Evaluation of DNA extraction procedures for traceability of various tomato products

Extraction, Purification, and Characterization of Olive (Olea europaea L., cv. Chemlal) Polyphenol Oxidase

Among fruits susceptible to enzymatic browning, olive polyphenol oxidase (OePPO) stood out as being unisolated from a natural source until this study, wherein we successfully purified and characterized the enzyme. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of heated and nonheated OePPO revealed distinct molecular weights of 35 and 54 kDa, respectively, indicative of its oligomeric nature comprising active and C-terminal subunits. OePPO displayed latency, fully activating with 5 mM SDS under optimal conditions of pH 7.5 and 15 °C. The enzyme demonstrated monophenolase activity and showcased the highest efficiency toward hydroxytyrosol. Despite its low optimal temperature, OePPO exhibited high thermal resistance, maintaining stability up to 90 °C. However, beyond this threshold, the oligomeric enzyme disassociated, yielding a denatured main subunit and C-terminal fragments. Six OePPO genes were found in the fruits. Tryptic digestion identified the enzyme as mature OePPO1 (INSDC OY733096), while mass spectrometry detected the active form mass alongside several C-terminal fragments, revealing potential cleavage sites (Gly407, Tyr408).

Honey Quality Control: Review of Methodologies for Determining Entomological Origin

Honey is a widely consumed natural product, and its entomological origin can significantly influence its market value. Therefore, traceability of the entomological origin of honey should also be considered in honey quality control protocols. Although several methods exist, such as physicochemical characterization and bioactivity profiling of honey of different entomological origins, the most promising three methods for entomological authentication of honey include protein-based identification, chemical profiling, and a DNA-based method. All of these methods can be applied for reliable identification of the entomological origin of honey. However, as the honey is a complex matrix, the inconsistency of the results obtained by these methods is a pragmatic challenge, and therefore, the use of each method in all the cases is questionable. Most of these methodologies can be used for authentication of newly harvested honey and it is worth understanding the possibility of using these methods for authentication of relatively old samples. Most probably, using DNA-based methods targeting small fragments of DNA can provide the best result in old samples, however, the species-specific primers targeting short fragments are limited and not available for all species. Therefore, using universal primers in combination with a DNA metabarcoding approach can be a good solution that requires further investigation. This present article describes the applications of different methods, their pros, and their cons to identify honey based on entomological origin.

Optimum DNA Extraction Methods for Edible Bird's Nest Identification Using Simple Additive Weighting Technique

A simple additive weighting (SAW) technique was used to determine and compare the overall performance of five DNA extraction methods from conventional (SDS method) to commercial kits (Qiagen, Wizard, and NucleoSpin) for identifying origins of edible bird’s nest (EBN) using end-point polymerase chain reaction (PCR). A hybrid method (SDS/Qiagen) which has been developed by combining the conventional SDS method with commercialised Qiagen was determined as the most suitable in terms of speed and cost-effectiveness. The determination of optimum extraction method was by the performances on efficiency and feasibility, extracted DNA concentration, purity, PCR amplifiability, handling time and safety of reagents used. The hybrid SDS/Qiagen method is less costly compared to the commercial kits and offered a more rapid alternative to the conventional SDS method with significant improvement in the yield, purity and PCR amplifiability. The developed hybrid SDS/Qiagen method provides a more practical alternative over the lengthy process using conventional method and expensive process using commercial kits. Using the simple additive weighting (SAW) technique and analysis, the Qiagen method is considered the most efficient and feasible method without consideration of cost as it yielded the purest extracted DNA and achieved the highest PCR amplifiability with the shortest turnaround time.

Biodegradable Food Packaging Materials and Prospects of the Fourth Industrial Revolution for Tomato Fruit and Product Handling

The environment and food safety are major areas of concern influencing the development of biodegradable packaging for partial replacement of petrochemical-based polymers. This review is aimed at updating the recent advances in biodegradable packaging material and the role of virtual technology and nanotechnology in the tomato supply chain. Some of the common biodegradable materials are gelatin, starch, chitosan, cellulose, and polylactic acid. The tensile strength, tear resistance, permeability, degradability, and solubility are some of the properties defining the selection and utilization of food packaging materials. Biodegradable films can be degraded in soil by microbial enzymatic actions and bioassimilation. Nanoparticles are incorporated into blended films to improve the performance of packaging materials. The prospects of the fourth industrial revolution can be realized with the use of virtual platforms such as sensor systems in authentification and traceability of food and packaging products. There is a research gap on the development of a hybrid sensor system unit that can integrate sampling headspace (SHS), detection unit, and data processing of big data for heterogeneous tomato-derived volatiles. Principal component analysis (PCA), linear discriminant analysis (LDA), and artificial neutral network (ANN) are some of the common mathematical models for data interpretation of sensor systems.

