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Synthesis and Biological Evaluation of Small Molecule Inhibitors of BMPR1bMachicao Tello, Paulo Andre 01 July 2016 (has links)
Methods for preparing an array of potential small molecule inhibitors of Bone Morphogenetic Protein Receptor 1b (BMPR1b) are described. Target molecules were prepared from two general classes: (1) N9-aryl-N6-ureidoadenines, and (2) dicarbamyl iodoacetamides. Recent data from the Peterson lab indicated that both classes might bind to BMPR1b and thus inhibit this key receptor. Docking studies performed using Sureflex Dock suggested the N9-aryl-N6-ureidoadenines would bind to the active site of BMPR1b. In addition antiproliferative activities of dicarbamyl iodoacetamides previously synthesized in the Peterson lab pointed to this moiety as an attractive target for structure activity relationship (SAR) development. Compounds were prepared in good to excellent yields and 40 derivatives were screened for antiproliferative activity. Of the N9-aryl-N6-ureidoadenine derivatives, N9-phenyl-N6-N-phenylureaadenine was most potent and exhibited selective activity against HeLa cells (IC50 = 11± 1 uM). Dicarbamyl iodoacetamide derivatives had similar activities compared to the previously reported compound (JRS-150).
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Interactions entre l'ARN 23S et les protéines uL24 et uL4 dans l'assemblage de la grande sous-unité du ribosome : mesures de force par piège optique / Interactions between 23S RNA and proteins uL24 and uL4 during the assembly of the large ribosomal subunit : force measurements by optical tweezersGeffroy, Laurent 04 December 2017 (has links)
Le ribosome est un organite essentiel de la cellule qui assure la synthèse des protéines. C'est une structure très conservée, composée d'ARN et de protéines ribosomiques organisés en deux sous-unités. Les expériences de reconstitution in vitro du ribosome d'E. coli ont montré que l'assemblage est un processus coordonné impliquant de nombreuses interactions entre les différents constituants. En particulier, les premières étapes de l'assemblage de la grande sous-unité dépendent fortement de la fixation coopérative de cinq protéines ribosomiques à l'ARN 23S, mais les mécanismes moléculaires sous-jacents sont mal connus.Cette étude à l'échelle de la molécule unique vise à préciser ces mécanismes et porte sur un fragment constitué des hélices H18, H19 et H20 du domaine I de l'ARN ribosomique 23S contenant les sites de fixation des protéines uL24 et uL4. Ce fragment d'ARN a été préparé dans une configuration qui permet la mesure de force via un double piège optique. Les courbes de force obtenues ont permis de dresser une cartographie de la stabilité des structures du fragment d'ARN.Ces cartes ont été comparées en absence et en présence des protéines ribosomiques uL24 et/ou uL4, démontrant ainsi que le fragment d'ARN est stabilisé par la fixation des protéines uL24 et/ou uL4. Leur fixation est coopérative et la présence conjointe des deux protéines sur-stabilise les structures du fragment d'ARN.Ces résultats sont discutés dans la perspective de préciser le rôle du fragment d'ARN et des protéines ribosomiques uL24 et uL4 dans l'assemblage de la grande sous-unité du ribosome. / Ribosomes are essential organelles of the cell responsible for the synthesis of proteins. Their well conserved structure made of RNA and proteins is organized into two subunits. In vitro reconstitution of E. coli ribosomes showed that their assembly is a coordinated process which involves many interactions between the components. More specifically, the early stages of the large subunit assembly depend strongly on the cooperative binding of five ribosomal proteins to the 23S RNA. The underlying molecular mechanisms however remain poorly understood.The aim of this study is to shine new light on these mechanisms at the single molecule level. It focuses on a 23S ribosomal RNA fragment composed of the helices H18, H19 and H20 in domain I which encompasses the binding sites of the ribosomal proteins uL24 and uL4. This RNA fragment has been prepared in a dumbbell configuration and force versus displacement measurements have been performed using a dual optical trap. From these measurements, a map summarizing the mechanical stability of the RNA fragment has been determined.The maps obtained in absence and in presence of the ribosomal proteins uL24 and/or uL4 have been compared consequently demonstrating mechanical stabilization of the RNA fragment induced by the binding of uL24 and/or uL4. Moreover, their binding is cooperative and when both are present, the mechanical stabilization of the RNA fragment is enhanced.These results are discussed to specify the role of the RNA fragment and proteins uL24 and uL4 in the large ribosomal subunit assembly.
