A fast and accurate method for controlling the correct labeling of products containing buffalo meat using High Resolution Melting (HRM) analysis

Advancements and future prospective of DNA barcodes in the herbal drug industry

Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology. Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations. Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification. Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.

Accurate identification of taxon-specific molecular markers in plants based on DNA signature sequence

Accurate identification of plants remains a significant challenge for taxonomists and is the basis for plant diversity conservation. Although DNA barcoding methods are commonly used for plant identification, these are limited by the low amplification success and low discriminative power of selected genomic regions. In this study, we developed a k-mer-based approach, the DNA signature sequence (DSS), to accurately identify plant taxon-specific markers, especially at the species level. DSS is a constant-length nucleotide sequence capable of identifying a taxon and distinguishing it from other taxa. In this study, we performed the first large-scale study of DSS markers in plants. DSS candidates of 3,899 angiosperm plant species were calculated based on a chloroplast dataset with 4,356 assemblies. Using Sanger sequencing of PCR amplicons and high-throughput sequencing, DSSs were validated in four and 165 species, respectively. Based on this, the universality of the DSSs was over 79.38%. Several indicators influencing DSS marker identification and detection have also been evaluated, and common criteria for DSS application in plant identification have been proposed.

Study of Meat Species Adulteration in Indonesian Commercial Beef Meatballs Related to Halal Law Implementation

Meatballs are processed meat products that are susceptible to adulteration. Indonesia enforces a halal product guarantee regulation so that all products in circulation are free from non-halal ingredients. This study aimed to detect with the PCR method the contamination by pork and chicken of commercial beef meatballs. The samples of commercial meatballs were obtained from 36 meatball shops in Bojonegoro Regency, East Java, and Boyolali Regency, Central Java Province, Indonesia. Reference meatballs as a positive control were prepared in the laboratory. DNA isolation was performed on commercial sample meatballs, reference meatballs, and 13 species of fresh meat for specificity tests. DNA concentrations were measured using a spectrophotometer, and visualization of the isolation and PCR results was conducted using agarose gel electrophoresis and a UV transilluminator. DNA isolates were amplified by PCR using gene targets 1.711B bovine repeat for identifying bovine species, CR1 SINE repeat element for identifying chicken species, and mitochondrial gene subunit ND1 for identifying pork species. The results showed that there was contamination by chicken meat in meatballs labeled as beef meatballs in 30 of 36 samples in Bojonegoro Regency and 33 of 36 samples in Boyolali Regency. The results also showed that 22 samples of commercial beef meatballs in the Boyolali Regency contained pork. The implementation of the PCR method using the three specific primers proved the presence of meat contamination that did not match the label on the meatballs circulating in the Indonesian market. The contamination by pork if beef meatballs has violated the regulation on halal product guarantees.

Detection of Species Substitution in the Meat Value Chain by High-Resolution Melting Analysis of Mitochondrial PCR Products

Substituting high commercial-value meats with similar cheaper or undesirable species is a common form of food fraud that raises ethical, religious, and dietary concerns. Measures to monitor meat substitution are being put in place in many developed countries. However, information about similar efforts in sub-Saharan Africa is sparse. We used PCR coupled with high-resolution melting (PCR-HRM) analysis targeting three mitochondrial genes—cytochrome oxidase 1 (CO1), cytochrome b (cyt b), and 16S rRNA—to detect species substitution in meat sold to consumers in Nairobi, Kenya. Out of 107 meat samples representing seven livestock animals, 11 (10.3%) had been substituted, with the highest rate being observed in samples sold as goat. Our results indicate that PCR-HRM analysis is a cost- and time-effective technique that can be employed to detect species substitution. The combined use of the three mitochondrial markers produced PCR-HRM profiles that successfully allowed for the consistent distinction of species in the analysis of raw, cooked, dried, and rotten meat samples, as well as of meat admixtures. We propose that this approach has broad applications in the protection of consumers against food fraud in the meat industry in low- and middle-income countries such as Kenya, as well as in developed countries.

