WorldCat Identities

Hersen, Pascal

Works: 17 works in 20 publications in 2 languages and 23 library holdings
Roles: Thesis advisor, Other, Opponent, Author
Publication Timeline
Most widely held works by Pascal Hersen
Identification of individual cells from z-stacks of bright-field microscopy images by Jean-Baptiste Lugagne( )

1 edition published in 2018 in English and held by 2 WorldCat member libraries worldwide

A quantitative approach to microbial population growth using tailored cylindrical yeast colonies by Clément Vulin( Book )

2 editions published in 2014 in English and held by 2 WorldCat member libraries worldwide

Microbes can form complex structures composed of millions to billions of cells. These cellular assemblies contrast with the classical view we have of the "unicellulars" microbes. In fact, given their environment, they likely form heterogeneous connected structures. Our understanding of these assemblies is still scarce. The problem is that the models we develop suffer from the lack of experimental tools to understand these groups of cells. In this thesis, I propose to study they yeast Saccharomyces cerevisiae colonies by defining the flux of nutrients the colony receives. I use patterned filtration membranes intercalated between colonies and nutritive gel, leading to well controlled chapes. Using the cylindrical geometry resulting from a disc pattern, I first propose a quick study of the pillar organization, and then propose a simple model for colony growth in order to explain experimental growth in different environmental conditions, with respect to glucose levels, colony diameter and oxygen availability. I then discuss the biological relevance of this model with respect to cell division and nutrient absorption. To go further in investigations, I propose a automated measure of colony volume using a laser based measure with a 10 µm height precision. A microfluidic setup that mimics a two-dimensional colony growth is also proposed, where cells can be directly observed under a microscope
Balancing a genetic toggle switch by real-time feedback control and periodic forcing by Jean-Baptiste Lugagne( )

1 edition published in 2017 in English and held by 2 WorldCat member libraries worldwide

Real-time feedback control of gene expression by Jannis Uhlendorf( Book )

2 editions published in 2013 in English and held by 2 WorldCat member libraries worldwide

L'expression génétique est un processus cellulaire fondamental réglé de manière ne. Les promoteurs inducibles permettent de perturber l'expression génétique en changeant l'expression d'une protéine par rapport à son niveau physiologique de référence. Cette propriété en fait un outil incontournable pour décrypter le fonctionnement des processus biologiques via la comparaison du comportement de la cellule sous divers niveaux d'induction. Toutefois, une limite actuelle à l'utilisation des promoteurs inducibles provient de la difficulté à appliquer des perturbations précises et dynamiques. Les deux obstacles principaux étant : (i) la variabilité intercellulaire ainsi qu'à la nature aléatoire de l'expression génétique qui limite la précision de la perturbation appliquée. (ii) la difficulté à prédire quantitativement le comportement des systèmes biologiques sur les longues periodes requises pour des objectifs d'expression variables dans le temps. Or des perturbations précises et changeant dans le temps permettent d'obtenir de riches informations sur la dynamique d'un système biologique. Est présenté ici une plate-forme de contrôle temps réel en boucle fermée qui permet le contrôle quantitatif sur une longue durée de l'expression génétique chez la levure. Cette plate-forme utilise la microscopie par fluorescence pour suivre l'expression génétique, un système micro fluidique pour interagir avec l'environnement cellulaire ainsi qu'un logiciel permettent l'analyse d'image en temps réel et le calcul de la stratégie de contrôle à appliquer. Ce système permet le contrôle de l'expression d'un gène chez la levure, tant au niveau d'une population cellulaire qu'au niveau de la cellule seule et ceci pour un objectif d'expression constant ou dépendant du temps. Le système de réponse aux chocs hyper-osmotiques de la levure S. cerevisiae (HOG pathway) a été utilisé pour influencer l'expression génétique. Toutefois, la possibilité d'utiliser un autre système d'induction sans profondes modifications de la plate-forme est démontré. De surcroît au développement de cette plate-forme est également ici démontré la possibilité de contrôler le système HOG. Afin de comprendre la dynamique cellulaire et de pouvoir la quantifier, il est nécessaire de pouvoir appliquer des perturbations précises. La plate-forme de contrôle de l'expression génétique présentée ici permet de perturber avec précision le niveau d'expression d'une protéine et représente donc une contribution majeure dans cette direction
Morphogenèse et Dynamique des Barchanes by Pascal Hersen( Book )

