Foamyviren (FV) gehören zur Familie der Retroviridae, werden aber aufgrund besonderer Eigenschaften in eine eigene Unterfamilie, die Spumaretrovirinae, eingeordnet. FV besitzen vor allem in vitro einen sehr breiten Tropismus, so dass bisher keine Zelllinie bekannt war, die nicht durch FV infiziert werden konnte. Obwohl diese Besonderheit darauf schließen lässt, dass ein sehr ubiquitäres Molekül auf der Wirtszelloberfläche für die FV-Bindung verwendet wird, ist der Rezeptor für die Virus-Aufnahme noch nicht bekannt. Dass FV einen pH-abhängigen Aufnahmemechanismus verwenden, lässt eine endozytotische Aufnahme vermuten. Dennoch sind die frühen Replikationsschritte, die zur Fusion der viralen und Wirtszellmembran führen, nur unzureichend charakterisiert. Deswegen wurden in der vorliegenden Arbeit funktionelle autofluoreszierende FV hergestellt, um die Bindung und Aufnahmemechanismen foamyviraler Partikel in Wirtszellen mit fluoreszenzmikroskopischen Analysen zu untersuchen. Mit diesen Methoden konnten erstmalig vier Zelllinien identifiziert werden, die nicht mit FV infizierbar sind, und damit mögliche Kandidaten für die Identifizierung des unbekannten FV Rezeptors darstellen. Des Weiteren wurden die fluoreszierenden FV erfolgreich eingesetzt, um die Fusionsereignisse zwischen viraler und zellulärer Membran in Echtzeit in lebenden Zellen zu untersuchen. Die durchgeführte „Single Virus Tracking“-Analyse zeigte, dass PFV (Prototype FV) Env-tragende Partikel sowohl an der Plasmamembran als auch in vermeintlichen Endosomen fusionieren können, wohingegen SFV (Simian FV) Env-tragende Partikel die Fusion wahrscheinlich nur in Endosomen auslösen können. Hinweis zur Nutzung der Filmdateien: Öffnen mit QuickTimePlayer bzw. ImageJ

The KdpFABC complex from E. coli functions as a high affinity K uptake system and belongs to the superfamily of P-type ATPases. So far, no information is available about the orientation of the subunits within the complex as well as its oligomeric state. By chemical crosslinking, gel filtration, electron transmission microscopy and single particle FRET analysis this study shows that the KdpFABC complex occurs as a homodimer with a dissociation constant between 30 to 50 nM. Furthermore, by means of single particle analysis of transmission electron micrographs, the solution structure of the complex at 1.9 nm resolution could be solved, thus providing the first structural analysis resolving all subunits of the holoenzyme. Based on crystal structures, it is generally assumed that P-type ATPases undergo large domain movements during catalysis. However, these conformational changes have never been shown directly. By use of single molecule FRET with alternating laser excitation, distance changes could be measured directly within KdpB during ATP hydrolysis. With this technique, distances and dwell times were determined for three conformational states in the working enzyme as well as in the orthovanadate- and the OCS-inhibited state.