Comparison of Long Non-Coding RNA Expression Profiles of Cattle and Buffalo Differing in Muscle Characteristics

Buffalo meat consist good qualitative characteristics as it contains “thined tender” which is favorable for cardavascular system. However, the regulatory mechanisms of long non-coding RNA (lncRNA), differences in meat quality are not well known. The chemical-physical parameters revealed the muscle quality of buffalo that can be equivalent of cattle, but there are significant differences in shearing force and muscle fiber structure. Then, we examined lncRNA expression profiles of buffalo and cattle skeletal muscle that provide first insights into their potential roles in buffalo myogenesis. Here, we profiled the expression of lncRNA in cattle and buffalo skeletal muscle tissues, and 16,236 lncRNA candidates were detected with 865 up-regulated lncRNAs and 1,296 down-regulated lncRNAs when comparing buffalo to cattle muscle tissue. We constructed coexpression and ceRNA networks, and found lncRNA MSTRG.48330.7, MSTRG.30030.4, and MSTRG.203788.46 could be as competitive endogenous RNA (ceRNA) containing potential binding sites for miR-1/206 and miR-133a. Tissue expression analysis showed that MSTRG.48330.7, MSTRG.30030.4, and MSTRG.203788.46 were highly and specifically expressed in muscle tissue. Present study may be used as a reference tool for starting point investigations into the roles played by several of those lncRNAs during buffalo myogenesis.

Monitoring of sausage products sold in Sichuan Province, China: a first comprehensive report on meat species' authenticity determination

Presently, there is growing concern worldwide regarding the adulteration of meat products. However, no reports on determining meat authenticity have been reported in China. To verify labelling compliance and evaluate the existence of fraudulent practices, 250 sausage samples were purchased from local markets in Sichuan Province and analysed for the presence of chicken, pork, beef, duck and genetically modified soybean DNA using real-time and end-point PCR methods, providing a Chinese case study on the problem of world food safety. In total, 74.4% (186) of the samples were properly labelled, while the other 25.6% (64) were potentially adulterated samples, which involved three illicit practices: product removal, addition and substitution. The most common mislabelling was the illegal addition of, or contamination with, duck. Therefore, meat authenticity monitoring should be routinely conducted. Additionally, the strict implementation of the nation’s food safety laws, along with regular surveillance, should be compulsory to alleviate and deter meat adulteration.

Rapid Identification of Rainbow Trout Adulteration in Atlantic Salmon by Raman Spectroscopy Combined with Machine Learning

This study intends to evaluate the utilization potential of the combined Raman spectroscopy and machine learning approach to quickly identify the rainbow trout adulteration in Atlantic salmon. The adulterated samples contained various concentrations (0-100% w/w at 10% intervals) of rainbow trout mixed into Atlantic salmon. Spectral preprocessing methods, such as first derivative, second derivative, multiple scattering correction (MSC), and standard normal variate, were employed. Unsupervised algorithms, such as recursive feature elimination, genetic algorithm (GA), and simulated annealing, and supervised K-means clustering (KM) algorithm were used for selecting important spectral bands to reduce the spectral complexity and improve the model stability. Finally, the performances of various machine learning models, including linear regression, nonlinear regression, regression tree, and rule-based models, were verified and compared. The results denoted that the developed GA-KM-Cubist machine learning model achieved satisfactory results based on MSC preprocessing. The determination coefficient (R2) and root mean square error of prediction sets (RMSEP) in the test sets were 0.87 and 10.93, respectively. These results indicate that Raman spectroscopy can be used as an effective Atlantic salmon adulteration identification method; further, the developed model can be used for quantitatively analyzing the rainbow trout adulteration in Atlantic salmon.

