Biotechnology and Bioprocess Engineering:BBE

The Korean Society for Biotechnology and Bioengineering (한국생물공학회)
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Development of DNA Microarray for Pathogen Detection

  • Yoo, Seung Min (Department of Chemical & Biomolecular Engineering and BioProcess Engineering Research Center, KAIST) ;
  • Keum, Ki Chang (Medigenes Co.,) ;
  • Yoo, So Young (Department of Radiation Oncology, Yonsei University College of Medicine, Department of Medicine and Pharmacology, Yale University School of Medicine) ;
  • Choi, Jun Yong (Medigenes Co., Department of Chemical & Biomolecular Engineering and BioProcess Engineering, Research Center, KAIST) ;
  • Chang, Kyung Hee (Department of Internal Medicine, Yonsei University College of Medicine) ;
  • Yoo, Nae Choon (Department of Internal Medicine, Yonsei University College of Medicine) ;
  • Yoo, Won Min (Department of Oncology and Cancer Center, Yonsei University College of Medicine) ;
  • Kim, June Myung (Department of Plastic & Reconstructive Surgery, Yonsei University College of Medicine, Department of Medicine and Pharmacology, Yale University, School of Medicine) ;
  • Lee, Duke (Department of Internal Medicine, Yonsei University College of Medicine) ;
  • Lee, Sang Yup (Department of Chemical & Biomolecular Engineering and BioProcess Engineering Research Center, KAIST)
  • Published : 2004.03.01
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Abstract

Pathogens pose a significant threat to humans, animals, and plants. Consequently, a considerable effort has been devoted to developing rapid, convenient, and accurate assays for the detection of these unfavorable organisms. Recently, DNA-microarray based technology is receiving much attention as a powerful tool for pathogen detection. After the target gene is first selected for the unique identification of microorganisms, species-specific probes are designed through bioinformatic analysis of the sequences, which uses the info rmation present in the databases. DNA samples, which were obtained from reference and/or clinical isolates, are properly processed and hybridized with species-specific probes that are immobilized on the surface of the microarray for fluorescent detection. In this study, we review the methods and strategies for the development of DNA microarray for pathogen detection, with the focus on probe design.