2 editions published in 2004 in French and held by 2 WorldCat member libraries worldwide

Spatial structuring and size selection as collective behaviours in an agent-based model for barchan fields by Mathieu Génois( )

1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide

Les fourmis et les machines : interfacer systèmes vivants et systèmes artificiels by Raphaël Ponthieu( )

1 edition published in 2018 in French and held by 1 WorldCat member library worldwide

Within the animal kingdom social insects fascinate humans. Especially ants, which are capable of adapting to various environments and taking advantage of their biotopes. Observing practices that we would have thought to be exclusive to humans - such as farming (of mushrooms) or breeding (of aphids) - spurs the will to understand by which mean ants operate. It turns out that ants achieve certain tasks in different ways than humans. For instance, to find the shortest path to a food source, or the best nest to migrate to; the colony can make a collective decision, decentralized and without the need of direct comparisons by individuals. My work has consisted of the elaboration and use of new methods to study ants. Two complementary objectives have been chosen to drive the work: implementation of a biohybrid system and assessing the means of and limits to controlling the behaviour of ants. The first objective consists of asking ourselves what will happen if we connected an ant colony with a computer For this I have designed apparatus that permit interaction between those two entities. It involved giving sight to the computer into what the colony was doing, then providing ways for the computer to act on the colony. To do so, I designed and tried out tools to monitor the activity of colonies as well as modular environments which ants can inhabit. I designed an embedded system that records and analyses activity of ant colonies on a micro-computer. I designed and 3D printed modules of various sizes that can be assembled together to form a structurally varied environment. For the computer to be able to act upon ant behaviour, I chose to endow it with the capability of modifying environmental conditions, at particular temperatures. Once the system was built, I conducted experiments to assess how local changes of temperature affect ant behaviour. This characterisation of behaviour under temperature changes sheds light on the relation of ants with their environment. This permitted the exploration of questions of control of behaviour of ants by a machine. The use of temperature having proved its capacity to modulate the local occupancy density, I then have been able to show that it was possible to confine an ant in a set location. Finally, I implemented a closed feedback loop system, in which the temperature used to confine the ant is dependent on the ant activity in real time. This last experiment shed light on the complexity of the dynamic relation between ants and their environments and opened new perspectives for future investigations. During this research, many tools were developed. Functional prototypes of moduary environments have demonstrated the relevance of using 3D printers for the study of ants. The various tools for monitoring, recording and processing video data provide new and innovative experimental possibilities and can be used for other studies, especially over long periods of time. Temperature control devices have as well been designed using rapid prototyping tools, making them accessible, scalable and reproducible in an open source approach
Peut-on déléguer le tri des urgences ophtalmologiques à un algorithme informatisé auto-implémenté par le patient ? : le projet ICARE (Interactive Care Assessment of Risk factors and Emergency levels) by Mikaël Guedj( )

1 edition published in 2018 in French and held by 1 WorldCat member library worldwide

