References
- Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ. Emerging fungal threats to animal, plant and ecosystem health. Nature 2012; 484(7393):186-94; PMID:22498624; https://doi.org/https://doi.org/10.1038/nature10947
- Nucci M, Marr KA. Emerging fungal diseases. Clin Infect Dis 2005; 41(4):521-6; PMID:16028162; https://doi.org/https://doi.org/10.1086/432060
- Enguita F, Costa M, Fusco-Almeida A, Mendes-Giannini M, Leitão A. Transcriptomic Crosstalk between Fungal Invasive Pathogens and Their Host Cells: Opportunities and Challenges for Next-Generation Sequencing Methods. J Fungi 2016; 2(1):7; https://doi.org/https://doi.org/10.3390/jof2010007
- Schulze S, Schleicher J, Guthke R, Linde J. How to Predict Molecular Interactions between Species? Front Microbiol 2016; 7(March):1-13.
- Westermann AJ, Gorski SA, Vogel J. Dual RNA-seq of pathogen and host. Nature Rev Microbiol 2012; 10(9):618-30; PMID:22890146; https://doi.org/https://doi.org/10.1038/nrmicro2852
- Blehert DS, Hicks AC, Behr M, Meteyer CU, Berlowski-Zier BM, Buckles EL, Coleman JT, Darling SR, Gargas A, Niver R, et al. Bat white-nose syndrome: an emerging fungal pathogen? Science 2009; 323(5911):227.
- Leopardi S, Blake D, Puechmaille SJ. White-nose syndrome fungus introduced from Europe to North America. Curr Biol 2015; 25(6):R217-19; PMID:25784035; https://doi.org/https://doi.org/10.1016/j.cub.2015.01.047
- Zukal J, Bandouchova H, Brichta J, Cmokova A, Jaron KS, Kolarik M, Kovacova V, Kubátová A, Nováková A, Orlov O, et al. White-nose syndrome without borders: Pseudogymnoascus destructans infection tolerated in Europe and Palearctic Asia but not in North America. Sci Rep 2016; 6(January):19829; PMID:26821755; https://doi.org/https://doi.org/10.1038/srep19829
- Frick WF, Puechmaille SJ, Hoyt JR, Nickel BA, Langwig KE, Foster JT, Barlow KE, Bartonička T, Feller D, Haarsma A-J, et al. Disease alters macroecological patterns of North American bats. Global Ecology and Biogeography 2015; 24(7):741-9; https://doi.org/https://doi.org/10.1111/geb.12290
- Langwig KE, Frick WF, Bried JT, Hicks AC, Kunz TH, Marm Kilpatrick A. Sociality, density-dependence and microclimates determine the persistence of populations suffering from a novel fungal disease, white-nose syndrome. Ecol Lett 2012; 15(9):1050-57; PMID:22747672; https://doi.org/https://doi.org/10.1111/j.1461-0248.2012.01829.x
- Turner GG, Reeder D, Coleman JTH. A Five-year Assessment of Mortality and Geographic Spread of White-Nose Syndrome in North American Bats, with a look to the future. Update of White-Nose Syndrome in bats. Bat Res News 2011; 52(2):13-27.
