Разработка систем идентификации фитопатогенов различных таксономических групп методом FLASH-PCR

выводы.

1. Разработана общая стратегия диагностики фитопатогенов методом ПЦР в формате FLASH.

2. Подтверждено, что зонд типа «молекулярный маячок» обладает меньшим уровнем фоновой флуоресценции, чем TaqMan, и также, как и TaqMan, разрушается Taq-полимеразой с 5'-3' экзонуклеазной активностью, а следовательно лучше всего подходит для ПНР в формате FLASH.

3. Созданы SCAR-маркеры для детекции 18 фитопатогенов методом ПЦР в формате FLASH по унифицированному алгоритму.

4. Для каждой тест-системы сконструированы и проклонированы положительные контроли.

5. Разработанные тест-системы внедрены в производство на базе ЗАО «НПФ ДНК-Технология».

1. Апасов И. В. (2007). Ризомания в России: мифы или реальность? Сах. Свекла. № 8, 10−6.

2. Баранов В. И., Ушаков В. В. (2000). Разработка и внедрение в практику элитного семеноводства картофеля технологии ускоренного промышленного производства оздоровленного материала картофеля: Отчет о НИР / Пущ. высш. агробиотехнол. Колледж. Пущино, 8.

3. Блоцкая Ж. В. (1998). Биоразнообразие вирусов картофеля// Защита и карантин растений. № 7, 41.

4. Гринько H.H. (2003). Аскохитоз огурцов Защищенный грунт. Защита и карантин растений. № 4, 32−33.5. Ёлов A.A., Федоров H.A., Жибурт Е. Б., Кофиади И. А., Трофимов Д. Ю. (2005). Здравоохранение и медтехника. № 2. С. 10.

5. Зайнуллин A.A., Зайнуллина A.C. (2003). Разработка тест-системы на основе ОТ-ПЦР для определения вируса картофеля М (PVM). Материалы отчет. Сес. молодых ученых ТатНИИСХ/Татар.НИИСХ. Казань, 22−29.

6. Лаптинов И. А. (2005). ПЦР-диагностика без электрофореза. Лабораторная диагностика России. Ежегодный справ. Мир медицины. М. Изд-во «Человек», 2004/2005.

7. Логинова Г. Л. (1993). Вирусы и продуктивность картофеля 1993./ Селекция, семеноводство и технологии возделывания картофеля на Северо-Западе РФ. 44−48.

8. Перечень вредителей, возбудителей болезней растений, сорняков, имеющих карантинное значение для Российской Федерации (Утвержден МСХ РФ в 2003 г.). (2003).

9. Перечень карантинных вредителей, болезней растений и сорняков для стран СНГ. 6-я конференция по карантину растений государствучастников Содружества Независимых Государств и государств Балтии от 12−14 августа 1997 года. (1997).

10. П. Трускинов Э. В. (2001). Андийские вирусы картофеля. Защита и карантин растений. № 3, 34−5.

11. Фолимонова С. Ю., Фолимонов A.C., Аграновский A.A., Атабеков И. Г. (1998). Идентификация штамма У-вируса картофеля, вызывающего кольцевой некроз клубней, с помощью иммуноспецифической ПНР. Доклады РАСХН. № 5, 16−17.

12. Хромова Л. М., Завриев С. К., Аршава Н. В., Бойко В. В. (2001). Диагностика PSTV-D методом RT-PCR. Биотехнология на рубеже двух тысячелетий. 39−40.

13. Abu-Halaweh М., Bates J., Patel B.K. (2005). Rapid detection anddifferentiation of pathogenic Campylobacter jejuni and Campylobacter coli by real-time PCR. Res Microbiol. 156, 107−14.

14. Afonina I., Metcalf M., Mills A., Mahoney W. (2008). Evaluation of 5'-MGB hybridization probes for detection of Bordetella pertussis and Bordetella parapertussis using different real-time PCR instruments. Diagn Microbiol Infect Dis. 60, 429−32.

15. Agindotan B.O., Shiel P.J., Berger P.H. (2007). Simultaneous detection of potato viruses, PLRV, PVA, PVX and PVY from dormant potato tubers by TaqMan real-time RT-PCR. J Virol Methods. 142, 1−9.

16. Agrios G.N. (1988). Plant Pathology, 3rd ed. Academic Press, Inc. New York. 803pp.

17. Allen R.C., Rogelj S., Cordova S.E., Kieft T.L. (2006). An immuno-PCR method for detecting Bacillus thuringiensis CrylAc toxin. J Immunol Methods. 308, 109−15.

18. Alvarez A.M. Integarted approaches for detection of plant pathogenic bacteria and bacterial diseases. (2004). Annual Review of Phytopathology. 42, 339−66.

19. Angelini E., Luca Bianchi G., Filippin L., Morassutti C., Borgo M. (2007). A new TaqMan method for the identification of phytoplasmas associated with grapevine yellows by real-time PCR assay. J Microbiol Methods. 68, 613−22.

20. Atallah Z.K., Stevenson W.R. (2006). A Methodology to Detect and Quantify Five Pathogens Causing Potato Tuber Decay Using Real-Time Quantitative Polymerase Chain Reaction: Phytopathology. 96, 1037−45.

