Gliomas are the most common primary brain tumours and are associated with poor prognosis. Among them, diffuse gliomas – which include their most aggressive form glioblastoma (GBM) – are known to be highly infiltrative. The diagnosis and follow-up of gliomas rely on positron emission tomography (PET) and magnetic resonance imaging (MRI). However, these imaging techniques do not currently allow to assess the whole extent of such infiltrative tumours nor to anticipate their preferred invasion patterns, leading to sub-optimal treatment planning. Mathematical tumour growth modelling has been proposed to address this problem. Reaction-diffusion tumour growth models, which are probably the most commonly used for diffuse gliomas growth modelling, propose to capture the proliferation and migration of glioma cells by means of a partial differential equation. Although the potential of such models has been shown in many works for patient follow-up and therapy planning, only few limited clinical applications have seemed to emerge from these works. This thesis aims at revisiting reaction-diffusion tumour growth models using state-of-the-art medical imaging and data processing technologies, with the objective of integrating multi-parametric PET/MRI data to further personalise the model. Brain tissue segmentation on MR images is first addressed with the aim of defining a patient-specific domain to solve the model. A previously proposed method to derive a tumour cell diffusion tensor from the water diffusion tensor assessed by diffusion-tensor imaging (DTI) is then implemented to guide the anisotropic migration of tumour cells along white matter tracts. The use of dynamic [S-methyl-11C]methionine ([11C]MET) PET is also investigated to derive patient-specific proliferation potential maps for the model. These investigations lead to the development of a microscopic compartmental model for amino acid PET tracer transport in gliomas. Based on the compartmental model results, a novel methodology is proposed to extract parametric maps from dynamic [11C]MET PET data using principal component analysis (PCA). The problem of estimating the initial conditions of the model from MR images is then addressed by means of a translational MRI/histology study in a case of non-operated GBM. Numerical solving strategies based on the widely used finite difference and finite element methods are finally implemented and compared. All these developments are embedded within a common framework allowing to study glioma growth in silico and providing a solid basis for further research in this field. However, commonly accepted hypothesis relating the outlines of abnormalities visible on MRI to tumour cell density iso-contours have been invalidated by the translational study carried out, leaving opened the questions of the initialisation and the validation of the model. Furthermore, the analysis of the temporal evolution of real multi-treated glioma patients demonstrates the limitations of the formulated model. These latter statements highlight current obstacles to the clinical application of reaction-diffusion tumour growth models and pave the way to further improvements. / Les gliomes sont les tumeurs cérébrales primitives les plus communes et sont associés à un mauvais pronostic. Parmi ces derniers, les gliomes diffus – qui incluent la forme la plus agressive, le glioblastome (GBM) – sont connus pour être hautement infiltrants. Le diagnostic et le suivi des gliomes s'appuient sur la tomographie par émission de positons (TEP) ainsi que l'imagerie par résonance magnétique (IRM). Cependant, ces techniques d'imagerie ne permettent actuellement pas d'évaluer l'étendue totale de tumeurs aussi infiltrantes ni d'anticiper leurs schémas d'invasion préférentiels, conduisant à une planification sous-optimale du traitement. La modélisation mathématique de la croissance tumorale a été proposée pour répondre à ce problème. Les modèles de croissance tumorale de type réaction-diffusion, qui sont probablement les plus communément utilisés pour la modélisation de la croissance des gliomes diffus, proposent de capturer la prolifération et la migration des cellules tumorales au moyen d'une équation aux dérivées partielles. Bien que le potentiel de tels modèles ait été démontré dans de nombreux travaux pour le suivi des patients et la planification de thérapies, seules quelques applications cliniques restreintes semblent avoir émergé de ces derniers. Ce travail de thèse a pour but de revisiter les modèles de croissance tumorale de type réaction-diffusion en utilisant des technologies de pointe en imagerie