Em concentrações elevadas no plasma ou no tecido renal a Angiotensina II (Ang II) induz, alterações na hemodinâmica renal, injúria glomerular, aumento da síntese de componentes da matriz extracelular glomerular, estresse oxidativo e apoptose de células glomerulares, incluindo os podócitos. Os podócitos possuem um sistema reninaangiotensina (SRA) próprio e expressam os receptores AT1 e AT2 para o peptídeo, além do trocador Na+/H+ isoforma 1 (NHE1). O NHE1 está envolvido com a resistência e indução de apoptose, controle do volume celular e manutenção do fenótipo celular. Assim, o objetivo deste estudo foi investigar em podócitos, o papel da Ang II na indução de apoptose, e os eventos intracelulares associados à atividade do NHE1 nesta condição. Nossos resultados indicam que o tratamento com Ang II em alta concentração por 24 horas promove apoptose em podócitos. Nesta condição o NHE1, promove ativação da via de sinalização intracelular p38 MAPK e aumenta a atividade do NHE1 levando a alcalose, ativação da Bax e apoptose nos podócitos. / It has been observed that high plasma, or kidney tissue concentrations of angiotensin II (Ang II) leads to changes in renal hemodynamics, severe glomerular injury, increased synthesis of glomerular extracellular matrix components, oxidative stress and apoptosis in glomerular cells, including podocyte and mesangial cells. Podocytes a local renin-angiotensin system (RAS), expresses the AT1 and AT2 receptors for Ang II and the Na + / H + exchanger (NHE1). The NHE1 is involved with resistance and induction of apoptosis, cell volume control and maintenance of cell phenotype. Thus, the goal of this study was to investigate in podocytes the role of Ang II in the induction of apoptosis, and intracellular events linked to the NHE1 activity in this condition. Our results indicate that the treatment with Ang II, in a high dose, for 24 hours induces apoptosis in podocytes, and promotes oxidative stress. However, the activation of NADPH oxidase subunits Nox4 and p22 (phox) and pro- apoptotic pprotein Bax, came before the late apoptosis observed in 24 hours of treatment with Ang II. Under physiological conditions, the NHE1 activity contributes to cell survival by preventing cytosolic acidification. Moreover, Ang II via the AT1 receptor, activates intracellular signaling pathway p38 MAPK and increases the NHE1 activiy leading to alkalosis, Bax activation and apoptosis in podocytes.

The mammalian Na+/H+ exchanger isoform 1 (NHE1) is a ubiquitously expressed membrane protein that regulates intracellular pH. In the myocardium, NHE1 has been implicated in ischemia/reperfusion (I/R) and cardiac hypertrophy (CH). Hormonal, autocrine and paracrine stimuli, acidosis, cardiotoxic metabolites released during I/R and CH increases NHE1 protein expression and activity. The involvement of NHE1 in CH and I/R has been further supported with the use of NHE1 inhibitors, which have been beneficial in the prevention/regression of several models of CH and I/R injury. Despite the fact that elevation of NHE1 expression and activity have been demonstrated in several models of heart disease, it was unclear whether elevation of NHE1 protein expression was sufficient to induce a specific cardiac pathology, or whether activation of the protein was required. To understand the direct role of NHE1 in CH and I/R, an in vivo and in vitro gain-of-function model, expressing varying levels and activities of NHE1 were examined. In vivo, our N-line mice expressed wild type NHE1 and our K-line mice expressed constitutively active NHE1. In vitro, neonatal rat ventricular cardiomyocytes were infected with the IRM adenovirus containing wild type NHE1 or the K-IRM adenovirus containing active NHE1. We demonstrated that expression of constitutively active NHE1 promotes CH to a much greater degree than expression of wild type NHE1 alone, both in vivo and in vitro. This NHE1-dependent hypertrophic response occurred independent of signaling pathways involved in CH including, mitogen activated protein kinases, p90 ribosomal S6 kinase, calcineurin and glycogen synthase kinase. The NHE1-dependent hypertrophic effect also occurred independent of gender. In addition, the expression of active NHE1 increased the susceptibility of intact mice to neurohormonal stimulation and progressed the hypertrophic response. When these hearts expressing active NHE1 were subjected to I/R using the ex vivo working heart perfusion model, fatty acid (FA) oxidation and glycolysis rates increased, thus generating greater ATP production rates. This was associated with cardioprotective effects in the myocardium, as well as a more energetically efficient myocardium. Expression of the endoplasmic reticulum (ER) stress response proteins, calreticulin and PDI were also shown to be increased relative to controls, and may contribute to the cardioprotection observed. We demonstrate that active NHE1 induces cardioprotection and alters cardiac metabolism in working hearts subjected to I/R. Overall, our results suggest that expression of active NHE1 has a double edged sword effect, on one side it induces CH while on the other side, it protects the heart against I/R injury.

