Functional proteomic analysis predicts beef tenderness and the tenderness differential

The effect of the production system on the proteomics profiles of the Longissimus thoracis muscle in Arouquesa cattle

Arouquesa cattle breed is an autochthonous Portuguese breed produced under a traditional mountain system that need improvement without affecting beef quality. The aim of this work is to compare the proteomics profiles of the Longissimus thoracis muscle from Arouquesa animals produced under different production systems. Sixty weaners were produced under the following systems: traditional (TF) and traditional with starter feed supplementation (TF + S1) with weaning and slaughtering at 9 months, the S1 + S2 (weaning at 5 months and grower supplement until slaughter) and two rearing periods with finishing supplementation (TF + S3 and S3). Upon slaughter, samples of L. thoracis were taken and analyzed using a shotgun proteomics workflow. Several putative markers of beef quality for the Arouquesa breed were identified: VIM, FSCN1, SERPINH1, ALDH1A1, NDUFB5, ANXA1, PDK4, CEMIP2, NDUFB9, PDLIM1, OXCT1, MYH4. These proteins are involved in actin binding, skeletal muscle development and in the mitochondrial respiratory chain and they can influence mostly meat tenderness and color. We identified specific proteins for each group related to different metabolisms involved in several aspects that affect meat quality parameters. Our results demonstrate the link between production practices and putative meat characteristics, which have the potential to improve the traceability of certified products. SIGNIFICANCE: Arouquesa breed is produced in a sustainable system using natural resources and contributing to the economy of low-populated rural regions in Northern Portugal. Besides their economic relevance, producing autochthonous breeds can counter rural depopulation and maintain local heritage. Additionally, consumer awareness about product quality is increasing and PDO products contribute to satisfying this demand. However, it is necessary to increase production so that it is possible to sell these products outside the production region. To ensure robust traceability and that PDO label characteristics are maintained despite increasing production yield, product analysis is of paramount importance. For this reason, proteomic approaches can provide insight into how production changes will affect beef quality and generate putative biomarkers of certified production systems.

Leveraging Functional Genomics for Understanding Beef Quality Complexities and Breeding Beef Cattle for Improved Meat Quality

Consumer perception of beef is heavily influenced by overall meat quality, a critical factor in the cattle industry. Genomics has the potential to improve important beef quality traits and identify genetic markers and causal variants associated with these traits through genomic selection (GS) and genome-wide association studies (GWAS) approaches. Transcriptomics, proteomics, and metabolomics provide insights into underlying genetic mechanisms by identifying differentially expressed genes, proteins, and metabolic pathways linked to quality traits, complementing GWAS data. Leveraging these functional genomics techniques can optimize beef cattle breeding for enhanced quality traits to meet high-quality beef demand. This paper provides a comprehensive overview of the current state of applications of omics technologies in uncovering functional variants underlying beef quality complexities. By highlighting the latest findings from GWAS, GS, transcriptomics, proteomics, and metabolomics studies, this work seeks to serve as a valuable resource for fostering a deeper understanding of the complex relationships between genetics, gene expression, protein dynamics, and metabolic pathways in shaping beef quality.

Electrical Stimulation Induces Activation of Mitochondrial Apoptotic Pathway and Down-Regulates Heat Shock Proteins in Pork: An Innovative Strategy for Enhancing the Ripening Process and Quality of Dry-Cured Loin Ham

A fundamental regulatory framework to elucidate the role of electrical stimulation (ES) in reducing long production cycles, enhancing protein utilization, and boosting product quality of dry-cured ham is essential. However, how mitochondria and enzymes in meat fibers are altered by ES during post-processing, curing, and fermentation procedures remains elusive. This study sought to explore the impact of ES on the regulation of heat shock proteins (HSP27, HSP70), apoptotic pathways, and subsequent influences on dry-cured pork loin quality. The gathered data validated the hypothesis that ES notably escalates mitochondrial oxidative stress and accelerates mitochondrial degradation along the ripening process. The proapoptotic response in ES-treated samples was increased by 120.7%, with a cellular apoptosis rate 5-fold higher than that in control samples. This mitochondrial degradation is marked by increased ratios of Bax/Bcl-2 protein along the time course, indicating that apoptosis could contribute to the dry-cured ham processing. ES was shown to further down-regulate HSP27 and HSP70, establishing a direct correlation with the activation of mitochondrial apoptosis pathways, accompanied by dry-cured ham quality improvements. The findings show that ES plays a crucial role in facilitating the ripening of dry-cured ham by inducing mitochondrial apoptosis to reduce HSP expression. This knowledge not only explains the fundamental mechanisms behind myofibril degradation in dry-cured ham production but also offers a promising approach to enhance quality and consistency.

