Combining Finite Element Method and L-Systems Using Natural Information Flow Propagation to Simulate Growing Dynamical Systems

International audienceThis paper shows how to solve a system of di↵erential equa-tions controlling the development of a dynamical system based on finite element method and L-Systems. Our methods leads to solve a linear system of equations by propagating the flow of information throughout the structure of the developing system in a natural way. The method is illustrated on the growth of a branching system whose axes bend under their own weight

Élucidation des rôles de YAP1 et TAZ dans l'ovaire chez la souris

L’ovaire est un organe indispensable à la fonction reproductive, car il permet la production, la maturation et la libération de la cellule germinale femelle, l’ovocyte. Malgré son rôle central dans la régulation de la reproduction chez la femme, plusieurs de ses processus physiologiques et de ses conditions pathologiques sont encore imparfaitement décrits. La caractérisation du rôle de nouveaux régulateurs pourrait permettre l’élucidation de plusieurs questionnements actuels en physiologie ovarienne. Initialement étudiée dans l’organogenèse et l’oncogenèse pour son implication dans la prolifération, la migration, la différenciation et l’apoptose cellulaire, la voie de signalisation Hippo pourrait s’avérer être un facteur déterminant dans la physiologie ovarienne. En effet, elle a été récemment rapportée comme participant à la régulation de l’activation folliculaire, de la prolifération des cellules de la granulosa et de l’ovulation. La voie Hippo consiste en une cascade de kinases menant ultimement à la phosphorylation des deux co-régulateurs transcriptionnels YAP1 (yes-associated protein 1) et TAZ (transcriptional coactivator with a PDZ-binding motif). L’objectif général de ce projet de thèse était de caractériser les rôles de Yap1/Taz dans la physiologie ovarienne en utilisant des modèles murins transgéniques d’inactivation conditionnelle de ces gènes dans les cellules de la granulosa. La première portion du projet a conduit à la caractérisation d’un phénotype inattendu de défaut des oviductes. Les souris femelles adultes étaient sous-fertiles et leur fonction ovarienne était intacte. En fait, la sous-fertilité était causée par le piégeage des embryons dans des dilatations de la paroi de l’oviducte, empêchant ainsi leur transport adéquat vers l’utérus. Nous sommes parvenus à démontrer que la perte d’expression de YAP1/TAZ dans les couches musculeuses de l’oviducte conduisait à un amincissement progressif de sa paroi et était ultimement responsable de l’échec du transport embryonnaire. Dans la seconde portion du projet, nous avons utilisé la culture primaire de cellules de la granulosa afin de décrire l’implication de la voie Hippo dans l’ovulation. Nous avons identifié la protéine kinase A comme modulateur clé de l’activation de la voie Hippo par l’hormone lutéinisante (LH). En utilisant un système adénoviral de délétion de Yap1/Taz, nous avons mis en évidence l’importance de leur expression pour l’induction de plusieurs gènes cibles de la LH. Ensuite, au moyen d’une expérience d’immunoprécipitation de la chromatine, nous avons démontré l’implication de YAP1 dans la régulation de la transcription de l’amphiréguline, un effecteur central de la cascade de signalisation de la LH. Dans son ensemble, ce projet a permis de mettre la lumière sur de nouveaux rôles de la voie de signalisation Hippo dans la régulation des cellules musculaires lisses de l’oviducte et des cellules de la granulosa durant l’ovulation chez la souris. Elles ouvrent la voie à une investigation plus précise de l’implication de la voie Hippo dans ces deux organes clés du système reproducteur femelle.The ovary is a central organ of the female reproductive tract involved in oocyte production, maturation and release. Still, many physiological and pathological ovarian processes remain to be described more comprehensively. The precise characterization of the roles of new ovarian regulators would contribute to a better understanding of its physiology. The Hippo signaling pathway was initially studied for its roles in cellular proliferation, apoptosis, migration and differentiation during organ and tumor development. Recently, it has been shown to be involved during normal physiological processes of multiple organs, including the ovary. Hippo was shown to be involved in the activation of primordial follicles, in the proliferation of granulosa cells and during ovulation. Hippo consists of a central kinase cascade leading to the phosphorylation of YAP1 (yes-associated protein 1) and TAZ (transcriptional coactivator with a PDZ-binding motif), the two transcriptional coactivators of the pathway. The objective of this thesis was to characterize the precise roles of Yap1/Taz in ovarian physiology using transgenic mouse models of their genetic deletion in granulosa cells. The first part of this thesis project led to the characterization of an unexpected oviductal phenotype. Adult females were subfertile and their ovarian function was unaffected. The subfertility was rather caused by the entrapment of embryos in oviductal dilations, preventing their normal transport to the uterus. We demonstrated that loss of YAP1/TAZ expression in oviductal smooth muscle cells led to a gradual thinning of the oviductal wall and was responsible for the embryo transport impediment. In the second part of this project, we cultured primary mouse granulosa cells to characterize the roles of the Hippo signaling pathway during ovulation. We showed that protein kinase A is a key effector of Hippo activation following the luteinizing hormone (LH) surge. We then demonstrated that Yap1/Taz expression is required for the induction of several LH target genes. Using a chromatin immunoprecipitation experiment, we were able to show that YAP1 drives the expression of amphiregulin, a key paracrine transmitter of the LH signal, during the early events of ovulation. Together, these results identified new roles of the Hippo signaling pathway in the regulation of oviductal smooth muscle cells and of granulosa cells during ovulation. This thesis project opens the door to new avenues of investigation of Hippo involvement in the regulation of the female reproductive system

