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2010
I. A. Arif, Bakir, M. A., Khan, H. A., Farhan, A. H. Al, Homaidan, A. A. Al, Bahkali, A. H., M. Sadoon, A., and Shobrak, M., Application of RAPD for molecular characterization of plant species of medicinal value from an arid environment, vol. 9, pp. 2191-2198, 2010.
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Development of SCAR markers for the discrimination of three species of medicinal plants, Angelica decursiva (Peucedanum decursivum), Peucedanum praeruptorum and Anthricus sylvestris, based on the internal transcribed spacer (ITS) sequence and random amplified polymorphic DNA (RAPD). Biol. Pharm. Bull. 32: 24-30. http://dx.doi.org/10.1248/bpb.32.24 PMid:19122275   Collard BCY and Mackill DJ (2009). Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene targeted markers in plants. Plant Mol. Biol. Rep. 27: 86-93. http://dx.doi.org/10.1007/s11105-008-0060-5   De Benedetti L, Mercuri A, Bruna S, Burchi G, et al. (2001). Genotype identification of ornamental species by RAPD analysis. Acta Hort. 546: 391-394.   Devi PU, Akagi K, Ostapenko V, Tanaka Y, et al. (1996). Withaferin A: a new radiosensitizer from the Indian medicinal plant Withania somnifera. Int. J. Radiat. Biol. 69: 193-197. http://dx.doi.org/10.1080/095530096146020 PMid:8609455   Echeverrigaray S, Agostini G, Atti-Serfini L, Paroul N, et al. (2001). Correlation between the chemical and genetic relationships among commercial thyme cultivars. J. Agric. Food Chem. 49: 4220-4223. http://dx.doi.org/10.1021/jf010289j PMid:11559114   Ghazanfar SA (1994). Handbook of Arabian Medicinal Plants. CRC Press, Florida.   Grace NN, Rainer BW, Barbara G, Eric NL, et al. (2004). Utilization of weed species as sources of traditional medicines in central Kenya. Lyonia 7: 71-87.   Hegazy AK, Hammouda O, Lovett-Doust J and Gomaa NH (2009). Variations of the germinable soil seed bank along the altitudinal gradient in the northwestern Red Sea region. Acta Ecol. Sin. 2: 20-29. http://dx.doi.org/10.1016/j.chnaes.2009.04.004   Heneidy SZ and Bidak LM (2004). Potential uses of plant species of the coastal Mediterranean region, Egypt. Pak. J. Biol. Sci. 7: 1010-1023. http://dx.doi.org/10.3923/pjbs.2004.1010.1023   Jones CJ, Edwards KJ, Castaglione S, Winfield MO, et al. (1997). Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol. Breed. 3: 381-390. http://dx.doi.org/10.1023/A:1009612517139   Joshi K, Chavan P, Warude D and Patwardhan B (2004). Molecular markers in herbal drug technology. Curr. Sci. 87: 159-165.   Liu P, Yang YS, Hao CY and Guo WD (2007). Ecological risk assessment using RAPD and distribution pattern of a rare and endangered species. Chemosphere 68: 1497-1505. http://dx.doi.org/10.1016/j.chemosphere.2007.03.018 PMid:17498776   Lu HP, Cai YW, Chen XY, Zhang X, et al. (2006). High RAPD but no cpDNA sequence variation in the endemic and endangered plant, Heptacodium miconioides Rehd. (Caprifoliaceae). Genetica 128: 409-417. http://dx.doi.org/10.1007/s10709-006-7542-x PMid:17028968   Micheli MR, Bova R, Pascale E and D'Ambrosio E (1994). Reproducible DNA fingerprinting with the random amplified polymorphic DNA (RAPD) method. Nucleic Acids Res. 22: 1921-1922. http://dx.doi.org/10.1093/nar/22.10.1921 PMid:8208620 PMCid:308096   Middleditch BS and Amer AM (1991). Kuwaiti Plants. In: Studies in Plant Science Elsevier Science, Amsterdam,   Mishra LC, Singh BB and Dagenais S (2000). Scientific basis for the therapeutic use of Withania somnifera (Ashwagandha): a review. Altern. Med. Rev. 5: 335-346.   Mossa JS, Al-Yahya MA and Al-Meshal IA (1987). Medicinal Plants of Saudi Arabia. King Saud University Press, Riyadh.   