Identification of specific oxidatively modified proteins in chicken muscles using a combined immunologic and proteomic approach

Effect of protein oxidation in meat and exudates on the water holding capacity in bighead carp (Hypophthalmichthys nobilis) subjected to frozen storage

This study aimed to investigate the effect of myofiber changes and protein oxidation on water holding capacity (WHC) of bighead carp fillets stored at -20 °C. WHC, microstructure, protein oxidation parameters, and specific modifications of oxidized amino acids were analyzed during 9 months of frozen storage. Results indicated that WHC decreased accompanied by myofibers' structural changes (including the formation of cavities among myofibers, breakage of myofibrils and myofibers, and shortening of sarcomeres) and protein oxidation. SDS-PAGE and carbonyl and sulfhydryl content determination of myofibrillar proteins and exudates gave a detailed description of the protein oxidation. LC-MS/MS analysis demonstrated that oxidation, di-oxidation, and 4-hydroxy-2-nonenal (HNE) and malondialdehyde (MDA) adduction were the top four oxidative modifications of proteins. Oxidative modifications impaired configuration and polarity of proteins, which may further affect WHC. This study provides plausible explanations to support the role of protein oxidation in the decrease of WHC in frozen fillets.

Effect of High Voltage Cold Plasma on Oxidation, Physiochemical, and Gelling Properties of Myofibrillar Protein Isolate from Asian Sea Bass (Lates calcarifer)

The effects of in-bag dielectric barrier discharge high voltage cold plasma (IB-DBD-HVCP) on myofibrillar protein isolate (MPI) from Asian sea bass (ASB) and its impact on the physiochemical and gelling properties of MPI gels were elucidated. A mixture of argon (90%) and oxygen (10%) was used for generating IB-DBD-HVCP. MPI was subjected to IB-DBD-HVCP for varying times (5–15 min). Total carbonyl content was increased, while total sulfhydryl content was decreased in MPI, especially with augmenting treatment time (TT) (p < 0.05). Surface hydrophobicity initially increased when IB-DBD-HVCP TT of 5 min (DBD-HVCP5) was implemented, followed by subsequent decrease with increasing TT. Based on gel electrophoresis, lower actin and myosin heavy chain (MHC) band intensities were found for MPI subjected to IB-DBD-HVCP, particularly when a TT longer than 10 min was used, compared to those of the control. Gel made from DBD-HVCP5 had higher breaking force, deformation, and highest G′ value compared to others. A more ordered and fibrous network was found in DBD-HVCP5 treated gel. Therefore, IB-DBD-HVCP treatment, particularly for 5 min, enhanced cross-linking of proteins in ASB myofibrillar proteins, which resulted in the improved gel elasticity and strength.

Effect of L-cysteine, Boswellia serrata, and Whey Protein on the Antioxidant and Physicochemical Properties of Pork Patties

This study investigated the effects of L-cysteine (C) combined with Boswellia serrata (B) and whey protein (W) on the antioxidant and physicochemical properties of pork patties. Proximate composition, water holding capacity (WHC), pH, texture profile analysis, sensory evaluation, thiobarbituric acid-reactive substances (TBARS), DPPH radical-scavenging activity, volatile basic nitrogen (VBN), and color stability were assessed. Patty VBN gradually increased throughout the storage period. However, VBN for the C treatment increased relatively slowly, indicating that cysteine can delay spoilage and extend the shelf life of patties. The protein content of the whey powder treatment group increased to a greater extent than that of the C and control (CON) groups. Pork patties supplemented with antioxidants showed significantly higher WHC and significantly lower cooking loss and hardness than the CON. Moreover, the addition of 2% whey, 1% B. serrata, and 0.25% cysteine (WBC) significantly enhanced the relative DPPH radical-scavenging activity and sensory characteristics of the patties. After 7-day storage, the MetMb and TBARS values of all treatments were significantly lower than those of the untreated. The results indicated that there was synergy among the cysteine, B. serrata, and whey protein. This finding is of great importance to the production of high-quality pork patties with enhanced shelf life.

Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model

Food proteins may get nitrated by various exogenous or endogenous mechanisms. As individuals might get recurrently exposed to nitrated proteins via daily diet, we aimed to investigate the effect of repeatedly ingested nitrated food proteins on the subsequent immune response in non-allergic and allergic mice using the milk allergen beta-lactoglobulin (BLG) as model food protein in a mouse model. Evaluating the presence of nitrated proteins in food, we could detect 3-nitrotyrosine (3-NT) in extracts of different foods and in stomach content extracts of non-allergic mice under physiological conditions. Chemically nitrated BLG (BLGn) exhibited enhanced susceptibility to degradation in simulated gastric fluid experiments compared to untreated BLG (BLGu). Gavage of BLGn to non-allergic animals increased interferon-γ and interleukin-10 release of stimulated spleen cells and led to the formation of BLG-specific serum IgA. Allergic mice receiving three oral gavages of BLGn had higher levels of mouse mast cell protease-1 (mMCP-1) compared to allergic mice receiving BLGu. Regardless of the preceding immune status, non-allergic or allergic, repeatedly ingested nitrated food proteins seem to considerably influence the subsequent immune response.

