Tackling proteome changes in the longissimus thoracis bovine muscle in response to pre-slaughter stress

In-depth exploration of the high and normal pH beef proteome: First insights emphasizing the dynamic protein changes in Longissimus thoracis muscle from pasture-finished Nellore bulls over different postmortem times

This study aimed to evaluate for the first time the temporal dynamic changes in early postmortem proteome of normal and high ultimate pH (pHu) beef samples from the same cattle using a shotgun proteomics approach. Ten selected carcasses classified as normal (pHu < 5.8; n = 5) or high (pHu ≥ 6.2; n = 5) pHu beef from pasture-finished Nellore (Bos taurus indicus) bulls were sampled from Longissimus thoracis muscle at 30 min, 9 h and 44 h postmortem for proteome comparison. The temporal proteomics profiling quantified 863 proteins, from which 251 were differentially abundant (DAPs) between high and normal pHu at 30 min (n = 33), 9 h (n = 181) and 44 h (n = 37). Among the myriad interconnected pathways regulating pH decline during postmortem metabolism, this study revealed the pivotal role of energy metabolism, cellular response to stress, oxidoreductase activity and muscle system process pathways throughout the early postmortem. Twenty-three proteins overlap among postmortem times and may be suggested as candidate biomarkers to the dark-cutting condition development. The study further evidenced for the first time the central role of ribosomal proteins and histones in the first minutes after animal bleeding. Moreover, this study revealed the disparity in the mechanisms underpinning the development of dark-cutting beef condition among postmortem times, emphasizing multiple dynamic changes in the muscle proteome. Therefore, this study revealed important insights regarding the temporal dynamic changes that occur in early postmortem of high and normal muscle pHu beef, proposing specific pathways to determine the biological mechanisms behind dark-cutting determination.

Sequential window acquisition of all theoretical mass spectra (SWATH-MS) as an emerging proteomics approach for the discovery of dark-cutting beef biomarkers

Recent advances in "omics" technologies have enabled the identification of new beef quality biomarkers and have also allowed for the early detection of quality defects such as dark-cutting beef, also known as DFD (dark, firm, and dry) beef. However, most of the studies conducted were carried out on a small number of animals and mostly applied gel-based proteomics. The present study proposes for the first time a Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) proteomics approach to characterize and comprehensively quantify the post-mortem muscle proteome of DFD (pH24 ≥ 6.2) and CONTROL (5.4 ≤ pH24 ≤ 5.6) beef samples within the largest database of DFD/CONTROL beef samples to date (26 pairs of the Longissimus thoracis muscle samples of young bulls from Asturiana de los Valles breed, n = 52). The pairwise comparison yielded 35 proteins that significantly differed in their abundances between the DFD and CONTROL samples. Chemometrics methods using both PLS-DA and OPLS-DA revealed 31 and 36 proteins with VIP > 2.0, respectively. The combination of different statistical methods these being Volcano plot, PLS-DA and OPLS-DA allowed us to propose 16 proteins as good candidate biomarkers of DFD beef. These proteins are associated with interconnected biochemical pathways related to energy metabolism (DHRS7B and CYB5R3), binding and signaling (RABGGTA, MIA3, BPIFA2B, CAP2, APOBEC2, UBE2V1, KIR2DL1), muscle contraction, structure and associated proteins (DMD, PFN2), proteolysis, hydrolases, and activity regulation (AGT, C4A, GLB1, CAND2), and calcium homeostasis (ANXA6). These results evidenced the potential of SWATH-MS and chemometrics to accurately identify novel biomarkers for meat quality defects, providing a deeper understanding of the molecular mechanisms underlying dark-cutting beef condition.

Molecular Changes of Meat Proteins During Processing and Their Impact on Quality and Nutritional Values

Meats are rich in lipids and proteins, exposing them to rapid oxidative changes. Proteins are essential to the human diet, and changes in the structure and functional attributes can greatly influence the quality and nutritional value of meats. In this article, we review the molecular changes of proteins during processing, their impact on the nutritional value of fresh and processed meat, the digestibility and bioavailability of meat proteins, the risks associated with high meat intake, and the preventive strategies employed to mitigate these risks. This information provides new research directions to reduce or prevent oxidative processes that influence the quality and nutritional values of meat.

Improving animal welfare status and meat quality through assessment of stress biomarkers: A critical review

Stress induces various physiological and biochemical alterations in the animal body, which are used to assess the stress status of animals. Blood profiles, serum hormones, enzymes, and physiological conditions such as body temperature, heart, and breathing rate of animals are the most commonly used stress biomarkers in the livestock sector. Previous exposure, genetics, stress adaptation, intensity, duration, and rearing practices result in wide intra- and inter-animal variations in the expression of various stress biomarkers. The use of meat proteomics by adequately analyzing the expression of various muscle proteins such as heat shock proteins (HSPs), acute phase proteins (APPs), texture, and tenderness biomarkers help predict meat quality and stress in animals before slaughter. Thus, there is a need to identify non-invasive, rapid, and accurate stress biomarkers that can objectively assess stress in animals. The present manuscript critically reviews various aspects of stress biomarkers in animals and their application in mitigating preslaughter stress in meat production.

