Deciphering mechanisms underlying the genetic variation of general production and liver quality traits in the overfed mule duck by pQTL analyses.

BACKGROUND: The aim of this study was to analyse the mechanisms that underlie phenotypic quantitative trait loci (QTL) in overfed mule ducks by identifying co-localized proteomic QTL (pQTL). The QTL design consisted of three families of common ducks that were progeny-tested by using 294 male mule ducks. This population of common ducks was genotyped using a genetic map that included 334 genetic markers located across 28 APL chromosomes (APL for Anas platyrhynchos). Mule ducks were phenotyped for 49 traits related to growth, metabolism, overfeeding ability and meat and fatty liver quality, and 326 soluble fatty liver proteins were quantified. RESULTS: One hundred and seventy-six pQTL and 80 phenotypic QTL were detected at the 5% chromosome-wide significance threshold. The great majority of the identified pQTL were trans-acting and localized on a chromosome other than that carrying the coding gene. The most significant pQTL (1% genome-wide significance) were found for alpha-enolase on APL18 and fatty acid synthase on APL24. Some proteins were associated with numerous pQTL (for example, 17 and 14 pQTL were detected for alpha-enolase and apolipoprotein A1, respectively) and pQTL hotspots were observed on some chromosomes (APL18, 24, 25 and 29). We detected 66 co-localized phenotypic QTL and pQTL for which the significance of the two-trait QTL (2t-QTL) analysis was higher than that of the strongest QTL using a single-trait approach. Among these, 16 2t-QTL were pleiotropic. For example, on APL15, melting rate and abundance of two alpha-enolase spots appeared to be impacted by a single locus that is involved in the glycolytic process. On APLZ, we identified a pleiotropic QTL that modified both the blood level of glucose at the beginning of the force-feeding period and the concentration of glutamate dehydrogenase, which, in humans, is involved in increased glucose absorption by the liver when the glutamate dehydrogenase 1 gene is mutated. CONCLUSIONS: We identified pleiotropic loci that affect metabolic pathways linked to glycolysis or lipogenesis, and in the end to fatty liver quality. Further investigation, via transcriptomics and metabolomics approaches, is required to confirm the biomarkers that were found to impact the genetic variability of these phenotypic traits.

Metabolomic study of fatty livers in ducks: Identification by 1H-NMR of metabolic markers associated with technological quality.

The control of fatty liver fat loss during cooking is a major issue. Previous studies showed that fat loss was influenced by bird production factors and liver technological treatments. However, part of the variability in fat loss remained uncontrolled. To provide enhanced insights into the determinism of fatty liver quality, liver hydrophilic metabolite profiles were measured by nuclear magnetic resonance of the proton ((1)H-NMR). The study aimed at i) comparing fatty livers with extreme fat loss values and ii) at characterizing the effect of postmortem evolution of livers during chilling. A group of 240 male mule ducks (Cairina moschata × Anas platyrhynchos) was reared and overfed. Their livers were sampled at 20 min and 6 h postmortem. Of these birds, 2 groups of ducks were built with extreme values on the technological yield (TY; TY = 100 - % fat loss; the low-fat-loss group, TY = 89.9%, n = 13; and the high-fat-loss group, TY = 68.3%, n = 12, P < 0.001). The (1)H-NMR analyses showed that the high-fat-loss livers were more advanced in postmortem biochemical and structural changes than low-fat-loss livers early postmortem. The high-fat-loss livers were characterized by hydrolysis of glycogen into glucose, worse integrity of cell membrane with diminution of compounds of phospholipids, and higher catabolic processes. The accelerated postmortem processes may be the origin of the differences in fat loss during cooking. During the early postmortem period, the adenosine triphosphate amount in liver cells was strongly reduced and lipolysis of triglycerides seemed to be enhanced. The glycogen stored in liver was first converted into glucose, but contrary to what happens in postmortem muscles, glucose was not converted into lactate.

Development of hepatic steatosis in male and female mule ducks after respective force-feeding programs.

Male and female mule ducks were subjected to a force-feeding diet to induce liver steatosis as it is generally done only with male ducks for the production of foie gras. The different biochemical measurements indicated that the course of hepatic steatosis development was present in both sexes and associated with a huge increase in liver weight mainly due to the synthesis and accumulation of lipids in hepatocytes. In livers of male and female ducks, this lipid accumulation was associated with oxidative stress and hypoxia. However, certain specific modifications (kinetics of lipid droplet development and hepatic inflammation) indicate that female ducks may tolerate force-feeding less well, at least at the hepatic level. This is in contradiction with what is generally reported concerning hepatic steatosis induced by dietary disturbances in mammals but could be explained by the very specific conditions imposed by force-feeding. Despite this, force-feeding female ducks seems entirely feasible, provided that the final quality of the product is as good as that of the male ducks, which will remain to be demonstrated in future studies.

