• Application of class-modelling techniques to near infrared data for food authentication purposes

      Oliveri, P.; Di Egidio, V.; Woodcock, T.; Downey, Gerard; European Union (Elsevier, 2011)
      Following the introduction of legal identifiers of geographic origin within Europe, methods for confirming any such claims are required. Spectroscopic techniques provide a method for rapid and non-destructive data collection and a variety of chemometric approaches have been deployed for their interrogation. In this present study, class-modelling techniques (SIMCA, UNEQ and POTFUN) have been deployed after data compression by principal component analysis for the development of class-models for a set of olive oil and honey. The number of principal components, the confidence level and spectral pre-treatments (1st and 2nd derivative, standard normal variate) were varied, and a strategy for variable selection was tried. Models were evaluated on a separate validation sample set. The outcomes are reported and criteria for selection of the most appropriate models for any given application are discussed.
    • A case of bovine raw milk contamination with Listeria monocytogenes

      Hunt, Karen; Drummond, Niall; Murphy, Mary; Butler, Francis; Buckley, James F.; Jordan, Kieran; Teagasc Walsh Fellowship Programme; Department of Agriculture, Food and the Marine, Ireland; European Union (Biomed Central, 06/07/2012)
      During routine sampling of bulk raw milk on a dairy farm, the pathogenic bacteria Listeria monocytogenes was found to be a contaminant, at numbers < 100 cfu/ml. A strain with an indistinguishable pulsed-field gel electrophoresis pattern was isolated from the bulk milk two months later. Environmental swabs taken at the dairy environment were negative for the presence of L. monocytogenes, indicating a possible case of excretion of the L. monocytogenes directly into the milk. Milk samples were collected from the individual cows and analysed, resulting in the identification of L. monocytogenes excretion (at 280 cfu/ml) from one of the 4 mammary quarters of one dairy cow out of 180. When the infected cow was isolated from the herd, no L. monocytogenes was detected from the remaining herd. The pulsed-field gel electrophoresis pattern of the strain from the individual cow was indistinguishable from that originally isolated from the bulk milk. The infected cow did not show any clinical signs of disease, nor did the appearance of the milk have any physical abnormalities. Antibiotic treatment of the infected mammary quarter was found to be ineffective. This study shows that there can be risks associated with direct contamination of raw milk with L. monocytogenes.
    • Confirmation of brand identity of a Trappist beer by mid-infrared spectroscopy coupled with multivariate data analysis

      Engel, J.; Blanchet, L.; Buydens, L.M.C.; Downey, Gerard; European Union (Elsevier, 2012)
      Authentication of foods is of importance both to consumers and producers for e.g. confidence in label descriptions and brand protection respectively. The authentication of beers has received limited attention and in most cases only small data sets were analysed. In this study, Fourier-transform infrared attenuated total reflectance (FT-IR ATR) spectroscopy was applied to a set of 267 beers (53 different brands) to confirm claimed identity for samples of a single beer brand based on their spectral profiles. Skewness-adjusted robust principal component analysis (ROBPCA) was deployed to detect outliers in the data. Subsequently, extended canonical variates analysis (ECVA) was used to reduce the dimensionality of the data while simultaneously achieving maximum class separation. Finally, the reduced data were used as inputs to various linear and non-linear classifiers. Work focused on the specific identification of Rochefort 8º (a Trappist beer) and both direct and indirect (using an hierarchical approach) identification strategies were studied. For the classification problems Rochefort versus non-Rochefort, Rochefort 8º versus non-Rochefort 8º and Rochefort 8º versus Rochefort 6º and 10º, correct prediction abilities of 93.8%, 93.3% and 97.3% respectively were achieved.
    • Effect of Cold Plasma on Meat Cholesterol and Lipid Oxidation

      Pérez-Andrés, Juan M.; Cropotova, Janna; Harrison, Sabine M.; Brunton, Nigel P.; Cullen, Patrick J.; Rustad, Turid; Tiwari, Brijesh K; European Union; Project ProHealth; Teagasc Walsh Scholarship Programme; et al. (Multidisciplinary Digital Publishing Institute, 2020-12-01)
      Cold atmospheric plasma (CAP) is a novel non-thermal technology with potential applications in inactivating microorganisms in food products. However, its impact on food quality is not yet fully understood. The aim of this research is to study the impact of in-package plasma technology on the stability of cholesterol and total lipid in four different types of meat (beef, pork, lamb and chicken breast). Additionally, any changes in the primary or secondary lipid oxidation, which is undesirable from a health perspective, is investigated. CAP was not found to have any impact on the cholesterol or lipid content. However, higher peroxide and thiobarbituric acid reactive substances (TBARS) values were found for the treated samples, indicating that plasma can induce the acceleration of primary and secondary lipid oxidation. Finally, color was not affected by the treatment supporting the suitability of the technology for meat products.
    • Genome-wide association analysis and functional annotation of positional candidate genes for feed conversion efficiency and growth rate in pigs

