Cell biophysical properties are a new class of biomarkers that can characterize cells into subgroups that indicate differences in phenotypes that may correlate with disease and cell state. Microfluidic biophysical cell sorters are platforms that utilize these newly developed biomarkers to expand biomedical capabilities for improvements in cell state detection and characterization. Cell biophysical properties are important indicators for cell state and function because they point to differences in cell structures, such as cytoskeletal arrangement and nuclear content. In particular, some diseases, such as cancer and malaria, can cause significant changes in cell biophysical properties. Therefore, cell biophysical properties have the potential to be used for disease diagnostics. Microfluidic systems which can interrogate these biophysical properties and exploit changes in biophysical properties to separate cells into subpopulations will provide important biomedical capabilities. In this combined theoretical and experimental investigation, we explore a new type of cell sorter which utilizes differences in biophysical properties of cells. These biophysical properties that can be utilized to sort cells include size, elasticity and viscosity. We invented a microfluidic system for continuous, label-free cell separation that utilizes variations in cell biophysical properties. A microfluidic channel is decorated by periodic diagonal ridges that are designed to compress flowing cells in rapid succession. The physical compression, in combination with hydrodynamic secondary flows induced by the ridged microfluidic channel, translates each cell perpendicular to the channel axis in proportion to its biophysical properties. Through careful experimental and computational studies, we found that the cell trajectories in the microfluidic cell sorter correlated to these biophysical properties. Furthermore, we examine the effect of channel design parameters under various experimental conditions to derive cell separation models that can be used to qualitatively predict cell sorting outcome. A variety of biophysical measurement tools, including atomic force microscopy and high-speed optical microscopy are used to directly characterize the heterogeneous population of cells before and after separation. Taken together, we describe the physical principles that our microfluidic approach can be effectively used to separate a variety of cell types. The major contribution is the creation and characterization of a novel microfluidic cell- sorting platform that utilizes cell biophysical properties to enrich cells into phenotypic subtypes. This innovative approach opens new ways for conducting rapid and low-cost cell analysis and disease diagnostics through biophysical markers.

No / Growing three dimensional (3D) cells is an emerging research in tissue engineering. Biophysical properties of the 3D cells regulate the cells growth, drug diffusion dynamics and gene expressions. Scaffold based or scaffoldless techniques for 3D cell cultures are rarely being compared in terms of the physical features of the microtissues produced. The biophysical properties of the microtissues cultured using scaffold based microencapsulation by flicking and scaffoldless liquid crystal (LC) based techniques were characterized. Flicking technique produced high yield and highly reproducible microtissues of keratinocyte cell lines in alginate microcapsules at approximately 350 ± 12 pieces per culture. However, microtissues grown on the LC substrates yielded at lower quantity of 58 ± 21 pieces per culture. The sizes of the microtissues produced using alginate microcapsules and LC substrates were 250 ± 25 μm and 141 ± 70 μm, respectively. In both techniques, cells remodeled into microtissues via different growth phases and showed good integrity of cells in field-emission scanning microscopy (FE-SEM). Microencapsulation packed the cells in alginate scaffolds of polysaccharides with limited spaces for motility. Whereas, LC substrates allowed the cells to migrate and self-stacking into multilayered structures as revealed by the nuclei stainings. The cells cultured using both techniques were found viable based on the live and dead cell stainings. Stained histological sections showed that both techniques produced cell models that closely replicate the intrinsic physiological conditions. Alginate microcapsulation and LC based techniques produced microtissues containing similar bio-macromolecules but they did not alter the main absorption bands of microtissues as revealed by the Fourier transform infrared spectroscopy. Cell growth, structural organization, morphology and surface structures for 3D microtissues cultured using both techniques appeared to be different and might be suitable for different applications. / (Science Fund Vot No.: 0201-01-13-SF0104 or S024) awarded by Malaysia Ministry of Science and Technology (MOSTI) and IGSP Grant Vot No. U679 awarded by Universiti Tun Hussein Onn Malaysia.

