Two sequential PCR amplifications for detection of Schistosoma mansoni in stool samples with low parasite load

Schistosomiasis constitutes a major public health problem, with an estimated 200 million individuals infected worldwide and 700 million people living in risk areas. In Brazil there are areas of high, medium and low endemicity. Studies have shown that in endemic areas with a low prevalence of Schistosoma infection the sensitivity of parasitological methods is clearly reduced. Consequently diagnosis is often impeded due to the presence of false-negative results. The aim of this study is to present the PCR reamplification (Re-PCR) protocol for the detection of Schistosoma mansoni in samples with low parasite load (with less than 100 eggs per gram (epg) of feces). Three methods were used for the lysis of the envelopes of the S. mansoni eggs and two techniques of DNA extraction were carried out. Extracted DNA was quantified, and the results suggested that the extraction technique, which mixed glass beads with a guanidine isothiocyanate/phenol/chloroform (GT) solution, produced good results. PCR reamplification was conducted and detection sensitivity was found to be five eggs per 500 mg of artificially marked feces. The results achieved using these methods suggest that they are potentially viable for the detection of Schistosoma infection with low parasite load.

Speciation and fractionation of Ca and the REE in fresh and marine waters

This study is concerned with speciation and fractionation of the rare earth elements (REE) and calcium (Ca) in aqueous solutions. The aim is to investigate the chemical states and physical sizes in which these elements can be present. The REE (including neodymium) and Ca have contrasting geochemical behavior in aqueous solutions. Ca is a major dissolved element, while the REE are trace components and highly reactive with aquatic particles. The major interests of the five papers included in this thesis are the following: · Papers I and V deal with the behavior of neodymium (Nd) and its isotopes in the Kalix River and some marine waters. · The diffusive gradients in thin-films (DGT) method is developed for measuring Ca and Mg in Paper II. · Paper III presents a speciation and fractionation study of Ca in the Kalix and Amazonian rivers. · The rare earth elements and their carrier phases are investigated in the Kalix river in Paper IV. For most elements a detailed study of speciation and fractionation can not be performed using only one method. This is due to the overall heterogeneity of the material, considering both size and chemical composition, which is present in aquatic solutions. During this project the aquatic geochemistry of the REE and Ca has been studied using mainly three methods; cross-flow filtration (CFF), field-flow fractionation (FFF) and diffusive gradients in thin-films (DGT). Field work has to a large part been conducted in the Kalix River, in northern Sweden, which is one of the last pristine river systems in Europe. Some field work has also been conducted in the Baltic Sea and the Arctic Ocean. Results from Amazonian rivers are also presented. These are the main conclusions from this work: The DGT technique works equally well for measuring Ca and Mg in natural waters as previously reported for trace metal. A significant colloidal phase for Ca could be detected in the Kalix River and in different Amazonian rivers. This was concluded independently using both CFF and FFF. Variations in REE signatures in the Kalix River suggests two different pathways for the REE during weathering and release form soil profiles and transport in the river. No significant variation in Nd-isotopic composition could be detected in the Kalix River although concentrations varied by a factor of ~10. This suggests that there is one major source for Nd in the river although different pathways for the REE may exist. A study of Nd in the Kalix River, the Baltic Sea and the Arctic Ocean showed that the isotopic compositions in the diffusible fractions were similar to water samples. However, the relative amount of diffusible Nd increased with salinity, probably reflecting the lower concentration of colloidal and particulate material in marine waters.

