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Recent Advances in OMICs Technologies and Application for Ensuring Meat...
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Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Meat".

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 35232

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Dr. Mohammed Gagaoua

E-Mail Website
Guest Editor
Food Quality and Sensory Science Department, Teagasc Ashtown Food Research Centre, Ashtown, Dublin 15, Ireland
Interests: foodomics; meat science; proteomics; muscle and meat biochemistry; biomarkers of meat quality; novel strategies to improve meat quality; meat tenderization; meat products
Special Issues, Collections and Topics in MDPI journals
Dr. Brigitte Picard

E-Mail Website
Guest Editor
Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
Interests: meat; skeletal muscle; beef quality; proteomics; muscle biochemistry; muscle fibres; muscle development; sensory quality; biomarkers of meat quality; prediction of meat quality; rearing practices and beef quality
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The meat industry has been increasingly requested by consumers to guarantee both high-quality products, as well as a stable sensory quality. To do so, it is necessary to understand the mechanisms that underlie the conversion of muscle into meat, as well as the impact of pre- and post-harvest procedures on the final quality and safety of meat products. Over the last two decades, sophisticated “-OMICs” technologies—genomics, transcriptomics, proteomics, peptidomics, metabolomics, and lipidomics—are a novelty in food sciences, and were successfully implemented to address meat-quality issues. These powerful techniques were also extensively used to elucidate the biological basis/mechanisms for phenotypic variation in the technological and sensory quality traits of meat from pork, cattle, poultry, fish, lamb, rabbit, camel, and many other muscle foods.

Accordingly, in this Special Issue, we invite authors to submit cutting edge innovative research papers or review papers on the application of OMICs tools to characterize or manage the quality of meat and meat products, wherever the source; the applications of OMICs for the evaluation of the risk assessment of meat products; and the use of foodomics to determine the foodstuff molecular profile of meat and meat products in the light of an improvement of human nutrition. This Special Issue also seeks to provide a fundamental understanding of the nutritional, sensory, and physical properties of meat and meat products using the latest applications of OMICs in meat science to identify biomarkers. Papers dealing with the application of OMICs as innovative tools to characterize the safety and the authenticity of meat and meat products are further welcomed. In short, we are also highly interested and encourage papers that address the application of OMICs to assess the fundamental pathways and biochemical processes driving the final quality of meat products.

Dr. Brigitte Picard
Dr. Mohammed Gagaoua
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Foods is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • OMICs to study the quality of meat (and fish) and meat products
  • Genomics and meat quality, safety, and authenticity
  • Transcriptomics and meat quality, safety, and authenticity
  • Proteomics and meat quality, safety, and authenticity
  • Peptidomics and meat quality, safety, and authenticity
  • Metabolomics and meat quality, safety, and authenticity
  • Lipidomics and meat quality, safety, and authenticity
  • OMICs and meat tenderness, color, pH decline, water-holding capacity, marbling, and so on
  • Functional pathways and biological properties influencing meat quality
  • Current statistical tools to manage OMICs data and predict meat quality
  • Meta-analyses and integromics (integrative studies) of OMICs data
  • Biomarkers of meat and meat product qualities

Published Papers (12 papers)

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Editorial

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4 pages, 197 KiB  
Editorial
Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity
by Mohammed Gagaoua
Foods 2022, 11(16), 2532; https://0-doi-org.brum.beds.ac.uk/10.3390/foods11162532 - 22 Aug 2022
Cited by 2 | Viewed by 1701
Abstract
Consumers and stakeholders are increasingly demanding that the meat industry guarantees high-quality meat products with stable and acceptable sensory and safety properties [...] Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)