Les récepteurs de type kaïnate (rKA) appartiennent, avec les récepteurs de type NMDA (rNMDA) et les recepteurs de type AMPA (rAMPA), à la famille des récepteurs canaux glutamatergiques (iGluR). Les propriétés fonctionelles des rKA contenant la sous-unité GluK3 en font des récepteurs tout à fait singuliers. Une étude réalisée dans le laboratoire a montré que la faible sensibilité de ces récepteurs au glutamate est liée à une entrée très rapide dans l’état désensibilisé et que la fonction de ces récepteurs pourrait être amplifiée par des modulateurs endogènes.Parmi les modulateurs potentiels de la fonction des rKA pré-synaptiques, nous avons choisi d’étudier le zinc, en raison de sa concentration importante dans les vésicules des terminaisons des axones des cellules granulaires du gyrus denté (fibres moussues). En dépit du rôle proposé des rKA contenant la sous unité GluK3 dans la régulation pré-synaptique aux synapses MF-CA3, la modulation de ces récepteurs par le zinc n’a jamais été étudiée.Grâce à l’enregistrement électrophysiologique des courants GluK3 exprimés dans les cellules HEK-293, nous avons montré que le zinc facilite les courants des récepteurs contenant la sous-unité GluK3, activés par le glutamate. L’analyse des cinétiques, ainsi que la modélisation, montrent que l’effet facilitateur du zinc est dû à la réduction de l’entrée dans l’état désensibilisé des récepteurs GluK3. Grâce à la mutagénèse dirigée et l’étude cristallographique, nous avons pu déterminer le site de liaison du zinc, constitué de l’aspartate 759, de l’histidine 762 et de l’aspartate 730, et localisé dans l’interface de dimérisation du domaine de liaison de l’agoniste (LBD).Cette étude décrit pour la première fois un nouveau site de modulation positive de la fonction des rKA. / Glutamate released at excitatory synapses acts on ligand-gated ionotropic receptors which fall into three classes: NMDA, AMPA and kainate receptors.At hippocampal mossy fiber synapses onto CA3 pyramidal cells, KARs are present both at the pre- and postsynaptic levels. Postsynaptic KARs are composed of the GluK2, GluK4 and GluK5 subunits, whereas presynaptic KARs are thought to comprise the GluK2 and GluK3 subunits. The functional properties of GluK3 (and GluK2/GluK3) receptors set it apart from the other ionotropic glutamate receptors. In particular, its sensitivity to glutamate is the lowest of all known ionotropic glutamate receptors, due in large part to fast desensitization of receptors with one or two bound glutamate molecules. The low agonist sensitivity of this receptor raises questions about its relevance for synaptic function. Therefore, it is possible that endogenous modulators may potentiate its function.Among potential endogenous modulators of KAR function, we chose to address the role of zinc, because of the large amounts contained in mossy fiber terminals. Zinc is thought to be accumulated into synaptic vesicles, and is co-released with glutamate in the extracellular milieu during neuronal activity. Zinc has been reported to inhibit most of native and recombinant KARs. Despite the proposed role of at hippocampal mossy fiber synapses, although modulation of GluK3-containing KARs by zinc has not yet been addressed.In this study, we show that zinc greatly potentiates recombinant GluK3 receptor currents evoked by glutamate. Zinc markedly slows receptor desensitization and increases apparent affinity for glutamate. Crystallographic studies and analysis of chimeric GluK2/GluK3 KARs and of GluK3 bearing selected point mutations, allowed us to identify the zinc binding domain defined by D759, H762, Q756 and D730, and localized in a region forming the interface between two GluK3 subunits in an LBD dimer assembly. Based on these structure-function studies and on modeling of KAR activity, we show that zinc plays a very distinct role on GluK3-KARs by stabilizing the interaction between dimers of LBD thereby reducing desensitization.Given the proposed localization of GluK3 close to zinc containing synaptic vesicles, zinc may be an endogenous allosteric modulator for native GluK3-KARs, and its binding site a new pharmacological target.