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Gamma-protocadherin Cis- and Trans-interactions regulate the development of dendrite arbors and synapses in the cerebral cortexMolumby, Michael Jacob 01 August 2017 (has links)
The alpha-, beta-, and gamma-Protocadherins (gamma-Pcdhs) are cadherin superfamily adhesion molecules encoded by clustered gene families. The 22 gamma-Pcdhs are combinatorially expressed in the central nervous system (CNS) by neurons and astrocytes, and play critical roles in synaptogenesis, dendrite arborization, and the survival of subsets of neurons. The gamma-Pcdhs promiscuously form cis-multimers that interact strictly homophilically in trans (Molumby et al., 2016; Schreiner and Weiner, 2010); the alpha- and beta-Pcdhs were subsequently shown to interact in a similar homophilic manner (Rubinstein et al., 2015; Thu et al., 2014). The Pcdh gene clusters thus have the potential to generate millions of distinct adhesive interfaces, providing CNS cells with molecular identities that shape neuronal morphology.
We demonstrated previously that, in mice lacking the gamma-Pcdhs in the cerebral cortex, pyramidal neurons exhibit severely reduced dendrite arborization (Garrett et al., 2012a). This, combined with many studies of gamma-Pcdh interactions in vitro, suggests that homophilic, adhesive gamma-Pcdh interactions between neurons, and between neurons and glia, provide a positive signal for dendrite growth. However, in retinal starburst amacrine cells and cerebellar Purkinje cells, loss of the gamma-Pcdhs resulted in aberrant dendrite fasciculation and self-crossing (Lefebvre et al., 2012), suggesting that these molecules can mediate repulsive self-avoidance between a neuron’s own dendrites.
In Chapter I of this thesis I utilized transgenic mice to manipulate expression in vivo, to show that the complexity of a cortical neuron’s dendritic arbor is determined by homophilic gamma-Pcdh isoform matching with other cells. Expression of the same single isoform in a neuron can result in either exuberant, or minimal, dendrite complexity depending on whether surrounding cells express the same isoform. Additionally, loss of gamma-Pcdh in astrocytes, or induced astrocyte-neuron mis-matching, reduces dendrite complexity cell non-autonomously. This indicates a neuron’s pattern of connectivity is indeed regulated by specific interactions between cells that are distinct from the repulsive self-avoidance seen in isoneuronal processes of planar cell types.
In addition to modulating dendrite branch development, the gamma-Pcdhs have been shown to regulate the progression of spinal cord synaptogenesis (Garrett and Weiner, 2009). A role for these molecules in cortical dendritic spines and synapses, however, had yet not been examined. In Chapter II of this thesis, I provide evidence that the gamma-Pcdhs negatively regulate synapse formation and spine morphogenesis in forebrain neurons. Mice lacking all gamma-Pcdhs in the cortex exhibit significantly increased spine and synapse density in vivo, while spine density is significantly decreased in mice overexpressing one of the 22 gamma-Pcdh isoforms. To explain this functional result, we present in vitro evidence to show that gamma-Pcdhs physically and functionally interact with the synaptic cell adhesion molecule neuroligin-1. This work suggests a potential new mechanism by which gamma-Pcdhs regulate the “choice” between dendrite arbor growth and formation and/or stabilization of dendritic spines and synapses in the developing brain.
Given that disruptions in the pattern and density of dendritic arbors and spines are a hallmark of neurodevelopmental disorders such as autism and Down, Rett, and fragile X syndromes, my work may provide the basic science foundation for future therapeutic approaches focused on Pcdhs and their associated signaling pathways.
