|
1. Zieglgansberger, W. &; Tolle, T.R. The pharmacology of pain signalling. Curr Opin Neurobiol 3, 611-8 (1993).
2. Odds, F.C., Webster, C.E., Mayuranathan, P. &; Simmons, P.D. Candida concentrations in the vagina and their association with signs and symptoms of vaginal candidosis. J Med Vet Mycol 26, 277-83 (1988).
3. Gudlaugsson, O. et al. Attributable mortality of nosocomial candidemia, revisited. Clinical Infectious Diseases 37, 1172-1177 (2003).
4. Odds, F.C. Candida and candidosis (University Park Press, Baltimore, 1979).
5. Calderone, R.A. Candida and candidiasis (ASM Press, Washington, D.C., 2002).
6. Hajjeh, R.A. et al. Incidence of bloodstream infections due to Candida species and in vitro susceptibilities of isolates collected from 1998 to 2000 in a population-based active surveillance program. J Clin Microbiol 42, 1519-27 (2004).
7. Gow, N.A., Brown, A.J. &; Odds, F.C. Fungal morphogenesis and host invasion. Curr Opin Microbiol 5, 366-71 (2002).
8. Navarro-Garcia, F., Sanchez, M., Nombela, C. &; Pla, J. Virulence genes in the pathogenic yeast Candida albicans. FEMS Microbiol Rev 25, 245-68 (2001).
9. Sundstrom, P. Adhesion in Candida spp. Cell Microbiol 4, 461-9 (2002).
10. Hube, B. From commensal to pathogen: stage- and tissue-specific gene expression of Candida albicans. Current opinion in microbiology 7, 336-41 (2004).
11. Naglik, J.R., Challacombe, S.J. &; Hube, B. Candida albicans secreted aspartyl proteinases in virulence and pathogenesis. Microbiol Mol Biol Rev 67, 400-28 (2003).
12. Wachtler, B., Wilson, D., Haedicke, K., Dalle, F. &; Hube, B. From attachment to damage: defined genes of Candida albicans mediate adhesion, invasion and damage during interaction with oral epithelial cells. PLoS One 6, e17046 (2011).
13. Wilson, D. et al. Identifying infection-associated genes of Candida albicans in the postgenomic era. Fems Yeast Research 9, 688-700 (2009).
14. Biswas, S., Van Dijck, P. &; Datta, A. Environmental sensing and signal transduction pathways regulating morphopathogenic determinants of Candida albicans. Microbiol Mol Biol Rev 71, 348-76 (2007).
15. Utzinger, J., N'Goran, E.K., Tanner, M. &; Lengeler, C. Simple anamnestic questions and recalled water-contact patterns for self-diagnosis of Schistosoma mansoni infection among schoolchildren in western Cote d'Ivoire. Am J Trop Med Hyg 62, 649-55 (2000).
16. Soll, D.R. Candida commensalism and virulence: the evolution of phenotypic plasticity. Acta Trop 81, 101-10 (2002).
17. Navarro-Garcia, F., Eisman, B., Roman, E., Nombela, C. &; Pla, J. Signal transduction pathways and cell-wall construction in Candida albicans. Med Mycol 39 Suppl 1, 87-100 (2001).
18. Filler, S.G. &; Sheppard, D.C. Fungal invasion of normally non-phagocytic host cells. PLoS Pathog 2, e129 (2006).
19. Ernst, J.F. Transcription factors in Candida albicans - environmental control of morphogenesis. Microbiology 146 ( Pt 8), 1763-74 (2000).
20. Naglik, J., Albrecht, A., Bader, O. &; Hube, B. Candida albicans proteinases and host/pathogen interactions. Cell Microbiol 6, 915-26 (2004).
21. Filler, S.G. Candida-host cell receptor-ligand interactions. Curr Opin Microbiol 9, 333-9 (2006).
22. Verstrepen, K.J. &; Klis, F.M. Flocculation, adhesion and biofilm formation in yeasts. Mol Microbiol 60, 5-15 (2006).
23. Lorenz, M.C., Bender, J.A. &; Fink, G.R. Transcriptional response of Candida albicans upon internalization by macrophages. Eukaryotic Cell 3, 1076-1087 (2004).
24. Rubin-Bejerano, I., Fraser, I., Grisafi, P. &; Fink, G.R. Phagocytosis by neutrophils induces an amino acid deprivation response in Saccharomyces cerevisiae and Candida albicans. Proceedings of the National Academy of Sciences of the United States of America 100, 11007-11012 (2003).