Application of 2-D DIGE to study the effect of ageing on horse meat myofibrillar sub-proteome

Considering the high relevance of meat tenderness for consumer acceptability, the aim of this study was to investigate post-mortem changes in myofibrillar sub-proteome in steaks from longissimus thoracis et lumborum muscle of six Hispano-Bretón horses. Indeed, the ageing process that leads to meat tenderization has been scarcely studied in this species. Steaks (n = 24) were aged (4 °C) in the dark under vacuum for 0, 7, 14 and 21 days and the myofibrillar sub-proteome was extracted. Using 2-D DIGE minimal labelling, 35 spots that were differentially abundant between 0 and 21 days aged meat were detected. Of them, 24 were analysed by LC-MS/MS, identifying a total of 29 equine proteins. These were structural and metabolic proteins, and among them, four (Actin, Troponin T and Myosin binding proteins 1 and 2) were selected for Western blot analysis, reporting changes in their abundance after 0, 7, 14 and 21 days of ageing. Results revealed that they should be further studied as potential protein biomarkers of horse meat tenderization. Additionally, several protein fragments increased after ageing, as was the case of glyceraldehyde-3-phosphate dehydrogenase. Fragments of this protein were present in four protein spots, and their study could be useful for monitoring horse meat tenderization. SIGNIFICANCE: Tenderization during ageing has been widely studied in meat from several farm animal species; however, both research and standardized ageing practices are lacking for the particular case of horse meat. In this regard, this study presents novel proteomic findings related to post-mortem evolution of horse muscle proteins. Acquired knowledge would support the development and optimization of efficient ageing practices by horse meat industry.

The potential of proteomics in the study of processed meat products

Proteomics is a field that has grown rapidly since its emergence in the mid-1990s, reaching many disciplines such as food technology. The application of proteomic techniques in the study of complex biological samples such as foods, specifically meat products, allows scientists to decipher the underlying cellular mechanisms behind different quality traits. Lately, much emphasis has been placed on the discovery of biomarkers that facilitate the prediction of biochemical transformations of the product and provide key information on parameters associated with traceability and food safety. This review study focuses on the contribution of proteomics in the improvement of processed meat products. Different techniques and strategies have recently been successfully carried out in the study of the proteome of these products that can help the development of foods with a higher sensory quality, while ensuring consumer safety through early detection of microbiological contamination and fraud. SIGNIFICANCE: The food industry and the academic world work together with the aim of responding to market demands, always seeking excellence. In particular, the meat industry has to face a series of challenges such as, achieving sensory attributes in accordance with the standards required by the consumer and maintaining a high level of safety and transparency, avoiding deliver adulterated and/or contaminated products. This review work exposes how the aforementioned challenges are attempted to be solved through proteomic technology, discussing the latest and most outstanding research in this regard, which undoubtedly contribute to improving the quality, in all the extension of the word, of meat products, providing relevant knowledge in the field of proteomic research.

Development of a Portable Near-Infrared Spectroscopy Tool for Detecting Freshness of Commercial Packaged Pork

Real-time monitoring of meat quality requires fast, accurate, low-cost, and non-destructive analytical methods that can be used throughout the entire production chain, including the packaged product. The aim of this work was to evaluate the potential of a portable near-infrared (NIR) spectroscopy tool for the on-site detection of freshness of pork loin fillets in modified atmosphere packaging (MAP) stored on display counters. Pork loin slices were sealed in MAP trays under two proportions of O2/CO2/N2: High-Ox-MAP (30/40/30) and Low-Ox-MAP (5/20/75). Changes in pH, color, thiobarbituric acid reactive substances (TBARS), Warner−Bratzler shear force (WBSF), and microbiology (total viable counts, Enteriobacteriaceae, and lactic acid bacteria) were monitored over 15 days post-mortem at 4 °C. VIS-NIR spectra were collected from pork fillets before (through the film cover) and after opening the trays (directly on the meat surface) with a portable LABSPEC 5000 NIR system in diffuse reflectance mode (350−2500 nm). Quantitative NIR models by partial least squares regression (PLSR) showed a promising prediction ability for meat color (L*, a*, C*, and h*) and microbiological variables (R2VAL > 0.72 and RPDVAL > 2). In addition, qualitative models using PLS discriminant analysis obtained good accuracy (over 90%) for classifying pork samples as fresh (acceptable for consumption) or spoiled (not acceptable) based on their microbiological counts. VIS-NIR spectroscopy allows rapid evaluation of product quality and shelf life and could be used for on-site control of pork quality.

Phosphoproteome Analysis Using Two-Dimensional Electrophoresis Coupled with Chemical Dephosphorylation

Protein phosphorylation is a reversible post-translational modification (PTM) with major regulatory roles in many cellular processes. However, the analysis of phosphoproteins remains the most challenging barrier in the prevailing proteome research. Recent technological advances in two-dimensional electrophoresis (2-DE) coupled to mass spectrometry (MS) have enabled the identification, characterization, and quantification of protein phosphorylation on a global scale. Most research on phosphoproteins with 2-DE has been conducted using phosphostains. Nevertheless, low-abundant and low-phosphorylated phosphoproteins are not necessarily detected using phosphostains and/or MS. In this study, we report a comparative analysis of 2-DE phosphoproteome profiles using Pro-Q Diamond phosphoprotein stain (Pro-Q DPS) and chemical dephosphorylation of proteins with HF-P from longissimus thoracis (LT) muscle samples of the Rubia Gallega cattle breed. We found statistically significant differences in the number of identified phosphoproteins between methods. More specifically, we found a three-fold increase in phosphoprotein detection with the HF-P method. Unlike Pro-Q DPS, phosphoprotein spots with low volume and phosphorylation rate were identified by HF-P technique. This is the first approach to assess meat phosphoproteome maps using HF-P at a global scale. The results open a new window for 2-DE gel-based phosphoproteome analysis.

