Towards muscle-specific meat color stability of Chinese Luxi yellow cattle: A proteomic insight into post-mortem storage

Quantitative proteomic analysis to identify potential biomarkers linked to quality traits of beef tripe from different sources

In this work, the 4D data-independent acquisition (DIA) quantitative strategy was used for differential proteomic analysis of four beef tripe samples from different sources to explore the associations between differentially expressed proteins (DEPs) and meat quality traits. A total of 68 shared DEPs were identified in all comparison groups, which were mainly involved in phosphorylation signaling pathway, peroxisome proliferator-activated receptor (PPAR) signaling pathway, and glucuronic acid pathway. In the correlation analysis between DEPs and quality traits of beef tripe, it was found that 21 proteins were significantly associated with the quality traits in beef tripe, which could be considered as the potential biomarkers of beef tripe quality. This study has successfully uncovered the protein composition of beef tripe for the very first time, which helps to understand the key proteins and biological processes associated with the quality traits of beef tripe from different sources and improve the quality control of beef tripe.

Genome-wide analysis reveals genomic diversity and signatures of selection in Qinchuan beef cattle

BACKGROUND

Indigenous Chinese cattle have abundant genetic diversity and a long history of artificial selection, giving local breeds advantages in adaptability, forage tolerance and resistance. The detection of selective sweeps and comparative genome analysis of selected breeds and ancestral populations provide a basis for understanding differences among breeds and for the identification and utilization of candidate genes. We investigated genetic diversity, population structure, and signatures of selection using genome-wide sequencing data for a new breed of Qinchuan cattle (QNC, n = 21), ancestral Qinchuan cattle (QCC, n = 20), and Zaosheng cattle (ZSC, n = 19).

RESULTS

A population structure analysis showed that the ancestry components of QNC and ZSC were similar. In addition, the QNC and ZSC groups showed higher proportions of European taurine ancestry than that of QCC, and this may explain the larger body size of QNC, approaching that of European cattle under long-term domestication and selection. A neighbor-joining tree revealed that QCC individuals were closely related, whereas QNC formed a distinct group. To search for signatures of selection in the QNC genome, we evaluated nucleotide diversity (θπ), the fixation index (FST) and Tajima's D. Overlapping selective sweeps were enriched for one KEGG pathway, the apelin signaling pathway, and included five candidate genes (MEF2A, SMAD2, CAMK4, RPS6, and PIK3CG). We performed a comprehensive review of genomic variants in QNC, QCC, and ZSC using whole-genome sequencing data. QCC was rich in novel genetic diversity, while diversity in QNC and ZSC cattle was reduced due to strong artificial selection, with divergence from the original cattle.

CONCLUSIONS

We identified candidate genes associated with production traits. These results support the success of selective breeding and can guide further breeding and resource conservation of Qinchuan cattle.

Quantitative Proteomics Reveals the Relationship between Protein Changes and Volatile Flavor Formation in Hunan Bacon during Low-Temperature Smoking

This study aimed to investigate the changes in proteins and volatile flavor compounds that occur in bacon during low-temperature smoking (LTS) and identify potential correlations between these changes. To achieve this, a combination of gas chromatography-mass spectrometry and proteomics was employed. A total of 42 volatile flavor compounds were identified in the bacon samples, and, during LTS, 11 key volatile flavor compounds with variable importance were found at a projection value of >1, including 2',4'-dihydroxyacetophenone, 4-methyl-2H-furan-5-one, Nonanal, etc. In total, 2017 proteins were quantified at different stages of LTS; correlation coefficients and KEGG analyses identified 27 down-regulated flavor-related proteins. Of these, seven were involved in the tricarboxylic acid (TCA) cycle, metabolic pathways, or amino acid metabolism, and they may be associated with the process of flavor formation. Furthermore, correlation coefficient analysis indicated that certain chemical parameters, such as the contents of free amino acids, carbonyl compounds, and TCA cycle components, were closely and positively correlated with the formation of key volatile flavor compounds. Combined with bioinformatic analysis, the results of this study provide insights into the proteins present in bacon at various stages of LTS. This study demonstrates the changes in proteins and the formation of volatile flavor compounds in bacon during LTS, along with their potential correlations, providing a theoretical basis for the development of green processing methods for Hunan bacon.

