Calcium (Ca²⁺) influx through Caᵥ1.2 channels mediates cardiac excitation-contraction coupling, tunes cardiac action potential duration and excitability, and regulates cardiomyocytes’ (CM) gene expression. Mechanisms regulating the sub-cellular localization, trafficking, and dynamics of surface Caᵥ1.2 in ventricular CMs are poorly understood though these are critical determinants of cardiac function. To gain new insights into Caᵥ1.2 organization, dynamics, and regulation at the CM surface we generated transgenic mice expressing an αMHC controlled cardiac-specific, dihydropyridine (DHP)- resistant α₁_ᴄ construct, tagged at the N-terminus with FLAG and HA epitopes, at the C- terminus with YFP, a 13-residue bungarotoxin binding site (BBS) inserted into in the third extracellular loop of domain II, and mutations that prevent cleavage of the C-terminus. We found robust inducible expression of DHP-resistant FLAG-HA-BBS-α₁_ᴄ-YFP in the heart that targeted to dyadic junctions, generated nisoldipine-resistant Ca²⁺ currents, supported cardiac excitation-contraction coupling, and was normally up-regulated by β-adrenergic activation with isoproterenol. Incubating transgenic CMs with AlexaFluor₆₄₇-conjugated α- bungarotoxin (BTX₆₄₇) enabled selective labeling of surface BBS-tagged Caᵥ1.2 channels. We used total internal fluorescence (TIRF) microscopy to investigate the spatiotemporal organization and dynamics of surface Caᵥ1.2 channels. Similar to endogenous Caᵥ1.2, transgenic α1C-YFP forms clusters with exponentially distributed sizes at the cell surface. A flow cytometry-based optical pulse-chase assay revealed surface Caᵥ1.2 channels in adult cardiomyocytes fully turn over within two hours. Application of angiotensin II (Ang II) decreased transgenic Caᵥ1.2 surface density and this effect was blocked by the selective Ang II receptor type I (AT1R) blocker losartan. Application of losartan by itself increased Caᵥ1.2 surface density, suggesting the potential presence of constitutively active Ang II receptors in adult CMs. Our results provide new insights into spatiotemporal organization, dynamics, and regulation of Caᵥ1.2 channels in adult CMs and introduce an approach that can be widely applied to elucidate spatiotemporal dynamics of cardiac ion channels and membrane proteins.

Improved diagnosis, prognosis and disease follow-up is a fundamental procedure and a constant challenge in medicine.  Among the different molecular biomarkers, proteins are the essential regulatory component in blood; hence, by developing enhanced specific and sensitive molecular tools will gives great insight into the different processes in disease treatment.  In this thesis, we build on the proximity ligation assay to develop and apply new adaptable methods to facilitate protein detection. In paper I, I present a variant of the proximity ligation assay (we call PLARCA) using micro titer plate for detection and quantification of protein using optical density as readout in the fluorometer. PLARCA detected femtomolar levels of these proteins in patient samples, which was considerably below the detection threshold for ELISA. In paper II, we developed and adapted a new method into the in situ PLA methods for detection and identification of extracellular vesicles (EVs) using flow cytometry as readout (a method we call ExoPLA).  We identified five target proteins on the surface of the Evs and using three colors, we identified the EV using flow cytometer. In paper III, we aim to improve the efficiency of in situ PLA by creating and developing new designs and versions of the assay we called Unfold probes Through comparison of detection of protein using in situ PLA versus Unfold probes, we observed considerable decrease in non-specific signals, and also a lower detection threshold. In paper IV, we describe the development of a solid phase proximity extension (sp-PEA) assay for protein detection and quantification. We compared detection of IL-8, TNF-alpha, IL-10 and IL-6 using spPEA and PEA; spPEA demonstrations over 2 orders of magnitudes in the lower detection concentrations by decreased in background noise.

