Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation

The slime mold Dictyostelium discoideum is one of the model systems of biological pattern formation. One of the most successful answers to the challenge of establishing a spiral wave pattern in a colony of homogeneously distributed D. discoideum cells has been the suggestion of a developmental path the cells follow (Lauzeral and coworkers). This is a well-defined change in properties each cell undergoes on a longer time scale than the typical dynamics of the cell. Here we show that this concept leads to an inhomogeneous and systematic spatial distribution of spiral waves, which can be predicted from the distribution of cells on the developmental path. We propose specific experiments for checking whether such systematics are also found in data and thus, indirectly, provide evidence of a developmental path

Differentiable PKC activation on pacemaking activity of cardiomyocytes derived from mouse embryonic stem cells

Les maladies cardiovasculaires sont souvent causées par des arythmies qui proviennent d'une obstruction du système de conduction cardiaque. L'intervenant clé de ce système est le nœud sinu-atrial (SA), qui est responsable de l’initiation de chaque battement cardiaque. L’activation électrique à intervalles réguliers, assurant que le rythme cardiaque est un rythme normal. Le dysfonctionnement du nœud SA entraînerait des instabilités électriques dans le cœur. Une maladie cardiaque acquise, comme la cardiopathie rhumatismale, ou un bloc de conduction ne sont que quelques-uns des nombreux cas qui nécessitent un stimulateur cardiaque électronique pour surveiller la fréquence cardiaque et générer une impulsion lorsqu'elle bat anormalement. Bien que le stimulateur cardiaque électrique soit considéré comme une thérapie fiable, il n'est pas sans limites. Ces limites comprennent les complications chirurgicales, l'infection au plomb ainsi que la durée de vie limitée de la batterie, qui doit être remplacée à intervalles de quelques années, ce qui alourdit le fardeau hospitalier. Plusieurs approches ont été adoptées pour développer une méthode thérapeutique plus adéquate. Une stratégie qui sera étudiée implique l'utilisation d'une greffe de cellules de stimulateur cardiaque, créant fondamentalement un stimulateur biologique. Les approches de thérapie cellulaire utilisent des cellules souches embryonnaires pour évoluer vers les lignées de cellules cardiaques, y compris les cellules stimulatrices cardiaques. Ces cellules de stimulation sont caractérisées par une dépolarisation spontanée qui crée les impulsions rythmiques dans le cœur et contrôle la fréquence cardiaque. Un élément important des cellules du stimulateur cardiaque qui donne lieu à la dépolarisation spontanée sont les canaux « hyperpolarization-activated and cyclic nucleotide-gated » qui sont activés pendant l’hyperpolarisation et conduisent le courant sous le nom de « funny current ». Ce courant augmente la perméabilité intérieure de la cellule aux courants de sodium et de potassium conduisant à la dépolarisation de la cellule. D'autre part, le taux de conduction est déterminé par la connexine 30.2 et la connexine 45, qui sont des protéines transmembranaires qui s’assemblent pour former des jonctions lacunaires. L'expression de HCN et l'expression de la connexine ont toutes deux étés liés au facteur T-box 3 (Tbx3) dans le développement des myocytes auriculaires. Une approche praticable pour moduler l'expression des gènes et par conséquent l'expression des protéines est l'utilisation du conditionnement chimique. Le Phorbol 12- myristate 13-acétate (PMA) est un activateur de Protéine Kinase C (PKC) lié à l'expression de Tbx3, et par conséquent à l'expression de HCN et de connexine, et entraînant une modification de l'activité spontanée. Les cellules souches embryonnaires de souris sont des cellules qui sont isolées de la masse cellulaire interne des embryons. Ces cellules ont la capacité de se différencier en tous les types de cellules somatiques. En combinant les facteurs de croissance, ces cellules peuvent se différencier en cardiomyocytes. Nous émettons l'hypothèse que le conditionnement chronique de cardiomyocytes de souris avec PMA entraîne une régulation à la hausse de l'expression de Tbx3 et par conséquent une régulation à la hausse de l'expression de HCN et de l'expression de connexine, favorisant ainsi le développement des cellules stimulatrices cardiaques dans la population des cardiomyocytes. Afin