Synechococcus elongatus PCC 7942 is a model organism used to study the circadian rhythm, a process that is driven by an endogenous biological clock that can be modulated by external cues such as light and temperature. Some proteins have been identified that are involved in circadian signal transduction in S. elongatus. Of them, KaiA, KaiB and KaiC comprise the central oscillator components, which are essential for internal timekeeping. SasA is an important protein in the output pathway, which passes the information from central oscillator to downstream components, and thus controls metabolic and behavioral processes. CikA is a major component in the input pathway, which maintains synchrony of the oscillator with the environment. CikA is an unusual phytochrome-like histidine protein kinase. It has a pseudo receiver domain which can not accept a phosphoryl group. CikA is thought to be located at the poles of the cell through interaction between PsR and some protein or protein complex that is also localized at the poles. One of the potential CikA-interacting proteins identified through a yeast two hybrid screen is called hypothetical protein 1. It specifically recognizes a PsR bait in a yeast two hybrid assay. A bioinformatics analysis showed that there are predicted signal peptide and transmembrane domains at the N-terminal and a cytochrome C homolog domain at the C-terminal of Hyp1. Elucidating the features and function of Hyp1 will provide us with useful information to understand the function and working mechanism of CikA, and therefore will help us to clarify the signal transduction in the clock. In this research, I used genetic, cell biological and biochemical approaches to study the features and function of this newly identified clock component Hyp1. To confirm the interaction between PsR and Hyp1 and complement the yeast two hybrid data, I truncated Hyp1 (Thyp1) and purified soluble Thyp1. At the same time, I obtained purified PsR. I tried to copurify the PsR and 6-histidine-tagged Hyp1 on a nickel affinity column. However, PsR non-specifically bound to the column, which eliminated the utility of this approach to study their interaction. In addition to using a biochemical approach to study Hyp1, I constructed three hyp1 overexpression alleles for genetic analysis and two hyp1-yfp overexpression fusion alleles for subcellular localization studies. All of them will help us to understand the features and function of Hyp1.

DNA is both the oldest and newest of targets for cancer therapy. While it is already being targeted by many anticancer drugs in the clinic, the development of sequence-specific DNA binders has brought it back to the limelight as a valuable anticancer drug target.My studies on DNA interacting agents was initiated with the DNA intercalator campotothecin, and also included topoisomerase I enzyme. I have evaluated the structure of topoisomerase I C-terminal domain that consists of the active site tyrosine. My data indicate that this domain exists in a molten globule conformation with a fluctuating tertiary structure. These fluctuations are suggested to be important in interaction with the topoisomerase I core domain and DNA. I have also evaluated the DNA interactions of the camptothecin analogue homocamptothecin and have determined that homocamptothecin intercalate with DNA in the absence of topoisomerase I, and that such intercalation results in its lactone stabilization. Subsequently, the mechanism of topoisomerase I mediated inhibition of HIF-1 by camptothecin was explored. I have shown that camptothecin stimulate topoisomerase I cleavage complex formation in the HIF-1 binding site, which is suggested to prevent the DNA binding of HIF-1.The second part of this study was focused on understanding the mechanism of action of another DNA binder, XR5944. Designed as a dual topoisomerase inhibitor, XR5944 was subsequently shown to have a different mechanism of action - inhibition of trancription. The NMR structural analysis, in our lab, of the drug-DNA complex showed that XR5944 bis-intercalate with DNA, while binding in the DNA major groove. Driven by these combined interaction modes, XR5944 is shown to inhibit the DNA binding and the subsequent transcriptional activity of specific transcription factors such as estrogen receptors and AP-1, which are overexpressed in certain cancers.Finally, I have analyzed G-quadruplex structures formed by telomeric DNA. The formation and stabilization of DNA G-quadruplexes in the human telomeric sequence have been shown to inhibit the activity of telomerase. Thus the telomeric DNA G-quadruplex has been considered as an attractive anticancer drug target. Telomeric DNA forms multiple G-quadruplex conformations, and my data reveal the conformations of the major G-quadruplexes formed by human telomeres.

