Quantitative proteomics methods for the analysis of histone post-translational modifications

Les histones sont des protéines nucléaires hautement conservées chez les cellules des eucaryotes. Elles permettent d’organiser et de compacter l’ADN sous la forme de nucléosomes, ceux-ci representant les sous unités de base de la chromatine. Les histones peuvent être modifiées par de nombreuses modifications post-traductionnelles (PTMs) telles que l’acétylation, la méthylation et la phosphorylation. Ces modifications jouent un rôle essentiel dans la réplication de l’ADN, la transcription et l’assemblage de la chromatine. L’abondance de ces modifications peut varier de facon significative lors du developpement des maladies incluant plusieurs types de cancer. Par exemple, la perte totale de la triméthylation sur H4K20 ainsi que l’acétylation sur H4K16 sont des marqueurs tumoraux spécifiques a certains types de cancer chez l’humain. Par conséquent, l’étude de ces modifications et des événements determinant la dynamique des leurs changements d’abondance sont des atouts importants pour mieux comprendre les fonctions cellulaires et moléculaires lors du développement de la maladie. De manière générale, les modifications des histones sont étudiées par des approches biochimiques telles que les immuno-buvardage de type Western ou les méthodes d’immunoprécipitation de la chromatine (ChIP). Cependant, ces approches présentent plusieurs inconvénients telles que le manque de spécificité ou la disponibilité des anticorps, leur coût ou encore la difficulté de les produire et de les valider. Au cours des dernières décennies, la spectrométrie de masse (MS) s’est avérée être une méthode performante pour la caractérisation et la quantification des modifications d’histones. La MS offre de nombreux avantages par rapport aux techniques traditionnelles. Entre autre, elle permet d’effectuer des analyses reproductibles, spécifiques et facilite l’etude d’un large spectre de PTMs en une seule analyse. Dans cette thèse, nous présenterons le développement et l’application de nouveaux outils analytiques pour l’identification et à la quantification des PTMs modifiant les histones. Dans un premier temps, une méthode a été développée pour mesurer les changements d’acétylation spécifiques à certains sites des histones. Cette méthode combine l’analyse des histones intactes et les méthodes de séquençage peptidique afin de déterminer les changements d’acétylation suite à la réaction in vitro par l’histone acétyltransférase (HAT) de levure Rtt109 en présence de ses chaperonnes (Asf1 ou Vps75). Dans un second temps, nous avons développé une méthode d’analyse des peptides isomériques des histones. Cette méthode combine la LC-MS/MS à haute résolution et un nouvel outil informatique appelé Iso-PeptidAce qui permet de déconvoluer les spectres mixtes de peptides isomériques. Nous avons évalué Iso-PeptidAce avec un mélange de peptides synthétiques isomériques. Nous avons également validé les performances de cette approche avec des histones isolées de cellules humaines érythroleucémiques (K562) traitées avec des inhibiteurs d’histones désacétylases (HDACi) utilisés en clinique, et des histones de Saccharomyces cerevisiae liées au facteur d’assemblage de la chromatine (CAF-1) purifiées par chromatographie d’affinité. Enfin, en utilisant la méthode présentée précédemment, nous avons fait une analyse approfondie de la spécificité de plusieurs HATs et HDACs chez Schizosaccharomyces pombe. Nous avons donc déterminé les niveaux d’acétylation d’histones purifiées à partir de cellules contrôles ou de souches mutantes auxquelles il manque une HAT ou HDAC. Notre analyse nous a permis de valider plusieurs cibles connues des HATs et HDACs et d’en identifier de nouvelles. Nos données ont également permis de définir le rôle des différentes HATs et HDACs dans le maintien de l’équilibre d’acétylation des histones. Dans l’ensemble, nous anticipons que les méthodes décrites dans cette thèse permettront de résoudre certains défis rencontrés dans l’étude de la chromatine. De plus, ces données apportent de nouvelles connaissances pour l’élaboration d’études génétiques et biochimiques utilisant S. pombe.

