<p>Our knowledge of the fine structure of the Human Spiral Ganglion (HSG) is still inadequate and new treatment techniques for deafness using electric stimulation, call for further information and studies on the neuronal elements of the human cochlea. This thesis presents results of analyses of human cochlear tissue and specimens obtained during neurosurgical transpetrosal removal of life-threatening meningeomas. The use of surgical biopsies produced a well-preserved material suitable for ultrastructural and immunohistochemical studies on the human inner ear. The SG was studied with respect to fine structure, using TEM technique and the immunostaining pattern of synaptophysin, which is an integral membrane protein of neuronal synaptic vesicles. The immunostaining patterns of the tight junctional protein ZO-1 and the gap junctional proteins Cx26 and Cx43 in the human cochlea were also studied. The ultrastructural morphology revealed an absence of myelination pattern in the HSG, thus differing from that in other species. Furthermore, formation of structural units as well as signs of neural interaction between the type 1 neurons could be observed. Type 1 cells were tightly packed in clusters, sharing the ensheathment of Schwann cells. The cells frequently made direct physical contact in Schwann cell gaps in which membrane specializations appeared. These specializations consisted of symmetrically or asymmetrically distributed filamentous densities along the apposed cell membranes. The same structures were also present between individual unmyelinated nerve fibres and the type 1 cells. Synapses were observed on the type 2 neurons, with nerve fibres originating from the intraganglionic spiral bundle. Such synapses, though rare, were also observed on the type 1 cells. The ultrastructural findings were confirmed by the synaptophysin study. A 3-D model of a Schwann cell gap between two type 1 cells was constructed, describing the distribution pattern of membrane specializations. In the immunohistochemical studies on the human cochlea, ZO-1 was expressed in tissues lining scala media, thus contributing to the formation of a closed compartment system, important for the maintenance of the specific ionic composition of the endolymph. Protein Cx26 could be identified in non-sensory epithelial cells of the organ of Corti, in connective tissue cells of the spiral ligament and spiral limbus, as well as in the basal and intermediate cell layers of stria vascularis. Cx26 in this region may be involved in the recycling of potassium. Protein Cx43 stained weakly in the spiral ligament, but intense staining in the SG may indicate that gap junctions exist between these neurons. A different functional role for the HSG can be assumed from the morphological characteristics and the signs of a neural interaction between the SG cells. This might be relevant for neural processing mechanisms in speech coding and could have implications for cochlear implant techniques.</p>

<p>Disruption of coordinated impulse propagation in the heart as a result of fibrosis or myocardial infarction can create an asynchronous substrate with poor conduction and impaired contractility. This can ultimately lead to cardiac failure and make the heart more vulnerable to life-threatening arrhythmias and sudden cardiac death. The transplantation of exogenous cells into the diseased myocardium, "cardiac cell therapy," has been proposed as a treatment option to improve compromised cardiac function. Clinical trials of stem cell-based cardiac therapy have shown promising results, but also raised concerns about our inability to predict or control the fate of implanted cells and the electrical consequences of their interactions with host cardiomyocytes. Alternatively, genetically engineered somatic cells could be implanted to selectively and safely modify the cardiac electrical substrate, but their unexcitable nature makes them incapable of electrically repairing large conduction defects. The objective of this thesis was thus to develop a methodology to generate actively conducting excitable cells from an unexcitable somatic cell source and to demonstrate their utility for studies of basic electrophysiology and cardiac cell therapy.