In-depth characterization of the sarcoplasmic muscle proteome changes in lambs fed with hazelnut skin by-products: Relationships with meat color

This study investigated the effect of agro-industrial hazelnut skin by-products supplementation on lamb meat color variation and the changes in the sarcoplasmic muscle proteome during post-mortem storage (0, 4 and 7 days). Gel-based proteomics and bioinformatics approaches were applied to better understand the potential role of feeding strategies in modulating the mechanisms underpinning meat discoloration and post-mortem changes during storage. Therefore, twenty-two Valle del Belice male lambs were randomly assigned to two dietary treatments: control (C), lambs fed with maize-barley diet, and hazelnut skin (H), lambs fed hazelnut skin by-product as maize partial replacer in the concentrate diet. Hazelnut dietary treatment led to better lamb meat color stability as evidenced by the lowest decrease in redness and saturation index values. Proteomics and bioinformatics results revealed changes in the abundance of 41 proteoforms, which were mainly involved in glycolytic processes, responses to oxidative stress, and immune and endocrine system. The proteins allowed revealing interconnected pathways to be behind meat color variation as a consequence of using hazelnut skin by-products to sustainable feed lamb. The proteins can be used as potential predictors of lamb meat color variation. Accordingly, the regression equations developed in this paper revealed triosephosphate isomerase (TPI1) as a reliable candidate biomarker of color stability in lamb meat. SIGNIFICANCE: The use of agro-industrial by-products in animal feeding can be a potential sustainable strategy to reduce the environmental impacts of the food production chain and consequently improve animal welfare and product quality. The inclusion of hazelnut skin by-products in the animal's diet, due to the high concentration of polyphenols, represents an effective strategy to improve the oxidative stability of meat, with significant implications on color. The use of proteomics combined with bioinformatics on the sarcoplasmic proteome is a powerful approach to decipher the underlying mechanism. Accordingly, this approach allowed in this trial a deeper understanding of the molecular mechanisms involved in the post-mortem processes through the discovery of several biological pathways linked with lamb meat color variation. Glycolysis, followed by responses to oxidative stress, and other proteins involved in the immune and endocrine system were found as the major interconnected pathways that could act as potential predictors of lamb meat color stability. Candidate proteins biomarkers were further revealed in this study to be related with multiple meat color traits.

Molecular mechanisms contributing to the development of beef sensory texture and flavour traits and related biomarkers: Insights from early post-mortem muscle using label-free proteomics

Beef sensory quality comprises a suite of traits, each of which manifests its ultimate phenotype through interaction of muscle physiology with environment, both in vivo and post-mortem. Understanding variability in meat quality remains a persistent challenge, but omics studies to uncover biological connections between natural variability in proteome and phenotype could provide validation for exploratory studies and offer new insights. Multivariate analysis of proteome and meat quality data from Longissimus thoracis et lumborum muscle samples taken early post-mortem from 34 Limousin-sired bulls was conducted. Using for the first-time label-free shotgun proteomics combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS), 85 proteins were found to be related with tenderness, chewiness, stringiness and flavour sensory traits. The putative biomarkers were classified in five interconnected biological pathways; i) muscle contraction, ii) energy metabolism, iii) heat shock proteins, iv) oxidative stress, v) regulation of cellular processes and binding. Among the proteins, PHKA1 and STBD1 correlated with all four traits, as did the GO biological process 'generation of precursor metabolites and energy'. Optimal regression models explained a high level (58-71%) of phenotypic variability with proteomic data for each quality trait. The results of this study propose several regression equations and biomarkers to explain the variability of multiple beef eating quality traits. Thanks to annotation and network analyses, they further suggest protein interactions and mechanisms underpinning the physiological processes regulating these key quality traits. SIGNIFICANCE: The proteomic profiles of animals with divergent quality profiles have been compared in numerous studies; however, a wide range of phenotypic variation is required to better understand the mechanisms underpinning the complex biological pathways correlated with beef quality and protein interactions. We used multivariate regression analyses and bioinformatics to analyse shotgun proteomics data to decipher the molecular signatures involved in beef texture and flavour variations with a focus on multiple quality traits. We developed multiple regression equations to explain beef texture and flavour. Additionally, potential candidate biomarkers correlated with multiple beef quality traits are suggested, which could have utility as indicators of beef overall sensory quality. This study explained the biological process responsible for determining key quality traits such as tenderness, chewiness, stringiness, and flavour in beef, which will provide support for future beef proteomics studies.

Early postmortem muscle proteome and metabolome of beef longissimus thoracis muscle classified by pH at 6 hours postmortem

The objective was to identify metabolome and proteome differences at 1 h and 1 d postmortem between longissimus thoracis (LT) muscle classified based on 6 h pH values. Twenty beef LT rib sections were sorted based on 6 h postmortem pH values into low (LpH; pH < 5.55; n = 9) and high (HpH; pH > 5.84; n = 8) pH classifications. Warner-Bratzler shear force (WBSF), desmin degradation, and calpain-1 autolysis were measured. Two-dimensional difference in gel electrophoresis (3-10, 4-7, and 6-9 pH range) and Tandem mass tagging (TMT) protein analyses were employed to determine how the sarcoplasmic protein profile varied across pH classification. Non-targeted metabolomic analyses were conducted on extracts prepared at 1 h and 1 d postmortem. The LpH classification had a lower WBSF value at 1 d postmortem, which was explained by greater calpain-1 autolysis and desmin degradation at 1 d postmortem. Proteome and metabolome analysis revealed a phenotype that promotes more rapid energy metabolism in the LpH group. Proteome and metabolome analyses identified energy production, apoptotic, calcium homeostasis, and proteasome systems influencing pH classifications that could explain the observed pH, proteolysis, and beef tenderness differences. SIGNIFICANCE: This study is the first to identify proteomic and metabolomic variations early (1 h and 1 day) postmortem that are linked to differences in early (6 h) postmortem pH values and to tenderness differences at 1 day postmortem. This study integrates postmortem biochemical features (protein degradation, proteome, and metabolome variations) to postmortem pH decline and eating quality of beef steaks. Potential biomarkers of more rapid postmortem metabolism linked to earlier tenderization in beef are suggested. Identification of these biochemical features will assist in predicting the eating quality of beef products.

