Unusual bismuth-containing surface layers of III-V compound semiconductors

The understanding and engineering of bismuth (Bi) containing semiconductor surfaces are signi cant in the development of novel semiconductor materials for electronic and optoelectronic devices such as high-e ciency solar cells, lasers and light emitting diodes. For example, a Bi surface layer can be used as a surfactant which oats on a III-V compound-semiconductor surface during the epitaxial growth of IIIV lms. This Bi surfactant layer improves the lm-growth conditions if compared to the growth without the Bi layer. Therefore, detailed knowledge of the properties of the Bi/III-V surfaces is needed. In this thesis, well-de ned surface layers containing Bi have been produced on various III-V semiconductor substrates. The properties of these Bi-induced surfaces have been measured by low-energy electron di raction (LEED), scanning-tunneling microscopy and spectroscopy (STM), and synchrotron-radiation photoelectron spectroscopy. The experimental results have been compared with theoretically calculated results to resolve the atomic structures of the studied surfaces. The main ndings of this research concern the determination of the properties of an unusual Bi-containing (2×1) surface structure, the discovery and characterization of a uniform pattern of Bi nanolines, and the optimization of the preparation conditions for this Bi-nanoline pattern.

Detection of Illicit Drugs and Drug Precursors with Cantilever-Enhanced Photoacoustic Spectroscopy

In this study, cantilever-enhanced photoacoustic spectroscopy (CEPAS) was applied in different drug detection schemes. The study was divided into two different applications: trace detection of vaporized drugs and drug precursors in the gas-phase, and detection of cocaine abuse in hair. The main focus, however, was the study of hair samples. In the gas-phase, methyl benzoate, a hydrolysis product of cocaine hydrochloride, and benzyl methyl ketone (BMK), a precursor of amphetamine and methamphetamine were investigated. In the solid-phase, hair samples from cocaine overdose patients were measured and compared to a drug-free reference group. As hair consists mostly of long fibrous proteins generally called keratin, proteins from fingernails and saliva were also studied for comparison. Different measurement setups were applied in this study. Gas measurements were carried out using quantum cascade lasers (QLC) as a source in the photoacoustic detection. Also, an external cavity (EC) design was used for a broader tuning range. Detection limits of 3.4 particles per billion (ppb) for methyl benzoate and 26 ppb for BMK in 0.9 s were achieved with the EC-QCL PAS setup. The achieved detection limits are sufficient for realistic drug detection applications. The measurements from drug overdose patients were carried out using Fourier transform infrared (FTIR) PAS. The drug-containing hair samples and drug-free samples were both measured with the FTIR-PAS setup, and the measured spectra were analyzed statistically with principal component analysis (PCA). The two groups were separated by their spectra with PCA and proper spectral pre-processing. To improve the method, ECQCL measurements of the hair samples, and studies using photoacoustic microsampling techniques, were performed. High quality, high-resolution spectra with a broad tuning range were recorded from a single hair fiber. This broad tuning range of an EC-QCL has not previously been used in the photoacoustic spectroscopy of solids. However, no drug detection studies were performed with the EC-QCL solid-phase setup.

Characterization Of Process Efficiency Improvement In Laser Additive Manufacturing

Laser additive manufacturing (LAM), known also as 3D printing, has gained a lot of interest in past recent years within various industries, such as medical and aerospace industries. LAM enables fabrication of complex 3D geometries by melting metal powder layer by layer with laser beam. Research in laser additive manufacturing has been focused in development of new materials and new applications in past 10 years. Since this technology is on cutting edge, efficiency of manufacturing process is in center role of research of this industry. Aim of this thesis is to characterize methods for process efficiency improvements in laser additive manufacturing. The aim is also to clarify the effect of process parameters to the stability of the process and in microstructure of manufactured pieces. Experimental tests of this thesis were made with various process parameters and their effect on build pieces has been studied, when additive manufacturing was performed with a modified research machine representing EOSINT M-series and with EOS EOSINT M280. Material used was stainless steel 17-4 PH. Also, some of the methods for process efficiency improvements were tested. Literature review of this thesis presents basics of laser additive manufacturing, methods for improve the process efficiency and laser beam – material- interaction. It was observed that there are only few public studies about process efficiency of laser additive manufacturing of stainless steel. According to literature, it is possible to improve process efficiency with higher power lasers and thicker layer thicknesses. The process efficiency improvement is possible if the effect of process parameter changes in manufactured pieces is known. According to experiments carried out in this thesis, it was concluded that process parameters have major role in single track formation in laser additive manufacturing. Rough estimation equations were created to describe the effect of input parameters to output parameters. The experimental results showed that the WDA (width-depth-area of cross-sections of single track) is correlating exponentially with energy density input. The energy density input is combination of the input parameters of laser power, laser beam spot diameter and scan speed. The use of skin-core technique enables improvement of process efficiency as the core of the part is manufactured with higher laser power and thicker layer thickness and the skin with lower laser power and thinner layer thickness in order to maintain high resolution. In this technique the interface between skin and core must have overlapping in order to achieve full dense parts. It was also noticed in this thesis that keyhole can be formed in LAM process. It was noticed that the threshold intensity value of 106 W/cm2 was exceeded during the tests. This means that in these tests the keyhole formation was possible.

