The role of the efflux mechanisms in multidrug resistance in Mycobacterium tuberculosis

Abstract The emergence of multi and extensively drug resistant tuberculosis (MDRTB and XDRTB) has increased the concern of public health authorities around the world. The World Health Organization has defined MDRTB as tuberculosis (TB) caused by organisms resistant to at least isoniazid and rifampicin, the main first-line drugs used in TB therapy, whereas XDRTB refers to TB resistant not only to isoniazid and rifampicin, but also to a fluoroquinolone and to at least one of the three injectable second-line drugs, kanamycin, amikacin and capreomycin. Resistance in Mycobacterium tuberculosis is mainly due to the occurrence of spontaneous mutations and followed by selection of mutants by subsequent treatment. However, some resistant clinical isolates do not present mutations in any genes associated with resistance to a given antibiotic, which suggests that other mechanism(s) are involved in the development of drug resistance, namely the presence of efflux pump systems that extrude the drug to the exterior of the cell, preventing access to its target. Increased efflux activity can occur in response to prolonged exposure to subinhibitory concentrations of anti-TB drugs, a situation that may result from inadequate TB therapy. The inhibition of efflux activity with a non-antibiotic inhibitor may restore activity of an antibiotic subject to efflux and thus provide a way to enhance the activity of current anti-TB drugs. The work described in this thesis foccus on the study of efflux mechanisms in the development of multidrug resistance in M. tuberculosis and how phenotypic resistance, mediated by efflux pumps, correlates with genetic resistance. In order to accomplish this goal, several experimental protocols were developed using biological models such as Escherichia coli, the fast growing mycobacteria Mycobacterium smegmatis, and Mycobacterium avium, before their application to M. tuberculosis. This approach allowed the study of the mechanisms that result in the physiological adaptation of E. coli to subinhibitory concentrations of tetracycline (Chapter II), the development of a fluorometric method that allows the detection and quantification of efflux of ethidium bromide (Chapter III), the characterization of the ethidium bromide transport in M. smegmatis (Chapter IV) and the contribution of efflux activity to macrolide resistance in Mycobacterium avium complex (Chapter V). Finally, the methods developed allowed the study of the role of efflux pumps in M. tuberculosis strains induced to isoniazid resistance (Chapter VI). By this manner, in Chapter II it was possible to observe that the physiological adaptation of E. coli to tetracycline results from an interplay between events at the genetic level and protein folding that decrease permeability of the cell envelope and increase efflux pump activity. Furthermore, Chapter III describes the development of a semi-automated fluorometric method that allowed the correlation of this efflux activity with the transport kinetics of ethidium bromide (a known efflux pump substrate) in E. coli and the identification of efflux inhibitors. Concerning M. smegmatis, we have compared the wild-type M. smegmatis mc2155 with knockout mutants for LfrA and MspA for their ability to transport ethidium bromide. The results presented in Chapter IV showed that MspA, the major porin in M. smegmatis, plays an important role in the entrance of ethidium bromide and antibiotics into the cell and that efflux via the LfrA pump is involved in low-level resistance to these compounds in M. smegmatis. Chapter V describes the study of the contribution of efflux pumps to macrolide resistance in clinical M. avium complex isolates. It was demonstrated that resistance to clarithromycin was significantly reduced in the presence of efflux inhibitors such as thioridazine, chlorpromazine and verapamil. These same inhibitors decreased efflux of ethidium bromide and increased the retention of [14C]-erythromycin in these isolates. Finaly, the methods developed with the experimental models mentioned above allowed the study of the role of efflux pumps on M. tuberculosis strains induced to isoniazid resistance. This is described in Chapter VI of this Thesis, where it is demonstrated that induced resistance to isoniazid does not involve mutations in any of the genes known to be associated with isoniazid resistance, but an efflux system that is sensitive to efflux inhibitors. These inhibitors decreased the efflux of ethidium bromide and also reduced the minimum inhibitory concentration of isoniazid in these strains. Moreover, expression analysis showed overexpression of genes that code for efflux pumps in the induced strains relatively to the non-induced parental strains. In conclusion, the work described in this thesis demonstrates that efflux pumps play an important role in the development of drug resistance, namely in mycobacteria. A strategy to overcome efflux-mediated resistance may consist on the use of compounds that inhibit efflux activity, restoring the activity of antimicrobials that are efflux pump substrates, a useful approach particularly in TB where the most effective treatment regimens are becoming uneffective due to the increase of MDRTB/XDRTB.

