Developmental Origin of Patchy Axonal Connectivity in the Neocortex: A Computational Model

Injections of neural tracers into many mammalian neocortical areas reveal a common patchy motif of clustered axonal projections. We studied in simulation a mathematical model for neuronal development in order to investigate how this patchy connectivity could arise in layer II/III of the neocortex. In our model, individual neurons of this layer expressed the activator-inhibitor components of a Gierer-Meinhardt reaction-diffusion system. The resultant steady-state reaction-diffusion pattern across the neuronal population was approximately hexagonal. Growth cones at the tips of extending axons used the various morphogens secreted by intrapatch neurons as guidance cues to direct their growth and invoke axonal arborization, so yielding a patchy distribution of arborization across the entire layer II/III. We found that adjustment of a single parameter yields the intriguing linear relationship between average patch diameter and interpatch spacing that has been observed experimentally over many cortical areas and species. We conclude that a simple Gierer-Meinhardt system expressed by the neurons of the developing neocortex is sufficient to explain the patterns of clustered connectivity observed experimentall

Turing pattern formation on the sphere for a morphochemical reaction-diffusion model for electrodeposition

The present paper deals with the pattern formation properties of a specific morpho- electrochemical reaction-diffusion model on a sphere. The physico-chemical background to this study is the morphological control of material electrodeposited onto spherical parti- cles. The particular experimental case of interest refers to the optimization of novel metal- air flow batteries and addresses the electrodeposition of zinc onto inert spherical supports. Morphological control in this step of the high-energy battery operation is crucial to the energetic efficiency of the recharge process and to the durability of the whole energy- storage device. To rationalise this technological challenge within a mathematical modeling perspective, we consider the reaction-diffusion system for metal electrodeposition intro- duced in [Bozzini et al., J. Solid State Electr.17, 467–479 (2013)] and extend its study to spherical domains. Conditions are derived for the occurrence of the Turing instability phe- nomenon and the steady patterns emerging at the onset of Turing instability are investi- gated. The reaction-diffusion system on spherical domains is solved numerically by means of the Lumped Surface Finite Element Method (LSFEM) in space combined with the IMEX Euler method in time. The effect on pattern formation of variations in the domain size is investigated both qualitatively, by means of systematic numerical simulations, and quan- titatively by introducing suitable indicators that allow to assign each pattern to a given morphological class. An experimental validation of the obtained results is finally presented for the case of zinc electrodeposition from alkaline zincate solutions onto copper spheres

A theoretical and computational study of cavity formation in biological systems

In this thesis, I present my work on the emergence of self-organised structure within cellular systems, with a particular emphasis on the formation of fluid filled cavities. Self-organisation is a striking hallmark of living systems, and plays a particularly import role in developmental biology. To study such systems, I develop a novel hydrodynamic theory of cells in a background fluid of water and solutes. The solutes and water can move passively across the membrane of the cells. Furthermore, solutes can be actively transported in or out of the cell both isotropi- cally and along a polar axis. Within this theory I demonstrate the existence of two potential mechanisms for cavity formation: spinodal phase separation driven by cell-cell adhesions, and an instability driven by active pumping of solutes into defects in the polarity field. This theory is general in scope, i.e. it is a framework to describe a variety of behaviours of any system consisting of adhering cells that can polarise and actively pump fluid. I also present a study of a specific experimental system: mouse embryonic stem cell (mESC) aggregates. When grown from wild type cells, these aggregates form a spherical structure with cells polarised towards the centre. Fluid is pumped into the centre and a cavity opens. Such aggregates are the simplest example of mESC organoids that recapitulate key in vivo developmental processes in vitro. In order to quantify the growth of mESC aggregates, I develop an image segmentation and analysis pipeline. This pipeline allows me to extract meaningful, structured information from noisy 3D experimental time series data. In order to model the growth of mESC aggregates in silico, I develop a novel 2D model of polarised, deformable cells with continuous boundaries, called the Spline Model. Using the Spline Model as a prototype, I recapitulate key features of the experiments. Finally, I develop a 3D model of polarised, deformable cells. I demonstrate quantitative agreement between cell shapes produced by this model and in experiment. I study the dynamics of cell aggregates for the case where adhesion forces are coupled to apicobasal polarity, and make quantitative comparisons between these simulations and experiments. I find a positive correlation between the measured polarity of E- cadherin and predictions based on integration of extracellular matrix signalling. Furthermore, by coupling polarity to increased apical adhesion, I demonstrate the ability of extended cellular aggregates to undergo a transition to a compact state. When the coupling is removed, the transition no longer occurs. This behaviour is reminiscent of β1-KO cells, in which polarity alignment mechanisms are disrupted, that fail to form compact, organised aggregates