Polymer-modified bitumen (PMB) is a high-performance material for road construction and maintenance. But its storage stability and phase separation behaviour are still not sufficiently understood and need to be studied toward a more successful and sustainable application of PMB. In this thesis, the equilibrium thermodynamics and phase separation dynamics of PMB are investigated with the aim at a fundamental understanding on PMB storage stability and phase separation behaviour. The development of polymer modifiers for paving bitumen is reviewed. The phase separation process in unstable PMBs is captured by fluorescence microscopy at the storage temperature (180 °C). A coupled phase-field model of diffusion and flow is developed to simulate and predict the PMB storage stability and phase separation behaviour. The temperature dependency of PMB phase separation behaviour is modelled by introducing temperature-dependent model parameters between 140 °C and 180 °C. This model is implemented in a finite element software package and calibrated with the experimental observations of real PMBs. The results indicate that storage stability and phase separation behaviour of PMB are strongly dependent on the specific combination of the base bitumen and polymer. An unstable PMB starts to separate into two phases by diffusion, because of the poor polymer-bitumen compatibility. Once the density difference between the two phases becomes sufficiently significant, gravity starts to drive the flow of the two phases and accelerates the separation in the vertical direction. The proposed model, based on the Cahn-Hilliard equation, Flory-Huggins theory and Navier-Stokes equations, is capable of capturing the stability differences among the investigated PMBs and their distinct microstructures at different temperatures. The various material parameters of the PMBs determine the differences in the phase separation behaviour in terms of stability and temperature dependency. The developed model is able to simulate and explain the resulting differences due to the material parameters. The outcome of this study may thus assist in future efforts of ensuring storage stability and sustainable application of PMB. / Polymermodifierade bitumen (PMB) är ett högpresterande material för väganläggning och underhåll. Men PMB:s lagringsstabilitet och fassepareringsegenskaper är inte tillräckligt förstådda än och behöver studeras för en mer framgångsrik och hållbar användning av PMB. I denna avhandling studeras termodynamisk jämvikt och fasseparation av PMB med målsättning att uppnå en grundläggande förståelse av PMB:s lagringsstabilitet och fassepareringsegenskaper. Utvecklingen av polymermodifierade bitumen sammanfattas. Fasseparationsprocessen av instabil PMB:s studeras med hjälp av fluorescens mikroskopi vid lagringstemperatur (180 °C). En kopplad fas-fälts modell som beskriver diffusion och flöde har utvecklats för att simulera och förutsäga PMB:s lagringsstabilitet och fassepareringsegenskaper. Temperaturberoendet hos PMB:s fasseparation har beskrivits genom att införa temperaturberoende modellparametrar mellan 140 °C och 180 °C. Denna modell är införd i ett finit element program och kalibrerad med experimentella observationer på verkliga PMB. Resultaten indikerar att lagringsstabiliteten och fasseparationen hos PMB är starkt beroende av den specifika kombinationen av basbitumen och polymer. En instabil PMB börjar separera i två faser genom diffusion, beroende på dålig bitumen-polymer kompatibilitet. När skillnaden i densitet mellan de två faserna blir tillräckligt stor kommer gravitationen att driva flödet av de två faserna och accelerera separationen i vertikalled. Den föreslagna modellen, baserad på Cahn-Hilliards ekvation, Flory-Huggins teori och Navier-Stokes ekvation, kan beskriva stabilitetsskillnaderna mellan de undersökta PMB:erna och deras distinkta mikrostruktur vid olika temperaturer. De olika materialparametrarna hos PMB bestämmer skillnaden i fassepareringsegenskaper i termer av stabilitet och temperaturberoende. Den utvecklade modellen kan simulera och förklara de resulterande skillnaderna på grund av materialparametrarna. Resultatet av denna studie kan bidra till att säkerställa lagringsstabilitet och hållbara applikationer för PMB. / <p>QC 20161102</p>

No description available.

