The immunological, environmental, and phylogenetic perpetrators of metastatic leishmaniasis.

Cutaneous leishmaniases have persisted for centuries as chronically disfiguring parasitic infections affecting millions of people across the subtropics. Symptoms range from the more prevalent single, self-healing cutaneous lesion to a persistent, metastatic disease, where ulcerations and granulomatous nodules can affect multiple secondary sites of the skin and delicate facial mucosa, even sometimes diffusing throughout the cutaneous system as a papular rash. The basis for such diverse pathologies is multifactorial, ranging from parasite phylogeny to host immunocompetence and various environmental factors. Although complex, these pathologies often prey on weaknesses in the innate immune system and its pattern recognition receptors. This review explores the observed and potential associations among the multifactorial perpetrators of infectious metastasis and components of the innate immune system.

Case Study of Seasonal Variation in the Subgrade and Subbase Layers of Highway US 20, TR-516, 2008

Seasonal variations in ground temperature and moisture content influence the load carrying capacity of pavement subgrade layers. To improve pavement performance, pavement design guidelines require knowledge of environmental factors and subgrade stiffness relationships. As part of this study, in-ground instrumentation was installed in the pavement foundation layers of a newly constructed section along US Highway 20 near Fort Dodge, Iowa, to monitor the seasonal variations in temperature, frost depth, groundwater levels, and moisture regime. Dynamic cone penetrometer (DCP), nuclear gauge, and Clegg hammer tests were performed at 64 test points in a 6-ft x 6-ft grid pattern to characterize the subgrade stiffness properties (i.e., resilient modulus) prior to paving. The purpose of this paper is to present the field instrumentation results and the observed changes in soil properties due to seasonal environmental effects.

The environmental roots of non-communicable diseases (NCDs) and the epigenetic impacts of globalization

BACKGROUND: Non-communicable diseases (NCDs) are increasing worldwide. We hypothesize that environmental factors (including social adversity, diet, lack of physical activity and pollution) can become "embedded" in the biology of humans. We also hypothesize that the "embedding" partly occurs because of epigenetic changes, i.e., durable changes in gene expression patterns. Our concern is that once such factors have a foundation in human biology, they can affect human health (including NCDs) over a long period of time and across generations. OBJECTIVES: To analyze how worldwide changes in movements of goods, persons and lifestyles (globalization) may affect the "epigenetic landscape" of populations and through this have an impact on NCDs. We provide examples of such changes and effects by discussing the potential epigenetic impact of socio-economic status, migration, and diet, as well as the impact of environmental factors influencing trends in age at puberty. DISCUSSION: The study of durable changes in epigenetic patterns has the potential to influence policy and practice; for example, by enabling stratification of populations into those who could particularly benefit from early interventions to prevent NCDs, or by demonstrating mechanisms through which environmental factors influence disease risk, thus providing compelling evidence for policy makers, companies and the civil society at large. The current debate on the '25 × 25 strategy', a goal of 25% reduction in relative mortality from NCDs by 2025, makes the proposed approach even more timely. CONCLUSIONS: Epigenetic modifications related to globalization may crucially contribute to explain current and future patterns of NCDs, and thus deserve attention from environmental researchers, public health experts, policy makers, and concerned citizens.

Ecology and the challenge of a multifunctional use of soil

Soil zoology and soil ecology have become very active fields of research since the early 1990s. A search in the ISI Web of Science databases showed a steady increase in publications about that theme over the last two decades, and 3,612 bibliographic references were found for that theme for the period of 2004 to 2008. The researches covered mostly soil environmental issues, toxicology and ecology. The issue of theoretical development in soil ecology is discussed, and arguments are presented against the idea that the soil ecology theory is deficient. Finally, the need for a general model of soil function and soil management is discussed and some options are presented to reach this goal.

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.

