Dissertations / Theses on the topic 'GYF domain'

Le paludisme est l'une des maladies infectieuses les plus répandues, menaçant 40% de la population mondiale, provoquant environ 300 millions de cas et 450 000 décès chaque année, touchant principalement les enfants de moins de 5 ans. En l'absence d'un vaccin efficace et face à l'émergence de la résistance aux médicaments, il y a un besoin urgent pour mieux comprendre la biologie du parasite afin de proposer des traitements innovants. Le parasite du paludisme, Plasmodium, responsable de la maladie, présente un cycle de vie complexe et un processus de division cellulaire unique. Par rapport aux systèmes bien étudiés, la connaissance limitée de la biologie du Plasmodium empêche le développement thérapeutique. La phosphorylation des protéines, un mécanisme de régulation important, est moins comprise dans Plasmodium que dans les cellules mammifères ou de levure. Les kinases et les phosphatases impliquées dans la phosphorylation et la déphosphorylation respectivement sont des cibles potentielles de médicaments. La sous-unité catalytique de la protéine phosphatase de type 1 (PP1c) (PF3D7_1414400) opère en combinaison avec diverses protéines régulatrices pour diriger et contrôler spécifiquement son activité phosphatase. Cependant, peu d'informations sont disponibles sur cette phosphatase et ses régulateurs dans le parasite du paludisme humain, Plasmodium falciparum. Pour combler cette lacune de connaissances, nous avons mené une étude approfondie sur les caractéristiques structurelles et fonctionnelles d'un régulateur spécifique du Plasmodium appelé, Gametocyte EXported Protein 15, GEXP15 (PF3D7_1031600). Par analyses in silico, nous avons identifié trois régions d'intérêt significatives dans GEXP15 : une région N-terminale couvrant un motif RVxF interagissant avec PP1, un domaine conservé dont la fonction est inconnue, et un domaine de type GYF qui facilite potentiellement des interactions spécifiques protéine-protéine. Pour élucider davantage le rôle de GEXP15, nous avons réalisé des études d'interaction in vitro qui ont démontré une interaction directe entre GEXP15 et PP1 via le motif de liaison RVxF. Cette interaction avec PfGEXP15 a été montrée capable d'augmenter l'activité phosphatase de PP1 in vitro. De plus, en utilisant une lignée transgénique de P. falciparum exprimant la GEXP15-GFP, nous avons observé une forte expression de GEXP15 dans les stades asexués tardifs du parasite, avec une localisation principalement dans le noyau. Des expériences d'immunoprécipitation suivies d'analyses en spectrométrie de masse ont révélé l'interaction de GEXP15 avec des protéines de liaison aux ribosomes et à l'ARN. De plus, grâce à des analyses de capture de domaines fonctionnels recombinants de GEXP15 marqués avec un tag His, nous avons confirmé sa liaison avec PfPP1et au complexe ribosomal via le domaine GYF. Dans l'ensemble, notre étude éclaire l'interaction PfGEXP15-PP1-ribosome, qui joue un rôle crucial dans la traduction des protéines. Ces découvertes suggèrent que PfGEXP15 pourrait être une cible potentielle pour le développement de médicaments contre le paludisme
Malaria is one of the most prevalent vector-borne infectious diseases threatening 40% of the global population, causing around 300 million cases and 450,000 deaths annually, mostly affecting children under 5. With no effective vaccine and drug resistance emerging, there is an urgent need for innovative treatments. The malaria-causing Plasmodium parasite has a complex life cycle and unique cell division process. Compared to well-studied systems, limited knowledge of Plasmodium biology hampers therapeutic development. Protein phosphorylation, a key regulatory mechanism, is less understood in Plasmodium than in mammalian or yeast cells. Kinases and phosphatases involved in phosphorylation and dephosphorylation processes respectively are potential drug targets. The Protein Phosphatase type 1 catalytic subunit (PP1c) (PF3D7_1414400) operates in combination with various regulatory proteins to specifically direct and control its phosphatase activity. However, there is little information about this phosphatase and its regulators in the human malaria parasite, Plasmodium falciparum. To address this knowledge gap, we conducted a comprehensive investigation into the structural and functional characteristics of a conserved Plasmodium-specific regulator called Gametocyte EXported Protein 15, GEXP15 (PF3D7_1031600). Through in silico analysis, we identified three significant regions of interest in GEXP15: an N-terminal region hous-ing a PP1-interacting RVxF motif, a conserved domain whose function is unknown, and a GYF-like domain that potentially facilitates specific protein-protein interactions. To further elucidate the role of GEXP15, we conducted in vitro interaction studies that demonstrated a direct interaction between GEXP15 and PP1 via the RVxF-binding motif. This interaction was found to enhance the phosphatase activity of PP1. Additionally, utilizing a transgenic GEXP15-tagged line and live microscopy, we observed high expression of GEXP15 in late asexual stages of the parasite, with localization predominantly in the nucleus. Immunoprecipitation assays followed by mass spectrometry analyses revealed the interaction of GEXP15 with ribosomal- and RNA-binding proteins. Furthermore, through pull-down analyses of recombinant functional domains of His-tagged GEXP15, we confirmed its binding to PfPP1 and to the ribosomal complex via the GYF domain. Collectively, our study sheds light on the PfGEXP15-PP1-ribosome interaction, which plays a crucial role in protein translation. These findings suggest that PfGEXP15 could serve as a potential target for the development of malaria drugs

