Development and Evaluation of a Real-Time PCR Multiplex Assay for the Detection of Allergenic Peanut Using Chloroplast DNA Markers

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.

Rapid and Simultaneous Authentication of Six Laver Species Using Capillary Electrophoresis-Based Multiplex PCR

Lavers are typically consumed in dried or seasoned forms. However, commercially processed lavers can lead to seafood fraud because it is impossible to authenticate the original species based on morphological characteristics alone. In this study, we developed a capillary electrophoresis-based multiplex polymerase chain reaction (PCR) to authenticate six different laver species. The species-specific primer sets to target the chloroplast rbcL or rbcS genes were newly designed. We successfully established both singleplex and multiplex conditions, which resulted in specific amplicons for each species (N. dentata, 274 bp; N. yezoensis, 211 bp; N. seriata, 195 bp; N. tenera, 169 bp; N. haitanensis, 127 bp; P. suborbiculata, 117 bp). Moreover, the assays were sensitive enough to detect DNA ranging from 10 to 0.1 pg of DNA. The optimized capillary electrophoresis-based multiplex PCR was successfully applied to 40 commercial laver products. In addition to detecting the laver species as stated on the commercial label, the assay discovered cases where less expensive species were mixed in. With its advantageous properties, such as short amplicon size, high specificity, and superior sensitivity, this assay could be used for the authentication of the six laver species.

Optimised multiplex droplet digital PCR is more precise, but not more sensitive, than real-time PCR for the detection of allergenic peanut

The United States requires labelling of food products containing major allergens, such as peanut, through the Food Allergen Labeling and Consumer Protection Act. Accurate labelling requires sensitive, specific and robust detection methods, and PCR-based techniques have proven highly effective. This article describes the transition of a previously developed multiplex real-time PCR assay for allergenic peanut to a droplet digital PCR format. The triplex droplet digital PCR assay was developed in a probe mixing format and directly compared to the established real-time PCR assay. Data are provided for thorough optimisation in the digital format, including the effects of primer and probe concentration, cycle number and annealing/extension time. Optimisation parameters influenced relative location and separation of droplet clusters but not final copy number. The droplet digital PCR assay was linear over five orders of magnitude; its lower limit of detection was 0.05 pg DNA per reaction, more sensitive than published digital PCR allergen assays. It was more precise, but not more sensitive, than the previously established real-time PCR assay.

An Ultrasensitive Silicon-Based Electrolyte-Gated Transistor for the Detection of Peanut Allergens

The highly sensitive detection of peanut allergens (PAs) using silicon-based electrolyte-gated transistors (Si-EGTs) was demonstrated. The Si-EGT was made using a top-down technique. The fabricated Si-EGT showed excellent intrinsic electrical characteristics, including a low threshold voltage of 0.7 V, low subthreshold swing of <70 mV/dec, and low gate leakage of <10 pA. Surface functionalization and immobilization of antibodies were performed for the selective detection of PAs. The voltage-related sensitivity (S_V) showed a constant behavior from the subthreshold regime to the linear regime. The current-related sensitivity (S_I) was high in the subthreshold regime and then significantly decreased as the drain current increased. The limit of detection (LOD) was calculated to be as low as 25 pg/mL based on S_I characteristics, which is the lowest value reported to date in the literature for various sensor methodologies. The Si-EGT showed selective detection of PA through a non-specific control test. These results confirm that Si-EGT is a high-sensitivity and low-power biosensor for PA detection.

Reference-free discovery of nuclear SNPs permits accurate, sensitive identification of Carya (hickory) species and hybrids

PREMISE

DNA-based species identification is critical when morphological identification is restricted, but DNA-based identification pipelines typically rely on the ability to compare homologous sequence data across species. Because many clades lack robust genomic resources, we present here a bioinformatics pipeline capable of generating genome-wide single-nucleotide polymorphism (SNP) data while circumventing the need for any reference genome or annotation data.

METHODS

Using the SISRS bioinformatics pipeline, we generated de novo ortholog data for the genus Carya, isolating sites where genetic variation was restricted to a single Carya species (i.e., species-informative SNPs). We leveraged these SNPs to identify both full-species and hybrid Carya specimens, even at very low sequencing depths.

RESULTS

We identified between 46,000 and 476,000 species-identifying SNPs for each of eight diploid Carya species, and all species identifications were concordant with the species of record. For all putative F1 hybrid specimens, both parental species were correctly identified in all cases, and more punctate patterns of introgression were detectable in more cryptic crosses.

