Recent genetic advances on boar taint reduction as an alternative to castration: a review.

peer reviewe

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase 1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age  6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score  652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc = 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N = 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in Asia and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Caracterização do consumo alimentar residual em bovinos Nelore através de expressão gênica, do perfil lipodômico e meta-análises para vias metabólicas

Increase in feed efficiency result in decrease in feed costs. Thus, to improve profitability in beef cattle production system is necessary to select animals more efficient in the use of feed sources. The residual feed intake (RFI) has become the preferable measure for feed efficiency, once that RFI is not correlated with growth rate or other production trait. Researchers have demonstrated that many physiological mechanisms contribute to variation in RFI, among them are protein turnover, tissue metabolism, synthesis and transportation of fatty acid, inflammatory response, glucose absorption and fatty acid oxidation. Even so, the molecular bases controlling this trait are not well elucidate yet. Thus, we aimed to investigate the biological bases that could be responsible for differences in animals classified for RFI. For that, we performed a pathway meta-analysis approach using several genome association studies results to search for significant pathways that may explain the genetic mechanism underlying this trait. We used an efficient permutation hypothesis test that takes into account the linkage disequilibrium patterns between SNPs. One significant pathway (valine, leucine and isoleucine degradation) related to RFI was found. This pathway is related to protein turnover and gluconeogenic process. In addition, we evaluated samples from muscle and liver tissue of 27 Nellore steers, classified as high, medium and low RFI. The samples were used to evaluate the mRNA expression of genes involved in the lipid metabolism and to carry out lipidomic analysis. None significant differences in mRNA expression were found. In the lipidomic analysis, it was found that animals from the high RFI group exhibited higher levels of fatty acids and triglycerides compared to medium and low RFI animals, indicating a possible increase in the requirement of lipid energy sources in the low RFI animals and also an increase in fat deposition in high RFI animals. In addition, it was observed differences in the lipid main components of cell membrane, which are related with cell signaling and molecules transportation. These results suggest that difference in RFI is associated with changes in lipid metabolism, but these changes are not caused by differences in the mRNA expression of the genes involved in this metabolism.O aumento na eficiência alimentar resulta em diminuição no custo de alimentação. Assim, para melhorar a rentabilidade do sistema de produção de bovinos é necessário selecionar animais com maior eficiência alimentar. O consumo alimentar residual (CAR) tornou-se a medida preferencial para eficiência alimentar, uma vez que o CAR não está correlacionado com a taxa de crescimento. Pesquisadores demonstraram que muitos mecanismos fisiológicos contribuem para a variação do CAR, entre eles a o turnover proteico, metabolismo dos tecidos, síntese e transporte de ácidos graxos, resposta inflamatória, absorção de glicose e oxidação de ácidos graxos. Mesmo assim, as bases moleculares que controlam essa característica ainda não estão bem elucidadas. Assim, objetivamos investigar as bases biológicas que poderiam ser responsáveis por diferenças na classificação de animais quanto ao CAR. Para isso, realizamos uma meta-análise para vias metabólicas usando vários resultados de estudos de associação genômica com o intuito de procurar vias que possam explicar o mecanismo de controle dessa característica. Uma via significativa (degradação de valina, leucina e isoleucina) relacionada ao CAR foi encontrada. Esta via está relacionada ao turnover proteico e a gliconeogênese. Além disso, foram avaliadas amostras de tecido muscular e hepático de 27 novilhos da raça Nelore, classificadas como alto, médio e baixo CAR. As amostras foram utilizadas para avaliar a expressão de mRNA de genes envolvidos no metabolismo lipídico e para realizar análises lipidômicas. Não foram encontradas diferenças significativas na expressão de mRNA. Na análise lipidômica, verificou-se que os animais do grupo alto CAR apresentaram maiores níveis de ácidos graxos e triglicerídeos em comparação aos animais de médio e baixo CAR, indicando um possível aumento no uso de fontes de energia lipídica nos animais de baixo CAR e um aumento na deposição de lipídeos nos animais de alto CAR. Além disso, foram observadas diferenças nos principais componentes lipídicos da membrana celular, que estão relacionados com a sinalização celular e com o transporte de moléculas. Estes resultados sugerem que a diferença no CAR está associada a alterações no metabolismo lipídico, porém essas alterações não são causadas por diferenças na expressão de mRNA dos genes envolvidos neste metabolismo.Conselho Nacional de Desenvolvimento Científico e Tecnológic

Validação estudos de associação genômica para qualidade de carne e características de carcaça em suínos através de redes gênicas e meta-análise