L'utilisation du LiDAR en télédétection permet une description précise de l'architecture du couvert végétal. L'objet de cette thèse est le développement des approches d'inversion de mesures LiDAR à l'aide d'une modélisation physique et statistique du signal dans le but d'estimer des propriétés biophysiques de cultures dominantes (blé, maïs) du Sud-Ouest de la France et d'un couvert forestier en Chine. Le travail a tout d'abord porté sur l'estimation du LAI et la hauteur des cultures par inversion de formes d'onde LiDAR à faible empreinte. Une base de données de simulations de formes d'onde réalistes des cultures est réalisée à l'aide du modèle de transfert radiatif (MTR) DART. L'inversion consiste à utiliser la technique de table de correspondance qui consiste à chercher la simulation la plus proche de l'observation réelle. Le travail a ensuite porté sur l'estimation du profil de LAI des arbres de la forêt. Une approche variationnelle d'estimation du profil de LAI par inversion de formes d'ondes est proposée. Elle repose sur un MTR simplifié et une technique de lissage du profil de LAI s'appuyant sur les chaines de Markov. La formulation bayésienne du problème, nous amène à une fonction de coût non-linéaire. Elle est minimisée à l'aide d'une nouvelle technique de gradient multi-échelle. Les approches développées montrent bien leurs performances en les appliquant sur des données réelles de cultures (maïs et blé) et de milieu forestier. / The use of LiDAR in remote sensing allows a precise description of the vegetation cover architecture. The aim of this thesis is the development of LiDAR data inversion approaches using physical and statistical signal modeling in order to estimate the biophysical properties of dominant crops (wheat, maize) of the South-West of France and a forest cover in China. The work firstly focused on estimating LAI and crop height by small footprint LiDAR waveforms inversion. A realistic crop waveform simulations database is performed using the Radiative Transfer Model (MTR) DART. The inversion consists in using the Look up Table technique which consists of looking for the closest simulation to the actual observation. The second inversion approach focused on LAI profile estimation of the forest trees. A variational approach to estimate LAI by waveform inversion is proposed. It relies on a simplified MTR and LAI profile smoothing technique based on Markov chains. The Bayesian formulation of the problem leads us to a non-linear cost function. It is minimized using a new multi-scale gradient technique. The developed approaches show clearly their performance by applying them to real crop data (corn and wheat) and forest.

La cryopréservation engendre des dégradations variables de l’activité biologique et des fonctionnalités des bactéries lactiques, notamment chez Lactobacillus delbrueckii subsp. bulgaricus, un starter de l’industrie laitière. Le but de ce travail a été d’identifier les marqueurs cellulaires de cryorésitance et de cryosensibilité afin de mieux comprendre les mécanismes de dégradation sous-jacents et d’améliorer les performances industrielles des bactéries lactiques. La cryopresérvation a ici été considérée comme une combination de deux stress majoritaires : froid et osmotique. Une attention particulière a été portée à l’analyse de la membrane cellulaire, un site majeur de dégradation lié à la congélation, mais également à la paroi cellulaire et aux protéines. De plus, les cellules ont été analysées à différentes échelles d’observation, de la population jusqu’à la cellule unique, afin de quantifier l’hétérogénéité des propriétés cellulaires existant au sein de populations. Dans une première partie de ce travail, des conditions de culture ont été comparées pour identifier deux souches de L. bulgaricus présentant des résistances contrastées vis-à-vis de la congélation. Une analyse génomique comparative des souches a également été menée dans le but de fournir des pistes de compréhension de ces comportements différents. Dans une seconde partie, des propriétés membranaires des cellules ont été évaluées en réponse aux stress froid et osmotique : composition en acides gras, organisation au niveau des chaînes d’acides gras et des têtes phospholipidiques, et fluidité.Leur fluidité membranaire a également été caractérisée à une échelle subcellulaire par microscopie de fluorescence au moyen du rayonnement synchrotron, permettant la quantification des hétérogénéités inter- et intra-cellulaires. Enfin, un développement technique et méthodologique a été entrepris afin de permettre l’analyse de bactéries individuelles en milieu aqueux par spectroscopie infrarouge à transformée de Fourier, et ainsi leur signature biochimique en conditions natives. Ces approches complémentaires et multidisciplinaires ont révélé l’existence de propriétés et d’organisation différentes de la membrane des deux souches de L. bulgaricus. Différents types d’interaction entre les molécules cryoprotectrices du milieu extracellulaire et la membrane des deux souches a été proposé, pouvant être à l’origine des dommages causés à la souche sensible. De plus, une hétérogénéité plus importante au sein de la population sensible a été identifiée, attribuée à des différences en termes de composition biochimique et d’organisation au niveau de la membrane et de la paroi. Finalement, ce travail suggère quelques marqueurs cellulaires d’évaluation de la cryorésistance des bactéries lactiques, et fournit des méthodes de caractérisation de l’hétérogénéité biochimique au sein des populations. Ceux-ci pourraient être appliqués à l’étude de toute autre