      Horodyska, Justyna; Hamill, Ruth; Varley, Patrick F.; Wimmers, Klaus; European Union; 311794 (PLOS, 12/06/2017)
      Feed conversion efficiency is a measure of how well an animal converts feed into live weight and it is typically expressed as feed conversion ratio (FCR). FCR and related traits like growth rate (e.g. days to 110 kg—D110) are of high interest for animal breeders, farmers and society due to implications on animal performance, feeding costs and environmental sustainability. The objective of this study was to identify genomic regions associated with FCR and D110 in pigs. A total of 952 terminal line boars, showing an individual variation in FCR, were genotyped using 60K SNP-Chips. Markers were tested for associations with estimated breeding values (EBV) for FCR and D110. For FCR, the largest number of associated SNPs was located on chromosomes 4 (30 SNPs), 1 (25 SNPs), X (15 SNPs) and 6 (12 SNPs). The most prominent genomic regions for D110 were identified on chromosomes 15 (10 SNPs), 1 and 4 (both 9 SNPs). The most significantly associated SNPs for FCR and D110 mapped 129.8 Kb from METTL11B (chromosome 4) and 32Kb from MBD5 (chromosome 15), respectively. A list of positional genes, closest to significantly associated SNPs, was used to identify enriched pathways and biological functions related to the QTL for both traits. A number of candidate genes were significantly overrepresented in pathways of immune cell trafficking, lymphoid tissue structure, organ morphology, endocrine system function, lipid metabolism, and energy production. After resequencing the coding region of selected positional and functional candidate genes, six SNPs were genotyped in a subset of boars. SNPs in PRKDC, SELL, NR2E1 and AKRIC3 showed significant associations with EBVs for FCR/D110. The study revealed a number of chromosomal regions and candidate genes affecting FCR/D110 and pointed to corresponding biological pathways related to lipid metabolism, olfactory reception, and also immunological status.
    • Influence of chaperone-like activity of caseinomacropeptide on the gelation behaviour of whey proteins at pH 6.4 and 7.2.

      Gaspard, Sophie J.; Sharma, Prateek; Fitzgerald, Ciarán; Tobin, John T.; O’Mahony, James A.; Kelly, Alan L.; Brodkorb, Andre; Dairy Research Ireland; Teagasc Walsh Fellowship Programme; European Union; et al. (Elsevier, 2020-08-15)
      The effect of caseinomacropeptide (CMP) on the heat-induced denaturation and gelation of whey proteins (2.5–10%, w/v) at pH 6.4 and 7.2, at a whey protein:CMP ratio of 1:0.9 (w/w), was investigated using differential scanning calorimetry (DSC), oscillatory rheology (90 °C for 20 min) and confocal microscopy. Greater frequency-dependence in the presence of CMP suggested that the repulsive interactions between CMP and the whey proteins affected the network generated by the non-heated whey protein samples. At pH 6.4 or 7.2, CMP increased the temperature of denaturation of β-lactoglobulin by up to 3 °C and increased the gelation temperature by up to 7 °C. The inclusion of CMP strongly affected the structure of the heat-induced whey protein gels, resulting in a finer stranded structure at pH 6.4 and 7.2. The presence of CMP combined with a lower heating rate (2 °C/min) prevented the formation of a solid gel of whey proteins after heating for 20 min at 90 °C and at pH 7.2. These results show the potential of CMP for control of whey protein denaturation and gelation.
    • Influence of high-pressure processing on quality attributes of haddock and mackerel minces during frozen storage, and fishcakes prepared thereof