- Meteyer CU, Buckles EL, Blehert DS, Hicks AC, Green DE, Shearn-Bochsler V, Thomas NJ, Gargas A, Behr MJ. Histopathologic criteria to confirm white-nose syndrome in bats. J Vet Diagn Invest 2009; 21(4):411-4; PMID:19564488; https://doi.org/https://doi.org/10.1177/104063870902100401
- Reeder DM, Frank CL, Turner GG, Meteyer CU, Kurta A, Britzke ER, Vodzak ME, Darling SR, Stihler CW, Hicks AC, et al. Frequent arousal from hibernation linked to severity of infection and mortality in bats with white-nose syndrome. PLoS ONE 2012; 7(6):e38920; PMID:22745688; https://doi.org/https://doi.org/10.1371/journal.pone.0038920
- Warnecke L, Turner JM, Bollinger TK, Misra V, Cryan PM, Blehert DS, Wibbelt G, Willis CKR. Pathophysiology of white-nose syndrome in bats: a mechanistic model linking wing damage to mortality. Biol Lett 2013; 9:20130177; PMID:23720520; https://doi.org/https://doi.org/10.1098/rsbl.2013.0177
- Cryan PM, Meteyer CU, Blehert DS, Lorch JM, Reeder DM, Turner GG, Webb J, Behr M, Verant M, Russell RE, et al. Electrolyte depletion in white-nose syndrome bats. J Wildl Dis 2013; 49(2):398-402; PMID:23568916; https://doi.org/https://doi.org/10.7589/2012-04-121
- Verant ML, Meteyer CU, Speakman JR, Cryan PM, Lorch JM, Blehert DS. White-nose syndrome initiates a cascade of physiologic disturbances in the hibernating bat host. BMC Physiol 2014; 14(1):10; PMID:25487871; https://doi.org/https://doi.org/10.1186/s12899-014-0010-4
- Langwig KE, Frick WF, Reynolds R, Parise KL, Drees KP, Hoyt JR, Cheng TL, Kunz TH, Foster JT, Kilpatrick AM. Host and pathogen ecology drive the seasonal dynamics of a fungal disease, white-nose syndrome. Proceedings of the Royal Society B. 2015; 282(1799):20142335; PMID:25473016; https://doi.org/https://doi.org/10.1098/rspb.2014.2335
- Hoyt JR, Langwig KE, Sun K, Lu G, Parise KL, Jiang T, Frick WF, Foster JT, Feng J, Kilpatrick AM. Host persistence or extinction from emerging infectious disease: insights from white-nose syndrome in endemic and invading regions. Proceedings of the Royal Society B: Biological Sciences 2016; 283(1826):20152861; https://doi.org/https://doi.org/10.1098/rspb.2015.2861
- Wibbelt G, Puechmaille SJ, Ohlendorf B, Mühldorfer K, Bosch T, Görföl T, Passior K, Kurth A, Lacremans D, Forget F. Skin Lesions in European Hibernating Bats Associated with Geomyces destructans, the Etiologic Agent of White-Nose Syndrome. PLoS ONE 2013; 8(9):e74105; PMID:24023927; https://doi.org/https://doi.org/10.1371/journal.pone.0074105
- Zukal J, Bandouchova H, Bartonicka T, Berkova H, Brack V, Brichta J, Dolinay M, Jaron KS, Kovacova V, Kovarik M, et al. White-nose syndrome fungus: A generalist pathogen of hibernating bats. PLoS ONE 2014; 9(5):e97224; https://doi.org/https://doi.org/10.1371/journal.pone.0097224
- Pikula J, Bandouchova H, Novotný L, Meteyer CU, Zukal J, Irwin NR, Zima J, Martínková N. Histopathology confirms white-nose syndrome in bats in Europe. J Wildl Dis 2012; 48(1):207-11; PMID:22247393; https://doi.org/https://doi.org/10.7589/0090-3558-48.1.207
- Van der Meij T, Van Strien AJ, Haysom KA, Dekker J, Russ J, Biala K, Bihari Z, Jansen E, Langton S, Kurali A, et al. Return of the bats? A prototype indicator of trends in European bat populations in underground hibernacula. Mammalian Biology 2015; 80(3):170-7; https://doi.org/https://doi.org/10.1016/j.mambio.2014.09.004
- Paterson S, Vogwill T, Buckling A, Benmayor R, Spiers AJ, Thomson NR, Quail M, Smith F, Walker D, Libberton B, et al. Antagonistic coevolution accelerates molecular evolution. Nature 2010; 464(7286):275-8; PMID:20182425; https://doi.org/https://doi.org/10.1038/nature08798
- Thogmartin WE, Sanders-Reed CA, Szymanski JA, McKann PC, Pruitt L, King RA, Runge MC, Russell RE. White-nose syndrome is likely to extirpate the endangered Indiana bat over large parts of its range. Biological Conservation 2013; 160:162-72; https://doi.org/https://doi.org/10.1016/j.biocon.2013.01.010
- Stevens RB. Cultural Practices in Disease Control. In: Horsfall J, Dimond A, editors. Plant pathology, an advanced treatise, Vol. 3. New York, NY, USA: Academic Press; 1960. p. 357-429.
