The transactivator of transcription protein (Tat) of human immunodeficiency virus (HIV) plays an important role in both viral replication and AIDS pathogenesis. Tat is responsible for enhancing HIV-specific transcription, without which production of infectious virus is severely limited. Ongoing research, however, has identified a plethora of additional functions attributable to Tat including regulating additional HIV processes, altering the homeostasis of both infected and uninfected cells, and being directly involved in AIDS-related neuropathology and cancer. Tat thus plays a diverse role in both viral replication and pathogenesis. What is the relative importance of Tat’s additional functions compared to its principle function of transactivation? This question is explored in Chapter 2 in which tat clones from an epidemiologicallylinked transmission cohort were functionally tested. tat sequences were isolated and cloned from the cohort members at various time points and assessed for transactivation potential. The data revealed that transmission of HIV resulted in the selection of mutations in tat that were host specific and that impacted on the Tat clones’ abilities to transactivate. No correlation, however, was observed between the transactivation potentials of the Tat clones and the AIDS progression statuses of the hosts. The host-specific tat mutations may instead reflect the selection of variants fitter in one or more of Tat’s other functions. This therefore leads to the hypothesis that Tat functions in addition to transactivation are influential in AIDS pathogenesis and are subject to selective pressures during HIV transmission. Tat’s flexibility and diversity of functions are mediated by defined functional domains. One of the most important of these is the basic domain, a highly conserved region encompassing a unique nuclear localisation signal (NLS). The NLS allows Tat to localise to the cell nucleus to participate in transactivation. However, many of Tat’s additional functions require Tat to be outside of the nucleus or even outside of the cell. It is currently unknown how the NLS is modulated to enable Tat nuclear egress, but it may involve post-translational modifications of NLS residues. In Chapter 3, protein arginine methyltransferase 6 (PRMT6) is demonstrated to alter the localisation of Tat within the nucleus and increase the half-life of Tat within the cell. Both of these effects require the methylation activity of PRMT6 and two NLS residues, arginines 52 and 53, previously described to be substrates for PRMT6 methylation. The results suggest that PRMT6 primes Tat for functions outside of the nucleus by altering its subcellular localisation and increasing its stability. The critical role of the basic domain in Tat function is highlighted in Chapter 4 in which mutation of the basic domain led to dysregulation of HIV replication. The mutant, referred to as Nullbasic, has characteristics similar to transdominant Tat mutants, such as suppressing transactivation and localising to the cell cytoplasm. Surprisingly, Nullbasic potently inhibits HIV infectivity by strongly downregulating the expression of envelope, the key molecule involved in cell attachment and entry. Part of this downregulation is attributable to Nullbasic interfering with the nuclear export of envelope-encoding mRNA as a result of altering the subcellular localisation of Rev. However, an additional mechanism of interference is required to fully explain the strong suppression of envelope protein observed in cells. The data allude to a role for Tat in promoting envelope mRNA translation, a role subverted by mutating the basic domain. Taken together, these studies highlight the importance of a diversity of Tat functions to HIV replication and AIDS pathogenesis. Further, they emphasise the critical role of the basic domain to Tat function. Modifications of the basic domain not only influence function, but also regulate Tat spatially and temporally. Dysregulation of the basic domain by mutation not only subverts Tat function, but also elicits antiviral activity at multiple steps of the HIV lifecycle. The study of Tat and its basic domain is crucial in order to understand its role in HIV/AIDS and to recognise Tat as a pathogenic agent in its own right.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2010.

Lung cancer is the most common cause of cancer-related mortality worldwide with current treatments providing limited therapeutic benefit in most cases. TP53 (Trp53, p53) mutations occur in approximately 50% of lung adenocarcinoma cases and are associated with poor prognosis and so novel therapies that target these p53 mutant lung tumours are urgently needed. Despite the high frequency of p53 mutations in lung tumours, the impact these mutations have on response to therapy remains unclear in this cancer type. The aim of my project is to characterise the gain-of-function and dominant-negative effects of p53 mutations in lung tumours and to identify ways of therapeutically targeting these p53 mutant tumours based on dependencies and susceptibilities that our analysis uncovers. To characterise the gain-of-function and dominant-negative effects of p53 mutations I compared p53 mutant murine lung tumour cells that endogenously express either a contact (R270H, equivalent to R273H in humans) or conformational (R172H, equivalent to R175H in humans) p53 mutant protein and p53 null lung tumour cell lines; both in the presence and absence of wild-type p53. Interestingly, transcriptional and functional analysis uncovered metabolic gain-of-functions that are specific to the type of p53 mutation. Upregulation of mevalonate pathway expression was observed only in R270H lung tumours and consequently R172H and R270H lung tumours displayed distinct sensitivities to simvastatin, a mevalonate pathway inhibitor widely used in the clinic. Furthermore, the transcriptional signature underlying this sensitivity to simvastatin was also present in human lung tumours with contact p53 mutations, indicating that these findings may be clinically relevant. On the other hand, our analysis of the potential dominant-negative effects of the p53 mutants on wild-type p53 demonstrated that wild-type p53 was able to induce typical p53 target genes to a similar level in p53 null and mutant cells. Furthermore, wild-type p53 restoration resulted in comparable tumour suppressive responses in p53 mutant and null tumours and thus, p53-restoration therapy will likely be of benefit to patients with p53 mutations in lung cancer. Hence, I have demonstrated that lung tumours harbouring contact and conformational p53 mutations display common and distinct therapeutic susceptibilities.