Environmental influence on the phenotype of ant workers revealed by common garden experiment

Many organism traits vary along environmental gradients. Common garden experiments provide powerful means to disentangle the role of intrinsic factors, such as genetic or maternal effects, from extrinsic environmental factors in shaping phenotypic variation. Here, we investigate body size and lipid content variation in workers of the socially polymorphic ant Formica selysi along several independent elevation gradients in Switzerland. We compare field-collected workers and workers sampled as eggs from the same colonies but reared in common laboratory conditions. Overall, field-collected workers from high elevation are larger than those from low elevation, but the trend varies substantially among valleys. The same pattern is recovered when the eggs are reared in a common garden, which indicates that body size variation along elevation gradients and valleys is partly explained by genetic or maternal effects. However, both body size and lipid content exhibit significantly greater variation in field-collected workers than in laboratory-reared workers. Hence, much of the phenotypic variation results from a plastic response to the environment, rather than from genetic differences. Eggs from different elevations also show no significant difference in development time in the common garden. Overall, selection on individual worker phenotypes is unlikely to drive the altitudinal distribution of single- and multiple-queen colonies in this system, as phenotypic variation tends to be plastic and can be decoupled from social structure. This study provides insights into the interplay between individual phenotypic variation and social organization and how the two jointly respond to differing environmental conditions.

Ympäristöteknologioiden verifioinnin mahdollisuudet pilaantuneiden maiden laadukkaan käsittelyn edistämisessä

EU on käynnistämässä ympäristöteknologioiden verifiointijärjestelmää, jonka avulla voidaan tarjota käyttäjille ja sijoittajille riippumatonta tietoa innovatiivisten teknologioiden toimivuudesta ja suorituskyvystä ja parantaa niiden markkina-asemaa. Verifioinnilla tarkoitetaan kolmannen osapuolen suorittamaa prosessia tai mekanismia, jonka avulla tuotteen toiminta ja suorituskyky voidaan todentaa. Kansallinen ympäristöteknologioiden verifiointijärjestelmä on käytössä mm. Yhdysvalloissa ja Kanadassa. Euroopassa järjestelmä otettaneen käyttöön vuonna 2011–2012. Suomessa tehdään nykyisin noin 300 pilaantuneen maan puhdistushanketta koskevaa lupa- ja ilmoituspäätöstä vuosittain. Noin 85 prosentissa kohteista käytetään kunnostusmenetelmänä massanvaihtoa. Massanvaihto tulee ainakin toistaiseksi säilymään yleisimpänä kunnostusmenetelmänä, mutta mm. in situ -menetelmien käytön arvioidaan lisääntyvän. Tämän diplomityön tavoitteena oli arvioida voidaanko verifiointia hyödyntää pilaantuneiden maiden laadukkaan käsittelyn edistämisessä ja voiko verifiointi nopeuttaa innovatiivisten kunnostusmenetelmien markkinoillepääsyä. Aihetta tarkasteltiin mm. kahden erityyppisen pilaantuneen maan ja pohjaveden kunnostusmenetelmän, reaktiivisten seinämien (in situ) ja bitumistabiloinnin (ex situ) kautta. Pilaantuneiden maiden kunnostusmenetelmien toimivuus riippuu monista eri tekijöistä, joista osaa ei voida hallita tai mallintaa luotettavasti. Verifiointi soveltuukin parhaiten laitteiden tai PIMA-menetelmiä yksinkertaisempien puhdistusmenetelmien suorituskyvyn todentamiseen. Verifiointi saattaa kuitenkin hyvin toimia PIMA-kunnostuksen kohdalla esimerkiksi tiedollisena ohjauskeinona. Reaktiivisten seinämien ja bitumistabiloinnin verifioinnin työvaiheet ovat hyvin samankaltaiset, suurimpana erona seinämien kohdalla tulee kuvata myös kohde johon seinämä on asennettu. Reaktiivisten seinämien toiminta on riippuvaista monista ympäristötekijöistä, toisin kuin erillisellä laitteistolla suoritettavan bitumistabiloinnin. Tulosten perusteella voidaan yleistää, että verifiointi soveltuu paremmin ex situ -, kuin in situ -kunnostusmenetelmille.

Plantas medicinais: fatores de influência no conteúdo de metabólitos secundários

Since secondary metabolites represent a chemical interface between plants and surrounding environment, their syntheses are frequently affected by environmental conditions. Thus, variations in the total content and/or of the relative proportions of secondary metabolites in plants can take place. We review the main environmental factors that can streamline or alter the production or concentration of secondary metabolites in plants. How seasonality, circadian rhythm, developmental stage and age, temperature, water availability, UV radiation, soil nutrients, altitude, atmospheric composition and tissue damage influence secondary metabolism are discussed.