Using 2-DE for the differentiation of local chicken breeds.

The aim of this study was to apply a proteomic approach for the characterisation of local chicken breeds. The experiment involved a total of 29 males of three local Italian chicken breeds: Pépoi, Padovana and Ermellinata di Rovigo. Sarcoplasmic protein fractions of breast muscle were analysed by 2-DE. Image analysis followed by statistical analysis enabled to differentiate groups of individuals based on the similarities of protein expression. Individuals were distinguished into clusters and groups, corresponding to the breed of origin. Distances among individuals, calculated using data on spot volumes, were used to draw a neighbour-joining tree, showing clear individual and breed grouping. The most relevant spots regarding breed differentiation were detected; 11 were identified by MS revealing preliminary evidences on the mechanisms of the breed differentiation process. The results evidenced the ability of proteomic analyses for the characterisation of chicken breeds.

Chloroquine enhances human CD8+ T cell responses against soluble antigens in vivo.

The presentation of exogenous protein antigens in a major histocompatibility complex class I-restricted fashion to CD8+ T cells is called cross-presentation. We demonstrate that cross-presentation of soluble viral antigens (derived from hepatitis C virus [HCV], hepatitis B virus [HBV], or human immunodeficiency virus) to specific CD8+ T cell clones is dramatically improved when antigen-presenting dendritic cells (DCs) are pulsed with the antigen in the presence of chloroquine or ammonium chloride, which reduce acidification of the endocytic system. The export of soluble antigen into the cytosol is considerably higher in chloroquine-treated than in untreated DCs, as detected by confocal microscopy of cultured cells and Western blot analysis comparing endocytic and cytosolic fractions. To pursue our findings in an in vivo setting, we boosted groups of HBV vaccine responder individuals with a further dose of hepatitis B envelope protein vaccine with or without a single dose of chloroquine. Although all individuals showed a boost in antibody titers to HBV, six of nine individuals who were administered chloroquine showed a substantial CD8+ T cell response to HBV antigen, whereas zero of eight without chloroquine lacked a CD8 response. Our results suggest that chloroquine treatment improves CD8 immunity during vaccination.

Evolution of liver fattening and foie gras technological yield during the overfeeding period in mule duck.

In foie gras production the technological yield after the cooking process is one of the main issues of processors as it is closely linked to the cooking melting rate. This rate is subjected to strict laws and regulations since it directly affects the organoleptic and technological qualities of this gourmet product. The objective of the study was to better understand the liver fattening and the technological yield decrease during the overfeeding kinetics. A flock of 210 mule ducks was reared and then overfed during 12 D with 2 overfeeding programs; in the test group the amounts of corn in the first meals were higher than in the control group (+430 g during the whole period). Ducks were slaughtered at the end of the rearing period (D0, n = 15) and every other day (D2 to D12, n = 15 by group). Duck performances, anatomical dissections and physical and biochemical liver characteristics were registered. The performances were equivalent in the groups (P > 0.1). The evolution of the liver weight was then analyzed in detail in relation with the evolution of its biochemical composition. A two-step evolution occurred in the liver metabolism, first a main glycogen storage and then a strong lipid storage. A model to predict the liver weight was established with only BWs and feed intakes (R² = 0.83). The technological yield was determined on foie gras weighing more than 300 g (D6 to D12). The melting process was high during the last 2 D. The technological yield reached 72% at D12, for 758 g foie gras, and a strong negative correlation was observed with liver weight (-0.83; P < 0.001). A model to predict the technological yield was established with the liver weight and the liver color parameters (R² = 0.71). This study highlights the compromise between foie gras weight and its quality.

Effects of dietary protein level during rearing period and age at overfeeding on magret and foie gras quality in male mule ducks.

