Transcriptional response to an alternative diet on liver, muscle, and rumen of beef cattle.

Feed cost represents a major economic determinant within cattle production, amounting to an estimated 75% of the total variable costs. Consequently, comprehensive approaches such as optimizing feed utilization through alternative feed sources, alongside the selection of feed-efficient animals, are of great significance. Here, we investigate the effect of two diets, traditional corn-grain fed and alternative by-product based, on 14 phenotypes related to feed, methane emission and production efficiency and on multi-tissue transcriptomics data from liver, muscle, and rumen wall, derived from 52 Nellore bulls, 26 on each diet. To this end, diets were contrasted at the level of phenotype, gene expression, and gene-phenotype network connectivity. As regards the phenotypic level, at a P value < 0.05, significant differences were found in favour of the alternative diet for average daily weight gain at finishing, dry matter intake at finishing, methane emission, carcass yield and subcutaneous fat thickness at the rib-eye muscle area. In terms of the transcriptional level of the 14,776 genes expressed across the examined tissues, we found 487, 484, and 499 genes differentially expressed due to diet in liver, muscle, and rumen, respectively (P value < 0.01). To explore differentially connected phenotypes across both diet-based networks, we focused on the phenotypes with the largest change in average number of connections within diets and tissues, namely methane emission and carcass yield, highlighting, in particular, gene expression changes involving SREBF2, and revealing the largest differential connectivity in rumen and muscle, respectively. Similarly, from examination of differentially connected genes across diets, the top-ranked most differentially connected regulators within each tissue were MEOX1, PTTG1, and BASP1 in liver, muscle, and rumen, respectively. Changes in gene co-expression patterns suggest activation or suppression of specific biological processes and pathways in response to dietary interventions, consequently impacting the phenotype. The identification of genes that respond differently to diets and their associated phenotypic effects serves as a crucial stepping stone for further investigations, aiming to build upon our discoveries. Ultimately, such advancements hold the promise of improving animal welfare, productivity, and sustainability in livestock farming.

Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle.

Background: Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission. Results: The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate. Conclusion: Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.

Prune homolog 2 with BCH domain (PRUNE2) gene expression is associated with feed efficiency-related traits in Nelore steers.

Animal feeding is a critical factor in increasing producer profitability. Improving feed efficiency can help reduce feeding costs and reduce the environmental impact of beef production. Candidate genes previously identified for this trait in differential gene expression studies (e.g., case-control studies) have not examined continuous gene-phenotype variation, which is a limitation. The aim of this study was to investigate the association between the expression of five candidate genes in the liver, measured by quantitative real-time PCR and feed-related traits. We adopted a linear mixed model to associate liver gene expression from 52 Nelore steers with the following production traits: average daily gain (ADG), body weight (BW), dry matter intake (DMI), feed conversion ratio (FCR), feed efficiency (FE), Kleiber index (KI), metabolic body weight (MBW), residual feed intake (RFI), and relative growth ratio (RGR). The total expression of the prune homolog 2 (PRUNE2) gene was significantly associated with DMI, FCR, FE, and RFI (P < 0.05). Furthermore, we have identified a new transcript of PRUNE2 (TCONS_00027692, GenBank MZ041267) that was inversely correlated with FCR and FE (P < 0.05), in contrast to the originally identified PRUNE2 transcript. The cytochrome P450 subfamily 2B (CYP2B6), early growth response protein 1 (EGR1), collagen type I alpha 1 chain (COL1A1), and connective tissue growth factor (CTGF) genes were not associated with any feed efficiency-related traits (P > 0.05). The findings reported herein suggest that PRUNE2 expression levels affects feed efficiency-related traits variation in Nelore steers.

DNA methylation may affect beef tenderness through signal transduction in Bos indicus.

