2019-07-Paris

PhD thesis in machine learning and image analysis methods development for cryo-electron microscopy
Context
Focus
The PhD thesis will be focused on machine learning and image analysis methods development for studying conformational variability of biomolecular complexes by cryo-electron microscopy.
Activities
The candidate will work on the development of methods combining machine learning with cryo-electron microscopy image processing and molecular mechanics simulation for studying continuous conformational changes of various biomolecular complexes, building on a previous work of the team on this topic (https://doi.org/10.1016/j.str.2014.01.004 ; https://doi.org/10.1016/j.bpj.2016.03.019 ; https://doi.org/10.1016/j.sbi.2016.12.011).
Skills
- Strong background in Machine Learning, Image Processing, Computer Vision or related fields
- Strong programming skills
- Creative mind
- Interest in machine learning and image processing for life sciences
Work Context
The candidate will work in the context of an ANR funded project. The work will be performed at the Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC-UMR 7590, Sorbonne Université, 75005 Paris), a joint research unit of the CNRS, the Sorbonne Université, and the Muséum National d'Histoire Naturelle, counting around 200 members. The IMPMC is a highly pluridisciplinary laboratory, with teams composed of researchers, researchers-teachers, and engineers with different backgrounds (physics, Earth science, biology, chemistry, computer science, electrical and mechanical engineering, etc.). The laboratory keeps the balance between the experimental and theoretical research regarding different topics such as elucidation of the structure of materials and macromolecular assemblages, investigation of their dynamic properties, study of interactions between the living world and the mineral world, etc.
Contract duration: 36 months
Thesis director: Slavica Jonic
http://www.impmc.upmc.fr/~jonic
Application
Documents to be provided by the applicant:
- CV
- Motivation letter
- Name and contact details of at least one reference
The applications should be sent to: Slavica.Jonic@upmc.fr

2019-06-Wageningen/Jouy-en-Josas

Novel universal delivery systems for mucosal vaccination: a whole-body approach for application in warm water fish
Context
Aquaculture is the fastest growing food-producing sector worldwide. However, aquaculture has to face the impact of infectious diseases and establishing prophylactic and therapeutic strategies is of utmost importance, especially within One Heath context1.
Currently, most effective vaccines for aquaculture species are delivered by injection. However, injection is associated with handling stress and local side effects. Although, mucosal vaccination of farmed fish, e.g. via immersion, would be preferred, it generally triggers only weak and/or short-lasting protection. The problem is that mucosal surfaces (skin, gills, intestine), have an intrinsic irresponsiveness referred to as ‘mucosal tolerance’. The mechanisms underlining mucosal tolerance in fish and the conditions required to overcome tolerance are largely unknown. In humans and veterinary species, live recombinant viral vectors are very effective, representing the latest generation of mucosal vaccines.
Our interdisciplinary project combines novel vaccine technology never used in fish before with whole-body advanced high-resolution microscopy in the context of a long-standing collaboration between the laboratories of the involved Partners. This will allow us to 1) develop novel mucosal vaccines against warm-water fish pathogens, and 2) provide a whole-body analysis of vaccine delivery and mucosal responses to immersion vaccination in an adult fish.
For the in vivo selection of promising candidates and detailed analysis of mucosal response, we will use transgenic zebrafish marking relevant leukocyte subpopulations. Their small size and transparency, combined with high-resolution real-time microscopy, will allow visualization of antigen capture, leukocyte recruitment, antigen presentation, and cell-cell interactions at mucosal sites after vaccination. Finally, we will provide the proof-of-principle of the efficacy of selected candidates in a commercially relevant warm water species, common carp.
Project
Your main tasks:
- Synthesis of antigens and nucleic acids vaccines using molecular biology and virology approaches applied to live viral vectors and/or replicon particles.
- Development and optimisation of delivery strategies in larval and adult zebrafish
- Selection and characterization of promising vaccine candidates using advanced microscopy approaches in transgenic zebrafish lines marking immune cells.
- Description of antigen, vaccine biodistribution and associated immune response (ie Antigen capture, leukocyte recruitment and cell-cell interactions with APC) in targeted mucosal tissues using real-time imaging combined with 3D deep imaging on cleared tissue post vaccination.
- Establishment of proof-of-principle of the efficacy of selected candidates in common carp used as a commercially relevant warm water species.
Application
We require:
• an MSc in (Medical) Biotechnology, Molecular Life Sciences, Biology or equivalent.
• good proficiency of written and spoken English language (fulfilment of the IELT test is a prerequisite to start in the PhD program).
• excellent presentation and communication skills
• excellent project and time management skills
• an interest in working with in vivo animal models and microscopy.
• enthusiasm in working in a very international team and in two countries (The Netherlands and France)
Research teams: you will perform approximately 50% of your work at the Cell Biology and Immunology Group (CBI) of Wageningen University and Research (WUR, the bets University of the Netherlands for 14 consecutive years) and 50% at the Fish Infection and Immunity team of INRA, Jouy-en-Josas (France, the top Agricultural Institute in France); the project is also in collaboration with the Virology group of the Wageningen Bioveterinary Research (WBVR) in Lelystad (the reference institute for animal health in the Netherlands, also equipped with unique BSLIII facilities).

You can only apply via the website of Wageningen University & Research https://www.wur.nl/en/Jobs/Vacancies.htm or https://www.academictransfer.com/en/. Please include a cover letter (max. 1 A4) with a statement of research interests, explanation of your motivation and suitability for the project, a CV, and names and contact information of at least two professional references who can document the applicant is self-motivated and can work independently.
For additional questions regarding the project, you can contact Dr. Maria Forlenza: maria.forlenza@wur.nl. Applications via e-mails are not eligible.
Applications will be open until the 30th of August 2019. The candidate should be available to start preferably by the 1st of December 2019.