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Cargo Transport By Myosin Va Molecular Motors Within Three-Dimensional In Vitro Models Of The Intracellular Actin Cytoskeletal NetworkLombardo, Andrew Thomas 01 January 2018 (has links)
Intracellular cargo transport involves the movement of critical cellular components (e.g. vesicles, organelles, mRNA, chromosomes) along cytoskeletal tracks by tiny molecular motors. Myosin Va motors have been demonstrated to play a vital role in the transport of cargos destined for the cell membrane by navigating their cargos through the three-dimensional actin networks of the cell. Transport of cargo through these networks presents many challenges, including directional and physical obstacles which teams of myosin Va-bound to a single cargo must overcome. Specifically, myosin Va motors are presented with numerous actin-actin intersections and dense networks of filaments which can act as a physical barrier to transport. Due to the complexities of studying myosin Va cargo transport in cells, much effort has been focused on the in vitro observation and analysis of myosin Va transport along single actin filaments or simple actin cytoskeletal models. However, these model systems often rely on non-physiological cargos (e.g. beads, quantum dots) and two-dimensional arrangements of actin attached to glass surfaces. Interestingly, a disconnect exists between the transport of cargo on these simple model systems and studies of myosin Va transport on suspended 3D actin arrangements or cellular networks which show longer run lengths, increased velocities, and straighter, more directed trajectories. One solution to this discrepancy is that the cell may use the fluidity of the cargo surface, the recruitment of myosin Va motor teams, and the 3D geometry of the actin, to finely tune the transport of intracellular cargo depending on cellular need.
To understand how myosin Va motors transport their cargo through 3D networks of actin, we investigated myosin Va motor ensembles transporting fluorescent 350 nm lipid-bilayer cargo through arrangements of suspended 3D actin filaments. This was accomplished using single molecule fluorescent imaging, three-dimensional super resolution Stochastic Optical Reconstruction Microscopy (STORM), optical tweezers, and in silico modeling. We found that when moving along 3D actin filaments, myosin motors could be recruited from across the fluid lipid cargo’s surface to the filaments which enabled dynamic teams to be formed and explore the full actin filaments binding landscape. When navigating 3D actin-actin intersections these teams capable of maneuvering their cargo through the intersection in a way that encouraged the vesicles to continue straight rather than switch filaments and turn at the intersection. We hypothesized that this finding may be the source of the relatively straight directed runs by myosin Va-bound cargo observed in living cells. To test this, we designed 3D actin networks where the vesicles interacted with 2-6 actin filaments simultaneously. Actin forms polarized filaments, which, in cells, generally have their plus-ends facing the exterior of the cell; the same direction in which myosin Va walks. We found that to maintain straight directed trajectories and not become stationary within the network, vesicles needed to move along filaments with a bias in their polarity. This allows for cargo-bound motors to align their motion along the polarized networks and produced productive motion despite physical and directional obstacles. Together this work demonstrates the physical properties of the cargo, the geometric arrangement of the actin, and the mechanical properties of the motor are all critical aspects of a robust myosin Va transport system.
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Discrimination and Sequencing of Polymers with Biological Nanopores / Interaction de polymères naturels et synthétiques avec des pores protéiquesBoukhet, Mordjane 19 November 2018 (has links)
La technique de détection à l'aide de nanopores au niveau de la molécule unique est l'une des plus puissantes pour l'analyse de diverses molécules, dont les polymères biologiques et synthétiques, les protéines et les peptides, les molécules de sucre ou les nanoparticules métalliques. Ces pores peuvent également servir de plate-forme pour l'étude de phénomènes physiques et biologiques fondamentaux. Dans le cadre de l'analyse de molécules, ce travail, expérimenté en utilisant la technique de la peinture de bicouche lipidique, porte principalement sur la détection des polymères et leur utilité pour sonder les processus fondamentaux des de l'α-hémolysine et de l'aérolysine.Le premier chapitre de résultats décrit l’analyse des flux à travers l'hémolysine et l'aérolysine