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2010
M. A. Moslem, Bahkali, A. H., Abd-Elsalam, K. A., and Wit, P. J. G. M., An efficient method for DNA extraction from Cladosporioid fungi, vol. 9, pp. 2283-2291, 2010.
Abd-Elsalam KA, Asran-Amal A and El-Samawaty A (2007). Isolation of high quality DNA from cotton and its fungal pathogens. J. Plant Dis. Prot. 114: 113-116.   Bulat SA, Lübeck M, Mironenko N, Jensen DF, et al. (1998). UP-PCR analysis and ITS1 ribotyping of strains of Trichoderma and Gliocladium. Mycol. Res. 102: 933-943. http://dx.doi.org/10.1017/S0953756297005686   Cenis JL (1992). Rapid extraction of fungal DNA for PCR amplification. Nucleic Acids Res. 20: 2380. http://dx.doi.org/10.1093/nar/20.9.2380 PMid:1594460 PMCid:312363   Ghahfarokhi MS, Fazli A, Lotfi A and Abyane MR (2004). Cellobiose dehydrogenase production by the genus Cladosporium. Iran. Biomed. J. 8: 107-111.   Griffin DW, Kellogg CA, Peak KK and Shinn EA (2002). A rapid and efficient assay for extracting DNA from fungi. Lett. Appl. Microbiol. 34: 210-214. http://dx.doi.org/10.1046/j.1472-765x.2002.01071.x PMid:11874544   Jin J, Lee YK and Wickes BL (2004). Simple chemical extraction method for DNA isolation from Aspergillus fumigatus and other Aspergillus species. J. Clin. Microbiol. 42: 4293-4296. http://dx.doi.org/10.1128/JCM.42.9.4293-4296.2004 PMid:15365025 PMCid:516345   Karakousis A, Tan L, Ellis D, Alexiou H, et al. (2006). An assessment of the efficiency of fungal DNA extraction methods for maximizing the detection of medically important fungi using PCR. J. Microbiol. Methods 65: 38-48. http://dx.doi.org/10.1016/j.mimet.2005.06.008 PMid:16099520   Loeffler J, Hebart H, Cox P, Flues N, et al. (2001). Nucleic acid sequence-based amplification of Aspergillus RNA in blood samples. J. Clin. Microbiol. 39: 1626-1629. http://dx.doi.org/10.1128/JCM.39.4.1626-1629.2001 PMid:11283102 PMCid:87985   Lugert R, Schettler C and Gross U (2006). Comparison of different protocols for DNA preparation and PCR for the detection of fungal pathogens in vitro. Mycoses 49: 298-304. http://dx.doi.org/10.1111/j.1439-0507.2006.01255.x PMid:16784444   Meyer W, Maszewska K and Sorrell TC (2001). PCR fingerprinting: a convenient molecular tool to distinguish between Candida dubliniensis and Candida albicans. Med. Mycol. 39: 185-193. PMid:11346267   Moyo M, Amoo SO, Bairu MW, Finnie JF, et al. (2008). Optimizing DNA isolation for medicinal plants. South Afr. J. Bot. 74: 771-775. http://dx.doi.org/10.1016/j.sajb.2008.07.001   Pitkäranta M, Meklin T, Hyvarinen A, Paulin L, et al. (2008). Analysis of fungal flora in indoor dust by ribosomal DNA sequence analysis, quantitative PCR, and culture. Appl. Environ. Microbiol. 74: 233-244. http://dx.doi.org/10.1128/AEM.00692-07 PMid:17981947 PMCid:2223223   Qiu-Xia C, Chang-Xing L, Wen-Ming H, Jiang-Qiang S, et al. (2008). Subcutaneous phaeohyphomycosis caused by Cladosporium sphaerospermum. Mycoses 51: 79-80. PMid:18076601   Rogers SO (1994). Phylogenetic and Taxonomic Information from Herbarium and Mummified DNA. In: Conservation of Plant Genes II: Utilization of Ancient and Modern DNA. Monographs in Systematic Botany 48 (Miller JS, Golenberg EM and Adams JE, eds.). Missouri Botanical Garden, St. Louis.   Schubert K (2005). Morphotaxonomic Revision of Foliicolous Cladosporium species (Hyphomycetes). PhD thesis, Martin-Luther-University, Halle-Wittenberg.   Sharma R, Mahla HR, Mohapatr T, Bhargava SC, et al. (2003). Isolating plant genomic DNA without liquid nitrogen. Plant Mol. Biol. Rep. 21: 43-50. http://dx.doi.org/10.1007/BF02773395   White TM, Bruns T, Lee S and Taylor J (1990). Amplification and Direct Sequencing of Fungal Ribosomal RNA for Phylogenetics. In: PCR Protocols: A Guide to Methods and Applications (Innis MA, Gelfand DH, Sninsky JJ and White TJ, eds.). Academic Press, San Diego, 315-321. PMid:1696192   Williamson EC, Leeming JP, Palmer HM, Steward CG, et al. (2000). Diagnosis of invasive aspergillosis in bone marrow transplant recipients by polymerase chain reaction. Br. J. Haematol. 108: 132-139. http://dx.doi.org/10.1046/j.1365-2141.2000.01795.x PMid:10651736   Wong SF, Mak JW and Pook PC (2007). New mechanical disruption method for extraction of whole cell protein from Candida albicans. Southeast Asian J. Trop. Med. Public Health 38: 512-518. PMid:17877228   Yano S, Koyabashi K and Kato K (2003). Intrabronchial lesion due to Cladosporium sphaerospermum in a healthy, non-asthmatic woman. Mycoses 46: 348-350. http://dx.doi.org/10.1046/j.1439-0507.2003.00885.x PMid:12950908   Yeo SF and Wong B (2002). Current status of nonculture methods for diagnosis of invasive fungal infections. Clin. Microbiol. Rev. 15: 465-484. http://dx.doi.org/10.1128/CMR.15.3.465-484.2002 PMid:12097252 PMCid:118074
