Oligonucleotide microarray for the identification of potential mycotoxigenic fungi

BMC Microbiology

Volumn 10, Issue , 2010, Pages

  Lezar, Sabine ^a   Barros, Eugenia ^a  

^a DSI CSIR Nanotechnology Innovation Centre   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

ELONGATION FACTOR 1ALPHA; INTERNAL TRANSCRIBED SPACER; LOCKED NUCLEIC ACID; MYCOTOXIN; RIBOSOME RNA; FUNGAL DNA;

ALTERNARIA; ARTICLE; ASPERGILLUS; CLAVICEPS; CONTROLLED STUDY; CURVULARIA; DNA MICROARRAY; DNA POLYMORPHISM; DNA SEQUENCE; FOOD; FUNGAL GENE; FUNGAL STRAIN; FUNGUS; FUNGUS IDENTIFICATION; FUNGUS ISOLATION; FUSARIUM; GENE CASSETTE; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE MICROARRAY; OLIGONUCLEOTIDE PROBE; PENICILLIUM; PROMOTER REGION; RNA STRUCTURE; SIGNAL TRANSDUCTION; DEUTEROMYCETES; FLUORESCENCE IN SITU HYBRIDIZATION; FOOD CONTROL; GENETICS; METHODOLOGY; POLYMERASE CHAIN REACTION; REPRODUCIBILITY;

ANIMALIA; FUNGI; ZEA MAYS;

DNA, FUNGAL; FOOD MICROBIOLOGY; IN SITU HYBRIDIZATION, FLUORESCENCE; MITOSPORIC FUNGI; MYCOTOXINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS;

EID: 77951677457     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-10-87     Document Type: Article

References (48)