</p><p>First, based on the principles of cardiac action potential propagation, we applied genetic engineering techniques to convert human unexcitable cells (HEK-293) into an autonomous source of excitable and conducting cells by the stable forced expression of only three genes encoding an inward rectifier potassium (Kir2.1), a fast sodium (Na_v1.5), and a gap junction (Cx43) channel. Systematic pharmacological and electrical pacing studies in these cells revealed the individual contributions of each expressed channel to action potential shape and propagation speed. Conduction slowing and instability of induced arrhythmic activity was shown to be governed by specific mechanisms of I_Na inhibition by TTX, lidocaine, or flecainide. Furthermore, expression of the Na_v1.5 A1924T mutant sodium channel or Ca_v3.3 T-type calcium channel was utilized to study the specific roles of these channels in action potential conduction and demonstrate that genetic modifications of the engineered excitable cells in this platform allow quantitative correlations between single-cell patch clamp data and tissue-level function.</p><p>We further performed proof-of-concept experiments to show that networks of biosynthetic excitable cells can successfully repair large conduction defects within primary excitable tissue cultures. Specifically, genetically engineered excitable cells supported active action potential propagation between neonatal rat ventricular myocytes (NRVMs) separated by at least 2.5 cm in 2-dimensional and 1.3 cm in 3-dimensional cocultures. Using elastic films with micropatterned zig-zag NRVM networks that mimicked the tortuous conduction patterns observed in cardiac fibrosis, we showed that electrical resynchronization of cardiomyocyte activation by application of engineered excitable cells improved transverse conduction by 370% and increased cardiac twitch force amplitude by 64%. This demonstrated that despite being noncontractile, engineered excitable cells could potentially improve both the electrical and mechanical function of diseased myocardial tissue. </p><p>Lastly, we investigated how activation and repolarization gradients at the interface between cardiomyocytes and other excitable cells influence the vulnerability to conduction block. Microscopic optical mapping of action potential propagation was used to quantify dispersion of repolarization (DOR) in micropatterned heterocellular strands in which either well-coupled or poorly-coupled engineered excitable cells with a short action potential duration (APD), seamlessly interfaced with NRVMs that had a significantly longer APD. The resulting electrical gradients originating from the underlying heterogeneity in intercellular coupling and APD dispersion were further manipulated by the application of barium chloride (BaCl2) to selectively prolong APD in the engineered cells. We measured how the parameters of DOR affected the vulnerable time window (VW) of conduction block and found a strong linear correlation between the size of the repolarization gradient and VW. Reduction of DOR by BaCl2 significantly reduced VW and showed that VW correlated directly with dispersion height but not width. Conversely, at larger DOR, VW was inversely correlated with the dispersion width but independent of the dispersion height. In addition, despite their similar APDs, poorly-coupled excitable cells were found to significantly increase the maximum repolarization gradient and VW compared to well-coupled excitable cells, but only at larger DOR.</p><p>In summary, this thesis presents the novel concept of genetically engineering membrane excitability and impulse conduction in previously unexcitable somatic cells. This biosynthetic excitable cell platform is expected to enable studies of ion channel function in a reproducible tissue-level setting, promote the integration of theoretical and experimental studies of action potential propagation, and stimulate the development of novel gene and cell-based therapies for myocardial infarction and cardiac arrhythmias.</p> / Dissertation

<p>Cardiac arrhythmias triggered by both reentrant and focal sources are closely correlated with regions of tissue characterized by significant structural heterogeneity. Experimental and modeling studies of electrical activity in the heart have shown that local microscopic heterogeneities which average out at the macroscale in healthy tissue play a much more important role in diseased and aging cardiac tissue which have low levels of coupling and abnormal or reduced membrane excitability. However, it is still largely unknown how various combinations of microheterogeneity in the intracellular and interstitial spaces affect wavefront propagation in these critical regimes. </p> <p>This thesis uses biophysically realistic 1-D and 2-D computer models to investigate how heterogeneity in the interstitial and intracellular spaces influence both the initiation of ectopic beats and the escape of multiple ectopic beats from a poorly coupled region of tissue into surrounding well-coupled tissue. An approximate discrete monodomain model that incorporates local heterogeneity in both the interstitial and intracellular