Caracterização da comunidade microbiana de solo coberto por pastagem e de fragmento de floresta através de análise metagenômica.

A degradação de pastagens é um problema mundial. No Brasil, esse problema afeta a sustentabilidade da pecuária. Em São Paulo, estima-se que em torno de 9.800.000 ha sejam ocupados pela pecuária, principalmente no oeste do estado. O mercado tem exigido a aplicação de técnicas sustentáveis de manejo e a mitigação de pastagens degradadas. Para a avaliação da qualidade de um solo, discute-se a necessidade de identificação de parâmetros de seu estado de conservação ou degradação. Neste caso, a diversidade microbiana tem sido utilizada como um desses parâmetros. O objetivo do presente estudo foi avaliar a diversidade taxonômica e funcional da comunidade microbiana presente em uma propriedade agrícola localizada no oeste do Estado de São Paulo. Para tanto, amostras de solo foram coletadas aleatoriamente em 10 pontos, na profundidade de 0-5 cm, em duas áreas da propriedade: (a) pasto coberto por Brachiaria e (b) fragmento de floresta. As amostras foram homogeneizadas e o DNA metagenômico foi extraído com o Power Max Soil kit. A qualidade e quantidade de DNA extraído foram avaliadas através de eletroforese em gel de agarose 0,8% e espectrofotometria. O DNA metagenômico obtido foi utilizado na construção de bibliotecas que foram sequenciadas na plataforma GS FLX Roche 454. As sequências foram comparadas ao banco de dados do NCBI e os ?top hits? utilizados em análises com o software MEGAN para analisar a diversidade taxonômica. Para analisar as potencias funções metabólicas foi utilizado o banco de dados SEED. Os resultados obtidos demonstraram que, no domínio Bacteria, os filos Proteobacteria, Fibrobacter/Acidobacteria e Actinobacteria são predominantes nas duas áreas, sendo que na área de pastagem degradada esses grupos foram observados em um maior número de reads. Com relação às categorias funcionais, os genes relacionados à virulência e metabolismo de carboidratos são os mais abundantes nas duas áreas, seguido por metabolismo de aminoácidos, proteínas e DNA. Os dados obtidos permitem sugerir que, o aumento da diversidade, principalmente de proteobactérias, nas áreas degradadas suscita discussão ampla sobre a qualidade dos solos, em relação aos micro-organismos necessários para fechamento dos ciclos biogeoquímicos para manutenção de altos níveis produtivos, além do incremento de micro-organismos de interesse clínico humano-veterinário. Apoio: MAPASTORE, CNPq, FAPER

Detection of co-expressed pathway modules associated with mineral concentration and meat quality in nelore cattle

Meat quality is a complex trait that is influenced by genetic and environmental factors, which includes mineral concentration. However, the association between mineral concentration and meat quality, and the specific molecular pathways underlying this association, are not well explored. We therefore analyzed gene expression as measured with RNA-seq in Longissimus thoracis muscle of 194 Nelore steers for association with three meat quality traits (intramuscular fat, meat pH, and tenderness) and the concentration of 13 minerals (Ca, Cr, Co, Cu, Fe, K, Mg, Mn, Na, P, S, Se, and Zn). We identified seven sets of co-expressed genes (modules) associated with at least two traits, which indicates that common pathways influence these traits. From pathway analysis of module hub genes, we further found an over-representation for energy and protein metabolism (AMPK and mTOR signaling pathways) in addition to muscle growth, and protein turnover pathways. Among the identified hub genes FASN, ELOV5, and PDE3B are involved with lipid metabolism and were affected by previously identified eQTLs associated to fat deposition. The reported hub genes and over-represented pathways provide evidence of interplay among gene expression, mineral concentration, and meat quality traits. Future studies investigating the effect of different levels of mineral supplementation in the gene expression and meat quality traits could help us to elucidate the regulatory mechanism by which the genes/pathways are affected

Allele specific expression analysis in bovine muscle tissue.

Imprinted genes have been target of many studies, mainly in human and mouse, and lately in bovines due to the interest of understanding the epigenetic mechanisms underlying important meat quality phenotypes and the possibility of applying it in animal breeding programs in the future. Genomic DNA from 146 steers was genotyped using the Illumina BovineHD BeadChip in order to identify heterozygous individuals with known allele origin.ISMB/ECCB 2015. Pôster D17

Allele specific expression analysis in bovine muscle tissue.

Imprinted genes have been target of many studies, mainly in human and mouse, and lately in bovines due to the interest of understanding the epigenetic mechanisms underlying important meat quality phenotypes and the possibility of applying it in animal breeding programs in the future. Genomic DNA from 146 steers was genotyped using the Illumina BovineHD BeadChip in order to identify heterozygous individuals with known allele origin.X-meeting 2015

Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake.

Residual feed intake (RFI), a measure of feed efficiency (FE), is defined as the difference between the observed and the predictable feed intake considering size and growth of the animal. It is extremely important to beef production systems due to its impact on the allocation of land areas to alternative agricultural production, animal methane emissions, food demand and cost of production. Global differential gene expression analysis between high and low RFI groups (HRFI and LRFI: less and more efficient, respectively) revealed 73 differentially expressed (DE) annotated genes in Longissimus thoracis (LT) muscle of Nelore steers. These genes are involved in the overrepresented pathways Metabolism of Xenobiotics by Cytochrome P450 and Butanoate and Tryptophan Metabolism. Among the DE transcripts were several proteins related to mitochondrial function and the metabolism of lipids. Our findings indicate that observed gene expression differences are primarily related to metabolic processes underlying oxidative stress. Genes involved in the metabolism of xenobiotics and antioxidant mechanisms were primarily down-regulated, while genes responsible for lipid oxidation and ketogenesis were up-regulated in HRFI group. By using LT muscle, this study reinforces our previous findings using liver tissue and reveals new genes and likely tissue-specific regulators playing key-roles in these processes

A single nucleotide polymorphism in NEUROD1 is associated with production traits in nelore beef cattle.

