Submitted by Jéssica Moraes Malheiros (jessicamalheiros@yahoo.com.br) on 2018-05-03T18:53:41Z No. of bitstreams: 1 TESE MALHEIROS, J. M..pdf: 1363679 bytes, checksum: 33291bc89815d196826e037eeda5b237 (MD5) / Approved for entry into archive by Alexandra Maria Donadon Lusser Segali null (alexmar@fcav.unesp.br) on 2018-05-04T18:11:25Z (GMT) No. of bitstreams: 1 malheiros_jm_dr_jabo.pdf: 1400936 bytes, checksum: bf9a223495b522a13300edf9c4026a2e (MD5) / Made available in DSpace on 2018-05-04T18:11:25Z (GMT). No. of bitstreams: 1 malheiros_jm_dr_jabo.pdf: 1400936 bytes, checksum: bf9a223495b522a13300edf9c4026a2e (MD5) Previous issue date: 2018-03-02 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O presente trabalho teve como objetivo avaliar a associação da expressão gênica e proteômica com a maciez da carne de bovinos da raça Nelore. A partir de uma população de 90 animais foram selecionados três grupos experimentais por meio da análise de força de cisalhamento (FC) e índice de fragmentação miofibrilar (MFI), sendo: carne moderadamente macia, carne moderadamente dura e carne muito dura. A expressão dos genes foi avaliada por meio da análise de PCR em tempo real e a análise proteômica foi realizada com base na separação de proteínas por meio da eletroforese bidimensional (2D-PAGE) e caracterizção por espectrometria de massas com ionização eletrospray (ESI-MS/MS). A expressão da isoforma da calpastatina (CAST2) mostrou-se up regulated (P<0,05) nos grupos de carne moderadamente dura e muito dura. Os genes HSP90AA1, DNAJA1 e HSPB1, os quais representam as proteínas de choque térmico Hsp90, Hsp40 e Hsp27, respectivamente, mostraram expressão down regulated (P<0,05) no grupo de carne moderadamente macia em relação ao grupo de carne muito dura. Na análise proteômica, a expressão do spot protéico das enzimas metabólicas TPI e PGM1, proteína estrutural PFN1 e aminiopeptidase LAP3 se mostraram up regulated (P<0,05) no grupo de carne moderadamente macia, enquanto que a expressão das proteínas estruturais (ACTA1, ACTB, ACTG1 e MLC1), estresse oxidativo (PRDX6, PRDX2, PRDX1 and PARK7), proteínas de choque térmico (HSP90AA1, HSP90AB1, HSPA1A, HSPA1B, HSPA1L, HSPD1 e HSPB1), e co-chaperonas e regulação celular (CD37, STIP1 e ARHGDIA) se mostraram down regulated (P>0,05) no mesmo grupo experimental. Estes resultados fornecem uma visão importante de novos possíveis marcadores biológicos atuantes no processo de amaciamento da carne, o que pode colaborar para melhor entender e gerar novas estratégias de seleção nos programas de melhoramento genético de bovinos Nelore. / The objective of this study was to evaluate the association of gene expression and proteomics with meat tenderness in Nellore cattle. From population of 90 animals three experimental groups were selected by shear force (SF) and/or myofibrillar fragmentation index (MFI): moderately tender meat, moderately tough meat and very tough meat. Gene expression was evaluated by real-time PCR and proteomics analysis was performed based on protein separation by two-dimensional gel electrophoresis (2D-PAGE) and characterisation by eletrospray ionisation mass spectrometry (ESI-MS/MS). Expression of the calpastatin isoform (CAST2) was up-regulated (P<0.05) in the moderately tough and very tough meat groups. Expression of the HSP90AA1, DNAJA1 and HSPB1 genes, wich represent the heat shock proteins Hsp90, Hsp40 and Hsp27, respectively, were down-regulated (P<0.05) in the moderately tender meat in relation to the very tough group. In the proteomics analysis, the expression of the protein spots of metabolism TPI1 and PGM1, structural protein PFN1, and aminopeptidase LAP3 were up regulated (P<0.05) in the moderately tender meat, while the expression of structural proteins (ACTA1, ACTB, ACTG1 and MLC1), oxidative stress (PRDX6, PRDX2, PRDX1 and PARK7), heat shock protein (HSP90AA1, HSP90AB1, HSPA1A, HSPA1B, HSPA1L, HSPD1 and HSPB1) and co-chaperones and cellular regulatory (CD37, STIP1 and ARHGDIA) were down regulated (P>0.05) in the same experimental group. The present results suggest an important view of possible new biological markers in the meat tenderization process, wich permit to unsderstand and generate new strategies for selection in Nellore cattle breeding programs. / FAPESP: 15/13021-1

