Multiplex DNA detection of food allergens on a digital versatile disk

Development of a Novel System Consisting of a Reductase-Like Nanozyme and the Reaction of Resazurin and Ammonia Borane for Sensitive Fluorometric Sensing

We report a novel system consisting of a redox reaction and a highly efficient reductase-like nanozyme, silica-palladium nanoparticles (Pd@SiO2 NPs), as a novel detection platform for fluorometric sensing. In a proof-of-concept demonstration using an oligonucleotide as the detection target, a glass fiber-based sensor is fabricated by covalently conjugating two oligo probes, which are complementary to the adjacent segments of the target oligonucleotide, on Pd@SiO2 NPs and glass fiber, respectively. In the presence of the target oligonucleotide, the two probes are drawn together by the target through sequence-specific hybridization, bringing the Pd@SiO2 NPs to the glass fiber. When the glass fiber is subsequently immersed in a mixture of resazurin and ammonia borane solution, the Pd@SiO2 NPs on the glass fiber trigger the catalytic conversion of resazurin (blue, slightly fluorescent) to resorufin (pink, highly fluorescent) with massive signal amplification, indirectly signaling the presence of the target oligonucleotide. We show that the glass fiber-based fluorometric sensor can detect a target oligonucleotide associated with the BRAF mutation linearly in the concentration range of 20 to 400 pM with a detection limit (LOD) of 15 pM and the specificity to differentiate targets with single-base difference. These results demonstrate a new frontier for the development of a sensitive, specific, and inexpensive nonenzyme-based fluorometric sensing platform as an alternative to conventional enzyme-based assays.

Disposable amperometric biotool for peanut detection in processed foods by targeting a chloroplast DNA marker

This work reports the development and application of a disposable amperometric sensor built on magnetic microcarriers coupled to an Express PCR strategy to amplify a specific DNA fragment of the chloroplast trnH-psbA. The procedure involves the selective capture of a 68-mer synthetic target DNA (or unmodified PCR products) through sandwich hybridization with RNA capture probe-modified streptavidin MBs and RNA signaling probes, labeled using antibodies specific to the heteroduplexes and secondary antibodies tagged with horseradish peroxidase. Amperometric measurements were performed on screen-printed electrodes using the H2O2/hydroquinone system. Achieving a LOD of 3 pM for the synthetic target, it was possible to detect 2.5 pg of peanut DNA and around 10 mg kg-1 of peanut in binary mixtures (defatted peanut flours prepared in spelt wheat). However, the detectability decreased between 10 and 1000 times in processed samples depending on the treatment. The Express PCR-bioplatform was applied to the detection of peanut traces in foodstuff.

Progress and Challenge of Sensors for Dairy Food Safety Monitoring

One of the most consumed foods is milk and milk products, and guaranteeing the suitability of these products is one of the major concerns in our society. This has led to the development of numerous sensors to enhance quality controls in the food chain. However, this is not a simple task, because it is necessary to establish the parameters to be analyzed and often, not only one compound is responsible for food contamination or degradation. To attempt to address this problem, a multiplex analysis together with a non-directed (e.g., general parameters such as pH) analysis are the most relevant alternatives to identifying the safety of dairy food. In recent years, the use of new technologies in the development of devices/platforms with optical or electrochemical signals has accelerated and intensified the pursuit of systems that provide a simple, rapid, cost-effective, and/or multiparametric response to the presence of contaminants, markers of various diseases, and/or indicators of safety levels. However, achieving the simultaneous determination of two or more analytes in situ, in a single measurement, and in real time, using only one working 'real sensor', remains one of the most daunting challenges, primarily due to the complexity of the sample matrix. To address these requirements, different approaches have been explored. The state of the art on food safety sensors will be summarized in this review including optical, electrochemical, and other sensor-based detection methods such as magnetoelastic or mass-based sensors.

