The role of type 4 phosphodiesterases in generating microdomains of cAMP: Large scale stochastic simulations

Cyclic AMP (cAMP) and its main effector Protein Kinase A (PKA) are critical for several aspects of neuronal function including synaptic plasticity. Specificity of synaptic plasticity requires that cAMP activates PKA in a highly localized manner despite the speed with which cAMP diffuses. Two mechanisms have been proposed to produce localized elevations in cAMP, known as microdomains: impeded diffusion, and high phosphodiesterase (PDE) activity. This paper investigates the mechanism of localized cAMP signaling using a computational model of the biochemical network in the HEK293 cell, which is a subset of pathways involved in PKA-dependent synaptic plasticity. This biochemical network includes cAMP production, PKA activation, and cAMP degradation by PDE activity. The model is implemented in NeuroRD: novel, computationally efficient, stochastic reaction-diffusion software, and is constrained by intracellular cAMP dynamics that were determined experimentally by real-time imaging using an Epac-based FRET sensor (H30). The model reproduces the high concentration cAMP microdomain in the submembrane region, distinct from the lower concentration of cAMP in the cytosol. Simulations further demonstrate that generation of the cAMP microdomain requires a pool of PDE4D anchored in the cytosol and also requires PKA-mediated phosphorylation of PDE4D which increases its activity. The microdomain does not require impeded diffusion of cAMP, confirming that barriers are not required for microdomains. The simulations reported here further demonstrate the utility of the new stochastic reaction-diffusion algorithm for exploring signaling pathways in spatially complex structures such as neurons

Heart Failure Remodeling and Ventricular Arrhythmia: The Role of Altered L-type Calcium Channel Function in the Development of Lethal Arrhythmias

Heart failure (HF) is one of the most common causes of morbidity and mortality worldwide. Although many patients suffering from HF die from sudden cardiac death caused by arrhythmias, the mechanism linking HF remodeling to an increased arrhythmogenic propensity remains incomplete. Independently of the etiology of the disease, HF is typically characterized by a progressive loss of transverse tubule (T-tubule) domains, which leads to an altered distribution of L-type Calcium channels (LTCCs). Ischemic cardiomyopathy (ICM) is usually accompanied by an increase in LTCC open probability (Po) in the T-tubules which depends on the activity of protein kinase A (PKA). In dilated cardiomyopathy (DCM) on the other hand, the increased LTCC Po on the non-T-tubule sarcolemma results from enhanced calcium-calmodulin kinase II (CaMKII) modulation. Microdomain degradation also causes the disruption of the β2 adrenergic receptor (β2AR) and phosphodiesterase (PDE) signaling localizations, normally confined to the dyadic space. The goal of this study was to analyze how these subcellular changes affect the function of LTCCs and lead to the emergence of ventricular cell-level triggers of arrhythmias. Furthermore, we aimed to compare how the two different pathways lead to different phenotypes in ICM vs. DCM. Using computational modeling, we analyzed the behavior of the LTCC current (ICaL) under basal and sympathetic stimulation and its effect on cellular action potentials (APs). Our results showed that channels redistributed from the T-tubular membrane to the bulk of the sarcolemma displayed an altered function in their new, non-native signaling domain. The changes in LTCC current led to the development of early afterdepolarizations (EADs) in both types of HF, and triggered reentrant arrhythmias only in the DCM model. Thus, our work shows that altered LTCC function is a potential cause for the emergence of cell-level triggers of arrhythmia, and that CaMKII, β2ARs and PDEs present useful therapeutic targets for treatment of HF and prevention of sudden cardiac death

Degradation of T-Tubular Microdomains and Altered cAMP Compartmentation Lead to Emergence of Arrhythmogenic Triggers in Heart Failure Myocytes: An in silico Study

