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Tsui et al. ARTICLE Lizardi PM, Huang X, Zhu Z, Bray-Ward P, Thomas DC, Ward DC (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nature Genetics 19: 225– 232. Lu Q, Gerrits van den Ende AH, Bakkers JM, Sun J, Lackner M, Najafzadeh MJ, Melchers WJ, Li R, de Hoog GS (2011). Identification of Pseudallescheria and Scedosporium species by three molecular methods. Journal of Clinical Microbiology 49: 960-7 Lucas S, da Luz Martins M, Flores O, Meyer W, Spencer-Martins I, Inácio J (2010) Differentiation of Cryptococcus neoformans varieties and Cryptococcus gattii using CAP59-based loopmediated isothermal DNA amplification. Clinical Microbiology and Infection 16: 711–714. McArthur FA, Bärlocher MO, McLean NAB, Hiltz MD, Bärlocher F (2001) Asking probing questions: can fluorescent in situ hybridization identify and localize aquatic hyphomycetes on leaf litter? International Review of Hydrobiology 86: 429-438. Mori Y, Notomi T (2009) Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases. Journal of Infection and Chemotherapy 15: 62–69. Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP, Landegren U (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265: 2085–2088. Nilsson M, Krejci K, Koch J, Kwiatkowski M, Gustavsson P, Landegren U (1997) Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21. Nature Genetics 16: 252–255. Nilsson M, Dahl F, Larsson C, Gullberg M, Stenberg J (2006) Analyzing genes using closing and replicating circles. Trends in Biotechnology 24: 83–88. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Research 28: E63. Ohori A, Endo S, Sano A, Yokoyama K, Yarita K, Yamaguchi M, Kamei K, Miyaji M, Nishimura K (2006) Rapid identification of Ochroconis gallopava by a loop-mediated isothermal amplification (LAMP) method. Veterinary Microbiology 114: 359–365. Okubara PA, Schroeder KL, Li C, Schumacher RT, Lawrence NP (2007) Improved extraction of Rhizoctonia and Pythium DNA from wheat roots and soil samples using pressure cycling technology. Canadian Journal of Plant Pathology 29: 304– 310. Ophel-Keller K, McKay A, Hartley D, Herdina A, Curran J (2008) Development of a routine DNA-based testing service for soilborne diseases in Australia. Australasian Plant Pathology 37: 243–253. Parida M, Sannarangaiah S, Dash PK, Rao PV, Morita K (2008) Loop mediated isothermal amplification (LAMP): a new generation of innovative gene amplification technique; perspectives in clinical diagnosis of infectious diseases. Reviews in Medical Virology 18: 407–421. Pernthaler A, Pernthaler J, Amann R (2002) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Applied and Environmental Microbiology 68: 3094–3101. Pickering J, Bamford A, Godbole V, Briggs J, Scozzafava G, Roe P, Wheeler C, Ghouze F, Cuss S (2002) Integration of DNA ligation and rolling circle amplification for the homogeneous, end-point detection of single nucleotide polymorphisms. Nucleic Acids Research 30: e60. Pozhitkov A, Noble PA, Domazet-Losˇo T, Nolte AW, Sonnenberg R, Staehler P, Beier M, Tautz D (2006) Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Research 34: e66. Pozhitkov AE, Tautz D, Noble PA (2007) Oligonucleotide microarrays: widely applied – poorly understood. Briefings in Functional Genomics & Proteomics 6: 141–148. Prins TW, van Dijk JP, Beenen HG, Van Hoef AA, Voorhuijzen MM, Schoen CD, Aarts HJ, Kok EJ (2008) Optimised padlock probe ligation and microarray detection of multiple (non-authorised) GMOs in a single reaction. BMC Genomics 9: 584. Punja ZK, Wan A, Goswami RS, Verma N, Rahman M, Barasubiye T, Seifert KA, Lévesque CA (2007) Diversity of Fusarium species associated with discolored ginseng roots in British Columbia. Canadian Journal of Plant Pathology 29: 340–353. Reeleder RD, Capella BB, Tomlinson LD, Hickey WJ (2003) The extraction of fungal DNA from multiple large soil samples. Canadian Journal of Plant Pathology 25: 182–191. Robideau GP, Caruso FL, Oudemans PV, McManus PS, Renaud MA, Auclair ME, Bilodeau GJ, Yee D, Désaulniers NL, DeVerna JW, Lévesque CA (2008) Detection of cranberry fruit rot fungi using DNA array hybridization. Canadian Journal of Plant Pathology 30: 226–240. Robin BJ, Arffa RC, Avni I, Rao NA (1986) Rapid visualization of three common fungi using fluorescein-conjugated lectins. Investigative Ophthalmology & Visual Science 27: 500–506. Scupham AJ, Presley LL, Wei B, Bent E, Griffith N, McPherson M, Zhu F, Oluwadara O, Rao N, Braun J, Borneman J (2006) Abundant and diverse fungal microbiota in the murine intestine. Applied and Environmental Microbiology 72: 793–801. Seifert, KA, Lévesque CA (2004) Phylogeny and molecular diagnosis of mycotoxigenic fungi. European Journal of Plant