Metabolic, proteomic and microbial changes postmortem and during beef aging

The purpose of this review is to provide an overview of the current knowledge about proteomic and metabolic changes in beef, the microbiological alteration postmortem and during aging, and observe the influence on beef quality parameters, such as tenderness, taste and flavor. This review will also focus on the different aging types (wet- and dry-aging), the aging or postmortem time of beef and their effect on the proteome and metabolome of beef. The Ca2+ homeostasis and adenosine 5'-triphosphate breakdown are the main reactions in the pre-rigor phase. After rigor mortis, the enzymatic degradation of connective tissues and breakdown of energy metabolism dominate molecular changes in beef. Important metabolic processes leading to the formation of saccharides, nucleotides, organic acids (e.g. lactic acid), creatine and fatty acids are considered in this context as possible flavor precursors or formers of beef flavor and taste. Flavor precursors are substrates for lipid oxidation, Strecker degradation and Maillard reaction during cooking or roasting. The findings presented should serve as a basis for a better understanding of beef aging and its molecular effects and are intended to contribute to meeting the challenges of improving beef quality.

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.

Proteomics as a promising biomarker in food authentication, quality and safety: A review

Adulteration and mislabeling have become a very common global malpractice in food industry. Especially foods of animal origin are prepared from plant sources and intentionally mislabeled. This type of mislabeling is an important concern in food safety as the replaced ingredients may cause a food allergy or toxicity to vulnerable consumers. Moreover, foodborne pathogens also pose a major threat to food safety. There is a dire need to develop strong analytical tools to deal with related issues. In this context, proteomics stands out as a promising tool used to report the aforementioned issues. The development in the field of omics has inimitable advantages in enabling the understanding of various biological fields especially in the discipline of food science. In this review, current applications and the role of proteomics in food authenticity, safety, and quality and food traceability are highlighted comprehensively. Additionally, the other components of proteomics have also been comprehensively described. Furthermore, this review will be helpful in the provision of new intuition into the use of proteomics in food analysis. Moreover, the pathogens in food can also be identified based on differences in their protein profiling. Conclusively, proteomics, an indicator of food properties, its origin, the processes applied to food, and its composition are also the limelight of this article.

Early postmortem degradation of actin muscle protein in Algerian Sahraoui dromedaries

The present study aimed to evaluate actin degradation during the early postmortem time in Longissimus Lumborum muscle according to Sahraoui dromedary's age. A sample of eight males, young (2 years old) and adult (8 years old) dromedaries, was used to investigate meat quality traits and actin proteolysis during the conversion of muscle to meat. Results demonstrated higher pH values in young compared to adult with a polyphasic pH drop profile. While, age did not affect drip loss (DL) and the values at 72 h postmortem varied from 5 to 9%. Western blot revealed that actin proteolysis occurred since 1 h postmortem and that it was affected by age and postmortem time. In particular, the 32 and 25 kDa actin fragments could be potential markers of ongoing meat tenderization.

Housekeeping Proteins in Meat Quality Research: Are They Reliable Markers for Internal Controls in Western Blot? A Mini Review

Advancements in technology and analytical methods enable researchers to explore the biochemical events that cause variation in meat quality. Among those, western blot techniques have been successfully used in identifying and quantifying the key proteins that have critical functions in the development of meat quality. Housekeeping proteins, like β-actin, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and tubulins are often used as internal controls in western blots to normalize the abundance of the protein of interest. However, there are increasing concerns about using housekeeping proteins for western blot normalization, as these proteins do not demonstrate any loading differences above the relatively small total protein loading amounts of 10μg. In addition, the interaction between these housekeeping proteins and programmed cell death processes highlights the concerns about using the housekeeping protein as the internal control in meat quality research. Moreover, recent proteomic research has indicated that the abundance of some housekeeping proteins, like β-actin, GAPDH, and tubulin, can be altered by preslaughter stress, dietary supplementation, sex, slaughter method, genotype, breed, aging period, muscle type, and muscle portion. Furthermore, these housekeeping proteins could have differential expression in meat with differing color stability, tenderness, and water holding capacity. Therefore, this review aims to examine the realities of using housekeeping proteins as the loading control in meat quality research and introduce some alternative methods that can be used for western blot normalization.

Is beef quality affected by the inclusion of distiller grains in cattle diets?

