Chaotropic Solid-phase Extraction Research Articles

Comparison of polymerase chain reaction methods and plating for analysis of enriched cultures of Listeria monocytogenes when using the ISO11290-1 method

Analysis for Listeria monocytogenes by ISO11290-1 is time-consuming, entailing two enrichment steps and subsequent plating on agar plates, taking five days without isolate confirmation. The aim of this study was to determine if a polymerase chain reaction (PCR) assay could be used for analysis of the first and second enrichment broths, saving four or two days, respectively. In a comprehensive approach involving six European laboratories, PCR and traditional plating of both enrichment broths from the ISO11290-1 method were compared for the detection of L. monocytogenes in 872 food, raw material and processing environment samples from 13 different dairy and meat food chains. After the first and second enrichments, total DNA was extracted from the enriched cultures and analysed for the presence of L. monocytogenes DNA by PCR. DNA extraction by chaotropic solid-phase extraction (spin column-based silica) combined with real-time PCR (RTi-PCR) was required as it was shown that crude DNA extraction applying sonication lysis and boiling followed by traditional gel-based PCR resulted in fewer positive results than plating. The RTi-PCR results were compared to plating, as defined by the ISO11290-1 method. For first and second enrichments, 90% of the samples gave the same results by RTi-PCR and plating, whatever the RTi-PCR method used. For the samples that gave different results, plating was significantly more accurate for detection of positive samples than RTi-PCR from the first enrichment, but RTi-PCR detected a greater number of positive samples than plating from the second enrichment, regardless of the RTi-PCR method used. RTi-PCR was more accurate for non-food contact surface and food contact surface samples than for food and raw material samples especially from the first enrichment, probably because of sample matrix interference. Even though RTi-PCR analysis of the first enrichment showed less positive results than plating, in outbreak scenarios where a rapid result is required, RTi-PCR could be an efficient way to get a preliminary result to be then confirmed by plating. Using DNA extraction from the second enrichment broth followed by RTi-PCR was reliable and a confirmed result could be obtained in three days, as against seven days by ISO11290-1.

Evidence for wheat, rye, and barley presence in gluten free foods by PCR method - comparison with ELISA method

A method of the evidence for the presence of wheat, rye, and barley in gluten free foods, based on the polymerase chain reaction (PCR), was validated. DNA was isolated from foods by chaotropic solid phase extraction. The PCR method applied was focused on the intron of the chloroplast gene trnL and utilised primers WBR11 and WBR13. Electrophoresed wheat and rye DNAs were characterised by a 201 bp fragment, barley DNA by a 196 bp fragment. The validated PCR method was applied to the selection of 18 gluten free foods, previously found by ELISA method to contain 1 mg or more of gliadin per 100 g food. The presence of wheat was confirmed by PCR method in all foods analysed. The comparison with the results obtained by ELISA method reliably verified the detection limit of PCR method, i.e., 0.02% wheat.

Identification of animal skin of historical parchments by polymerase chain reaction (PCR)-based methods

This study deals with establishing of a PCR-based strategy with the aim to recognize the animal origin of different historical parchments. This is one of relatively rare studies on the analysis of ancient DNA from parchments. Robustness of the PCR technology is demonstrated by successful identification of the animal species using only a small amount of DNA isolated from 12 parchment samples. Ten PCR-based assays specific for the detection of different animal species ( Bos taurus, Ovis aries, Capra hircus, Sus scrofa, Oryctolagus domestica, Cervus elaphus, Capreolus capreolus, Dama dama) and two PCR assays utilizing universal primers were evaluated and optimized with the aim to find a rapid parchment identification method, which would be more reliable than the classical microscopic examination. The optimized PCR methods produced satisfactory results. Out of 12 investigated parchments, 9 items were unambiguously identified, DNA from 2 samples could not be amplified with any of the species-specific PCR assays, and only one parchment produced controversial results. The species-specific PCR results were confirmed by direct sequencing and PCR cloning with consequent sequencing. Our approach, including isolation of parchment DNA by chaotropic solid-phase extraction, optimization of the PCR programs and high-stringency annealing temperatures, demonstrated to be effective, easy and reliable for the analysis of historical parchment DNA. We consider this PCR-based strategy potentially useful also for investigation of other types of animal items conserved in museums, galleries or libraries.

