Christophe Chambon

French National Institute for Agricultural Research, Lutetia Parisorum, Île-de-France, France

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Publications (93)286.73 Total impact

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    T. Sayd · C. Chambon · V. Santé-Lhoutellier
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    ABSTRACT: We aimed to identify and quantify the peptides generated during in vitro digestion of cooked meat by liquid chromatography coupled with high resolution mass spectrometer. A total of 940 non-redundant peptides in the gastric compartment and 989 non-redundant peptides in the intestinal compartment were quantified and identified. Among the 71 different proteins identified, 43 meat proteins were found in the two digestive compartments, 20 proteins were specific to the gastric compartment and 8 proteins to the intestinal compartment. In terms of estimation, the proteins involved in muscle contraction and structure were preferentially enzymatically hydrolyzed in the small intestine. The effect of cooking provided different but less clear patterns of digestion. To the best of our knowledge, this constitutes the highest number of peptides identified in beef meat digests and provides a comprehensive database for meat protein digestion associated with cooking conditions. Such quantitative and qualitative differences may have important nutritional consequences.
    Full-text · Article · Nov 2015 · Food Chemistry
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    ABSTRACT: Wheat grain end-use value is determined by complex molecular interactions that occur during grain development, including those in the cell nucleus. However, our knowledge of how the nuclear proteome changes during grain development is limited. Here, we analyzed nuclear proteins of developing wheat grains collected during the cellularization, effective grain-filling, and maturation phases of development, respectively. Nuclear proteins were extracted and separated by two-dimensional gel electrophoresis. Image analysis revealed 371 and 299 reproducible spots in gels with first dimension separation along pH 4–7 and pH 6–11 isoelectric gradients, respectively. The relative abundance of 464 (67%) protein spots changed during grain development. Abundance profiles of these proteins clustered in six groups associated with the major phases and phase transitions of grain development. Using nano liquid chromatography-tandem mass spectrometry to analyse 387 variant and non-variant protein spots, 114 different proteins were identified that were classified into 16 functional classes. We noted that some proteins involved in the regulation of transcription, like HMG1/2-like protein and histone deacetylase HDAC2, were most abundant before the phase transition from cellularization to grain-filling, suggesting that major transcriptional changes occur during this key developmental phase. The maturation period was characterized by high relative abundance of proteins involved in ribosome biogenesis. Data are available via ProteomeXchange with identifier PXD002999.
    Preview · Article · Oct 2015 · Frontiers in Plant Science
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    ABSTRACT: Wheat grain end-use value is determined by complex molecular interactions that occur during grain development, including those in the cell nucleus. However, our knowledge of how the nuclear proteome changes during grain development is limited. Here, we analyzed nuclear proteins of developing wheat grains collected during the cellularization, effective grain-filling, and maturation phases of development, respectively. Nuclear proteins were extracted and separated by two-dimensional gel electrophoresis. Image analysis revealed 371 and 299 reproducible spots in gels with first dimension separation along pH 4–7 and pH 6–11 isoelectric gradients, respectively. The relative abundance of 464 (67%) protein spots changed during grain development. Abundance profiles of these proteins clustered in six groups associated with the major phases and phase transitions of grain development. Using nano liquid chromatography-tandem mass spectrometry to analyse 387 variant and non-variant protein spots, 114 different proteins were identified that were classified into 16 functional classes. We noted that some proteins involved in the regulation of transcription, like HMG1/2-like protein and histone deacetylase HDAC2, were most abundant before the phase transition from cellularization to grain-filling, suggesting that major transcriptional changes occur during this key developmental phase. The maturation period was characterized by high relative abundance of proteins involved in ribosome biogenesis. Data are available via ProteomeXchange with identifier PXD002999.