L’identification de biomarqueurs des maladies mentales telles que l’autisme, la schizophrénie ou la maladie d’Alzheimer, est d’une importance capitale non seulement pour établir un diagnostic objectif, mais aussi pour suivre l’effet des traitements. La création et le maintien de fonctions neuronales sub-cellulaires, telle que la plasticité synaptique, sont fortement dépendants du transport intraneuronal, essentiel pour acheminer d’importants composants à des positions spécifiques. Un transport actif défaillant semble être partiellement responsable d’anomalies de la plasticité synaptique et de la morphologie neuronale présentes dans de nombreuses maladies neuropsychiatriques. Cette thèse décrit (i) la mise au point d’une méthode de quantification du transport intraneuronal reposant sur le suivi de nanoparticules de diamants fluorescents (fNDs); (ii) l’application de cette technique simple et faiblement invasive à l’analyse fonctionnelle de variants génétiques associés à des maladies neuropsychiatriques. Ce manuscrit comporte quatre chapitres. Le premier détaille l’architecture polygénique complexe des maladies mentales et démontre la pertinence d’étudier le transport intraneuronal. Les deuxième et troisième chapitres sont dédiés à la méthode et détaillent les stratégies d’internalisation des fNDs, les outils de quantification du transport intraneuronal et la validation de la technique. La forte brillance, la photo-stabilité parfaite et l’absence de toxicité cellulaire font des fNDs un outil de choix pour étudier la dynamique du transport intraneuronal sur une durée d’observation de plusieurs heures avec une haute résolution spatiotemporelle et une bonne puissance statistique. Enfin, dans le quatrième chapitre, nous appliquons cette nouvelle méthode d’analyse fonctionnelle pour étudier l’effet de variants génétiques associés à l’autisme et à la schizophrénie. Pour cela, nous utilisons des lignées de souris transgéniques ayant une faible surexpression des gènes MARK1 et SLC25A12, ainsi que des AAV-shRNA pour induire une haplo-insuffisance du gène AUTS2. Notre méthode de diagnostic moléculaire s’avère suffisamment sensible pour déceler des variations fines de la dynamique du transport intraneuronal, ouvrant la voie à de futurs développements en nanomédecine translationnelle. / The identification of molecular biomarkers of brain diseases as diverse as autism, schizophrenia and Alzheimer’s disease, is of crucial importance not only for an objective diagnosis but also to monitor response to treatments. The establishment and maintenance of sub-cellular neuronal functions, such as synaptic plasticity, are highly dependent on intracellular transport, which is essential to deliver important materials to specific locations. Abnormalities in such active transport are thought to be partly responsible for synaptic plasticity and neuronal morphology impairment found in many neuropsychiatric and neurodegenerative diseases. This thesis reports (i) the development of a quantification technic of intraneuronal transport based on fluorescent nanodiamonds (fNDs) tracking; (ii) the application of this simple and minimally invasive approach to the functional analysis of neuropsychiatric disease-related genetic variants.This manuscript falls into four chapters. The first one details the complex polygenic architecture of mental disorders and demonstrates the disease relevance of monitoring the intraneuronal transport. The second and the third chapters are dedicated to the nanodiamond-tracking assay and describe the fNDs internalisation strategies, the spatiotemporal quantitative readouts and the validation of the technic. The high brightness, the perfect photostability and the absence of cytotoxicity make fNDs a tool of choice to perform high throughput long-term bioimaging at high spatiotemporal resolution. Finally, in the fourth chapter, we apply this new functional analysis method to study the effect of genetic variants associated to autism and schizophrenia. We established transgenic mouse lines in which MARK1 and SLC25A12 genes were slightly overexpressed, and AAV-shRNA to induce AUTS2 gene haploinsufficiency. Our molecular diagnosis assay proves sufficiently sensitive to detect fine changes in intraneuronal transport dynamic, paving the way for future development in translational nanomedicine.

No description available.

Les nanoparticules d’argent (Ag NPs) sont considérablement utilisées dans l’industrie alimentaire. Elles sont fortement appliquées comme enrobages d’emballages alimentaires afin d’assurer une meilleure qualité des aliments et une plus longue durée de conservation sur les étagères des supermarchés. En revanche, les risques associés aux Ag NPs sont inquiétants. Leurs effets potentiels sur les humains et sur l’environnement suscitent un grand intérêt scientifique. C’est pourquoi il est important de valider des méthodes analytiques pour détecter, caractériser et quantifier les Ag NPs dans la nourriture mise en contact avec ce type de contenant. Les méthodes permettront de mieux comprendre la migration de l'argent vers les aliments directement ingérés par l’humain. La spectrométrie de masse à plasma à couplage inductif en mode particule unique (SP-ICP-MS) est une technique prometteuse pour caractériser et quantifier de petites particules (de quelques nanomètres) à de faibles concentrations (dans l'ordre du ng L-1). Contrairement aux techniques analytiques conventionnelles, telles que les techniques de microscopie et de diffusion de la lumière, le SP-ICP-MS distingue la forme ionique