Microarray on digital versatile disc for identification and genotyping of Salmonella and Campylobacter in meat products.

Highly portable, cost-effective, and rapid-response devices are required for the subtyping of the most frequent food-borne bacteria; thereby the sample rejection strategies and hygienization techniques along the food chain can be tailor-designed. Here, a novel biosensor is presented for the generic detection of Salmonella and Campylobacter and the discrimination between their most prevalent serovars (Salmonella Enteritidis, Salmonella Typhimurium) and species (Campylobacter jejuni, Campylobacter coli), respectively. The method is based on DNA microarray developed on a standard digital versatile disc (DVD) as support for a hybridization assay and a DVD driver as scanner. This approach was found to be highly sensitive (detection limit down to 0.2 pg of genomic DNA), reproducible (relative standard deviation 4-19 %), and high working capacity (20 samples per disc). The inclusivity and exclusivity assays indicated that designed oligonucleotides (primers and probes) were able to discriminate targeted pathogens from other Salmonella serovars, Campylobacter species, or common food-borne pathogens potentially present in the indigenous microflora. One hundred isolates from meat samples, collected in a poultry factory, were analyzed by the DVD microarraying and fluorescent real-time PCR. An excellent correlation was observed for both generic and specific detection (relative sensitivity 93-99 % and relative specificity 93-100 %). Therefore, the developed assay has been shown to be a reliable tool to be used in routine food safety analysis, especially in settings with limited infrastructure due to the excellent efficiency-cost ratio of compact disc technology. Graphical Abstract DNA microarray performed by DVD technology for pathogen genotyping.

Development and validation study of compact biophotonic platform for detection of serum biomarkers.

The application of advances in personalized medicine requires the support of in vitro diagnostic techniques aimed at the accurate, fast, sensitive, and precise determination of selected biomarkers. Herein, a novel optical centrifugal microfluidic device is developed for clinical analysis and point-of-care diagnostics. Based on compact disc technology, the integrated biophotonic system enables multiple immunoassays in miniaturized mode. The disposable microfluidic discs are made in cyclic olefin copolymer (COP), containing arrays of immobilized probes. In the developed approach, up to six patient samples can each be tested simultaneously. A portable instrument (<2 kg) controls the assay and the high-sensitive reproducible optical detection in transmission mode. Also, the instrument incorporates specific functionalities for personalized telemedicine. The device (analytical method, disc platform, reader, and software) has been validated to diagnose IgE-mediated drug allergies, such as amoxicillin and penicillin G. The total and specific IgE to ß-lactam antibiotics were determined in human serum from patients (25 µL). The excellent analytical performances (detection limit 0.24 ng/mL, standard deviation 7-20 %) demonstrated that the developed system could have the potential for a broader impact beyond the allergy field, as it applies to other IVD tests.

Design of Oligonucleotides for Allele-Specific Amplification Based on PCR and Isothermal Techniques.

Single-nucleotide variations have been associated to various genetic diseases, variations on drug efficiency, and differences in cancer prognostics. The detection of these changes in nucleic acid sequences from patient samples is particularly useful for accurate diagnosis, therapeutics, and disease management. A reliable allele-specific amplification is still an important challenge for molecular-based diagnostic technologies. In the last years, allele-specific primers have been designed for promoting the enrichment of certain variants, based on a higher stability of primer/template duplexes. Also, several methods are based on the addition of a blocking oligonucleotide that prevent the amplification of a specific variant, enabling that other DNA variants can be observed. In this context, genotyping methods based on isothermal amplification techniques are increasing, especially those assays aimed to be deployed at point-of-care applications. The correct selection of target sequences is crucial for reaching the required analytical performances, in terms of reaction time, amplification yield, and selectivity. The present chapter describes the design criteria for the selection of primers and blockers for relevant PCR approaches and novel isothermal strategies. Several successful examples are provided in order to highlight the main design restrictions and the potential to be extended to other applications.

DNA Genotyping Based on Isothermal Amplification and Colorimetric Detection by Consumer Electronics Devices.

