Identification of Mycoplasmas Using a Fluorophore-Free Microarray and Infrared Chemical Imaging (IRCI)

Mossoba, Magdi M.; Chizhikov, Vladimir E.; Volokhov, Dmitry; Milians, K. Martinez-Diaz; Schoen, Brianna; Al-Khaldi, Sufian F.

doi:10.1016/j.mimet.2011.06.003

Cited by 2 publications

(5 citation statements)

References 14 publications

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“…In this proof-of-concept study, we have applied a microarray assay with vibrational spectroscopic detection methods 22 previously used to identify bacterial species in our laboratory 23,24 to demonstrate that this methodology can also be successfully used to identify catfish species. Oligonucleotide probes were carefully designed and tested in silico and then printed in triplicate arrays to a slide (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Microarray Chip Development Using Infrared Imaging for the Identification of Catfish Species

et al. 2014

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Several families of catfish species are extensively aquacultured around the world; however, only those from the family Ictaluridae can be labeled as catfish in the United States. Non-Ictalurid catfish species that are marketed as "catfish" in the USA are considered misbranded. Misbranding in general has led to an increased interest in developing deoxyribonucleic acid (DNA)-based methods such as DNA barcoding, polymerase chain reaction restriction fragment length polymorphism, and DNA microarrays with fluorescence detection for the identification of fish species. In this proof-of-concept study, DNA microarrays coupled with a newly developed mid-infrared imaging detection method were applied to the identification of seven species of catfish for the first time. Species-specific DNA probes targeting three regions per species of the cytochrome c oxidase 1 (barcoding) gene were developed and printed as microarrays on glass slides. Deoxyribonucleic acid targets labeled with biotin were hybridized to their complementary probes using a strategy that allowed the selective formation of a silver layer on hybridized spots needed for detection. Using this three-probe format, the seven species were all identified correctly, even when a limited number of false positive spots were observed. Raman spectroscopy was employed to further characterize the arrays.

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Section: Resultsmentioning

confidence: 99%

“…This IRCI detection method was successfully applied to the microarray-based genomic analysis of microorganisms in our laboratory. 23,24…”

Section: Introductionmentioning

confidence: 99%

Microarray Chip Development Using Infrared Imaging for the Identification of Catfish Species

et al. 2014

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“…DNA microarray technology is a well-established and efficient molecular biological tool that allows for the simultaneous analysis of multiple genes (or their transcripts) in a single experiment by measuring the hybridization signal between sequence-specific microarray probes attached to a solid surface and complementary regions of DNA or RNA of the organism under investigation. 1,–4 Recently, we described in detail the application of mid-infrared chemical imaging (IRCI) in the external reflection mode as a novel read-out tool 2 for the analysis of microarrays in which hybridized spots had been selectively augmented with nanogold-silver to facilitate detection. 2,–4 The adlayer of silver, selectively bound to only hybridized spots (approximately 120 μm in diameter) in a microarray, formed the external reflective IR substrate that was necessary for the detection of DNA hybridization by IRCI.…”

Section: Introductionmentioning

confidence: 99%

“…1,–4 Recently, we described in detail the application of mid-infrared chemical imaging (IRCI) in the external reflection mode as a novel read-out tool 2 for the analysis of microarrays in which hybridized spots had been selectively augmented with nanogold-silver to facilitate detection. 2,–4 The adlayer of silver, selectively bound to only hybridized spots (approximately 120 μm in diameter) in a microarray, formed the external reflective IR substrate that was necessary for the detection of DNA hybridization by IRCI. 2 In that proof-of-concept study, 2 IRCI detection was evaluated and applied to the analysis of five virulence genes— cpb, etx, cpe, cpa, and cpia —in samples of the bacterium Clostridium perfringens.…”

Section: Introductionmentioning

confidence: 99%

“…All detailed experimental conditions for microarray printing, PCR amplification of targeted genes, preparation of biotinylated ssDNA targets from PCR amplicons, microarray hybridization to oligonucleotide probes immobilized on glass slides, conjugation to the streptavidin loaded with gold nanoparticles, silver enhancement, and detection by IRCI 2 were previously reported. 2,–4 Brief accounts of some procedures are provided below. Brain heart infusion medium was used to grow the 19 Y. enterocolitica strains.…”

Section: Introductionmentioning

confidence: 99%

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Enhanced Mid-Infrared Chemical Imaging (IRCI) Detection of DNA Microarrays

et al. 2012

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We report on the optimization of a recently proposed mid-infrared chemical imaging (IRCI) detection method for the analysis of DNA microarrays. The improved protocol allowed for a ten-fold reduction in the time needed to generate a mosaic image of an entire microarray and the production of IR images with high contrast that would facilitate data analysis and interpretation. Advantages of using this protocol were evaluated by applying it to the analysis of four virulence genes in the genomes of 19 strains of the food bacterial pathogen Yersinia enterocolitica.

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Identification of Mycoplasmas Using a Fluorophore-Free Microarray and Infrared Chemical Imaging (IRCI)

Cited by 2 publications

References 14 publications

Microarray Chip Development Using Infrared Imaging for the Identification of Catfish Species

Microarray Chip Development Using Infrared Imaging for the Identification of Catfish Species

Enhanced Mid-Infrared Chemical Imaging (IRCI) Detection of DNA Microarrays

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