Effect of environmental variables on buffaloes physiology

The objective of this work was to evaluate the effect of environmental variables on dairy buffaloes physiology in two different places after milking, shaded plus artificial ventilation and another one non-shaded, in Ribeira Valley, São Paulo State, Brazil. Data on the respiratory rate (RR) and the surface temperature (ST) at udder, neckmiddle, forehead, back middle and rump were collected in 12 dairy buffaloes at autumn. In the same way, it were recorded the black globe temperature in the sun (GTS) and in the shade (GTNS), air temperature and wind speed at padronized height of 1.60 meters. All data were collected at 10:30am and 1:30pm. The results showed statistical difference among black globe temperature, wind speed, RR and ST (P<0.01) in two treatments.The results showed the necessity of protection against the solar radiation in the buffaloes, even in periods of warm climates.

Method of numerical correction of errors occasioned by delay of records during the monitoring of environmental variables of interest for animal production

As condições de ambiente térmico e aéreo, no interior de instalações para animais, alteram-se durante o dia, devido à influência do ambiente externo. Para que análises estatísticas e geoestatísticas sejam representativas, uma grande quantidade de pontos distribuídos espacialmente na área da instalação deve ser monitorada. Este trabalho propõe que a variação no tempo das variáveis ambientais de interesse para a produção animal, monitoradas no interior de instalações para animais, pode ser modelada com precisão a partir de registros discretos no tempo. O objetivo deste trabalho foi desenvolver um método numérico para corrigir as variações temporais dessas variáveis ambientais, transformando os dados para que tais observações independam do tempo gasto durante a aferição. O método proposto aproximou os valores registrados com retardos de tempo aos esperados no exato momento de interesse, caso os dados fossem medidos simultaneamente neste momento em todos os pontos distribuídos espacialmente. O modelo de correção numérica para variáveis ambientais foi validado para o parâmetro ambiental temperatura do ar, sendo que os valores corrigidos pelo método não diferiram pelo teste Tukey, a 5% de probabilidade dos valores reais registrados por meio de dataloggers.

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species.

Trends in NE Atlantic landings (southern Portugal): identifying the relative importance of fisheries and environmental variables

Time series of commercial landings from the Algarve (southern Portugal) from 1982 to 1999 were analyzed using min/max autocorrelation factor analysis (MAFA) and dynamic factor analysis (DFA). These techniques were used to identify trends and explore the relationships between the response variables (annual landings of 12 species) and explanatory variables [sea surface temperature, rainfall, an upwelling index, Guadiana river (south-east Portugal) flow, the North Atlantic oscillation, the number of licensed fishing vessels and the number of commercial fishermen]. Landings were more highly correlated with non-lagged environmental variables and in particular with Guadiana river flow. Both techniques gave coherent results, with the most important trend being a steady decline over time. A DFA model with two explanatory variables (Guadiana river flow and number of fishermen) and three common trends (smoothing functions over time) gave good fits to 10 of the 12 species. Results of other models indicated that river flow is the more important explanatory variable in this model. Changes in the mean flow and discharge regime of the Guadiana river resulting from the construction of the Alqueva dam, completed in 2002, are therefore likely to have a significant and deleterious impact on Algarve fisheries landings.

Multivariate analysis of the effects of soil parameters and environmental factors on the flavonoid content of leaves of Passiflora incarnata L., Passifloraceae

The aim of the present study was to evaluate the effect of soil characteristics (pH, macro- and micro-nutrients), environmental factors (temperature, humidity, period of the year and time of day of collection) and meteorological conditions (rain, sun, cloud and cloud/rain) on the flavonoid content of leaves of Passiflora incarnata L., Passifloraceae. The total flavonoid contents of leaf samples harvested from plants cultivated or collected under different conditions were quantified by high-performance liquid chromatography with ultraviolet detection (HPLC-UV/PAD). Chemometric treatment of the data by principal component (PCA) and hierarchic cluster analyses (HCA) showed that the samples did not present a specific classification in relation to the environmental and soil variables studied, and that the environmental variables were not significant in describing the data set. However, the levels of the elements Fe, B and Cu present in the soil showed an inverse correlation with the total flavonoid contents of the leaves of P. incarnata.

