Applied evolution: An integrated approach to studying life history traits in response to drug selection

The use of chemical control measures to reduce the impact of parasite and pest species has frequently resulted in the development of resistance. Thus, resistance management has become a key concern in human and veterinary medicine, and in agricultural production. Although it is known that factors such as gene flow between susceptible and resistant populations, drug type, application methods, and costs of resistance can affect the rate of resistance evolution, less is known about the impacts of density-dependent eco-evolutionary processes that could be altered by drug-induced mortality. The overall aim of this thesis was to take an experimental evolution approach to assess how life history traits respond to drug selection, using a free-living dioecious worm (Caenorhabditis remanei) as a model. In Chapter 2, I defined the relationship between C. remanei survival and Ivermectin dose over a range of concentrations, in order to control the intensity of selection used in the selection experiment described in Chapter 4. The dose-response data were also used to appraise curve-fitting methods, using Akaike Information Criterion (AIC) model selection to compare a series of nonlinear models. The type of model fitted to the dose response data had a significant effect on the estimates of LD50 and LD99, suggesting that failure to fit an appropriate model could give misleading estimates of resistance status. In addition, simulated data were used to establish that a potential cost of resistance could be predicted by comparing survival at the upper asymptote of dose-response curves for resistant and susceptible populations, even when differences were as low as 4%. This approach to dose-response modeling ensures that the maximum amount of useful information relating to resistance is gathered in one study. In Chapter 3, I asked how simulations could be used to inform important design choices used in selection experiments. Specifically, I focused on the effects of both within- and between-line variation on estimated power, when detecting small, medium and large effect sizes. Using mixed-effect models on simulated data, I demonstrated that commonly used designs with realistic levels of variation could be underpowered for substantial effect sizes. Thus, use of simulation-based power analysis provides an effective way to avoid under or overpowering a study designs incorporating variation due to random effects. In Chapter 4, I 3 investigated how Ivermectin dosage and changes in population density affect the rate of resistance evolution. I exposed replicate lines of C. remanei to two doses of Ivermectin (high and low) to assess relative survival of lines selected in drug-treated environments compared to untreated controls over 10 generations. Additionally, I maintained lines where mortality was imposed randomly to control for differences in density between drug treatments and to distinguish between the evolutionary consequences of drug treatment versus ecological processes affected by changes in density-dependent feedback. Intriguingly, both drug-selected and random-mortality lines showed an increase in survivorship when challenged with Ivermectin; the magnitude of this increase varied with the intensity of selection and life-history stage. The results suggest that interactions between density-dependent processes and life history may mediate evolved changes in susceptibility to control measures, which could result in misleading conclusions about the evolution of heritable resistance following drug treatment. In Chapter 5, I investigated whether the apparent changes in drug susceptibility found in Chapter 4 were related to evolved changes in life-history of C. remanei populations after selection in drug-treated and random-mortality environments. Rapid passage of lines in the drug-free environment had no effect on the measured life-history traits. In the drug-free environment, adult size and fecundity of drug-selected lines increased compared to the controls but drug selection did not affect lifespan. In the treated environment, drug-selected lines showed increased lifespan and fecundity relative to controls. Adult size of randomly culled lines responded in a similar way to drug-selected lines in the drug-free environment, but no change in fecundity or lifespan was observed in either environment. The results suggest that life histories of nematodes can respond to selection as a result of the application of control measures. Failure to take these responses into account when applying control measures could result in adverse outcomes, such as larger and more fecund parasites, as well as over-estimation of the development of genetically controlled resistance. In conclusion, my thesis shows that there may be a complex relationship between drug selection, density-dependent regulatory processes and life history of populations challenged with control measures. This relationship could have implications for how resistance is monitored and managed if life histories of parasitic species show such eco-evolutionary responses to drug application.

A Belief rule-based environmental responsibility assessment system for small and medium-sized enterprises