Effect of Different Forms of Poly o-Toluidine /Poly Vinyl Chloride Composites on Dielectric Propertiesin the Microwave Field

In this paper we report the preparation and dielectric properties of poly o-toluidine:poly vinyl chloride composites in pellet and film forms. The composites were prepared using ammonium persulfate initiator and HCl dopant. The characterization is done by TGA and DSC. The dielectric properties including dielectric loss, conductivity, dielectric constant, dielectric heating coefficient, absorption coefficient, and penetration depth were studied in the microwave field. An HP8510 vector network analyzer with rectangular cavity resonator was used for the study. Sbands (2-4 GHz), C band (5-8 GHz), and X band (8-12 GHz) frequencies were used in the microwave field. Comparisons between the pellet and film forms of composites were also included. The result shows that the dielectric properties in the microwave field are dependent on the frequency and on the method of preparation.

Field Equilibrium Finite Elements for Structural Analysis

Many finite elements used in structural analysis possess deficiencies like shear locking, incompressibility locking, poor stress predictions within the element domain, violent stress oscillation, poor convergence etc. An approach that can probably overcome many of these problems would be to consider elements in which the assumed displacement functions satisfy the equations of stress field equilibrium. In this method, the finite element will not only have nodal equilibrium of forces, but also have inner stress field equilibrium. The displacement interpolation functions inside each individual element are truncated polynomial solutions of differential equations. Such elements are likely to give better solutions than the existing elements.In this thesis, a new family of finite elements in which the assumed displacement function satisfies the differential equations of stress field equilibrium is proposed. A general procedure for constructing the displacement functions and use of these functions in the generation of elemental stiffness matrices has been developed. The approach to develop field equilibrium elements is quite general and various elements to analyse different types of structures can be formulated from corresponding stress field equilibrium equations. Using this procedure, a nine node quadrilateral element SFCNQ for plane stress analysis, a sixteen node solid element SFCSS for three dimensional stress analysis and a four node quadrilateral element SFCFP for plate bending problems have been formulated.For implementing these elements, computer programs based on modular concepts have been developed. Numerical investigations on the performance of these elements have been carried out through standard test problems for validation purpose. Comparisons involving theoretical closed form solutions as well as results obtained with existing finite elements have also been made. It is found that the new elements perform well in all the situations considered. Solutions in all the cases converge correctly to the exact values. In many cases, convergence is faster when compared with other existing finite elements. The behaviour of field consistent elements would definitely generate a great deal of interest amongst the users of the finite elements.

Optimization of Preparation Techniques and Dielectric Study of Polyanilines in the Microwave & High Frequency Field

The thesis deals with the preparation and dielectric characterization of Poly aniline and its analogues in ISM band frequency of 2-4 GHz that includes part of the microwave region (300 MHz to 300 GHz) of the electromagnetic spectrum and an initial dielectric study in the high frequency [O.05MHz-13 MHz]. PolyaniIine has been synthesized by an in situ doping reaction under different temperature and in the presence of inorganic dopants such as HCl H2S04, HN03, HCl04 and organic dopants such as camphorsulphonic acid [CSA], toluenesulphonic acid {TSA) and naphthalenesulphonic acid [NSA]. The variation in dielectric properties with change in reaction temperature, dopants and frequency has been studied. The effect of codopants and microemulsions on the dielectric properties has also been studied in the ISM band. The ISM band of frequencies (2-4 GHz) is of great utility in Industrial, Scientific and Medical (ISM) applications. Microwave heating is a very efficient method of heating dielectric materials and is extensively used in industrial as well as household heating applications.