K. A. Abd-Elsalam, Almohimeed, I., Moslem, M. A., and Bahkali, A. H., M13-microsatellite PCR and rDNA sequence markers for identification of Trichoderma (Hypocreaceae) species in Saudi Arabian soil, vol. 9, pp. 2016-2024, 2010.
Abd-Elsalam KA, Asran-Amal A and El-Samawaty A (2007). Isolation of high-quality DNA from cotton and its fungal pathogens. J. Plant Dis. Prot. 114: 113-116.   Asran-Amal A, Abd-Elsalam KA, Omar MR and Aly AA (2005). Antagonistic potential of Trichoderma spp. against Rhizoctonia solani and use of M13 minisatellite-primed PCR to evaluate of the antagonist genetic variation. J. Plant Dis. Prot. 112: 550-561.   Chaverri P, Castlebury LA, Overton BE and Samuels GJ (2003). Hypocrea/Trichoderma: species with conidiophore elongations and green conidia. Mycologia 95: 1100-1140. http://dx.doi.org/10.2307/3761915 PMid:21149016   Druzhinina I and Kubicek CP (2005). Species concepts and biodiversity in Trichoderma and Hypocrea: from aggregate species to species clusters? J. Zhejiang. Univ. Sci. B 6: 100-112. PMid:15633245 PMCid:1389624   Druzhinina IS, Kopchinskiy AG, Komon M, Bissett J, et al. (2005). An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genet. Biol. 42: 813-828. http://dx.doi.org/10.1016/j.fgb.2005.06.007 PMid:16154784   Druzhinina IS, Kopchinskiy AG, Komon M and Kubicek CP (2006). An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Proceedings of the 8th International Mycological Congress, 21-25 August, 2006. Queensland, Australia, 1630-1700 IS2-0357.   Howell CR (2003). Mechanisms employed by Trichoderma species in the biological control of plant diseases: the history and evolution of current concepts. Plant Dis. 87: 4-10. http://dx.doi.org/10.1094/PDIS.2003.87.1.4   Kredics L, Antal Z, Doczi I, Manczinger L, et al. (2003). Clinical importance of the genus Trichoderma. A review. Acta Microbiol. Immunol. Hung. 50: 105-117. http://dx.doi.org/10.1556/AMicr.50.2003.2-3.1 PMid:12894482   Kullnig-Gradinger CM, Szakacs G and Kubicek CP (2002). Phylogeny and evolution of the genus Trichoderma: a multigene approach. Mycol. Res. 106: 757-767. http://dx.doi.org/10.1017/S0953756202006172   Nagy E, Kredics L, Antal Z and Papp T (2004). Molecular diagnosis, epidemiology and taxonomy of emerging medically important filamentous fungi. Rev. Med. Microbiol. 15: 153-162. http://dx.doi.org/10.1097/00013542-200410000-00004   Rifai M (1969). A revision of the genus Trichoderma. Mycol. Pap. 116: 1-56.   Sambrook JE, Fritsch F and Maniatis T (2001). Molecular Cloning: a Laboratory Manual. 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.   Samuels GJ, Dodd SL, Gams W, Castlebury LA, et al. (2002). Trichoderma species associated with the green mold epidemic of commercially grown Agaricus bisporus. Mycologia 94: 146-170. http://dx.doi.org/10.2307/3761854 PMid:21156486   Sariah M, Choo CW, Zakaria H and Norihan MS (2005). Quantification and characterisation of Trichoderma spp. from different ecosystems. Mycopathologia 159: 113-117. http://dx.doi.org/10.1007/s11046-004-4432-6 PMid:15750742   Sieburg HB (1990). Physiological studies in silico. Stud. Sci. Complexity 12: 321-342.   White TJ, Burns T, Lee S and Taylor J (1990). Amplication and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics. In: PCR Protocols: A Guide to Methods and Applications (Innis MA, Gelfand DH, Sninsky JJ and White TJ, eds.). Academic Press, San Diego, 315-322. PMid:1696192
M. A. Moslem, Mashraqi, A., Abd-Elsalam, K. A., Bahkali, A. H., and Elnagaer, M. A., Molecular detection of ochratoxigenic Aspergillus species isolated from coffee beans in Saudi Arabia, vol. 9, pp. 2292-2299, 2010.
