Adaptive Copy Number Evolution in Malaria Parasites
Tóm tắt
Từ khóa
Tài liệu tham khảo
GM Cooper, 2007, Mutational and selective effects on copy-number variants in the human genome., Nat Genet, 39, S22, 10.1038/ng2054
GH Perry, 2006, Hotspots for copy number variation in chimpanzees and humans., Proc Natl Acad Sci U S A, 103, 8006, 10.1073/pnas.0602318103
JL Freeman, 2006, Copy number variation: new insights in genome diversity., Genome Res, 16, 949, 10.1101/gr.3677206
EB Dopman, 2007, A portrait of copy-number polymorphism in <italic>Drosophila melanogaster</italic>., Proc Natl Acad Sci U S A, 104, 19920, 10.1073/pnas.0709888104
G Cutler, 2007, Significant gene content variation characterizes the genomes of inbred mouse strains., Genome Res, 17, 1743, 10.1101/gr.6754607
X Estivill, 2007, Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies., PLoS Genet, 3, 1787, 10.1371/journal.pgen.0030190
DQ Nguyen, 2006, Bias of Selection on Human Copy-Number Variants., PLoS Genet, 2, e20, 10.1371/journal.pgen.0020020
BE Stranger, 2007, Relative impact of nucleotide and copy number variation on gene expression phenotypes., Science, 315, 848, 10.1126/science.1136678
E Gonzalez, 2005, The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility., Science, 307, 1434, 10.1126/science.1101160
R Redon, 2006, Global variation in copy number in the human genome., Nature, 444, 444, 10.1038/nature05329
GH Perry, 2007, Diet and the evolution of human amylase gene copy number variation., Nat Genet
C Kidgell, 2006, A systematic map of genetic variation in <italic>Plasmodium falciparum</italic>., PLoS Pathog, 2, e57, 10.1371/journal.ppat.0020057
U Ribacke, 2007, Genome wide gene amplifications and deletions in <italic>Plasmodium falciparum</italic>., Mol Biochem Parasitol, 155, 33, 10.1016/j.molbiopara.2007.05.005
S Nair, 2007, Recurrent gene amplification and soft selective sweeps during evolution of multidrug resistance in malaria parasites., Mol Biol Evol, 24, 562, 10.1093/molbev/msl185
RN Price, 2004, Mefloquine resistance in <italic>Plasmodium falciparum</italic> and increased <italic>pfmdr1</italic> gene copy number., Lancet, 364, 438, 10.1016/S0140-6736(04)16767-6
AB Sidhu, 2006, Decreasing pfmdr1 copy number in plasmodium falciparum malaria heightens susceptibility to mefloquine, lumefantrine, halofantrine, quinine, and artemisinin., J Infect Dis, 194, 528, 10.1086/507115
X Su, 2007, Genetic linkage and association analyses for trait mapping in <italic>Plasmodium falciparum</italic>., Nat Rev Genet, 8, 497, 10.1038/nrg2126
S Dittrich, 2008, An atypical orthologue of 6-pyruvoyltetrahydropterin synthase can provide the missing link in the folate biosynthesis pathway of malaria parasites., Mol Microbiol, 67, 609, 10.1111/j.1365-2958.2007.06073.x
T Yoneyama, 2001, GTP cyclohydrolase I feedback regulatory protein-dependent and -independent inhibitors of GTP cyclohydrolase I., Arch Biochem Biophys, 388, 67, 10.1006/abbi.2001.2288
CV Plowe, 1998, <italic>P. falciparum</italic> dihydrofolate reductase and dihydropteroate synthase mutations: epidemiology and role in clinical resistacne to antifolates., Drug Resistance Updates, 1, 389, 10.1016/S1368-7646(98)80014-9
LM Fohl, 2003, Fitness effects of DHFR-TS mutations associated with pyrimethamine resistance in apicomplexan parasites., Mol Microbiol, 50, 1319, 10.1046/j.1365-2958.2003.03756.x
W Sirawaraporn, 1997, Antifolate-resistant mutants of <italic>Plasmodium falciparum</italic> dihydrofolate reductase., Proc Natl Acad Sci U S A, 94, 1124, 10.1073/pnas.94.4.1124
CI Sandefur, 2007, Pyrimethamine-resistant dihydrofolate reductase enzymes of <italic>Plasmodium falciparum</italic> are not enzymatically compromised in vitro., Mol Biochem Parasitol, 154, 1, 10.1016/j.molbiopara.2007.03.009
NJ White, 1992, Antimalarial drug resistance: the pace quickens., J Antimicrob Chemother, 30, 571, 10.1093/jac/30.5.571
TJ Anderson, 2005, Geographical Distribution of Selected and Putatively Neutral SNPs in SE Asian Malaria Parasites., Mol Biol Evol, 22, 2362, 10.1093/molbev/msi235
M Mayxay, 2007, Diagnosis and management of malaria by rural community health providers in the Lao People's Democratic Republic (Laos)., Trop Med Int Health, 12, 540, 10.1111/j.1365-3156.2007.01820.x