Comparative Proteomics of Potato Cultivars with a Variable Dormancy Period

The control of the duration of the dormancy phase is a significant challenge in the potato industry and for seed producers. However, the proteome landscape involved in the regulation of the length of the dormancy period over potato cultivars remains largely unexplored. In this study, we performed for the first time a comparative proteome profiling of potato cultivars with differential duration of tuber dormancy. More specifically, the proteome profiling of Agata, Kennebec and Agria commercial potato varieties with short, medium and medium-long dormancy, respectively, was assessed at the endodormancy stage using high-resolution two-dimensional electrophoresis (2-DE) coupled to reversed-phase liquid chromatography–tandem mass spectrometry (LC-TripleTOF MS/MS). A total of 11 proteins/isoforms with statistically significant differential abundance among cultivars were detected on 2-DE gels and confidently identified by LC-TripleTOF MS/MS. Identified proteins have known functions related to tuber development, sprouting and the oxylipins biosynthesis pathway. Fructokinase, a mitochondrial ADP/ATP carrier, catalase isozyme 2 and heat shock 70 kDa were the proteins with the strongest response to dormancy variations. To the best of our knowledge, this study reports the first candidate proteins underlying variable dormancy length in potato cultivars.

Tandem mass tag labeling to assess proteome differences between intermediate and very tender beef steaks

Tenderness is considered as one of the most important quality attributes dictating consumers' overall satisfaction and future purchasing decisions of fresh beef. However, the ability to predict and manage tenderness has proven very challenging due to the numerous factors that contribute to variation in end-product tenderness. Proteomic profiling allows for global examination of differentially abundant proteins in the meat and can provide new insight into biological mechanisms related to meat tenderness. Hence, the objective of this study was to examine proteomic profiles of beef longissimus lumborum (LL) steaks varying in tenderness, with the intention to identify potential biomarkers related to tenderness. For this purpose, beef LL muscle samples were collected from 99 carcasses at 0 and 384 h postmortem. Based on Warner-Bratzler shear force values at 384 h, 16 samples with the highest (intermediate tender, IT) and lowest (very tender, VT) values were selected to be used for proteomic analysis in this study (n = 8 per category). Using tandem mass tag-based proteomics, a total of 876 proteins were identified, of which 51 proteins were differentially abundant (P < 0.05) between the tenderness categories and aging periods. The differentially identified proteins encompassed a wide array of biological processes related to muscle contraction, calcium signaling, metabolism, extracellular matrix organization, chaperone, and apoptosis. A greater (P < 0.05) relative abundance of proteins associated with carbohydrate metabolism and apoptosis, and a lower (P < 0.05) relative abundance of proteins involved in muscle contraction was observed in the VT steaks after aging compared with the IT steaks, suggesting that more proteolysis occurred in the VT steaks. This may be explained by the greater (P < 0.05) abundance of chaperonin and calcium-binding proteins in the IT steaks, which could have limited the extent of postmortem proteolysis in these steaks. In addition, a greater (P < 0.05) abundance of connective tissue proteins was also observed in the IT steaks, which likely contributed to the difference in tenderness due to added background toughness. The established proteomic database obtained in this study may provide a reference for future research regarding potential protein biomarkers that are associated with meat tenderness.

The Investigation of Protein Profile and Meat Quality in Bovine Longissimus thoracic Frozen under Different Temperatures by Data-Independent Acquisition (DIA) Strategy

The influence of freezing on the protein profile and quality traits in bovine Longissimus thoracic (LT) muscle was investigated by the data-independent acquisition (DIA) technique. Compared to fresh meat, a total of 262 proteins were identified as differential abundance proteins (DAPs) in four frozen groups (−12 °C, −18 °C, −38 °C, and −80 °C). According to the bioinformatics analysis, most of the DAPs in the significant Go terms and the KEGG pathway were structure proteins and enzymes. Proteome changes in the frozen bovine muscle at −12 °C and −18 °C were more significant than those at −38 °C and −80 °C. The result was consistent with the deterioration trend of the meat quality. The correlation analysis revealed that 17 proteins were correlated closely with the color, shear force, thawing loss, and cooking loss of the frozen meat, which could be used as putative biomarkers for frozen meat quality. MYO18A and ME3 are newly discovered proteins that are associated with frozen beef quality. In addition, CTTN and SERPINB6 were identified in frozen groups, which exhibited a significant inverse correlation with thawing loss (p < 0.01). These findings reveal the quality changes induced by freezing at the protein molecular level and provide new insights into the control of quality deterioration.

