RESUMO
BACKGROUND: Positively correlated with carcass weight and animal growth, the ribeye area (REA) and the backfat thickness (BFT) are economic important carcass traits, which impact directly on producer's payment. The selection of these traits has not been satisfactory since they are expressed later in the animal's life and multigene regulated. So, next-generation technologies have been applied in this area to improve animal's selection and better understand the molecular mechanisms involved in the development of these traits. Correlation network analysis, performed by tools like WGCNA (Weighted Correlation Network Analysis), has been used to explore gene-gene interactions and gene-phenotype correlations. Thus, this study aimed to identify putative candidate genes and metabolic pathways that regulate REA and BFT by constructing a gene co-expression network using WGCNA and RNA sequencing data, to better understand genetic and molecular variations behind these complex traits in Nelore cattle. RESULTS: The gene co-expression network analysis, using WGCNA, were built using RNA-sequencing data normalized by transcript per million (TPM) from 43 Nelore steers. Forty-six gene clusters were constructed, between them, three were positively correlated (p-value< 0.1) to the BFT (Green Yellow, Ivory, and Light Yellow modules) and, one cluster was negatively correlated (p-value< 0.1) with REA (Salmon module). The enrichment analysis performed by DAVID and WebGestalt (FDR 5%) identified eight Gene Ontology (GO) terms and three KEGG pathways in the Green Yellow module, mostly associated with immune response and inflammatory mechanisms. The enrichment of the Salmon module demonstrated 19 GO terms and 21 KEGG pathways, related to muscle energy metabolism, lipid metabolism, muscle degradation, and oxidative stress diseases. The Ivory and Light yellow modules have not shown significant results in the enrichment analysis. CONCLUSION: With this study, we verified that inflammation and immune response pathways modulate the BFT trait. Energy and lipid metabolism pathways, highlighting fatty acid metabolism, were the central pathways associated with REA. Some genes, as RSAD2, EIF2AK2, ACAT1, and ACSL1 were considered as putative candidate related to these traits. Altogether these results allow us to a better comprehension of the molecular mechanisms that lead to muscle and fat deposition in bovine.
Assuntos
Adiposidade/genética , Bovinos/crescimento & desenvolvimento , Bovinos/genética , Desenvolvimento Muscular/genética , Animais , Bovinos/metabolismo , Metabolismo Energético/genética , Expressão Gênica , Redes Reguladoras de Genes , Estudos de Associação Genética , Metabolismo dos Lipídeos/genética , Redes e Vias Metabólicas/genética , Análise de Sequência de RNARESUMO
BACKGROUND: MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs are involved in the regulation of many processes including cell proliferation, differentiation, neurogenesis, angiogenesis, and apoptosis. Beef tenderness is an organoleptic characteristic of great influence in the acceptance of meat by consumers. Previous studies have shown that collagen level, marbling, apoptosis and proteolysis are among the many factors that affect beef tenderness. Considering that miRNAs can modulate gene expression, this study was designed to identify differentially expressed miRNAs that could be modulating biological processes involved with beef tenderness. RESULTS: Deep sequence analysis of miRNA libraries from longissimus thoracis muscle allowed the identification of 42 novel and 308 known miRNAs. Among the known miRNAs, seven were specifically expressed in skeletal muscle. Differential expression analysis between animals with high (H) and low (L) estimated breeding values for shear force (EBVSF) revealed bta-mir-182 and bta-mir-183 are up-regulated (q value < 0.05) in animals with L EBVSF, and bta-mir-338 is up-regulated in animals with H EBVSF. The number of bovine predicted targets for bta-mir-182, bta-mir-183 and bta-mir-338 were 811, 281 and 222, respectively, which correspond to 1204 unique target genes. Among these, four of them, MEF2C, MAP3K2, MTDH and TNRC6B were common targets of the three differentially expressed miRNAs. The functional analysis identified important pathways related to tenderness such as apoptosis and the calpain-calpastatin system. CONCLUSION: The results obtained indicate the importance of miRNAs in the regulatory mechanisms that influence muscle proteolysis and meat tenderness and contribute to our better understanding of the role of miRNAs in biological processes associated with beef tenderness.