    Full-text · Article · Oct 2015 · Frontiers in Plant Science
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    ABSTRACT: Escherichia coli é um microrganismo comensal do trato gastrointestinal de animais e humanos. Esta pode ser utilizada em diversos estudos biológicos e genéticos sobre a resistência aos antibióticos. A presença do plasmídeo pMdT1 é de grande relevância no estudo da resistência aos antibióticos, visto que contém um gene que codifica uma variante da proteína AAC(6’)-lb-cr e que esta, quando ativa, confere resistência à tobramicina e à canamicina, e diminui a suscetibilidade à ciprofloxacina e à norfloxacina. Foram utilizadas duas amostras, Escherichia coli Electromax DH10B, recetora do processo de transformação e Escherichia coli TF-Se20 sendo esta transformada, pois contém o plasmídeo pMdT1 que expressa o gene da acetilase. Após a extração proteica, a separação e quantificação das proteínas foi realizada mediante eletroforese monodimensional (SDS-PAGE) e posteriormente bidimensional (IEF x SDS-PAGE). A identificação das proteínas foi realizada através da técnica MALDI-TOF/MS. Para determinar a sequência da proteína de interesse, utilizou-se a técnica LC-MS/MS. As proteínas identificadas participam em diversos processos biológicos, designadamente nos processos de glicólise, oxidação-redução e biossíntese de proteínas. A proteína de interesse, aminoglycoside N(6’)-acetyltransferase type 1, foi identificada e posteriormente sequenciada concluindo-se, desta forma, que a proteómica pode ser usada para obter mais informação sobre os mecanismos de resistência.
    Full-text · Conference Paper · Oct 2015
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    ABSTRACT: Ku70-dependent canonical nonhomologous end-joining (c-NHEJ) DNA repair system is fundamental to the genome maintenance and B-cell lineage. c-NHEJ is upregulated and error-prone in incurable forms of chronic lymphocytic leukemia which also displays telomere dysfunction, multiple chromosomal aberrations and the resistance to DNA damage-induced apoptosis. We identify in these cells a novel DNA damage inducible form of phospho-Ku70. In vitro in different cancer cell lines, Ku70 phosphorylation occurs in a heterodimer Ku70/Ku80 complex within minutes of genotoxic stress, necessitating its interaction with DNA damage-induced kinase pS2056-DNA-PKcs and/or pS1981-ATM. The mutagenic effects of phospho-Ku70 are documented by a defective S/G2 checkpoint, accelerated disappearance of γ-H2AX foci and kinetics of DNA repair resulting in an increased level of genotoxic stress-induced chromosomal aberrations. Together, these data unveil an involvement of phospho-Ku70 in fast but inaccurate DNA repair; a new paradigm linked to both the deregulation of c-NHEJ and the resistance of malignant cells.
    Full-text · Article · Aug 2015 · Oncotarget
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    ABSTRACT: For many years Staphylococcus aureus has been recognized as an important human pathogen. In this study, the surfacome and exoproteome of a clinical sample of MRSA was analyzed. The C2355 strain, previously typed as ST398 and spa-t011 and showing a phenotype of multiresistance to antibiotics, has several resistance genes. Using shotgun proteomics and bioinformatics tools, 236 proteins were identified in the surfaceome and 99 proteins in the exoproteome. Although many of these proteins are related to basic cell functions, some are related to virulence and pathogenicity like catalase and isdA, main actors in S. aureus infection, and others are related to antibiotic action or eventually resistance like penicillin binding protein, a cell-wall protein. Studying the proteomes of different subcellular compartments should improve our understanding of this pathogen, a microorganism with several mechanisms of resistance and pathogenicity, and provide valuable data for bioinformatics databases.
    Full-text · Article · Jul 2015
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    ABSTRACT: The aleurone layer (AL) is the grain peripheral tissue; it is rich in micronutrients, vitamins, antioxidants, and essential amino acids. This highly nutritive part of the grain has been less studied partly because its isolation is so laborious. In the present study, the ALs of Triticum aestivum (variety Récital) were separated manually at 15 stages of grain development. A total of 327 proteins were identified using 2-DE LC-MS/MS. They were classified in six main groups and 26 sub-groups according to their biochemical function. Proteomic analysis revealed seven different profiles distributed among three main development stages: (i) early AL development, with proteins involved in intense metabolic activities in the growth and development of the cell wall compounds; (ii) the intermediate stage, characterized by oxidative stress and defense proteins (65%) linked with loss of water in peripheral layers during grain filling; and (iii) AL maturation, involving the production of amino acids and the control of reactive oxidative species to enable the accumulation and maturation of globulins within the AL. The present study provides the first insights into developing proteome in the AL. We describe the numerous AL enzymes involved in the accumulation of storage protein and in the protection of the endosperm over time.
