 30(5):1196-205
|
| [46] | Martin DP, Lemey P, Lott M, Moulton V, Posada D et al. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462-2463. doi:10.1093/bioinformatics/btq467. PubMed: 20798170.
|
| [47] | Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512-526. PubMed: 8336541.
|
