Geographic differentiation of polymorphism in the Plasmodium falciparum malaria vaccine candidate gene SERA5

SERA5 is regarded as a promising malaria vaccine candidate of the most virulent human malaria parasite Plasmodium falciparum. SERA5 is a 120 kDa abundantly expressed blood-stage protein containing a papain-like protease. Since substantial polymorphism in blood-stage vaccine candidates may potentially limit their efficacy, it is imperative to fully investigate polymorphism of the SERA5 gene (sera5). In this study, we performed evolutionary and population genetic analysis of sera5. The level of inter-species divergence (kS = 0.076) between P. falciparum and Plasmodium reichenowi, a closely related chimpanzee malaria parasite is comparable to that of housekeeping protein genes. A signature of purifying selection was detected in the proenzyme and enzyme domains. Analysis of 445 near full-length P. falciparum sera5 sequences from nine countries in Africa, Southeast Asia, Oceania and South America revealed extensive variations in the number of octamer repeat (OR) and serine repeat (SR) regions as well as substantial level of single nucleotide polymorphism (SNP) in non-repeat regions (2562 bp). Remarkably, a 14 amino acid sequence of SERA5 (amino acids 59-72) that is known to be the in vitro target of parasite growth inhibitory antibodies was found to be perfectly conserved in all 445 worldwide isolates of P. falciparum evaluated. Unlike other major vaccine target antigen genes such as merozoite surface protein-1, apical membrane antigen-1 or circumsporozoite protein, no strong evidence for positive selection was detected for SNPs in the non-repeat regions of sera5. A biased geographical distribution was observed in SNPs as well as in the haplotypes of the sera5 OR and SR regions. In Africa, OR- and SR-haplotypes with low frequency (<5%) and SNPs with minor allele frequency (<5%) were abundant and were mostly continent-specific. Consistently, significant genetic differentiation, assessed by the Wright's fixation index (FST) of inter-population variance in allele frequencies, was detected for SNPs and both OR- and SR-haplotypes among almost all parasite populations. The exception was parasite populations between Tanzania and Ghana, suggesting frequent gene flow in Africa. The present study points to the importance of investigating whether biased geographical distribution for SNPs and repeat variants in the OR and SR regions affect the reactivity of human serum antibodies to variants. (C) 2011 Elsevier Ltd. All rights reserved.

Understanding bias in geographic range size estimates

Aim Estimates of geographic range size derived from natural history museum specimens are probably biased for many species. We aim to determine how bias in these estimates relates to range size. Location We conducted computer simulations based on herbarium specimen records from localities ranging from the southern United States to northern Argentina. Methods We used theory on the sampling distribution of the mean and variance to develop working hypotheses about how range size, defined as area of occupancy (AOO), was related to the inter-specific distribution of: (1) mean collection effort per area across the range of a species (MC); (2) variance in collection effort per area across the range of a species (VC); and (3) proportional bias in AOO estimates (PBias: the difference between the expected value of the estimate of AOO and true AOO, divided by true AOO). We tested predictions from these hypotheses using computer simulations based on a dataset of more than 29,000 herbarium specimen records documenting occurrences of 377 plant species in the tribe Bignonieae (Bignoniaceae). Results The working hypotheses predicted that the mean of the inter-specific distribution of MC, VC and PBias were independent of AOO, but that the respective variance and skewness decreased with increasing AOO. Computer simulations supported all but one prediction: the variance of the inter-specific distribution of VC did not decrease with increasing AOO. Main conclusions Our results suggest that, despite an invariant mean, the dispersion and symmetry of the inter-specific distribution of PBias decreases as AOO increases. As AOO increased, range size was less severely underestimated for a large proportion of simulated species. However, as AOO increased, range size estimates having extremely low bias were less common.

Do Higher Temperatures Increase Growth in the Nocturnal Gecko Homonota darwini (Gekkota: Phyllodactylidae)? A Skeletochronological Assessment Analyzed at Temporal and Geographic Scales

Recent studies predict that several lineages of tropical animals are at particular risk given current estimates of global climate change. Yet, much uncertainty exists on the effects of climate shifts in ectothermic species from cool temperate regions such as Patagonia. In this study, we focus on the impact of environmental temperature on growth, age at sexual maturity, and life-span of the Patagonian gecko Homonota darwini. Skeletochronological methods were used to assess the bone growth rates Of individuals from three populations at different geographic and temporal scales: two populations from Chubut (warm site; 1941 and 2010) and one population from Rio Negro (cold site; 1997-1998). Populations displayed similar bone arrangement and the growth patterns fit a von Bertalanffy curve. Three populations attained reproductive size at a minimum age of 3 yr, but at the cold site two specimens were shown to mature in 4 yr. We found no differences in juvenile growth rates in body size or bone zone width between juveniles of 1 to 3 yr of age from the 1941 warm site and the 2010 warm site. However, these traits appeared to be higher at these two warm sites than at the cold site, which is consistent with the climatic differences among the three localities. Our results suggest that higher temperatures positively affect growth, denoting that global warming might benefit H. darwini, especially the southern populations.