The release of zinc and lead from mine tailings

Mining and processing of metal ores are important causes of soil and groundwater contamination in many regions worldwide. Metal contaminations are a serious risk for the environment and human health. The assessment of metal contaminations in the soil is therefore an important task. A common approach to assess the environmental risk emanating from inorganic contaminations to soil and groundwater is the use of batch or column leaching tests. In this regard, the suitability of leaching tests is a controversial issue. In the first part of this work the applicability and comparability of common leaching tests in the scope of groundwater risk assessment of inorganic contamination is reviewed and critically discussed. Soil water sampling methods (the suction cup method and centrifugation) are addressed as an alternative to leaching tests. Reasons for limitations of the comparability of leaching test results are exposed and recommendations are given for the expedient application of leaching tests for groundwater risk assessment. Leaching tests are usually carried out in open contact with the atmosphere disregarding possible changes of redox conditions. This can affect the original metal speciation and distribution, particularly when anoxic samples are investigated. The influence of sample storage on leaching test results of sulfide bearing anoxic material from a former flotation dump is investigated in a long-term study. Since the oxidation of the sulfide-bearing samples leads to a significant overestimation of metal release, a feasible modification for the conduction of common leaching tests for anoxic material is proposed, where oxidation is prevented efficiently. A comparison of leaching test results to soil water analyzes have shown that the modified saturation soil extraction (SSE) is found to be the only of the tested leaching procedures, which can be recommended for the assessment of current soil water concentrations at anoxic sites if direct investigation of the soil water is impossible due to technical reasons. The vertical distribution and speciation of Zn and Pb in the flotation residues as well as metal concentrations in soil water and plants were investigated to evaluate the environmental risk arising from this site due to the release of metals. The variations in pH and inorganic C content show an acidification of the topsoil with pH values down to 5.5 in the soil and a soil water pH of 6 in 1 m depth. This is due to the oxidation of sulfides and depletion in carbonates. In the anoxic subsoil pH conditions are still neutral and soil water collected with suction cups is in equilibrium with carbonate minerals. Results from extended x-ray absorption fine-structure (EXAFS) spectroscopy confirm that Zn is mainly bound in sphalerite in the subsoil and weathering reactions lead to a redistribution of Zn in the topsoil. A loss of 35% Zn and S from the topsoil compared to the parent material with 10 g/kg Zn has been observed. 13% of total Zn in the topsoil can be regarded as mobile or easily mobilizable according to sequential chemical extractions (SCE). Zn concentrations of 10 mg/L were found in the soil water, where pH is acidic. Electron supply and the buffer capacity of the soil were identified as main factors controlling Zn mobility and release to the groundwater. Variable Pb concentrations up to 30 µg/L were observed in the soil water. In contrast to Zn, Pb is enriched in the mobile fraction of the oxidized topsoil by a factor of 2 compared to the subsoil with 2 g/kg Pb. 80% of the cation exchange capacity in the topsoil is occupied by Pb. Therefore, plant uptake and bioavailability are of major concern. If the site is not prevented from proceeding acidification in the future, a significant release of Zn, S, and Pb to the groundwater has to be expected. Results from this study show that the assessment of metal release especially from sulfide bearing anoxic material requires an extensive comprehension of leaching mechanisms on the one hand and on weathering processes, which influence the speciation and the mobility of metals, on the other hand. Processes, which may change redox and pH conditions in the future, have to be addressed to enable sound decisions for soil and groundwater protection and remediation.

Speciation of Pu(III) in the environmental system humic substances-groundwater-kaolinite

For the safety assessments of nuclear waste repositories, the possible migration of the radiotoxic waste into environment must be considered. Since plutonium is the major contribution at the radiotoxicity of spent nuclear waste, it requires special care with respect to its mobilization into the groundwater. Plutonium has one of the most complicated chemistry of all elements. It can coexist in 4 oxidation states parallel in one solution. In this work is shown that in the presence of humic substances it is reduced to the Pu(III) and Pu(IV). This work has the focus on the interaction of Pu(III) with natural occurring compounds (humic substances and clay minerals bzw. Kaolinite), while Pu(IV) was studied in a parallel doctoral work by Banik (in preparation). As plutonium is expected under extreme low concentrations in the environment, very sensitive methods are needed to monitor its presence and for its speciation. Resonance ionization mass spectrometry (RIMS), was used for determining the concentration of Pu in environmental samples, with a detection limit of 106- 107 atoms. For the speciation of plutonium CE-ICP-MS was routinely used to monitor the behaviour of Pu in the presence of humic substances. In order to reduce the detection limits of the speciation methods, the coupling of CE to RIMS was proposed. The first steps have shown that this can be a powerful tool for studies of pu under environmental conditions. Further, the first steps in the coupling of two parallel working detectors (DAD and ICP_MS ) to CE was performed, for the enabling a precise study of the complexation constants of plutonium with humic substances. The redox stabilization of Pu(III) was studied and it was determined that NH2OHHCl can maintain Pu(III) in the reduced form up to pH 5.5 – 6. The complexation constants of Pu(III) with Aldrich humic acid (AHA) were determined at pH 3 and 4. the logß = 6.2 – 6.8 found for these experiments was comparable with the literature. The sorption of Pu(III) onto kaolinite was studied in batch experiments and it was determine dthat the pH edge was at pH ~ 5.5. The speciation of plutonium on the surface of kaolinite was studied by EXAFS/XANES. It was determined that the sorbed species was Pu(IV). The influence of AHA on the sorption of Pu(III) onto kaolinite was also investigated. It was determined that at pH < 5 the adsorption is enhanced by the presence of AHA (25 mg/L), while at pH > 6 the adsorption is strongly impaired (depending also on the adding sequence of the components), leading to a mobilization of plutonium in solution.