à l’aide des polyéthylèneglycols (PEG) et des α-cyclodextrines, ainsi que les effets des sels de KCl et de LiCl sur l'interaction des PEG avec ces pores. L'une des principales conclusions est qu'il existe un flux électoosmotique plus fort dans l'aérolysine, responsable du transport des molécules neutres, les α-cyclodextrines. La seconde constatation concerne la dynamique des PEG avec les nanopores qui semblait être fortement dépendante du sel, montrant des différences drastiques de fréquence et de durée d’interaction en fonction de la tension pour les deux sels, bien que la détection de la masse de PEG dans les deux conditions indique que la nature de l'interaction avec le pore est similaire dans les deux types de sels.Le but des travaux présentés dans le deuxième chapitre de résultats était de détecter les polymères de précision et à trouver les meilleures conditions pouvant conduire à leur séquençage avec des nanopores. Des homopolymères et copolymères de poly(phosphodiester)s ont été sondés en utilisant l'hémolysine, l'aérolysine et MspA. Le premier type de polymères étudiés contenant une amorce 3-polythymidine et une suite de comonomères de type (0) a montré une forte interaction avec les pores qui a été interprétée comme la promotion de la liaison avec les pores, due à l'amorce d’ADN simple brin, combinée à une grande flexibilité du premier type de polymères. Les polymères qui contenaient des chaînes latérales alcyne et triazole se sont révélés avoir des interactions plus complexes, mais ont interagi pendant des durées plus courtes avec les pores indiquant qu'ils étaient plus rigides. Le second type de polymères semble s’agréger en solution du fait de l’interaction entre les chaînes latérales, ce qui prouve l’importance de la caractérisation de ces molécules en solution par diffusion de rayons, dans le cadre de la détection et finalement de leur séquençage.L'étude du troisième chapitre de résultats, a porté sur la dynamique de petits oligonucléotides avec le pore d’aerolysine. Les polyadénines (A3, A4, A5) ont montré une dynamique complexe d’interaction avec le pore, qui a été étudiée par l'analyse et la quantification des différentes propriétés des événements. L'ensemble du processus s'est avéré être régi par deux sites de liaison et des barrières énergétiques à l'intérieur du pore que les molécules doivent surmonter. Ces résultats ont été combinés à un modèle cinétique qui a permis une description complète de la liaison et de la translocation (ou son non succès) des polyadénines.Le dernier chapitre des résultats décrit l’interaction de plus grandes polyadénines (A6-A7-A8-A9-A10) avec l’aérolysine. L’analyse de l'amplitude des courants des blocs induits par l'adénine à l'intérieur de ce pore montre une interaction dépendante de l'orientation des molécules avec le pore. Cette interaction dépendante de l'orientation a commencé à apparaître pour la molécule A7 et est devenue l'effet dominant pour A9 et A10. En raison de la flexibilité de l'ANDsb, cet effet n'est pas observé pour les molécules de plus petite taille (A6 et inférieures) en raison de leur possibilité de réorientation à l'intérieur du pore. / The technique of detection with nanopores at the single molecule level, is one of the most powerful method for the analysis of various molecules, of which biological and synthetic polymers, proteins and peptides, sugar molecules or metal nanoparticles. These pores can also serve as a platform for the study of fundamental physical and biological phenomenons. In the context of molecule analysis, this work, which is experimented using the technique of planar lipid bilayer painting, focuses mainly on the detection of polymers and their utility to portray fundamental processes of the α-hemolysin and aerolysin biological nanopores.The first results chapter described the probing of flows through α-hemolysin and aerolysin using polyethylene glycols (PEGs) and α-cyclodextrines, and the effects of KCl and LiCl salts on the interaction of PEGs with these pores. One main finding was that there exists a stronger electoosmotic flow in aerolysin, responsible for the transport of the neutral molecules α-cyclodextrines. The second finding was that the dynamics of PEGs with the nanopores are strongly dependent on the salt, showing drastic differences of frequency and dwell times vs. voltage for the two salts, although, the results of detection of mass of PEGs pointed to the fact that the nature of the interaction with the pore is similar in both salts.The aim of the work presented in the second results chapter, was to detect precision polymers, and find the best conditions, which can lead to their sequencing with nanopores. The homo- an copolymers of poly(phosphodiester)s were probed using α-hemolysin, aerolysin and MspA. The