The Use of Agricultural Chemicals and Mosquito Response to Pyrethroids in Bungoma Sub-county,Western Kenya

Insecticide treated bed nets and indoor residual spraying are the most widely used vector control methods in Africa. The World Health Organization now recommends four classes of insecticides for use against adult mosquitoes in public health programs. Of these four classes of insecticides, pyrethroids have become the insecticides of choice in treating mosquito bed nets and in the use of indoor spraying to prevent malaria transmission. Pyrethroids are not only used in malaria control but also in agriculture to protect against pest insects. This concurrent use of pyrethroids in vector control and protection of crops from pests in agriculture may exert selection pressure on mosquito larval population and induce resistance to this class of insecticides. The main objective of our study was to explore the role of agricultural chemicals and the response of mosquitoes to pyrethroids in an area of high malaria transmission.

We used a cross-sectional study design. This was a two-step study involving both mosquitoes and human subjects. In this study, we collected larvae growing in breeding sites affected by different agricultural practices. We used purposive sampling to identify active mosquito breeding sites and then interviewed households adjacent to those breeding sites to learn about their agricultural practices that might influence the response of mosquitoes to pyrethroids. We also performed secondary analysis of larval data from a previous case-control study by Obala et al.

Enzymatic Polymerization of High Molecular Weight DNA

The use of DNA as a polymeric building material transcends its function in biology and is exciting in bionanotechnology for applications ranging from biosensing, to diagnostics, and to targeted drug delivery. These applications are enabled by DNA’s unique structural and chemical properties, embodied as a directional polyanion that exhibits molecular recognition capabilities. Hence, the efficient and precise synthesis of high molecular weight DNA materials has become key to advance DNA bionanotechnology. Current synthesis methods largely rely on either solid phase chemical synthesis or template-dependent polymerase amplification. The inherent step-by-step fashion of solid phase synthesis limits the length of the resulting DNA to typically less than 150 nucleotides. In contrast, polymerase based enzymatic synthesis methods (e.g., polymerase chain reaction) are not limited by product length, but require a DNA template to guide the synthesis. Furthermore, advanced DNA bionanotechnology requires tailorable structural and self-assembly properties. Current synthesis methods, however, often involve multiple conjugating reactions and extensive purification steps.

The research described in this dissertation aims to develop a facile method to synthesize high molecular weight, single stranded DNA (or polynucleotide) with versatile functionalities. We exploit the ability of a template-independent DNA polymerase−terminal deoxynucleotidyl transferase (TdT) to catalyze the polymerization of 2’-deoxyribonucleoside 5’-triphosphates (dNTP, monomer) from the 3’-hydroxyl group of an oligodeoxyribonucleotide (initiator). We termed this enzymatic synthesis method: TdT catalyzed enzymatic polymerization, or TcEP.

Specifically, this dissertation is structured to address three specific research aims. With the objective to generate high molecular weight polynucleotides, Specific Aim 1 studies the reaction kinetics of TcEP by investigating the polymerization of 2’-deoxythymidine 5’-triphosphates (monomer) from the 3’-hydroxyl group of oligodeoxyribothymidine (initiator) using in situ 1H NMR and fluorescent gel electrophoresis. We found that TcEP kinetics follows the “living” chain-growth polycondensation mechanism, and like in “living” polymerizations, the molecular weight of the final product is determined by the starting molar ratio of monomer to initiator. The distribution of the molecular weight is crucially influenced by the molar ratio of initiator to TdT. We developed a reaction kinetics model that allows us to quantitatively describe the reaction and predict the molecular weight of the reaction products.

Specific Aim 2 further explores TcEP’s ability to transcend homo-polynucleotide synthesis by varying the choices of initiators and monomers. We investigated the effects of initiator length and sequence on TcEP, and found that the minimum length of an effective initiator should be 10 nucleotides and that the formation of secondary structures close to the 3’-hydroxyl group can impede the polymerization reaction. We also demonstrated TcEP’s capacity to incorporate a wide range of unnatural dNTPs into the growing chain, such as, hydrophobic fluorescent dNTP and fluoro modified dNTP. By harnessing the encoded nucleotide sequence of an initiator and the chemical diversity of monomers, TcEP enables us to introduce molecular recognition capabilities and chemical functionalities on the 5’-terminus and 3’-terminus, respectively.