BACKGROUND: Beef tenderness is a complex trait of economic importance for the beef industry. Understanding the epigenetic mechanisms underlying this trait may help improve the accuracy of breeding programs. However, little is known about epigenetic effects on Bos taurus muscle and their implications in tenderness, and no studies have been conducted in Bos indicus. RESULTS: Comparing methylation profile of Bos indicus skeletal muscle with contrasting beef tenderness at 14 days after slaughter, we identified differentially methylated cytosines and regions associated with this trait. Interestingly, muscle that became tender beef had higher levels of hypermethylation compared to the tough group. Enrichment analysis of predicted target genes suggested that differences in methylation between tender and tough beef may affect signal transduction pathways, among which G protein signaling was a key pathway. In addition, different methylation levels were found associated with expression levels of GNAS, PDE4B, EPCAM and EBF3 genes. The differentially methylated elements correlated with EBF3 and GNAS genes overlapped CpG islands and regulatory elements. GNAS, a complex imprinted gene, has a key role on G protein signaling pathways. Moreover, both G protein signaling pathway and the EBF3 gene regulate muscle homeostasis, relaxation, and muscle cell-specificity. CONCLUSIONS: We present differentially methylated loci that may be of interest to decipher the epigenetic mechanisms affecting tenderness. Supported by the previous knowledge about regulatory elements and gene function, the methylation data suggests EBF3 and GNAS as potential candidate genes and G protein signaling as potential candidate pathway associated with beef tenderness via methylation.

High throughput analysis of MHC-I and MHC-DR diversity of Brazilian cattle populations.

The major histocompatibility complex (MHC) contains many genes that play key roles in initiating and regulating immune responses. This includes the polymorphic MHCI and MHCII genes that present epitopes to CD8+ and CD4+ T-cells, respectively. Consequently, the characterisation of the repertoire of MHC genes is an important component of improving our understanding of the genetic variation that determines the outcomes of immune responses. In cattle, MHC (BoLA) research has predominantly focused on Holstein-Friesian animals (as the most economically important breed globally), although the development of high-throughput approaches has allowed the BoLA-DRB3 repertoire to be studied in a greater variety of breeds. In a previous study we reported on the development of a MiSeq-based method to enable high-throughput and high-resolution analysis of bovine MHCI repertoires. Herein, we report on the expansion of this methodology to incorporate analysis of the BoLA-DRB3 and its application to analyse MHC diversity in a large cohort of cattle from Brazil (>500 animals), including representatives from the three major Bos indicus breeds present in Brazil - Guzerat, Gir and Nelore. This large-scale description of paired MHCI-DRB3 repertoires in Bos indicus cattle has identified a small number of novel DRB3 alleles, a large number of novel MHCI alleles and haplotypes, and provided novel insights into MHCI-MHCII association - further expanding our knowledge of bovine MHC diversity.

Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle.

MicroRNAs (miRNAs) are key regulators of gene expression, potentially affecting several biological processes, whose function can be altered by sequence variation. Hence, the integration of single nucleotide polymorphisms (SNP) and miRNAs can explain individual differences in economic traits. To provide new insights into the effects of SNPs on miRNAs and their related target genes, we carried out a multi-omic analysis to identify SNPs in miRNA mature sequences (miR-SNPs) associated with fatty acid (FA) composition in the Nelore cattle. As a result, we identified 3 miR-SNPs in different miRNAs (bta-miR-2419-3p, bta-miR-193a-2, and bta-miR-1291) significantly associated with FA traits (p-value < 0.02, Bonferroni corrected). Among these, the rs110817643C>T, located in the seed sequence of the bta-miR-1291, was associated with different ω6 FAs, polyunsaturated FA, and polyunsaturated:saturated FA ratios. Concerning the other two miR-SNPs, the rs43400521T>C (located in the bta-miR-2419-3p) was associated with C12:0 and C18:1 cis-11 FA, whereas the rs516857374A>G (located in the bta-miR-193a-2) was associated with C18:3 ω6 and ratio of ω6/ω3 traits. Additionally, to identify potential biomarkers for FA composition, we described target genes affected by these miR-SNPs at the mRNA or protein level. Our multi-omics analysis outlines the effects of genetic polymorphism on miRNA, and it highlights miR-SNPs and target candidate genes that control beef fatty acid composition.

Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes.

Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3'UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits.

Genomic regions and pathways associated with gastrointestinal parasites resistance in Santa Inês breed adapted to tropical climate.

