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.

[EN] The Saccharomyces cerevisiae protein kinases Sat4 (Hal4) and Hal5 are required for the plasma membrane stability of the high affinity K+ transporter Trk1 and some amino acid and glucose permeases. A transcriptomic analysis of the hal4 hal5 strain revealed that the absence of these genes causes general alterations in the metabolism of amino acids and glucose. This data is confirmed by the following approaches: activity of the Gcn2-Gcn4 pathway, uptake of methionine and leucine, activity of succinate dehydrogenase (SDH), glucose consumption and ethanol production of this mutant. In this thesis, we demonstrated that the high affinity permease Mup1 is internalized and degraded in the vacuole in the absence of potassium supplementation, like other plasma membrane permeases such as Hxt1 (glucose), Can1 (arginine), Fur4 (uracil) and Gap1 (amino acids). This destabilization of the Mup1 permease is likely to explain the reduction in the uptake of methionine in the double mutant hal4 hal5 and suggests that Hal4 and Hal5 are involved in a general mechanism of regulation of the stability of permeases in the plasma membrane. This hypothesis was corroborated by studies with inhibitors of endocytosis and mutant isoforms of the E3 ubiquitin ligase Rsp5, which is responsible for the ubiquitination and subsequent vacuolar degradation of the permeases studied. The process of Rsp5-mediated ubiquitination requires, in many cases, specific adapters for recognition of the target protein. So far, 19 Rsp5 adapter proteins have been described, among which there are 9 ARTs proteins (Arrestin-Related Trafficking adaptor). In this study, we investigated whether there is a functional connection between Hal4 and Hal5 kinases and ARTs, since this mechanism could explain the observed phenotypes. We studied whether Art1, a regulator of Mup1 and Can1 endocytosis, is involved in the internalization of these permeases in hal4 hal5 strains. Our data indicates that Art1 is not necessary for internalizing Mup1 in the hal4 hal5 strain in the absence of potassium supplementation, therefore suggesting a new role for the Hal4 and Hal5 kinases. We extended the study to include the transporter of aspartic and glutamic acid, Dip5, whose endocytosis is mainly mediated by Aly2 (Art3). The results were positive, providing support for a more general mechanism of regulation of the permeases of the plasma membrane by these kinases. It has been proposed that Npr1, a kinase that is an effector of the Target of Rapamycin Complex 1 (TORC1), controls the activity of Art1, Aly1 (Art6) and Aly2 (Art3), leading to the accumulation of some permeases in the plasma membrane. We observe lower expression levels of Npr1 in hal4 hal5 strains. We also observe a state of constitutive hyperphosphorylation, similar to WT cells under limiting potassium. Furthermore, overexpression of the Npr1 kinase partially rescues the growth defects and instability of the permeases in the plasma membrane described in the hal4 hal5 mutant. Therefore, we identify part of the pathway regulated by the Hal4 and Hal5 kinases. In eukaryotes, TOR (Target of Rapamycin) exists in two distinct multiprotein complexes, TOR complex 1 (TORC1) and TOR complex 2 (TORC2). We have analyzed the direct substrates of TORC1 (Sch9) and TORC2 (Ypk1) in hal4 hal5 and trk1 trk2 mutants in potassium limiting conditions, observing alterations in the phosphorylation levels of both effectors. Finally, we observed that hal4 hal5 and trk1 trk2 mutants are highly sensitive to the TORC1 inhibitor, rapamycin, and that this sensitivity is rescued by increased external potassium. We confirmed that cells treated with rapamycin had lower internal potassium levels, an effect which is dependent on TORC1 and independent of Trk1 and Trk2. Therefore, our data indicates that the Hal4 and Hal5 kinases have a more specific effect on Npr1 and that there is a reciprocal regulation between potassium and the TOR signaling pathway. / [ES] Las proteínas quinasa de Saccharomyces cerevisiae Sat4 (Hal4) y Hal5 son necesarias para la estabilidad del transportador de K+ de alta afinidad Trk1 y de algunas permeasas de aminoácidos y de glucosa. El análisis transcriptómico del mutante hal4 hal5 reveló que la ausencia de estos genes origina alteraciones generales en el metabolismo de aminoácidos y de glucosa, datos que confirmamos mediante la medida de la ruta Gcn2-Gcn4, de la toma de metionina y de leucina, de la actividad de la succinato deshidrogenasa (SDH), del consumo de glucosa y de la producción de etanol. En esta tesis, hemos demostrado que la permeasa de alta afinidad de metionina, Mup1 se degrada en la vacuola en ausencia de un suplemento de potasio en el mutante hal4 hal5, igual que otras permeasas de la membrana plasmática como Hxt1, Can1, Fur4 y Gap1. Esta desestabilización de Mup1 podría explicar el defecto en la toma de metionina observado y sugiere que Hal4 y Hal5 