Meat quality traits and proteome profile of woody broiler breast (pectoralis major) meat

Woody breast meat has recently become prevalent in the broiler industry in both the United States and European Union. Recent publications have described the meat quality characteristics of woody breast meat as having hardened areas and pale ridge-like bulges at both the caudal and cranial regions of the breast. The present study investigated the meat quality (pH, color, cooking loss, and shear force) and protein quality characteristics (protein and salt-soluble protein content) in woody breast meat as compared to normal breast meat. In addition, the differences in the muscle proteome profiles of woody and normal breast meat were characterized. Results indicated that woody breast meat had a greater average pH (P < 0.0001) and cooking loss (P = 0.001) than normal breast meat, but woody breast meat did not differ in shear force (P > 0.05) in comparison to normal breast meat samples. The L*, a*, and b* values of woody breast fillets were greater than normal breast fillets (P < 0.0001 to L*; P = 0.002 to a*; P = 0.016 to b*). The woody breast meat had more fat (P < 0.0001) and moisture (P < 0.021) and less protein (P < 0.0001) and salt-soluble protein (P < 0.0001) when compared with normal breast fillets. Whole muscle proteome analysis indicated 8 proteins that were differentially expressed (P < 0.05) between normal and woody breast meat samples. The differences in muscle proteome between normal and woody breast meat indicated an increased oxidative stress in woody breast meat when compared to normal meat. In addition, the abundance of some glycolytic enzymes, which are critical to the regeneration of adenosine triphosphate (ATP) in postmortem muscles, was lower in woody breast meat than in normal breast meat. Proteomic differences provide additional information on the biochemical pathways and genetic variations that lead to woody breast meat. Further research should be conducted to elucidate the genetic and nutritional contributions to the proliferation of woody breast meat in the United States.

TRIENNIAL LACTATION SYMPOSIUM: Nutrigenomics in livestock: Systems biology meets nutrition

The advent of high-throughput technologies to study an animal's genome, proteome, and metabolome (i.e., "omics" tools) constituted a setback to the use of reductionism in livestock research. More recent development of "next-generation sequencing" tools was instrumental in allowing in-depth studies of the microbiome in the rumen and other sections of the gastrointestinal tract. Omics, along with bioinformatics, constitutes the foundation of modern systems biology, a field of study widely used in model organisms (e.g., rodents, yeast, humans) to enhance understanding of the complex biological interactions occurring within cells and tissues at the gene, protein, and metabolite level. Application of systems biology concepts is ideal for the study of interactions between nutrition and physiological state with tissue and cell metabolism and function during key life stages of livestock species, including the transition from pregnancy to lactation, in utero development, or postnatal growth. Modern bioinformatic tools capable of discerning functional outcomes and biologically meaningful networks complement the ever-increasing ability to generate large molecular, microbial, and metabolite data sets. Simultaneous visualization of the complex intertissue adaptations to physiological state and nutrition can now be discerned. Studies to understand the linkages between the microbiome and the absorptive epithelium using the integrative approach are emerging. We present examples of new knowledge generated through the application of functional analyses of transcriptomic, proteomic, and metabolomic data sets encompassing nutritional management of dairy cows, pigs, and poultry. Published work to date underscores that the integrative approach across and within tissues may prove useful for fine-tuning nutritional management of livestock. An important goal during this process is to uncover key molecular players involved in the organismal adaptations to nutrition.

Development of microbial spoilage and lipid and protein oxidation in rabbit meat

This experiment aimed to determine microbial spoilage and lipid and protein oxidation during aerobic refrigerated (4°C) storage of rabbit meat. Forty male New Zealand white rabbits were slaughtered according to the Halal slaughter procedure. The hind limbs were used for microbial analysis while the Longissimus lumborum m. was used for determination of lipid and protein oxidation. Bacterial counts generally increased with aging time and the limit for fresh meat (10(8)cfu/g) was reached at d 7 postmortem. Significant differences in malondialdehyde content were observed after 3d of storage. The thiol concentration significantly decreased with increase in aging time. The band intensities of myosin heavy chain and troponin T significantly reduced with increased refrigerated storage while actin remained relatively stable. This study thus proposes protein oxidation as a potential deteriorative change in refrigerated rabbit meat along with microbial spoilage and lipid oxidation.