Mechanobiological computational model for the development and formation of synovial joints

El desarrollo de las articulaciones sinoviales se debe a diferentes factores genéticos, bioquímicos y mecánicos. Comienza en el brote de las extremidades, que tienen una masa ininterrumpida de células mesenquimales dentro de su núcleo, el blastema esquelético. La mayoría de estas células blastemales se diferencian en condrocitos; sin embargo, algunas de estas células permanecen, sin diferenciar, en el sitio de la futura articulación (interzona). La separación de los rudimentos ocurre con el proceso de cavitación dentro de la interzona. Después de la cavitación, se produce la morfogénesis articular y el hueso toma su forma final. Una vez finalizado el período embrionario, la articulación sinovial y sus estructuras internas se han desarrollado completamente. Aunque una vez que se forman las articulaciones sinoviales, pueden sufrir, a lo largo de la vida, distintas patologías, como la osteoartritis (OA). Hay varios tratamientos que se han propuesto para regenerar el cartílago articular, entre los cuales, los andamiajes (scaffolds) sin fuentes celulares han mostrado grandes resultados. Comprender los procesos por los que pasa el tejido articular es importante para desarrollar nuevos tratamientos directos y efectivos para las patologías relacionadas con las articulaciones. Los modelos computacionales parecen ser una buena herramienta para complementar el estudio de los procesos articulares. Por lo tanto, fue de nuestro interés estudiar, a través de modelos computacionales, la interacción bioquímica de la aparición de la interzona, la cavitación y la morfogénesis durante el desarrollo de articulaciones. Analizamos estos fenómenos en el desarrollo de una articulación interfalángica y el desarrollo de la rótula. Además, también estábamos interesados en analizar, mediante un modelo computacional, los procesos que ocurren cuando un defecto en el cartílago articular se trata con la implantación de un andamiaje polimérico. Todos los modelos computacionales desarrollados en este estudio aplicaron teorías sobre el comportamiento de los tejidos bajo estímulos mecánicos y bioquímicos. Los resultados obtenidos, fueron comparados con los trabajos experimentales encontrados en la literatura, todos los modelos mostraron resultados prometedores. Por lo tanto, consideramos que los procedimientos y las suposiciones tomadas para cada modelo computacional propuesto no están lejos de lo que realmente está sucediendo en los fenómenos biológicos analizados. Además, pudimos evaluar las condiciones mecánicas y bioquímicas de los fenómenos biológicos analizados, difíciles de probar a través de enfoques experimentales. Esperamos que estos modelos sean útiles para las investigaciones médicas y biológicas, ayudando en el diseño de estrategias de prevención y terapia para enfermedades relacionadas con las articulaciones. Esta tesis está estructurada en ocho partes, incluida una introducción que trata de exponer la importancia del estudio y los objetivos de la tesis. Posteriormente, en la segunda parte exponemos algunos conceptos generales relacionados con los temas y métodos empleados para desarrollar la investigación. Luego, la tercera parte describe un modelo computacional propuesto para explicar el desarrollo de articulaciones desde el inicio de la interzona hasta el proceso de cavitación. La cuarta parte se centra en la morfogénesis de las articulaciones como parte del proceso de desarrollo de las mismas. Posteriormente, la quinta sección está dedicada a explicar el desarrollo de los huesos sesamoideos a través de una comparación de tres teorías del desarrollo de la rótula, evaluadas mediante modelos computacionales. La séptima parte de este trabajo es un modelo computacional propuesto para comprender los procesos que rodean la regeneración del cartílago cuando se implanta un andamiaje polimérico en el cartílago articular. En la última parte, se concluyen los logros y se