Effective PCR detection of animal species in highly processed animal byproducts and compound feeds

Inorganic Characterization of Feeds Based on Processed Animal Protein Feeds

The potential of utilizing inorganic constituents in processed animal proteins (PAPs) for species identification in animal feeds was investigated, with the aim of using these constituents to ensure the quality and authenticity of the products. This study aimed to quantify the inorganic content across various PAP species and assess whether inorganic analysis could effectively differentiate between PAP species, ultimately aiding in the identification of PAP fractions in animal feeds. Four types of PAPs, namely bovine, swine, poultry, and fish-based, were analyzed and compared to others made up of feathers of vegetal-based feed. Also, three insect-based PAPs (Cricket, Silkworm, Flour Moth) were considered in this study to evaluate the differences in terms of the nutrients present in this type of feed. Ionic chromatography (IC) was used to reveal the concentrations of NO3-, NO2, Cl-, and SO42-, and inductively coupled plasma optical emission spectroscopy (ICP-OES) to detect Al, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Mo, Na, Ni, P, Si, Sr, Ti, and Zn. The application of multivariate chemometric techniques to the experimental results allowed us to determine the identification capability of the inorganic composition to identify correlations among the variables and to reveal similarities and differences among the different species. The results show the possibility of using this component for discriminating between different PAPS; in particular, fish PAPs are high in Cd, Sr, Na, and Mg content; swine PAPs have lower metal content due to high fat; feathers and vegetal feed have similar Al, Si, and Ni, but feathers are higher in Fe and Zn; and insect PATs have nutrient levels comparable to PAPs of other origins but are very high in Zn, Cu, and K.

Preliminary Feed Sedimentation Step for the Sensitive and Specific Detection of Processed Animal Proteins by Mass Spectrometry-Based Proteomics

The circular economy is one of the main building blocks of the European Green Deal. In this context, the use of former foodstuffs containing ruminant gelatin was recently authorized in nonruminant feed. This minor modification makes it more challenging, if not impossible, to interpret the analytical results of the official control for animal proteins. The presence of ruminant DNA from authorized byproducts (i.e., milk and/or gelatin) may hide the use of prohibited byproducts. The objective of this work was to evaluate the use of sedimentation to increase the sensitivity and specificity of bovine-processed animal proteins (PAPs) detection by mass spectrometry-based proteomics. Both approaches (standard versus optimized method) were evaluated by UHPLC-MS/MS on various animal feeds and samples from an interlaboratory study. The optimized method was able to achieve the adulteration level below the level of 0.1% PAPs required by the European Commission. This approach presents a simple and economical solution to improve the method without the need for new equipment or expertise since it is already in place in the control laboratories.

Challenges related to the application of analytical methods to control insect meals in the context of European legislation

Since their approval for use in aquaculture in 2017, processed insect proteins have been extensively studied for their nutritional quality in animal feed. This new type of meal is highly promising but requires, as for other products used in animal feed, strict sanitary control in accordance with European legislation. Within this legal framework, light microscopy and PCR remain the official methods but have some analytical limitations that other methods could overcome. This paper aims to provide an overview of the European legislation concerning use of processed insect proteins, but also to highlight the advantages and disadvantages of the official methods for their analysis. It also points out other analytical methods, which have already proved their worth for the analysis of processed animal proteins, which could be used as complementary methods.

Development of real-time PCR based molecular markers for two medicinal herb Artemisia species A. capillaris and A. iwayomogi

Artemisia capillaris and Artemisia iwayomogi are well-known herbal medicines which are used as hepatotherapeutic drugs. These two herbal species can be confused with each other, owing to their morphological similarity and similar Korean common names of "Injinho" and "Haninjin," respectively. Molecular markers to distinguish between the two plants were developed. Six primer sets were designed and verified, and their efficiencies were found to range from 90.28 to 98.29%. The developed primer sets had significant correlation coefficient values between the cycle threshold values and the logarithm of DNA concentration for their target species (R2 > 0.98), with slopes ranged from - 3.3637 to - 3.5793. The specificity of the quantitative polymerase chain reaction (qPCR) was confirmed with 14 other species. Additionally, 16 commercial medicinal herbs and 40 blind samples were tested to evaluate their reliability. Collectively, the findings indicate that developed qPCR-based target-specific primer sets have potential applicability toward protection of consumers' rights.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01166-0.

