Dissertations / Theses on the topic 'Cargo receptor'

Arenaviruses and hantaviruses are human pathogens that cause significant morbidity and mortality. The current lack of vaccines and treatment options for these viruses is a global concern. Despite producing only 4 proteins, these viruses are able to maintain a persistent and asymptomatic infection in wild rodents while being continuously shed into the environment. In humans, these viruses cause a spectrum of diseases ranging from aseptic meningitis to severe hemorrhagic fever syndromes. Little is known about how arenavirus and hantavirus proteins engage and interact with the human proteome during the complex process of viral biogenesis, or how the interactions with human proteins contribute to viral propagation as well as the onset and progression of disease. This dissertation provides a road map of the protein interactions formed between a prototypic envelope glycoprotein encoded by either an arenavirus or hantavirus, and the human proteome. The viral envelope glycoprotein (GP) decorates the surface of the virion. The primary function of the GP is to mediate attachment of the virus to specific cellular receptors, and after internalization of the virion, fuse the viral membrane with an internal endosomal membrane. In order to carry out these specific tasks, the viral GPs must first co-opt the extensive machinery found within the cellular secretory pathway to coordinate the proper glycosylation, folding, proteolytic maturation, and targeting of the GP during its biosynthesis. We identified a human protein with a conserved interaction amongst these two groups of viral GPs termed the Endoplasmic Reticulum (ER)-Golgi Intermediate Compartment Protein of 53 kiloDaltons (ERGIC-53). ERGIC-53 is an intracellular cargo receptor that normally cycles within the early secretory pathway of cells, where it is responsible for ferrying a small subset of cellular glycoproteins, most notably the coagulation factors FV and FVIII, from the ER to the Golgi apparatus. Herein we describe a novel role for ERGIC-53 in the propagation of not only arenaviruses, but also coronaviruses and filoviruses. Following infection with an arenavirus, ERGIC-53 leaves the early secretory pathway and becomes incorporated into the virus as it pinches off from the cell surface. Newly formed viruses lacking ERGIC-53 are no longer infectious due, in part, to a defect in their ability to attach to host cells. We suggest that ERGIC-53 represents a promising broad-spectrum antiviral target because of its association with the GPs from many families of pathogenic viruses, as well as its ability to exert control over their infectivity; and finally, because ERGIC-53 itself is not required for human health. The discovery of ERGIC-53 outside of its normal location inside of cells suggests that it may have additional unknown functions. Lastly, by revealing the importance of the cellular protein in controlling viral infectivity, we provide insight into the ongoing co-evolution of virus and host.