Heart failure (HF) is one of the most common causes of morbidity and mortality worldwide. Although many patients suffering from HF die from sudden cardiac death caused by arrhythmias, the mechanism linking HF remodeling to an increased arrhythmogenic propensity remains incomplete. HF is typically characterized by a progressive loss of transverse tubule (T-tubule) domains, which leads to an altered distribution of L-type calcium channels (LTCCs). Microdomain degradation also causes the disruption of the β2 adrenergic receptor (β2AR) and phosphodiesterase (PDE) signaling localization, normally confined to the dyadic space. The goal of this study was to analyze how these subcellular changes affect the function of LTCCs and lead to the emergence of ventricular cell-level triggers of arrhythmias. To accomplish this, we developed a novel computational model of a human ventricular HF myocyte in which LTCCs were divided into six different populations, based on their location and signaling environment they experience. To do so, we included T-tubular microdomain remodeling which led to a subset of LTCCs to be redistributed from the T-tubular to the surface membrane and allowed for different levels of phosphorylation of LTCCs by PKA, based on the presence of β2ARs and PDEs. The model was used to study the behavior of the LTCC current (ICaL) under basal and sympathetic stimulation and its effect on cellular action potential. Our results showed that channels redistributed from the T-tubular membrane to the bulk of the sarcolemma displayed an altered function in their new, non-native signaling domain. Incomplete calcium dependent inactivation, which resulted in a longer-lasting and larger-in-magnitude LTCC current, was observed when we decoupled LTCCs from ryanodine receptors and removed them from the dyadic space. The magnitude of the LTCC current, especially in the surface sarcolemma, was also increased via phosphorylation by the redistributed β2ARs and PDEs. These changes in LTCC current led to the development of early afterdepolarizations. Thus, our study shows that altered LTCC function is a potential cause for the emergence of cell-level triggers of arrhythmia, and that β2ARs and PDEs present useful therapeutic targets for treatment of HF and prevention of sudden cardiac death

AKAP7γ Regulation of PKA Substrate Phosphorylation

In the cell, cAMP-protein kinase A (PKA) signaling is compartmentalized. Two different receptor types, both utilizing cAMP and PKA as second messenger and signal effector, are able to convey separate signals that result in phosphorylation of distinct substrates. Signal compartmentation is possible primarily because of A Kinase Anchoring Proteins (AKAPs) that bind both PKA and a target substrate, effectively co-localizing them. AKAPs are also capable of binding to other necessary signaling components like adenylate cyclase and phosphodiesterase, thus enabling AKAPs to coordinate a signaling microdomain containing many of necessary components. In this thesis I present multiple lines of evidence demonstrating how AKAP7g is able to regulate PKA phosphorylation. First, I show that AKAP7g is able to self-associate, forming dimers and possibly higher order oligomers. I predict via computational modeling that this behavior will increase both the speed and magnitude of PKA signaling. Next, I demonstrate that AKAP7g participates in a highly dynamic phosphorylation-state dependent interaction with phospholamban (PLB), and predict via computational modeling that this allows low concentrations of AKAP7g to regulate phosphorylation of much higher concentrations of substrate. Finally I demonstrate via computational modeling that contrary to the widely accepted hypothesis of AKAP signaling, the catalytic subunit of PKA is likely retained within the AKAP-PKA complex during signaling events. I further show that the structure of the complex is an important determinant of substrate phosphorylation. This work offers new insight into the function of AKAPs and offers an update to the AKAP signaling hypothesis