étape critique du procédé de production des bactéries lactiques, et pourraient être utiles pour aller vers la production de ferments homogènes au niveau de leur résistance. / Cryopreservation leads to variable degradation of the biological activity and functionality among lactic acid bacteria (LAB), particularly Lactobacillus delbrueckii subsp. bulgaricus, a dairy starter of industrial relevance. The aim of this work was to identify cellular markers of cryoresistance or cryosensitivity for better understanding the mechanisms of cell cryoinjury and increasing LAB industrial performances. Cryopreservation was here considered as a combination of cold and osmotic stresses. A particular focus was given to the analysis of the cell membrane, recognised as a primary site of cryoinjury, but also of the cell wall and proteins. Moreover, cells were analysed from the population level down to the single-cell level to quantify the heterogeneity of cell properties within populations. In the first part of this work, bacterial cultivation conditions were compared to identify two L. bulgaricus strains with markedly different cell cryoresistance. Moreover, a comparative genomic analysis of the strains was performed to provide some clues for the explanation of their different behaviours. In the second part of this work, the membrane properties were evaluated in response to the cold and osmotic stresses: fatty acid composition, organisation of fatty acyl and phospholipid headgroups, and fluidity.Subcellular membrane fluidity was also characterised by fluorescence microscopy using synchrotron radiation, enabling the quantification of inter- and intra-cellular heterogeneities. Finally, original methodological and technical developments were undertaken to achieve the analysis of individual bacterial cells in an aqueous environment by Fourier transform infrared (FTIR) spectroscopy, for the analysis of the biochemical signature of cells under native conditions. These complementary multidisciplinary approaches revealed different properties and organisation of the membrane of both L. bulgaricus strains. It was proposed that different types of interaction between cryoprotectants of the extracellular matrix and the membrane of both strains could be at the origin of cryoinjury for the sensitive strain. Moreover, a high population heterogeneity characterised the cryosensitive strain, ascribed to differences in terms of biochemical composition and organisation of the membrane and cell wall. Altogether, this work suggests some cellular markers to evaluate LAB cryoresistance and provides methods to characterize population biochemical heterogeneity. These could be applied to any other stressful step of their production process, and should be useful for future production of homogeneous populations of resistant LAB.

Ion channels are fundamental molecules in the nervous system that catalyze the flux of ions across the cell membrane. There are mounting evidences suggesting that the kinetic properties of ion channels undergo activity-dependent changes in various pathophysiological conditions. Here such activity-dependent changes were studied in case of two different ion channels; the rat brain derived voltage-gated Na+ channel, rNav1.2 and the human background leak K+ channel, hTREK1 using the single channel patch-clamp technique. Our results on the voltage-gated Na+ channel (Chapter III) illustrated that sustained membrane depolarization, as seen in pathophysiological conditions like epilepsy, induced a defined non-linear variation in the unitary conductance, activation, inactivation and recovery kinetic properties of the channel. Signal processing tools attributed a pseudo-oscillatory nature to the non-linearity observed in the channel properties. Prolonged membrane depolarization also induced a “molecular memory” phenomenon, characterized by clustering of dwell time events and strong autocorrelation in the dwell time series. The persistence of such molecular memory was found to be dependent on the duration of depolarization. Similar plastic changes were observed in case of the hTREK1 channel in presence of saturating concentrations of agonist, trichloroethanol (TCE) (Chapter IV). TREK1 channel behaves similar to single enzyme molecules with a single binding site for the substrate K+ ion whereas TCE acts as an allosteric activator of the channel. We observed that with increasing concentration of TCE (10 M to 10 mM) the catalytic turnover rate exhibited progressive departure from monoexponential to multi-exponential distribution suggesting the presence of ‘dynamic disorder’ analogous to single enzyme molecules. In addition, we observed the induction of strong correlation in successive waiting times and flux intensities, exemplified by distinct mode switching between high and low flux activity, which implied the induction of memory in single ion channel. Our observation of such molecular memory in two different ion channels in different experimental conditions highlights the importance and generality of the phenomenon which is normally hidden under the ensemble behaviour of ion channels. In the final part of the work (chapter V) we observed strong negative cooperativity and half-of-sites saturation kinetics in the interaction of local anesthetic, lidocaine with hTREK1 channel. We also mapped the specific anesthetic binding site in the c-terminal domain of the channel. Further, single channel analysis and the heterodimer studies enabled us to propose a model for this interaction and provide a plausible paradigm for the inhibitory action of lidocaine on hTREK1.