1. Mycotoxins: Of molds and maladies. JR Barrett, Environ Health Perspectives 2000 108 20 A27 10.2307/3454282
2. Problem of Mycotoxins and some solutions. S Mellor, Pig progress 2003 5 12 15
3. Toxigenic fungi and mycotoxins in South African foods and feeds. CJ Rabie GJ Marais, Report to the Department of Health, Pretoria 2000
4. Toxic effects of mycotoxin in humans. M Peraica B Radic A Lucic M Pavlovic, Bulletin WHO 1999 77 754 756
5. PCR-based diagnosis and quantification ofmycotoxin producing fungi. L Niessen, Int J Food Microbiol 2007 119 38 46 10.1016/j.ijfoodmicro.2007.07.023 17804102 (Pubitemid 350051464)
6. Early detection of Aspergillus infection after allogeneic stem cell transplatation by polymerase chain reaction screening. HJ Hebart J Loffler C Meissner F Serey D Schmidt A Bohme H Martin A Engel D Bunje WV Kern U Schumacher L Kanz H Einsele, J Infec Dis 2000 181 1713 1719 10.1086/315435 (Pubitemid 30387765)
7. Identification of pathogenic Aspergillus species by a PCR-restriction enzyme method. H Mirhendi K Diba P Kordbacheh N Jalalizand K Makimura, J Med Microbiol 2007 56 1568 1570 10.1099/jmm.0.47319-0 17965363 (Pubitemid 350175088)
8. Development of a PCR-based assay for rapid and reliable identification of pathogenic Fusaria. PK Mishra RTV Fox A Culham, FEMS Microbiol Lett 2003 218 329 332 10.1111/j.1574-6968.2003.tb11537.x 12586412 (Pubitemid 36183516)
9. Synteny in toxigenic Fusarium species: the fumonisin gene cluster and the mating type region as examples. C Waalwijk T van der Lee I de Vries T Hesselink J Arts GHJ Kema, Eur J Plant Pathol 2004 110 533 544 10.1023/B:EJPP.0000032393. 72921.5b (Pubitemid 39001455)
10. A gene probe for the patulin metabolic pathway with potential for use in patulin and novel disease control. RRM Paterson S Archer Z Kozakiewicz A Lea T Locke E O'Grady, Biocontrol Science and Technol 2000 10 509 512 10.1080/09583150050115098 (Pubitemid 30647984)
11. DNA microarray to detect and identify trichothecene- and moniliformin-producing Fusarium species. R Kristensen G Gauthier KG Berdal S Hamels J Remacle A Holst-Jensen, J Appl Microbiol 2007 102 1060 1070 17381750 (Pubitemid 46457488)
12. Applications of microarrays in pathogen detection and biodefence. M Uttamchandani JL Neo BNZ Ong S Moochhala, Trends Biotechnol 2008 27 53 61 10.1016/j.tibtech.2008.09.004 19008003
13. Development of a DNA microarray for detection and identification of fungal pathogens involved in invasive mycoses. DM Leinberger U Schumacher IB Autenrieth TT Bachmann, J Clinical Microbiol 2005 43 4943 4953 10.1128/JCM.43.10.4943-4953.2005 (Pubitemid 41483988)
14. Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray. TZ DeSantis CE Stone SR Murray JP Moberg GL Andersen, FEMS Microbiol Lett 2005 245 271 278 10.1016/j.femsle.2005.03.016 15837382
15. A microarray for monitoring the production of mycotoxins in food. M Schmidt-Heydt R Geisen, Int J Food Microbiol 2007 117 131 140 10.1016/j.ijfoodmicro.2007.01.014 17512074 (Pubitemid 46813168)
16. Nucleic acid amplification strategies for DNA-microarray-based pathogen detection. GJ Vora CE Meador DA Stenger JD Andreadis, Appl Environ Microbiol 2004 70 3047 3054 10.1128/AEM.70.5.3047-3054.2004 15128566 (Pubitemid 38657823)
17. Locked nucleic acids (LNA) singlenucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. MP Johnson LM Haupt LR Griffiths, NAR 2004 32 55 10.1093/nar/gnh046 15047860
18. Design of LNA probes that improve mismatch discrimination. Y You BG Moreira MA Behlke R Owczarzy, Nucleic Acids Res 2006 34 60 10.1093/nar/gkl175 16670427 (Pubitemid 43985690)
19. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. TJ White T Bruns S Lee J Taylor, PCR Protocols: A Guide to Methods and Applications San Diego: Academic Press Inc, Innis MA, Gelfand DH, Sninsky JJ, White TJ, 1990 315 322
20. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. MD Kane TA Jatkoe CR Stumpf J Lu JD Thomas SJ Madore, Nucleic Acids Res 2000 28 4552 4557 10.1093/nar/28.22.4552 11071945
21. Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays. J Letowski R Brousseau L Masson, J Microbiol Methods 2004 57 269 278 10.1016/j.mimet.2004.02. 002 15063067 (Pubitemid 38450733)
22. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. RM Anthony TJ Brown GL French, J Clinical Microbiol 2000 38 781 788
23. Identification of Listeria species by microarray-based assay. D Volokhov A Rasooly K Chumakov V Chizhikov, J Clinical Microbiol 2002 40 4720 4728 10.1128/JCM.40.12.4720-4728.2002 (Pubitemid 35434973)
24. Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays. A Graf B Gasser M Dragostis M Sauer GG Leparc T Tuechler DP Kreil D Mattanovich, BMC Genomics 2008 9 390 10.1186/1471-2164-9-390 18713468
25. Amplicon structure prevents target hybridization to oligonucleotide microarrays. S Lane J Everman F Logea DR Call, Biosensors and Bioelec 2004 20 728 725 10.1016/j.bios.2004.04.014 (Pubitemid 39441251)