In silico study of calcium handling in the human failing heart

Tesis por compendio[EN] Heart failure, a cardiomyopathy that produces mechanical dysfunction and sudden cardiac death following fatal arrhythmias, is one of the main causes of mortality worldwide that also causes elevated morbidity rates. Current clinical therapies are challenged by the complexity of this cardiac pathology, in which many factors are involved in the electrical instabilities that lead to an altered function. The electrical activity of the heart comprises a wide range of spatial and temporal scales. Ion transport across transmembrane proteins initiate the cellular depolarization that is propagated cell to cell through the myocardium depolarizing and then repolarizing the entire heart in an orchestrated manner. The electrical excitation of cardiomyocytes triggers the cellular contraction, a process in which Ca2+ ions are the main mediators. Ca2+ dynamics plays a relevant role in controlling excitation-contraction coupling and consequently, investigations have focused on Ca2+-handling proteins and the regulation of Ca2+ homeostasis to elucidate the causes of impaired contractility and pro-arrhythmic conditions in cardiac diseases. This thesis takes advantage of the existence of mathematical models with detailed representation of the subcellular processes to perform computational simulations of cardiac electrophysiology and understand the altered mechanisms that govern heart failure, especially those related with intracellular Ca2+ cycling. It is known that failing myocytes undergo a specific remodeling of ion channels and Ca2+-handling proteins that lead to an impaired excitation-contraction coupling. Initially, it was analyzed, in the human action potential model of ventricular myocytes selected for the whole study, the effects of modulating ionic mechanisms on the electrical activity and Ca2+ dynamics. In tissue, heart failure induces additional changes affecting cellular coupling. The development of fibroblasts and impact on myocyte electrophysiology was investigated, including the vulnerability to generate alternans, a common precursor to arrhythmogenesis. Finally, the beta-adrenergic signaling model was integrated with the action potential model because of the electrophysiological modulation exerted by the sympathetic nervous system, which is aggravated under heart failure conditions. Results highlighted the need of studying heart failure therapies on failing cells because of the different response of ion channels and membrane proteins to drugs. Functional Ca2+ proteins were important to maintain Ca2+ homeostasis and to avoid malignant electrical consequences, being SERCA pump the most critical factor. Apart from the electrophysiological remodeling, fibroblast interaction contributed to alter Ca2+ dynamics in myocytes and, when analyzing Ca2+ alternans, spatial electrical discordances predominated in failing tissues. The inclusion of beta-adrenergic stimulation showed that the inotropic response was diminished in heart failure as well as the antiarrhythmic benefits provided by catecholamines in the normal heart. These findings contribute to gain insight into the pathophysiology of heart failure and the development of new pharmacological agents targeted to restore Ca2+ dynamics. The control of intracellular Ca2+ cycling is crucial to ensure both the mechanical force and the electrical activity that lead to a rhythmic contraction of the heart.[ES] La insuficiencia cardíaca, una cardiomiopatía que provoca disfunción mecánica y muerte súbita tras arritmias cardíacas letales, es una de las principales causas de mortalidad en todo el mundo que además causa tasas de morbilidad elevadas. Las terapias usadas actualmente en la clínica están comprometidas por la complejidad de esta patología cardíaca, ya que son muchos los factores que están implicados en las inestabilidades eléctricas que conllevan a alteraciones funcionales. La actividad eléctrica del corazón abarca un amplio rango escalas espaciales y temporales. El transporte de iones a través de las proteínas transmembrana inicia la despolarización celular que se propaga de célula en célula a través del miocardio, despolarizando y luego repolarizando todo el corazón de manera sincronizada. La excitación eléctrica de los cardiomiocitos desencadena la contracción celular, un proceso en el que los iones de Ca2+ son los principales intermediarios. La dinámica de Ca2+ tiene un papel relevante en el control del acoplamiento excitación-contracción y, como consecuencia, las investigaciones se han centrado en las proteínas que controlan el ciclo del Ca2+ y la regulación homeostática para encontrar las causas que empeoran la contractilidad y conducen a condiciones proarrítmicas en casos de insuficiencia cardíaca. Esta tesis hace uso de la existencia de modelos matemáticos con una representación detallada de los procesos subcelulares para realizar simulaciones computacionales de electrofisiología cardíaca y comprender los mecanismos que están alterados y predominan en insuficiencia cardíaca, especialmente aquellos relacionados con el ciclo intracelular de Ca2+ . Se sabe que los miocitos dañados por insuficiencia cardíaca experimentan un remodelado específico en los canales iónicos y en las proteínas partícipes en el ciclo de Ca2+, ocasionando fallos en el acoplamiento excitación-contracción. Inicialmente, se analizaron, en el modelo de potencial de acción humano de miocitos ventriculares seleccionado para todo el estudio, los efectos de la modulación de los mecanismos iónicos sobre la actividad eléctrica y la dinámica de Ca2+. En los tejidos, la insuficiencia cardíaca induce cambios adicionales que afectan el acoplamiento celular. Se ha investigado la