A Comparative Study of Some Procedures for Isolation of Fruit DNA of Sufficient Quality for PCR-Based Assays

Food fraud has been and still is a problem in the food industry. It is detectable by several approaches, such as high performance liquid chromatography (HPLC), chemometric assays, or DNA-based techniques, each with its own drawbacks. This work addresses one major drawback of DNA-based methods, in particular their sensitivity to inhibitors contained in particular matrices from which DNA is isolated. We tested five commercial kits and one in-house method characterized by different ways of sample homogenization and DNA capture and purification. Using these methods, DNA was isolated from 10 different fruit species commonly used in plant-based foodstuffs. The quality of the DNA was evaluated by UV-VIS spectrophotometry. Two types of qPCR assays were used for DNA quality testing: (i) Method specific for plant ITS2 region, (ii) methods specific for individual fruit species. Based mainly on the results of real-time PCR assays, we were able to find two column-based kits and one magnetic carrier-based kit, which consistently provided fruit DNA isolates of sufficient quality for PCR-based assays useful for routine analysis and identification of individual fruit species in food products.

Traceability of fruits and vegetables

Food safety and traceability are nowadays a constant concern for consumers, and indeed for all actors in the food chain, including those involved in the fruit and vegetable sector. For the EU, the principles and legal requirements of traceability are set out in Regulation 178/2002. Currently however the regulation does not describe any analytical traceability tools. Furthermore, traceability systems for fruits and vegetables face increasing competition due to market globalization. The current challenge for actors in this sector is therefore to be sufficiently competitive in terms of price, traceability, quality and safety to avoid scandal and fraud. For all these reasons, new, flexible, cheap and efficient traceability tools, as isotopic analysis, DNA fingerprinting and metabolomic profiling coupled with chemometrics are needed.

Analysis of Microsatellites (SSRs) in Processed Olives as a Means of Cultivar Traceability and Authentication

Select cultivars of table olives have more desirable traits and a higher economic value. There are suspected issues with cultivar mislabeling and traceability in the supply chain. Here, we describe a method to identify cultivars by genotyping of processed olives. DNA was extracted from leaves and California-style olives of seven commonly packed cultivars. Processed olive fruits yielded relatively low DNA concentrations (0.04-0.86 μg/g), and extracts had more impurities compared with leaves. From 15 candidate SSRs, five markers showing the highest number of unique allele combinations and discriminatory power were selected. These SSRs were successfully amplified and analyzed in all cultivars of olives except one. When directly comparing any two cultivars, different allele combinations were typically present for at least four of the five SSRs. Microsatellite analysis shows potential as a simple yet robust diagnostic tool. The method can be expanded to include other cultivars, styles of table olives, and potentially other processed plant-based foods.

Exploiting formalin-preserved fish specimens for resources of DNA barcoding

With the development of the DNA barcoding project, a large number of specimens are required to establish the library of reference barcode. Formalin-fixed samples from museums provide a potential resource for it. However, recovery of DNA and amplification of the target gene from formalin-fixed samples are challenging. In this study, a hot alkali pre-treatment accompanied by the use of cetyltrimethylammonium bromide (CTAB) method was employed for DNA recovery from formalin-preserved samples, with the purpose of pursuing the optimal condition for high quantity and quality of DNA and minimizing PCR inhibition. Meanwhile, a semi-nested PCR-based method was developed to enhance the efficacy of amplification. This advanced protocol was demonstrated to be reliable and effective. Even for 23-year-old samples, genomic DNA could be extracted, and COI gene was correctly sequenced.