Efecto de los usos del suelo en la emisión de dióxido de carbono del suelo a la atmósfera en un agroecosistema semiárido del Valle del Ebro

Los cambios en los usos del suelo han contribuido de manera importante al incremento de gases de efecto invernadero en la atmósfera, especialmente de dióxido de carbono, aumentando sus emisiones desde 1970 en un 80%. Estos cambios causan la alteración de los suelos provocando un impacto sobre el ciclo del carbono, aumentando las tasas de descomposición de la fracción orgánica creando así un flujo de CO2 a la atmosfera. Entre las recomendaciones del Panel Intergubernamental de expertos sobre el Cambio Climático (IPCC, en inglés), y contemplado en el Protocolo de Kyoto, se encuentra el proceso de secuestro de carbono en suelos, que implica la eliminación del CO2 atmosférico por parte de las plantas y su almacenamiento como materia orgánica del suelo. Para poder favorecer dicho proceso, en un determinado tipo de ecosistema, es fundamental conocer cuáles son los factores que gobiernan la respiración del suelo y el impacto que tienen los diferentes usos en la emisión de CO2. En el presente trabajo se han estudiado 4 usos del suelo representativos del secano aragonés: un monocultivo de cebada en siembra directa (NT), un suelo abandonado labrado (AC), un suelo abandonado no alterado (AU) y un suelo forestal (FR) con el objetivo de conocer sus tasas de respiración, la influencia de diferentes parámetros edáficos en ellas, y proponer cambios en el uso del suelo que ayuden a mitigar estas emisiones. Además, se ha dedicado un apartado para conocer cómo influyen diferentes técnicas de fertilización nitrogenada (mineral y orgánica) en la respiración de un monocultivo de cebada en siembra directa. En cuanto a los usos, los resultados obtenidos tanto in situ como en laboratorio muestran una mayor respiración en AC, siendo los valores más bajos los de NT y FR. Una de las principales conclusiones es que la supresión del laboreo y del periodo de barbecho largo, así como la conversión de tierras abandonadas y marginales a cultivos y zonas forestales se presentan en este tipo de ecosistemas como prácticas de secuestro de carbono. En el estudio de aplicación de fertilizantes, no se observó ningún cambio en la respiración del suelo después de la aplicación de nitrógeno mineral. En cambio, el suelo fertilizado con purín sí que mostró picos de emisión durante las siguientes horas a la incorporación de éste, debido fundamentalmente a su alto contenido de carbono lábil.

Classification, comorbidity, heredity, and risk factors of female sexual dysfunctions