Quand des facteurs humains interviennent dans une large majorité des accidents de la route, l’amélioration de la sécurité routière passe par l’introduction de systèmes d’assistance, afin d’aider le conducteur dans les tâches de conduites les plus complexes. Les systèmes de conduites « by-wire », en facilitant le partage des tâches de conduites entre le conducteur et les systèmes d’assistance, représentent une avancée majeure vers une automatisation progressive de la conduite.Cependant, le déploiement de ces systèmes est freiné pour des questions de sûreté de fonctionnement, et nécessite la mise en œuvre d’outils de diagnostique pour détecter et corriger d'éventuelles défaillances. Dans le cadre de cette thèse, nous évaluons un algorithme de détection et de localisation des fautes compatible avec une architecture « by-wire », basé sur l’approche multi-modèles interagissants. Cette méthode nécessite l'estimation probabiliste de l’état du véhicule, pour laquelle différents observateurs non linéaires sont comparés. Pour cette démarche, l’accent est mis sur la validation expérimentale des résultats qui a nécessité l’équipement d’un véhicule de test.Une fois que la faute est localisée, nous étudions les différentes stratégies de contrôle du véhicule en fonction des actionneurs encore disponibles.Cette étude montre que les effets d'une défaillance sur les directions découplées sont particulièrement difficiles à corriger. / The improvement of the road safety implies to increase the place of driving assistance systems for road vehicles. Paving the road of the fully autonomous vehicle, the drive-by-wire technology could improve the potential of the vehicle control. The implementation of these new embedded systems is still limited, mainly for reliability reasons, thus requiring the development of diagnostic mechanisms to detect occurring faults. In a first step, we evaluate a fault detection and isolation algorithm, based on the interacting multiple models approach. The method relies on a probabilistic estimation of the vehicle state, for which different non-linear observer schemes are compared. The experimental validation required the preparation of a test vehicle.Then, when a fault is identified, the optimal back-up control strategies are investigated according to the availability of actuators.Thus study points out that faults on steer-by-wire systems are particularly difficult to treat.

This thesis studies two Markov processes describing the evolution of a system of many interacting random components. These processes undergo an absorbing-state phase transition, i.e., as one variates the parameter values, the process exhibits a transition from a convergence regime to one of the absorbing-states to an active regime. In Chapter 2 we study Activated Random Walk, which is an interacting particle system where the particles can be of two types and their number is conserved. Firstly, we provide a new lower bound for the critical density on Z as a function of the jump distribution and of the sleeping rate and we prove that the critical density is not a constant function of the jump distribution. Secondly, we prove that on Zd in the case of biased jump distribution the critical density is strictly less than one, provided that the sleeping rate is small enough. This answers a question that has been asked by Dickman, Rolla, Sidoravicius [9, 28] in the case of biased jump distribution. Our results have been presented in [33]. In Chapter 3 we study a class of probabilistic cellular automata which are related by a natural coupling to a special type of oriented percolation model. Firstly, we consider the process on a finite torus of size n, which is ergodic for any parameter value. By employing dynamic-renormalization techniques, we prove that the average absorption time grows exponentially (resp. logarithmically) with n when the model on Z is in the active (resp. absorbing) regime. This answers a question that has been asked by Toom [37]. Secondly, we study how the neighbourhood of the model affects the critical probability for the process on Z. We provide a lower bound for the critical probability as a function of the neighbourhood and we show that our estimates are sharp by comparing them with our numerical estimates. Our results have been presented in [34, 35].

We present two different interacting dark sector models: one in which the dark matter particle is charged under a non-abelian dark gauge group, whose gauge bosons constitute a dark radiation component; and one in which a fraction of the dark matter has efficient number-changing self-interactions that keep it warm. We find that in general the structure formation is slowed down in these models, which addresses a discrepancy in the measurement of the σ8 parameter of large-scale structure. We also perform fits to cosmological data for a generalization of the non-abelian model (in which only a fraction of the dark matter interacts with the dark gauge bosons) and show that it can ease the current experimental tension in the measurement of the Hubble expansion rate H0.