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.

Metabolomics and bioinformatic analyses to determine the effects of oxygen exposure within longissimus lumborum steak on beef discoloration

Meat discoloration starts from the interior and spreads to oxymyoglobin layer on the surface. The effects of oxygen exposure within a steak on the metabolome have not been evaluated. Therefore, the objective of this study was to evaluate the impact of oxygen exposure on the metabolome of the longissimus lumborum muscle. Six United States Department of Agriculture (USDA) Low Choice beef strip loins were sliced into steaks (1.91-cm) and packaged in polyvinyl chloride overwrap trays for 3 or 6 d of retail display. The oxygen exposed (OE) surface was the display surface during retail, and the non-oxygen exposed (NOE) surface was the intact interior muscle. The instrumental color was evaluated using a HunterLab MiniScan spectrophotometer. To analyze the NOE surface on days 3 and 6, steaks were sliced parallel to the OE surface to expose the NOE surface. Metmyoglobin reducing ability (MRA) was determined by nitrite-induced metmyoglobin reduction. A gas chromatography-mass spectrometry was used to identify metabolites. The a* values of steaks decreased (P < 0.05) with display time. MRA was greater (P < 0.05) in the NOE surface compared with the OE surface on days 3 and 6. The KEGG pathway analysis indicated the tricarboxylic acid (TCA) cycle, pentose and glucuronate interconversions, phenylalanine, tyrosine, and tryptophan metabolism were influenced by the oxygen exposure. The decrease in abundance of succinate from days 0 to 6 during retail display aligned with a decline in redness during display. Furthermore, citric acid and gluconic acid were indicated as important metabolites affected by oxygen exposure and retail display based on the variable importance in the projection in the PLS-DA plot. Citric acid was lower in the NOE surface than the OE surface on day 6 of retail display, which could relate to the formation of succinate for extended oxidative stability. Greater alpha-tocopherol (P < 0.05) in the NOE surface supported less oxidative changes compared to the OE surface during retail display. These results indicate the presence of oxygen can influence metabolite profile and promote migration of the metmyoglobin layer from interior to surface.

Quality changes and indicator proteins of Litopenaeus vannamei based on label-free proteomics analysis during partial freezing storage

Litopenaeus vannamei are known to deteriorate in quality during low-temperature storage. This study demonstrated the potential protein indicators of partial freezing of stored shrimp by traditional quality parameters and label-free based proteomic techniques. The carbonyl content and myofibril fragmentation index (MFI) of shrimp increased from 0.56 ± 0.03 to 2.14 ± 0.03 nmol/mg and 13.09 ± 0.14 to 54.93 ± 0.96, respectively. Within the extension of storage, the trichloroacetic acid (TCA), cooking loss and whiteness significantly increased. A total of 240 proteins changed in abundance at 10, 20, and 30 days compared to fresh samples. Projectin, ribosomal protein and histone were potential biomarkers for protein denaturation and oxidation in shrimp muscle. Myosin heavy chain and glyceraldehyde-3-phosphate dehydrogenase corresponded with the degradation of muscle proteins. Myosin light chain, tubulin alpha chain, and heat shock protein correlated with tenderness and water holding capacity; meantime, malate dehydrogenase and hemocyanin can serve as color indicators. Further study of the properties of these indicator proteins can inform their exploitation as quality indicator proteins during partial freezing storage.

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.

Strategies to improve meat-like properties of meat analogs meeting consumers' expectations

Due to environmental and ethical concerns, meat analogs represent an emerging trend to replace traditional animal meat. However, meat analogs lacking specific sensory properties (flavor, texture, color) would directly affect consumers' acceptance and purchasing behavior. In this review, we discussed the typical sensory characteristics of animal meat products from texture, flavor, color aspects, and sensory perception during oral processing. The related strategies were detailed to improve meat-like sensory properties for meat analogs. However, the upscaling productions of meat analogs still face many challenges (e.g.: sensory stability of plant-based meat, 3D scaffolds in cultured meat, etc.). Producing safe, low cost and sustainable meat analogs would be a hot topic in food science in the next decades. To realize these promising outcomes, reliable robust devices with automatic processing should also be considered. This review aims at providing the latest progress to improve the sensory properties of meat analogs and meet consumers' requirements.

Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout

The visual appearance of the fish fillet is a significant determinant of consumers' purchase decisions. Depending on the rainbow trout diet, a uniform bright white or reddish/pink fillet color is desirable. Factors affecting fillet color are complex, ranging from the ability of live fish to accumulate carotenoids in the muscle to preharvest environmental conditions, early postmortem muscle metabolism, and storage conditions. Identifying genetic markers of fillet color is a desirable goal but a challenging task for the aquaculture industry. This study used weighted, single-step GWAS to explore the genetic basis of fillet color variation in rainbow trout. We identified several SNP windows explaining up to 3.5%, 2.5%, and 1.6% of the additive genetic variance for fillet redness, yellowness, and whiteness, respectively. SNPs are located within genes implicated in carotenoid metabolism (β,β-carotene 15,15'-dioxygenase, retinol dehydrogenase) and myoglobin homeostasis (ATP synthase subunit β, mitochondrial (ATP5F1B)). These genes are involved in processes that influence muscle pigmentation and postmortem flesh coloration. Other identified genes are involved in the maintenance of muscle structural integrity (kelch protein 41b (klh41b), collagen α-1(XXVIII) chain (COL28A1), and cathepsin K (CTSK)) and protection against lipid oxidation (peroxiredoxin, superoxide dismutase 2 (SOD2), sestrin-1, Ubiquitin carboxyl-terminal hydrolase-10 (USP10)). A-to-G single-nucleotide polymorphism in β,β-carotene 15,15'-dioxygenase, and USP10 result in isoleucine-to-valine and proline-to-leucine non-synonymous amino acid substitutions, respectively. Our observation confirms that fillet color is a complex trait regulated by many genes involved in carotenoid metabolism, myoglobin homeostasis, protection against lipid oxidation, and maintenance of muscle structural integrity. The significant SNPs identified in this study could be prioritized via genomic selection in breeding programs to improve fillet color in rainbow trout.

Estimation of the proteome affecting changes in tenderness of yak meat during storage by label-free mass spectrometry

Background

Tenderness is the main quality of meat products. However, the meat tenderness formation is a complex biological process, and pathways and proteins that affect the tenderness of yak meat are unknown.

Methods

Label‐free proteomics method was used to explore the effects of differentially expressed proteins on the tenderness of yak skeletal muscle (tenderloin) during post‐mortem storage (0, 3, and 7 days) at 3 ± 1°C.

Results

The tenderness of yak skeletal muscle improved significantly during storage. A total of 91 differentially expressed proteins of yak skeletal muscle during post‐mortem storage were identified by the following comparisons: day 3 versus 0, day 7 versus 0, and day 7 versus 3. NDUFS6, CYCS, COX6A2, LDB3, HSPB7, TPM4, TAGLN, COL1A1, LUM, MYH11, ACTC1, and MYOZ1 proteins showed a significant difference during yak skeletal muscle post‐mortem storage. Furthermore, bioinformatics analyses revealed that the identified proteins were related to carbon metabolism, citrate cycle, glycolysis, oxidative phosphorylation, and RNA degradation.

Conclusion

The results of the present study could provide proteomic insights into changes in yak skeletal muscle tenderness during storage and may be a valuable resource for future investigations.

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.

DIA-based quantitative proteomic analysis on the meat quality of porcine Longissimus thoracis et lumborum cooked by different procedures

A DIA-based quantitative proteomic strategy was used to investigate the effects of different cooking procedures (steaming and boiling) on pork meat quality. Results showed that steamed meats had higher redness, cohesion, springiness, but lower lightness, yellowness, shear force, hardness, chewiness and cooking loss than boiled meats. In total of 1608 proteins were identified and 103 proteins exhibited significant difference (fold change > 1.5, P < 0.05). These DAPs mainly involved in protein structure, metabolic enzyme, protein turnover and oxidation stress. ALDOC, PVALB, PPP1R14C, AMPD1, CRYAB and SOD1 were validated as potential indicators of color variations in cooked meat. CFL1, COL1A1, COL3A1, RTN4, NRAP, NT5C3A, and SOD1 might be potential biomarker for texture changes of cooked meats. Moreover, these validated proteins exhibited significant (P < 0.05) correlation with cooking loss and could be serve as candidate predictors for cooking loss changes of meats in different cooking procedures.