- Casadevall A, Pirofski L. Host-pathogen interactions: the attributes of virulence. J Infect Dis 2001; 184(3):337-44; PMID:11443560; https://doi.org/https://doi.org/10.1086/322044
- Field KAKA, Johnson JS, Lilley TMTM, Reeder SMSM, Rogers EJEJ, Behr MJMJ, Reeder DMDM. The White-Nose Syndrome Transcriptome: Activation of Anti-fungal Host Responses in Wing Tissue of Hibernating Little Brown Myotis. PLoS Pathogens 2015; 11(10):1-29; https://doi.org/https://doi.org/10.1371/journal.ppat.1005168
- Whittington A, Gow NAR, Hube B. From Commensal to Pathogen: Candida albicans. In: Kurzai O, editor. Human Fungal Pathogens. 2nd ed. Berlin Heidelberg; 2014. p. 3-18.
- Brunke S, Mogavero S, Kasper L, Hube B. Virulence factors in fungal pathogens of man. Curr Opin Microbiol 2016; 32:89-95; PMID:27257746; https://doi.org/https://doi.org/10.1016/j.mib.2016.05.010
- Pannkuk EL, Risch TS, Savary BJ. Isolation and identification of an extracellular subtilisin-like serine protease secreted by the Bat Pathogen Pseudogymnoascus destructans. PLoS ONE. 2015; 10(3):e0120508; PMID:25785714; https://doi.org/https://doi.org/10.1371/journal.pone.0120508
- O'Donoghue AJ, Knudsen GM, Beekman C, Perry J a, Johnson AD, DeRisi JL, Craik CS, Bennett RJ. Destructin-1 is a collagen-degrading endopeptidase secreted by Pseudogymnoascus destructans, the causative agent of white-nose syndrome. Proc Natl Acad Sci 2015; 112(24):7478-83; https://doi.org/https://doi.org/10.1073/pnas.1507082112
- Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, et al. Pfam: The protein families database. Nucleic Acids Res 2014; 42(D1):D222-30; https://doi.org/https://doi.org/10.1093/nar/gkt1223
- Bandouchova H, Bartonicka T, Berkova H, Brichta J, Cerny J, Kovacova V, Kolarik M, Köllner B, Kulich P, Martínková N, et al. Pseudogymnoascus destructans: Evidence of Virulent Skin Invasion for Bats Under Natural Conditions, Europe. Transbound Emerg Dis 2015; 62(1):1-5; PMID:25268034; https://doi.org/https://doi.org/10.1111/tbed.12282
- Frank CL, Michalski A, McDonough AA, Rahimian M, Rudd RJ, Herzog C. The resistance of a North American bat species (Eptesicus fuscus) to White-Nose Syndrome (WNS). PLoS ONE 2014; 9(12):e113958; https://doi.org/https://doi.org/10.1371/journal.pone.0113958
- Mayer FL, Wilson D, Hube B. Candida albicans pathogenicity mechanisms. Virulence 2013; 4(2):119-28; PMID:23302789; https://doi.org/https://doi.org/10.4161/viru.22913
- Lilley TMTM, Johnson JS, Ruokolainen L, Rogers EJEJ, Wilson CACA, Schell SMSM, Field KAKA, Reeder DMDDM. White-nose syndrome survivors do not exhibit frequent arousals associated with Pseudogymnoascus destructans infection. Frontiers in Zoology 2016; 13(1):12; PMID:26949407; https://doi.org/https://doi.org/10.1186/s12983-016-0143-3
- Wheeler RT, Kombe D, Agarwala SD, Fink GR. Dynamic, morphotype-specific Candida albicans beta-glucan exposure during infection and drug treatment. PLoS Pathogens 2008; 4(12):1-12; https://doi.org/https://doi.org/10.1371/journal.ppat.1000227
- Romani L. Immunity to fungal infections. Nat Rev Immunol 2011; 11(4):275-88; PMID:21394104; https://doi.org/https://doi.org/10.1038/nri2939