Environmental conditions and rodent infestation in Campo Limpo district, Sao Paulo municipality, Brazil

Rodents are involved in the transmission to human beings of several diseases, including liptospirosis, which shows high lethality rates in Sao Paulo municipality. Despite this, few studies have assessed the relationship existing between urban environmental conditions and building rodent infestation. With the purpose of clarifying this relationship, an analysis has been conducted in order to quantify the influence of environmental factors upon rodent infestation on a low-income district. Diagnosis of the environmental situation has been performed to evaluate the frequency according to which harborage, food and access sources occur, and a survey on infestation rates in 2175 dwellings in the area studied. The logistic regression analysis showed that among the environmental variables, the one that showed the closest association with rodent infestation was access; followed by harborage, and food. It was concluded that poor socioeconomic and environmental conditions in the area propitiate the occurrence of high rodent infestation rates

Intestinal parasitoses and environmental factors in a rural population of Argentina, 2002-2003

We evaluate the prevalence of intestinal parasites in 504 people and the degree of association between environmental variables and parasites found in population, soil and water in a rural area of Argentina during 2002-2003. A structured survey was used to evaluate the environmental variables and fecal-human, soil and water samples were analyzed. The prevalence of parasites was 45.4%. Most prevalent protozoa were Blastocystis hominis (27.2%) and Giardia lamblia (6.9%), while the most prevalent helminth was Ascaris lumbricoides (3.8%). The analyzed environmental variables showing association (p < 0.05) with presence of parasites in population were: cardboard-tin or wooden house, dirt floor, home or communal water pump, faucet outside the house or public faucet and cesspool or latrine. Parasite forms were found in 82.3% of the soil samples and in 84.2% of the water samples. In both samples we found parasites that were also found in people. In this study we have found deficient sanitary conditions associated with presence of parasites in population and we have evidenced that contaminated soil and water were the source of these parasites.

Epidemiological and environmental aspects of visceral leishmaniasis in children under 15 years of age between 2007 and 2012 in the City of Araguaína, State of Tocantins, Brazil

Introduction Visceral leishmaniasis (VL) stands out as a zoonosis observed on four continents and also in urban expansion zones in several regions of Brazil. Methods A cross-sectional epidemiological study of VL cases in children under 15 years of age in the period from 2007 to 2012. Clinical data were gathered from medical reports; meteorological data were obtained at the Meteorological Measurement Department of UFT. Environmental variables were divided into two periods, rainy and dry. Results The study revealed no difference by gender (p=0.67) among the 821 patients. However, the most affected age group was between one and five years of age (58.6%; p<0.01); the highest prevalence of the disease (99.03%; p<0.01) occurred in urban zones; and the most affected ethnic group (85.5%; p<0.01) was mixed race. The highest incidence coefficients in this population occurred in 2007 and 2008 (578.39/100,000 inhabitants; 18.5/100,000 inhabitants, respectively), whereas the highest lethality coefficients occurred in 2008 and 2011 (0.85/100 deaths). There was no significant correlation between average rainfall and the number of VL cases. The correlation between temperature and number of VL cases was negative (r = -0.4039; p<0.01). Conclusions In Araguaína, visceral leishmaniasis in children under 15 years is an urban-based endemic disease distributed across all districts of the city wherein temperature as an environmental factor, a higher prevalence in mixed race children between one and five years of age, and a high incidence coefficient all strongly contribute to child mortality.

Environmental determinants for natural regeneration of gallery forest at the Cerrado/Amazonia boundaries in Brazil

Natural regeneration and structure and their relationship to environmental variables were studied in three sections of a gallery forest, in Eastern Mato Grosso, Brazil (14º43′S and 52º21′W). The assumption was that natural regeneration is constrained by environmental determinants at all stages of development of the tree community. The objective was to analyse the forest structure and to verify the relationship between species distribution and abundance at different stages of regeneration and environmental variables. In each section, 47 contiguous (10x10m) permanent plots were established to sample trees (gbh≥15cm), following a systematic design. Seedlings (0.01 to 1m height), saplings (1.01 to 2m) and poles (from 2.01m height to gbh<15cm) were sampled in sub-plots of 1x1m, 2x2m and 5x5m, respectively. In each plot, soil properties, gaps projection, bamboos, rocky cover, declivity and depth of ground watertable were determined. The relationships between the environmental variables with trees and seedling communities were assessed by canonical correspondence analysis. In spite of the sections being near to each other, they presented large differences in floristics, structure and site conditions. The forest soil presented a low cation exchange capacity and a high level of Al saturation. The occurrence of bamboos and gaps and the depth of ground watertable limited the occurrence of poles and trees. The high degree of structural heterogeneity for each regeneration category was related primarily to a humidity gradient; but soil fertility (Ca+Mg) was also a determinant of seedling and sapling communities.