Next Generation Sequencing-based DNA metabarcoding for animal species profiling in fish feed

The expansion of worldwide aquaculture has been accompanied by extensive growth in the fish feed industry. However, improper labelling of many commercially available fish feeds has raised security and safety concerns over the species' origin of the ingredients. The inclusion of ruminants-derived ingredients in fish feed is prohibited according to EU legislation while porcine inclusion in fish feed has been a great concern among Muslim farmers. In contrast to the limited species that could be simultaneously determined using multiplex PCR, this study utilised Next Generation Sequencing-based DNA metabarcoding assay to determine the compositional profiles of animal species in fish feed samples in a more holistic manner. In relation to the religious issue associated with porcine-derived ingredients in fish feed, this study firstly aimed to determine the sensitivity of the methods in profiling fish feed adulterated with porcine blood and muscle tissues. Next, 10 commercially available fish feed samples were analysed. As a result, a detection limit of as low as 3% (w/w) porcine muscle and blood in the laboratory-prepared fish feed was obtained. The analysis of 10 commercial fish feeds shows surprising findings: 50% of the feeds contain Sus scrofa and 80% contain Bos taurus, a ruminant. Only one commercial fish feed was found to be solely composed of marine species. This study shows that commercial fish feeds sold in Malaysia contain undesirable animal species, and emphasises the need for accurate and legally enforced labelling of mammalian species in fish feed products.

Real-Time PCR Assay for the Detection and Quantification of Roe Deer to Detect Food Adulteration-Interlaboratory Validation Involving Laboratories in Austria, Germany, and Switzerland

Game meat products are particularly prone to be adulterated by replacing game meat with cheaper meat species. Recently, we have presented a real-time polymerase chain reaction (PCR) assay for the identification and quantification of roe deer in food. Quantification of the roe deer content in % (w/w) was achieved relatively by subjecting the DNA isolates to a reference real-time PCR assay in addition to the real-time PCR assay for roe deer. Aiming at harmonizing analytical methods for food authentication across EU Member States, the real-time PCR assay for roe deer has been tested in an interlaboratory ring trial including 14 laboratories from Austria, Germany, and Switzerland. Participating laboratories obtained aliquots of DNA isolates from a meat mixture containing 24.8% (w/w) roe deer in pork, roe deer meat, and 12 meat samples whose roe deer content was not disclosed. Performance characteristics included amplification efficiency, level of detection (LOD_95%), repeatability, reproducibility, and accuracy of quantitative results. With a relative reproducibility standard deviation ranging from 13.35 to 25.08% (after outlier removal) and recoveries ranging from 84.4 to 114.3%, the real-time PCR assay was found to be applicable for the detection and quantification of roe deer in raw meat samples to detect food adulteration.

Validation and Optimization of qPCR Method for Identification of Actaea racemosa (Black Cohosh) NHPs

BACKGROUND

Actaea racemosa (black cohosh) herbal dietary supplements are commonly used to treat menopausal symptoms in women. However, there is a considerable risk of contamination of A. racemosa herbal products in the natural health product (NHP) industry, impacting potential efficacy. Authentication of A. racemosa products is challenging because of the standard, multi-part analytical chemistry methods that may be too costly and not appropriate for both raw and finished products.

OBJECTIVE

In this paper, we discuss developing and validating quick alternative biotechnology methods to authenticate A. racemosa herbal dietary supplements, based on the use of a species-specific hydrolysis PCR probe assay.

METHODS

A qPCR-based species-specific hydrolysis probe assay was designed, validated, and optimized for precisely identifying the species of interest using the following analytical validation criteria: (1) specificity (accuracy) in determining the target species ingredient, while not identifying other non-target species; (2) sensitivity in detecting the smallest amount of the target material; and (3) reliability (repeatability and reproducibility) in detecting the target species in raw materials on a real-time PCR platform.

RESULTS

The results show that the species-specific hydrolysis probe assay was successfully developed for the raw materials and powders of A. racemosa. The specificity of the test was 100% to the target species. The efficiency of the assay was observed to be 99%, and the reliability of the assay was 100% for the raw/starting and powder materials.