This study aimed to analyze the effect of including increasing levels of distiller grains (DG) in beef cattle feeding diets on meat quality from an integral approach. To this end, we analyzed the meat from 36 yearling steers fed with four dietary treatments: 0DG (control corn-based diet), 15DG, 30DG, and 45DG (containing 15%, 30%, or 45% of DG on DM basis). Crude protein, ash, and fat contents of diets increased with DG level. The fatty acid profile of DG diets was reflected in the fatty acid profile of plasma samples. Feeding diets with DG had no effect on the biochemical parameters analyzed in plasma. In addition, it did not influence the water holding capacity, the muscle or fat color at 72 h post mortem or at retail display, or the contents of SFAs, MUFAs, and PUFAs in beef. The DG diets led to lower values of cooking loss. Meat from 15DG and 30DG showed greater percentage of troponin C and fragments of 30 to 27 kDa than meat from 45DG. Also, meat from 30DG showed the lowest values of Warner-Bratzler shear force. Hence, including up to 30% corn DG in beef cattle feeding diets had positive effects on meat quality.

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.

Proteomic profile and morphological characteristics of skeletal muscle from the fast- and slow-growing yellow perch (Perca flavescens)

The objective of the present study was to compare skeletal muscle proteomic profiles, histochemical characteristics, and expression levels of myogenic regulatory factors (MRFs) between fast- versus slow-growing yellow perch Perca flavescens and identify the proteins/peptides that might play a crucial role in the muscle growth dynamic. Yellow perch were nursed in ponds for 6 weeks from larval stage and cultured in two meter diameter tanks thereafter. The fingerlings were graded to select the top 10% and bottom 10% fish which represented fast- and slow-growing groups (31 yellow perch per each group). Our statistical analyses showed 18 proteins that had different staining intensities between fast- and slow-growing yellow perch. From those proteins 10 showed higher expression in slow-growers, and 8 demonstrated higher expression in fast-growers. Fast-growing yellow perch with a greater body weight was influenced by both the muscle fiber hypertrophy and mosaic hyperplasia compared to slow-growing fish. These hyperplastic and hypertrophic growth in fast-grower were associated with not only metabolic enzymes, including creatine kinase, glycogen phosphorylase, and aldolase, but also myoD and myogenin as MRFs. Overall, the results of the present study contribute to the identification of different expression patterns of gene products in fast- and slow-growing fish associated with their muscle growth.

Quantitative proteomic analysis of beef tenderness of Piemontese young bulls by SWATH-MS

Quantitative proteomic approach is a suitable way to tackle the beef tenderness. Ten aged-beef samples from Longissimus thoracis of Piemontese breed classified as tender (n = 5) and tough (n = 5) meat were evaluated using SWATH-MS and bioinformatic tools for the identification of the proteins and pathways most influencing tenderness variability. Between the two textural groups, proteomic changes were mainly caused by 43 differentially abundant proteins (DAPs) arranged in reference patterns as displayed by the heat map analysis. Most of these DAPs were associated with energy metabolism. From the functional proteomic analysis, two clusters of proteins, including ACO2, MDH1, MDH2 and CS in one cluster and FBP2, PFKL, LDHA, TPI1 and GAPDH/S in the other cluster, suggest gluconeogenesis, glycolysis and citrate cycle as key pathways for Piemontese breed beef tenderness. These findings contribute to a deeper insight into molecular pathways related to beef tenderness.

Molecular signatures of beef tenderness: Underlying mechanisms based on integromics of protein biomarkers from multi-platform proteomics studies

Over the last two decades, proteomics have been employed to decipher the underlying factors contributing to variation in the quality of muscle foods, including beef tenderness. One such approach is the application of high-throughput protein analytical platforms in the identification of meat quality biomarkers. To broaden our understanding about the biological mechanisms underpinning meat tenderization across a large number of studies, an integromics study was performed to review the current status of protein biomarker discovery targeting beef tenderness. This meta-analysis is the first to gather and propose a comprehensive list of 124 putative protein biomarkers derived from 28 independent proteomics-based experiments, from which 33 robust candidates were identified worthy of evaluation using targeted or untargeted data-independent acquisition proteomic methods. We further provide an overview of the interconnectedness of the main biological pathways impacting tenderness determination after multistep analyses including Gene Ontology annotations, pathway and process enrichment and literature mining, and specifically discuss the major proteins and pathways most often reported in proteomics research.

Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction

This study evaluated the potential of a panel of 20 protein biomarkers, quantified by Reverse Phase Protein Array (RPPA), to explain and predict two important meat quality traits, these being beef tenderness assessed by Warner-Bratzler shear force (WBSF) and the intramuscular fat (IMF) content (also termed marbling), in a large database of 188 Protected Designation of Origin (PDO) Maine-Anjou cows. Thus, the main objective was to move forward in the progression of biomarker-discovery for beef qualities by evaluating, at the same time for the two quality traits, a list of candidate proteins so far identified by proteomics and belonging to five interconnected biological pathways: (i) energy metabolic enzymes, (ii) heat shock proteins (HSPs), (iii) oxidative stress, (iv) structural proteins and (v) cell death and protein binding. Therefore, three statistical approaches were applied, these being Pearson correlations, unsupervised learning for the clustering of WBSF and IMF into quality classes, and Partial Least Squares regressions (PLS-R) to relate the phenotypes with the 20 biomarkers. Irrespective of the statistical method and quality trait, seven biomarkers were related with both WBSF and IMF, including three small HSPs (CRYAB, HSP20 and HSP27), two metabolic enzymes from the oxidative pathway (MDH1: Malate dehydrogenase and ALDH1A1: Retinal dehydrogenase 1), the structural protein MYH1 (Myosin heavy chain-IIx) and the multifunctional protein FHL1 (four and a half LIM domains 1). Further, three more proteins were retained for tenderness whatever the statistical method, among which two were structural proteins (MYL1: Myosin light chain 1/3 and TNNT1: Troponin T, slow skeletal muscle) and one was glycolytic enzyme (ENO3: β-enolase 3). For IMF, two proteins were, in this trial, specific for marbling whatever the statistical method: TRIM72 (Tripartite motif protein 72, negative) and PRDX6 (Peroxiredoxin 6, positive). From the 20 proteins, this trial allowed us to qualify 10 and 9 proteins respectively as strongly related with beef tenderness and marbling in PDO Maine-Anjou cows.