Abarca ML, Accensi F, Cano J and Cabanes FJ (2004). Taxonomy and significance of black aspergilli. Antonie Van Leeuwenhoek 86: 33-49. http://dx.doi.org/10.1023/B:ANTO.0000024907.85688.05 PMid:15103236   Al-Musallam A (1980). Revision of the Black Aspergillus Species. PhD thesis, State University Utrecht, The Netherlands.   Bahkali AH, Abd-Elsalam KA, Moslem MA and Al-Khedhairy AA (2008). In-house protocol for isolation of restrictable and amplifiable genomic DNA from plants, fungi and bacteria. Genes Genomes Genomics 2: 77-88.   Borman AM, Linton CJ, Miles SJ and Johnson EM (2008). Molecular identification of pathogenic fungi. J. Antimicrob. Chemother. 1 (Suppl 61): i7-i12. http://dx.doi.org/10.1093/jac/dkm425 PMid:18063605   Caba-es FJ, Accensi F, Bragulat MR, Abarca ML, et al. (2002). What is the source of ochratoxin A in wine? Int. J. Food Microbiol. 79: 213-215. http://dx.doi.org/10.1016/S0168-1605(02)00087-9   Cenis JL (1992). Rapid extraction of fungal DNA for PCR amplification. Nucleic Acids Res. 20: 2380. http://dx.doi.org/10.1093/nar/20.9.2380 PMid:1594460 PMCid:312363   Dao HP, Mathieu F and Lebrihi A (2005). Two primer pairs to detect OTA producers by PCR method. Int. J. Food Microbiol. 104: 61-67. http://dx.doi.org/10.1016/j.ijfoodmicro.2005.02.004 PMid:15975678   de Vries RP, Frisvad JC, van de Vondervoort PJ, Burgers K, et al. (2005). Aspergillus vadensis, a new species of the group of black aspergilli. Antonie Van Leeuwenhoek 87: 195-203. http://dx.doi.org/10.1007/s10482-004-3194-y PMid:15803385   Fungaro MH, Vissotto PC, Sartori D, Vilas-Boas LA, et al. (2004). A molecular method for detection of Aspergillus carbonarius in coffee beans. Curr. Microbiol. 49: 123-127. PMid:15297917   Geisen R, Mayer Z, Karolewiez A and Farber P (2004). Development of a real time PCR system for detection of Penicillium nordicum and for monitoring ochratoxin A production in foods by targeting the ochratoxin polyketide synthase gene. Syst. Appl. Microbiol. 27: 501-507. http://dx.doi.org/10.1078/0723202041438419 PMid:15368856   Geiser DM, Klich MA, Frisvad JC, Peterson SW, et al. (2007). The current status of species recognition and identification in Aspergillus. Stud. Mycol. 59: 1-10. http://dx.doi.org/10.3114/sim.2007.59.01 PMid:18490947 PMCid:2275194   Klich MA (2002). Identification of Common Aspergillus Species. Centraalbureau Voor Schimmelcultures, Utrecht.   Leong SL, Hien LT, An TV, Trang NT, et al. (2007). Ochratoxin A-producing aspergilli in Vietnamese green coffee beans. Lett. Appl. Microbiol. 45: 301-306. http://dx.doi.org/10.1111/j.1472-765X.2007.02189.x PMid:17718843   Logrieco A, Bottalico A, Mulé G, Moretti A, et al. (2003). Epidemiology of toxigenic fungi and their associated mycotoxins for some Mediterranean crops. Eur. J. Plant Pathol. 109: 645-667. http://dx.doi.org/10.1023/A:1026033021542   Murakami H (1979). Some experimental methods and cultural characteristics of the black aspergilli. Taxonomic studies on Japanese Industrial strains of the Aspergillus. J. Soc. Brew. 74 (Part 26): 323-327.   Niessen L (2007). Current Trends in Molecular Diagnosis of Ochratoxin A Producing Fungi. In: Mycotechnology: Present Status and Future Prospects (Rai M, ed.). I.K. International Publishing House, New Delhi, 84-105.   