Assuntos
Cruzamento , Bovinos/genética , MicroRNAs/metabolismo , Músculo Esquelético/metabolismo , Carne Vermelha , Animais , Apoptose , Proteínas de Ligação ao Cálcio/metabolismo , MAP Quinase Quinase Quinase 2/genética , MAP Quinase Quinase Quinase 2/metabolismo , Fatores de Transcrição MEF2/genética , Fatores de Transcrição MEF2/metabolismo , Manitol Desidrogenases/genética , Manitol Desidrogenases/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismoRESUMO
BACKGROUND: The amount of intramuscular fat can influence the sensory characteristics and nutritional value of beef, thus the selection of animals with adequate fat deposition is important to the consumer. There is growing knowledge about the genes and pathways that control the biological processes involved in fat deposition in muscle. MicroRNAs (miRNAs) belong to a well-conserved class of non-coding small RNAs that modulate gene expression across a range of biological functions in animal development and physiology. The aim of this study was to identify differentially expressed (DE) miRNAs, regulatory candidate genes and co-expression networks related to intramuscular fat (IMF) deposition. To achieve this, we used mRNA and miRNA expression data from the Longissimus dorsi muscle of 30 Nelore steers with high (H) and low (L) genomic estimated breeding values (GEBV) for IMF deposition. RESULTS: Differential miRNA expression analysis between animals with extreme GEBV values for IMF identified six DE miRNAs (FDR 10%). Functional annotation of the target genes for these microRNAs indicated that the PPARs signaling pathway is involved with IMF deposition. Candidate regulatory genes such as SDHAF4, FBXO17, ALDOA and PKM were identified by partial correlation with information theory (PCIT), phenotypic impact factor (PIF) and regulatory impact factor (RIF) co-expression approaches from integrated miRNA-mRNA expression data. Two DE miRNAs (FDR 10%), bta-miR-143 and bta-miR-146b, which were upregulated in the Low IMF group, were correlated with regulatory candidate genes, which were functionally enriched for fatty acid oxidation GO terms. Co-expression patterns obtained by weighted correlation network analysis (WGCNA), which showed possible interaction and regulation between mRNAs and miRNAs, identified several modules related to immune system function, protein metabolism, energy metabolism and glucose catabolism according to in silico analysis performed herein. CONCLUSION: In this study, several genes and miRNAs were identified as candidate regulators of IMF by analyzing DE miRNAs using two different miRNA-mRNA co-expression network methods. This study contributes to the understanding of potential regulatory mechanisms of gene signaling networks involved in fat deposition processes measured in muscle. Glucose metabolism and inflammation processes were the main pathways found in silico to influence intramuscular fat deposition in beef cattle in the integrative mRNA-miRNA co-expression analysis.
Assuntos
Composição Corporal/genética , Metabolismo Energético/genética , Regulação da Expressão Gênica , MicroRNAs/genética , Interferência de RNA , RNA Mensageiro/genética , Animais , Bovinos , Biologia Computacional/métodos , Ontologia Genética , Redes Reguladoras de Genes , Sequenciamento de Nucleotídeos em Larga Escala , Fenótipo , Análise de Sequência de DNA , Transdução de SinaisRESUMO
BACKGROUND: Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification of genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a whole genome scale. Intramuscular fat (IMF) content and carcass composition play important roles in metabolic and physiological processes in mammals because they influence insulin sensitivity and consequently prevalence of metabolic diseases such as obesity and type 2 diabetes. However, limited information is available on the genetic variants and mechanisms associated with IMF deposition in mammals. Thus, our hypothesis was that eQTL analyses could identify putative regulatory regions and transcription factors (TFs) associated with intramuscular fat (IMF) content traits. RESULTS: We performed an integrative eQTL study in skeletal muscle to identify putative regulatory regions and factors associated with intramuscular fat content traits. Data obtained from skeletal muscle samples of 192 animals was used for association analysis between 461,466 SNPs and the transcription level of 11,808 genes. This yielded 1268 cis- and 10,334 trans-eQTLs, among which we identified nine hotspot regions that each affected the expression of > 119 genes. These putative regulatory regions overlapped with previously identified QTLs for IMF content. Three of the hotspots respectively harbored the transcription factors USF1, EGR4 and RUNX1T1, which are known to play important roles in lipid metabolism. From co-expression network analysis, we further identified modules significantly correlated with IMF content and associated with relevant processes such as fatty acid metabolism, carbohydrate metabolism and lipid metabolism. CONCLUSION: This study provides novel insights into the link between genotype and IMF content as evident from the expression level. It thereby identifies genomic regions of particular importance and associated regulatory factors. These new findings provide new knowledge about the biological processes associated with genetic variants and mechanisms associated with IMF deposition in mammals.