The Quality Changes and Proteomic Analysis of Cattle Muscle Postmortem during Rigor Mortis

Rigor mortis occurs in a relatively early postmortem period and is a complex biochemical process in the conversion of muscle to meat. Understanding the quality changes and biomarkers during rigor mortis can provide a theoretical basis for maintaining and improving meat quality. Herein, a tandem mass tag proteomic method is used to investigate the effects of differentially expressed proteins on the meat quality of cattle Longissimus lumborum muscle postmortem (0, 6, and 24 h). The pH, total sulfhydryl content and sarcomere length decrease significantly during storage. In contrast, meat color values (L*, a*, and b*) and the myofibril fragmentation index increase significantly. Altogether, 147 differentially expressed proteins are identified, most being categorized as metabolic enzymes, mitochondrial proteins, necroptosis and ferroptosis proteins and structural proteins. The results also reveal additional proteins that are potentially involved in rigor mortis, such as cardiac phospholamban, acetyl-coenzyme A acyltransferase, and ankyrin repeat domain 2. The current results provide proteomic insights into the changes in meat quality during rigor mortis.

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.

Proteomics discovery of protein biomarkers linked to yak meat tenderness as determined by label-free mass spectrometry

Tenderness is one of the most important qualities in meat. A proteomic approach is a suitable way to ensure meat tenderness. Thirty-six tenderloin samples from yak were classified as exhibiting high (n = 12) or low (n = 12) tenderness and were evaluated using label-free proteomics for the identification of the proteins and pathways most influential in tenderness variability. Between the two groups, proteomic changes were mainly caused by 33 differentially expressed proteins as displayed in reference patterns in heat maps. The expression of ENO2, SUCLG2, ETFDH, PGM1, TNNT3, TNNT1, HSDL2, GPI, ALAD, and COL1A1 proteins was very different between yak meats with high and low tenderness, and therefore, they are candidate biomarkers of yak meat tenderness. Furthermore, bioinformatics analyses revealed that the identified proteins are related to pentose phosphate, glycolysis, the citrate cycle, fatty acid metabolism, and the calcium signaling pathway.

Proteomic Changes in Sarcoplasmic and Myofibrillar Proteins Associated with Color Stability of Ovine Muscle during Post-Mortem Storage

The objective of this study was to investigate the proteomic characteristics for the sarcoplasmic and myofibrillar proteomes of M. longissimus lumborum (LL) and M. psoasmajor (PM) from Small-tailed Han Sheep. During post-mortem storage periods (1, 3, and 5 days), proteome analysis was applied to elucidate sarcoplasmic and myofibrillar protein changes in skeletal muscles with different color stability. Proteomic results revealed that the identified differentially abundant proteins were glycolytic enzymes, energy metabolism enzymes, chaperone proteins, and structural proteins. Through Pearson’s correlation analysis, a few of those identified proteins (Pyruvate kinase, Adenylate kinase isoenzyme 1, Creatine kinase M-type, and Carbonic anhydrase 3) were closely correlated to representative meat color parameters. Besides, bioinformatics analysis of differentially abundant proteins revealed that the proteins mainly participated in glycolysis and energy metabolism pathways. Some of these proteins may have the potential probability to be predictors of meat discoloration during post-mortem storage. Within the insight of proteomics, these results accumulated some basic theoretical understanding of the molecular mechanisms of meat discoloration.