25. Huang, Q. et al. The plasticity of dendritic cell responses to pathogens and their components. Science 294, 870-875 (2001).
26. Barker, K.S., Liu, T. &; Rogers, P.D. Coculture of THP-1 human mononuclear cells with Candida albicans results in pronounced changes in host gene expression. Journal of Infectious Diseases 192, 901-912 (2005).
27. Barker, K.S. et al. Transcriptome profile of the vascular endothelial cell response to Candida albicans. Journal of Infectious Diseases 198, 193-202 (2008).
28. Fradin, C. et al. Stage-specific gene expression of Candida albicans in human blood. Molecular Microbiology 47, 1523-1543 (2003).
29. Lieschke, G.J. &; Currie, P.D. Animal models of human disease: zebrafish swim into view. Nat Rev Genet 8, 353-367 (2007).
30. Zon, L.I. &; Peterson, R.T. In vivo drug discovery in the zebrafish. Nat Rev Drug Discov 4, 35-44 (2005).
31. Alarco, A.M. et al. Immune-deficient Drosophila melanogaster: a model for the innate immune response to human fungal pathogens. J Immunol 172, 5622-8 (2004).
32. Cotter, G., Doyle, S. &; Kavanagh, K. Development of an insect model for the in vivo pathogenicity testing of yeasts. FEMS Immunol Med Microbiol 27, 163-9 (2000).
33. Pukkila-Worley, R., Peleg, A.Y., Tampakakis, E. &; Mylonakis, E. Candida albicans hyphal formation and virulence assessed using a Caenorhabditis elegans infection model. Eukaryot Cell 8, 1750-8 (2009).
34. Cotter, G., Doyle, S. &; Kavanagh, K. Development of an insect model for the in vivo pathogenicity testing of yeasts. Fems Immunology and Medical Microbiology 27, 163-169 (2000).
35. Chamilos, G., Lionakis, M.S., Lewis, R.E. &; Kontoyiannis, D.P. Role of mini-host models in the study of medically important fungi. Lancet Infect Dis 7, 42-55 (2007).
36. Mylonakis, E., Casadevall, A. &; Ausubel, F.M. Exploiting amoeboid and non-vertebrate animal model systems to study the virulence of human pathogenic fungi. PLoS Pathog 3, e101 (2007).
37. Chamilos, G. et al. Drosophila melanogaster as a facile model for large-scale studies of virulence mechanisms and antifungal drug efficacy in Candida species. J Infect Dis 193, 1014-22 (2006).
38. Breger, J. et al. Antifungal chemical compounds identified using a C. elegans pathogenicity assay. PLoS Pathog 3, e18 (2007).
39. Chamilos, G. et al. Candida albicans Cas5, a regulator of cell wall integrity, is required for virulence in murine and toll mutant fly models. J Infect Dis 200, 152-7 (2009).
40. Meeker, N.D. &; Trede, N.S. Immunology and zebrafish: spawning new models of human disease. Dev Comp Immunol 32, 745-57 (2008).
41. Carradice, D. &; Lieschke, G.J. Zebrafish in hematology: sushi or science? Blood 111, 3331-42 (2008).
42. Sullivan, C. &; Kim, C.H. Zebrafish as a model for infectious disease and immune function. Fish Shellfish Immunol 25, 341-50 (2008).
43. Chao, C.C. et al. Zebrafish as a model host for Candida albicans infection. Infection and immunity 78, 2512-21 (2010).
44. Hughes, T.R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109-126 (2000).
45. van't Veer, L.J. et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536 (2002).
46. Chu, S. et al. The transcriptional program of sporulation in budding yeast. Science 282, 699-705 (1998).
47. Spellman, P.T. et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9, 3273-3297 (1998).
48. Callow, M.J., Dudoit, S., Gong, E.L., Speed, T.P. &; Rubin, E.M. Microarray expression profiling identifies genes with altered expression in HDL-deficient mice. Genome Research 10, 2022-2029 (2000).
49. Tusher, V.G., Tibshirani, R. &; Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences of the United States of America 98, 5116-5121 (2001).
50. de Souto, M.C., Costa, I.G., de Araujo, D.S., Ludermir, T.B. &; Schliep, A. Clustering cancer gene expression data: a comparative study. BMC Bioinformatics 9, 497 (2008).
51. Golub, T.R. et al. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286, 531-537 (1999).
52. Alizadeh, A.A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503-511 (2000).
53. McLachlan, G.J., Bean, R.W. &; Peel, D. A mixture model-based approach to the clustering of microarray expression data. Bioinformatics 18, 413-422 (2002).