Les éléments transposables d’ADN sont presque ubiquitaires dans le monde vivant et leur mobilité peut être délétère pour le génome. Leur régulation dans les tissus germinaux animaux passe par la voie de silencing des piRNAs (PIWI-interacting RNAs). Les piRNAs sont produits à partir de loci contenant des fragments d’éléments transposables insérés en clusters. Nous étudions l’émergence de ces clusters de piRNAs chez la drosophile.Nous avons activé de novo un cluster de transgènes par héritage maternel de piRNAs homologues. Il s’agit d’un cas de paramutation, ou conversion épigénétique stable et récurrente.Nous avons montré que ce cluster paramuté produit de novo des piRNAs, et étonnement dessiRNAs.J’ai caractérisé de façon fonctionnelle et moléculaire ce phénomène de paramutation par l’utilisation de mutants. J’ai montré que les propriétés de silencing, ainsi que la production depiRNAs et de siRNAs, sont abolies en contexte mutant pour tous les gènes testés de la voie despiRNAs (voies primaire et secondaire). Parallèlement, j’ai étudié un cas de paramutation« partiellement homologue » dans laquelle le cluster reçoit des piRNAs homologues seulement àune partie de sa séquence. J’ai montré qu’il y a production de piRNAs par la totalité du cluster dès la 3e génération.J’ai montré, enfin, que des clusters activés de novo par la chaleur, présentent des propriétés fonctionnelles et moléculaires semblables aux clusters activés par les piRNAsmaternels.Ces travaux apportent des éléments clés pour la compréhension de la mise en place de l’épigénome, tant d’un point de vue mécanistique qu’évolutif. / DNA transposable elements are almost ubiquitous in the living world and their mobility can be deleterious for the genome. Their regulation in germaria is mediated by the piRNAsilencing pathway (PIWI-interacting RNAs). piRNAs are produced by loci formed by clusters of fragments of transposable elements. We are studying the emergence of these piRNA-producing clusters in Drosophila.We have de novo activated a cluster of transgenes via maternal inheritance of homologous piRNAs. This is a case of paramutation i.e. a stable and recurrent epigenetic conversion process.We have shown that this paramutated cluster produces de novo piRNAs and, surprisingly, also siRNAs. I have characterized this paramutation functionally and molecularly, by a mutant approach. I have shown that its silencing properties, as well as piRNA and siRNA production are abolished in mutant contexts for all the genes from the primary and secondary piRNA pathways I have tested. At the same time, I have studied the case of a partially homologous paramutation, in which piRNAs maternally inherited by the cluster are homologous to only a part of its sequence. I have shown that piRNA are produced all along the cluster as early as the 3rdgeneration.Finally, I have shown that a cluster activated de novo by an environmental stress shows the same functional and molecular properties as a cluster paramutated via maternal piRNA inheritance.These studies provide key elements for understanding the emergence of the epigenome from a mechanistic and an evolutionary perspective.