están implicadas en un mecanismo general de regulación de la estabilidad de las permeasas en la membrana plasmática. Esta hipótesis fue corroborada mediante estudios con inhibidores de la endocitosis y mutantes en la E3 ubiquitina ligasa Rsp5, responsable de la ubiquitinación y posterior degradación vacuolar de las permeasas estudiadas. El proceso de ubiquitinación, en muchos casos, precisa de adaptadores específicos para reconocer la proteína diana. Se han descrito 19 proteínas adaptadoras de Rsp5, entre las que se encuentran 9 proteínas ARTs (Adaptadores de tráfico relacionados con arrestina). En este trabajo, hemos investigado si existe una conexión funcional entre las quinasas Hal4 y Hal5 y los ARTs; este mecanismo podría explicar los fenotipos observados. Estudiamos si Art1, regulador de la endocitosis de Mup1 y Can1, está implicado en la internalización de estas permeases en la cepa hal4 hal5. Nuestros datos indican que Art1 no es necesario para la internalización de Mup1 y Can1 en una cepa hal4 hal5 en ausencia de un suplemento de potasio, sugiriendo un papel novedoso de las quinasas Hal4 y Hal5. Ampliamos el estudio al transportador de ácido aspártico y glutámico, Dip5, cuya endocitosis viene mediada principalmente por Aly2 (Art3). Los resultados fueron positivos apoyando un mecanismo más general de regulación de las permeasas de la membrana plasmática por parte de estas quinasas. Se ha propuesto que Npr1, una quinasa efectora del Target of Rapamycin Complex 1 (TORC1), controla la actividad de Art1, Aly1 (Art6) y Aly2 (Art3) generando la acumulación de algunas permeasas en la membrana plasmática. Observamos menores niveles de expresión de Npr1 en mutantes hal4 hal5, además de un estado de hiperfosforilación constitutivo similar al de células WT en condiciones de potasio limitante. Además, la sobreexpresión de NPR1 rescata los defectos de crecimiento observados en medios con baja disponibilidad de potasio e inestabilidad de permeasas de la membrana plasmática descritos en el mutante hal4 hal5. Por tanto, identificamos parte de la ruta regulada por las quinasas Hal4 y Hal5. En los organismos eucariotas TOR (Target of Rapamycin) existe en dos complejos multiproteicos distintos, complejo TOR1 (TORC1) y complejo TOR2 (TORC2). Hemos analizado los sustratos directos de TORC1 (Sch9) y TORC2 (Ypk1) en mutantes hal4 hal5 y trk1 trk2 y en condiciones de potasio limitante observando alteraciones en los niveles de fosforilación de ambos efectores. Finalmente, hemos observado que los mutantes hal4 hal5 y trk1 trk2 son altamente sensibles al inhibidor de TORC1, rapamicina y que esta sensibilidad se rescata con un exceso de potasio en el medio. Comprobamos que células tratadas con rapamicina presentan una disminución del potasio interno dependiente de TORC1 e independiente de Trk1 y Trk2. Por tanto, nuestros datos indican que las quinasas Hal4 y Hal5 tienen un efecto más específico sobre Npr1 y que hay una regulación reciproca entre el potasio y la r / [CAT] Les proteïnes quinasa de Saccharomyces cerevisiae Sat4 (Hal4) i Hal5 són necessàries per a l'estabilitat del transportador de K+ d'alta afinitat Trk1 i d'algunes permeases d'aminoàcids i de glucosa. L'anàlisi transcriptòmic d'una soca mutant hal4 hal5 revela que l'absència d'aquests gens origina alteracions generals en el metabolisme d'aminoàcids i de glucosa, dades que confirmem mitjançant la mesura de la ruta Gcn2-Gcn4, de la presa de metionina i leucina, de l'activitat de succinat deshidrogenasa (SDH), del consum de glucosa i de la producció d'etanol d'aquest mutant. En aquesta tesi, hem demostrat que la permeasa d'alta afinitat de metionina, Mup1 es degrada en el vacúol en absència d'un suplement de potassi en el mutant hal4 hal5, igual que altres permeases de la membrana plasmàtica com Hxt1, Can1, Fur4 i Gap1. Aquesta desestabilització de Mup1 podria explicar el defecte en la presa de metionina observat i suggereix que Hal4 i Hal5 estan implicades en un mecanisme general de regulació de l'estabilitat de les permeases a la membrana plasmàtica. Aquesta hipòtesi va ser corroborada mitjançant estudis amb inhibidors de l'endocitosi i mutants en l'E3 ubiquitina ligasa Rsp5, responsable de la ubiquitinació i posterior degradació vacuolar de les permeases estudiades. El procés d'ubiquitinació, en molts casos, precisa d'adaptadors específics per reconèixer la proteïna diana. Fins al moment s'han descrit 19 proteïnes adaptadores de Rsp5, entre les quals es troben 9 proteïnes ART (Adaptadors de trànsit relacionats amb arrestina). En aquest treball hem investigat si existeix una connexió funcional entre les quinases Hal4 i Hal5 i els ARTs; aquest mecanisme podria explicar els fenotips observats. Estudiem si Art1, regulador de l'endocitosi de Mup1 i Can1, està implicat en la internalització d'aquestes permeases a la soca hal4 hal5. Les nostres dades indiquen que Art1 no és necessari per a la internalització de Mup1 i Can1 en una soca hal4 hal5 en absència d'un