Pardo E, Marin S, Ramos AJ and Sanchis V (2004). Occurrence of Ochratoxigenic Fungi and Ochratoxin A in Green Coffee from Different Origins. Food Sci. Technol. Int. 10: 45-49. http://dx.doi.org/10.1177/1082013204041509   Pati-o B, González-Salgado A, Gonzalez-Jaen MT and Vázquez C (2005). PCR detection assays for the ochratoxin-producing Aspergillus carbonarius and Aspergillus ochraceus species. Int. J. Food Microbiol. 104: 207-214. http://dx.doi.org/10.1016/j.ijfoodmicro.2005.02.011 PMid:15967531   Perrone G, Susca A, Cozzi G, Ehrlich K, et al. (2007). Biodiversity of Aspergillus species in some important agricultural products. Stud. Mycol. 59: 53-66. http://dx.doi.org/10.3114/sim.2007.59.07 PMid:18490950 PMCid:2275197   Perrone G, Varga J, Susca A, Frisvad JC, et al. (2008). Aspergillus uvarum sp nov., an uniseriate black Aspergillus species isolated from grapes in Europe. Int. J. Syst. Evol. Microbiol. 58: 1032-1039. http://dx.doi.org/10.1099/ijs.0.65463-0 PMid:18398215   Pitt JI and Hocking AD (1997). Fungi and Food Spoilage. Vol. II. Blackie Academic and Professional, London. http://dx.doi.org/10.1007/978-1-4615-6391-4   Samson RA, Noonim P, Meijer M, Houbraken J, et al. (2007). Diagnostic tools to identify black aspergilli. Stud. Mycol. 59: 129-145. http://dx.doi.org/10.3114/sim.2007.59.13 PMid:18490945 PMCid:2275192   Sánchez-Hérvas M, Gil JVV, Bisbal F, Rámon D, et al. (2008). Mycobiota and mycotoxin producing fungi from cocoa beans. Int. J. Food Microbiol. 125: 336-340. http://dx.doi.org/10.1016/j.ijfoodmicro.2008.04.021 PMid:18539350   Schmidt H, Ehrmann M, Vogel RF, Taniwaki MH, et al. (2003). Molecular typing of Aspergillus ochraceus and construction of species specific SCAR-primers based on AFLP. Syst. Appl. Microbiol. 26: 138-146. http://dx.doi.org/10.1078/072320203322337434 PMid:12747422   Schmidt H, Taniwaki MH, Vogel RF and Niessen L (2004). Utilization of AFLP markers for PCR-based identification of Aspergillus carbonarius and indication of its presence in green coffee samples. J. Appl. Microbiol. 97: 899-909. http://dx.doi.org/10.1111/j.1365-2672.2004.02405.x PMid:15479404   Serra R, Abrunhosa L, Kozakiewicz Z and Venancio A (2003). Black Aspergillus species as ochratoxin A producers in Portuguese wine grapes. Int. J. Food Microbiol. 88: 63-68. http://dx.doi.org/10.1016/S0168-1605(03)00085-0   Susca A, Stea G, Mule G and Perrone G (2007). Polymerase chain reaction (PCR) identification of Aspergillus niger and Aspergillus tubingensis based on the calmodulin gene. Food Addit. Contam. 24: 1154-1160. http://dx.doi.org/10.1080/02652030701546206 PMid:17886188   Taniwaki MH, Pitt JI, Teixeira AA and Iamanaka BT (2003). The source of ochratoxin A in Brazilian coffee and its formation in relation to processing methods. Int. J. Food Microbiol. 82: 173-179. http://dx.doi.org/10.1016/S0168-1605(02)00310-0   Téren J, Varga J, Hamari Z, Rinyu E, et al. (1996). Immunochemical detection of ochratoxin A in black Aspergillus strains. Mycopathologia 134: 171-176. http://dx.doi.org/10.1007/BF00436726 PMid:8981783   Varga J, Kocsube S, Toth B, Frisvad JC, et al. (2007). Aspergillus brasiliensis sp nov., a biseriate black Aspergillus species with world-wide distribution. Int. J. Syst. Evol. Microbiol. 57: 1925-1932. http://dx.doi.org/10.1099/ijs.0.65021-0 PMid:17684283