Speciation of tetravalent plutonium in contact with humic substances and kaolinite under environmental conditions

Plutonium represents the major contribution to the radiotoxicity of spent nuclear fuel over storage times of up to several hundred thousand years. The speciation of plutonium in aquifer systems is important in order to assess the risks of high-level nuclear waste disposal and to acquire a deep knowledge of the mobilization and immobilization behavior of plutonium. In aqueous solutions, plutonium can coexist in four oxidation states and each one of them has different chemical and physical behavior. Tetravalent plutonium is the most abundant under natural conditions. Therefore, detailed speciation studies of tetravalent plutonium in contact with humic substances (HS) and kaolinite as a model clay mineral have been performed in this work. Plutonium is present in the environment at an ultratrace level. Therefore, speciation of Pu at the ultratrace level is mandatory. Capillary electrophoresis (CE) coupled to resonance ionization mass spectrometry (RIMS) was used as a new speciation method. CE-RIMS enables to improve the detection limit for plutonium species by 2 to 3 orders of magnitude compared to the previously developed CE-ICP-MS. For understanding the behavior of Pu(IV) in aqueous systems, redox reactions, complexation, and sorption behavior of plutonium were studied. The redox behavior of plutonium in contact with humic acid (HA) and fulvic acid (FA) was investigated. A relatively fast reduction of Pu(VI) in contact with HS was observed. It was mainly reduced to Pu(IV) and Pu(III) within a couple of weeks. The time dependence of the Pu(IV) complexation with Aldrich HA was investigated and a complex constant (logßLC) between 6.4 - 8.4 of Pu(IV) was determined by means of ultrafiltration taking into account the loading capacity (LC). The sorption of tetravalent plutonium onto kaolinite was investigated as a function of pH in batch experiments under aerobic and anaerobic conditions. The sorption edge was found at about pH = 1 and a maximum sorption at around pH = 8.5. In the presence of CO2 at pH > 8.5, the sorption of plutonium was decreased probably due to the formation of soluble carbonate complexes. For comparison, the sorption of Th(IV) onto kaolinite was also investigated and consistent results were found. The Pu(IV) sorption onto kaolinite was studied by XANES and EXAFS at pH 1, 4, 9 and the sorbed species on kaolinite surface was Pu(IV). Depending on the pH, only 1 - 10 % of the sorbed plutonium is desorbed from kaolinite and released into a fresh solution at the same pH value. Furthermore, the sorption of HS onto kaolinite was studied as a function of pH at varying concentrations of HS, as a prerequisite to understand the more complex ternary system. The sorption of HA onto kaolinite was found to be higher than that of FA. The investigation of the ternary systems (plutonium-kaolinite-humic substances) is performed as a function of pH, concentration of HS, and the sequences of adding the reactants. The presence of HS strongly influences the sorption of Pu(IV) onto kaolinite over the entire pH range. For comparison, the influence of HS on the sorption of Th(IV) onto kaolinite was also investigated and a good agreement with the results of Pu(IV) was obtained.