Every year in France, 4 million emergency consultations are not justified from a medical point of view and almost half of the patients presenting to the Emergency Department could be treated elsewhere, thus releasing the Emergency Departments to take care of the real urgent situations. The overcrowding of the ERs led the services to set up a prioritization of care for the reception of patients; this prioritization is not standardized nor rationalized. We designed a computerized tool to sort emergency levels based on a patient's symptoms, background, and medical context. By this tool, called iCare, the patient alone or assisted by a third party, must be able to detect and prioritize his symptoms leading to an urgent consultation, as opposed to less urgent or non-urgent symptoms. The evaluation of the iCare algorithm regarding ocular pathologies aims to run a generalizable and reproducible sorting tool within the different care units, but also to improve patient autonomy in the understanding of their symptoms and their use of the healthcare system (e-health concept of empowerment). The main objective of our "interventional research involving only minimal risks and constraints" was to validate the iCare sorting algorithm, determining the appropriate level of urgency corresponding to the clinical situations encountered. This validity was based on the calculations of sensitivity, specificity, positive and negative predictive values. The chosen gold-standard was the level of emergency determined by the doctor after his consultation. A number of 1000 patients presenting for an ophthalmological emergency were offered to participate in research upon arrival at the reception of two Parisian health centers (Rothschild Foundation, Vernes Institute), from the date of protocol acceptance by the Committee for the Protection of Persons in biomedical research (CPP). If the patient consented to participate in research, a Clinical Study Technician (CST) made him fill in the iCare algorithm, presented as an interactive questionnaire on touchscreen tablet, whose implementation took less than two minutes. At the end of this implementation, a level of emergency A, B, C or D was provided by the program. The level of emergency attributed by the algorithm was unknown to either the patient or the doctor who was going to examine him. The level of emergency determined by the physician at the end of his clinical examination (gold standard of the primary endpoint) was collected as a level A, B, C, D or as binary choice Urgent / No Urgent (U / NU). Other parameters, such as the time required and the need for filling assistance, the reason for consultation, demographics and on-site waiting time were also analyzed. This thesis outlines a state of the art of the word "e-health" in 2018, addresses the current public health issues related to high traffic in emergency services in France, and features the iCare tool as a potential solution to simplify and rationalize the sorting of emergency levels in ophthalmology (public health feature), as a means of health education and empowerment of patients in the reading of their symptoms (empowerment feature), but also as a generalizable tool for big data reporting of the reasons for consultation in the emergency wards, private practices or even at home health-related internet researches (epidemiological feature)
Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform( )

1 edition published in 2017 in English and held by 1 WorldCat member library worldwide

Abstract : With the continuous expansion of single cell biology, the observation of the behaviour of individual cells over extended durations and with high accuracy has become a problem of central importance. Surprisingly, even for yeast cells that have relatively regular shapes, no solution has been proposed that reaches the high quality required for long-term experiments for segmentation and tracking (S & T) based on brightfield images. Here, we present CellStar, a tool chain designed to achieve good performance in long-term experiments. The key features are the use of a new variant of parametrized active rays for segmentation, a neighbourhood-preserving criterion for tracking, and the use of an iterative approach that incrementally improves S & T quality. A graphical user interface enables manual corrections of S & T errors and their use for the automated correction of other, related errors and for parameter learning. We created a benchmark dataset with manually analysed images and compared CellStar with six other tools, showing its high performance, notably in long-term tracking. As a community effort, we set up a website, the Yeast Image Toolkit, with the benchmark and the Evaluation Platform to gather this and additional information provided by others
Drug Delivery: Extracellular Vesicle Production Loaded with Nanoparticles and Drugs in a Trade-off between Loading, Yield and Purity: Towards a Personalized Drug Delivery System (Adv. Biosys. 5/2017)( )

1 edition published in 2017 in English and held by 1 WorldCat member library worldwide

Abstract : The human body possesses its own outperforming delivery device in extracellular vesicles that circulate in all body fluids and act as a farreaching intercellular communication pathway. Engineering extracellular vesicles with therapeutic and imaging agents opens up unprecedented perspectives with a new generation of personalized drug delivery systems. In article number1700044, Florence Gazeau, Amanda K.A. Silva, and co-workers compare methods of production, engineering, and purification of extracellular vesicles that challenge the road towards clinical translation
Real-time control of a genetic toggle switch by Jean-Baptiste Lugagne( )

1 edition published in 2016 in English and held by 1 WorldCat member library worldwide

