Reverse Phase Protein array for the quantification and validation of protein biomarkers of beef qualities: The case of meat color from Charolais breed

Abstract

Reverse Phase Protein Arrays (RPPA) were applied for the quantification and validation of protein biomarkers of beef qualities on M. longissimus thoracis sampled early post-mortem from young Charolais bulls. pHu was related to six proteins, three of which are glycolytic enzymes (ENO1, ENO3 and TPI1), while others belong to structural (TTN and α-actin) and proteolytic (μ-calpain) pathways. For color traits, several correlations were found, interestingly with structural proteins. The relationships were in some cases trait-dependent. To understand the mechanisms and explore animal variability, color data were categorized into three classes. α-actin and TTN allowed efficient separation of the classes and were strongly related with all color traits. Biomarkers belonging to heat stress and metabolism pathways were also involved. Two identified proteins, namely Four and a half LIM domains 1 (FHL1) and Tripartite motif-containing 72 (TRIM72), were for the first time related to beef color. Overall, these relationships could be used to develop muscle-specific processing strategies to improve beef color stability.

Contribution of connective tissue components, muscle fibres and marbling to beef tenderness variability in longissimus thoracis, rectus abdominis, semimembranosus and semitendinosus muscles

“…Accordingly, to check the suitability of the factorial model, the Kaiser–Meyer–Olkin (KMO) measure, known also as Kaiser's measure of sampling adequacy was applied to test sampling adequacy was used. The overall KMO value of the PCA was 0.72, which is acceptable …”

“…The overall KMO value of the PCA was 0.72, which is acceptable. 24 Z-scores were computed in a stepwise manner using multivariate regression analyses to consider the fixed effects of M and to avoid the effects as a result of other factors of variation present in the database by taking into account the differences in the number of animals for LT and RA muscle compared to SM and ST. Zscores represent the deviation of each trait observation relative to the mean of the corresponding animal irrespective of the breed, experiment and other confounded effects and were calculated using PROC STANDARD of SAS (SAS Institute Inc., Cary, NC, USA), which standardizes data to a mean of 0 and a SD of 1. Subsequently, and using the Z-scores, Pearson correlations were performed to investigate simple relationships between muscle characteristics and sensory tenderness.…”

Decision tree, a learning tool for the prediction of beef tenderness using rearing factors and carcass characteristics

“…Using the residual scores of tenderness, the k ‐means and HCA algorithms gave the best results, as reported in Gagaoua et al K‐ means is an iterative clustering method used to automatically partition a dataset into k groups where the number of clusters k is assumed to be fixed a priori by minimizing relative distances . This algorithm consists of two separate phases: the first phase is to define k centroids, one for each cluster, and the second phase is to take each point belonging to the given dataset and associate it with the nearest centroid. HCA is a cluster analysis that seeks to build a hierarchy and binary tree of clusters .…”

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

“…The muscle proteins were extracted by homogenization of the samples in “Precellys 24” tissue homogenizer (Bertin technologies, Saint Quentin-en-Yvelines, France) following the previously described protocol [ 41 ]. Briefly, 80 mg of frozen muscle were ground using 1.4 mm ceramic beads in an extraction buffer containing 50 mM Tris (pH 6.8), 5% glycerol, 2% SDS, 2 mM DTT, 2.5 mM EDTA, 2.5 mM EGTA, 1 × HALT Phosphatase inhibitor, Protease inhibitor cocktail complete MINI EDTA-free, 2 mM Na 3 VO 4 and 10 mM NaF.…”

“…The relative abundances of 20 protein biomarkers of tenderness and/or IMF ( Table 1 ) were quantified by the Reverse Phase Protein Array [ 42 ] following exactly the same protocol recently detailed by our group on bovine muscle [ 26 , 35 , 36 , 41 ]. The 20 proteins belong to five biological pathways that are:…”