CONCLUSION

The method developed in this study can be used to authenticate and perform qualitative analysis of A. racemosa supplements.

Selected Instrumental Techniques Applied in Food and Feed: Quality, Safety and Adulteration Analysis

This review presents an overall glance at selected instrumental analytical techniques and methods used in food analysis, focusing on their primary food science research applications. The methods described represent approaches that have already been developed or are currently being implemented in our laboratories. Some techniques are widespread and well known and hence we will focus only in very specific examples, whilst the relatively less common techniques applied in food science are covered in a wider fashion. We made a particular emphasis on the works published on this topic in the last five years. When appropriate, we referred the reader to specialized reports highlighting each technique's principle and focused on said technologies' applications in the food analysis field. Each example forwarded will consider the advantages and limitations of the application. Certain study cases will typify that several of the techniques mentioned are used simultaneously to resolve an issue, support novel data, or gather further information from the food sample.

Official Feed Control Linked to the Detection of Animal Byproducts: Past, Present, and Future

In the context of the expansion of the human population, availability of food, and in extension of animal feed, is a big issue. Favoring a circular economy by the valorization of byproducts is a sustainable way to be more efficient. Animal byproducts are an interesting source of feed materials due to their richness in proteins of high nutritional value. Prevention and control efforts have allowed a gradual lifting of the feed ban regarding the use of animal byproducts. Nevertheless, the challenge remains the development of analytical methods enabling a distinction between authorized and unauthorized feed materials. This Review focuses on the historical and epidemiological context of the official control, the evaluation of current and foreseen legislation, and the available methods of analysis for the detection of constituents of animal origin in feedingstuffs. It also underlines the analytical limitations of the approach and discusses some prospects of novel methods to ensure food and feed safety.

Application of real-time polymerase chain reaction using species specific primer targeting on mitochondrial cytochrome-b gene for analysis of pork in meatball products

OBJECTIVE

This study aimed to design specific primers derived from mitochondrial cytb of Sus Scrofa (1F1R primer) used in the pork meatball analysis using real time polymerase chain reaction (RT-PCR) method.

MATERIALS AND METHODS

Such designed primers were validated and these included specificity of primer, linearity, and sensitivity of the method as well as the repeatability test. The primers were specifically affirmed in the fresh tissue of chickens, cows, pigs, and goats. The linearity and sensitivity of the method was conducted by measuring the amplification curve from a series of dilution (0, 1, 1, 10, 100, 1,000, and 10,000 pg/μl of DNA) extracted from 100% pork meatball formulation. The repeatability test was conducted by determining the cycle threshold (Ct) values of RT-PCR amplification from 100% pork meatball formulation as many as six times.

RESULTS

Primer of 1F1R (forward: 5'-ACG CGA TAT AAG CAG GTA AA-3'; reverse: 5'-CTG CTT TCG TAG CAC GTA TT-3') was specific in analyzing the presence of pork in meatball formulation at 47.1°C, which was optimum annealing temperature. The DNA identification was able to use the primers by RT-PCR with 1 pg as the limit of detection, efficiency value was 242.58%, and the coefficient of determination value (R 2) was 0.956. The coefficient of variance was 4.13%. The developed method was also fruitfully applied to analyze commercial meatballs.

CONCLUSION

RT-PCR method using specific primers targeting on mitochondrial gene (1F1R primer) could be used as the standard method for identification of pork in food samples intended for halal authentication studies.

Simultaneous Detection of Carnosine and Anserine by UHPLC-MS/MS and Its Application on Biomarker Analysis for Differentiation of Meat and Bone Meal

A novel ultra-high performance liquid chromatography (UHPLC) procedure, coupled with tandem mass spectrometry (MS/MS), was established for the analysis of anserine (ANS) and carnosine (CAR) in meat and bone meal (MBM) (bovine, ovine, porcine, and poultry origins). The pretreatment strategies were optimized for four types of MBM samples prior to UHPLC-MS/MS analysis. This method allowed determining CAR and ANS in short analysis time (18 min per sample). The limits of detection (LODs) and limits of quantification (LOQs) of two analytes in four types of MBM samples were in the ranges of 0.41–3.07 ng/g and 0.83–5.71 ng/g, respectively. The recovery rates spiked with low, intermediate, and high levels of two analytes in four types of MBM samples were 48.53–98.93%, 60.12–98.94%, and 67.90–98.92%, respectively. Acceptable inter-day reproducibility (RSD < 12.63%) supported the application of this proposed method for determining CAR and ANS in MBM samples. Overall, this rapid, effective, and robust method was successfully applied for quantitative detection of CAR and ANS in MBM samples. Furthermore, The CAR/ANS ratio was found to be in the decreasing order: porcine > bovine > ovine > poultry MBM. This proposed methodology was novelly applied to identify the biomarker (CAR/ANS ratio) for species-specific identification of MBM.