Protein oxidation and protein nitration influenced by sodium nitrite in two different meat model systems

The effect of NaNO2 on protein oxidation was studied in isolated myofibrillar protein isolates (100 and 1000 mg NaNO2/kg) and in porcine patties (18 and 180 mg NaNO2/kg). In addition, the potential use of 3-nitrotyrosine as a specific marker for reactive nitrogen species mediated nitration was investigated. Overall, no distinct pro- or antioxidant effect of NaNO2 against carbonyl formation was observed in the isolates or in the patties. However, in the isolates, higher protein carbonyl concentrations were found in the NaNO2-treated samples compared to the treatment without added nitrite immediately after the addition of oxidants and NaNO2. Addition of 180 mg NaNO2/kg to patties resulted in significantly lower thiol concentrations at 4 and 7 days of illuminated chilled display compared to the treatments with 0 and 18 mg/kg NaNO2, whereas no effect was observed in the isolates. No effect of NaNO2 was found on the protein solubility of either meat model. 3-Nitrotyrosine was present in all samples, but no clear effect of NaNO2 addition or oxidation time was observed.

Protein thiols undergo reversible and irreversible oxidation during chill storage of ground beef as detected by 4,4'-dithiodipyridine

Quantification of protein thiols and disulfides in ground beef during storage under high-oxygen atmosphere at 4 °C was performed by thiol detection using 4,4'-dithiodipyridine (4-DPS) before and after disulfide reduction using sodium borohydride. Two independent storage trials were performed, and in trial 1, only reversible thiol oxidation was observed (thiol loss was 30%). In trial 2, irreversible thiol oxidation occurred during the first days of storage, while further loss of thiols was caused by reversible disulfide formation (thiol loss was 33%, of which ca. half was lost because of irreversible oxidation). The results were compared to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of cross-linked myosin heavy chain formed by disulfide bonding. Both methods confirmed increasing disulfide formation because of thiol oxidation in meat during storage, but the 4-DPS method showed higher disulfide percentages than the SDS-PAGE method (22.2 ± 0.3% and 8.5 ± 1.2%, respectively). The 4-DPS assay provides an accurate method to evaluate the thiol-disulfide redox state in meat.

Oxidative and nitrosative stress induced in myofibrillar proteins by a hydroxyl-radical-generating system: impact of nitrite and ascorbate

Understanding the chemistry behind the redox properties of nitrite and ascorbate is essential to identify the impact of curing agents on food quality and optimize the formulation of cured meat products. This study was designed to gain insight into the interactions between curing agents and myofibrillar proteins (MPs) during in vitro oxidation by a hydroxyl-radical-generating system. MPs (4 mg/mL) were oxidized for 4 days at 37 °C under constant stirring with 25 μM iron(III) and 2.5 mM hydrogen peroxide. Dependent upon the addition of nitrite (0, 75, and 150 mg/L) and ascorbate (0, 250, and 500 mg/L), nine different reaction units were prepared in triplicate (n = 3) according to a total factorial design. Upon completion of the oxidation assay, samples were analyzed for the concentration of tryptophan (TRP), α-aminoadipic semialdehyde (AAS), Schiff bases (SBs), and 3-nitrotyrosine (3NT). Ascorbate at 250 mg/L significantly inhibited the depletion of TRP (∼20% inhibition) and the formation of AAS and SBs (>90% inhibition) in MP suspensions. Nitrite, alone, had a negligible effect on protein oxidation but induced the formation of a specific marker of nitrosative stress, namely, 3NT. Ascorbate was also efficient at inhibiting the formation of 3NT by a dose-dependent anti-nitrosative effect and enabled the antioxidant action of nitrite.

Oxidative stress response: a proteomic view

The oxidative stress response is characterized by various effects on a range of biologic molecules. When examined at the protein level, both expression levels and protein modifications are altered by oxidative stress. While these effects have been studied in the past by classic biochemical methods, the recent onset of proteomics methods has allowed the oxidative stress response to be studied on a much wider scale. The input of proteomics in the study of oxidative stress response and in the evidence of an oxidative stress component in biologic phenomena is reviewed in this paper.