2019-06-Marseille/Montpellier

Development of enhanced TIRF microscopy to study the dynamics of viral assembly at the single molecule level
Context
The plasma membrane is the exit or the entry gate of many intracellular pathogens (bacteria, viruses). These processes have a precise temporality and they are spatially regulated at the scale of a few molecules. Recent optical microscopy methods have allowed to measure the
dynamics and the localization of these molecules at the membrane of living host cells, leading to a strong input in the understanding of these mechanisms. Amongst these optical microscopy methods, evanescent field excitation microscopies (such as TIRF microscopy) have been implemented in a multimode way (space, time) this last decade, either by analyzing temporal fluctuations of these molecules (Im-FCS) or by using a spatial super resolution approach combined to trajectories analyses of single molecules (spt-PALM). However, these methods suffer from their weak sensitivities.
Project
The main goal of this thesis is to drastically improve this sensitivity in order to locate and track these molecules with high spatial and temporal accuracy. For this purpose, we will use resonant multi-dielectric stacks. The enhancement of the local field induced by the stacking will allow a sharp increase in this sensitivity over the entire cell surface and thus an improvement in the pointing accuracy (~ 10 nm) or temporal resolution (<1 ms) of these single molecules positions and motions. This enhanced excitation will open new perspectives not only for monitoring virus assemblies in the cell at the single molecule level but also in numerous other applications.
This thesis is an interdisciplinary thesis supervised by an experimentalist physicist (Aude Lereu / Institut Fresnel) and a biophysicist/biologists (Cyril Favard / IRIM). The position is funded for three years (36 months) by the CNRS. The CNRS is an equal opportunity employer and supports gender equality.
Application
We are looking for a highly motivated and excellent candidate with a strong background in general physics, optics and microscopy and a commitment for technological applications, and a strong interest in understanding molecular mechanisms occurring in cell biology/virology. For this position, the candidate is expected to be enthusiastic about a collaborative interdisciplinary environment. Programing skills will be an added value. The candidate will be mainly located in Marseilles for the 6/8 first months of the contract and then move to Montpellier during the 28/30 last months. If your profile matches the description, please send your application including all documents (motivation letter, CV and contact details) until August 31, 2019 preferably by e-mail in a single pdf file.
For further information please contact: Cyril Favard e-mail: cyril.favard@irim.cnrs.fr  Aude Lereu e-mail: aude.lereu@fresnel.fr

2019-06-Paris

Deep learning for advanced microscopy
Context
Deep learning (machine learning using artificial neural networks) is at the core of the currentrenaissance of artificial intelligence (AI) and holds great potential for addressing outstanding questions and technical bottlenecks in life science and medicine.
Our lab is applying and adapting state-of-the-art deep learning methods to selected topics in the fields of biophysics, advanced microscopy, and medicine (see e.g. Ouyang et al. 2018, Samacoits et al. 2018; Ouyang et al. 2019).
Project
We propose to study these new behaviors in the framework of a PhD. Diffrerent aspects of the cell/nanoparticle interaction will be addressed:
- the modulation of the interaction force between particles and surfaces, the modification of surface chemistry, particle size and density.
- the biochemical response triggered by the particle monolayer, the behavior of different cell types in regard to nanoparticle coatings and the caracterization of the pathways involved in the internatization process.
This work at the interface between cell biology and material science will give a dual competency to the student.
Application
In general, we are always looking for highly motivated individuals with a strong background in one or more of the following or related fields:
• physics, biophysics
• applied mathematics, computer science, image processing, AI
• light microscopy
• cell biology
For questions or applications please contact Christophe Zimmer: czimmer@pasteur.fr
Unité Imagerie et Modélisation CNRS UMR 3691 Département de Biologie Cellulaire et Infections Institut Pasteur 25, rue du Docteur Roux 75015 Paris France

2019-05-Mulhouse

Cellular internalization mechanism of nanoparticle-based coatings
Context
Interaction between cells and micro or nanoparticles is a topic still widely discused in the literature, especially in the frame of the internalization process and biochemical response of the cell. This question concerns the developpement of new biomaterials as well as therapeutical strategies and public healt in the cace of exposure and dispersion of nanoobjects. The most common configuration for studying these interactions is when cells and particles are both dispersed in solution. Cells interacting with particles already adsorbed on a surface is never considerd. It is however representative of many situations such as particlebased biofunctionnal coatings or particles adorbed on tissues for example. This configuiration also modelizes interactions between cells and adosrbed bacteria or any other adsorbed pathogenes. Our first results on the interactions between macrophages and silica particles monolayers (diameter ranging from 30 nm to 450 nm diameter) have shown internalization efficiencies remarkably different from those obtained with particles in solution.
Project
We propose to study these new behaviors in the framework of a PhD. Diffrerent aspects of the cell/nanoparticle interaction will be addressed:
- the modulation of the interaction force between particles and surfaces, the modification of surface chemistry, particle size and density.
- the biochemical response triggered by the particle monolayer, the behavior of different cell types in regard to nanoparticle coatings and the caracterization of the pathways involved in the internatization process.
This work at the interface between cell biology and material science will give a dual competency to the student.
Application
LAURENT VONNA – LAURENT PIEUCHOT
IS2M, 15 RUE JEAN STARCKY, 68057 MULHOUSE CEDEX
E-MAIL : LAURENT.VONNA@UHA.FR OU LAURENT.PIEUCHOT@UHA.FR

2019-05-Illkirch

Validation et optimisation de nouvelles sondes fluorogéniques pour l’imagerie super-résolutive DNAPAINT
Projet
L’émergence des microscopies super-résolutives a transformé en profondeur la recherche en biologie cellulaire et moléculaire en permettant de visualiser de structures et organelles sous la limite de diffraction de la lumière. Parmi les principales variantes, les microscopies de super-localisation PALM (photoactivatable and photoconvertible localization microscopy) et dSTORM (direct stochastic optical reconstruction microscopy) sont particulièrement performantes, permettant des résolutions de l’ordre d’une dizaine de nanomètres. Toutefois, l’une des principales limites de ces approches est la maitrise du clignotement stochastique des marqueurs fluorescents. Une variante est la technique DNA-PAINT (accumulation de points pour une imagerie topographique à l’échelle nanométrique) qui exploite l’hybridation transitoire programmable de brins d’ADN fluorescents courts (brins d’ADN imageurs) à un brin complémentaire lié de manière covalente à une cible. L’ADN imageur lié de façon transitoire au brin complémentaire génère des flux de photons localisés contrastant avec le bruit de fond des molécules diffusantes dans le champ d’observation. Le processus d’activation / désactivation est donc principalement contrôlé par la constante de diffusion de l’ADN imageur et de sa constante de dissociation avec sa séquence cible. L’objectif de cette thèse est de diminuer le bruit de fond lié de l’ADN imageur libre en l’étiquetant avec des sondes fluorogéniques, presque non fluorescentes dans l’ADN simple brin, mais qui deviennent hautement fluorescentes une fois l’hybridation avec le brin cible effectuée. Ce projet soutenu par un financement de l’Agence Nationale pour la Recherche (ANR) sera réalisé dans le laboratoire d’Yves Mély (Strasbourg), en collaboration avec l’équipe d’Alain Burger. Le(la) candidat(e) aura dans un premier temps pour objectif de caractériser et valider ces ADN en molécule unique. Les meilleurs brins d’ADN imageurs fluorogéniques ainsi identifiés seront ensuite utilisés pour localiser et imager par DNA-PAINT un ARNm cible dans des échantillons cellulaires.
Profil
Ce sujet s’adresse à un(e) étudiant(e) (biophysicien, physico-chimiste ou biologiste) souhaitant travailler sur des approches de microscopie innovantes. Des connaissances en microscopie et/ou spectroscopie de fluorescence ainsi qu’une forte volonté de s’investir dans ces domaines seraient un atout.
Candidature
Les personnes intéressées sont invitées envoyer leur curriculum vitae, leurs relevés de notes en M1 et M2, et les coordonnées d’au moins un référant par courriel à yves.mely@unistra.fr.