presencia de fibroblastos y su impacto en la electrofisiología de los miocitos, incluida la vulnerabilidad para generar alternantes, un precursor común de la arritmogénesis. Finalmente, se ha incluido el modelo de señalización -adrenérgica integrado con el modelo de potencial de acción debido a la modulación electrofisiológica ejercida por el sistema nervioso simpático, que se agrava en condiciones de insuficiencia cardíaca. Los resultados han destacado la necesidad de estudiar las terapias de insuficiencia cardíaca en células de estos corazones debido a la diferente respuesta de los canales iónicos y las proteínas de membrana a los medicamentos. El buen funcionamiento de las proteínas reguladoras del Ca2+ es importantes para mantener la homeostasis del Ca2+ y evitar consecuencias eléctricas malignas, siendo la bomba SERCA el factor más crítico. Además del remodelado electrofisiológico, la interacción con fibroblastos contribuye a alterar la dinámica de Ca2+ en los miocitos y, al analizar los alternantes de Ca2+, predominan las discordancias eléctricas espaciales en los tejidos de corazones con insuficiencia cardíaca. La inclusión de la estimulación -adrenérgica ha mostrado que la respuesta inotrópica disminuye en insuficiencia cardíaca, así como los beneficios antiarrítmicos proporcionados por las catecolaminas en un corazón normal. Estos hallazgos contribuyen a obtener información sobre la fisiopatología de la insuficiencia cardíaca y el desarrollo de nuevos agentes farmacológicos destinados a restaurar la dinámica de Ca 2+. El control del ciclo de Ca2+ intracelular es crítico para garantizar tanto la fuerza mecánica como la actividad eléctrica que conducen a una contracción rítmica del corazón.[CA] La insuficiència cardíaca, una cardiomiopatia que provoca disfunció mecànica i mort sobtada després d'arrítmies cardíaques letals, és una de les principals causes de mortalitat a tot el món que a més causa taxes de morbiditat elevades. Les teràpies utilitzades actualment en la clínica estan compromeses per la complexitat d'aquesta patologia cardíaca, ja que són molts els factors que estan implicats en les inestabilitats elèctriques que comporten a alteracions funcionals. L'activitat elèctrica del cor abasta un ampli rang d'escales espacials i temporals. El transport d'ions a través de les proteïnes transmembrana inicia la despolarització cel·lular que es propaga de cèl·lula en cèl·lula a través del miocardi, despolaritzant i després repolaritzant tot el cor de manera sincronitzada. L'excitació elèctrica dels cardiomiòcits desencadena la contracció cel·lular, un procés en el qual els ions de Ca2+ són els principals intermediaris. La dinàmica de Ca2+ té un paper rellevant en el control de l'acoblament excitació-contracció i, com a conseqüència, les investigacions s'han centrat en les proteïnes que controlen el cicle del Ca2+ i la regulació homeostàtica per a trobar les causes que empitjoren la contractilitat i condueixen a condicions proarrítmiques en casos d'insuficiència cardíaca. Aquesta tesi fa ús de l'existència de models matemàtics amb una representació detallada dels processos subcel·lulars per a realitzar simulacions computacionals de l'electrofisiologia cardíaca i comprendre els mecanismes que estan alterats i predominen en insuficiència cardíaca, especialment aquells relacionats amb el cicle intracel·lular de Ca2+. Se sap que els miòcits danyats per insuficiència cardíaca experimenten un remodelat específic en els canals iònics i en les proteïnes partícips en el cicle de Ca2+, ocasionant fallades en l'acoblament excitació-contracció. Inicialment, es van analitzar, en el model de potencial d'acció humà de miòcits ventriculars seleccionat per a tot l'estudi, els efectes de la modulació dels mecanismes iònics sobre l'activitat elèctrica i la dinàmica de Ca2+. En els teixits, la insuficiència cardíaca indueix canvis addicionals que afecten l'acoblament cel·lular. S'ha investigat la presència de fibroblasts i el seu impacte en l'electrofisiologia dels miòcits, inclosa la vulnerabilitat per a generar alternants, un precursor comú de l'arritmogènesi. Finalment, s'ha inclòs el model de senyalització beta-adrenèrgica integrat amb el model de potencial d'acció a causa de la modulació electrofisiològica exercida pel sistema nerviós simpàtic, que s'agreuja en condicions d'insuficiència cardíaca. Els resultats han destacat la necessitat d'estudiar les teràpies d'insuficiència cardíaca en cèl·lules d'aquests cors a causa de la diferent resposta dels canals iònics i les proteïnes de membrana als medicaments. El bon funcionament de les proteïnes reguladores del Ca2+ és importants per a mantindre l'homeòstasi del Ca2+ i evitar conseqüències elèctriques malignes, sent la bomba SERCA el factor més crític. A més del remodelat electrofisiològic, la interacció amb fibroblasts contribueix a alterar la dinàmica de Ca2+ en els miòcits i, en analitzar els alternants de Ca2+, predominen les discordances elèctriques espacials en els teixits de cors amb insuficiència cardíaca. La inclusió de l'estimulació beta-adrenèrgica ha mostrat que la resposta inotròpica disminueix en insuficiència cardíaca, així com els beneficis antiarrítmics proporcionats per les catecolamines en un cor normal. Aquestes troballes contribueixen a obtindre informació sobre la fisiopatologia de la insuficiència cardíaca i el desenvolupament de nous agents farmacològics destinats a restaurar la dinàmica de Ca2+. El control del cicle de Ca2+ intracel·lular és crític per a garantir tant la força mecànica com l'activitat elèctrica per a una contracció rítmica del cor.Mora Fenoll, MT. (2020). In silico study of calcium handling in the human failing heart [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/153143TESISCompendi

