Selection of internal reference genes for SYBR green qRT-PCR studies of rhesus monkey (Macaca mulatta) tissues

<p>Abstract</p> <p>Background</p> <p>The rhesus monkey (<it>Macaca mulatta</it>) is a valuable and widely used model animal for biomedical research. However, quantitative analyses of rhesus gene expression profiles under diverse experimental conditions are limited by a shortage of suitable internal controls for the normalization of mRNA levels. In this study, we used a systematic approach for the selection of potential reference genes in the rhesus monkey and compared their suitability to that of the corresponding genes in humans.</p> <p>Results</p> <p>Eight housekeeping genes (HKGs) (<it>GAPDH, SDHA, ACTB, RPL13A, RPL32, UBA52, PGK1Y</it>, and <it>YWHAZ</it>) from rhesus monkeys and humans were selected to test for normalization of expression levels in six different tissue types (brain, colon, kidney, liver, lung, and stomach). Their stability and suitability as reference genes were validated by <it>geNorm</it>, <it>NormFinder </it>and <it>BestKeeper </it>programs. Intriguingly, <it>RPL13A </it>and <it>RPL32 </it>were selected as ideal reference genes only in rhesus monkeys.</p> <p>Conclusion</p> <p>The results clearly indicated the necessity of using different reference genes for normalization of expression levels between rhesus monkeys and humans in various tissues.</p

Changes in Sensitization Rate to Weed Allergens in Children with Increased Weeds Pollen Counts in Seoul Metropolitan Area

The prevalence of allergic diseases in children has increased for several decades. We evaluated the correlation between pollen count of weeds and their sensitization rate in Seoul, 1997-2009. Airborne particles carrying allergens were collected daily from 3 stations around Seoul. Skin prick tests to pollen were performed on children with allergic diseases. Ragweed pollen gradually increased between 1999 and 2005, decreased after 2005 and plateaued until 2009 (peak counts, 67 in 2003, 145 in 2005 and 83 grains/m3/day in 2007). Japanese hop pollen increased between 2002 and 2009 (peak counts, 212 in 2006 and 492 grains/m3/day in 2009). Sensitization rates to weed pollen, especially ragweed and Japanese hop in children with allergic diseases, increased annually (ragweed, 2.2% in 2000 and 2.8% in 2002; Japanese hop, 1.4% in 2000 and 1.9% in 2002). The age for sensitization to pollen gradually became younger since 2000 (4 to 6 yr of age, 3.5% in 1997 and 6.2% in 2009; 7 to 9 yr of age, 4.2% in 1997 and 6.4% in 2009). In conclusion, sensitization rates for weed pollens increase in Korean children given increasing pollen counts of ragweed and Japanese hop

The Revised Edition of Korean Calendar for Allergenic Pollens

The old calendar of pollens did not reflect current pollen distribution and concentrations that can be influenced by changes of weather and environment of each region in South Korea. A new pollen calendar of allergenic pollens was made based on the data on pollen concentrations obtained in eight regions nationwide between 1997 and 2009. The distribution of pollen was assessed every day at 8 areas (Seoul, Guri, Busan, Daegu, Jeonju, Kwangju, Kangneung, and Jeju) for 12 years between July 1, 1997 and June 30, 2009. Pollens were collected by using Burkard 7-day sampler (Burkard Manufacturing Co Ltd, UK). Pollens which were stained with Calberla's fuchsin staining solution were identified and counted. Pine became the highest pollen in May, and the pollen concentrations of oak and birch also became high. Ragweed appeared in the middle of August and showed the highest pollen concentration in the middles of September. Japanese hop showed a high concentration between the middle of August and the end of September, and mugwort appeared in the middles of August and its concentration increased up until early September. In Kangneung, birch appeared earlier, pine showed a higher pollen concentration than in the other areas. In Daegu, Oriental thuja and alder produced a large concentration of pollens. Pine produced a large concentration of pollens between the middle of April and the end of May. Weeds showed higher concentrations in September and mugwort appeared earlier than ragweed. In Busan the time of flowering is relatively early, and alder and Oriental thuja appeared earliest among all areas. In Kwangju, Oriental thuja and hazelnut appeared in early February. Japanese cedar showed the highest pollen concentration in March in Jeju. In conclusion, update information on pollen calendar in South Korea should be provided for allergic patients through the website to manage and prevent the pollinosis