first type of polymers investigated which contained a 3-polythymidine primer and a sequence of comonomers of type (0) showed a strong interaction with the pores that was interpreted as the promotion of ssDNA-primer to the binding with the pore, combined to a high flexibility of the first type of polymers. The polymers which contained alkyne and triazole side chains, were found to have more complex interactions, but interacted for shorter durations with the pore indicating them to be stiffer. The second type of polymers seemed to be clustering in solution due the interaction between side chains, which proved the importance of performing characterization of these molecules in solution using wave scattering in the context of detection and ultimately sequencing.The study of the third result chapter, focused on the dynamics of small oligonucleotides with the aerolysin pore. The interaction of polyadenines (A3, A4, A5) showed complex dynamics and kinetics with pore, which was investigated via analysis of the events pattern. The whole process was found to be governed by two binding sites and energy barriers inside the pore that the molecules have to overcome. These results were combined to a developed kinetic model which allowed a complete description of the binding and translocation (or failure of it) of these polyadenines.The last results chapter described the interaction of bigger polyadenines (A6-A7-A8-A9-A10) with the aerolysin nanopore. The analysis of amplitude of currents of the adenine-induced blocks inside this pore showed an orientation dependent interaction of the molecules with the pore. This orientation dependent interaction started to be apparent for the A7 molecule and became the dominant effect for A9 and A10. Due to the flexibility of ssDNA, this effect is not observed for smaller sized molecules (A6 and below) because of their possibility of reorientation while inside the pore.
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Quantitative confocal imaging of nanoporous silicaHu, Yan 01 May 2016 (has links)
Nanoporous materials have been widely used in the fields of biological and chemical sensing, chemical separation, heterogeneous catalysis and biomedicine due to their merits of high surface area-to-volume ratio, chemical and thermal stabilities, and flexible surface modification. However, as the nature of nanoporous materials, they are inherently heterogeneous in the micro- and nanoenvironments. The environmental heterogeneity plays a decisive role in determining the performance of various applications of nanoporous materials. In order to provide an in-depth understanding of the nanoporous materials, it is of great interest to investigate the environmental heterogeneity in them. Single molecule spectroscopy, combined the quantitative confocal fluorescence imaging which possesses the capability of optical sectioning, has demonstrated to be a powerful tool to approach the environmental heterogeneity inside nanoporous materials. Single molecule spectroscopy is an ultrasensitive technique for probing molecular transport and properties of individual molecules. This technique has been extensively used in the research of environmental heterogeneity in nanoporous materials since it removes the issues of ensemble averaging and directly approaches detailed information that is obscured in ensemble measurements. In order to proficiently interpret single molecule data, we developed a comprehensive methodology – single molecule counting – for characterizing molecular transport in nanoporous silica. With this methodology as a tool, the nanoenvironmental heterogeneity inside the nanopores of C18-derivatized silica particles was explored by probing single molecular diffusion inside the pores. By employing single molecule ratiometric spectroscopy and a solvatochromic fluorophore as viii reporter of local environment, the gradient in nanopolarity as well as the nanoviscosity along the C18 layer after the inclusion of solvent was uncovered. The chemical properties of solute molecules at the nanopore surface are ultimately controlled by the energetics of the solute-interface interactions. The imaging of distribution of energies would be a decisive approach to assess the fundamental heterogeneity of the interface. To this end, we investigated the ΔG distribution of C18-derivatized nanoporous silica particles with quantitative confocal imaging. The pixel-to-pixel and particle-to-particle analysis showed the existence of ΔG heterogeneity between particles as well as within individual particles. The heterogeneity in ΔG could be partially responsible for band broadening in chemical separations and significantly affect overall reaction yield when using nanoporous materials as solid support for heterogeneous catalysis.