Metabolic Dynamics in Skeletal Muscle during Acute Reduction in Blood Flow and Oxygen Supply to Mitochondria: In-Silico Studies Using a Multi-Scale, Top-Down Integrated Model

Control mechanisms of cellular metabolism and energetics in skeletal muscle that may become evident in response to physiological stresses such as reduction in blood flow and oxygen supply to mitochondria can be quantitatively understood using a multi-scale computational model. The analysis of dynamic responses from such a model can provide insights into mechanisms of metabolic regulation that may not be evident from experimental studies. For the purpose, a physiologically-based, multi-scale computational model of skeletal muscle cellular metabolism and energetics was developed to describe dynamic responses of key chemical species and reaction fluxes to muscle ischemia. The model, which incorporates key transport and metabolic processes and subcellular compartmentalization, is based on dynamic mass balances of 30 chemical species in both capillary blood and tissue cells (cytosol and mitochondria) domains. The reaction fluxes in cytosol and mitochondria are expressed in terms of a general phenomenological Michaelis-Menten equation involving the compartmentalized energy controller ratios ATP/ADP and NADH/NAD+. The unknown transport and reaction parameters in the model are estimated simultaneously by minimizing the differences between available in vivo experimental data on muscle ischemia and corresponding model outputs in coupled with the resting linear flux balance constraints using a robust, nonlinear, constrained-based, reduced gradient optimization algorithm. With the optimal parameter values, the model is able to simulate dynamic responses to reduced blood flow and oxygen supply to mitochondria associated with muscle ischemia of several key metabolite concentrations and metabolic fluxes in the subcellular cytosolic and mitochondrial compartments, some that can be measured and others that can not be measured with the current experimental techniques. The model can be applied to test complex hypotheses involving dynamic regulation of cellular metabolism and energetics in skeletal muscle during physiological stresses such as ischemia, hypoxia, and exercise

Geometric principles of second messenger dynamics in dendritic spines.