Building on TcEP’s synthesis capacities, in Specific Aim 3 we invented a two-step strategy to synthesize diblock amphiphilic polynucleotides, in which the first, hydrophilic block serves as a macro-initiator for the growth of the second block, comprised of natural and/or unnatural nucleotides. By tuning the hydrophilic length, we synthesized the amphiphilic diblock polynucleotides that can self-assemble into micellar structures ranging from star-like to crew-cut morphologies. The observed self-assembly behaviors agree with predictions from dissipative particle dynamics simulations as well as scaling law for polyelectrolyte block copolymers.

In summary, we developed an enzymatic synthesis method (i.e., TcEP) that enables the facile synthesis of high molecular weight polynucleotides with low polydispersity. Although we can control the nucleotide sequence only to a limited extent, TcEP offers a method to integrate an oligodeoxyribonucleotide with specific sequence at the 5’-terminus and to incorporate functional groups along the growing chains simultaneously. Additionally, we used TcEP to synthesize amphiphilic polynucleotides that display self-assemble ability. We anticipate that our facile synthesis method will not only advance molecular biology, but also invigorate materials science and bionanotechnology.

A recessionary debate: who suffered more? A study of sectoral well-being and economic insecurity in Ireland

The aim of this thesis is to identify the relationship between subjective well-being and economic insecurity for public and private sector workers in Ireland using the European Social Survey 2010-2012. Life satisfaction and job satisfaction are the indicators used to measure subjective well-being. Economic insecurity is approximated by regional unemployment rates and self-perceived job insecurity. Potential sample selection bias and endogeneity bias are accounted for. It is traditionally believed that public sector workers are relatively more protected against insecurity due to very institution of public sector employment. The institution of public sector employment is made up of stricter dismissal practices (Luechinger et al., 2010a) and less volatile employment (Freeman, 1987) where workers are subsequently less likely to be affected by business cycle downturns (Clark and Postal-Vinay, 2009). It is found in the literature that economic insecurity depresses the well-being of public sector workers to a lesser degree than private sector workers (Luechinger et al., 2010a; Artz and Kaya, 2014). These studies provide the rationale for this thesis in testing for similar relationships in an Irish context. Sample selection bias arises when a selection into a particular category is not random (Heckman, 1979). An example of this is non-random selection into public sector employment based on personal characteristics (Heckman, 1979; Luechinger et al., 2010b). If selection into public sector employment is not corrected for this can lead to biased and inconsistent estimators (Gujarati, 2009). Selection bias of public sector employment is corrected for by using a standard Two-Step Heckman Probit OLS estimation method. Following Luechinger et al. (2010b), the propensity for individuals to select into public sector employment is estimated by a binomial probit model with the inclusion of the additional regressor Irish citizenship. Job satisfaction is then estimated by Ordinary Least Squares (OLS) with the inclusion of a sample correction term similar as is done in Clark (1997). Endogeneity is where an independent variable included in the model is determined within in the context of the model (Chenhall and Moers, 2007). The econometric definition states that an endogenous independent variable is one that is correlated with the error term (Wooldridge, 2010). Endogeneity is expected to be present due to a simultaneous relationship between job insecurity and job satisfaction whereby both variables are jointly determined (Theodossiou and Vasileiou, 2007). Simultaneity, as an instigator of endogeneity, is corrected for using Instrumental Variables (IV) techniques. Limited Information Methods and Full Information Methods of estimation of simultaneous equations models are assed and compared. The general results show that job insecurity depresses the subjective well-being of all workers in both the public and private sectors in Ireland. The magnitude of this effect differs among sectoral workers. The subjective well-being of private sector workers is more adversely affected by job insecurity than the subjective well-being of public sector workers. This is observed in basic ordered probit estimations of both a life satisfaction equation and a job satisfaction equation. The marginal effects from the ordered probit estimation of a basic job satisfaction equation show that as job insecurity increases the probability of reporting a 9 on a 10-point job satisfaction scale significantly decreases by 3.4% for the whole sample of workers, 2.8% for public sector workers and 4.0% for private sector workers. Artz and Kaya (2014) explain that as a result of many austerity policies implemented to reduce government expenditure during the economic recession, workers in the public sector may for the first time face worsening perceptions of job security which can have significant implications for their well-being (Artz and Kaya, 2014). This can be observed in the marginal effects where job insecurity negatively impacts the well-being of public sector workers in Ireland. However, in accordance with Luechinger et al. (2010a) the results show that private sector workers are more adversely impacted by economic insecurity than public sector workers. This suggests that in a time of high economic volatility, the institution of public sector employment held and was able to protect workers against some of the well-being consequences of rising insecurity. In estimating the relationship between subjective well-being and economic insecurity advanced econometric issues arise. The results show that when selection bias is corrected for, any statistically significant relationship between job insecurity and job satisfaction disappears for public sector workers. Additionally, in order to correct for endogeneity bias the simultaneous equations model for job satisfaction and job insecurity is estimated by Limited Information and Full Information Methods. The results from two different estimators classified as Limited Information Methods support the general findings of this research. Moreover, the magnitude of the endogeneity-corrected estimates are twice as large as those not corrected for endogeneity bias which is similarly found in Geishecker (2010, 2012). As part of the analysis into the effect of economic insecurity on subjective well-being, the effects of other socioeconomic variables and work-related variables are examined for public and private sector workers in Ireland.

