Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii

Alonso-Monge, 1999, Role of the mitogen-activated protein kinase Hog1p in morphogenesis and virulence of Candida albicans, J. Bacteriol., 181, 3058, 10.1128/JB.181.10.3058-3068.1999 Alonso-Monge, 2003, The Hog1 mitogen-activated protein kinase is essential in the oxidative stress response and chlamydospore formation in Candida albicans, Eukaryot. Cell, 2, 351, 10.1128/EC.2.2.351-361.2003 Bendtsen, 2004, Improved prediction of signal peptides: SignalP 3.0, J. Mol. Biol., 340, 783, 10.1016/j.jmb.2004.05.028 Boyle, 1994, Potential molecular targets of metabolic pathways, J. Med. Vet. Mycol., 32, 79, 10.1080/02681219480000741 Bozdech, 2003, Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray, Genome Biol., 4, R9, 10.1186/gb-2003-4-2-r9 Brem, 2002, Genetic dissection of transcriptional regulation in budding yeast, Science, 296, 752, 10.1126/science.1069516 Breslau, 1964, Continuous in vitro cultivation of spherules of Coccidioides immitis, J. Bacteriol., 87, 468, 10.1128/JB.87.2.468-472.1964 Cole, 1988, Immunoreactivity of a surface wall fraction produced by spherules of Coccidioides immitis, Infect. Immun., 56, 2695, 10.1128/IAI.56.10.2695-2701.1988 Cole, 1988, Isolation and morphology of an immunoreactive outer wall fraction produced by spherules of Coccidioides immitis, Infect. Immun., 56, 2686, 10.1128/IAI.56.10.2686-2694.1988 Converse, 1957, Effect of surface active agents on endosporulation of Coccidioides immitis in a chemically defined medium, J. Bacteriol., 74, 106, 10.1128/JB.74.1.106-107.1957 Crameri, 1998, Recombinant Aspergillus fumigatus allergens: from the nucleotide sequences to clinical applications, Int. Arch. Allergy Imm., 115, 99, 10.1159/000023889 Delgado, 2004, Profiling gene expression in Coccidioides posadasii, Med. Mycol., 42, 59, 10.1080/1369378031000156890 Delgado, 2003, A recombinant beta-1,3-glucanosyltransferase homolog of Coccidioides posadasii protects mice against coccidioidomycosis, Infect. Immun., 71, 3010, 10.1128/IAI.71.6.3010-3019.2003 Diatchenko, 1999, Suppression subtractive hybridization: a versatile method for identifying differentially expressed genes, Method Enzymol., 303, 349, 10.1016/S0076-6879(99)03022-0 Drnevich, 2004, Quantitative evolutionary genomics: differential gene expression and male reproductive success in Drosophila melanogaster, Proc. Biol. Sci., 271, 2267, 10.1098/rspb.2004.2880 Fay, 2004, Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae, Genome Biol., 5, R26, 10.1186/gb-2004-5-4-r26 Fisher, 2002, Molecular and phenotypic description of Coccidioides posadasii sp nov., previously recognized as the non-California population of Coccidioides immitis, Mycologia, 94, 73, 10.2307/3761847 Fisher, 2002, Disease surveillance in recombining pathogens: multilocus genotypes identify sources of human Coccidioides infections, Proc. Natl. Acad. Sci. USA, 99, 9067, 10.1073/pnas.132178099 Fritz, 2002, Dependence of Mycobacterium bovis BCG on anaerobic nitrate reductase for persistence is tissue specific, Infect. Immun., 70, 286, 10.1128/IAI.70.1.286-291.2002 Galagan, 2003, The genome sequence of the filamentous fungus Neurospora crassa, Nature, 422, 859, 10.1038/nature01554 Galgiani, 1999, Coccidioidomycosis: a regional disease of national importance—rethinking approaches for control, Ann. Intern. Med., 130, 293, 10.7326/0003-4819-130-4-199902160-00015 Gancedo, 2004, The importance of a functional trehalose biosynthetic pathway for the life of yeasts and fungi, FEMS Yeast Res., 4, 351, 10.1016/S1567-1356(03)00222-8 Guevara-Olvera, 2000, Sequence, expression and functional analysis of the Coccidioides immitis ODC (ornithine decarboxylase) gene, Gene, 242, 437, 10.1016/S0378-1119(99)00496-5 Hung, 2000, A major cell surface antigen of Coccidioides immitis which elicits both humoral and cellular immune responses, Infect. Immun., 68, 584, 10.1128/IAI.68.2.584-593.2000 Hung, 2002, A parasitic phase-specific adhesin of Coccidioides immitis contributes to the virulence of this respiratory fungal pathogen, Infect. Immun., 70, 3443, 10.1128/IAI.70.7.3443-3456.2002 Hwang, 2003, Identifying phase-specific genes in the fungal pathogen Histoplasma capsulatum using a genomic shotgun microarray, Mol. Biol. Cell, 14, 2314, 10.1091/mbc.E03-01-0027 Ivey, 2003, Identification of a protective antigen of Coccidioides immitis by expression library immunization, Vaccine, 21, 4359, 10.1016/S0264-410X(03)00485-7 Jedd, 2000, A new self-assembled peroxisomal vesicle required for efficient resealing of the plasma membrane, Nat. Cell Biol., 2, 226, 10.1038/35008652 Johannesson, 2005, Concerted evolution in the repeats of an immunomodulating cell surface protein, sowgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii, Genetics, 171, 109, 10.1534/genetics.105.040923 