Who were the miners of Allumiere? A multidisciplinary approach to reconstruct the osteobiography of an Italian worker community

This research presents an in-depth study of the skeletal remains collected from the archaeological site of Allumiere (15th-16th centuries CE; Rome, Italy). A multidisciplinary approach was used, combining skeletal biology, molecular anthropology and archaeobotany with the aim of reconstructing the osteobiography of the alum miners buried at the site. Since 1460, the area of the Tolfa Mountains was significant for the exploitation of alum which was used for a wide range of purposes in the Middle Ages, ranging from woven production to medical practice. A total of 70 individuals (63 adults and 7 juveniles) were studied. The sex ratio of the community indicated a higher prevalence of males with respect to females. Morphological examination indicated occupational musculoskeletal stress markers, which might reflect the specific phase of alum production that each individual was occupied in. Dietary reconstruction was primarily performed through carbon and nitrogen stable isotope analysis with integration of the results obtained by microscopic, genetic and GC-MS investigations on dental calculus. The diet was omnivorous, indicating a reliance on C3-terrestrial protein and evidence for limited C4 consumption by some individuals. Herbivores, such as sheep and cattle, appear to have contributed to the diet more than pigs and chickens. Consumption of Fagaceae and Poaceae species was predominant; moreover, indicators of Brassicaceae and milk and its derivatives were abundantly recurrent in the population, followed by plant oils and theophylline. Furthermore, the detection of pharmacological alkaloids indicated the knowledge and application of medicinal plants by the community. The novel use of multiple techniques based on cutting-edge technologies has provided a unique window on the lifestyles of individuals from one of the first Italian settlements of alum workers.

A rapid and simple UPLC-MS/MS method using collagen marker peptides for identification of porcine gelatin

Gelatin, which is mainly derived from bovine and porcine sources, has been used in many foods and pharmaceutical products. To ensure the compliance of food products with halal regulations, reliable analytical methods are very much required. In this study, one unique marker peptide for porcine gelatins was selected to develop an UPLC-MS/MS multiple reaction monitoring method. The capability of this method to identify porcine materials was demonstrated by analyzing in-house-made gelatins containing different amounts of porcine gelatins and commercial gelatin products. The adulteration of porcine gelatin could be sensitively detected at a low level of 0.04%. When combined with HPLC and mass spectrometry, this method is an accurate and sensitive quantitative method to identify porcine gelatins. Thus, the strategy can be used to verify halal authenticity of gelatin.

Gelatin, which is mainly derived from bovine and porcine sources, has been used in many foods and pharmaceutical products.

LC-MS/MS Identification of Species-Specific Muscle Peptides in Processed Animal Proteins

An innovative analytical strategy has been applied to identify signature peptides able to distinguish among processed animal proteins (PAPs) derived from bovine, pig, fish, and milk products. Proteomics was first used to elucidate the proteome of each source. Starting from the identified proteins and using a funnel based approach, a set of abundant and well characterized peptides with suitable physical-chemical properties (signature peptides) and specific for each source was selected. An on-target LC-ESI-MS/MS method (MRM mode) was set up using standard peptides and was then applied to selectively identify the PAP source and also to distinguish proteins from bovine carcass and milk proteins. We believe that the method described meets the request of the European Commission which has developed a strategy for gradually lifting the "total ban" toward "species to species ban", therefore requiring official methods for species-specific discrimination in feed.