Muscle Fiber Properties in Cattle and Their Relationships with Meat Qualities: An Overview

The control of meat quality traits constitutes an important target for any farm animal production, including cattle. Therefore, better understanding of the biochemical properties that drive muscle development and final outcomes constitutes one of the main challenging topics of animal production and meat science. Accordingly, this review has focused on skeletal muscle fibers in cattle and their relationships with beef qualities. It aimed to describe the chemical and structural properties of muscle fibers as well as a comprehensive review of their contractile and metabolic characteristics during the life of the animal. The existing methods for the classification of muscle fibers were reviewed, compared, and discussed. Then, the different stages of myogenesis in cattle were defined. The main factors regulating fetal and postnatal growth and the plasticity of muscle fibers were evidenced, especially the role of myostatin growth factor and the impact of nutritional factors. This review highlights that the knowledge about muscle fibers is paramount for a better understanding of how to control the muscle properties throughout the life of the animal for better management of the final eating qualities of beef. Accordingly, the associations between bovine muscle fibers and different meat eating qualities such as tenderness, pH decline, and color traits were further presented.

Investigation of the Sarcoplasmic Proteome Contribution to the Development of Pork Loin Tenderness

The study objectives were to determine the extent to which the sarcoplasmic proteome explains variations in aged pork loin star probe value. Pork loins (n=12) were categorized by differences in star probe at 21 d post mortem from a larger set of loins. Loins were categorized into low star probe (LSP) group (n=6; star probe&lt;5.80 kg) and high star probe (HSP) group (n=6; star probe&gt;7.00 kg) based on 21-d star probe value with inclusion criteria of marbling score (1.0–3.0) and 24-h pH (5.69–5.98). Quality traits were measured at 1-, 8-, 14-, and 21-d aging. Desmin and troponin-T degradation, peroxiredoxin-2 abundance, calpain-1 autolysis, and sarcomere length were determined. Two-dimensional difference gel electrophoresis and mass spectrometry were used to identify proteins that differed in abundance due to category. Star probe values were lower (P&lt;0.01) in LSP at each day of aging compared with HSP. Greater pH values were observed (P&lt;0.05)in LSP compared with HSP at each day of aging. Marbling score was greater (P&lt;0.05) in LSP compared with HSP at each day of aging. Greater (P&lt;0.05) desmin and troponin-T degradation was detected in LSP chops at 14- and 21-d aging and 8-, 14-, and 21-d aging, respectively. Greater (P&lt;0.05) sarcomere length was determined in LSP compared with HSP at 1-,8-, and 21-d aging. Sarcoplasmic proteins from HSP chops had greater abundance (P&lt;0.10) of metabolic and regulatory proteins, whereas the LSP chops had greater abundance (P&lt;0.10) of stress response proteins. Star probe values were affected by pH, marbling score, protein degradation, sarcomere length, and sarcoplasmic proteome.

The associations between proteomic biomarkers and beef tenderness depend on the end-point cooking temperature, the country origin of the panelists and breed

Steaks of 74 animals from 3 young bull breeds (Aberdeen Angus, Limousin and Blond d'Aquitaine) were cooked at two end-point cooking temperatures (55 and 74 °C) and evaluated for tenderness by trained panelists from France (FR) and the United Kingdom (UK). Using principal component regressions, the tenderness scores of each breed, country origin of the panelists and cooking temperature were linked with the abundances of 21 protein biomarkers belonging to five biological pathways. Twelve regression equations were built and explained 68 to 95% of tenderness variability. A high dissimilarity in the retained biomarkers was observed among the equations and differences exist among breeds, cooking temperatures and country origin of the panelists. Among the 21 biomarkers, 6 proteins including structural (MyHC-I, MyHC-IIa, MyHC-IIx), oxidative stress (DJ-1, PRDX6) and proteolysis (CAPN1) were retained robustly in positive or negative directions in the tenderization process of Longissimus thoracis, regardless the breed, the end-point cooking temperature or the country origin of the panelist.