Female sexual dysfunctions, including desire, arousal, orgasm and pain problems, have been shown to be highly prevalent among women around the world. The etiology of these dysfunctions is unclear but associations with health, age, psychological problems, and relationship factors have been identified. Genetic effects explain individual variation in orgasm function to some extent but until now quantitative behavior genetic analyses have not been applied to other sexual functions. In addition, behavior genetics can be applied to exploring the cause of any observed comorbidity between the dysfunctions. Discovering more about the etiology of the dysfunctions may further improve the classification systems which are currently under intense debate. The aims of the present thesis were to evaluate the psychometric properties of a Finnish-language version of a commonly used questionnaire for measuring female sexual function, the Female Sexual Function Index (FSFI), in order to investigate prevalence, comorbidity, and classification, and to explore the balance of genetic and environmental factors in the etiology as well as the associations of a number of biopsychosocial factors with female sexual functions. Female sexual functions were studied through survey methods in a population based sample of Finnish twins and their female siblings. There were two waves of data collection. The first data collection targeted 5,000 female twins aged 33–43 years and the second 7,680 female twins aged 18–33 and their over 18–year-old female siblings (n = 3,983). There was no overlap between the data collections. The combined overall response rate for both data collections was 53% (n = 8,868), with a better response rate in the second (57%) compared to the first (45%). In order to measure female sexual function, the FSFI was used. It includes 19 items which measure female sexual function during the previous four weeks in six subdomains; desire, subjective arousal, lubrication, orgasm, sexual satisfaction, and pain. In line with earlier research in clinical populations, a six factor solution of the Finnish-language version of the FSFI received supported. The internal consistencies of the scales were good to excellent. Some questions about how to avoid overestimating the prevalence of extreme dysfunctions due to women being allocated the score of zero if they had had no sexual activity during the preceding four weeks were raised. The prevalence of female sexual dysfunctions per se ranged from 11% for lubrication dysfunction to 55% for desire dysfunction. The prevalence rates for sexual dysfunction with concomitant sexual distress, in other words, sexual disorders were notably lower ranging from 7% for lubrication disorder to 23% for desire disorder. The comorbidity between the dysfunctions was substantial most notably between arousal and lubrication dysfunction even if these two dysfunctions showed distinct patterns of associations with the other dysfunctions. Genetic influences on individual variation in the six subdomains of FSFI were modest but significant ranging from 3–11% for additive genetic effects and 5–18% for nonadditive genetic effects. The rest of the variation in sexual functions was explained by nonshared environmental influences. A correlated factor model, including additive and nonadditive genetic effects and nonshared environmental effects had the best fit. All in all, every correlation between the genetic factors was significant except between lubrication and pain. All correlations between the nonshared environment factors were significant showing that there is a substantial overlap in genetic and nonshared environmental influences between the dysfunctions. In general, psychological problems, poor satisfaction with the relationship, sexual distress, and poor partner compatibility were associated with more sexual dysfunctions. Age was confounded with relationship length but had over and above relationship length a negative effect on desire and sexual satisfaction and a positive effect on orgasm and pain functions. Alcohol consumption in general was associated with better desire, arousal, lubrication, and orgasm function. Women pregnant with their first child had fewer pain problems than nulliparous nonpregnant women. Multiparous pregnant women had more orgasm problems compared to multiparous nonpregnant women. Having children was associated with less orgasm and pain problems. The conclusions were that desire, subjective arousal, lubrication, orgasm, sexual satisfaction, and pain are separate entities that have distinct associations with a number of different biopsychosocial factors. However, there is also considerable comorbidity between the dysfunctions which are explained by overlap in additive genetic, nonadditive genetic and nonshared environmental influences. Sexual dysfunctions are highly prevalent and are not always associated with sexual distress and this relationship might be moderated by a good relationship and compatibility with partner. Regarding classification, the results supports separate diagnoses for subjective arousal and genital arousal as well as the inclusion of pain under sexual dysfunctions.

Coffee water use in agroforestry system with rubber trees

Water uptake and use by plants are essentially energy processes that can be largely modified by percentage of soil cover, plant type; foliage area and its distribution; phenological stage and several environmental factors. Coffee trees (Coffea arabica - cv. Obatã IAC 1669-20) in Agrforestry System (AFS) spaced 3.4x0.9m apart, were planted inside and along rows of 12- year-old rubber trees (Hevea spp.) in Piracicaba-SP, Brazil (22 42'30" S, 47 38'00" W - altitude: 546m). Sap flow of one-year-old coffee plants exposed to 35; 45; 80; 95 and 100% of total solar radiation was estimated by the heat balance technique (Dynamax Inc.). Coffee plants under shade showed greater water loss per unit of incident irradiance. On the other hand, plants in monocrop (full sun) had the least water loss per unit of incident irradiance. For the evaluated positions average water use was (gH2O.m-2Leaf area.MJ-1): 64.71; 67.75; 25.89; 33.54; 27.11 in Dec./2002 and 97.14; 72.50; 40.70; 32.78; 26.13 in Feb./2003. This fact may be attributed to the higher stomata sensitivity of the coffee plants under more illuminated conditions, thus plants under full sun presented the highest water use efficiency. Express transpiration by leaf mass can be a means to access plant adaptation to the various environments, which is inaccessible when the approach is made by leaf area.