    Full-text · Article · Apr 2015 · Journal of proteomics
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    ABSTRACT: Une période de mise à jeûne des animaux permet de diminuer les risques de contamination des carcasses lors de l’éviscération. Les objectifs de cet essai sont d’étudier en détails les effets de la durée de jeûne et de la digestibilité du maïs sur les performances zootechniques de canards mulards gavés et sur la qualité de leurs foies. Les relations entre ces performances et le métabolisme des foies ont été étudiées. Un lot de 60 canards mulards a été élevé jusqu’à 12 semaines d’âge dans des conditions standards. Puis les canards ont été gavés soit avec du maïs waxy (riche en amylopectine et rapidement digestible) soit avec du maïs témoin. Pour étudier le métabolisme du foie en fonction du type de maïs et de la durée du jeûne, des analyses biochimiques, transcriptomiques et protéomiques ont été réalisées sur les foies obtenus après 9h et 15h de jeûne. Les foies de tous les canards ont un poids équivalent même si le taux de lipides est supérieur après 15h de jeûne (p=0,019). Mais le rendement technologique est supérieur de 7,0 points pour les canards gavés au maïs waxy à 9h de jeûne (p=0,039). Ces différences de rendement technologique semblent s’expliquer par le taux de lipides qui est inférieur de 3,9 points lorsque le maïs waxy est utilisé (p=0,019) et par un niveau d’expression plus élevé des protéines et transcrits impliqués dans la glycolyse et la lipogenèse.
    Preview · Article · Mar 2015
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    ABSTRACT: As commonly seen in monoderm bacteria, Listeria monocytogenes possesses multiple membrane-bound signal peptidases of Type I (SPases I) called SipX, SipY and SipZ. In order to decipher their respective contribution in an integrated and global view, the complement of the secretome corresponding to the exoproteome was resolved by two-dimensional gel electrophoresis (2-DE). This was performed for L. monocytogenes sipX(-), sipY(-), sipZ(-) single mutants, as well as for ΔsipXY and ΔsipYZ double mutants, and then compared to that of the wild type strain. Remarkably, the amounts of listeriolysin O (LLO), phosphatidylcholine phospholipase C (PlcB) and zinc metalloproteinase Mpl in the extracellular milieu was significantly decreased upon inactivation of SipZ. For the majority of the Sec-secreted exoproteins identified, protein secretion was not affected by the inactivation of one or two of the SPases I, supporting the concept that the three SPases I have overlapping specificities for the cleavage of the signal peptides. The current study reveals that the role of SipZ as the major SPase I of L. monocytogenes applies only to a small subset of the secreted exoproteins. Rather than absolute, the notion of major and minor SPases thus appears to be relative. In addition to new insight into bacterial physiology, this investigation of the contribution of the SPases I to the exoproteome of L. monocytogenes paves the way for further characterization of other complements of the secretome under various environmental conditions. L. monocytogenes encodes three orthologous signal peptidases of Type I (SPases I). SipZ improves the secretion efficiency for a subset of extracellular virulence factors. Multiple SPases I are functionally redundant for the majority of the Sec-secreted exoproteins of L. monocytogenes. The concepts of major and minor SPases are not absolute but relative. Copyright © 2015. Published by Elsevier B.V.