analizan las principales conclusiones de la tesis, así como el trabajo futuro recomendado y las perspectivas. Como capítulo adicional, agregamos una descripción general de la tesis en inglés y en valenciano.The onset and development of the synovial joints is due to different genetic, biochemical, and mechanical factors. It starts at the limb buds, which have an uninterrupted mass of mesenchymal cells within its core, also known as skeletal blastema. Most of these blastemal cells differentiate into chondrocytes; however, some of these cells remain undifferentiated at the site of the future joint (interzone). The separation of the rudiments occurs with cavitation process within the interzone. After the joint cleavage (cavitation), joint morphogenesis occurs, and the bones take their final shape. Once the embryonic period has finished, the synovial joint and its internal structures has developed completely. Though, once the synovial joints are formed, they might suffer several pathologies, such as the osteoarthritis (OA). There are several treatments that have been proposed to regenerate the articular cartilage, among which scaffolds without cellular sources have shown great results. Understand the processes that the joint tissue goes through are important to develop new direct and effective treatments for joint related pathologies. Computational models seem a good alternative tool to complement the study of the joint processes. Therefore, it was of our interest to study, through computational models, the biochemical interaction for the interzone onset, the cavitation and morphogenesis processes during the joint development. We analyzed these phenomena within the development of an interphalangeal joint and the patella onset. Moreover, we were also interested on analyzing, through a computational model, the processes happening when a defect in the articular cartilage is treated with the implantation of a polymeric scaffold. All the computational models developed in this study applied theories about tissue behavior under mechanical and biochemical stimuli. The obtained results were compared to experimental works found in the literature, all of them showed promising outcomes. Hence, we consider that the procedures and considerations taken for each proposed computational model are not far from what is really happening on the analyzed biological phenomena. Moreover, we were able to evaluate mechanical and biochemical conditions the biological phenomena, that would be hard to test through experimental approaches. We hope that these models become useful to medical and biological researches, helping in the design of prevention and therapy strategies for joint related diseases. This thesis is structured in eight parts including an introduction which tries to aware the importance of the study and the objectives of the thesis. Afterwards, on the second part, we expose some general concepts related to the topics and methods employed to develop the research. Then, the third part describes a computational model proposed to explain joint development from the interzone onset to the cavitation process. The fourth part is focus on the joint morphogenesis as part of the joint development process. Subsequently, the fifth section is dedicated to explaining the sesamoid bones development through a comparison of three theories of the patella onset, evaluated via computational models. The seventh part of this work is a computational model proposed to understand the processes that surround the cartilage regeneration when a polymeric scaffold is implanted in the articular cartilage. In the last part, we concluded the achievements and discussed the main conclusions of the thesis, as well as the recommended future work and perspectives. As an additional chapter, we added a general overview of the thesis in English and in Valencian

Implantable microelectrodes on soft substrate with nanostructured active surface for stimulation and recording of brain activities