Morphological, molecular and cross-breeding analysis of geographic populations of coconut-mite associated predatory mites identified as Neoseiulus baraki: evidence for cryptic species?

Surveys were conducted in Brazil, Benin and Tanzania to collect predatory mites as candidates for control of the coconut mite Aceria guerreronis Keifer, a serious pest of coconut fruits. At all locations surveyed, one of the most dominant predators on infested coconut fruits was identified as Neoseiulus baraki Athias-Henriot, based on morphological similarity with regard to taxonomically relevant characters. However, scrutiny of our own and published descriptions suggests that consistent morphological differences may exist between the Benin population and those from the other geographic origins. In this study, we combined three methods to assess whether these populations belong to one species or a few distinct, yet closely related species. First, multivariate analysis of 32 morphological characters showed that the Benin population differed from the other three populations. Second, DNA sequence analysis based on the mitochondrial cytochrome oxidase subunit I (COI) showed the same difference between these populations. Third, cross-breeding between populations was unsuccessful in all combinations. These data provide evidence for the existence of cryptic species. Subsequent morphological research showed that the Benin population can be distinguished from the others by a new character (not included in the multivariate analysis), viz. the number of teeth on the fixed digit of the female chelicera.

Evaluation of the detection and quantification limits in electroanalysis using two popular methods: application in the case study of paraquat determination

In this work, the reduction reaction of paraquat herbicide was used to obtain analytical signals using electrochemical techniques of differential pulse voltammetry, square wave voltammetry and multiple square wave voltammetry. Analytes were prepared with laboratory purified water and natural water samples (from Mogi-Guacu River, SP). The electrochemical techniques were applied to 1.0 mol L-1 Na2SO4 solutions, at pH 5.5, and containing different concentrations of paraquat, in the range of 1 to 10 mu mol L-1, using a gold ultramicroelectrode. 5 replicate experiments were conducted and in each the mean value for peak currents obtained -0.70 V vs. Ag/AgCl yielded excellent linear relationships with pesticide concentrations. The slope values for the calibration plots (method sensitivity) were 4.06 x 10(-3), 1.07 x 10(-2) and 2.95 x 10(-2) A mol(-1) L for purified water by differential pulse voltammetry, square wave voltammetry and multiple square wave voltammetry, respectively. For river water samples, the slope values were 2.60 x 10(-3), 1.06 x 10(-2) and 3.35 x 10(-2) A mol(-1) L, respectively, showing a small interference from the natural matrix components in paraquat determinations. The detection limits for paraquat determinations were calculated by two distinct methodologies, i.e., as proposed by IUPAC and a statistical method. The values obtained with multiple square waves voltammetry were 0.002 and 0.12 mu mol L-1, respectively, for pure water electrolytes. The detection limit from IUPAC recommendations, when inserted in the calibration curve equation, an analytical signal (oxidation current) is smaller than the one experimentally observed for the blank solution under the same experimental conditions. This is inconsistent with the definition of detection limit, thus the IUPAC methodology requires further discussion. The same conclusion can be drawn by the analyses of detection limits obtained with the other techniques studied.

Considerations for Assessing Maximum Critical Temperatures in Small Ectothermic Animals: Insights from Leaf-Cutting Ants

The thermal limits of individual animals were originally proposed as a link between animal physiology and thermal ecology. Although this link is valid in theory, the evaluation of physiological tolerances involves some problems that are the focus of this study. One rationale was that heating rates shall influence upper critical limits, so that ecological thermal limits need to consider experimental heating rates. In addition, if thermal limits are not surpassed in experiments, subsequent tests of the same individual should yield similar results or produce evidence of hardening. Finally, several non-controlled variables such as time under experimental conditions and procedures may affect results. To analyze these issues we conducted an integrative study of upper critical temperatures in a single species, the ant Atta sexdens rubropiosa, an animal model providing large numbers of individuals of diverse sizes but similar genetic makeup. Our specific aims were to test the 1) influence of heating rates in the experimental evaluation of upper critical temperature, 2) assumptions of absence of physical damage and reproducibility, and 3) sources of variance often overlooked in the thermal-limits literature; and 4) to introduce some experimental approaches that may help researchers to separate physiological and methodological issues. The upper thermal limits were influenced by both heating rates and body mass. In the latter case, the effect was physiological rather than methodological. The critical temperature decreased during subsequent tests performed on the same individual ants, even one week after the initial test. Accordingly, upper thermal limits may have been overestimated by our (and typical) protocols. Heating rates, body mass, procedures independent of temperature and other variables may affect the estimation of upper critical temperatures. Therefore, based on our data, we offer suggestions to enhance the quality of measurements, and offer recommendations to authors aiming to compile and analyze databases from the literature.