NIR-Vis Up-Conversion Luminescence in the Yb3+,Er3+ Doped Y2O2S, ZrO2, and NaYF4 Nanomaterials

Since the discovery of the up-conversion phenomenon, there has been an ever increasing interest in up-converting phosphors in which the absorption of two or more low energy photons is followed by emission of a higher energy photon. Most up-conversion luminescence materials operate by using a combination of a trivalent rare earth (lanthanide) sensitizer (e.g. Yb or Er) and an activator (e.g. Er, Ho, Tm or Pr) ion in a crystal lattice. Up-converting phosphors have a variety of potential applications as lasers and displays as well as inks for security printing (e.g. bank notes and bonds). One of the most sophisticated applications of lanthanide up-conversion luminescence is probably in medical diagnostics. However, there are some major problems in the use of photoluminescence based on the direct UV excitation in immunoassays. Human blood absorbs strongly UV radiation as well as the emission of the phosphor in the visible. A promising way to overcome the problems arising from the blood absorption is to use a long wavelength excitation and benefit from the up-conversion luminescence. Since there is practically no absorption by the whole-blood in the near IR region, it has no capability for up-conversion in the excitation wavelength region of the conventional up-converting phosphor based on the Yb3+ (sensitizer) and Er3+ (activator) combination. The aim of this work was to prepare nanocrystalline materials with high red (and green) up-conversion luminescence efficiency for use in quantitative whole-blood immunoassays. For coupling to biological compounds, nanometer-sized (crystallite size below 50 nm) up-converting phosphor particles are required. The nanocrystalline ZrO2:Yb3+,Er3+, Y2O2S:Yb3+,Er3+, NaYF4:Yb3+,Er3+ and NaRF4-NaR’F4 (R: Y, Yb, Er) materials, prepared with the combustion, sol-gel, flux, co-precipitation and solvothermal synthesis, were studied using the thermal analysis, FT-IR spectroscopy, transmission electron microscopy, EDX spectroscopy, XANES/EXAFS measurements, absorption spectroscopy, X-ray powder diffraction, as well as up-conversion and thermoluminescence spectroscopies. The effect of the impurities of the phosphors, crystallite size, as well as the crystal structure on the up-conversion luminescence intensity was analyzed. Finally, a new phenomenon, persistent up-conversion luminescence was introduced and discussed. For efficient use in bioassays, more work is needed to yield nanomaterials with smaller and more uniform crystallite sizes. Surface modifications need to be studied to improve the dispersion in water. On the other hand, further work must be carried out to optimize the persistent up-conversion luminescence of the nanomaterials to allow for their use as efficient immunoassay nanomaterials combining the advantages of both up-conversion and persistent luminescence.

Defining the keyhole modes – the effects on the weld geometry and the molten pool behaviour in high power laser welding of stainless steels