BACKGROUND: The aim of this study was to estimate variance components and to identify genomic regions and pathways associated with resistance to gastrointestinal parasites, particularly Haemonchus contortus, in a breed of sheep adapted to tropical climate. Phenotypes evaluations were performed to verify resistance to gastrointestinal parasites, and were divided into two categories: i) farm phenotypes, assessing body condition score (BCS), degree of anemia assessed by the famacha chart (FAM), fur score (FS) and feces consistency (FC); and ii) lab phenotypes, comprising blood analyses for hematocrit (HCT), white blood cell count (WBC), red blood cell count (RBC), hemoglobin (HGB), platelets (PLT) and transformed (log10) egg per gram of feces (EPGlog). A total of 576 animals were genotyped with the Ovine SNP12k BeadChip (Illumina, Inc.), that contains 12,785 bialleleic SNP markers. The variance components were estimated using a single trait model by single step genomic BLUP procedure. RESULTS: The overall linkage disequilibrium (LD) mean between pairs of markers measured by r2 was 0.23. The overall LD mean between markers considering windows up to 10 Mb was 0.07. The mean LD between adjacent SNPs across autosomes ranged from 0.02 to 0.10. Heritability estimates were low for EPGlog (0.11), moderate for RBC (0.18), PLT (0.17) HCT (0.20), HGB (0.16) and WBC (0.22), and high for FAM (0.35). A total of 22, 21, 23, 20, 26, 25 and 23 windows for EPGlog for FAM, WBC, RBC, PLT, HCT and HGB traits were identified, respectively. Among the associated windows, 10 were shown to be common to HCT and HGB traits on OAR1, OAR2, OAR3, OAR5, OAR8 and OAR15. CONCLUSION: The traits indicating gastrointestinal parasites resistance presented an adequate genetic variability to respond to selection in Santa Inês breed, and it is expected a higher genetic gain for FAM trait when compared to the others. The level of LD estimated for markers separated by less than 1 Mb indicated that the Ovine SNP12k BeadChip might be a suitable tool for identifying genomic regions associated with traits related to gastrointestinal parasite resistance. Several candidate genes related to immune system development and activation, inflammatory response, regulation of lymphocytes and leukocytes proliferation were found. These genes may help in the selection of animals with higher resistance to parasites.

Avaliação da dor no período puerperal: estudo comparativo entre os tipos de parto / Evaluation of pain during postpartum: study comparing types of birth

Objetivo ­ Comparar a frequência, o local e a intensidade da dor referida pelas puérperas submetidas ao parto normal e à cesárea, e verificar as limitações das atividades diárias em função da algia. Métodos ­ Estudo descritivo, transversal, com abordagem quantitativa. Resultados ­ Desenvolvido com 424 mulheres assistidas em duas maternidades de São Paulo durante o período de setembro a dezembro de 2012. A dor foi referida por 71,3% das puérperas com parto normal e por 75,1% das que tiveram parto cesárea. A algia na região supra-púbica foi a mais citada (44%), seguida pela abdominal (29,4%), sem diferença estatisticamente significativa entre os tipos de parto. A dificuldade para sentar (72,6%) e andar (59,4%) foram as limitações mais referidas pelas puérperas. Conclusão ­ Conclui-se que a dor foi referida pela maioria das participantes, sem diferença estatisticamente significativa entre o parto normal e a cesárea, com predominância de limitações durante as atividades de sentar e andar.

Objective ­ To compare the frequency, location, and intensity of pain reported by women undergoing vaginal delivery and cesarean section, and check the activity limitations caused by this symptom. Methods ­ Descriptive, cross-sectional study with a quantitative approach. Results ­ Developed with 424 women seen at two hospitals of São Paulo during the period from September to December 2012. Pain was reported by 71.3% of postpartum women with vaginal delivery and 75.1% of who had cesarean delivery. A localized pain in the suprapubic region was the most frequently cited (44%) followed by abdominal (29.4%) with no statistically significant difference between the types of delivery. Difficulties to sit (72.6%) and to walk (59.4%) were the most common limitations related by women. Conclusions ­ It is concluded that most of the mothers interviewed reported experiencing pain in the postpartum period, regardless of the type of delivery, with a predominance of limitations during activities of sitting and walking.

Iron Content Affects Lipogenic Gene Expression in the Muscle of Nelore Beef Cattle.