Proteomic Technologies and their Application for Ensuring Meat Quality, Safety and Authenticity

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Proteomic tools were extensively used to understand the relationship between muscle proteome and conversion of muscle to meat, post-mortem proteolysis, meat texture, and variation in meat color. Developments in proteomic tools have also resulted in their application for addressing the safety and authenticity issues including meat species identification, detection of animal byproducts, non-meat ingredients and tissues in meat products, traceability, identification of genetically modified ingredients, chemical residues and other harmful substances. Proteomic tools are also being used in some of the potential areas like understanding the effect of animal transportation, stunning, slaughter stress, halal authentication and issues related to animal welfare. Emerging advances in proteomic and peptidomic technologies and their application in traceability, meat microbiology, safety and authentication are taking a major stride as an interesting and complementary alternative to DNA-based methods currently in use. Future research in meat science need to be linked to emerging metabolomic, lipidomic and other omic technologies for ensuring integrated meat quality and safety management. In this paper, a comprehensive overview of the use of proteomics for the assessment of quality and safety in the meat value chain and their potential application is discussed.

New Insights on the Impact of Cattle Handling on Post-Mortem Myofibrillar Muscle Proteome and Meat Tenderization

This study investigated the effect of different cattle management strategies at farm (Intensive vs. Extensive) and during transport and lairage (mixing vs. non-mixing with unfamiliar animals) on the myofibrillar subproteome of Longissimus thoracis et lumborum (LTL) muscle of "Asturiana de los Valles" yearling bulls. It further aimed to study the relationships with beef quality traits including pH, color, and tenderness evaluated by Warner-Bratzler shear force (WBSF). Thus, comparative proteomics of the myofibrillar fraction along meat maturation (from 2 h to 14 days post-mortem) and different quality traits were analyzed. A total of 23 protein fragments corresponding to 21 unique proteins showed significant differences among the treatments (p < 0.05) due to any of the factors considered (Farm, Transport and Lairage, and post-mortem time ageing). The proteins belong to several biological pathways including three structural proteins (MYBPC2, TNNT3, and MYL1) and one metabolic enzyme (ALDOA) that were affected by both Farm and Transport/Lairage factors. ACTA1, LDB3, and FHL2 were affected by Farm factors, while TNNI2 and MYLPF (structural proteins), PKM (metabolic enzyme), and HSPB1 (small Heat shock protein) were affected by Transport/Lairage factors. Several correlations were found between the changing proteins (PKM, ALDOA, TNNI2, TNNT3, ACTA1, MYL1, and CRYAB) and color and tenderness beef quality traits, indicating their importance in the determination of meat quality and their possible use as putative biomarkers.

Assessment of Stress by Serum Biomarkers in Calves and Their Relationship to Ultimate pH as an Indicator of Meat Quality

Simple Summary

The routine handling of cattle during the rearing period and during antemortem events is an inevitable source of animal stress that can have negative impacts on the quality of meat, resulting in economic losses for the meat industry. This study assesses the breed, the farm management system, and the pre-mortem handling of animals and their impact on serum stress biomarkers, as well as their relationship with pH_u. The findings indicate that breed, together with farm management, had the highest impact; cortisol, lactate, and serum amyloid A were identified as potential stress biomarkers in relation to pH_u. We believe that these findings might help in the assessment of stress in cattle at the stage prior to slaughter.

Abstract

Seventy-eight calves from Asturiana de los Valles, Retinta, and Rubia Gallega breeds, under extensive and intensive farm systems and animal mixing and non-mixing conditions, and during the transport and lairage in slaughterhouses, were studied. This research aimed to study the effect of breed, farm system and mixing conditions on serum biomarkers (cortisol, lactate, glucose, serum amyloid A, haptoglobin, and C-reactive protein) and their relationship with pH_u at slaughter time, and to evaluate the response of the serum biomarkers of calves throughout fattening period. Moreover, this study aims to evaluate the response of the biomarkers in each breed during the fattening period. At slaughter time, cortisol and lactate were affected by BreedxFarm; Retinta showed the opposite pattern to the others and revealed the highest glucose in extensive farm systems. Rubia Gallega in mixing revealed the highest Amyloid A and haptoglobin. Extensive calves in mixing conditions showed the highest glucose. There was a relationship among the variables cortisol, lactate, Amyloid A, and pH_u. Slaughter time was a major stressor, and the stress response was mainly affected by breed. At slaughter, several biomarkers should be considered.

Protein Biomarkers of Bovine Defective Meats at a Glance: Gel-Free Hybrid Quadrupole-Orbitrap Analysis for Rapid Screening

An understanding of biological mechanisms that could be involved in the stress response of animal cattle prior to slaughter is critical to create effective strategies aiming at the production of high-quality meat. The sarcoplasmic proteome of directly extracted samples from normal and high ultimate pH (pHu) meat groups was studied through a straightforward gel-free strategy supported by liquid chromatography hybrid quadrupole-Orbitrap high-resolution mass spectrometry (LC-HRMS) analysis. A stepped proteomic pipeline combining rapid biomarker hunting supported by qualitative protein Mascot scores followed by targeted label-free peptide quantification revealed 26 descriptors that characterized meat groups assayed. The functional study of the proposed biomarkers suggested their relevant role in metabolic, chaperone/stress-related, muscle contractility/fiber organization, and transport activities. The efficiency, flexibility, rapidity, and easiness of the methodology proposed can positively contribute to the creation of innovative proteomic alternatives addressing meat quality assessment.