Penner GA, Bush A, Wise R, Kim W, et al. (1993). Reproducibility of random amplified polymorphic DNA (RAPD) analysis among laboratories. Genome Res. 2: 341-345. http://dx.doi.org/10.1101/gr.2.4.341   Ranade SA, Farooqui N, Bhattacharya E and Verma A (2001). Gene tagging with random amplified polymorphic DNA (RAPD) marker for molecular breeding in plants. Crit. Rev. Plant Sci. 20: 251-275.   Sathiyamoorthy P, Lugasi-Evgi H, Schlesinger P, Kedar I, et al. (1999). Screening for cytotoxic and antimalarial activities in desert plants of the Negev and Bedouin market plant products. Pharm. Biol. 37: 188-195. http://dx.doi.org/10.1076/phbi.37.3.188.6298   Shinde VM, Dhalwal K, Mahadik KR, Joshi KS, et al. (2007). RAPD analysis for determination of components in herbal medicine. Evid. Based Complement Alternat. Med. 4: 21-23. http://dx.doi.org/10.1093/ecam/nem109 PMid:18227927 PMCid:2206231   Skroch P and Nienhuis J (1995). Impact of scoring error and reproducibility of RAPD data on RAPD based estimates of genetic distance. Theor. Appl. Genet. 91: 1086-1091.   Temiesak P, Ponpim Y and Harada T (1993). RAPD analysis for varietal identification in Brassica. Kasetsart J. Nat. Sci. 27: 37-42.   Tochika-Komatsu Y, Asaka I and Ii I (2001). A random amplified polymorphic DNA (RAPD) primer to assist the identification of a selected strain, aizu K-111 of Panax ginseng and the sequence amplified. Biol. Pharm. Bull. 24: 1210-1213. http://dx.doi.org/10.1248/bpb.24.1210 PMid:11642336   Um JY, Chung HS, Kim MS, Na HJ, et al. (2001). Molecular authentication of Panax ginseng species by RAPD analysis and PCR-RFLP. Biol. Pharm. Bull. 24: 872-875. http://dx.doi.org/10.1248/bpb.24.872 PMid:11510476   Vanijajiva O, Sirirugsa P and Suvachittanont W (2005). Confirmation of relationships among Boesenbergia (Zingiberaceae) and related genera by RAPD. Biochem. Syst. Ecol. 33: 159-170. http://dx.doi.org/10.1016/j.bse.2004.06.012   Wang Y, Wang S, Zhao Y, Khan DM, et al. (2009). Genetic characterization of a new growth habit mutant in tomato (Solanum lycopersicum). Plant Mol. Biol. Rep. 27: 431-438. DOI:10.1007/s11105-009-0095-2. http://dx.doi.org/10.1007/s11105-009-0095-2   Wang ZS, An SQ, Liu H, Leng X, et al. (2005). Genetic structure of the endangered plant Neolitsea sericea (Lauraceae) from the Zhoushan archipelago using RAPD markers. Ann. Bot. 95: 305-313. http://dx.doi.org/10.1093/aob/mci027 PMid:15546928   Weder JKP (2002). Influence of experimental conditions on the reproducibility of RAPD-PCR identification of legumes and cereals. Lebensm. Wiss. Technol. 35: 233-238. http://dx.doi.org/10.1006/fstl.2001.0844   Welsh J and McClelland M (1990). Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18: 7213-7218. http://dx.doi.org/10.1093/nar/18.24.7213 PMid:2259619 PMCid:332855   Williams JG, Kubelik AR, Livak KJ, Rafalski JA, et al. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18: 6531-6535. http://dx.doi.org/10.1093/nar/18.22.6531 PMid:1979162 PMCid:332606   Zhang YB, Shaw PC, Sze CW, Wang ZT, et al. (2007). Molecular authentication of Chinese herbal materials. J. Food Drug Anal. 15: 1-9.   Zheng W, Wang L, Meng L and Liu J (2008). Genetic variation in the endangered Anisodus tanguticus (Solanaceae), an alpine perennial endemic to the Qinghai-Tibetan Plateau. Genetica 132: 123-129. http://dx.doi.org/10.1007/s10709-007-9154-5 PMid:17516136
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
I. A. Arif, Khan, H. A., Shobrak, M., Homaidan, A. A. Al, M. Sadoon, A., Farhan, A. H. Al, and Bahkali, A. H., Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx, vol. 9, pp. 259-265, 2010.