Thesis (MSc)--Stellenbosch University, 2004. / ENGLISH ABSTRACT: In this thesis, generalized Dyson boson-fermion mappings are considered. These are techniques used in the analysis of the quantum many-body problem, and are instances of so-called boson expansion methods. A generalized Dyson boson-fermion mapping, or a Dyson mapping for short, is a one-to-one linear but non-unitary operator that can be applied to vectors representing the states of a many-fermion system. A vector representing a fermion system maps onto a vector that is most naturally interpreted as representing a state of a many-body system that contains both bosons and fermions. The motivation for doing such a mapping is the hope that the mapping will reveal some property of the system that simplifies its analysis and that was hidden in the original form. The aims of this thesis are 1. to review the theory of generalized Dyson boson-fermion mappings, 2. by considering a tutorial example, to demonstrate that it is feasible to implement the theory and 3. to find a useful application for a generalized Dyson boson-fermion mapping, by considering a non-trivial model, namely the Richardson model for superconductivity. The realization of the first two aims mainly involve the collecting together of ideas that have already appeared in the literature, into one coherent text. Some subtle points that were treated only briefly due to space restrictions in the journal publications where the theory was first expounded, are elaborated on in the present work. On the other hand, the analysis of the Richardson Hamiltonian that uses a Dyson mapping, goes beyond what has already appeared in the literature. It is the first time that a boson expansion technique is implemented for a system where the roles of both collective and non-collective fermion pairs are important. (The Dyson mapping associates bosons with Cooper pairs, while the fermions not bound in Cooper pairs result in fermions being present in the mapped system as well.) What is found is that the Dyson mapping uncovers non-trivial properties of the system. These properties aid the construction of time-independent perturbation expansions for the stationary states of the system, as well as time-dependent expansions for transition amplitudes between states. The time-independent expansions agree with results that other authors obtained through methods other than boson expansions. The time-dependent expansions, that one would be hard-pressed to develop without a Dyson mapping, might in future prove useful in understanding aspects of the dynamics of ultracold fermi gases, when time-dependent magnetic fields are used to vary the atom-atom interaction strenght. / AFRIKAANSE OPSOMMING: In hierdie tesis word veralgemeende Dyson boson-fermion-afbeeldings ondersoek. Hierdie afbeeldings word gebruik in die analise van die kwantum veeldeeltjie probleem, en is voorbeelde van sogenaamde boson-uitbreidingstegnieke. 'n Veralgemeende Dyson bosonfermion- afbeelding, of kortweg 'n Dyson afbeelding, is 'n een-tot-een, lineêre maar nie-unitêre operator wat inwerk op vektore wat toestande verteenwoordig van 'n veel-fermion sisteem. 'n Vektor wat 'n fermionsisteem verteenwoordig word so afgebeeld op 'n vektor waarvoor die mees natuurlike interpretasie is dat dit 'n toestand verteenwoordig van 'n sisteem waarin beide bosone en fermione aanwesig is. So 'n afbeelding word gewoonlik gemaak in die hoop dat eienskappe van die sisteem, wat versteek was in die oorspronklike weergawe, voor-die-hand-liggend is na die afbeelding. Hierdie tesis het ten doel 1. om die teorie van veralgemeende Dyson boson-fermion-afbeeldings te hersien, 2. om 'n eenvoudige voorbeeld deur te werk, en so te demonstreer dat die teorie sonder moeite geïmplimenteer kan word en 3. om 'n nuttige toepassing te vind vir 'n veralgemeende Dyson boson-fermion-afbeelding deur 'n nie-triviale model, naamlik die Richardson model vir supergeleiding, te ondersoek. Die eerste twee van hierdie doelwitte behels hoofsaaklik dat idees wat reeds in die literatuur verskyn het, saamgevat word in een koherente teks. Sommige subtiele punte wat, vanwee beperkte ruimte, slegs kortliks bespreek is in die joernaalartikels waarin die teorie oorspronklik verskyn het, word in hierdie tesis meer breedvoering bespreek. Daarteenoor verteenwoordig die analise van die Richardson model met behulp van 'n Dyson afbeelding 'n nuwe bydra. Dit is naamlik die eerste keer dat 'n bosonuitbreiding ingespan word vir 'n sisteem waar sowel kollektiewe as nie-kollektiewe fermionpare 'n belangrike rol speel. (Die Dyson afbeelding assosieer bosone met die oorspronklike sisteem se Cooper pare, terwyl die fermione wat in die oorspronklike sisteem nie tot Cooper pare gebind is nie, sorg dat daar ook fermione teenwoordig is in die afgebeelde sisteem.) Ons vind dat die Dyson afbeelding nie-triviale eienskappe van die sisteem aan die lig bring. Hierdie eienskappe is nuttig vir die konstruksie van beide tyd-onafhanklike steuringsreekse vir die stasionêre toestande van die sisteem en vir tyd-afhanklike steuringsreekse vir oorgangsamplitudes tussen toestande. Die tyd-onafhanklike uitbreidings stem ooreen met resultate wat ander outeurs afgelei het sonder die gebruik van 'n Dyson afbeelding. Die tyd-afhanklike uitbreidings, wat kwalik afgelei kan word sonder 'n Dyson afbeelding, mag vorentoe nuttig wees om aspekte van die dinamika van baie koue Fermi gasse te verstaan, wanneer tydafhanklike magneetvelde gebruik word om die inter-atoomwisselwerking te manipuleer.

