Les travaux de cette thèse portent principalement sur le développement d'une méthodologie pour la modélisation de systèmes biologiques. Cette méthodologie, basée sur une modélisation en équations différentielles, intègre aussi bien des méthodes formelles (solveur sur intervalles, solveur de formules STL), qu'analytiques (calcul de stabilité d'état stationnaire) ou numériques (algorithme d'optimisation, analyses statistiques). Elle permet l'intégration de différents types de données, telles la réponse comportementale à une perturbation ou des données quantitatives (demie-vie, concentrations). En collaboration avec une équipe de biologistes, cette méthodologie est appliquée, avec succès, au système de l'homéostasie du fer : nous étudions la réponse intracellulaire du système, via des protéines régulatrices spécifiques (protéines IRP), face à une situation de carence en fer. Un résultat majeur de cette étude est l'amélioration des connaissances sur la concentration de fer intracellulaire nécessaire à la prolifération des cellules : cette concentration est mise en avant par l'étude du modèle, puis est confirmée expérimentalement.Le deuxième volet de ces travaux portent sur le développement d'un outil pour la modélisation de réseaux de gènes avec le formalisme des réseaux de Thomas. Cet outil, développé en ASP (Answer Set Programming), permet l'intégration de différents types de données telles des données sur des mutants ou l'existence de différents états stationnaires. Cet outil permet d'éviter automatiquement l'incohérence en cas de contradiction entre différentes hypothèses sur le système. Il permet également l'inférence de propriétés biologiques telles que l'ordre entre paramètres cinétiques. / The major part of this PhD consists in the creation of a methodology to model biological systems. This methodology considers models based on differential equations, and uses formal methods (interval solver, verification of STL formula), analytical methods (study of stability) and numerical methods (optimization algorithm, statistical analysis). Moreover, many kind of data, like behavioral response to perturbation, or quantitative data (metabolite half-life and concentration) can be incorporated. In collaboration with a biologist team, this methodology is successfully applied to the iron homeostasis network : we study the response of the system to an iron depletion, at the intracellular level, based on specific regulatory proteins (IRP proteins). A major output of this study is insight into the level of iron cells need to proliferate : this concentration is pointed out by the study of the model, and is experimentally validated.The second part of the PhD is the creation of a tool to model genetic regulatory networks, using Thomas' formalism. This tool, developed using ASP (Answer Set Programming) programming language, can integrate many kind of data, like mutation data, or the existence of many steady states. It automatically avoids inconsistency in case of contradiction between different hypotheses. It also infers biological properties such as relationships between kinetic parameters.

Magíster en Ciencias de la Ingeniería, Mención Matemáticas Aplicadas. Ingeniero Civil Matemático / La homeostasis es un estado de equilibrio sobre las distintas condiciones internas que pre- servan los organismos vivos [17]. Como tales condiciones son afectadas por los estímulos del medio externo, los organismos vivos desarrollan complejos mecanismos de adaptación que les permiten mantener este estado de armonía interna. Casi la mitad de las enzimas, piezas claves en la maquinaria metabólica de los sistemas biológicos, necesitan de ciertos metales como el cobre, el hierro o el zinc para cumplir sus funciones [73]. Sin embargo, altas concentraciones de estos metales pueden producir la muerte del organismo [71]. Como resultado de esta di- námica, las bacterias han evolucionado complejos mecanismos homeostáticos para equilibrar la presencia de estos metales [71]. Basándose en evidencia experimental [51, 57, 39] y en trabajos de modelamiento previos [49], en el transcurso de esta memoria se busca describir matemáticamente la dinámica de la homeostasis del cobre en E. faecalis, haciendo uso de la teoría clásica de sistemas de ecuaciones diferenciales ordinarias y, recurriendo a herramientas recientes, provenientes de la teoría de sistemas dinámicos monótonos [22, 21, 6, 28]. Para enfrentar la complejidad y la no-linealidad de las ecuaciones que aparecen en los sistemas, provenientes de los formalismos de modelamiento de reacciones químicas, se divide el análisis en el estudio de dos modelos: a) un modelo que incluye solo ecuaciones polinomiales y b) un modelo más realista que incluye la descripción de fenómenos como la cooperatividad y saturación, usando funciones de regulación. Como resultados derivados de este análisis, se describe la homeostasis en términos cualitativos, concluyendo con la demostración de que este estado es un atractor global al cual el sistema tiende, a partir de una dinámica transiente. Además, se presentan simulaciones numéricas en las que se constata este tipo de comportamiento. Los hallazgos planteandos en este trabajo constituyen un primer paso para el estudio de estas propiedades en sistemas homeostáticos más generales. Esto último tiene una importan- cia crítica para el desarrollo de aplicaciones biotecnológicas en la industria como lo son, por ejemplo, los procesos de bioloxividación en la minería del cobre [1, 2]. / Este trabajo ha sido parcialmente financiado por el proyecto Fondecyt de Iniciación 11150679 y el proyecto Fondap CRG 15090007