      Cropotova, Janna; Mozuraityte, Revilija; Standal, Inger Beate; Ojha, Shikha; Rustad, Turid; Tiwari, Brijesh K; European Union; RCN 259582/E50 (Elsevier BV, 2020-01)
      The study focused on assessing quality parameters of haddock and mackerel minces subjected to a high-pressure treatment (HP) at 200 and 300 MPa and frozen storage at −40 °C. Dry matter, water-holding capacity, protein solubility and oxidation, lipid oxidation, microbiological parameters, low molecular weight metabolites (LMW) and color parameters, were analyzed. The texture of fishcakes prepared on the basis of these fish minces was also studied, showing a decrease in firmness along with an increase in pressure. A marked inhibition of microbial growth was observed in fish minces when increasing the pressure level of HP-treatment. However, no significant effect (p < 0.05) on the content of primary and secondary lipid oxidation products was observed between untreated and 300 MPa-pressurized fish samples. The results suggested that HP-treatment could be successfully applied to both lean and fatty fish samples for reduction of microbial growth with minor changes in product quality. Industrial relevance. The application of high pressure (HP) treatment of 200 and 300 MPa could be successfully applied to both lean and fatty fish species before freezing for reduction of microbial growth. The degree of lipid oxidation is decreasing with an increase in pressure as a result of inactivation of prooxidative endogenous enzymes. Fish minces become slightly lighter and softer after HP-treatment conducted at 200 MPa due to denaturation of proteins, thus enhancing sensory properties of fishcakes prepared thereof.
    • Mechanical Grading of beef carcasses

      Allen, Paul; Finnerty, Nicholas; European Union; European Union (Teagasc, 2001-10)
      Three beef carcass classification systems that use Video Image Analysis (VIA) technology were tested in two trials at Dawn Meats Midleton, Co. Cork. The VIA systems were BCC2, manufactured by SFK Technology, Denmark, VBS2000, manufactured by E+V, Germany, and VIAscan, manufactured by Meat and Livestock Australia. The first trial, conducted over a 6-week period in July/August 1999, calibrated the VIA systems on a large sample of carcasses and validated these calibrations on a further sample obtained at the same time. The second trial, conducted in the first two weeks of March 2000, was a further validation trial. The reference classification scores were determined by a panel of three experienced classifiers using the EUROP grid with 15 subclasses for conformation class and 15 sub-classes for fat. In the first trial the accuracy of the VIA systems at predicting saleable meat yield in steer carcasses was also assessed.
    • Predicting the eating quality of meat

      Mullen, Anne Maria; Murray, Brendan; Troy, Declan J.; European Union (Teagasc, 2000-12)
      A novel, water soluble protein fragment [1735Da] was isolated from beef striploin and characterised. As soluble components of the proteolytic system are easily extracted from muscle they may be suitable for routine factory analysis. This fragment originated from the important myofibrillar protein, troponin T and may serve as a tenderness indicator.
    • Proteomic biomarkers of beef colour

      Gagaoua, Mohammed; Hughes, Joanne; Terlouw, E.M. Claudia; Warner, Robyn D.; Purslow, Peter P.; Lorenzo, José M.; Picard, Brigitte; European Union; Enterprise Ireland; 713654; et al. (Elsevier BV, 2020-07)
      Background Implementation of proteomics over the last decade has been an important step toward a better understanding of the complex biological systems underlying the conversion of muscle to meat. These sophisticated analytical tools have helped to reveal the biochemical pathways involved in fresh meat colour and have identified key protein biomarkers. Scope and approach Until recently, there have been no detailed or critical studies on the role of protein biomarkers in determining meat colour. This review presents an integromics of recent muscle proteomic studies to investigate pathways and mechanisms of beef colour. A database was created from 13 independent proteomic-based studies including data on five muscles and a list of 79 proteins which were significantly correlated with colour traits. The database was subjected to a multistep analysis including Gene Ontology annotations, pathway analysis and literature mining. This report discusses the key protein biomarkers and the biological pathways associated with fresh beef colour. Biomarkers were prioritised by the frequency of identification and the need for future validation experiments is discussed. Key findings and conclusions This review identifies six pathways involved in beef colour including energy metabolism, heat shock and oxidative stress, myofibril structure, signalling, proteolysis and apoptosis. The data-mining of the list of the putative biomarkers showed that certain proteins, such as β-enolase (ENO3), Peroxiredoxin 6 (PRDX6), HSP27 (HSPB1), Phosphoglucomutase 1 (PGM1), Superoxide Dismutase [Cu-Zn] (SOD1) and μ-calpain (CAPN1) were consistently reported by multiple studies as being differentially expressed and having a significant role in beef colour. This integromics work proposes a list of 27 putative biomarkers of beef colour for validation using adapted high-throughput methods.
    • RNA-seq of muscle from pigs divergent in feed efficiency and product quality identifies differences in immune response, growth, and macronutrient and connective tissue metabolism