Development of Free Space Method for Material Characterisation and GPR Study & A Case Study on Biological Samples

The thesis mainly focuses on material characterization in different environments: freely available samples taken in planar fonn, biological samples available in small quantities and buried objects.Free space method, finds many applications in the fields of industry, medicine and communication. As it is a non-contact method, it can be employed for monitoring the electrical properties of materials moving through a conveyor belt in real time. Also, measurement on such systems at high temperature is possible. NID theory can be applied to the characterization of thin films. Dielectric properties of thin films deposited on any dielectric substrate can be determined. ln chemical industry, the stages of a chemical reaction can be monitored online. Online monitoring will be more efficient as it saves time and avoids risk of sample collection.Dielectric contrast is one of the main factors, which decides the detectability of a system. lt could be noted that the two dielectric objects of same dielectric constant 3.2 (s, of plastic mine) placed in a medium of dielectric constant 2.56 (er of sand) could even be detected employing the time domain analysis of the reflected signal. This type of detection finds strategic importance as it provides solution to the problem of clearance of non-metallic mines. The demining of these mines using the conventional techniques had been proved futile. The studies on the detection of voids and leakage in pipes find many applications.The determined electrical properties of tissues can be used for numerical modeling of cells, microwave imaging, SAR test etc. All these techniques need the accurate determination of dielectric constant. ln the modem world, the use of cellular and other wireless communication systems is booming up. At the same time people are concemed about the hazardous effects of microwaves on living cells. The effect is usually studied on human phantom models. The construction of the models requires the knowledge of the dielectric parameters of the various body tissues. lt is in this context that the present study gains significance. The case study on biological samples shows that the properties of normal and infected body tissues are different. Even though the change in the dielectric properties of infected samples from that of normal one may not be a clear evidence of an ailment, it is an indication of some disorder.ln medical field, the free space method may be adapted for imaging the biological samples. This method can also be used in wireless technology. Evaluation of electrical properties and attenuation of obstacles in the path of RF waves can be done using free waves. An intelligent system for controlling the power output or frequency depending on the feed back values of the attenuation may be developed.The simulation employed in GPR can be extended for the exploration of the effects due to the factors such as the different proportion of water content in the soil, the level and roughness of the soil etc on the reflected signal. This may find applications in geological explorations. ln the detection of mines, a state-of-the art technique for scanning and imaging an active mine field can be developed using GPR. The probing antenna can be attached to a robotic arm capable of three degrees of rotation and the whole detecting system can be housed in a military vehicle. In industry, a system based on the GPR principle can be developed for monitoring liquid or gas through a pipe, as pipe with and without the sample gives different reflection responses. lt may also be implemented for the online monitoring of different stages of extraction and purification of crude petroleum in a plant.Since biological samples show fluctuation in the dielectric nature with time and other physiological conditions, more investigation in this direction should be done. The infected cells at various stages of advancement and the normal cells should be analysed. The results from these comparative studies can be utilized for the detection of the onset of such diseases. Studying the properties of infected tissues at different stages, the threshold of detectability of infected cells can be determined.

Buried-object detection using free-space time-domain near-field measurements

The detection of buried objects using time-domain freespace measurements was carried out in the near field. The location of a hidden object was determined from an analysis of the reflected signal. This method can be extended to detect any number of objects. Measurements were carried out in the X- and Ku-bands using ordinary rectangular pyramidal horn antennas of gain 15 dB. The same antenna was used as the transmitter and recei er. The experimental results were compared with simulated results by applying the two-dimensional finite-difference time-domain(FDTD)method, and agree well with each other. The dispersi e nature of the dielectric medium was considered for the simulation.

Modeling premartensitic effects in Ni2MnGa: A mean-field and Monte Carlo simulation study

ic first-order transition line ending in a critical point. This critical point is responsible for the existence of large premartensitic fluctuations which manifest as broad peaks in the specific heat, not always associated with a true phase transition. The main conclusion is that premartensitic effects result from the interplay between the softness of the anomalous phonon driving the modulation and the magnetoelastic coupling. In particular, the premartensitic transition occurs when such coupling is strong enough to freeze the involved mode phonon. The implication of the results in relation to the available experimental data is discussed.

Studies in molecular mechanics using spectroscopic data exact force field and bond in homogeneity

This thesis deals with some studies in molecular mechanic using spectroscopic data. It includes an improvement in the parameter technique for the evaluation of exact force fields, the introduction of a new and simple algebraic method for the force field calculation and a study of asymmetric variation of bonding forces along a bond.

