DNA microarrays and their potential applications for the detection of plant viruses, viroids, and phytoplasmas

Journal of Plant Pathology

Volumn 86, Issue 2, 2004, Pages 97-104

  Hadidi, A ^a   Czosnek, H ^b   Barba, M ^c  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^c Istituto Sperimentale per la Patologia Vegetale   (Italy)

Author keywords

Arrays; cDNA microarrays; Detection; Diagnostics; DNA chip; DNA macroarrays; DNA microarrays; Gene expression; GeneChip; High density arrays; Hybridization; Identification; Low density arrays; Microarrays; Oligo chip; Oligonucleotide microarrays; PCR; Phytoplasmas

Indexed keywords

VIROIDS;

EID: 4444304333     PISSN: 11254653     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (54)

1. Afshari C.A., 2002. Perspective microarray technology, seeing more than spots. Endocrinology 143: 1983-1989.
2. Barba M., Gumpf D.J., Hadidi A., 2003. Quarantine of imported germplasm. In: Hadidi A., Flores R., Randles J.W., Semancik J.S. (eds.). Viroids, pp. 303-311. CSIRO Publishing, Collingwood, Victoria, Australia.
3. Beisson F., Koo A.J.K., Ruuska S., Schwender J., Pollard M., Thelen J.J., Paddock T., Salas J.J., Savage L., Milcamps A., Mhaske V.B., Cho Y.H., Ohlrogge J.B., 2003. Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database. Plant Physiology 132: 681-697.
4. Bertucci F., Bernard K., Loroid B., Chang Y., Granjeaud S., Bimbaum D., Nguyen C., Peck K., Jordan B., 1999a. Sensitivities issues in DNA array-based expression measurements and performance of nylon microarrays for small samples. Human Molecular Genetics 8: 1715-1722.
5. Bertucci F., Van Hulst S., Bernard K., Loroid B., Granjeaud S., Tagette R., Starkey M., Nguyen C., Jordan B., Brimbaum D., 1999b. Expression scanning of an array of growth control genes in human cell lines. Oncogene 18: 3905-3912.
6. Bertucci F., Loriod B., Tagett R., Granjeaud S., Bimbaum D., Nguyen C., Houlgattte R., 2001. DNA arrays: technological aspects and applications. Cancer Bulletin 88: 243-255.
7. Bodrossy E., Stralis-Pavese N., Sessitsch A., 2003. Diagnostic microarrays in microbiology. In: Abstracts Agricultural Biomarkers for Array Technology, Management Committee Meeting, Wadenswil 2002, 12.
8. Bonants P., De Weerdt M., Van Beckhoven J., Hilhorst R., Chan A., Boender P., Zijlstra C., Schoen C., 2002. Multiplex detection of plant pathogens by microarrays: an innovative tool for plant health management. In: Abstracts Agricultural Biomarkers for Array Technology, Management Committee Meeting, Wadenswil 2002, 20.
9. Boonham N., Walsh K., Madagan K., Barker I., 2002. Detection of potato viruses using microarrays. In: Abstracts Agricultural Biomarkers for Array Technology, Management Committee Meeting, Wadenswil 2002, 18.
10. Bystricka D., Lenz O., Mraz I., Dedic P., Sip M., 2003. DNA microarrays: parallel detection of potato viruses. Acta Virologica 47: 41-44.
11. Chen J., Wu R., Yang P., Huang J., Sher Y., Han M., Kao W., Lee P., Chiu T., Chang F., Chu Y., Wu C., Peck K., 1998. Profiling expression patterns and isolating differentially expressed genes by cDNA microarray system with colorimetry detection. Genomics 51: 313-324.
12. rd International Symposium - Biodetection Technologies, Arlington 2003, 4.
13. Cullen P., Lorkowski S., 2002. DNA microarrays in medicine: manufacturing techniques and potential applications. Expert Opinion Therapeutic Patents 12: 1-12.
14. Da Silva E.J., 1999. Biological warfare, bioterrorism, biodefence and the biological and toxin weapons convention. Electronic Journal of Biotechnology 2: 99-129.
15. Debouck C., Goodfellow P.N., 1999. DNA microarrays in drug discovery and development. Nature Genetics 21 (Suppl. 1): 48-50.