de la forme particulaire de l'analyte. Cette présente étude valide une méthode pour la caractérisation et la quantification des Ag NPs et de l’argent ionique dans deux boissons et trois simulants: jus d'orange, préparation en poudre pour nourrissons, eau Milli-Q, acide acétique à 3% et éthanol à 10%. De plus, une meilleure compréhension du devenir et de la migration de l’argent provenant d'emballages alimentaires nano-activés a pu être obtenue. En effet, les milieux acides et les traitements thermiques ont engendré de plus grands relargages d’argent, sous forme ionique, contrairement aux milieux dits « lipophiles » tels que la préparation pour nourrissons et l’éthanol. En conclusion, ce mémoire nous démontre que les voies de libération des NPs des contenants nano-activés ne sont pas encore très bien comprises. De plus amples études doivent être entreprises afin de pouvoir établir des modèles de migration clairs et afin de mieux comprendre les risques associés à leurs utilisations. / Silver nanoparticles (Ag NPs) are increasingly used in the food industry. They are integrated into coatings of various food packaging to help ensure longer product shelf life. However, the risks associated with Ag NPs are currently not well known and their potential effects on humans are causing growing concern. Furthermore, it is not clear whether NPs have greater or lesser risk than dissolved silver ions or bulk phase Ag. Consequently, it is necessary to detect and to characterize the release of silver from silver-enhanced containers into real food matrices using sensitive analytical techniques that allow one to distinguish between silver ions and nanoparticles. Single particle ICP-MS is a promising technique to count and size small particles at low concentrations. Compared to other conventional instrumentation, it can distinguish between ionic and particulate forms of the analyte. This thesis focused firstly on the validation of an analytical method for the analysis of Ag NPs and ionic silver in three different food simulants (Milli-Q water, 10% ethanol and 3% acetic acid) and in two drinks (orange juice and infant milk formula). A better understanding of the aging and of the migration of silver has been reached in these matrices. Essentially, acidic media caused significant NP oxidation whereas organic macromolecules like lipids, proteins and polysaccharides appeared to increase the stability of the NPs. Subsequently, a migration study from silver-enhanced containers showed significant release of dissolved Ag in 3% acetic acid and a lower release in milk formula. Also, heating led to a considerable release of silver from the container. To conclude, further studies are needed to obtain clear release models to better understand the risk on humans and on the environment.

No description available.

Batterimodeller används för att representera batterier. För ändamål som batterihanteringssystem används idag främst empiriska modeller som representerar ett batteri med en motsvarande kretsmodell. Några nackdelar för dessa modeller ligger i dess oförmåga att simulera interna tillstånd och en tidskrävande parametriseringsprocess. Dessa nackdelar motiverar ingenjörer att vända sig till modeller som är baserade på fysiska lagar som ett alternativ eftersom de kan ge insikt i vad som händer inuti batteriet. Batterimodellerna som är baserade på de fysiska lagarna har alltför krävande beräkningar för att kunna användas för vissa applikationer, som batterihanteringssystem. Singel-partikelmodellen (SPM) är en fysikbaserad modell som används i detta avhandlingsprojekt. Syftet med projektet var att hitta en metod för att parametrisera SPM för nya kommersiella cylindriska HTPFR18650 1100mAh 3.2V litiumjärnfosfatceller. En litteraturundersökning och experiment användes för att extrahera parametervärdena. 17 parametrar valdes från litteraturundersökningen eftersom de kunde användas för att parametrisera modellen. Geometriska parametrar hittades genom en cellöppning. Tre typer av icke-destruktiva experiment som var inspirerade av litteraturen utfördes för att extrahera värden för de andra icke-geometriska parametrarna. Ett cykeltest med låg strömhastighet utfördes för att få en pseudo-OCV-kurva och för att extrahera kapacitetsrelaterade parametrarna. En känslighetsanalys genomfördes för galvanostatisk intermittent titreringsteknik testet (GITT) och pulstestet för de parametrar som var kopplade till transportoch kinetiska fenomen. Python matematisk batterimodellering (PyBaMM) användes för att simulera experimenten. Parametersamlingen Prada 2013 användes som standardvärden. Standardvärdena för de valda parametrarna ersattes av de värden som hittades genom experiment. Känslighetsanalysen visade att några av de valda parametrarna var känsliga för experimenten medan andra inte var det. Parametrarna extraherades genom fysiska relationer och genom att anpassa parametervärde för simuleringen så att den passar den experimentella datan under urladdningsförloppet. Värden för 14 av de 17 parametrarna extraherades i metoden. Den parametriserade modellen validerades mot två potentiella applikationer, en för ett batterielfordon och den andra för ett mild-hybridfordon. Den parametriserade modellen visade att den negativa partikelradien inte kan hittas med den föreslagna parametriseringsmetoden. Simuleringen visade sig också matchade den experimentella datan bättre under urladdning av cellerna jämfört till uppladdning. Flera förbättringar för framtida arbete har föreslagits, såsom att utvidgning av känslighetsanalysen, att erhålla