Deletion-Compliance in the Absence of Privacy

Garg, Goldwasser and Vasudevan (Eurocrypt 2020) invented the notion of deletion-compliance to formally model the right to be forgotten , a concept that confers individuals more control over their digital data. A requirement of deletion-compliance is strong privacy for the deletion requesters since no outside observer must be able to tell if deleted data was ever present in the first place. Naturally, many real world systems where information can flow across users are automatically ruled out. The main thesis of this paper is that deletion-compliance is a standalone notion, distinct from privacy. We present an alternative definition that meaningfully captures deletion-compliance without any privacy implications. This allows broader class of data collectors to demonstrate compliance to deletion requests and to be paired with various notions of privacy. Our new definition has several appealing properties: - It is implied by the stronger definition of Garg et al. under natural conditions, and is equivalent when we add a privacy requirement. - It is naturally composable with minimal assumptions. - Its requirements are met by data structure implementations that do not reveal the order of operations, a concept known as history-independence. Along the way, we discuss the many challenges that remain in providing a universal definition of compliance to the right to be forgotten

L008 Défaut de différenciation veino-lymphatique embyonnaire par modulation de l’ARN interférence

L’ARN interférence, mécanisme de régulation de l’expression des gènes, est médiée par les siARNs et les microARNs, ARN non-codants de 20 à 22 nucléotides affectant la régulation post-transcriptionnelle d’ARNm cibles avec lesquels ils s’apparient.La RNase DICER est une enzyme centrale de la biosynthèse des siARNs et microARNs. Les souris dont le gène dicer est invalidé ont un phénotype complexe, et meurent très tôt pendant le développement, notamment à cause d’un défaut d’angiogenèse.Afin d’étudier l’ARN interférence au cours de l’angiogenèse embryonnaire, des souris dont le gène dicer est floxé (mutant conditionnel) sont croisées avec des souris exprimant la recombinase Cre, de manière constitutive, sous le contrôle du promoteur du gène tie2, dirigeant ainsi son expression dans les cellules endothéliales (CE) et les cellules hématopiétiques.Nos résultats montrent que l’invalidation de dicer sous le contrôle du promoteur du gène tie2 entraine une mortalité embryonnaire suite à un œdème et des hémorragies au treizième jour du développement (E13,5). L’analyse histologique montre des vaisseaux lymphatiques remplis de sang, suggérant une mauvaise séparation du réseau sanguin et lymphatique. Cette hypothèse est étudiée par marquage des vaisseaux lymphatiques (LYVE-1) et des vaisseaux sanguins (PECAM) sur embryon entier et peaux isolées à différents stades précédant la mort.Ces embryons présentent également un problème de développement du foie, probablement dû à l’activité du promoteur tie2 dans les lignées hématopoiétiques. La mise en culture de ces foies fœtaux à E13,5 révèle une atteinte des précurseurs hématopoétiques.L’étude de ces précurseurs à des stades plus précoces (E8,5) est en cours au laboratoire.Nos résultats démontrent donc un rôle important de l’ARN interférence dans le contrôle épigénétique de l’angiogenèse et de la lymphangiogenèse embryonnaire mais également dans le développement de l’hématopoièse, suggérant son implication dans la différenciation veino-lymphangiogenèse, dont les mécanismes moléculaires seront discutés