16. Foster J.A., Hadidi A., 1998. Exclusion of plant viruses. In: Hadidi A., Khetarpal R.K., Koganezawa H. (eds.). Plant Virus Disease Control, pp. 208-229. The American Phytopathological Society Press, St. Paul, Minnesota, USA.
17. Gillespie D., Spiegelman S.A., 1965. Quantitative assay for DNA-RNA hybrids with DNA immobilized on a membrane. Journal of Molecular Biology 12: 829-842.
18. Hadidi A., Candresse T., 2001. Virus detection-PCR. In: Maloy O.G., Murray T.D. (eds.). Encyclopedia of Plant Pathology, pp. 1095-1100. John Wiley & Sons, Inc., New York, USA.
19. Hadidi A., Candresse T., 2003. Polymerase chain reaction. In: Hadidi A., Flores R., Randles J.W., Semancik J.S. (eds.). Viroids, pp. 115-122. CSIRO Publishing, Collingwood, Victoria, Australia.
20. Hadidi A., Khetarpal R.K., Koganezawa H., 1998. Plant Virus Disease Control. The American Phytopathological Society Press, St. Paul, Minnesota, USA.
21. Hadidi A., Flores R., Randles J.W., Semancick J.S., 2003. Viroids. CSIRO Publishing, Collingwood, Victoria, Australia.
22. rd International Symposium - Biodetection Technologies, Arlington 2003, 3.
23. Kafatos F., Jones C., Efstratiadis A., 1979. Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. Nucleic Acids Research 7: 1541-1552.
24. Kirkpatrick B.C., 1991. Mycoplasma-like organisms: plant and invertebrate pathogens. In: Balows A., Truper H.G., Dworkin M., Harder W., Schliefer K.H. (eds.). The Prokaryotes, pp. 4050-4067. Springer-Verlag, New York, USA.
25. Koppal T., 2004. Microarrays: migrating from discovery to diagnostics. Drug Discovery 9: 30-34.
26. Lipshutz R., Fodor S., Gingeras T., Lockhart D., 1999. High density synthetic oligonucleotide arrays. Nature Genetics 21 (Suppl. 1): 20-24.
27. Lockhart D., Dong H., Byme M., Follettie M., Gallo M., Chee M., Mittmann M., Wang C., Kobayashi M., Horton H., Brown E. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology 14: 1675-1680.
28. Loi N., Ermacora P., Carraro L., Osler R., Chen TA, 2002 Production of monoclonal antibodies against apple proliferation phytoplasma and their use in serological detection. European Journal of Plant Pathology 108: 81-86.
29. Lorenz K.H., Schneider B., Ahrens U., Seemüller E., 1995. Detection of the apple proliferation and pear decline phytoplasmas by PCR amplification of ribosomal and nonribosomal DNA. Phytopathology 85: 771-776.
30. Lübeck M., 2002. Detection of genetically modified plants - methods to sample and analyze GMO content in plants and plant products. http://www.sns.dk/erhvogadm/biotek/REPORT_rev%20maj.pdf
31. Nicolaisen M., 2002. DNA chip diagnostics: related work at Danish Institute of Agricultural Sciences. In: Abstracts Agricultural Biomarkers for Array Technology, Management Committee Meeting, Wadenswil 2002, 22.
32. Parker M., Emanuel P., Wilson J., Estacio P., Callahan M., Cullin D., 2003. In: Proceedings of the Consensus Conference on the Role of Biosensors in the Detection of Agents of Bioterrorism. U.S. Army Medical Research and Materiel Command. http://biodefense.georgetown.edu/files/Sept%2003%20Biosensor%20Conf. pdf.
33. Pasquini G., Faggioli F., Barba M., 1999. Sample preparation and RT-PCR assays for large-scale detection of fruit tree viruses covered by certification standards. Petria 9: 157-162.
34. Pasquini G., Marzachì C., Poggi Pollini C., Faggioli F., Ragozzino A., Bissani R., Barba M., Giunchedi L., Boccardo G., 2000. Molecular characterization of phytoplasmas affecting olive (Olea europea L.) trees in Italy. Journal of Plant Pathology 82: 213-219.
35. Perez-Ortin J.E., 2002. Microarray methods for the detection of pathogenic bacterias and viruses in plants. In: Abstracts Agricultural Biomarkers for Array Technology, Management Committee Meeting, Wadenswil 2002, 13.