Assuntos
Locos de Características Quantitativas/genética , Fatores de Transcrição/metabolismo , Animais , Metabolismo dos Carboidratos/genética , Metabolismo dos Carboidratos/fisiologia , Ácidos Graxos/metabolismo , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica/genética , Regulação da Expressão Gênica/fisiologia , Metabolismo dos Lipídeos/genética , Metabolismo dos Lipídeos/fisiologia , Doenças Metabólicas/genética , Doenças Metabólicas/metabolismo , Fatores de Transcrição/genéticaRESUMO
BACKGROUND: Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits. RESULTS: By comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis. CONCLUSION: In this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production.
Assuntos
Redes e Vias Metabólicas , Músculos Paraespinais/metabolismo , Fenótipo , Transdução de Sinais , Transcriptoma , Criação de Animais Domésticos , Animais , Cruzamento , Bovinos/genética , Bovinos/metabolismo , Proteínas Quinases Ativadas por Mitógeno , Músculos Paraespinais/fisiologia , Análise de Sequência de RNARESUMO
BACKGROUND: Lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. In the last few decades, it has been reported that long-chain fatty acids (FAs) are involved in several biological functions from transcriptional regulation to physiological processes. Several fatty acids have been both positively and negatively implicated in different biological processes in skeletal muscle and other tissues. To gain insight into biological processes associated with fatty acid content in skeletal muscle, the aim of the present study was to identify differentially expressed genes (DEGs) and functional pathways related to gene expression regulation associated with FA content in cattle. RESULTS: Skeletal muscle transcriptome analysis of 164 Nellore steers revealed no differentially expressed genes (DEGs, FDR 10%) for samples with extreme values for linoleic acid (LA) or stearic acid (SA), and only a few DEGs for eicosapentaenoic acid (EPA, 5 DEGs), docosahexaenoic acid (DHA, 4 DEGs) and palmitic acid (PA, 123 DEGs), while large numbers of DEGs were associated with oleic acid (OA, 1134 DEGs) and conjugated linoleic acid cis9 trans11 (CLA-c9t11, 872 DEGs). Functional annotation and functional enrichment from OA DEGs identified important genes, canonical pathways and upstream regulators such as SCD, PLIN5, UCP3, CPT1, CPT1B, oxidative phosphorylation mitochondrial dysfunction, PPARGC1A, and FOXO1. Two important genes associated with lipid metabolism, gene expression and cancer were identified as DEGs between animals with high and low CLA-c9t11, specifically, epidermal growth factor receptor (EGFR) and RNPS. CONCLUSION: Only two out of seven classes of molecules of FA studied were associated with large changes in the expression profile of skeletal muscle. OA and CLA-c9t11 content had significant effects on the expression level of genes related to important biological processes associated with oxidative phosphorylation, and cell growth, survival, and migration. These results contribute to our understanding of how some FAs modulate metabolism and may have protective health function.