La microscopie par fluorescence de cellules vivantes produit de grandes quantités de données. Ces données sont composées d’une grande diversité au niveau de la forme des objets d’intérêts et possèdent un ratio signaux/bruit très bas. Pour concevoir un pipeline d’algorithmes efficaces en traitement d’image de microscopie par fluorescence, il est important d’avoir une segmentation robuste et fiable étant donné que celle-ci constitue l’étape initiale du traitement d’image. Dans ce mémoire, je présente MinSeg, un algorithme de segmentation d’image de microscopie par fluorescence qui fait peu d’assomptions sur l’image et utilise des propriétés statistiques pour distinguer le signal par rapport au bruit. MinSeg ne fait pas d’assomption sur la taille ou la forme des objets contenus dans l’image. Par ce fait, il est donc applicable sur une grande variété d’images. Je présente aussi une suite d’algorithmes pour la quantification de petits complexes dans des expériences de microscopie par fluorescence de molécules simples utilisant l’algorithme de segmentation MinSeg. Cette suite d’algorithmes a été utilisée pour la quantification d’une protéine nommée CENP-A qui est une variante de l’histone H3. Par cette technique, nous avons trouvé que CENP-A est principalement présente sous forme de dimère. / Live-cell fluorescence microscopy produces high amounts of data with a high variability in shapes at low signal-to-noise ratio. An efficient design of image analysis pipelines requires a reliable and robust initial segmentation step that needs little parameter fine-tuning. Here, I present a segmentation algorithm called MinSeg for fluorescence image data that relies on minimal assumptions about the image, and uses statistical considerations to distinguish signal from background. More importantly, the algorithm does not make assumptions about feature size or shape, and is thus universally applicable. I also present a pipeline for the quantification of small complexes with single-molecule fluorescence microscopy using this segmentation algorithm as the first step of the workflow. This pipeline was used for the quantification of a small histone H3 variant protein called CENP-A. We found that the CENP-A nucleosomes are dimers.

A major goal in biological imaging is to visualize interactions of different tissues, often fluorescently labeled, during dynamic processes. Only a few of these labels fit into the available spectral range without overlap, but can be separated computationally if the full spectrum of every single pixel is known. In medical imaging, hyperspectral techniques show promise to identify different tissue types without any staining. Yet, microscopists still commonly acquire spectral information either with filters, thus integrating over a few broad bands only, or point-wise, dispersing the spectra onto a multichannel detector, which is inherently slow. Light sheet fluorescence microscopy (LSFM) and optical projection tomography (OPT) are two techniques to acquire 3D microscopic data fast, photon-efficiently and gently on the specimen. LSFM works in fluorescence mode and OPT in transmission. Both are based on a fast widefield detection scheme where a 2D detector records the spatial information but leaves no room to acquire dispersed spectra. Hyperspectral imaging had not yet been demonstrated for either technique. In this work, I developed a line-scanning hyperspectral LSFM and an excitation scanning OPT to acquire 5D data (3D spatial, 1D temporal, 1D spectral) and optimized the performance of both setups to minimize acquisition times without sacrificing image contrast, spatial or spectral information. I implemented and assessed different evaluation pipelines to classify and unmix relevant features. I demonstrate the efficiency of my workflow by acquiring up to five fluorescent markers and the autofluorescence in \\zf and fruit fly embryos on my hyperspectral LSFM. I extracted both concentration maps and spectra for each of these fluorophores from the multidimensional data. The same methods were applied to investigate the transmission data from my spectral OPT, where I found evidence that OPT image formation is governed by refraction, whereas scattering and absorption only play a minor role. Furthermore, I have implemented a robust, educational LSFM on which laymen have explored the working principles of modern microscopies. This eduSPIM has been on display in the Technische Sammlungen Dresden for one year during the UNESCO international year of light. / Ein wichtiges Ziel biologischer Bildgebung ist die Visualisierung des Zusammenspiels von verschiedenen, meist fluoreszent markierten, Geweben bei dynamischen Prozessen. Nur