OCV-kurvan från GITT istället för att använda pseudo-OCVkurvan, att använda strängare gränser vid kurvanpassningarna samt att skapa mer optimala tester för att extrahera parametervärdena. / Battery models are used to represent batteries. For purposes like battery management systems, empirical based models like the equivalent circuit models are widely used. These models have downsides regarding for example inability to simulate internal states and parametrization time that make engineers look at physics-based models as an alternative. The physics-based models are made up of physical relationships that offer insights into what is happening inside the battery. These are too computationally demanding to be used for certain applications, like battery managements systems. The Single Particle Model (SPM) is a physics-based model that is utilized in this thesis project. The aim of the project is to find a method to parametrize the SPM for fresh commercial cylindrical HTPFR18650 1100mAh 3.2V lithium iron phosphate cells. Literature survey and experiments were used to extract the parameter values. 17 parameters were selected from the literature survey since they could be used to parametrize the model. Geometrical parameters were found through a cell opening. Three types of nondestructive experiments inspired by literature were performed to extract values for the other non-geometric parameters. A low-rate cycling test was performed to get pseudo-OCV curve and to extract capacity related parameters. A sensitivity analysis is done for the GITT and the Pulse test for the parameters that were connected to the transport and kinetic phenomena. Python mathematical battery modelling (PyBaMM) was used to simulate the experiments. The Prada 2013 parameter set was be used as default values. The default values for the selected parameters were replaced by the values found through experiments. The sensitivity analysis showed that some of the selected parameters were sensitive while others were not. The parameters were extracted through physical relations and through curve fitting procedures during discharge. Values for 14 out of the 17 parameters were extracted in the method. The parametrized model was validated against two potential applications, one for a battery electric vehicle and the other for a mild hybrid. The parametrized model showed that the negative particle radius cannot be found through the proposed parametrization procedure. The simulation matched the experimental data better for discharging cells than charging cells. Several improvements for future work have been suggested such as extending the sensitivity analysis, obtaining the OCV-curve from GITT instead of low-rate cycling, having stricter bounds for the curve fitting as well as creating more optimal tests to extract the parameter values.

Biological systems carry inherent complexity, which pose difficulties observing behavioural properties, such as diffusion coefficients, kinetic constants and state switching occurrences. With constantly improving computing power and microscopy technologies, single molecule methods have become a viable alternative when probing the behaviour of proteins, enzymes, lipids and other molecules. Processed microscopy images and videos provide information such as particle intensities and trajectories, avoiding ensemble averaging and therefore allowing for a detailed breakdown of particle mobility and interactions. A single particle tracking (SPT) algorithm was developed which implements detection, localization and position linking on image stacks. Sub-pixel precise detection is done via either centroid determination, Gaussian fit, or radial symmetry centres, while tracking makes use of distance based global cost optimization. The detection algorithm is also used for single particle spectroscopy, where intensity information is used to determine the size of oligomers, as well as their interaction with other molecules through channel intensity cross-correlation. The algorithm underwent benchmarking with simulated videos and was applied to three different biological systems with comparison to other established methods of analysis. The first system studied was the diffusion of the fluorescent lipophilic dye DiD in a five-component mitochondria-like solid-supported lipid bilayer. Comparing line-scanning fluorescence correlation spectroscopy (FCS) and single particle tracking, the measured diffusion coefficients were found to be statistically different, with DFCS = 3 μm2s-1 and DSPT = 2 μm2s-1, indicating different operational ranges for the two methods. FCS outperforms SPT when the diffusion coefficient exceeds 1 μm2s-1, making it ideal for lipid diffusion in fluid membranes and proteins in solution with weak membrane interaction. SPT is best suited for mobile and immobile membrane inserted proteins, as well as lipid diffusion in viscous membranes. The second system studied was the interaction between the two proteins Bax and Bid when inserted in a membrane. Bax and Bid are both members of the Bcl-2 family of proteins, which plays a vital role in the apoptosis mechanism, by inducing mitochondrial outer membrane permeabilization. To study this system with single particle spectroscopy, fluorescently labelled Bax and truncated Bid (tBid) were imaged when interacting with a mitochondria-like supported lipid bilayer with confocal microscopy. Immobile and mobile particles were detected and distinguished based on the eccentricity of the observed fluorescence spot. The intensity of the particle signal was used to determine