Fabrication et caractérisation de cellules solaires organiques nanostructurées par la méthode de nanoimpression thermique

La morphologie des couches actives des cellules solaires organiques joue un rôle important sur l’efficacité de conversion de l’énergie solaire en énergie électrique de ces dispositifs. Les hétérojonctions planaires et les hétérojonctions en volume sont les plus communément utilisées. Cependant, la morphologie idéale pour l’efficacité se situerait à mis chemin entre celles-ci. Il s’agit de l’hétérojonction nanostructurée qui augmenterait la surface entre les couches actives de matériaux tout en favorisant le transport des porteurs de charge. L’objectif de ce projet de maîtrise est d’étudier l’impact de l’implantation de nanostructures dans les cellules solaires organiques sur leurs performances photovoltaïques. Pour ce faire, on utilise la méthode de nanoimpression thermique sur le matériau donneur, le P3HT, afin que celui-ci forme une interface nanostructurée avec le matériau accepteur, le PCBM. Pour effectuer les nanoimpressions, des moules en alumine nanoporeuse ont été fabriqués à l’aide du procédé d’anodisation en deux temps développé par Masuda et al. Ces moules ont subi un traitement afin de faciliter leur séparation du P3HT. Les agents antiadhésifs PDMS et FTDS ont été utilisés à cette fin. Les résultats obtenus témoignent de la complexité d’exécution du procédé de nanoimpression. Il a été démontré que la pression appliquée durant le procédé, la tension superficielle des éléments en contact et les dimensions des nanopores des moules sont des paramètres critiques pour le succès des nanoimpressions. Ceux-ci ont donc dû être optimisés de manière à réussir cette opération. Ainsi, des cellules à interface nanostructurée à 25% avec des nanobâtonnets de 35 nm de hauteur ont pu être fabriquées. Les cellules nanostructurées ont démontré une efficacité 2,3 ± 0,6 fois supérieure aux cellules sans nanostructures, dites planaires. D’autre part, un solvant a été proposé pour diminuer l’interdiffusion entre les couches de P3HT et de PCBM pouvant altérer les nanostructures. Ce phénomène bien connu survient lors du dépot de la couche de PCBM avec le dichlorométhane, un solvant orthogonal avec ces matériaux. Des mesures au TOF-SIMS ont démontré que le limonène permet de diminuer l’interdiffusion entre les couches de P3HT et de PCBM, ce qui en fait un meilleur solvant orthogonal que le dichlorométhane.