wenige dieser Farbstoffe passen ohne Überlapp in das zur Verfügung stehende Spektrum. Sie können jedoch rechnerisch getrennt werden, wenn das gesamte Spektrum jedes Pixels bekannt ist. In medizinischen Anwendungen versprechen hyperspektrale Techniken, verschiedene Gewebetypen markierungsfrei zu identifizieren. Dennoch ist es in der Mikroskopie noch immer üblich, spektrale Information entweder mit Filtern über breiten Bändern zu integrieren, oder Punktspektren mithilfe von Dispersion zu trennen und auf einem Multikanaldetektor aufzunehmen, was inhärent langsam ist. Light Sheet Fluorescence Microscopy (LSFM) und Optical Projection Tomography (OPT) nehmen 3D Mikroskopiedaten schnell, photoneneffizient und sanft für die Probe auf. LSFM arbeitet mit Fluoreszenz, OPT in Transmission. Beide basieren auf schneller Weitfelddetektion, wobei die räumliche Information mit einem 2D Detektor aufgenommen wird, der keinen Raum lässt, um die getrennten Spektren zu messen. Hyperspektrale Bildgebung wurde bis jetzt für keine der zwei Techniken gezeigt. Ich habe ein hyperspektrales LSFM mit Linienabtastung und ein OPT mit Wellenlängenabtastung entwickelt, um 5D Daten (3D räumlich, 1D zeitlich, 1D spektral) aufzunehmen. Beide Aufbauten wurden hinsichtlich minimaler Aufnahmezeit optimiert, ohne dabei Kontrast, räumliche oder spektrale Auflösung zu opfern. Ich habe verschiedene Abläufe zum Klassifizieren und Trennen der Hauptkomponenten implementiert. Ich nehme bis zu fünf Fluorophore und Autofluoreszenz in Zebrafisch- und Fruchtfliegenembryos mit dem hyperspektralen LSFM auf und zeige die Effizienz des gesamten Ablaufes, indem ich Spektren und räumliche Verteilung aller Marker extrahiere. Die Transmissionsdaten des spektralen OPT werden mit denselben Methoden untersucht. Ich konnte belegen, dass die Bildformation im OPT massgeblich von Brechung bestimmt ist, und Streuung und Absorption nur einen geringen Beitrag leisten. Außerdem habe ich ein robustes, didaktisches LSFM gebaut, damit Laien die Funktionsweise moderner Mikroskopie erkunden können. Dieses eduSPIM war ein Jahr lang in den Technischen Sammlungen Dresden ausgestellt.

Résumé : La compréhension des contraintes qui régissent l'assemblage des machineries supramoléculaires – qu'elles soient solubles ou bien ancrées dans les membranes biologiques – est un enjeu scientifique majeur.Le système de de sécrétion type VI (T6SS) est un organelle bactérien récemment mis en évidence qui a pour particularité de posséder une origine évolutive commune avec le bactériophage T4. En raison de cette origine évolutive commune, certaines sous unités du T6SS et du bactériophage T4 présentent des structures comparables. Cependant, un grand nombre des sous unités du T6SS reste à caractériser. Parmi celles-ci, les protéines SciB et SciC sont retrouvées dans tous les systèmes de sécrétion de type VI suggérant que ces deux protéines participent à la formation du "core-complexe": le complexe minimal requis pour le fonctionnement du T6SS. / The recently identified type VI secretion system has been demonstrated to be involved in most of these processes. The T6SS is a highly complex macromolecular machine that allows Gram-negative bacteria to deliver effector proteins to both prokaryotic and eukaryotic cells in a contact-dependent manner. The T6SS promotes therefore antibacterial competition, virulence towards eukaryotes or even both. The T6SS is composed of a minimal set of 13 subunits, which are currently believed to form the core apparatus. They assemble two distinct sub-complexes: one is a cytosolic contractile structure related to the tail of contractile bacteriophages, whereas the other spans the whole cell envelope. Therefore, the T6SS is generally depicted as an inverted phage tail anchored to the cell envelope through its membrane-associated complex. Contractile tails are currently thought to assemble from four structural elements: the baseplate, the internal tube, the contractile sheath and the tail terminator. The aim of my Ph.D. work was to further characterize the assembly and function of the T6SS phage tail-like complex in enteroaggregative E. coli. In this thesis document, I provide evidence that the internal tube assembles from Hcp hexamers stacked in a head-to-tail manner and that this internal cylinder is used as a template during sheath assembly. I also characterized a sub-complex of three proteins (TssEFG) that forms the baseplate of the T6SS and controls the polymerization of the tube and sheath. Finally, I recently showed that the T6SS functions like a nano-crossbow to kill target cells as the contraction of the T6SS results in prey cell death during interbacterial competition.