spaces was developed to represent the tissue domain. </p> <p>The results showed that increasing the effective interstitial resistivity in poorly coupled fibers alters the distribution of electrical load at the microscale and causes propagation to become more like that observed in continuous fibers. In poorly coupled domains, this nearly continuous state is modulated by cell length and is characterized by decreased gap junction delay, sustained conduction velocity, increased sodium current, reduced maximum upstroke velocity, and increased safety factor. In inhomogeneous fibers with adjacent well-coupled and poorly coupled regions, locally increasing the effective interstitial resistivity in the poorly coupled region reduces the size of the focal source needed to generate an ectopic beat, reduces dispersion of repolarization, and delays the onset of conduction block that is caused by source-load mismatch at the boundary between well-coupled and poorly-coupled regions. In 2-D tissue models, local increases in effective interstitial resistivity as well as microstructural variations in cell arrangement at the boundary between poorly coupled and well-coupled regions of tissue modulate the distribution of maximum sodium current which facilitates the unidirectional escape of focal beats. Variations in the distribution of sodium current as a function of cell length and width lead to directional differences in the response to increased effective interstitial resistivity. Propagation in critical regimes such as the ectopic substrate is very sensitive to source-load interactions and local increases in maximum sodium current caused by microheterogeneity in both intracellular and interstitial structure.</p> / Dissertation

Our knowledge of the fine structure of the Human Spiral Ganglion (HSG) is still inadequate and new treatment techniques for deafness using electric stimulation, call for further information and studies on the neuronal elements of the human cochlea. This thesis presents results of analyses of human cochlear tissue and specimens obtained during neurosurgical transpetrosal removal of life-threatening meningeomas. The use of surgical biopsies produced a well-preserved material suitable for ultrastructural and immunohistochemical studies on the human inner ear. The SG was studied with respect to fine structure, using TEM technique and the immunostaining pattern of synaptophysin, which is an integral membrane protein of neuronal synaptic vesicles. The immunostaining patterns of the tight junctional protein ZO-1 and the gap junctional proteins Cx26 and Cx43 in the human cochlea were also studied. The ultrastructural morphology revealed an absence of myelination pattern in the HSG, thus differing from that in other species. Furthermore, formation of structural units as well as signs of neural interaction between the type 1 neurons could be observed. Type 1 cells were tightly packed in clusters, sharing the ensheathment of Schwann cells. The cells frequently made direct physical contact in Schwann cell gaps in which membrane specializations appeared. These specializations consisted of symmetrically or asymmetrically distributed filamentous densities along the apposed cell membranes. The same structures were also present between individual unmyelinated nerve fibres and the type 1 cells. Synapses were observed on the type 2 neurons, with nerve fibres originating from the intraganglionic spiral bundle. Such synapses, though rare, were also observed on the type 1 cells. The ultrastructural findings were confirmed by the synaptophysin study. A 3-D model of a Schwann cell gap between two type 1 cells was constructed, describing the distribution pattern of membrane specializations. In the immunohistochemical studies on the human cochlea, ZO-1 was expressed in tissues lining scala media, thus contributing to the formation of a closed compartment system, important for the maintenance of the specific ionic composition of the endolymph. Protein Cx26 could be identified in non-sensory epithelial cells of the organ of Corti, in connective tissue cells of the spiral ligament and spiral limbus, as well as in the basal and intermediate cell layers of stria vascularis. Cx26 in this region may be involved in the recycling of potassium. Protein Cx43 stained weakly in the spiral ligament, but intense staining in the SG may indicate that gap junctions exist between these neurons. A different functional role for the HSG can be assumed from the morphological characteristics and the signs of a neural interaction between the SG cells. This might be relevant for neural processing mechanisms in speech coding and could have implications for cochlear implant techniques.