Cross priming amplification with nucleic acid test strip analysis of mutton in meat mixtures

A simple, sensitive, accurate and affordable rapid detection of meat species authentication is urgently needed in food industry. In this study, a cross priming amplification (CPA) combining nucleic acid test strip (CPA-Strip) assay for rapid detection of mutton from meat mixture were developed and its feasibility was investigated. In an isothermal CPA system, cytochrome b (cytb) gene as target was amplified at 63°C for 60min. The nucleic acid strip was able to show the corresponding test line in the presence of target gens in 5min. Non-targeting gene interference was not evident. The CPA-Strip has been applied for the detection of 0.1-100% mutton in a thermal treated meat mixtures with a detection limit of a detect limit of 1%. CPA-Strip assay would be a promising simple, rapid and sensitive method for identification of target species in raw and processed meat mixtures.

Species-specific identification of collagen components in Colla corii asini using a nano-liquid chromatography tandem mass spectrometry proteomics approach

Colla corii asini (CCA) is a protein-based traditional Chinese medicine made from donkey skins. Because it has the ability to nourish blood, its demand is increasing rapidly. The shortage of donkey skins increases the risk of the adulteration of CCA products with other animal skins. To ensure the drug efficacy and safety of CCA products, a proteomics technique was applied to reveal proteins in the skins of donkey, horse, cattle, and pig. Species-specific peptides for each animal species were predicted using bioinformatics, and their presence in the skins and gelatin samples was examined by nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS). One unique marker peptide for each animal species was selected to develop an LC-MS/MS multiple reaction monitoring method. The capability of this method to identify donkey, horse, cattle, and pig materials was demonstrated by analyzing in-house-made donkey gelatins containing different amounts of other animal skins and commercial CCA products. The adulteration of non-donkey species could be sensitively detected at a low level of 0.5%. Hybrid animals, such as mules and hinnies, were also differentiated from donkeys. We provide a practical tool for the quality control of CCA products. The strategy can also be used to study other important traditional Chinese medicines which contain animal proteins.

Identification of specific bovine blood biomarkers with a non-targeted approach using HPLC ESI tandem mass spectrometry

Animal by-products are valuable protein sources in animal nutrition. Among them are blood products and blood meal, which are used as high-quality material for their beneficial effects on growth and health. Within the framework of the feed ban relaxation, the development of complementary methods in order to refine the identification of processed animal proteins remains challenging. The aim of this study was to identify specific biomarkers that would allow the detection of bovine blood products and processed animal proteins using tandem mass spectrometry. Seventeen biomarkers were identified: nine peptides for bovine plasma powder; seven peptides for bovine haemoglobin powder, including six peptides for bovine blood meal; and one peptide for porcine blood. They were not detected in several commercial compound feed or feed materials, such as blood by-products of other animal origins, milk-derived products and fish meal. These biomarkers could be used for developing a species-specific and blood-specific detection method.

Species and tissues specific differentiation of processed animal proteins in aquafeeds using proteomics tools

The rapidly growing aquaculture industry drives the search for sustainable protein sources in fish feed. In the European Union (EU) since 2013 non-ruminant processed animal proteins (PAP) are again permitted to be used in aquafeeds. To ensure that commercial fish feeds do not contain PAP from prohibited species, EU reference methods were established. However, due to the heterogeneous and complex nature of PAP complementary methods are required to guarantee the safe use of this fish feed ingredient. In addition, there is a need for tissue specific PAP detection to identify the sources (i.e. bovine carcass, blood, or meat) of illegal PAP use. In the present study, we investigated and compared different protein extraction, solubilisation and digestion protocols on different proteomics platforms for the detection and differentiation of prohibited PAP. In addition, we assessed if tissue specific PAP detection was feasible using proteomics tools. All work was performed independently in two different laboratories. We found that irrespective of sample preparation gel-based proteomics tools were inappropriate when working with PAP. Gel-free shotgun proteomics approaches in combination with direct spectral comparison were able to provide quality species and tissue specific data to complement and refine current methods of PAP detection and identification.

SIGNIFICANCE

To guarantee the safe use of processed animal protein (PAP) in aquafeeds efficient PAP detection and monitoring tools are required. The present study investigated and compared various proteomics workflows and shows that the application of shotgun proteomics in combination with direct comparison of spectral libraries provides for the desired species and tissue specific classification of this heat sterilized and pressure treated (≥133°C, at 3bar for 20min) protein feed ingredient.