The Amazon basin has about 7000 km2 of extension and a vast biodiversity providing an ichthyofauna of approximately 5000 species of fish. Myxozoan parasites cause diseases in fish in both the natural environment and the breeding systemand they are responsible for high mortality rates. Myxozoans show a great diversity of species with some of them, highly pathogenic and, therefore, have been receiving attention of the researchers. In Brazil, due to the great diversity of fish species, the study of these parasites has been gaining the attention of the researchers, focusing on diversity, biology and parasite-host interaction. In this context, the objective of this work was to explore the parasite diversity of the Myxozoa subphylum, through morphological and molecular analyses of myxosporean parasites of Amazonian fish, important for the food market such as Colossoma macropomum (tambaqui) and Piaractus brachypomus (pirapitinga). For the taxonomic study, morphological analyses were performed using light microscopy and molecular analyses using ssrDNA. The fish were captured in the Amazon basin, in the Tapajós and Solimões Rivers, Santarém, PA and Manaus, AM, respectively. Two new myxosporean species, Myxobolus n. sp. 1 and Myxobolus n. sp. 2, were described infecting C. macropomum, based on morphological and molecular data. Myxobolus colossomatis, found infecting C. macropomum, was considered a distinct species of Myxobolus cf. colossomatis described in Piaractus mesopotamicus, through molecular and phylogenetic data. For P. brachypomus four new species were described. Henneguya n. sp. 1 and Myxobolus n. sp. 3, were described through of morphological, histological, ultra-structural and molecular analyses. Henneguya n. sp. 2 and Myxobolus n. sp. 4 were described based in morphological and molecular data. After observing the mitochondrial behavior of myxospores through electron microscopy studies, we performed an experiment of mitochondrial fluorescence microscopy and the results showed that few Henneguya sp. myxospores presented labeling for mitochondrial activity. / A bacia Amazônica tem cerca de 7000 km2 de extensão e uma vasta biodiversidade abrigando uma ictiofauna de, aproximadamente, 5000 espécies de peixes. Parasitos mixozoários são causadores de doenças em peixes de ambiente natural e de sistemas de criação sendo responsáveis por altas taxas de mortalidade. Mixosporídeos apresentam uma grande diversidade de espécies com algumas destas, altamente patogênicas e, por isso, vêm recebendo atenção dos pesquisadores. No Brasil, devido à grande diversidade de espécies de peixes, o estudo destes parasitos vem ganhando cada vez mais destaque, com foco para a diversidade, biologia e a interação parasito-hospedeiro. Neste contexto, o objetivo deste trabalho foi explorar a diversidade de parasitos do subfilo Myxozoa, através de análises morfológicas e moleculares de mixosporídeos parasitos de peixes amazônicos, importantes para o mercado de alimentos como Colossoma macropomum (tambaqui) e Piaractus brachypomus (pirapitinga). Para o estudo taxonômico foram realizadas análises morfológicas, utilizando microscopia de luz, e análises moleculares utilizando o sequenciamento do ssrDNA. Os peixes foram capturados na bacia Amazônica, nos rios Tapajós e Solimões, Santarém, PA e Manaus, AM, respectivamente. Duas novas espécies de mixosporídeos, Myxobolus sp. n. 1 e Myxobolus sp. n. 2, foram descritas infectando C. macropomum, baseado em dados morfológicos e moleculares. Myxobolus colossomatis encontrada infectando C. macropomum foi considerada uma espécie distinta de Myxobolus cf. colossomatis descrita em Piaractus mesopotamicus, através de dados moleculares e filogenéticos. Para P. brachypomus quatro novas espécies foram descritas. Henneguya sp. n. 1 e Myxobolus sp. n. 3 foram descritas através de análises morfológicas, histológicas, ultra-estruturais e moleculares. Henneguya sp. n. 2 e Myxobolus sp. n. 4 foram descritas baseadas em dados morfológicos e moleculares. Após a observação do comportamento mitocondrial de mixosporídeos através de estudos de microscopia eletrônica, nós realizamos um experimento de microscopia de fluorescência mitocondrial e os resultados obtidos demonstraram que poucos mixosporos de Henneguya sp. apresentaram marcação para a atividade mitocondrial.