The O’Brien lab has demonstrated that Heat shock protein 27 (HSP27)shows attenuated expression in human coronary arteries as the degree of atherosclerosis progresses. Moreover, over-expression of HSP27 reduces atherogenesis in mice. The precise mechanism(s) for HSP27-mediated "atheroprotection" are incompletely understood. Nuclear Factor-kappaB (NF-κB) is a key signaling modulator in atherogenesis. Hence, this project sought to determine if recombinant HSP27 (rHSP27) alters NF-κB signaling to affect atheroprotection. Treatment of THP1 macrophages with rHSP27 resulted in degradation of IκBα, coincided with nuclear translocation of the p65 subunit and produced transcriptional evidence of activation of NF-κB signaling. When the transcriptional profile of THP1 macrophages treated with rHSP27 was analyzed using NF-κB-pathway-specific qRT-PCR arrays, among the regulated genes, IL-10 and GM-CSF mRNA levels were markedly increased, as were parallel translational effects observed. These data provide new mechanistic insights into the atheroprotective effects of HSP27.

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Glutamate carboxypeptidase II (GCPII) usually called prostate specific membrane antigen (PSMA) is membrane bound metallopeptidase expressed mainly in prostate carcinoma (PCa). Agents targeting GCPII suitable for both imaging and treatment of PCa are in development and they show promising results in advanced clinical trials. Some studies showed that GCPII may serve also as PCa blood serum marker, but this has not been validated due to the lack of methods suitable for accurate detection of GCPII in human blood. Moreover, GCPII is also expressed in brain, where it cleaves inhibitory N-acetyl-α-L- aspartyl-L-glutamate (NAAG) to release excitatory L-glutamate and GCPII inhibition has been shown to be neuroprotective in animal models of several neuropathies. Tight binding inhibitors of GCPII have been identified by rational design, but all have poor bioavailability and thus cannot be used in clinics. Identifying new scaffolds by 'brute force' screening methods is thus essential; however, no such method for GCPII has been developed so far. Glutamate carboxypeptidase III (GCPIII) is also expressed in brain and cleaves NAAG. It is thus an important protein for understanding of GCPII function as well as GCPII targeting in medicine. Here, we focused on development of novel methods for quantification of both...

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No description available.

Aspergillus fumigatus is an opportunistic fungal pathogen responsible for invasive aspergillosis in immunocompromised individuals. Current detection and treatment strategies for invasive aspergillosis, as well as other invasive fungal infections, are poor. Iron has been shown to be essential for Aspergillus fumigatus virulence. Furthermore, mechanisms in the iron regulatory network are believed to be potential drug targets since iron management in fungi is vastly different from that in mammals and other eukaryotes. Therefore a better understanding of iron homeostasis in Aspergillus fumigatus could help improve drug therapies for invasive aspergillosis. In this research a discrete model of iron uptake, storage and utilization in Aspergillus fumigatus with particular focus on siderophore-mediated iron acquisition is constructed. The model predicts oscillations in gene expression as the fungus adapts to a switch from an iron depleted to an iron replete environment. The model is validated via in vitro experiments. / Master of Science

Mycoplasma hominis est une bactérie opportuniste qui peut être responsable d’infections du tractus urogénital, d’infections néonatales ou d’infections disséminées notamment chez les patients immunodéprimés. La membrane des mycoplasmes constitue l’interface d’interaction directe avec le milieu extérieur en raison de l’absence de paroi. Cette membrane contient de nombreuses lipoprotéines qui ont le pouvoir d’activer des cellules dendritiques humaines (hDCs), d’induire la production de cytokines et de polariser le système immunitaire adaptatif. Nous avons étudié l’interaction de M. hominis PG21 avec les hDCs en nous penchant d’une part sur la fraction du mycoplasme qui active les hDCs et d’autre part sur la réponse immunitaire innée des hDCs. Apres avoir déterminé les lipoprotéines contenues dans un extrait TX-114 de M. hominis PG21, nous