Keyhole welding, meaning that the laser beam forms a vapour cavity inside the steel, is one of the two types of laser welding processes and currently it is used in few industrial applications. Modern high power solid state lasers are becoming more used generally, but not all process fundamentals and phenomena of the process are well known and understanding of these helps to improve quality of final products. This study concentrates on the process fundamentals and the behaviour of the keyhole welding process by the means of real time high speed x-ray videography. One of the problem areas in laser welding has been mixing of the filler wire into the weld; the phenomena are explained and also one possible solution for this problem is presented in this study. The argument of this thesis is that the keyhole laser welding process has three keyhole modes that behave differently. These modes are trap, cylinder and kaleidoscope. Two of these have sub-modes, in which the keyhole behaves similarly but the molten pool changes behaviour and geometry of the resulting weld is different. X-ray videography was used to visualize the actual keyhole side view profile during the welding process. Several methods were applied to analyse and compile high speed x-ray video data to achieve a clearer image of the keyhole side view. Averaging was used to measure the keyhole side view outline, which was used to reconstruct a 3D-model of the actual keyhole. This 3D-model was taken as basis for calculation of the vapour volume inside of the keyhole for each laser parameter combination and joint geometry. Four different joint geometries were tested, partial penetration bead on plate and I-butt joint and full penetration bead on plate and I-butt joint. The comparison was performed with selected pairs and also compared all combinations together.

Low-level red laser therapy alters effects of ultraviolet C radiation on Escherichia coli cells

Low-level lasers are used at low power densities and doses according to clinical protocols supplied with laser devices or based on professional practice. Although use of these lasers is increasing in many countries, the molecular mechanisms involved in effects of low-level lasers, mainly on DNA, are controversial. In this study, we evaluated the effects of low-level red lasers on survival, filamentation, and morphology of Escherichia colicells that were exposed to ultraviolet C (UVC) radiation. Exponential and stationary wild-type and uvrA-deficientE. coli cells were exposed to a low-level red laser and in sequence to UVC radiation. Bacterial survival was evaluated to determine the laser protection factor (ratio between the number of viable cells after exposure to the red laser and UVC and the number of viable cells after exposure to UVC). Bacterial filaments were counted to obtain the percentage of filamentation. Area-perimeter ratios were calculated for evaluation of cellular morphology. Experiments were carried out in duplicate and the results are reported as the means of three independent assays. Pre-exposure to a red laser protected wild-type and uvrA-deficient E. coli cells against the lethal effect of UVC radiation, and increased the percentage of filamentation and the area-perimeter ratio, depending on UVC fluence and physiological conditions in the cells. Therapeutic, low-level red laser radiation can induce DNA lesions at a sub-lethal level. Consequences to cells and tissues should be considered when clinical protocols based on this laser are carried out.

Low-intensity red and infrared laser effects at high fluences on Escherichia coli cultures

Semiconductor laser devices are readily available and practical radiation sources providing wavelength tenability and high monochromaticity. Low-intensity red and near-infrared lasers are considered safe for use in clinical applications. However, adverse effects can occur via free radical generation, and the biological effects of these lasers from unusually high fluences or high doses have not yet been evaluated. Here, we evaluated the survival, filamentation induction and morphology of Escherichia coli cells deficient in repair of oxidative DNA lesions when exposed to low-intensity red and infrared lasers at unusually high fluences. Cultures of wild-type (AB1157), endonuclease III-deficient (JW1625-1), and endonuclease IV-deficient (JW2146-1) E. coli, in exponential and stationary growth phases, were exposed to red and infrared lasers (0, 250, 500, and 1000 J/cm2) to evaluate their survival rates, filamentation phenotype induction and cell morphologies. The results showed that low-intensity red and infrared lasers at high fluences are lethal, induce a filamentation phenotype, and alter the morphology of the E. coli cells. Low-intensity red and infrared lasers have potential to induce adverse effects on cells, whether used at unusually high fluences, or at high doses. Hence, there is a need to reinforce the importance of accurate dosimetry in therapeutic protocols.

Thick Section Laser Beam Welding of Structural Steels: Methods for Improving Welding Efficiency