54. Liu, L., Hawkins, D.M., Ghosh, S. &; Young, S.S. Robust singular value decomposition analysis of microarray data. Proceedings of the National Academy of Sciences of the United States of America 100, 13167-13172 (2003).
55. Brunet, J.P., Tamayo, P., Golub, T.R. &; Mesirov, J.P. Metagenes and molecular pattern discovery using matrix factorization. Proceedings of the National Academy of Sciences of the United States of America 101, 4164-4169 (2004).
56. Tseng, G.C., Oh, M.K., Rohlin, L., Liao, J.C. &; Wong, W.H. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Research 29, 2549-2557 (2001).
57. Chen, Y., Dougherty, E.R. &; Bittner, M.L. Ratio-based decisions and the quantitative analysis of cDNA microarray images. Journal of Biomedical Optics 2, 364-374 (1997).
58. Yang, Y.H. et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 30 (2002).
59. Yang, I.V. et al. Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biology 3 (2002).
60. Cleveland, W.S. Robust locally weighted regression and smoothing scatterplots. Journal of the American Statistical Association 74, 829-836 (1979).
61. Smyth, G.K. &; Speed, T. Normalization of cDNA microarray data. Methods 31, 265-273 (2003).
62. Hilsenbeck, S.G. et al. Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. Journal of the National Cancer Institute 91, 453-459 (1999).
63. Craig, J.C. et al. Developmental expression of morphoregulatory genes in the mouse embryo: An analytical approach using a novel technology. Biochemical and Molecular Medicine 60, 81-91 (1997).
64. Vohradsky, J., Li, X.M. &; Thompson, C.J. Identification of procaryotic developmental stages by statistical analyses of two-dimensional gel patterns. Electrophoresis 18, 1418-1428 (1997).
65. Ray, S. &; Turi, R.H. Determination of number of clusters in K-means clustering and application in colour image segmentation. Proceedings of the 4th International Conference on Advances in Pattern Recognition and Digital Techniques (ICAPRDT'99), 27-29 (1999).
66. Skrzypek, M.S. et al. New tools at the Candida Genome Database: biochemical pathways and full-text literature search. Nucleic Acids Research 38, D428-D432 (2010).
67. Albrecht, A. et al. Glycosylphosphatidylinositol-anchored proteases of Candida albicans target proteins necessary for both cellular processes and host-pathogen interactions. The Journal of biological chemistry 281, 688-94 (2006).
68. Almeida, R.S. et al. The Hyphal-Associated Adhesin and Invasin Als3 of Candida albicans Mediates Iron Acquisition from Host Ferritin. Plos Pathogens 4 (2008).
69. Homann, O.R., Dea, J., Noble, S.M. &; Johnson, A.D. A Phenotypic Profile of the Candida albicans Regulatory Network. Plos Genetics 5 (2009).
70. Ramanan, N. &; Wang, Y. A high-affinity iron permease essential for Candida albicans virulence. Science 288, 1062-4 (2000).
71. Sarthy, A.V. et al. Phenotype in Candida albicans of a disruption of the BGL2 gene encoding a 1,3-beta-glucosyltransferase. Microbiology 143 ( Pt 2), 367-76 (1997).
72. Thewes, S. et al. In vivo and ex vivo comparative transcriptional profiling of invasive and non-invasive Candida albicans isolates identifies genes associated with tissue invasion. Mol Microbiol 63, 1606-28 (2007).
73. Weissman, Z. &; Kornitzer, D. A family of Candida cell surface haem-binding proteins involved in haemin and haemoglobin-iron utilization. Molecular Microbiology 53, 1209-20 (2004).
74. Weissman, Z., Shemer, R., Conibear, E. &; Kornitzer, D. An endocytic mechanism for haemoglobin-iron acquisition in Candida albicans. Molecular Microbiology 69, 201-17 (2008).
75. Enjalbert, B. et al. Role of the Hog1 stress-activated protein kinase in the global transcriptional response to stress in the fungal pathogen Candida albicans. Molecular Biology of the Cell 17, 1018-32 (2006).
76. Kadosh, D. &; Johnson, A.D. Rfg1, a protein related to the Saccharomyces cerevisiae hypoxic regulator Rox1, controls filamentous growth and virulence in Candida albicans. Molecular and cellular biology 21, 2496-505 (2001).
77. Zaragoza, O., Rodriguez, C. &; Gancedo, C. Isolation of the MIG1 gene from Candida albicans and effects of its disruption on catabolite repression. Journal of bacteriology 182, 320-6 (2000).