Single side damage simulations and detection in beam-like structures

Beam-like structures are the most common components in real engineering, while single side damage is often encountered. In this study, a numerical analysis of single side damage in a free-free beam is analysed with three different finite element models; namely solid, shell and beam models for demonstrating their performance in simulating real structures. Similar to experiment, damage is introduced into one side of the beam, and natural frequencies are extracted from the simulations and compared with experimental and analytical results. Mode shapes are also analysed with modal assurance criterion. The results from simulations reveal a good performance of the three models in extracting natural frequencies, and solid model performs better than shell while shell model performs better than beam model under intact state. For damaged states, the natural frequencies captured from solid model show more sensitivity to damage severity than shell model and shell model performs similar to the beam model in distinguishing damage. The main contribution of this paper is to perform a comparison between three finite element models and experimental data as well as analytical solutions. The finite element results show a relatively well performance.

Gammaretroviral and lentiviral vectors for gene therapy: stability and inactivation mechanisms

Dissertation presented to obtain a Ph.D degree in Engineering and Technology Sciences, Gene Therapy at the Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa

Liver dysfunction in patients bitten by Crotalus durissus terrificus (Laurenti, 1768) snakes in Botucatu (State of São Paulo, Brazil)

Thirty-two patients bitten by venomous snakes sixteen by Bothrops spp. and sixteen by Crotalus durissus terrificus were studied. The group comprised thirty males and two females, aged eight to sixty-three years (mean 33±15). Bromsulphalein tests were increased in the majority of patients bitten by Crotalus durissus terrificus. The correlation coefficient of Spearman was positive between bromsulphalein tests and alanine aminotransferase levels, and between alanine aminotransferase and aspartate aminotransferase levels only in the Crotalus group. The only patient who died was bitten by Crotalus durissus terrificus and showed hydropic degeneration and mitochondrial injury in the liver. It was concluded that the hepatic damage might have been caused by at least two possible mechanisms: venom effect on liver mitochondria and cytokine effects on hepatocyte, specially interleukin-6.

Neural mechanisms of stimulus generalization in auditory fear conditioning

Dissertation presented to obtain the Ph.D degree in Neuroscience Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Enterococcus and biocides: mechanisms of tolerance and selection for vancomycin resistance

Dissertation presented to obtain a Doctoral degree in Biology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa.

Análise de Integridade Estrutural de uma Flare Industrial

Para garantir que um equipamento opere com segurança e fiabilidade durante o seu ciclo de vida, desde a sua instalação ao desmantelamento, devem ser realizadas inspeções e/ou monitorizações que, dependendo dos dados recolhidos, podem implicar avaliações Fitness- For-Service (FFS) que definirão a necessidade de reparação ou alteração do equipamento ou das condições processuais. A combinação de inspeção ou monitorização com os melhores procedimentos e técnicas de avaliação atuais fazem sobressair insuficiências dos procedimentos mais antigos. Usando métodos mais avançados de avaliação, validados e suportados através de uma vasta experiência de campo, pode-se agora avaliar defeitos nos ativos (equipamentos) e determinar a adequação ao serviço com uma análise FFS. As análises FFS tornaram-se cada vez mais aceites em toda a indústria ao longo dos últimos anos. A norma API 579 - 1/ASME FFS-1: 2007 fornece diretrizes para avaliar os tipos de danos que afetam os equipamentos processuais e a norma API RP 571: 2011 descreve os mecanismos de degradação que afetam os equipamentos nas petroquímicas e refinarias, que incluem os danos por corrosão, desalinhamentos, deformações plásticas, laminações, fissuras, entre outros. Este trabalho consiste na análise de Integridade Estrutural de uma Flare Industrial que surgiu da necessidade real de análise do equipamento no âmbito da atividade profissional do candidato. O estudo realizado a nível profissional é de grande abrangência, incluindo a inspeção do equipamento, identificação da falha ou dano, recolha e registo de dados, definição de estratégia de atuação e seleção de técnicas de avaliação da condição para posterior alteração, reparação ou desmantelamento. Na presente dissertação de mestrado em Engenharia Mecânica, Ramo Construções Mecânicas, pretende-se efetuar o estudo aprofundado de uma das etapas de projeto, nomeadamente estudar a causa, avaliar a falha e implicações estruturais ou processuais devido à degradação interior do riser de uma flare, com base numa análise FFS, assumindo a operabilidade em segurança e garantindo resolutas condições de funcionamento. A presente análise FFS tem como finalidade validar ou não a integridade atual (avaliação técnica quantitativa) de modo a conhecer se o item em questão é seguro e confiável para continuar a operar em condições específicas durante um período de tempo determinado, tendo em consideração as condições verificadas no ato de inspeção e especificações de projeto, segundo os itens de verificação de segurança estabelecidos na norma EN 1990:2002/A1:2005/AC:2010 e com base na norma API 579-1/ASME FFS-1: 2007. No âmbito do presente trabalho foram realizadas as seguintes tarefas: - Identificar e analisar os mecanismos de degradação com base na norma API RP 571: 2011, face às condições processuais e geométricas que o equipamento em análise está sujeito de modo a perceber a evolução da degradação estrutural e quais as implicações na sua longevidade. - Avaliar e propor soluções de reparação e ou alterações processuais e ou geométricas do equipamento em análise de modo a permitir a continuidade em funcionamento sem afetar as condições de segurança e por conseguinte minimizar ou evitar o elevado custo económico associado a um novo equipamento e tempo de paragem processual. - Assumir limites estruturais face às condições processuais e ações externas ou adjacentes. - Garantir a segurança e qualidade da vida humana ou meio que o rodeia, do equipamento, das instalações, das infraestruturas envolventes e evitar o colapso económico, quer por motivos processuais, quer indeminizações ou agravamento do prémio do seguro. Verificou-se que os resultados serão a base para as alterações inerentes, tais como reforço estrutural, alteração da geometria do defletor, ajuste no tensionamento dos cabos e controlo da espessura mínima, de modo a alargar o período de vida útil da flare com segurança.