Thesis (M.Arch.)--Massachusetts Institute of Technology, Dept. of Architecture, 2002.
Includes bibliographical references (p. 78-79).
In the present urban space, where an individual is exposed to the conditions of heterogeneity and anonymity, a conventional Bodybuilding Gym opens up certain issues of emplacement of un/nder-spoken men's body and its close(t)ed placement in the society. While the rituals of entering and exiting the gym and 'building' the muscularity raise questions of men's reflected societal states in North America, the changing social appreciation of the 'new' body images, and emerging holistic approach of wellness of body-mind have become the thresholds to rethink the previously hyper-masculine gym space and to reinvent a way to accommodate these new conditions. I have explored the design of a contemporary gym as a subterranean-heterotopic- site rooted in the current urban context to reflect its various and changing socio-spatial identities of each user. The design focus is to recognize the updated characteristics of the user spaces when the gym is introduced with the new programs of Totality of Body-Mind, or, a further embodied Mind Zone coming into the body activity program concepts, to create new physical and psychological inter-relationships, or Proximity of Heterotopic Stages, to the individual users.
by Hyung Suk Lee.
M.Arch.

A new family of methionine-sulfoxide reductase (Msr) was recently discovered, and was named free methionine sulfoxide reductase (fRMsr). This family includes enzymes with a reductase activity toward the free R isomer of a methionine sulfoxide substrate. The fRMsrs have a GAF domain topology, a domain, which was previously identified as having in some cases a cyclic nucleotide phosphodiesterase activity. The classification of fRMsrs as GAF domains revealed a new function can be added to the GAF domain family. Interestingly the four members identified in the fRMsr family share the GAF domain structure and the presence of three conserved cysteines in the active site with free R methionine sulfoxide substrate specificity. This thesis presents the crystal structures of reduced, free Met-SO substrate-bound and MES-bound forms of a new fRMsr from Burkholderia pseudomallei (BPSL2418). BPSL2418 was cloned, overexpressed and purified to enable protein crystallization. The crystallization trials for reduced, Met-SO-bound and MES-bound forms of BPSL2418 were prepared and reasonable crystals of each form were produced. The crystal structures of BPSL2418MES, BPSL2418Met-SO and BPSL2418Reduced were solved at 1.18, 1.4 and 2.0Å, respectively by molecular replacement. The BPSL2418MES crystal belongs to space group P 21 21 21 while BPSL2418Met-SO and BPSL2418Reduced crystals belong to space group P 1 21 1. All three forms share the GAF domain structure of six antiparallel β-strands and four a-helices with connecting loops. The antiparallel β- strands (β1, β2, β5 and β6) are located in the center of the BPSL2418 structure flanked on one side by a three a-helices (a1, a2 and a4) and on the other side by a (loop1, β3, loop2, a3, β4 loop4) unit where loop4 forms a capping flap and covers the active site. The structural comparison of the three forms of BPSL2418 indicates that the catalytically important cysteine is CYS109, where the resolving cysteine is CYS75, which forms a disulfide bond with CYS109. They also suggest that the third conserved cysteine in the active site, CYS85, which is located in a3, is a nonessential cysteine for the catalytic function but it may play a role in the binding of the substrate. The structural comparison of the three forms reveals that conformational changes appear in the active site particularly involving loop4 and CYS109 during catalysis. The 3D structure of BPSL2418 shows strong structure similarity to fRMsrs enzymes, which further suggests that BPSL2418 acts as a free Met-R-SO reductase and shares the catalytic mechanism of fRMsr family.