Specific PCR assays to determine bovine, porcine, fish and plant origin of gelatin capsules of dietary supplements

Gelatin, a purified protein derived mostly from pig skin and bovine tissue, is used widely in both food and pharmaceutical industries. Here, to determine the species of origin of capsule gelatin, we developed a sensitive and reliable test using the polymerase chain reaction (PCR) method, which included 1) species-specific or universal primer sets, designed to detect short 16S ribosomal RNA (rRNA) gene sequences from cow, pig, and fish (tilapia) as well as genes encoding the large subunit of plant ribulose-1,5-bisphosphate carboxylase oxygenase and 2) species-specific PCR coupled with whole-genome amplification. This method was used to verify manufacturing label claims of 28 gelatin capsule samples sold as dietary supplements. The results from 27 samples were consistent with gelatin-related information on the manufacturer label, while one sample that mentioned tilapia gelatin was found to contain only bovine DNA. This rapid method can therefore be used to verify the authenticity of gelatin capsules.

Species Identification of Bovine, Ovine and Porcine Type 1 Collagen; Comparing Peptide Mass Fingerprinting and LC-Based Proteomics Methods

Collagen is one of the most ubiquitous proteins in the animal kingdom and the dominant protein in extracellular tissues such as bone, skin and other connective tissues in which it acts primarily as a supporting scaffold. It has been widely investigated scientifically, not only as a biomedical material for regenerative medicine, but also for its role as a food source for both humans and livestock. Due to the long-term stability of collagen, as well as its abundance in bone, it has been proposed as a source of biomarkers for species identification not only for heat- and pressure-rendered animal feed but also in ancient archaeological and palaeontological specimens, typically carried out by peptide mass fingerprinting (PMF) as well as in-depth liquid chromatography (LC)-based tandem mass spectrometric methods. Through the analysis of the three most common domesticates species, cow, sheep, and pig, this research investigates the advantages of each approach over the other, investigating sites of sequence variation with known functional properties of the collagen molecule. Results indicate that the previously identified species biomarkers through PMF analysis are not among the most variable type 1 collagen peptides present in these tissues, the latter of which can be detected by LC-based methods. However, it is clear that the highly repetitive sequence motif of collagen throughout the molecule, combined with the variability of the sites and relative abundance levels of hydroxylation, can result in high scoring false positive peptide matches using these LC-based methods. Additionally, the greater alpha 2(I) chain sequence variation, in comparison to the alpha 1(I) chain, did not appear to be specific to any particular functional properties, implying that intra-chain functional constraints on sequence variation are not as great as inter-chain constraints. However, although some of the most variable peptides were only observed in LC-based methods, until the range of publicly available collagen sequences improves, the simplicity of the PMF approach and suitable range of peptide sequence variation observed makes it the ideal method for initial taxonomic identification prior to further analysis by LC-based methods only when required.

Degradation and detection of transgenic Bacillus thuringiensis DNA and proteins in flour of three genetically modified rice events submitted to a set of thermal processes

This study aimed to investigate the degradation of three transgenic Bacillus thuringiensis (Bt) genes (Cry1Ab, Cry1Ac, and Cry1Ab/Ac) and the corresponding encoded Bt proteins in KMD1, KF6, and TT51-1 rice powder, respectively, following autoclaving, cooking, baking, or microwaving. Exogenous Bt genes were more stable than the endogenous sucrose phosphate synthase (SPS) gene, and short DNA fragments were detected more frequently than long DNA fragments in both the Bt and SPS genes. Autoclaving, cooking (boiling in water, 30 min), and baking (200 °C, 30 min) induced the most severe Bt protein degradation effects, and Cry1Ab protein was more stable than Cry1Ac and Cry1Ab/Ac protein, which was further confirmed by baking samples at 180 °C for different periods of time. Microwaving induced mild degradation of the Bt and SPS genes, and Bt proteins, whereas baking (180 °C, 15 min), cooking and autoclaving led to further degradation, and baking (200 °C, 30 min) induced the most severe degradation. The findings of the study indicated that degradation of the Bt genes and proteins somewhat correlated with the treatment intensity. Polymerase chain reaction, enzyme-linked immunosorbent assay, and lateral flow tests were used to detect the corresponding transgenic components. Strategies for detecting transgenic ingredients in highly processed foods are discussed.