21. Atkins D.S., Clark I.M. (2004). Fungal diagnostics: a mini review. J. Appl Genet. 45, 3−15.

22. Balme-Sinibaldi V., Tribodet M., Croizat F., Lefeuvre P., Kerlan C., Jacquot E. (2006). Improvement of Potato virus Y (PVY) detection and quantitation using PVY (N) — and PVY (0)-specific real-time RT-PCR assays. J Virol Methods. 134, 261−6.

23. Bartels R. (1971). Potato Virus A. Description, of plant viruses. № 54.

24. Beckhoven van J.R., Stead D.E., van der Wolf J.M. (2002). Detection of Clavibacter michiganensis subsp. sepedonicus by AmpliDet RNA, a new technology based on real time monitoring of NASBA amplicons with a molecular beacon. J Appl Microbiol. 93, 840−9.

25. Belkum A van ., Niesters H.G. (1995). Nucleic acid amplification and related techniques in microbiological diagnostics and epidemiology. Cell Mol Biol. 41, 615−23.

26. Belkum van A. (1994). DNA fingerprinting of medically importantmicroorganisms by use of PCR. Clin Microbiol Rev. 7, 174−84.

27. Bellis P., Schena L., Cariddi C. (2007). Real-time Scorpion-PCR detection and quantification of Erwinia amylovora on pear leaves and flowers. European Journal of Plant Pathology. 118, 11−22.

28. Bentsink L., Leone G.O., van Beckhoven J.R., van Schijndel H.B., van Gemen B., van der Wolf J.M. (2002). Amplification of RNA by NASBA allows direct detection of viable cells of Ralstonia solanacearum in potato. J Appl Microbiol. 93, 647−55.

29. Berg T., Tesonero L., Hailstones D.L. (2006). A multiplex real-time PCR assay for detection of Xanthomonas campestris from brassicas. Lett Appl Microbiol. 42, 624−30.

30. Bergervoet J.H., Peters J., van Beckhoven J.R., van den Bovenkamp G.W., Jacobson J.W., van der Wolf J.M. (2008). Multiplex microsphere immunodetection of potato virus Y, X and PLRV. J Virol Methods. 149, 63−68.

31. Bextine B., Blua M., Harshman D., Miller T.A. (2005). A SYBR green-based real-time polymerase chain reaction protocol and novel DNA extraction technique to detect Xylella fastidiosa in Homalodisca coagulata. J Econ Entomol. 98, 667−72.

32. Birch D.E. (1996). Simplified hot start PCR. Nature. 381, 445−6.

33. Bluhm B.H., Cousin M.A., Woloshuk CP. (2004). Multiplex real-time PCR detection of fumonisin-producing and trichothecene-producing groups of Fusarium species. J Food Prot. 67, 536−43.

34. Boonham N., Perez L.G., Mendez M.S., Peralta E.L., Blockley A., Walsh K., Barker I., Mumford R.A. (2004). Development of a real-time RT-PCR assay for the detection of potato spindle tuber viroid. J Virol Methods. 116, 139−46.

35. Boonham N., Walsh K., Smith P., Madagan K., Graham I., Barker I. (2003). Detection of potato viruses using microarray technology: towards a generic method for plant viral disease diagnosis. Jornal of Virological method. 108, 181−7.

36. Borman A.M., Linton Chr.J., Miles S.-J., Johnson E.M. (2008). Molecular identification of pathogenic fungi. Jornal of Antimicrobial Chemotherapy. 61, I7-I12.

37. Braasch H., Burgermeister W, Pastrik K.-H. (1995). Differentiation of three Bursaphelenchus species by means of RAPD-PCR. Nachrichtenblatt des Deutschen Pflanzenschutzdiensts 47, 310−314.

38. Brownie J., Shawcross S., Theaker J. (1997). The elimination of primer-dimer accumulation in PCR. Nucl. Acids Res. 25, 3235−41.

39. Bulman S.R., Marshall J.W. (1997). Differentiation of Australian potato cyst nematode (PCN) populations using the polymerase chain reaction (PCR). N Z J Crop Horticult Sei. 25:123−9.

40. Burggraf S., Olgemoller B. (2004). Simple Technique for Internal Control of.

41. Real-Time Amplification Assays. Clinical Chemistry. 50, 819−25.

42. Burokiene D. (2006). Early detection of Clavibacter michiganensis subsp. michiganensi in tomato seedlings. Agronomy Research. 4 (Special issue), 1514.

43. Bustamante P.I., Hull R. (1998). Plant virus gene expression strategies. EJB Electronic Journal of Biotechnology. 1.

44. Bystricka D., Lenz O., Mraza I., Piherovad L., Kmochd S., Sipc M. (2005). Oligonucleotide-based microarray: A new improvement in microarray detection of plant viruses. Journal of Virological Methods. 128(1−2), 176−82.

45. Chen R., Huang W., Lin Z., Zhou Z., Yu H., Zhu D. (2004). Development of a novel real-time RT-PCR assay with LUX primer for the detection of swine transmissible gastroenteritis virus. J Virol Methods. 122, 57−61.