Association of calpain and calpastatin activity to postmortem myofibrillar protein degradation and sarcoplasmic proteome changes in bovine Longissiumus lumborum and Triceps brachii

The aim of this study was to determine the extent to which calpastatin (CASN) variants (based on two chromatographic peaks; CASN-P1 and CASN-P2) explain variation in μ-calpain autolysis, protein degradation, and changes in the sarcoplasmic proteome observed during postmortem aging of beef. The Longissimus lumborum (LL) and Triceps brachii (TB) muscles were obtained from six crossbred steers and samples prepared from day 0, 1 and 7 postmortem (pm). The decline of CASN activity during aging was due to decrease of CASN-P2 in both muscles. The CASN-P2:μ-calpain ratio at day 0 was greater for TB, which presented lesser calpain autolysis, myofibrillar protein degradation, and fewer sarcoplasmic proteome changes during aging. Changes in abundance of Heat shock protein 70 family in the sarcoplasmic fraction were positively associated to proteolysis during aging, with greater differences in LL.

Pharmaceutical Advances and Proteomics Researches

Proteomics enables understanding the composition, structure, function and interactions of the entire protein complement of a cell, a tissue, or an organism under exactly defined conditions. Some factors such as stress or drug effects will change the protein pattern and cause the present or absence of a protein or gradual variation in abundances. The aim of this study is to explore relationship between proteomics application and drug discovery. "proteomics", "Application", and "pharmacology were the main keywords that were searched in PubMed (PubMed Central), Web of Science, and Google Scholar. The titles that were stablished by 2019, were studied and after study of the appreciated abstracts, the full texts of the 118 favor documents were extracted. Changes in the proteome provide a snapshot of the cell activities and physiological processes. Proteomics shows the observed protein changes to the causal effects and generate a complete three-dimensional map of the cell indicating their exact location. Proteomics is used in different biological fields and is applied in medicine, agriculture, food microbiology, industry, and pharmacy and drug discovery. Biomarker discovery, follow up of drug effect on the patients, and in vitro and in vivo proteomic investigation about the drug treated subjects implies close relationship between proteomics advances and application and drug discovery and development. This review overviews and summarizes the applications of proteomics especially in pharmacology and drug discovery.

Data from the Farmgate-to-Meat Continuum Including Omics-Based Biomarkers to Better Understand the Variability of Beef Tenderness: An Integromics Approach

This study is based on an integromic approach of 71 young bulls' data from the farmgate-to-meat continuum including omics-based biomarkers, to understand beef tenderness variability in two muscle cuts that differ by their contractile and metabolic properties. By the means of chemometrics using partial least-squares (PLS) and principal component regressions (PCR), important variables from a list of 49 that characterize four levels of the continuum (rearing factors-carcass-muscle-meat) were identified to explain tenderness of Longissimus thoracis (LT) and Semitendinosus (ST) muscles evaluated by a sensory panel and instrumental Warner-Bratzler shear force (WBSF). The PLS and PCR analyses validated 16 and 15 variables for LT and 12 and 14 for ST from the whole continuum to explain sensory tenderness and WBSF, respectively. Among the explanatory variables in the four models and in line with the role of apoptosis in tenderness determinism, HSP70-1A/B (a heat shock protein) was retained to explain beef tenderness irrespective of muscle and evaluation method. Similarly, dressing percentage from the carcass level was another robust predictor but in a muscle-dependent direction manner. HSP20, ENO3, and MyHC-I as three muscle protein biomarkers and dry matter intake (DMI) as a rearing factor were involved in three models to explain beef tenderness. This study highlighted also that several variables were muscle-specific irrespective of the evaluation method of tenderness. For LT muscle, six variables including three carcass traits (fatness score, fat carcass %, and muscle carcass %), two muscle biomarkers (HSP70-8 and MyHC-IIx/b), and one meat quality trait (pH_3h) were found. For ST muscle, five variables were validated from two rearing factors (average daily gain and feed efficiency) and three structural protein biomarkers (α-actin, MyBP-H, and CapZ-β). Finally, for WBSF only, lactate dehydrogenase chain B (LDH-B) was retained positively for LT and negatively for ST muscles. Overall, this trial showed that tenderness of LT and ST muscle cuts is influenced by variables belonging to the whole continuum with relationships that depend on both the muscle type and the evaluation method. It further highlighted the potential of integromic/chemometric approaches on the farmgate-to-meat continuum data to better understand the sophisticated biological processes that orchestrate the conversion of muscle into meat and tenderness determinism.

Meat quality traits and proteome profile of woody broiler breast (pectoralis major) meat

Woody breast meat has recently become prevalent in the broiler industry in both the United States and European Union. Recent publications have described the meat quality characteristics of woody breast meat as having hardened areas and pale ridge-like bulges at both the caudal and cranial regions of the breast. The present study investigated the meat quality (pH, color, cooking loss, and shear force) and protein quality characteristics (protein and salt-soluble protein content) in woody breast meat as compared to normal breast meat. In addition, the differences in the muscle proteome profiles of woody and normal breast meat were characterized. Results indicated that woody breast meat had a greater average pH (P < 0.0001) and cooking loss (P = 0.001) than normal breast meat, but woody breast meat did not differ in shear force (P > 0.05) in comparison to normal breast meat samples. The L*, a*, and b* values of woody breast fillets were greater than normal breast fillets (P < 0.0001 to L*; P = 0.002 to a*; P = 0.016 to b*). The woody breast meat had more fat (P < 0.0001) and moisture (P < 0.021) and less protein (P < 0.0001) and salt-soluble protein (P < 0.0001) when compared with normal breast fillets. Whole muscle proteome analysis indicated 8 proteins that were differentially expressed (P < 0.05) between normal and woody breast meat samples. The differences in muscle proteome between normal and woody breast meat indicated an increased oxidative stress in woody breast meat when compared to normal meat. In addition, the abundance of some glycolytic enzymes, which are critical to the regeneration of adenosine triphosphate (ATP) in postmortem muscles, was lower in woody breast meat than in normal breast meat. Proteomic differences provide additional information on the biochemical pathways and genetic variations that lead to woody breast meat. Further research should be conducted to elucidate the genetic and nutritional contributions to the proliferation of woody breast meat in the United States.

