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AVRIL 2016 ACTUALITES : PRIX DE THESE 2015 Le prix de thèse 2015 a été attribué à Gilles Storelli (Travaux réalisés dans le Laboratoire de François Leulier, à l’ Ecole Normale Supérieure de Lyon) pour sa thèse intitulée : « Caractérisation de l’interaction mutualiste liant Drosophila melanogaster à son symbionte Lactobacillus plantarum” Gilles présentera ces travaux lors du prochain congrès de la SFBD « Shaping Life » qui se tiendra du 24 au 27 mai à Marseille (voir section suivante). Meeting SFBD 2016 : « SHAPING LIFE » 24-27 mai 2016 à Marseille J‐4 pour soumettre un abstract !! Programme et inscriptions ici : http://www.atoutcom.com/shapinglife‐sfbd/ Et toujours: APPEL à l'organisation de Journée thématique ITMO BCDE Notre Société lance un appel à thématique pour organiser, avant fin juin 2016, une Journée thématique soutenue et financée par ITMO BCDE qui met à disposition un amphithéâtre d’environ 100 personnes à Paris. Ceux qui sont intéressés par l’organisation de cette Journée sont priés de se manifester le plus rapidement possible en écrivant à Christine Lemaître ([email protected]) et à Krzysztof Jagla ([email protected]). BON A SAVOIR : RENOUVELLEMENT ADHESION 2016 Pour renouveler votre adhésion il vous suffit de confirmer votre cotisation en précisant votre mode de règlement. Pensez à mettre à jour les informations vous concernant, s’il y a eu des changements. Les bons de commande sont à envoyer à: [email protected] Les chèques à : SFBD (à l’attention de Svetlana de Joussineau) Laboratoire GReD, Faculté de médecine, 28 place H. Dunant, 63000 Clermont-Ferrand Adhésion individuelle : 50€ pour les titulaires et post-doctorants 25€ pour les doctorants. Adhésion par équipe: équipes jusqu’à 10 personnes - 200 euros; équipes 10 personnes et plus - 300 euros. PERMANENCE TELEPHONIQUE/COMPTE TWITTER Une permanence téléphonique est assurée pour la Société les lundis et les jeudis de 14h à 16h au 04 73 17 81 83. De plus, vous pouvez nous rejoindre sur Twitter "SFBD-BioDev". OFFRES DE POSTES (voir détail des offres en fin de lettre) ASSISTANT PROFESSOR IN “MULTISCALE ANALYSES IN DEVELOPMENTAL BIOLOGY” The Center for Developmental Biology (CBD) http://www-cbd.ups-tlse.fr/ in Toulouse (France) recruits an assistant professor in multiscale analyses in developmental biology. Contact: F. PITUELLO 05 61 55 67 39 [email protected] Website:https://www.galaxie.enseignementsuprecherche.gouv.fr/ensup/ListesPostesPublies/FIDIS/0311384L/FOPC_0 311384L_4437.pdf POSTE D’INGENIEUR D’ETUDE AU LBCMCP, CBI, A TOULOUSE pour un CCD d'une durée d’un an dans l’équipe de Luisa di Stefano Les candidats peuvent transmettre leur CV et leur lettre de motivation à Luisa Di Stefano e-mail: [email protected]). Website: (http://cbi-toulouse.fr/fr/equipe-distefano). L’UNIVERSITE PARIS DIDEROT ET LE CNRS RECHERCHENT UNE DIRECTRICE/UN DIRECTEUR POUR L’INSTITUT JACQUES MONOD renseignements ici : https://www.dgdr.cnrs.fr/drh/cadres-sup/pdf/2016/IJM_DUDAS5C.pdf POST-DOCTORAL POSITION at the Institute of Human Genetics, CNRS, Montpellier, France. Please submit a curriculum vitae and contact information of two referees to Marcel Méchali, Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier, France. Tel: +33 (0) 434 359 917; e-mail: [email protected] website: www.igh.cnrs.fr./equip/mechali/ THREE POSTDOC POSITIONS IN EVO DEVO AND ECO DEVO OF HORNED BEETLES At Moczek-Lab, Indiana University, Bloomington To apply, please submit a letter of application indicating which position is being applied for, a CV, research interests, and the contact information for three references to https://indiana.peopleadmin.com/postings/2277 or send to Jeremy Bennett, 1001 E. Third St., Bloomington, IN 47405 ([email protected]). Review of applications will start immediately and will continue until positions are filled. Preferred start date is July '16 (position #1) and September '16 (positions #2,3) though some flexibility exists. Inquiries about each position can be directed to Armin Moczek ([email protected]). Additional information about research in the Moczek lab can be found at http://ecoevodevo.com/. PHD POSITION AT THE INTEGRATIVE BIOLOGY OF MARINE ORGANISMS LAB (cnrs umr7232) in Banyuls, France. Open position for an interdisciplinary collaborative PhD project focusing on early morphogenesis in a non-conventional vertebrate model organism (catshark, cartilaginous fish). Applications should be sent before the 4th of April to Sylvie Mazan ([email protected]) and René Doursat ([email protected]), who will submit the application of the selected candidate to the Interfaces Pour le Vivant (IPV) Doctoral School (deadline 16th April). The final selection of the candidate will involve an oral presentation to the IPV committee (19th-20th May). PHD POSITION OPENED IN SWITZERLAND DEVELOPMENTAL / CELL BIOLOGIST in GENEVA FOR A On “Evolutionary developmental genetics of reptile skin colour” Candidates must have a Master in biology or biochemistry. Skills and experience with developmental biology and/or cell biology are mandatory Candidates must send their application - in the form of a single PDF file including a brief letter of interest, a CV, as well as contact information (not support letters) of two persons of reference - to: Prof. Michel Milinkovitch, Laboratory of Artificial & Natural Evolution, University of Geneva, Switzerland. e-mail: [email protected], website: www.lanevol.org PHD PROGRAM ON QUANTITATIVE BIOLOGY - OPEN CALL The LabEx INFORM (interdisciplinary program) opens up to 5 positions this year. Recruitment campaign is now open until April 10th 2016 LabEx inform is a interdisciplinary and international research consortium on Quantitative Biology of Signaling, in Marseille, France (http://labex-inform.com/). We encourage the application of graduate students (master degree or equivalent) with backgrounds in biology but also engineering, physics and mathematics.This PhD program is integrated in the international training program called BIOTRAIL, providing excellent support to welcome and train international students. Et toujours : 8 POSTDOCTORAL POSITIONS AT the CENTER FOR INTEGRATIVE BIOLOGY TOULOUSE Applications deadline: April 10 th More informations at http://cbi-toulouse.fr/eng/; http://cbi-toulouse.fr/eng/programme-post-doc PHD INTERNATIONAL PROGRAM AT CENTER FOR INTEGRATIVE BIOLOGY TOULOUSE More informations at http://cbi-toulouse.fr/eng/programme-phd Deadline for applications: April 10, 201 ANNONCES An introduction with lectures and hands-on for scientists and students having completed 3 years of university Contact et infos: http://esc.u-strasbg.fr WINTER SCHOOL AT LES HOUCHES CHAMONIX ” 13-25 mars 2017 “Interplay between physics and integrative biology… …illustrated on two research fields Contact: [email