Population dynamics of intermediate snail hosts of Fasciola hepatica and some environmental factors in San Juan y Martinez municipality, Cuba

The variation of abundances of intermediate snail hosts of Fasciola hepatica in Cuba (Fossaria cubensis and Pseudosuccinea columella) was studied during one year under natural conditions at five sampling sites in San Juan y Martinez municipality, Pinar del Rio province, Cuba. The effect of some environmental variables on the lymnaeid abundances was also studied. A canonical correspondence analysis showed that both species do not generally occur together in the same habitat and that most factors affect them in an opposite fashion, although both of them correlate positively through time to the diversity of the habitats. F. cubensis prefers the sites that are in or closer to the city whereas P. columella is more abundant in rural sites. Lymnaeid abundances are mainly affected by nitrite and nitrate concentrations as well as by the abundance of the thiarid Tarebia granifera. F. cubensis is more abundant in polluted habitats with low densities (or absence) of T. granifera whereas P. columella prefers cleaner habitats and can coexist with the thiarid, even at its higher densities. The implications of divergent preferences of the two lymnaeids for the control of fasciolosis are discussed.

Analysis and estimative of schistosomiasis prevalence for the state of Minas Gerais, Brazil, using multiple regression with social and environmental spatial data

The aim of this work is to establish a relationship between schistosomiasis prevalence and social-environmental variables, in the state of Minas Gerais, Brazil, through multiple linear regression. The final regression model was established, after a variables selection phase, with a set of spatial variables which contains the summer minimum temperature, human development index, and vegetation type variables. Based on this model, a schistosomiasis risk map was built for Minas Gerais.

Delimitation of kala-azar risk areas in the district of Vaishali in Bihar (India) using a geo-environmental approach

Remote sensing and geographical information technologies were used to discriminate areas of high and low risk for contracting kala-azar or visceral leishmaniasis. Satellite data were digitally processed to generate maps of land cover and spectral indices, such as the normalised difference vegetation index and wetness index. To map estimated vector abundance and indoor climate data, local polynomial interpolations were used based on the weightage values. Attribute layers were prepared based on illiteracy and the unemployed proportion of the population and associated with village boundaries. Pearson's correlation coefficient was used to estimate the relationship between environmental variables and disease incidence across the study area. The cell values for each input raster in the analysis were assigned values from the evaluation scale. Simple weighting/ratings based on the degree of favourable conditions for kala-azar transmission were used for all the variables, leading to geo-environmental risk model. Variables such as, land use/land cover, vegetation conditions, surface dampness, the indoor climate, illiteracy rates and the size of the unemployed population were considered for inclusion in the geo-environmental kala-azar risk model. The risk model was stratified into areas of "risk"and "non-risk"for the disease, based on calculation of risk indices. The described approach constitutes a promising tool for microlevel kala-azar surveillance and aids in directing control efforts.

Computational analysis of the genetic and environmental contributions to disease-related human phenotypes: From predicting adverse lipid response of HIV patients receiving antiretroviral therapy to genome-wide association studies of cardiovascular and lipid related disorders