Actin carbonylation: from cell dysfunction to organism disorder

Protein carbonylation is an important event in the context of proteostasis because of its frequency, non-enzymatic nature and irreversible effects. The carbonylation of proteins disturbs their function and leads to protein aggregates, which may precede cellular senescence and cell death. Actin, an evolutionarily conserved cytoskeletal protein that is involved in important cellular processes, is one of the proteins most susceptible to carbonylation. Conditions resulting in oxidative stress are likely to lead to its carbonylation, loss of function and aggregate formation. In this review, we summarise actin susceptibility to carbonylation, as verified in cell free extracts, cell lines and animal models, and review its fate through the activation of cell mechanisms aimed at removing damaged proteins. Their insufficient activity may underlie age-related diseases and the ageing process. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.

Formation of 3-nitrotyrosines in carbonic anhydrase III is a sensitive marker of oxidative stress in skeletal muscle

Oxidation of skeletal muscle proteins has been reported to occur following contractions, with ageing, and with a variety of disease states, but the nature of the oxidised proteins has not been identified. A proteomics approach was utilised to identify major proteins that contain carbonyls and/or 3-nitrotyrosine (3-NT) groups in the gastrocnemius (GTN) muscles of adult (5-11 months of age) and old (26-28 months of age) wild type (WT) mice and adult mice lacking copper, zinc superoxide dismutase (Sod1(-/-) mice), manganese superoxide dismutase (Sod2(+/-) mice) or glutathione peroxidase 1 (GPx1(-/-) mice). In quiescent GTN muscles of adult and old WT mice, protein carbonylation and/or formation of 3-NT occurred in several proteins involved in glycolysis, as well as creatine kinase and carbonic anhydrase III. Following contractions, the 3-NT intensity was increased in specific protein bands from GTN muscles of both adult and old WT mice. In quiescent GTN muscles from adult Sod1(-/-) , Sod2(+/-) or GPx1(-/-) mice compared with age-matched WT mice only carbonic anhydrase III showed a greater 3-NT content. We conclude that formation of 3-NT occurs readily in response to oxidative stress in carbonic anhydrase III and this may provide a sensitive measure of oxidative damage to muscle proteins.

Proteomic analysis and differential expression in protein extracted from chicken with a varying growth rate and water-holding capacity

Chickens from a randomly bred genetic line were segregated into high and low growth rates and high and low water-holding capacities (WHCs). The objective of this study was to identify protein markers associated with slow and fast growth rates and low and high WHCs from water-soluble protein (WSP) and crude myofibrillar protein (CMP) extracts of chicken breast muscle. Proteins were fractionated using two-dimensional electrophoresis, and a total of 22 protein spots were selected, excised, and analyzed by in-gel tryptic digestion and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proteins expressed in extracts from slow and fast growth rates and low and high WHCs included metabolic enzymes, such as creatine kinase, pyruvate kinase, triosephosphate isomerase, and ubiqitin; housekeeping proteins, such as heat shock protein; contractile proteins, such as myosin heavy chain; actin; and also MHC isoforms and actin isoforms. The mass spectra of 20 protein spots significantly matched (protein score >83; P < 0.05) an online database. In CMP, there were unique proteins that were present only in the fast-growth population: gi|118099530 , gi|20664362 , gi|71895043 , gi|114794125 , gi|297343122 , and gi|71895043 . This information identified protein markers associated with growth rate and water holding capacity. Some of those protein markers could be added to the chicken database.

Fish proteins as targets of ferrous-catalyzed oxidation: identification of protein carbonyls by fluorescent labeling on two-dimensional gels and MALDI-TOF/TOF mass spectrometry

Protein oxidation in fish meat is considered to affect negatively the muscle texture. An important source of free radicals taking part in this process is Fenton's reaction dependent on ferrous ions present in the tissue. The aim of this study was to investigate the susceptibility of cod muscle proteins in sarcoplasmic and myofibril fractions to in vitro metal-catalyzed oxidation and to point out protein candidates that might play a major role in the deterioration of fish quality. Extracted control proteins and proteins subjected to free radicals generated by Fe(II)/ascorbate mixture were labeled with fluorescein-5-thiosemicarbazide (FTSC) to tag carbonyl groups and separated by two-dimensional gel electrophoresis. Consecutive visualization of protein carbonyl levels by capturing the FTSC signal and total protein levels by capturing the SyproRuby staining signal allowed us to quantify the relative change in protein carbonyl levels corrected for changes in protein content. Proteins were identified using MALDI-TOF/TOF mass spectrometry and homology-based searches. The results show that freshly extracted cod muscle proteins exhibit a detectable carbonylation background and that the incubation with Fe(II)/ascorbate triggers a further oxidation of both sarcoplasmic and myofibril proteins. Different proteins exhibited various degrees of sensitivity to oxidation processes. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), nucleoside diphosphate kinase B (NDK), triosephosphate isomerase, phosphoglycerate mutase, lactate dehydrogenase, creatine kinase, and enolase were the sarcoplasmic proteins most vulnerable to ferrous-catalyzed oxidation. Moreover, NDK, phosphoglycerate mutase, and GAPDH were identified in several spots differing by their pI, and those forms showed different susceptibilities to metal-catalyzed oxidation, indicating that post-translational modifications may change the resistance of proteins to oxidative damage. The Fe(II)/ascorbate treatment significantly increased carbonylation of important structural proteins in fish muscle, mainly actin and myosin, and degradation products of those proteins were observed, some of them exhibiting increased carbonylation levels.