protected] More on Les Houches: http://www.leshouches.ujfgrenoble.fr APPEL A CANDIDATURES POUR L’OCTROI FELLOWSHIPS AU CHURCHILL COLLEGE L’UNIVERSITE DE CAMBRIDGE DE DE Le Service pour la Science et la Technologie de l’Ambassade de France au Royaume-Uni offre chaque année la possibilité à des chercheurs confirmés français de séjourner au Churchill College à Cambridge pour une durée allant de 6 à 11 mois, afin d’effectuer une activité de recherche dans cette prestigieuse université. Pour plus d’information, cf.le site du College http://www.chu.cam.ac.uk/) ou contacter The Bursar ([email protected] ou The Fellowship Secretary ([email protected]). Deadline : lundi 18 avril 17h00 GMT. LANCEMENT DU PROGRAMME HETEROGENEITE TUMORALE ET ECOSYSTEME 2016 Ce Programme HTE est organisé par l’ITMO Cancer, en collaboration avec l’ITMO BCDE (Biologie cellulaire, développement et évolution) et de l’ITMO Technologies pour la santé de l’alliance nationale pour les sciences de la vie et de la santé (AVIESAN) avec l’Institut National du Cancer (INCa) et l’Inserm dans le cadre du Plan Cancer. Les objectifs du Programme sont de promouvoir la mise en place d’une masse critique aussi bien en ressources qu’en compétences afin de conduire des projets de recherche interdisciplinaires nécessitant la coopération d’équipes provenant de domaines différents, Plus d’infos ici : https://www.eva2.inserm.fr/EVA/jsp/AppelsOffres/CANCER/HFR/index_F.jsp DETAIL DES ANNONCES ET DES OFFRES DE POSTE Le poste de Maitre de conférences (MCF) « Analyse multi-échelles en Biologie du Développement » à pourvoir au Centre de Biologie du Développement (CBD) de Toulouse est maintenant ouvert (référence Galaxie 4437) Recherche : Les équipes du Centre de Biologie du Développement ambitionnent de décrypter les mécanismes fondamentaux du développement animal en particulier l’acquisition et la maintenance de l’identité cellulaire et l’organisation des cellules dans les tissus et les organes. Ces questions sont abordées à différents niveaux : expression des génomes, organisation/plasticité des cellules, des tissus dans l’organisme entier, avec divers modèles animaux (drosophile, poulet, xénope, souris, poisson zèbre), et en utilisant une gamme étendue d’approches génétiques, génomiques, biochimiques et de biologie cellulaire. Ces dernières années, l’accent a été mis sur des études systémiques et des analyses dynamiques du vivant par imagerie quantitative et en temps réel. La/le Maitre de Conférences recruté(e) renforcera une des 11 équipes du CBD en 2016, en y apportant des nouvelles compétences. Profil scientifique : Le(a) candidat(e) MCF recruté(e) sera spécialiste de l’étude multi-échelle du développement animal. Son activité visera à renforcer une équipe de recherche du CBD (UMR 5547 CNRS-UT3) par l’apport de nouvelles compétences. Une expérience dans les stratégies d’analyses à grande échelle, les techniques d’imagerie du vivant ou les stratégies innovantes en génétique serait particulièrement appréciée. Des connaissances en modélisation mathématique et biophysique des processus développementaux seront un plus pour favoriser l’interface avec les collaborateurs de l’axe Biologie computationnelle et Biologie des systèmes du Centre de Biologie Intégrative. Enseignement : Biologie du Développement, Evo-devo. Le Centre de Biologie du Développement (http://www-cbd.ups-tlse.fr/) fait partie de la Fédération « Centre de Biologie Intégrative de Toulouse » (CBI ; http://cbi-toulouse.fr/). Contact : Fabienne PITUELLO 05 61 55 67 39 [email protected] Référence Galaxie 4437 : https://www.galaxie.enseignementsuprecherche.gouv.fr/ensup/ListesPostesPublies/FIDIS/0311384L/FOPC_0311384L_4437.pdf Dépôt des candidatures du 1 Avril au 1 Mai (16h heure de Paris) 2016 - campagne emplois Enseignants‐chercheurs 2016 Université Toulouse 3 (http://www.univ-tlse3.fr/). The Center for Developmental Biology (CBD) in Toulouse (France) wishes to strengthen its research and teaching by recruiting an assistant professor in “Multiscale analyses in Developmental Biology” Research: Our goal is to understand the genetic and molecular rules governing animal development. Using vertebrate and invertebrate models (drosophila, chicken, xenopus, mouse, zebrafish), our research interests range from gene organization and evolution to cell and tissue architecture, and include the physiological/behavioral aspects of living organisms. Several groups have started studying the systemic and dynamic aspects of complex gene regulatory networks, controlling different processes such as cell and tissue morphogenesis. Likewise, studies at the cellular/tissue level and the dynamics of cell populations are now analyzed in whole embryos, larvae or juveniles, using state of the art live imaging strategies. The successful candidate will reinforce one of these groups with his/her new skills. The candidate must have expertise in multiscale analyses of animal development. Research experience in either bioinformatics or quantitative real time imaging and modeling would be an asset. Teaching: Developmental Biology and Evolution The ability to teach in French is required. The Center for Developmental Biology (http://www-cbd.ups-tlse.fr/) is a founding member of the Center for Integrative Biology in Toulouse (CBI; http://cbi-toulouse.fr/). Contact: Fabienne PITUELLO 33 (0)5 61 55 67 39 [email protected] For more information please refer to Galaxie reference 4437: https://www.galaxie.enseignementsuprecherche.gouv.fr/ensup/ListesPostesPublies/FIDIS/0311384L/FOPC_0311384L_4437.pdf Applications will be considered from April 1 to Mai 1 (16h-Paris) 2016. Please retrieve your application on the University Toulouse 3 internet site (http://www.univ-tlse3.fr/) starting on 1 April 2016. CDD Ingénieur d’étude Biologie Moléculaire/Génétique Un contrat CDD d’un an est proposé à partir de Mai 2016 pour un emploi de Ingénieur d’étude Biologie Moléculaire/Génétique dans l’équipe de Luisa Di Stefano au Centre de Biologie Integrative/Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université Paul Sabatier CNRS-LBCMCP UMR 5088, Toulouse (http://cbi-toulouse.fr/fr/equipe-di-stefano). Le ou la candidate participera à la caractérisation de nouvelles interactions génétiques entre l’histone déméthylase dLsd1 et autres régulateurs de la chromatine chez la drosophile. Activités : Assurer le développement et la réalisation d'un projet d’épigénétique, mettant en oeuvre des approches de biologie moléculaire, biochimie, génétique et microscopie confocale S'impliquer dans la formation de stagiaires et étudiants de l'équipe Diffuser et valoriser les résultats au travers de publications et présentations orales Responsabilité de la maintenance et de l’entretien des souches de drosophiles Commander les produits biologiques de l’équipe et assurer l’interaction avec les