Pathology 110: 449–471. Seifert KA, Samson RA, deWaard JR, Houbraken J, Lévesque CA, Moncalvo J-M, Louis-Seize G and Hebert PDN (2007) Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proceedings of the National Academy of Sciences, USA 104: 3901–3906. Shepard JR, Addison RM, Alexander BD, Della-Latta P, Gherna M, Haase G, Hall G, Johnson JK, Merz WG, Peltroche- Llacsahuanga H, Stender H, Venezia RA, Wilson D., Procop GW, Wu F, Fiandaca MJ (2008) Multicenter evaluation of the Candida albicans/Candida glabrata peptide nucleic acid fluorescent in situ hybridization method for simultaneous dual-color identification of C. albicans and C. glabrata directly from blood culture bottles. Journal of Clinical Microbiology 46: 50–55. Sholberg PL, O’Gorman D, Bedford K, Lévesque CA (2005) Development of a DNA macroarray for detection and monitoring of economically important apple diseases. Plant Disease 89: 1143–1150. 188 ima fUNGUS
Molecular identification and detection of fungi Sholberg PL, O’Gorman D, Bedford KE (2006) Monitoring Erwinia amylovora in pome fruit orchards using reverse dot-blot hybridization. Acta Horticulturae 704: 91-98. Stanley KK, Szewczuk E (2005) Multiplexed tandem PCR: gene profiling from small amounts of RNA using SYBR Green detection. Nucleic Acids Research 33: e180. Summerbell RC, Lévesque CA, Seifert KA, Bovers M, Fell JW, Diaz MR, Boekhout T, de Hoog GS, Stalpers J, Crous PW (2005) Microcoding: the second step in DNA barcoding. Philosophical Transactions of the Royal Scoiety, B 360: 1897–1903. Sun J, Li X, Zeng H, Xie Z, Lu C, Xi L, de Hoog GS (2010a) Development and evaluation of loop-mediated isothermal amplification (LAMP) for the rapid diagnosis of Penicillium marneffei in archived t<strong>issue</strong> samples. FEMS Immunology and Medical Microbiology 58: 381–388. Sun J, Najafzadeh MJ, Vicente V, Xi L, de Hoog GS (2010b) Rapid detection of pathogenic fungi using loop-mediated isothermal amplification, exemplified by Fonsecaea agents of chromoblastomycosis. Journal of Microbiological Methods 80: 19–24. Szemes M, Bonants P, de Weerdt M, Baner J, Landegren U, Schoen CD (2005) Diagnostic application of padlock probes – multiplex detection of plant pathogens using universal microarrays. Nucleic Acids Research 33: e70. Tambong JT, de Cock AWAM, Tinker NA, Lévesque CA (2006) Oligonucleotide array for identification and detection of Pythium species. Applied and Environmental Microbiology 72: 2691– 2706. Tatibana BT, Sano A, Uno J, Kamei K, Igarashi T, Mikami Y, Miyaji M, Nishimura K, Itano EN (2009) Detection of Paracoccidioides brasiliensis gp43 gene in sputa by loop-mediated isothermal amplification method. Journal of Clinical Laboratory Analysis 23: 139–143. Tomita N, Mori Y, Kanda H, Notomi T (2008) Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nature Protocols 3: 877–882. Tsui CKM, Wang B, Khadempour L, Alamouti SM, Bohlmann J, Murray BW, Hamelin RC (2010) Rapid identification and detection of pine pathogenic fungi associated with mountain pine beetles by padlock probes. Journal of Microbiological Methods 83: 26–33. Tsui CKM, Wang B, Schoen C, Hamelin RC (2012) Padlock probe for the detection of pathogenic fungi. In Laboratory Protocols in Fungal Biology: Current Methods in Fungal Biology (Gupta VA, Tuohy M, Ayyachamy M, Turner KM, O’Donovan A, eds): in press. Springer-Verlag. Uehara T, Kushida A, Momota Y (1999) Rapid and sensitive identification of Pratylenchus spp. using reverse dot blot hybridization. Nematology 1: 549–555. Urakawa H, Fantroussi SE, Smidt H, Smoot JC, Tribou EH, Kelly JJ, Noble PA, Stahl DA (2003) Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Applied and Environmntal Microbiology 69: 2848–2856. van Doorn R, Szemes M, Bonants P, Kowalchuk GA, Salles JF, Ortenberg E, Schoen CD (2007) Quantitative multiplex detection of plant pathogens using a novel ligation probe-based system coupled with universal, high-throughput real-time PCR on OpenArrays ® . BMC Genomics 8: 276. van Doorn R, Slawiak M, Szemes M, Dullemans AM, Bonants P, Kowalchuk GA, Schoen CD (2009) Robust detection and identification of multiple oomycetes and fungi in environmental samples by using a novel cleavable padlock probe-based ligation detection assay. Applied and Environmental Microbiology 75: 4185–4193. Wang B, Dwyer DE, Chew CB, Kol C, He ZP, Joshi H, Steain MC, Cunningham AL, Saksena NK (2009) Sensitive detection of the K103N non-nucleoside reverse transcriptase inhibitor resistance mutation in treatment-naive HIV-1 infected individuals by rolling circle amplification. Journal of Virological Methods 161: 128–135. Wang B, Dwyer DE, Blyth CC, Soedjono M, Shi H, Kesson A, Ratnamohan M, McPhie K, Cunningham AL, Saksena NK (2010) Detection