de vérifier notre hypothèse, nous avons acheté des cellules de la lignée cellulaire E14TG2A de souris. Ces cellules ont été cultivées dans des pétris et différenciées en cardiomyocytes à l'aide d'un protocole en trois étapes (voir la section Méthodes). Les cardiomyocytes sont ensuite exposés à la PMA à des concentrations variables (0.1 µM vs 1 µM) pendant 1h (exposition aiguë) ou 24 h (exposition chronique). Les résultats variaient d'un groupe expérimental à l'autre par rapport au groupe témoin. Dans toutes les conditions expérimentales, il semble y avoir une augmentation initiale de l'activité spontanée, mais elle s'inverse rapidement à la marque des 24 heures, où le rythme diminue. Différentes concentrations jouent un rôle dose-dépendant dans l'effet inhibiteur de longue durée sur la stimulation des cellules.Cardiovascular diseases are often caused by arrhythmias that originate from an obstruction within the cardiac conduction system. The key player within that system is the sinoatrial (SA) node, which is responsible for initiation the electrical impulses at a regular interval, insuring the heartbeat at a normal pace. Dysfunction of the SA node would lead to electrical instabilities in the heart. An acquired heart disease, such as rheumatic heart disease, or a conduction block are just some of many cases that would require an electronic pacemaker to monitor the heart rate and generate an impulse when it beats abnormally. Although the electric pacemaker is considered as a reliable therapy, it is not without limitations. These limitations include surgery complication, lead infection as well as limited battery lifespan, which requires replacement every few years thus adding to the hospital burden. Several approaches have been taken to develop a more adequate therapeutic method. A strategy that will be investigated involves using a graft of pacemaker cells, fundamentally creating a biological pacemaker. Cell therapy approaches use embryonic stem cells to evolve into the cardiac cell lines, including pacemaker cells. These pacing cells are characterized by spontaneous depolarization that create the rhythmic impulses in the heart and control the heart rate. An important element of the pacemaker cells that give rise to the spontaneous depolarization are the hyperpolarization- activated and cyclic nucleotide-gated (HCN) channels that are activated during hyperpolarization and conduct the funny current by increasing the cell’s inward permeability to sodium-potassium currents. On the other hand, the conduction rate is determined by connexin 30.2 and connexin 45, which are transmembrane proteins that assemble to form gap junctions. Both HCN expression and connexin expression has been linked to T-box factor 3 (Tbx3) in the development of atrial myocytes. A practicable approach to modulate gene expression and consequently protein expression is using chemical conditioning. Phorbol 12-myristate 13-acetate (PMA) is a Protein Kinase C (PKC) activator that has linked to Tbx3 expression, and consequently HCN and connexin expression, and lead to a modification in spontaneous activity. Mouse embryonic stem cells (ESCs) are cells that are isolated from the inner cell mass of early embryos. These cells can differentiate into all somatic cell types. Given the proper combination of growth factors, these cells can differentiate into cardiomyocytes. We hypothesize that chronic conditioning of mice cardiomyocytes with PMA lead to an upregulation of Tbx3 expression and consequently an upregulation of HCN expression and connexin expression, therefore promoting the development of pacemaker cells within the cardiomyocyte population. In order to test our hypothesis, we purchased cells from the mouse E14TG2A cell line. These cells were cultured in glass bottom petri dishes and differentiated into cardiomyocytes using a three-step protocol (shown in Methods section). The cardiomyocytes are then exposed to PMA in varying concentration (0.1 µM vs 1 µM) for either 1h (acute exposure) or 24 h (chronic exposure). The results varied between the experimental groups compared to the control. In all experimental conditions there seems to be an initial increase in spontaneous activity, but this is quickly reversed at the 24 h mark, where pacing decreased. Different concentration plays a dose-dependent role in long-lasting inhibitory effect on the pacing of the cell

Using Phylogenomic Data to Untangle the Patterns and Timescale of Flowering Plant Evolution