2019-04-Troyes

Structurations spatialement contrôlées de boîtes quantiques pour l’étude dynamique d’intégrines α5β1
Projet
L’adhésion et la migration cellulaire sont des processus importants qui jouent un rôle critique dans les différentes étapes du développement d’un cancer (prolifération, angiogénèse, métastase...). Pour adhérer et se déplacer la cellule va devoir établir des liens physicochimiques forts avec son environnement. Ce dernier est constitué d’une matrice extracellulaire extrêmement complexe, résultant de l'agencement de différentes protéines (collagène, fibronectine...), sur laquelle les cellules se déplacent. L’ancrage entre une cellule et cette matrice est principalement contrôlé par une famille de récepteur membranaire, les intégrines, qui relayent différentes voies de signalisation régulant adhésion et migration. On observe ainsi dans de nombreux cancers, une augmentation de l’expression des intégrines qui favorise l’invasion tumorale mais aussi la résistance aux thérapies. Les intégrines offrent donc une cible thérapeutique fondamentale pour le traitement des cancers. Ainsi, de petites molécules chimiques antagonistes des intégrines (mimant la séquence peptidique RGD de certaines protéines matricielles) ont été développées en essais cliniques. Ces molécules sont capables de bloquer la signalisation intracellulaire induite par l’activation des intégrines lors de la liaison avec la matrice extracellulaire. Leur action est communément mise en évidence par des mesures macroscopiques d’adhésion et de migration in vitro. Cependant, il est fréquent d’enregistrer des résultats contradictoires à l'aide des techniques de caractérisation conventionnelle (augmentation ou diminution de la migration lorsque l’adhésion semble inhibée). Le but de ce projet est d’explorer les possibilités offertes par une technique de nanoscopie de fluorescence développée au sein du laboratoire L2n afin d'étudier la dynamique spatio-temporelle des intégrines à l’échelle nanométrique (sur cellules vivantes). Cette technique est basée sur le FRET (Förster Resonance Energy Transfer) via l’activation d’une surface de verre par des boîtes quantiques (QDs). Elle résulte d’une excitation indirecte des molécules fluorescentes via un transfert d’énergie de type FRET entre un substrat activé par des QDs et la membrane d’une cellule rendue fluorescente par l’ajout de fluorophores. Cette technique vise à réduire, jusqu’à des dimensions nanométriques (<10nm), l’extension axiale du volume d’observation en microscopie de fluorescence. Au cours d’un récent travail, nous avons montré que cette technique permettait d’imager les distances entre une membrane lipidique et une surface avec une précision de 1 nm. Nous souhaitons donc utiliser l’immense potentialité de cette technique en patternant les QDs sur des surfaces. Le pattern ainsi obtenu servira de support au greffage de protéines permettant alors l’adhésion et la migration des cellules. Dans la perspective de faire la preuve de concept de l’intérêt d’une telle approche en cancérologie, nous avons choisi d’étudier l’adhésion et la migration d’une lignée cellulaire issue d’une tumeur cérébrale particulièrement agressive (glioblastome) : la lignée U87MG. Nous souhaitons notamment mettre en évidence les propriétés inhibitrices de molécules antagonistes d’intégrines sur l’adhésion et la migration des cellules U87MG individuelles exprimant des quantités variables de l’intégrine α5β1. Ce sont ces intégrines qui seront rendues fluorescentes via l’utilisation d’aptamères fluorescents s’accrochant spécifiquement sur la partie extracellulaire des intégrines sans interférer sur leurs fonctionnements.
Profil
Le candidat ou la candidate devra avoir des connaissances solides en physico-chimie des surfaces ainsi qu'en biophysique. Des connaissances dans les techniques d'imagerie par fluorescence ainsi que dans la culture cellulaire sera un plus. Le ou la candidate devra naviguer dans les interface entre la biologie, la chimie et la physique. Une grande adaptabilité ainsi qu'une grande curiosité est attendue.
Candidature
Merci d’envoyer un CV, une lettre de motivation et vos résultats de master à Cyrille Vézy (cyrille.vezy@utt.fr) pour début mai au plus tard. Le financement se fera sur la base d’une bourse de thèse du ministère et il est acquis à 100% et se monte à 1400 euros net par mois. Il sera aussi possible de faire des enseignements au cours du doctorat et d’avoir donc une augmentation de la bourse de thèse.

Laboratoire Lumière, nanomatériaux, nanotechnologies (L2n), Université de Technologie de Troyes : Le L2n fait partie de l’Université de technologie de Troyes. Plus de 80 personnes (enseignants chercheurs, ingénieurs, post doctorant et doctorants) travaillent sur la nano-optique, la plasmonique moléculaire, la photonique et la nanobiophotonique. Les équipements du laboratoire sont composés d’une plateforme de fabrication dévolue aux nanostructures (salle blanche, lithographie optique, RIE, évaporateur, MEB etc etc), de microscopes optiques, d’AFM, de lasers ultrarapides etc etc.