Με την βοήθεια τεχνικών για συστήματα αλληλεπιδρώντων σωματιδίων, σκιαγραφήθηκαν και αποδείχθηκαν θεωρήματα για μοντέλα γνώμης και πολιτιστικής δυναμικής. Τα χωρικά αυτά στοχαστικά μοντέλα εξετάζονται ως γενικεύσεις με μια παράμετρο εμπιστοσύνης ε του γνωστού μοντέλου ψηφοφόρου. Το κεντρικό ερώτημα είναι ο καθορισμός της ασυμπτωτικής δυναμικής, η οποία ενδέχεται να εμφανίζει μετάβαση φάσης από μια ποιοτική συμπεριφορά σε κάποια άλλη. Τα παραχθέντα θεωρήματα αφορούν: α) στην επέκταση του θεωρήματος ομαδοποίησης του Lanchier (2012) σε αυθαίρετους γράφους απόψεων, και β) στην εφαρμογή της μεθοδολογίας των Bramson και Griffeath (1989) σε δυο συστήματα με ουδέτερες αλληλεπιδράσεις, την ουδέτερη εκδοχή των κυκλικών συστημάτων σωματιδίων και γ) το μοντέλο Axelrod για την διάχυση των πολιτιστικών περιοχών. Στα δυο τελευταία μοντέλα εξετάζονται τα φαινόμενα τόσο της καθήλωσης (η άποψη κάθε δράστη μεταβάλλεται πεπερασμένα συχνά) όσο και του κατακερματισμού (μη ομαδοποίηση) του άπειρου συστήματος. / By the use of techniques from interacting particle systems, heuristics and proof have been produced for opinion and cultural dynamical models. These stochastic spatial models are investigated as generalizations with a confidence parameter ε of the well-known voter model. The main question is the characterization of dynamics in the asymptotic limit of time, which may exhibit phase transition from one qualitative behavior to another. The produced theorems are: a) an extension of the clustering theorem by Lanchier (2012) to arbitrary opinion graphs, and b) the appropriation of the Bramson and Griffeath (1989) methodology for systems with neutral interactions, namely, a neutral version of cyclic particle systems and c) the model of Axelrod for the diffusion of cultural domains. In the last two models, the studied phenomena is the fixation of the infinite system (each agent changes her opinion finitely often) to a fragmented configuration (non-clustering).

Esta tese apresenta resultados sobre a estrutura, relações de escala e cinemática para 48 galáxias em 22 grupos compactos de Hickson, sendo que a apresentação de mapas de velocidades, monocromáticos (na linha H alpha) e de dispersão de velocidades são feitos pela primeira vez para 35 galáxias em 12 dos grupos. A partir dos mapas de velocidades e imagens óticas, foi possível obter os parâmetros cinemáticos, morfológicos e as curvas de rotação das galáxias da presente amostra. Usando as velocidades máximas de rotação para cada galáxia (derivadas das curvas de rotação) e as luminosidades óticas, infravermelhas, as massas estelares e bariônicas, foram estudadas as diferentes relações de Tuly-Fisher (TF) para as galáxias dos grupos compactos. Comparando esses resultados com os apresentados por uma amostra de galáxias de campo, foi encontrado que as galáxias de grupos compactos seguem a relação de TF definida pelas galáxias em ambientes menos densos, no entanto algumas galáxias de baixa massa apresentam altas luminosidades para as suas velocidades de rotação. Surtos de formação estelar e atividade nuclear parecem ser os principais fatores que fazem com que as galáxias de baixas massas dos grupos compactos não estejam na relação de TF definida pelas galáxias do campo. Este resultado indica que as velocidades máximas de rotação não são alteradas em galáxias em interação e portato não há um stripping de massa significativo nas galáxias de grupos compactos, dentro de R(25). O uso das curvas de rotação para estudar a distribuição de massas nestas galáxias revelou que estas curvas apresentam um alto grau de assimetria, a qual seria produzida em eventos de interação galáxia-galáxia. Esses eventos, além de perturbar as curvas de rotação, conseguem expulsar parte do gás neutro das galáxias ao meio intra grupo. Usando dados ultravioleta, nesta tese foram encontradas vários sistemas estelares jovens no meio intergaláctico de grupos compactos. Esses sistemas podem se converter em galáxias satélites ou simplesmente serem dissolvidos, enriquecendo o meio intragrupo. / This thesis presents results on the kinematics, scaling relations and structures of 48 galaxies in 22 compact groups. For 