Ortsaufgelöste Speziation von Schwermetallen in geogenen Proben mit Röntgenabsorptionsspektrometrie (my-XAS)

Die Vergesellschaftung und Bindungsform von Arsen in Düngekalk wurde durch chemische und mineralogische Analysen sowie XANES/EXAFS-Messungen untersucht. Die durch-schnittliche As-Konzentration im Düngekalk (70 mg/kg) überschreitet den Grenzwert der DüMV (40 mg/kg). Arsen ist in Mn- (Romanechit) und Fe-Dendriten (Goethit, Ferrihydrit) angereichert. Seine Oxidationsstufe ist jeweils 5+. µ-EXAFS-Untersuchungen ergaben Hin-weise auf zweizähnige und einzähnige mononukleare Durchdringungskomplexe mit Eisen-oxid. Das Mobilisierungsverhalten von Arsen wurde durch sequentielle Extraktion des Dün-gekalks und Mobilisierungsversuche mit wassergesättigtem Boden untersucht. Die Lösung erfolgte vorwiegend im dritten Extraktionsschritt gemeinsam mit kristallinen Eisenoxiden. Unter moderat anoxischen Bedingungen war im Boden keine zusätzliche Mobilisierung von Arsen aus dem Düngekalk nachweisbar. Erhöhte As-Konzentrationen und As3+-Anteile im Porenwasser traten bei niedrigem Eh unabhängig von Kalkzugabe auf. Eine Kopplung des Arsen-Grenzwerts an den Eisenoxidgehalt erscheint sinnvoll. Ein Messaufbau für Mikro-XAS Imaging wurde in Betrieb genommen. Er ermöglicht die si-multane Erfassung einer Probenfläche von 26,6×6,6 mm² wahlweise im Transmissions- oder Fluoreszenzmodus mit der räumlichen Auflösung 52×52 µm² durch eine CCD-Kamera. Zur Datenverarbeitung wurden IDL-Programme sowie die Fernerkundungssoftware ENVI ver-wendet. Die Messergebnisse zeigen weniger Störungen und Rauschen als die Ergebnisse frü-herer Messungen mit einem Prototyp. Die Ergebnisse und Erfahrungen der Messungen liefern Hinweise für die weitere erfolgreiche Nutzung des Messaufbaus.

Study of the interactions of Neptunium with humic substances and the clay mineral montmorillonite by direct and non direct speciation methods

For the safety assessment of radioactive waste, the possibility of radionuclide migration has to be considered. Since Np (and also Th due to the long-lived 232-Th) will be responsible for the greatest amount of radioactivity one million years after discharge from the reactor, its (im)-mobilization in the geosphere is of great importance. Furthermore, the chemistry of Np(V) is quite similar (but not identical) to the chemistry of Pu(V). Three species of neptunium may be found in the near field of the waste disposal, but pentavalent neptunium is the most abundant species under a wide range of natural conditions. Within this work, the interaction of Np(V) with the clay mineral montmorillonite and melanodins (as model substances for humic acids) was studied. The sorption of neptunium onto gibbsite, a model clay for montmorillonite, was also investigated. The sorption of neptunium onto γ-alumina and montmorillonite was studied in a parallel doctoral work by S. Dierking. Neptunium is only found in ultra trace amounts in the environment. Therefore, sensitive and specific methods are needed for its determination. The sorption was determined by γ spectroscopy and LSC for the whole concentration range studied. In addition the combination of these techniques with ultrafiltration allowed the study of Np(V) complexation with melanoidins. Regrettably, the available speciation methods (e.g. CE-ICP-MS and EXAFS) are not capable to detect the environmentally relevant neptunium concentrations. Therefore, a combination of batch experiments and speciation analyses was performed. Further, the preparation of hybrid clay-based materials (HCM) montmorillonitemelanoidins for sorption studies was achieved. The formation of hybrid materials begins in the interlayers of the montmorillonite, and then the organic material spreads over the surface of the mineral. The sorption of Np onto HCM was studied at the environmentally relevant concentrations and the results obtained were compared with those predicted by the linear additive model by Samadfam. The sorption of neptunium onto gibbsite was studied in batch experiments and the sorption maximum determined at pH~8.5. The sorption isotherm pointed to the presence of strong and weak sorption sites in gibbsite. The Np speciation was studied by using EXAFS, which showed that the sorbed species was Np(V). The influence of M42 type melanodins on the sorption of Np(V) onto montmorillonite was also investigated at pH 7. The sorption of the melanoidins was affected by the order in which the components were added and by ionic strength. The sorption of Np was affected by ionic strength, pointing to outer sphere sorption, whereas the presence of increasing amounts of melanoidins had little influence on Np sorption.