Genome-wide analysis of DNA methylation patterns in horse

Background: DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known. Results: We report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density. Conclusions: We provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses.open1

Vascular responses of the extremities to transdermal application of vasoactive agents in Caucasian and African descent individuals

This is an accepted manuscript of an article published by Springer in European Journal of Applied Physiology on 04/04/2015, available online: https://doi.org/10.1007/s00421-015-3164-2 The accepted version of the publication may differ from the final published version.© 2015, Springer-Verlag Berlin Heidelberg. Purpose: Individuals of African descent (AFD) are more susceptible to non-freezing cold injury than Caucasians (CAU) which may be due, in part, to differences in the control of skin blood flow. We investigated the skin blood flow responses to transdermal application of vasoactive agents. Methods: Twenty-four young males (12 CAU and 12 AFD) undertook three tests in which iontophoresis was used to apply acetylcholine (ACh 1 w/v %), sodium nitroprusside (SNP 0.01 w/v %) and noradrenaline (NA 0.5 mM) to the skin. The skin sites tested were: volar forearm, non-glabrous finger and toe, and glabrous finger (pad) and toe (pad). Results: In response to SNP on the forearm, AFD had less vasodilatation for a given current application than CAU (P = 0.027–0.004). ACh evoked less vasodilatation in AFD for a given application current in the non-glabrous finger and toe compared with CAU (P = 0.043–0.014) with a lower maximum vasodilatation in the non-glabrous finger (median [interquartile], AFD n = 11, 41[234] %, CAU n = 12, 351[451] %, P = 0.011) and non-glabrous toe (median [interquartile], AFD n = 9, 116[318] %, CAU n = 12, 484[720] %, P = 0.018). ACh and SNP did not elicit vasodilatation in the glabrous skin sites of either group. There were no ethnic differences in response to NA. Conclusion: AFD have an attenuated endothelium-dependent vasodilatation in non-glabrous sites of the fingers and toes compared with CAU. This may contribute to lower skin temperature following cold exposure and the increased risk of cold injuries experienced by AFD.Published versio

Genome-Wide Analysis of DNA Methylation before- and after Exercise in the Thoroughbred Horse with MeDIP-Seq

Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre- and post-exercise blood samples of superior and inferior horses were identified. Exercise altered the methylation patterns. After 30 min of exercise, 596 genes were hypomethylated and 715 genes were hypermethylated in the superior horse, whereas in the inferior horse, 868 genes were hypomethylated and 794 genes were hypermethylated. These genes were analyzed based on gene ontology (GO) annotations and the exercise-related pathway patterns in the two horses were compared. After exercise, gene regions related to cell division and adhesion were hypermethylated in the superior horse, whereas regions related to cell signaling and transport were hypermethylated in the inferior horse. Analysis of the distribution of methylated CpG islands confirmed the hypomethylation in the gene-body methylation regions after exercise. The methylation patterns of transposable elements also changed after exercise. Long interspersed nuclear elements (LINEs) showed abundance of DMRs. Collectively, our results serve as a basis to study exercise-based reprogramming of epigenetic traitsclose

Circuits neuronaux impliqués dans la discrimination de la mémoire de peur contextuelle