fournisseurs Compétences : Une expérience préalable en génétique de drosophile (croisement, maintien des stocks), biochimie (immunoprécipitation, western blot…), biologie moléculaire (clonage, q-PCR, préparation des ADN et ARN …) et microscopie est préférée. Savoir interpréter et diffuser des résultats scientifiques Savoir travailler en équipe Etre doté d'une bonne capacité d'organisation et d'adaptation Maitrise de l'anglais écrite et orale Aptitudes: Autonomie et sens des initiatives dans l'exercice de ses attributions Rigueur et fiabilité Sens des responsabilités. Il est demandé aux candidats de transmettre leur CV et leur lettre de motivation à Luisa Di Stefano ([email protected]). L’Université Paris Diderot et le CNRS recherchent une Directrice/un Directeur pour l’Institut Jacques Monod L'Institut Jacques Monod (UMR7592, http://www.ijm.fr) constitue l'un des principaux pôles de recherche fondamentale en biologie de la région parisienne. Composé de 31 équipes employant des organismes modèles variés, l’IJM s’organise autour de 3 thèmes de recherche (Dynamique du génome et des chromosomes, Dynamique cellulaire et signalisation, Développement et évolution) et 2 axes transversaux (Biologie quantitative et modélisation, Pathologies moléculaires et cellulaires). Les recherches interdisciplinaires, à l'interface de la physique, des mathématiques, de la chimie et de la médecine, y sont vivement encouragées. L’institut dispose de plateformes de haut niveau dans les domaines de la cytométrie en flux, de la microscopie électronique et photonique, de la protéomique, de la génomique, de la transgenèse, ainsi que de l’hébergement et l’expérimentation animale. Le(la) directeur(trice) définira la stratégie, la politique scientifique, l’animation et la cohésion scientifique. Il/elle assurera la gestion des moyens de l’Institut, décidera de leur utilisation en liaison avec les tutelles et établira des partenariats renforcés, académiques ou industriels, au niveau national et international. En parallèle, il/elle poursuivra son activité de recherche et éventuellement d’enseignement. Cette mission prendra effet au 1er janvier 2019, pour une période de 5 ans renouvelable une fois. Une intégration du (de la) futur(e) directeur(trice) et de son équipe pourra cependant être envisagée préalablement à cette date. Pourront candidater les personnes titulaires d’un poste du CNRS ou de l’Université Paris Diderot ou, sous réserve d’un détachement, d’une autre université ou d’un autre établissement de recherche. Le dossier de candidature comportant CV, lettre de motivation et notice de Titres et Travaux devra être adressé à Giuseppe Baldacci, directeur de l’Institut, avant le 15 mai 2016. Pour tout renseignement, contacter : [email protected] (tel : 33 1 57 27 81 39). Pour télécharger l’appel d’offre détaillé: https://www.dgdr.cnrs.fr/drh/cadres-sup/pdf/2016/IJM_DU-DAS5C.pdf POSTDOCTORAL POSITION IN DNA REPLICATION A postdoctoral position is open in our laboratory at the Institute of Human Genetics, CNRS, Montpellier, France. Place of work The Institute of Human Genetics (www.igh.cnrs.fr) is a modern large CNRS Institute located in the University and Hospital campus in Montpellier. Fully endowed with state-of-the-art scientific equipment, the IGH generates a stimulating and international research environment, for high-quality and intensive scientific life. The working language is English. The city is one of the most lively and concentrated areas for research scientists in France. The team Our multinational team wishes to understand how DNA replication origins are recognized, and how their organization is coordinated with the cell fate. Our model systems include cell cultures from both mouse and human cells, as well as in-vitro DNA replication systems from Xenopus eggs. Recently, our laboratory unravelled how genetic and epigenetic features shape DNA replication origin recognition and organization. The project is focused on functional aspects of metazoan DNA replication origins, using in-vivo cell systems as well as in-vitro cell systems to analyse the regulation of DNA replication and its associated factors. Some Recent publications • Fragkos, M., Ganier, O., Coulombe, P. and Méchali, M. (2015) DNA replication origin activation in space and time. Nature Rev. Mol. Cell Biol. 16, 360-374. • Cayrou C, Ballester B, Peiffer I, Fenouil R, Coulombe P, Andrau JC, van Helden J, Méchali M. (2015), The chromatin environment shapes DNA replication origin organization and defines origin classes. Genome Res., 12, 1873-1885. • Traver, S., Coulombe, P., Kitzmann, M., Peiffer, I., Hutchins, J., Latreille, D., and Méchali, M. (2014) MCM9 is Required for Mammalian DNA Mismatch Repair. Mol. Cell, 59, 831-839. • Coulombe, P., Grégoire, D., Tsanov, N., and Méchali, M. (2013) A spontaneous Cdt1 mutation in 129 mouse strains reveals a regulatory domain restraining replication licensing. Nature Com. 4, 110. • Lutzmann, M., Grey, C., Traver, S., Ganier, O., Maya-Mendoza, A., Ranisavljevic, N., Bernex, F., Nishiyama, A., Montel, N., Gavois, E., Forichon, L., de Massy, B., and Méchali, M. (2012) MCM8- and MCM9-Deficient Mice Reveal Gametogenesis Defects and Genome Instability Due to Impaired Homologous Recombination. Mol Cell. 47, 523-534. Qualification We would be glad to receive applications from highly motivated scientists, able to work independently, with a solid background in nuclear metabolism and strong expertise in molecular biology. The position is for at least two years. Please submit a curriculum vitae and contact information of two referees to Marcel Méchali, Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier, France. Tel: +33 (0) 434 359 917; e-mail: [email protected] website: www.igh.cnrs.fr./equip/mechali/ THREE POSTDOC POSITIONS IN EVO DEVO AND ECO DEVO OF HORNED BEETLES (Moczek-Lab, Indiana University, Bloomington) Three (3) full-time postdoctoral positions are available in Armin Moczek’s lab, Department of Biology, Indiana University, Bloomington. Our lab conducts research in the evolutionary developmental (evo-devo) and ecological developmental (eco-devo) biology of insects. We focus on the genetic, developmental, and ecological mechanisms, and their interactions, that mediate the origins and diversification of novel complex traits (such as beetle horns, firefly lanterns, or treehopper helmets) and functions (such as nutrition-responsive development, sexual dimorphisms, or alternative reproductive tactics). The first position will focus on identifying the genes and pathways underlying the origin and diversification of horns in the extraordinarily diverse beetle genus Onthophagus. Specifically, the work will use genomic and candidate-gene approaches to identify and functionally characterize the developmental-genetic mechanisms that regulate horn