Application of proteomics to understand the molecular mechanisms determining meat quality of beef muscles during postmortem aging

Proteomics profiling disclosed the molecular mechanism underlying beef poor meat quality. This study aimed to identify protein markers indicating the quality of beef during postmortem storage at 4°C. Beef longissimus dorsi samples were stored at 4°C. The meat water holding capacity (WHC), pH value and moisture content were determined at different time points during the storage period. The iTRAQ MS/MS approach was used to determine the proteomics profiling at 0, 3.5 and 7 d during storage at 4°C. Bioinformatics analysis was performed to investigate the potential correlated proteins associated with meat quality. Storage at 4°C gradually decreased the pH value, WHC, and hence the moisture content. The iTRAQ proteomic analysis revealed that a cluster of glycolytic enzymes including malate dehydrogenase, cytoplasmic, L-lactate dehydrogenase, phosphoglycerate mutase and pyruvate kinase, and another cluster of proteins involved in oxygen transport and binding (myoglobin) and hemoglobin complex (including Globin A1 and hemoglobin subunit alpha) were decreased during the postmortem storage. These results suggest that the decreased glycolysis, oxygen, and heme-binding activities might be associated with the beef muscle low quality and the decline of tenderness during postmortem storage at 4°C.

Investigation of muscle-specific beef color stability at different ultimate pHs

OBJECTIVE

This study was aimed to investigate the muscle-specific beef color stability at normal and high ultimate pHs.

METHODS

The impact of muscle (Longissimus lumborum [LL] vs psoas major [PM]) and pH (normal ultimate pH [Np] vs high pH dark cutting beef [Hp]) on color stability, indicated by basic color traits, metmyoglobin reducing activity (MRA) and oxygen consumption (OC), as well as the lipid oxidation, were determined over 7 days of display at 4°C.

RESULTS

Hp-LL had the highest pH (6.92), followed by Hp-PM (6.01), Np-PM (5.76), and Np-LL (5.52). Hp-LL had increased (p<0.05) a*, chroma and % oxymyoglobin during display. Hp-LL also had the highest metmyoglobin (MMb) reducing activity and OC among all the samples, thus, the greatest color stability, although very dark throughout storage, with lowest values for lightness (L*) and yellowness (b*). Np-LL also exhibited relatively high color stability, as a result of its lower % MMb and OC and higher MRA than psoas muscle samples. The 0.2 unit difference of the pH between Hp and Np psoas muscle, resulted in the difference of the color intensity, not the color stability. Interestingly, high pH psoas muscle (Hp-PM) did not have better color stability than Np-PM, and in fact had lower color stability than even Np-LL. The similar level of OC and lipid oxidation cannot explain the difference in color stability between Hp-PM and Np-LL.

CONCLUSION

The Hp does not always show better color stability compared with Np beef, which depends on the muscle type. The balance of MRA and OC is important to keep the color in great intensity and stability in the meantime.

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.

Recent Updates in Meat Color Research: Integrating Traditional and High-Throughput Approaches

Deviation from a bright cherry-red color of fresh meat results in less consumer acceptance and either discounted or discarded products in the value chain. Tissue homeostasis changes immediately after exsanguination, leading to acidification of muscle. Any alteration in pH drop can influence both muscle structure and enzymatic activity related to oxygen consumption and the redox state of myoglobin. This review focuses on both fundamental and applied approaches to under-stand the effects of pH on biochemical changes, oxygen diffusion, and its impact on meat color. Recent updates utilizing high-throughput “omics” approaches to elucidate the biochemical changes associated with high-pH meat are also dis-cussed. The fundamental aspects affecting fresh meat color are complex and highly interrelated with factors ranging from live animal production to preharvest environmental issues, muscle to meat conversion, and numerous facets along the merchandising chain of marketing meat to consumers.

Comparative transcriptomics to reveal muscle-specific molecular differences in the early postmortem of Chinese Jinjiang yellow cattle

Differences in the expression of functional genes between beef Longissimus Lumborum (LL) and Psoas Major (PM) are not well understood. The aim of present study is to reveal transcriptome changes of beef LL and PM during early postmortem by high-throughput Illumina Hiseq4000 Sequencing. Hierarchical clustering analysis indicated significant differences in transcriptome profiles between LL and PM as well as 1 h and 12 h postmortem. A total of 65 genes differentially expressed between LL and PM (fold change ≥3, and p < 0.05; 34 were up-regulated in LL and 31 in PM), and the majority of them (53 genes) occurred at 12 h postmortem. These differentially expressed genes mainly involved in energy production and conversion, nucleotide metabolic, posttranslational modification, and transcription. KEGG analysis revealed that oxidative phosphorylation was one of the important pathways. This study gave new perspectives to understand the underlying mechanisms associated with muscle-specific beef quality.