Assuntos
Ácidos Graxos/metabolismo , Perfilação da Expressão Gênica , Músculo Esquelético/metabolismo , Transcriptoma , Animais , Bovinos , Qualidade dos Alimentos , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Redes e Vias Metabólicas , Ácido Oleico/metabolismo , Fenótipo , Carne Vermelha/normas , Reprodutibilidade dos TestesRESUMO
Metagenomics has made it feasible to elucidate the intricacies of the ruminal microbiome and its role in the differentiation of animal production phenotypes of significance. The search for mobile genetic elements (MGEs) has taken on great importance, as they play a critical role in the transfer of genetic material between organisms. Furthermore, these elements serve a dual purpose by controlling populations through lytic bacteriophages, thereby maintaining ecological equilibrium and driving the evolutionary progress of host microorganisms. In this study, we aimed to identify the association between ruminal bacteria and their MGEs in Nellore cattle using physical chromosomal links through the Hi-C method. Shotgun metagenomic sequencing and the proximity ligation method ProxiMeta were used to analyze DNA, getting 1,713,111,307 bp, which gave rise to 107 metagenome-assembled genomes from rumen samples of four Nellore cows maintained on pasture. Taxonomic analysis revealed that most of the bacterial genomes belonged to the families Lachnospiraceae, Bacteroidaceae, Ruminococcaceae, Saccharofermentanaceae, and Treponemataceae and mostly encoded pathways for central carbon and other carbohydrate metabolisms. A total of 31 associations between host bacteria and MGE were identified, including 17 links to viruses and 14 links to plasmids. Additionally, we found 12 antibiotic resistance genes. To our knowledge, this is the first study in Brazilian cattle that connect MGEs with their microbial hosts. It identifies MGEs present in the rumen of pasture-raised Nellore cattle, offering insights that could advance biotechnology for food digestion and improve ruminant performance in production systems.
Assuntos
Sequências Repetitivas Dispersas , Rúmen , Animais , Bovinos , Rúmen/microbiologia , Sequências Repetitivas Dispersas/genética , Metagenômica/métodos , Metagenoma , Microbiota/genética , Microbioma Gastrointestinal/genética , Bactérias/genética , Bactérias/classificação , Genoma Bacteriano , FilogeniaRESUMO
Animal production and health are of significant economic importance, particularly regarding the world food supply. Animal and veterinary sciences have evolved immensely in the past six decades, particularly in genetics, nutrition, housing, management and health. To address major challenges such as those posed by climate change or metabolic disorders, it is of utmost importance to use state-of-the-art research tools. Proteomics and the other post-genomic tools (transcriptomics or metabolomics) are among them. Proteomics has experienced a considerable development over the last decades. This brought developments to different scientific fields. The use and adoption of proteomics tools in animal and veterinary sciences has some limitations (database availability or access to proteomics platforms and funding). As a result, proteomics' use by animal science researchers varies across the globe. In this viewpoint article, we focus on the developments of domestic animal proteomics over the last decade in different regions of the globe and how the researchers have coped with such challenges. In the second part of the article, we provide examples of funding, educational and laboratory establishment initiatives designed to foster the development of (animal-based) proteomics. International scientific collaboration is a definitive and key feature in the development and advancement of domestic animal proteomics. SIGNIFICANCE: Animal production and health are very important for food supply worldwide particularly as a source of proteinaceous foods. Animal and veterinary sciences have evolved immensely in the last decades. In order to address the major contemporary challenges facing animal and veterinary sciences, it is of utmost importance to use state-of-the-art research tools such as Proteomics and other Omics. Herein, we focus on the major developments in domestic animal proteomics worldwide during the last decade and how different regions of the world have used the technology in this specific research field. We address also major international efforts aiming to increase the research output in this area and highlight the importance of international cooperation to address specific problems inherent to domestic animal proteomics.