Rapid identification of common medicinal snakes and their adulterants using the Bar-HRM analysis method

Effective identification methods for snake species are lacking, exacerbating the extermination of medicinal and commercially valuable snake species. Hence, it is imperative to find fast and reliable methods to distinguish snake samples available on the market. Seventy-three samples from four families belonging to 13 genera were collected in China and found to contain common medicinal snakes and their adulterants. Cytochrome oxidase I (COI) was utilized as a DNA barcode to analyse these common snakes, and a DNA mini-barcode was employed for fast detection. Then, the DNA mini-barcode assays were coupled with a high-resolution melting (HRM) analysis (Bar-HRM) to realize the rapid discrimination of these snake species. The results showed the power of DNA barcoding with COI, which was capable of distinguishing all collected snake samples, and the combined Bar-HRM method can successfully identify the adulterants and different snake species. In particular, Bar-HRM revealed Bungarus fasciatus adulterants in B. multicinctus at concentrations as low as 1.6%. Moreover, the results of the study confirmed the effectiveness of the technique in terms of the rapid identification of snakes, which has great potential for ensuring the safety of commercially valuable snake species.

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.

ITS2 barcoding DNA region combined with high resolution melting (HRM) analysis of Hyoscyami Semen, the mature seed of Hyoscyamus niger

Hyoscyami Semen, the mature dried seed of Hyoscyamus niger L., has long been used as a traditional Chinese medicine to treat human diseases. Hyoscyami Semen is found in local markets in China. In markets, sellers and buyers commonly inadvertently mix the seeds of H. niger with the seeds of related species such as Hygrophila salicifolia (Vahl) Nees, Astragalus complanatus R. Br., Cuscuta australis R. Br., Cuscuta chinensis Lam., and Impatiens balsamina L. because of their similar morphologies or similar names. Thus, developing a reliable method for discriminating H. niger seeds from its adulterants is necessary to reduce confusion and ensure the safe use of Hyoscyami Semen. The present study was designed to evaluate the efficiency of high-resolution melting analysis combined with DNA barcoding (Bar-HRM) with internal transcribed spacer 2 to discriminate H. niger. Our results show that Bar-HRM successfully identified the adulterants and detected the proportion of H. niger DNA extract within an admixture. In particular, HRM detected H. niger DNA extract in A. complanatus DNA extract at concentrations as low as 1%. In conclusion, the Bar-HRM method developed in the present study for authenticating H. niger is rapid and cost-effective. It can be used in the future to guarantee the purity of Hyoscyami Semen for the clinical use.

Double Gene Targeting Multiplex Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Assay Discriminates Beef, Buffalo, and Pork Substitution in Frankfurter Products

Beef, buffalo, and pork adulteration in the food chain is an emerging and sensitive issue. Current molecular techniques to authenticate these species depend on polymerase chain reaction (PCR) assays involving long and single targets which break down under natural decomposition and/or processing treatments. This novel multiplex polymerase chain reaction-restriction fragment length polymorphism assay targeted two different gene sites for each of the bovine, buffalo, and porcine materials. This authentication ensured better security, first through a complementation approach because it is highly unlikely that both sites will be missing under compromised states, and second through molecular fingerprints. Mitochondrial cytochrome b and ND5 genes were targeted, and all targets (73, 90, 106, 120, 138, and 146 bp) were stable under extreme boiling and autoclaving treatments. Target specificity and authenticity were ensured through cross-amplification reaction and restriction digestion of PCR products with AluI, EciI, FatI, and CviKI-1 enzymes. A survey of Malaysian frankfurter products revealed rampant substitution of beef with buffalo but purity in porcine materials.

Quantitative detection of pork in commercial meat products by TaqMan® real-time PCR assay targeting the mitochondrial D-loop region

The TaqMan® real-time PCR assay using the mitochondrial D-loop region was developed for the quantitative detection of pork in processed meat products. The newly designed primers and probe specifically amplified pork without any cross-reactivity with non-target animal species. The limit of detection of the real-time PCR assay was 0.1pg of heat-treated pork meat and 0.1% (w/w) pork meat in beef and chicken meat mixtures. The quantitative real-time PCR assay was applied to analyze the pork meat content in 22 commercial processed meat products including jerkies, press hams, sausages, hamburger patties and steaks, grilled short rib patties, and nuggets. The developed real-time PCR method was able to detect pork meat in various types of processed meat products that declared the use of pork meat on their label. All processed meat products that declared no use of pork meat showed a negative result in the assay. The method developed in this study showed sensitivity and specificity in the quantification of pork meat in commercial processed meat products.