Angiosperms are one of the most dominant groups on Earth, and have fundamentally changed global ecosystem patterns and function. Therefore, unravelling their evolutionary history is key to understanding how the world around us was formed, and how it might change in the future. In this thesis, I use genome-scale data to investigate the evolutionary patterns and timescale of angiosperms at multiple taxonomic levels, ranging from angiosperm-wide to genus-level data sets. I begin by using the largest combination of taxon and gene sampling thus far to provide a novel estimate for the timing of angiosperm origin in the Triassic period. Through a range of sensitivity analyses, I demonstrate that this estimate is robust to many important components of Bayesian molecular dating. I then explore tactics for phylogenomic dating using multiple molecular clocks. I evaluate methods for estimating the number and assignment of molecular clock models, and strategies for partitioning molecular clock models in analyses of multigene data sets. I also demonstrate the importance of critically evaluating the precision in age estimates from molecular dating analyses. Finally, I assess the utility of plastid data sets for resolving challenging phylogenetic relationships, focusing on Pimelea Banks & Sol. ex Gaertn. Through analysis of a multigene data set, sampled from many taxa, I provide an improved phylogeny for Pimelea and its close relatives. I then generate a plastome-scale data set for a representative sample of species to further refine the Pimelea phylogeny, and characterise discordant phylogenetic signals within their chloroplast genomes. The work in this thesis demonstrates the power of genome- scale data to address challenging phylogenetic questions, and the importance of critical evaluation of both methods and results. Future progress in our understanding of angiosperm evolution will depend on broader and denser taxon sampling, and the development of improved phylogenetic methods

Aspects of Pacemakers

Outstanding steps forward were made in the last decades in terms of identification of endogenous pacemakers and the exploration of their controllability. New "artifical" devices were developed and are now able to do much more than solely pacemaking of the heart. In this book different aspects of pacemaker - functions and interactions, in various organ systems were examined. In addition, various areas of application and the potential side effects and complications of the devices were discussed

Reconstruction, mobility, and synchronization in complex networks

During the last decades, it has become clear that systems formed by many interacting parts show emergent dynamical properties which are inherently related to the topology of the underlying pattern of connections among the constituent parts. Such systems, usually known as complex systems, are in general suitably described through their networks of contacts, that is, in terms of nodes (representing the system's components) and edges (standing for their interactions), which allows to catch their essential features in a simple and general representation. In recent years, increasing interest on this approach, thanks also to a favorable technological progress, led to the accumulation of an increasing amount of data. This situation has allowed the arising of new questions and, therefore, the diversification of the scientific work. Among them, we can point out three general issues that have been receiving a lot of interest: (i) is the available information always reliable and complete? (ii) how does a complex interaction pattern affect the emergence of collective behavior in complex systems? And (iii) which is the role of mobility within the framework of complex networks? This thesis has been developed along these three lines, which are strictly interrelated. We expand on three case-studies, each one of which deals with two the above mentioned macro-issues. We consider the issue of the incompleteness of the available information both in the case of natural (Chapter 2) and artificial (Chapter 3) networks. As a paradigmatic emergent behavior, we focus on the synchronization of coupled phase oscillators (Chapter 2 and Chapter 4), deeply investigating how different patterns of connections can affect the achievement of a globally coherent state. Finally, we include moving agents in two different frameworks, using them as explorers of unknown networks (Chapter 3) and considering them as interacting units able to establish connections with their neighbors (Chapter 4). In Chapter 2, we study the problem of the reconstruction of an unknown interaction network, whose nodes are Kuramoto oscillators. Our aim is to extract topological features of the connectivity pattern from purely dynamical measures, based on the fact that in a heterogeneous network the global dynamics is not only affected by the distribution of the natural frequencies but also by the location of the different values. The gathered topological information ranges from local features, such as the single node connectivity, to the hierarchical structure of functional clusters, and even to the entire adjacency matrix. In Chapter 4, instead, we present a model of integrate and fire oscillators that are moving agents, freely displacing on a plane. The phase of the oscillators evolves linearly in time and when it reaches a threshold value they fire at their neighbors. In this way, the interaction network is a dynamical object by itself since it is re-created at each time step by the motion of the units. Depending on the velocity of the motion, the average number of neighbors, the coupling strength and the size of the agents population, we identify different regimes. Moving agents are employed also in Chapter 3 where they play the role of explorers of unknown artificial networks, having the mission to recover information about their structures. We propose a model in which random walkers with previously assigned home nodes navigate through the network during a fixed amount of time. We consider that the exploration is successful if the walker gets the information gathered back home, otherwise, no data is retrieved. We show that there is an optimal solution to this problem in terms of the average information retrieved and the degree of the home nodes and design an adaptive strategy based on the behavior of the random walker.Durante las últimas décadas, se ha empezado a poner de manifiesto que sistemas formados por muchos elementos en interacción pueden mostrar propiedades dinámicas emergentes relacionadas con la topología del patrón de conexiones entre las partes constituyentes. Estos sistemas, generalmente conocidos como sistemas complejos, en muchos casos pueden ser descritos a través de sus redes de contactos, es decir, en términos de nodos (que representan los componentes del sistema) y de enlaces (sus interacciones). De esta manera es posible capturar sus características esenciales en una representación simple y general. En esta última década, el creciente interés en este enfoque, gracias también a un progreso tecnológico favorable, ha llevado a la acumulación de una cantidad ingente de datos. Eso, a su vez, ha permitido el surgimiento de nuevas preguntas y, por lo tanto, la diversificación de la actividad científica. Entre ellas, podemos destacar tres cuestiones generales que son objeto de mucho interés: (i) ¿la información disponible es siempre fiable y completa? (ii) ¿cómo un patrón de interacción complejo puede afectar el surgimiento de comportamientos colectivos? Y (iii) ¿cual es el papel de la movilidad en el marco de las redes complejas? Esta tesis se ha desarrollado siguiendo estas tres líneas, que están íntimamente relacionadas entre sí. Hemos profundizado en tres casos de estudio, cada uno de los cuales se ocupa de dos de los macro-temas mencionados. Consideramos la cuestión del carácter incompleto de la información disponible tanto en el caso de redes naturales (Capítulo 2) como de redes artificiales (Capítulo 3). Nos centramos en la sincronización de los osciladores de fase acoplados (Capítulos 2 y 4) en cuanto comportamiento emergente paradigmático, investigando en profundidad cómo los diferentes patrones de conexión puedan afectar la consecución de un estado coherente a nivel global. Por último, analizamos el rol de la movilidad incluyendo agentes móviles en dos marcos diferentes. En un caso, los utilizamos como exploradores de redes desconocidas (Capítulo 3), mientras que en otro los consideramos como unidades que interaccionan y son capaces de establecer conexiones con sus vecinos (Capítulo 4)