Various environmental management systems, standards and tools are being created to assist companies to become more environmental friendly. However, not all the enterprises have adopted environmental policies in the same scale and range. Additionally, there is no existing guide to help them determine their level of environmental responsibility and subsequently, provide support to enable them to move forward towards environmental responsibility excellence. This research proposes the use of a Belief Rule-Based approach to assess an enterprise’s level commitment to environmental issues. The Environmental Responsibility BRB assessment system has been developed for this research. Participating companies will have to complete a structured questionnaire. An automated analysis of their responses (using the Belief Rule-Based approach) will determine their environmental responsibility level. This is followed by a recommendation on how to progress to the next level. The recommended best practices will help promote understanding, increase awareness, and make the organization greener. BRB systems consist of two parts: Knowledge Base and Inference Engine. The knowledge base in this research is constructed after an in-depth literature review, critical analyses of existing environmental performance assessment models and primarily guided by the EU Draft Background Report on "Best Environmental Management Practice in the Telecommunications and ICT Services Sector". The reasoning algorithm of a selected Drools JBoss BRB inference engine is forward chaining, where an inference starts iteratively searching for a pattern-match of the input and if-then clause. However, the forward chaining mechanism is not equipped with uncertainty handling. Therefore, a decision is made to deploy an evidential reasoning and forward chaining with a hybrid knowledge representation inference scheme to accommodate imprecision, ambiguity and fuzzy types of uncertainties. It is believed that such a system generates well balanced, sensible and Green ICT readiness adapted results, to help enterprises focus on making improvements on more sustainable business operations.

An A Posteriori Error Indicator for Discontinuous Galerkin Approximations of Fourth Order Elliptic Problems

We introduce a residual-based a posteriori error indicator for discontinuous Galerkin discretizations of the biharmonic equation with essential boundary conditions. We show that the indicator is both reliable and efficient with respect to the approximation error measured in terms of a natural energy norm, under minimal regularity assumptions. We validate the performance of the indicator within an adaptive mesh refinement procedure and show its asymptotic exactness for a range of test problems.

Improving photofermentative hydrogen production through metabolic engineering and DOE (Design of Experiments)

A l’heure actuelle, les biocarburants renouvelables et qui ne nuit pas à l'environnement sont à l'étude intensive en raison de l'augmentation des problèmes de santé et de la diminution des combustibles fossiles. H2 est l'un des candidats les plus prometteurs en raison de ses caractéristiques uniques, telles que la densité d'énergie élevée et la génération faible ou inexistante de polluants. Une façon attrayante pour produire la H2 est par les bactéries photosynthétiques qui peuvent capter l'énergie lumineuse pour actionner la production H2 avec leur système de nitrogénase. L'objectif principal de cette étude était d'améliorer le rendement de H2 des bactéries photosynthétiques pourpres non sulfureuses utilisant une combinaison de génie métabolique et le plan des expériences. Une hypothèse est que le rendement en H2 pourrait être améliorée par la redirection de flux de cycle du Calvin-Benson-Bassham envers du système de nitrogénase qui catalyse la réduction des protons en H2. Ainsi, un PRK, phosphoribulose kinase, mutant « knock-out » de Rhodobacter capsulatus JP91 a été créé. L’analyse de la croissance sur des différentes sources de carbone a montré que ce mutant ne peut croître qu’avec l’acétate, sans toutefois produire d' H2. Un mutant spontané, YL1, a été récupéré qui a retenu l'cbbP (codant pour PRK) mutation d'origine, mais qui avait acquis la capacité de se développer sur le glucose et produire H2. Une étude de la production H2 sous différents niveaux d'éclairage a montré que le rendement d’YL1 était de 20-40% supérieure à la souche type sauvage JP91. Cependant, il n'y avait pas d'amélioration notable du taux de production de H2. Une étude cinétique a montré que la croissance et la production d'hydrogène sont fortement liées avec des électrons à partir du glucose principalement dirigés vers la production de H2 et la formation de la biomasse. Sous des intensités lumineuses faibles à intermédiaires, la production d'acides organiques est importante, ce qui suggère une nouvelle amélioration additionnel du rendement H2 pourrait être possible grâce à l'optimisation des processus. Dans une série d'expériences associées, un autre mutant spontané, YL2, qui a un phénotype similaire à YL1, a été testé pour la croissance dans un milieu contenant de l'ammonium. Les résultats ont montré que YL2 ne peut croître que avec de l'acétate comme source de carbone, encore une fois, sans produire de H2. Une incubation prolongée dans les milieux qui ne supportent pas la croissance de YL2 a permis l'isolement de deux mutants spontanés secondaires intéressants, YL3 et YL4. L'analyse par empreint du pied Western a montré que les deux souches ont, dans une gamme de concentrations d'ammonium, l'expression constitutive de la nitrogénase. Les génomes d’YL2, YL3 et YL4 ont été séquencés afin de trouver les mutations responsables de ce phénomène. Fait intéressant, les mutations de nifA1 et nifA2 ont été trouvés dans les deux YL3 et YL4. Il est probable qu'un changement conformationnel de NifA modifie l'interaction protéine-protéine entre NifA et PII protéines (telles que GlnB ou GlnK), lui permettant d'échapper à la régulation par l'ammonium, et donc d'être capable d'activer la transcription de la nitrogénase en présence d'ammonium. On ignore comment le nitrogénase synthétisé est capable de maintenir son activité parce qu’en théorie, il devrait également être soumis à une régulation post-traductionnelle par ammonium. Une autre preuve pourrait être obtenue par l'étude du transcriptome d’YL3 et YL4. Une première étude sur la production d’ H2 par YL3 et YL4 ont montré qu'ils sont capables d’une beaucoup plus grande production d'hydrogène que JP91 en milieu d'ammonium, qui ouvre la porte pour les études futures avec ces souches en utilisant des déchets contenant de l'ammonium en tant que substrats. Enfin, le reformage biologique de l'éthanol à H2 avec la bactérie photosynthétique, Rhodopseudomonas palustris CGA009 a été examiné. La production d'éthanol avec fermentation utilisant des ressources renouvelables microbiennes a été traitée comme une technique mature. Cependant, la plupart des études du reformage de l'éthanol à H2 se sont concentrés sur le reformage chimique à la vapeur, ce qui nécessite généralement une haute charge énergetique et résultats dans les émissions de gaz toxiques. Ainsi le reformage biologique de l'éthanol à H2 avec des bactéries photosynthétiques, qui peuvent capturer la lumière pour répondre aux besoins énergétiques de cette réaction, semble d’être plus prometteuse. Une étude précédente a démontré la production d'hydrogène à partir d'éthanol, toutefois, le rendement ou la durée de cette réaction n'a pas été examiné. Une analyse RSM (méthode de surface de réponse) a été réalisée dans laquelle les concentrations de trois facteurs principaux, l'intensité lumineuse, de l'éthanol et du glutamate ont été variés. Nos résultats ont montré que près de 2 moles de H2 peuvent être obtenus à partir d'une mole d'éthanol, 33% de ce qui est théoriquement possible.