A large number of quantitative trait loci (QTLs) for meat quality and carcass traits has been identified in several studies, but the genetic architecture remains poorly understood. Thus, a methodology that allows study genes and pathways that affect these traits would offers many advantages and increase the knowledge of physiological mechanisms. With this purpose, a methodology named Association Weight Matrix (AWM) was used to investigate the genetic basis of these traits and generate gene network based on the co-association of pair-wise SNPs across phenotypes. We performed genome association studies for 12 traits and 144 SNPs was found to be significant. A meta-analysis was performed to validate the results obtained in the genome association study in this present study. Some significant SNPs found in the genome association studies of this work are close to QTLs findings in the studies from meta-analysis. Therefore the results from meta-analysis corroborated those of the genome association studies of the present work. The significant SNPs from genome association studies were selected to build the AWM. Through this methodology, we could found 45 genes, these genes were used to build a gene network based on pairwise correlations between them. Besides, we identified 25 transcription factors (TF) strongly related (p-value<0.001) with genes in the network. The top three TF (Sox5, Nkx2- 5 and T) were choosing for construction of a network with their pathways and gene ontology. The genes from network and associated with this TF were involved in metabolism of adipose tissue and skeletal muscle. Our results suggest that genes and TF identified here are important in the control of meat quality and carcass traits. However, further efforts should be made in order to study in more detail the new gene-gene interactions here identified, as well as, the key transcription factors and pathways involved in these traits.Um grande número de locus de características quantitativas (QTLs) para qualidade de carne e carcaça tem sido identificado em diversos estudos, mas a arquitetura genética envolvida nessas características ainda é pouco compreendida. Dessa forma, uma metodologia que permite estudar genes e vias que afetam essas características oferece vantagens e aumenta o conhecimento dos mecanismos fisiológicos. Com esta finalidade, uma metodologia chamada Matriz de Pesos de Associação (AWM) foi utilizado para investigar a base genética dessas características e gerar redes gênicas com base na co- associação de pares de SNPs através dos fenótipos. Foi realizado estudos de associação genômica para 12 características e 144 SNPs foram significativos. Uma meta-análise foi realizada para validar os resultados obtidos no estudo de associação genômica do presente estudo. Alguns SNPs significativos encontrados nos estudos de associação genômica deste trabalho estão perto de QTLs achados nos estudos usados na meta-análise. Portanto, os resultados da meta-análise corroboram os resultados do estudo de associação genômica do presente trabalho. Os SNPs considerados significativos nos estudos de associação genômica foram selecionados para a construção da AWM. Através dessa metodologia, foi possível encontrar 45 genes e estes foram usados para a construção de uma rede com base na correlação entre eles. Além disso, foram identificados 25 fatores de transcrição (FT) fortemente relacionados (p <0,001) com os genes dessa rede. Os três top FT (Sox5, NKX2-5 e T) foram escolhidos para a construção de uma rede com suas vias e ontologia gênica. Os genes da rede e associado com os FT estão envolvidos no metabolismo do tecido adiposo e do músculo esquelético. Nossos resultados sugerem que os genes e FT identificados aqui são importantes no controle de características de qualidade de carne e carcaça. No entanto, esforços devem ser feitos a fim de estudar mais detalhadamente as novas interações gene-gene aqui identificados, bem como, os fatores de transcrição chave e vias envolvidas nestas características.Fundação de Amparo à Pesquisa do Estado de Minas Gerai

Genome-wide association studies pathway-based meta-analysis forresidual feed intake in beef cattle

Genome-wide association studies (GWASes) have been performed to search for genomicregions associated with residual feed intake (RFI); however inconsistent results have beenobtained. A meta-analysis may improve these results by decreasing the false-positive rate.Additionally, pathway analysis is a powerful tool that complements GWASes, as it enablesidentification of gene sets involved in the same pathway that explain the studied phenotype.Because there are no reports on GWAS pathways-based meta-analyses for RFI in beef cattle,we used several GWAS results to search for significant pathways that may explain thegenetic mechanism underlying this trait. We used an efficient permutation hypothesis testthat takes into account the linkage disequilibrium patterns between SNPs and thefunctional feasibility of the identified genes over the whole genome. One significant pathway(valine, leucine and isoleucine degradation) related to RFI was found. The three genes inthis pathway—methylcrotonoyl-CoA carboxylase 1(MCCC1), aldehyde oxidase 1(AOX1) andpropionyl-CoA carboxylase alpha subunit(PCCA)—were found in three different studies. Thissame pathway was also reported in a transcriptome analysis from two cattle populationsdivergently selected for high and low RFI. We conclude that a GWAS pathway-based meta-analysis can be an appropriate method to uncover biological insights into RFI by combininguseful information from different studies

Desenvolvimento do portal NUFENA (Núcleo de Fenômica Animal)

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Isotonic regression analysis of Guzerá cattle growth curves

The objective of this study was to apply data transformation via isotonic regression in growth curves studies of Guzerá cattle whose data presented disturbances characterized by decreased body weight in certain age groups. Weightage data were collected on newly weaned Guzerá males according to the methodology of weight gain tests (WGT) defined by the Brazilian Association of Zebu Breeders (ABCZ). The Logistic, Von Bertalanffy and Gompertz models were fitted to weight-age data using the generalized least squares method for non-linear regression models through the Gauss-Newton algorithm. The proposed transformation based on isotonic regression theory proved to be efficient; and the Logistic model was the best to describe the growth of animals, with a high percentage of convergence (100%) and goodness of fit assessed by the mean squared error (MSE) and the coefficient of determination (R2)