médicale et traitement de données, avec pour objectif d'y intégrer des données TEP/IRM multi-paramétriques pour personnaliser davantage le modèle. Le problème de la segmentation des tissus cérébraux dans les images IRM est d'abord adressé, avec pour but de définir un domaine propre au patient pour la résolution du modèle. Une méthode proposée précédemment permettant de dériver un tenseur de diffusion tumoral à partir du tenseur de diffusion de l'eau évalué par imagerie DTI a ensuite été implémentée afin de guider la migration anisotrope des cellules tumorales le long des fibres de matière blanche. L'utilisation de l'imagerie TEP dynamique à la [S-méthyl-11C]méthionine ([11C]MET) est également investiguée pour la génération de cartes de potentiel prolifératif propre au patient afin de nourrir le modèle. Ces investigations ont mené au développement d'un modèle compartimental pour le transport des traceurs TEP dérivés des acides aminés dans les gliomes. Sur base des résultats du modèle compartimental, une nouvelle méthodologie est proposée utilisant l'analyse en composantes principales pour extraire des cartes paramétriques à partir de données TEP dynamiques à la [11C]MET. Le problème de l'estimation des conditions initiales du modèle à partir d'images IRM est ensuite adressé par le biais d'une étude translationelle combinant IRM et histologie menée sur un cas de GBM non-opéré. Différentes stratégies de résolution numérique basées sur les méthodes des différences et éléments finis sont finalement implémentées et comparées. Tous ces développements sont embarqués dans un framework commun permettant d'étudier in silico la croissance des gliomes et fournissant une base solide pour de futures recherches dans le domaine. Cependant, certaines hypothèses communément admises reliant les délimitations des anormalités visibles en IRM à des iso-contours de densité de cellules tumorales ont été invalidée par l'étude translationelle menée, laissant ouverte les questions de l'initialisation et de la validation du modèle. Par ailleurs, l'analyse de l'évolution temporelle de cas réels de gliomes multi-traités démontre les limitations du modèle. Ces dernières affirmations mettent en évidence les obstacles actuels à l'application clinique de tels modèles et ouvrent la voie à de nouvelles possibilités d'amélioration. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished

The open nature of Cell-Free Protein Synthesis (CFPS) systems has enabled flexible design, easy manipulation, and novel applications of protein engineering in therapeutic production, biocatalysis, and biosensors. This dissertation reports on three advances in the application of CFPS systems for 1) improving biocatalysis performance in industrial applications by site-specific covalent enzyme immobilization, 2) expressing and optimizing a difficult to express a mammalian protein in bacterial-based CFPS systems and its application for cost-effective, on-demand biosensors compatible with human body fluids, and 3) streamlining the procedure of an E. coli extract with built-in compatibility with human body fluid biosensors. Site-specific covalent immobilization stabilizes enzymes and facilitates recovery and reuse of enzymes which improves the net profit margin of industrial enzymes. Yet, the suitability of a given site on the enzyme for immobilization remains a trial-and-error procedure. This dissertation reports the reliability of several design heuristics and a coarse-grain molecular simulation in predicting the optimum sites for covalent immobilization of a target enzyme, TEM-1 ?-lactamase. This work demonstrates that the design heuristics can successfully identify a subset of favorable locations for experimental validation. This approach highlights the advantages of combining coarse-grain simulation and high-throughput experimentation using CFPS to efficiently identify optimal enzyme immobilization sites. Additionally, this dissertation reports high-yield soluble expression of a difficult-to-express protein (murine RNase Inhibitor or m-RI) in E. coli-lysate-based CFPS. Several factors including reaction temperature, reaction time, redox potential, and presence of folding chaperones in CFPS reactions were altered to find suitable conditions for m-RI expression. m-RI with the highest activity and stability was used to develop a lyophilized CFPS biosensor in human body fluids which reduced the cost of biosensor test by ~90%. Moreover, an E. coli extract with RNase inhibition activity was developed and tested which further streamlines the production of CFPS biosensors compatible with human body fluids.