DISCUSSION

Bioinformatics pipelines that use only short-read sequencing data provide vital new tools enabling rapid expansion of DNA identification assays for model and non-model clades alike.

Detection of Peanut Allergen by Real-Time PCR: Looking for a Suitable Detection Marker as Affected by Processing

Peanut (Arachis hypogaea) contains allergenic proteins, which make it harmful to the sensitised population. The presence of peanut in foods must be indicated on label, to prevent accidental consumption by allergic population. In this work, we use chloroplast markers for specific detection of peanut by real-time PCR (Polymerase Chain Reaction), in order to increase the assay sensitivity. Binary mixtures of raw and processed peanut flour in wheat were performed at concentrations ranging from 100,000 to 0.1 mg/kg. DNA isolation from peanut, mixtures, and other legumes was carried out following three protocols for obtaining genomic and chloroplast-enrich DNA. Quantity and quality of DNA were evaluated, obtaining better results for protocol 2. Specificity and sensitivity of the method has been assayed with specific primers for three chloroplast markers (mat k, rpl16, and trnH-psbA) and Ara h 6 peanut allergen-coding region was selected as nuclear low-copy target and TaqMan probes. Efficiency and linear correlation of calibration curves were within the adequate ranges. Mat k chloroplast marker yielded the most sensitive and efficient detection for peanut. Moreover, detection of mat K in binary mixtures of processed samples was possible for up to 10 mg/kg even after boiling, and autoclave 121 °C 15 min, with acceptable efficiency and linear correlation. Applicability of the method has been assayed in several commercial food products.

HPLC-UV, Metabarcoding and Genome Skims of Botanical Dietary Supplements: A Case Study in Echinacea

The use of DNA-based methods to authenticate botanical dietary supplements has been vigorously debated for a variety of reasons. More comparisons of DNA-based and chemical methods are needed, and concordant evaluation of orthogonal approaches on the same products will provide data to better understand the strengths and weaknesses of both approaches. The overall application of DNA-based methods is already firmly integrated into a wide array of continually modernizing stand alone and complementary authentication protocols. Recently, the use of full-length chloroplast genome sequences provided enhanced discriminatory capacity for closely related species of Echinacea compared to traditional DNA barcoding approaches (matK and rbcL). Here, two next-generation sequencing approaches were used: (1) genome skimming and (2) PCR amplicon (metabarcoding). The two genetic approaches were then combined with HPLC-UV to evaluate 20 commercially available dietary supplements of Echinacea representing "finished" products. The trade-offs involved in different DNA approaches were discussed, with a focus on how DNA methods support existing, accepted chemical methods. In most of the products (19/20), HPLC-UV suggested the presence of Echinacea spp. While metabarcoding was not useful with this genus and instead only resolved 7 products to the family level, genome skimming was able to resolve to species (9) or genus (1) with the 10/20 products where it was successful. Additional ingredients that HPLC-UV was unable to identify were also found in four products along with the relative sequence proportion of the constituents. Additionally, genome skimming was able to identify one product that was a different Echinacea species entirely.

Visible on-site detection of Ara h 1 by the switchable-linker-mediated precipitation of gold nanoparticles

Biosensors have been widely applied in tests for allergens, but on-site detection remains a challenge. Herein, we proposed a detection procedure for peanut Ara h 1 as a representative allergen, which was extracted from a cookie, thereby minimising the need for any complex pretreatment that was difficult to perform, and enabling the visual detection of the target without the use of analytical equipment. The extraction procedure was performed in less than 30 min using a syringe and filter (0.45 μm). The detection method for Ara h 1 was based on the aggregation of switchable linkers (SL) and gold nanoparticles (AuNP), and the presence of 0.19 mg peanut protein per 30 g of cookie could be confirmed within 30 min based on the AuNP/SL concentration ratio by the precipitation. This proposed procedure could be successfully applied to the detection of a wide range of food allergens.