Evolutionary Expansions and Neofunctionalization of Ionotropic Glutamate Receptors in Cnidaria

Reef ecosystems are composed of a variety of organisms, transient species of fish and invertebrates, microscopic bacteria and viruses, and structural organisms that build the living foundation, coral. Sessile cnidarians, corals and anemones, interpret dynamic environments of organisms and abiotic factors through a molecular interface. Recognition of foreign molecules occurs through innate immunity via receptors identifying conserved molecular patterns. Similarly, chemosensory receptors monitor the environment through specific ligands. Chemosensory receptors include ionotropic glutamate receptors (iGluRs), transmembrane ion channels involved in chemical sensing and neural signal transduction. Recently, an iGluR homolog was implicated in cnidarian immunological resistance to recurrent infections of bacterial pathogens. I postulate that iGluRs in cnidarians may act as danger-sensing and/or pathogen recognition receptors adjacent to immune defense and nervous system signaling. In Chapter One, I explain the exploration of diversity and divergence within cnidarian iGluRs, complimented with predicted functions in the context of correlated response to biological and environmental signals, setting the groundwork for functional characterization. In Chapter Two, I characterized the divergence of cnidarian iGluRs in comparison to other metazoans through maximum likelihood phylogenetic analyses, which revealed greater evolutionary expansion of cnidarian iGluR lineages, including a Cnidaria-specific class. Gene expression differentiation implies select iGluRs respond transcriptionally to bacterial challenge, supporting the hypothesis that cnidarian iGluRs respond to pathogen signals. In Chapter Three, I investigated a putative endogenous rhythm to iGluR expression, as chemosensory receptors may have the capacity to anticipate daily environmental fluctuations. While a circadian rhythm does not appear to be a primary contributor to biological rhythms in iGluR gene expression, symbiosis and diurnal fluctuations are implicated factors. In Chapter Four, I chromogenically localized Exaiptasia pallidaiGluR expression to the epidermis and concentrated within sensory tentacles, alongside cnidocytes. Expression of iGluRs in proximity of sensory cells is consistent with the putative function of iGluRs in cnidarian neural signaling. In the final chapter, I synthesized my research in its entirety; highlighting that cnidarian iGluRs expansions indicate cnidarian-specific neofunctionalization towards functions of chemosensory cnidarian-environmental signaling. New hypotheses and future research are presented to continue the study of iGluRs as chemosensory receptors within the cnidarian nervous system