Magister Educationis - MEd / Pupils experience various problems when trying to solve problems in Biology, particularly on Higher Grade. This problem was profound in the area of Homeostasis, an aspect of Human Physiology. During this investigation a number of pupils, the PIONEER GROUP, were screened for cognitive deficiencies. Major common deficiencies were identified as IMPULSIVITY, THE USE TWO OR MORE SOURCES OF INFORMATION SIMULTANEOUSLY, SPATIAL AND TEMPORAL ORIENTATION. A second phase, the essence of this investigation, sought ways in which to teach pupils the cognitive skills to facilitate their concept formation in the area of Homeostasis. Since the subjects displaying these cognitive deficiencies were already in their final year of High School a method was sought which would benefit them in the short term. Simultaneously a way had to be found to teach these skills so that it could be of use to pupils on a long term basis. This study revealed that for short term benefit the cognitive skills have to be subtly introduced and integrated with the subject content. Teaching cognitive skills in concentrated form over such a short period had a detrimental effect on the group subjected to this treatment. However, the PIONEER GROUP, had been taught these skills in a very short period in concentrated form. Feedback from them reveals that they were not able to apply the skills in their Senior Certificate Examination but all of them are now adept at using these skills to their benefit. This leads to the conclusion that if these skills are to be taught separately it should be started as early as possible in the school career. In the last year of High School it is more of a burden to the pupil than a benefit. In such a case it should be done integrated with subject content.

Grado de magister en nuerociencias / La homeostasis de sueño REM refiere el proceso mediante el cual la cantidad de tiempo en este estado se mantiene dentro de límites mínimos aceptables; sin embargo existen reportes contradictorios respecto a si el sueño REM posee efectivamente este tipo de regulación. Utilizando la herramienta de Estimulación Fótica provocamos un exceso de sueño REM. Aplicando Pulsos de Oscuridad (PO) durante el periodo de luz, se logra con alta probabilidad y corta latencia una transición de sueño NREM a sueño REM en ratas albinas. De esta manera provocamos un exceso del estado y evaluamos la respuesta posterior. Se implementaron tres protocolos: (1) 4R, privación selectiva de sueño REM durante 4 horas (Zeitgeber time 4-7); (2) 10d, aplicación de Pulsos de Oscuridad de 10 minutos, alternados con 20 minutos de luz durante 2 horas (Zeitgeber time 8-9) y por último (3) 4R10d, que involucra la combinación de ambas condiciones experimentales. Los protocolos 4R y 4R10d mostraron una respuesta homeostática de rebote significativa posterior a la privación. Durante el periodo de Estimulación Fótica se observó un importante incremento del tiempo en sueño REM en 4R10d en relación a BL y 4R que se extendió incluso durante el periodo de actividad de la rata. En el protocolo 10d se observó un incremento del tiempo en sueño REM equivalente al rebote post-privación obtenido en 4R, y el incremento ocurrido en 4R10d constituye la sumatoria del sueño REM obtenido producto de la privación más la acción de los Pulsos de Oscuridad. En conclusión, la recuperación post-privación mostró características homeostáticas, sin embargo no consideró el exceso de sueño REM obtenido mediante Estimulación Fótica. / There is a homeostatic mechanism that preserves the daily REM sleep quota. To be truly homeostatic, the underlying REM sleep hourglass process that keeps track of the cumulated REM sleep time should promote REM sleep in response to REM sleep deficits, as occurs after selective REM sleep deprivation (RD) in humans and rodent models, and postpone REM sleep occurrence when challenged by REM sleep excesses. In the albino rat, short dark pulses (DP) transiently increase REM sleep amount by shortening the latency of NREM to REM sleep transitions, phenomenon known as photic masking. Photic masking provides a useful strategy to explore the REM sleep hourglass process in response to REM sleep excess. Male albino rats were subjected to 4 hours of RD during the rest phase (zeitgeber time, ZT, 4-7; light:dark cycle= 12:12). It was compared the subsequent REM sleep rebound when occurring in the presence or absence of 10-minute DP given in the ZT 8-9 interval. REM sleep rebound in the ZT 8-11 interval after RD was 10.9 minutes and when occurring in the presence of DP was 22.2 minutes. Whereas REM sleep rebound after RD alone fully compensated REM sleep debt within 6 hours, REM sleep rebound with DP provoked a sustained REM sleep excess that was present after 16 hours of recordings. The additive effect of photic masking suggest that REM sleep hourglass process is insensitive to the activation of REM-on neurons targeted by retinofugal projections.