Juvenile Parkinson disease caused by parkin mutations: large deletions and pathogenic mechanisms

Dissertação para obtenção do Grau de Mestre em Genética Molecular e Biomedicina

Immune response and tissue cytoprotection: two sides of the same coin in immunopathology

Dissertation presented to obtain the Ph.D degree in Biochemistry

Failure of nitric oxide production by macrophages and decrease in CD4+ T cells in oral paracoccidioidomycosis: possible mechanisms that permit local fungal multiplication

Paracoccidioidomycosis is a chronic granulomatous disease that induces a specific inflammatory and immune response. The participation of nitric oxide (NO), a product of the inducible nitric oxide synthase enzyme (iNOS), as an important fungicidal molecule against Paracoccidioides brasiliensis has been demonstrated. In order to further characterize the Oral Paracoccidioidomycosis (OP), we undertook an immunohistochemical study of iNOS+, CD45RO+, CD3+, CD8+, CD20+, CD68+ cells and mast cells. The samples were distributed in groups according to the number of viable fungi per mm². Our results showed weak immunolabeling for iNOS in the multinucleated giant cells (MNGC) and in most of the mononuclear (MN) cells, and the proportion of iNOS+ MN/MNGC cells in the OP were comparable to Control (clinically healthy oral tissues). Additionally, our analysis revealed a similarity in the number of CD4+ cells between the Control and the OP groups with higher numbers of fungi. These findings suggest that a low expression of iNOS and a decrease in the CD4+ T cells in OP may represent possible mechanisms that permit the local fungal multiplication and maintenance of active oral lesions.

Damage assessment of fibre reinforced laminates

The use of solid wastes and natural fibres to the production of innovative composites is now a matter of environmental need. A set of hybrid composites constituted of waste rubber particles and sugarcane bagasse fibres into a thermoset composite material are drilled to determine the effect of rubber particle addition and size, sugarcane fibre addition and length and fibre chemical treatment on damage extension and related mechanical properties. Damage extension is determined by enhanced radiography for further damage measurement – diameter and areas – and correlated with mechanical test results — bearing test. The results demonstrated significant effect of the rubber and fibre additions on mechanical properties of the composites.

Neural Mechanisms of Exercise: Anti-Depression, Neurogenesis, and Serotonin Signaling

Depression is associated with decreased serotonin metabolism and functioning in the central nervous system, evidenced by both animal models of depression and clinical patient studies. Depression is also accompanied by decreased hippocampal neurogenesis in diverse animal models. Neurogenesis is mainly defined in dentate gyrus of hippocampus as well as subventricular zone. Moreover, hypothalamus, amygdala, olfactory tubercle, and piriform cortex are reported with evidences of adult neurogenesis. Physical exercise is found to modulate adult neurogenesis significantly, and results in mood improvement. The cellular mechanism such as adult neurogenesis upregulation was considered as one major mood regulator following exercise. The recent advances in molecular mechanisms underlying exercise-regulated neurogenesis have widen our understanding in brain plasticity in physiological and pathological conditions, and therefore better management of different psychiatric disorders.

Neural Mechanisms of Exercise: Effects on Gut Miccrobiota and Depression

Microbiota is a set of microorganisms resident in gut ecosystem that reacts to psychological stressful stimuli, and is involved in depressed or anxious status in both animals and human being. Interestingly, a series of studies have shown the effects of physical exercise on gut microbiota dynamics, suggesting that gut microbiota regulation might act as one mediator for the effects of exercise on the brain. Recent studies found that gut microbiota dynamics are also regulated by metabolism changes, such as through physical exercise or diet change. Interestingly, physical exercise modulates different population of gut bacteria in compared to food restriction or rich diet, and alleviates gut syndromes to toxin intake. Gut microbiota could as well contribute to the beneficial effects of exercise on cognition and emotion, either directly through serotonin signaling or indirectly by modulating metabolism and exercise performance.