Research

Jump to: Editorial

30 pages, 2463 KiB  
Article
Interlaboratory Validation of a DNA Metabarcoding Assay for Mammalian and Poultry Species to Detect Food Adulteration
by Stefanie Dobrovolny, Steffen Uhlig, Kirstin Frost, Anja Schlierf, Kapil Nichani, Kirsten Simon, Margit Cichna-Markl and Rupert Hochegger
Foods 2022, 11(8), 1108; https://0-doi-org.brum.beds.ac.uk/10.3390/foods11081108 - 12 Apr 2022
Cited by 9 | Viewed by 2162
Abstract
Meat species authentication in food is most commonly based on the detection of genetic variations. Official food control laboratories frequently apply single and multiplex real-time polymerase chain reaction (PCR) assays and/or DNA arrays. However, in the near future, DNA metabarcoding, the generation of [...] Read more.
Meat species authentication in food is most commonly based on the detection of genetic variations. Official food control laboratories frequently apply single and multiplex real-time polymerase chain reaction (PCR) assays and/or DNA arrays. However, in the near future, DNA metabarcoding, the generation of PCR products for DNA barcodes, followed by massively parallel sequencing by next generation sequencing (NGS) technologies, could be an attractive alternative. DNA metabarcoding is superior to well-established methodologies since it allows simultaneous identification of a wide variety of species not only in individual foodstuffs but even in complex mixtures. We have recently published a DNA metabarcoding assay for the identification and differentiation of 15 mammalian species and six poultry species. With the aim to harmonize analytical methods for food authentication across EU Member States, the DNA metabarcoding assay has been tested in an interlaboratory ring trial including 15 laboratories. Each laboratory analyzed 16 anonymously labelled samples (eight samples, two subsamples each), comprising six DNA extract mixtures, one DNA extract from a model sausage, and one DNA extract from maize (negative control). Evaluation of data on repeatability, reproducibility, robustness, and measurement uncertainty indicated that the DNA metabarcoding method is applicable for meat species authentication in routine analysis. Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)
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14 pages, 2560 KiB  
Communication
Preliminary Results about Lamb Meat Tenderness Based on the Study of Novel Isoforms and Alternative Splicing Regulation Pathways Using Iso-seq, RNA-seq and CTCF ChIP-seq Data
by Zehu Yuan, Ling Ge, Weibo Zhang, Xiaoyang Lv, Shanhe Wang, Xiukai Cao and Wei Sun
Foods 2022, 11(8), 1068; https://0-doi-org.brum.beds.ac.uk/10.3390/foods11081068 - 07 Apr 2022
Cited by 7 | Viewed by 2054
Abstract
Tenderness is an important indicator of meat quality. Novel isoforms associated with meat tenderness and the role of the CCCTC-binding factor (CTCF) in regulating alternative splicing to produce isoforms in sheep are largely unknown. The current project studied six sheep from two crossbred [...] Read more.
Tenderness is an important indicator of meat quality. Novel isoforms associated with meat tenderness and the role of the CCCTC-binding factor (CTCF) in regulating alternative splicing to produce isoforms in sheep are largely unknown. The current project studied six sheep from two crossbred populations (Dorper × Hu × Hu, DHH and Dorper × Dorper × Hu, DDH) with divergent meat tenderness. Pooled Iso-seq data were used to annotate the sheep genomes. Then, the updated genome annotation and six RNA-seq data were combined to identify differentially expressed isoforms (DEIs) in muscles between DHH and DDH. These data were also combined with peaks detected from CTCF ChIP-seq data to investigate the regulatory role of CTCF for the alternative splicing. As a result, a total of 624 DEIs were identified between DDH and DHH. For example, isoform 7.524.18 transcribed from CAPN3 may be associated with meat tenderness. In addition, a total of 86 genes were overlapped between genes with transcribed DEIs and genes in differential peaks identified by CTCF ChIP-seq. Among these overlapped genes, ANKRD23 produces different isoforms which may be regulated by CTCF via methylation. As preliminary research, our results identified novel isoforms associated with meat tenderness and revealed the possible regulating mechanisms of alternative splicing to produce isoforms. Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)
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22 pages, 2341 KiB  
Article
New Insights on the Impact of Cattle Handling on Post-Mortem Myofibrillar Muscle Proteome and Meat Tenderization