46. Clavibacter michiganensis subsp. michiganensis. Bull. OEPP. (2005). Organisation Europ. et mediterraneene pour la protection des plantes. Oxford, 35, 275−83.

47. Clavibacter michiganensis subsp. sepedonicus. Bull. OEPP. (2004). Organisation europ. et mediterraneenne pour la protection des plantes. Oxford, 34, 323−5.

48. Coplin D.L., Majerczak D.R. (2002). Identification of Pantoea stewartii subsp. stewartii by PCR and strain differentiation by PFGE. Plant Disease. 86, 30 411.

49. Coutelle C. (1991). New DNA-analysis techniques (minireview). Biomed BiochimActa. 50,3−10.

50. Cubero J., Wolf van der J., Beckhoven van J., Lopez M.M. (2002). An internal control for the diagnosis of crown gall by PCR. J. Microbiol Methods. 51, 38 792.

51. Dang C., Jayasena S.D. (1996). Oligonucleotide inhibitors of Taq DNA polymerase facilitate detection of low copy number targets by PCR. J. Mol. Biol. 264, 68−278.

52. Degola F., Berni E., Dall’Asta C., Spotti E., Marchelli R., Ferrero I., Restivo F.M. (2007). A multiplex RT-PCR approach to detect aflatoxigenic strains of Aspergillus flavus. J Appl Microbiol. 103,409−17.

53. Deiman B., van Aarle P, Sillekens P. (2002). Characteristics and applications of nucleic acid sequence-based amplification (NASBA). Mol Biotechnol. 20, 163−79.

54. Diagnostic Beet necrotic yellow vein virus (benyvirus). (2006). European and Mediterranean Plant Protection Organization. Blackwell Publishing Ltd PM 7/30 (2).

55. Diagnostic protocol for regulated pests Bursaphelenchus xylophilus. (2002). EPPO Standards. PM 7/4(1) English.

56. Diagnostic protocols for regulated pests PM 7/40. (2004) EPPO Standards. OEPP/EPPO Bulletin 34, 155−7.

57. Dreier J., Bermpohl A., Eichenlaub R. (1995). Southern hybridization and PCR for specific detection of phytopathogenic Clavibacter michiganensis subsp. michiganensis. Phytopathology. 85, 462−8.

58. Du Z., Chen J., Hiruki C. (2006). Optimization and application of a multiplex RT-PCR system for simultaneous detection of five potato viruses using 18S rRNA as an internal control. Plant Dis. 90, 185−189.

59. Du Z., Jin B., Liu W., Chen L., Chen J. (2007). Highly sensitive fluorescent-labeled probes and glass slide hybridization for the detection of plant RNA viruses and a viroid. Acta Biochim Biophys Sin. 39, 326−334.

60. Faggioli F., Pasquini G., Barba M. Comparison of different methods of RNA isolation for plum pox virus detection by reverse transcription-polymerase chain reaction. (1998). Acta Virol. 42,219−21.

61. Fessehaie A., De Boer S.H., Levesque C.A. (2003). An Oligonucleotide Array for the Identification and Differentiation of Bacteria Pathogenic on Potato. Phytopathology. 93, 262−9.

62. Filion M., St-Arnaud M., Jabaji-Hare S.H. (2003). Direct quantification of fungal DNA from soil substrate using real-time PCR. J Microbiol Methods. 53, 67−76.

63. Finetti Sialer M.M., Rosso L. (2007). Molecular detection in integrated pest and disease managemtnt. General Concepts in Integrated Pest and Disease Management. 305−28.

64. Fischer A., von Eiff C., Kuczius T., Omoe K., Peters G., Becker K. (2007). A quantitative real-time immuno-PCR approach for detection of staphylococcal enterotoxins. J Mol Med. 85, 461−9.

65. Gill P., Ghaemi A. (2008). Nucleic acid isothermal amplification technologies: a review. Nucleosides Nucleotides Nucleic Acids. 27(3):224−43.

66. Glen M., Smith A.H., Langrell S.R.H., Mohammed C.L. (2007). Development of nested polymerase chain reaction detection of mycosphaerella spp. and its application to the study of leaf disease in eucalyptus plantations. Phytopathology. 97, 132−44.

67. Goel G, Kumar A, Puniya AK, Chen W, and Singh K (2005) Molecular beacon: a multitask probe. J Appl Microbiol. 99, 435−442.

68. Goldmeyer J., Kong H., Tang W. (2007). Development of a Novel One-Tube Isothermal Reverse Transcription Thermophilic HelicaseDependent Amplification Platform for Rapid RNA Detection. Journal of Molecular Diagnostics. 9, 639−44.

69. Grothaus G.D., Bandla M., Currier T., Giroux R., Jenkins G.R., Lipp M., Shan G., Stave J.W., Pantella V. (2006). Immunoassay as an analytical tool in agricultural biotechnology. J AO AC Int. 89, 913−928.

70. Guglielmo R, Bergemann S.E., Gonthier P., Nicolotti G., Garbelotto M. (2007). A multiplex PCR-based method for the detection and early identification of wood rotting fungi in standing trees. J Appl Microbiol. 103, 1490−507.