Assuntos
Animais Domésticos , Proteômica , Animais , Biologia Computacional , Metabolômica , Estudos RetrospectivosRESUMO
The present study investigated the inclusion of yerba mate extract (YME) in the lamb's diet on meat quality traits, antioxidant activity, and shelf-life. Thirty-six lambs were distributed according to a block design with the following groups: control group without YME (0%) and three treatment groups with 1, 2, and 4% YME inclusion in the dry matter. The animals were fed these diets for 53 days. Samples were collected from the Longissimusthoracis (LT) muscle to analyze antioxidant activity and meat quality. Samples were placed on a counter display simulating a retail environment for 0, 3, and 6 days at 4 ± 2 °C. All data were analyzed using a MIXED model with orthogonal contrasts. Inclusion of 1 and 4% YME in the diet changed the yellow (b*) and the chroma (C*) of the meat (p ≤ 0.05). The pH, colour, thiobarbituric acid reactive substances, and carbonyl values were influenced by the retail display time for all the evaluated treatments (p ≤ 0.03). However, neither diet nor the retail display time influenced the oxidation of proteins or the antioxidant enzyme activities of catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPX) and glutathione activity (GSH) in meat. Therefore, the inclusion of 4% YME showed positive results in the yellow and colour stability parameters of the meat without increasing the lipid peroxidation values or altering the normal meat quality parameters in lambs.
RESUMO
Oleic acid (OA) and cis-9, trans-11 conjugated linoleic acid (c9t11-CLA) are fatty acids found in beef with beneficial effects in human health. This study investigated differentially abundant proteins (DAPs) in skeletal muscle of bovines with extreme values of OA, and c9t11-CLA. For each one of the fatty acids, twenty muscle samples were divided into two groups (N = 10_High; N = 10_Low) and analyzed by high definition mass spectrometry. We identified 103 and 133 DAPs between the groups for each fatty acid. We found 64 and 45 up-regulated and 39 and 68 down-regulated proteins for OA and c9t11-CLA, respectively. Comparative analysis between proteomic and transcriptomic data revealed eight and ten genes with a consistent between mRNA expression levels and protein abundance for OA and c9t11-CLA, respectively. Unconventional myosin-Id (MYO1D), mineralocorticoid receptor (NR3C2), geranylgeranyl transferase type-2 subunit-alpha (RABGGTA), and uveal autoantigen with coiled-coil domains and ankyrin repeats (UACA) were found as putative candidate proteins for OA content. Fatty acid synthase (FASN), tubulin alpha-4A chain (TUBA4A), vinculin (VCL), NADH dehydrogenase 1 alpha subcomplex 5 (NDUFA5), and prefoldin subunit 6 (PFDN6) for c9t11-CLA. Our findings contribute to a deeper understanding of the molecular mechanisms behind the regulation of the OA and c9t11-CLA content in cattle skeletal muscle. SIGNIFICANCE: Questions about the association between meat intake and disease incidence in humans has driven animal scientist to pursue a better understanding of the biological processes associated with differences in the intramuscular fat composition. The beneficial effects of oleic acid and conjugated linoleic acid in human health have been demonstrated by improving the immune system and preventing atherosclerosis, different types of cancers, hypertension, and diabetes. Previous genome-wide association and gene expression studies identified genomic regions and differentially expressed genes associated with the fatty acid profile in skeletal muscle. In this work, differences were evaluated at the protein level. The use of a label-free quantitative proteomic approach, compared with muscle transcriptome results obtained by RNA-sequencing, allowed us to earn new insights into the variability in fatty acid deposition in skeletal muscle of farm animals. This study opens new avenues to explore the effect of the fatty acids in the skeletal muscle of livestock animals, which is associated with nutritional values of the meat, and perhaps to understand the mechanisms correlated with metabolic diseases in other species.
Assuntos
Ácidos Linoleicos Conjugados , Animais , Bovinos , Ácidos Graxos , Estudo de Associação Genômica Ampla , Músculo Esquelético , Ácido Oleico , Proteoma , ProteômicaRESUMO
The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and productivity. This would surely benefit regions where resource quality and quantity are increasingly unstable, and research is still very incipient, which is the case of many regions in the tropics. The purpose of this review is to demonstrate how omics-based approaches play a major role in animal science, particularly concerning ruminant production systems and research associated to the tropics and developing countries. SIGNIFICANCE: Environmental conditions in the tropics make livestock production harder, compared to temperate regions. Due to global warming, the sustainability of livestock production will become increasingly problematic. The use of novel omics technologies could generate useful information to understand adaptation mechanisms of resilient breeds and/or species. The application of omics to tropical animal production is still residual in the currently available literature. With this review, we aim to summarize the most notable results in the field whilst encouraging further research to deal with the future challenges that animal production in the tropics will need to face.