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New approaches in super-resolution microscopy / Nouvelles approches microscope de super-résolutionYang, Bin 13 April 2015 (has links)
La première méthode vise à améliorer la vitesse d’imagerie de la microscopie super-résolue àtempérature ambiante pour des applications biologiques. En tant qu’une technique de scan, lamicroscopie STED a besoins d’être parallélisé pour faire de l’imagerie rapide en champ large. Nousavons obtenu une parallélisation massive de la microscopie STED en utilisant les réseaux d’optiqueavec une excitation en en champ large et une caméra rapide pour détection. Les images super-résoluesd’un champ de 3 μm par 3 μm sont acquises en scannant une maille élémentaire du réseau optique, quipeut être aussi petite que 290 nm * 290 nm. La microscopie Lattice-STED est démontrée avec unerésolution allant jusqu'à 70 nm à une cadence de 12,5 images par seconde.La deuxième méthode étend la microscopie super-résolue à la température de l’hélium liquide pourdes applications aux technologies quantiques. Des résolutions optiques à l'échelle nanométrique desémetteurs quantique est une étape cruciale vers le contrôle des états délocalisés formés par lesinteractions fortes et cohérentes entre des émetteurs. Dans ce contexte, nous avons développé unetechnique de microscopie à des températures cryogéniques, dénommée la microscopie Essat. Cettetechnique est basée sur la saturation optique de l'état excité des molécules fluorescentes uniques parl’excitation d’un faisceau en forme d’anneau. Une résolution moins de 10 nm est obtenue avec debasses intensités d'excitation, plus de millions de fois plus faibles que celles utilisées dans lamicroscopie STED à la température ambiante. Par rapport aux approches basées sur la superlocalisation,notre technique offre une occasion unique de résoudre sous la limite de diffraction lesmolécules uniques ayant des fréquences de résonance optiques qui se chevauchent. Ceci ouvre la voieà l'étude des interactions cohérentes entre émetteurs uniques et à la manipulation de leur degréd'intrication. / The first technique aims at improving the imaging speed of super-resolution microscopy at roomtemperature for biological applications. As a scanning technique, STED (Stimulated EmissionDepletion) microscopy needs parallelization for fast wide-field imaging. Using well-designed opticallattices for depletion together with wide-field excitation and a fast camera for detection, we achievelarge parallelization of STED microscopy. Wide field of view super-resolved images are acquired byscanning over a single unit cell of the optical lattice, which can be as small as 290 nm * 290 nm.Lattice-STED imaging is demonstrated with a resolution down to 70 nm at 12.5 frames per second.The second one extends super-resolution microscopy to liquid helium temperature for applications inquantum technologies. Optical resolution of solid-state single quantum emitters at the nanometer scaleis a challenging step towards the control of delocalized states formed by strongly and coherentlyinteracting emitters. ESSat (Excited State Saturation) microscopy operating at cryogenic temperaturesis based on optical saturation of the excited state of single fluorescent molecules with a doughnutshapedbeam. Sub-10 nm resolution is achieved with extremely low excitation intensities, more thanmillion times lower than those used in room temperature STED microscopy. Compared to superlocalisationapproaches, our technique offers a unique opportunity to super-resolve single moleculeshaving overlapping optical resonance frequencies, paving the way to the study of coherent interactionsbetween single emitters and to the manipulation of their degree of entanglement.
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Identification and Validation of Small Molecules Inhibiting Human Adenovirus ReplicationSaha, Bratati 01 October 2019 (has links)
Human adenovirus (HAdV) mainly causes minor illnesses, but can lead to severe disease and death in both immunocompromised and immunocompetent patients. In such cases, the current standards of treatment often do not improve disease outcome and no approved antiviral therapy against HAdV exists. Since HAdV relies on cellular machinery to assist in the progression of the virus lifecycle, we hypothesized that small molecules targeting certain cellular proteins/pathways, without severely affecting cell health, may serve as effective anti-HAdV compounds. Thus, we aimed to identify novel inhibitors of HAdV, and investigate the molecular mechanism to determine new therapeutic targets for intervention in HAdV infection. We first examined the antiviral properties of pan-histone deacetylase (HDAC) inhibitor SAHA and found that the drug affects multiple stages of the HAdV lifecycle, resulting in significant reductions in virus yield. SAHA was effective in decreasing gene expression from clinically relevant HAdV serotypes. Subsequent investigations on the role of HDACs in HAdV infection led us to determine that class I HDAC activity, mainly HDAC2, is necessary for optimal viral gene expression. Using a wildtype-like HAdV reporter construct that allows us to monitor virus replication by fluorescence microscopy, we then designed an efficient system for screening small molecules to identify novel HAdV inhibitors. We screened over 1300 small molecules, and the screen was sensitive enough to detect compounds with both robust and modest antiviral activity. Several positive hits were validated to reduce HAdV gene expression and yield from infected cells. Further investigation on the efficacy of these compounds and the mechanism behind their inhibition of HAdV can lead to the discovery of new pharmacological targets and the development of more effective antivirals.