Modeling of light transmission under heterogeneous forest canopy: model description and validation

International audienceGrowth and survival of regeneration saplings and understorey vegetation development is closely related to light available below the forest trees. Manipulating the forest structure by thinning adult trees is a major tool to control light transmission to the understorey. The transmission is related to the attenuation of light which is usually estimated with the Beer-Lambert law assuming homogeneous foliage within the canopy. However forest canopies are far from homogeneous, which requires models that can take into account the effect of clumping between and within trees. In this work we present a model that can be readily used with both coarse or detailed parameterization to generate any type of stand and compute the distribution of light transmitted below the canopy. To evaluate the accuracy of the model, we compared model results with field measurements from several stands of Pinus sylvestris L. in the French Massif Central.no abstrac

Selected plasma fatty acid levels in subsistence fed sled dogs along the Yukon River: a pilot study for biomonitoring

The introduction of the ‘western diet' marked a decline in omega-3 fatty acids rich foods and a concurrent increase in saturated and omega-6 fatty acids that persists today. Historically, circumpolar people have had a low incidence of obesity, diabetes and cardiovascular disease and this has been largely attributed to polyphenolic compounds and omega-3 fatty acids offered from subsistence foods. In this report, we studied sled dogs as an Arctic sentinel species for monitoring the effect of a changing diet on lipid profiles along the Yukon River. Subsistence fed village sled dogs along the Yukon River, maintained largely on salmon were compared with a control kennel maintained on commercial food. Profiles showed higher levels for long chain omega-3 fatty acids in village subsistence fed dogs compared to control dogs and an opposite trend for omega-6 fatty acids, establishing baseline levels for follow up studies. A comparison with data for previously published mercury levels from the same cohort of dogs revealed a positive correlation with alpha-linolenic fatty acid and a negative correlation with linoleic fatty acid. Food and nutritional security is a concern in the Arctic as the impacts of climate change and transport of contaminants become obvious. This study supports not only the nutritional value of a subsistence diet but also the utility of sled dogs as a sentinel for human dietary chang

Addition of Red Clover or Birdsfoot Trefoil in Alfalfa-based Mixtures to Improve the Forage Energy to Protein Balance

The low ratio of sugars (S) to crude proteins (CP) in alfalfa (AL, Medicago sativa L.) leads to inefficient use of nitrogen by ruminants. The objective was to determine if adding red clover (RC, Trifolium pratense L.) or birdsfoot trefoil (BT, Lotus corniculatus L.) with or without a grass species to AL improved the forage S/CP ratio. Treatments were 100% AL (control) or AL-based mixtures with RC or BT in three proportions (75, 50, or 25% of seeded legumes) with either no grass or with timothy (Phleum pratense L.) or tall fescue (Schedonorus arundinaceus Schreb. Dumort.), resulting in 21 treatments assigned to a randomized complete block design with four replications at three sites in Canada (Agassiz, BC; St-Anne-de-Bellevue, QC; StAugustin-de-Desmaures, QC). Species contribution and nutritive attributes measured at each harvest were weighted for yield as a proportion of the seasonal yield and expressed yearly for the first two post-seeding years. Regression analyses showed that forage S concentration increased, CP concentration tended to decrease, and the S/CP ratio increased from 0.3 to 0.5 (y = 0.002 x + 0.3; P = 0.003, R2 = 0.53) with the addition of up to 92% RC or up to 66% BT to AL-based mixtures. The addition of up to 61% TI or 55% TF did not impact the S/CP ratio of AL-based mixtures. Further studies are needed to determine if the improved forage S/CP ratio following the addition of RC or BT to AL-based mixtures leads to an improved N-use efficiency in ruminants