by Verónica Sierra, Laura González-Blanco, Yolanda Diñeiro, Fernando Díaz, María Josefa García-Espina, Ana Coto-Montes, Mohammed Gagaoua and Mamen Oliván
Foods 2021, 10(12), 3115; https://0-doi-org.brum.beds.ac.uk/10.3390/foods10123115 - 15 Dec 2021
Cited by 14 | Viewed by 3791
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)
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14 pages, 3082 KiB  
Article
Proteomic Changes in Sarcoplasmic and Myofibrillar Proteins Associated with Color Stability of Ovine Muscle during Post-Mortem Storage
by Xiaoguang Gao, Dandan Zhao, Lin Wang, Yue Cui, Shijie Wang, Meng Lv, Fangbo Zang and Ruitong Dai
Foods 2021, 10(12), 2989; https://0-doi-org.brum.beds.ac.uk/10.3390/foods10122989 - 03 Dec 2021
Cited by 8 | Viewed by 2187
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)
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12 pages, 1685 KiB  
Article
Development of a Duck Genomic Reference Material by Digital PCR Platforms for the Detection of Meat Adulteration
by Xiaoyun Chen, Yi Ji, Kai Li, Xiaofu Wang, Cheng Peng, Xiaoli Xu, Xinwu Pei, Junfeng Xu and Liang Li
Foods 2021, 10(8), 1890; https://0-doi-org.brum.beds.ac.uk/10.3390/foods10081890 - 15 Aug 2021
Cited by 8 | Viewed by 2083
Abstract
Low-cost meat, such as duck, is frequently used to adulterate more expensive foods like lamb or beef in many countries. However, the lack of DNA-based reference materials has limited the quality control and detection of adulterants. Here, we report the development and validation [...] Read more.
Low-cost meat, such as duck, is frequently used to adulterate more expensive foods like lamb or beef in many countries. However, the lack of DNA-based reference materials has limited the quality control and detection of adulterants. Here, we report the development and validation of duck genomic DNA certified reference materials (CRMs) through the detection of the duck interleukin 2 (IL2) gene by digital PCR (dPCR) for the identification of duck meat in food products. The certified value of IL2 in CRMs was 5.78 ± 0.51 × 103 copies/μL with extended uncertainty (coverage factor k = 2) based on IL2 quantification by eight independent collaborating laboratories. Quantification of the mitochondrial gene cytb revealed a concentration of 2.0 × 106 copies/μL, as an information value. The CRMs were also used to determine the limit of detection (LOD) for six commercial testing kits, which confirmed that these kits meet or exceed their claimed sensitivity and are reliable for duck detection. Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)
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16 pages, 2215 KiB  
Article
Impact of Extraction Method on the Detection of Quality Biomarkers in Normal vs. DFD Meat
by Laura González-Blanco, Yolanda Diñeiro, Andrea Díaz-Luis, Ana Coto-Montes, Mamen Oliván and Verónica Sierra
Foods 2021, 10(5), 1097; https://0-doi-org.brum.beds.ac.uk/10.3390/foods10051097 - 15 May 2021
Cited by 6 | Viewed by 2758
Abstract
The objective of this work was to demonstrate how the extraction method affects the reliability of biomarker detection and how this detection depends on the biomarker location within the cell compartment. Different extraction methods were used to study the sarcoplasmic and myofibrillar fractions [...] Read more.
The objective of this work was to demonstrate how the extraction method affects the reliability of biomarker detection and how this detection depends on the biomarker location within the cell compartment. Different extraction methods were used to study the sarcoplasmic and myofibrillar fractions of the Longissimus thoracis et lumborum muscle of young bulls of the Asturiana de los Valles breed in two quality grades, standard (Control) or dark, firm, and dry (DFD) meat. Protein extractability and the expression of some of the main meat quality biomarkers—oxidative status (lipoperoxidation (LPO) and catalase activity (CAT)), proteome (SDS-PAGE electrophoretic pattern), and cell stress protein (Hsp70)—were analyzed. In the sarcoplasmic fraction, buffers containing Triton X-100 showed significantly higher protein extractability, LPO, and higher intensity of high-molecular-weight protein bands, whereas the TES buffer was more sensitive to distinguishing differences in the protein pattern between the Control and DFD meat. In the myofibrillar fraction, samples extracted with the lysis buffer showed significantly higher protein extractability, whereas samples extracted with the non-denaturing buffer showed higher results for LPO, CAT, and Hsp70, and higher-intensity bands in the electrophoretic pattern. These findings highlight the need for the careful selection of the extraction method used to analyze the different biomarkers considering their cellular location to adapt the extractive process. Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)
