Age and microenvironment outweigh genetic influence on the Zucker rat microbiome

Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed; we investigated the role of experimental design on one such rodent model. We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6) and lean (homozygous n = 6; heterozygous n = 6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance, but large differences seen between cages. Importantly, the genetically induced obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than the host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?

Effects of agricultural management practices on earthworm populations and crop yield: validation and application of a mechanistic modelling approach

There is little consensus on how agriculture will meet future food demands sustainably. Soils and their biota play a crucial role by mediating ecosystem services that support agricultural productivity. However, a multitude of site-specific environmental factors and management practices interact to affect the ability of soil biota to perform vital functions, confounding the interpretation of results from experimental approaches. Insights can be gained through models, which integrate the physiological, biological and ecological mechanisms underpinning soil functions. We present a powerful modelling approach for predicting how agricultural management practices (pesticide applications and tillage) affect soil functioning through earthworm populations. By combining energy budgets and individual-based simulation models, and integrating key behavioural and ecological drivers, we accurately predict population responses to pesticide applications in different climatic conditions. We use the model to analyse the ecological consequences of different weed management practices. Our results demonstrate that an important link between agricultural management (herbicide applications and zero, reduced and conventional tillage) and earthworms is the maintenance of soil organic matter (SOM). We show how zero and reduced tillage practices can increase crop yields while preserving natural ecosystem functions. This demonstrates how management practices which aim to sustain agricultural productivity should account for their effects on earthworm populations, as their proliferation stimulates agricultural productivity. Synthesis and applications. Our results indicate that conventional tillage practices have longer term effects on soil biota than pesticide control, if the pesticide has a short dissipation time. The risk of earthworm populations becoming exposed to toxic pesticides will be reduced under dry soil conditions. Similarly, an increase in soil organic matter could increase the recovery rate of earthworm populations. However, effects are not necessarily additive and the impact of different management practices on earthworms depends on their timing and the prevailing environmental conditions. Our model can be used to determine which combinations of crop management practices and climatic conditions pose least overall risk to earthworm populations. Linking our model mechanistically to crop yield models would aid the optimization of crop management systems by exploring the trade-off between different ecosystem services.

Multivariate measurement error models based on scale mixtures of the skew-normal distribution

Scale mixtures of the skew-normal (SMSN) distribution is a class of asymmetric thick-tailed distributions that includes the skew-normal (SN) distribution as a special case. The main advantage of these classes of distributions is that they are easy to simulate and have a nice hierarchical representation facilitating easy implementation of the expectation-maximization algorithm for the maximum-likelihood estimation. In this paper, we assume an SMSN distribution for the unobserved value of the covariates and a symmetric scale mixtures of the normal distribution for the error term of the model. This provides a robust alternative to parameter estimation in multivariate measurement error models. Specific distributions examined include univariate and multivariate versions of the SN, skew-t, skew-slash and skew-contaminated normal distributions. The results and methods are applied to a real data set.

Environmental Objectives, Cost Efficiency, and Multivariate Stochastic Control

This paper is concerned with the cost efficiency in achieving the Swedish national air quality objectives under uncertainty. To realize an ecologically sustainable society, the parliament has approved a set of interim and long-term pollution reduction targets. However, there are considerable quantification uncertainties on the effectiveness of the proposed pollution reduction measures. In this paper, we develop a multivariate stochastic control framework to deal with the cost efficiency problem with multiple pollutants. Based on the cost and technological data collected by several national authorities, we explore the implications of alternative probabilistic constraints. It is found that a composite probabilistic constraint induces considerably lower abatement cost than separable probabilistic restrictions. The trend is reinforced by the presence of positive correlations between reductions in the multiple pollutants.

Output convergence in Mercosur: multivariate time series evidence

The aim of this paper is to provide evidence on output convergence among the Mercosur countries and associates, using multivariate time-series tests. The methodology is based on a combination of tests and estimation procedures, both univariate and multivariate, applied to the differences in per capita real income. We use the definitions of time-series convergence proposed by Bernard & Durlauf and apply unit root and tests proposed by Abuaf & Jorion and Taylor & Sarno. In this same multivariate context, the Flôres, Preumont & Szafarz and Breuer, MbNown & Wallace tests, which allow for the existence of correlations across the series without imposing a common speed of mean reversion, identify the countries that convergence. Concerning the empirical results, there is evidence of long-run convergence or, at least, catching up, for the smaller countries, Bolivia, Paraguay, Peru and Uruguay, towards Brazil and, to some extent, Argentina. In contrast, the evidence on convergence for the larger countries is weaker, as they have followed different (or rather opposing) macroeconomic policy strategies. Thus the future of the whole area will critically depend on the ability of Brazil, Argentina and Chile to find some scope for more cooperative policy actions.