26. Molecular interactions on microarrays. E Southern K Mir M Shepinov, Nature Genet 1999 21 5 9 10.1038/4429 9915493 (Pubitemid 29031484)
27. Reverse Line Blot Hybridization Assay for Identification of Medically Important Fungi from Culture and Clinical Specimens. XZ Zheng F Kong C Halliday S Chen A Lau G Playford TC Sorrell, J Clinical Microbiol 2007 45 2872 2880 10.1128/JCM.00687-07 (Pubitemid 47417329)
28. Comparison of environmental profiles for growth and deoxynivalenol production by Fusarium culmorum and F. graminearum on wheat grain. D Hope D Aldred N Magan, Lett Appl Microbiol 2005 40 295 300 10.1111/j.1472-765X.2005. 01674.x 15752221 (Pubitemid 40470582)
29. Rapid preparation of DNA from filamentous fungi. U Raeder P Broda, Lett Appl Microbiol 1985 1 17 20 10.1111/j.1472-765X.1985.tb01479.x (Pubitemid 16253847)
30. The CLUSTL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tool. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins, Nucleic Acids Res 1997 25 4876 4882 10.1093/nar/25.24. 4876 9396791
31. Two divergent intragenomic rRNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. K O'Donnell E Cigelnik, Molecular Phylogenet Evol 1997 7 103 116 10.1006/mpev.1996.0376 (Pubitemid 127347168)
32. 2007. A Prototype Taxonomic Microarray Targeting the rpsA Housekeeping Gene Permits Species Identification within the Rhizobial Genus. M Martens S Weidner B Link P de Vos M Gillis A Willems, Syst Appl Microbiol 2007 30 5 390 400 10.1016/j.syapm.2007.01.002 17291704 (Pubitemid 46962944)
33. NCBI Gene Expression Omnibus (GEO). http://ncbi.nlm.nih.gov/geo/
34. Multiplex polymerase chain reaction assay for the differential detection of trichothecene- and fumonisin-producing species of Fusarium in cornmeal. BH Bluhm JE Flaherty MA Cousin CP Woloshuk, J Food Proteomics 2002 65 1955 1961
35. Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. KJ Martin PT Rygiewicz, BMC Microbiology 2005 5 28 10.1186/1471-2180-5-28 15904497
36. A DNA-based method to quantify Stenocarpella maydis in maize. E Barros M Crampton G Marais S Lezar, Maydica 2008 53 125 129
37. The use of species-specific PCR-based assays to analyse Fusarium ear blight of wheat. FM Doohan DW Parry P Jenkinson P Nicholson, Plant Path 1998 47 197 205 10.1046/j.1365-3059.1998.00218.x (Pubitemid 28228834)
38. The application of species-specific assays based on the polymerase chain reaction to analyse Fusarium crown rot of durum wheat. KJ Williams JI Dennis C Smyl H Wallwork, Australasian Plant Path 2002 31 119 127 10.1071/AP01079 (Pubitemid 36425261)
39. Species-specific primers resolve members of Fusarium section Fusarium - Taxonomic status of the edible "Quorn" fungus reevaluated. WT Yoder LM Christianson, Fungal Genet and Biol 1998 23 68 80 10.1006/fgbi.1997.1027 (Pubitemid 28403139)
40. Species-specific PCR assays for the fungal pathogens Fusarium moniliforme and Fusarium subglutinans and their application to diagnose maize ear rot disease. EM Möller J Chelkowski HH Geiger, J Phytopath 1999 147 497 502 10.1111/j.1439-0434.1999.tb03856.x
41. Detection and quantification of Fusarium culmorum and Fusarium graminearum in cereals using PCR assays. P Nicholson DR Simpson G Weston HN Rezanoor AK Lees DW Parry D Joyce, Physiol and Mol Plant Path 1998 53 17 37 10.1006/pmpp.1998.0170 (Pubitemid 28564655)
42. A species-specific PCR assay based on the calmodulin partial gene for identification of Fusarium verticillioides, F. proliferatum and F. subglutinans. G Mulé A Susca G Stea A Moretti, Eur J Plant Path 2004 110 495 502 10.1023/B:EJPP.0000032389.84048.71 (Pubitemid 39001451)
43. Quantification of the copy number of nor-1, a gene of the aflatoxin biosynthetic pathway by real-time PCR, and its correlation to the cfu of Aspergillus flavus in foods. Z Mayer A Bagnara P Färber R Geisen, Int J Food Microbiol 2003 82 143 151 10.1016/S0168-1605(02)00250-7 12568754 (Pubitemid 36144018)
44. The sequence of the isoepoxydon dehydrogenase gene of the patulin biosynthetic pathway in Penicillium species. MA Dombrink-Kurtzman, Antonie van Leeuwenhoek 2007 91 179 189 10.1007/s10482-006-9109-3 17043910 (Pubitemid 46267511)
45. The isoepoxydon dehydrogenase gene of the patulin metabolic pathway differs for Penicillium griseofulvum and Penicillium expansum. MA Dombrink-Kurtzman, Antonie van Leeuwenhoek 2005 89 1 8 10.1007/s10482-005-9002-5 16328863
46. Tri13 and Tri7 Determine Deoxynivalenol- and Nivalenol-Producing Chemotypes of Gibberella zeae. L Lee Y-K Han K-H Kim S-H Yun Y-W Lee, Appl and Environ Microbiol 2002 68 2148 2154 10.1128/AEM.68.5.2148-2154.2002 (Pubitemid 34477807)
47. Detection and differentiation of trichothecene and enniatin-producing Fusarium species on small-grain cereals. P Nicholson DR Simpson AH Wilson E Chandler M Thomsett, Eur J Plant Path 2004 110 503 514 10.1023/B:EJPP. 0000032390.65641.a7 (Pubitemid 39001452)
48. Group specific PCR-detection of potential trichothecene-producing Fusarium-species in pure cultures and cereal samples. ML Niessen RF Vogel, Syst Appl Microbiol 1998 21 618 631 9924828