      Horodyska, Justyna; Wimmers, Klaus; Reyer, Henry; Trakooljul, Nares; Mullen, Anne Maria; Lawlor, Peadar G; Hamill, Ruth M; European Union; 311794 (Biomed Central, 2018-11-01)
      Background Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to differences in FE are not fully elucidated, therefore the objective of this study was to profile the porcine Longissimus thoracis et lumborum (LTL) muscle transcriptome, examine the product quality from pigs divergent in FE and investigate the functional networks underpinning the potential relationship between product quality and FE. Results RNA-Seq (n = 16) and product quality (n = 40) analysis were carried out in the LTL of pigs differing in FE status. A total of 272 annotated genes were differentially expressed with a P < 0.01. Functional annotation revealed a number of biological events related to immune response, growth, carbohydrate & lipid metabolism and connective tissue indicating that these might be the key mechanisms governing differences in FE. Five most significant bio-functions altered in FE groups were ‘haematological system development & function’, ‘lymphoid tissue structure & development’, ‘tissue morphology’, ‘cellular movement’ and ‘immune cell trafficking’. Top significant canonical pathways represented among the differentially expressed genes included ‘IL-8 signalling’, ‘leukocyte extravasation signalling, ‘sphingosine-1-phosphate signalling’, ‘PKCθ signalling in T lymphocytes’ and ‘fMLP signalling in neutrophils’. A minor impairment in the quality of meat, in relation to texture and water-holding capacity, produced by high-FE pigs was observed. High-FE pigs also had reduced intramuscular fat content and improved nutritional profile in terms of fatty acid composition. Conclusions Ontology analysis revealed enhanced activity of adaptive immunity and phagocytes in high-FE pigs suggesting more efficient conserving of resources, which can be utilised for other important biological processes. Shifts in carbohydrate conversion into glucose in FE-divergent muscle may underpin the divergent evolution of pH profile in meat from the FE-groups. Moreover, altered amino acid metabolism and increased mobilisation & flux of calcium may influence growth in FE-divergent muscle. Furthermore, decreased degradation of fibroblasts in FE-divergent muscle could impact on collagen turnover and alter tenderness of meat, whilst enhanced lipid degradation in high-FE pigs may potentially underlie a more efficient fat metabolism in these animals.
    • Technology transfer of research results (The 2xtra project)

      McDonagh, Ciara; Byrne, Briege; Troy, Declan J.; Mullen, Anne Maria; Downey, Gerard; European Commission; European Union (Teagasc, 2008-02)
      The 2XTRA project (Technology Transfer Research Results Atlantic Area) was carried out with the aim of promoting economic activity based on research results and technologies developed within universities, research and technology institutes and companies in the European Atlantic Area. This collaborative work was carried out by a strong partnership of 13 entities across this region and included universities, research and technology institutes, private consultants and TBC (technology-based company) incubators. The specific goals of the project were: ● The exchange of information and experiences on technology transfer (TT) with a view to assisting project partners directly and feeding into their regional innovation systems. ● The promotion of new technology-based companies by drawing on collective experiences and developing methodologies relating to - identification and evaluation of business ideas - production of business plans, and - support of early stage companies internationalising. ● The creation of an Atlantic Area Network to support and promote technology-based companies (TBCs) and the technology transfer process. These objectives were achieved through defined activities carried out in three separate stages of this project.
    • What are the drivers of beef sensory quality using metadata of intramuscular connective tissue, fatty acids and muscle fiber characteristics?