Crop sequences in no-tillage system: effects on soil fertility and soybean, maize and rice yield

Os resíduos vegetais das culturas, ao se decomporem, alteram os atributos químicos do solo e, como consequência, influenciam a produtividade das culturas em sucessão. O objetivo deste trabalho foi avaliar os atributos químicos do solo e a produtividade das culturas de soja, milho e arroz, cultivadas no verão, em sucessão a culturas de inverno em semeadura direta. O experimento foi realizado em Jaboticabal-SP (48 ° 18 ' 58 '' W e 21 ° 15 ' 22 '' S), em um Latossolo Vermelho eutrófico. O delineamento experimental foi em blocos ao acaso, no esquema em faixas, com três repetições. Os tratamentos foram constituídos pela combinação de quatro sequências de culturas de verão (monoculturas de milho e soja e rotações soja/milho e arroz/feijão/algodão) com sete culturas de inverno (milho, girassol, nabo forrageiro, milheto, guandu, sorgo e crotalária). Os cultivos iniciaram-se em 2002. Após o manejo das culturas de inverno e antes da semeadura das culturas de verão do ano agrícola 2006/2007, foram coletadas amostras de solo nas camadas de 0-2,5; 2,5-5,0; 5-10; 10-20; e 20-30 cm. Nas amostras de solo, foram determinados: teores de matéria orgânica, pH, teores de P (resina), K, Ca e Mg trocáveis e acidez potencial (H + Al). As sequências de verão rotação soja/milho e milho em monocultura proporcionaram no solo menores teores de matéria orgânica na camada de 0-10 cm e de P do solo na camada de 0-20 cm. Na sequência de verão arroz/feijão/algodão, maiores teores de K foram proporcionados pelas culturas de inverno crotalária e nabo forrageiro, na camada de 0-10 cm, e milheto, na de 0-2,5 cm. Crotalária, milheto, nabo forrageiro e sorgo, cultivados no inverno, proporcionaram maiores teores de matéria orgânica no solo na camada de 0-30 cm. Maiores teores de P no solo foram proporcionados pela crotalária, na camada de 0-2,5 cm, e pelo nabo forrageiro, na de 0-5 cm. Maiores produtividades de soja, como monocultura de verão, foram obtidas após nabo forrageiro e crotalária e, quando em rotação com milho no verão, após nabo forrageiro, crotalária e milheto. Maiores produtividades de milho foram obtidas após nabo forrageiro, milheto e guandu, e menor produtividade de arroz foi obtida após sorgo.

Spatial relationships between soil attributes and corn yield in no-tillage system

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Soil sampling intensity and spatial distribution pattern of soils attributes and corn yield in no-tillage system

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effects of energy level in finisher diets and slaughter age of on the performance and carcass yield in broiler chickens

Male broilers were used to evaluate the effects of different energy levels in finisher diets and age of slaughter on performance, production pattern and carcass yield. Experimental design was a 2x3 factorial arrangement: energy level (ME) in the finisher diet (3,200 and 3,600 kcal ME/kg) and age of slaughter (42, 49 and 56 days), resulting in six treatments with four replicates. The finisher diet was fed only in the last week of the growing period. Characteristics evaluated were feed consumption (FC), body weight gain (WG), feed conversion (FC), energy intake (EI), caloric conversion (CC), efficiency production index, production pattern, and carcass yield. The results showed better WG and CC for broilers fed 3,200 kcal ME/kg finisher diet. Broilers slaughtered at 42 and 49 days of age had better performance and higher annual production than broilers slaughtered at 56 days of age. Carcass yield was influenced by slaughter age and better breast yield was seen at 49 and 56 days than at 42 days of age. It was concluded that 3,200 kcal ME/kg induced the best overall performance. Poultry houses were efficiently used when broilers were slaughtered at 42 days of age. Meat:bone ratio was improved for broilers slaughtered at 49 and 56 days of age.