A smartphone-integrated portable rotating platform for estimation of concentration level of plasma-creatinine using whole human blood

The measurement of creatinine concentration is performed to monitor the renal health. The devices available in modern clinical laboratories for measuring creatinine concentration are accurate and provide results rapidly but may be prohibitively expensive for resource-poor settings. Therefore, developing an inexpensive yet accurate device for measuring creatinine concentration is needed. Consequently, we developed a simple, affordable, and portable spinning disc for measuring plasma-creatinine concentration with 10 μL of whole human blood. 5 μL of the alkaline picrate solution is loaded into the device and rotated at 1000 rpm to transport this solution to the periphery of the microchannel. Further, 10 μL whole blood is loaded in the same channel and spun at 1300 rpm for 10 min. The creatinine in plasma reacts with alkaline picrate (Jaffe reaction), and the color of the mixture changes to yellow-orange color. The resulting color is captured with a smartphone, and creatinine concentration is estimated using an in-house developed app (CREA-SESE). The value of creatinine measured with the present device and the gold standard device are highly correlated (R² = 0.998). The bias and standard deviation of the difference between the two measurements are 0.134 mg/dL and 0.143 mg/dL. This study demonstrates the feasibility of a simple, inexpensive, and portable rotating device for measuring creatinine concentration using 10 μL of whole human blood, which can easily be deployed to the underserved population in resource-constrained settings to monitor renal diseases.

Development of Multiplex PCR Coupled DNA Chip Technology for Assessment of Endogenous and Exogenous Allergens in GM Soybean

Allergenicity assessment of transgenic plants and foods is important for food safety, labeling regulations, and health protection. The aim of this study was to develop an effective multi-allergen diagnostic approach for transgenic soybean assessment. For this purpose, multiplex polymerase chain reaction (PCR) coupled with DNA chip technology was employed. The study was focused on the herbicide-resistant Roundup Ready soya (RRS) using a set of certified reference materials consisting of 0, 0.1%, 0.5%, and 10% RRS. Technically, the procedure included design of PCR primers and probes; genomic DNA extraction; development of uniplex and multiplex PCR systems; DNA analysis by agarose gel electrophoresis; microarray development, hybridization, and scanning. The use of the asymmetric multiplex PCR method is shown to be very efficient for DNA hybridization with biochip probes. We demonstrate that newly developed fourplex PCR methods coupled with DNA-biochips enable simultaneous identification of three major endogenous allergens, namely, Gly m Bd 28K, Gly m Bd 30K, and lectin, as well as exogenous 5-enolppyruvyl shikimate-phosphate synthase (epsps) expressed in herbicide-resistant roundup ready GMOs. The approach developed in this study can be used for accurate, cheap, and fast testing of food allergens.

Whey allergens: Influence of nonthermal processing treatments and their detection methods

Whey and its components are recognized as value-added ingredients in infant formulas, beverages, sports nutritious foods, and other food products. Whey offers opportunities for the food industrial sector to develop functional foods with potential health benefits due to its unique physiological and functional attributes. Despite all the above importance, the consumption of whey protein (WP) can trigger hypersensitive reactions and is a constant threat for sensitive individuals. Although avoiding such food products is the most successful approach, there is still a chance of incorrect labeling and cross-contamination during food processing. As whey allergens in food products are cross-reactive, the phenomenon of homologous milk proteins of various species may escalate to a more serious problem. In this review, nonthermal processing technologies used to prevent and eliminate WP allergies are presented and discussed in detail. These processing technologies can either enhance or mitigate the impact of potential allergenicity. Therefore, the development of highly precise analytical technologies to detect and quantify the existence of whey allergens is of considerable importance. The present review is an attempt to cover all the updated approaches used for the detection of whey allergens in processed food products. Immunological and DNA-based assays are generally used for detecting allergenic proteins in processed food products. In addition, mass spectrometry is also employed as a preliminary technique for detection. We also highlighted the latest improvements in allergen detection toward biosensing strategies particularly immunosensors and aptasensors.

Are current analytical methods suitable to verify VITAL® 2.0/3.0 allergen reference doses for EU allergens in foods?