Banhos A, Hrbeck T, Gravena W, Sanaiotti T, et al. (2008). Genomic resources for the conservation and management of the harpy eagle (Harpia harpyja, Falconiformes, Accipitridae). Genet. Mol. Biol. 31: 146-154. http://dx.doi.org/10.1590/S1415-47572008000100025   Bonin A, Bellemain E, Bronken EP, Pompanon F, et al. (2004). How to track and assess genotyping errors in population genetics studies. Mol. Ecol. 13: 3261-3273. http://dx.doi.org/10.1111/j.1365-294X.2004.02346.x PMid:15487987   Chan CH, Zhao Y, Cheung MY and Chambers GK (2008). Isolation and characterization of microsatellites in the kakerori (Pomarea dimidiata) using feathers as source of DNA. Conserv. Genet. 9: 1067-1070. http://dx.doi.org/10.1007/s10592-007-9456-2   Harker N (2001). Collection, Reporting and Storage of Microsatellite Genotype Data. In: Plant Genotyping: the DNA Fingerprinting of Plants (Henry RJ, ed.). CAB International, Wallingford, UK & New York, USA, 251-264. http://dx.doi.org/10.1079/9780851995151.0251   Hoffman JI and Amos W (2005). Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Mol. Ecol. 14: 599-612. http://dx.doi.org/10.1111/j.1365-294X.2004.02419.x PMid:15660949   Johansson A, Karlsson P and Gyllensten U (2003). A novel method for automatic genotyping of microsatellite markers based on parametric pattern recognition. Hum. Genet. 113: 316-324. http://dx.doi.org/10.1007/s00439-003-0973-x PMid:12883999   Kawka M, Horbanczuk JO, Sacharczuk M, Zieba G, et al. (2007). Genetic characteristics of the Ostrich population using molecular methods. Poult. Sci. 86: 277-281. PMid:17234840   Li Y, Wongprasert K, Shekhar M, Ryan J, et al. (2007). Development of two microsatellite multiplex systems for black tiger shrimp Penaeus monodon and its application in genetic diversity study for two populations. Aquaculture 266: 279-288. http://dx.doi.org/10.1016/j.aquaculture.2007.01.038   MacHugh DE, Shriver MD, Loftus RT, Cunningham P, et al. (1997). Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics 146: 1071-1086. PMid:9215909 PMCid:1208036   Ryberg WA, Fitzgerald LA, Honeycutt RL and Cathey JC (2002). Genetic relationships of American alligator populations distributed across different ecological and geographic scales. J. Exp. Zool. 294: 325-333. http://dx.doi.org/10.1002/jez.10207 PMid:12461812   Selkoe KA and Toonen RJ (2006). Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol. Lett. 9: 615-629. http://dx.doi.org/10.1111/j.1461-0248.2006.00889.x PMid:16643306   Zhou H, Li D, Zhang Y, Yang T, et al. (2007). Genetic diversity of microsatellite DNA loci of Tibetan antelope (Chiru, Pantholops hodgsonii) in Hoh Xil National Nature Reserve, Qinghai, China. J. Genet. Genomics 34: 600-607. http://dx.doi.org/10.1016/S1673-8527(07)60068-X
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. 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