Dark-cutting beef: A brief review and an integromics meta-analysis at the proteome level to decipher the underlying pathways

Comprehensive characterization of the post-mortem muscle proteome defines a fundamental goal in meat proteomics. During the last decade, proteomics tools have been applied in the field of foodomics to help decipher factors underpinning meat quality variations and to enlighten us, through data-driven methods, on the underlying mechanisms leading to meat quality defects such as dark-cutting meat known also as dark, firm and dry (DFD) meat. In cattle, several proteomics studies have focused on the extent to which changes in the post-mortem muscle proteome relate to dark-cutting beef development. The present data-mining study firstly reviews proteomics studies which investigated dark-cutting beef, and secondly, gathers the protein biomarkers that differ between dark-cutting versus beef with normal-pH in a unique repertoire. A list of 130 proteins from eight eligible studies was curated and mined through bioinformatics for Gene Ontology annotations, molecular pathways enrichments, secretome analysis and biological pathways comparisons to normal beef color from a previous meta-analysis. The major biological pathways underpinning dark-cutting beef at the proteome level have been described and deeply discussed in this integromics study.

Injection of iodoacetic acid into pre-rigor bovine muscle simulates dark cutting conditions

The purpose of this study was to develop an in situ model for dark cutting beef. Iodoacetic acid (IAA) was injected at different concentrations (0, 0.625, 1.25, 2.5, 3.75, 5, or 10 μmol/g of muscle) into pre-rigor bovine longissimus thoracis et lumborum (LTL) muscle samples, and pH and color were evaluated over a 48 h period. Injection of IAA blunted muscle pH decline and lowered lightness (L*), redness (a*), and yellowness (b*) values (P ≤ 0.05) in a concentration dependent fashion. In a follow-up study, LTL muscle samples were injected with 5 μmol IAA/g of muscle to test whether IAA maintains its effect over a 336 h post-mortem storage period. In addition to inhibiting pH decline and decreasing color values, IAA increased LTL muscle water holding capacity (WHC) and firmness (P ≤ 0.05) throughout the 336 h post-mortem storage period. Collectively, these data suggest that pre-rigor injection of IAA generates beef with dark cutting-like characteristics.

Proteomic pipeline for biomarker hunting of defective bovine meat assisted by liquid chromatography-mass spectrometry analysis and chemometrics

A wide variety of factors prior to slaughter may affect the stress status of beef cattle, giving rise to well-known 'dark-cutting' defective meats characterised by a high ultimate pH (pHu). To understand the underlying mechanisms of pHu fluctuations in beef cattle there was studied the proteome changes caused by pre-slaughter stress through a gel-free proteomic approach. Comparative peptidomic analysis was carried out on 12 loin samples at 24 h post-mortem from Longissimus thoracis et lumborum bovine muscle of crossbred animals, previously sorted into two different groups according to their pHu values: normal (pHu < 6.0) and high (pHu ≥ 6.0). Tryptic peptides from direct protein extracts were approached by combining untargeted (intact mass, MS¹) and targeted (Selected Reaction Monitoring, SRM) quantitative LC-MS assays followed by chemometric analysis. Seventeen peptide biomarkers belonging to 10 different proteins appropriately discriminated sample groups assayed. Results may promote the use of this simple and effective methodology towards the creation of new insights in meat quality research. SIGNIFICANCE: The significance of this study was the optimization of an affordable straightforward gel-free proteomic approach addressing the differentiation of the muscle sub-proteome of normal and high pHu meat samples. This strategy allowed the study of tryptic peptides from direct meat protein extracts by combining untargeted MS¹ and targeted SRM quantitative assays performed by conventional LC-MS detection. Affordability, simplicity and robustness of this methodology can facilitate its readily implementation in routine protocols for quality assessment of meat.

Omics Application in Animal Science-A Special Emphasis on Stress Response and Damaging Behaviour in Pigs

Increasing stress resilience of livestock is important for ethical and profitable meat and dairy production. Susceptibility to stress can entail damaging behaviours, a common problem in pig production. Breeding animals with increased stress resilience is difficult for various reasons. First, studies on neuroendocrine and behavioural stress responses in farm animals are scarce, as it is difficult to record adequate phenotypes under field conditions. Second, damaging behaviours and stress susceptibility are complex traits, and their biology is not yet well understood. Dissecting complex traits into biologically better defined, heritable and easily measurable proxy traits and developing biomarkers will facilitate recording these traits in large numbers. High-throughput molecular technologies (“omics”) study the entirety of molecules and their interactions in a single analysis step. They can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways. Here, we provide a general overview of different omics approaches and we give examples of how these techniques could be applied to discover biomarkers. We discuss the genetic dissection of the stress response by different omics techniques and we provide examples and outline potential applications of omics tools to understand and prevent outbreaks of damaging behaviours.

Effects of Farm Management Practices and Transport Time on Post-Mortem Changes of Longissimus lumborum Muscle Proteins in Suckling Goat Kids

The combined effect of farm management practices, transport time, and ageing time on the electrophoretic changes of sarcoplasmic (SPP) and myofibrillar (MFP) protein fractions of goat kids was studied. A total of 64 suckling goat kids were withdrawn from two farms with "high" (GW) and "low" (DW) welfare-friendly management practices, and they were transported for 2 or 6 h immediately before slaughtering. Longissimus lumborum samples were obtained at 3, 8, and 21 days post-mortem, and muscle proteins were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis SDS-PAGE. Both protein extracts displayed significant changes attributable to meat maturation. Managing conditions of kids in DW farms increased the post-mortem susceptibility of muscle proteins. Some MFP of Longissimus lumborum muscle, such as troponin T, as well as 26-30 and 35-37 kDa fractions were influenced significantly by deficient on-farm management, and therefore, these protein fragments might be considered as indicators of low-welfare on-farm management in goat kids.