Iodine speciation in atmospheric aerosols in the marine boundary layer

Iodine chemistry plays an important role in the tropospheric ozone depletion and the new particle formation in the Marine Boundary Layer (MBL). The sources, reaction pathways, and the sinks of iodine are investigated using lab experiments and field observations. The aims of this work are, firstly, to develop analytical methods for iodine measurements of marine aerosol samples especially for iodine speciation in the soluble iodine; secondly, to apply the analytical methods in field collected aerosol samples, and to estimate the characteristics of aerosol iodine in the MBL. Inductively Coupled Plasma – Mass Spectrometry (ICP-MS) was the technique used for iodine measurements. Offline methods using water extraction and Tetra-methyl-ammonium-hydroxide (TMAH) extraction were applied to measure total soluble iodine (TSI) and total insoluble iodine (TII) in the marine aerosol samples. External standard calibration and isotope dilution analysis (IDA) were both conducted for iodine quantification and the limits of detection (LODs) were both 0.1 μg L-1 for TSI and TII measurements. Online couplings of Ion Chromatography (IC)-ICP-MS and Gel electrophoresis (GE)-ICP-MS were both developed for soluble iodine speciation. Anion exchange columns were adopted for IC-ICP-MS systems. Iodide, iodate, and unknown signal(s) were observed in these methods. Iodide and iodate were separated successfully and the LODs were 0.1 and 0.5 μg L-1, respectively. Unknown signals were soluble organic iodine species (SOI) and quantified by the calibration curve of iodide, but not clearly identified and quantified yet. These analytical methods were all applied to the iodine measurements of marine aerosol samples from the worldwide filed campaigns. The TSI and TII concentrations (medians) in PM2.5 were found to be 240.87 pmol m-3 and 105.37 pmol m-3 at Mace Head, west coast of Ireland, as well as 119.10 pmol m-3 and 97.88 pmol m-3 in the cruise campaign over the North Atlantic Ocean, during June – July 2006. Inorganic iodine, namely iodide and iodate, was the minor iodine fraction in both campaigns, accounting for 7.3% (median) and 5.8% (median) in PM2.5 iodine at Mace Head and over the North Atlantic Ocean, respectively. Iodide concentrations were higher than iodate in most of the samples. In the contrast, more than 90% of TSI was SOI and the SOI concentration was correlated significantly with the iodide concentration. The correlation coefficients (R2) were both higher than 0.5 at Mace Head and in the first leg of the cruise. Size fractionated aerosol samples collected by 5 stage Berner impactor cascade sampler showed similar proportions of inorganic and organic iodine. Significant correlations were obtained in the particle size ranges of 0.25 – 0.71 μm and 0.71 – 2.0 μm between SOI and iodide, and better correlations were found in sunny days. TSI and iodide existed mainly in fine particle size range (< 2.0 μm) and iodate resided in coarse range (2.0 – 10 μm). Aerosol iodine was suggested to be related to the primary iodine release in the tidal zone. Natural meteorological conditions such as solar radiation, raining etc were observed to have influence on the aerosol iodine. During the ship campaign over the North Atlantic Ocean (January – February 2007), the TSI concentrations (medians) ranged 35.14 – 60.63 pmol m-3 among the 5 stages. Likewise, SOI was found to be the most abundant iodine fraction in TSI with a median of 98.6%. Significant correlation also presented between SOI and iodide in the size range of 2.0 – 5.9 μm. Higher iodate concentration was again found in the higher particle size range, similar to that at Mace Head. Airmass transport from the biogenic bloom region and the Antarctic ice front sector was observed to play an important role in aerosol iodine enhancement. The TSI concentrations observed along the 30,000 km long cruise round trip from East Asia to Antarctica during November 2005 – March 2006 were much lower than in the other campaigns, with a median of 6.51 pmol m-3. Approximately 70% of the TSI was SOI on average. The abundances of inorganic iodine including iodine and iodide were less than 30% of TSI. The median value of iodide was 1.49 pmol m-3, which was more than four fold higher than that of iodate (median, 0.28 pmol m-3). Spatial variation indicated highest aerosol iodine appearing in the tropical area. Iodine level was considerably lower in coastal Antarctica with the TSI median of 3.22 pmol m-3. However, airmass transport from the ice front sector was correlated with the enhance TSI level, suggesting the unrevealed source of iodine in the polar region. In addition, significant correlation between SOI and iodide was also shown in this campaign. A global distribution in aerosol was shown in the field campaigns in this work. SOI was verified globally ubiquitous due to the presence in the different sampling locations and its high proportion in TSI in the marine aerosols. The correlations between SOI and iodide were obtained not only in different locations but also in different seasons, implying the possible mechanism of iodide production through SOI decomposition. Nevertheless, future studies are needed for improving the current understanding of iodine chemistry in the MBL (e.g. SOI identification and quantification as well as the update modeling involving organic matters).