Seed germination of a rare neotropical canopy tree dormancy and the effects of abiotic factors

The purpose of this study was to examine if germination is a critical phase on Enterolobium glaziovii regeneration. Hence, the germinative response of E. glaziovii seeds was investigated in relation to some of the main environmental factors (temperature, light and water stress) to which its seeds are subjected in the forest, as well as its dormancy and the longevity of its burial seeds. According to our results, its seeds may be regarded as photoblastic neutral. They do not need alternating temperatures to germinate and can germinate under a broad range of water stress. However, only about 10% of E. glaziovii seeds remain viable after one year. In other words, the annual fruiting, instead seed longevity, seems to maintain the long-term seed availability of this species. Consequently, the seed longevity could be a critical phase of E. glaziovii germination.

Germination and emergence of Stachytarpheta cayennensis and Ipomoea asarifolia

Understanding how weed seed germination and emergence respond to environmental factors is critical to determining their adaptive capabilities and potential for infestations, and could also aid in the development of effective control practices. Germination of Ipomoea asarifolia (Desr.) Roem. & Schultz and Stachytarpheta cayennensis (Rich) Vahl. decreased linearly with decreasing osmotic potentials. Also, increasing osmotic stress delayed germination of Ipomoea more than that of Stachytarpheta. Ipomoea germination was insensitive to light, while Stachytarpheta showed a positive photoblastic behavior. Nitrate had a negative effect on germination of Ipomoea seed under both light and dark conditions but stimulated dark germination of Stachytarpheta. Ipomoea emergence was not significantly affected by planting depth. However, for Stachytarpheta emergence was restrited to seeds planted at the soil surface. Emergence of Ipomoea seedlings from greater than 6cm significantly decreased the amount of biomass allocated to roots, while biomass allocated to leaves was decreased for seedlings that emerged from depths greater than 2cm. These germination and emergence responses are discussed in relation to their ecological implications and to weed control strategies.

Germination ecology of Rhynchosia capitata: an emerging summer weed in Asia

Rhynchosia capitata is becoming an increasing problem in summer crops, such as cotton, soybean, pearl millet and mungbean in many Asian countries. Laboratory and greenhouse studies have been conducted to determine the effects of several environmental factors on seed germination patterns and seedling emergence of R. capitata. We investigated whether the diverse ecological factors such as temperature, light, salinity, moisture stress, pH, and soil depth affected germination and seedling emergence of R. capitata. Germination increased as temperature increased from 25ºC and significantly reduced at 45ºC. Presence or absence of light did not influence germination. Germination of R. capitata was sensitive to increased salt and moisture stress, as well as to seed burial depth. Only 48% of seeds germinated at 150 mM salt concentration compared to 100% in control (distilled water). Similarly, 15% of seeds germinated at an osmotic potential of ‑0.8 MPa compared to 88% at ‑0.2 MPa. The optimum pH for seed germination of R. capitata was 7 (98% germination), but the seeds also germinated at lower level of pH 5 (85%) and at higher level of pH 10 (75%). In seed burial trial, maximum seedling emergence of 93% occurred at 2 cm depth, and seedling did not emerge from a depth of 12 cm. The high germination ability of R. capitata under a wide range of ecological factors suggests that this species is likely to be the one to cause more problems in a near future, if not managed appropriately.

Germination ecology of wild onion: a rainfed crop weed

Asphodelus tenuifolius is becoming a more common weed in rain-fed area in Pakistan. Laboratory and greenhouse experiments were conducted to determine the effect of different environmental factors on germination and emergence of A.tenuifolius. Results showed that A.tenuifolius can tolerate a wide range of varying environmental factors. Greatest percentage of germination (80%) was recorded at 15 ºC constant temperature; however, considerable germination occurred at 20 and 25 ºC. Light for 10 h photoperiod stimulate germination of Asphodelus tenuifolius compared with complete darkness. Germination was totally inhibited at osmotic stress higher than -0.8 MPa. There was no significant difference in germination at pH 6 to 8; however, there was a slightly decrease at pH 9, compared with distilled water. Asphodelus tenuifolius was very sensitive to salinity; however, a few seeds of A.tenuifolius were able to germinate even at 150 mM NaCl concentration. Greatest emergence occurred with seed placed at soil surface and emergence decreased with increase in burial depth. No emergence occurred from 4 cm or greater. This information may aid in developing tools and strategies for management.