    Full-text · Article · Jan 2015 · Journal of Proteomics
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    ABSTRACT: Muscle ageing contributes to both loss of functional autonomy and increased morbidity. Muscle atrophy accelerates after 50 years of age, but the mechanisms involved are complex and likely result from the alteration of a variety of interrelated functions. In order to better understand the molecular mechanisms underlying muscle chronological ageing in human, we have undertaken a top-down differential proteomic approach to identify novel biomarkers after the fifth decade of age. Muscle samples were compared between adult (56 years) and old (78 years) post-menopausal women. In addition to total muscle extracts, low-ionic strength extracts were investigated to remove high abundance myofibrillar proteins and improve the detection of low abundance proteins. Two-dimensional gel electrophoreses with overlapping IPGs were used to improve the separation of muscle proteins. Overall, 1919 protein spots were matched between all individuals, 95 were differentially expressed and identified by mass spectrometry, and they corresponded to 67 different proteins. Our results suggested important modifications in cytosolic, mitochondrial and lipid energy metabolism, which may relate to dysfunctions in old muscle force generation. A fraction of the differentially expressed proteins were linked to the sarcomere and cytoskeleton (myosin light-chains, troponin T, ankyrin repeat domain-containing protein-2, vinculin, four and a half LIM domain protein-3), which may account for alterations in contractile properties. In line with muscle contraction, we also identified proteins related to calcium signal transduction (calsequestrin-1, sarcalumenin, myozenin-1, annexins). Muscle ageing was further characterized by the differential regulation of several proteins implicated in cytoprotection (catalase, peroxiredoxins), ion homeostasis (carbonic anhydrases, selenium-binding protein 1) and detoxification (aldo-keto reductases, aldehyde dehydrogenases). Notably, many of the differentially expressed proteins were central for proteostasis, including heat shock proteins and proteins involved in proteolysis (valosin-containing protein, proteasome subunit beta type-4, mitochondrial elongation factor-Tu). This study describes the most extensive proteomic analysis of muscle ageing in humans, and identified 34 new potential biomarkers. None of them were previously recognized as differentially expressed in old muscles, and each may represent a novel starting point to elucidate the mechanisms of muscle chronological ageing in humans.
    Full-text · Article · Dec 2014 · BMC Genomics
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    ABSTRACT: Annexin A1 deregulation is often associated with cancer. Indeed we have shown that annexin A1 is overexpressed in melanoma and promotes metastases by formyl peptide receptor stimulation and MMP2 expression. Here, we demonstrated in different melanoma cell lines that annexin A1-MMP2 induction is mediated by MAPK and STAT3 pathways. To decipher endogenous annexin A1 action mode, we showed that annexin A1 is externalized in A375 cells and cleaved by a membrane-associated serine protease, allowing the release of a pro-invasive annexin A1 peptide in the extra cellular environment. Finally, a biochemical and proteomic approach allowed to enrich eight out of 12 members of the annexin family and to identify an original annexin A1 cleavage site localized between Ser28 and Lys29. Altogether, these data identify signaling pathways involved in annexin A1 pro-invasive role and suggest that externalized full-length annexin A1 interacts with formyl peptide receptors in a juxtacrine manner while ANXA 2–28 release allows autocrine and paracrine interaction.
    No preview · Article · Nov 2014 · Archives for Dermatological Research
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    ABSTRACT: The aleurone layer (AL) is an inner tissue of the wheat grain. It contains micronutrients, vitamins, antioxidants and fibre, and can greatly increase the nutritional quality of flour if it is not removed from the kernel with the bran. The AL of mature kernels of three varieties of the two major cultivated wheat species T. aestivum (genome A, B and D) and T. monococcum (genome A) were manually dissected and analyzed using two-dimensional gel-based proteomics. In T. monococcum although composed of only genome A, the maximum number of Coomassie stained AL spots was close to the number found in the bread wheat varieties (1320 and 1258, respectively). Inter-variety variation in spots was higher in the three T. monococcum varieties (103 spots) than in the three T. aestivum varieties (79 spots). Comparison of the two species revealed that only 88 spots differed significantly either in abundance or presence/absence. The B and D genome did not drastically modify the AL proteome, as demonstrated by the fact that 93% of the spots present in T. Monococcum AL spots were also present in T. aestivum. Proteins which differed within and between species were identified using MALDI-TOF and LC-MS/MS Mass Spectrometry. Among the 182 spots that differed, 115 were identified, 53 differed between the two species and 44 (83%) were globulin (Glo) storage proteins. The remarkable environmental stability of the AL proteome previously observed in T. durum and T. aestivum species was confirmed in the variety T. monococcum DV92, grown for two consecutive years in field conditions. Only 15 proteins (out of 1320 AL spots) exhibited significant quantitative variations.