Le récepteur atypique ACKR3 et le récepteur CXCR4 sont des récepteurs couplés aux protéines G appartenant à la famille des récepteurs CXC des chimiokines. Ces deux récepteurs sont activés par la chimiokine CXCL12 et sont surexprimés dans de nombreux cancers comme les gliomes, dont ils favorisent la prolifération et le caractère invasif. Le récepteur CXCR4 active des voies de signalisation qui dépendent de la protéine Gi et des β-arrestines et s’associe à plusieurs protéines impliquées dans la transduction du signal, le trafic et la localisation cellulaire du récepteur. Par contre, les mécanismes de signalisation impliqués dans les effets d’ACKR3 restent mal connus. Le récepteur déclenche une signalisation dépendant des β-arrestines, mais son couplage aux protéines G dépend du type cellulaire ou se fait par un mécanisme indirect via son association au récepteur CXCR4. Le récepteur ACKR3 s’associe également au récepteur de l’EGF pour induire la prolifération cellulaire par un mécanisme indépendant de sa stimulation par un agoniste. Ces données illustrent l’intérêt de caractériser de façon systématique l’interactome de ces récepteurs pour comprendre leurs rôles physiologiques et pathologiques. Cette thèse a poursuivi cet objectif grâce à la mise en œuvre d’une approche protéomique combinant la purification des partenaires des deux récepteurs par affinité suivie de leur identification par spectrométrie de masse. J’ai ainsi identifié respectivement 19 et 151 partenaires protéiques potentiels des récepteurs CXCR4 et ACKR3 exprimés dans les cellules HEK-293T. Parmi les protéines recrutées par ACKR3, nous nous sommes focalisés sur la connexine 43 (Cx43, une des protéines constituant les jonctions Gap) du fait de la similitude des effets du récepteur et de la Cx43 dans la pénétration des leucocytes dans le parenchyme cérébral, la migration des interneurones et la progression des gliomes. J’ai confirmé par Western blot et par BRET l’association spécifique de la Cx43 à l’ACKR3 et non pas au CXCR4. De la même façon, j’ai montré une co-localisation de la Cx43 et de l’ACKR3 dans des cellules de gliome humain, ainsi que dans les astrocytes de la zone sous-ventriculaire et les pieds astrocytaires entourant les capillaires cérébraux chez la souris, suggérant que les deux protéines forment un complexe protéique dans un contexte biologique authentique. Des études fonctionnelles ont révélé que l’ACKR3 module les fonctions de la Cx43 par différents mécanismes. L’expression de l’ACKR3 dans les cellules HEK-293T (mimant la surexpression du récepteur dans les tumeurs), induit par elle-même une inhibition de l’activité jonctionnelle de la Cx43. De même, la stimulation du récepteur par un agoniste réduit l’activité jonctionnelle de la Cx43 par un mécanisme impliquant l’activation d’une protéine Gi, la β-arrestine2 et l’internalisation de la Cx43. Cette thèse établit donc pour la première fois un lien fonctionnel entre le système constitué par les chimiokines CXCL11, CXCL12 et leur récepteur ACKR3 d’une part et les jonctions Gap d’autre part qui pourrait jouer un rôle critique dans la progression des gliomes. / The Atypical Chemokine Receptor 3 (ACKR3) and CXCR4 are two G protein-coupled receptors (GPCR) belonging to the CXC chemokine receptor family. Both receptors are activated upon CXCL12 binding and are over-expressed in various tumours, including glioma, where they have been found to promote proliferation and invasive behaviours. Upon CXCL12 binding, CXCR4 activates canonical GPCR signalling pathways involving Gαi protein and β-arrestins. In addition, CXCR4 was found to interact with several proteins able to modify its signalling, trafficking and localization. In contrast, the cellular pathways underlying ACKR3-dependent effects remain poorly characterized. Several reports show that ACKR3 engages β-arrestin-dependent signalling pathways, but its coupling to G proteins is restricted to either specific cellular populations, including astrocytes, or occurs indirectly via its interaction with CXCR4. ACKR3 also associates with the epidermal growth factor receptor to promote proliferation of tumour cells in an agonist-independent manner. These examples suggest that the extensive characterization of ACKR3 and CXCR4 interactomes might be a key step in understanding or clarifying their roles in physiological and pathological contexts. This thesis addressed this issue employing an affinity purification coupled to high-resolution mass spectrometry proteomic strategy that identified 19 and 151 potential protein partners of CXCR4 and ACKR3 transiently