Root system markup language: toward an unified root architecture description language

The number of image analysis tools supporting the extraction of architectural features of root systems has increased over the last years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tool is able to extract in an efficient way growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML) that has been designed to overcome two major challenges: (i) to enable portability of root architecture data between different software tools in an easy and interoperable manner allowing seamless collaborative work, and (ii) to provide a standard format upon which to base central repositories which will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store 2D or 3D image metadata, plant and root properties and geometries, continuous functions along individual root paths and a suite of annotations at the image, plant or root scales, at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An xml-schema describes the features and constraints of RSML and open-source packages have been developed in several languages (R, Excel, Java, Python, C#) to enable researchers to integrate RSML files into popular research workflow

Vascular smooth muscle contractility assays for inflammatory and immunological mediators

The blood vessels are one of the important target tissues for the mediators of inflammation and allergy; further cytokines affect them in a number of ways. We review the use of the isolated blood vessel mounted in organ baths as an important source of pharmacological information. While its use in the bioassay of vasoactive substances tends to be replaced with modern analytical techniques, contractility assays are effective to evaluate novel synthetic drugs, generating robust potency and selectivity data about agonists, partial agonists and competitive or insurmountable antagonists. For instance, the human umbilical vein has been used extensively to characterize ligands of the bradykinin B2 receptors. Isolated vascular segments are live tissues that are intensely reactive, notably with the regulated expression of gene products relevant for inflammation (e.g., the kinin B1 receptor and inducible nitric oxide synthase). Further, isolated vessels can be adapted as assays of unconventional proteins (cytokines such as interleukin-1, proteases of physiopathological importance, complement-derived anaphylatoxins and recombinant hemoglobin) and to the gene knockout technology. The well known cross-talks between different cell types, e.g., endothelium-muscle and nerve terminal-muscle, can be extended (smooth muscle cell interaction with resident or infiltrating leukocytes and tumor cells). Drug metabolism and distribution problems can be modeled in a useful manner using the organ bath technology, which, for all these reasons, opens a window on an intermediate level of complexity relative to cellular and molecular pharmacology on one hand, and in vivo studies on the other

Androgen-Regulated Expression of Arginase 1, Arginase 2 and Interleukin-8 in Human Prostate Cancer

BACKGROUND: Prostate cancer (PCa) is the most frequently diagnosed cancer in North American men. Androgen-deprivation therapy (ADT) accentuates the infiltration of immune cells within the prostate. However, the immunosuppressive pathways regulated by androgens in PCa are not well characterized. Arginase 2 (ARG2) expression by PCa cells leads to a reduced activation of tumor-specific T cells. Our hypothesis was that androgens could regulate the expression of ARG2 by PCa cells. METHODOLOGY/PRINCIPAL FINDINGS: In this report, we demonstrate that both ARG1 and ARG2 are expressed by hormone-sensitive (HS) and hormone-refractory (HR) PCa cell lines, with the LNCaP cells having the highest arginase activity. In prostate tissue samples, ARG2 was more expressed in normal and non-malignant prostatic tissues compared to tumor tissues. Following androgen stimulation of LNCaP cells with 10 nM R1881, both ARG1 and ARG2 were overexpressed. The regulation of arginase expression following androgen stimulation was dependent on the androgen receptor (AR), as a siRNA treatment targeting the AR inhibited both ARG1 and ARG2 overexpression. This observation was correlated in vivo in patients by immunohistochemistry. Patients treated by ADT prior to surgery had lower ARG2 expression in both non-malignant and malignant tissues. Furthermore, ARG1 and ARG2 were enzymatically active and their decreased expression by siRNA resulted in reduced overall arginase activity and l-arginine metabolism. The decreased ARG1 and ARG2 expression also translated with diminished LNCaP cells cell growth and increased PBMC activation following exposure to LNCaP cells conditioned media. Finally, we found that interleukin-8 (IL-8) was also upregulated following androgen stimulation and that it directly increased the expression of ARG1 and ARG2 in the absence of androgens. CONCLUSION/SIGNIFICANCE: Our data provides the first detailed in vitro and in vivo account of an androgen-regulated immunosuppressive pathway in human PCa through the expression of ARG1, ARG2 and IL-8