Metastasis Associated in Colon Cancer 1 (MACC1) ist ein prognostischer und prädiktiver Biomarker für Tumorprogression und Fernmetastasierung von Darmkrebs. Der exponentielle Anstieg der MACC1-verbundenen Publikationen seit dessen Entdeckung im Jahr 2009 verdeutlicht Mitwirkung von MACC1 am Krankheitsfortschritt vieler solider Tumore. Dies umfasst sich nicht nur die erhöhte Tumorinvasion und Metastasierung, sondern ebenso erhöhte Tumorangiogenese, dessen Stammzellfähigkeit und die Vermeidung von Apoptose. Obwohl unsere Forschungsarbeiten in den letzten Jahren neue Erkenntnisse über die Auswirkung von MACC1 in der Tumorprogression brachten, ist über dessen Proteinstruktur und der damit verbundenen Funktion in physiologischen Prozessen wenig bekannt. In dieser Arbeit wird zum ersten Mal die Rolle von MACC1 in der Clathrin-abhängigen Endozytose (CME) untersucht. Nach massenspektrometrischer Analyse des MACC1-Interaktoms wurde die Proteinbindung von MACC1 und den CME-verbundenen Faktoren CLTC, DNM2 und AP-2α, bzw. dem CME-Cargo TfR experimentell bestätigt. Davon ausgehend wurde der Endozytoseweg von TfR und MACC1-abhängige Änderungen in dessen Oberflächenverteilung, Internalisierung, Recycling und Proteinabbau mittels neu etablierter Methoden untersucht und ergab einen deutlichen Einfluss von MACC1 auf die Internalisierung und das Recycling von TfR. Daraufhin wurden durch Sequenzanalyse der MACC1-Proteinstruktur vorhergesagte N-terminale Interaktionsbereiche mit CME-Faktoren betrachtet, die eine Clathrin-Box sowie NPF- bzw. DPF-Motive umfassen. Deletionsvarianten von MACC1 wurden zunächst auf ihre Interaktionsfähigkeit mit CLTC, DNM2 und TfR getestet, deren subzelluläre Lokalisation bestimmt, sowie deren Einfluss auf den Endozytoseweg von TfR geprüft. Das erhöhte Recycling von TfR in Abhängigkeit von MACC1 wurde für EGFR als wichtigen Vertreter von krebsrelevanten Rezeptor-Tyrosinkinasen überprüft. Die Analyse des TfR-EGFR gekoppelten frühen Endozytosewegs ergab eine erhöhte Recyclingrate des Rezeptors in verschiedenen MACC1-überexprimierenden Zelllinien. Um den Einfluss der N-terminalen Interaktionsbereiche von MACC1 auf den Endozytoseweg von EGFR zu verstehen, wurden die MACC1-Deletionsvarianten nicht nur auf Änderungen im Verlauf der EGFR-Endozytose geprüft, sondern ebenfalls auf die Aktivierung des Rezeptors sowie nachgelagerter Signaltransduktoren wie PI3K/AKT und ERK1/2. Die Wichtigkeit der Interaktionsbereiche von MACC1 wurde durch eine Analyse der EGF-induzierten Zellproliferation bestätigt. Die Ergebnisse dieser Arbeit, die die Rolle von MACC1 in der Endozytose beschreiben, erweitern die Interventionsmöglichkeiten gegenüber der Fernmetastasierung solider Tumore und könnten helfen, das Überleben betroffener Patienten zu verlängern.
Metastasis Associated in Colon Cancer 1 (MACC1) is a newly discovered prognostic and predictive biomarker associated with tumor progression and metastasis development. Since our first report concerning MACC1 in 2009, MACC1-related research has been exponentially increasing. At present, MACC1 involvement in the progression of many cancer types has become increasingly clear. MACC1 does not only promote invasion and metastasis formation, but it also induces angiogenesis, stemness and prevents apoptosis. Although in the last years our research concerning MACC1 gained new insights into cancer progression, little is known about its structural role and functions in physiological processes. In this thesis, I will address for the first time the role of MACC1 during CME (clathrin-mediated endocytosis). Importantly, MACC1’s role in CME was first suggested by interactome analysis. Thus, MACC1’s CME interactors (CLTC, DNM2, AP2α and TfR), were first identified and validated. In addition, MACC1’s impact on TfR endocytic traffic was addressed by studying its effect on surface distribution, uptake, recycling and degradation of the receptor with pioneering and newly established methods. As a result of this research, MACC1 shows a clear impact on TfR internalization and recycling. Thus, the present work dissects the MACC1 protein structure containing predicted CME domains such as clathrin box, NPFs and DPF. By deleting these domains, first the impact on the binding between MACC1 and CLTC, DNM2 and TfR were analyzed. Also, we characterized the distribution of MACC1 in the cell depending on the presence of its CME domains, and then I addressed their specific impact during TfR endocytic traffic. After we elucidated the MACC1-dependent increase in TfR recycling, we compared its newly discovered function during EGFR endocytic traffic. By analyzing TfR -EGFR coupled early endocytic traffic during EGF-stimulated internalization in MACC1 overexpressing cell lines, we discovered that MACC1 promotes faster recycling of EGFR to PM, in two different cell lines. In order to understand the MACC1 CME domains impact on EGFR endocytic traffic, we dissected not only EGFR endocytic fate in MACC1 CME mutant cell lines but also the impact on EGFR trans-activation after EGF-stimulated internalization and downstream signaling, in particular, AKT and ERK1/2. To conclude with functional analysis, we also addressed MACC1 CME domains impact on cell proliferation revealing that CME domains integrity is important for efficient cell proliferation. The present work sheds new light on MACC1’s role during endocytosis, opening a possibility of intervention on metastasis development in CRC to improve the survival of patients.

Biomolecular simulations have been widely used in the study of protein-ligand interactions; comprehending the mechanisms involved in the prediction of binding affinities would have a significant repercussion in the pharmaceutical industry. Notwithstanding the intrinsic difficulty of sampling the phase space, hardware and methodological developments make computer simulations a promising candidate in the resolution of biophysically relevant problems. In this context, the objective of the thesis is the development of a protocol that permits studying protein-ligand interactions, in view to be applied in drug discovery pipelines. The author contributed to the rewriting PELE, our Monte Carlo sampling procedure, using good practices of software development. These involved testing, improving the readability, modularity, encapsulation, maintenance and version control, just to name a few. Importantly, the recoding resulted in a competitive cutting-edge software that is able to integrate new algorithms and platforms, such as new force fields or a graphical user interface, while being reliable and efficient. The rest of the thesis is built upon this development. At this point, we established a protocol of unbiased all-atom simulations using PELE, often combined with Markov (state) Models (MSM) to characterize the energy landscape exploration. In the thesis, we have shown that PELE is a suitable tool to map complex mechanisms in an accurate and efficient manner. For example, we successfully conducted studies of ligand migration in prolyl oligopeptidases and nuclear hormone receptors (NHRs). Using PELE, we could map the ligand migration and binding pathway in such complex systems in less than 48 hours. On the other hand, with this technique we often run batches of 100s of simulations to reduce the wall-clock time. MSM is a useful technique to join these independent simulations in a unique statistical model, as individual trajectories only need to characterize the energy landscape locally, and the global characterization can be extracted from the model. We successfully applied the combination of these two methodologies to quantify binding mechanisms and estimate the binding free energy in systems involving NHRs and tyorsinases. However, this technique represents a significant computational effort. To reduce the computational load, we developed a new methodology to overcome the sampling limitations caused by the ruggedness of the energy landscape. In particular, we used a procedure of iterative simulations with adaptive spawning points based on reinforcement learning ideas. This permits sampling binding mechanisms at a fraction of the cost, and represents a speedup of an order of magnitude in complex systems. Importantly, we show in a proof-of-concept that it can be used to estimate absolute binding free energies. Overall, we hope that the methodologies presented herein help streamline the drug design process.
Las simulaciones biomoleculares se han usado ampliamente en el estudio de interacciones proteína-ligando. Comprender los mecanismos involucrados en la predicción de afinidades de unión tiene una gran repercusión en la industria farmacéutica. A pesar de las dificultades intrínsecas en el muestreo del espacio de fases, mejoras de hardware y metodológicas hacen de las simulaciones por ordenador un candidato prometedor en la resolución de problemas biofísicos con alta relevancia. En este contexto, el objetivo de la tesis es el desarrollo de un protocolo que introduce un estudio más eficiente de las interacciones proteína-ligando, con vistas a diseminar PELE, un procedimiento de muestreo de Monte Carlo, en el diseño de fármacos. Nuestro principal foco ha sido sobrepasar las limitaciones de muestreo causadas por la rugosidad del paisaje de energías, aplicando nuestro protocolo para hacer analsis detallados a nivel atomístico en receptores nucleares de hormonas, receptores acoplados a proteínas G, tirosinasas y prolil oligopeptidasas, en colaboración con una compañía farmacéutica y de varios laboratorios experimentales. Con todo ello, esperamos que las metodologías presentadas en esta tesis ayuden a mejorar el diseño de fármacos.