(Table 1) Age determination of North Atlantic sediment cores

Stable isotope, trace metal, alkenone paleothermometry, and radiocarbon methods have been applied to sediment cores in the western subpolar North Atlantic between Hudson Strait and Cape Hatteras to reveal the history of climate in that region over the past ~11 kyr. We focus on cores from the Laurentian Fan, which is known to have rapid and continuous accumulation of hemipelagic sediment. Although results among our various proxy data are not always in agreement, the weight of the evidence (alkenone sea surface temperature (SST), d18O and abundance of Globigerinoides ruber) indicates a continual cooling of surface waters over Laurentian Fan, from about 18°C in the early Holocene to about 8°C today. Alternatively, Mg/Ca data on planktonic foraminifera indicate no systematic change in Holocene SST. The inferred long-term decrease in SST was probably driven by decreasing seasonality of Northern Hemisphere insolation. Two series of proxy data show the gradual cooling was interrupted by a two-step cold pulse that began 8500 years ago, and lasted about 700 years. Although this event is associated with the final deglaciation of Hudson Bay, there is no d18O minimum anywhere in the Labrador Sea, yet there is some evidence for it as far south as Cape Hatteras. Finally, although the 8200 year B.P. event has been implicated in decreasing North Atlantic ventilation, and hence widespread temperature depression on land and at sea, we find inconsistent evidence for a change at that time in deep ocean nutrient content at ~4 km water depth.

Mass accumulation rates of IODP Hole 320-U1333C

Understanding changes in export production through time provides insight into the response of the biological pump to global climate change, particularly during periods of rapid climate change. In this study we consider what role changes in export production may have had on carbon sequestration and how this may have contributed to the onset of the Eocene-Oligocene transition (EOT). In addition, we consider if these export production variations are dominantly controlled by orbitally driven climate variability. To accomplish these objectives, we report changes in export production in the Eastern Equatorial Pacific (EEP) from Site U1333 across the EOT reconstructed from a high-resolution record of marine barite accumulation rates (BAR). BAR fluctuations suggest synchronous declines in export production associated with the two-step increases in oxygen isotopes that define the transition. The reduction in productivity across the EOT suggests that the biological pump did not contribute to carbon sequestration and the cooling over this transition. We also report a previously undocumented peak in EEP export productivity before the EOT onset. This peak is consistent with export production proxies from the Southern Ocean, potentially implying a global driver for this precursor event. We propose that this enhanced export production and the associated carbon sequestration in the late Eocene may have contributed to the pCO2 drawdown at the onset of Antarctic glaciation.

Planktic foraminifera isotopes, temperature and d18O of seawater at the central Walvis Ridge for Termination II (MIS 6 to 5), sediment core 64PE-174P13

Salty and warm Indian Ocean waters enter the South Atlantic via the Agulhas leakage, south of Africa. Model simulations and proxy evidence of Agulhas leakage strengthening during glacial terminations led to the hypothesis that it was an important modulator of the Atlantic Ocean circulation. Yet, the fate of the leakage salinity and temperature anomalies remains undocumented beyond the southern tip of Africa. Downstream of the leakage, new paleoceanographic evidence from the central Walvis Ridge (southeast Atlantic) shows that salinity increased at the thermocline, and less so at the surface, during glacial termination II. Thermocline salinity change coincided with higher frequency of Agulhas rings passage at the core location and with salinity maxima in the Agulhas leakage area, suggesting that leakage waters were incorporated in the Atlantic circulation through the thermocline. Hydrographic changes at the Walvis Ridge and in the leakage area display a distinct two-step structure, with a reversal at ca. 134 ka. This matched a wet interlude within the East Asia weak monsoon interval of termination II, and a short-lived North Atlantic warming. Such concurrence points to a Bølling-Allerød-like recovery of the Atlantic circulation amidst termination II, with a northward shift of the Intertropical Convergence Zone and Southern Hemisphere westerlies, and attendant curtailment of the interocean connection south of Africa.