Desenvolvimento de uma célula a combustível de glicerol direto em meio alcalino

Dissertação (mestrado)—Universidade de Brasília, Instituto de Química, Programa de Pós-Graduação em Química, 2015.

Desenvolvimento de uma célula a combustível de glicerol direto em meio alcalino

Dissertação (mestrado)—Universidade de Brasília, Instituto de Química, Programa de Pós-Graduação em Química, 2015.

Small and medium enterprise competitiveness: Internationalization strategy

Field lab: SME competitiveness

Topological massive Dirac edge modes and long-range superconducting Hamiltonians

We discover novel topological effects in the one-dimensional Kitaev chain modified by long-range Hamiltonian deformations in the hopping and pairing terms. This class of models display symmetry-protected topological order measured by the Berry/Zak phase of the lower-band eigenvector and the winding number of the Hamiltonians. For exponentially decaying hopping amplitudes, the topological sector can be significantly augmented as the penetration length increases, something experimentally achievable. For power-law decaying superconducting pairings, the massless Majorana modes at the edges get paired together into a massive nonlocal Dirac fermion localized at both edges of the chain: a new topological quasiparticle that we call topological massive Dirac fermion. This topological phase has fractional topological numbers as a consequence of the long-range couplings. Possible applications to current experimental setups and topological quantum computation are also discussed.

Understanding the CO Preoxidation and the Intrinsic Catalytic Activity of Step Sites in Stepped Pt Surfaces in Acidic Medium

In order to deepen the knowledge about the origin of the CO preoxidation process and the intrinsic catalytic activity of Pt superficial steps toward CO oxidation, a series of CO stripping experiments were performed on stepped Pt electrodes in acidic medium. For the occurrence of CO preoxidation, it was found that it arises (reproducibly) whenever four interconnected conditions are simultaneously fulfilled: (1) CO adsorption at potentials lower than about 0.2 V; (2) on surfaces saturated with COads; (3) in the presence of traces of CO in solution; (4) in the presence of surface steps. If any of these four conditions is not satisfied, the CO preoxidation pathway does not appear, even though the steps on the electrode surface are completely covered by CO. By controlling the removal of the CO adlayer (voltammetrically), we show that once the CO adlayer has been partially oxidized, the (111) terrace sites of stepped surfaces are released earlier than the (110) step sites. Moreover, if (110) steps are selectively decorated with CO, its oxidation occurs only at potentials ∼150 mV higher than the CO preoxidation peak. Our results systematically demonstrate that step sites are less active to oxidize CO than those ones responsible for the CO preoxidation process. Once the sites responsible for the CO preoxidation are made free, there is no apparent motion of the remaining adsorbed CO layer, suggesting that the activation of the surface controls the whole process, rather than the diffusion of COads toward hypothetically “most active sites”. Voltammetric and chronoamperometric experiments performed on partially covered CO adlayers suggest that adsorbed CO behave as a motionless species during its oxidation, in which the CO adlayer is removed piece by piece. By means of in situ FTIR experiments, the stretching frequency of CO selectively adsorbed on (110) step sites was examined. Band frequency results confirm that those molecules adsorbed on steps are fully coupled with the adsorbed CO on (111) terraces when the surface reaches full coverage.