Ce projet de thèse s'inscrit dans une dynamique de développement des polyrotaxanes de cyclodextrines pour des applications biomédicales. L'objectif est d'obtenir, par une approche modulaire et convergente, des polyrotaxanes fonctionnalisés pour l'imagerie par microscopie optique dans le proche infrarouge et l'IRM. Une bibliothèque de cyclodextrines fonctionnalisées a été générée par CuAAC entre des fluorophores (BODIPY, Cyanine) ou un agent de contraste (monoamide-DOTA-Gd) et des ?-cyclodextrines mono- ou bis-azotures. Leurs propriétés d'auto-assemblage ont été étudiées sur un axe court et ont permis le développement de [3]rotaxanes fonctionnalisés pour l'IRM dont les expérimentations in vivo ont démontré l'apport bénéfique de la structure supramoléculaire pour les propriétés d'agent de contraste. L'extension de l'architecture aux polyrotaxanes multimodaux a été réalisée par l'utilisation d'un axe polyammonium. Une nouvelle classe d'axes anioniques a été développée avec l'étude cinétique et thermodynamique de l'enfilage sélectif d'une ou deux cyclodextrines sur des monomères diphosphates et montre l'intérêt des pseudo-bouchons phosphates pour le contrôle de la barrière d'activation par le pH. L'extension à une structure pseudopolyrotaxane est obtenue par la synthèse d'un poly(hexylène phosphate) et permet de valider l'utilisation du polymère pour la synthèse de composés fonctionnalisés. En perspective de ces développements, des voies de post-fonctionnalisation des polyrotaxanes, une nouvelle voie de synthèse par polymérisation de pseudo-rotaxanes et l'obtention d'une cyclodextrine pour le relargage contrôlé par stimuli acido-basiques sont abordées. / This PhD project is focused on the development of cyclodextrin-based polyrotaxanes for biomedical applications. The objective is to use a modular building-block approach to synthesize functionalized polyrotaxanes for NIR fluorescence and magnetic resonance imaging. A library of functionalized cyclodextrins was obtained by a versatile ‘click’ reaction between fluorescent probes (BODIPY, Cyanine) or contrast agent (GdDOTA-monoamide) and mono- or bis-azido α-cyclodextrins. Their self-assembly properties were first studied on short axles and allowed the development of functionalized [3]rotaxanes for MRI. In vitro and in vivo studies demonstrated the advantages of the supramolecular approach for the design of contrast agent with an enhancement of the relaxivities and better retention times in kidneys. The strategy was extended to obtain multimodal polyrotaxane architectures based on a poly(alkyl)ammonium thread. A new family of anionic threads based on alkylphosphate moieties was also developed. Thorough kinetic and thermodynamic studies revealed the ability of phosphates to act as pH-responsive stoppers enabling a selective threading of one or two cyclodextrins on small alkanediphosphate threads. Pseudopolyrotaxanes of α-CD were then obtained with poly(hexylene phosphate) and pave the way for the synthesis of functionalized ones. Finally, significant investigations in the post-functionalization of polyrotaxanes, polymerization of pseudo-rotaxanes as new synthetic pathway and pH-switchable rotaxane for controlled release were realized.

Most of the protein coding genes of higher eukaryotes contain introns which have to be removed from primary transcripts to make mRNA which can be used as a template for protein synthesis. This crucial step in the pre-mRNA processing is carried out by the spliceosome, a complex ribonucleoprotein machine formed from small ribonucleoprotein particles (snRNPs). snRNPs biogenesis is a complex process composed of several steps which take place in both the cytoplasm and the nucleus. Spliceosome assembly is highly dynamic and tightly regulated and pre-mRNA splicing depends not only on the sequence of the pre-mRNA itself but also on the nuclear context, such as the chromatin modifications. How do cells regulate where and when the spliceosome would be assembled? What determines which introns will be spliced? These are fundamental, yet unanswered, biological questions. In this work we analyzed the formation of splicing machinery in the context of the cell nucleus from several different points of view. First, we investigated the unexpected connection between splicing factor U1-70K and the survival of motor neurons (SMN) complex which is a major player in the snRNP biogenesis pathway. We revealed that U1-70K interacts with the SMN complex and that this interaction is crucial for the stability of nuclear gems, small...