Food allergy affects up to 6% of Europeans. Allergen identification is important for the risk assessment and management of the inadvertent presence of allergens in foods. The VITAL® initiative for voluntary incidental trace allergen labeling suggests protein reference doses, based on clinical reactivity in food challenge studies, at or below which voluntary labelling is unnecessary. Here, we investigated if current analytical methodology could verify the published VITAL® 2.0 doses, that were available during this analysis, in serving sizes between 5 and 500 g. Available data on published and commercial ELISA, PCR and mass spectrometry methods, especially for the detection of peanuts, soy, hazelnut, wheat, cow's milk and hen's egg were reviewed in detail. Limit of detection, quantitative capability, matrix compatibility, and specificity were assessed. Implications by the recently published VITAL® 3.0 doses were also considered. We conclude that available analytical methods are capable of reasonably robust detection of peanut, soy, hazelnut and wheat allergens for levels at or below the VITAL® 2.0 and also 3.0 doses, with some methods even capable of achieving this in a large 500 g serving size. Cow's milk and hen's egg are more problematic, largely due to matrix/processing incompatibility. An unmet need remains for harmonized reporting units, available reference materials, and method ring-trials to enable validation and the provision of comparable measurement results.

Application of real-time PCR for tree nut allergen detection in processed foods

Currently, food allergies are an important health concern worldwide. The presence of undeclared allergenic ingredients or the presence of traces of allergens due to accidental contamination during food processing poses a great health risk to sensitized individuals. Therefore, reliable analytical methods are required to detect and identify allergenic ingredients in food products. Real-time PCR allowed a specific and accurate amplification of allergen sequences. Some processing methods could induce the fragmentation and/or degradation of genomic DNA and some studies have been performed to analyze the effect of processing on the detection of different targets, as thermal treatment, with and without applying pressure. In this review, we give an updated overview of the applications of real-time PCR for the detection of allergens of tree nut in processed food products. The different variables that contribute to the performance of PCR methodology for allergen detection are also review and discussed.

Sub-femtomolar detection of DNA and discrimination of mutant strands using microwell-array assisted digital enzyme-linked oligonucleotide assay

Detection methods that do not rely on the amplification of DNA but can reach sensitivity, specificity and throughput of gold standard methods, such as qPCR, have been extensively explored in recent years. Here, we present a hydrophilic-in-hydrophobic (HIH)-microwell array platform that empowers a panel of different amplification-free DNA bioassays: digital enzyme-linked oligonucleotide assay (ELONA), ligation-assisted (LA) digital ELONA and so-called 'analog' bioassays. We developed all three bioassays by using magnetic beads for capturing DNA target, followed by hybridization of enzyme-labelled detection probes and sealing of the built complexes into the femtoliter HIH microwells to achieve the fluorescent readout of single DNA molecules. With the optimized digital ELONA bioassay, we successfully detected 97 and 200 nt-long ssDNA molecules down to 68 and 92 aM, respectively, demonstrating extremely high sensitivity of the bioassay and its flexibility towards targets of different lengths. Importantly, we also proved that the same bioassay concept was suited to detect substantially higher concentrations of ssDNA (up to picomolar levels) by quantifying the total fluorescent intensity rather than counting fluorescent events for digital quantification. Finally, we advanced this concept towards LA digital ELONA capable of differentiating wildtype strands from those carrying single-point mutations even when the former were constituting only 1% of the DNA mixture and were present at 2 fM concentration. In conclusion, the developed platform showed remarkably high sensitivity, specificity and versatility for amplification-free detection of DNA and as such can be valuable for numerous applications in medical diagnostics, gene analysis, food safety and environmental monitoring.

Recent Advances in the Detection of Allergens in Foods

Food allergy is a public health issue that has significantly increased worldwide in the past decade affecting consumers' quality of life and making increasing demands on health service resources. Despite recent advances in many areas of diagnosis and treatment, our general knowledge of the basic mechanisms of the disease remained limited, i.e., not at pace with the exponential number of new cases and the explosion of the new technologies. For sensitized individuals, the only effective way to prevent allergic reactions is the strict avoidance of the offending food. For this reason, a number of regulatory bodies in several countries have recognized the importance of providing information about the presence of food allergens by enacting laws, regulations, or standards for food labeling of "priority allergens." This has resulted in the need for the development of analytical methods for protection of food-allergic consumers that should be among others highly specific, sensitive, and not influenced by the presence of the food matrix components. Several analytical approaches target either the allergen itself or a corresponding allergen marker such as peptide fragment or gene segment and have been used in the detection and quantification of allergens in food products. In this short review, some of the conventional and new methods for the detection of allergens in food are listed and briefly discussed.