The Potential Power of Bar-HRM Technology in Herbal Medicine Identification

The substitution of low-cost or adulterated herbal products for high-priced herbs makes it important to be able to identify and trace herbal plant species and their processed products in the drug supply chain. PCR-based methods play an increasing role in monitoring the safety of herbal medicines by detecting adulteration. Recent studies have shown the potential of DNA barcoding combined with high resolution melting (Bar-HRM) analysis in herbal medicine identification. This method involves precisely monitoring the change in fluorescence caused by the release of an intercalating DNA dye from a DNA duplex as it is denatured by a gradual increase in temperature. Since the melting profile depends on the GC content, length, and strand complementarity of the amplification product, Bar-HRM analysis opens up the possibility of detecting single-base variants or species-specific differences in a short region of DNA. This review summarizes key factors affecting Bar-HRM analysis and describes how Bar-HRM is performed. We then discuss advances in Bar-HRM analysis of medicinal plant ingredients (herbal materia medica) as a contribution toward safe and effective herbal medicines.

Specific identification of chicken and soybean fraud in premium burgers using multiplex-PCR method

The increased consumption of meat products, such as hamburger in large cities such as Tehran, has highlighted the importance of quality control for these products. Due to the escalating cost of red meat, and the difficulty of detecting adulteration in ground meat, the replacement of red meat with cheaper animal and plant proteins in these products is clearly possible. As a result, the aim of this study was to investigate the validity of labeling in premium hamburgers made of beef. In addition, the presence of soybean and chicken meat, which constitutes commercial fraud in premium hamburgers, was detected using a sensitive and quick multiplex-PCR method. In total, 10 specified brands of premium hamburgers purported to consist of beef were collected from markets in Tehran City, Iran. DNA was extracted from the premium hamburgers, then, simplex-PCR and multiplex-PCR fwere optimized using specific beef, chicken and soybean primers. The 118, 183, and 274 bp fragments, were amplified in all samples from soybean lectin, 12 s rRNA, and mitochondrial cytochrome b genes, respectively. The results indicated the addition of chicken meat and soybean in the premium hamburgers which were not indicated on their labels.

Quantitative high resolution melting: two methods to determine SNP allele frequencies from pooled samples

Background

The advent of next-generation sequencing has brought about an explosion of single nucleotide polymorphism (SNP) data in non-model organisms; however, profiling these SNPs across multiple natural populations still requires substantial time and resources.

Results

Here, we introduce two cost-efficient quantitative High Resolution Melting (qHRM) methods for measuring allele frequencies at known SNP loci in pooled DNA samples: the “peaks” method, which can be applied to large numbers of SNPs, and the “curves” method, which is more labor intensive but also slightly more accurate. Using the reef-building coral Acropora millepora, we show that both qHRM methods can recover the allele proportions from mixtures prepared using two or more individuals of known genotype. We further demonstrate advantages of each method over previously published methods; specifically, the “peaks” method can be rapidly scaled to screen several hundred SNPs at once, whereas the “curves” method is better suited for smaller numbers of SNPs.

Conclusions

Compared to genotyping individual samples, these methods can save considerable effort and genotyping costs when relatively few candidate SNPs must be profiled across a large number of populations. One of the main applications of this method could be validation of SNPs of interest identified in population genomic studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0222-z) contains supplementary material, which is available to authorized users.