The aim of this trial was to study the effects of dietary protein content during the rearing period on the performance of mule ducks, according to age at overfeeding (O). Ducks (n = 612) were divided into four groups differing in the protein content in the diet offered during the starting period (S, 0-20 days; Sl vs. Sh : 150 vs. 175 g/kg crude protein (CP)) and growing-finishing period (GF; 21-67 or 81 days, depending on age at O; GFl vs. GFh : 133 vs. 152 g/kg CP). The relative weight of pectoral muscle was lower when ducks were fed a low protein diet during S (-5%, P < 0.01) or GF period (-6%, P < 0.001) at 68 days and higher in ducks of the Sl GFh group (+6%; P < 0.05) at 82 days. Both foie gras and magret weights fell when ducks were fed Sl or GFl (P < 0.05 and < 0.01). Mortality during the O period was higher in ducks fed the Sl diet and overfed at late age (7.4% vs. 0%; P < 0.01). In conclusion, a reduction in the dietary protein supply should be recommended only during the GF period for ducks overfed at a late age.

Proteome response of fish under multiple stress exposure: Effects of pesticide mixtures and temperature increase.

Aquatic systems can be subjected to multiple stressors, including pollutant cocktails and elevated temperature. Evaluating the combined effects of these stressors on organisms is a great challenge in environmental sciences. To the best of our knowledge, this is the first study to assess the molecular stress response of an aquatic fish species subjected to individual and combined pesticide mixtures and increased temperatures. For that, goldfish (Carassius auratus) were acclimated to two different temperatures (22 and 32°C) for 15 days. They were then exposed for 96h to a cocktail of herbicides and fungicides (S-metolachlor, isoproturon, linuron, atrazine-desethyl, aclonifen, pendimethalin and tebuconazole) at two environmentally relevant concentrations (total concentrations of 8.4µgL-1 and 42µgL-1) at these two temperatures (22 and 32°C). The molecular response in liver was assessed by 2D-proteomics. Identified proteins were integrated using pathway enrichment analysis software to determine the biological functions involved in the individual or combined stress responses and to predict the potential deleterious outcomes. The pesticide mixtures elicited pathways involved in cellular stress response, carbohydrate, protein and lipid metabolisms, methionine cycle, cellular functions, cell structure and death control, with concentration- and temperature-dependent profiles of response. We found that combined temperature increase and pesticide exposure affected the cellular stress response: the effects of oxidative stress were more marked and there was a deregulation of the cell cycle via apoptosis inhibition. Moreover a decrease in the formation of glucose by liver and in ketogenic activity was observed in this multi-stress condition. The decrease in both pathways could reflect a shift from a metabolic compensation strategy to a conservation state. Taken together, our results showed (1) that environmental cocktails of herbicides and fungicides induced important changes in pathways involved in metabolism, cell structure and cell cycle, with possible deleterious outcomes at higher biological scales and (2) that increasing temperature could affect the response of fish to pesticide exposure.

Mule duck "foie gras" shows different metabolic states according to its quality phenotype by using a proteomic approach.

This study aimed at identifying the mechanisms implicated in "foie gras" quality variability through the study of the relationships between liver protein compositions and four liver quality phenotypes: liver weight, melting rate, and protein contents on crude or dry matter. Spots of soluble proteins were separated by bidimensional electrophoresis, and the relative abundance of proteins according to quality traits values was investigated. Twenty-three protein spots (19 unique identified proteins) showed different levels of abundance according to one or more of the traits' values. These abundance differences highlighted two groups of livers with opposite trends of abundance levels. Proteins of the first group, associated with low liver weight and melting rate, are involved in synthesis and anabolism processes, whereas proteins of the second group, associated with high liver weight and melting rate, are proteins involved in stress response. Altogether, these results highlight the variations in metabolic states underlying foie gras quality traits.

Protein matrix involved in the lipid retention of foie gras during cooking: a multimodal hyperspectral imaging study.

Denaturation of the protein matrix during heat treatment of duck foie gras was studied in relationship to the amount of fat loss during cooking. A low fat loss group was compared with a high fat loss group by histochemistry, FT-IR, and synchrotron UV microspectroscopy combination to characterize their protein matrix at different scales. After cooking, the high fat loss group showed higher densification of its matrix, higher ultraviolet tyrosine autofluorescence, and an infrared shift of the amide I band. These results revealed a higher level of protein denaturation and aggregation during cooking in high fat loss than in low fat loss foie gras. In addition, the fluorescence and infrared responses of the raw tissue revealed differences according to the level of fat losses after cooking. These findings highlight the importance of the supramolecular state of the protein matrix in determining the fat loss of foie gras.