morphology (size, shape, position), context-dependent expression of horns (sex- and nutrition-specificity), and how evolutionary changes in these mechanisms have mediated diversification within and among species. The second position will utilize diverse horned beetle species and populations to explore the role of developmental plasticity in facilitating, biasing, or hindering phenotypic evolution. Focusing on morphological and physiological phenotypes, this work will combine genomic, transcriptomic, and candidate-pathway approaches to contrast ancestral and descendant patterns of gene expression and function in natural as well as mesocosm populations. The third position will explore the relative significances of - and interactions among - the horned beetle microbiome, niche construction behaviors, and nematode symbionts in the ecological radiation of horned beetles. This work will combine genomic, transcriptomic, and candidate-pathway approaches in both beetles and nematodes to characterize the role of co-development in the ecology and evolution of dung beetles, and the developmental mechanisms and evolutionary consequences of interspecific epistasis. All postdoctoral candidates would have opportunities to develop additional independent lines of research in these and related areas. We seek three collegial, self-motivated, independent, and intellectually curious individuals with recent PhDs in Evolutionary Biology, Developmental Biology, or related fields. Applicants for either position must have strong bench skills, and familiarity with techniques such as RNAinterference, qPCR, cloning, immuno-histochemistry, and the bioinformatic analyses of next-gen sequencing data is strongly desirable (though training in these techniques will also be provided as necessary). In addition, candidates must have demonstrated written and oral communication skills. Experience working with insects is helpful but not required. All three positions are initially available for 24 months, with possible extension for a third year funds permitting. Salary will be commensurate with experience, and full benefits are included. Indiana University has a large and interactive group at the interface of evolutionary and developmental biology and ecology. Bloomington is situated in scenic, hilly southern Indiana, near several parks and wilderness areas. The cultural environment provided by the University is exceptionally rich in art, music, and theater. To apply, please submit a letter of application indicating which position is being applied for, a CV, a statement of research interests, and the contact information for three references tohttps://indiana.peopleadmin.com/postings/2277 or send to Jeremy Bennett, 1001 E. Third St., Bloomington, IN 47405 ([email protected]). Review of applications will start immediately and will continue until positions are filled. Preferred start date is July '16 (position #1) and September '16 (positions #2,3) though some flexibility exists. Inquiries about each position can be directed to Armin Moczek ([email protected]). Additional information about research in the Moczek lab can be found at http://ecoevodevo.com/. Indiana University is an Equal Employment and Affirmative Action employer and a provider of ADA services. All qualified applicants will receive consideration for employment without regard to age, ethnicity, color, race, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status. Programme doctoral Interfaces pour le Vivant 2016 Projet MORPHOSHARK ____________________________________________________________________________ MORPHOSHARK: MULTI-SCALE ANALYSIS OF EARLY MORPHOGENESIS IN A NON-CONVENTIONAL VERTEBRATE MODEL, THE CATSHARK S. CANICULA Open position for an interdisciplinary collaborative PhD project focusing on early morphogenesis in a non-conventional vertebrate model organism (catshark, cartilaginous fish). The project relies on a combination of computational modeling, 4D imaging and developmental genetic analysis. It will be conducted in the Integrative Biology of Marine Organisms lab (CNRS UMR7232) in Banyuls, France. It will benefit from the local support of marine facilities and the Banyuls outpost of the BioEmergences platform (CNRS USR3695, Dir. Nadine Peyriéras), including an unlimited access to on-site dedicated confocal facilities and expertise in 4D imaging and modelling. It will be co-supervised by Sylvie Mazan, Observatoire Océanologique, Banyuls, France, and René Doursat, Manchester Metropolitan University, UK. Applications should be sent before the 4th of April to Sylvie Mazan ([email protected]) and René Doursat ([email protected]), who will submit the application of the selected candidate to the Interfaces Pour le Vivant (IPV) Doctoral School (deadline 16th April). The final selection of the candidate will involve an oral presentation to the IPV committee (19th-20th May). Summary Understanding how variations in individual cell behaviours can drive the overwhelming diversification of embryonic forms across metazoans is a major challenge of modern biology. The project addresses this general issue, focussing on the variability of early embryonic architectures in vertebrates and using an interdisciplinary approach at the crossroads of evolutionary developmental biology, physics and bioinformatics. Its general objective is to generate a theoretical model connecting a quantified characterization of individual cell behaviours to tissue deformations and global embryo growth during early development in a non-conventional model, the catshark S. canicula. At blastula-gastrula stages, it exhibits complex cell movements, similar to zebrafish (epiboly), amphibians (involution) and amniotes (ingressions). This makes it a unique model for comparisons with established vertebrate models and the reconstruction of the gnathostome ancestral state. The project will rely on four tasks: (i) obtaining a quantified description of cell behaviours during catshark early development using fluorescence live imaging; (ii) constructing a molecular and cellular atlas of the early catshark embryo also integrating genetic expression profiles; (iii) building a multi-scale model connecting individual cell behaviours to global shape changes of the blastoderm using the multi-agent based modelling platform MecaGen (developed by the co-supervisor); (iv) testing the model by the introduction of controlled experimental perturbations of early morphogenesis. The thesis supervision will be ensured by S. Mazan, a developmental biologist specialist of early development in the catshark, and R. Doursat, who has a strong background in the modeling of morphogenesis. The recruited student will also benefit from the support of the Banyuls outpost of the BioEmergences platform, including an unlimited access to on-site dedicated confocal facilities and expertise in 4D imaging and modelling. 