Fast and reliable detection of toxic Crotalaria spectabilis Roth. in Thunbergia laurifolia Lindl. herbal products using DNA barcoding coupled with HRM analysis

Background

Nowadays, medicinal plants are used as a popular alternative to synthetic drugs. Many medicinal plant products have now been commercialized throughout various markets. These products are commonly sold in processed or modified forms such as powders, dried material and capsules, making it almost impossible to accurately identify the constituent species. The herbal plant known as ‘Rang Chuet’ in Thai has been widely used as remedies for various ailments. However, two medicinal plants species, Thunbergia laurifolia and Crotalaria spectabilis share this name. Duo to the similarity in nomenclature, the commercial products labeled as ‘Rang Chuet’ could be any of them. Recently, the evidence of hepatotoxic effects linked to use of C. spectabilis were reported and is now seriously concern. There is a need to find an approach that could help with species identification of these herbal products to ensure the safety and efficacy of the herbal drug.

Methods

Here DNA barcoding was used in combination with High Resolution Melting analysis (Bar-HRM) to authenticate T. laurifolia species. Four DNA barcodes including matK, rbcL, rpoC and trnL were selected for use in primers design for HRM analysis to produce standard melting profiles of the selected species. Commercial products labeled as ‘Rang Chuet’ were purchased from Thai markets and authentication by HRM analyses.

Results

Melting data from the HRM assay using the designed primers showed that the two ‘Rang Chuet’ species could easily be distinguished from each other. The melting profiles of the all four region amplicons of each species are clearly separated in all three replicates. The method was then applied to authenticate products in powdered form. HRM curves of all ten test samples indicated that three of the tested products did not only contain the T. laurifolia species.

Conclusion

The herbal drugs derived from different plants must be distinguished from each other even they share the same vernacular name. The Bar-HRM method developed here proved useful in the identification and authentication of herbal species in processed samples. In the future, species authentication through Bar-HRM could be used to promote consumer trust, as well as raising the quality of herbal products.

Electronic supplementary material

The online version of this article (doi:10.1186/s12906-015-0692-6) contains supplementary material, which is available to authorized users.

Reliable discrimination of 10 ungulate species using high resolution melting analysis of faecal DNA

Identifying species occupying an area is essential for many ecological and conservation studies. Faecal DNA is a potentially powerful method for identifying cryptic mammalian species. In New Zealand, 10 species of ungulate (Order: Artiodactyla) have established wild populations and are managed as pests because of their impacts on native ecosystems. However, identifying the ungulate species present within a management area based on pellet morphology is unreliable. We present a method that enables reliable identification of 10 ungulate species (red deer, sika deer, rusa deer, fallow deer, sambar deer, white-tailed deer, Himalayan tahr, Alpine chamois, feral sheep, and feral goat) from swabs of faecal pellets. A high resolution melting (HRM) assay, targeting a fragment of the 12S rRNA gene, was developed. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behaviour for each species. The method was developed using tissue from each of the 10 species, and was validated in blind trials. Our protocol enabled species to be determined for 94% of faecal pellet swabs collected during routine monitoring by the New Zealand Department of Conservation. Our HRM method enables high-throughput and cost-effective species identification from low DNA template samples, and could readily be adapted to discriminate other mammalian species from faecal DNA.

A universal method for species identification of mammals utilizing next generation sequencing for the analysis of DNA mixtures

Species identification can be interesting in a wide range of areas, for example, in forensic applications, food monitoring and in archeology. The vast majority of existing DNA typing methods developed for species determination, mainly focuses on a single species source. There are, however, many instances where all species from mixed sources need to be determined, even when the species in minority constitutes less than 1 % of the sample. The introduction of next generation sequencing opens new possibilities for such challenging samples. In this study we present a universal deep sequencing method using 454 GS Junior sequencing of a target on the mitochondrial gene 16S rRNA. The method was designed through phylogenetic analyses of DNA reference sequences from more than 300 mammal species. Experiments were performed on artificial species-species mixture samples in order to verify the method's robustness and its ability to detect all species within a mixture. The method was also tested on samples from authentic forensic casework. The results showed to be promising, discriminating over 99.9 % of mammal species and the ability to detect multiple donors within a mixture and also to detect minor components as low as 1 % of a mixed sample.