Caracterização de múltiplos polimorfismos de Pneumocystis Jirovecii por multiplex-PCR/Single base extension

Pneumocystis jirovecii é conhecido por causar infecções específicas no aparelho respiratório de seus hospedeiros, principalmente em doentes imunocomprometidos, manifestando-se por uma pneumonia grave e por vezes fatal, normalmente designada por pneumonia por Pneumocystis. A caracterização da diversidade genética de P. jirovecii tem demonstrado que determinados polimorfismos de base única poderão ser reconhecidos como marcadores moleculares de eleição para o estudo da distribuição geográfica, vias de transmissão, resistência/susceptibilidade a fármacos, factores de virulência e genética populacional de subtipos genéticos. Este estudo teve como objectivo a caracterização de polimorfismos de P. jirovecii, através da metodologia PCR multiplex/Extensão de base única (do inglês single base extension), com a principal finalidade de constatar eventuais associações entre polimorfismos de base única, genótipos multilocus, e dados clínicos e demográficos da infecção. Sessenta e seis espécimes pulmonares, previamente considerados positivos para P. jirovecii, obtidos entre 2001 e 2012, a partir de doentes portugueses imunocomprometidos, foram seleccionados de forma aleatória para este estudo multilocus. PCR multiplex foi utilizada para a amplificação simultânea de três regiões genómicas: subunidade grande do rRNA mitocondrial, superóxido dismutase e dihidropteroato sintetase. Cinco polimorfismos de base única, previamente correlacionados com parâmetros da doença, foram genotipados por extensão de base única: mt85, SOD110, SOD215, DHPS165 e DHPS171. Um total de 330 polimorfismos de base única e 29 genótipos multilocus putativos de P. jirovecii foram identificados e caracterizados nos espécimes pulmonares analisados. Os padrões de distribuição dos polimorfismos foram analisados, sendo considerada a variação temporal e/ou geográfica das suas formas alélicas. Constatou-se grande diversidade genotípica entre os isolados de P. jirovecii que poderá ter influência a nível epidemiológico. Foram observadas associações estatísticas entre mt85/genótipos multilocus e parâmetros demográficos e clínicos. A correlação mais importante verificou-se entre mt85C e cargas parasitárias baixas a moderadas, enquanto mt85T foi associado com cargas parasitárias altas; MLG5, MLG9 e MLG13 foram associados com cargas parasitárias baixas, moderadas e altas, respectivamente. Tais associações demonstram que potenciais marcadores moleculares da infecção por P. jirovecii poderão existir e que polimorfismos/genótipos específicos poderão determinar perfis epidemiológicos da pneumonia por Pneumocystis. A análise genética cruzada permitiu verificar associações entre polimorfismos de base única. Os polimorfismos SOD110T e SOD215C, SOD110C e SOD215T, DHPS165A e DHPS171C, DHPS165G e DHPS171T foram associados estatisticamente. Os genótipos multilocus mais prevalentes foram considerados para o teste recombinatório d1. Dois genótipos multilocus (MLG7 e MLG9) foram observados com elevada frequência, e a análise genética indicou que estes se encontravam sobre-representados na população de P. jirovecii estudada. Estas evidências indicam que o fenómeno de desequilíbrio de ligação e a propagação clonal de subtipos genéticos é frequente, considerando que a espécie P. jirovecii poderá ser representada por uma população com estrutura epidémica. O presente trabalho confirmou a importância do estudo de polimorfismos em P. jirovecii, sugerindo que a caracterização multilocus poderá fornecer informação relevante para a compreensão dos padrões, causas e controlo da infecção, melhorando assim a investigação deste importante patogéneo.

Gas tungsten arc welding of NiTi shape memory alloy

Shape memory alloys are characterized by the ability of recovering their initial shape after being deformed and by superelasticity. Since the discovery of these alloys, a new field of interest emerged not only for the scientific community but also to many industries. However, these alloys present poor machinability which constitute a constrain in the design of complex components for new applications. Thus, the demand for joining techniques able to join these alloys without compromising their properties became of great importance to enlarge the complexity of existing applications. Literature shows that these alloys are joined mainly using laser welding. In the present study, similar NiTi butt joints, were produced using TIG welding. The welds were performed in 1.5 mm thick plates across the rolling direction. A special fixture and gas assist device was designed and manufactured. Also a robot arm was adapted to accommodate the welding torch to assure the repeatability of the welding parameters. Welds were successfully achieved without macroscopic defects, such as pores and distortions. Very superficial oxidation was seen on the top surface due to insufficient shielding gas flow on the weld face. The welded joints were mechanically tested and structurally characterized. Testing methods were used to evaluate macro and microstructure, as well as the phase transformation temperatures, the mechanical single and cyclic behaviour and the shape recovery ability. Differential Scanning Calorimetry (DSC), Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy (EDS), microhardness measurements were techniques also used to evaluate the welded joints. A depletion in Ni in the fusion zone was seen, as well as a shift in Ms temperature. For strain values of 4% the accumulated irrecoverable strain was of about 30% and increased with the strain imposed during cycling. Nevertheless, a complete recovery of initial shape was observed when testing the shape memory effect on a dedicated device that introduces a deformation of 6.7%. That is, the welding procedure does not remove the ability of the specimens to recover their initial shape.