Recent progresses in microfluidics, synthetic biology and microscopy automation now make it possible to control gene expression externally and in real time. Among the challenges facing the field of external real-time control of gene expression is the control of intricate, multistable gene regulation networks as well as the control of several target genes at the same time. To advance the domain in this direction we studied the controllability of a simple bistable two-genes network, the so-called genetic toggle switch, in the vicinity of its unstable equilibrium point for extended periods of time. Throughout this document, we present the development of a custom control platform for external control of gene expression at the single-cell level as well as a bacterial cellular chassis and a library of toggle switch genetic circuits for us to control. We use the platform to drive and maintain our genetic system in its region of unstability with both closed-loop and open-loop strategies. Not only do we demonstrate that in silico control platforms can control genetic systems in out-of-equilibrium states, we also notably maintain a population of cells in their unstable area with open-loop periodic stimulations. These results suggest the possible emergence of different regimes of stability in gene regulation networks submitted to fluctuating environments, and can potential insights in the study of cellular decision making. We also introduce a new approach for microscopy image analysis which exploits information hidden in several focal planes around the specimen instead of using only a single-plane image. The objective of this method is to automatically label different parts of an image with machine learning techniques inspired by hyperspectral imaging. The method is then shown to facilitate segmentation and be easily adaptable to various different organisms
Severe osmotic compression of the yeast Saccharomyces cerevisiae by Agnès Miermont( Book )

1 edition published in 2013 in English and held by 1 WorldCat member library worldwide

Cells have developed several signaling pathways and transcriptional regulatory networks to regulate their size and coordinate their growth with the cell division. Importantly, the interior of a cell is naturally packed with macromolecules and is said to be crowded. Macromolecular crowding has been intensely studied in vitro and is known to affect the kinetics of reactions. However, studying the effects of crowding in vivo is more challenging due to the high level of complexity and heterogeneity in the cytoplasm. In this thesis, we address the effects of changing the cellular volume on the kinetics of biochemical reactions in live Saccharomyces cerevisiae cells. We osmotically compressed yeast cells, thus increasing the total macromolecular density and investigated the impact of such crowding on the kinetics of signal transduction. Cell shrinkage is expected to increase the intracellular viscosity and may severely slow down the functioning of signaling pathways and cellular processes. Indeed, by progressively increasing the level of compression, we recorded a progressive slow-down of several, unrelated biological processes until a point for which cell dynamics were arrested. We propose that this slowing down upon cellular compression is very general and is reminiscent of a soft colloidal glassy-like transition. Our results suggest the importance for cells to regulate their volume and their cytoplasmic crowding to function properly
Self-organization of Saccharomyces cerevisiae colonies by Zoran Marinkovic( )

1 edition published in 2017 in English and held by 1 WorldCat member library worldwide

The natural environment of yeast is often a community of cells but researchers prefer to study them in simpler homogeneous environments like single cell or bulk liquid cultures, losing insight into complex spatiotemporal growth, differentiation and self-organization and how those features are intertwined and shaped through evolution and ecology. I developed a multi-layered microfluidic device that allows us to grow yeast colonies in spatially controlled dynamically structured changing environments from a monolayer of single yeast cells to a multi-layered colony. Colony growth, as a whole and at specific locations, is a result of the nutrient gradient formation within a colony through interplay of nutrient diffusion rates, nutrient uptake rates by the cells and starting nutrient concentrations. Once a limiting nutrient (e.g. glucose or amino acids) is depleted at a specific distance from the nutrients source the cells within a colony stop to grow. I was able to modulate this specific distance by changing the starting nutrient concentrations and uptake rates of cells. Colony gene expression patterns gave us information on specific micro environments formation and consequential development, differentiation and self-organization. I quantified the patterns of expression of seven glucose transporter genes (HXT1-7), each of them specifically expressed depending on the glucose concentration. This enabled us to reconstruct glucose gradients formation in a colony. I further followed the expression of fermentation and respiration specific genes and observed differentiation between two subpopulations. We also mapped other genes specific for different parts of carbohydrate metabolism, followed and quantified the spatiotemporal dynamics of growth and gene expression, and finally modelled the colony growth and nutrient gradient formation. For the first time, we were able to observe growth, differentiation and self-organization of S. cerevisiae colony with such an unprecedented spatiotemporal resolution
Étude d'agrégats d'anticorps monoclonaux sous écoulement microfluidique by Charles Duchêne( )