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13 pages, 26254 KiB  
Article
A Simple and Reliable Single Tube Septuple PCR Assay for Simultaneous Identification of Seven Meat Species
by Zhendong Cai, Song Zhou, Qianqian Liu, Hui Ma, Xinyi Yuan, Jiaqi Gao, Jinxuan Cao and Daodong Pan
Foods 2021, 10(5), 1083; https://0-doi-org.brum.beds.ac.uk/10.3390/foods10051083 - 13 May 2021
Cited by 11 | Viewed by 2658
Abstract
Multiplex PCR methods have been frequently used for authentication of meat product adulteration. Through screening of new species-specific primers designed based on the mitochondrial DNA sequences, a septuple PCR method is ultimately developed and optimized to simultaneously detect seven species including turkey (110 [...] Read more.
Multiplex PCR methods have been frequently used for authentication of meat product adulteration. Through screening of new species-specific primers designed based on the mitochondrial DNA sequences, a septuple PCR method is ultimately developed and optimized to simultaneously detect seven species including turkey (110 bp), goose (194 bp), pig (254 bp), sheep (329 bp), beef (473 bp), chicken (612 bp) and duck (718 bp) in one reaction. The proposed method has been validated to be specific, sensitive, robust and inexpensive. Taken together, the developed septuple PCR assay is reliable and efficient, not only to authenticate animal species in commercial meat products, but also easily feasible in a general laboratory without special infrastructures. Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)
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20 pages, 1748 KiB  
Article
A Proteomic Study for the Discovery of Beef Tenderness Biomarkers and Prediction of Warner–Bratzler Shear Force Measured on Longissimus thoracis Muscles of Young Limousin-Sired Bulls
by Yao Zhu, Mohammed Gagaoua, Anne Maria Mullen, Alan L. Kelly, Torres Sweeney, Jamie Cafferky, Didier Viala and Ruth M. Hamill
Foods 2021, 10(5), 952; https://0-doi-org.brum.beds.ac.uk/10.3390/foods10050952 - 27 Apr 2021
Cited by 22 | Viewed by 3394
Abstract
Beef tenderness is of central importance in determining consumers’ overall liking. To better understand the underlying mechanisms of tenderness and be able to predict it, this study aimed to apply a proteomics approach on the Longissimus thoracis (LT) muscle of young Limousin-sired bulls [...] Read more.
Beef tenderness is of central importance in determining consumers’ overall liking. To better understand the underlying mechanisms of tenderness and be able to predict it, this study aimed to apply a proteomics approach on the Longissimus thoracis (LT) muscle of young Limousin-sired bulls to identify candidate protein biomarkers. A total of 34 proteins showed differential abundance between the tender and tough groups. These proteins belong to biological pathways related to muscle structure, energy metabolism, heat shock proteins, response to oxidative stress, and apoptosis. Twenty-three putative protein biomarkers or their isoforms had previously been identified as beef tenderness biomarkers, while eleven were novel. Using regression analysis to predict shear force values, MYOZ3 (Myozenin 3), BIN1 (Bridging Integrator-1), and OGN (Mimecan) were the major proteins retained in the regression model, together explaining 79% of the variability. The results of this study confirmed the existing knowledge but also offered new insights enriching the previous biomarkers of tenderness proposed for Longissimus muscle. Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)
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25 pages, 8888 KiB  
Article
Upstream Regulator Analysis of Wooden Breast Myopathy Proteomics in Commercial Broilers and Comparison to Feed Efficiency Proteomics in Pedigree Male Broilers
by Walter G. Bottje, Kentu R. Lassiter, Vivek A. Kuttappan, Nicholas J. Hudson, Casey M. Owens, Behnam Abasht, Sami Dridi and Byungwhi C. Kong
Foods 2021, 10(1), 104; https://0-doi-org.brum.beds.ac.uk/10.3390/foods10010104 - 06 Jan 2021
Cited by 8 | Viewed by 2441
Abstract
In an effort to understand the apparent trade-off between the continual push for growth performance and the recent emergence of muscle pathologies, shotgun proteomics was conducted on breast muscle obtained at ~8 weeks from commercial broilers with wooden breast (WB) myopathy and compared [...] Read more.