The point-of-care testing of DNA biomarkers requires compact biosensing systems and consumer electronic technologies provide fascinating opportunities. Their portability, mass-produced components, and high-performance readout capabilities are the main advantages for the development of novel bioanalytical methods.This chapter describes the detection of single nucleotide polymorphisms (SNP) through methods based on user-friendly optical devices (e.g., USB digital microscope, flatbed scanner, smartphone, and DVD drive). Loop mediated isothermal amplification (LAMP) enables the required discrimination of each specific variant prior to the optical reading. In the first method, products are directly hybridized to the allele-specific probes attached to plastic chips in an array format. The second method, allele-specific primers are used, enabling the direct end-point detection based a colorimetric dyer and a microfluidic chamber chip. In both approaches, devices are employed for chip scanning.A representative application to the genotyping of a clinically relevant SNP from human samples is provided, showing the excellent features achieved. Consumer electronic devices are able to register sensitive precise measurements in terms of signal-to-noise ratios, image resolution, and scan-to-scan reproducibility. The integrated DNA-based method lead a low detection limit (100 genomic DNA copies), reproducible (variation <15%), high specificity (genotypes validated by reference method), and cheap assays (<10 €/test). The underlying challenge is the reliable implementation into minimal-specialized clinical laboratories, incorporating additional advantages, such as user-friendly interface, low cost, and connectivity for telemedicine needs.

Temperature effect of tapered element oscillating microbalance (TEOM) system measuring semi-volatile organic particulate matter.

The tapered element oscillating microbalance (TEOM) system is widely used to measure continuous particle mass concentrations in air quality networks. However, the semi-volatile aerosol material is lost under normal operation conditions (50 °C). This study has evaluated the error in the organic fraction of the TEOM-measured secondary organic aerosols formed from the degradation of biogenic pollutants. Experiments were carried out under controlled, water-free conditions in a fully equipped, high volume atmospheric simulator--the European PhotoReactor (EUPHORE). The ozonolysis of α-pinene, ß-pinene and limonene provided a reproducible source of organic aerosol. Particulate matter concentration profiles were registered for different TEOM operating temperatures. When these values were compared with values from a filter-based gravimetric method and a scanning mobility particle sizer (SMPS), they showed that the differences between monitoring systems increased with increasing TEOM temperature. According to our results, when the TEOM is operated at 50 °C, it fails to measure 32-46% of the organic particulate material, depending on the aerosol precursor. This study has also identified and quantified the multi-oxygenated organic compounds lost in the TEOM monitoring by using a method based on the gas chromatography-mass spectrometry technique. Important losses have been calculated for relevant ambient aerosol compounds such as pinonic acid, pinonaldehyde, norpinone and limonalic acid. In conclusion, the present study has demonstrated that a high operating temperature of the TEOM monitor reduces the humidity interference but underestimates the semi-volatile organic fraction.

Determination of reduced sulfur compounds in air samples for the monitoring of malodor caused by landfills.

A reliable method for determining malodorous reduced sulfur compounds (RSC) in atmospheric samples has been developed. The method uses an activated coconut solid-phase sorbent for active sampling, hexane as desorption solvent, and gas chromatography-mass spectrometry (GC-MS) technique for specific and sensitive separation-detection. The compounds analyzed were hydrogen sulfide, ethyl mercaptan, dimethyl sulfide, carbon disulfide, butyl mercaptan and dimethyl disulfide. Recovery efficiency varied between 75% and 97% and no detectable losses were observed during storage at -20°C. Satisfactory analytical parameters were reported, such as good linearity (r(2)>0.98), low detection limits (0.6-59 pg m(-3)), adequate repeatability (9%) and reproducibility (17%), and fast GC-MS analysis (<6.5 min). The accurate determination of RSCs, free of interferences from atmospheric components, such as ozone or water was demonstrated. The method has been applied to analyze the composition of environmental air close to three landfills processing urban and industrial solid wastes. The results indicated that hydrogen sulfide and ethyl mercaptan were the main molecules responsible of malodor phenomenon in the study areas.

Isothermal DNA amplification strategies for duplex microorganism detection.

A valid solution for micro-analytical systems is the selection of a compatible amplification reaction with a simple, highly-integrated efficient design that allows the detection of multiple genomic targets. Two approaches under isothermal conditions are presented: recombinase polymerase amplification (RPA) and multiple displacement amplification (MDA). Both methods were applied to a duplex assay specific for Salmonella spp. and Cronobacter spp., with excellent amplification yields (0.2-8.6 · 10(8) fold). The proposed approaches were successfully compared to conventional PCR and tested for the milk sample analysis as a microarray format on a compact disc (support and driver). Satisfactory results were obtained in terms of resistance to inhibition, selectivity, sensitivity (10(1)-10(2)CFU/mL) and reproducibility (below 12.5%). The methods studied are efficient and cost-effective, with a high potential to automate microorganisms detection by integrated analytical systems working at a constant low temperature.