A simple and efficient method for processing of cell lysates for two-dimensional gel electrophoresis

Sample preparation is one of the major issues in 2-DE for the separation of proteins. Although a 100% representation of cellular proteins onto a 2-DE is virtually impossible, maximum representation of cellular proteins compared with the original cell lysate is important in the subsequent analysis. We demonstrate that lysis of cells in urea/thiourea solution with subsequent sonication to disrupt the nucleic acids and concentration of the lysate using centri-con led to enrichment of proteins. The procedure resulted in minimal nucleic acid contamination with better resolution of spots. 2-DE spot patterns of proteins prepared using urea-thiourea solubilization/centri-con method to other protein enrichment methods such as phenol/chloroform/isoamyl alcohol extraction, methanol/ammonium acetate precipitation, acetone precipitation and ethanol precipitation were compared. Urea-thiourea solubilization combined with centri-con method of protein enrichment represented higher number/unique spots particularly in the 50-250 kDa M(r) compared with others. Lysis of cells in urea/thiourea from the beginning of lysate preparation preserves the proteins from protease activity due to denaturation of proteases. Thus, we demonstrate that the centri-con methodology is simple and effective for the preparation of high-quality sample that can be used for a qualitative representation of cellular proteins on a 2-DE for proteomic analysis.

Extralysosomal protein degradation in myofibrillar myopathies

Myofibrillar myopathies (MFMs) are a group of heterogeneous muscle disorders morphologically defined by the presence of foci of dissolution of the myofibrils, accumulation of the products of myofibrillar degradation and ectopic expression of multiple proteins. MFMs represent the paradigm of conformational protein diseases of skeletal and cardiac muscles. Protein aggregation in MFMs is now considered to be the result of a failure of the extralysosomal proteolytic degradation system. Several factors including mutant proteins, aggresome formation and oxidative stress may compromise the ubiquitin-proteasome system, promoting the accumulation of potentially toxic protein aggregates within muscle cells.

Use of conventional and -omics based methods for health claims of dietary antioxidants: a critical overview

This article describes the principles and limitations of methods used to investigate reactive oxygen species (ROS) protective properties of dietary constituents and is aimed at providing a better understanding of the requirements for science based health claims of antioxidant (AO) effects of foods. A number of currently used biochemical measurements aimed of determining the total antioxidant capacity and oxidised lipids and proteins are carried out under unphysiological conditions and are prone to artefact formation. Probably the most reliable approaches are measurements of isoprostanes as a parameter of lipid peroxidation and determination of oxidative DNA damage. Also the design of the experimental models has a strong impact on the reliability of AO studies: the common strategy is the identification of AO by in vitro screening with cell lines. This approach is based on the assumption that protection towards ROS is due to scavenging, but recent findings indicate that activation of transcription factors which regulate genes involved in antioxidant defence plays a key role in the mode of action of AO. These processes are not adequately represented in cell lines. Another shortcoming of in vitro experiments is that AO are metabolised in vivo and that most cell lines are lacking enzymes which catalyse these reactions. Compounds with large molecular configurations (chlorophylls, anthocyans and polyphenolics) are potent AO in vitro, but weak or no effects were observed in animal/human studies with realistic doses as they are poorly absorbed. The development of -omics approaches will improve the scientific basis for health claims. The evaluation of results from microarray and proteomics studies shows that it is not possible to establish a general signature of alterations of transcription and protein patterns by AO. However, it was shown that alterations of gene expression and protein levels caused by experimentally induced oxidative stress and ROS related diseases can be normalised by dietary AO.