Platinum–rhodium–tin/carbon electrocatalysts for ethanol oxidation in acid media: effect of the precursor addition order and the amount of tin

Carbon-supported Pt x –Rh y –Sn z catalysts (x:y:z = 3:1:4, 6:2:4, 9:3:4) are prepared by Pt, Rh, and Sn precursors reduction in different addition order. The materials are characterized by X-ray diffraction, transmission electron microscopy, and X-ray photoelectron spectroscopy techniques and are evaluated for the electrooxidation of ethanol in acidic media by cyclic voltammetry, chronoamperometry, and anode potentiostatic polarization. The influence of both the order in which the precursors are added and the composition of metals in the catalysts on the electrocatalytic activity and physico-chemical characteristics of Pt x –Rh y –Sn z /C catalysts is evaluated. Oxidized Rh species prevail on the surface of catalysts synthesized by simultaneous co-precipitation, thus demonstrating the influence of synthesis method on the oxidation state of catalysts. Furthermore, high amounts of Sn in composites synthesized by co-precipitation result in very active catalysts at low potentials (bifunctional effect), while medium Sn load is needed for sequentially deposited catalysts when the electronic effect is most important (high potentials), since more exposed Pt and Rh sites are needed on the catalyst surface to alcohol oxidation. The Pt3–Rh1–Sn4/C catalyst prepared by co-precipitation is the most active at potentials lower than 0.55 V (related to bifunctional effect), while the Pt6–Rh2–Sn4/C catalyst, prepared by sequential precipitation (first Rh and, after drying, Pt + Sn), is the most active above 0.55 V.

Estudo da variação de propriedades de geomembranas de PVC devido a danos mecânicos

Dissertação (mestrado)—Universidade de Brasília, Faculdade de Tecnologia, Departamento de Engenharia Civil e Ambiental, 2015.

Posidonia oceanica (L.) Delile in its westernmost biogeographical limit (northwestern Alboran Sea): Meadows characterisation, phenology and flowering events

Posidonia oceanica is a Mediterranean endemic seagrass species that forms meadows covering ca. 2.5–4.5 millions of hectares, representing ca.25 % of the infralittoral and shallow circalittoral (down to 50m) bottoms of the Mediterranean. This seagrass is considered a habitat-engineer species and provides an elevated number of ecosystem services. In addition the Marine Strategy Framework Directive (MSFD, 2008/56/EC) includes seagrass like elements to evaluate the “Good Environmental Status” of the European coasts. Information about their phenological characteristic and structure of the meadows is needed for indicator estimations in order to establish their conservation status. The studied meadows are located in the westernmost limit of the P. oceanica distribution (North-western Alboran Sea) in the vecinity of the Strait of Gibraltar, an Atlantic-Mediterranean water transition area. Four sites were selected from East to West: Paraje Natural de Acantilados de Maro-Cerro Gordo (hereafter Maro), Special Area of Conservation “Calahonda” (hereafter Calahonda), Site of Community Importance Estepona (hereafter Estepona) and Punta Chullera (hereafter Chullera) where P. oceanica present their westernmost meadows. Phenological data were recorded from mid November to mid December in P. oceanica patches located at 2 – 3 m depth. At each site three types of patches (patch area <1m2, small patches; 1-2 m2, medium patches and >2 m2, large patches) were sampled. At each patch and site, 3 quadrants of 45 x 45 cm were sampled for shoot and inflorescences density measurements. In each quadrant, 10 random shoots were sampled for shoot morphology (shoot height and number of leaves). Shoot and inflorescences densities were standardized to squared meters. All the studied P. oceanica meadows develop on rocks and they present a fragmented structure with a coverage ranging between ca. 45% in Calahonda and Estepona and ca. 31% in Maro. The meadows of Chullera are reduced to a few small - medium patches with areas ranging between 0.5-1.5 m2 (Fig. 1). The meadows of Chullera and Estepona presented similar values of shoot density (ca. 752 – 662 shoots m-2, respectively) and leaf height (ca. 25 cm). Similarly, the Calahonda and Maro meadows also showed similar values of shoot density (ca. 510 – 550 shoots m-2, respectively) but displaying lower values than those of sites located closer to the Strait of Gibraltar. Regarding patch sizes and leaf height, the longest leaves (ca. 25 cm) were found in medium and large patches, but the number of leaves per shoot were higher in the small and the medium size patches (ca. 6.3 leaves per shoot). Flowering was only detected at the Calahonda meadows with maximum values of ca. 330 inflorescences m-2 (115.2 ± 98.2 inflorescences m-2, n= 9; mean ± SD) (Fig.1). Inflorescence density was not significant different among patches of different sizes. In the Alboran Sea and unlike the studied meadows, extensive beds of P. oceanica occur at the National Park of Cabo de Gata (northeastern Alboran Sea), but from east to west (Strait of Gibraltar), meadows are gradually fragmenting and their depth range decrease from 30m to 2m depth between Cabo de Gata and Chullera, respectively. Probably, the Atlantic influence and the characteristic oceanographic conditions of the Alboran Sea (i.e., higher turbidity, higher water turbulence) represent a developmental limiting factor for P. oceanica at higher depths. Similarities between the meadows located closer to Strait of Gibraltar (Chullera and Estepona) were detected as well as between those more distant (Calahonda and Maro). The first ones showed higher values of shoot densities and leaf heights than the formers, which could be relating to the higher hydrodynamic exposure found at Chullera and Estepona meadows. Regarding flowering events, sexual reproduction in P. oceanica is not common in different locations of the Mediterranean Sea. The available information seems to indicate that flowering represent an irregular event and it is related to high seawater temperature. In fact, the flowering episodes that occurred in Calahonda in November 2015, match with the warmest year ever recorded. This is the third flowering event registered in these meadows located close to the westernmost distributional limit of P. oceanica (Málaga, Alboran Sea), which could indicates that these meadows presents a healthy status. Furthermore, the absence of significant differences in relation to inflorescence density between patches of different sizes may be indicating that the fragmentation does not necessarily influence on the flowering of this seagrass species.