Real-time loop-mediated isothermal DNA amplification in compact disc micro-reactors

An integrated device composed of micro-reactors embedded onto compact discs is proposed for real-time targeted DNA determination. The method principle is based on in-disc loop-mediated isothermal amplification (iD-LAMP) and quantitative optical read-out by a disc drive. In the presence of a target, the turbidimetric or colorimetric properties of reaction solution change, and the transmitted intensity of the disc drive laser modifies according to reaction yield. Monitoring real-time curves allowed the quantitative determination of DNA template amounts. The best amplification/detection results were obtained with micro-reactors (2mm diameter and 1.1mm in depth) drilled on a digital video disc (DVD) and detection based on the colorimetric mode. As proof-of-concept, the assay was applied to detect pathogenic bacteria Salmonella spp. and to identify bovine meat in food samples. Ninety-six samples were simultaneously analysed in 15 min, with high selectivity and sensitivity (5 CFU/mL and 10 µg/g for bacteria and meat, respectively). The in-disc results were comparable to those obtained by conventional LAMP or qPCR approaches. The developed device allows low sample and reagent consumption (3 µL of reaction), portability, ease-of-use, and rapid low-cost high-throughput analyses.

Isothermal solid-phase recombinase polymerase amplification on microfluidic digital versatile discs (DVDs)

The proposed device, for massive DNA-based screening in limited-resource settings, comprises a centrifugal platform to perform isothermal solid-phase amplification in microarray format and a digital versatile disc drive to read the results.

Toward point-of-care diagnostics with consumer electronic devices: the expanding role of nanoparticles

A review of the role that nanoparticles can play in point-of-care diagnostics that utilize consumer electronic devices such as cell phones and smartphones for readout, including an overview of important concepts and examples from the literature.

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.

DVD technology-based molecular diagnosis platform: quantitative pregnancy test on a disc

A diagnosis platform based entirely on DVD technology was developed for on-site quantitation of molecular analytes of interest, e.g., human chorionic gonadotropin (hCG) in urine samples ("quantitative pregnancy test on a disc"). An hCG-specific monoclonal antibody-binding assay prepared on a regular DVD-R was labeled with nanogold-streptavidin conjugates for signal enhancement with a customized silver-staining protocol. An unmodified, conventional computer optical drive was used for assay reading, and free disc-quality analysis software for data processing. The performance (sensitivity and selectivity) of this DVD assay is comparable to that of well-established colorimetric methods (determination of optical darkness ratios) and standard enzyme-linked immunosorbent assays (ELISA). As validated by examining its linear correlation with the ELISA results on the same set of samples, the DVD assay promises to be a low-cost, multiplex, point-of-care (POC) diagnostic tool for physicians and even for individuals at home, producing prompt results.

Simultaneous detection of RNA and DNA targets based on multiplex isothermal amplification

The detection of pathogenic microorganisms present in food, feed, plant, and other samples is important for providing safe food as well as for preventing the spread of microbes. The genome of pathogens is made of DNA or RNA, therefore a multiplex diagnostics tool would ideally be able to amplify and detect both RNA and DNA targets in parallel. With this goal we have developed an isothermal nucleic acid sequence based amplification [NASBA] implemented microarray analysis (NAIMA) procedure, suitable for the simultaneous multiplex amplification of RNA and DNA targets, coupled with the detection on ArrayTubes. The method is demonstrated to be very sensitive and specific for the detection of two economically important quarantine plant pathogens of potato, the potato spindle tuber viroid (RNA target) and Ralstonia solanacearum (DNA target). Because of its isothermal amplification and simple detection equipment, the method is also applicable for on-site analyses. NAIMA can be used in any domain where there is the need to detect RNA and DNA targets simultaneously.

Analysis to support allergen risk management: Which way to go?