Les Méthionine sulfoxyde réductases (Msr) catalysent la réduction spécifique des méthionine sulfoxydes (Met-O) en méthionines (Met). Elles sont impliquées dans la résistance des cellules à un stress oxydant et dans la virulence des bactéries pathogènes du genre Neisseria. Cette famille d'enzyme se compose de trois classes, les MsrA et B, structuralement distinctes, et présentant une stéréosléctivité respectivement pour l'isomère S et R de la fonction sulfoxyde du substrat. Une troisième classe, découverte récemment, et appelée fRMsr, catalyse la réduction spécifique de la forme libre de l'isomère R de la fonction sulfoxyde. La fRMsr appartient à la famille des domaines GAF, généralement impliqués dans la signalisation cellulaire, et les fRMsr représentent le premier domaine GAF présentant une activité enzymatique. Les études réalisées au cours de ma thèse sur la fRMsr de Neisseria meningitidis ont permis de montrer que : 1) fRMsr de N. meningitidis présente un mécanisme catalytique identique à MsrA/B avec la formation d'au moins un pont disulfure intramoléculaire Cys84-Cys118 réduit par la thiorédoxine (Trx) ; 2) La Cys118 est le résidu catalytique sur lequel l'intermédiaire acide sulfénique doit se former ; 3) L'étape réductase est l'étape cinétiquement déterminante du mécanisme à deux étapes conduisant à la formation du pont disulfure Cys84-Cys118. La combinaison de l'analyse des résultats cinétiques, et de la structure tridimensionnelle de la fRMsr de N. meningitidis en complexe avec le substrat ont permis de montrer : 1) L'existence d'un site de reconnaissance oxyanion impliqué dans la stabilisation de la fonction carboxylate ; 2) Un rôle de la fonction carboxylate du résidu Asp143 dans la catalyse de l'étape réductase ; 3) Le résidu Glu125 est impliqué dans la reconnaissance et/ou le positionnement du substrat Met-O probablement via la stabilisation du groupement NH3+ ; 4) Un rôle du résidu Asp141 dans le positionnement des résidus Asp143 et Glu125 ; 5) le noyau indole du Trp62 est impliqué dans la stabilisation du groupe méthyle-[epsilon]
Methionine sulfoxide reductases (Msr) catalyze the specific reduction of methionine sulfoxides (Met-O) into methionine (Met). They are involved in cell defences against oxidative stress and virulence of pathogenic bacteria of Neisseria genius. This family of enzymes consists of three classes, MsrA and MsrB, structurally-unrelated, Specific for the S and the R epimer of the sulfoxide function of the substrate, respectively. A third class, recently discovered and called fRMsr, selectively reduce the free form of the R epimer of the sulfoxide function. The fRMsr belongs to the family of GAF domains, they are usually involved in cell signaling, and fRMsr represent the first GAF domain to show enzymatic activity. The studies of the Neisseria meningitidis fRMsr have shown that: 1) The Neisseria meningitidis fRMsr have a identical catalytic mechanism to MsrA and MsrB with the formation of at least one intramolecular disulfide bond, Cys84-Cys118 reduced by thioredoxin (Trx) ; 2) The Cys118 is demonstrated to be the catalytic Cys on which a sulfenic acid is formed ; 3) The Reductase step is the rate determining step of the mechanism leading to the formation of the disulfide bond Cys84-Cys118. The combination of the biochemical and kinetics data, and the examination of the 3D structure of the N. meningitidis fRMsr in complex with its substrate shown: 1) an oxyanion hole involved in the accommodation of the carboxylate group ; 2) the carboxylate group of the Asp143 residue involved in the catalysis of step reductase, and 3) The Glu125 residue involved in the recognition and/or positioning of the Met-O probably by the stabilization of the NH3+; 4) the Asp141 residue involved in the positioning of Asp143 and Glu125 residues ; 5) the indole ring of the Trp62 residue involved in stabilizing of the epsilon-methyl group