Les interactions de tous les jours nécessitent de prendre en compte le contexte afin de réagir de manière appropriée. Par exemple, la rencontre d’un lion dans un environnement ouvert ou bien derrière la vitre d’un zoo doit amener à des réactions différentes. Cette évaluation permanente de l’environnement est donc essentielle par bien des aspects. Un cerveau sain a donc la capacité permanente de sélectionner et garder distincts de nombreux stimuli sensoriels constitutifs de notre environnement et de les rendre résistants au temps et à la confusion. L’altération de cette capacité amène à des désordres psychologiques et est au coeur d’un nombre important de pathologies telles que l’anxiété et les désordres post-traumatiques. Étant donné le rôle important de l’évaluation contextuelle dans les émotions et la cognition, la compréhension des mécanismes cérébraux qui la sous-tendent et qui permettent sa restitution est fondamentale, ainsi que leur modulation par les émotions associées aux contextes. Au sein des laboratoires, la mise en place d’une aversion contextuelle est aisée et est classiquement utilisée pour étudier les circuits neuronaux impliqués. Ce protocole, appelé conditionnement contextuel à la peur, consiste à placer un animal dans une enceinte de conditionnement dans laquelle il va recevoir un stimulus aversif. Comme ce contexte va devenir prédictif de l’arrivée de ce stimulus, l’animal conditionné va adopter un comportement de crainte lorsqu’il sera repositionné dans ce contexte quelques jours plus tard. Cette réponse comportementale sera spécifique à ce contexte, n’étant pas observée dans un autre contexte même proche. Ce phénomène est appelé discrimination contextuelle. Mon but est de visualiser les phénomènes neurophysiologiques qui sont en jeu à ce moment crucial où les contextes sont ambigus et doivent être évalués afin de déterminer la réponse à adopter. La difficulté est d’abord méthodologique : il est difficile de modifier le niveau d’ambiguïté d’un contexte dans une seule modalité sensorielle qui doit également être perçue. Le début de mon travail de thèse a donc été de déterminer expérimentalement la meilleure modalité à utiliser, qui s’est avérée être la forme de l’enceinte de conditionnement. Ensuite, j’ai mis en place des enregistrements extracellulaires multisites ciblant trois zones impliquées dans la peur contextuelle : le cortex préfrontal médian (mPFC), l’amygdale basolatérale (BLA) et l’hippocampe ventral (vHPC). Les enregistrements ont été menés sur plusieurs jours, incluant les phases de tests ainsi que les phases de repos, qui sont essentiels pour la consolidation de la mémoire. Une attention particulière a été portée aux phases de transition entre les contextes que notre appareillage permet de mener de façon progressive. Nous avons voulu répondre à plusieurs questions ambitieuses : 1. Quels sont les mécanismes fonctionnels instruisant le cortex préfrontal lors de l’expressions de la peur contextuelle ? 2. Quels sont les mécanismes fonctionnels ayant lieu au sein du circuit mPFC-BLA-vHPC qui permettent l’ajustement de la réponse comportementale a un changement de la valence contextuelle ? 3. Au niveau cellulaire, quels sont les déterminants entrainant la sélection d’un neurone dans l’encodage de la peur ou la discrimination contextuelle ? De façon générale, nous pensons qu’une meilleure compréhension du processus par lequel le cerveau décode le contexte environnant est essentielle afin de comprendre la flexibilité comportementale que nous montrons quotidiennement, et dont l’importance est démontrée par les pathologie associée à son dysfonctionnement. Le propos de ce travail était d’apporter une petite brique supplémentaire à cet édifice.Encountering a particular stimulus may require radically different responses in different situations. Imagine yourself facing a lion, an animal that is generally integrated in our consciousness as threatening. This lion would express a different meaning when it is encountered in the wild or when it is seen behind glass in a zoo. This observation emphasizes the context processing allowing to elicit the most appropriate response. Normal brains keep biologically significant events distinct and resistant to confusion. If not, it may lead to psychological dysfunction because of inaccurate context processing. This is a one of the core symptoms observed in patients suffering from anxiety disorders and posttraumatic stress disorder (PTSD). Given the essential role of the context in emotion and cognition, a major scientific challenge is to understand how the brain processes and restitute contextual information between neutral and aversive emotional valance. In the laboratory condition, the classical contextual fear conditioning (CFC) is a useful model for studying neural circuits of associative learning processes. In its most basic form, it consists of placing the animal in a conditioning chamber in which is delivered an aversive stimulus. In rodent studies the environmental context itself act as an “occasion setter” to predict the arrival of the US, thus replacing the animal back in this context leads to the expression of conditioned responses (CR) usually freezing behavior. The latter observation is highly context specific, such that when placed in another context animals do not exhibit any fear behavior, a phenomenon called contextual fear discrimination. My goal is to visualize how brain deals with moments of context ambiguity! But how to catch them! It is first a methodological problem: it is difficult to manipulate the level of ambiguity in the surrounding context along a single sensory dimension. During my thesis, I tested and validated smooth area shape transitions as unique context changes to elicit contextual fear discrimination. Among areas potentially involved in the contextual fear processing, three brain regions - the medial prefrontal cortex (mPFC), the basolateral amygdala (BLA), and the hippocampus (HPC) - are particularly important, and share functional connectivity. We therefore performed extracellular recording simultaneously in the three aforementioned areas, along the contextual fear learning process, i.e., fear acquisition, retrieval and discrimination, with a particular focus on transition periods to let emerge the “partition of the symphony”. We wanted to answer a few specific questions: 1. What are the functional mechanisms instructing the PFC during contextual fear expression? 2. What are the functional mechanisms within the interconnected tripartite circuit that mediate appropriate behavior according to the contextual valence? 3. At cellular level, what will determine if a neuron is implicated or not in contextual discrimination? In general, we believe that a more comprehensive view of the brain circuits that mediate contextual processing and modulation will greatly enrich the future understanding of flexible, adaptive responses to environmental stimuli, and pathophysiological processes that interfere with this flexibility. The purpose of this thesis is to bring another brick in this wal