expressed in HEK-293T cells, respectively. Amongst ACKR3 interacting proteins identified, we paid particular attention on the gap junction protein Connexin-43 (Cx43), in line with its overlapping roles with the receptor in the control of leukocyte entry into the brain, interneuron migration and glioma progression. Western blotting and BRET confirmed the specific association of Cx43 with ACKR3 compared to CXCR4. Likewise, Cx43 is co-localized with ACKR3 but not CXCR4 in glioma initiating cell lines, and ACKR3 and Cx43 are co-expressed in astrocytes of the sub-ventricular zone and surrounding blood vessels in adult mouse brain, suggesting that both proteins form a complex in authentic cell or tissue contexts. Further functional studies showed that ACKR3 influences Cx43 trafficking and functionality at multiple levels. Transient expression of ACKR3 in HEK-293T cells to mimic ACKR3 overexpression detected in several cancer types, induces Gap Junctional Intercellular Communication (GJIC) inhibition in an agonist-independent manner. In addition, agonist stimulation of endogenously expressed ACKR3 in primary cultured astrocytes inhibits Cx43-mediated GJIC through a mechanism that requires activation of Gαi protein, and dynamin- and β-arrestin2-dependent Cx43 internalisation. Therefore, this thesis work provides the first functional link between the CXCL11/CXCL12/ACKR3 axis and gap junctions that might underlie their critical role in glioma progression.

Light entering the eye is transformed by the retina into electrical signals. Extensive processing takes place in the retina before these signals are transmitted to the brain. Beginning in the outer retina, light-evoked electrical signals are distributed into parallel pathways specialized for different visual tasks, such as the detection of dark vs. bright ambient light, the onset or offset of light, and the direction of stimulus motion. Pathway diversity is a consequence of cell type diversity, differential cell connectivity, synapse organization, receptor expression, or any combination thereof. Cell connectivity itself can be accomplished through excitatory or inhibitory chemical synapses, or electrical coupling via gap junctions. Gap junctions are further specialized based on the expression of different connexin subunit isoforms. In aggregate, this diversity gives rise to ganglion cells with highly specialized functions, including ON and/or OFF responses, contrast-tuning and direction-selectivity (DS). The directionally-selective circuit, a circuit specialized for the encoding of stimulus motion, makes use of many of these circuit specializations. Bipolar cells, in response to glutamate release from cone photoreceptors, provide highly-sensitive glutamatergic input to amacrine cells and DS ganglion cells (DSGCs) in this circuit, while amacrine cells provide cholinergic and directionally-tuned GABAergic input to DSGCs. One population of DSGCs also transmit signals laterally to one another via gap junctions. Thus numerous specializations in bipolar cells, amacrine cells and ganglion cells endow DSGCs with their unique encoding abilities. In Chapters 2 and 3 of this dissertation I focus on synchronized firing between gap junction-coupled DSGCs. sDSGCs exhibit fine-scale correlations, with action potentials in an sDSGC more likely within ~2ms of action potential firing in a coupled neighbour. I first characterize electrical coupling of DSGCs through the identification of the molecular composition of DSGC gap junctions (Chapter 2). Physiological and immunohistochemical methods allowed me to demonstrate an important role for connexin 36 subunits in DSGC electrical coupling. Next (Chapter 3) I investigate the sub-cellular mechanisms underlying neuronal correlations between electrically coupled DSGCs. Using paired recordings, I show that chemical input (from bipolar cells and amacrine cells), electrical input (from gap junctions), and Na+ channel activity in DSGC dendrites underlie the generation of correlated spiking activity. While a common feature of electrically coupled networks, the mechanisms underlying correlations were previously unclear. In Chapter 4 I focus on the mechanisms within the DS circuit that endow these neurons with impressive sensitivity to stimulus contrast. Using physiological and pharmacological methods I first assess the relative contrast sensitivity of ganglion cells and starburst amacrine cells (SACs) in the DS circuit. The sensitivity of DSGC and SAC excitatory currents to antagonists of Na+ channels suggests an important role for these channels in amplifying low contrast responses and other weak inputs to the circuit. This role is later attributed to the differential expression of voltage-gated Na+ channels in specific bipolar cell populations. In aggregate, this dissertation describes several novel circuit mechanisms within the well-studied DS circuit. I also provide specific roles for such specializations in visual coding. / Graduate