Studies in quantum field theory at finite temperature

The thesis deals with certain quantum field systems exhibiting spontaneous symmetry breaking and their response to temperature. These models find application in diverse branches such as particle physics, solid state physics and non~linear optics. The nature of phase transition that these systems may undergo is also investigated. The thesis contains seven chapters. The first chapter is introductory and gives a brief account of the various phenomena associated with spontaneous symmetry breaking. The chapter closes with anote on the effect of temperature on quantum field systems. In chapter 2, the spontaneous symmetry breaking phenomena are reviewed in more detail. Chapter 3, deals with the formulation of ordinary and generalised sine-Gordon field theories on a lattice and the study of the nature of phase transition occurring in these systems. In chapter 4, the effect of temperature on these models is studied, using the effective potential method. Chapter 5 is a continuation of this study for another model, viz, the m6 model. The nature of phase transition is also studied. Chapters 5 and 6 constitute a report of the investigations on the behaviour of coupling constants under thermal excitation D1 $4 theory, scalar electrodynamics, abelian and non-abelian gauge theories

Normalization factors for magnetic relaxation of small particle systems in non-zero magnetic field.

We critically discuss relaxation experiments in magnetic systems that can be characterized in terms of an energy barrier distribution, showing that proper normalization of the relaxation data is needed whenever curves corresponding to different temperatures are to be compared. We show how these normalization factors can be obtained from experimental data by using the Tln (t/t0) scaling method without making any assumptions about the nature of the energy barrier distribution. The validity of the procedure is tested using a ferrofluid of Fe3O4 particles.

Variational Wigner-Kirkwood approach to relativistic mean field theory

The recently developed variational Wigner-Kirkwood approach is extended to the relativistic mean field theory for finite nuclei. A numerical application to the calculation of the surface energy coefficient in semi-infinite nuclear matter is presented. The new method is contrasted with the standard density functional theory and the fully quantal approach.

Underwater Target Localization, Tracking and Classification

Underwater target localization and tracking attracts tremendous research interest due to various impediments to the estimation task caused by the noisy ocean environment. This thesis envisages the implementation of a prototype automated system for underwater target localization, tracking and classification using passive listening buoy systems and target identification techniques. An autonomous three buoy system has been developed and field trials have been conducted successfully. Inaccuracies in the localization results, due to changes in the environmental parameters, measurement errors and theoretical approximations are refined using the Kalman filter approach. Simulation studies have been conducted for the tracking of targets with different scenarios even under maneuvering situations. This system can as well be used for classifying the unknown targets by extracting the features of the noise emanations from the targets.

Studies on the interaction of two level atoms with quantized electromagnetic field

The present study described about the interaction of a two level atom and squeezed field with time varying frequency. By applying a sinusoidal variation in the frequency of the field, the randomness in population inversion is reduced and the collapses and periodic revivals are regained. Quantum optics is an emerging field in physics which mainly deals with the interaction of atoms with quantised electromagnetic fields. Jaynes-Cummings Model (JCM) is a key model among them, which describes the interaction between a two level atom and a single mode radiation field. Here the study begins with a brief history of light, atom and their interactions. Also discussed the interaction between atoms and electromagnetic fields. The study suggest a method to manipulate the population inversion due to interaction and control the randomness in it, by applying a time dependence on the frequency of the interacting squeezed field.The change in behaviour of the population inversion due to the presence of a phase factor in the applied frequency variation is explained here.This study also describes the interaction between two level atom and electromagnetic field in nonlinear Kerr medium. It deals with atomic and field state evolution in a coupled cavity system. Our results suggest a new method to control and manipulate the population of states in two level atom radiation interaction,which is very essential for quantum information processing.We have also studied the variation of atomic population inversion with time, when a two level atom interacts with light field, where the light field has a sinusoidal frequency variation with a constant phase. In both coherent field and squeezed field cases, the population inversion variation is completely different from the phase zero frequency modulation case. It is observed that in the presence of a non zero phase φ, the population inversion oscillates sinusoidally.Also the collapses and revivals gradually disappears when φ increases from 0 to π/2. When φ = π/2 the evolution of population inversion is identical to the case when a two level atom interacts with a Fock state. Thus, by applying a phase shifted frequency modulation one can induce sinusoidal oscillations of atomic inversion in linear medium, those normally observed in Kerr medium. We noticed that the entanglement between the atom and field can be controlled by varying the period of the field frequency fluctuations. The system has been solved numerically and the behaviour of it for different initial conditions and different susceptibility values are analysed. It is observed that, for weak cavity coupling the effect of susceptibility is minimal. In cases of strong cavity coupling, susceptibility factor modifies the nature in which the probability oscillates with time. Effect of susceptibility on probability of states is closely related to the initial state of the system.