1 1. Context: a quantitative and evolutionary approach of morphogenesis From cell behaviours to embryo construction. Understanding how individual cell behaviours shape embryonic structures in a coordinated fashion is a central question of developmental biology (reviewed in [1]). In the past ten years, this field has been deeply impacted by major advances in in vivo imaging, especially the development of novel, genetically encoded or engineered fluorescent probes and of innovative microscopy techniques, leading to higher spatio-temporal resolution, larger fields of data acquisition, minimal damage to living specimens and direct measurement of local mechanical forces [2-4]. These technical advances were accompanied by new concepts and methods, such as quantitative image analysis workflows and computational models that integrate cell genetic properties and behaviours to predict tissue deformations during development. The combination of these approaches at the crossroads of physics, bioinformatics and biology has led to breakthroughs in our understanding of cell behaviours during early development [5-9]. As they allow quantitative descriptions of cell behaviours, they also open novel perspectives to bridge the gap between cell behaviours and the morphogenesis of a whole organ, or embryo. The evolution of early morphogenesis: the catshark reference. These innovations have also paved the way to another, related major challenge of modern developmental biology, understanding how variations of individual cell behaviours and the diversification of embryonic forms are coordinated during evolution. Early development in vertebrates provides an excellent paradigm to explore this issue. Early embryonic architectures indeed extensively vary across the taxon, depending on the mode of embryonic nutrition and yolk expansion [10,11]. How individual cell behaviours and genetic regulatory networks are concomitantly modified remains poorly understood. The catshark Scyliorhinus canicula unites a number of interesting characteristics to address this issue: as a member of cartilaginous fishes, it holds a reference phylogenetic position for an evolutionary approach, relying on a phylogenetic reconstruction of ancestral gnathostome characteristics [12,13] the early embryo is endowed with a relatively simple geometry, which can be easily modelled (as a growing oval shaped blastodisc, comprising two cell sheets: a superficial, epithelial-like one and a deep one of endodermal identity [14] early development involves complex cell movements including epiboly, involution and ingression, thus exhibiting similarities with each of the major osteichthyan model organisms [15,16] most importantly, the catshark is amenable to molecular and functional approaches and pioneering experiments conducted in collaboration between the Mazan group and USR 3695 BioEmergences (Dir. N. Peyriéras) have validated it as a suitable model organism for 4D imaging analyses (Figure 1). Figure 1: Example of 4D imaging raw data showing axis formation in the catshark during early gastrulation. The territory shown corresponds to the anterior neural plate at stage 13. Images were obtained following Syto16 nuclear labelling. Arrows represent represent averaged displacement vector fields from stage 12 to 12+, the length and colour being related to the intensity of the displacement in the time window studied (unpublished data obtained by R. Lagadec, Mazan group, and B. Rizzi, Peyriéras group, using the BioEmergences platform confocal equipment and image analysis tools). 2. Objectives General objective. The general aim of this project is to generate, for the first time in a chondrichthyan, a theoretical model connecting a quantified characterization of individual cell behaviours to global embryo growth and deformation. This requires an interdisciplinary approach, gathering complementary expertise in developmental genetics, bioinformatics, and modelling. The general strategy proposed will consist of obtaining first a global description of the local properties (cells behaviours and characteristics) of the embryo integrating time and space, in order to delineate cell clusters sharing related properties and design a relevant geometrical model. This information will be used to generate a higher level model of development integrating time and space, which will be proofed by the introduction of experimental perturbations in the system. Specific objectives. The project will aim at four specific objectives: 2.1. Optimize 4D imaging techniques and obtain a quantified description of cell behaviours during catshark early development. Our preliminary tests show the feasibility of 4D imaging analysis of the superficial layer development in the catshark. This part of the work will aim at (i) an optimization of the conditions of data acquisition and (ii) a comprehensive description of local cell behaviours and characteristics. We will additionally 2 test the possibility to conduct a similar analysis in the deep cell layer, which may be involved in the control of superficial cell movements. 2.2. Create a molecular and cellular atlas of catshark early development. A higher level description of the early catshark embryo requires a comprehensive and dynamic description of local cellular and molecular characteristics of the developing superficial layer. This part of the work will aim at creating a map of this layer, integrating signalling activities, genetic expression data and quantified cell behaviours and characteristics determined as part of objective 1 at the stages studied. This descriptive step is crucial to partition the embryo into relevant subdivisions, exhibiting similar cellular and molecular characteristics [14]. 2.3. Build a semantic and geometric model of early morphogenesis in the catshak. This will rely on the generation of a mechanistic digital model, using the MecaGen platform [17,18]. Considering its specific characteristics (large embryo size, slow development), modelling the dynamics of the catshark early embryo implies the development of original methods of classification and quantification. This will be linked to high-level spatial reasoning in order to create an automated, intuitive, yet realistic description of morphogenesis. 2.4. Develop functional tools to test the model. The power of any model relies in its predictive potential. This part of the project aims at assessing this potential, by testing whether theoretically predicted effects match those observed in vivo, following controlled experimental perturbations. 