avons enrichi en lipoprotéines bioactives une fraction de vésicules membranaires du mycoplasme par une double extraction utilisant deux détergents non dénaturants, le Sarkosyl puis le Triton X-114. Apres séparation par SDS-PAGE, nous avons identifié vingt lipoprotéines qui pourraient entrainer la sécrétion d’IL-23 par les hDCs, notamment la lipoprotéine MHO_4720. Un lipopeptide synthétique correspondant à la fraction N-terminale de MHO_4720 est capable de stimuler les hDCs. En analysant les variations transcriptionnelles des gènes codant pour les 48 lipoprotéines de M. hominis PG21 par qRT-PCR, nous avons également déterminé que 21 lipoprotéines sont surexprimées après 4h ou 24h de contact entre le mycoplasme et les hDCs. Enfin, la réponse cellulaire a été évaluée par PCR array et ELISA. Nous avons observé l’activation d’inflammasome(s) par la mise en évidence de la production d’IL-1β dépendant de la caspase 5. / Mycoplasma hominis is involved in urogenital tract infections, neonatal infections or disseminated infections particularly in immunocompromised patients. Mycoplasmas have no cell wall and their membrane is the main interface mediating the interaction between the mycoplasma and its environment. Lipoproteins that are anchored to the extracellular side of the plasma membrane are known to induce the maturation of human dendritic cells (hDCs), to stimulate the pro-inflammatory cytokine production by hDCs and to polarize the adaptive immune system. We studied the interaction of M. hominis PG21 with hDCs in order to assess the lipoproteins that can induce the stimulation of hDCs, to determine the lipoproteins that are regulated upon interaction of the mycoplasma with the host cell and to evaluate the innate host cell response. Using a double extraction strategy with two non-denaturing detergents, Sarkosyl then Triton X-114, and separation by SDS-PAGE, we found that 20 lipoproteins may induce the secretion of IL-23 by the hDCs, especially the MHO_4720 lipoprotein. We showed that a synthetic lipopeptide corresponding to the N-terminus part of the MHO_4720 lipoprotein can stimulate the hDCs in a dose-dependent manner. Using qRT-PCR for the evaluation of the transcriptional regulation of the 48 lipoprotein-coding genes of M. hominis PG21, we also determined that 21 lipoproteins were upregulated upon 4h and 24h of contact of M. hominis with hDCs. Finally, the hDC innate immune response was evaluated by PCR array and ELISA. We observed a caspase 5-dependent production of IL- 1β corresponding to the activation of an inflammasome.

Der Embryonale Stammzelltest (EST) ist ein validierter In-vitro-Embryotoxizitätstest, der zur Untersuchung embryotoxischer Wirkungen von Chemikalien eingesetzt werden kann. Während des zehntägigen Differenzierungsassays differenzieren sich die pluripotenten murinen embryonalen Stammzellen (ES-Zellen) der Linie D3 in vitro in spontan kontrahierende Herzmuskelzellen. Dabei rekapitulieren sie Prozesse der frühen Embryogenese in vivo. Ein Zytotoxizitätsassay mit D3-Zellen und ausdifferenzierten, adulten 3T3-Maus-Fibroblasten dient der Ermittlung allgemeiner zytotoxischer Effekte und unterschiedlicher Sensitivitäten beider Zelllinien. Somit basiert der EST auf den beiden wichtigsten Mechanismen pränataler Toxizität, der Störung der Differenzierung und der Zytotoxizität. Ziel dieser Arbeit war es, mit Hilfe des EST das embryotoxische Potential der vier Chemikalien Trichostatin A (TSA), Methylazoxymethanolacetat (MAMac), Natriumdodecylsulfat (SDS) und Benzoesäure (BA) abzuschätzen. Dazu wurde mikroskopisch ermittelt, bei welcher Testsubstanzkonzentration in 50 % der während der In-vitro-Differenzierung gebildeten Embryonalkörperchen die Kardiomyozytendifferenzierung inhibiert wird (ID50). Außerdem wurde die halbmaximale Hemmkonzentration des Zellwachstums auf die beiden Zelllinien bestimmt (IC50D3 bzw. IC503T3). Als Erweiterung dieses konventionellen EST wurden mittels quantitativer Real Time-PCR an den Tagen 5, 7 und 10 der Differenzierung zusätzlich Genexpressionsanalysen etablierter herzmuskelspezifischer Markergene (Mesoderm Posterior 1, Tag 5; Myosin light chain 1, Tag 7 und 10) durchgeführt. Deren Expression korreliert in den ES-Zellen mit der embryonalen Herzdifferenzierung in vivo und kann zur Ermittlung der von der Prüfsubstanz hervorgerufenen halbmaximalen