Resting-state fMRI (rsfMRI) has been widely used to map intrinsic brain network organization of the human brain both in health and in pathological conditions. However, the neural underpinnings and dynamic rules governing brain-wide rsfMRI coupling remain unclear. Filling this knowledge gap is of crucial importance, given our current inability to decode and reverse-engineer clinical signatures of aberrant connectivity into interpretable neurophysiological events that can help understand or diagnose brain disorders. Toward this goal, here we combined chemogenetics, rsfMRI, and in vivo electrophysiology in the mouse to investigate how regional manipulations of brain activity (i.e. neural inhibition, or excitation) causally contribute to whole-brain fMRI network organization. In a first set of proof of concept investigations, we empirically probed the widely held notion that neural inhibition of a cortical node would result in reduced fMRI coupling of the silenced area and its long-range terminals. Surprisingly, we found that chronic inhibition of the mouse medial prefrontal cortex (PFC) via viral overexpression of a potassium channel paradoxically increased fMRI connectivity between the inhibited area and its direct thalamo-cortical targets. Notably, acute chemogenetic inhibition of the PFC reproduced analogous patterns of fMRI overconnectivity. Using in vivo electrophysiology, we found that chemogenetic inhibition of the PFC enhances low frequency (0.1 - 4 Hz) oscillatory power via suppression of neural firing not phase-locked to slow rhythms, resulting in increased slow and δ band coherence between areas that exhibit fMRI overconnectivity. These results provide causal evidence that cortical inactivation can counterintuitively increase fMRI connectivity via enhanced, less-localized slow oscillatory processes, with important implications for neural modeling and interpretation of fMRI overconnectivity in brain disorders. Importantly, our observation that neural inhibition of the PFC results in fMRI overconnectivity allowed us to predict that neural activation of the same area might produce opposite results, i.e. fMRI underconnectivity and neural desynchronization. To test this hypothesis, we used chemogenetics to increase local excitatory-inhibitory (E/I) balance in the PFC. As predicted, chemogenetic stimulation of CamkII-expressing neurons, or inhibition of fast-spiking parvalbumin-expressing neurons, produced similar rsfMRI signatures of rsfMRI underconnectivity. Both manipulations produced analogous electrophysiological signatures characterized by increased firing activity and a robust LFP power shift towards higher (i.e. γ) frequencies, effectively reversing the corresponding neural signature observed in DREADD inhibition studies. Importantly, the same E/I affecting perturbations were also associated with socio-communicative deficits in behaving mice hence underscoring the behavioral relevance of the employed manipulations. These results show that excitatory/inhibitory balance critically biases brain-wide fMRI coupling, pointing at a possible unifying mechanistic link between E/I imbalance and rsfMRI connectivity disruption in developmental disorders. More broadly, these investigations reveal a set of fundamental rules linking regional brain activity to macroscale functional connectivity, offering opportunities to physiologically interpret rsfMRI signatures of functional dysconnectivity in human brain disorders.

The DNA damage response is a cell-wide response that coordinates repair and cell-cycle progression. Crucial to fidelity of genetic propagation, survival, and apoptosis, dysfunctions in the response are at the root of genome instability syndromes and cancer predisposition in mammalian cells. Within the response lie hubs of coordination, called checkpoints, whose members and organization are ubiquitous amongst eukaryotes. The high conservation of these checkpoints enable the study of their dynamics by proxy via simpler model organisms. We use the budding yeast, Saccharomyces cerevisiae, to study the replication and DNA damage checkpoints --- both implicated in DNA damage repair. Using a yEGFP reporter driven by the RNR3 promoter and reporter-based synthetic genetic array analysis, we created a detector of potential checkpoint activation in response to two doses of MMS, 0.015% and 0.060% (v/v). The high-throughput screens and differential epistasis miniarray analyses (EMAPs) yield unanticipated involvement of oxidative stress response, ribosomal biogenesis, and chromatin remodelling genes.