oligomer type (homo-oligomerization) while the interaction with the particles' counterpart (hetero-oligomerization) was determined by channel cross-correlation. This allowed the measurement of the 2D-KD values for mobile (0.6 μm-2) and immobile (0.08 μm-2) Bax/tBid complexes, showing that the degree of insertion of the proteins in the membrane greatly affect their affinity for each other. The third and final system studied was the motion of cellulases on cellulose fibers. Enzymatic hydrolysis of crystalline cellulose is a costly step in the generation of fermentable sugars for biofuel production. Due to the complex structure and many possible interaction states of the enzymes with cellulose, single particle tracking is a well-adapted technique to the gathering of information on the enzyme dynamics, which is essential for process optimization. The movement of cellulases on cellulose substrate was observed via labelled Thermobifidia fusca Cel5A, Cel6B and Cel9A on bacterial micro-crystalline cellulose substrate. The detected trajectories were analyzed using multiple diffusion models. A simple one-state diffusion model was insufficient to describe the observed radial displacement distributions and so a two-state model was introduced and confronted with the data using conventional least-squares fits , as well as a hidden Markov approach. The diffusion coefficients of the two states are found to be on the order of Dfast = 10-3 μm2s-1 and Dslow = 10-4 μm2s-1, with the slow state being more stable and therefore more likely to occur. Single particle tracking can give us better insight into complex interactions, such as synergistic binding of proteins existing in several different states and processive enzymatic behaviour, where ensemble averaging techniques can fall short. The uses of single molecule methods are plentiful and with the current rise of machine learning, higher levels of abstraction will provide us with more detailed insights into biological processes, driving promising developments in the medical field, as well as new technologies in many sectors of industry. / Thesis / Doctor of Science (PhD) / Proteins are the motors that drive most cellular processes, for example steering a cell’s life cycle, or decomposing sources of nutrients. Being able to observe the motion of individual proteins is key to understanding their behaviour. In this work a single particle tracking (SPT) program was developed to extract protein trajectories from fluorescence microscopy experiments. With this tool-set we investigated the following two systems. The first system of interest is the Bcl-2 protein family, which is vital during the pro- grammed cell death at the end of each cell’s life span. The failure of a controlled cell death can have dire consequences, such as necrosis and cancer. The Bcl-2 family proteins Bid and Bax are active on the outer membrane of the mitochondria, where they initiate the process of terminating the cell’s functions by forming pores. For our experiments we ar- tificially mimicked the outer membrane of the mitochondria, introduced Bid and Bax and observed their preferential groupings on the membrane surface. This provided indications of the mechanisms involved during binding and pore formation. The motivation behind the investigation of the second system is the improvement of biofuel generation from a renewable source: plant-based biomass. Cellulases are enzymes from bacteria or fungi that break down cellulose – one of the main building blocks of all plant cell walls – into fermentable sugars. In fluorescence microscopy experiments a purified cellulose substrate was used to monitor the motion of three types of cellulases. The insight which we gained into the cellulase behaviour may allow the optimization of the process of cellulose decomposition.

Droplet Interface Bilayers (DIBs) have a number of attributes that distinguish them from conventional artificial lipid bilayers. In particular, the ability to manipulate bilayers mechanically is explored in this thesis. Directed bilayer area changes are used to make precise measurements of the specific capacitance of DIBs and to control the two dimensional concentration of a membrane protein reconstituted in the bilayer. Chapter 1 provides a general introduction to the role of the lipid membrane en- vironment in the function of biological membranes and their integral proteins. An overview of model lipid bilayer systems is given. Chapter 2 introduces work carried out in this laboratory previously and illustrates the experimental setup of DIBs. Some important bilayer biophysical concepts are covered to provide the theoretical background to experiments in this and in later chapters. Results from the characterisation of DIBs are reported, and an account of the development of methods to manipulate the bilayer by mechanical means is given. Chapter 3 describes experiments that apply bilayer area manipulation in DIBs to achieve precise measurement of specific capacitance in a range of lipid systems. Chapter 4 reports results from experiments investigating the response of bilayer specific capacitance to an applied potential. Chapter 5 covers the background and experimental setup for total internal fluo- rescence microscopy experiments in DIBs and describes the expression, purification and characterisation of the bacterial β-barrel membrane protein pore α-Hemolysin. Chapter 6 describes experiments that apply the mechanical manipulation of bilayer area in DIBs to the corralling and control of the surface density of α-Hemolysin.