Phylogeographic Structure and Karyotypic Diversity of the Brazilian Shrew Mouse (Blarinomys breviceps, Sigmodontinae) in the Atlantic Forest

Blarinomys breviceps possesses cryptic and burrowing habits with poorly documented genetics and life history traits. Due to its rarity, only a few specimens and DNA sequences have been deposited in collections worldwide. Here, we present the most comprehensive cytogenetic and molecular characterization of this rare genus. Phylogenetic analyses based on partial cytochrome b sequences were performed, attempting to establish the relationships among individuals with distinct karyotypes along the geographic distribution of the genus in the Atlantic Forest. Classical and molecular cytogenetics, using banding patterns and FISH of telomeric and whole chromosome X-specific painting probes (obtained from the Akodontini Akodon cursor) were used to characterize and compare the chromosomal complements. Molecular phylogenetic analyses recovered 2 main geographically structured clades, northeastern and southeastern with pair-wise sequence divergences among specimens varying between 4.9 and 8.4%. Eight distinct karyomorphs are described: (A) 2n = 52 (50A, XX), (B) 2n = 52 (48A, XY+2Bs), (C) 2n = 45 (42A, XY+1B), (D) 2n = 43 (37A, XX+4Bs), (E) 2n = 37 (34A, XY+1B), (F) 2n = 34 (32A, XX), (G) 2n = 31 (27A, XX+2Bs), (H) 2n = 28 (26A, XY), all with the same number of autosomal arms (FNA = 50). Variation of 0-4 supernumerary chromosomes (Bs) presenting heterogeneity in morphology and distribution of interstitial telomeric sequences (ITSs) is reported. ITSs are also found in some metacentric autosomes. The phylogeographic separation between 2 major lineages with high levels of genetic divergence, and the wide karyotypic diversity indicate that B. breviceps is a diverse group that warrants taxonomic re-evaluation. Copyright (C) 2012 S. Karger AG, Basel

Cadmium Uptake by Lettuce (Lactuca sativa L.) as Basis for Derivation of Risk Limits in Soils

The availability and uptake of Cd by lettuce (Lactuca sativa L.) in two common tropical soils (before and after liming) were studied in order to derive human health-based risk soil concentration. Cadmium concentrations ranging from 1 to 12 mg kg(-1) were added to samples from a clayey Oxisol and a sandy-loam Ultisol under glasshouse conditions. After incubation, a soil sample was taken from each pot, the concentration of Cd in the soil was determined, lettuce was grown during 36 d, and the edible parts were harvested and analyzed for Cd. A positive linear correlation was observed between total soil Cd and the Cd concentration in lettuce. The amount of Cd absorbed by lettuce grown in the Ultisol was about twice the amount absorbed in the Oxisol. Liming increased the soil pH and slightly reduced Cd availability and uptake. CaCl2 extraction was better than DTPA to reflect differences in binding strength of Cd between limed and unlimed soils. Risk Cd concentrations in the Ultisol were lower than in the Oxisol, reflecting the greater degree of uptake from the Ultisol. The derived risk Cd values were dependent on soil type and the exposure scenario.

A Dark Matter Search with AMANDA : Limits on the Muon Flux from Neutralino Annihilations at the Centre of the Earth with 1997-99 Data

The nature of the dark matter in the Universe is one of the greatest mysteries in modern astronomy. The neutralino is a nonbaryonic dark matter candidate in minimal supersymmetric extensions to the standard model of particle physics. If the dark matter halo of our galaxy is made up of neutralinos some would become gravitationally trapped inside massive bodies like the Earth. Their pair-wise annihilation produces neutrinos that can be detected by neutrino experiments looking in the direction of the centre of the Earth. The AMANDA neutrino telescope, currently the largest in the world, consists of an array of light detectors buried deep in the Antarctic glacier at the geographical South Pole. The extremely transparent ice acts as a Cherenkov medium for muons passing the array and using the timing information of detected photons it is possible to reconstruct the muon direction. A search has been performed for nearly vertically upgoing neutrino induced muons with AMANDA-B10 data taken over the three year period 1997-99. No excess above the atmospheric neutrino background expectation was found. Upper limits at the 90 % confidence level has been set on the annihilation rate of neutralinos at the centre of the Earth and on the muon flux induced by neutrinos created by the annihilation products.