Different timing of whitefly control and soybean yield

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Antimicrobial use and incidence of multidrug-resistant Pseudomonas aeruginosa in a teaching hospital: an ecological approach

Introduction: Multidrug-resistant Pseudomonas aeruginosa is a major threat in healthcare settings. The use of antimicrobials can influence the incidence of resistant strains by direct and indirect mechanisms. The latter can be addressed by ecological studies. Methods: Our group attempted to analyze the relation between the use of antipseudomonal drugs and the incidence of MDR-PA among 18 units from a 400-bed teaching hospital. The study had a retrospective, ecological design, comprising data from 2004 and 2005. Data on the use of four antimicrobials (amikacin, ciprofloxacin, ceftazidime and imipenem) were tested for correlation with the incidence of MDR-PA (defined as isolates resistant to the four antimicrobials of interest) in clinical cultures. Univariate and multivariate linear regression analyses were performed. Results: Significant correlations were determined between use and resistance for all antimicrobials in the univariate analysis: amikacin (standardized correlation coefficient = 0.73, p = 0.001); ciprofloxacin (0.71, p = 0.001); ceftazidime (0.61, p = 0.007) and imipenem (0.87, p < 0.001). In multivariate analysis, only imipenem (0.67, p = 0.01) was independently related to the incidence of multidrug-resistant strains. Conclusions: These findings share similarities with those reported in individual-based observational studies, with possible implications for infection control.

Trends and patterns of exclusive breastfeeding for under-6-month-old children

Objective: To study the trends and patterns of exclusive breastfeeding (EBF) for under-6-month-old infants in the city of Bauru, southeastern Brazil.Methods: We compared data from three cross-sectional surveys, using similar methodologies, which were part of a project for monitoring breastfeeding indicators in the state of São Paulo, Brazil. The sample included infants aged 0 to 6 months who attended one of the two rounds of the nationwide infant vaccination campaign in 1999, 2003 and 2006 (respectively: 496, 674 and 509 infants). Descriptive statistics were used to compare the prevalence of EBF according to age (in months) and group of children under 6 months of age. Differences in prevalence were expressed as percentage-points and submitted to statistical analysis (Pearson's chi-square and tendency), and the level of significance was set at p < 0.05. Factors associated with EBF interruption in 2006 were evaluated by univariate and multivariate analyses.Results: An increase in the prevalence of EBF was observed in under-6-month-old infants: 1999-2003, increase of 9.1 percentage-points; 2003-2006, increase of 6.6 percentage-points, resulting in an annual increase rate of 2.3 percentage-points for the first period and 2.2 percentage-points for the second period. Significant inverse association was observed between EBF and the use of pacifiers (prevalence ratio = 2.03; 95% confidence interval 1.44-2.84).Conclusion: EBF prevalence in under-6-month-old infants in the city of Bauru, southeastern Brazil, increased almost threefold over the period studied, from 8.5% in 1999 to 24.2% in 2006, a total increase of 184.7%. The use of pacifiers was the only factor strongly associated with the interruption of EBF.

Effect of nucleotides on broiler performance and carcass yield

This study aimed at evaluating the effect of nucleotides on the performance and carcass yield of broilers fed diets with no antibiotic growth promoters (AGP), anticoccidials, or animal feedstuffs. In the trial, 600 Ross 308 male broilers were distributed in a completely randomized experimental design into six treatments with four replicates of 25 birds each. Treatments consisted of a control diet (CD), CD + AGP, CD + 0.04%, CD + 0.05%, CD + 0.06%, and CD + 0.07% nucleotides. The experimental diets did not contain anticoccidials, and birds were vaccinated against coccidiosis at three days of age. No significant differences were detected among broilers submitted to the different treatments in none of the studied parameters. Under the conditions of this experiment, diets supplemented with nucleotides did not influence broiler performance or carcass yield at 42 days of age, and were not different from the feeds not containing any additive or with AGP.

Relationship between udder measurements and milk yield in Bergamasca ewes in Brazil

The present work aimed to evaluate udders of Bergamasca ewes and their correlation with milk yield in a mix system of milk yield. Seventy-seven ewes were fed with balanced concentrate starting 20 days before lambing until the end of the experiment. The lambs stayed with their mothers in pastures during the day and were separated at night. They returned to their mothers after the morning milking and were weaned at 45 days of age. Forty-eight hours after lambing, ewes were machine milked once daily at 7 am and the milk yield was recorded for a period of 60 days. Measurements of circumference, depth and width of the udder, and width and length of teats, at 30 and 60 days, were taken. A higher average daily yield of commercial milk was observed after lambs weaning (0.509 vs. 0.435 kg/ewe/day) than before. In the same way, the correlations between udder depth, circumference and width and milk yield were positive and significant only after weaning (0.74, 0.75 and 0.62, respectively). Udder measures had positive correlations with milk yield and can be used in programs of milk yield improvement. (c) 2007 Elsevier B.V. All rights reserved.