Les prothèses neuronales implantables offrent de nos jours une réelle opportunité pour restaurer des fonctions perdues par des patients atteints de lésions cérébrales ou de la moelle épinière, en associant un canal non-musculaire au cerveau ce qui permet la connexion de machines au système nerveux. La fiabilité sur le long terme de ces dispositifs, se présentant sous la forme d'électrodes implantables, est un facteur crucial pour envisager des applications dans le domaine des interfaces cerveau-machine. Cependant, les électrodes actuelles pour l'enregistrement et la stimulation se détériorent en quelques mois voire quelques semaines. Ce défaut de fiabilité sur le long terme, principalement lié à une réaction chronique contre un corps étranger, est induit au départ par le traumatisme consécutif à l'insertion du dispositif et s'aggrave ensuite, durant les mouvements du cerveau, à cause des propriétés mécaniques inadaptées de l'électrode par rapport à celles du tissu. Au cours du temps, l'ensemble de ces facteurs inflammatoires conduit à l'encapsulation de l'électrode par une couche isolante de cellules réactives détériorant ainsi la qualité de l'interface entre le dispositif implanté et le tissu cérébral. Pour s'affranchir de ce phénomène, la biocompatibilité des matériaux et des procédés, ainsi que les propriétés mécaniques de l'électrode doivent être pris en considération. Durant cette thèse, nous avons abordé la question en développant un procédé de fabrication simple pour réaliser des dispositifs implantables souples en parylène. Les électrodes flexibles ainsi obtenues sont totalement biocompatibles et leur compliance est adaptée à celle du tissu cérébral ce qui limite fortement la réaction inflammatoire occasionnée par les mouvements du cerveau. Après avoir optimisé le procédé de fabrication, nous avons focalisé notre étude sur les performances du dispositif et sa stabilité. L'utilisation d'une grande densité d'électrodes micrométriques, avec un diamètre de 10 à 50 µm, permet de localiser les zones d'enregistrement en rendant possible, par exemple, la conversion d'un ensemble de signaux électrophysiologiques en une commande de mouvement. En contrepartie, la réduction de la taille des électrodes conduit à une augmentation de l'impédance ce qui dégrade la qualité d'enregistrement des signaux. Ici, un polymère conducteur organique, le poly(3,4-ethylenedioxythiophene), PEDOT, a été utilisé pour améliorer les caractéristiques électriques d'enregistrement d'électrodes de petites dimensions. Le PEDOT a été déposé sur la surface des électrodes par électrochimie avec une grande reproductibilité. Des dépôts homogènes avec des conductivités électriques très élevées ont été obtenus en utilisant différents procédés électrochimiques. Grâce à l'augmentation du rapport surface/volume induit par la présence de la couche de PEDOT, une diminution significative de l'impédance de l'électrode (jusqu'à 3 ordres de grandeur) a été obtenue sur une large plage de fréquences. De tests de vieillissement thermique accéléré ont également été effectués sans influence notable sur les propriétés électriques démontrant ainsi la stabilité de la couche de PEDOT durant plusieurs mois. Les dispositifs ainsi obtenus, fabriqués en parylène avec un dépôt de PEDOT sur la surface active des électrodes, ont été testés in vitro et in vivo sur des cerveaux de souris. Un meilleur rapport signal sur bruit a été mesuré durant des enregistrements neuronaux en comparaison avec des résultats obtenus avec des électrodes commerciales. En conclusion, la technologie décrite ici, associant stabilité sur le long terme et faible impédance, a permis d'obtenir des électrodes implantables parfaitement adaptées pour le développement d'interfaces neuronales chroniques.Implantable neural prosthetics devices offer, nowadays, a promising opportunity for the restoration of lost functions in patients affected by brain or spinal cord injury, by providing the brain with a non-muscular channel able to link machines to the nervous system. The long term reliability of these devices constituted by implantable electrodes has emerged as a crucial factor in view of the application in the "brain-machine interface" domain. However, current electrodes for recording or stimulation still fail within months or even weeks. This lack of long-term reliability, mainly related to the chronic foreign body reaction, is induced, at the beginning, by insertion trauma, and then exacerbated as a result of mechanical mismatch between the electrode and the tissue during brain motion. All these inflammatory factors lead, over the time, to the encapsulation of the electrode by an insulating layer of reactive cells thus impacting the quality of the interface between the implanted device and the brain tissue. To overcome this phenomenon, both the biocompatibility of materials and processes, and the mechanical properties of the electrodes have to be considered. During this PhD, we have addressed both issues by developing a simple process to fabricate soft implantable devices fully made of parylene. The resulting flexible electrodes are fully biocompatible and more compliant with the brain tissue thus limiting the inflammatory reaction during brain motions. Once the fabrication process has been completed, our study has been focused on the device performances and stability. The use of high density micrometer electrodes with a diameter ranging from 10 to 50 µm, on one hand, provides more localized recordings and allows converting a series of electrophysiological signals into, for instance, a movement command. On the other hand, as the electrode dimensions decrease, the impedance increases affecting the quality of signal recordings. Here, an organic conductive polymer, the poly(3,4-ethylenedioxythiophene), PEDOT, has been used to improve the recording characteristics of small electrodes. PEDOT was deposited on electrode surfaces by electrochemical deposition with a high reproducibility. Homogeneous coatings with a high electrical conductivity were obtained using various electrochemical routes. Thanks to the increase of the surface to volume ratio provided by the PEDOT coating, a significant lowering of the electrode impedance (up to 3 orders of magnitude) has been obtained over a wide range of frequencies. Thermal accelerated ageing tests were also performed without any significant impact on the electrical properties demonstrating the stability of the PEDOT coatings over several months. The resulting devices, made of parylene with a PEDOT coating on the active surface of electrodes, have been tested in vitro and in vivo in mice brain. An improved signal to noise ratio during neural recording has been measured in comparison to results obtained with commercially available electrodes. In conclusion, the technology described here, combining long-term stability and low impedance, make these implantable electrodes suitable candidates for the development of chronic neural interfaces