71. Han H., Han B.Y., Chung Y.J., Shin S.C. (2008). A Simple PCR-RFLP for Idenficiation of Bursaphelenchus spp. Collected from Korea. Plant Pathol. J. 24, 159−63.

72. Harris S, Jones DB. (1997). Optimisation of the polymerase chain reaction. Br JBiomed Sci. 54, 166−73.

73. Harrison B. D. (1984). Potato leafroll virus. Description of plant viruses. № 291.

74. Harrison B.D., Reavy B. (2002). Potato mop-top virus. Description of plant viruses. № 389.

75. Hassan M., Myrta A., Polak J. (2006). Simultaneous detection and identification of four pome fruit viruses by one-tube pentaplex RT-PCR. J.

76. Virol Methods. 133, 124−9.

77. Havis N.D., Oxley S.P., Piper S.R., Langrell S.R. (2006). Rapid nested PCR-based detection of Ramularia collo-cygni direct from barley. FEMS Microbiol Lett. 256,217−23.

78. Henry C.M., Barker I., Morris J., Hugo S.A. (1995). Detection of beet necrotic yellow vein virus using reverse transcription and polymerase chain reaction. Journal of Virological Methods. 54, 15−28.

79. S6. Hermansson A., Lindgren P-E. (2001). Quantification of Ammonia-Oxidizing Bacteria in Arable Soil by Real-Time PCR. Applied and Environmental Microbiology. 67, 972−6.

80. Hiroyuki U., Shinya T. (2005). A One-Step Reverse Transcription-Polymerase Chain Reaction System for the Simultaneous Detection and Identification of Multiple Tospovirus Infections. PHYTOPATHOLOGY. 95, 166−71.

81. Holland P.M., Abramson R.D., Watson R., Gelfand, D.H. (1991). Detection of specific polymerase chain reaction product by utilizing the 5−3' exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci USA. 88, 7276−80.

82. Horita M., Yano K., Tsuchiya K. (2004). PCR-based specific detection of Ralstonia solanacearum race 4 strains. J Gen Plant Pathol. 70, 278−83.

83. Kalantidis K., Denti M.A., Tzortzakaki S., Marinou E., Tabler M., Tsargris M. (2007). Virpl is a host protein with a major role in Potato Spindle Tuber Viroid infection in Nicotiana plants. Journal of virology. 81, 12 872−80.

84. Kekarainen T., Savilahti H., Valkonen J.P.T. (2002). Functional Genomics on Potato Virus A: Virus Genome-Wide Map of Sites Essential for Virus Propagation. Genome Res. 12, 584−94.

85. Kellogg D.E., Rybalkin I., Chen S. (1997). TaqStartTM Antibody: «Hot Start» PCR Facilitated by a Neutralizing Monoclonal Antibody Directed Against Taq DNA Polymerase. Biotechniques. 16, 1134−7.

86. Kerlan C. (2006). Potato Virus Y. Description of plant viruses. № 414.

87. Kleppe K., Ohtsuka E., Kleppe R., Molineux I., Khorana H.G. (1971). Studies on polynucleotides. XCVI. Repair replications of short synthetic DNA’s as catalyzed by DNA polymerases. In: J. Mol. Biol. Bd. 56, 341−361.

88. Koenig R., Lesemann D.-E. (1989). Potato Virus X. Description of plant viruses. № 354;

89. Kogovsek P., Gow L., Pompe-Novak M., Gruden K., Foster G.D., Boonham N., Ravnikar M. (2008). Single-step RT real-time PCR for sensitive detection and discrimination of Potato virus Y isolates. Journal of Virological Methods. 149(1), 1−11.

90. Kovarova M., Draber P. (2000). New specificity and yield enhancer of polymerase chain reactions. Nucleic Acids Res.Jul. 28, E70-e70.

91. Kramer M.F., Coen D.M. (2001). Enzymatic amplification of DNA by PCR: standard procedures and optimization. Curr Protoc Cell Biol. Appendix 3'.Appendix 3 °F.

92. Kubista M., Andrade J.M., Bengtsson M., Forootan A., Jonak J., Lind K., Sindelka R., Sjoback R., Sjogreen B., Strombom L., Stahlberg A., Zoric N.2006). The real-time polymerase chain reaction. Mol Aspects Med. 27, 95 125.

93. Kumar S, Balakrishna K, Batra HV. (2008).Enrichment-ELISA for detection of Salmonella typhi from food and water samples. Biomed Environ Sci. 21(2), 137−43.

94. Lam, http://ihome.cuhk.edu.hk/~z045513/ coursematerial/blast.pdf.

95. Lamhoujeb S., Fliss I., Ngazoa S.E., Jean J. (2008). Evaluation of the Persistence of Infectious Human Noroviruses on Food Surfaces using Molecular Beacon-Based Nucleic Acid Sequence-Based Amplification. Appl Environ Microbiol. Epub ahead of print.

96. Langrell S.R. (2005). Development of a nested PCR detection procedure for Nectria fuckeliana direct from Norway spruce bark extracts. FEMS Microbiol Lett. 242,185−93.