Circuits neuronaux impliqués dans la discrimination de la mémoire de peur contextuelle

Encountering a particular stimulus may require radically different responses in different situations. Imagine yourself facing a lion, an animal that is generally integrated in our consciousness as threatening. This lion would express a different meaning when it is encountered in the wild or when it is seen behind glass in a zoo. This observation emphasizes the context processing allowing to elicit the most appropriate response. Normal brains keep biologically significant events distinct and resistant to confusion. If not, it may lead to psychological dysfunction because of inaccurate context processing. This is a one of the core symptoms observed in patients suffering from anxiety disorders and posttraumatic stress disorder (PTSD). Given the essential role of the context in emotion and cognition, a major scientific challenge is to understand how the brain processes and restitute contextual information between neutral and aversive emotional valance. In the laboratory condition, the classical contextual fear conditioning (CFC) is a useful model for studying neural circuits of associative learning processes. In its most basic form, it consists of placing the animal in a conditioning chamber in which is delivered an aversive stimulus. In rodent studies the environmental context itself act as an “occasion setter” to predict the arrival of the US, thus replacing the animal back in this context leads to the expression of conditioned responses (CR) usually freezing behavior. The latter observation is highly context specific, such that when placed in another context animals do not exhibit any fear behavior, a phenomenon called contextual fear discrimination. My goal is to visualize how brain deals with moments of context ambiguity! But how to catch them! It is first a methodological problem: it is difficult to manipulate the level of ambiguity in the surrounding context along a single sensory dimension. During my thesis, I tested and validated smooth area shape transitions as unique context changes to elicit contextual fear discrimination. Among areas potentially involved in the contextual fear processing, three brain regions - the medial prefrontal cortex (mPFC), the basolateral amygdala (BLA), and the hippocampus (HPC) - are particularly important, and share functional connectivity. We therefore performed extracellular recording simultaneously in the three aforementioned areas, along the contextual fear learning process, i.e., fear acquisition, retrieval and discrimination, with a particular focus on transition periods to let emerge the “partition of the symphony”. We wanted to answer a few specific questions: 1. What are the functional mechanisms instructing the PFC during contextual fear expression? 2. What are the functional mechanisms within the interconnected tripartite circuit that mediate appropriate behavior according to the contextual valence? 3. At cellular level, what will determine if a neuron is implicated or not in contextual discrimination? In general, we believe that a more comprehensive view of the brain circuits that mediate contextual processing and modulation will greatly enrich the future understanding of flexible, adaptive responses to environmental stimuli, and pathophysiological processes that interfere with this flexibility. The purpose of this thesis is to bring another brick in this wallLes interactions de tous les jours nécessitent de prendre en compte le contexte afin de réagir de manière appropriée. Par exemple, la rencontre