2019-04-Suisse/France

6 PhD positions available at multiple Institutions within a collaborative Quantitative Cell Biology project
Context
Funded by a Swiss National Science Foundation Sinergia grant, we are looking for ambitious PhD/postdoc students with interest in quantitative cell biology approaches within a consortium made of four labs with complementary expertise. The multidisciplinary project aims at understanding signaling mechanisms that regulate contractile cytoskeletal structures in processes such as cell migration, organogenesis and cytokinesis. The project will mix state of the art live cell imaging methods in cultured cells and Drosophila embryos, optogenetic and microfabrication techniques to manipulate single living cells, and analysis of cytoskeletal/signaling processes using tools and concepts from theoretical physics. The positions are available in different groups within the consortium.
Candidates with a Degree in Biology, Biochemistry, Bioengineering, Physics or a closely related field should apply. Experience with molecular biology, cell culture, live cell imaging and programing are advantages, but are not an absolute requirement. The students are expected to interact within a multidisciplinary environment including cell biology, physics and mathematics, and to closely collaborate with all members of the consortium. An important goal is the development of new optogenetic tools, signaling biosensors, and cytoskeletal reporters that can be applied across different model systems. Excellent spoken and written English are required. All positions are initially offered for 1 year, and can be renewed for up to 4 years. Salaries are in accordance with guidelines from the Swiss National Science Foundation. We aim to start this project around June 2019. Only short-listed candidates will be contacted.
Application
Applications with a full CV, 3 references and a cover letter with a short research statement should be submitted by email to the PIs of the labs that most accurately matches the applicant’s research interests, as listed below:
• Prof Olivier Pertz (University of Bern, Switzerland): Study of cell migration in cultured cells. 2 PhD positions available. Email: olivier.pertz@izb.unibe.ch
http://www.izb.unibe.ch/research/prof_dr_olivier_pertz/index_eng.html
https://www.pertzlab.net/
• Prof Damian Brunner (University of Zurich, Switzerland): Study of Drosophila Organogenesis. 2 PhD positions available. Email: damian.brunner@imls.uzh.ch
https://www.imls.uzh.ch/en/research/brunnerd.html
• Prof Daniel Riveline (IGBMC, Strasbourg, France): Study of cytokinesis/epithelial contractile arrays in cultured cells. 2 PhD positions available. Email:
daniel.riveline@igbmc.fr
http://www.igbmc.fr/riveline/

2019-04-Nantes

Computer vision for correlative microscopies for the biological characterisation of cardiac diseases
PROJECT
Correlative microscopy allows to combine different scales of observations and different types of content, functional and morphological, thanks to all the microscopy technologies available for the life sciences. To decipher the fundamental mechanisms of dysfunction of the heart valve, these approaches are particularly interesting because of the heterogeneity of cellular remodeling involved in the development of the disease. Mitral valve prolapse is indeed a disorder affecting nearly 2% of the population. L’institut du Thorax (INSERM CNRS Univ Nantes CHU Nantes) has recently developped a KI rat model for one of the mutations identified in patients: FlnA-P637Q. This unique model offers the opportunity to analyze the development and etiology of valvular dystrophy. We thus wish to correlate the morphological and functional phenotypes of the valve observed at the level of the whole heart with cellular and molecular defects detected with high resolution imaging approaches on the same samples. The objective of the Phd thesis is to develop a generic method of multi-scale and multimodality image data fusion, able to adapt to the different acquisition protocols of the project. In particular we believe that the point cloud based approaches, with suitable descriptors, allow the work of different methodological contributions thesis: in particular the proposal for new imaging protocols optimized and automated by these approaches but also to increase accuracy and confidence in matching by selecting deformation patterns learned on the data through an error prediction approaches. The first task will be to contribute to an image database of these different modalities, uncorrelated and manually correlated, or simulated, to test the algorithms developped. The second major step will be to work on the automatic extraction of the common elements between two modalities, taking into account the biomedical problematic, even to suggest new or automatized acquisition protocols. The third major step is to improve the data fusion algorithm, and to adapt its use to the various protocols to make automatic then study physical basic non-rigid transformations for taking into account deformations in the various protocols adapted the different questions asked (influence of pulling forces, local organization of the extracellular matrix). The thesis will therefore rely on the candidate’s ability to understand the team’s biological issues, in addition to the development of his technical skills.
The candidate will have initial training in biomedical engineering, particularly in computer vision, and object-oriented programming skills. He/she will have an interest in biology and its medical applications, and be able to work in a highly multidisciplinary environment (scientific curiosity and sense of organization)
FRAMEWORK
This thesis is already funded, and to be filled as soon as possible.
Contact: P. Paul-Gilloteaux

2019-04-Toulouse/Paris

Candida albicans “on-chip”: Biomechanical approach of morphogenetic plasticity of the yeast C. albicans
CONTEXT
Candida albicans is an opportunistic pathogen yeast that exists in three morphotypes: rugbyshaped yeasts, elongated filamentous hyphae, and intermediate pseudo-hyphae types (see Graphical abstract). The switch from one morphotype to another one has been associated with benign (candidiasis) to deed-seated infections in which C. albicans cells invade biological tissues. Different regions of the body have different physico-chemical characteristics, resulting notably in various sources of confinement and mechanical stresses that C. albicans cells may experience. Recently, we have shown that the switch from one morphotype to another one was highly dependent on mechanics, raising the question of the role of such stresses in promoting or restraining virulence.
PROJECT
The goal of this PhD project is to investigate morphotype regulation under mechanical stress. To this end, various microfluidic devices will be developed in order to control the physico-chemical environment cells are subjected to. In particular, the yeast-to-hyphal and the pseudo-hyphal-tohyphal transitions will be investigated. The results from these biophysical studies will serve as a basis to study C. albicans invasiveness into mammalian cells within “organ-on-a-chip”-like devices. This PhD will take place into a larger collaborative network involving Pasteur Institute in Paris (C. d’Enfert team) and the theoretical group in Physico-Chimie Curie (P. Sens)
FRAMEWORK
We are looking for a highly motivated student who is eager to work at the interface between physics and biology. Among others, the candidate will learn microbiology techniques and microfabrication. The thesis will be in between two laboratories: the LAAS-CNRS (Toulouse), under the supervision of M. Delarue, and the Institut Curie – IPGG (Paris) under the supervision of C. Villard. The first half of the PhD program will be at LAAS-CNRS, where the student would be studying the yeast-to-hyphal transition under well-defined physico-chemical conditions, learning microfabrication in the state-of-the-art 1500m2 clean room. The second half of the PhD will be at Institut Curie/Institut Pierre-Gilles de Gennes for microfluidics, investigating the role of confinement in hyphal growth and the pseudo-hyphal-to-hyphal transition. The PhD student would sign in the PSL-“Physique Ile de France” doctoral school in Paris, and regular bimonthly meetings will be organized, either in Paris or in Toulouse.
If you are interested, please send your CV, a short statement of interest, and the contact information of at least one reference to: catherine.villard@curie.fr and morgan.delarue@laas.fr .