Hemmung der Genexpression in den Kardiomyozyten (IC50 Exp) herangezogen werden. Um letztlich embryotoxische Effekte in vivo auf Grundlage der ermittelten In-vitro-Daten abschätzen zu können, wurden die ermittelten Parameter mittels eines für den EST empirisch abgeleiteten mathematischen Prädiktionsmodells (PM) zur Klassifizierung der Testsubstanzen als nicht, schwach oder stark embryotoxisch herangezogen. Für jede der Substanzen waren die ermittelten Halbhemmkonzentrationen in den überwiegenden Fällen vergleichbar und führten unter Verwendung des PMs im konventionellen und im molekularen EST zu deren identischer Klassifizierung. TSA wurde als „stark embryotoxisch“ klassifiziert und beeinflusste insbesondere das Differenzierungspotential der ES-Zellen. Das als „schwach embryotoxisch“ klassifizierte SDS wirkte auf die D3-Zellen stärker differenzierungsinhibierend als zytotoxisch, hemmte jedoch das Wachstum der 3T3-Zellen bereits in deutlich niedrigeren Konzentrationen. MAMac und BA wurden als „nicht embryotoxisch“ klassifiziert. Bei ihnen stand die zytotoxische Wirkung deutlich im Vordergrund. Diese Prädiktionen stimmten mit In-vivo-Befunden überein, was von der Stabilität und der Brauchbarkeit der im konventionellen und molekularen EST ermittelten Parameter zeugte. Einzige Ausnahme war das als Entwicklungsneurotoxin in vivo bekannte MAMac. Da der EST auf mesodermaler Differenzierung basiert, können spezifische Effekte auf neuronale Entwicklungsprozesse offenbar nicht vollständig erfasst werden. Substanzkonzentrationen, die sich als differenzierungsinhibierend auf die morphologische Kardiomyozytendifferenzierung erwiesen haben, führten auch zu einer messbaren Repression der herzmuskelspezifischen Genexpression. Dabei erwies sich die IC50 Exp als ebenso sensitiv wie die konventionellen Parameter und als nutzbringende Ergänzung zu diesen, da sie bereits nach 5 bzw. 7 Tagen der In-vitro-Differenzierung eine mit dem mikroskopischen Parameter übereinstimmende Einschätzung des embryotoxischen Potentials der Chemikalien in vivo ermöglichte. Genexpressionsanalysen weiterer differenzierungsspezifischer Gene können zusätzlich zur Aufklärung zu Grunde liegender Mechanismen der Embryotoxizität von Testsubstanzen dienen. Somit kann der EST durch die Vorteile der Stammzelltechnologie und der Genexpressionsanalyse als neues prädiktives Screening-Instrument zur frühzeitigen Detektion embryotoxischer Substanzeffekte in der pharmazeutischen und chemischen Industrie genutzt werden. / The embryonic stem cell test (EST) represents a validated in vitro embryotoxicity test that can be utilised for investigations of embryotoxic effects of chemical substances. During the 10-day differentiation assay the pluripotent murine embryonic stem cells (ES cells) of the D3 line differentiate in vitro into spontaneously beating cardiac muscle cells that can be observed microscopically. Thereby, ES cells recapitulate processes of early embryogenesis in vivo. A cytotoxicity assay with D3 cells as well as differentiated, adult 3T3 mouse fibroblasts is used to determine general cytotoxic effects and to consider differences in the sensitivity of both cell lines. Hence the EST is based on the two most important mechanisms of prenatal toxicity, such as inhibition of differentiation and cytotoxicity. The aim of the presented work consisted in the evaluation of the embryotoxic potential of the four chemicals trichostatin A (TSA), methylazoxymethanolacetate (MAMac), sodium dodecyl sulfate (SDS) and benzoic acid (BA) by means of the EST. For this purpose the concentration of the test substance that causes an inhibition of cardiomyocyte differentiation in 50 % of the embryoid bodies which are formed during the in vitro differentiation (ID50-value) and the halfmaximal inhibiting concentration of cell proliferation of D3 and 3T3 cell lines (IC50D3 and IC503T3) were determined. As extension of this conventional EST, the effect of test substances was investigated at the molecular level by gene expression analyses of cardiac specific genes (Mesoderm Posterior 1, day 5; Myosin light chain 1, day 7 and 10). Their expression in ES cells correlates with the embryonic heart differentiation in vivo. Quantitative Real Time-PCR gene expression analysis was used to determine the halfmaximal inhibition of the cardiomyocyte gene expression (IC50 Exp) caused by the test compound. To predict embryotoxic effects in vivo from the determined in vitro data, these parameters were used for the classification of the test chemicals as non, weak or strong embryotoxic via a mathematical prediction model (PM). In the majority of cases comparable halfmaximal inhibiting concentrations were calculated in the conventional and molecular EST that resulted in the identical classification of the tested chemicals concerning their embryotoxic potential. TSA was estimated as “strongly embryotoxic” and affected particularly the differentiation potential of the ES cells. SDS was classified as “weakly embryotoxic” and acted by inhibiting the differentiation of D3 cells at concentrations lower than cytotoxic concentrations but already repressed the growth of the 3T3 cells in significantly lower ranges. As to MAMac and BA that were classified as “non-embryotoxic” the cytotoxic effects on both cell lines predominated. These predictions were consistent with in vivo findings that testifies the stability and the usefulness of the parameters used in the conventional and molecular EST. MAMac, which is known as a developmental neurotoxin in vivo, represented the single exception. Its misclassification as compared to in vivo data may originate from the limitations of the model system that is based on mesodermal differentiation. Thus, specific effects on neuronal developmental processes obviously cannot be detected completely. Gene expression analysis showed that test substance concentrations which were proved to be inhibiting on the morphological differentiation of cardiomyocytes caused a repression of cardiac-specific marker gene expression as well. Thereby, IC50 Exp-values proved to be just as sensitive as the conventional parameters and can provide valuable and supportive data. They allowed a prediction of the embryotoxic potential of the chemicals in vivo already at day 5 and day 7 of in vitro differentiation. Moreover, gene expression analysis of appropriate differentiation specific genes could be used to investigate mechanisms that are responsible for embryotoxic properties of the test compounds. Thus, the EST is considered to represent a new, predictive screening test especially in the pharmaceutical industry to detect the embryotoxic potential of chemical compounds early in the process of compound development.

Made available in DSpace on 2015-03-26T13:42:23Z (GMT). No. of bitstreams: 1 texto completo.pdf: 636309 bytes, checksum: ca1e7c510537c62820f228b759c5a23d (MD5) Previous issue date: 2011-07-25 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O suíno (Sus scrofa) é considerado um animal de grande importância para produção de carne, sendo seu potencial de crescimento muscular objeto de grande interesse e geralmente associado com características determinadas na fase pré-natal durante a miogênese. Para o estudo de genes responsáveis por estas características, as etiquetas de sequências expressas (Expressed Sequence Tags - EST) fornecem informações diretas sobre o transcriptoma e indiretas sobre a relação entre o genoma e diferentes fenótipos, proporcionando o conhecimento sobre genes diferencialmente expressos (GDE) bem como sequências genômicas transcritas para o controle da expressão gênica como, por exemplo, alguns RNAs não codificantes. Características de tecidos musculares em suínos podem ser influenciadas diretamente por genes, e estes sendo regulados como, por exemplo, através de miRNAs, em diferentes fases de desenvolvimento. O presente trabalho teve como objetivo a identificação e a anotação in sílico de GDE e sequências não codificantes, com enfoque aos miRNAs, de bibliotecas de cDNA construídas a partir do músculo esquelético semi-membranoso de três diferentes raças de suínos (Duroc, Large White e naturalizada brasileira Piau) bem como a análise dos níveis de expressão dos genes identificados e miRNAs em sete fases de desenvolvimento do Longissimus Dorsi (21, 40, 70 e 90 dias pré-natal e 107, 121 e 171 dias pós-natal) de animais de linha comercial. Foram identificados 34 GDE sendo 21 pertencentes a uma rede gênica musculo-específica. Destes, 13 genes tiveram seus perfis de expressão analisados com o uso do qRT-PCR durante os sete períodos citados, formando quatro grupos de expressão semelhantes, um com maior expressão na fase pós-natal