d’un lion dans un environnement ouvert ou bien derrière la vitre d’un zoo doit amener à des réactions différentes. Cette évaluation permanente de l’environnement est donc essentielle par bien des aspects. Un cerveau sain a donc la capacité permanente de sélectionner et garder distincts de nombreux stimuli sensoriels constitutifs de notre environnement et de les rendre résistants au temps et à la confusion. L’altération de cette capacité amène à des désordres psychologiques et est au coeur d’un nombre important de pathologies telles que l’anxiété et les désordres post-traumatiques. Étant donné le rôle important de l’évaluation contextuelle dans les émotions et la cognition, la compréhension des mécanismes cérébraux qui la sous-tendent et qui permettent sa restitution est fondamentale, ainsi que leur modulation par les émotions associées aux contextes. Au sein des laboratoires, la mise en place d’une aversion contextuelle est aisée et est classiquement utilisée pour étudier les circuits neuronaux impliqués. Ce protocole, appelé conditionnement contextuel à la peur, consiste à placer un animal dans une enceinte de conditionnement dans laquelle il va recevoir un stimulus aversif. Comme ce contexte va devenir prédictif de l’arrivée de ce stimulus, l’animal conditionné va adopter un comportement de crainte lorsqu’il sera repositionné dans ce contexte quelques jours plus tard. Cette réponse comportementale sera spécifique à ce contexte, n’étant pas observée dans un autre contexte même proche. Ce phénomène est appelé discrimination contextuelle. Mon but est de visualiser les phénomènes neurophysiologiques qui sont en jeu à ce moment crucial où les contextes sont ambigus et doivent être évalués afin de déterminer la réponse à adopter. La difficulté est d’abord méthodologique : il est difficile de modifier le niveau d’ambiguïté d’un contexte dans une seule modalité sensorielle qui doit également être perçue. Le début de mon travail de thèse a donc été de déterminer expérimentalement la meilleure modalité à utiliser, qui s’est avérée être la forme de l’enceinte de conditionnement. Ensuite, j’ai mis en place des enregistrements extracellulaires multisites ciblant trois zones impliquées dans la peur contextuelle : le cortex préfrontal médian (mPFC), l’amygdale basolatérale (BLA) et l’hippocampe ventral (vHPC). Les enregistrements ont été menés sur plusieurs jours, incluant les phases de tests ainsi que les phases de repos, qui sont essentiels pour la consolidation de la mémoire. Une attention particulière a été portée aux phases de transition entre les contextes que notre appareillage permet de mener de façon progressive. Nous avons voulu répondre à plusieurs questions ambitieuses : 1. Quels sont les mécanismes fonctionnels instruisant le cortex préfrontal lors de l’expressions de la peur contextuelle ? 2. Quels sont les mécanismes fonctionnels ayant lieu au sein du circuit mPFC-BLA-vHPC qui permettent l’ajustement de la réponse comportementale a un changement de la valence contextuelle ? 3. Au niveau cellulaire, quels sont les déterminants entrainant la sélection d’un neurone dans l’encodage de la peur ou la discrimination contextuelle ? De façon générale, nous pensons qu’une meilleure compréhension du processus par lequel le cerveau décode le contexte environnant est essentielle afin de comprendre la flexibilité comportementale que nous montrons quotidiennement, et dont l’importance est démontrée par les pathologie associée à son dysfonctionnement. Le propos de ce travail était d’apporter une petite brique supplémentaire à cet édifice