D Nash, 2005, Selection strength and hitchhiking around two antimalarial resistance genes., Proc Biol Sci, 272, 1153, 10.1098/rspb.2004.3026
S Nair, 2002, Rapid genotyping of loci involved in antifolate drug resistance in <italic>Plasmodium falciparum</italic> by primer extension., Int J Parasitol, 32, 852, 10.1016/S0020-7519(02)00033-4
WG Hill, 1995, Estimation of numbers of malaria clones in blood samples., Proc R Soc Lond B Biol Sci, 262, 249, 10.1098/rspb.1995.0203
DJ Conway, 1999, High recombination rate in natural populations of <italic>Plasmodium falciparum</italic>., Proc Natl Acad Sci U S A, 96, 4506, 10.1073/pnas.96.8.4506
S Nair, 2003, A Selective Sweep Driven by Pyrimethamine Treatment in SE Asian Malaria Parasites., Mol Biol Evol, 20, 1526, 10.1093/molbev/msg162
TJ Anderson, 1999, Twelve microsatellite markers for characterization of <italic>Plasmodium falciparum</italic> from finger-prick blood samples., Parasitology, 119(Pt 2), 113, 10.1017/S0031182099004552
TJ Anderson, 2000, Microsatellite markers reveal a spectrum of population structures in the malaria parasite <italic>Plasmodium falciparum</italic>., Mol Biol Evol, 17, 1467, 10.1093/oxfordjournals.molbev.a026247
M Schuelke, 2000, An economic method for the fluorescent labeling of PCR fragments., Nat Biotechnol, 18, 233, 10.1038/72708
M Nei, 1987, Molecular Evolutionary Genetics
PC Sabeti, 2002, Detecting recent positive selection in the human genome from haplotype structure., Nature, 419, 832, 10.1038/nature01140
JC Mueller, 2004, Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosity., Bioinformatics, 20, 786, 10.1093/bioinformatics/btg481
CC Cockerham, 1984, Estimating F-Statistics for the Analysis of Population Structure., Evolution, 38, 1358, 10.2307/2408641
J Goudet, 2001
MA Beaumont, 2004, Identifying adaptive genetic divergence among populations from genome scans., Mol Ecol, 13, 969, 10.1111/j.1365-294X.2004.02125.x
JM Akey, 2002, Interrogating a high-density SNP map for signatures of natural selection., Genome Res, 12, 1805, 10.1101/gr.631202
D Bunnag, 1987, The current status of drug resistance in malaria., Int J Parasitol, 17, 169, 10.1016/0020-7519(87)90038-5
SK Volkman, 2007, A genome-wide map of diversity in <italic>Plasmodium falciparum</italic>., Nat Genet, 39, 113, 10.1038/ng1930
J Mu, 2007, Genome-wide variation and identification of vaccine targets in the <italic>Plasmodium falciparum</italic> genome., Nat Genet, 39, 126, 10.1038/ng1924
CM Egan, 2007, Recurrent DNA copy number variation in the laboratory mouse., Nat Genet, 39, 1384, 10.1038/ng.2007.19
E Kugelberg, 2006, Multiple pathways of selected gene amplification during adaptive mutation., Proc Natl Acad Sci U S A, 103, 17319, 10.1073/pnas.0608309103
JK Iyer, 2001, Plasmodium falciparum cross-resistance between trimethoprim and pyrimethamine., Lancet, 358, 1066, 10.1016/S0140-6736(01)06201-8
AI Nilsson, 2006, Reducing the fitness cost of antibiotic resistance by amplification of initiator tRNA genes., Proc Natl Acad Sci U S A, 103, 6976, 10.1073/pnas.0602171103
CV Plowe, 1997, Mutations in <italic>Plasmodium falciparum</italic> dihydrofolate reductase and dihydropteroate synthase and epidemiologic patterns of pyrimethamine-sulfadoxine use and resistance., J Infect Dis, 176, 1590, 10.1086/514159
C Roper, 2004, Intercontinental spread of pyrimethamine resistant malaria., Science, 305, 1124, 10.1126/science.1098876
PC Sabeti, 2007, Genome-wide detection and characterization of positive selection in human populations., Nature, 449, 913, 10.1038/nature06250
K Hayton, 2004, Genetic and biochemical aspects of drug resistance in malaria parasites., Curr Drug Targets Infect Disord, 4, 1, 10.2174/1568005043480925
AM Snijders, 2003, Shaping of tumor and drug-resistant genomes by instability and selection., Oncogene, 22, 4370, 10.1038/sj.onc.1206482
SH Craven, 2007, Double trouble: medical implications of genetic duplication and amplification in bacteria., Future Microbiol, 2, 309, 10.2217/17460913.2.3.309
C Guimond, 2003, Modulation of gene expression in <italic>Leishmania</italic> drug resistant mutants as determined by targeted DNA microarrays., Nucleic Acids Res, 31, 5886, 10.1093/nar/gkg806