Abstract
Background:A rapid, accurate, flexible and reliable diagnostic method may significantly decrease the costs of diagnosis and treatment. Designing an appropriate microarray chip reduces noises and probable biases in the final result.Objective:The aim of this study was to design and construct a DNA Microarray Chip for a rapid detection and identification of 10 important bacterial agents.Method:In the present survey, 10 unique genomic regions relating to 10 pathogenic bacterial agents including Escherichia coli (E.coli), Shigella boydii, Sh.dysenteriae, Sh.flexneri, Sh.sonnei, Salmonella typhi, S.typhimurium, Brucella sp., Legionella pneumophila, and Vibrio cholera were selected for designing specific long oligo microarray probes. For this reason, the in-silico operations including utilization of the NCBI RefSeq database, Servers of PanSeq and Gview, AlleleID 7.7 and Oligo Analyzer 3.1 was done. On the other hand, the in-vitro part of the study comprised stages of robotic microarray chip probe spotting, bacterial DNAs extraction and DNA labeling, hybridization and microarray chip scanning. In wet lab section, different tools and apparatus such as Nexterion® Slide E, Qarraymini spotter, NimbleGen kit, TrayMixTM S4, and Innoscan 710 were used.Results:A DNA microarray chip including 10 long oligo microarray probes was designed and constructed for detection and identification of 10 pathogenic bacteria.Conclusion:The DNA microarray chip was capable to identify all 10 bacterial agents tested simultaneously. The presence of a professional bioinformatician as a probe designer is needed to design appropriate multifunctional microarray probes to increase the accuracy of the outcomes.
Highlights
Food and water borne pathogenic bacteria including E. coli, Shigella, Salmonella, Vibrio cholera, Brucella and Legionella are considered as the most important causes of life-threatening diseases throughout the world
The presence of a professional bioinformatician as a probe designer is needed to design appropriate multifunctional microarray probes to increase the accuracy of the outcomes
The dry laboratory of microarray technique includes the processes of probe designing and finalizing data analysis which are known as in-silico study
Summary
Food and water borne pathogenic bacteria including E. coli, Shigella, Salmonella, Vibrio cholera, Brucella and Legionella are considered as the most important causes of life-threatening diseases throughout the world. The infections caused by these bacterial pathogens are endemic in many countries including Iran [1 - 7]. The conventional methods for detection of bacterial infections may take several days to be completed. DNA microarray technology is a proper and high-throughput diagnostic tool for detection and identification pathogenic microorganisms. It is flexible, sensitive, specific and very sharp technique. The process of this technology is divided into two sections of dry laboratory (in-silico) (Bioinformatic practices) and wet laboratory (in-vitro). The dry laboratory of microarray technique includes the processes of probe designing and finalizing data analysis which are known as in-silico study. Designing an appropriate microarray chip reduces noises and probable biases in the final result
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