Genetic variants influence the risk to develop certain diseases or give rise to differences in drug response. Recent progresses in cost-effective, high-throughput genome-wide techniques, such as microarrays measuring Single Nucleotide Polymorphisms (SNPs), have facilitated genotyping of large clinical and population cohorts. Combining the massive genotypic data with measurements of phenotypic traits allows for the determination of genetic differences that explain, at least in part, the phenotypic variations within a population. So far, models combining the most significant variants can only explain a small fraction of the variance, indicating the limitations of current models. In particular, researchers have only begun to address the possibility of interactions between genotypes and the environment. Elucidating the contributions of such interactions is a difficult task because of the large number of genetic as well as possible environmental factors.In this thesis, I worked on several projects within this context. My first and main project was the identification of possible SNP-environment interactions, where the phenotypes were serum lipid levels of patients from the Swiss HIV Cohort Study (SHCS) treated with antiretroviral therapy. Here the genotypes consisted of a limited set of SNPs in candidate genes relevant for lipid transport and metabolism. The environmental variables were the specific combinations of drugs given to each patient over the treatment period. My work explored bioinformatic and statistical approaches to relate patients' lipid responses to these SNPs, drugs and, importantly, their interactions. The goal of this project was to improve our understanding and to explore the possibility of predicting dyslipidemia, a well-known adverse drug reaction of antiretroviral therapy. Specifically, I quantified how much of the variance in lipid profiles could be explained by the host genetic variants, the administered drugs and SNP-drug interactions and assessed the predictive power of these features on lipid responses. Using cross-validation stratified by patients, we could not validate our hypothesis that models that select a subset of SNP-drug interactions in a principled way have better predictive power than the control models using "random" subsets. Nevertheless, all models tested containing SNP and/or drug terms, exhibited significant predictive power (as compared to a random predictor) and explained a sizable proportion of variance, in the patient stratified cross-validation context. Importantly, the model containing stepwise selected SNP terms showed higher capacity to predict triglyceride levels than a model containing randomly selected SNPs. Dyslipidemia is a complex trait for which many factors remain to be discovered, thus missing from the data, and possibly explaining the limitations of our analysis. In particular, the interactions of drugs with SNPs selected from the set of candidate genes likely have small effect sizes which we were unable to detect in a sample of the present size (<800 patients).In the second part of my thesis, I performed genome-wide association studies within the Cohorte Lausannoise (CoLaus). I have been involved in several international projects to identify SNPs that are associated with various traits, such as serum calcium, body mass index, two-hour glucose levels, as well as metabolic syndrome and its components. These phenotypes are all related to major human health issues, such as cardiovascular disease. I applied statistical methods to detect new variants associated with these phenotypes, contributing to the identification of new genetic loci that may lead to new insights into the genetic basis of these traits. This kind of research will lead to a better understanding of the mechanisms underlying these pathologies, a better evaluation of disease risk, the identification of new therapeutic leads and may ultimately lead to the realization of "personalized" medicine.

Coliform density in oyster culture waters and its relationship with environmental factors

The objective of this work was to evaluate the total and thermotolerant coliform densities in the oyster culture water of Cananeia, SP, Brazil, correlating these densities with environmental variables and tidal variations. Superficial water samples were collected in two tide conditions (spring and neap) from three areas of Cananéia municipality (Mandira, Itapitangui and Cooperostra). The three studied areas showed good conditions for the culture regarding coliform densities. The two tidal conditions differed significantly as to total coliform concentration; however, the same procedure was not performed for thermotolerant coliforms. No correlation was observed between water temperature, pH, and concentrations of total and thermotolerant coliforms. Coliform density was positively correlated with rainfall and negatively correlated with salinity. Spring and neap tides differed significantly as to coliform number. Simple diagnosis of environmental conditions of the crop fields is insufficient to assess water quality of shellfish cultivation. A continuous monitoring program of planted areas is necessary both for the assessment of water quality potential for marine culture and for ensuring safe consumption of seafood, besides constituting an important tool to understand the relationships between contamination and the involved environmental variables.

Environmental factors, spatial variation, and specific requirements of Chironomidae in Mediterranean reference streams

Chironomidae spatial distribution was investigated at 63 near-pristine sites in 22 catchments of the Iberian Mediterranean coast. We used partial redundancy analysis to study Chironomidae community responses to a number of environmental factors acting at several spatial scales. The percentage of variation explained by local factors (23.3%) was higher than that explained by geographical (8.5%) or regional factors(8%). Catchment area, longitude, pH, % siliceous rocks in the catchment, and altitude were the best predictors of Chironomidae assemblages. We used a k-means cluster analysis to classified sites into 3 major groups based on Chironomidae assemblages. These groups were explained mainly by longitudinal zonation and geographical position, and were defined as 1) siliceous headwater streams, 2) mid-altitude streams with small catchment areas, and 3) medium-sized calcareous streams. Distinct species assemblages with associated indicator taxa were established for each stream category using IndVal analysis. Species responses to previously identified key environmental variables were determined, and optima and tolerances were established by weighted average regression. Distinct ecological requirements were observed among genera and among species of the same genus. Some genera were restricted to headwater systems (e.g., Diamesa), whereas others (e.g., Eukiefferiella) had wider ecological preferences but with distinct distributions among congenerics. In the present period of climate change, optima and tolerances of species might be a useful tool to predict responses of different species to changes in significant environmental variables, such as temperature and hydrology.