Most patients undergoing androgen deprivation therapy relapse eventually and progress to androgen-independent (AI) prostate cancer. Although the mechanisms underlying progression to AI prostate cancer are not well understood, studies suggest that androgen receptor (AR) is still required for AI prostate cancer. Our lab found that Vav3, a Rho GTPase guanine nucleotide exchange factor (GEF), is up-regulated during the progression of androgen-dependent human prostate cancer cells to androgen-independence in vivo and in cell-based experiments. Since Vav3 significantly increases ligand-dependent AR transcriptional activity and this action requires the Vav3 pleckstrin homology (PH) domain but not Vav3 GEF activity, we explored the role of the Vav3 PH domain in ligand-dependent AR coactivation by Vav3. We found that targeting the Vav3 PH mutant into nuclei but not the plasma membrane restored Vav3 PH mutant in AR coactivation. Targeting Vav3 to the plasma membrane eliminated the capacity of Vav3 to coactivate AR. In agreement with nuclear targeting of Vav3 via its PH domain, chromatin immunoprecipitation assays showed that Vav3 enhancement of AR transcriptional activity was accompanied by Vav3 recruitment to AR transcriptional complexes at an AR target gene enhancer. Further, Vav3 increased AR occupancy at the target gene enhancer upon androgen treatment and this may underlie the capacity of Vav3 to enhance AR transcriptional activity. Because Vav3 can also be activated by growth factors (GFs) and GFs activate AR in the absence of androgen (ligand-independent), we investigated the crosstalk between Vav3 and GF activation of AR and found Vav3 strongly enhanced AR transcriptional activity induced by GFs. GEF function and the downstream Rho GTPase, Rac1 were required for constitutively active (Ca) Vav3 activation of AR, which differs from Vav3 activation of AR in the presence of androgen. We also investigated the possible signal pathways contributing to AR activation by Ca Rac1. Ca Rac1 caused ligand-independent activation of AR in part through MAPK/ERK signaling and conferred prostate cancer growth in the absence of androgen in cell culture, soft agar and mouse tumor xenografts. Thus, our findings indicate that Vav3 activates AR in the presence or absence of ligand through two distinct mechanisms, which supports a versatile regulatory effect of Vav3 in AR signaling and prostate cancer progression.

This diploma thesis deals with the design of a new marketing strategy for the Brno gym Velký Průvan. Based on theoretical knowledge, an analysis of the current state and the state of competition is prepared, which is the basis of the design part, which focuses on the modification of the current product due to the global pandemic, new PPC advertising and marketing on social networks. These changes should increase the competitiveness and, ultimately, the gym's sales.

Cette thèse porte sur les relations entre les processus SLE, les ensembles CLE et le champ libre Gaussien. Dans le chapitre 2, nous donnons une construction des processus SLE(k,r) à partir des boucles des CLE(k) et d'échantillons de restriction chordale. Sheffield et Werner ont prouvé que les CLE(k) peuvent être construits à partir des processus d'exploration symétriques des SLE(k,r).Nous montrons dans le chapitre 3 que la configuration des boucles construites à partir du processus d'exploration asymétrique des SLE(k,k-6) donne la même loi CLE(k). Le processus SLE(4) peut être considéré comme les lignes de niveau du champ libre Gaussien et l'ensemble CLE(4) correspond à la collection des lignes de niveau de ce champ libre Gaussien. Dans la deuxième partie du chapitre 3, nous définissons un paramètre de temps invariant conforme pour chaque boucle appartenant à CLE(4) et nous donnons ensuite dans le chapitre 4 un couplage entre le champ libre Gaussien et l'ensemble CLE(4) à l'aide du paramètre de temps. Les processus SLE(k) peuvent être considérés comme les lignes de flot du champ libre Gaussien. Nous explicitons la dimension de Hausdorff de l'intersection de deux lignes de flot du champ libre Gaussien. Cela nous permet d'obtenir la dimension de l'ensemble des points de coupure et des points doubles de la courbe SLE, voir le chapitre 5. Dans le chapitre 6, nous définissons la mesure de restriction radiale, prouvons la caractérisation de ces mesures, et montrons la condition nécessaire et suffisante de l'existence des mesures de restriction radiale.

Il lavoro è stato suddiviso in tre macro-aree. Una prima riguardante un'analisi teorica di come funzionano le intrusioni, di quali software vengono utilizzati per compierle, e di come proteggersi (usando i dispositivi che in termine generico si possono riconoscere come i firewall). Una seconda macro-area che analizza un'intrusione avvenuta dall'esterno verso dei server sensibili di una rete LAN. Questa analisi viene condotta sui file catturati dalle due interfacce di rete configurate in modalità promiscua su una sonda presente nella LAN. Le interfacce sono due per potersi interfacciare a due segmenti di LAN aventi due maschere di sotto-rete differenti. L'attacco viene analizzato mediante vari software. Si può infatti definire una terza parte del lavoro, la parte dove vengono analizzati i file catturati dalle due interfacce con i software che prima si occupano di analizzare i dati di contenuto completo, come Wireshark, poi dei software che si occupano di analizzare i dati di sessione che sono stati trattati con Argus, e infine i dati di tipo statistico che sono stati trattati con Ntop. Il penultimo capitolo, quello prima delle conclusioni, invece tratta l'installazione di Nagios, e la sua configurazione per il monitoraggio attraverso plugin dello spazio di disco rimanente su una macchina agent remota, e sui servizi MySql e DNS. Ovviamente Nagios può essere configurato per monitorare ogni tipo di servizio offerto sulla rete.