Reactive electron scattering from biomolecules and technologically relevant molecules

The role of a set of gases relevant within the context of biomolecules and technologically relevant molecules under the interaction of low-energy electrons was studied in an effort to contribute to the understanding of the underlying processes yielding negative ion formation. The results are relevant within the context of damage to living material exposed to energetic radiation, to the role of dopants in the ion-molecule chemistry processes, to Electron Beam Induced Deposition (EBID) and Ion Beam Induced Deposition (IBID) techniques. The research described in this thesis addresses dissociative electron attachment (DEA) and electron transfer studies involving experimental setups from the University of Innsbruck, Austria and Universidade Nova de Lisboa, Portugal, respectively. This thesis presents DEA studies, obtained by a double focusing mass spectrometer, of dimethyl disulphide (C2H6S2), two isomers, enflurane and isoflurane (C3F5Cl5) and two chlorinated ethanes, pentachloroethane (C2HCl5) and hexachloroethane (C2Cl6), along with quantum chemical calculations providing information on the molecular orbitals as well as thermochemical thresholds of anion formation for enflurane, isoflurane, pentachloroethane and hexachloroethane. The experiments represent the most accurate DEA studies to these molecules, with significant differences from previous work reported in the literature. As far as electron transfer studies are concerned, negative ion formation in collisions of neutral potassium atoms with N1 and N3 methylated pyrimidine molecules were obtained by time-of-flight mass spectrometry (TOF). The results obtained allowed to propose concerted mechanisms for site and bond selective excision of bonds.

NAV Portugal's performance within the single European Sky Initiative

NAV Portugal is the Air Navigation Service Provider in Portugal, providing air traffic control services in the airspace under the country’s responsibility. Recently, the company has been included in an initiative launched by the European Commission, called the Single European Sky. This aims for a unification of the European airspace, improving it in four main pillars: safety, capacity, environment, and cost-efficiency. To each of them, Key Performance Indicators need to be computed and monitored, all having pre-defined targets. The presented work project will be analyzing how NAV Portugal is doing in the pillar of capacity, proving suggestions if needed.

Electron driven reactions in sulphur containing biological prototypes

The interaction of ionising radiation with living tissues may direct or indirectly generate several secondary species with relevant genotoxic potential. Due to recent findings that electrons with energies below the ionisation threshold can effectively damage DNA, radiation-induced damage to biological systems has increasingly come under scrutiny. The exact physico-chemical processes that occur in the first stages of electron induced damage remain to be explained. However, it is also known that free electrons have a short lifetime in the physiological medium. Hence, electron transfer processes studies represent an alternative approach through which the role of "bound" electrons as a source of damage to biological tissues can be further explored. The thesis work consists of studying dissociative electron attachment (DEA) and electron transfer to taurine and thiaproline. DEA measurements were executed in Siedlce University with Prof. Janina Kopyra under COST action MP1002 (Nanoscale insights in ion beam cancer therapy). The electron transfer experiments were conducted in a crossed atom(potassium)-molecule beam arrangement. In these studies the anionic fragmentation patterns were obtained. The results of both mechanisms are shown to be significantly different, unveiling that the damaging potential of secondary electrons can be underestimated. In addition, sulphur atoms appear to strongly influence the dissociation process, demonstrating that certain reactions can be controlled by substitution of sulphur at specific molecular sites.