78. Almeida, R.S., Wilson, D. &; Hube, B. Candida albicans iron acquisition within the host. FEMS yeast research 9, 1000-12 (2009).
79. Baek, Y.U., Li, M. &; Davis, D.A. Candida albicans ferric reductases are differentially regulated in response to distinct forms of iron limitation by the Rim101 and CBF transcription factors. Eukaryotic Cell 7, 1168-79 (2008).
80. Hsu, P.C., Yang, C.Y. &; Lan, C.Y. Candida albicans Hap43 is a repressor induced under low-iron conditions and is essential for iron-responsive transcriptional regulation and virulence. Eukaryotic Cell 10, 207-25 (2011).
81. Johnson, D.C., Cano, K.E., Kroger, E.C. &; McNabb, D.S. Novel regulatory function for the CCAAT-binding factor in Candida albicans. Eukaryotic Cell 4, 1662-76 (2005).
82. Murad, A.M. et al. Transcript profiling in Candida albicans reveals new cellular functions for the transcriptional repressors CaTup1, CaMig1 and CaNrg1. Molecular Microbiology 42, 981-93 (2001).
83. Lan, C.Y. et al. Regulatory networks affected by iron availability in Candida albicans. Molecular Microbiology 53, 1451-69 (2004).
84. Huang, D.W., Sherman, B.T. &; Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols 4, 44-57 (2009).
85. Ernst, J. &; Bar-Joseph, Z. STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics 7 (2006).
86. Costa, I.G., Schonhuth, A. &; Schliep, A. The Graphical Query Language: a tool for analysis of gene expression time-courses. Bioinformatics 21, 2544-2545 (2005).
87. Bendel, C.M. et al. Systemic infection following intravenous inoculation of mice with Candida albicans int1 mutant strains. Molecular genetics and metabolism 67, 343-51 (1999).
88. Hoyer, L.L., Payne, T.L., Bell, M., Myers, A.M. &; Scherer, S. Candida albicans ALS3 and insights into the nature of the ALS gene family. Current genetics 33, 451-9 (1998).
89. Soloviev, D.A., Jawhara, S. &; Fonzi, W.A. Regulation of Innate Immune Response to Candida albicans Infections by alpha(M)beta(2)-Pra1p Interaction. Infection and Immunity 79, 1546-1558 (2011).
90. Alvarez, F.J. &; Konopka, J.B. Identification of an N-acetylglucosamine transporter that mediates hyphal induction in Candida albicans. Molecular Biology of the Cell 18, 965-75 (2007).
91. Uhl, M.A., Biery, M., Craig, N. &; Johnson, A.D. Haploinsufficiency-based large-scale forward genetic analysis of filamentous growth in the diploid human fungal pathogen C.albicans. The EMBO journal 22, 2668-78 (2003).
92. Barwell, K.J., Boysen, J.H., Xu, W. &; Mitchell, A.P. Relationship of DFG16 to the Rim101p pH response pathway in Saccharomyces cerevisiae and Candida albicans. Eukaryotic Cell 4, 890-9 (2005).
93. Bensen, E.S., Clemente-Blanco, A., Finley, K.R., Correa-Bordes, J. &; Berman, J. The mitotic cyclins Clb2p and Clb4p affect morphogenesis in Candida albicans. Molecular Biology of the Cell 16, 3387-400 (2005).
94. Yamaguchi, Y., Ota, K. &; Ito, T. A novel Cdc42-interacting domain of the yeast polarity establishment protein Bem1. Implications for modulation of mating pheromone signaling. The Journal of biological chemistry 282, 29-38 (2007).
95. Alonso-Monge, R. et al. Role of the mitogen-activated protein kinase Hog1p in morphogenesis and virulence of Candida albicans. Journal of bacteriology 181, 3058-68 (1999).
96. San Jose, C., Monge, R.A., Perez-Diaz, R., Pla, J. &; Nombela, C. The mitogen-activated protein kinase homolog HOG1 gene controls glycerol accumulation in the pathogenic fungus Candida albicans. Journal of bacteriology 178, 5850-2 (1996).
97. Calera, J.A., Zhao, X.J. &; Calderone, R. Defective hyphal development and avirulence caused by a deletion of the SSK1 response regulator gene in Candida albicans. Infection and immunity 68, 518-25 (2000).
98. Chauhan, N. et al. Candida albicans response regulator gene SSK1 regulates a subset of genes whose functions are associated with cell wall biosynthesis and adaptation to oxidative stress. Eukaryotic Cell 2, 1018-24 (2003).