Food allergy represents an important food safety issue because of the potential lethal effects; the only effective treatment is the complete removal of the allergen involved from the diet. However, due to the growing complexity of food formulations and food processing, foods may be unintentionally contaminated via allergen-containing ingredients or cross-contamination. This affects not only consumers' well-being but also food producers and competent authorities involved in inspecting and auditing food companies. To address these issues, the food industry and control agencies rely on available analytical methods to quantify the amount of a particular allergic commodity in a food and thus to decide upon its safety. However, no "gold standard methods" exist for the quantitative detection of food allergens. Nowadays mostly receptor-based methods and in particular commercial kits are used in routine analysis. However, upon evaluation of their performances, commercial assays proved often to be unreliable in processed foods, attributed to the chemical changes in proteins that affect the molecular recognition with the receptor used. Unfortunately, the analytical outcome of other methods, among which are chromatographic combined with mass spectrometric techniques as well as DNA-based methods, seem to be affected in a comparable way by food processing. Several strategies can be employed to improve the quantitative analysis of allergens in foods. Nevertheless, issues related to extractability and matrix effects remain a permanent challenge. In view of the presented results, it is clear that the food industry needs to continue to make extra efforts to provide accurate labeling and to reduce the contamination with allergens to an acceptable level through the use of allergen risk management on a company level, which needs to be supported inevitably by a tailor-validated extraction and detection method.

Reading disc-based bioassays with standard computer drives

Traditional methods of disease diagnosis are both time-consuming and labor-intensive, and many tests require expensive instrumentation and trained professionals, which restricts their use to biomedical laboratories. Because patients can wait several days (even weeks) for the results, the consequences of delayed treatment could be disastrous. Therefore, affordable and simple point-of-care (POC) biosensor devices could fill a diagnostic niche in the clinic or even at home, as personal glucose meters do for diabetics. These devices would allow patients to check their own health conditions and enable physicians to make prompt treatment decisions, which could improve the chances for rapid recovery and cure. Compact discs (CDs) provide inexpensive substrate materials for the preparation of microarray biochips, and conventional computer drives/disc players can be adapted as precise optical reading devices for signal processing. Researchers can employ the polycarbonate (PC) base of a CD as an alternative substrate to glass slides or silicon wafers for the preparation of microanalytical devices. Using the characteristic optical phenomena occurring on the metal layer of a CD, researchers can develop biosensors based on advanced spectroscopic readout (interferometry or surface plasmon resonance). If researchers integrate microfluidic functions with CD mechanics, they can control fluid transfer through the spinning motion of the disc, leading to "lab-on-a-CD" devices. Over the last decade, our laboratory has focused on the construction of POC biosensor devices from off-the-shelf CDs or DVDs and standard computer drives. Besides the initial studies of the suitability of CDs for surface and materials chemistry research (fabrication of self-assembled monolayers and oxide nanostructures), we have demonstrated that an ordinary optical drive, without modification of either the hardware or the software driver, can function as the signal transducing element for reading disc-based bioassays quantitatively. In this Account, we first provide a brief introduction to CD-related materials chemistry and microfluidics research. Then we describe the mild chemistry developed in our laboratory for the preparation of computer-readable biomolecular screening assays: photochemical activation of the polycarbonate (PC) disc surface and immobilization and delivery of probe and target biomolecules. We thoroughly discuss the analysis of the molecular recognition events: researchers can "read" these devices quantitatively with an unmodified optical drive of any personal computer. Finally, and critically, we illustrate our digitized molecular diagnosis approach with three trial systems: DNA hybridization, antibody-antigen binding, and ultrasensitive lead detection with a DNAzyme assay. These examples demonstrate the broad potential of this new analytical/diagnostic tool for medical screening, on-site food/water safety testing, and remote environmental monitoring.

Detection of food-borne pathogens with DNA arrays on disk

A DNA oligonucleotide array for duplex pathogen detection on a DVD platform is developed. The assay involves hybridization of PCR products and optical detection using compact disc technology. Different DNA array constructions for attachment of synthetic oligonucleotides on to DVD surface are evaluated, finding that streptavidin-biotin coupling method yielded the highest sensitivity in combination with enzymatic signal amplification. Issues of importance for the DNA array construction such immobilized probes design, PCR product labeling strategy and composition of the hybridization buffer were addressed. The methodology was proved scoring single nucleotide polymorphisms with high selectivity. The assay capability was also demonstrated by the identification of two pathogenic microorganisms in powder milk samples. In fifty minutes, the DVD-array system identifies Salmonella spp. and Cronobacter spp. (previously named Enterobacter sakazakii) precise and simultaneously with a sensitivity of 10(0) and 10(2) cfu/mL, respectively, in infant milk. Results were in good agreement with those obtained by quantitative real-time PCR.