Dendritic spines are small, bulbous protrusions along dendrites in neurons and play a critical role in synaptic transmission. Dendritic spines come in a variety of shapes that depend on their developmental state. Additionally, roughly 14-19% of mature spines have a specialized endoplasmic reticulum called the spine apparatus. How does the shape of a postsynaptic spine and its internal organization affect the spatio-temporal dynamics of short timescale signaling? Answers to this question are central to our understanding the initiation of synaptic transmission, learning, and memory formation. In this work, we investigated the effect of spine and spine apparatus size and shape on the spatio-temporal dynamics of second messengers using mathematical modeling using reaction-diffusion equations in idealized geometries (ellipsoids, spheres, and mushroom-shaped). Our analyses and simulations showed that in the short timescale, spine size and shape coupled with the spine apparatus geometries govern the spatiotemporal dynamics of second messengers. We show that the curvature of the geometries gives rise to pseudo-harmonic functions, which predict the locations of maximum and minimum concentrations along the spine head. Furthermore, we showed that the lifetime of the concentration gradient can be fine-tuned by localization of fluxes on the spine head and varying the relative curvatures and distances between the spine apparatus and the spine head. Thus, we have identified several key geometric determinants of how the spine head and spine apparatus may regulate the short timescale chemical dynamics of small molecules that control synaptic plasticity

A Compartmentalized Mathematical Model of the b1-Adrenergic Signaling System in Mouse Ventricular Myocytes

The b1-adrenergic signaling system plays an important role in the functioning of cardiac cells. Experimental data shows that the activation of this system produces inotropy, lusitropy, and chronotropy in the heart, such as increased magnitude and relaxation rates of [Ca2+]i transients and contraction force, and increased heart rhythm. However, excessive stimulation of b1-adrenergic receptors leads to heart dysfunction and heart failure. In this paper, a comprehensive, experimentally based mathematical model of the b1-adrenergic signaling system for mouse ventricular myocytes is developed, which includes major subcellular functional compartments (caveolae, extracaveolae, and cytosol). The model describes biochemical reactions that occur during stimulation of b1-adrenoceptors, changes in ionic currents, and modifications of Ca2+ handling system. Simulations describe the dynamics of major signaling molecules, such as cyclic AMP and protein kinase A, in different subcellular compartments; the effects of inhibition of phosphodiesterases on cAMP production; kinetics and magnitudes of phosphorylation of ion channels, transporters, and Ca2+ handling proteins; modifications of action potential shape and duration; magnitudes and relaxation rates of [Ca2+]i transients; changes in intracellular and transmembrane Ca2+ fluxes; and [Na+]i fluxes and dynamics. The model elucidates complex interactions of ionic currents upon activation of b1- adrenoceptors at different stimulation frequencies, which ultimately lead to a relatively modest increase in action potential duration and significant increase in [Ca2+]i transients. In particular, the model includes two subpopulations of the L-type Ca2+ channels, in caveolae and extracaveolae compartments, and their effects on the action potential and [Ca2+]i transients are investigated. The presented model can be used by researchers for the interpretation of experimental data and for the developments of mathematical models for other species or for pathological conditions

A Compartmentalized Mathematical Model of the b1-Adrenergic Signaling System in Mouse Ventricular Myocytes