Suitability of DNA Sequencing Tools for Identifying Edible Seaweeds Sold in the United States

Seaweeds have been consumed by billions of people around the world and are increasingly popular in United States (US) diets. Some seaweed species have been associated with adverse health effects-such as heavy metal toxicity-and higher priced seaweeds may be more prone to adulteration. Knowing which species of seaweeds are being marketed in the US is important for protecting human health and preventing economic adulteration. Therefore, the United States Food and Drug Administration is developing new DNA-based species identification tools to complement established chemical methods for verifying the accurate labeling of products. Here, seaweed products available in the United States were surveyed using a tiered approach to evaluate a variety of DNA extraction techniques followed by traditional DNA barcoding via Sanger sequencing; if needed, genome skimming of total extracted nuclear DNA via next-generation sequencing was performed. This two-tiered approach of DNA barcoding and genome skimming could identify most seaweed samples (41/46), even those in blends (2/2, 1 out of 3 labeled species in each). Only two commercial samples appeared to be mislabeled or to contain unintended algal species. Five samples, labeled as "hijiki" or "arame", could not be confirmed by these DNA-based identification methods.

A Systematic Review of Food Allergy: Nanobiosensor and Food Allergen Detection

Several individuals will experience accidental exposure to an allergen. In this sense, the industry has invested in the processes of removing allergenic compounds in food. However, accidental exposure to allergenic proteins can result from allergenic substances not specified on labels. Analysis of allergenic foods is involved in methods based on immunological, genetic, and mass spectrometry. The traditional methods have some limitations, such as high cost. In recent years, biosensor and nanoparticles combined have emerged as sensitive, selective, low-cost, and time-consuming techniques that can replace classic techniques. Nevertheless, each nanomaterial has shown a different potential to specific allergens or classes. This review used Preferred Reporting Items for Systematic Reviews and the Meta-Analysis guidelines (PRISMA) to approach these issues. A total of 104 articles were retrieved from a standardized search on three databases (PubMed, Scopus and Web of Science). The systematic review article is organized by the category of allergen detection and nanoparticle detection. This review addresses the relevant biosensors and nanoparticles as gold, carbon, graphene, quantum dots to allergen protein detection. Among the selected articles it was possible to notice a greater potential application on the allergic proteins Ah, in peanuts and gold nanoparticle-base as a biosensor. We envision that in our review, the association between biosensor and nanoparticles has shown promise in the analysis of allergenic proteins present in different food samples.

Development and Validation of a Real-Time PCR Based Assay to Detect Adulteration with Corn in Commercial Turmeric Powder Products

Turmeric, or Curcuma longa, is commonly consumed in the South East Asian countries as a medical product and as food due to its therapeutic properties. However, with increasing demand for turmeric powder, adulterated turmeric powders mixed with other cheap starch powders, such as from corn or cassava, are being distributed by food suppliers for economic benefit. Here, we developed molecular markers using quantitative real-time PCR to identify adulteration in commercial turmeric powder products. Chloroplast genes, such as matK, atpF, and ycf2, were used to design species-specific primers for C. longa and Zea mays. Of the six primer pairs designed and tested, the correlation coefficients (R²) were higher than 0.99 and slopes were -3.136 to -3.498. The efficiency of the primers was between 93.14 and 108.4%. The specificity of the primers was confirmed with ten other species, which could be intentionally added to C. longa powders or used as ingredients in complex turmeric foods. In total, 20 blind samples and 10 commercial C. longa food products were tested with the designed primer sets to demonstrate the effectiveness of this approach to detect the addition of Z. mays products in turmeric powders. Taken together, the real-time PCR assay developed here has the potential to contribute to food safety and the protection of consumer's rights.

Heptaplex Polymerase Chain Reaction Assay for the Simultaneous Detection of Beef, Buffalo, Chicken, Cat, Dog, Pork, and Fish in Raw and Heat-Treated Food Products

Species authentication of meat and fish products is crucial to safeguard public health, economic investment, and religious sanctity. We developed a heptaplex polymerase chain reaction assay targeting short amplicon length (73-198 bp) for the simultaneous detection and differentiation of cow, buffalo, chicken, cat, dog, pig, and fish species in raw and processed food using species-specific primers targeting mitochondrial cytb, ND5, and 16s rRNA genes. Assay validation of adulterated and various heat-treated meatball matrices showed excellent stability and sensitivity under all processing conditions. The detection limit was 0.01-0.001 ng of DNA under pure states and 0.5% meat in meatball products. Buffalo was detected in 86.7% (13 out of 15) of tested commercial beef products, while chicken, pork, and fish products were found to be pure. The developed assay was efficient enough to detect target species simultaneously, even in highly degraded and processed food products at reduced time.