97. Leal I., Green M., Allen E., Humble L., Rott M. (2005). An effective PCR-based diagnostic method for the detection of Bursaphelenchus xylophilus (Nematoda: Aphelenchoididae) in wood samples from lodgepole pine. Nematology. 7, 833−42.

98. Leal I., Green M., Allen E., Humble L., Rott M. (2007). Application of a real-time PCR method for the detection of pine wood nematode, Bursaphelenchus xylophilus, in wood samples from lodgepole pine. Nematology. 9, 351−62.

99. Lee I.-M., Bartoszyk I.M., Gundersen D.E., Mogen B., DAavis R.E.1997). Nested PCR for Ultrasensitive Detection of the Potato Ring Rot Bacterium, Clavibacter michiganensis subsp. sepedonicus. Applied and Environmental Microbiology. 63, 2625−30.

100. Lee L., Kaplan I.B., Ripoll D.R., Liang D., Palukaitis P., Gray S.M. (2005). A surface loop of the potato leafroll virus coat protein is involved in virion assembly, systemic movement, and aphid transmission. J Virol. 79, 1207−14.

101. Leijon M., Mousavi-Jazi M., Kubista M. (2006). LightUp probes in clinical diagnostics. Mol Aspects Med. 27, 160−75.

102. Leone G., van Schijndel H., van Gemen B., Kramer F.R., Schoen C.D.1998). Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA. Nucleic Acids Res. 26, 2150−5.

103. Liming S.H., Bhagwat A.A. (2004). Application of a molecular beacon-real-time PCR technology to detect Salmonella species contaminating fruits and vegetables. Int J Food Microbiol. 95, 177−87.

104. Ling K.S., Wechter W.P., Jordan R. (2007). Development of a one-step immunocapture real-time TaqMan RT-PCR assay for the broad spectrum detection of Pepino mosaic virus. J Virol Methods. 144, 65−72.

105. Loeffler J., Hebart H., Cox P., Flues N., Schumacher U., Einsele H. (2001). Nucleic acid sequence-based amplification of Aspergillus RNA in blood samples. J Clin Microbiol. 39, 1626−9.

106. Lopez M.M., Bertolini E., Olmos A., Caruso P., Gorris M.T., Llop P., Penyalver R., Cambra M. (2003). Innovative tools for detection of plant pathogenic viruses and bacteria. Int Microbiol. 6, 233−43.

107. Lopez M.M., Llop P., Olmos A., Marco-Noales E., Cambra M., Bertolini E. (2009). Molecular tools solving the challenges posed by detection of plant pathogenic bacteria and viruses? Curr. Issues MoL. Biol. 11, 13−46.

108. Lopez R., Asensio C., Guzman M.M., Boonham N. (2006). Development of real-time and conventional RT-PCR assays for the detection of potato yellow vein virus (PYVV). J Virol Methods. 136, 24−9.

109. Lou X.J., Panaro N.J., Wilding P., Fortina P., Kricka L.J. (2004). Mutation detection using ligase chain reaction in passivated silicon-glass microchips and microchip capillary electrophoresis. Biotechniques. 37, 396−8.

110. Lynch J.R., Brown J.M. (1990) The polymerase chain reaction: current and future clinical applications. Med Genet. 27, 2—7.

111. MadaniaM., Subbotin S.A., Moensa M. (2005). Quantitative detection of the potato cyst nematode, Globodera pallida, and the beet cyst nematode, Heterodera schachtii, using Real-Time PCR with SYBR green I dye. Molecular and Cellular Probes. 19, 81−6.

112. Maliogka V., Dovas C.I., Efthimiou K., Katis N.I. (2004). Detection and differentiation of Comoviridae species using a semi-nested RT-PCR and a phylogenetic analysis based on the polymerase protein. Journal of phytopathology. 152, 404−9.

113. Markoulatos P., Siafakas N., Katsorchis T., Moncany M. (2003). Multiplex PCR: rapid DNA cycling in a conventional thermal cycler. J Clin Lab Anal. 17, 108−12.

114. Markoulatos P., Siafakas N., Moncany M. (2002). Multiplex polymerase chain reaction: a practical approach. J Clin Lab Anal. 16, 47−51.

115. Marone M., Mozzetti S., De Ritis D., Pierelli L., Scambia G. (2001). Semiquantitative RT-PCR analysis to assess the expression levels of multipletranscripts from the same sample. Biol Proced Online. 16, 19−25.

116. Matsunaga K., Togashi K. (2004). A simple method for discriminating Bursaphelenchus xylophilus and B. mucronatus by species specific polymerase chain reaction primer pairs. Nematology. 6, 273−7.

117. McCartney H.A., Foster S.J., Fraaije B.A., Ward E. (2003). Molecular diagnostics for fungal plant pathogens. Pest Manag Sci. 59, 129−42.

118. Menzel W., Jelkmann W., Maiss E. (2002). Detection of four apple viruses by multiplex RT-PCR assays with coamplification of plant mRNA as internal control. J Virol Methods. 99, 81−92.

119. Mills D., Russel B.W. (2003). Parameters for Specific Detection of Clavibacter michiganensis subsp, sepedonicus in Potato Stems and Tubers By Multiplexed PCR-ELISA. Amer J of Potato Res. 80, 223−34.