L’utilisation accrue des nanomatériaux manufacturés (NM) fait en sorte que les différents acteurs de réglementation se questionnent de plus en plus par rapport à leur destin et leurs impacts sur les écosystèmes et la santé humaine suite à leur rejet dans l’environnement. Le développement de techniques analytiques permettant de détecter et de caractériser les NM en matrice environnementale est impératif étant donné la nécessité d’évaluer le risque relié à ces polluants émergents. Une des approches de plus en plus favorisée est d’utiliser une technique chromatographique et un ou plusieurs détecteurs sensibles dans les buts de réduire les effets de matrice, d’identifier des nanoparticules (NP) selon leurs temps de rétention et de les quantifier à des concentrations représentatives de la réalité environnementale. Une technique analytique utilisant la chromatographie hydrodynamique (HDC) et des détecteurs en ligne ou hors ligne (détecteurs de diffusion statique ou dynamique de la lumière, spectromètre de masse par torche à plasma en mode particule unique (SP-ICPMS), l’ultracentrifugation analytique) a donc été développée. Le couplage de la colonne HDC avec ces détecteurs a permis de caractériser des NP standards et l’optimisation des conditions de séparation de ces nanoparticules de polystyrène, d’or et d’argent a permis de confirmer que les NP y sont bel et bien séparées seulement selon leur taille, tel que la théorie le prédit. De plus, l’utilisation de la colonne HDC couplée au SP-ICPMS a permis de séparer un mélange de nanoparticules d’argent (nAg) et de les détecter à des concentrations représentatives de celles rencontrées dans l’environnement, soit de l’ordre du μg L-1 au ng L-1. Par exemple, dans un échantillon d’eau usée (effluent), un mélange de nAg de 80 et de 40 nm a été séparé et les nAg ont été détectées à l’aide du SP-ICPMS connecté à la colonne HDC (temps de rétention de 25.2 et 25.6 minutes et diamètres déterminés de 71.4 nm et 52.0 nm). Finalement, pour plusieurs échantillons environnementaux auxquels aucun ajout de nanoparticules n’a été fait, les analyses HDC-SP-ICPMS effectuées ont permis de déterminer qu’ils ne contenaient initialement pas de nAg. / Due to the widespread use of engineered nanoparticles (ENP), regulatory agencies are very concerned about their fate and their impacts on the environment and on human health. The development of analytical techniques, which will allow the detection, characterization and quantification of ENP in environmental matrices, is therefore critical in order to properly evaluate the exposure associated with these emerging pollutants. One promising approach to detect and quantify the nanoparticles is to couple a chromatographic technique to a sensitive detector in order to: (i) reduce matrix effects; (ii) identify nanoparticles from their retention times and (iii) quantify the ENP at environmentally relevant concentrations. Consequently, the coupling of hydrodynamic chromatography (HDC) was performed with both on-line and off-line detectors (light scattering detectors, inductively coupled plasma mass spectrometer in its single particle mode (SP-ICPMS) and an analytical ultracentrifuge). HDC was first used for the characterization of ENP standards. Separation conditions were optimized for standard nanoparticle suspensions of polystyrene, gold and silver, which allowed us to confirm that the separation was occurring, based on hydrodynamic size, as predicted by theory. By coupling the HDC column to the ICPMS detector in its ‘‘single particle’’ mode, it was possible to separate an ENP mixture and to detect the nanoparticles at environmental concentrations, i.e., in the μg L-1 to ng L-1 range. For example, in a wastewater sample (effluent wastewater), a mixture of two silver nanoparticles (nAg) of 40 and 80 nm were separated and the nAg were detected by SP-ICPMS at retention times of 25.2 and 25.6 minutes. Diameters of 71.4 nm and 52.0 nm were found. HDC-SP-ICPMS analysis carried out on different non-spiked wastewater samples allowed us to conclude that nAg was below the detection limit of 0.1 µg L-1.