Massively parallel whole transcriptome sequencing and its ability to generate full transcriptome data at the single transcript level provides a powerful tool with multiple interrelated applications, including transcriptome reconstruction, gene/isoform expression estimation, also known as transcriptome quantification. As a result, whole transcriptome sequencing has become the technology of choice for performing transcriptome analysis, rapidly replacing array-based technologies. The most commonly used transcriptome sequencing protocol, referred to as RNA-Seq, generates short (single or paired) sequencing tags from the ends of randomly generated cDNA fragments. RNA-Seq protocol reduces the sequencing cost and significantly increases data throughput, but is computationally challenging to reconstruct full-length transcripts and accurately estimate their abundances across all cell types. We focus on two main problems in transcriptome data analysis, namely, transcriptome reconstruction and quantification. Transcriptome reconstruction, also referred to as novel isoform discovery, is the problem of reconstructing the transcript sequences from the sequencing data. Reconstruction can be done de novo or it can be assisted by existing genome and transcriptome annotations. Transcriptome quantification refers to the problem of estimating the expression level of each transcript. We present a genome-guided and annotation-guided transcriptome reconstruction methods as well as methods for transcript and gene expression level estimation. Empirical results on both synthetic and real RNA-seq datasets show that the proposed methods improve transcriptome quantification and reconstruction accuracy compared to previous methods.

No description available.

Reduced neo-adipogenesis and dysfunctional lipid-overloaded adipocytes are hallmarks of hypertrophic obesity linked to insulin resistance. Identifying molecular features of hypertrophic adipocytes requires appropriate in vitro models. We describe the generation of a model of human hypertrophic-like adipocytes directly comparable to normal adipose cells and the pathologic evolution toward hypertrophic state. We generate in vitro hypertrophic cells from mature adipocytes, differentiated from human mesenchymal stem cells. Combining optical, confocal, and transmission electron microscopy with mRNA/protein quantification, we characterize this cellular model, confirming specific alterations also in subcutaneous adipose tissue. Specifically, we report the generation and morphological/molecular characterization of human normal and hypertrophic-like adipocytes. The latter displays altered morphology and unbalance between canonical and dominant negative (PPARGΔ5) transcripts of PPARG, paralleled by reduced expression of PPARγ targets, including GLUT4. Furthermore, the unbalance of PPARγ isoforms associates with GLUT4 down-regulation in subcutaneous adipose tissue of individuals with overweight/obesity or impaired glucose tolerance/type 2 diabetes, but not with normal weight or glucose tolerance. In conclusion, the hypertrophic-like cells described herein are an innovative tool for studying molecular dysfunctions in hypertrophic obesity and the unbalance between PPARγ isoforms associates with down-regulation of GLUT4 and other PPARγ targets, representing a new hallmark of hypertrophic adipocytes.

No description available.