The b1-adrenergic signaling system plays an important role in the functioning of cardiac cells. Experimental data shows that the activation of this system produces inotropy, lusitropy, and chronotropy in the heart, such as increased magnitude and relaxation rates of [Ca2+]i transients and contraction force, and increased heart rhythm. However, excessive stimulation of b1-adrenergic receptors leads to heart dysfunction and heart failure. In this paper, a comprehensive, experimentally based mathematical model of the b1-adrenergic signaling system for mouse ventricular myocytes is developed, which includes major subcellular functional compartments (caveolae, extracaveolae, and cytosol). The model describes biochemical reactions that occur during stimulation of b1-adrenoceptors, changes in ionic currents, and modifications of Ca2+ handling system. Simulations describe the dynamics of major signaling molecules, such as cyclic AMP and protein kinase A, in different subcellular compartments; the effects of inhibition of phosphodiesterases on cAMP production; kinetics and magnitudes of phosphorylation of ion channels, transporters, and Ca2+ handling proteins; modifications of action potential shape and duration; magnitudes and relaxation rates of [Ca2+]i transients; changes in intracellular and transmembrane Ca2+ fluxes; and [Na+]i fluxes and dynamics. The model elucidates complex interactions of ionic currents upon activation of b1- adrenoceptors at different stimulation frequencies, which ultimately lead to a relatively modest increase in action potential duration and significant increase in [Ca2+]i transients. In particular, the model includes two subpopulations of the L-type Ca2+ channels, in caveolae and extracaveolae compartments, and their effects on the action potential and [Ca2+]i transients are investigated. The presented model can be used by researchers for the interpretation of experimental data and for the developments of mathematical models for other species or for pathological conditions

Global neural rhythm control by local neuromodulation

Neural oscillations are a ubiquitous form of neural activity seen across scales and modalities. These neural rhythms correlate with diverse cognitive functions and brain states. One mechanism for changing the oscillatory dynamics of large neuronal populations is through neuromodulator activity. An intriguing phenomenon explored here is when local neuromodulation of a distinct neuron type within a single brain nucleus exerts a powerful influence on global cortical rhythms. One approach to investigate the impact of local circuits on global rhythms is through optogenetic techniques. My first project involves the statistical analysis of electrophysiological recordings of an optogenetically-mediated Parkinsonian phenotype. Empirical studies demonstrate that Parkinsonian motor deficits correlate with the emergence of exaggerated beta frequency (15-30 Hz) oscillations throughout the cortico-basal ganglia-thalamic network. However, the mechanism of these aberrant oscillatory dynamics is not well understood. A previous modeling study predicted that cholinergic neuromodulation of medium spiny neurons in the striatum of the basal ganglia may mediate the pathologic beta rhythm. Here, this hypothesis was tested using selective optogenetic stimulation of striatal cholinergic interneurons in normal mice; stimulation robustly and reversibly amplified beta oscillations and Parkinsonian motor symptoms. The modulation of global rhythms by local networks was further studied using computational modeling in the context of intrathalamic neuromodulation. While intrathalamic vasoactive intestinal peptide (VIP) is known to cause long-lasting excitation in vitro, its in vivo dynamical effects have not been reported. Here, biophysical computational models were used to elucidate the impact of VIP on thalamocortical dynamics during sleep and propofol general anesthesia. The modeling results suggest that VIP can form robust sleep spindle oscillations and control aspects of sleep architecture through a novel homeostatic mechanism. This homeostatic mechanism would be inhibited by general anesthesia, representing a new mechanism contributing to anesthetic-induced loss of consciousness. While the previous two projects differed in their use of empirical versus theoretical methods, a challenge common to both domains is the difficulty in visualizing and analyzing large multi-dimensional datasets. A tool to mitigate these issues is introduced here: GIMBL-Vis is a Graphical Interactive Multi-dimensional extensiBLe Visualization toolbox for Matlab. This toolbox simplifies the process of exploring multi-dimensional data in Matlab by providing a graphical interface for visualization and analysis. Furthermore, it provides an extensible open platform for distributed development by the community