Genetic characterization of Italian tomato varieties and their traceability in tomato food products-Sardaro-2012-Food Science & Nutrition-Wiley Online Library

Genetic diversity underlies the improvement of crops by plant breeding. Landraces of tomato (Solanum lycopersicum L.) can contain valuable alleles not common in modern germplasms. The aim was to measure genetic diversity present in 47 most common tomato varieties grown in Italy, 35 were varieties used for processing and 12 were landraces considered “salad varieties”. Furthermore, we demonstrated the possibility that the variety traceability can be extended through the entire production chain. Diversity was measured using 11 microsatellite markers and 94 genotypes. Among the markers used, a total of 48 alleles were detected. A dendrogram based on total microsatellite polymorphism grouped 47 varieties into three major clusters at 0.75 similarity coefficient, differentiating the modern varieties from tomatoes landraces. The DNA markers developed confirmed the possibility to support the genotype identification all along the tomato production chain. The number of alleles and genotypes identified in the present work is the largest considering papers on food traceability.

Ammonium secretion during Colletotrichum coccodes infection modulates salicylic and jasmonic acid pathways of ripe and unripe tomato fruit

The postharvest pathogens Colletotrichum coccodes remains quiescent after infection of unripe fruit. However, during fruit ripening, the pathogen assumes a necrotrophic life style, rapidly colonizing the tissue. C. coccodes secretes ammonium during germination and colonization of host tissue that induces host programmed cell death. We further examined the role of ammonia in the infection process by analyzing transcriptome expression from infected and ammonia-treated fruit tissue compared with healthy tissue. The analysis revealed 82 and 237 common upregulated and downregulated genes, respectively. Quantitative reverse-transcriptase polymerase chain reaction analysis of select transcripts in normal and transgenic NADPH oxidase antisense plants revealed that their expression was NADPH oxidase dependent. Common-upregulated genes showed overrepresentation of salicylic acid (SA)-dependent genes as well as genes related to biotic stress. The downregulated genes showed overrepresentation of jasmonic acid (JA)-dependent genes. Indeed, direct application of SA to the fruit enhanced C. coccodes necrotrophic colonization, whereas the application of JA delayed colonization. Importantly, green fruit and red fruit displayed similar gene expression patterns although only red fruit is susceptible to colonization. Thus, it is likely that the resistance of green fruit to C. coccodes colonization is due to additional factors.

Comparison of DNA extraction methods and development of duplex PCR and real-time PCR to detect tomato, carrot, and celery in food

Traceability is of particular importance for those persons who suffer allergy or intolerance to some food component(s) and need a strict avoidance of the allergenic food. In this paper, methodologies are described to fingerprint the presence of allergenic species such as carrot, tomato, and celery by DNA detection. Three DNA extraction methods were applied on vegetables and foods containing or not containing the allergens, and the results were compared and discussed. Fast SYBR Green DNA melting curve temperature analyses and duplex PCR assays with internal control have been developed for detection of these allergenic vegetables and have been tested on commercial foods. Spiking food experiments were also performed, assessing that limits of detection (LOD) of 1 mg/kg for carrot and tomato DNA and 10 mg/kg for celery DNA have been reached.

Investigating the origin of tomatoes and triple concentrated tomato pastes through multielement determination by inductively coupled plasma mass spectrometry and statistical analysis

The concentration of 32 elements (Al, As, Ba, Be, Ca, Cd, Ce, Cu, Dy, Fe, K, La, Lu, Mg, Mn, Na, Nd, Pb, Rb, Sm, Sr, Th, U, V, Zn) was determined in tomatoes harvested in different four Italian regions and in triple concentrated tomato paste samples coming from Italy, China, Greece and California. The resulting multielement profiles were processed using three chemometric techniques to evaluate the possibility of discrimination between different cultivation areas. The closed-vessel microwave digested samples were diluted and analyzed by DRC-ICP-MS with CH(4) as reaction gas. The accuracy of the proposed method was considered acceptable (values in the range 75-120%) for 25 out of the 35 elements of the reference material NCS ZC85006 Tomato. The origin of tomato fruits and the areas of production as "Italy" and "non-Italy" of the triple concentrated pastes were evaluated by three supervised pattern recognition procedures, linear discriminant analysis (LDA), soft independent modeling of class analogy (SIMCA) and K-nearest neighbors (KNN).