A unique subcellular structure found in Leishmania donovani is the glycosome. This organelle compartmentalizes the enzymatic machinery required for multiple metabolic pathways, including glycolysis. Correct targeting of glycosomal enzymes is essential for parasite viability. Proteins targeted to the glycosome have either a C-terminal PTS1 or N-terminal PTS2 topogenic signal sequence, which is recognized by cytosolic receptors LdPEX5 or LPEX7, respectively. These cargo-loaded receptors interact with the peroxin protein LdPEX14, located on the cytosolic face of the glycosomal membrane, an event required for import of the cargo proteins into the glycosomal lumen. However, the complete glycosomal protein import pathway has not been fully elucidated. This work has been undertaken to better understand the protein-protein interactions involved in the trafficking of cargo proteins across the glycosomal membrane.The cytosolic fraction from L. donovani parasites was used to determine protein-protein interactions of receptors LdPEX5 and LPEX7. Size exclusion chromatography, isoelectric focusing, and affinity pull-downs showed that in the cytosol these receptors form large heterologous PTS1-LdPEX5-LPEX7-PTS2 complexes. Purified glycosomes were used to evaluate the effects of receptor-cargo complexes on glycosomal LdPEX14 conformation. Limited trypsin proteolysis showed that interaction of receptor-cargo complexes with native LdPEX14 protected this protein from digestion, whereas native LdPEX14 alone was highly sensitive to proteolysis. Protection was not dependent on membrane integrity as disruption of the lipid bilayer did not alter the effect of trypsin on these proteins. Native gel electrophoresis showed that native LdPEX14 forms large ~800 kDa complexes; however, when associated with receptor-cargo complexes the molecular weight of LdPEX14 complexes increased to ~1200 kDa. Alkaline carbonate extractions showed that native LdPEX14 acts like a peripheral glycosomal membrane protein; however loading with receptor-cargo complexes caused LdPEX14 to behave like an integral membrane protein. Furthermore, membrane insertion of LdPEX14 drove insertion of LdPEX5 and LPEX7 into the glycosomal membrane. Receptor-cargo complex association causes LdPEX14 to undergo a conformational change resulting in deeper membrane insertion and increase in complex size.Purification of recombinant LPEX7 was hampered by its association with bacterial chaperone protein GroEL. A refolding technique was developed to purify LPEX7 from inclusion bodies free of bacterial proteins. Far Western and protein-protein affinity assays showed that refolded LPEX7 specifically bound PTS2 proteins as both a monomer and a dimer, the co-receptor LdPEX5, and LdPEX14. Mapping of the interaction domains on LPEX7 showed that LPEX7-PTS2 interaction required the entire receptor protein, while LdPEX5 and LdPEX14 interaction motifs were situated in the N-terminal region of LPEX7.There are metabolites in glycosomes that are not imported via the peroxin based glycosomal import pathway but by glycosomal membrane transporters. L-arginine is one such metabolite; it is the substrate for the PTS1 glycosomal enzyme arginase, which catalyses the first step in the polyamine biosynthetic pathway. L-arginine is scavenged from the extracellular milieu and by the L-arginine transporter, amino acid permease 3 (LdAAP3). Subcellular fractionation showed that LdAAP3 localized to both the plasma and glycosomal membranes. Furthermore, L. donovani promastigotes were capable of sensing the L-arginine levels in the media and upregulated LdAAP3 expression on the plasma and glycosome membrane in the absence of L-arginine. These studies provide evidence that metabolite specific transporters are present on the glycosomal membrane.Together these studies contribute to the elucidation of glycosomal function in Leishmania donovani, and a better understanding of some of the mechanisms required for glycosomal import.
Le glycosome est une structure subcellulaire unique qui se trouve dans le parasite Leishmania donovani. Cette organelle compartimente la machinerie enzymatique requise pour de multiples voies métaboliques, y compris la glycolyse. Le bon ciblage des enzymes du glycosome est essentiel pour la viabilité du parasite. Les protéines ciblées pour le glycosome ont une séquence signal topogénique, un PTS1 C-terminale ou un PTS2 N-terminale, qui est reconnue par les récepteurs cytosoliques, le LdPEX5 ou le LPEX7, respectivement. Ces complexes de récepteurs chargés s'interagissent avec la protéine LdPEX14, située du côté cytosolique de la membrane glycosomale, un événement requis pour le transport des protéines à travers la membrane du glycosome. Cependant, la voie complète d'importation de protéines glycosomales n'a pas été totalement élucidée. Ce travail a été entrepris pour mieux comprendre ces interactions protéine-protéine.La fraction cytosolique des parasites L.donovani a été utilisée pour déterminer les interactions protéine-protéine des récepteurs LdPEX5 et LPEX7. La chromatographie d'exclusion de taille, la focalisation isoélectrique, et les interactions d'affinité proteine-proteine ont montré que, dans les cytosols, ces récepteurs forment des grands complexes hétérologues. Les glycosomes purifiés ont été utilisés pour évaluer l'effet des complexes récepteur sur la conformation du LdPEX14. Une protéolyse limitée a montré que l'interaction du LdPEX14 chargé avec les complexes récepteur l'à protèger de la digestion à la surface de la membrane. L'électrophorèse sur gel natif a montré que le LdPEX14 forme des grands complexes de ~ 800 kDa et que lorsqu'il est associé à des complexes récepteur, le poids moléculaire des complexes LdPEX14 passe à ~ 1200 kDa. Les extractions avec le carbonate alcalin a déterminé que le LdPEX14 seul s'agit comme une protéine périphérique; mais son chargement avec des complexes récepteur l'entrainer à s'agir comme une protéine membranaire intégrale. L'insertion de LdPEX14 dans la membrane du glycosome conduit à l'insertion du LdPEX5 et LPEX7 dans la membrane aussi. L'association des complexes récepteur à causer LdPEX14 à subir un changement de conformation causant l'insertion profonde dans la membrane et l'augmentation de la taille des complexes.La purification du récepteur LPEX7 recombinante été entravée par son association avec la protéine chaperonne bactérienne GroEL. Une technique de repliement a été développé pour purifier LPEX7 en évitant l'association de protéines bactériennes. Les techniques de Far Western et d'affinité protéine-protéine ont montré que ce LPEX7 replier est spécifiquement associé à des protéines PTS2, le co-récepteur LdPEX5, et le LdPEX14. La cartographie des domaines d'interaction de LPEX7 a montré que l'interaction LPEX7-PTS2 nécessit le LPEX7 entière, alors que les motifs d'interaction avec LdPEX5 et LdPEX14 étaient situés dans sa région N-terminale.Il y a des métabolites glycosomal qui ne sont pas importés par la voie de l'importation glycosomale, mais par des transporteurs membranaires du glycosome. L-arginine est un de ces métabolites, substrat de l'enzyme glycosomale PTS1 arginase. L-arginine est récupéré dans le milieu extracellulaire par son transporteur, LdAAP3. Un fractionnement subcellulaire a été utilisés pour séparer les membranes plasmiques des glycosomes, et LdAAP3 a été localisé sur les deux membranes. De plus, des promastigotes de L. donovani sont capable de detecter le niveau de L-arginine dans le millieu, ce qui provoque une régulation positive de l'expression de LdAAP3 à la fois dans la membrane plasmique et dans la membrane du glycosome. Ces études fournissent des preuves que des transporteurs de métabolites spécifique sont présent dans la membrane du glycosome.Ensemble, ces études contribuent à l'élucidation de la fonction glycosomale de Leishmania donovani, et une meilleure compréhension de certains mécanismes nécessaires pour l'importation glycosomale.