Assuntos
Gado , Ruminantes , Aclimatação , Animais , Bovinos , Mudança ClimáticaRESUMO
In the present study, 155 Nellore cattle were genotyped for the CAPN4751 and UOGCAST polymorphisms and phenotyped for shear force (SF) at 1, 7 and 14days aging. The effects of different genotypic combinations were evaluated on the Longissimus muscle proteomic profile using 2DE and mass spectrometry. A significant association was found between genotypes for UOGCAST and CAPN4751 and meat tenderness. The CC genotype for both markers was favorable for lesser shear force than TT. A total of 40 spots showed significant differential expression profiles (P<0.05), of which eight had a main effect for the CAPN4751 marker, 11 for UOGCAST, two for both markers, and 19 had interactions between markers, including myosin (MYL1, MYL2, MYLPF and MYL6B), actin (ACTA1 and CAPZß), troponin (TNNT1 and TNNT3) and heat shock proteins (HSPB6, HSPB1 and HSP70-2). The results demonstrated that UOGCAST and CAPN4751 genotypes led to variability on the expression of proteins that are involved in muscle metabolism, and consequently affect meat tenderness.
Assuntos
Bovinos/genética , Músculo Esquelético/metabolismo , Proteoma/genética , Carne Vermelha/análise , Animais , Genótipo , Proteínas de Choque Térmico/análise , Masculino , Proteínas Musculares/análiseRESUMO
The proteomic data presented in this article are associated with the research article entitled "Longissimus dorsi muscle label-free quantitative proteomic reveals biological mechanisms associated with intramuscular fat deposition" published in Journal of Proteomics [1]. In this article, we characterized the proteomic profile of bovine Longissimus dorsi muscle from Nelore steers and identified differentially abundant proteins associated with the intramuscular fat (IMF) content. An integrated transcriptome-assisted label-free quantitative proteomic approach by High Definition Mass Spectrometry (HDMSE) was employed to identify and quantify the proteins. A functional enrichment analysis using the differentially abundant proteins list was performed to understand the biological processes involved in IMF deposition. Moreover, to explore and clarify the biological mechanisms that influence IMF content, the mRNA data for the same trait from Cesar and collaborators [2] obtained by RNA-sequencing technology was compared with proteomic data. The mRNA data is deposited in the European Nucleotide Archive (ENA) repository (EMBL-EBI), under accession PRJEB13188.
RESUMO
The pathways involved in intramuscular fat (IMF) deposition in Longissimus dorsi muscle were investigated using an integrated transcriptome-assisted label-free quantitative proteomic approach by High Definition Mass Spectrometry. We quantified 1582 proteins, of which 164 were differentially abundant proteins (DAPs, pâ¯<â¯0.05) between animals with high (H) and low (L) genomic estimated breeding values (GEBV) for IMF content. Ingenuity pathway analysis (IPA) revealed that these DAPs were mainly involved in glycolysis metabolism, actin cytoskeleton signaling, cell-cell adherens junction and pathways for MAPK and insulin. A comparative study between transcriptomic (mRNA) and proteomic data showed 17 differentially expressed genes corresponding to DAPs, of which three genes/proteins did not agree on the direction of the fold change between groups. Moreover, we investigated microRNAs data to explain these differences in fold change direction, being able to unravel two of the three unexpected mRNA/protein relationships. Results demonstrated that changes in protein/mRNA levels of sarcomere organization, intracellular signal transduction and regulation of actin cytoskeleton, are involved in IMF deposition. These findings provide a deeper understanding of the highly complex regulatory mechanisms involved in IMF deposition in cattle and indicate target pathways for future studies. SIGNIFICANCE: Intramuscular fat is the amount of fat deposited inside muscle and plays an important role in human health and meat quality attributes, influencing energy metabolism of skeletal muscle, as well as, tenderness, flavor, and juiciness of beef. We performed for the first time the utilization of integrated transcriptome-assisted label-free quantitative proteomic approach using High Definition Mass Spectrometry for characterization of the changes in the proteomic profile of the Longissimus dorsi muscle associated with intramuscular fat deposition in cattle. Furthermore, we compared the muscle proteome with the muscle transcriptome (mRNA and microRNAs), obtained by RNA-sequencing, to better understand the relationship between expression of mRNAs and proteins and to unravel essential biological mechanisms involved in bovine skeletal muscle IMF deposition.