No / The alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate receptor (AMPAR) subunit GluR2, which regulates excitotoxicity and the inflammatory cytokine tumour necrosis factor alpha (TNFalpha) have both been implicated in motor neurone vulnerability in amyotrophic lateral sclerosis/motor neurone disease. TNFalpha has been reported to increase cell surface expression of AMPAR subunits to increase synaptic strength and enhance excitotoxicity, but whether this mechanism occurs in motor neurones is unknown. We used primary cultures of mouse motor neurones and cortical neurones to examine the interaction between TNFalpha receptor activation, GluR2 availability, AMPAR-mediated calcium entry and susceptibility to excitotoxicity. Short exposure to a physiologically relevant concentration of TNFalpha (10 ng/mL, 15 min) caused a marked redistribution of both GluR1 and GluR2 to the cell surface as determined by cell surface biotinylation and immunofluorescence. Using fura-2-acetoxymethyl ester microfluorimetry, we showed that exposure to TNFalpha caused a rapid reduction in the peak amplitude of AMPA-mediated calcium entry in a PI3-kinase and p38 kinase-dependent manner, consistent with increased insertion of GluR2-containing AMPAR into the plasma membrane. This resulted in a protection of motor neurones against kainate-induced cell death. Our data therefore, suggest that TNFalpha acts primarily as a physiological regulator of synaptic activity in motor neurones rather than a pathological drive in amyotrophic lateral sclerosis.

The Protein Data Bank (PDB) is the definitive electronic repository for experimentally-derived protein structures, composed mainly of those determined by X-ray crystallography. Approximately 200 new structures are added weekly to the PDB, and at the time of writing, it contains approximately 97,000 structures. This represents an expanding wealth of high-quality information but there seem to be few bioinformatics tools that consider and analyse these data as an ensemble. This thesis explores the development of three efficient, fast algorithms and software implementations to study protein structure using the entire PDB. The first project is a crystal-form matching tool that takes a unit cell and quickly (< 1 second) retrieves the most related matches from the PDB. The unit cell matches are combined with sequence alignments using a novel Family Clustering Algorithm to display the results in a user-friendly way. The software tool, Nearest-cell, has been incorporated into the X-ray data collection pipeline at the Diamond Light Source, and is also available as a public web service. The bulk of the thesis is devoted to the study and prediction of protein disorder. Initially, trying to update and extend an existing predictor, RONN, the limitations of the method were exposed and a novel predictor (called MoreRONN) was developed that incorporates a novel sequence-based clustering approach to disorder data inferred from the PDB and DisProt. MoreRONN is now clearly the best-in-class disorder predictor and will soon be offered as a public web service. The third project explores the development of a clustering algorithm for protein structural fragments that can work on the scale of the whole PDB. While protein structures have long been clustered into loose families, there has to date been no comprehensive analytical clustering of short (~6 residue) fragments. A novel fragment clustering tool was built that is now leading to a public database of fragment families and representative structural fragments that should prove extremely helpful for both basic understanding and experimentation. Together, these three projects exemplify how cutting-edge computational approaches applied to extensive protein structure libraries can provide user-friendly tools that address critical everyday issues for structural biologists.