Feed efficiency and carcass characteristics are late-measured traits. The detection of molecular markers associated with them can help breeding programs to select animals early in life, and to predict breeding values with high accuracy. The objective of this study was to identify polymorphisms in the functional and positional candidate gene NEUROD1 (neurogenic differentiation 1), and investigate their associations with production traits in reference families of Nelore cattle. A total of 585 steers were used, from 34 sires chosen to represent the variability of this breed. By sequencing 14 animals with extreme residual feed intake (RFI) values, seven single nucleotide polymorphisms (SNPs) in NEUROD1 were identified. The investigation of marker effects on the target traits RFI, backfat thickness (BFT), ribeye area (REA), average body weight (ABW), and metabolic body weight (MBW) was performed with a mixed model using the restricted maximum likelihood method. SNP1062, which changes cytosine for guanine, had no significant association with RFI or REA. However, we found an additive effect on ABW (P ≤ 0.05) and MBW (P ≤ 0.05), with an estimated allele substitution effect of -1.59 and -0.93 kg0.75, respectively. A dominant effect of this SNP for BFT was also found (P ≤ 0.010). Our results are the first that identify NEUROD1 as a candidate that affects BFT, ABW, and MBW. Once confirmed, the inclusion of this SNP in dense panels may improve the accuracy of genomic selection for these traits in Nelore beef cattle as this SNP is not currently represented on SNP chips

Genetic regulators of mineral amount in Nelore cattle muscle predicted by a new co-expression and regulatory impact factor approach.

Mineral contents in bovine muscle can affect meat quality, growth, health, and reproductive traits. To better understand the genetic basis of this phenotype in Nelore (Bos indicus) cattle, we analysed genome-wide mRNA and miRNA expression data from 114 muscle samples. The analysis implemented a new application for two complementary algorithms: the partial correlation and information theory (PCIT) and the regulatory impact factor (RIF), in which we included the estimated genomic breeding values (GEBVs) for the phenotypes additionally to the expression levels, originally proposed for these methods. We used PCIT to determine putative regulatory relationships based on significant associations between gene expression and GEBVs for each mineral amount. Then, RIF was adopted to determine the regulatory impact of genes and miRNAs expression over the GEBVs for the mineral amounts. We also investigated over-represented pathways, as well as pieces of evidences from previous studies carried in the same population and in the literature, to determine regulatory genes for the mineral amounts. For example, NOX1 expression level was positively correlated to Zinc and has been described as Zinc-regulated in humans. Based on our approach, we were able to identify genes, miRNAs and pathways not yet described as underlying mineral amount. The results support the hypothesis that extracellular matrix interactions are the core regulator of mineral amount in muscle cells. Putative regulators described here add information to this hypothesis, expanding the knowledge on molecular relationships between gene expression and minerals.Article: 8436

Inequities in maternal postnatal visits among public and private patients: 2004 Pelotas cohort study

<p>Abstract</p> <p>Background</p> <p>The postnatal period is the ideal time to deliver interventions to improve the health of both the newborn and the mother. However, postnatal care shows low-level coverage in a large number of countries. The objectives of this study were to: 1) investigate inequities in maternal postnatal visits, 2) examine differences in postnatal care coverage between public and private providers and 3) explore the relationship between the absence of maternal postnatal visits and exclusive breastfeeding, use of contraceptive methods and maternal smoking three months after birth.</p> <p>Methods</p> <p>In the calendar year of 2004 a birth cohort study was started in the city of Pelotas, Brazil. Mothers were interviewed soon after delivery and at three months after birth. The absence of postnatal visits was defined as having no consultations between the time of hospital discharge and the third month post-partum. Logistic regression analysis was used to estimate the association between absence of postnatal visits and type of insurance scheme adjusting for potential confounding factors.</p> <p>Results</p> <p>Poorer women, black/mixed, those with lower level of education, single mothers, adolescents, multiparae, smokers, women who delivered vaginally and those who were not assisted by a physician were less likely to attend postnatal care. Postnatal visits were also less frequent among women who relied in the public sector than among private patients (72.4% vs 96% among public and private patients, respectively, <it>x</it>²p < 0.001) and this difference was not explained either by maternal characteristics or by health care utilization patterns. Women who attended postnatal visits were more likely to exclusively breastfeed their infants, to use contraceptive methods and to be non-smokers three months after birth.</p> <p>Conclusion</p> <p>Postpartum care is available for every woman free of charge in the Brazilian Publicly-funded health care system. However, low levels of postpartum care were seen in the study (77%). Efforts should be made to increase the percentage of women receiving postpartum care, particularly those in socially disadvantaged groups. This could include locally-adapted health education interventions that address women's beliefs and attitudes towards postpartum care. There is a need to monitor postpartum care and collected data should be used to guide policies for health care systems.</p