Maintaining wakefulness is associated with a progressive increase in the need for sleep. This phenomenon has been linked to changes in synaptic function. The synaptic adhesion molecule Neuroligin-1 (NLG1) controls the activity and synaptic localization of N-methyl-D-aspartate receptors, which activity is impaired by prolonged wakefulness. We here highlight that this pathway may underlie both the adverse effects of sleep loss on cognition and the subsequent changes in cortical synchrony. We found that the expression of specific Nlg1 transcript variants is changed by sleep deprivation in three mouse strains. These observations were associated with strain-specific changes in synaptic NLG1 protein content. Importantly, we showed that Nlg1 knockout mice are not able to sustain wakefulness and spend more time in nonrapid eye movement sleep than wild-type mice. These changes occurred with modifications in waking quality as exemplified by low theta/alpha activity during wakefulness and poor preference for social novelty, as well as altered delta synchrony during sleep. Finally, we identified a transcriptional pathway that could underlie the sleep/wake-dependent changes in Nlg1 expression and that involves clock transcription factors. We thus suggest that NLG1 is an element that contributes to the coupling of neuronal activity to sleep/wake regulation.

Maintaining wakefulness is associated with a progressive increase in the need for sleep. This phenomenon has been linked to changes in synaptic function. The synaptic adhesion molecule Neuroligin-1 (NLG1) controls the activity and synaptic localization of N-methyl-D-aspartate receptors, which activity is impaired by prolonged wakefulness. We here highlight that this pathway may underlie both the adverse effects of sleep loss on cognition and the subsequent changes in cortical synchrony. We found that the expression of specific Nlg1 transcript variants is changed by sleep deprivation in three mouse strains. These observations were associated with strain-specific changes in synaptic NLG1 protein content. Importantly, we showed that Nlg1 knockout mice are not able to sustain wakefulness and spend more time in nonrapid eye movement sleep than wild-type mice. These changes occurred with modifications in waking quality as exemplified by low theta/alpha activity during wakefulness and poor preference for social novelty, as well as altered delta synchrony during sleep. Finally, we identified a transcriptional pathway that could underlie the sleep/wake-dependent changes in Nlg1 expression and that involves clock transcription factors. We thus suggest that NLG1 is an element that contributes to the coupling of neuronal activity to sleep/wake regulation.

Simple regulatory mechanisms based on the idea of the saturable 'common stomach' can control the regulation of protein foraging and protein allocation in honeybee colonies and colony-level responses to environmental changes. To study the economic benefits of pollen and nectar foraging strategies of honeybees to both plants and honeybees under different environmental conditions, a model was developed and analyzed. Reallocation of the foraging workforce according to the quality and availability of resources (an 'adaptive' strategy used by honeybees) is not only a successful strategy for the bees but also for plants, because intensified pollen foraging after rain periods (when nectar quality is low) compensates a major fraction of the pollination flights lost during the rain. The 'adaptive' strategy performed better than the'fixed' (steady, minimalistic, and non-adaptive foraging without feedback) or the 'proactive' (stockpiling in anticipation of rain) strategies in brood survival and or in nectar/sugar economics. The time pattern of rain periods has profound effect on the supply-and-demand of proteins. A tropical rain pattern leads to a shortage of the influx of pollen and nectar, but it has a less profound impact on brood mortality than a typical continental rainfall pattern. Allocating more bees for pollen foraging has a detrimental effect on the nectar stores, therefore while saving larvae from starvation the 'proactive' strategy could fail to collect enough nectar for surviving winter.

Immune homeostasis is a host characteristic that maintains biological balance within a host. Humans have evolved many host defence mechanisms that ensure the survival of individuals upon encountering a pathogenic infection, with recovery or persistence from a viral infection being determined by both viral factors and host immunity. Chronic viral infections, such as hepatitis B virus, hepatitis C virus and HIV, often result in chronic fluctuating viraemia in the face of host cellular and humoral immune responses, which are dysregulated by multi-faceted mechanisms that are incompletely understood. This review attempts to illuminate the mechanisms involved in this process, focusing on immune homeostasis in the setting of persistent viral infection from the aspects of host defence mechanism, including interferon-stimulated genes, apolipoprotein B mRNA editing enzyme catalytic polypeptide 3 (APOBEC3), autophagy and interactions of various immune cells, cytokines and regulatory molecules.

Research has shown that when individuals are in situations that do not occasion one form of motoric responding, they will engage in another so that the overall level of motoric responding is homeostatic. The purpose of this study was to test whether students would substitute task-related behaviors for stereotypic or other challenging behaviors when the opportunity for active responding did or did not match the level of motoric responding in a free-operant baseline. Four students with mental retardation participated. Results showed that they did substitute behaviors, with stereotypic and other challenging behaviors occurring 1.5-14 times as much in the Non-matched condition for the four students. Further analysis showed considerably more of these behaviors in passive than in active tasks (by a factor up to 21 times as much). Results were discussed in terms of homeostasis, functional assessment, and opportunities to improve educational behaviors.