Sorption and direct speciation of neptunium(V) on aluminium oxide and montmorillonite

This study comprised batch experiments, direct speciation studies via EXAFS, and modelling with the 2SPNE SC/CE model to elucidate the mechanisms of Np(V) sorption on montmorillonite and, for reference, on γ-Al2O3. The sorption of pM 239Np(V) and µM 237Np(V) on montmorillonite (STx-1, 4 g/L) and γ-Al2O3 (0.5 g/L) was studied at room temperature in the presence and absence of ambient CO2 covering a pH-range from 2.5 (STx-1) or 5 (γ-Al2O3) to 10.5 with 0.01 or 0.1M NaClO4 as background electrolyte. The Np(V) uptake was determined by γ spectroscopy of the supernatants and calculated as percentage as well as distribution coefficient Kd. Sorption starts from pH ~6 and, under exclusion of CO2, increases continuously, while, in the presence of ambient air, it reaches a maximum at pH ~8.5 (γ-Al2O3: log Kd max ≈ 4 mL/g; STx-1: log Kd max ≈ 2.7 mL/g). Beyond that it decreases again due to the formation of queous neptunium carbonate complexes. Furthermore, neptunium sorption on montmorillonite is influenced by ionic strength at pH <6 through ion exchange processes pointing towards the formation of outer-sphere surface complexes there. Isotherms measured at the sorption maximum showed the precipitation of resumably neptunium carbonate complexes above 3∙10^-5 M under ambient air conditions. Additionally, they indicated progressive saturation of the sorption sites of γ-Al2O3. At selected pH (STx-1: 5.0, 7.0, 8.0, 8.5, 9.0, 9.5; γ-Al2O3: 8.5, 9.5) EXAFS samples were prepared as wet pastes with µM 237Np and measured at room temperature in fluorescence mode at ANKA and ESRF. Several spectra were averaged and analysed with EXAFSPAK and FEFF 8.20 employing models of NaNpO2(CO3) or soddyite, (UO2)2SiO4∙2(H2O). The shorter atomic distances of the neptunyl ion at pH 5 compared to the others hinted at the retention of the hydration shell and, thus, at outer-sphere sorption. On average the bond lengths for Np(V) sorbed on STx-1 at high pH were Oax ≈ 1.84 Å and Oeq ≈ 2.53 Å. At high pH, ternary neptunyl carbonate surface complexes could be identified for montmorillonite (C ≈ 3.00 Å), but not for γ-Al2O3, where an interaction of neptunium with the aluminium surface atoms according to the soddyite model gave better agreement with the experimental data. However, neither structure as suggested by the two models could be excluded for both systems rendering a combination most likely. Modelling of the sorption data provided further evidence for the existence of ternary neptunium carbonate surface complexes in both cases. The results of this study can aid environmental risk assessment for clay-based nuclear waste repositories by providing valuable input data for simulations of radionuclide migration from a final disposal site.