Molecular pathology of myofibrillar myopathies

Myofibrillar myopathies (MFMs) are clinically and genetically heterogeneous muscle disorders that are defined morphologically by the presence of foci of myofibril dissolution, accumulation of myofibrillar degradation products, and ectopic expression of multiple proteins. MFMs are the paradigm of conformational protein diseases of the skeletal (and cardiac) muscles characterised by intracellular protein accumulation in muscle cells. Understanding of this group of disorders has advanced in recent years through the identification of causative mutations in various genes, most of which encode proteins of the sarcomeric Z-disc, including desmin, alphaB-crystallin, myotilin, ZASP and filamin C. This review focuses on the MFMs arising from defects in these proteins, summarising genetic and clinical features of the disorders and then discussing emerging understanding of the molecular pathogenic mechanisms leading to muscle fibre degeneration. Defective extralysosomal degradation of proteins is now recognised as an important element in this process. Several factors--including mutant proteins, a defective ubiquitin-proteasome system, aggresome formation, mutant ubiquitin, p62, oxidative stress and abnormal regulation of some transcription factors--are thought to participate in the cascade of events occurring in muscle fibres in MFMs.

Detection and localization of oxidized proteins in muscle cells by fluorescence microscopy

In meat, no detailed studies on the intracellular distribution of oxidized proteins during oxidative stress have been performed, to our knowledge. Therefore, we used fluorescence microscopy to detect and locate protein carbonyls, oxidation products of basic amino acids, generated in bovine M. Rectus abdominis during either exposition to a chemical free radical generating system, or refrigerated storage, or cooking. The technique consisted of an immunohistochemical detection of carbonyls by reaction with the specific probe DNPH (2,4-dinitrophenylhydrazine) followed by the sequential addition of a first antibody against DNPH-carbonylated proteins and a CY3-labeled secondary antibody. The fluorescence of the CY3 probe increased regularly with level of free radical generating system and storage time. Moreover, an important heterogeneity of carbonyl distribution was observed, with a higher oxidation level at the periphery than inside the muscle cells. Cooking induced fluorescence increase only at the periphery of cells. Specific coloration of collagen by Sirius red showed that collagen was not involved in fluorescence. We can deduce that accumulation of oxidized proteins observed in the cell periphery was linked to membrane protein oxidation and not to connective tissue oxidation. Biochemical assays were performed in parallel on membrane and myofibrillar proteins to provide complementary quantitative data on level of oxidized proteins.

Functional genomics of the chicken--a model organism

Since the sequencing of the genome and the development of high-throughput tools for the exploration of functional elements of the genome, the chicken has reached model organism status. Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scale. Systems biology attempts to integrate functional information derived from multiple high-content data sets into a holistic view of all biological processes within a cell or organism. Generation of a large collection ( approximately 600K) of chicken expressed sequence tags, representing most tissues and developmental stages, has enabled the construction of high-density microarrays for transcriptional profiling. Comprehensive analysis of this large expressed sequence tag collection and a set of approximately 20K full-length cDNA sequences indicate that the transcriptome of the chicken represents approximately 20,000 genes. Furthermore, comparative analyses of these sequences have facilitated functional annotation of the genome and the creation of several bioinformatic resources for the chicken. Recently, about 20 papers have been published on transcriptional profiling with DNA microarrays in chicken tissues under various conditions. Proteomics is another powerful high-throughput tool currently used for examining the dynamics of protein expression in chicken tissues and fluids. Computational analyses of the chicken genome are providing new insight into the evolution of gene families in birds and other organisms. Abundant functional genomic resources now support large-scale analyses in the chicken and will facilitate identification of transcriptional mechanisms, gene networks, and metabolic or regulatory pathways that will ultimately determine the phenotype of the bird. New technologies such as marker-assisted selection, transgenics, and RNA interference offer the opportunity to modify the phenotype of the chicken to fit defined production goals. This review focuses on functional genomics in the chicken and provides a road map for large-scale exploration of the chicken genome.

Desmin is oxidized and nitrated in affected muscles in myotilinopathies and desminopathies

Degenerative diseases with abnormal protein aggregates are characterized by the accumulation of proteins with variable posttranslational modifications including phosphorylation, glycoxidation, oxidation, and nitration. Myofibrillar myopathies, including myotilinopathies and desminopathies, are characterized by the intracytoplasmic focal accumulation of proteins in insoluble aggregates in muscle cells. By using single immunohistochemistry, monodimensional gel electrophoresis and Western blotting, and bidimensional gel electrophoresis, in-gel digestion, and mass spectometry, desmin was demonstrated to be a major target of oxidation and nitration in both desminopathies and myotilinopathies. Because oxidized and nitrated proteins may have toxic effects and may impair ubiquitin-proteasomal function, modified desmin can be considered to be an additional element in the pathogenesis of myofibrillar myopathies. In addition to desmin, pyruvate kinase muscle splice form M1 is oxidized, thus supporting complemental mitochondrial damage, at least in some cases of myotilinopathy.