Submitted by Marcelo Andrade Silva (marcelo.andradesilva@ufpe.br) on 2015-03-09T14:28:37Z No. of bitstreams: 2 DISSERTAÇÃO Joelma Carvalho Santos.pdf: 2064030 bytes, checksum: 9d9c233bec668a94294f6d19471cb844 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5)
Made available in DSpace on 2015-03-09T14:28:37Z (GMT). No. of bitstreams: 2 DISSERTAÇÃO Joelma Carvalho Santos.pdf: 2064030 bytes, checksum: 9d9c233bec668a94294f6d19471cb844 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2014
A presença de polimorfismos de único nucleotídeo (SNPs) e a expressão variante dos genes das citocinas IFN-α1, IFN-γ e do receptor IFN-α r1 em pacientes com infecção crônica pelo vírus da hepatite B (HBV), podem ser considerados fatores etiopatogênicos relacionados aos níveis séricos do HBV, resultando em complicações da doença. Desta forma, o presente estudo teve como objetivo verificar a associação entre as frequências genotípicas e proporções alélicas dos genes IFNG, IFNA1, IFNAR1 em relação aos níveis de expressão desses genes e à carga viral do HBV, em pacientes com infecção crônica pelo HBV sem tratamento antiviral. Foi realizado um estudo de caso-controle com amostras de sangue total de 208 indivíduos (94 pacientes com infecção crônica e 114 indivíduos imunes ao HBV) no período de outubro de 2012 a agosto de 2013, no ambulatório de hepatologia do Hospital das Clínicas da Universidade Federal de Pernambuco (HC/UFPE) e no Hospital Escola Dr. Helvio Auto da Universidade Estadual de Ciências da Saúde de Alagoas (HEHA/UNCISAL). Para a identificação dos polimorfismos foi utilizada a PCR em tempo real (qPCR) de acordo com técnica de alta resolução de melting (HRM). A quantificação da carga viral e a expressão absoluta dos genes IFNG (-5 A>G), IFNA1 (-2 C>T), IFNAR1 (-97 T>C) foram realizadas por qPCR. Em todos os pacientes com infecção crônica pelo HBV os níveis de expressão foram menores para o gene IFNA1 (mediana=2,56x10-1ηg/μL), em relação aos genes IFNG (mediana=4,54x105ηg/μL) e IFNAR1 (mediana=6,92x109ηg/μL), e a média de carga viral foi de 3,2 log10. Pacientes com genótipo heterozigoto IFNA1(-2) CT e alelo polimórfico IFNA1 (-2) T apresentaram maiores chances de desenvolver proteção pelo HBV quando comparados a indivíduos imunes com genótipo IFNA1(-2) CC e alelo tipo selvagem C, respectivamente (IFNA1 CT/CC: OR=0,45; p=0,01 e IFNA T/C: OR=0,54; p<0,01). Em pacientes com infecção crônica e genótipo tipo selvagem TT do IFNAR1, os baixos níveis de expressão do gene desse receptor, quando comparado aos outros genótipos, explicam em 40% os altos níveis de carga viral desses pacientes (r2=0,40 | p=0,04) conferindo um risco para o desenvolvimento da cronicidade. Para o genes IFNG(-5) não foi observada diferença estatisticamente significante entre os níveis de expressão e os genótipos. Assim, a presença da variante polimórfica do gene IFNA1 (-2) em pacientes com infecção crônica, pode estar associada à proteção da cronicidade quando comparada ao grupo controle. Os altos níveis de expressão do gene IFNAR1 e baixos níveis de IFNA1 podem contribuir para a cronicidade nestes indivíduos. Os pacientes que com genótipo polimórfico IFNA1 (-2) CT e alelo T apresentaram maior proteção para a cronicidade pelo HBV.