3. Work program and methodology 3.1. Fluorescence live imaging of early catshark embryos. This part of the work will be conducted in collaboration with the BioEmergences platform, using the platform imaging facilities settled in the Banyuls Marine station. Its feasibility has been validated by tests conducted in collaboration between the Mazan and Peyriéras groups. Briefly, various concentrations of the nuclear dye Syto 16 were injected in ovo through the shell. Following a one hour incubation, the upper third of the eggshell was removed, thus exposing the labelled embryo, which developed for extended periods at 17°C in these conditions. Time-lapse imaging (interval=15 mn) was conducted on a Leica SP8 multiphoton microscope at 17°C, at x20 magnification (1NA, water dipping lens). In order to optimize these conditions, a set of additional dyes labelling nuclei and membranes will be tested at various concentrations. The trade-off between field size and resolution will also be assessed, in order to maximize the former while retaining the possibility to track single cells. The second phase of the work will aim at data acquisition and analysis from the earliest accessible blastula stages to the start of mesendoderm involution. We will more specifically focus on cell division rates and planes, cell displacements, ingressions and apoptosis. Data will be collected in different sectors of the blastodisc (anterior/lateral/posterior; medial/marginal) from stages 6 to 11, from 5-10 embryos in order to assess inter-individual variations. This part of the work will be conducted using a Leica SP8 microscope and advanced software tools developed by the BioEmergences platform. These algorithms support the automated analysis and reconstruction of collective cell movements based on time-lapse microscopy of organism development. We expect from these studies a precise map of cell behaviours and tissue flows and deformation during gastrulation. 3.2. Constructing a molecular and cellular atlas of the early catshark embryo. Expression characterizations of key candidate regional markers have already been conducted, suggesting a dynamic partitioning of the early blastoderm in at least three sectors at stages 6-9 (anterior, posterior-medial, posterior-marginal) and 4 at stage 10 (with the individualization of an additional posterior-marginal territory: [13-16]). This molecular characterization will be extended to components of signalling pathways known to control cell movements (Wnt-PCP, FGF, Sphingosine-1-Phosphate, CXCR-SDF) and markers of cell junctions, cell polarity and cell adhesion. In the absence of transgenic tools in the catshark, this analysis will rely on in situ hybridization and immunohistochemistry, which should allow a partitioning of the blastodisc in sectors, exhibiting similar molecular properties. While this does not allow a single cell resolution, this is a reasonable strategy in view of embryo size and slow development. 3.3. Developing a multi-scale model connecting cell individual behaviours to global shape changes of the blastoderm. This part of the project will rely on (1) the implementation of a higher level system clustering cell populations exhibiting similar properties (kinematics and gene expression) and (2) an integration of the data into the MecaGen platform developed by the Peyriéras group [17]. The data reconstruction stage provided by BioEmergences can be followed by agent-based modelling and simulation with MecaGen. Embryogenesis is viewed here as an emergent, self-organized phenomenon based on the individual behaviour of a large number of cells, via their genetically regulated, and regulating, biomechanical behaviour. Cells’ mechanical properties (such as division rate, adhesion strength, or intrinsic motility) are closely correlated with their spatial location and temporal state of genetic and molecular dynamics (such as internal protein and external ligand concentrations) and affect each other concurrently. MecaGen has already been applied to the exploration of the different morphogenetic episodes occurring through the first 10 hours of the zebrafish and sea urchin development: egg cell cleavage, enveloping layer formation, epiboly, endomesoderm internalization and convergence-extension [17,18]. 3 Modeling high-level cell behaviours: In order to build a multi-scale model for development, the semantic aspect is important since it is the essential link between purely numerical aspects and biology. We propose the development of both analysis and modeling methodologies. The analysis will summarize numerical aspects into a semantic description, by mainly clustering cells showing similar displacements and/or similar molecular content, and inferring spatial relationship between these clusters (“close”, “touching”, “surrounding”, …). The subsequent model based on semantic description of cells aggregates and relationships between them will be translated into numerical components into the MecaGen program. We will use different methodologies for analysis and modeling the different scales: cellular scale (Mereotopology: [19]), tissue scale (graphs or α-shapes: [20]) and global scale (spatial statistics: [21]). We already successfully developed a model of multi-scale organization of cells and tissues mixing mereotopology (how cells are organized one to another) and spatial statistics (global pattern of spatial distribution, random, aggregated or uniform). We will apply these methodologies to study cell behaviours and extend it to temporal aspects. 3.4. Implementation of functional approaches. This phase aims at coupling 4D imaging with the introduction of controlled experimental perturbations of development. The former will rely on pharmacological treatments directed against candidate signaling pathways, known to control morphogenesis and cell movements. We now routinely conduct such approaches by drug injections in ovo. We will adapt these conditions by direct addition of pharmacological reagents on top of the developing embryo during 4D image acquisitions. Nodal signaling loss-of-function, which results in a well-characterized molecular phenotype (loss of posterior margin identity: [15]) will be taken as a positive control. This pathway may also be involved in the control of morphogenesis, as suggested by other abnormalities observed (larger blastoderm size than in control embryos, absence of posterior thickening). 4. Perspectives Beyond the specific objectives mentioned above, this program will open new challenges. First, we anticipate that it will allow an accurate delimitation of embryonic territories from blastula to gastrula stages with unprecedented resolution, in both time and space. This should pave the way for transcriptomic characterization, a technique of choice in the catshark considering its embryo size, which could allow the identification of novel molecular actors involved in these processes. Second, the imaging and modelling tools developed for the catshark will be of more general application in species displaying a large embryo size and slow development. Such features have generally been counter-selected in traditional model organisms but they prevail in many emergent models, which currently raise a growing interest in parallel with the acceleration of sequencing techniques, also amenable to a wide range of species. 