99. Tebarth, B. et al. Adaptation of the Efg1p morphogenetic pathway in Candida albicans by negative autoregulation and PKA-dependent repression of the EFG1 gene. Journal of molecular biology 329, 949-62 (2003).
100. Hnisz, D., Majer, O., Frohner, I.E., Komnenovic, V. &; Kuchler, K. The Set3/Hos2 histone deacetylase complex attenuates cAMP/PKA signaling to regulate morphogenesis and virulence of Candida albicans. Plos Pathogens 6, e1000889 (2010).
101. Davis, D. Adaptation to environmental pH in Candida albicans and its relation to pathogenesis. Current Genetics 44, 1-7 (2003).
102. Fonzi, W.A. PHR1 and PHR2 of Candida albicans encode putative glycosidases required for proper cross-linking of beta-1,3-and beta-1,6-glucans. Journal of Bacteriology 181, 7070-7079 (1999).
103. Khalaf, R.A. &; Zitomer, R.S. The DNA binding protein Rfg1 is a repressor of filamentation in Candida albicans. Genetics 157, 1503-12 (2001).
104. Murad, A.M. et al. NRG1 represses yeast-hypha morphogenesis and hypha-specific gene expression in Candida albicans. EMBO J 20, 4742-52 (2001).
105. Brand, A. et al. Hyphal orientation of Candida albicans is regulated by a calcium-dependent mechanism. Current biology : CB 17, 347-52 (2007).
106. Arnaud, M.B. et al. The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. Nucleic Acids Research 33, D358-D363 (2005).
107. Arnaud, M.B., Costanzo, M.C., Shah, P., Skrzypek, M.S. &; Sherlock, G. Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans. Trends in microbiology 17, 295-303 (2009).
108. Shaw, G.C. et al. Mitoferrin is essential for erythroid iron assimilation. Nature 440, 96-100 (2006).
109. Nairz, M., Schroll, A., Sonnweber, T. &; Weiss, G. The struggle for iron - a metal at the host-pathogen interface. Cellular Microbiology 12, 1691-702 (2010).
110. Schaible, U.E. &; Kaufmann, S.H. Iron and microbial infection. Nature reviews. Microbiology 2, 946-53 (2004).
111. Wang, L. &; Cherayil, B.J. Ironing out the wrinkles in host defense: interactions between iron homeostasis and innate immunity. Journal of innate immunity 1, 455-64 (2009).
112. Chen, C., Pande, K., French, S.D., Tuch, B.B. &; Noble, S.M. An Iron Homeostasis Regulatory Circuit with Reciprocal Roles in Candida albicans Commensalism and Pathogenesis. Cell Host Microbe 10, 118-35 (2011).
113. Singh, R.P., Prasad, H.K., Sinha, I., Agarwal, N. &; Natarajan, K. Cap2-HAP Complex Is a Critical Transcriptional Regulator That Has Dual but Contrasting Roles in Regulation of Iron Homeostasis in Candida albicans. Journal of Biological Chemistry 286, 25154-25170 (2011).
114. Dunkel, N. &; Morschhauser, J. Loss of Heterozygosity at an Unlinked Genomic Locus Is Responsible for the Phenotype of a Candida albicans sap4 Delta sap5 Delta sap6 Delta Mutant. Eukaryotic Cell 10, 54-62 (2011).
115. Nantel, A. et al. Transcription profiling of Candida albicans cells undergoing the yeast-to-hyphal transition. Molecular Biology of the Cell 13, 3452-3465 (2002).
116. Dunkler, A., Walther, A., Specht, C.A. &; Wendland, J. Candida albicans CHT3 encodes the functional homolog of the Cts1 chitinase of Saccharomyces cerevisiae. Fungal Genetics and Biology 42, 935-947 (2005).
117. Lee, K.H., Jun, S., Hur, H.S., Ryu, J.J. &; Kim, J. Candida albicans protein analysis during hyphal differentiation using an integrative HA-tagging method. Biochemical and Biophysical Research Communications 337, 784-790 (2005).
118. Sorgo, A.G. et al. Effects of Fluconazole on the Secretome, the Wall Proteome, and Wall Integrity of the Clinical Fungus Candida albicans. Eukaryotic Cell 10, 1071-1081 (2011).
119. Almeida, R.S., Wilson, D. &; Hube, B. Candida albicans iron acquisition within the host. Fems Yeast Research 9, 1000-1012 (2009).
120. Bonhomme, J. et al. Contribution of the glycolytic flux and hypoxia adaptation to efficient biofilm formation by Candida albicans. Molecular Microbiology 80, 995-1013 (2011).
|