Organic field-effect transistors and phototransistors based on amorphous materials

A comparison between the charge transport properties in low molecular amorphous thin films of spiro-linked compound and their corresponding parent compound has been demonstrated. The field-effect transistor method is used for extracting physical parameters such as field-effect mobility of charge carriers, ON/OFF ratios, and stability. In addition, phototransistors have been fabricated and demonstrated for the first time by using organic materials. In this case, asymmetrically spiro-linked compounds are used as active materials. The active materials used in this study can be divided into three classes, namely Spiro-linked compounds (symmetrically spiro-linked compounds), the corresponding parent-compounds, and photosensitive spiro-linked compounds (asymmetrically spiro-linked com-pounds). Some of symmetrically spiro-linked compounds used in this study were 2,2',7,7'-Tetrakis-(di-phenylamino)-9,9'-spirobifluorene (Spiro-TAD),2,2',7,7'-Tetrakis-(N,N'-di-p-methylphenylamino)-9,9'-spirobifluorene (Spiro-TTB), 2,2',7,7'-Tetra-(m-tolyl-phenylamino)-9,9'-spirobifluorene (Spiro-TPD), and 2,2Ž,7,7Ž-Tetra-(N-phenyl-1-naphtylamine)-9,9Ž-spirobifluorene (Spiro alpha-NPB). Related parent compounds of the symmetrically spiro-linked compound used in this study were N,N,N',N'-Tetraphenylbenzidine (TAD), N,N,N',N'-Tetrakis(4-methylphenyl)benzidine (TTB), N,N'-Bis(3-methylphenyl)-(1,1'-biphenyl)-4,4'-diamine (TPD), and N,N'-Diphenyl-N,N'-bis(1-naphthyl)-1,1'-biphenyl-4,4'-diamine (alpha-NPB). The photosensitive asymmetrically spiro-linked compounds used in this study were 2,7-bis-(N,N'-diphenylamino)-2',7'-bis(biphenyl-4-yl)-9,9'-spirobifluorene (Spiro-DPSP), and 2,7-bis-(N,N'-diphenylamino)-2',7'-bis(spirobifluorene-2-yl)-9,9'-spirobifluorene (Spiro-DPSP^2). It was found that the field-effect mobilities of charge carriers in thin films of symmetrically spiro-linked compounds and their corresponding parent compounds are in the same order of magnitude (~10^-5 cm^2/Vs). However, the thin films of the parent compounds were easily crystallized after the samples have been exposed in ambient atmosphere and at room temperature for three days. In contrast, the thin films and the transistor characteristics of symmetrically spiro-linked compound did not change significantly after the samples have been stored in ambient atmosphere and at room temperature for several months. Furthermore, temperature dependence of the mobility was analyzed in two models, namely the Arrhenius model and the Gaussian Disorder model. The Arrhenius model tends to give a high value of the prefactor mobility. However, it is difficult to distinguish whether the temperature behaviors of the material under consideration follows the Arrhenius model or the Gaussian Disorder model due to the narrow accessible range of the temperatures. For the first time, phototransistors have been fabricated and demonstrated by using organic materials. In this case, asymmetrically spiro-linked compounds are used as active materials. Intramolecular charge transfer between a bis(diphenylamino)biphenyl unit and a sexiphenyl unit leads to an increase in charge carrier density, providing the amplification effect. The operational responsivity of better than 1 A/W can be obtained for ultraviolet light at 370 nm, making the device interesting for sensor applications. This result offers a new potential application of organic thin film phototransistors as low-light level and low-cost visible blind ultraviolet photodetectors.