120. Monis P.T., Giglio S. (2006). Nucleic acid amplification-based techniques for pathogen detection and identification. Infect Genet Evol. 6, 212.

121. Morris J., Clover G.R.G., Harju V.A., Hugo S.A., Henry C.M. (2001). Development of a highly sensitive nested RT-PCR method for Beet necrotic yellow vein virus detection. Journal of Virological Methods. 95, 163−9.

122. Mumford R.A., Seal S.E. (1997). Rapid single-tube immunocapture RT-PCR for the detection of two yam potyviruses. J Virol Methods. 69, 73−9.

123. Nazarenko I, Lowe B, Darfler M, Ikonomi P, Schuster D, Rashtchian A. (2002). Multiplex quantitative PCR using self-quenched primers labeled with a single fluorophore. Nucleic Acids Res. 30, e37.

124. Nazarenko I., Pires R., Lowe B., Obaidy M., Rashtchian A. (2002b). Effect of primary and secondary structure of oligodeoxyribonucleotides on the fluorescent properties of conjugated dyes. Nucleic Acids Res. 30, 2089;195.

125. Nickerson D.A., Ankener W., Delahunty C., Kwok P.Y. (2001). Genotyping by ligation assays. Curr Protoc Hum Genet. Chapter 2, Unit 2.6.

126. Nie X., Bai Y., Molen T.A., Desjardins D.C. (2008). Development of universal primers for detection of potato carlaviruses by RT-PCR. J Virol Methods. 149, 209−216.

127. Niemeyer C.M., Adler M., Wacker R. (2007). Detecting antigens by quantitative immuno-PCR. Nat Protoc. 2, 1918;30.

128. Nilsson M. (2006). Lock and roll: single-molecule genotyping in situ using padlock probes and rolling-circle amplification. Histochemistry and Cell Biology. 126, 159−164.

129. Nowaczyk K., Dobosz R., Kornobis S., Obrepalska-Steplowska A. (2008). TaqMan REAL-Time PCR-based approach for differentiation between Globodera rostochiensis (golden nematode) and Globodera artemisiae species. Parasitol Res. 103,577−81.

130. Olmos A., Bertolini E., Cambra M. (2007). Isothermal amplification coupled with rapid flow-through hybridisation for sensitive diagnosis of Plum pox virus. J Virol Methods. 139, 111−5.

131. Osman F., Leutenegger C., Golino D., Rowhani A. (2008). Comparison of low-density arrays, RT-PCR and real-time TaqMan RT-PCR in detection of grapevine viruses. J Virol Methods. 149, 292−9.

132. Pantoea stewartii subsp. stewartii. Diagnostic protocols for regulated pests. (2004). OEPP/EPPO Standards PM 7/60. Bulletin 36, 111−115.

133. Park S.H., Kim H.J., Kim J.H., Kim T.W., Kim H.Y. (2007). Simultaneous detection and identification of Bacillus cereus group bacteria using multiplex PCR. J Microbiol Biotechnol. 17, 1177−82.

134. Pasquini G., Simeone A.M., Conte L., Barba M. (1998). Detection of plum pox virus in apricot seeds. Acta Virol. 42,260−3.

135. Pastrik K.H. (2000). Detection of Clavibacter michiganensis subsp. sepedonicus in potato tubers by multiplex PCR with coapmlifications of host DNA. Eur. J. Plant Pathol. 106, 155−165.

136. Pastrik K.H., Rainey F.A. (1999). Identification and differentiation of Clavibacter michiganensis subspecies by Polymerase Chain Reaction-based techniques. Journal of Phytopathology. 147, 687−93.

137. Peiman M., Xie C. (2006). Development and evaluation of a multiplex RT-PCR for detecting main viruses and a viroid of potato. Acta Virol. 50, 12 933.

138. Penyalver R., Garcia A., Ferrer A., Bertolini E., Lopez M.M. (2002). Detection of Pseudomonas savastanoi pv. savastanoi in olive plants by enrichment and PCR. 66, 2673−7.

139. Persson P., Sletten A. (1995). Fatty acid analysis for the identification of Erwinia carotovora subsp. atroseptica and E. carotovora subsp. Carotovora. EPPO Bull. 25:151−156.

140. Poussier S., Cheron J.-J., Couteau A., Luisetti J. (2002). Evaluation of procedures for reliable PCR detection of Ralstonia solanacearum in common natural substrates. Journal of Microbiological Methods. 51, 349 — 59.

141. Provost G. Le., Iskra-Caruana M.L., Acina I., Teycheney P.Y. (2006). Improved detection of episomal Banana streak viruses by multipleximmunocapture PCR. J Virol Methods. 137, 7−13.

142. Punithalingam E., P. Holliday. (1972). Didymella bryoniae. CMI Descriptions of Pathogenic Fungi and Bacteria. № 332.

143. Ralstonia solanacearum. Bull. OEPP. (2004). / Organisation europ. et mediterraneenne pour la protection des plantes. Oxford, 34, 173−8.