Proteomic analysis of duck fatty liver during post-mortem storage related to the variability of fat loss during cooking of "foie gras".

Fat loss during cooking of duck "foie gras" is the main problem for both manufacturers and consumers. Despite the efforts of the processing industry to control fat loss, the variability of fatty liver cooking yields remains high and uncontrolled. To understand the biochemical effects of postslaughter processing on fat loss during cooking, this study characterizes for the first time the protein expression of fatty liver during chilling using a proteomic approach. For this purpose the proteins were separated according to their solubility: the protein fraction soluble in a buffer of low ionic strength (S) and the protein fraction insoluble in the same buffer (IS). Two-dimensional electrophoresis was used to analyze the S fraction and mass spectrometry for the identification of spots of interest. This analysis revealed 36 (21 identified proteins) and 34 (26 identified proteins) spots of interests in the low-fat-loss and high-fat-loss groups, respectively. The expression of proteins was lower after chilling, which revealed a suppressive effect of chilling on biological processes. The shot-gun strategy was used to analyze the IS fraction, with the identification of all the proteins by mass spectrometry. This allowed identification of 554 and 562 proteins in the low-fat-loss and high-fat-loss groups, respectively. Among these proteins, only the proteins that were up-regulated in the high-fat-loss group were significant (p value = 3.17 × 10(-3)) and corresponded to protein from the cytoskeleton and its associated proteins. Taken together, these results suggest that the variability of technological yield observed in processing plants could be explained by different aging states of fatty livers during chilling, most likely associated with different proteolytic patterns.

Identification by proteomic analysis of early post-mortem markers involved in the variability in fat loss during cooking of mule duck "foie gras".

Fat loss during cooking of duck "foie gras" is the main quality issue for both processors and consumers. Despite the efforts of the processing industry to control fat loss, the variability of fatty liver cooking yield remains high and uncontrolled. To better understand the biological basis of this phenomenon, a proteomic study was conducted. To analyze the protein fraction soluble at low ionic strength (LIS), we used bidimensional electrophoresis and mass spectrometry for the identification of spots of interest. To analyze the protein fraction not soluble at low ionic strength (NS), we used the shotgun strategy. The analysis of data acquired from both protein fractions suggested that at the time of slaughter, livers with low fat loss during cooking were still in anabolic processes with regard to energy metabolism and protein synthesis, whereas livers with high fat loss during cooking developed cell protection mechanisms. The variability in the technological yield observed in processing plants could be explained by a different physiological stage of liver steatosis.

Skeletal muscle proteomics in livestock production.

Proteomics allows studying large numbers of proteins, including their post-translational modifications. Proteomics has been, and still are, used in numerous studies on skeletal muscle. In this article, we focus on its use in the study of livestock muscle development and meat quality. Changes in protein profiles during myogenesis are described in cattle, pigs and fowl using comparative analyses across different ontogenetic stages. This approach allows a better understanding of the key stages of myogenesis and helps identifying processes that are similar or divergent between species. Genetic variability of muscle properties analysed by the study of hypertrophied cattle and sheep are discussed. Biological markers of meat quality, particularly tenderness in cattle, pigs and fowl are presented, including protein modifications during meat ageing in cattle, protein markers of PSE meat in turkeys and of post-mortem muscle metabolism in pigs. Finally, we discuss the interest of proteomics as a tool to understand better biochemical mechanisms underlying the effects of stress during the pre-slaughter period on meat quality traits. In conclusion, the study of proteomics in skeletal muscles allows generating large amounts of scientific knowledge that helps to improve our understanding of myogenesis and muscle growth and to control better meat quality.

Cross-presentation of caspase-cleaved apoptotic self antigens in HIV infection.

We found that the proteome of apoptotic T cells includes prominent fragments of cellular proteins generated by caspases and that a high proportion of distinct T cell epitopes in these fragments is recognized by CD8+ T cells during HIV infection. The frequencies of effector CD8+ T cells that are specific for apoptosis-dependent epitopes correlate with the frequency of circulating apoptotic CD4+ T cells in HIV-1-infected individuals. We propose that these self-reactive effector CD8+ T cells may contribute to the systemic immune activation during chronic HIV infection. The caspase-dependent cleavage of proteins associated with apoptotic cells has a key role in the induction of self-reactive CD8+ T cell responses, as the caspase-cleaved fragments are efficiently targeted to the processing machinery and are cross-presented by dendritic cells. These findings demonstrate a previously undescribed role for caspases in immunopathology.