Neuronal mechanisms underlying contextual fear memory discrimination

Les interactions de tous les jours nécessitent de prendre en compte le contexte afin de réagir de manière appropriée. Par exemple, la rencontre d’un lion dans un environnement ouvert ou bien derrière la vitre d’un zoo doit amener à des réactions différentes. Cette évaluation permanente de l’environnement est donc essentielle par bien des aspects. Un cerveau sain a donc la capacité permanente de sélectionner et garder distincts de nombreux stimuli sensoriels constitutifs de notre environnement et de les rendre résistants au temps et à la confusion. L’altération de cette capacité amène à des désordres psychologiques et est au coeur d’un nombre important de pathologies telles que l’anxiété et les désordres post-traumatiques. Étant donné le rôle important de l’évaluation contextuelle dans les émotions et la cognition, la compréhension des mécanismes cérébraux qui la sous-tendent et qui permettent sa restitution est fondamentale, ainsi que leur modulation par les émotions associées aux contextes. Au sein des laboratoires, la mise en place d’une aversion contextuelle est aisée et est classiquement utilisée pour étudier les circuits neuronaux impliqués. Ce protocole, appelé conditionnement contextuel à la peur, consiste à placer un animal dans une enceinte de conditionnement dans laquelle il va recevoir un stimulus aversif. Comme ce contexte va devenir prédictif de l’arrivée de ce stimulus, l’animal conditionné va adopter un comportement de crainte lorsqu’il sera repositionné dans ce contexte quelques jours plus tard. Cette réponse comportementale sera spécifique à ce contexte, n’étant pas observée dans un autre contexte même proche. Ce phénomène est appelé discrimination contextuelle. Mon but est de visualiser les phénomènes neurophysiologiques qui sont en jeu à ce moment crucial où les contextes sont ambigus et doivent être évalués afin de déterminer la réponse à adopter. La difficulté est d’abord méthodologique : il est difficile de modifier le niveau d’ambiguïté d’un contexte dans une seule modalité sensorielle qui doit également être perçue. Le début de mon travail de thèse a donc été de déterminer expérimentalement la meilleure modalité à utiliser, qui s’est avérée être la forme de l’enceinte de conditionnement. Ensuite, j’ai mis en place des enregistrements extracellulaires multisites ciblant trois zones impliquées dans la peur contextuelle : le cortex préfrontal médian (mPFC), l’amygdale basolatérale (BLA) et l’hippocampe ventral (vHPC). Les enregistrements ont été menés sur plusieurs jours, incluant les phases de tests ainsi que les phases de repos, qui sont essentiels pour la consolidation de la mémoire. Une attention particulière a été portée aux phases de transition entre les contextes que notre appareillage permet de mener de façon progressive. Nous avons voulu répondre à plusieurs questions ambitieuses : 1. Quels sont les mécanismes fonctionnels instruisant le cortex préfrontal lors de l’expressions de la peur contextuelle ? 2. Quels sont les mécanismes fonctionnels ayant lieu au sein du circuit mPFC-BLA-vHPC qui permettent l’ajustement de la réponse comportementale a un changement de la valence contextuelle ? 3. Au niveau cellulaire, quels sont les déterminants entrainant la sélection d’un neurone dans l’encodage de la peur ou la discrimination contextuelle ? De façon générale, nous pensons qu’une meilleure compréhension du processus par lequel le cerveau décode le contexte environnant est essentielle afin de comprendre la flexibilité comportementale que nous montrons quotidiennement, et dont l’importance est démontrée par les pathologie associée à son dysfonctionnement. Le propos de ce travail était d’apporter une petite brique supplémentaire à cet édifice.Encountering a particular stimulus may require radically different responses in different situations. Imagine yourself facing a lion, an animal that is generally integrated in our consciousness as threatening. This lion would express a different meaning when it is encountered in the wild or when it is seen behind glass in a zoo. This observation emphasizes the context processing allowing to elicit the most appropriate response. Normal brains keep biologically significant events distinct and resistant to