Infraestructura polivalente basada en sensores inalámbricos aplicada a la monitorización medioambiental georreferenciada.

Máster Universitario en Sistemas Inteligentes y Aplicaciones Numéricas en Ingeniería (SIANI)

Existence of solutions and asymtptotic limits of the Euler-Poisson and the quantum drift-diffusion systems

My work concerns two different systems of equations used in the mathematical modeling of semiconductors and plasmas: the Euler-Poisson system and the quantum drift-diffusion system. The first is given by the Euler equations for the conservation of mass and momentum, with a Poisson equation for the electrostatic potential. The second one takes into account the physical effects due to the smallness of the devices (quantum effects). It is a simple extension of the classical drift-diffusion model which consists of two continuity equations for the charge densities, with a Poisson equation for the electrostatic potential. Using an asymptotic expansion method, we study (in the steady-state case for a potential flow) the limit to zero of the three physical parameters which arise in the Euler-Poisson system: the electron mass, the relaxation time and the Debye length. For each limit, we prove the existence and uniqueness of profiles to the asymptotic expansion and some error estimates. For a vanishing electron mass or a vanishing relaxation time, this method gives us a new approach in the convergence of the Euler-Poisson system to the incompressible Euler equations. For a vanishing Debye length (also called quasineutral limit), we obtain a new approach in the existence of solutions when boundary layers can appear (i.e. when no compatibility condition is assumed). Moreover, using an iterative method, and a finite volume scheme or a penalized mixed finite volume scheme, we numerically show the smallness condition on the electron mass needed in the existence of solutions to the system, condition which has already been shown in the literature. In the quantum drift-diffusion model for the transient bipolar case in one-space dimension, we show, by using a time discretization and energy estimates, the existence of solutions (for a general doping profile). We also prove rigorously the quasineutral limit (for a vanishing doping profile). Finally, using a new time discretization and an algorithmic construction of entropies, we prove some regularity properties for the solutions of the equation obtained in the quasineutral limit (for a vanishing pressure). This new regularity permits us to prove the positivity of solutions to this equation for at least times large enough.

Applications of remote sensing and geographic information systems in geomorphological studies: Safaga - El Quseir area, Red Sea coast, Egypt as an example