1 edition published in 2018 in French and held by 1 WorldCat member library worldwide

The formation of aggregates in solutions of monoclonal antibodies is difficult to prevent. Even if the occurrence of large aggregates is rather rare, their existence can have dramatic effects in injection devices, as they can lead to partial or total clogging of constrictions in the latter. This leads to badly controlled injection or even total obstruction of the device. Little is know on the role of aggregate size and applied pressure on such clogging events. In this thesis, we present a microfluidic model system, mimicking medical injection devices to gain fundamental understanding of the clogging of constrictions of given size. Highly concentrated solutions of monoclonal antibodies allow us to create protein aggregates (bigger than 50 micrometers) using mechanical or heat stress. We show that clogging occurs when aggregates reach the size of the constriction and can in some cases be undone by increasing the applied pressure. The observed possibility to eject aggregates from constrictions via an increase in pressure indicates the important role of protein aggregate deformability, so far completely unexplored. We perform systematic experiments for different relative aggregate size and the applied pressure, and measure the flow-rate. Despite their different shapes and density, we can predict the number of clogging events for a given constriction size by Flow Imaging Microscopy (MFI) measurements. In addition our device can detect the occurrence of very rare big aggregates often overlooked by other detection techniques. With a simple mechanical model where we neglected the friction, we could estimate for the first time an order of magnitude for the Young modulus and a porous diameter for monoclonal antibodies aggregates. We also develop another model experiment with an hyperbolic channel coupled with a flow focusing to observe deformation of the aggregates under extensional flow. We describe their behavior by analyzing their trajectories which are for most of them tumbling and alignment with the flow. Moreover, we develop a mechanical model which took into account the friction force in a controlled model experiment with polymeric solution. We thus investigate the role of a minimal applied pressure to generate the particle movement into the constriction, and then link it with protein aggregates
Extracellular Vesicle Production Loaded with Nanoparticles and Drugs in a Trade-off between Loading, Yield and Purity: Towards a Personalized Drug Delivery System( )

1 edition published in 2017 in English and held by 1 WorldCat member library worldwide

Abstract : Extracellular vesicles (EVs) released by cells and circulating in body fluids are recognized as potent vectors of intercellular self-communication. Due to their cellular origin, EVs hold promise as naturally targeted "personalized" drug delivery system insofar as they can be engineered with drugs or theranostic nanoparticles. However, technical hurdles related to their production, drug loading, purification, and characterization restrain the translation of self-derived EVs into a clinical drug delivery system. Herein, different methods are compared to generate and to purify EVs encapsulating iron oxide nanoparticles and a clinical photosensitizer drug (Foscan) as biocamouflaged agents for photodynamic therapy, magnetic resonance imaging, magnetic manipulation, and hyperthermia. Theranostic EVs are produced from drug- and nanoparticle-loaded endothelial cells either by spontaneous release in complete medium, by starvation in serum-free medium or by mechanical stress in a microfluidic chip mimicking vessel shear stress, and purified by ultracentrifugation or magnetic sorting. The impact of the production and purification protocols is investigated on EV yield and size, nanoparticle and drug cargo, and finally on their therapeutic efficacy. EV production by starvation combined with purification by ultracentrifugation may be considered a reasonable trade-off between loading, yield, and purity for biogeneration of theranostic EVs. Abstract : Cell-released extracellular vesicles are potent vectors of intercellular communication. Their potential as naturally targeted "personalized" drug delivery system depends on technical hurdles related to their production, drug and nanoparticle loading, purification, and characterization. Herein, different methods are compared to generate and purify extracellular vesicles with theranostic properties
Pre-evolutionary dynamics in autocatalytic RNA networks by Simon Arsene( )