Transposable elements dynamics in taxa with different reproductive strategies or speciation rate

In recent years the advances in genomics allowed to understand the importance of Transposable Elements (TE) in the evolution of eukaryotic genomes. In this thesis I face two aspects of the TE impact on the in the animal kingdom. The first part is a comparison of the dynamics of the TE dynamics in three species of stick-insects of the Genus Bacillus. I produced three random genomic libraries of 200 Kbps for the three parental species of the taxon: a gonochoric population of Bacillus rossius (facultative parthenogenetic), Bacillus grandii (gonochoric) and Bacillus atticus (obligate parthenogenetic). The unisexual taxon Bacillus atticus does not shows dramatic differences in TE total content and activity with respect to Bacillus grandii and Bacillus rossius. This datum does not confirm the trend observed in other animal models in which unisexual taxa tend to repress the activity of TE to escape the extinction by accumulation of harmful mutations. In the second part I tried to add a contribute to the debate initiated in recent years about the possibility that a high TE content is linked to a high rate of speciation. I designed an evolutionary framework to establish the different rate of speciation among two or more taxa, then I compared TE dynamics considering the different rates of speciation. The species dataset comprises: 29 mammals, four birds, two fish and two insects. On the whole the majority of comparisons confirms the expected trend. In particular the amount of species analyzed in Mammalia allowed me to get a statistical support (p<0,05) of the fact that the TE activity of recently mobilized elements is positively related with the rate of speciation.

Deadlock analysis of asynchronous sequential processes

In this thesis we present ad study an object-oriented language, characterized by two different types of objects, passive and active objects, of which we define the operational syntax and semantics. For this language we also define the type system, that will be used for the type checking and for the extraction of behavioral types, which are an abstract description of the behavior of the methods, used in deadlock analysis. Programs can manifest deadlock due to the errors of the programmer. To statically identify possible unintended behaviors we studied and implemented a technique for the analysis of deadlock based on behavioral types.

A sequential Cox approach for estimating the causal effect of treatment in the presence of time-dependent confounding applied to data from the Swiss HIV Cohort Study

When estimating the effect of treatment on HIV using data from observational studies, standard methods may produce biased estimates due to the presence of time-dependent confounders. Such confounding can be present when a covariate, affected by past exposure, is both a predictor of the future exposure and the outcome. One example is the CD4 cell count, being a marker for disease progression for HIV patients, but also a marker for treatment initiation and influenced by treatment. Fitting a marginal structural model (MSM) using inverse probability weights is one way to give appropriate adjustment for this type of confounding. In this paper we study a simple and intuitive approach to estimate similar treatment effects, using observational data to mimic several randomized controlled trials. Each 'trial' is constructed based on individuals starting treatment in a certain time interval. An overall effect estimate for all such trials is found using composite likelihood inference. The method offers an alternative to the use of inverse probability of treatment weights, which is unstable in certain situations. The estimated parameter is not identical to the one of an MSM, it is conditioned on covariate values at the start of each mimicked trial. This allows the study of questions that are not that easily addressed fitting an MSM. The analysis can be performed as a stratified weighted Cox analysis on the joint data set of all the constructed trials, where each trial is one stratum. The model is applied to data from the Swiss HIV cohort study.

Sequential female assessment drives complex sexual selection on bower shape in a cichlid fish

In many animals, sexual selection on male traits results from female mate choice decisions made during a sequence of courtship behaviors. We use a bower-building cichlid fish, Nyassachromis cf. microcephalus, to show how applying standard selection analysis to data on sequential female assessment provides new insights into sexual selection by mate choice. We first show that the cumulative selection differentials confirm previous results suggesting female choice favors males holding large volcano-shaped sand bowers. The sequential assessment analysis reveals these cumulative differentials are the result of selection acting on different bower dimensions during the courtship sequence; females choose to follow males courting from tall bowers, but choose to engage in premating circling with males holding bowers with large diameter platforms. The approach we present extends standard selection analysis by partitioning the variances of increasingly accurate estimates of male reproductive fitness and is applicable to systems in which sequential female assessment drives sexual selection on male traits.