The tegmentum vasculosum of the duckling consists of a highly folded epithelium which extends over the dorsal and lateral walls of the cochlear duct, separating the scala media from the scala vestibuli. This epithelium consists of two distinct cell types, dark cells and light cells, and is well vascularized. The surface of the epithelium is formed by a mosaic of alternating dark and light cells. The goblet-shaped dark cells have an electron-dense, organelle-rich cytoplasm, and are expanded basally by extensive basolateral plasma membrane infoldings, within which are numerous mitochondria. Dark cells are isolated from each other and from the capillaries within the epithelium by intervening light cells. In contrast, columnar light cells exhibit an electron-lucent, organelle-poor cytoplasm and may extend from the underlying capillaries to the endolymphatic surface. Light cells contain abundant, coated endocytic vesicles on their apical surfaces and are bound, apically, to other light cells or to dark cells by tight junctions and desmosomes. Laterally, light cells are linked to each other either by complex, fluid-filled membrane interdigitations or by extensive gap junctions. Plasma membrane interdigitations and obvious, fluid-filled intercellular spaces characterize the lateral borders between light and dark cells. Vascular corrosion casting reveals the three-dimensional anatomy of the cochlear vasculature. A continuous arteriolar loop fed by anterior and posterior cochlear arterioles encircles the cochlear duct. The rich capillary beds of the tegmentum vasculosum are supplied by arching arterioles arising from this loop. These capillaries are the continuous type and are situated primarily within the core of the epithelium or along its border with the scala vestibuli. The structure and blood supply of the tegmentum vasculosum are characteristic of an epithelium involved in active transport.

Cette thèse étudie l'origine de l'activité spontanée dans l'utérus. Cet organe n'a aucune activité jusqu'à la délivrance, où les contractions rapides et efficaces sont générés. Le but de ce travail est de fournir un aperçu de l'origine des oscillations spontanées et de la transition de l'activité asynchrone à synchronisé dans l'utérus gravide. Un aspect intéressant de l'utérus est l'absence de pacemaker. L'organe est composé de cellules musculaires, qui sont excitables, et conjonctives, dont le comportement est purement passif, aucune de ces cellules, pris isolément, oscillent spontanément. Nous développons une hypothèse basée sur l'augmentation grande du couplage électrique entre les cellules observée pendant la grossesse. L'étude est basée sur deux modèles des cellules excitables, couplé à l'autre sur un réseau régulier, et un nombre variable de cellules passives, en accord avec la structure connue de l'utérus. Les deux paramètres du modèle, le couplage entre les cellules excitables, et entre les cellules excitables et passive, croissent pendant la grossesse. En utilisant les deux modèles, nous démontrons que les oscillations peuvent apparaître spontanément lorsque l'on augmente les coefficients de couplage, conduisant finalement à des oscillations cohérentes sur l'ensemble du tissu. Nous étudions la transition vers un régime cohérent, à la fois numériquement et semi-analytique, en utilisant le modèle simple des cellules excitables. Enfin, nous montrons que le modèle réaliste reproduit irréguliers modes de la propagation d'action potentiels ainsi que le comportement de bursting, observé dans les expériences in vitro. / This thesis investigates the origin of spontaneous activity in the uterus. This organ does not show any activity until shortly before delivery, where fast and efficient contractions are generated. The aim of this work is to provide insight into the origin of spontaneous oscillations and into the transition from asynchronous to synchronized activity in the pregnant uterus. One intriguing aspect in the uterus is the absence of any pacemaker cell. The organ is composed of muscular cells, which are excitable, and connective cells, whose behavior is purely passive; None of these cells, taken in isolation, spontaneously oscillates. We develop