    Full-text · Article · Jul 2014 · Current Proteomics
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    ABSTRACT: Long chain omega 3 polyunsaturated fatty acids (LC-n-3PUFAs) exert potent anti-atherosclerotic action but the mechanisms of action at the vascular level remain unclear. The present study used a non-targeted nutrigenomic approach to investigate the modulations of the aortic proteome in atherosclerotic prone mice following DHA supplementation. LDLR−/− male mice received an atherogenic diet (20 weeks) in parallel with daily oral gavages with either oleic acid-rich oil (Control) or a mixture of oils providing 2% of energy as DHA. The overall protein expression was determined by a proteomic approach followed by bioinformatics analysis. In addition, protein oxidative modifications, namely 4-hydroxynonenal (4-HNE) protein adducts, were detected with a specific antibody followed by MS analysis of the identified spots. Nineteen differentially expressed proteins have been identified in the aorta of the DHA group. The top 5 canonical pathways analysis associated all proteins to metabolic pathways and showed that most of them were related to glucose or lipid metabolism. Up-regulation of superoxide dismutase also suggests an impact of DHA supplementation on vascular antioxidant defenses. The analysis of 4-HNE-protein adducts indicated that DHA supplementation did not enhance oxidative modification of proteins with 4-HNE. This study also identified some new proteins with 4-HNE adducts at the aortic level. In summary, DHA supplementation induces significant modifications of aorta proteome which point out the importance of metabolic changes occurring in the vascular tissue in the presence of LC-n-3PUFAs.
    Full-text · Article · Dec 2013 · European Journal of Lipid Science and Technology
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    ABSTRACT: Saccharomyces cerevisiae plays a primordial role in alcoholic fermentation and has a vast worldwide application in the production of fuel-ethanol, food and beverages. The dominance of S. cerevisiae over other microbial species during alcoholic fermentations has been traditionally ascribed to its higher ethanol tolerance. However, recent studies suggested that other phenomena, such as microbial interactions mediated by killer-like toxins, might play an important role. Here we show that S. cerevisiae secretes antimicrobial peptides (AMPs) during alcoholic fermentation that are active against a wide variety of wine-related yeasts (e.g. Dekkera bruxellensis) and bacteria (e.g. Oenococcus oeni). Mass spectrometry analyses revealed that these AMPs correspond to fragments of the S. cerevisiae glyceraldehyde 3-phosphate dehydrogenase (GAPDH) protein. The involvement of GAPDH-derived peptides in wine microbial interactions was further sustained by results obtained in mixed cultures performed with S. cerevisiae single mutants deleted in each of the GAPDH codifying genes (TDH1-3) and also with a S. cerevisiae mutant deleted in the YCA1 gene, which codifies the apoptosis-involved enzyme metacaspase. These findings are discussed in the context of wine microbial interactions, biopreservation potential and the role of GAPDH in the defence system of S. cerevisiae.
    Full-text · Article · Nov 2013 · Applied Microbiology and Biotechnology
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    ABSTRACT: Sarcopenia corresponds to the loss of muscle mass occurring during aging, and is associated with a loss of muscle functionality. Proteomic links the muscle functional changes with protein expression pattern. To better understand the mechanisms involved in muscle aging, we performed a proteomic analysis of Vastus lateralis muscle in mature and older women. For this, a shotgun proteomic method was applied to identify soluble proteins in muscle, using a combination of high performance liquid chromatography and mass spectrometry. A label-free protein profiling was then conducted to quantify proteins and compare profiles from mature and older women. This analysis showed that 35 of the 366 identified proteins were linked to aging in muscle. Most of the proteins were under-represented in older compared to mature women. We built a functional interaction network linking the proteins differentially expressed between mature and older women. The results revealed that the main biological functions altered during human muscle aging were defined by proteins involved in energy metabolism and proteins from the myofilament and cytoskeleton. This is the first time that label-free quantitative proteomics has been applied to study of aging mechanisms in human skeletal muscle. This approach highlights new elements for elucidating the alterations observed during aging and may lead to novel sarcopenia biomarkers.