A straightforward gel-free proteomics pipeline assisted by liquid isoelectric focusing (OFFGEL) and mass spectrometry analysis to study bovine meat proteome

Bovine sarcoplasmic sub-proteome was studied through a straightforward gel-free pipeline supported by liquid isoelectric focusing (OFFGEL) protein fractionation coupled to liquid chromatography-mass spectrometry (LC-MS) analysis. Full-MS and data-dependent MS/MS analyses were simultaneously performed by a conventional three-dimensional ion-trap addressing targeted quantitative and untargeted qualitative research, respectively. There were unambiguously identified 47 proteins distributed along 12 OFFGEL fractions assayed. Regarding intermediate- and high-abundant peptides, bulky quantitative data processing performed by MZmine 2 freeware yielded a satisfactory linearity and coefficient of variation with r2 in the 0.95–0.99 range and about 25%, respectively. Up to 41 peptides from 20 identified proteins were relatively quantified throughout OFFGEL fractions. This reliable, flexible and affordable gel-free proteomic approach could be readily implemented by industry to improve quality assessment of protein-based food products.

Measuring quantitative proteomic distance between Spanish beef breeds

Estimates of quantitative proteomic distance between populations have not been reported to date. Here, quantitative proteomic distances between three Spanish bovine breeds (Asturiana de los Valles, AV; Retinta, RE; and Rubia Gallega, RG) were estimated from two-dimensional electrophoresis profiles of meat samples of longissimus thoracis muscle at 2 h post-mortem. Statistically significant distances were detected between AV/RG and the most genetically different RE breed, using the novel QD measure of quantitative proteomic distance. In total, 18 differentially abundant myofibrillar and sarcoplasmic proteins/isoforms contributing to proteomic distances between breeds were confidently identified by tandem mass spectrometry. The fast skeletal myosin regulatory light chain 2 followed by other five interacting proteins exhibited the most pronounced relative change between breeds. In addition, most differentially represented proteins could be associated with variations in meat tenderness. Therefore, they could be candidate biomarkers for molecular breeding programs and authentication of the three Spanish beef breeds.

Proteomic Characterization of Normal and Woody Breast Meat from Broilers of Five Genetic Strains

Woody breast (WB) is an emergent broiler myopathy that is macroscopically characterized by hardened areas of the Pectoralis major muscle. Five genetic strains (strains 1–5) of mixed-sex broilers were fed either a control or an amino acid (AA)-reduced diet (20% reduction of digestible lysine, total sulfur AAs, and threonine) for 8 wk. Differences between whole-muscle proteome profiles of normal breast (NB; n = 6 gels) and WB tissue (n = 6 gels) were characterized for (1) broiler strains 1–5 that were fed with a control diet and collected at 0 min; (2) strain 5 (control diet) that were collected at 15 min, 4 h, and 24 h; (3) strain 5 (0 min) that were fed with a control and an AA-reduced diet. Birds that yielded WB were heavier and had a greater pH at death (pH0min) than normal birds. Results indicated that 21 proteins were more abundant (P &lt; 0.05) and 3 proteins were less abundant (P &lt; 0.05) in WB compared with NB. The differentially abundant proteins in each comparison were consistently upregulated or downregulated in WB tissue although the different protein profiles were noticed for each comparison. Strains 2 and 5 had more protein profile differences between WB and NB meat than strains 1, 3, and 4, which potentially indicates a stronger genetic component for strains 2 and 5 with respect to WB formation. The proteins that were more abundant in WB compared to NB are involved in carbohydrate metabolism, oxidative stress, cytoskeleton structure, and transport and signaling. Ingenuity Pathway Analysis indicated that regulated pathways in WB were mainly related to carbohydrate metabolism, cellular repair, cellular organization and maintenance, and cell death and survival. The results support the potential causes of WB myopathy, including the presence of hypoxia, oxidative stress, increased apoptosis, misfolded proteins, and inflammation.

Label-free quantitative proteomic analysis of M. longissimus dorsi from cattle during dietary restriction and subsequent compensatory growth

Compensatory growth (CG) is a naturally occurring physiological process whereby an animal has the ability to undergo enhanced growth following a period of restricted feeding. This studies objective was to identify key proteins involved in the expression of CG. Forty Holstein Friesian bulls were equally assigned to one of four groups. R1 and R2 groups were subjected to restricted feed allowance for 125 days (Period 1). A1 and A2 animals had ad libitum access to feed in Period 1. Following Period 1, all animals from R1 and A1 were slaughtered. Remaining animals (R2 and A2) were slaughtered following ad libitum access to feed for successive 55 days (Period 2). M. longissimus dorsi samples were collected at slaughter from all animals. Proteins were isolated from samples and subjected to label-free mass spectrometry proteomic quantification. Proteins which were differentially abundant during CG (n = 39) were involved in cellular binding processes, oxidative phosphorylation and mitochondrial function. There was also evidence for up regulation of three pathways involved in nucleotide biosynthesis. Genetic variants in or regulating genes pertaining to proteins identified in this study may hold potential for use as DNA based biomarkers for genomic selection of animals with a greater ability to undergo CG.