Analysis of Proteins Associated with Quality Deterioration of Grouper Fillets Based on TMT Quantitative Proteomics during Refrigerated Storage

A TMT (Tandem Mass Tag)-based strategy was applied to elucidate proteins that change in proteomes of grouper fillets during refrigerated storage. In addition, quality analyses on pH, centrifugal loss, color (L *, a *, b *) and texture (hardness, chewiness, and gumminess) for grouper fillets were performed. A total of 64 differentially significant expressed proteins (DSEPs) were found in the results in the Day 0 vs. Day 6 group comparison and the Day 0 vs. Day 12 group comparison. It is worth mentioning that more proteome changes were found in the Day 0 vs. Day 12 comparisons. Bioinformatics was utilized to analyze the DSEP. UniProt Knowledgebase (UniProtKB), Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein interaction network analysis were adopted. All DSEPs were classified into seven areas by function: binding proteins, calcium handling, enzymes, heat shock protein, protein turnover, structural proteins and miscellaneous. The numbers of proteins that correlated closely with pH, centrifugal loss, color (L *, a *, b *) and texture (hardness, chewiness, and gumminess) were 4, 3, 6 and 8, respectively.

Is the protein profile of pig Longissimus dorsi affected by gender and diet?

The impact of gender and diet on the proteome of Longissimus dorsi was addressed by 2D-PAGE analysis of male and female pigs, fed with a barley-based control diet and a diet enriched with extruded linseed and plant extracts. No statistically significant difference in protein number between female and male samples was found. Furthermore, PCA excluded gender-dependent protein clusters. For both the control and enriched diet, several spots exhibited at least a 1.5-fold intensity difference, but none showed a statistically relevant variation. Protein profiles PCA for both diets indicated that the first two principal components account up to 47% of total variance, with two diet-dependent separated clusters. Among 176 common spots, 29 exhibited >1.5 fold change, mostly more abundant in the control diet. PMF identified 14 distinct proteins, including myofibrillar proteins, glycolytic enzymes and myoglobin, thus suggesting a diet-dependent meat quality. A statistically significant increase in carbonylated proteins of enriched diet samples was detected using the 2,4-dinitrophenylhydrazine method but not using fluorescein-5-thiosemicarbazide-labeled bands. ROS induction and DNA oxidative damage, detected in a human cell line exposed to digested meat from both diets, further support the notion that the enriched diet does not protect against oxidative stress. SIGNIFICANCE: The comparison of the protein profile of female and male Longissimus dorsi from pigs fed by a control diet and a diet enriched with polyphenols, indicate no gender effect, whereas diet affects the abundance of several proteins, possibly linked to meat quality. Protein carbonylation was statistically higher in meat from the enriched diet, suggesting that polyphenols at the concentration present in the diet did not exert a protective effect against oxidation.

Proteomic analysis of the fast-twitch muscle of pacu (Piaractus mesopotamicus) after prolonged fasting and compensatory growth

Protocols that improve growth performance in fish while assuring product quality are important for aquaculture. Fasting followed by refeeding may promote compensatory growth, thus optimizing growth performance. During fasting and refeeding, fast-twitch muscle, which comprises most of fish fillet, undergoes intense plasticity. In this work, we studied the proteome of pacu (Piaractus mesopotamicus) fast-twitch muscle after 30 days of fasting (D30), 30 days of refeeding (D60) and 60 days of refeeding (D90) with two-dimensional electrophoresis, mass spectrometry and bioinformatics. Body mass, growth rate and muscle histology were also assessed. At D30, fish presented muscle catabolism and decreased growth. Proteomic analysis showed that metabolism proteins were the most affected, up and downregulated. Cytoskeleton and amino acid biosynthesis proteins were downregulated, while nuclear and regulatory proteins were upregulated. At D60, fish showed accelerated growth, despite the body mass not completely recovering. Metabolism proteins were still the most affected. Amino acid biosynthesis proteins became upregulated, while cytoskeleton proteins remained downregulated. At D90, the fish presented total compensatory growth. Many metabolic proteins were up or downregulated. Few cytoskeleton proteins remained differentially expressed. Amino acid biosynthesis proteins were mostly upregulated, but less than at D60. Prolonged fasting followed by refeeding also led to the regulation of possible meat quality biomarkers, such as antioxidant enzymes. This fact suggests possible consequences of this protocol on fish meat quality. Our work also enriches our knowledge on proteomic changes during muscle plasticity that occur during fasting and refeeding diet protocols.