Life Sciences Program Tasks and Bibliography for FY 1996

This document includes information on all peer reviewed projects funded by the Office of Life and Microgravity Sciences and Applications, Life Sciences Division during fiscal year 1996. This document will be published annually and made available to scientists in the space life sciences field both as a hard copy and as an interactive Internet web page

Three-dimensional electrode array for brain slice culture

Multielektroder arrays (MEA) er rækker af elektroder mest i mikrometer størrelse, som er blevet brugt i stor omfang til at stimulere og måle elektrisk aktivitet fra neuronale netværker. Brug af disse for at analysere hjerne slices (hjerneskiver) kan give indsigt i interaktioner mellem neuroner, eftersom dyrkninger af hjerneskiver in vitro beholder funktionaliteten af netværkerne i den levende hjerne. Elektroder var designet og fabrikeret med det formal at optimere MEA præstationen ved stimulering af og måling fra hjerneskiver in vitro. Meget af arbejdet beskrevet her beskæftiger sig med studiet af silicium mikrofabrikations teknikker for at opnå 3D elektroder med en høj dimensionsforhold, som er de mest egnede til at interagere med hjerneskiver. Elektroderne blev karakteriseret bade elektrisk og mekanisk for at demonstrere deres bedre egenskaber ved elektriske malinger og væv indtrægningsevne. Ved et andet sæt eksperimenter, det fabrikeret MEA system blev forsøgt integreret med et dyrkningsplatform som skal gøre længerevarende målinger mulige. Baseret på eksisterende litteratur mange forskellige platformer blev udviklet og tested med hjerneskiver. Selvom dyrkningen af væv ikke var mulig i disse systemer, eksperimenterne viser at de mikrofluidiske dele af systemet var funktionelle og det var muligt at integrere MEA systemet med ved at modificere den og lave den del af gennemstrømningsmekanismen. Til sidst en mekanisme som var I stand til at flytte elektroderne ind og ud af hjerneskiveren blev udviklet, simuleret og testet. Systemet var i stand til at flytte MEA chippen. Selvom mindre modifikationer vil være ønskelige for at forbedre bevægelsespræcisionen, integrering af denne mekanisme med MEA chippen var mulig og funktionaliteten af systemet blev påvist