This diploma thesis deals with DCE-MRI (Dynamic Contrast-Enhanced Magnetic Resonance Imaging) thus one of the contrast magnetic resonance imaging methods. It describes the principle of conventional continuous DCE-MRI, which uses single bolus of contrast agent and further it focuses on the dual bolus contrast agent techniques, especially the interleaved acquisition. The graphical interface for processing Bruker systems data was made. Synthetic data were used to evaluate the influence of this method on the perfusion parameters estimation. Simulations proved that the further the second bolus is from the first one, the better results are. Simulations of acquisition interruption did not lead to the clear result. However, two statements, which are expected to lead to as good estimation of perfusion parameters as possible, were formulated

Stroke is a serious brain injury, which causes sudden death or terminates in permanent neurological disability. Nowadays, tissue plasminogen activator (tPA) is used as the only effective treatment of stroke. One of the potential targets for novel therapy are T cells. Even though the explicit role of T cells in the pathogenesis of brain injury, amounts and timing of all T cell subtypes infiltrating into brain during the stroke still needs further investigation. The research in this field is complicated by the lack of efficient methods for in vivo cell tracking. Therefore the aim of this thesis was to develop a method of T cells labelling by MRI contrast agent in order to investigate T cells distribution in ischemic mice model using in vivo MR imaging. T cells were isolated from C57/BL6 mice in two step isolation protocol using gradient centrifugation and magnetic separation with the efficiency of 97 %. The isolated cells were labelled with 100 μg Fe/mL of Molday ION Rhodamine B contrast agent. The labelling efficiency after 17 hours of cells incubation was higher than 99 %. The labelled cells were cultured with CD3 and CD28 antibodies resulting into the 74 % viability of labelled T cells compared to 83 % viability of non labelled T cells. The labelled T cells were visualized by fluorescent...

Agriculture, with different Neolithic cultures, starts in the Near East more than 10,000 years ago. This new way of life has very different archaeological manifestations that previous Mesolithic. After its Near Eastern emergence, the farming practices rapidly penetrated into southeastern Europe and the first signs of Neolithic in Central Europe are already 7,000 years old. It is being considered that the cultural innovations influenced demographic growth of the populations that have taken part in the Neolithic spread. In such situation, new mutations would have to fix and could form new specific haplogroups for Europe with ancestral ties to the Near East. Phylogeographic studies such as founder analysis of European and Near Eastern mtDNA sequences found that the European Neolithic component was enriched mainly by haplogroups J and T1, and that the genetic contribution of farming economy in European gene pool is about 10 - 20%. However, studies like these have not been yet realized in particular parts of Europe. The aim of this thesis is to disentangle the internal variability of Central European haplogroups J and T1 thought to be involved in the Neolithic demic diffusion. We classified these haplogroups from the HVS-I mtDNA sequences of 281 samples of the recent population of the Czech Republic. We...

Clinical course of multiple sclerosis (MS) is heterogenous and white matter lesion count and volume on brain magnetic resonance imaging (MRI) correlate with clinical course only partially. Therefore, there is an urgent need for more reliable prognostic biomarkers. This work explored three imaging markers - spinal cord (SC) imaging (specifically SC volume measurement and assessment of focal and diffuse SC changes), atlas-based model of "disconnectome" (i.e. disruption of brain connectivity due to white matter lesions) and periventricular white matter gradient assessed with T1 relaxometry. For the SC projects, we assessed MRI from 2044 MS patients with a semi-automatic method for SC volume measurement. We confirmed (i) a relationship between diffuse SC changes, SC volume and disability; (ii) a novel finding was that in patients with EDSS ≤ 4.0, diffuse changes contributed to higher disability more than SC volume; (iii) SC volume explains the paradox in patients with dissociation between brain white matter lesion load and disability; (iv) SC focal and/or diffuse changes are present in 75% patients with early MS, of which 43% have diffuse changes that are related to brainstem lesions. In the disconnectome project, we evaluated the disruption of connectivity caused by white mater lesions in 745 patients...