As depicted in Chapter I, 2-oxoglutarate- (2OG) dependent oxygenases are ubiquitous in living systems and display a wide range of cellular functions, spanning metabolism, transcription, and translation. Although functionally diverse, the 2OG oxygenases share a high degree of structural similarities between their catalytic sites. From a medicinal chemistry point of view, the combination of biological diversity and structural similarity presents a rather challenging task for the development of selective small molecules for functional studies in vivo. The non-selective metal chelator 8-hydroxyquinoline (8HQ) was used as a template for the generation of tool compound <b>I</b> for the KDM4 subfamily of histone demethylases via application of the Betti reaction. Structural analogue <b>II</b> was used as the corresponding negative control (Figure A). These compounds were characterised in vitro against a range of 2OG oxygenases and subsequently used for studies in cells. <b>I</b> displays selectivity for KDM4 and increases the level of the H3K9me3 histone mark in cells. It has an effect on the post-translational modification pattern of histone H3, but not other histones, and reduces the viability of lung cancer cells, but not normal lung cells, derived from the same patient. <b>I</b> also stabilises hypoxia-inducable factor HIF in cells via a mechanism which seems to be independent from prolyl hydroxylase inhibition. This work is described in Chapters II and III. The chemical biology research in epigenetics is complemented by qualitative analysis conducted in the social sciences at Said Business School. With a global view on how innovation occurs and may actively be fostered, Chapter IV focuses on the potential of epigenetics in drug discovery and how this process may actively be promoted within the framework of open innovation. Areas of focus include considerations of incremental and disruptive technology; how to claim, demarcate, and control the market; how knowledge brokering occurs; and insights about process, management, organisation, and culture of open innovation. In contrast to the open-skies approach adopted for the development of a tool compound in Chapters II and III, a focused-library approach was taken for the generation of a tool compound for the OGFOD1 ribosomal prolyl hydroxylase. The development of a suitable in vitro activity assay for OGFOD1 in Chapter V enabled the development of lead compound <b>III</b> in Chapter VI. <b>III</b> is selective for OGFOD1 against the structurally closely related prolyl hydroxylase PHD2.

Der wichtigste exzitatorische Neurotransmitter Glutamat spielt eine grosse Rolle in der Gehirnentwicklung, wie neuronale Migration und Synaptogenese. Ob glutamaterge Stimulation für das Überleben entwickelnder Neuronen notwendig ist, war bislang jedoch unbekannt. Um zu untersuchen, ob eine Hemmung von Glutamatrezeptoren im unreifen Gehirn zu Neurodegeneration führt, wurden Ratten im Alter von 1 bis 31 Tagen für 24 Stunden mit dem N-Methyl-D-Aspartat-(NMDA) Glutamatrezeptorantagonisten Dizocilpin (MK801) behandelt. Die Dichte neuronaler Degeneration wurde mikroskopisch in Kupfer-Silber- und TUNEL- gefärbten Hirnschnittpräparaten ermittelt und Unterschiede mittels ANOVA analysiert (Signifikanzniveau p / The predominant excitatory neurotransmitter glutamate plays a major role in certain aspects of neural development. However, whether developing neurons depend on glutamate for survival remains unknown. To investigate if deprivation of glutamate stimulation in the immature mammalian brain causes neuronal cell death (apoptosis), rat pups aged 0 to 30 days were treated for 24 hours with dizocilpine maleate (MK801), an N-methyl-D-aspartate-(NMDA) glutamate receptor antagonist. Density of neural degeneration was evaluated by a stereological dissector method in cupric-silver and TUNEL-stained brain slices. Groups were compared by ANOVA and significance considered at p