Laser beam welding (LBW) is applicable for a wide range of industrial sectors and has a history of fifty years. However, it is considered an unusual method with applications typically limited to welding of thin sheet metal. With a new generation of high power lasers there has been a renewed interest in thick section LBW (also known as keyhole laser welding). There was a growing body of publications during 2001-2011 that indicates an increasing interest in laser welding for many industrial applications, and in last ten years, an increasing number of studies have examined the ways to increase the efficiency of the process. Expanding the thickness range and efficiency of LBW makes the process a possibility for industrial applications dealing with thick metal welding: shipbuilding, offshore structures, pipelines, power plants and other industries. The advantages provided by LBW, such as high process speed, high productivity, and low heat input, may revolutionize these industries and significantly reduce the process costs. The research to date has focused on either increasing the efficiency via optimizing process parameters, or on the process fundamentals, rather than on process and workpiece modifications. The argument of this thesis is that the efficiency of the laser beam process can be increased in a straightforward way in the workshop conditions. Throughout this dissertation, the term “efficiency” is used to refer to welding process efficiency, specifically, an increase in efficiency refers an increase in weld’s penetration depth without increasing laser power level or decreasing welding speed. These methods are: modifications of the workpiece – edge surface roughness and air gap between the joining plates; modification of the ambient conditions – local reduction of the pressure in the welding zone; modification of the welding process – preheating of the welding zone. Approaches to improve the efficiency are analyzed and compared both separately and combined. These experimentally proven methods confirm previous findings and contribute additional evidence which expand the opportunities for laser beam welding applications. The focus of this research was primarily on the effects of edge surface roughness preparation and pre-set air gap between the plates on weld quality and penetration depth. To date, there has been no reliable evidence that such modifications of the workpiece give a positive effect on the welding efficiency. Other methods were tested in combination with the two methods mentioned above. The most promising - combining with reduced pressure method - resulted in at least 100% increase in efficiency. The results of this thesis support the idea that joining those methods in one modified process will provide the modern engineering with a sufficient tool for many novel applications with potential benefits to a range of industries.

Feasibility of industrial implementation of laser cutting into paper making machine

Laser cutting implementation possibilities into paper making machine was studied as the main objective of the work. Laser cutting technology application was considered as a replacement tool for conventional cutting methods used in paper making machines for longitudinal cutting such as edge trimming at different paper making process and tambour roll slitting. Laser cutting of paper was tested in 70’s for the first time. Since then, laser cutting and processing has been applied for paper materials with different level of success in industry. Laser cutting can be employed for longitudinal cutting of paper web in machine direction. The most common conventional cutting methods include water jet cutting and rotating slitting blades applied in paper making machines. Cutting with CO2 laser fulfils basic requirements for cutting quality, applicability to material and cutting speeds in all locations where longitudinal cutting is needed. Literature review provided description of advantages, disadvantages and challenges of laser technology when it was applied for cutting of paper material with particular attention to cutting of moving paper web. Based on studied laser cutting capabilities and problem definition of conventional cutting technologies, preliminary selection of the most promising application area was carried out. Laser cutting (trimming) of paper web edges in wet end was estimated to be the most promising area where it can be implemented. This assumption was made on the basis of rate of web breaks occurrence. It was found that up to 64 % of total number of web breaks occurred in wet end, particularly in location of so called open draws where paper web was transferred unsupported by wire or felt. Distribution of web breaks in machine cross direction revealed that defects of paper web edge was the main reason of tearing initiation and consequent web break. The assumption was made that laser cutting was capable of improvement of laser cut edge tensile strength due to high cutting quality and sealing effect of the edge after laser cutting. Studies of laser ablation of cellulose supported this claim. Linear energy needed for cutting was calculated with regard to paper web properties in intended laser cutting location. Calculated linear cutting energy was verified with series of laser cutting. Practically obtained laser energy needed for cutting deviated from calculated values. This could be explained by difference in heat transfer via radiation in laser cutting and different absorption characteristics of dry and moist paper material. Laser cut samples (both dry and moist (dry matter content about 25-40%)) were tested for strength properties. It was shown that tensile strength and strain break of laser cut samples are similar to corresponding values of non-laser cut samples. Chosen method, however, did not address tensile strength of laser cut edge in particular. Thus, the assumption of improving strength properties with laser cutting was not fully proved. Laser cutting effect on possible pollution of mill broke (recycling of trimmed edge) was carried out. Laser cut samples (both dry and moist) were tested on the content of dirt particles. The tests revealed that accumulation of dust particles on the surface of moist samples can take place. This has to be taken into account to prevent contamination of pulp suspension when trim waste is recycled. Material loss due to evaporation during laser cutting and amount of solid residues after cutting were evaluated. Edge trimming with laser would result in 0.25 kg/h of solid residues and 2.5 kg/h of lost material due to evaporation. Schemes of laser cutting implementation and needed laser equipment were discussed. Generally, laser cutting system would require two laser sources (one laser source for each cutting zone), set of beam transfer and focusing optics and cutting heads. In order to increase reliability of system, it was suggested that each laser source would have double capacity. That would allow to perform cutting employing one laser source working at full capacity for both cutting zones. Laser technology is in required level at the moment and do not require additional development. Moreover, capacity of speed increase is high due to availability high power laser sources what can support the tendency of speed increase of paper making machines. Laser cutting system would require special roll to maintain cutting. The scheme of such roll was proposed as well as roll integration into paper making machine. Laser cutting can be done in location of central roll in press section, before so-called open draw where many web breaks occur, where it has potential to improve runability of a paper making machine. Economic performance of laser cutting was done as comparison of laser cutting system and water jet cutting working in the same conditions. It was revealed that laser cutting would still be about two times more expensive compared to water jet cutting. This is mainly due to high investment cost of laser equipment and poor energy efficiency of CO2 lasers. Another factor is that laser cutting causes material loss due to evaporation whereas water jet cutting almost does not cause material loss. Despite difficulties of laser cutting implementation in paper making machine, its implementation can be beneficial. The crucial role in that is possibility to improve cut edge strength properties and consequently reduce number of web breaks. Capacity of laser cutting to maintain cutting speeds which exceed current speeds of paper making machines what is another argument to consider laser cutting technology in design of new high speed paper making machines.