Le Système Nerveux Central (SNC) est un acteur majeur de la régulation de l’homéostasie énergétique, intégrant différents signaux nerveux, hormonaux ou nutritionnels. Le métabolisme lipidique joue un rôle essentiel notamment dans la détection des signaux lipidiques, et les enzymes y participant sont donc fortement impliquées dans la régulation de ces signaux et leur expression est cruciale au bon équilibre énergétique. La Lipoprotéine Lipase (LPL), enzyme clé de l'hydrolyse des triglycérides, nous est apparue comme une cible de choix dans la mesure où elle est exprimée dans différentes structures cérébrales comme l'hippocampe ou l'hypothalamus. L'hypothalamus a été identifié depuis de nombreuses années comme un centre de régulation de la prise alimentaire et donc de l'équilibre entre entrées et dépenses d'énergie. Ainsi, il est apparu comme légitime que de s'intéresser plus précisément au rôle de la LPL hypothalamique et son implication dans la régulation de l'homéostasie énergétique.L'objet de cette thèse a donc été d'étudier, dans un premier temps, les effets d'une délétion de LPL dans le VMH, réalisée grâce à une injection d'un AAV2/9 exprimant la Cre recombinase chez des souris LPL lox/lox âgées de 8 semaines. La diminution de l'activité LPL dans le VMH conduit au développement d'une obésité au bout de 3 semaines post-injection, ainsi qu'au développement d'une intolérance au glucose, d'une résistance à l'insuline ainsi qu'une diminution de l'activité locomotrice.Ce phénotype est dû à une diminution transitoire de la quantité de céramides synthétisées par l’enzyme CerS1 au sein de l'hypothalamus durant les semaines qui suivent l'injection et qui perturbent la signalisation homéostatique. Il apparait également que le système endocannabinoïde pourrait être impliqué dans la mise en place de ce phénotype. Les caractéristiques de ce phénotype rappelant celles d'un état de torpeur, nous avons cherché dans la deuxième partie de ce travail de thèse, à reproduire celui-ci pour pouvoir étudier plus précisément les liens et les conséquences entre torpeur et lipases cérébrales. Nous avons donc exposés les animaux à 4°C pendant 4 heures et étudié les répercussions de ce stress thermique sur les gènes des lipases centrales ainsi que ceux du rythme circadien : nous avons pu mettre en évidence une modification du rythme circadien. Nous avons également exposé des animaux délétés en LPL hypothalamique et pu établir que cette délétion centrale en LPL modifie la thermogenèse du tissu adipeux brun ainsi et favorise le développement du tissu adipeux beige. Ce travail de thèse a donc permis de mettre en lumière pour la première fois l'implication de la LPL hypothalamique dans la régulation de l'homéostasie énergétique ainsi que son rôle dans la réponse adaptative à une exposition aiguë au froid. / The Central Nervous System (CNS) is a major actor in the energy balance regulation, integrating different nervous, hormonal or nutritional signals. The lipid metabolism plays an essential role especially in the detection of lipid signals. So, the enzymes taking part in it are involved in the regulation of these signals and their expression is crucial to the energy balance. The Lipoprotein Lipase (LPL), the key enzyme in triglycerides hydrolysis appeared to us as a target of choice as it is expressed in different brain structures like the hypothalamus or the hippocampus.The hypothalamus has long been known as a regulation center of food intake and so of the balance between entrance and expenditure of energy. It seemed interesting to focus more precisely on the role of hypothalamic LPL and its implication in the regulation of energy homeostasis.This dissertation’s main objective was to identify the effects of LPL deletion in the VMH, achieved by injection of an AAV2/9 expressing the Cre-recombinase in LPL lox/lox mice aged of 8 weeks. The decrease of LPL activity in the VMH leads to obesity development around 3 weeks post-injection and to the development of glucose intolerance, resistance to insulin and a decrease in locomotor activity.This phenotype is probably due to a transient decrease of ceramides synthesized by the CerS1 enzyme in the hypothalamus during the weeks post-injection and which disrupts the homeostatic signalling. The endocannabinoid system also seems to be involved in the onset of this phenotype.As the characteristics of this phenotype were reminiscent of a torpor state, we tried in a second part of work to reproduce it to study more precisely the links between torpor and brain lipases. We exposed animals to 4°C for 4 hours and studied the repercussions of this thermic stress on the central lipases genes and on circadian rhythm genes: we were able to highlight a modulation of the circadian rhythm. We also exposed to the cold VMH-LPL-depleted mice and established that this depletion in VMH-LPL modifies the thermogenesis of brown adipose tissue and so promotes the development of beige adipocytes.This work highlights for the first time the implication of hypothalamic LPL in the regulation of energy homeostasis and its role in adaptive response to cold exposure.