Realisation de deux logiciels infographiques de modelisation moleculaire : 2d3d et mdnm, ecrits pour le systeme ps300 couple a un ordinateur vax. Avec 2d3d, construction de structures tridimensionnelles (3d) a partir du dessin interactif 2d, incorporant des contraintes structurales, afin de representer des structures 3d avec ou sans leur surface moleculaire. Emploi de mdnm pour representer les structures dynamiques issues de simulations par la methode de la dynamique moleculaire ou par la methode de monte carlo afin de visualiser de facon statique (par des vecteurs) ou dynamique des modes normaux de vibrations. Application a l'etude d'un recepteur macrotricyclique de synthese, le cryptand sc24 (neutre ou protone) et de divers cryptates de cations et d'anions en combinant 2d3d et mdnm pour des optimisations de mecanique moleculaires, des calculs de modes normaux de vibration, des simulations de dynamique moleculaire

Nesta tese foi desenvolvida uma nova classe de porfirinas supramoleculares contendo um grupo (4-nitrofenil)triazeno ligado na posição meso-aril do anel porfirínico. Suas propriedades estruturais e eletrônicas foram investigadas por espectrometria de massas, espectroscopia eletrônica de absorção e emissão, cálculos teóricos semi-empíricos, ressonância magnética nuclear de 1H e 13C, voltametria cíclica e espectroeletroquímica. Efeitos eletrônicos e estruturais diferenciados foram observados quando o grupo triazeno é inserido na porfirina, fazendo com que estes novos compostos apresentem novas propriedades quanto, por exemplo, às fragmentações no estado gasoso, deslocamento batocrômico nos espectros eletrônicos de absorção, variação das intensidades relativas e nos valores dos rendimentos quânticos de fluorescência, deslocalização eletrônica nos orbitais de fronteira evidenciando as transições de transferência de carga do ânion triazenido para o anel porfirínico e variações nos processos redox dos compostos até então estudados
In this thesis we has been developed a new class of supramolecular porphyrins containing (4-nitrophenyl)triazene group connected in the meso-aryl-position of the porphyrin ring. Their structural and electronic properties were investigated by mass spectrometry, absorption and emission electronic spectroscopy, semi-empirical theoretical calculations, nuclear magnetic resonance of 1H and 13C-NMR, cyclic voltammetry and spectroelectrochemistry. Different structural and electronic effects were observed when the unit is inserted into the triazene to porphyrin, so that these presents new properties such as, for example, to fragmentation in the gaseous state, bathocrimic shift in the electronic absorption spectra, relative intensity variation and values the fluorescence quantum yields, electron delocalization in the frontier orbitals showing the charge-transfer transitions from the triazenide anion to the porphyrin ring and changes in redox processes of compounds previously studied.