144. Randhawa P. S., Pannu S.S., Schaad N.W. (2001). Improved bio-PCR test for detection of Acidovorax avenae subsp citrulli in watermelon and cantaloupe seeds. APS/MSA/SON Joint Meeting. Salt Lake City, august, 2529.

145. Ratti C., Clover G.R., Autonell C.R., Harju V.A., Henry C.M. (2005). A multiplex RT-PCR assay capable of distinguishing beet necrotic yellow vein virus types A and B. J Virol Methods. 124, 41−7.

146. Rekhviashvili N., Stevens G., Scott L., Stevens W. (2006). Fluorogenic LUX primer for quantitation of HIV-1 by real-time RT-PCR. Molecular Biotechnology. 32, 101−109.

147. Rigotti S., Gugerli P. (2007). Rapid identification of potato virus Y strains by one-step triplex RT-PCR. J Virol Methods. 140, 90−94.

148. Rose E.A. (1991). Applications of the polymerase chain reaction to genome analysis. FASEB J. 5, 46−54.

149. Roy A., Fayad A., Barthe G., Brlansky R.H. (2005). A multiplex polymerase chain reaction method for reliable, sensitive and simultaneous detection of multiple viruses in citrus trees. J Virol Methods. 129, 47−55.

150. Rumsby G. (2006). An introduction to PCR techniques. Methods’Mol Biol. 324, 75−89.

151. Saiki R.K., Scharf S., Faloona F., Mullis K.B., Horn G.T., Erlich H.A., Arnheim N. (1985). Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 230, 1350−4.

152. Sakthivel N., Mortensen C.N., Mathur S.B. (2001). Detection of Xanthomonas oryzae pv. oryzae in artificially inoculated and naturally infected rice seeds and plants by molecular techniques. Appl Microbiol Biotechnol. 56, 435−41.

153. Sano T., Smith C.L., Cantor C.R. (1992). Immuno-PCR: Very sensitive antigen detection by means of specific antibody-DNA conjugates. Science. 258, 120−2.

154. Saponari M, Manjunath K, Yokomi RK. (2008). Quantitative detection of Citrus tristeza virus in citrus and aphids by real-time reverse transcription.

155. PCR (TaqMan). J Virol Methods. 147, 43−53.

156. Schaad N.W., Frederick R.D. (2002) Real-time PCR and its application for rapid plant disease diagnostics. Plant Pathol. 24: 250−8.

157. Schneider W.L., Sherman D.J., Stone A.L., Damsteegt V.D., Frederick R.D. (2004). Specific detection and quantification of Plum pox virus by realtime fluorescent reverse transcription-PCR. J Virol Methods. 120, 97−105.

158. Schonfeld J., Heuer H., van Elsas, J.D., Smalla K. (2003). Specific and Sensitive Detection of Ralstonia solanacearum in Soil on the Basis of PCR Amplification of fliC Fragments. Applied and Environmental Microbiology. 69, 7248−56.

159. Shim C.K., Seo I.K., Jee H.J., Kim H.K. (2006). Genetic Diversity of Didymella bryoniae for RAPD Profiles Substantiated by SCAR Marker in Korea. Plant Pathology Journal. 22, 36−45.

160. Siebert P.D., Larrick J.W. (1992). Competitive PCR. Nature. 359, 557−8.

161. Singh R.P., Valkonen J.P.T., Gray S.M.,. Boonham N,. Jones R.A.C, Kerlan C., Schubert J. (2008). Discussion paper: The naming of PVY. Archives of Virology. 153,1−13.

162. Somai B.M., Keinath A.P., Dean R.A. (2002b). Development of PCR-ELISA for detection and differentiation of Didymella bryoniae from related Phoma species (2) — 2002, vol. 86, no7, pp. 710−716 (40 ref.).

163. Song W.Y., Kim H.M., Hwang C.Y., Schaad N.W. (2004). Detection of Acidovorax avenae ssp. avenae in rice seeds using BIO-PCR. Journal of phytopathology. 152, 667−76.

164. Spooner D., van Treuren R., de Vicente M.C. (2005) Molecular markers for genebank management. IPGRI Technical bulletin № 10. International Plant Genetic Resources Institute, Rome, Italy.

165. Szemes M., Bonants P., Weerdt de M., Baner J., Landegren U., Schoen C.D. (2005). Diagnostic applications of padlock-probes — multiplex detection of plant pathogenes using universal microarrays. Nucleic acid Research. 33, e70.

166. Tabler M., Tsagris M. (2004). Viroids: petite RNA pathogens with distinguished talents. Trends Plant Sci. 9, 339−48.

167. Tamada T. (2002). Beet necrotic yellow vein virus. Description of plantviruses. № 391.

168. Tamura K., Dudley J., Nei M., & Kumar S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 24:1596−1599.

169. Templeton N.S. (1992). The polymerase chain reaction. History, methods, and applications. Diagn Mol Pathol. 1, 58−72.

170. Teycheney P.Y., Acina I., Lockhart B.E., Candresse T. (2007). Detection of Banana mild mosaic virus and Banana virus X by polyvalent degenerate oligonucleotide RT-PCR (PDO-RT-PCR). J Virol Methods. 142, 41−9.