La séparation de deux énantiomères est un procédé d’intérêt pour l’industrie pharmaceutique. En effet, souvent un seul des énantiomères exerce l'activité biologique requise. Cette problématique est abordée ici par l'utilisation d'enzymes énantiosélectives qui est une alternative intéressante aux méthodes conventionnelles (chromatographie chirale, synthèse asymétrique ou cristallisation). Cette approche a été mise en oeuvre pour les molécules de la famille des profènes (l’Ibuprofène, le Kétoprofène ou le Naproxène par exemple) qui sont des acides 2- arylpropioniques et constituent une classe importante de médicaments anti-inflammatoires non stéroïdiens. Tout d’abord, un travail de recherche dans le domaine de la catalyse enzymatique et de l’ingénierie d’enzymes a été effectué. Des enzymes aux potentialités prometteuses, issues de la levure Yarrowia lipolytica, pour la résolution de ces trois anti-inflammatoires ont été identifiées. S’appuyant sur la modélisation moléculaire, l’ingénierie moléculaire a été utilisée pour accéder à des enzymes performantes tant du point de vue de la sélectivité que de l’activité. Les réactions ont été réalisées conventionnellement dans un système diphasique phase aqueuse/décane car les profènes et les esters associés sont des substrats hydrophobes et très faiblement solubles dans l'eau, la réaction doit donc être effectuée dans un solvant apolaire en contact avec une phase aqueuse où l'enzyme libre est dissoute. Ce mode opératoire permet d'éviter une immobilisation de l'enzyme. Une enzyme pour chaque substrat avec une énantiosélectivité suffisante a pu être développée, à savoir Lip2p V232A pour l’ibuprofène, V235S pour le naproxène et V232F pour le kétoprofène. Les lipases de Candida rugosa se sont également avérées intéressantes pour la résolution des profènes mais moins que les lipases précédemment évoquées. Le deuxième aspect de cette thèse s’est intéressé à la mise oeuvre de cette technique de résolution enzymatique dans un procédé innovant de Chimie Verte où le dioxyde de carbone supercritique (CO2SC) remplace le décane. En effet, les solvants organiques tels que le décane peuvent être toxiques mais aussi difficiles à éliminer, à la fin du processus, ce qui conduit à des étapes fastidieuses et coûteuses de purification. Dans un premier temps l’étude a porté sur la résolution de l’acide 2-bromo phényl acétique par l’hydrolyse de son ester octylique (ester + eau <=> acide (profène) + alcool). L'acidification de la phase aqueuse en contact avec CO2SC (formation d'acide carbonique) s’est montrée préjudiciable pour obtenir des conversions élevées. Cet inconvénient a été atténué en utilisant des concentrations assez élevées de sels (Na2HPO4 et KH2PO4) pour tamponner la phase aqueuse. Une étude spécifique en cellule haute pression utilisant des sondes solvatochromiques a permis d’établir que l’utilisation de concentrations élevées de sels (de l’ordre de 1000 mmol/L) permettait de maintenir un pH de l‘ordre de 6. Dans ces conditions, des conversions élevées ont pu être obtenues pour des temps de réactions de l’ordre de 100 h. Cependant la cinétique s’est avérée plus lente par rapport à celle observée avec le décane. L’explication de cette différence n’est pas encore totalement élucidée mais deux pistes ont été privilégiées : la formation de carbamates dues aux interactions entre le CO2SC et les acides aminés composant l’enzyme ou une mauvaise ouverture du volet moléculaire qui recouvre le site actif de l’enzyme liée à la moindre hydrophobicité du CO2SC hydraté. Cette résolution énantiomérique a également été mise en oeuvre dans un système sans phase aqueuse en utilisant l‘enzyme sous sa forme immobilisée sur support solide en utilisant la réaction réverse, l’estérification. Utilisant les mêmes approches, la résolution énantiomérique de l’ibuprofène a également été réalisée. Les meilleurs résultats obtenus en système diphasique phase aqueuse/CO2SC permettent en 75 heures une résolution quasi-totale.