36. Pouthas F., Gentil C., Cote D., Bockelmann U., 2004. DNA detection on transistor arrays following mutation-specific enzymatic amplification. Applied Physics Letters 84: 1594-1596.
37. Ragozzino E., Faggioli F., Barba M., 2004. Development of a one tube-one step RT-PCR protocol for the detection of seven viroids in four genera: Apscaviroid, Hostunviroid, Pelamoviroid and Pospiviroid. Journal of Virological Methods (in press).
38. Randles J.W., 2003. Economic impact of viroid diseases. In: Hadidi A., Flores R., Randles J.W., Semancik J.S. (eds.). Viroids, pp. 3-11. CSIRO Publishing, Collingwood, Victoria, Australia.
39. Schena M., Shalon D., Davis R.W., Brown P.O., 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
40. Scherm B., Palomba M., Balmas V., Migheli Q., 2002. Identification of aflotoxin-producing and non-producing isolates of Aspergillus flavus and A. parasiticus by reverse transcription polymerse chain reaction (RT-PCR). In: Abstracts Agricultural Biomarkers for Array Technology, Management Committee Meeting, Wadenswil 2002, 23.
41. Schoen C., De Weerdt M., Hillhorst R., Chan A., Boender P., Zijlstra C., Bonants P., 2002. Use of novel 3D microarray flow through system for plant pathogen multiplex detection. In: Abstracts Agricultural Biomarkers for Array Technology, Management Committee Meeting, Wadenswil 2002, 11.
42. th International Symposium on Virus and Virus-like Diseases of Temperate Fruit Crops, Valencia 2003, 108.
43. Sip M., 2002. Parallel detection of potato pathogens: possibilities and problems. In: Abstracts Agricultural Biomarkers for Array Technology, Management Committee Meeting, Wadenswil 2002, 24.
44. Southern E., 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. Journal of Molecular Biology 98: 503-517.
45. Southern E.M., Mitchell A.R., 1971. Chromatography of nucleic acid digests on thin layers of cellulose impregnated with polyethyleneamine. Biochemical Journal 123: 613-617.
46. Thieblemont C., 2000. DNA microarrays and non Hodgkin's lymphoma: current and future applications. Journal of Oncology 2: 45-52.
47. Wang D., Coscoy L., Zylberberg M., Avila P.C., Boushey H.A., Genam D., DeRisi J.L., 2002. Microarray-based detection and genotyping of viral pathogens. Proceedings of the National Academy of Sciences U.S.A. 99: 15687-15692.
48. Waring J.F., Ciurlionis R., Jolly R.A., Heidel M., Ulrich R.G., 2001. Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanism of toxicity. Toxicology Letters 120: 359-368.
49. Warsen A., Krug M., LaFrentz S., Stanek D.R., Loge F.J., Call D.R., 2004. Simultaneous discrimination between 15 fish pathogens using 16S rDNA PCR and DNA microarrays. Applied and Environmental Microbiology (in press).
50. Waterworth H.E., Hadidi A., 1998. Economic losses due to plant viruses. In: Hadidi A., Khetarpal R.K., Koganezawa H. (eds.). Plant Virus Disease Control, pp. 1-13. The American Phytopathological Society Press, St. Paul, Minnesota, USA.
51. White K.P., Rifkin S.A., Hurban P., Hogness D.S., 1999. Microarray analysis of Drosophila development during metamorphosis. Science 286: 2179-2184.
52. Wodicka L., Dong H.L., Mittmann M., Ho M.H., Lockart D.J., 1997. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nature Biotechnology 15: 1359-1367.
53. Zahavy E., Fisher M., Bromberg A., Olshevsky U., 2003. Detection of frequency resonance energy transfer pair on double-labeled microsphere and Bacillus anthracis spores by flow cytometry. Applied and Environmental Microbiology 69: 2330-2339.
54. Zhu S.F., Hadidi A., Lee I.-M., Gundersen D.E., Zhang C.L., 1998. Characterization of the phytoplasmas associated with cherry leaf lethal yellows and jujube witches-broom diseases in China. Acta Horticulturae 472: 701-714.