Washington University Record, November 30, 2006

https://digitalcommons.wustl.edu/record/2091/thumbnail.jp

Its Skin is My Skin

This text examines the complexity of attempting to empathize with bodies that are vastly othered from my own. This broad yet nuanced subject crosses epistemological boundaries and complicates the dualities between both the mind and body, and between the corporeal and the virtual. My desire to better understand the conditions of another’s experience originates from a painful traumatic loss which caused me to feel isolated and incomplete. In response to this suffering, I long to emotionally connect with other beings and create artwork that attempts to bridge the qualia of individual experience. I am interested in the capacity (or lack thereof) to empathize with othered bodies; human, animal, non-human and virtual. As a result, my work involves discourse around the parameters that constitute being considered alive, the ability of cross-species empathy through shared experiences of embodiment, as well as corporeal relationships with digital technology and cyberspace. I utilize the media of digital photography along with 3D modeling and animation software to create abject amalgams of human flesh. Through the freedom of the digital medium, I can visually depict internal conflict in a way that transcends corporeal limitations. I manipulate representations of tangible bodies, placing them in surreal non-spaces that I intend to be suggestive of psychological states or digital voids. By doing so, I hope to not only convey intangible emotions of pain, but also speak to the complexity of understanding corporeal indeterminacy and a fragmentation of identity within a virtual environment unbound by physical limitations

Computational design of custom therapeutic cells to correct failing human cardiomyocytes

Background: Myocardial delivery of non-excitable cells—namely human mesenchymal stem cells (hMSCs) and c-kit+ cardiac interstitial cells (hCICs)—remains a promising approach for treating the failing heart. Recent empirical studies attempt to improve such therapies by genetically engineering cells to express specific ion channels, or by creating hybrid cells with combined channel expression. This study uses a computational modeling approach to test the hypothesis that custom hypothetical cells can be rationally designed to restore a healthy phenotype when coupled to human heart failure (HF) cardiomyocytes.Methods: Candidate custom cells were simulated with a combination of ion channels from non-excitable cells and healthy human cardiomyocytes (hCMs). Using a genetic algorithm-based optimization approach, candidate cells were accepted if a root mean square error (RMSE) of less than 50% relative to healthy hCM was achieved for both action potential and calcium transient waveforms for the cell-treated HF cardiomyocyte, normalized to the untreated HF cardiomyocyte.Results: Custom cells expressing only non-excitable ion channels were inadequate to restore a healthy cardiac phenotype when coupled to either fibrotic or non-fibrotic HF cardiomyocytes. In contrast, custom cells also expressing cardiac ion channels led to acceptable restoration of a healthy cardiomyocyte phenotype when coupled to fibrotic, but not non-fibrotic, HF cardiomyocytes. Incorporating the cardiomyocyte inward rectifier K+ channel was critical to accomplishing this phenotypic rescue while also improving single-cell action potential metrics associated with arrhythmias, namely resting membrane potential and action potential duration. The computational approach also provided insight into the rescue mechanisms, whereby heterocellular coupling enhanced cardiomyocyte L-type calcium current and promoted calcium-induced calcium release. Finally, as a therapeutically translatable strategy, we simulated delivery of hMSCs and hCICs genetically engineered to express the cardiomyocyte inward rectifier K+ channel, which decreased action potential and calcium transient RMSEs by at least 24% relative to control hMSCs and hCICs, with more favorable single-cell arrhythmia metrics.Conclusion: Computational modeling facilitates exploration of customizable engineered cell therapies. Optimized cells expressing cardiac ion channels restored healthy action potential and calcium handling phenotypes in fibrotic HF cardiomyocytes and improved single-cell arrhythmia metrics, warranting further experimental validation studies of the proposed custom therapeutic cells