2019-04-Grenoble

Microscopie hyperspectrale et tomographie en cohérence optique parallèle avec un spectro-imageur à transformée de Fourier statique
Résumé
Le Laboratoire des Systèmes d’Imagerie pour le Vivant (LSIV) du CEA Grenoble propose une thèse dans le domaine de la bio-photonique et de l’instrumentation. En Spectroscopie à Transformée de Fourier on mesure le degré de cohérence de la lumière dans un interféromètre pour remonter au spectre. On parle de spectromètre à Transformée de Fourier statique lorsque l’interférogramme est enregistré en une seule exposition, sans déplacement de pièce mécanique. Récemment ce concept a été étendu à l’imagerie hyperspectrale pour le domaine du Spatial en utilisant un nouvel arrangement d’interféromètre statique que l’on positionne devant un capteur matriciel. Outre l’imagerie hyperspectrale, une possibilité qui reste inexplorée à ce jour est d’employer cet interféromètre pour l’imagerie par Tomographie en Cohérence Optique (OCT). Dans la thèse, qui est une collaboration entre l’Institut de Planétologie et d’Astrophysique de Grenoble (IPAG) et le CEA Leti, nous proposons d’étudier cette nouvelle méthode d’imagerie OCT. On pourra également envisager de coupler les deux modalités (OCT et imagerie hyperspectrale) dans un système d’imagerie rapide permettant d’adresser de nombreuses applications santé et en imagerie du vivant. L’étudiant développera un système de microscopie autour de ce nouveau concept d’imageur ainsi que les outils numériques de traitement des interférogrammes. Ce sujet s’adresse à un étudiant avec une formation en optique et de solides compétences en traitement des données, ou bien un étudiant avec une formation générale. Un fort intérêt pour la biophotonique et l’imagerie du vivant est attendu.
Laboratoire d’accueil
Le LSIV développe des systèmes optiques pour l’analyse du matériel biologique et le diagnostic. Le laboratoire fait partie du Département des Technologies pour la Santé du CEA Leti qui est une unité multidisciplinaire dont les thèmes de recherche englobent la bio-photonique, la micro-fluidique, les systèmes électroniques bio-compatibles, et les capteurs chimiques et micro/nano-mécaniques. Les travaux menés actuellement au LSIV portent sur l’imagerie sans lentille, les spectroscopies Raman et Brillouin d’échantillons biologiques complexes, et l’analyse microbiologique par diffraction. Le travail de thèse sera réalisé en collaboration avec l’IPAG qui est très actif dans le développement d’instrumentation pour la spectroscopie.
Lieu : Grenoble.
Candidatures
Date limite de dépôt des candidatures : 15 Mai 2019.
Date de début : au plus tard 10/2019.
Durée : 3 ans.
Financement : CEA, acquis.
Contact : Jean-Charles Baritaux (jean-charles.baritaux@cea.fr)

2019-04-Paris

New super-resolution fluorescence microscopy
Description of the PhD project
Super-resolution optical microscopy, awarded by the Nobel Prize 2014, represents a true revolution in biology. Their ultimate sensitivities, allowing the tracking of unique molecules, as well as their nanometric resolution, unveil, for the first time, the organization and intracellular mechanisms at the molecular level. Diffraction has long been considered as a fundamental limitation to the spatial resolution of optical imaging systems. Numerous biological applications were thus excluded by the impossibility of imaging molecular structures smaller than 200 nm. Recent developments in super-localization microscopy techniques (dSTORM / PALM) make it possible to achieve a lateral positioning accuracy of about 10 nm, by acquiring at different times the emission of fluorophores which lie in the response function of the microscope. In our group at Langevin Institute, we are developing innovative strategies to improve both lateral and axial resolution to optimize the acquisition of biological information at the nanoscale (Nature Photonics 2015, Nature Communications 2015, ACS Nano 2017). We also focus on the ability to retrieve additional information at the single molecular level like the orientation or the chemical local environment. Accessing the local environment at the scale of an individual molecule within a cell would represent a true breakthrough in biology by allowing one to go beyond statistical averaged measurements. Despite the efforts of many research teams in this field, this remains very difficult, if not impossible. This project will use an innovative concept to retrieve information at the single molecule level without compromising the localization precision. It provides a direct access to this information through the acquisition of the molecule fluorescence lifetime. Being compatible with standard super-resolution microscopy, without degrading their performance, this concept takes advantage of the whole set of photons emitted by the molecule to extract information. Inter-molecular variability will become a new and extraordinary source of information for the understanding of cellular mechanisms. This interdisciplinary project involves the active collaboration of several groups. The first part of this project consists in implementing this new microscopy. After a step of validation of the performances of the device on calibrated samples, the observations of samples of biological interest will be performed in collaboration.

Keywords: Super-resolution microscopy, Cell imaging, Fluorescence, Lifetime, Multiplexing
Research unit: UMR7587 Langevin Institute
Description of the research Unit/subunit: The candidate will be hosted at the Langevin Institute. The Langevin Institute is a research unit affiliated with ESPCI Paris and CNRS. The researches conducted at the Institute aim at developing at the best world-level the physics of waves bringing together high level fundamental research, applied research, and company start ups in a thoroughly cross-disciplinary way.
Name of the supervisor: Emmanuel Fort (Emmanuel.Fort@espci.fr)
Intersectoriality: This project is directly connected to several key enabling technologies (photonics, nanotechnology, biotechnology with biochemistry and molecular labelling. The outcome of the project is of direct interest for this industrial partner Abbelight which cofund this PhD program. Abbelight is an innovative company in super-resolution microscopy that is interested in getting licensed for this patented technology.
Interdisciplinarity: This project has a very strong interdisciplinary component and involves optics, biochemistry, image processing and biology. The success of this project is based on the active collaborations with several groups, experts in the different fields.
International mobility: This interdisciplinary project involves several international collaborations in particular strong exchanges with the Tjian & Darzacq Group at Berkeley. Probable visits and exchanges with this group (to perform experiments) will take place during the project.
Expected Profile of the candidate
We seek a candidate with a MSc degree in Physics. The ideal candidate is highly motivated, has experience in experimental physics and enjoys working in an interdisciplinary team. Experience with super-resolution microscopy, single-molecule spectroscopy or software development (programming) is preferred but not required. Speaking French is not a requirement at all!
Important dates
Call for applications : from February 1st to March 31st 2019
Eligibility check results : Mid April
3i Committee evaluation results : Mid May
Interviews from the shortlisted candidates with the Selection Committee : Late June-Early July
Final results : Mid July

2019-04-Umea (Sweden)