Protein and lipid oxidation during frozen storage of rainbow trout (Oncorhynchus mykiss)

This study aimed at investigating protein and lipid oxidation during frozen storage of rainbow trout. Rainbow trout fillets were stored for 13 months at -20, -30, or -80 degrees C, and samples were analyzed at regular intervals for lipid and protein oxidation markers. Lipid oxidation was followed by measuring lipid hydroperoxides (PV), as well as secondary oxidation products (volatiles) using dynamic headspace GC-MS. Free fatty acids (FFA) were measured as an estimation of lipolysis. Protein oxidation was followed using the spectrophotometric determination of protein carbonyls and immunoblotting. Significant oxidation was observed in samples stored at -20 degrees C, and at this temperature lipid and protein oxidation seemed to develop simultaneously. FFA, PV, and carbonyls increased significantly for the fish stored at -20 degrees C, whereas the fish stored at -30 and -80 degrees C did not show any increase in oxidation during the entire storage period when these methods were used. In contrast, the more sensitive GC-MS method used for measurement of the volatiles showed that the fish stored at -30 degrees C oxidized more quickly than those stored at -80 degrees C. Detection of protein oxidation using immunoblotting revealed that high molecular weight proteins were oxidized already at t = 0 and that no new protein oxidized during storage irrespective of the storage time and temperature. The results emphasize the need for the development of more sensitive and reliable methods to study protein oxidation in order to gain more explicit knowledge about the significance of protein oxidation for food quality and, especially, to correlate protein oxidation with physical and functional properties of foods.

Oxidative stress in desminopathies and myotilinopathies: a link between oxidative damage and abnormal protein aggregation

Myotilinopathies and desminopathies are subgroups of myofibrillar myopathies (MFM) caused by mutations in myotilin and desmin genes, respectively. They are characterized by the presence of protein aggregates in muscle cells. As oxidation of proteins facilitates their aggregation and makes them more resistant to proteolysis, the present study was geared to analyze oxidative stress in MFM. For this purpose, markers of glycoxidation, lipoxidation and nitration were examined with gel electrophoresis and Western blotting, single immunohistochemistry, and double- and triple-labeling immunofluorescence and confocal microscopy in muscle biopsies from patients suffering from myotilinopathy and desminopathy. Increased levels of glycation-end products (AGEs), N-carboxymethyl-lysine (CML) and N-carboxyethyl-lysine (CEL), malondialdehyde-lysine (MDAL), 4-hydroxynonenal (HNE) and nitrotyrosine (N-tyr) were found in MFM. Furthermore, aberrant expression of AGE, CML, CEL, MDAL and HNE, as well as of neuronal, inducible and endothelial nitric oxide synthases (nNOS, iNOS, eNOS), and superoxide dismutase 2 (SOD2), was found in muscle fibers containing protein aggregates in myotilinopathies and desminopathies. AGE, ubiquitin and p62 co-localized in several muscle fibers in MFM. As oxidized proteins are vulnerable to misfolding and are resistant to degradation by the UPS, the present observations support a link between oxidative stress, protein aggregation and abnormal protein deposition in MFMs.

Avian proteomics: advances, challenges and new technologies

Proteomics is defined as an analysis of the full complement of proteins of a cell or tissue under given conditions. Avian proteomics, or more specifically chicken proteomics, has focussed on the study of individual tissues and organs of interest to specific researchers. Researchers have looked at skeletal muscle and growth, and embryonic development and have performed initial studies in avian disease. Traditional proteomics involves identifying and cataloguing proteins in a cell and identifying relative changes in populations between two or more states, be that physiological or disease-induced states. Recent advances in proteomic technologies have included absolute quantification, proteome simplification and the ability to determine the turnover of individual proteins in a global context. This review discusses the current developments in this relatively new field, new technologies and how they may be applied to biological questions, and the challenges faced by researchers in this ever-expanding and exciting field.

Using Proteomics to Understand Avian Systems Biology and Infectious Disease

The proteome is defined as the protein complement to the genome. Proteomics is the study of the proteome. Several techniques are frequently used in proteomics; these include 2-hybrid systems, 2-dimensional gel electrophoresis, and mass spectrometry. Systems biology is a scientific approach that takes into account the complex relationships among and between genes and proteins and determines how all of these interactions come together to form a functional organism. Proteomic tools can simultaneously probe the properties of numerous proteins and thus are a great aid to the emerging field of systems biology, in which the functional interactions of numerous proteins are studied instead of studying individual proteins as isolated entities. In the field of avian biology, proteomics has been used to study everything from the development and function of organs and systems to the interactions of infectious agents and the altered states that they induce in their hosts.