Control of a white organic light emitting diode’s emission parameters using a single doped RGB active layer

White Color tuning is an attractive feature that Organic Light Emitting Diodes (OLEDs) offer. Up until now, there hasn’t been any report that mix both color tuning abilities with device stability. In this work, White OLEDs (W-OLEDs) based on a single RGB blend composed of a blue emitting N,N′-Di(1-naphthyl)-N,N′-diphenyl-(1,1′-biphenyl)-4,4′-diamine (NPB) doped with a green emitting Coumarin-153 and a red emitting 4-(Dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran (DCM1) dyes were produced. The final device structure was ITO/Blend/Bathocuproine (BCP)/ Tris(8-hydroxyquinolinato)aluminium (Alq3)/Al with an emission area of 0.25 cm2. The effects of the changing in DCM1’s concentration (from 0.5% to 1% wt.) allowed a tuning in the final white color resulting in devices capable of emitting a wide range of tunes – from cool to warm – while also keeping a low device complexity and a high stabilitty. Moreover, an explanation on the optoelectrical behavior of the device is presented. The best electroluminescense (EL) points toward 160 cd/m2 of brightness and 1.1 cd/A of efficiency, both prompted to being enhanced. An Impedance Spectroscopy (IS) analysis allowed to study both the effects of BCP as a Hole Blocking Layer and as an aging probe of the device. Finally, as a proof of concept, the emission was increased 9 and 64 times proving this structure can be effectively applied for general lighting.

Field-effect transistors based on Zinc oxide nanoparticles

This work reports the development of field-effect transistors (FETs), whose channel is based on zinc oxide (ZnO) nanoparticles (NPs). Using screen-printing as the primary deposition technique, different inks were developed, where the semiconducting ink is based on a ZnO NPs dispersion in ethyl cellulose (EC). These inks were used to print electrolyte-gated transistors (EGTs) in a staggered-top gate structure on glass substrates, using a lithium-based polymeric electrolyte. In another approach, FETs with a staggered-bottom gate structure on paper were developed using a sol-gel method to functionalize the paper’s surface with ZnO NPs, using zinc acetate dihydrate (ZnC4H6O4·2H2O) and sodium hydroxide (NaOH) as precursors. In this case, the paper itself was used as dielectric. The various layers of the two devices were characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier Transform Infrared spectroscopy (FTIR), thermogravimetric and differential scanning calorimetric analyses (TG-DSC). Electrochemical impedance spectroscopy (EIS) was used in order to evaluate the electric double-layer (EDL) formation, in the case of the EGTs. The ZnO NPs EGTs present electrical modulation for annealing temperatures equal or superior to 300 ºC and in terms of electrical properties they showed On/Off ratios in the order of 103, saturation mobilities (μSat) of 1.49x10-1 cm2(Vs)-1 and transconductance (gm) of 10-5 S. On the other hand, the ZnO NPs FETs on paper exhibited On/Off ratios in the order of 102, μSat of 4.83x10- 3 cm2(Vs)-1and gm around 10-8 S.

Development of paper transistor with memory effect

This work will discuss the use of different paper membranes as both the substrate and dielectric for field-effect memory transistors. Three different nanofibrillated cellulose membranes (NFC) were used as the dielectric layer of the memory transistors (NFC), one with no additives, one with an added polymer PAE and one with added HCl. Gallium indium zinc oxide (GIZO) was used as the device’s semiconductor and gallium aluminium zinc oxide (GAZO) was used as the gate electrode. Fourier transform infrared spectroscopy (FTIR) was used to access the water content of the paper membranes before and after vacuum. It was found that the devices recovered their water too quickly for a difference to be noticeable in FTIR. The transistor’s electrical performance tests yielded a maximum ION/IOFF ratio of around 3,52x105 and a maximum subthreshold swing of 0,804 V/decade. The retention time of the dielectric charge that grants the transistor its memory capabilities was accessed by the measurement of the drain current periodically during 144 days. During this period the mean drain current did not lower, leaving the retention time of the device indeterminate. These results were compared with similar devices revealing these devices to be at the top tier of the state-of-the-art.

Targeting Heme with Single Domain Antibodies

Heme, i.e. iron (Fe) protoporphyrin IX, functions as a prosthetic group in a variety of hemoproteins that participate in vital biologic functions essential to sustain life. Heme is a highly reactive molecule, participating in redox reactions, and presumably for this reason it must be sequestered within the heme pockets of hemoproteins, controlling its reactivity. However, under biological stress conditions, hemoproteins can release their prosthetic groups, generating “free heme”, which binds loosely to proteins or to other molecules and presumably acquires unfettered redox activity. Moreover, a growing body of evidence supports the notion that “free heme” can act in a vasoactive, pro-inflammatory and cytotoxic manner when released from a subset of these hemoproteins, such as extracellular hemoglobin, generated during hemolytic conditions. (...)