Orientador: Sandra Cecilia Botelho Costa
Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas
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Resumo: O cytomegalovirus humano (HCMV) e o herpesvirus humano 6 (HHV-6) são ß-herpesvirus com homologia superior a 67% e alta soroprevalência na população adulta. A infecção primaria por estes herpesvirus ocorre comumente na infância e é normalmente subclinica, ou pode causar mononucleose (HCMV) ou exantema súbito (HHV-6) sendo resolvidos na maioria dos casos sem complicações. Após a infecção primária os vírus permanecem no hospedeiro por toda vida podendo ser reativado de seu estado de latência em indivíduos adultos imunocomprometidos como os receptores de células tronco hematopoiéticas (TCTH). A reativação ou reinfecção por estes vírus causam serias complicações em pacientes submetidos ao transplante de células tronco hematopoiéticas como pneumonia intersticial, febre, gastroenterite, mielossupressão, encefalite e doença do enxerto contra o hospedeiro (GVHD). A reativação do HHV-6 após o transplante é associada com o desenvolvimento de infecções oportunistas, doença causada pelo citomegalovírus humano e possíveis episódios de rejeição aguda. Com efetivos tratamentos antivirais disponíveis, um monitoramento adequado destes vírus distinguindo entre latência e reativação é critico para estes pacientes. Monitoramos 30 pacientes submetidos à TCTH quanto a infecção ativa por HCMV e HHV-6 pelas técnicas de nested-PCR em soro e células, PCR- em tempo real em soro e células e transcrição reversa acoplada a nestedPCR (RT-nPCR). 29 pacientes (96,66%) apresentaram infecção ativa por HCMV sendo 21 pacientes (70%) pela nested-PCR em células, 17 pacientes(56,66%) pela neste-PCR em soro ,23 pacientes(76,67%) pela PCR em tempo real em células,19 pacientes (63,33%) pela PCR em tempo real em soro e 15 pacientes (53,3%) pela RT-nPCR. 25pacientes (83,33%) apresentaram infecção ativa por HHV-6, sendo 14 pacientes (46,7%) pela nested-PCR em células, 2 pacientes(6,6%) pela PCR em tempo real em células,23 pacientes (76,67%) %) pela PCR em tempo real em soro e 9 pacientes (30%) pela RT-nPCR. Todos os pacientes que apresentaram infecção ativa por HCMV apresentaram também presença do HHV-6, e 25 pacientes (83,33%) apresentaram co-infecção HCMV/HHV-6, sendo a infecção por HHV-6 precoce em relação ao HCMV. O presente estudo encontrou também associação entre infecção ativa por HCMV e doença do enxerto contra o hospedeiro.
Abstract: Human cytomegalovirus (HCMV) and human herpesvirus type 6 (HHV-6) are ß-herpesvirinae extremely closely related with a homology > 67% with a high seroprevalence in the adult population. Primary infection commonly appears in early childhood and is usually subclinical, or may cause mononucleosis (HCMV) or febrile illness, including exanthema subitum (HHV-6), solving, in the majority of cases, without complications. After primary infection, the viruses persist in the infected individual through life and can be reactivated from their state of latency in immunocompromised hosts. Reactivation or reinfection causes severe clinical diseases in patients who underwent hematopoietic stem cell transplantation, like interstitial pneumonia, fever, gastroenteritis, myelossupression, encephalitis and graft-versus-host-disease (GVHD). A potential increase in virulence of HHV-6 in the course of a simultaneous CMV reactivation, leading to a great risk of CMV-associated disease. In this present study, 30 patients who received HSCT were monitoring for active HCMV and HHV-6 infection by Nested PCR in serum and peripheral blood leukocytes (PBL) samples, real time PCR in serum and PBL and RT-nPCR. In 29 patients (96,66%) active HCMV infection was detected: 21 patients (70%) by PBL nested-PCR, 17 patients (56,66%) by serum neste-PCR, 23 patients(76,67%) by PBL real-time-PCR,19 patients (63,33%) by serum real-time-PCR and 15 patients (53,3%) by RT-nPCR. In 25 patients (83,33%) active HHV-6 infection was detected : 14 patients (46,7%) by PBL nested-PCR, 2 patients(6,6%) by PBL real time -PCR,23 patients (76,67%) by serum real time-PCR and 9 patients (30%) by RT-nPCR. In all patients who had active HCMV infection, HHV-6 DNA was detected. 25 patients (83,33) had HCMV/HHV-6 co-infection, and the active HHV-6 infection was detected earlier in the majority of the cases. Our results showed a correlation between GVHD and active HCMV infection and detection of active HCMV infection by serum nested-PCR and PBL and serum real time-PCR.
Universidade Estadual de Campi
Ciencias Basicas
Doutor em Clínica Médica