Iron (Fe) is an essential mineral for metabolism and plays a central role in a range of biochemical processes. Therefore, this study aimed to identify differentially expressed (DE) genes and metabolic pathways in Longissimus dorsi (LD) muscle from cattle with divergent iron content, as well as to investigate the likely role of these DE genes in biological processes underlying beef quality parameters. Samples for RNA extraction for sequencing and iron, copper, manganese, and zinc determination were collected from LD muscles at slaughter. Eight Nelore steers, with extreme genomic estimated breeding values for iron content (Fe-GEBV), were selected from a reference population of 373 animals. From the 49 annotated DE genes (FDR<0.05) found between the two groups, 18 were up-regulated and 31 down-regulated for the animals in the low Fe-GEBV group. The functional enrichment analyses identified several biological processes, such as lipid transport and metabolism, and cell growth. Lipid metabolism was the main pathway observed in the analysis of metabolic and canonical signaling pathways for the genes identified as DE, including the genes FASN, FABP4, and THRSP, which are functional candidates for beef quality, suggesting reduced lipogenic activities with lower iron content. Our results indicate metabolic pathways that are partially influenced by iron, contributing to a better understanding of its participation in skeletal muscle physiology.

Perfil obstétrico e neonatal de puérperas atendidas em maternidades de São Paulo / Perfil obstétrico y neonatal de madres atendidas en maternidades en São Paulo / The obstetrical and newborn profile of postpartum women in maternities in São Paulo

Objective: To describe the sociodemographic and obstetric profile of postpartum women in São Paulo, to check the perinatal data and to identify the type of delivery. Method: A descriptive, cross-sectional study involving 424 postpartum women. Data was collected through structured interviews and medical records. We used descriptive statistics for analysis. Results: There was a predominance of women between 21 and 30 years (60.6%), mulatto (55.2%), high school education (65.8%), without payment (57.3%), with a partner( 85.4%), primiparous (34.9%) and without previous abortion (78.8%). The vaginal delivery was performed in 58.3% of women. Most newborns were male (52.2%), with appropriate weight and height (89.5% and 80.7%), and na Apgar score between eight and ten in the first minutes of life (> 90.0 %). Conclusion: There was a predominance of women with little education and unfavorable financial conditions, factors that hinder access to health services, contributing to increased maternal and neonatal morbidity and mortality...

Objetivo: Descrever o perfil sociodemográfico e obstétrico das puérperas atendidas em São Paulo, verificar os dados perinatais e identificar o tipo de parto realizado. Método: Estudo descritivo, transversal,realizado com 424 puérperas. Os dados foram obtidos por meio de entrevista estruturada e dos prontuários. Utilizou-se a estatística descritiva para a análise. Resultados: Constatou-se predomínio de mulheres entre 21 e 30 anos (60,6%), cor parda (55,2%), ensino médio (65,8%), sem remuneração (57,3%),com companheiro (85,4%), primíparas (34,9%) e sem aborto anterior (78,8%). O parto normal foi realizado em 58,3% das mulheres. A maioria dos recém-nascidos era do sexo masculino (52,2%), com peso e estatura adequados (89,5% e 80,7%), e Apgar entre oito e dez nos primeiros minutos de vida (>90,0%). Conclusão: Houve predomínio de mulheres com pouca escolaridade e condições financeiras desfavoráveis, fatores que dificultam o acesso aos serviços de saúde, contribuindo para o aumento da morbimortalidade materna e neonatal...

Objetivo: Describir el perfil sociodemográfico y obstétrico de mujeres recién paridas en São Paulo, comprobar los datos perinatales e identificar el tipo de parto. Método: Estudio descriptivo, transversal,que involucra 424 mujeres en el posparto. Los datos fueron recolectados a través de entrevistas estructuradas y registros médicos. Se utilizó estadística descriptiva para analizar. Resultados: Hubo un predominio de las mujeres entre 21 y 30 años (60,6%), mulatos (55,2%), de la escuela secundaria (65,8%),sin pago (57,3%), con un compañero (85,4%), primíparas (34,9%) y sin aborto anterior (78,8%). El parto vaginal se realizó en el 58,3% de las mujeres. La mayoría de los recién nacidos eran varones (52,2%), conpeso y la altura adecuado (89,5% y 80,7%), y la puntuación de Apgar entre ocho y diez en los primeros minutos de vida (> 90,0 %). Conclusión: Se observó un predominio de mujeres con poca educación y las condiciones financieras desfavorables, factores que dificultan el acceso a los servicios de salud, contribuyendo al aumento de la morbilidad y mortalidad materna y neonatal...