Optical and photoelectric properties of dry bacteriorhodopsin sensors

In this thesis, bacteriorhodopsin (BR) photosensor’s optical and electrical properties were studied. The BR sensor consisted of a dry film with BR in polyvinyl alcohol and covered with transparent conductors. In the experiments the BR photocycle was started with two lasers. The characteristics of the BR sensor were measured in two ways. The first approach was theoretical and it required knowing the laser parameters. The second way required assembling a measurement setup for the optical response measurements. However, no measurable results were obtained due to low laser power. The photoelectric response was measured in the experiments with two laser systems and the amplifier was tested. In the experiment with a Cavitar laser, the photoelectric response was obtained. In the experiment with FemtoFiber Pro laser, the photoelectric response was not measured. The expected amplitude of the response was obtained. The experimental data was analyzed and possible solutions for reducing the interference were given.

Far infrared spectroscopy of heavy fermion superconductor CeCoIn5

The optical response to far infrared radiation has been measured on a mosaic of heavy fermion CeColnssingle crystals. The superconducting transition temperature of the crystals has been determined by van der Pauw resistivity and ac-susceptibility measurements as Tc = 2.3 K. The optical measurements were taken above and below the transition temperature using a 3He cryostat and step and integrate Martin-Puplett type polarizing interferometer. The absolute reflectance of the heavy fermion CeColns in the superconducting state in range (0, 100)cm-1 was calculated from the measured thermal reflectance, using the normal state data of Singley et al and a low frequency extrapolation for a metallic material in the Hagen-Rubens regime. By means of Kramers-Kronig analysis the absolute reflectance was used to calculate the optical conductivity of the sample. The real part of the calculated complex conductivity 0-(w) ofCeColns indicates a possible opening of an energy gap close to 50 em-I.

Far infrared spectroscopy of heavy fermion superconductor CeCoIn5 /

The optical response to far infrared radiation has been measured on a mosaic of heavy fermion CeCoIns single crystals. The superconducting transition temperature of the crystals has been determined by van der Pauw resistivity and ac-susceptibility measurements as Tc = 2.3 K. The optical measurements were taken above and below the transition temperature using a ^He cryostat and step and integrate Martin-Puplett type polarizing interferometer. The absolute reflectance of the heavy fermion CeCoIns in the superconducting state in range (0, 100)cm~^ was calculated from the measured thermal reflectance, using the normal state data of Singley et al and a low frequency extrapolation for a metallic material in the Hagen-Rubens regime. By means of Kramers-Kronig analysis the absolute reflectance was used to calculate the optical conductivity of the sample. The real part of the calculated complex conductivity a{u)) of CeCoIns indicates a possible opening of an energy gap close to 50 cm~^.

La Visualisation in vivo des « espèces oxygénées radiculaires» au niveau des cellules ganglionnaires de la rétine.