Aggregation of Omic Data and Secretome Prediction Enable the Discovery of Candidate Plasma Biomarkers for Beef Tenderness

Beef quality is a complex phenotype that can be evaluated only after animal slaughtering. Previous research has investigated the potential of genetic markers or muscle-derived proteins to assess beef tenderness. Thus, the use of low-invasive biomarkers in living animals is an issue for the beef sector. We hypothesized that publicly available data may help us discovering candidate plasma biomarkers. Thanks to a review of the literature, we built a corpus of articles on beef tenderness. Following data collection, aggregation, and computational reconstruction of the muscle secretome, the putative plasma proteins were searched by comparison with a bovine plasma proteome atlas and submitted to mining of biological information. Of the 44 publications included in the study, 469 unique gene names were extracted for aggregation. Seventy-one proteins putatively released in the plasma were revealed. Among them 13 proteins were predicted to be secreted in plasma, 44 proteins as hypothetically secreted in plasma, and 14 additional candidate proteins were detected thanks to network analysis. Among these 71 proteins, 24 were included in tenderness quantitative trait loci. The in-silico workflow enabled the discovery of candidate plasma biomarkers for beef tenderness from reconstruction of the secretome, to be examined in the cattle plasma proteome.

The first evidence of global meat phosphoproteome changes in response to pre-slaughter stress

BACKGROUND

Pre-slaughter stress (PSS) impairs animal welfare and meat quality. Dark, firm and dry (DFD) are terms used to designate poor quality meats induced by PSS. Protein phosphorylation can be a potentially significant mechanism to explain rapid and multiple physiological and biochemical changes linked to PSS-dependent muscle-to-meat conversion. However, the role of reversible phosphorylation in the response to PSS is still little known. In this study, we report a comparative phosphoproteomic analysis of DFD and normal meats at 24 h post-mortem from the longissimus thoracis (LT) bovine muscle of male calves of the Rubia Gallega breed. For this purpose, two-dimensional gel electrophoresis (2-DE), in-gel multiplex identification of phosphoproteins with PRO-Q Diamond phosphoprotein-specific stain, tandem (MALDI-TOF/TOF) mass spectrometry (MS), novel quantitative phosphoproteomic statistics and bioinformatic tools were used.

RESULTS

Noticeable and statistically significant differences in the extent of protein phosphorylation were detected between sample groups at the qualitative and quantitative levels. Overall phosphorylation rates across significantly changed phosphoproteins were about three times higher in DFD than in normal meat. Significantly changed phosphoproteins involved a variable number of isoforms of 13 myofibrillar and sarcoplasmic nonredundant proteins. However, fast skeletal myosin light chain 2 followed by troponin T, F-actin-capping and small heat shock proteins showed the greatest phosphorylation change, and therefore they were the most important phosphoproteins underlying LT muscle conversion to DFD meat in the Rubia Gallega breed.

CONCLUSIONS

This is the first study reporting global meat phosphoproteome changes in response to PSS. The results show that reversible phosphorylation is a relevant mechanism underlying PSS response and downstream effects on meat quality. This research opens up novel horizons to unravel the complex molecular puzzle underlying muscle-to-meat conversion in response to PSS.

A proteomic-based approach for the search of biomarkers in Iberian wild deer (Cervus elaphus) as indicators of meat quality

The positive perception of deer meat among consumers is growing. Consequently, further efforts are needed to control its meat quality. Specifically, the aim of this study was to search protein biomarkers in connection with tenderness and intramuscular fat (IMF) content of Iberian wild red deer (Cervus elaphus) meat. Twelve venison samples classified as tender, intermediate and tough meat, as well as with different IMF were studied, using quantitative proteomic by SWATH-MS combined with bioinformatic analyses. The study of muscle proteome showed significant differences among these three groups of meat samples, since five differentially abundant proteins (IVD, LAMB1, MYL3, SDHC and SDHA) and six (FABP4, IVD, LAMB1, MYL3, CRYZ and SERPINB6) were strongly correlated with tenderness and IMF, respectively. The proteomic approach provides protein biomarkers linked to venison meat quality and marked changes in proteins related to oxidoreductase complex in skeletal muscle. SIGNIFICANCE: Meat tenderness and IMF are major concerns in game meat. The proteomic approach demonstrated a strong correlation between proteins and these quality traits, despite the complexity of samples (wild animals hunted at different ages). Our results suggest that several proteins can be biomarkers and provide a molecular insight.

The Discovery of Proteins Associated with Freshness of Coregonus Peled Muscle During Refrigerated Storage

The aim of this study is to identify the protein indicator of freshness of Coregonus peled using two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization-time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS) methods. Samples were obtained prior to (control group) and 2, 4, 6, and 8 days after refrigerated storage for quality and proteomics analysis. Three proteins were found to have significant differential abundance in sample groups during the refrigerated storage, including l-lactate dehydrogenase, adenylate kinase isoenzyme 1, and myosin heavy chain, which were associated with freshness changes of C. peled. The freshness of C. peled fish during the refrigerated storage can be differentiated from the comparison of the specific proteins. PRACTICAL APPLICATION: The changes of food quality pose not only the relative economical loses but also the potential implications on consumer's health. Proteomics can represent a powerful tool to explore potential biomarkers that may be related to meat quality defects. The identification of key protein biomarkers linked to freshness of Coregonus peled allows to monitor the response of the food matrix during storage and try to minimizes these defects.