171. Tian P., Mandrell R. (2006). Detection of norovirus capsid proteins in faecal and food samples by a real time immuno-PCR method. J Appl Microbiol. 100, 564−74.

172. Toth I.K., Avrova A.O., Hyman L.J. (2001). Rapid Identification and Differentiation of the Soft Rot Erwinias by 16S-23S Intergenic Transcribed Spacer-PCR and Restriction Fragment Length Polymorphism Analyses. Appl Environ Microbiol. 67, 4070−6.

173. Tyagi S, Bratu DP, and Kramer FR (1998) Multicolor molecular beacons for allele discrimination. Nat Biotechnol. 16, 49−53.

174. Tyagi S., Landedren U., Tazi M. (1996). Extremely sensitive, background-free gene detection using binary probes and QP replicase. Proc. Nat. Acad. Sci. 93, 5395−400.

175. Varga A., James D. (2006). Use of reverse transcription lopp-mediated isothermal amplification for the detection of Plum pox virus. J. Virol. Methods. 123,213−20.

176. Verchot-Lubicz J., YE C.-M., Bamunusinghe D. (2007). Molecular biology of potexviruses: recent advances. Journal of general virology. 88, 1643−55.

177. Vigano F., Stevens M. (2007). Development of a multiplex immunocapture-RT-PCR for simultaneous detection of BMYV and BChV in plants and single aphids. J Virol Methods. 146, 196−201.

178. Vincent M., Xu Y., Kong H., (2004). Helicase-dependent isothermal DNA amplification. EMBO reports. 5, 795−800.

179. Vora G.J., Meador C.E., Stenger D.A., Andreadis J.D. (2004). Nucleicacid amplification strategies for DNA microarray-based pathogen detection. Applied and enviromental microbiology. 70, 3047−54.

180. Vosberg H. P (1989). The polymerase chain reaction: an improved method for the analysis of nucleic acids. Hum Genet. 83, 1−15.

181. Wang L., Li P.C.H. (2007). Flexible Microarray Construction and Fast DNA Hybridization Conducted on a Microfluidic Chip for Greenhouse Plant Fungal Pathogen Detection. J. Agric. Food Chem. 55, 10 509−16.

182. Wang L., Li P.C.H. Yu H.-Z., Parameswaran A.M. (2008). Fungal pathogenic nucleic acid detection achieved with a microfluidic microarray device. Analytica chimica acta. 610, 97−104.

183. Weller S.A., Elphinstone J.G., Smith N.C., Boonham N., Stead D.E. (2000). Detection of Ralstonia solanacearum strains with a quantitative, multiplex, real-time, fluorogenic PCR (TaqMan) assay. Appl Environ Microbiol. 66, 2853−8.

184. Wells J.M., Moline H.E. (1991). Differentiation of the soft-rotting Erwinia of the carotovora group by fatty acid composition. J. Phytopathol. 131, 22−32.

185. Westin L., Xu X., Miller C. (2000). Anchored multiplex amplification on a microelectronic chip array. Nature Biotechnol. 18, 199−204.

186. Wetter C. (1971). Potato Virus S. Description of plant viruses. № 60.

187. Wetter C. (1972). Potato Virus M. Description of plant viruses. № 87.

188. Xu L.Z., Larzul D. (1991). The polymerase chain reaction: basic methodology and applications. Comp Immunol Microbiol Infect Dis. 14, 20 921.

189. Zeng Q.Y., Hansson P., Wang X.R. (2005). Specific and sensitive detection of the conifer pathogen Gremmeniella abietina by nested PCR. BMC Microbiol. 5, 65.

190. Zhang D., Wu J., Ye F., Feng T., Lee I., Yin B. (2006). Amplification of circularizable probes for the detection of target nucleic acids and proteins. Clinica chimica acta. 363, 61−70.

191. Zhang W., Bielaszewska M., Pulz M., Becker K., Friedrich A.W., Karch H., Kuczius TJ. (2008). New immuno-PCR assay for detection of low concentrations of shiga toxin 2 and its variants. Clin Microbiol. 46, 1292−7.

192. Zhang Y., Zhang D., Li W., Chen J., Peng Y., Cao W. (2003). A novel real-time quantitative PCR method using attached universal template probe. Nucleic Acids Res. 31, el23.

193. Zhao W-J., Chen H-Y., Zhu S-F., Xia M-F., Tan T-W. (2007) One-step detection of Clavibacter michiganensis subsp. Michiganensis. Journal of Plant Pathology. 89:349−51.

194. Zijlstra C., van Hoof R. A. (2006). A Multiplex Real-Time Polymerase Chain Reaction (TaqMan) Assay for the Simultaneous Detection of Meloidogyne chitwoodi andM. fallax. Phytopatology. 96, 1255−62.

195. Zizyte M., Staniulis J., Zitikaite I. (2006). Identification of Beet necrotic yellow vein virus isolate detected in Lithuania. Agronomy Research 4 (Special issue), 475−478.

196. Zouhar M, Rysanek O., Kocova M. (2000). Detection and differentiation of the potato cyst nematodes Globodera rostochiensis and Globodera pallida by PCR. Plant Protection Science. 36, 81−84.