In an effort to understand the apparent trade-off between the continual push for growth performance and the recent emergence of muscle pathologies, shotgun proteomics was conducted on breast muscle obtained at ~8 weeks from commercial broilers with wooden breast (WB) myopathy and compared with that in pedigree male (PedM) broilers exhibiting high feed efficiency (FE). Comparison of the two proteomic datasets was facilitated using the overlay function of Ingenuity Pathway Analysis (IPA) (Qiagen, CA, USA). We focused on upstream regulator analysis and disease-function analysis that provides predictions of activation or inhibition of molecules based on (a) expression of downstream target molecules, (b) the IPA scientific citation database. Angiopoeitin 2 (ANGPT2) exhibited the highest predicted activation Z-score of all molecules in the WB dataset, suggesting that the proteomic landscape of WB myopathy would promote vascularization. Overlaying the FE proteomics data on the WB ANGPT2 upstream regulator network presented no commonality of protein expression and no prediction of ANGPT2 activation. Peroxisome proliferator coactivator 1 alpha (PGC1α) was predicted to be inhibited, suggesting that mitochondrial biogenesis was suppressed in WB. PGC1α was predicted to be activated in high FE pedigree male broilers. Whereas RICTOR (rapamycin independent companion of mammalian target of rapamycin) was predicted to be inhibited in both WB and FE datasets, the predictions were based on different downstream molecules. Other transcription factors predicted to be activated in WB muscle included epidermal growth factor (EGFR), X box binding protein (XBP1), transforming growth factor beta 1 (TGFB1) and nuclear factor (erythroid-derived 2)-like 2 (NFE2L2). Inhibitions of aryl hydrocarbon receptor (AHR), AHR nuclear translocator (ARNT) and estrogen related receptor gamma (ESRRG) were also predicted in the WB muscle. These findings indicate that there are considerable differences in upstream regulators based on downstream protein expression observed in WB myopathy and in high FE PedM broilers that may provide additional insight into the etiology of WB myopathy. Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)
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23 pages, 1580 KiB  
Article
Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction
by Mohammed Gagaoua, Muriel Bonnet and Brigitte Picard
Foods 2020, 9(9), 1180; https://0-doi-org.brum.beds.ac.uk/10.3390/foods9091180 - 26 Aug 2020
Cited by 31 | Viewed by 4002
Abstract
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) [...] Read more.
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. Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)
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11 pages, 2192 KiB  
Article
Gas Chromatography–Mass Spectrometry-Based Metabolite Profiling for the Assessment of Freshness in Gilthead Sea Bream (Sparus aurata)
by Athanasios Mallouchos, Theano Mikrou and Chrysavgi Gardeli
Foods 2020, 9(4), 464; https://0-doi-org.brum.beds.ac.uk/10.3390/foods9040464 - 09 Apr 2020
Cited by 14 | Viewed by 3968
Abstract
Gilthead sea bream (Sparus aurata) is one of the most important farmed Mediterranean fish species, and there is considerable interest for the development of suitable methods to assess its freshness. In the present work, gas chromatography–mass spectrometry-based metabolomics was employed to [...] Read more.
Gilthead sea bream (Sparus aurata) is one of the most important farmed Mediterranean fish species, and there is considerable interest for the development of suitable methods to assess its freshness. In the present work, gas chromatography–mass spectrometry-based metabolomics was employed to monitor the hydrophilic metabolites of sea bream during storage on ice for 19 days. Additionally, the quality changes were evaluated using two conventional methods: sensory evaluation according to European Union’s grading scheme and K-value, the most widely used chemical index of fish spoilage. With the application of chemometrics, the fish samples were successfully classified in the freshness categories, and a partial least squares regression model was built to predict K-value. A list of differential metabolites were found, which were distinguished according to their evolution profile as potential biomarkers of freshness and spoilage. Therefore, the results support the suitability of the proposed methodology to gain information on seafood quality. Full article
(This article belongs to the Special Issue Recent Advances in OMICs Technologies and Application for Ensuring Meat Quality, Safety and Authenticity)
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