Keywords

References

  1. Arch. Pathol. Lab. Med. v.125 Solitary blood cultures David,A.;A.Novis;C.D.Jane;B.S.Ron;G.R.Stephen;K.W.Molly
  2. Curr. Opin. Biotechnol. v.12 Advances in the analysis of DNA sequence variations using oligonucleotide microchip technology Tillib,S.V.;A.D.Mirzabekov https://doi.org/10.1016/S0958-1669(00)00168-3
  3. Nat. Biotechnol. v.14 Expression monitoring by hybridization to high-density oligonucleotide arrays Lockhart,D.J.;H.Dong;M.C.Byrne;M.T.Follettie;M.V.Gallo;M.S.Chee;M.Mittmann;C.Wang;M.Kobayashi;H.Horton;E.L.Brown https://doi.org/10.1038/nbt1296-1675
  4. Mol Cell Probe v.16 Sequence-specific identification of 18 pathogenic microorganisms using microarray technology Wilson,W.J.;C.L.Strout;T.Z.Desantis;J.L.Stilwell;A.V.Carrano;G.L.Andersen https://doi.org/10.1006/mcpr.2001.0397
  5. FEMS Microbiol. Lett v.213 no.2 Design and evaluation of microarray oligonucleotidemethod for the detection of human intestinal bacteria in fecal samples Wang, R.F.;M.L.Beggs;L.H.Robertson;C.E.Cerniglia https://doi.org/10.1111/j.1574-6968.2002.tb11302.x
  6. Int. J. Food Microbiol. v.78 Development and application of new nucleic acid-based technologies for microbial community analyses in foods Rudi,K.;H.K.Nogva;B.Moen;H.Nissen;S.Bredholt;T.Moretro;K.Naterstad;A.Holck https://doi.org/10.1016/S0168-1605(02)00236-2
  7. Int. J. Syst. Bacterial. v.42 How close is close: 16S rRNA sequence identify may not be sufficient to guarantee species identity Fox,G.E.;J.D.Wisotzkey;P.Jurtshuk https://doi.org/10.1099/00207713-42-1-166
  8. FEMS Microbiol. Rev. v.24 Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology Amann,R.;W.Ludwig https://doi.org/10.1111/j.1574-6976.2000.tb00557.x
  9. Microbiol. Rev. v.51 Bacterial evolution Woose,C.R.
  10. Appl. Environ. Microbial. v.68 Phylogeny of culturable estuarine bacteria catabolizing riverine organic matter in the Northern Baltic sea Kisand,V.;R.Cuadros;J.Wikner https://doi.org/10.1128/AEM.68.1.379-388.2002
  11. Appl. Environ. Microbiol. v.68 Parallel characterization of anaerobic toluene-and ethylbenzene-degrading consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology Koizumi,Y.;J.J.Kelly;T.Nakagawa;H.Urakawa;S.El-Fantroussi;S.Al-Muzaini;M.Fukui;Y.Urushigawa;D.A.Stahl https://doi.org/10.1128/AEM.68.7.3215-3225.2002
  12. Nucleic Acids Res. v.27 A new version of the RDP (Ribosomal Database Project) Maidak,B.L.;J.R.Cole;C.T.Parker,Jr;G.M.Garrity;R.Overbe;S.Pramanik;T.M.Schmidt;J.M.Tiedje;C.R.Woese https://doi.org/10.1093/nar/27.1.171
  13. J. Clin. Microbiol. v.38 Detection and identification of mycobacteria by amplification of the internal transcribed spacer regions with genus-and species-specific PCR primers Park,H.;H.Jang;C.Kim;B.Chung;C.L.Chang;S.K.Park;S.Song
  14. J. Clin. Microbiol. v.38 Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array Anthony,R.M.;T.J.Brown;G.L.French
  15. J. Clin. Microbiol. v.41 Microarray-based identification of thermophilic Campylobacter jejuni, C. coli, C. lari, and C. upsaliensis Volokhov,D.;V.Chizhikov;K.Chumakov;A.Rasooly https://doi.org/10.1128/JCM.41.9.4071-4080.2003
  16. Appl. Environ. Microbiol. v.67 Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays Cho,J.C.;J.M.Tiedje https://doi.org/10.1128/AEM.67.8.3677-3682.2001
  17. Appl. Environ. Microbiol. v.60 Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization Raskin,L.;L.K.Poulsen;D.R.Noguera;B.E.Rittmann;D.A.Stahl
  18. Appl. Environ. Microbiol. v.59 Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA Muyzer,G.;E.C.De Waal;A.G.Uitterlinden
  19. Appl. Environ. Microbiol. v.63 Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA Liu,W.T.;T.L.Marsh;H.Cheng;L.J.Forney
  20. Genome Informatics v.13 Design of ITS and 23S rDNA-targeted probes and its usefulness for the identification of bacterial pathogens Yoo,S.Y.;K.H.Chang;S.M.Yoo;S.Y.Park;N.C.Yoo;K.C.Keum;W.M.Yoo;J.M.Kim;S.Y.Lee
  21. Nucleic Acids Res. v.27 Database on the structure of small subunit ribosomal RNA Van de Peer,Y.;E.Robbrecht;S.de Hoog;A.Caers;P.de Rijk;R.de Wachter https://doi.org/10.1093/nar/27.17.e17
  22. Bioinformatics v.17 Selection of optimal DNA oligos for gene expression arrays Li,F.;G.D.Stormo https://doi.org/10.1093/bioinformatics/17.1.107
  23. Methods Mol. Biol. v.132 Primer 3 on the WWW for general users and for biologist programmers Rozen,S.;H.J.Skaletsky
  24. Bioinformatics v.18 OligoArray: Genome-scale oligonucleotide design for microarrays Rouillard,J.M.;C.J.Herbert;M.Zuker https://doi.org/10.1093/bioinformatics/18.3.486
  25. Nucleic Acids Res. v.29 GST-PRIME: A genome-wide primer design software for the generation of gene sequence tags Varotto,C.;E.Richly;F.Salamini;D.Leister https://doi.org/10.1093/nar/29.21.4373
  26. Appl. Environ. Microbiol. v.68 Sequencing-independent method to generate oligonucleotide probes targeting a variable region in bacterial 16S rRNA by PCR with detachable primers Bertilsson,S.;C.M.Cavanaugh;M.F.Polz https://doi.org/10.1128/AEM.68.12.6077-6086.2002