of the rapid emergence of the H275Y mutation associated with oseltamivir resistance in severe pandemic influenza virus A/ H1N1 09 infections. Antiviral Research 87: 16–21. Wang Y, Kang Z, Gao H, Gao Y, Qin L, Lin H, Yu F, Qi X, Wang X (2011) A one-step reverse transcription loop-mediated isothermal amplification for detection and discrimination of infectious bursal disease virus. Virology Journal 8: 108. Weber SD, Ludwig W, Schleifer K-H, Fried J (2007) Microbial composition and structure of aerobic granular sewage biofilms. Applied and Environmental Microbiology 73: 6233–6240. Wilson DA, Joyce MJ, Hall LS, Reller LB, Roberts GD, Hall GS, Alexander BD, Procop W (2005) Multicenter evaluation of a Candida albicans peptide nucleic acid fluorescent in situ hybridization probe for characterization of yeast isolates from blood cultures. Journal of Clinical Microbiology 43: 2909–2912. Xiong L, Kong F, Yang Y, Cheng J, Gilbert GL (2006) Use of PCR and reverse line blot hybridization macroarray based on 16S-23S rRNA gene internal transcribed spacer sequences for rapid identification of 34 Mycobacterium species. Journal of Clinical Microbiology 44: 3544–3550. Yang YP, Corley N, Garcia-Heras J (2001) Reverse dot-blot hybridization as an improved tool for the molecular diagnosis of point mutations in congenital adrenal hyperplasia caused by 21-hydroxylase deficiency. Molecular Diagnostics 6: 193–199. Zhang N, Geiser MD, Smart CD (2007) Macroarray detection of solanaceous plant pathogens in the Fusarium solani species complex. Plant disease 91: 1612–1620. Zhang N, McCarthy ML, Smart CD (2008) A macroarray system for the detection of fungal and oomycete pathogens of solanaceous crops. Plant disease 92: 953–960. Zhang Y, Coyne MY, Will SG, Levenson CH, Kawasaki ES (1991) Single-base mutational analysis of cancer and genetic diseases using membrane bound modified oligonucleotides. Nucleic Acids Research 19: 3929–3933. Zhao K, Shi W, Han F, Xu Y, Zhu L, Zou Y, Wu X, Zhu H, Tan F, Tao S, Tang X (2011). Specific, simple and rapid detection of porcine circovirus type 2 using the loop-mediated isothermal amplification method. Virology Journal 8: 126. Zhou X, Kong F, Sorrell TC, Wang H, Duan Y, Chen SC (2008) Practical method for detection and identification of Candida, Aspergillus, and Scedosporium spp. by use of rolling-circle amplification. Journal of Clinical Microbiology 46: 2423–2427. ARTICLE volume 2 · no. 2 189
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T h e G l o b a l M y c o l o g i c
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ONE FUNGUS ONE NAME: A PLANT PATHOL
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1000 fungal genomes to be sequenced
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change and evolve through mutation
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INSTITUTE OF MICROBOLOGY CHINESE AC
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and the research facilities feature
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30 th ECCO Annual Meeting in Utrech
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20 th Nordic Mycological Congress (
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this Medal based on her research an
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eflecting his personal interests an
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Horizontal Gene Transfer (HGT) from
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A new system for the arbuscular myc
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involved; E. alphitoides (syn. Micr
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Evolution of Fungi and Fungal-like
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December 2010 was the centenary of
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FORTHCOMING MEETINGS International
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doi:10.5598/imafungus.2011.02.02.01
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One Fungus = One Name: DNA and fung
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doi:10.5598/imafungus.2011.02.02.02
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Penicillium menonorum sp. nov. ARTI
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Penicillium menonorum sp. nov. syno
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What is Scirrhia? DNA isolation, am
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What is Scirrhia? ARTICLE Fig. 3. S
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What is Scirrhia? Acknowledgements
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Page 65 and 66: Tropical lichen fungi: ascospore di
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