Determination of the ruminant origin of bone particles using fluorescence in situ hybridization (FISH)

Molecular biology techniques such as PCR constitute powerful tools for the determination of the taxonomic origin of bones. DNA degradation and contamination by exogenous DNA, however, jeopardise bone identification. Despite the vast array of techniques used to decontaminate bone fragments, the isolation and determination of bone DNA content are still problematic. Within the framework of the eradication of transmissible spongiform encephalopathies (including BSE, commonly known as "mad cow disease"), a fluorescence in situ hybridization (FISH) protocol was developed. Results from the described study showed that this method can be applied directly to bones without a demineralisation step and that it allows the identification of bovine and ruminant bones even after severe processing. The results also showed that the method is independent of exogenous contamination and that it is therefore entirely appropriate for this application.

Detection of rabbit and hare processed material in compound feeds by TaqMan real-time PCR

Food and feed traceability has become a priority for governments due to consumer demand for comprehensive and integrated safety policies. In the present work, a TaqMan real-time PCR assay targeting the mitochondrial 12S rRNA gene was developed for specific detection of rabbit and hare material in animal feeds and pet foods. The technique is based on the use of three species-specific primer/probe detection systems targeting three 12S rRNA gene fragments: one from rabbit species, another one from hare species and a third fragment common to rabbit and hare (62, 102 and 75 bp length, respectively). A nuclear 18S rRNA PCR system, detecting a 77-bp amplicon, was used as positive amplification control. Assay performance and sensitivity were assessed through the analysis of a batch of laboratory-scale feeds treated at 133°C at 3 bar for 20 min to reproduce feed processing conditions dictated by European regulations. Successful detection of highly degraded rabbit and hare material was achieved at the lowest target concentration assayed (0.1%). Furthermore, the method was applied to 96 processed commercial pet food products to determine whether correct labelling had been used at the market level. The reported real-time PCR technique detected the presence of rabbit tissues in 80 of the 96 samples analysed (83.3%), indicating a possible labelling fraud in some pet foods. The real-time PCR method reported may be a useful tool for traceability purposes within the framework of feed control.

A nuclear DNA-based species determination and DNA quantification assay for common poultry species

DNA testing for food authentication and quality control requires sensitive species-specific quantification of nuclear DNA from complex and unknown biological sources. We have developed a multiplex assay based on TaqMan® real-time quantitative PCR (qPCR) for species-specific detection and quantification of chicken (Gallus gallus), duck (Anas platyrhynchos), and turkey (Meleagris gallopavo) nuclear DNA. The multiplex assay is able to accurately detect very low quantities of species-specific DNA from single or multispecies sample mixtures; its minimum effective quantification range is 5 to 50 pg of starting DNA material. In addition to its use in food fraudulence cases, we have validated the assay using simulated forensic sample conditions to demonstrate its utility in forensic investigations. Despite treatment with potent inhibitors such as hematin and humic acid, and degradation of template DNA by DNase, the assay was still able to robustly detect and quantify DNA from each of the three poultry species in mixed samples. The efficient species determination and accurate DNA quantification will help reduce fraudulent food labeling and facilitate downstream DNA analysis for genetic identification and traceability.

Sensitive detection of porcine DNA in processed animal proteins using a TaqMan real-time PCR assay

A TaqMan real-time PCR method was developed for specific detection of porcine-prohibited material in industrial feeds. The assay combines the use of a porcine-specific primer pair, which amplifies a 79 bp fragment of the mitochondrial (mt) 12 S rRNA gene, and a locked nucleic acid (LNA) TaqMan probe complementary to a target sequence lying between the porcine-specific primers. The nuclear 18 S rRNA gene system, yielding a 77 bp amplicon, was employed as a positive amplification control to monitor the total content of amplifiable DNA in the samples. The specificity of the porcine primers-probe system was verified against different animal and plant species, including mammals, birds and fish. The applicability of the real-time PCR protocol to detect the presence of porcine mt DNA in feeds was determined through the analysis of 190 industrial feeds (19 known reference and 171 blind samples) subjected to stringent processing treatments. The performance of the method allows qualitative and highly sensitive detection of short fragments from porcine DNA in all the industrial feeds declared to contain porcine material. Although the method has quantitative potential, the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing conditions of the feeds, which affect the amount and quality of amplifiable DNA.