Diet, gut microbiota, mucosal barrier function
Context / Background
In the group of Björn O. Schröder at The Laboratory for Molecular Infection Medicine Sweden (MIMS), the EMBL Nordic Node at Umeå University, Sweden, new PhD student and Postdoc opportunities are available. The laboratory is located in the Department for Molecular Biology at Umeå University. To prevent infection by or translocation of the gut microbiota into underlaying tissues, the intestinal epithelium exhibits defense mechanisms, such as the production of intestinal mucus and antimicrobial peptides (AMPs). Our research projects will focus on how dietary and other factors influence the interaction between gut microbiota and the mucosal barrier (intestinal mucus and AMPs) and we will investigate the relevance of this interaction in the context of diseases, such as inflammatory bowel disease and metabolic diseases. In the laboratory we will use a combination of gut microbiota analyses, microbiota transplantations (FMT), state-of-the-art ex vivo mucus measurements, antimicrobial assays, as well as confocal and fluorescence microscopy. In addition, we will use dietary interventions in mice and humans and closely work with Norrlands University Hospital Umeå (NUS) to analyze relevant patient samples.
Qualifications
Successful candidates must hold a university degree (PhD or equivalent for postdoctoral applications) in a subject area relevant for the positions. Furthermore, applicants for a postdoctoral position should have experience in mucosal barrier function and/or gut microbiota research and must have good knowledge of standard molecular biology and biochemical methods. For all candidates, working experience with mouse studies, gut microbiota analyses + manipulations and/or imaging techniques are strong merits. Successful candidates need to be highly motivated, have very good communication skills and are expected to be at ease collaborating with other scientists. They should have high capacity to independently organize and lead projects. International experience is a merit while good skills in both oral and written communication in English is a must. Great emphasis will be placed on personal suitability.
Contact/ Application
Interested candidates are welcome to contact Björn Schröder for more information and/or send a letter of interest as one .pdf file in English to bjorn.schroder@umu.se, including: (i) a cover letter, summarizing qualifications and motives for applying, (ii) a curriculum vitae, and (iii) the names and contacts of three references (up to two references for PhD student applications).

2019-04-Hannover

The relevance of lipid droplet biogenesis to the hepatitis C virus replication cycle
Context / Project description
The Institute of Experimental Virology of Prof. Dr. Thomas Pietschmann at the TWINCORE- Center for Experimental and Clinical Infection Research in Hannover, Germany is seeking a doctoral Researcher (f/m/d). Job announcement No. 29/2019.

Lipid droplets are intracellular lipid storage organelles. As a key metabolic hub of the cells, they are targeted by a number of pathogens, including viruses, bacteria and parasites. Hepatitis C virus (HCV) is a liver-tropic human pathogen that chronically infects 71 million people worldwide. Symptoms include steatosis, the accumulation of lipid droplets in the liver, and may evolve to hepatocarcinoma. At the cellular level, HCV hijacks lipid droplets for its morphogenesis. As a result, the circulating virion resembles host lipoproteins, and this mimicry helps the virus to evade the host immune defences.
Your main project will be the investigation of the role of lipid droplets in HCV replication cycle using cell culture infection models and a broad spectrum of techniques ranging from molecular and cell biology (e.g. cloning, transfections, flow cytometry), biochemistry (e.g. Western Blots, Elisas), and virology (e.g. HCV, lentiviral vectors) to high-end microscopy techniques (confocal microscopy, live cell imaging, advanced image analysis). A particular interest in microscopy is desirable. The project is funded by the DFG and will be conducted under the supervision of Dr. Gabrielle Vieyres. Note that the project involves work in laboratories of biosafety levels 2 and 3.
Qualifications:
BMaster’s Degree in biology, biochemistry, biotechnology, or a related field within the life sciences
- Excellent education/training in molecular and cell biology
- Excellent English communication skills (written and spoken)
- Ability to work independently and as part of an international team
- Experience in virology and/or in microscopy will be of advantage
Equal Opportunities are part of our personnel policy. Qualified applicants with a disability will be given preference, provided their equal aptitude and suitability.
Application:
Starting date: August 2019 or later - Initial contract for 3 years
Salary: alike TVöD E13 (50%) with the possibility of an additional payment of 15%
Probation period: 6 months
Published on: 20.03.2019
Closing date: 14.04.2019
Application: Applicants are required to complete the online application form here: https://hzi.opencampus.net/ (Please select Job No. 29/2019).
For more details regarding the position, please contact Dr. Gabrielle Vieyres via email: gabrielle.vieyres@twincore.de, or by phone: +49 511 22 00 27 146.
TWINCORE is a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI). Further information about the institute can be found on our website: https://www.twincore.de/en/institutes/experimental-virology/

2019-04-Paris

Mécanismes contrôlant la migration cellulaire au cours du développement
de la nageoire pectoral chez le poisson zébré
TOPIC
Cell migration is a fundamental process in development, proper body function, and pathological conditions such as cancer. During zebrafish pectoral fin development, somitic mesodermal cells migrate from neighbouring somites into the fin bud. This happens between 30 and 48 hours of development. Very little is known about the mechanisms underlying somitic mesodermal cell migration. The goal of this project is to study the mechanisms controlling their migration into the developing fin bud. We expect to discover the molecular and cellular basis of this process. The project has three specific aims. Aim1: identification of the biochemical and mechanical cues that direct cells during their migration toward the fin bud; Aim 2: characterization of the migration mode such as actin-rich protrusions, blebbing or other mechanisms never described so far; Aim 3: consequences for the development of the fin in case of impaired migration of the somitic cells.
Foreseen methods include: functional genetics, optogenetics, biosensors (FRET), live imaging microscopy (2-photon LSM and light sheet), image analysis for the quantification of relevant parameters and computer modelling to discriminate between possible models. By the end of this project, we expect to understand how somitic cells leave the somites, invade the fin bud and differentiate. More generally, we expect to shed light on the diversity of migration in morphogenesis.
PROFILE/SKILLS - FUNDING /APPLICATION - WHERE
Basic molecular biology and biochemistry skills, strong computer skills, English usage. Motivation and dedication to science and developmental biology is very important Zebrafish experience is desired by not necessary.

Doctoral School ED 568 "Signaling and Integrated Networks in Biology"

Laboratory : BioEmergences USR3695
Hosting team : Zebrafin
Laboratory director : Peyriéras Nadine
Institution of affiliation : CNRS, Université Paris Saclay

Name and first name of the team leader : Elena Kardash
E-mail : elena.kardash@cnrs.fr