A novel real-time polymerase chain reaction method for the detection of macadamia nuts in food

A real-time PCR-based method for the detection of macadamia nuts (fruits of Macadamia integrifolia or M. tetraphylla or their hybrids) in food products is described. The method consists of DNA isolation by chaotropic solid phase extraction and subsequent PCR with macadamia-specific primers and a TaqMan fluorescent probe. The primers and the probe were targeted to the gene encoding for vicilin precursor. The method was positive for M. integrifolia and M. tetraphylla and negative for 16 other plant species used in food industry, including peanuts, walnuts, hazelnuts, almonds, pistachio nuts, cashew nuts, Brazil nuts, and chestnuts. The DNA-based detection limit of the method was 1.45 pg. Using a series of model samples with defined macadamia nut contents, a practical detection limit of 0.02% (w/w) macadamia nuts was determined. Practical applicability of the PCR method was tested by the analysis of 14 confectionery samples. For all of the samples, results conforming to the labeling were obtained. The presented PCR method is useful for relatively fast, highly selective, and moderately sensitive detection of macadamia nuts in food samples.

A novel real-time polymerase chain reaction (PCR) method for the detection of hazelnuts in food

A real-time PCR (polymerase chain reaction)-based method for the detection of hazelnuts (nuts of Corylus avellana or C. maxima) in confectionery and bakery products is described. The method consists of DNA isolation by chaotropic solid phase extraction and the subsequent PCR with hazelnut-specific primers and a TaqMan fluorescent probe. The primers and the probe are targeted to the hsp1 gene encoding for a low molecular weight heat-shock protein. The method was positive for five hazelnut varieties approved in Slovakia and negative for all other tested plant materials used in food industry including peanuts, walnuts, almonds, pistachio nuts, cashews and chestnuts. The intrinsic detection limit of the method was 13 pg hazelnut DNA, which corresponds to approximately 27 genome equivalents (1C). Using a series of model pastry samples with defined hazelnut contents, a practical detection limit of 0.01% (w/w) hazelnut was determined. Practical applicability of the PCR method was tested by the analysis of 20 food samples (confectionery and bakery products) along with ELISA. For all of the food samples, identical results were obtained by both methods, which conformed to the labelling. The presented PCR method is useful for sensitive and selective detection of hazelnuts in food samples and can be performed in one working day.

A novel real-time polymerase chain reaction method for the detection of pecan nuts in food

A real-time PCR-based method for the detection of the pecan (Carya illinoiensis) component in food is described. The method consists of DNA isolation by chaotropic solid phase extraction and the subsequent PCR with pecan-specific primers and a TaqMan fluorescent probe. The primers and the probe are targeted to the putative gene for allergenic vicilin-like seed storage protein of pecan. The method was positive for 10 pecan varieties and negative for all other tested plant materials used in food industry, including walnut. The intrinsic detection limit of the method was 1 pg pecan DNA which corresponds to 1.2 haploid genome copies. Using a series of model pastry samples with defined pecan contents, a practical detection limit of 0.01% (w/w) pecan was estimated. Practical applicability of the PCR method was tested by the analysis of 13 food samples; no discrepancies between the declared and detected pecan contents were found. The presented PCR method is useful for sensitive and selective detection of pecans in food samples and can be performed in one working day.