Muscle-specific color stability in fresh beef from grain-finished Bos indicus cattle

Objective

To investigate the color and oxidative stabilities of longissimus lumborum (LL) and psoas major (PM) muscles from grain-finished Bos indicus cattle in Brazil.

Methods

The LL and PM muscles were obtained 24 h post-mortem from eight (n = 8) Nellore bull carcasses, fabricated into 1.5-cm steaks, aerobically packaged, and stored at 4°C for nine days. Steaks were analyzed for myoglobin concentration, pH, instrumental color, metmyoglobin reducing activity (MRA) and lipid oxidation.

Results

The LL steaks exhibited greater (p<0.05) redness, color stability, and MRA than their PM counterparts on days 5 and 9. The LL and PM steaks demonstrated similar (p>0.05) lightness and yellowness on days 0, 5, and 9. On the other hand, PM steaks exhibited greater (p<0.05) myoglobin concentration, pH, and lipid oxidation than their LL counterparts.

Conclusion

These results indicated that muscle source influenced the color and oxidative stabilities of beef from grain-finished Bos indicus animals. These results highlighted the necessity of muscle-specific strategies to improve the color stability of beef from grain-fed Bos indicus cattle.

Comparing SRM and SWATH Methods for Quantitation of Bovine Muscle Proteomes

Mass spectrometry (MS) has become essential for efficient and accurate quantification of proteins and proteomes and, thus, a key technology throughout all biosciences. However, validated MS methods are still scarce for meat quality research applications. The objective of this work was to develop and compare two targeted proteomic methods, namely, selected reaction monitoring (SRM) and sequential window acquisition of all theoretical spectra (SWATH), for the quantification of 11 bovine muscle proteins that may be indicators of meat color. Both methods require evaluation of spectra from proteotypic and quantotypic peptides, and we here report our evaluation of which peptides and MS parameters are best suited for robust quantification of these 11 proteins. We observed that the SRM approach provides better reproducibility, linearity, and sensitivity than SWATH and is therefore ideal for targeted quantification of low-abundance proteins, while the SWATH approach provides a more time-efficient method for targeted protein quantification of high-abundance proteins and, additionally, supports the search for novel biomarkers.

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.

Proteomic analysis to investigate color changes of chilled beef longissimus steaks held under carbon monoxide and high oxygen packaging

This study investigated the proteome basis for color stability variations in beef steaks packaged under two modified atmosphere packaging (MAP) methods: HiOx-MAP (80% O₂/20% CO₂) and CO-MAP (0.4% CO/30% CO₂/69.6% N₂) during 15 days of storage. The color stability, pH, and sarcoplasmic proteome analysis of steaks were evaluated on days 0, 5, 10 and 15 of storage. Proteomic results revealed that the differential expression of the sarcoplasmic proteome during storage contributed to the variations in meat color stability between the two MAP methods. Compared with HiOx-MAP steaks, some glycolytic and energy metabolic enzymes important in NADH regeneration and antioxidant processes, antioxidant peroxiredoxins (thioredoxin-dependent peroxide reductase, peroxiredoxin-2, peroxiredoxin-6) and protein DJ-1 were more abundant in CO-MAP steaks. The over-expression of these proteins could induce CO-MAP steaks to maintain high levels of metmyoglobin reducing activity and oxygen consumption rate, resulting in CO-MAP steaks exhibiting better color stability than HiOx-MAP steaks during storage.