- Ketudat Cairns JR, Esen A. β-Glucosidases. Cell Mol Life Sci: CMLS 2010; 67(20):3389-405; PMID:20490603; https://doi.org/https://doi.org/10.1007/s00018-010-0399-2
- Kitagaki H, Wu H, Shimoi H, Ito K. Two homologous genes, DCW1 (YKL046c) and DFG5, are essential for cell growth and encode glycosylphosphatidylinositol (GPI)-anchored membrane proteins required for cell wall biogenesis in Saccharomyces cerevisiae. Mol Microbiol 2002; 46(4):1011-22; PMID:12421307; https://doi.org/https://doi.org/10.1046/j.1365-2958.2002.03244.x
- Ene I V, Adya AK, Wehmeier S, Brand AC, Maccallum DM, Gow NAR, Brown AJP. Host carbon sources modulate cell wall architecture, drug resistance and virulence in a fungal pathogen. Cell Microbiol 2012; 14(9):1319-35; PMID:22587014; https://doi.org/https://doi.org/10.1111/j.1462-5822.2012.01813.x
- Ene I V, Heilmann CJ, Sorgo AG, Walker LA, de Koster CG, Munro CA, Klis FM, Brown AJP. Carbon source-induced reprogramming of the cell wall proteome and secretome modulates the adherence and drug resistance of the fungal pathogen Candida albicans. PROTEOMICS 2012; 12(21):3164-79; PMID:22997008; https://doi.org/https://doi.org/10.1002/pmic.201200228
- Gargas A, Trest MT, Christensen M, Volk TJ, Blehert DS. Geomyces destructans sp. nov. associated with bat white-nose syndrome. Mycotaxon 2009; 108(June):147-54; https://doi.org/https://doi.org/10.5248/108.147
- Raudabaugh DB, Miller AN. Morphogenetic Effect of L-cysteine on Pseudogymnoascus destructans and Related Species. Mycosphere 2014; 5(6):737-46.
- Collette JR, Lorenz MC. Mechanisms of immune evasion in fungal pathogens. Curr Opin Microbiol 2011; 14(6):668-75; PMID:21955887; https://doi.org/https://doi.org/10.1016/j.mib.2011.09.007
- Johnson JS, Reeder DM, Lilley TM, Czirják G, Voigt CC, McMichael JW, Meierhofer MB, Seery CW, Lumadue SS, Altmann AJ, et al. Antibodies to Pseudogymnoascus destructans are not sufficient for protection against white-nose syndrome. Ecol Evol 2015; 5(11):2203-14; PMID:26078857; https://doi.org/https://doi.org/10.1002/ece3.1502
- Lilley TM, Prokkola JM, Johnson JS, Rogers EJ, Gronsky S, Kurta A, Reeder DM, Field KA. Immune responses in hibernating little brown myotis (Myotis lucifugus) with white-nose syndrome. Proceedings of the Royal Society B. 2017; 284 (1848):20162232; PMID:28179513; https://doi.org/https://doi.org/10.1098/rspb.2016.2232
- Bromuro C, Romano M, Chiani P, Berti F, Tontini M, Proietti D, Mori E, Torosantucci A, Costantino P, Rappuoli R, et al. Beta-glucan-CRM197 conjugates as candidates antifungal vaccines. Vaccine 2010; 28(14):2615-23; PMID:20096763; https://doi.org/https://doi.org/10.1016/j.vaccine.2010.01.012
- Shen HD, Lin WL, Tam MF, Chou H, Wang CW, Tsai JJ, Wang SR, Han SH. Identification of vacuolar serine proteinase as a major allergen of Aspergillus fumigatus by immunoblotting and N-terminal amino acid sequence analysis. Clin Exp Allergy 2001; 31(2):295-302; PMID:11251631; https://doi.org/https://doi.org/10.1046/j.1365-2222.2001.01026.x
- Hood MI, Skaar EP. Nutritional immunity: transition metals at the pathogen-host interface. Nat Rev Microbiol 2012; 10(8):525-37; PMID:22796883; https://doi.org/https://doi.org/10.1038/nrmicro2836