Reverse phase protein arrays for the identification/validation of biomarkers of beef texture and their use for early classification of carcasses

The validation of biomarkers and tools for the prediction of beef texture remains a challenging task. In this study, reverse phase protein arrays (RPPA) quantified 29 protein biomarkers in the m. Longissimus thoracis of Charolais cattle sampled early post-mortem. Myosin heavy chain 1 (MHC1, slow-oxidative fibers) and Retinal dehydrogenase 1 (ALDH1A1, oxidative enzyme) discriminated between tender and juicy vs. tough meat with residues classes and are validated as prime biomarkers of beef texture. Several proteins belonging to energy metabolism, heat shock and oxidative stress, cytoskeletal, cell signaling and apoptosis were related with tenderness. Among the unusual proteins, Four and a half LIM domains 1 (FHL1) and Tripartite motif protein 72 (TRIM72) correlated respectively negatively and positively with beef tenderness. Principal component regression was used for the first time to explain beef texture traits using biomarkers. The results are very promising as they revealed sophisticated mechanisms behind the tenderizing process.

Identification and partial characterization of a sex specific protein in Koi carp (Cyprinus carpio haematopterus)

Gender identification of fish species is carried out mainly by examining external morphological characteristics, which in general, it is very complex and not always a reliable approach. Electrophoresis of plasma proteins can be used as an alternative and useful molecular tool for a more precise sex determination. The presence of female specific proteins in the plasma is a starting point for the application of this technique. In this study, reducing discontinuous sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was applied to analyze plasma proteins of male and female koi carp (Cyprinus carpio haematopterus). Image analyses of electrophoregrams with resolved plasma proteins by SDS-PAGE showed that it is an appropriate technique to discriminate male from female samples. It is based on the presence of apolipoprotein B-100 which can be used as a suitable marker. Further amino acid characterization of apolipoprotein B-100 confirmed that it is a specific protein for female individuals.

Use of Foodomics for Control of Food Processing and Assessing of Food Safety

Food chain, food safety, and food-processing sectors face new challenges due to globalization of food chain and changes in the modern consumer preferences. In addition, gradually increasing microbial resistance, changes in climate, and human errors in food handling remain a pending barrier for the efficient global food safety management. Consequently, a need for development, validation, and implementation of rapid, sensitive, and accurate methods for assessment of food safety often termed as foodomics methods is required. Even though, the growing role of these high-throughput foodomic methods based on genomic, transcriptomic, proteomic, and metabolomic techniques has yet to be completely acknowledged by the regulatory agencies and bodies. The sensitivity and accuracy of these methods are superior to previously used standard analytical procedures and new methods are suitable to address a number of novel requirements posed by the food production sector and global food market.

Proteomic and peptidomic differences and similarities between four muscle types from New Zealand raised Angus steers

Four muscles from New Zealand-raised Angus steers were evaluated (musculus semitendinosus, m. longissimus thoracis et lumborum, m. psoas major and m. infraspinatus) to test their differences and common features in protein and peptide abundances. The ultimate goal of such a comparison is to match muscle types to products with targeted properties. Protein profiling based on two-dimensional electrophoresis showed that the overall profiles were similar, but, between muscle types, significant (p<0.05) intensity differences were observed in twenty four protein spots. Profiling of endogenous peptides allowed characterisation of 346 peptides. Quantitative analysis showed a clear distinction between the muscle types. Forty-four peptides were identified that showed a statistically significant (p<0.05) and substantial (>2-fold change) difference between at least two muscle types. These analyses demonstrate substantial similarities between these four muscle types, but also clear distinctions in their profiles; specifically a 25% difference between at least two muscles at the peptidomic level, and a 14% difference at the proteomic level.

Expression Marker-Based Strategy to Improve Beef Quality

For beef cattle research, a main objective is to control concomitantly the development of muscles and the qualities of beef cuts. Beef quality is a complex phenotype that is only detectable after slaughter and is highly variable. The beef industry is in need of tools to estimate beef quality of live cattle or online in abattoirs, with specific attention towards sensory attributes (tenderness, juiciness, flavour, and colour). Identification of relevant genetic and genomic markers is ongoing, especially for tenderness—a top priority quality attribute. In this paper, we describe the steps of an expression marker-based strategy to improve beef sensory quality, from the discovery of biomarkers that identify consistent beef and the biological functions governing beef tenderness to the integration of the knowledge into detection tests for desirable animals. These tools should soon be available for the management of sensory quality in the beef production chain for meeting market's demands and assuring good quality standards.