Assuntos
Tecido Adiposo/metabolismo , Metabolismo Energético/fisiologia , Músculo Esquelético/metabolismo , Proteoma/metabolismo , Transcriptoma/fisiologia , Animais , Cruzamento , Bovinos , MicroRNAs/metabolismo , RNA Mensageiro/metabolismo , Análise de Sequência de RNARESUMO
Our objective was to evaluate the diagnosis of swine cysticercosis by examining "ante mortem" (inspection of the tongue), "post mortem" (inspection and detailed necropsy) and ELISA for research in serum of antibodies (Ab-ELISA) and antigens (Ag-ELISA). Seven (7) pigs were experimentally infected orally with eggs of Taenia solium and another 10 were naturally infected. In the pigs experimentally infected, inspection of the tongue was negative in all animals, in the routine inspection detailed necropsy and cysticercis were identified in all of them. In pigs with heavy natural infection, inspection of the tongue identified cysticerci in two (20%), while at inspection with necropsy the parasites were identified in large quantities in all animals. In ELISA for antibody search (Ab-ELISA) TS-14 recombinant protein was used, and in search for antigen (Ag-ELISA) a monoclonal antibody against this protein. In animals experimentally infected, blood was collected weekly for 140 days. The Ab-ELISA identified an increase in titers of antibody to cysticerci 21 days after infection, and at the end of the experimental period six animals (86%) were positive to the test. The search for circulating antigens (Ag-ELISA) was positive in two pigs 28 to 91 days after infection. All naturally infected pigs were positive for Ag-ELISA and Ab-ELISA. The search for antibodies and antigens by ELISA in serum from 30 pigs of a local farm and without history of cysticercosis was negative. Thus, the use of TS-14 antigen in ELISA test (Ab-ELISA) can be useful for the diagnosis of cysticercosis in pigs with low infection.
Nosso objetivo foi avaliar o diagnóstico de cisticercose suína através do exame "ante mortem" (inspeção da língua), "post mortem" (inspeção e necropsia detalhada) e teste de ELISA para a pesquisa no soro de anticorpos (Ab-ELISA) e antígenos (Ag -ELISA). Sete (7) suínos foram infectados experimentalmente por via oral com ovos de Taenia solium e outros 10 eram portadores de infecção natural generalizada. Nos suínos experimentalmente infectados, a inspeção da língua foi negativa em todos os animais, na inspeção 4 (57%) estavam infectados, a necropsia detalhada identificou cisticercos em todos os animais. Nos animais com infecção natural generalizada, a inspeção da língua identificou cisticercos em 2 (20%), enquanto que a inspeção e a necropsia os parasitas foram identificados em grande quantidade em todos os animais. No teste de ELISA para a pesquisa de anticorpos (Ab-ELISA) foi utilizada a proteína recombinante TS-14 e para a pesquisa de antígenos (Ag-ELISA) um anticorpo monoclonal produzido contra esta proteína. Nos animais experimentalmente infectados o sangue foi coletado semanalmente por um período de 140 dias. O Ab-ELISA identificou um aumento nos títulos de anticorpos para cisticercos 21 dias após a infecção, sendo que no final do período experimental 6 animais (86%) foram positivos ao teste. A pesquisa de antígenos circulantes (Ag-ELISA), foi positiva em 2 animais, entre os dias 21 e 91 após a infecção . Todos os suínos com infecção natural generalizada foram positivos para Ag-ELISA e Ab-ELISA.A pesquisa de anticorpos e antígenos pelo ELISA realizada no soro de 30 suínos procedentes de uma criação local sem historia de cisticercose foi negativa. Assim o uso do antígeno TS-14 (Ac-ELISA), pode ser útil para o diagnóstico da cisticercose em suínos com baixa infecção.