Common crystallization procedures, X-ray diffraction method and crystallographic software to determine and refine the structure of haloalkane dehalogenase enzyme were used in this thesis.

Mutation analysis is a fault-based method used for introducing small changes into a program, producing mutants based on mutation operators, classes of commonly occurring faults. Mutation analysis has been used in the last couple of decades for evaluating how good test cases produced by software testing are at detecting faults. Software testing is the process of executing software based on certain input parameters and evaluating its behavior with the purpose of finding faults and making sure that the software works as expected.   In automotive systems, MATLAB Simulink is the facto standard for implementing the electronic control software of vehicle functions. As such, the application of software testing and mutation analysis to Simulink models becomes a crucial aspect for providing a framework to evaluate existing test cases by introducing mutations into these models.   In this thesis, we propose a mutation generation framework for Simulink by using a set of mutation operators defined based on our own classification based on the Simulink project structure and previously defined operators. Our method is supported by the tool SIMUTATOR, which we also introduce and apply on an industrial prototype called the Brake-By-Wire system. This work enables the mutation analysis of industrial Simulink models. In addition, we show how SIMUTATOR can be used together with SIMPAAL (a tool for transforming Simulink models to timed automata) and MATS (a tool for test generation) for mutation testing. The results show that SIMUTATOR is efficient and can be used successfully on industrial-sized Simulink software

A evolução in vitro é um método laboratorial criado para a evolução de moléculas, principalmente de proteínas. Por meio de mutações, o método busca novas propriedades de moléculas, objetivando criar novas proteínas e, com isso, intensificar o estudo e a cura de doenças, pelo desenvolvimento de novos fármacos. O grande desafio na evolução in vitro é criar o maior número possível de moléculas de proteínas que atinjam propriedades desejadas, uma vez que apenas uma fração infinitesimal das diversidades geradas utilizando-se seqüências de DNA é aproveitada. Para se obter moléculas com funcionalidade adequada por meio dessa técnica, é requerido muito tempo e aporte financeiro. Com o objetivo de avaliar computacionalmente a funcionalidade de proteínas variantes a partir das seqüências de aminoácidos buscando reduzir o custo e o tempo desprendido em laboratório, este trabalho propõe o uso de técnicas de computação inteligentes (evolução in silicio), baseadas em aprendizado de máquina e computação evolutiva. Para o emprego de técnicas de AM, bancos de dados com elevado número de informações são fundamentais. Neste sentido, escolheu-se investigar as moléculas mutantes de hemoglobina, uma vez que a quantidade de informações disponíveis sobre a mesma é bastante extensa na literatura. Os resultados obtidos mostram que é possível desenvolver algoritmos eficientes para determinar a funcionalidade de variantes de hemoglobina. Com esses resultados, busca-se contribuir no desenvolvimento de técnicas de evolução dirigida com suporte computacional / In vitro evolution is a laboratorial method developed to molecule evolution mainly proteins. By producing mutations, this method looks for new molecule properties, aiming achieve new proteins for the development of drugs for diseases. The great challenge of in vitro evolution is the development of the highest possible number of molecules that reaches desired properties. This objective is a great challenge to be transposed, since only one infinitesimal fraction of generated proteins using DNA sequencies is usefull to obtain molecules with the desired function. Besides high financial support and time are required to apply this technique. With the objective of evaluating computacionaly and functionality of proteins mutants starting from aminoacids sequences looking for to reduce the cost and the time loosened at laboratory, this work proposes the use of intelligent computation techniques based on learning of it conspires and evolutionary computation. On the other hand, when machine learning techniques are used, it is fundamental to access data mining with high number of information. In order to reduce these difficulties, this work proposes a machine learning (ML) based on approach to evaluate computationaly hemoglobin variants. ML techniques require, in general, large data base. In order to supply this requirement, hemoglobin variants were used because there is a large number of hemoglobin variants available in the literature. The obtained results shown that is possible to develop efficient algorithms to determine hemoglobin variant function. These results can contribute for development of molecule evolution techniques

Brachypod (bpH/bpH), an autosomal mutation in mice, is characterized by a shortening of the long bones and paws, and a delay or absence of ossification in some of the distal limb elements. The present study represents a detailed description of the brachypod phenotype in day 12 hindlimb buds maintained for 6 days in a submerged, serum-free organ culture system. Using this in vitro system, the proximal-to-distal effect on the severity of cartilage reduction was intensified in the brachypod explants with an intermediate expression in the heterozygotes. Immunofluorescent staining of the brachypod cartilage revealed a deficiency in and an abnormal distribution of the proteoglycans. Although there was no recognizable difference in the immunofluorescent staining for type II collagen between the mutant and wild-type, electron micrographs showed the presence of thick fibrils in the matrix. Other atypical structures in the brachypod cartilage included pleomorphic nuclei, reduced intracellular glycogen granules and profuse intercellular contacts. It is proposed that with the use of this in vitro system which supports the autonomous development of the individual limb elements, experiments concerning the pathogenesis of skeletal mutations such as brachypod should be more feasible.