Silicon Photonic Device for Wavelength Sensing and Monitoring

Over the last decade advances and innovations from Silicon Photonics technology were observed in the telecommunications and computing industries. This technology which employs Silicon as an optical medium, relies on current CMOS micro-electronics fabrication processes to enable medium scale integration of many nano-photonic devices to produce photonic integrated circuitry. However, other fields of research such as optical sensor processing can benefit from silicon photonics technology, specially in sensors where the physical measurement is wavelength encoded. In this research work, we present a design and application of a thermally tuned silicon photonic device as an optical sensor interrogator. The main device is a micro-ring resonator filter of 10 $\mu m$ of diameter. A photonic design toolkit was developed based on open source software from the research community. With those tools it was possible to estimate the resonance and spectral characteristics of the filter. From the obtained design parameters, a 7.8 x 3.8 mm optical chip was fabricated using standard micro-photonics techniques. In order to tune a ring resonance, Nichrome micro-heaters were fabricated on top of the device. Some fabricated devices were systematically characterized and their tuning response were determined. From measurements, a ring resonator with a free-spectral-range of 18.4 nm and with a bandwidth of 0.14 nm was obtained. Using just 5 mA it was possible to tune the device resonance up to 3 nm. In order to apply our device as a sensor interrogator in this research, a model of wavelength estimation using time interval between peaks measurement technique was developed and simulations were carried out to assess its performance. To test the technique, an experiment using a Fiber Bragg grating optical sensor was set, and estimations of the wavelength shift of this sensor due to axial strains yield an error within 22 pm compared to measurements from spectrum analyzer. Results from this study implies that signals from FBG sensors can be processed with good accuracy using a micro-ring device with the advantage of ts compact size, scalability and versatility. Additionally, the system also has additional applications such as processing optical wavelength shifts from integrated photonic sensors and to be able to track resonances from laser sources.

Lactobacillus rossiae, a vitamin B12 producer, represents a metabolically versatile species within the genus Lactobacillus

Lactobacillus rossiae is an obligately hetero-fermentative lactic acid bacterium, which can be isolated from a broad range of environments including sourdoughs, vegetables, fermented meat and flour, as well as the gastrointestinal tract of both humans and animals. In order to unravel distinctive genomic features of this particular species and investigate the phylogenetic positioning within the genus Lactobacillus, comparative genomics and phylogenomic approaches, followed by functional analyses were performed on L. rossiae DSM 15814(T), showing how this type strain not only occupies an independent phylogenetic branch, but also possesses genomic features underscoring its biotechnological potential. This strain in fact represents one of a small number of bacteria known to encode a complete de novo biosynthetic pathway of vitamin B-12 (in addition to other B vitamins such as folate and riboflavin). In addition, it possesses the capacity to utilize an extensive set of carbon sources, a characteristic that may contribute to environmental adaptation, perhaps enabling the strain's ability to populate different niches.