35 galaxies in 12 compact groups, velocity fields, monochromatic maps (derived from H alpha observations) and velocity dispersion maps are presented for the first time. By using these data, it was possible to determine the kinematic and morphological parameters, the rotation curves and to derive the Tully-Fisher relation for the galaxies in dense environments. By using the maximum rotational velocity for each galaxy (derived from its rotation curve) and its optical and near-infrared luminosity and mass, the different Tully-Fisher relations for galaxies in compact groups were derived. Comparing these results with the results displayed by galaxies in less dense environments, it was found that galaxies in compact groups agrees with the Tully-Fisher relation defined by non-interacting galaxies. However, some of the low-mass galaxies are off the Tully-Fisher relation, having too high luminosities for their maximum rotational velocities. This scenario can be explained by a burst of star formation and/or by nuclear activity. We conclude that the maximum rotational velocities of compact groups galaxies are not affected during galaxy-galaxy interactions which implies that there is no significant mass stripping in galaxies of compact groups inside their optical radius. The mass distribution of galaxies in compact groups indicates that the rotation curves of these galaxies are highly asymmetric. The asymmetry could be produced by interactions between galaxies. These interactions, besides affecting the shape of the rotation curve, can eject some neutral gas from the disk of the interacting galaxies into the intragroup medium. By using ultraviolet data, we find several young star-forming regions in the intragroup medium of compact groups. It is still an open question wether these young stellar systems can survive and become new members of the group or if they will fall back onto their parent galaxies.

Background. VAV interacting Krüppel-like factor (VIK) is a novel transcription factor. Previously our lab reported a series of breast cancer tumour samples where VIK methylation was associated with an increased risk of recurrence in tamoxifen-treated patients, indicating a role for VIK in ER positive breast cancer and endocrine resistance. Additionally VIK has been shown to be involved in cell cycle regulation, interacting with CDK4 and VAV1. The cyclin D-CDK4/6-Rb pathway is frequently dysregulated in ER positive breast cancer. Combined treatment of palbociclib, a highly selective CDK4/6 inhibitor, with endocrine therapy substantially improved outcome of patients with ER positive metastatic breast cancer. Increasing clinical use means acquired resistance to palbociclib is emerging as a major clinical challenge. Results. VIK was confirmed to be subject to regulation by DNA methylation in breast cancer. VIK methylation correlated to transcriptional silencing of mRNA in both cancer cell lines and primary tumours. To determine the functional significance of loss of VIK expression, VIK was knocked down in unmethylated breast cancer cell lines and a normal breast epithelial cell line. Knockdown resulted in cell death via induction of apoptosis. VIK knockdown altered cell cycle progression from G1 to S phase. Expression of multiple regulatory cell cycle proteins was altered, differentially in normal and tumour cells. Treatment with the CDK4/6 inhibitor, palbociclib, in cells with reduced VIK expression resulted in decreased sensitivity to the drug, inducing a shift in IC50 value towards resistance. In a model of acquired resistance, T47D cells were cultured long-term with palbociclib generating resistant clones. VIK was significantly downregulated in all resistant clones to barely detectable mRNA levels, suggesting a role for VIK in resistance to CDK4/6 inhibition. Conclusion. This PhD has confirmed VIK is a novel epigenetically regulated gene in breast cancer. VIK expression is essential to both normal and tumour breast cell survival and is involved in the regulation of the G1/S phase transition in the cell cycle. Loss of VIK expression potentially contributes to the development of acquired resistance to CDK4/6 inhibitors.