Made available in DSpace on 2017-07-20T12:40:20Z (GMT). No. of bitstreams: 1 Agnes Thiane Machado.pdf: 7176772 bytes, checksum: 01a4049f5c4aed0935803a0cf3a6468d (MD5) Previous issue date: 2017-03-22 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Study of protein three-dimensional structures allow us to investigate the relations between amino acid sequence, structure and function, what is important chiefly for proteins from pathogenic organisms or ones that belong to the same genus of these, such that they can be used as a structural model. In this context, this work aims at the structural characterization of the enzymes alanine racemase long isoform from Trypanosoma cruzi and glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi. The long isoform of alanine racemase catalyzes the conversion between L and D-alanine which, in turn, is part of one of the metabolic pathways in Trypanosoma cruzi, the etiologic agent of Chagas disease. The heterologous expression of this enzyme in Escherichia coli BL21 (DE3) GroEL was analyzed by SDS-PAGE, which revealed that the protein is in higher proportion in the insoluble fraction, thus it was necessary to establish a recovery protocol followed by an in vitro refolding. Data from enzymatic assays and circular dichroism revealed the success of the recovery/refolding protocol, which may in the future contribute to the search for specific inhibitors. Glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi catalyzes the sixth step of the organism’s glycolytic pathway. NgGAPDH enzyme was expressed in E. coli (DE3) using the pET-15b vector, and then purified by tree chromatographic steps, two of nickel affinity and one of size exclusion. The enzymatic characterization was investigated with the enzyme without the his-tag; NgGAPDH presented higher activity at pH 8.0, 25 °C and 10 mM of arsenate, and positive cooperativity for substrates G3P and NAD+. His-tag depleted NgGAPDH crystals appeared in 3 days after drop settings, the best crystal diffracted to 1.94 A resolution and belongs to space group P21 with cell parameters a = 83.74 A, b = 94.55 A, c = 90.93 A, = 99.96 °. The final refined structure presents R = 0.1652 and Rfree = 0.2029. The catalytic domain formed by residues 134 to 313 is highly conserved, as expected, with the exception of Asn145, present only in NgGAPDH, while the other GAPDHs present either Ser or Thr on the corresponding position. Molecular dynamics analysis revealed that Asn145 has correlated motion with residues Ala123, Thr125 and Pro126 that belong to what was called "bonded loop". It should be emphasized that this is the first GAPDH from the phylum Percolozoa that has its three dimensional structure determined and kinetic parameters established, such that we expect to have contributed to the understanding of the evolution of this class of proteins. / O estudo da estrutura tridimensional de proteínas nos permite investigar as relações entre sequência de aminoácidos, estrutura e função, o que é importante principalmente para proteínas de organismos patogênicos ou mesmo pertencente ao gênero destes, que podem ser utilizadas como modelo estrutural. Neste contexto, o presente trabalho visa caracterizar estruturalmente as enzimas alanina racemase isoforma longa de Trypanosoma cruzi e gliceraldeído-3-fosfato desidrogenase de Naegleria gruberi. A alanina racemase isoforma longa catalisa a conversão entre L e D-alanina em uma das vias metabólicas do T. cruzi, que é o agente etiológico da doença de Chagas. A análise por SDS-PAGE de amostras da expressão heteróloga dessa enzima em Escherichia coli BL21(DE3) GroEL revelou que a proteína está em maior proporção na fração insolúvel, por isso, foi necessário estabelecer um protocolo de recuperação seguido de um reenovelamento in vitro. Dados de ensaios enzimáticos e dicroísmo circular revelaram o sucesso do protocolo de recuperação/reenovelamento, o que poderá no futuro contribuir para a busca de inibidores específicos. A gliceraldeído-3-fosfato desidrogenase de Naegleria gruberi catalisa a sexta etapa da via glicolítica do organismo. A enzima NgGAPDH foi expressa em E. coli (DE3) usando-se o vetor pET-15b e então purificada em três passos de cromatografia, dois por afinidade a níquel e um por exclusão por tamanho. A caracterização enzimática foi realizada com a enzima sem a ―his-tag‖; a NgGAPDH apresentou maior atividade em pH 8,0, 25 °C e 10 mM de arsenato, e cooperatividade positiva frente aos substratos G3P e NAD+. Cristais de NgGAPDH sem a ―his-tag‖ apareceram em 3 dias após montagem das gotas e o melhor difratou a 1,94 A de resolução, pertencendo ao grupo espacial P21 com parâmetros de cela a = 83,74 Å, b = 94,55 A, c = 90,93 A e = 99,96 °. A estrutura final refinada apresenta R = 0,1652 e Rfree = 0,2029. O domínio catalítico formado pelos resíduos 134 a 313 é altamente conservado, como esperado, com exceção da Asn145, presente somente em NgGAPDH, enquanto que as demais GAPDHs apresentam Ser ou Thr na posição correspondente. Análises por dinâmica molecular revelaram que a Asn145 tem correlação de movimento com os resíduos Ala123, Thr125 e Pro126, pertencentes ao que se chamou de ―bonded loop‖. Ressalte-se que esta é a primeira GAPDH do filo Percolozoa que tem sua estrutura tridimensional determinada e parâmetros cinéticos estabelecidos, tal que se espera contribuir para o entendimento da evolução dessa classe de proteínas.