    Full-text · Article · Nov 2013 · Molecular & Cellular Proteomics
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    Full-text · Article · Sep 2013

  • No preview · Article · Jul 2013
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    ABSTRACT: Meat is an appropriate source of proteins and minerals for human nutrition. Technological treatments modify the physical-chemical properties of proteins, making them liable to decrease the nutritional potential of meat. To counteract this damage, antioxidants and chaperone proteins in muscle cells can prevent oxidation, restore the function of denatured proteins, and thus prevent aggregation. This study aimed to explore the impact of indoor vs outdoor-reared meat protein composition on digestion and to associate protein markers to in vitro digestion parameters. Indoor-reared meat tended to show less oxidation and denaturation than outdoor-reared meat and was characterised by an overexpression of contractile and chaperone proteins. Outdoor-reared meat showed amplification of antioxidant and detoxification metabolism defending against oxidised compounds. Impacts on digestion remained minor. Several protein markers of in vitro digestion parameters were found for aged and cooked meat, linked to the detoxification process and to muscle contraction.
    No preview · Article · Feb 2013 · Food Chemistry
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    ABSTRACT: As part of the Sec translocase, the accessory ATPase SecA2 is present in some pathogenic Gram-positive bacteria. In Listeria monocytogenes, deletion of secA2 results in filamentous cells that forms rough colonies and have lower virulence. However, only a few proteins have been identified that are secreted by this pathway. This investigation aims to provide the first exoproteomic analysis of the SecA2-dependent secretion in L. monocytogenes EGD-e. By using media and temperatures relevant to bacterial physiology, we demonstrated that the rough colony and elongated bacterial cell morphotypes are highly dependent on growth conditions. Subsequently, comparative exoproteomic analyses of the ΔsecA2 versus wt strains were performed in chemically defined medium at 20°C and 37°C. Analyzing the proteomic data following the secretomics-based method, part of the proteins appeared routed towards the Sec pathway and exhibited an N-terminal signal peptide. For another significant part, they were primarily cytoplasmic proteins, thus lacking signal peptide and with no predictable secretion pathway. In total, 13 proteins were newly identified as secreted via SecA2, which were essentially associated with cell-wall metabolism, adhesion and/or biofilm formation. From this comparative exoproteomic analysis, new insights into the L. monocytogenes physiology are discussed in relation to its saprophytic and pathogenic lifestyle.
    Full-text · Article · Jan 2013 · Journal of proteomics
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    ABSTRACT: In order to identify new markers of beef tenderness, a proteomic analysis was performed on Longissimus thoracis muscle to compare two extreme groups in terms of meat tenderness, consisting of 10 animals each of the three main French beef breeds: Blond d’Aquitaine, Charolais, and Limousin. Animals were grouped on the basis of an index combining a tenderness score estimated by a trained panel and mechanical shear force measurement (Warner-Bratzler). The large number of available experimental animals (more than 3,300 young bulls) allowed animals with different meat tenderness but similar main muscle characteristics (fibers, collagen, and lipids) to be chosen. The muscle proteins of the extreme groups considered 24 h after slaughter were analyzed by two-dimensional electrophoresis, statistical analysis, and mass spectrometry. Potential markers of tenderness were suggested for each breed; their marker status varied according to the breed. Only α actin appeared to be a potential marker of tenderness in the three studied breeds. We focused particularly on different abundances of HSP27 and Troponin T fast isoforms between tenderness groups and according to breed.
    Full-text · Chapter · Jan 2013