Nitrite consumption and associated isotope changes during a river flood event in the Elbe river

In oceans, estuaries, and rivers, nitrification is an important nitrate source, and stable isotopes of nitrate are often used to investigate recycling processes (e.g. remineralisation, nitrification) in the water column. Nitrification is a two-step process, where ammonia is oxidised via nitrite to nitrate. Nitrite usually does not accumulate in natural environments, which makes it difficult to study the single isotope effect of ammonia oxidation or nitrite oxidation in natural systems. However, during an exceptional flood in the Elbe River in June 2013, we found a unique co-occurrence of ammonium, nitrite, and nitrate in the water column, returning towards normal summer conditions within 1 week. Over the course of the flood, we analysed the evolution of d15N-[NH4]+ and d15N-[NO2]- in the Elbe River. In concert with changes in suspended particulate matter (SPM) and d15N SPM, as well as nitrate concentration, d15N-NO3 - and d18O-[NO3] -, we calculated apparent isotope effects during net nitrite and nitrate consumption. During the flood event, > 97 % of total reactive nitrogen was nitrate, which was leached from the catchment area and appeared to be subject to assimilation. Ammonium and nitrite concentrations increased to 3.4 and 4.4 µmol/l, respectively, likely due to remineralisation, nitrification, and denitrification in the water column. d15N-[NH4]+ values increased up to 12 per mil, and d15N-[NO2]- ranged from -8.0 to -14.2 per mil. Based on this, we calculated an apparent isotope effect 15-epsilon of -10.0 ± 0.1 per mil during net nitrite consumption, as well as an isotope effect 15-epsilon of -4.0 ± 0.1 per mil and 18-epsilon of -5.3 ± 0.1 per mil during net nitrate consumption. On the basis of the observed nitrite isotope changes, we evaluated different nitrite uptake processes in a simple box model. We found that a regime of combined riparian denitrification and 22 to 36 % nitrification fits best with measured data for the nitrite concentration decrease and isotope increase.

Deterministic Switching in Bismuth Ferrite Nanoislands

We report deterministic selection of polarization variant in bismuth BiFeO3 nanoislands via a two-step scanning probe microscopy procedure. The polarization orientation in a nanoisland is toggled to the desired variant after a reset operation by scanning a conductive atomic force probe in contact over the surface while a bias is applied. The final polarization variant is determined by the direction of the inhomogeneous in-plane trailing field associated with the moving probe tip. This work provides the framework for better control of switching in rhombohedral ferroelectrics and for a deeper under- standing of exchange coupling in multiferroic nanoscale hetero- structures toward the realization of magnetoelectric devices.

Catalyst screening: Refinement of the origin of the volcano curve and its implication in heterogeneous catalysis

Understanding the overall catalytic activity trend for rational catalyst design is one of the core goals in heterogeneous catalysis. In the past two decades, the development of density functional theory (DFT) and surface kinetics make it feasible to theoretically evaluate and predict the catalytic activity variation of catalysts within a descriptor-based framework. Thereinto, the concept of the volcano curve, which reveals the general activity trend, usually constitutes the basic foundation of catalyst screening. However, although it is a widely accepted concept in heterogeneous catalysis, its origin lacks a clear physical picture and definite interpretation. Herein, starting with a brief review of the development of the catalyst screening framework, we use a two-step kinetic model to refine and clarify the origin of the volcano curve with a full analytical analysis by integrating the surface kinetics and the results of first-principles calculations. It is mathematically demonstrated that the volcano curve is an essential property in catalysis, which results from the self-poisoning effect accompanying the catalytic adsorption process. Specifically, when adsorption is strong, it is the rapid decrease of surface free sites rather than the augmentation of energy barriers that inhibits the overall reaction rate and results in the volcano curve. Some interesting points and implications in assisting catalyst screening are also discussed based on the kinetic derivation. Moreover, recent applications of the volcano curve for catalyst design in two important photoelectrocatalytic processes (the hydrogen evolution reaction and dye-sensitized solar cells) are also briefly discussed.