Technological advancements in mass spectrometry allowing quantification of almost complete proteomes make proteomics a key platform for generating unique functional molecular data. Furthermore, the integrative analysis of genomic and proteomic data, termed proteogenomics, has emerged as a new field revealing insights into gene expression regulation, cell signalling, and disease processes. However, the lack of software tools for high-throughput integration and unbiased modification and variant detection hinder efforts for large-scale proteogenomics studies. The main objectives of this work are to address these issues by developing and applying new software tools and data analysis methods. Firstly, I address mapping of peptide sequences to reference genomes. I introduce a novel tool for high-throughput mapping and highlight its unique features facilitating quantitative and post-translational modification mapping alongside accounting for amino acid substitutions. The performance is benchmarked. Furthermore, I offer an additional tool that permits generation of web accessible hubs of genome wide mappings. To enable unbiased identification of post-translational modifications and amino acid substitutions for high resolution mass spectrometry data, I present algorithmic updates the mass tolerant blind spectrum comparison tool ’MS SMiV’. I demonstrate the applicability of the changes by benchmarking against a published mass tolerant database search of a high resolution tandem mass spectrometry dataset. I then present the application of ‘MS SMiV’ on a panel of 50 colorectal cancer cell lines. I show that the adaption of ‘MS SMiV’ outperforms traditional sequence database based identification of single amino acid variants. Furthermore, I highlight the utility of mass tolerant spectrum matching in combination with isobaric labelled quantitative proteomics in distinguishing between post-translational modifications and amino acid variants of similar mass. In the last part of this work I integrate both tools with a high-throughput proteogenomic identification pipeline and apply it to a pilot study of chondrocytes derived from 12 osteoarthritic individuals. I show the value of this approach in identifying variation between individuals and molecular levels and highlight them with individual examples. I show that multi-plexed proteogenomics can be used to infer genotypes of individuals.

Prion diseases are fatal neurodegenerative diseases that affect mammals, including humans, which are characterized by accumulation of pathologi- cal prion protein isoform (PrPTSE ) in the brain. The animals were commonly used for the prion disease research in the past but in recent years, the tissue cultures are being used as well. Tissue cultures have many advantages com- pared with animals. E.g. the possibility of a detailed study of the biochemical processes associated with prion diseases, and rapid and sensitive PrPTSE de- tecting method. However no reliable in vitro model was developed for human prion diseases so far. We focused on monitoring of transmission and propagation efficiency of different prion strains and on the influence of cultivation conditions on the transfer of the neuronal cell line CAD5, which is highly sensitive to prion infection. We confirmed the sensitivity of CAD5 cells to mouse-adapted scra- pie prion strains and we presented new facts about their ability to propagate mouse adapted prions of human strains and bovine spongiform encepha- lopathy. We have used CAD5 cell sensitivity to be infected with different prion strains in other parts of this work. In the second part, we focused on the cell sensitivity to prion infection and propagation of prion strains under different culture...