Assuntos
Animais , Autopsia , Cisticercose/diagnóstico , Cisticercose/veterinária , Ensaio de Imunoadsorção Enzimática , Suínos/parasitologia , Taenia solium/patogenicidade , Cysticercus/imunologia , Língua/fisiopatologiaRESUMO
Our objective was to evaluate the diagnosis of swine cysticercosis by examining "ante mortem" (inspection of the tongue), "post mortem" (inspection and detailed necropsy) and ELISA for research in serum of antibodies (Ab-ELISA) and antigens (Ag-ELISA). Seven (7) pigs were experimentally infected orally with eggs of Taenia solium and another 10 were naturally infected. In the pigs experimentally infected, inspection of the tongue was negative in all animals, in the routine inspection detailed necropsy and cysticercis were identified in all of them. In pigs with heavy natural infection, inspection of the tongue identified cysticerci in two (20%), while at inspection with necropsy the parasites were identified in large quantities in all animals. In ELISA for antibody search (Ab-ELISA) TS-14 recombinant protein was used, and in search for antigen (Ag-ELISA) a monoclonal antibody against this protein. In animals experimentally infected, blood was collected weekly for 140 days. The Ab-ELISA identified an increase in titers of antibody to cysticerci 21 days after infection, and at the end of the experimental period six animals (86%) were positive to the test. The search for circulating antigens (Ag-ELISA) was positive in two pigs 28 to 91 days after infection. All naturally infected pigs were positive for Ag-ELISA and Ab-ELISA. The search for antibodies and antigens by ELISA in serum from 30 pigs of a local farm and without history of cysticercosis was negative. Thus, the use of TS-14 antigen in ELISA test (Ab-ELISA) can be useful for the diagnosis of cysticercosis in pigs with low infection.(AU)
Nosso objetivo foi avaliar o diagnóstico de cisticercose suína através do exame "ante mortem" (inspeção da língua), "post mortem" (inspeção e necropsia detalhada) e teste de ELISA para a pesquisa no soro de anticorpos (Ab-ELISA) e antígenos (Ag -ELISA). Sete (7) suínos foram infectados experimentalmente por via oral com ovos de Taenia solium e outros 10 eram portadores de infecção natural generalizada. Nos suínos experimentalmente infectados, a inspeção da língua foi negativa em todos os animais, na inspeção 4 (57%) estavam infectados, a necropsia detalhada identificou cisticercos em todos os animais. Nos animais com infecção natural generalizada, a inspeção da língua identificou cisticercos em 2 (20%), enquanto que a inspeção e a necropsia os parasitas foram identificados em grande quantidade em todos os animais. No teste de ELISA para a pesquisa de anticorpos (Ab-ELISA) foi utilizada a proteína recombinante TS-14 e para a pesquisa de antígenos (Ag-ELISA) um anticorpo monoclonal produzido contra esta proteína. Nos animais experimentalmente infectados o sangue foi coletado semanalmente por um período de 140 dias. O Ab-ELISA identificou um aumento nos títulos de anticorpos para cisticercos 21 dias após a infecção, sendo que no final do período experimental 6 animais (86%) foram positivos ao teste. A pesquisa de antígenos circulantes (Ag-ELISA), foi positiva em 2 animais, entre os dias 21 e 91 após a infecção . Todos os suínos com infecção natural generalizada foram positivos para Ag-ELISA e Ab-ELISA.A pesquisa de anticorpos e antígenos pelo ELISA realizada no soro de 30 suínos procedentes de uma criação local sem historia de cisticercose foi negativa. Assim o uso do antígeno TS-14 (Ac-ELISA), pode ser útil para o diagnóstico da cisticercose em suínos com baixa infecção.(AU)