suplement de potassi, suggerint un paper nou de les quinases Hal4 i Hal5. Ampliem l'estudi per incloure el transportador d'àcid aspàrtic i glutàmic, Dip5, en l'endocitosi del qual intervé principalment Aly2 (Art3). Els resultats van ser positius recolzant un mecanisme més general de regulació de les permeases de la membrana plasmàtica per part d'aquestes quinases. S'ha proposat que Npr1, una quinasa que és un efector del Target of rapamycin Complex 1 (TORC1), controla l'activitat de Art1, Aly1 (Art6) i Aly2 (Art3) i genera l'acumulació d'algunes permeases a la membrana plasmàtica. Observem nivells menors d'expressió de Npr1 en mutants hal4 hal5, a més d'un estat d'hiperfosforilació constitutiu semblant al de cèl·lules WT en condicions de potassi limitant. A més, la sobreexpressió de la quinasa Npr1 rescata parcialment els defectes de creixement observats en medis amb baixa disponibilitat de potassi i la inestabilitat de permeases de la membrana plasmàtica descrits en el mutant hal4 hal5. Per tant, identifiquem part de la ruta regulada per les quinases Hal4 i Hal5. En els organismes eucariotes, TOR (Target of rapamycin) existeix en dos complexos multiproteics diferents, complex TOR1 (TORC1) i complex TOR2 (TORC2). Hem analitzat els substrats directes de TORC1 (Sch9) i TORC2 (Ypk1) en mutants hal4 hal5 i trk1 trk2 i en condicions de potassi limitant observant alteracions en els nivells de fosforilació dels dos efectors. Finalment, hem observat que els mutants hal4 hal5 i trk1 trk2 són altament sensibles a l'inhibidor de TORC1, rapamicina, i que aquesta sensibilitat es rescatada amb un excés de potassi en el medi. Vam comprovar que cèl·lules tractades amb rapamicina presenten una disminució del potassi intern dependent de TORC1 e independent de Trk1 i Trk2. Per tant, les nostres dades indiquen que les quinases Hal4 i Hal5 tenen un efecte més específic sobre Npr1 i que hi ha una regulació recíproca entre el potassi i / Primo Planta, C. (2015). Mecanismos de regulación post-traduccional de transportadores de la membrana plasmática: Papel de las quinasas Hal4 y Hal5 en el tráfico de transportadores de nutrientes e iones en el organismo modelo Saccharomyces cerevisiae [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/52697 / TESIS

The plant hormones gibberellins (GAs) and auxin display overlapping activities in the regulation of multiple developmental processes, including the differential growth that mediates the response to tropic stimuli and the formation of the apical hook. Several mechanisms have been proposed that explain the interaction between these two hormones, such as the regulation of auxin transport by GAs, and the regulation of GA biosynthesis by auxin. GAs are known to exert their action at the transcriptional level by promoting the degradation of DELLA proteins, which in turn interact with numerous transcription factors and modulate their activity. We have identified INDOLE-3-ACETIC ACID METHYLTRANSFERASE 1 (IAMT1) as one of the earliest target genes upregulated after conditional expression of the DELLA protein GAI in Arabidopsis thaliana. In this Thesis, we have addressed two main issues: (1) the contribution of IAMT1 to auxin homeostasis and its biological relevance; and (2) the molecular mechanism by which DELLAs are able to induce the expression of IAMT1. Using combinations of iamt1 loss-of-function mutants and reporter lines for auxin accumulation and activity, we have found that IAMT1 activity is essential for proper generation and maintenance of the auxin gradients that underlie differential growth. According to our results, the role of IAMT1 would be to restrict polar auxin transport especially during the response to tropic stimuli, preventing excessive auxin accumulation in the responding tissues, and IAMT1 exerts this function, at least in part, by inhibiting the expression of the PIN genes, encoding auxin efflux carriers. Regarding the regulation of IAMT1 expression by DELLAs, dissection of the promoter, in silico analysis of putative DELLA partners, and molecular genetic analysis of reporter lines has allowed us to identify two mechanisms with different relevance depending on the environmental conditions, and through different cis elements. In etiolated seedlings, DELLA proteins are recruited by DORNRÖSCHEN (DRN) to the IAMT1 promoter to induce IAMT1 expression. In the light and in a temperature-dependent manner, DELLA proteins inhibit the DNA-binding activity of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and BRI1 EMS-SUPPRESSOR1(BES1), which act as repressors of IAMT1 expression. The work presented here highlights how GAs may affect local accumulation of auxin, being particularly relevant in processes that involve differential growth. / Abbas, M. (2014). The control of auxin homeostasis through the regulation of IAMT1 by DELLA proteins [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/39348 / TESIS

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.