      Listrat, Anne; Gagaoua, Mohammed; Andueza, Donato; Gruffat, Dominique; Normand, Jérome; Mairesse, Guillaume; Picard, Brigitte; Hocquette, Jean-François; Agence de l'Environnement et de la Maîtrise de l'Energie, France; European Union; et al. (Elsevier BV, 2020-10)
      The aim of this integrative study was to investigate the relationships between biochemical traits (total, insoluble and soluble collagens (TCol, ICol, SCol), cross-links (CLs), proteoglycans (TPGs), proportion of fiber types, total lipids (TLips), main fatty acids (FAs) families, the n-6/n-3 polyunsaturated FA (n-6/n-3PUFA) ratio and the sensory attributes scores (tenderness, juiciness, flavor) of two muscles from beef: Rectus abdominis (RA) and Longissimus thoracis (LT). For robust analysis, a database was prepared using samples from three studies from animals raised under different production systems. The analyses were performed either on each study separately or on pooled data per muscle after removing as many experimental effects as possible in each study. The CLs (across the muscles and studies) and, to a lower extent, type IIA muscle fibers (mainly for RA muscles), saturated FAs (SFAs), monounsaturated FAs (MUFAs) (for the LT muscles) were the components the most frequently associated with tenderness. The CLs, type IIA muscle fibers (mainly for the RA muscles), TLips, SFAs, MUFAs, conjugated linoleic acids (CLAs) and n-6/n-3 PUFA ratio (mainly for the LT muscles) were the components the most associated with juiciness. The TLips and CLAs (across the muscles and studies), SFAs, MUFAs (mainly for the LT muscles), CLs (mainly for the RA muscles) and TPGs (mainly for the LT muscles) were the components the most associated with flavor liking. The CLs, CLAs, TLips, SFAs, MUFAs, n-6/n-3 PUFA ratio, type IIA and I muscle fibers were the components the most frequently associated with the 3 sensory scores taken together. The SCol, TPGs and type IIX+B muscle fibers were little associated with the sensory scores taken together. The TCol, ICol and PUFAs were components the least associated with sensory scores. The data of this integrative study highlighted for the first time that the CLs were negatively involved in the determination of the three sensory traits mainly in the RA muscle. The muscle fibers in this integrative study had a weak impact on the variations in beef sensory traits. The type IIA and IIX+B muscle fibers were respectively negatively and positively associated with tenderness, negatively associated with juiciness and flavor. The type I muscle fibers were overall positively associated with juiciness and flavor and negatively or positively with tenderness and these associations were muscle and study-dependent. Overall, the TLips and FAs were positively associated with the sensory scores and the n-6/n-3 PUFA ratio was negatively associated with them.
    • What are the drivers of beef sensory quality using metadata of intramuscular connective tissue, fatty acids and muscle fiber characteristics?

      Listrat, Anne; GAGAOUA, Mohammed; Andueza, Donato; Gruffat, Dominique; Normand, Jérome; Mairesse, Guillaume; Picard, Brigitte; Hocquette, Jean-François; Agence de l'Environnement et de la Maîtrise de l'Energie; European Union; et al. (Elsevier, 2020-08-14)
      The aim of this integrative study was to investigate the relationships between biochemical traits (total, insoluble and soluble collagens (TCol, ICol, SCol), cross-links (CLs), proteoglycans (TPGs), proportion of fiber types, total lipids (TLips), main fatty acids (FAs) families, the n-6/n-3 polyunsaturated FA (n-6/n-3PUFA) ratio and the sensory attributes scores (tenderness, juiciness, flavor) of two muscles from beef: Rectus abdominis (RA) and Longissimus thoracis (LT). For robust analysis, a database was prepared using samples from three studies from animals raised under different production systems. The analyses were performed either on each study separately or on pooled data per muscle after removing as many experimental effects as possible in each study. The CLs (across the muscles and studies) and, to a lower extent, type IIA muscle fibers (mainly for RA muscles), saturated FAs (SFAs), monounsaturated FAs (MUFAs) (for the LT muscles) were the components the most frequently associated with tenderness. The CLs, type IIA muscle fibers (mainly for the RA muscles), TLips, SFAs, MUFAs, conjugated linoleic acids (CLAs) and n-6/n-3 PUFA ratio (mainly for the LT muscles) were the components the most associated with juiciness. The TLips and CLAs (across the muscles and studies), SFAs, MUFAs (mainly for the LT muscles), CLs (mainly for the RA muscles) and TPGs (mainly for the LT muscles) were the components the most associated with flavor liking. The CLs, CLAs, TLips, SFAs, MUFAs, n-6/n-3 PUFA ratio, type IIA and I muscle fibers were the components the most frequently associated with the 3 sensory scores taken together. The SCol, TPGs and type IIX+B muscle fibers were little associated with the sensory scores taken together. The TCol, ICol and PUFAs were components the least associated with sensory scores. The data of this integrative study highlighted for the first time that the CLs were negatively involved in the determination of the three sensory traits mainly in the RA muscle. The muscle fibers in this integrative study had a weak impact on the variations in beef sensory traits. The type IIA and IIX+B muscle fibers were respectively negatively and positively associated with tenderness, negatively associated with juiciness and flavor. The type I muscle fibers were overall positively associated with juiciness and flavor and negatively or positively with tenderness and these associations were muscle and study-dependent. Overall, the TLips and FAs were positively associated with the sensory scores and the n-6/n-3 PUFA ratio was negatively associated with them.