Gas-phase and particulate products from the atmospheric degradation of the organothiophosphorus insecticide chlorpyrifos-methyl.

The phosphorothioate structure is highly present in several organophosphorus pesticides. However, there is insufficient information about its degradation process after the release to the atmosphere and the secondary pollutants formed. Herein, the atmospheric reaction of chlorpyrifos-methyl (o,o-dimethyl o-(3,5,6-trichloropyridin-2-yl) phosphorothioate), is described for semi-urban or rural locations. The photo-oxidation under low NOx conditions (5-55 ppbV) was reproduced in a large outdoor simulation chamber, observing a rapid degradation (lifetime<3.5 h). The formation of gaseous products and particulate matter (aerosol yield 2-8%) was monitored. The chemical composition of minor products (gaseous and particulate) was studied, identifying 15 multi-oxygenated derivatives. The most abundant products were ring-retaining molecules such as o,o-dimethyl o-(3,5,6-trichloropyridin-2-yl) phosphorothioate, dimethyl 3,5,6-trichloropyridin-2-yl phosphate, o-methyl o-(3,5,6-trichloropyridin-2-yl) hydrogen phosphorothioate, 3,5,6-trichloropyridin-2-yl dihydrogen phosphate, 3,5,6-trichloropyridin-2-ol, and 3,5,6-trichloropyridine-2,4-diol. An atmospheric degradation mechanism has been proposed based on an oxidation started with OH-nucleophilic attack to P=S bond. The results have been extrapolated to other organothiophosphorus molecules, such as malathion, parathion, diazinon and methidathion, among many others, to estimate their photo-oxidative degradation and the expected products.

Gas-phase and particulate products from the atmospheric degradation of an isoxazole fungicide.

The isoxazole structure is present in several pesticides. However, there is a lack of information about its degradation products after the release to the atmosphere. The main atmospheric reactions of hymexazol (5-methylisoxazol-3-ol), selected as representative model, were investigated at a large outdoor simulation chamber. The predominant products of atmospheric degradations were gaseous nitrogen derivates (nitric acid, nitrogen dioxide, nitrogen oxide, nitrous acid, and peroxyacetylnitrate), ozone, and small oxygenated compounds (formic acid, formaldehyde, and methylglyoxal). The aerosol yields were lower than 5%, and an OH rate-dependence was observed in the nucleation, particle growth, and size distribution. Also, the chemical composition of minor multi-oxygenated products was studied for OH-photo-oxidations. More than 20 products were detected in the gas or particulate phase. The most abundant were heterocyclic cleavage products with C4-chain and oxygenated moieties at positions 1 and 3, such as 3,4-dioxobutanoic acid, 3-oxobutanoic acid, and 3-oxobutanal. The suggested reaction pathway is the opening of heterocycle ring by the cleavage of N-O bond and C-N bond, releasing nitrogen oxides.

Immunoradiometric determination of thyroglobulin in serum samples by time calibration transfer.

BACKGROUND: A limitation of isotopic assays is decay of the radioactive signal and the need for a calibration curve in each run. Thus, calibration transfer has been proposed for immunoradiometric analysis (IRMA). The present study was undertaken to establish the main methodological issues applied to the determination of thyroglobulin (Tg). METHODS: Serum samples were analyzed at a different experimental time than Tg standards. Tg concentrations were then determined using a transferred calibration curve estimated from a calibration model based on a three-parameter antigen-antibody interaction model and a decay kinetic constant. RESULTS: A kinetic constant for decay of the radiolabeled antibody signal was calculated (-0.018+/- 0.002 day(-1)). This strategy avoided full recalibration, despite degradation of the radiolabeled immunoreagents or experimental variations. The calibration transfer was validated using addition, dilution and recovery protocols. Repeated analyses of serum samples were performed during the life of the commercial immunoreagents, and concentrations were determined using daily and transferred calibration curves. Results were statistically comparable, but significant reductions in reagent consumption, analysis time, radioactive waste and staff time were obtained. CONCLUSIONS: Transferred curves can be used to analyze samples by IRMA without simultaneous measurement of standards, and provide reliable concentrations. This principle has been demonstrated for Tg determination, but the key issues to extend to other IRMA methods have been established.