2019-04-Lille

Synchronization of the mammalian circadian clock with metabolism: biosensor approaches coupled with mathematical modeling
TOPIC
In most living organisms, the circadian clock synchronizes to the day/night cycle and or chestrates many biological functions. There is increasing evidence that disruption of the mammalian circadian clock in metabolic organs (liver, pancreas, …) plays a key role in pathologies such as obesity or type 2 diabetes. To clarify the mechanisms invol ved, we have designed a mathematical model of the liver clock synchronized to feeding/fasting cycles through the intracellular factors NAD+ and AMP, which reflect the cellular bioenergetics (Woller et al, Cell Reports 17, 1087, 2016). Experiments are now needed to validate and extend this model, as well as to verify the biological hypotheses it has suggested.
JOB DESCRIPTION
The PhD student will be in charge of acquiring relevant data to extend the model. For that purpose, she/he will transfect cells with fluorescence based biosensors available in the lab and monitor the evolu tion of cell energy along the circadian clock. The main goals of the PhD thesis are summarized below. Using reporters and biosensors for key metabolic actors such as NAD+/SIRT1 or AMPK, as well as for core clock genes (Bmal1, Rev Erbα), the PhD student wil l quantify how various factors reset the circadian clock depending on the time of the day and compare measurements with model predictions. The use of pharmacological or genetic tools will help unravelling the key components entraining the clock, which may be targeted to reset the clock through chronotherapic protocols. There will be a strong interaction with the modeling part of the project, which is handled by a post
doctoral researcher. Contribution to this part will be welcome but does not represent a main task for the PhD student.
CONTEXT
Marc Lefranc at PhLAM has a long experience in developing data driven mathematical models to describe the dynamics of the circadian clock, and will supervise the model refinement. Laurent Héliot at PhLAM has leading expertise in tracking molecular dynamics in living cells using real time fluorescence based bioph otonic approaches, and will supervise the cell preparation and data acquisition within the imaging facility. This project is in tight collaboration with Bart Staels and Hélène Duez, experts in metabolic diseases (U1011, Institut Pasteur de Lille). Marc Lefranc is coordinator of the “Mathematics and Physics for biology” axis of Labex CEMPI, which fosters interdisciplinary research and partly supports this project.
PROFILE/SKILLS - FUNDING /APPLICATION - WHERE
Candidates should have a good biological background and experience with cell cultures, transfection and imaging. Since the student will interact closely with researchers in an interdisciplinary environment, relational abilities and good communication skills are required. A great motivation for quantitative biological approaches combining cell cultures and imaging with mathematical modeling is expected. The contract is for 3 years, starting from September 2019. Funding is already secured from the University of Lille Nord Europe ISITE project. It is aligned with the recently upgraded CNRS salary scale. Candidates should send a cover letter stating their motivations and curriculum vitae, as well as two support letters, to Marc Lefranc ( marc.lefranc@univ lille.fr ) and Laurent Heliot laurent.heliot@univ lille.fr
On the Science and Technology campus of the University of Lille, in Northern France. Lille is the dynamic core of the 4 th French urban area (1.2 M people). It hosts many top research units in the various scientific disciplines. Will 67 000 students, the University of Lille is the largest french speaking university. Lille is connected by high speed trains to Brussels (40 min), Roissy airport (50 min.), Paris (60 min), and London (80 min). With a lively atmosphere and a reasonable cost of living, Lille is an attractive place to stay.

2019-03-Toulouse

Biophysical exploration of nanoscale dynamics at the immunological synapse - NanoTCell
Context
“NanoTCell” is an interdisciplinary project at the interface between quantitative biology and statistical biophysics aiming at elucidating how T cells regulate their cytotoxic activity, a key parameter conditioning the capability of the immune system to eliminate infected or cancer cells. It depends on the assembly of the immunological synapse (see figure), a highly dynamic structure that stabilizes the interaction between the T cell and its target cell, leads to the T cell activation, allows the secretion of lytic granules and potentiates the pore-forming activity of perforin by applying mechanical forces on the target cell plasma membrane. The synaptic cortical actin cytoskeleton is essential in this context as it has been proven to be a key-player of the synapse assembly and its integrity is essential for the cytotoxic activity. Exploring its organization, the molecular control of its remodeling and the ensuing physical forces will be crucial in order to understand how T cells convert molecular signals into a coordinated physical action. The NanoTCell project relies on the study of unique study models consisting in T cells from immunodeficient patients carrying mutations in genes encoding various actin cytoskeleton regulators (WASP, WIP, WRD1, Coronin-1A).
Main objectives
The main objectives of the thesis will be to:
- Characterize by superresolution microscopy (SIM) and dynamical microscopy (TIRF) the synapse spatial organization in T cells from immunodeficient patients and healthy donors, with a focus on the correlation between cortical actin density and the localization of membrane proteins;
- Test the relevance of different physical models used to describe protein organization in nanodomains (fence-and-picket model vs models based on protein-protein and/or protein-lipid interactions);
- Measure the physical forces exerted by the T cell at the synapse in the cytotoxic activity context with the help of micro-pillar experiments [Basu2016];
- Elaborate a quantitative numerical multiscale model of immunological synapse describing how actin cytoskeleton remodeling controls lytic granules release and cytotoxic activity.
The experimental work (microscopy) will be done under the supervision of Loïc Dupré, an immunologist expert in the study of primary immunodeficiencies related to the actin cytoskeleton, at the CPTP (cell imaging facility, directed by Sophie Allart, Genotoul network) [Dupré2002, Calvez2011, Dupré2015, Pfajfer2017, Houmadi2018, Pfajfer2018]. The numerical modeling will be done under the supervision of Nicolas Destainville (LPT), a physicist expert in data analysis and modeling of biophysical mechanisms at play at the cell surface [Destainville2016, Gueguen2017, Destainville2018]. The student will share its time equally between both laboratories. The part of the work related to the measurement of physical forces will be done during a stay in Morgan Huse’s team at the Memorial Sloan-Kettering Cancer Center, New York, USA.
Expected skills
the candidate must have followed a M.Sc. (or equivalent) in Physical Biology, Biophysics or Biological Physics. He/she must be as familiar as possible with modern fluorescence microscopy techniques, data processing, numerical simulation techniques and physical modeling.
Funding and Application
The 3-year PhD position is funded by the University of Toulouse and is expected to start in September 2019. It aligns with the French national PhD contract and includes health and social insurance coverage. Please send before May 15, 2019 a CV, letter of motivation and 2 references to Loïc Dupré (loic.dupre@inserm.fr) and Nicolas Destainville (destain@irsamc.ups-tlse.fr).