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Biomarker Assay Development and Sensing with Solid-State NanoporesBeamish, Eric 01 October 2019 (has links)
Broadly speaking, the work herein discussed encompasses the development of biomolecular assays for biomarker detection. Specific to the assays in this thesis is the design of reaction schemes that consider the unique requirements of one class of single-molecule sensors in particular: solid-state nanopores formed using a novel fabrication and conditioning technique discovered during this research at the University of Ottawa.
We present three unique assays for the detection of different biomolecular targets. The first uses a class of DNA origami structures termed nanoswitches to translate the presence of a short segment of single-stranded DNA Zika virus biomarker to a large configurational change in a double-stranded DNA scaffold. The signal amplification inherent in this topological change allowed us to a achieve a high degree of specificity for detecting a small nucleic acid target by requiring two separate binding events. Furthermore, through careful design of the configurational change, the number of topological states that a solid-state nanopore can sense is limited, providing unambiguous signals in ionic current recordings. Quantification of the Zika gene was performed by sensing the relative amounts of nanoswitches in looped and linear configurations from only hundreds of individual molecules.
We then explored the sensitivity of solid-state nanopores for detecting small molecular features along short DNA scaffolds. Leveraging the ability of our nanopores to detect the presence of these protrusions, we present results in which ATP, a molecule significantly too small to be directly detected by the nanopore sensor, initiated an aptamer-based DNA displacement reaction to form a protrusion along scaffolds, producing measurable changes in ionic current signatures in nanopore recordings.
Finally, we present an assay in which a microRNA, a biomarker linked to various cancers, was detected through the conjugation of two probes, each of which contained a binding site to different segments of the microRNA. In addition to examining different probe set structures for optimal performance, our two-probe design aimed to improve specificity over conventional single-probe-based assays which only require one recognition step, while still providing unambiguous signals due to the greater-than-doubling in molecular complex size upon conjugation. Furthermore, the use of two individual small probes, rather than one large nanoswitch, increased the resolution with which we could differentiate microRNA concentrations. The assay enabled the quantification of six concentrations of microRNA spanning a single order of magnitude, in only several hundred events, and allowed us to take advantage of the reduced cost, material and labour, as well as increased nanopore capture rates, associated with small assembled molecules.
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ORGANO-SPÉCIFICITÉ DE L'ENDOTHÉLIUM : MISE EN ÉVIDENCE ET CARACTÉRISATION D'UNE MOLÉCULE RÉGULATRICE DE L'ADHÉSION, NOMMEE ARM-1LAMERANT-FAYEL, Nathalie 17 December 2004 (has links) (PDF)
Afin d'identifier de nouvelles cibles organo-spécifiques de l'endothélium, nous avons comparé l'expression de gènes entre deux lignées de hautes cellules endothéliales et mis en évidence la protéine ARM-1. Des expériences de RT-PCR ont montré une expression spécifique d'ARM-1 dans certaines lignées de cellules endothéliales et de lymphocytes. La surexpression d'ARM-1 dans des cellules endothéliales de peau, n'exprimant pas cette protéine, augmente de façon préférentielle l'adhésion de certaines lignées lymphocytaires sur ces cellules. Ceci renforce l'hypothèse d'un rôle particulier d'ARM-1 au sein des cellules endothéliales. Une étude de fractionnement cellulaire a montré qu'ARM-1 était une protéine sécrétée, pouvant être associée à la membrane. Des expériences d'immunolocalisation n'ont cependant démontré aucune expression d'ARM-1 à la surface cellulaire. Ces résultats suggèrent une action indirecte d'ARM-1 dans l'adhésion plutôt qu'un rôle direct en tant que molécule d'adhésion.
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