5. Student supervision The thesis supervision will be ensured by S. Mazan, a developmental biologist specialist of catshark early development [12-16;22-27], and R. Doursat (http://doursat.free.fr), who has a strong background in the modeling of morphogenesis. The recruited student will benefit from the support of the Banyuls outpost of the BioEmergences platform, including unlimited access to on-site dedicated confocal facilities and expertise in 4D imaging and modelling. 6. References [1] Keller R. 2012. Science 338 :201-3 [2] Luengo-Oroz et al. 2011. Curr. Opin. Genet. Dev. 21:630-7. [3] Pantazis & Supatto. 2014. Nat.Rev. Mol. Cell Biol. 15:327-39. [4] Oates et al. 2009. Nat. Rev. Genet. 10:517-30. [5] Keller et al. 2008. Science 322:1065-9 [6] Olivier et al. 2010. Science 329:967-71 [7] Castro-Gonzalez et al. 2014. PLoS Comput. Biol. 10:e1003670. [8] Ichikawa et al. 2013. PLoS One 8:e64506. [9] Voiculescu et al. 2014. Elife 3:e01817. [10] Arendt and Nübler-Jung. 1999. Mech. Dev. 81:3-22. [11] Irie and Kuratani. 2011. Nature Commun. 2:248. [12]. Coolen et al. 2008. CSH Protoc. doi: 10.1101/pdb.emo111 [13] Coolen et al. 2007. PLoS One 2:e374 [14] Godard and Mazan. 2013. J. Anat. 222:56-66 [15] Godard et al. 2014. Biology Open. 3:1098-1107 [16] Sauka-Spengler et al. 2003. Dev. Biol. 263:296-307 [17]. Delile et al. 2013. In Computational Systems Biology, 2nd edition, A. Kriete & R. Eils, eds.: pp. 359-405. Academic Press, Elsevier, ISBN 978-0-124-05926-9 [18] Faure et al. 2016. Nature Commun. 7:8674. [19] Randell et al. 2012. IEEE Trans. Pattern Anal. Mach. Intell. 3 :568-581. [20] Loménie and Racoceanu. 2012. J. Pattern Recognition. 45:2894-2911 [21] Andrey et al. 2010. PLOS Comput. Biol. 6: e1000853 [22] Lagadec et al. 2015. Nature Commun. 6:6686 [23] Falcon et al. 2014. PNAS 111:314-319. [24] Campo-Paysaa et al. 2015. EvoDevo 6:18 [26] Santos-Dran et al. 2015. Front Neuroanat. 9:37 [27] Tulenko et al. 2016. Scientific Reports in press. 4 PhD position opened in Switzerland for a developmental / cell biologist Evolutionary developmental genetics of reptile skin colour In the context of evolutionary developmental biology analyses of reptilian skin colours and colour patterns, we offer one PhD position for an outstanding, highly motivated, and creative experimental wet-lab biologist with strong skills in developmental biology and cell biology. Michel Milinkovitch’s group at the University of Geneva (UNIGE) integrates the expertise of developmental biologists, evolutionary biologists, computer scientists and physicists for an improved understanding of the mechanisms generating a diversity of skin colours and colour patterns in reptiles. We have recently shown (Saenko et al. 2013) that the extensive variation of skin colours and patterns in Sauropsida reptiles is generated by precise co-localisation of interacting pigmentary and nano-structural elements. In this framework, we have also shown (Teyssier et al. 2015) that chameleons shift colour through active tuning of a lattice of guanine nanocrystals, which photonic effect is filtered by a layer of pigments. In addition, we have built extensive transcriptomic and genomic resources (Ullate-Agote et al. 2014; Tzika et al. 2015) for mapping colour mutations in our new model species of snakes and lizards. For example, we recently mapped and identified the mutation responsible for the amelanistic mutation in corn snakes (Saenko et al. 2015). The successful candidate will (i) participate to linkage mapping of multiple colour and colour pattern mutations in snakes and lizards and (ii) use molecular/cell/developmental biology methods (microscopy, immuno-histochemistry, in-situ hybridisation, transcriptomics, in-vivo assays, ex-vivo cultures, etc.) to characterise the effects of these mutations on neural-crest cell migration, as well as on the physiology of pigmentary and structural-colour cells. The new PhD student will also interact with a physicist PhD student who is mathematically modelling the reaction-diffusion processes that generate colour patterns in snakes and lizards. Candidates must have a Master in biology or biochemistry. Skills and experience with developmental biology and/or cell biology are mandatory. Skills in biophysics are useful. The successful candidate will have a genuine interest for organismal biology and will appreciate interactions with physicists and computer scientists. The University of Geneva (UNIGE) is world-renowned for its research in Biology and Physics. UNIGE is among the top 1% best th universities in the world and the Faculty of Sciences is ranked 32 world best (Shangai Academic Ranking of World Universities). PhD students are remunerated according to the standards of UNIGE, which are very generous when compared to other international programs. Geneva is an international city occupying a privileged geographical situation. Candidates must send their application - in the form of a single PDF file including a brief letter of interest, a CV, as well as contact information (not support letters) of two persons of reference - to: Prof. Michel Milinkovitch ([email protected]), Laboratory of Artificial & Natural Evolution (www.lanevol.org), University of Geneva, Switzerland. Refs: Saenko, Teyssier, van der Marel & Milinkovitch. Precise colocalization of interacting structural and pigmentary elements generates extensive color pattern variation in Phelsuma lizards. BMC Biology 2013, 11: 105; Teyssier Saenko van der Marel & Milinkovitch. Photonic Crystals Cause Active Colour Change in Chameleons. Nature Communications 6: 6368 (2015); Tzika, UllateAgote, Grbic & Milinkovitch. Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics. Genome Biol. Evol. 7: 1827-1841 (2015); Ullate-Agote, Milinkovitch & Tzika. The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates. Int. J. Dev. Biol. 58: 881-888 (2014); Saenko, Lamichhaney, Martinez Barrio, Rafati, Andersson & Milinkovitch. Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene. Scientific Reports 5, 17118 (2015) Integrative and quantitative biology network The INFORM program sets up an interdisciplinary consortium gathering 11 groups from 4 research institutes on campus (IBDM, CIML, LAI, AFM). The objective is to understand, through collaborations between biologists and physicists, the biochemical and mechanical basis of cell signaling in both normal and pathological conditions. Developmental Biology Institute of Marseille Centre for Immunology of Marseille Luminy Laboratory of Adhesion and Inflamation Structure and Assembly of membrane proteins by Atomic Force Microscopy For this purpose, we aim at: u u u u Developing innovative quantitative imaging techniques Developing new tools to monitor signaling in vivo Building quantitative models of signaling Linking these models with physiological functions We seek to build an interdisciplinary research community through a combination of: u Collaborative research projects u Innovative training u International networking through workshops and seminars The Labex INFORM is looking for talented and highly motivated students interested in interdisciplinary approaches to decipher biological processes (please visit the website for more details on the research projects). Students with background in biology, physics, engineering or applied mathematics/informatics, are highly encouraged to apply. Students enrolled in the PhD Program at the Labex INFORM will benefit of a three year fully funded fellowship starting October, travelling fellowship, specific training and personal mentoring in extremely well resourced laboratories with state of the art core technology facilities. http://labexinform.com/ BIOTRAIL The Labex INFORM supports the Biotrail program in the frame of the Académie d’excellence, Aix-Marseille Université. INFORM Labex is funded by the « Investissements d’Avenir » French Government program managed by the French National Research Agency (ANR-11-LABX-0054). http://sciences.univ-amu.fr/biotrail Biology at diff erent Sc ales The school will focus on the interplay between physics and biology to describe and understand biology at different scales, from the molecular level to cells and living organisms. The school is aimed at PhD students and early-stage researchers. Participants will learn how a biological problem can be tackled using an integrated approach, going from atomic resolution to a whole organism level. The school also aims at showing how physics and mathematics can contribute to model biological processes.! 13-25 March 2017! Interplay between physics and integrative biology… …illustrated on two research fields Les Houches Winter school Chamonix Links between cellular and structural biology! Cell and tissue morphogenesis! Remodeling of membranes and transport processes at ! !mesoscopic and molecular scales!!!!! Concepts and methods from physics applied to biology! Preliminary program! Plant morphogenesis from genes to flowers ! ! ! ! François Parcy (Grenoble) Floral development: bridging atomic and genomic scales (3 lectures)! Exocytosis and morphology of the synapse ! Olivier Hamant (Lyon) Forces in plant development (3 lectures)! ! Christophe Godin (Montpellier) Virtual plants: An introduction to modeling flower bud (3 lectures)! ! Dolf Weijers (Wageningen) Integrated biology of auxin (2 lectures)! ! + Seminars ! Michael Kozlov (Tel Aviv) Physical models of membrane shaping with the exocytosis of synaptic vesicles as an example (3 lectures)! Patricia Bassereau (Paris) Role of proteins in membrane remodeling, theory and experiments (3 lectures)! Reinhard Jahn (Göttingen) Molecular mechanisms of neuronal exocytosis (including different types of microscopies) (3 lectures)! Dirk-Jan Slotboom (Groningen) Membrane transporters: structure, dynamics and function (2 lectures)! Werner Kühlbrandt (Frankfurt, to be confirmed) The revolution in electron microscopy Organized by R. Jahn, H. Nury, F. Parcy, E.Pebay-Peyroula Contact: [email protected] More on Les Houches: http://www.leshouches.ujf-grenoble.fr Offre de séjour pour chercheurs confirmés au Churchill College, Cambridge Le Service pour la Science et la Technologie de l’Ambassade de France au Royaume-Uni offre chaque année la possibilité à des chercheurs confirmés français de séjourner au Churchill College à Cambridge pour une durée allant de 6 à 11 mois, afin d’effectuer une activité de recherche dans cette prestigieuse université. Les chercheurs retenus participeront à toutes les activités du College en tant que « French Government Fellows », soit comme « By-Fellows », soit comme « Overseas Fellows », selon leur niveau académique. Les frais d’hébergement sont pris en charge par l’Ambassade à travers une convention avec le College, les salaires restant à la charge de l’établissement d’origine des chercheurs. Les candidatures sont ouvertes pour deux postes pour l’année académique 2016-2017. Il n’y a aucune restriction sur les disciplines, étant toutefois précisé que Churchill College est un College particulièrement dédié aux sciences, à la technologie et à l’ingénierie. Le dossier de candidature devra obligatoirement comprendre les éléments suivants : une lettre de motivation, avec la durée souhaitée de son séjour une lettre d’invitation du laboratoire d’accueil à Cambridge un CV avec liste des publications une présentation en trois pages maximum du projet de recherche et des retombées attendues l’indication du nom de deux collègues (britannique et/ou français) pouvant servir de référents et susceptibles d’être contactés par le College. Les frais d’hébergement du chercheur, et le cas échéant de sa famille, ainsi que les frais d’électricité sont pris en charge par le Service pour la Science et la Technologie. Seules les factures téléphoniques sont à la charge du futur Fellow. Durant son séjour, le chercheur a accès aux services et installations du Collège : salle de sport, salle des professeurs, bibliothèque, etc. Il dispose également d’une carte universitaire qui lui permet de bénéficier de tarifs réduits pour les transports en commun, entre autres. Il a accès à la salle à manger du College, et bénéficie d’un certain nombre de dîners gratuits. A la fin de son séjour, il bénéficiera à vie de certains de ces privilèges. Pour plus d’information, cf.le site du College http://www.chu.cam.ac.uk/) ou contacter The Bursar ([email protected] ou The Fellowship Secretary ([email protected]). A noter toutefois que certains départements scientifiques de l’Université peuvent être amenés à facturer des frais d’accueil (bench fees) non couverts par ce financement. L’attention des candidats est donc appelée sur la nécessité pour eux de bien veiller à leurs conditions d’accueil dans leur département de rattachement. Candidature : L’ensemble des documents, rédigés en anglais uniquement, devra parvenir au Service pour la Science et la Technologie de l’Ambassade de France au Royaume-Uni par voie électronique à l’attention de M. Cyrille van Effenterre à l’adresse suivante : [email protected]. La date limite de dépôt des dossiers de candidature est fixée au lundi 18 avril 17h00 GMT. Les candidatures retenues par le Churchill College seront directement notifiées par celui-ci courant mai. Cyrille van EFFENTERRE, Conseiller pour la Science et la Technologie, 6 Cromwell Place, London, SW7 2JN. Tél : +44 20 7073 1391.