Indiana University-Purdue University Indianapolis (IUPUI) / Myelodysplastic syndrome (MDS) is a clonal disease arising from mutated hematopoietic stem cells (HSCs). MDS stem cells originate from pre-leukemic HSCs, which have enhanced competitive advantage over wild-type (WT) HSCs but normal differentiation capacity. Recently, acquired somatic gain-of-function (GOF) TP53 mutations were identified in the blood of aged healthy individuals as well as in patients with MDS. However, the role of GOF TP53 mutations in clonal hematopoiesis and the pathogenesis of MDS is largely unknown. Based upon our previous studies and clinical findings, I hypothesized that GOF mutant p53 drives the development of pre-leukemic HSCs with enhanced competitive advantage, leading to clonal expansion and the pathogenesis of MDS. To test my hypothesis, I examined HSC behaviors in young p53+/+ and p53R248W/+ mice. I discovered that p53R248W enhances the repopulating potential of HSCs without affecting terminal differentiation. I also found that GOF mutant p53 protects HSCs from genotoxic stress and promotes their expansion. To investigate the role of mutant p53 in the pathogenesis of hematological malignancies, I monitored disease development in p53+/+ and p53R248W/+ mice and observed that some mutant p53 mice develop MDS during aging. Therefore, I demonstrated that GOF mutant p53 enhances the repopulating potential of HSCs and drives the development of pre-leukemic HSCs, predisposing aged mutant p53 mice to MDS development. Mechanistically, I found that mutant p53 increases the chromatin accessibility to genes important for HSC maintenance, including pluripotent gene Sox2 and chemokine gene Cxcl9. By performing biochemical experiments, I discovered that GOF mutant p53, but not WT p53, interacts with histone methyltransferase EZH2 and enhances histone H3 lysine 27 trimethylation (H3K27me3) at genes, including Mef/Elf4 and Gadd45g, that negatively regulate HSC self-renewal. Collectively, these findings demonstrated that GOF mutant p53 drives pre-leukemic HSC development through modulating epigenetic pathways. Thus, our studies have uncovered novel mechanistic and functional links between GOF mutant p53 and epigenetic regulators in pre-leukemic HSCs. This research may identify epigenetic regulator EZH2 as a novel target for the prevention and treatment of MDS patients with TP53 mutations.

Indiana University-Purdue University Indianapolis (IUPUI) / Q fever is a heavily underdiagnosed and underreported infection caused by the obligate intracellular pathogen Coxiella burnetii. Following entry into the host cell, Coxiella replicates in the acidic phagolysosome-like parasitophorous vacuole termed the Coxiella Containing Vacuole (CCV). The CCV is a large and highly fusogenic compartment that actively fuses with the host endocytic pathway during maturation of the phagolysosome. Evidence suggests that the development of the CCV is sensitive to increasing cholesterol levels and leads to CCV acidification and bacterial death. Therefore, we hypothesize that CCV cholesterol concentration is carefully modulated through the Coxiella encoded sterol reductases (CBU1206 and CBU1158). A ∆CBU1206 mutant of Coxiella is hypersensitive to cholesterol and displays growth defects in intracellular replication and CCV development. Following fusion with the host endocytic pathway, the Coxiella NMII Phase II (WT) CCVs readily acquire host proteins such as LAMP1, CD63, Rab7, ORP1L, RILP, and LC3. These heterotypic events with the host endosomal cascade are presumed to provide selected subsets of endocytosed cargo and membrane. Therefore, I investigated whether ΔCBU1206 CCV heterotypic fusion events are defective due to altered lipid content on the CCV membrane. I observed increased accumulation of sterols on the ΔCBU1206 CCV membrane. Similar to WT, the mutant readily fuses host lysosomes and readily acquires the host glycoprotein LAMP1 but displays reduced localization of CD63 (LAMP3). Additionally, reduced localization of the late endosomal markers Rab7, ORP1L, and RILP was observed suggesting that late endosome fusion maybe defective in ΔCBU1206. Further, reduced localization of LC3 was also observed suggesting that the mutant may also be defective in fusing with autophagosomes. Finally, the mutant possesses a functional Type 4 Secretion System that secretes a moderate amount of effector proteins relative to WT. Considering the vast array of functions accomplished by the effectors secreted, the moderate effector secretion by the mutant could influence the endocytic pathway fusion processes as well as CCV development. Collectively, this body of work suggests that the lack of sterol reductase CBU1206 in Coxiella results in defective heterotypic fusion events of the CCV membrane that could alter pathogenesis and CCV expansion.