Titre: La Visualisation in vivo des « espèces oxygénées radiculaires» au niveau des cellules ganglionnaires de la rétine. Le But : Les espèces d'oxygène réactives sont non seulement produites à la suite de la blessure cellulaire, mais servent aussi des molécules faisantes des signes pour une variété de processus critiques, en incluant mitosis et de mort de cellule. Nous avons auparavant dit que la blessure à RGC axons incite un éclatement de superoxyde dans le corps de cellule, probablement de l'origine mitochondrial (Lieven et al, 2006). Nous décrivons maintenant une méthode pour refléter des espèces d'oxygène réactives dans la rétine de l'animal vivant en utilisant un confocal le lisant rapidement du laser ophthalmoscope a appelé la Rétine de Heidelberg Angiograph 2 (HRA2) équipé avec les lasers doubles. La méthodolologie : Après les études préliminaires en utilisant d'autres indicateurs (hydroethidium; HEt) pour les espèces d'oxygène réactives, nous avons essayé de refléter des espèces d'oxygène réactives dans le dans le modèle de vivo l'utilisation 5-(et 6)-chloromethyl-2', 7 '-dichlorodihydrofluorescein diacetate, l'acétyle ester (le CM-H2DCFDA). Un nerf optique de Longs-Evans rats a été écrasé intraorbitalement, en épargnant la circulation retinal. Dans certains rats colliculi supérieur de Longs rats Evans avait été auparavant exposé via craniotomy et surposé avec Gelfoam saturé avec le vert indocyanine (ICG). Aux points de temps variables les animaux ont été injectés intraveineusement ou intravitreally avec HEt ou le CM-H2DCFDA et reflétés avec fluorescein et-ou les filtres d'ICG en utilisant le HRA2. Les résultats: Nous avons démontré le foyer brillant multiple de fluorescence dans la couche de cellule de ganglion quand nous avons rétrogradement étiqueté d'ICG bilatéralement, en indiquant qu'ICG était un colorant rétrogradement transporté qui pourrait être découvert avec le HRA2. Après axotomy et l'injection intravitreal de CM-H2DCFDA, il y avait la fluorescence brillante dans le canal fluorescein dans quelques cellules dans la couche de cellule de ganglion, en accord avec la production d'une ou plusieurs espèces d'oxygène réactives. Les conclusions : RGCs peut être identifié et les niveaux d'espèces d'oxygène réactives mesurés en utilisant une fréquence double confocal Mots-clés : cellules ganglionnaires de la rétine; especes oxygenique radiculaire; la visualisation;

Développement et caractérisation d’une méthode photonique pour créer des distributions spatiales de protéines

Les cellules sont capables de détecter les distributions spatiales de protéines et ainsi de migrer ou s’étendre dans la direction appropriée. Une compréhension de la réponse cellulaire aux modifications de ces distributions spatiales de protéines est essentielle pour l’avancement des connaissances dans plusieurs domaines de recherches tels que le développement, l’immunologie ou l’oncologie. Un exemple particulièrement complexe est le guidage d’axones se déroulant pendant le développement du système nerveux. Ce dernier nécessite la présence de plusieurs distributions de molécules de guidages étant attractives ou répulsives pour connecter correctement ce réseau complexe qu’est le système nerveux. Puisque plusieurs indices de guidage collaborent, il est particulièrement difficile d’identifier la contribution individuelle ou la voie de signalisation qui est déclenchée in vivo, il est donc nécessaire d’utiliser des méthodes pour reproduire ces distributions de protéines in vitro. Plusieurs méthodes existent pour produire des gradients de protéines solubles ou liées aux substrats. Quelques méthodes pour produire des gradients solubles sont déjà couramment utilisées dans plusieurs laboratoires, mais elles limitent l’étude aux distributions de protéines qui sont normalement sécrétées in vivo. Les méthodes permettant de produire des distributions liées au substrat sont particulièrement complexes, ce qui restreint leur utilisation à quelques laboratoires. Premièrement, nous présentons une méthode simple qui exploite le photoblanchiment de molécules fluorescentes pour créer des motifs de protéines liées au substrat : Laser-assisted protein adsorption by photobleaching (LAPAP). Cette méthode permet de produire des motifs de protéines complexes d’une résolution micrométrique et d’une grande portée dynamique. Une caractérisation de la technique a été faite et en tant que preuve de fonctionnalité, des axones de neurones du ganglion spinal ont été guidés sur des gradients d’un peptide provenant de la laminine. Deuxièmement, LAPAP a été amélioré de manière à pouvoir fabriquer des motifs avec plusieurs composantes grâce à l’utilisation de lasers à différentes longueurs d’onde et d’anticorps conjugués à des fluorophores correspondants à ces longueurs d’onde. De plus, pour accélérer et simplifier le processus de fabrication, nous avons développé LAPAP à illumination à champ large qui utilise un modulateur spatial de lumière, une diode électroluminescente et un microscope standard pour imprimer directement un motif de protéines. Cette méthode est particulièrement simple comparativement à la version originale de LAPAP puisqu’elle n’implique pas le contrôle de la puissance laser et de platines motorisées, mais seulement d’envoyer l’image du motif désiré au modulateur spatial. Finalement, nous avons utilisé LAPAP pour démontrer que notre technique peut être utilisée dans des analyses de haut contenu pour quantifier les changements morphologiques résultant de la croissance neuronale sur des gradients de protéines de guidage. Nous avons produit des milliers de gradients de laminin-1 ayant différentes pentes et analysé les variations au niveau du guidage de neurites provenant d’une lignée cellulaire neuronale (RGC-5). Un algorithme pour analyser les images des cellules sur les gradients a été développé pour détecter chaque cellule et quantifier la position du centroïde du soma ainsi que les angles d’initiation, final et de braquage de chaque neurite. Ces données ont démontré que les gradients de laminine influencent l’angle d’initiation des neurites des RGC-5, mais n’influencent pas leur braquage. Nous croyons que les résultats présentés dans cette thèse faciliteront l’utilisation de motifs de protéines liées au substrat dans les laboratoires des sciences de la vie, puisque LAPAP peut être effectué à l’aide d’un microscope confocal ou d’un microscope standard légèrement modifié. Cela pourrait contribuer à l’augmentation du nombre de laboratoires travaillant sur le guidage avec des gradients liés au substrat afin d’atteindre la masse critique nécessaire à des percées majeures en neuroscience.