This thesis explores the reception of Johann Joachim Winckelmann in Italian art scholarship, 1755-1834. Winckelmann posed a problem: he was a presence in Italy that could not be ignored, yet the views he expounded were Italophobic and contentious to an Italian readership. In light of this dilemma, the research question asked is how did Italian art scholarship respond to Winckelmann in this period and why did it respond in that way. The core argument advanced is that there were two opposing reactions to Winckelmann, both of which were motivated by nationalism. On the one hand, Italian art scholars presented Winckelmann, his works, and his views as less attractive to an Italian readership than they would otherwise have appeared and, on the other hand, they presented him as more attractive. Through these reactions – termed foreignization and domestication respectively – art scholarship either defended against and ostracized Winckelmann or, when presented as less offensive, welcomed and embraced him amongst Italians. Thus this thesis argues that both reactions demonstrate a nationalistic attempt to portray Winckelmann in the manner most auspicious to the yet-to-be-united peninsula. In order to explore this response to the German scholar, the thesis centres on three media: translations, art literature, and artistic journalism. Both foreignization and domestication are evident throughout the sources analysed, yet there is a predominance of domestication, achieved through a variety of methods. This investigation adds to existing literature by examining the previously overlooked dilemma that Winckelmann posed. Moreover, employing the original conceptual framework of foreignization and domestication allows for a re-evaluation of how the art scholarship of the period engaged with the German scholar. Finally, demonstrating the infiltration of nationalistic sentiment in this period, even extending to Italian art scholarship, this thesis is the first to posit that nationalism played a significant role in Winckelmann's critical legacy.

Shen, Jinbo.
Thesis (Ph.D.)--Chinese University of Hong Kong, 2013.
Includes bibliographical references (leaves 110-119).
Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web.
Abstract also in Chinese.

碩士
國立中興大學
生物化學研究所
105
Plant selective autophagy plays a significant role in stress responses, delay aging and nutrient shortage. The main function of selective autophagy is to recycle the specific elements like organelles, aggregated proteins or specific proteins. Previous studies indicated that phytoene desaturase (pds) silencing not only lead to the decrease of carotenoid and chlorophyll contents, but also cause an albino phenotype. Here, we characterized the relationship between pds silencing and leaf albino were characterized. We observed the number of chloroplasts was reduced in the albino leaves via tissue slices. Chloroplast degradation has been reported via Rubisco-Containing Bodies (RCBs), which was regarded as autophagy. However, it is still unknown how specific chloroplast substrates are recognized and obtained in RCBs. In this study, we found that the expression level of cargo receptor Joka2 was highly increased in albino leaves. Moreover, in Joka2 silencing plant, vesicle-like structures were observed and accumulated after Amitrole, a PDS inhibitor, treatment. Taking together, these results suggest that Joka2 is involved in chloroplast degradation. It has been known that Xanthomonas can interfere to plant immunity by virulence effectors, which are secreted via type III secretion system. The overexpression of XopN(Xanthomonas outer protein N) and XopQ effectors in leaves could trigger severe hypersensitive response (HR) and cause cell death in tobacco leaves. In this study, we found that HR can also induce the expression of Joka2. Thus, these results suggest that Joka2 is also involved in HR triggered by Xanthominas type III effectors.

碩士
國立中興大學
生物化學研究所
107
Plants frequently encounter adverse environmental conditions, such as heat stress or salt stress. Autophagy not only plays an important role in nutrient recycling and utilization, but also can reduce energy consumption during stress conditions. Next to BRCA1 gene 1 (NBR1), a selective autophagy cargo receptor, is to recognize degraded protein.ACR1 is a homologous protein of NBR1.However, the function of ACR1 in rice is still unknown. In this study, the role of ACR1 in rice was explored. We found that the expression levels (protein and mRNA) of ACR1 were induced by salt, heat and chilling stresses. In addition, the T-DNA insertion mutant lines (ACR1 overexpression and acr1 knockout) were identified from the TRIM database. With RNA-seq analysis, 164 genes with significantly differential expression levels between ACR1 overexpression mutant and wild-type were identified; 65 genes with significantly differential expression levels between acr1 knockout mutant and wild-type were identified. Among them, genes involved in stress responds, such as heat stress and salt stress, were correlated with the expression of ACR1 to a certain extent. These results suggest that the selective autophagy cargo receptor, ACR1 might play an important role in stress response in rice.

碩士
國立中興大學
生物化學研究所
107
Both plant development and morphogenesis are regulated by brassinosteroid (BR) signal and multiple endogenous stresses. BR signal plays an important role in promoting cell elongation and expansion, which results in the distinct structure between plant tissues. Under nutrient-deficient condition, plants can regulate basal metabolism and reduce energy consumption by autophagy, which is a key factor that helps plants to survive under stressful environment. Previous studies indicated that the loss of autophagy not only affects the plants survival rate under stressful environment, but also influences the quantity of silique and seed yield. Next to the BRCA1 (NBR1), acts as a cargo receptor in selective autophagy pathway, which mainly functions in recognizing the degradation signals. In this study, we found a NBR1 homolog gene in rice and named as Autophagy Cargo Receptor 1 (ACR1). Here, we identified ACR1 overexpression and acr1 knockout T-DNA insertion lines from TRIM. Compared to the wild type (WT), ACR1 overexpression lines were shorter and displayed larger flag leaf angle; the acr1 knockout line showed fertility defects. Using qRT-PCR, the expression levels of BR signal related genes were measured. We found that BC1, which is involved in flag leaf angle regulation, was highly expressed in ACR1 overexpression lines than WT. As a result, ACR1 not only affects rice phenotypes and yields, but also regulates the BR pathway.