an hypothesis based on the observed strong increase in the electrical coupling between cells in the last days of pregnancy. The study is based on a mathematical model of excitable cells, coupled to each other on a regular lattice, and to a fluctuating number of passive cells, consistent with the known structure of the uterus. The two parameters of the model, the coupling between excitable cells, and between excitable and passive cells, grow during pregnancy.Using both a model based on measured electrophysiological properties, and a generic model of excitable cell, we demonstrate that spontaneous oscillations can appear when increasing the coupling coefficients, ultimately leading to coherent oscillations over the entire tissue. We study the transition towards a coherent regime, both numerically and semi-analytically, using the simple model of excitable cells. Last, we demonstrate that, the realistic model reproduces irregular action potential propagation patterns as well as the bursting behavior, observed in the in-vitro experiments.

Atherosclerosis is an inflammatory disease which develops focally in regions of the vasculature where there is dysfunction of endothelial cells modulated in part by shear stress from flowing blood. To address the clinical crisis of atherosclerosis, tissue engineering has focused on development of a living blood vessel substitute for use as a vascular graft in bypass surgery. Despite substantial progress in understanding the biological basis and developing clinical treatments for cardiovascular disease, critical challenges remain. As a novel strategy to improve understanding of basic human vascular biology and develop superior tissue engineered grafts, this dissertation combines the scientific and clinical approaches by using a tissue engineered blood vessel as a more physiologic in vitro model to study endothelial cell biology. Through the use of transcriptional profiling, results demonstrate significant changes in endothelial cell gene expression using the tissue engineered blood vessel model. Furthermore, the presence of a more physiologic substrate alters the cellular response to shear stress which is a critical mediator of vascular pathology. A case study of endothelial cell function in this system focuses on cell-cell communication through gap junctions. Endothelial cell connexins which form gap junctions are shown to be differentially regulated by substrate and shear stress. Moreover, gap junction communication between endothelial cells is modulated by the mechanical environment. Studies using RNA interference to knockdown expression of individual connexin isotypes demonstrate integrated regulation of connexins yet unique roles in endothelial cell function. Collectively, results exemplify the sensitivity of endothelial cell phenotype to substrate and shear stress and underline the importance of using more physiologic models in the study of basic cell biology.

A number of nanomachines that cooperatively communicate and share information in order to achieve specific tasks is envisioned as a nanonetwork. Due to size and capabilities of nanomachines, the traditional communication paradigms cannot be used for nanonetworks in which network nodes may be composed of just several atoms or molecules and scale on the orders of few nanometers. Instead, the molecular communication is a promising solution approach for nanoscale communication paradigm. However, molecular communication must be thoroughly investigated to realize the nanoscale communication and nanonetworks for many envisioned applications such as nanoscale body area networks, nanoscale molecular computers. In this thesis, a simulation framework (NanoSim) for nanoscale molecular communication networks is presented. The objective of the framework is to provide a simulation experimental tool in order to create a better understanding of nanonetworks and facilitate the development of new communication techniques and validation of theoretical results. The NanoSim framework is built on top of core components of widely used network simulator (ns-2). It incorporates the simulation modules for various nanoscale communication paradigms based on diffusive molecular, motor-based and gap junction-based molecular communication channels. The details of NanoSim are discussed and some functional scenarios are defined to validate NanoSim. In addition to this, the numerical analyses of these functional scenarios and the experimental results for them are presented. The validation of NanoSim is done by comparing these experimental and numerical results.