e três na fase pré-natal. Nas análises das sequências não codificantes um resultado importante foi a identificação de dois novos miRNAs em suínos, os quais tiveram suas sequências maduras similares aos miRNAs hsa-miR-1207-5p e hsa-miR-665 foram classificadas como verdadeiras pelo programa MiPred e formaram estruturas secundárias. Destes, encontrou-se 289 e 214 genes regulados por eles respectivamente, dos quais quatro são músculo-específicos. Os novos miRNAs tiveram seus perfis de expressão analisados com o uso do PCR em tempo real durante os sete períodos citados juntamente com outros três já identificados em suínos. Seus níveis de expressão mostraram diferenças entre os estágios pré- e pós-natal. Estes estudos podem fornecer valiosas informações possibilitando um maior entendimento dos mecanismos moleculares envolvidos no desenvolvimento muscular. As análises de GDE em fases pré e pós-natal sugerem a presença de genes atuando especificamente em determinados estágios de desenvolvimento do músculo, contribuindo para melhor explicar suas funções. A identificação de dois novos miRNAs, somados a outros já identificados e postados nos bancos de dados em suínos, podem contribuir para um maior entendimento dos modos de regulação gênica, sendo de importância para os estudos de genética e melhoramento animal, permitindo o entendimento da fisiologia da deposição de músculo para produção de carne em suínos. / The pig (Sus scrofa) is considered an important animal for meat production. This interest revolves around the potential for muscle growth, which usually is associated with certain characteristics during prenatal myogenesis. To study the genes responsible for these characteristics, expressed sequence tags (EST) provide direct information about the transcriptome and indirectly on the relationship between the genome and different phenotypes, supplying knowledge about differentially expressed genes (DEG) as well as other transcribed genomic sequences for the control of gene expression, e.g., some non-coding RNAs. Characteristics of muscle tissue in pigs may have been directly influenced by genes, and those being regulated, for example, by miRNAs, in different stages of development. This study aimed to identify by in silico annotation, DEG and non-coding sequences, focusing on miRNAs, using cDNA libraries constructed from semi-membranous skeletal muscle of three different pig breeds (Duroc, Large White and naturalized Brazilian Piau ) as well as analysis of gene expression profiles of identified genes and miRNAs during seven stages of development (21, 40, 70 and 90 days prenatal and 107, 121 and 171 days postnatal) from commercial line animals Longissimus Dorsi muscle. Twenty-one identified genes out of 34 DEGs belongs to the muscle-specific path. From these, 13 genes had their expression profiles analyzed by qRT-PCR during the seven periods, forming four clusters of similar expression, with one having greater expression in the postnatal period and three in the prenatal. In the analysis of non-coding sequences, an important result was the identification of two new miRNAs in pigs, which had their sequences similar to mature miRNAs hsa-miR-1207- 5p and hsa-miR-665 which had their precursor sequences forming secondary structures and classified as real precursor sequence by MiPred program. From these, we found 289 genes and 214 respectively regulated by them, of which four are muscle-specific. The new miRNAs and other three which have been identified in previous studies in pigs had their expression levels analyzed by quantitative real time PCR during the mentioned seven periods. Their levels of expression differed between pre-and postnatal stages. These studies may provide valuable information allowing a better understanding of the molecular mechanisms involved in muscle development. Analyses of DEG in the pre-and postnatal periods suggest the presence of genes acting specifically on certain stages of muscle development, contributing to better explain their functions. The identification of two new miRNAs, together with other previously identified and posted on the databases in pigs, may contribute to a better understanding of gene regulation and is important for studies of genetics and animal breeding, allowing the understanding of the muscle deposition physiology to meat production in pigs.