Kohlenhydrate und Proteine gehören neben Wasser und Fetten zu den quantitativ bedeutendsten Grundbestandteilen biologischer Systeme und der Lebensmittel. Unter milden Bedingungen in lebenden Organismen oder unter thermischer Belastung bei der Lebensmittelverarbeitung können reduzierende Kohlenhydrate amin-katalysiert durch die Abspaltung von Wasser und Fragmentierungen des Kohlenstoffgerüsts abgebaut werden, wobei die noch reaktiveren 1,2-Dicarbonylverbindungen entstehen. Aus der Reaktion der N-α-Aminogruppe und funktioneller Gruppen der Seitenketten von Aminosäuren mit Kohlenhydraten bzw. 1,2-Dicarbonylverbindungen können stabile Endprodukte entstehen. In vivo können proteingebundene Maillard-Produkte (MRPs) aus der Reaktion mit Glucose (Amadori-Produkte) oder 1,2-Dicarbonylverbindungen (Advanced Glycation Endproducts: AGEs) entstehen. Beispielsweise ist das „N-terminale“ N-α-Fructosylderivat der β-Kette des Hämoglobins ein etablierter Parameter zur Diagnose von Diabetes mellitus (HbA1c-Wert). Diese nicht-enzymatische, posttranslationale Modifizierung von Proteinen wird allgemein als Glykierung bezeichnet und kann die Funktionalität von Proteinen beeinträchtigen. Deshalb wird untersucht, ob die Trübung der Augenlinsen, die Versteifung von Blutgefäßen oder Schädigungen von Nervenzellen durch eine erhöhte Glykierung verursacht werden. Diese Veränderungen treten im Alter und bei Stoffwechselkrankheiten wie Diabetes mellitus und Urämie auf, die durch eine erhöhte Glucosekonzentration bzw. die Anreicherung von 1,2-Dicarbonylverbindungen im Blut gekennzeichnet sind. Zwar gibt es Publikationen zum Vorkommen N-terminaler Amadori-Produkte an Hämoglobin und in Lebensmitteln, aber die Bildung N-terminaler AGEs wurde bisher nur in wenigen Studien untersucht. Deshalb waren die Bildung und das Vorkommen N-terminaler AGEs im physiologischen Modell, in Hämoglobin und in Backwaren Gegenstand der vorliegenden Arbeit. In der vorliegenden Arbeit wurde erstmals systematisch die Sequenzabhängigkeit der Bildung der Fructosylderivate bzw. der CM-Derivate in Konkurrenz zu den Glyoxal-2(1H)-Pyrazinonen am N-Terminus von Peptiden unter physiologischen und backtechnologischen Bedingungen untersucht. Dabei wurde nachgewiesen, dass die Variation der C-terminalen Aminosäure in Dipeptiden den Glykierungsgrad und das Produktspektrum erheblich beeinflusst. Mit dem konsequenten Nachweis der N-terminalen von Glyoxal und Methylglyoxal ableitbaren Carboxyalkylderivate und 2(1H)-Pyrazinone in humanen Hämoglobin wurde die Relevanz der N-terminalen Glykierung in vivo untermauert. Damit wird eine umfassendere Beurteilung des Dicarbonylstresses und der Glykierung insbesondere bei Urämikern und Diabetikern ermöglicht. Am Beispiel von Backwaren wurde für Lebensmittel gezeigt, dass unter trockenen Reaktionsbedingungen die 2(1H)-Pyrazinone und in wasserhaltigen Systemen die Carboxyalkylderivate bevorzugt zu erwarten sind.

Kohlenhydrate und Proteine gehören neben Wasser und Fetten zu den quantitativ bedeutendsten Grundbestandteilen biologischer Systeme und der Lebensmittel. Unter milden Bedingungen in lebenden Organismen oder unter thermischer Belastung bei der Lebensmittelverarbeitung können reduzierende Kohlenhydrate amin-katalysiert durch die Abspaltung von Wasser und Fragmentierungen des Kohlenstoffgerüsts abgebaut werden, wobei die noch reaktiveren 1,2-Dicarbonylverbindungen entstehen. Aus der Reaktion der N-α-Aminogruppe und funktioneller Gruppen der Seitenketten von Aminosäuren mit Kohlenhydraten bzw. 1,2-Dicarbonylverbindungen können stabile Endprodukte entstehen. In