Multi-site MRI studies collect large amounts of data in a short time frame. Large sample sizes are desirable to address power and replicability issues that have been problematic for scientists in the past. Although multi-site MRI solves the sample size problem, it brings with it a new set of challenges. Scanning the same person at different sites might result in differences in MRI derived measurements. In this thesis we compared three approaches to facilitate the analysis of multi-site MRI data: quantitative R1 mapping, adding site as a covariate in a linear model, and using the ComBat method. We also investigated the relationship between two common MRI measurements: signal and volume. We collected data from 64 healthy participants across 3 GE scanners and 1 Siemens scanner at 3T. We found that signal intensity was different between vendors whereas volume was not. Our R1 method resulted in values that were different across vendor and significantly lower than those reported in the literature. B1+ maps used to calculate R1 were different across sites. Using a scale factor, we were able to compensate for mistakes in R1 mapping. We also found that adding site as a covariate corrected mean differences in signal intensity across sites, but not differences in variance. The ComBat method gave best similarity between sites. However, since different people were scanned at each site, we couldn’t evaluate the effectiveness of each method as variation in the data could have been due to site effects or heterogeneity in participants. White matter volume and signal intensity in the white matter were correlated in males but not in females. We found that this low correlation was caused by outliers in our female sample. The correlation between white matter volume and signal in males suggests that both metrics are measuring myelin and can be used as converging evidence to detect changes in brain myelination. / Thesis / Master of Science (MSc)

This thesis presents a high-resolution volumetric technique to measure the longitudinal relaxation time T1 in the vessel wall using MRI. The method of Variable Flip Angles (VFA) was applied using a new strategy for flip angle selection that allows measurement of T1 with high accuracy (< 10% mean error) and precision (T1-to-noise ratio > 10) over the wide range of anticipated values (300-3000ms) in the vessel wall. This strategy was validated in simulation, phantom and volunteer spinal cord experiments. Initial validation of vessel wall T1 measurements was performed in ex-vivo thoracic aorta samples from cholesterol-fed rabbits. For in-vivo vessel wall T1 mapping, the technique was augmented with spatial saturation bands for flow suppression and applied to the carotid arteries of three volunteers. Preliminary results from volunteers suggest that this approach may be useful in characterizing T1 changes associated with high-risk atherosclerotic disease.

This thesis presents a high-resolution volumetric technique to measure the longitudinal relaxation time T1 in the vessel wall using MRI. The method of Variable Flip Angles (VFA) was applied using a new strategy for flip angle selection that allows measurement of T1 with high accuracy (< 10% mean error) and precision (T1-to-noise ratio > 10) over the wide range of anticipated values (300-3000ms) in the vessel wall. This strategy was validated in simulation, phantom and volunteer spinal cord experiments. Initial validation of vessel wall T1 measurements was performed in ex-vivo thoracic aorta samples from cholesterol-fed rabbits. For in-vivo vessel wall T1 mapping, the technique was augmented with spatial saturation bands for flow suppression and applied to the carotid arteries of three volunteers. Preliminary results from volunteers suggest that this approach may be useful in characterizing T1 changes associated with high-risk atherosclerotic disease.

In this thesis, three different types of polymer-based gels are fabricated and characterized for passive and active applications. Silica aerogel is a 3D mesoporous solid material that can be used for thermal insulation or in the biomedical industry. In this thesis, silica aerogel is cross- linked with diisocyanate to improve its strength and flexibility, which greatly opens up the range of applications. Then, soft polymer gel with tissue equivalent characteristics is fabricated to mimic the spin-lattice (T1) and spin-spin (T2) relaxation times for the magnetic resonance imaging (MRI) phantom of a liver with lesions. This study demonstrates a relationship between the composition of a gelling agent, and T1 and T2 modifiers on its dielectric, mechanical and imaging properties. Finally, an ionic electroactive polymer (EAP) that can be actuated on an electric field is fabricated, and its swelling and bending behaviours on design parameters are closely examined.