Statistical evaluation of texture analysis from the biocrystallization method

The consumers are becoming more concerned about food quality, especially regarding how, when and where the foods are produced (Haglund et al., 1999; Kahl et al., 2004; Alföldi, et al., 2006). Therefore, during recent years there has been a growing interest in the methods for food quality assessment, especially in the picture-development methods as a complement to traditional chemical analysis of single compounds (Kahl et al., 2006). The biocrystallization as one of the picture-developing method is based on the crystallographic phenomenon that when crystallizing aqueous solutions of dihydrate CuCl2 with adding of organic solutions, originating, e.g., from crop samples, biocrystallograms are generated with reproducible crystal patterns (Kleber & Steinike-Hartung, 1959). Its output is a crystal pattern on glass plates from which different variables (numbers) can be calculated by using image analysis. However, there is a lack of a standardized evaluation method to quantify the morphological features of the biocrystallogram image. Therefore, the main sakes of this research are (1) to optimize an existing statistical model in order to describe all the effects that contribute to the experiment, (2) to investigate the effect of image parameters on the texture analysis of the biocrystallogram images, i.e., region of interest (ROI), color transformation and histogram matching on samples from the project 020E170/F financed by the Federal Ministry of Food, Agriculture and Consumer Protection(BMELV).The samples are wheat and carrots from controlled field and farm trials, (3) to consider the strongest effect of texture parameter with the visual evaluation criteria that have been developed by a group of researcher (University of Kassel, Germany; Louis Bolk Institute (LBI), Netherlands and Biodynamic Research Association Denmark (BRAD), Denmark) in order to clarify how the relation of the texture parameter and visual characteristics on an image is. The refined statistical model was accomplished by using a lme model with repeated measurements via crossed effects, programmed in R (version 2.1.0). The validity of the F and P values is checked against the SAS program. While getting from the ANOVA the same F values, the P values are bigger in R because of the more conservative approach. The refined model is calculating more significant P values. The optimization of the image analysis is dealing with the following parameters: ROI(Region of Interest which is the area around the geometrical center), color transformation (calculation of the 1 dimensional gray level value out of the three dimensional color information of the scanned picture, which is necessary for the texture analysis), histogram matching (normalization of the histogram of the picture to enhance the contrast and to minimize the errors from lighting conditions). The samples were wheat from DOC trial with 4 field replicates for the years 2003 and 2005, “market samples”(organic and conventional neighbors with the same variety) for 2004 and 2005, carrot where the samples were obtained from the University of Kassel (2 varieties, 2 nitrogen treatments) for the years 2004, 2005, 2006 and “market samples” of carrot for the years 2004 and 2005. The criterion for the optimization was repeatability of the differentiation of the samples over the different harvest(years). For different samples different ROIs were found, which reflect the different pictures. The best color transformation that shows efficiently differentiation is relied on gray scale, i.e., equal color transformation. The second dimension of the color transformation only appeared in some years for the effect of color wavelength(hue) for carrot treated with different nitrate fertilizer levels. The best histogram matching is the Gaussian distribution. The approach was to find a connection between the variables from textural image analysis with the different visual criteria. The relation between the texture parameters and visual evaluation criteria was limited to the carrot samples, especially, as it could be well differentiated by the texture analysis. It was possible to connect groups of variables of the texture analysis with groups of criteria from the visual evaluation. These selected variables were able to differentiate the samples but not able to classify the samples according to the treatment. Contrarily, in case of visual criteria which describe the picture as a whole there is a classification in 80% of the sample cases possible. Herewith, it clearly can find the limits of the single variable approach of the image analysis (texture analysis).