vivo können proteingebundene Maillard-Produkte (MRPs) aus der Reaktion mit Glucose (Amadori-Produkte) oder 1,2-Dicarbonylverbindungen (Advanced Glycation Endproducts: AGEs) entstehen. Beispielsweise ist das „N-terminale“ N-α-Fructosylderivat der β-Kette des Hämoglobins ein etablierter Parameter zur Diagnose von Diabetes mellitus (HbA1c-Wert). Diese nicht-enzymatische, posttranslationale Modifizierung von Proteinen wird allgemein als Glykierung bezeichnet und kann die Funktionalität von Proteinen beeinträchtigen. Deshalb wird untersucht, ob die Trübung der Augenlinsen, die Versteifung von Blutgefäßen oder Schädigungen von Nervenzellen durch eine erhöhte Glykierung verursacht werden. Diese Veränderungen treten im Alter und bei Stoffwechselkrankheiten wie Diabetes mellitus und Urämie auf, die durch eine erhöhte Glucosekonzentration bzw. die Anreicherung von 1,2-Dicarbonylverbindungen im Blut gekennzeichnet sind. Zwar gibt es Publikationen zum Vorkommen N-terminaler Amadori-Produkte an Hämoglobin und in Lebensmitteln, aber die Bildung N-terminaler AGEs wurde bisher nur in wenigen Studien untersucht. Deshalb waren die Bildung und das Vorkommen N-terminaler AGEs im physiologischen Modell, in Hämoglobin und in Backwaren Gegenstand der vorliegenden Arbeit. In der vorliegenden Arbeit wurde erstmals systematisch die Sequenzabhängigkeit der Bildung der Fructosylderivate bzw. der CM-Derivate in Konkurrenz zu den Glyoxal-2(1H)-Pyrazinonen am N-Terminus von Peptiden unter physiologischen und backtechnologischen Bedingungen untersucht. Dabei wurde nachgewiesen, dass die Variation der C-terminalen Aminosäure in Dipeptiden den Glykierungsgrad und das Produktspektrum erheblich beeinflusst. Mit dem konsequenten Nachweis der N-terminalen von Glyoxal und Methylglyoxal ableitbaren Carboxyalkylderivate und 2(1H)-Pyrazinone in humanen Hämoglobin wurde die Relevanz der N-terminalen Glykierung in vivo untermauert. Damit wird eine umfassendere Beurteilung des Dicarbonylstresses und der Glykierung insbesondere bei Urämikern und Diabetikern ermöglicht. Am Beispiel von Backwaren wurde für Lebensmittel gezeigt, dass unter trockenen Reaktionsbedingungen die 2(1H)-Pyrazinone und in wasserhaltigen Systemen die Carboxyalkylderivate bevorzugt zu erwarten sind.

Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.

Systematic studies of basal nonsense suppression, orthogonality of tRNAPyl variants, and cross recognition between codons and tRNA anticodons are reported. E. coli displays detectable basal amber and opal suppression but shows a negligible ochre suppression. Although detectable, basal amber suppression is fully inhibited when a pyrrolysyl-tRNA synthetase (PylRS)-tRNAPyl_CUA pair is genetically encoded. trnaPyl_CUA is aminoacylated by an E. coli aminoacyl-tRNA synthetase at a low level, however, this misaminoacylation is fully inhibited when both PylRS and its substrate are present. Besides that it is fully orthogonal in E. coli and can be coupled with PylRS to genetically incorporate a NAA at an ochre codon, tRNAPyl_UUA is not able to recognize an UAG codon to induce amber suppression. This observation is in direct conflict with the wobble base pair hypothesis and enables using an evolved M. jannaschii tyrosyl-tRNA synthetase-tRNAPyl_UUA pair and the wild type or evolved PylRS-tRNAPyl_UUA pair to genetically incorporate two different NAAs at amber and ochre codons. tRNAPyl_UCA is charged by E. coli tryptophanyl-tRNA synthetase, thus not orthogonal in E. coli. Mutagenic studies of trnaPyl_UCA led to the discovery of its G73U form which shows a higher orthogonality. Mutating trnaPyl_CUA to trnaPyl_UCCU not only leads to the loss of the relative orthogonality of tRNAPyl in E. coli but also abolishes its aminoacylation by PylRS.