L’asthme équin est une condition inflammatoire fréquente affectant les voies respiratoires inférieures. Cette maladie est caractérisée par une bronchoconstriction, une hyperréactivité bronchique, ainsi que des changements des différentes couches tissulaires des voies respiratoires que l’on regroupe sous le terme de remodelage pulmonaire. Le remodelage du muscle lisse bronchique dans l’asthme comprend une hyperplasie, une hypertrophie, ainsi qu’une altération des propriétés contractiles des myocytes. Bien que ces changements aient été décrits dans la forme sévère de l’asthme équin, la présence de telles altérations chez les chevaux atteints des formes légères à modérées de l’asthme demeure incertaine. L’objectif de notre étude est donc de déterminer si le muscle lisse bronchique présente un remodelage chez les chevaux asthmatiques légers à modérés. Des biopsies endobronchiques provenant de 18 chevaux asthmatiques et de 7 chevaux contrôles ont été étudiées. Le diagnostic était basé sur les signes cliniques et confirmé par cytologie du lavage bronchoalvéolaire. La prolifération des cellules du muscle lisse bronchique était évaluée par l’expression du proliferating cell nuclear antigen marqué par immunohistochimie, et l’expression génique de l’isoforme rapide de la myosine, une protéine hypercontractile, a été mesurée par RT-qPCR. Cette étude a permis de mettre en évidence une surexpression de l’isoforme rapide de la myosine chez les chevaux asthmatiques légers à modérés. Malgré l’absence de différence dans le taux de prolifération cellulaire du muscle lisse bronchique entre les groupes, le pourcentage de myocytes en prolifération était corrélé à l’inflammation pulmonaire neutrophilique ainsi qu’à l’expression de l’isoforme rapide de la myosine chez les chevaux asthmatiques. Cette première étude évaluant le remodelage du muscle lisse bronchique chez les chevaux asthmatiques légers à modérés a démontré une altération fonctionnelle du muscle lisse bronchique dans les formes légères de l’asthme équin, une possible influence de la neutrophilie pulmonaire sur la prolifération du muscle lisse, ainsi qu’une association entre les phénotypes prolifératifs et contractiles. Les altérations identifiées pourraient servir de biomarqueurs potentiels dans l’évolution de la maladie et de la réponse aux traitements. / Equine asthma is a common inflammatory condition affecting the lower airways. This disease is characterised by bronchoconstriction, airway hyperreactivity, and changes in the different tissue layers of the airways, which are referred to as airway remodelling. Remodelling of the smooth muscle in asthma includes hyperplasia, hypertrophy, and altered contractile properties of the myocytes. Although these changes have been described in severe equine asthma, their presence in horses with milder forms of asthma remains unclear. The aim of our study was therefore to determine whether airway smooth muscle remodelling occurs in horses with mild to moderate asthma. Endobronchial biopsies from 18 asthmatic horses and 7 control horses were studied. The diagnosis was based on clinical signs and confirmed by bronchoalveolar lavage cytology results. Airway smooth muscle cell proliferation was assessed by the expression of immunohistochemically labelled proliferating cell nuclear antigen, and the gene expression of the fast contracting myosin isoform, a hypercontractile protein, was measured by RT-qPCR. This study showed overexpression of the fast contracting myosin isoform in horses with mild to moderate asthma. Although there was no difference in the proliferation rate of airway smooth muscle myocyte between groups, it was correlated with neutrophilic lung inflammation as well as with the expression of the fast myosin isoform in asthmatic horses. This first study evaluating airway smooth muscle remodelling in mild to moderate asthmatic horses has demonstrated a functional alteration of airway smooth muscle in mild equine asthma, as well as a possible influence of pulmonary neutrophilia on smooth muscle proliferation, and an association between proliferative and contractile phenotypes. The identified alterations could eventually serve as biomarkers in the evolution of the disease and the response to treatments.