confusion. If not, it may lead to psychological dysfunction because of inaccurate context processing. This is a one of the core symptoms observed in patients suffering from anxiety disorders and posttraumatic stress disorder (PTSD). Given the essential role of the context in emotion and cognition, a major scientific challenge is to understand how the brain processes and restitute contextual information between neutral and aversive emotional valance. In the laboratory condition, the classical contextual fear conditioning (CFC) is a useful model for studying neural circuits of associative learning processes. In its most basic form, it consists of placing the animal in a conditioning chamber in which is delivered an aversive stimulus. In rodent studies the environmental context itself act as an “occasion setter” to predict the arrival of the US, thus replacing the animal back in this context leads to the expression of conditioned responses (CR) usually freezing behavior. The latter observation is highly context specific, such that when placed in another context animals do not exhibit any fear behavior, a phenomenon called contextual fear discrimination. My goal is to visualize how brain deals with moments of context ambiguity! But how to catch them! It is first a methodological problem: it is difficult to manipulate the level of ambiguity in the surrounding context along a single sensory dimension. During my thesis, I tested and validated smooth area shape transitions as unique context changes to elicit contextual fear discrimination. Among areas potentially involved in the contextual fear processing, three brain regions - the medial prefrontal cortex (mPFC), the basolateral amygdala (BLA), and the hippocampus (HPC) - are particularly important, and share functional connectivity. We therefore performed extracellular recording simultaneously in the three aforementioned areas, along the contextual fear learning process, i.e., fear acquisition, retrieval and discrimination, with a particular focus on transition periods to let emerge the “partition of the symphony”. We wanted to answer a few specific questions: 1. What are the functional mechanisms instructing the PFC during contextual fear expression? 2. What are the functional mechanisms within the interconnected tripartite circuit that mediate appropriate behavior according to the contextual valence? 3. At cellular level, what will determine if a neuron is implicated or not in contextual discrimination? In general, we believe that a more comprehensive view of the brain circuits that mediate contextual processing and modulation will greatly enrich the future understanding of flexible, adaptive responses to environmental stimuli, and pathophysiological processes that interfere with this flexibility. The purpose of this thesis is to bring another brick in this wal

Leaf Wetness Duration Models Using Advanced Machine Learning Algorithms: Application to Farms in Gyeonggi Province, South Korea

Leaf wetness duration (LWD) models have been proposed as an alternative to in situ LWD measurement, as they can predict leaf wetness using physical mechanism and empirical relationship with meteorological conditions. Applications of advanced machine learning (ML) algorithms in the development of empirical LWD model can lead to improvements in the LWD prediction. The current study developed LWD model using extreme learning machine, random forest method, and a deep neural network. Additionally, performances of these ML-based LWD models are evaluated and compared with existing models. Observed LWD and meteorological variable data are obtained from nine farms in South Korea. Temporal and geographical information were also used. Additionally, the priorities of the employed variables in the development of the ML-based LWD models were analyzed. As a result, the ML-based LWD models outperformed the existing models; the random forest led to the best performance for LWD prediction among the tested LWD models. Strengths of associations between input variables and leaf wetness were relative humidity, short wave radiation, air temperature, hour, latitude, longitude, and wind speed in descending order. Uses of the geographical and time information in development of LWD model can improve the performance of LWD model