A novel real-time polymerase chain reaction (PCR) method for the detection of walnuts in food

A real-time polymerase chain reaction (PCR)-based method for the detection of the walnut (Juglans regia) component in food is described here. The method consists of DNA isolation by chaotropic solid phase extraction and the subsequent PCR with walnut-specific primers and a TaqMan fluorescent probe. The primers and the probe are targeted to the jug r2, a major allergen gene of walnut. The method was positive for 8 varieties of walnut and negative for all other tested plant materials used in food industry, including pecan nuts. The intrinsic detection limit of the method was 0.24 ng walnut DNA. Using a series of model pastry samples with defined walnut contents, a practical detection limit of 0.01% walnut content was estimated. Practical applicability of the PCR method was tested by the analysis of 13 food samples (bakery and confectionery products), out of which two cakes were found to contain walnuts although they were not adequately labelled. The presented PCR method is useful for sensitive and selective detection of walnuts in food samples and can be performed in one working day.

Detection of pea in food by real-time polymerase chain reaction (PCR)

A qualitative 5′-nuclease real-time PCR-based method for the detection of pea (Pisum sativum) in food is described. The method consists of DNA isolation by chaotropic solid phase extraction and the subsequent PCR with pea-specific primers and a TaqMan fluorescent probe. The primers and the probe are oriented to the chloroplast DNA intron located between trnL and trnF exons encoding for tRNA. The analytical parameters of the method were inclusivity 100%, exclusivity 100% and the detection limit of 0.11±0.07 ng of pea DNA corresponding to 12±7 diploid pea genome copies. Using a set of model meat pâtes with defined pea contents, a matrix-related detection limit of 0.05% was determined and a linear calibration line was constructed. The presented analytical method was useful for qualitative detection or semiquantitative determination of pea in food products. The method was relatively fast because the analysis could be performed in one working day.

Detection of gluten-containing cereals in flours and “gluten-free” bakery products by polymerase chain reaction

A polymerase chain reaction-based method for the detection of gluten-containing cereals in flours and “gluten-free” bakery products was optimized and its intralaboratory validation was carried out. The optimized method involved DNA isolation by chaotropic solid-phase extraction and PCR with primers of Dahinden et al. [Dahinden I., von Büren M., Lüthy J., 2001. A quantitative competitive PCR system to detect contamination of wheat, barley and rye in gluten-free food for coeliac patients. European Food Research and Technology 212, 228–233]. Using purified DNA, intrinsic detection limit of 42 ± 12 pg was determined, which corresponds to 10° genome copies. By the analysis of a panel of 26 European wheat cultivars and flours from six non-gluten-containing plants, which are commonly used for the production of gluten-free bakery products, inclusivity of 100% and exclusivity of 100% were determined. By the analysis of model samples of soya flour and cakes, detection limit of 0.1% (w/w) of fine wheat flour was determined, which is suitable for the analysis of “gluten-free” food products, as it is approximately equivalent to the limit of 10 mg per 100 g for gluten stated by Codex Alimentarius. The method was successfully applied to four samples of flours and 13 brands of biscuits designated “gluten-free”, out of which two flours and one brand of biscuits were found positive for gluten-containing cereals. The method proved to be suitable for routine use, it was relatively straightforward and could be completed in one working day.

Comparison of three types of methods for the isolation of DNA from flours, biscuits and instant paps

Three types of methods for the isolation of DNA from food products, namely, cetyltrimethylammonium bromide solubilization with liquid-phase extraction (CTAB-LPE), chaotropic solid-phase extraction (SPE) and non-chaotropic SPE were compared on the basis of yields. These were measured by UV spectrophotometry, fluorimetry of the SYBR Green I-DNA complex and by the determination of the maximum amplifiable dilution. The latter parameter, which proved to be the most informative, was determined using polymerase chain reaction (PCR) for soya, maize and wheat, respectively, in series of flours, biscuits, chocolate-containing biscuits and instant paps (a baby food preparation) containing the respective major ingredients. All three types of DNA isolation methods performed well for practically all food products analysed, yielding ≥102×minimum amplifiable DNA concentration. Chaotropic SPE performed in most cases as well as to CTAB-LPE and may be recommended as a faster alternative for isolating DNA in PCR-based analyses of these types of food products.