In den letzten drei Jahrzehnten sind Fernerkundung und GIS in den Geowissenschaften zunehmend wichtiger geworden, um die konventionellen Methoden von Datensammlung und zur Herstellung von Landkarten zu verbessern. Die vorliegende Arbeit befasst sich mit der Anwendung von Fernerkundung und geographischen Informationssystemen (GIS) für geomorphologische Untersuchungen. Durch die Kombination beider Techniken ist es vor allem möglich geworden, geomorphologische Formen im Überblick und dennoch detailliert zu erfassen. Als Grundlagen werden in dieser Arbeit topographische und geologische Karten, Satellitenbilder und Klimadaten benutzt. Die Arbeit besteht aus 6 Kapiteln. Das erste Kapitel gibt einen allgemeinen Überblick über den Untersuchungsraum. Dieser umfasst folgende morphologische Einheiten, klimatischen Verhältnisse, insbesondere die Ariditätsindizes der Küsten- und Gebirgslandschaft sowie das Siedlungsmuster beschrieben. Kapitel 2 befasst sich mit der regionalen Geologie und Stratigraphie des Untersuchungsraumes. Es wird versucht, die Hauptformationen mit Hilfe von ETM-Satellitenbildern zu identifizieren. Angewandt werden hierzu folgende Methoden: Colour Band Composite, Image Rationing und die sog. überwachte Klassifikation. Kapitel 3 enthält eine Beschreibung der strukturell bedingten Oberflächenformen, um die Wechselwirkung zwischen Tektonik und geomorphologischen Prozessen aufzuklären. Es geht es um die vielfältigen Methoden, zum Beispiel das sog. Image Processing, um die im Gebirgskörper vorhandenen Lineamente einwandfrei zu deuten. Spezielle Filtermethoden werden angewandt, um die wichtigsten Lineamente zu kartieren. Kapitel 4 stellt den Versuch dar, mit Hilfe von aufbereiteten SRTM-Satellitenbildern eine automatisierte Erfassung des Gewässernetzes. Es wird ausführlich diskutiert, inwieweit bei diesen Arbeitsschritten die Qualität kleinmaßstäbiger SRTM-Satellitenbilder mit großmaßstäbigen topographischen Karten vergleichbar ist. Weiterhin werden hydrologische Parameter über eine qualitative und quantitative Analyse des Abflussregimes einzelner Wadis erfasst. Der Ursprung von Entwässerungssystemen wird auf der Basis geomorphologischer und geologischer Befunde interpretiert. Kapitel 5 befasst sich mit der Abschätzung der Gefahr episodischer Wadifluten. Die Wahrscheinlichkeit ihres jährlichen Auftretens bzw. des Auftretens starker Fluten im Abstand mehrerer Jahre wird in einer historischen Betrachtung bis 1921 zurückverfolgt. Die Bedeutung von Regentiefs, die sich über dem Roten Meer entwickeln, und die für eine Abflussbildung in Frage kommen, wird mit Hilfe der IDW-Methode (Inverse Distance Weighted) untersucht. Betrachtet werden außerdem weitere, regenbringende Wetterlagen mit Hilfe von Meteosat Infrarotbildern. Genauer betrachtet wird die Periode 1990-1997, in der kräftige, Wadifluten auslösende Regenfälle auftraten. Flutereignisse und Fluthöhe werden anhand von hydrographischen Daten (Pegelmessungen) ermittelt. Auch die Landnutzung und Siedlungsstruktur im Einzugsgebiet eines Wadis wird berücksichtigt. In Kapitel 6 geht es um die unterschiedlichen Küstenformen auf der Westseite des Roten Meeres zum Beispiel die Erosionsformen, Aufbauformen, untergetauchte Formen. Im abschließenden Teil geht es um die Stratigraphie und zeitliche Zuordnung von submarinen Terrassen auf Korallenriffen sowie den Vergleich mit anderen solcher Terrassen an der ägyptischen Rotmeerküste westlich und östlich der Sinai-Halbinsel.

Reproduction and maternal health care among young women in Kenya: geographic and socio-economic determinants

Many factors influence the propensity of young women to seek appropriate maternal healthcare, and they need to be considered when analyzing these women’s reproductive behavior. This study aimed to contribute to the analysis concerning Kenyan young women’s determinants on maternal healthcare-seeking behavior for the 5 years preceding the 2008/9 Kenya Demographic and Health Survey. The specific objectives were to: investigate the individual and contextual variables that may explain maternal healthcare habits; measure the individual, household and community effect on maternal healthcare attitudes in young women; assess the link between young women’s characteristics and the use of facilities for maternal healthcare; find a relationship between young women’s behavior and the community where they live; examine how the role of the local presence of healthcare facilities influences reproductive behavior, and if the specificity of services offered by healthcare facilities affects their inclination to use healthcare facilities, and measure the geographic differences that influence the propensity to seek appropriate maternal healthcare. The analysis of factors associated with maternal healthcare-seeking behavior for young women in Kenya was investigated using multilevel models. We performed three major analyses, which concerned the individual and contextual determinants influencing antenatal care (discussed in Part 6), delivery care (Part 7), and postnatal care (Part 8). Our results show that there is a significant variation in antenatal, delivery and postnatal care between communities, even if the majority of variability is explained by individual characteristics. There are differences at the women’s level on the probability of receiving antenatal care and delivering in a healthcare facility instead of at home. Moreover, community factors and availability of healthcare facilities on the territory are also crucial in influencing young women’s behavior. Therefore, policies addressed to youth’s reproductive health should also consider geographic inequalities and different types of barriers in access to healthcare facilities.

Measurement of the ZZ production cross section and limits on anomalous neutral triple gauge couplings with ATLAS

The main work of this thesis concerns the measurement of the production cross section using LHC 2011 data collected at a center-of-mass energy equal to 7 TeV by the ATLAS detector and resulting in a total integrated luminosity of 4.6 inverse fb. The ZZ total cross section is finally compared with the NLO prediction calculated with modern Monte Carlo generators. In addition, the three differential distributions (∆φ(l,l), ZpT and M4l) are shown unfolded back to the underlying distributions using a Bayesian iterative algorithm. Finally, the transverse momentum of the leading Z is used to provide limits on anoumalus triple gauge couplings forbidden in the Standard Model.