La capacité des organismes à survivre dans un environnement changeant dépendlargement de leur aptitude à prendre des décisions adaptées. Cette fonction complexerésulte notamment de l’intégration de processus de prédiction et de contrôle de l’action,classiquement étudiés dans le corpus théorique et méthodologique des apprentissagesassociatifs. Les bases neurobiologiques de ces processus sont largement distribués au seinde circuits au sein desquels le cortex préfrontal et son afférence principale, le thalamusmédiodorsal (MD) jouent un rôle important. Dans ce contexte, le travail entrepris au coursde ce travail de thèse visait à déterminer le rôle fonctionnel des échanges entre ces deuxstructures dans le cadre de la prise de décision.Une première partie de ce travail a visé à confirmer le rôle spécifique du MD dans lesprocessus de prise de décision. Par l’utilisation d’un protocole expérimental nécessitantl’intégration des contingences instrumentales et Pavloviennes pour obtenir unerécompense, nous avons démontré que des rats porteurs d’une lésion du MD n’étaient pascapables d’adapter leur comportement en fonction des changements de valeur de larécompense, confirmant ainsi le rôle fondamental du MD dans la représentation du but.Surla base de ce résultat, nous avons ensuite entrepris une étude d’anatomie descriptive visantà caractériser finement l’architecture des projections thalamocorticales issues du MD. Cetteétude nous a permis de démontrer que de multiples voies thalamocorticales issues du MDtrouvent leur origine dans des populations neuronales thalamiques essentiellementségrégées mais également que la région orbitofrontale était innervée par une régionthalamique méconnue, le thalamus submédian. Pour éprouver les fonctions de cesdifférentes voies, nous avons d’abord mis en place une stratégie d’inactivation réversible depopulations neuronales sélectionnées sur la base de leurs projections spécifiques par uneméthode pharmacogénétique conditionnelle. L’utilisation de cette méthode nous a permisde révéler que la capacité de l’animal à se représenter la valeur ou la relation actionrécompensedépend de la direction des échanges entre le MD et le cortex préfrontalmédian. Par ailleurs, une approche lésionnelle comparée plus classique nous a permisd’identifier un rôle fonctionnel spécifique du thalamus submédian dans la mise à jour descontingences Pavloviennes.12Pris dans leur ensemble, ces résultats sont en accord avec l’idée que des bouclesthalamocorticales distinctes sont impliquées dans les processus de prédiction et de contrôlede l’action nécessaires à une prise de décision adaptée. / Survival of living organisms depends on the ability to make decision adapted to theircurrent needs and desires. Such an ability results from the integration of multiple basiccognitive processes such as events prediction and action control. These processes are bestinvestigated within the framework of associative learning. Past research has demonstratedthat these processes are supported by a widespread neuronal circuit, in which the prefrontalcortex and his major afferent structure, the mediodorsal thalamus (MD), play a central role.In this context, this thesis work aimed at investigating the functional role of the exchangesbetween these two structures in decision making.In a first part of this work, we assessed the role of the MD in prediction and control.We showed that MD lesioned rats are unable to adapt their behavior to a change in rewardvalue, in an experimental procedure asking the integration of instrumental and Pavloviancontingencies. This result confirmed the fundamental role of MD in goal representation. As asecond step, we performed an anatomical study in order to characterize the architecture ofthe thalamocortical pathways arising from the MD. We first showed that multiplethalamocortical pathways originate from segregated neuronal populations within the MD.We also discovered a poorly known thalamic structure innervating the orbitofrontal cortex,the submedius nuclei. In order to understand the functional role of these pathways, we useda conditional chemogenetic technique aimed at inactivating neuronal populations selectedon the basis of their projections. Using this technique, we showed that the animal’s abilitiesto represent either the value or the action-reward relationship depend on the directionalityof MD and prefrontal cortex exchanges. Finally, we identified a specific role for thesubmedius nuclei in updating Pavlovian contingencies, by using a more classical lesioningapproach.Taken together, these results support the idea that decision making involved severalthalamocortical loops, differentially supporting prediction and action control.

Les sirtuines sont une famille conservée de déacétylases NAD+-dépendantes qui sont impliquées dans divers processus. Les humains possèdent 7 sirtuines (SIRT1-7) qui jouent un rôle dans plusieurs voies cellulaires, tandis que la levure Saccharomyces cerevisiae possède 5 membres (Sir2, Hst1-4) qui influencent plusieurs voies comme le cycle cellulaire ou le vieillissement. Une absence d’activité des sirtuines mène toutefois à des défauts de croissance, une thermosensibilité et l’apparition de dommages spontanés à l’ADN par des mécanismes mal élucidés. Pour mieux caractériser ce phénomène, ce mémoire met en lumière certains résultats venant d’un crible chimiogénétique réalisé par traitement au nicotinamide (NAM), un pan-inhibiteur des sirtuines. Nos résultats indiquent que le NAM entraîne chez la levure Saccharomyces cerevisiae une forte activation des voies de réponses aux dommages à l’ADN, et que les défauts de croissance sont principalement dus à l’hyperacétylation de la lysine 56 de l’histone H3 (H3K56), une modification post-traductionnelle qui est renversée par les sirtuines Hst3 et Hst4. Lors d’hyperacétylation de H3K56, la protéine Slx4 et le complexe PP4 sont requis pour la croissance de la levure en modulant les niveaux d’activation de la kinase Rad53 lors de la RDA. Également, certains résultats préliminaires inclus dans ce mémoire mettent en évidence un rôle de l’activité des sirtuines dans la régulation de la recombinaison homologue, l’une des voies de réparation de l’ADN. Ensemble, nos résultats suggèrent que la déacétylation des histones par les sirtuines permet de moduler la réponse aux dommages à l’ADN en présence de stress réplicatif. / Sirtuins are a conserved family of NAD+-dependent deacetylases that are involved in various processes. Humans have seven sirtuins (SIRT1-7) and play a role in several cellular pathways, while the budding yeast Saccharomyces cerevisiae has 5 members (Sir2, Hst1-4) and influence several pathways, such as the cell cycle or aging. Lack of sirtuin activity however leads to growth defects, thermosensitivity and spontaneous DNA damage by poorly understood mechanisms. To further characterize this phenomenon, this thesis highlights results obtained from a chemogenetic screen realized by treatment with nicotinamide (NAM), a pan-inhibitor of all sirtuins. Our results indicate that NAM causes strong activation of DNA damage-induced signaling in budding yeast Saccharomyces cerevisiae, and that growth defects are mainly due to histone H3 lysine 56 (H3K56) hyperacetylation, a post-translational modification reversed by sirtuins Hst3 and Hst4. During H3K56 hyperacetylation, the Slx4 protein and PP4 complex are both required for yeast growth by modulating the activation levels of Rad53 kinase during the DDR. Also, preliminary results included in this thesis highlight that proper regulation of homologous recombination, one of DNA repair pathways, is essential for growth in the presence of NAM-induced sirtuin inhibition. Together, our results suggest that chromosome-wide histone deacetylation by sirtuins can modulate DNA damage response in presence of replicative stress.