博士
國立臺灣大學
動物學研究所
101
The accumulation of certain misfolded protein aggregates in the brain is a common feature in various neurodegenerative diseases, and is accepted as a major causative factor of neurodegeneration. Aggrephagy, the process by which protein aggregates are selectively degraded through macroautophagy, plays an essential role in protecting neurons from aggregate-induced neurotoxicity. Recent findings have identified p62/sequestosome1 as a cargo receptor that interacts with the autophagosomal membrane associated protein LC3, and recruits ubiquitin-positive protein aggregates into autophagosomes. The finding that p62 is co-localized with inclusion bodies in the brains of patients with Huntington’s disease (HD) and Alzheimer’s disease (AD) suggests a critical role for p62 in neurodegeneration. Previous findings have identified residues in a yeast LC3 homologue, Atg8, that are essential for interaction of Atg8 with the cargo receptor Atg19 in selective autophagic processes. In the first part of my thesis, I describe our attempts to determine whether such interaction is evolutionally conserved from yeast to mammals. By using an amino acid replacement approach, we determined that three residues in LC3 corresponding to those in Atg8 were essential for p62 binding. Furthermore, while disruption of the LC3-p62 complex formation did not alter overall autophagic activity, it was sufficient to impede the autophagy-mediated clearance of aggregation–prone mutant Huntingtin (Htt), the cytotoxic protein which induces the pathological phenotypes of HD. The protective role of p62 in the clearance of aggregation-prone proteins prompted us to investigate how p62 expression is regulated under pathological conditions. In the second part of my thesis, I describe our discovery that p62 expression is transcriptionally regulated by presenilin 1 (PS1), a protein which is mutated in the majority of patients with early-onset familial Alzheimer’s disease (FAD). The PI3K/Akt/AP-1 pathway was found to be required for PS1-mediated regulation of p62 expression. Moreover, down-regulation of p62 by either PS1 deficiency or over-expression of FAD-linked PS1 mutants compromised clearance of aggregation-prone Tau, which forms intracellular neurofibrillary tangles in the AD brain; these findings thus confirm the essential role of p62 in the clearance of neurotoxic protein aggregates. Together, our studies emphasize the importance of the LC3-p62 interaction in selective autophagy, and the requirement of p62 for the removal of neurodegeneration-associated protein aggregates. Furthermore, the identification of PS1-dependent transcriptional regulation of p62 expression uncovers a novel PS1/p62-mediated molecular mechanism underlying the pathogenesis of AD and related neurodegenerative diseases.

Luo, Fang.
Thesis Ph.D. Chinese University of Hong Kong 2014.
Includes bibliographical references (leaves 121-132).
Abstracts also in Chinese.
Title from PDF title page (viewed on 08, November, 2016).

Cells express a variety of proteins on their surface that allows them to sample the world. These proteins are embedded in the plasma membrane, a bilayer of lipids that surrounds the cell. Since the lipid and protein dimensions are in the nanometer range, they are subject to thermal agitation by water molecules and show characteristic diffusive motion. The diffusive movement of these proteins plays a critical role in the cell's ability to react to external signals and regulate its internal environment.

One prominent application of protein diffusion is in the synaptic connection, where is the highly localized concentration of receptors. The receptive dendrite membrane contains many types of receptors that are accumulated to form functional microdomains opposite the presynaptic terminal buttons that release neurotransmitters. Experiments reveal that receptors move from extrasynaptic locations to synaptic locations by lateral diffusion, thereby concentrating receptors at synapses. Two key processes that control synaptic AMPAR numbers are receptor diffusion within the synaptic and extrasynaptic space and interactions between receptors and PSD scaffold proteins. Electron microscopy images suggest that the PSD is highly crowded potentially limiting the ability of receptors to diffuse and interact with scaffold proteins. However, the contribution of macromolecular crowding to receptor retention remains to be tested systematically.

Here, we combine experimental and computational approaches to test the effect of synaptic steric hindrance on receptor mobility and enrichment. We first investigate how the diffusion is influenced by membrane geometry. The membrane itself can have three-dimensional structure, which means that the actual path length of diffusion can be different from a projected path length. Here, we use a position Langevin equation for diffusion, which incorporates curvature and gradient effects of surfaces. Numeric simulation of the equation allows for the prediction of effective diffusion coefficients over corrugated surfaces.

In order to examine the distinct contributions of crowding and receptor-scaffold binding, we developed a computational model for AMPA-receptor diffusion in the synaptic and extrasynaptic space, which contains immobile obstacles, representing scaffolding, receptor and adhesion molecules in the PSD. The spatial distribution of scaffold proteins was determined directly from photo-activated localization microscopy measurements that mapped molecular positions with a resolution of ~20 nm. The AMPAR/scaffold association and dissociation rates were adjusted by computer simulations to fit single-particle tracking and fluorescence recovery after photobleaching measurements. The model predicts the recovery curves are influenced mostly by size changes while variation of kinetic rates did not significantly alter receptor residence time or mobility. We also examined the effect of binding, by adding a single synaptic binding motif to a small transmembrane protein, which slows its diffusion within the synapse. These results suggest that both protein size and binding play important roles in retaining surface-diffusing TM proteins within the excitatory synapse and shed light on the biophysical mechanisms that lead to high density of AMPARs at synapses.

Dissertation