1 edition published in 2018 in English and held by 1 WorldCat member library worldwide

Networks of interdependent molecules are considered plausible candidates for initiating the transition from biology to chemistry. Though they have been intensively scrutinized theoretically, there is still no experimental evidence for confirming or denying their supposed crucial role in the origins of life. In particular, we are still lacking experimental proofs of any of the three ingredients usually presented as required for Darwinian evolution: heredity, variation and selection. A system that would possess the three while being coupled to some sort of encapsulated replication process would theoretically be able to undergo Darwinian evolution. As a matter of fact, this has been shown theoretically for Collectively Autocatalytic Sets (CAS) where each molecule of the set is catalytically formed by another member of the ensemble. Here we use the Azoarcus recombination ribozyme system to experimentally form structurally diverse CASs to explore their evolutionary properties. In this system, the ribozymes can catalyze the assembly of other ribozymes from smaller fragments, present in the food set. We first use a droplet microfluidics set-up coupled with next-generation sequencing to conduct a large scale study on thousands of Azoarcus CASs. We develop a perturbative approach to identify the important topological parameters that control variations in CASs as a result of environmental perturbations, here the addition of a new species. We then determine the small set of network features governing memory of the initial conditions in Azoarcus CAS, a pre-requisite for heredity, by using a computational model validated by experimental data. Finally, we demonstrate that Azoarcus CAS possess catabolic processes which make them robust to perturbations in the food set and thus more prebiotic relevant. These results provide evidence for the crucial role of RNA CASs in the origins of life and illustrate how the network structure can be tailored to obtain CASs with properties interesting from an evolutionary point of view, paving the way to an experimental demonstration of Darwinian evolution with a purely molecular system
Memory of stress response in the budding yeast Saccharomyces cerevisiae. by Zacchari Ben Meriem( )

1 edition published in 2018 in English and held by 1 WorldCat member library worldwide

La mémoire cellulaire est une capacité critique dont font preuve les micro-organismes pour s'adapter aux fluctuations environnementales potentiellement néfastes. Chez l'eucaryote unicellulaire S. cerevisiae, il a été montré à l'échelle d'une population que la mémoire cellulaire peut prendre la forme d'une réponse plus rapide ou moins prononcée suite à des stress répétés. Nous présentons ici une étude sur la façon dont les levures réagissent à des stress hyperosmotiques de courte durée à l'échelle de la cellule unique. Nous avons analysé le comportement dynamique du promoteur STL1, exprimé en condition de stress osmotique, et fusionné à un rapporteur fluorescent en faisant usage de microfluidique et de microscopie à fluorescence. Nous avons établi que pSTL1 présente une variabilité dynamique dans ses activations successives après deux stress courts. Malgré cette variabilité, la plupart des cellules présentent une mémoire des stress passés caractérisée par une diminution de l'activité de pSTL1. Nous avons montré que cette mémoire ne nécessite pas de nouvelle synthèse de protéines. L'emplacement génomique est important pour cette mémoire puisque le déplacement du promoteur vers un domaine chromatinien péricentromérique entraîne une diminution de sa force transcriptionnelle ainsi que la perte de la mémoire. Nos résultats indiquent aussi une implication non rapportée du complexe SIR sur l'activité de pSTL1 lorsqu'il est déplacé dans le domaine péricentromérique, dans nos conditions expérimentales. Cette étude fournit une description quantitative d'une mémoire cellulaire qui inclut la variabilité cellulaire et prend en compte la contribution de la structure de la chromatine sur la mémoire du stress. Nos travaux pourraient servir de base à des études plus larges sur le positionnement des gènes de réponse au stress en positions subtélomériques dans la levure, tant d'un point de vue génétique qu'évolutif
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Alternative Names
Pascal Hersen researcher

Pascal Hersen wetenschapper

English (15)

French (5)