Approches bio-informatiques appliquées aux technologies émergentes en génomique

Les études génétiques, telles que les études de liaison ou d’association, ont permis d’acquérir une plus grande connaissance sur l’étiologie de plusieurs maladies affectant les populations humaines. Même si une dizaine de milliers d’études génétiques ont été réalisées sur des centaines de maladies ou autres traits, une grande partie de leur héritabilité reste inexpliquée. Depuis une dizaine d’années, plusieurs percées dans le domaine de la génomique ont été réalisées. Par exemple, l’utilisation des micropuces d’hybridation génomique comparative à haute densité a permis de démontrer l’existence à grande échelle des variations et des polymorphismes en nombre de copies. Ces derniers sont maintenant détectables à l’aide de micropuce d’ADN ou du séquençage à haut débit. De plus, des études récentes utilisant le séquençage à haut débit ont permis de démontrer que la majorité des variations présentes dans l’exome d’un individu étaient rares ou même propres à cet individu. Ceci a permis la conception d’une nouvelle micropuce d’ADN permettant de déterminer rapidement et à faible coût le génotype de plusieurs milliers de variations rares pour un grand ensemble d’individus à la fois. Dans ce contexte, l’objectif général de cette thèse vise le développement de nouvelles méthodologies et de nouveaux outils bio-informatiques de haute performance permettant la détection, à de hauts critères de qualité, des variations en nombre de copies et des variations nucléotidiques rares dans le cadre d’études génétiques. Ces avancées permettront, à long terme, d’expliquer une plus grande partie de l’héritabilité manquante des traits complexes, poussant ainsi l’avancement des connaissances sur l’étiologie de ces derniers. Un algorithme permettant le partitionnement des polymorphismes en nombre de copies a donc été conçu, rendant possible l’utilisation de ces variations structurales dans le cadre d’étude de liaison génétique sur données familiales. Ensuite, une étude exploratoire a permis de caractériser les différents problèmes associés aux études génétiques utilisant des variations en nombre de copies rares sur des individus non reliés. Cette étude a été réalisée avec la collaboration du Wellcome Trust Centre for Human Genetics de l’University of Oxford. Par la suite, une comparaison de la performance des algorithmes de génotypage lors de leur utilisation avec une nouvelle micropuce d’ADN contenant une majorité de marqueurs rares a été réalisée. Finalement, un outil bio-informatique permettant de filtrer de façon efficace et rapide des données génétiques a été implémenté. Cet outil permet de générer des données de meilleure qualité, avec une meilleure reproductibilité des résultats, tout en diminuant les chances d’obtenir une fausse association.