The Major Storage Protein in Potato Tuber Is Mobilized by a Mechanism Dependent on Its Phosphorylation Status

The role of the protein phosphorylation mechanism in the mobilization of vegetative storage proteins (VSPs) is totally unknown. Patatin is the major VSP of the potato (Solanum tuberosum L.) tuber that encompasses multiple differentially phosphorylated isoforms. In this study, temporal changes in the phosphorylation status of patatin isoforms and their involvement in patatin mobilization are investigated using phosphoproteomic methods based on targeted two-dimensional electrophoresis (2-DE). High-resolution 2-DE profiles of patatin isoforms were obtained in four sequential tuber life cycle stages of Kennebec cultivar: endodormancy, bud break, sprouting and plant growth. In-gel multiplex identification of phosphorylated isoforms with Pro-Q Diamond phosphoprotein-specific stain revealed an increase in the number of phosphorylated isoforms after the tuber endodormancy stage. In addition, we found that the phosphorylation status of patatin isoforms significantly changed throughout the tuber life cycle (P < 0.05) using the chemical method of protein dephosphorylation with hydrogen fluoride-pyridine (HF-P) coupled to 2-DE. More specifically, patatin phosphorylation increased by 32% from endodormancy to the tuber sprouting stage and subsequently decreased together with patatin degradation. Patatin isoforms were not randomly mobilized because highly phosphorylated Kuras-isoforms were preferably degraded in comparison to less phosphorylated non-Kuras isoforms. These results lead us to conclude that patatin is mobilized by a mechanism dependent on the phosphorylation status of specific isoforms.

Stress Effects on Meat Quality: A Mechanistic Perspective

Stress inevitably occurs from the farm to abattoir in modern livestock husbandry. The effects of stress on the behavioral and physiological status and ultimate meat quality have been well documented. However, reports on the mechanism of stress effects on physiological and biochemical changes and their consequent effects on meat quality attributes have been somewhat disjointed and limited. Furthermore, the causes of variability in meat quality traits among different animal species, muscle fibers within an animal, and even positions within a piece of meat in response to stress are still not entirely clear. This review 1st summarizes the primary stress factors, including heat stress, preslaughter handling stress, oxidative stress, and other stress factors affecting animal welfare; carcass quality; and eating quality. This review further delineates potential stress-induced pathways or mediators, including AMP-activated protein kinase-mediated energy metabolism, crosstalk among calcium signaling pathways and reactive oxygen species, protein modification, apoptosis, calpain and cathepsin proteolytic systems, and heat shock proteins that exert effects that cause biochemical changes during the early postmortem period and affect the subsequent meat quality. To obtain meat of high quality, further studies are needed to unravel the intricate mechanisms involving the aforementioned signaling pathways or mediators and their crosstalk.

Proteomic footprint of ultrasound intensification on sliced dry-cured ham subjected to mild thermal conditions

Ultrasound can intensify the heating process used to correct texture defects in dry-cured hams. The effect of ultrasound-assisted heating on the proteome of sliced dry-cured ham was evaluated. Dry-cured hams with high proteolysis index (PI > 36) were sliced, vacuum packed and subjected to conventional (CV) and ultrasound-assisted (US) thermal treatments. Comparative proteome profiling between sample groups was assessed by two-dimensional electrophoresis (2-DE) coupled to tandem mass spectrometry. It was found that protein fragmentation increased markedly after US thermal treatment. Specifically, fragments of the major myofibrillar protein, actin, were abundantly over-represented following US heating. In addition, five unfragmented sarcoplasmic proteins (i.e. fatty acid-binding protein, peroxiredoxin-6, superoxide dismutase, carbonyl reductase and aminoacylase) showed increased abundance in the US sample group. These results suggest candidate biomarkers to monitor proteolysis intensity and proteolysis-independent effects linked to cured ham quality by ultrasound application. SIGNIFICANCE: The present proteome profiling study of treated dry-cured ham demonstrates the impact of ultrasound action on proteins. Moreover, negative organoleptic effects can be appearing with ultrasound treatment due to proteolysis increase. Therefore, the proteolysis monitoring could help to control these effects. In this regards, our results suggest that actin can be a candidate biomarker to monitor proteolysis intensity.

Contribution of myofibril filament disassembly to textural deterioration of ice-stored grass carp fillet: Significance of endogenous proteolytic activity, loss of heat shock protein and dephosphorylation of myosin light chain

To investigate the underlying mechanism of softening of ice-stored grass carp fillet, changes in assembly structure of myofibrillar proteins and potential candidates for regulating this change including myosin regulatory chain phosphorylation, heat shock proteins (Hsp27, Hsp90, αB-crystallin and UNC45) and endogenous protease activity were studied. Comparison of SDS-PAGE pattern of myofibrillar proteins treated with EDC crosslinking showed that thin filament experienced rapid disassembly within initial 8 h, followed by depolymerization of thick filament consisting of myosin, which further exacerbated the myofibril disorganization of fillets. Pearson coefficient analysis showed that UNC45, Hsp90, Hsp27 and αB-crystallin concentration and cathepsin B, D, L activities were significantly correlated with dissociated MHC and actin. Therefore, the significant correlation between shear force and dissociated MHC and actin clearly demonstrated that post mortem disassembly of myofibril filaments, which was regulated by endogenous proteolytic activity and loss of Hsp, contributed to the softening of ice-stored grass carp fillets.