Understanding tenderness variability and ageing changes in buffalo meat: biochemical, ultrastructural and proteome characterization

Understanding of biological impact of proteome profile on meat quality is vital for developing different approaches to improve meat quality. Present study was conducted to unravel the differences in biochemical, ultrastructural and proteome profile of longissimus dorsi muscle between buffaloes (Bubalus bubalis) of different age groups (young v. old). Higher (P<0.05) myofibrillar and total protein extractability, muscle fibre diameter, and Warner-Bratzler shear force (WBSF) values was observed in old buffalo meat relative to meat from young buffaloes. Scanning electron microscopy photographs revealed reduced fibre size with increased inter-myofibrillar space in young compared with old buffalo meat. Transmission electron microscopy results revealed longer sarcomeres in young buffalo meat relative to meat from old buffaloes. Proteomic characterization using two-dimensional gel electrophoresis (2DE) found 93 differentially expressed proteins between old and young buffalo meat. Proteome analysis using 2DE revealed 191 and 95 differentially expressed protein spots after 6 days of ageing in young and old buffalo meat, respectively. The matrix assisted laser desorption ionization time-of flight/time-of flight mass spectrometry (MALDI-TOF/TOF MS) analysis of selected gel spots helped in identifying molecular markers of tenderness mainly consisting of structural proteins. Protein biomarkers identified in the present study have the potential to differentiate meat from young and old buffaloes and pave the way for optimizing strategies for improved buffalo meat quality.

Proteome Changes in biceps femoris Muscle of Iranian One-Humped Camel and Their Effect on Meat Quality Traits

In this study physicochemical and quality traits of biceps femoris and longissimus thoracis muscles of male and female Iranian one-humped camel were determined during 14 days of refrigeration storage. Analysis of variance of the results showed that only shear force and temperature were affected by the gender (p<0.05). Anatomical location of the muscle influenced the meat properties except for drip loss (p<0.05). Also, except for cooking loss, ageing influenced the physicochemical and quality properties of meat; during 14 days of storage, proteolysis resulted in an increase of L* and b* values, drip loss and myofibrillar fragmentation index, and the decrease of a* value, expressed juice, shear force and sarcomere length. Proteome changes (myofibrillar proteins) during storage were investigated. Gel analysis revealed that 19 protein spots were significantly changed during 24, 72 and 168 h post-mortem. Fifteen spots were identified by MALDI-TOF/TOF mass spectrometer. Correlation analysis revealed significant correlations of actin, troponin T, capping protein, heat shock proteins (HSP) and desmin with physicochemical and quality properties of meat (p<0.05). Actin might be a potential protein marker for colour, tenderness and water-holding capacity, and HSP27 and desmin are good candidate markers for colour and tenderness, respectively.

Biomarkers: Non-destructive Method for Predicting Meat Tenderization

Meat tenderness is the primary and most important quality attribute for the consumers worldwide. Tenderness is the process of breakdown of collagen tissue in meat to make it palatable. The earlier methods of tenderness evaluation like taste panels and shear force methods are destructive, time consuming and ill suited as they requires removing a piece of steak from the carcass for performing the test. Therefore, a non-destructive method for predicting the tenderness would be more desirable. The development of a meat quality grading and guarantee system through muscle profiling research can help to meet this demand. Biomarkers have the ability to identify if an exposure has occurred. Biomarkers of the meat quality are of prime importance for meat industry, which has ability to satisfy consumers' expectations. The biomarkers so far identified have been then sorted and grouped according to their common biological functions. All of them refer to a series of biological pathways including glycolytic and oxidative energy production, cell detoxification, protease inhibition and production of Heat Shock Proteins. On this basis, a detailed analysis of these metabolic pathways helps in identifying tenderization of meat having some domains of interest. It was, therefore, stressed forward that biomarkers can be used to determine meat tenderness. This review article summarizes the uses of several biomarkers for predicting the meat tenderness.

Genome-Wide H3K4me3 Analysis in Angus Cattle with Divergent Tenderness

Tenderness is one of the most important properties of meat quality, which is influenced by genetic and environmental factors. As an intensively studied epigenetic marker, histone methylation, occurring on arginine and lysine residues, has pivotal regulatory functions on gene expression. To examine whether histone methylation involves in beef tenderness variation, we analyzed the transcriptome and H3K4me3 enrichment profiles of muscle strips obtained from the longissimus dorsi (LD) of Angus steers previously classify to the tender or tough group. We first plotted a global bovine H3K4me3 map on chromosomes and called peak-enriched regions and genes. We found that majorities of H3K4me3 on genes were occupying the first intron and intergenic regions and its maps displayed similar patterns in tender and tough groups, with high H3K4me3 enrichment surrounding the transcription start site (TSS). We also explored the relationship of H3K4me3 and gene expression. The results showed that H3K4me3 enrichment is highly positively correlated with gene expression across the whole genome. Cluster analysis results confirmed the relationship of H3K4me3 enrichment and gene expression. By using a pathway-based approach in genes with H3K4me3 enrichment in promoter regions from the tender cluster, we revealed that those genes involved in the development of different tissues-connective tissue, skeletal and muscular system and functional tissues-; while in tough group those genes engaged in cell death, lipid metabolism and small molecule biochemistry. The results from this study provide a deep insight into understanding of the mechanisms of epigenetic regulations in meat quality and beef tenderness.