Identification of carbonylated protein in frozen rainbow trout (Oncorhynchus mykiss) fillets and development of protein oxidation during frozen storage

Frozen storage of fish is known to enhance lipid oxidation, resulting in the development of an unpleasant rancid taste and odor. Frozen storage of fish is also known to reduce protein solubility, and proteins are expected to be oxidatively modified; however, these oxidative mechanisms are poorly understood. Generally, protein oxidation leads to a wide range of modifications; the most studied being the formation of carbonyl groups. The present work shows, by UV spectrophometric determination of protein carbonyl groups in rainbow trout muscle, that storage at -20 degrees C resulted in a 2-fold increase in protein carbonylation compared to storage at -30 or -80 degrees C. Furthermore, low-salt-soluble proteins in fish that were either fresh or stored for 3 years at -80 degrees C were found to have similar extents of carbonylation. Proteome analysis and two-dimensional immunoblotting of rainbow trout low-salt- and high-salt-soluble proteins gave a detailed description of the protein carbonylation pattern. Several carbonylated proteins were identified by LC-MS/MS, such as nucleoside diphosphate kinase, adenylate kinase, pyruvate kinase, actin, creatine kinase, tropomyosin, myosin light chains 1 and 2, and myosin heavy chain. Furthermore, the results showed a reduced solubility of nucleoside diphosphate kinase in fish stored at -20 degrees C for 2 years compared to fish stored at -80 degrees C. It was observed that low-abundant proteins could be relatively more carbonylated than high-abundant proteins, thereby indicating that some proteins are more susceptible to oxidation than others, due to either their cellular localization, amino acid sequence, or biochemical function.

The use of proteomic techniques to explore the holistic effects of nutrients in vivo

The availability of ‘omics’ technologies is transforming scientific approaches to physiological problems from a reductionist viewpoint to that of a holistic viewpoint. This is of profound importance in nutrition, since the integration of multiple systems at the level of gene expression on the synthetic side through to metabolic enzyme activity on the degradative side combine to govern nutrient availability to tissues. Protein activity is central to the process of nutrition from the initial absorption of nutrients via uptake carriers in the gut, through to distribution and transport in the blood, metabolism by degradative enzymes in tissues and excretion through renal tubule exchange proteins. Therefore, the global profiling of the proteome, defined as the entire protein complement of the genome expressed in a particular cell or organ, or in plasma or serum at a particular time, offers the potential for identification of important biomarkers of nutritional state that respond to alterations in diet. The present review considers the published evidence of nutritional modulation of the proteome in vivo which has expanded exponentially over the last 3 years. It highlights some of the challenges faced by researchers using proteomic approaches to understand the interactions of diet with genomic and metabolic–phenotypic variables in normal populations.

Proteome analysis of the sarcoplasmic fraction of pig semimembranosus muscle: implications on meat color development

Two-dimensional electrophoresis was used to investigate sarcoplasmic protein expression in pig Semimembranosus muscles sampled 20 min after slaughter. Two groups (light and dark) of 12 animals were selected from 1000 pigs, based on meat L values measured 36 h postmortem. Twenty-two proteins or fragments (p < 0.05) were differentially expressed. Muscles leading to darker meat had a more oxidative metabolism, indicated by more abundant mitochondrial enzymes of the respiratory chain, hemoglobin, and chaperone or regulator proteins (HSP27, alphaB-crystallin, and glucose-regulated protein 58 kDa). Conversely, enzymes of glycolysis were overexpressed in the lighter group. Such samples were also characterized by higher levels of glutathione S-transferase omega, which can activate the RyR calcium channels, and higher levels of cyclophilin D. This protein pattern is likely to have severe implications on postmortem metabolism, namely, acceleration of ATP depletion and pH fall and subsequent enhanced protein denaturation, well-known to induce discoloration.

Proteome analysis of chicken embryonic gonads: identification of major proteins from cultured gonadal primordial germ cells

The domestic chicken (Gallus gallus) is an important model for research in developmental biology because its embryonic development occurs in ovo. To examine the mechanism of embryonic germ cell development, we constructed proteome map of gonadal primordial germ cells (gPGCs) from chicken embryonic gonads. Embryonic gonads were collected from 500 embryos at 6 days of incubation, and the gPGCs were cultured in vitro until colony formed. After 7-10 days in culture, gPGC colonies were separated from gonadal stroma cells (GSCs). Soluble extracts of cultured gPGCs were then fractionated by two-dimensional gel electrophoresis (pH 4-7). A number of protein spots, including those that displayed significant expression levels, were then identified by use of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry and LC-MS/MS. Of the 89 gPGC spots examined, 50 yielded mass spectra that matched avian proteins found in on-line databases. Proteome map of this type will serve as an important reference for germ cell biology and transgenic research.