- Haas H, Eisendle M, Turgeon BG. Siderophores in fungal physiology and virulence. Annu Rev Phytopathol 2008; 46(1):149-187; PMID:18680426; https://doi.org/https://doi.org/10.1146/annurev.phyto.45.062806.094338
- Flieger M, Bandouchova H, Cerny J, Chudíčková M, Kolarik M, Kovacova V, Martínková N, Novák P, Šebesta O, Stodůlková E, et al. Vitamin B2 as a virulence factor in Pseudogymnoascus destructans skin infection. Sci Rep 2016; 6:33200; PMID:27620349; https://doi.org/https://doi.org/10.1038/srep33200
- Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30(15):2114-20; PMID:24695404; https://doi.org/https://doi.org/10.1093/bioinformatics/btu170
- Andrews S. FastQC: A quality control tool for high throughput sequence data. Available from: http://www.bioinformatics.babraham.ac.uk/Projects/Fastqc/.2010
- Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 2013; 29(1):15-21; PMID:23104886; https://doi.org/https://doi.org/10.1093/bioinformatics/bts635
- Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, et al. Ensembl 2016. Nucleic Acids Res 2016; 44(D1):D710-D716; PMID:26687719; https://doi.org/https://doi.org/10.1093/nar/gkv1157
- Drees KP, Palmer JM, Sebra R, Lorch JM, Chen C, Wu C-C, Bok JW, Keller NP, Blehert DS, Cuomo CA, et al. Use of Multiple Sequencing Technologies To Produce a High-Quality Genome of the Fungus Pseudogymnoascus destructans, the Causative Agent of Bat White-Nose Syndrome. Genome Announc 2016; 4(3):e00445-16; PMID:27365344; https://doi.org/https://doi.org/10.1128/genomeA.00445-16
- Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011; 12(1):323; PMID:21816040; https://doi.org/https://doi.org/10.1186/1471-2105-12-323
- Busby MA, Stewart C, Miller CA, Grzeda KR, Marth GT. Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. Bioinformatics 2013; 29(5):656-7; PMID:23314327; https://doi.org/https://doi.org/10.1093/bioinformatics/btt015
- Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014; 15(12):550; PMID:25516281; https://doi.org/https://doi.org/10.1186/s13059-014-0550-8
- Robinson MD, McCarthy DJ, Smyth GK. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26(1):139-40; PMID:19910308; https://doi.org/https://doi.org/10.1093/bioinformatics/btp616
- Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 2010; 11(3):R25; PMID:20196867; https://doi.org/https://doi.org/10.1186/gb-2010-11-3-r25
- Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B (Methodological) 1995; 57:289-300.
- Suzuki R, Shimodaira H. Pvclust: An R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 2006; 22(12):1540-42; PMID:16595560; https://doi.org/https://doi.org/10.1093/bioinformatics/btl117
- McGinnis S, Madden TL. BLAST: At the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004; 32 (suppl_2): W20-W25; PMID: 15215342; https://doi.org/https://doi.org/10.1093/nar/gkh435
- Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, et al. InterProScan 5: Genome-scale protein function classification. Bioinformatics 2014; 30(9):1236-40; PMID:24451626; https://doi.org/https://doi.org/10.1093/bioinformatics/btu031
- Tang H, Flick P, Sato K, Ramirez F, Klopfenstein D, Mungall C, Yunes J, Pedersen B. GOATOOLS: Tools for Gene Ontology. 2015; https://doi.org/https://doi.org/10.5281/ZENODO.31628