Johannesson, 2004, Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C-posadasii and their closest relatives, Mol. Biol. Evol., 21, 1134, 10.1093/molbev/msh124 Kojima, 2004, Fungicide activity through activation of a fungal signalling pathway, Mol. Microbiol., 53, 1785, 10.1111/j.1365-2958.2004.04244.x Koufopanou, 1997, Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis, Proc. Natl. Acad. Sci. USA, 94, 5478, 10.1073/pnas.94.10.5478 Kraus, 2004, Identification of Cryptococcus neoformans temperature-regulated genes with a genomic-DNA microarray, Eukaryot. Cell, 3, 1249, 10.1128/EC.3.5.1249-1260.2004 Lan, 2002, Metabolic specialization associated with phenotypic switching in Candida albicans, Proc. Natl. Acad. Sci. USA, 99, 14907, 10.1073/pnas.232566499 Le Quere, 2004, Divergence in gene expression related to variation in host specificity of an ectomycorrhizal fungus, Mol. Ecol., 13, 3809, 10.1111/j.1365-294X.2004.02369.x Maddy, 1967, 309 Mannhaupt, 2003, What’s in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence, Nucleic Acid Res., 31, 1944, 10.1093/nar/gkg293 Pappagianis, 1988, Epidemiology of coccidioidomycosis, Curr. Top. Med. Mycol., 2, 199, 10.1007/978-1-4612-3730-3_6 Perfect, 2002, New antifungal agents, Transpl. Infect. Dis., 4, 52, 10.1034/j.1399-3062.4.s3.8.x Reichard, 2000, Disruption of the gene which encodes a serodiagnostic antigen and chitinase of the human fungal pathogen Coccidioides immitis, Infect. Immun., 68, 5830, 10.1128/IAI.68.10.5830-5838.2000 Rockman, 2002, Abundant raw material for cis-regulatory evolution in humans, Mol. Biol. Evol., 19, 1991, 10.1093/oxfordjournals.molbev.a004023 Saubolle, 1996, 1 Singh, 2001, ProPred: prediction of HLA-DR binding sites, Bioinformatics, 17, 1236, 10.1093/bioinformatics/17.12.1236 Sturniolo, 1999, Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices, Nat. Biotechnol., 17, 555, 10.1038/9858 Takasaki, 2004, Unusual transcription regulation of the niaD gene under anaerobic conditions supporting fungal ammonia fermentation, Biosci. Biotechnol. Biochem., 68, 978, 10.1271/bbb.68.978 Tarbet, 1953, Histochemical investigation of the spherule of Coccidioides immitis in relation to host reaction, J. Infect. Dis., 72, 183, 10.1093/infdis/92.2.183 Tey, 2005, Polarized gene expression determines Woronin body formation at the leading edge of the fungal colony, Mol. Biol. Cell, 16, 2651, 10.1091/mbc.E04-10-0937 Townsend, 2004, Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays, Bmc Bioinformatics, 5, 54, 10.1186/1471-2105-5-54 Townsend, 2003, Population genetic variation in genome-wide gene expression, Mol. Biol. Evol., 20, 955, 10.1093/molbev/msg106 Townsend, 2002, Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments, Genome Biol., 3, 0071, 10.1186/gb-2002-3-12-research0071 Townsend, 2005, Designing experiments using spotted microarrays to detect gene regulation differences within and among species, Methods Enzymol., 395, 597, 10.1016/S0076-6879(05)95031-3 Van Gelder, 1990, Amplified RNA synthesized from limited quantities of heterogeneous cDNA, Proc. Natl. Acad. Sci. USA, 87, 1663, 10.1073/pnas.87.5.1663 Vandenbossche, 1990, Biochemical basis for the activity and selectivity of oral antifungal drugs, Br. J. Clin. Pract., 44, 41 Weber, 2000, Anaerobic nitrate reductase (narGHJI) activity of Mycobacterium bovis BCG in vitro and its contribution to virulence in immunodeficient mice, Mol. Microbiol., 35, 1017, 10.1046/j.1365-2958.2000.01794.x Wheat, 1977, Comparison of Coccidioides immitis arthrospore, mycelium, and spherule cell walls, and influence of growth medium on mycelial cell wall composition, Infect. Immun., 17, 91, 10.1128/IAI.17.1.91-97.1977 Whitehead, 2005, Variation in tissue-specific gene expression among natural populations, Genome Biol., 6, R13, 10.1186/gb-2005-6-2-r13 Wills, E.A., Cox, G.M., Perfect, J.R., 2002. The trehalose complex and its interaction with calcineurin in Cryptococcus neoformans. 5th International Conference on Cryptococcus and Cryptococcosis, Adelaide. Winzeler, 2003, Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays, Genetics, 163, 79, 10.1093/genetics/163.1.79 Yuan, 2003, A HEX-1 crystal lattice required for Woronin body function in Neurospora crassa, Nat. Struct. Biol., 10, 264, 10.1038/nsb910 Zaragoza, 1998, Disruption of the Candida albicans TPS1 gene encoding trehalose-6-phosphate synthase impairs formation of hyphae and decreases infectivity, J. Bacteriol., 180, 3809, 10.1128/JB.180.15.3809-3815.1998 Zhang, 2002, Osmoregulation and fungicide resistance: the Neurospora crassa os-2 gene encodes a HOG1 mitogen-activated protein kinase homologue, Appl. Environ. Microbiol., 68, 532, 10.1128/AEM.68.2.532-538.2002 Zhou, 2002, Ammonia fermentation, a novel anoxic metabolism of nitrate by fungi, J. Biol. Chem., 277, 1892, 10.1074/jbc.M109096200