Domain Specific Modeling (DSM) aims to increase productivity of software development by raising the level of abstraction beyond code concepts and using domain concepts. By providing a generative model-driven tooling component and runtime support, the Eclipse Graphical Modeling Framework (GMF) aims to simplify the creation of diagram editors for specific domains based on a series of model creation and transformation steps. GMF leverages the Eclipse Modeling Framework (EMF) and the Eclipse Graphical Editing Framework (GEF) to allow the graphical modeling of Domain Specific Languages (DSL). A Domain Specific Language (DSL) is developed specifically for a specific task and specific domain. In this research, the State Machine Compiler (SMC) represents the specific domain for which a DSL in a form of a diagram editor is developed using GMF. SMC is an open source Java tool allowing generation of state pattern classes from textual descriptions of state machines. The main objective of this research is to describe the use of GMF, highlight potential pitfalls and identify strengths and weaknesses of GMF based on certain criteria. To be able to feed the SMC diagrams created with the editor into SMC, a Java Emitter Templates (JET) transformation is used to transform SMC model instances into textual format expected by SMC.
Thesis (Master, Computing) -- Queen's University, 2011-04-14 18:58:08.797

The South African Department of Basic Education and Department of Higher Education and Training (2011a) made a call for the development of mathematics knowledge and practice standards in the foundation phase to serve as guidelines for the preparation of foundation phase teachers in the different higher education institutions. The purpose of the study in hand was to develop draft knowledge and practice standards in the number domain for the preparation of foundation phase teachers (referred to as mathematics knowledge and practice standards). These standards have to be refined and improved in further studies and should in the end serve as knowledge and practice standards for the preparation of foundation phase teachers in South Africa. Through a conceptual qualitative research methodology the researcher purposefully collected documents and analysed them through content analysis. The data-gathering process took place in three phases. During the first phase, policy documents with regard to general standards for teacher preparation, written school curriculum documents and mathematical standards for the preparation of foundation phase teachers in South Africa, the United States of America, Australia and the Netherlands were gathered. The second phase involved the purposeful gathering of articles, research reports and teacher preparation textbooks with regard to the preparation of foundation phase teachers to teach the number domain. During the first and second phases of data gathering, the documents were analysed according to mathematical knowledge for teaching as described by Ball, Thames and Phelps (2008) and the first draft of mathematical knowledge and practice standards was compiled. During the third data-gathering phase, critical evaluation reports were gathered from experts in the field of mathematics education (including researchers at universities and practising foundation phase teachers). The critical evaluation includes gaps/shortcomings in the draft mathematics knowledge and practice standards, as well as comments with regard to the clarity, applicability and functionality of the document. The draft mathematics knowledge and practice standards (MKPSs) for the preparation of foundation phase teachers include: Standard 1: Common content knowledge – The foundation phase teacher has a clear understanding of the common content knowledge of the number domain. Standard 2: Specialised content knowledge – The foundation phase teacher has a clear understanding of the specialised content of the number domain. Standard 3: Knowledge at the mathematical horizon – The foundation phase teacher understands how mathematical themes in the number domain relate to other themes in the different foundation phase year groups and in other phases. Standard 4: Knowledge of content and teaching – The foundation phase teacher is able to plan lessons and knows how to teach the number domain. Standard 5: Knowledge of content and learners – The foundation phase teacher knows the foundation phase learners and knows how they learn the number domain. Standard 6: Knowledge of content and the curriculum – The foundation phase teacher understands the South African school curriculum, as well as international trends in the school curriculum concerning the number domain. Those experts in the field of mathematics education in the foundation phase who participated in the study all indicated that the mathematics knowledge and practice standards in the number domain have the potential to boost the preparation of foundation phase teachers in South Africa.
MEd (Mathematics Education), North-West University, Potchefstroom Campus, 2014