In this thesis, three different types of polymer-based gels are fabricated and characterized for passive and active applications. Silica aerogel is a 3D mesoporous solid material that can be used for thermal insulation or in the biomedical industry. In this thesis, silica aerogel is cross- linked with diisocyanate to improve its strength and flexibility, which greatly opens up the range of applications. Then, soft polymer gel with tissue equivalent characteristics is fabricated to mimic the spin-lattice (T1) and spin-spin (T2) relaxation times for the magnetic resonance imaging (MRI) phantom of a liver with lesions. This study demonstrates a relationship between the composition of a gelling agent, and T1 and T2 modifiers on its dielectric, mechanical and imaging properties. Finally, an ionic electroactive polymer (EAP) that can be actuated on an electric field is fabricated, and its swelling and bending behaviours on design parameters are closely examined.

Ce travail de thèse a comporté deux parties distinctes : l'une porte sur l'étude du complexe TAR/Tat/cycline T1 impliqué dans la transactivation de la transcription de l'ARN du virus HIV-1, l'autre concerne différentes facettes de la régulation de l'épissage de l'ARN du virus HIV-1. L'interaction de la protéine virale Tat avec l'élément TAR présent à l'extrémité 5' des ARN du virus HIV-1 d'une part, et la cycline T1, composant du complexe p-TEFb responsable de l'hyperphosphorylation de l'ARN polymérase II d'autre part, est primordial pour obtenir des ARN viraux de pleine longueur. Dans l'objectif de réaliser une étude structurale du complexe TAR/Tat/cycline T1, l'ARN TAR et un fragment de la cycline T1 ont été produits en grandes quantités. De nombreuses tentatives de complexation des trois partenaires (TAR, Tat et cycline T1) ont été effectuées, mais la qualité des cristaux n'était pas suffisante pour une étude radiocristallographique du complexe. L'épissage est une étape majeure du cycle de multiplication du virus HIV-1. Son ARN comporte 5 sites donneurs et 8 sites accepteurs dont l'utilisation combinée permet la production des 9 ORF virales. Les variations de l'épissage alternatif de l'ARN du virus HIV-1 en fonction de l'expression de protéines virales Tat et Nef ont été étudiées. Nous avons par ailleurs étudié l'effet des protéines SR sur l'utilisation des sites accepteurs A2 et A3. L'étude fine de l'élément régulateur ESEt du site A3 a révélé l'implication de la protéine SR 9G8 dans le schéma complexe de régulation de ce site. / This work of thesis contained two different parts : the one concerns the study of the TAR/Tat/cycline T1 complex involved in the transactivation of the transcription of the HIV-1 RNA, the other one concerns various facets of the regulation of the splicing of the HIV-1 RNA. The interaction of the viral protein Tat with the TAR element present in the 5 ' extremity of the HIV-1 RNA on one hand, and the cycline T1, composing of the complex p-TEFb responsible for the hyperphosphorylation of the RNA polymerase II on the other hand, is essential to obtain viral RNA of full length. In the objective to realize a structural study of the complex TAR/Tat/cycline T1, TAR RNA and a fragment of the cycline T1 were produced in appropriate quantities. Numerous attempts of complexation of three partners (TAR, Tat and cycline T1) were made, but the quality of crystals was not sufficient for a radiocristallographic study of the complex. Splicing is a major stage of the cycle of reproduction of the virus HIV-1. His RNA contains 5 donor splice sites and 8 acceptor splice sites whose combined use allows the production 9 viral ORF. The variations of the alternative épissage of HIV-1 RNA according to the expression of viral proteins Tat and Rev were studied. We besides studied the effect of proteins SR on the use of acceptor splice sites A2 and A3. The fine study of the regulating element ESEt of the site A3 revealed the involvement of the SR protein 9G8 in the complex regulation of this site.