2019-02-Liège

Development of novel deep/machine learning algorithms for quantitative multimodal biomedical image analysis
Context
The Montefiore Institute (http://www.montefiore.uliege.be) at the University of Liège, Belgium has an opening for a PhD candidate to work on the development of novel deep/machine learning algorithms for quantitative multimodal biomedical image analysis. More specifically, this PhD project entails the development of novel algorithms to automatically locate, measure, and classify elements in multimodal biomedical images with a specific focus on skeletal development applications. These algorithms will be disseminated to a wide audience through the open-source Cytomine web-based software platform (http://uliege.cytomine.org).
Candidate
The ideal candidate should have a Master in Computer Science or Biomedical Engineering, with a taste for deep/machine learning and modern software programming. The candidate will be supervised by senior scientific staff with a background in computer science (Prof. Wehenkel, Prof. Geurts, Dr. Raphaël Marée) in collaboration with biomedical researchers (Dr. Marc Muller) and other project partners. The candidate will actively participate in PhD training activities within the BioMedaqu consortium. It is a Marie Sklodowska-Curie Innovative Training Network (MCSA-ITN) with the primary research aim to create an innovative expertise combining research in skeletal biology of aquaculture fish species with that in biomedical models and humans. In total, 15 Early Stage Researchers (ESRs) will be appointed by the BioMedaqu consortium for 36 months each.
Eligibility
There are strict eligibility requirements for the ESR PhD positions in MSCA-ITN. Please ensure that you qualify before applying, as ineligible candidates cannot be considered. See more details here:
http://www.giga.uliege.be/cms/c_279692/en/biomedaqu-open-positions
Application
The position starts as soon as possible (and before July 2019). Interested and eligible candidates should send their résumé and application letter to Dr. Raphaël Marée (raphael.maree@uliege.be) and Dr. Marc Muller (m.muller@uliege.be).

2018-08-Grenoble

Imagerie photoacoustique endoscopique de la vascularisation de ménisque in vivo
Contexte et enjeux scientifiques
Cette thèse s’intègre dans le projet MenisCare qui rassemble les laboratoires Liphy (Université Grenoble-Alpes) et Creatis (Université Lyon 1), le CIC-IT (Centre d’Investigation Clinique- Innovation Technologique) du CHU Grenoble Alpes et deux PME, Cartimage Medical (La Tronche) et ACS Biotech (Lyon). Ce projet vise à proposer une nouvelle approche de la chirurgie du ménisque du genou, en favorisant la réparation des lésions méniscales plutôt que l'ablation (méniscectomie).

L’objectif de cette thèse est de réaliser un système d’imagerie photoacoustique endoscopique permettant de mesurer la densité de vascularisation d’un ménisque in vivo sur animal. En effet, à l'heure actuelle, la littérature montre un taux d'échec de la réparation méniscale entre 5% et 43% [1]. Un des critères majeurs pour l'établissement d'un pronostic de succès de la réparation du ménisque est la présence de capillaires sanguins (micro-vascularisation) dans la zone lésée à suturer. Or cette microvascularisation est à l'heure actuelle détectable uniquement par des techniques invasives comme l’immuno-histologie. Il est donc essentiel d’apporter une technique non invasive de mesure qui permette de déterminer, avec un niveau de certitude suffisant, si une suture peut être réalisée avec succès sur un ménisque. C’est dans ce contexte que s’intègre cette thèse.
Objectif
Nous proposons de développer un instrument pour détecter in vivo la densité de vascularisation d’un ménisque Pour cela, l’objectif sera de réaliser un système d’imagerie photoacoustique [2] dans les contraintes d’un dispositif médical endoscopique. L’imagerie photoacoustique permet de réaliser des images de contraste optique avec un signal de détection ayant les propriétés de propagation et de diffusion des ondes acoustiques. Son principe repose sur la génération d’une onde acoustique par effet thermoélastique suite à une variation thermique engendrée par absorption optique de l’objet à imager. Cette onde acoustique est ensuite détectée à l’aide d’un transducteur piézoélectrique. L’utilisation d’une longueur d’onde optique centrée sur l’absorption de l’hémoglobine permet alors d’obtenir une image à résolution acoustique (100μm) de la vascularisation avec un très fort contraste. Sur la base d’une sonde échographique intra-articulaire utilisée lors d’opérations sous-arthroscopie, il s’agit donc de développer un imageur photoacoustique endoscopique avec les mêmes contraintes de dimensions. Cet imageur sera testé et calibré sur des fantômes de ménisque. Il s’agit de circuits microfluidiques réalisés en PDMS qui doivent permettre de simuler le réseau micro vasculaire proche de celui du ménisque de façon être le plus réaliste possible (taille de canaux, densité, diffusion optique).
En parallèle de ce travail, des travaux d’immuno-histologie devront être réalisés dans le cadre de la collaboration MenisCare pour mieux comprendre le réseau vasculaire humain du ménisque et trouver le modèle animal le plus approprié. A partir des échantillons d’intérêt (humain et animaux), les paramètres optiques de l’imageur pourront être optimisés de façon à ne pas endommager le tissu méniscal.
L’objectif final est de pouvoir réaliser avec cet imageur une mesure sur animal in vivo en chirurgie ouverte.

[1] Pujol et al, "Amount of meniscal resection after failed meniscal repair", Am. J. Sports Med, (2011)
[2] Wang et al, “Photoacoustic Tomography: In Vivo Imaging from Organelles to Organs”, Science 335, 1458 (2012)
Environnement
L’équipe OPTIMA (OPTique et IMAgerie) du LIPhy dans lequel se déroulera cette thèse a acquis depuis une dizaine d’années une expertise en imagerie laser et plus récemment dans en imagerie photoacoustiques, activité financée depuis 2016 par un projet ERC. Ce travail de thèse sera mené en étroite collaboration avec tous les acteurs du projet Meniscare. Ce travail de thèse est financé par le FRI (Fond régional Innovation) de la région Rhône Alpes Auvergne (salaire net approximatif 1400 euros/mois).
Contact
eric.lacot@univ-grenoble-alpes.fr Tel: (33)4.76.51.43.58 - Fax: (33)4.76 63 54 95

2018-07-Reims

Développement d’Outils d’analyse du REmodelage Matriciel par Imagerie Haute Résolution (DOREMI).
Contexte
Les maladies cardiovasculaires et métaboliques sont les atteintes les plus observées au cours du vieillissement. Ces pathologies chroniques progressent lentement sans symptôme visible jusqu'à atteindre une situation critique où la maladie est définitivement installée. Lors de ce processus, la matrice extracellulaire vasculaire est dégradée. En particulier, les lames élastiques présentes au sein de la paroi vasculaire sont altérées et ne remplissent plus pleinement leurs rôles. Comme l’élastine qui les compose n’est plus produite au-delà de l’adolescence, toute altération survenant sur ces structures est fondamentalement irréversible et contribue au vieillissement vasculaire.
En collaboration avec nos collègues de l’Université de Manchester, notre laboratoire s’intéresse aux modifications survenant au sein des parois artérielles et à leur évolution, notamment dans le cadre de pathologies liées à l’âge comme le diabète ou l’insuffisance rénale chronique. Nous avons ainsi développé une technique d’imagerie par rayonnement synchrotron X (Diamond Light Source, Didcot, UK) sans agent de contraste qui permet d’obtenir des coupes optiques à très haute résolution (800 nm). Les images obtenues (définition : 2560x × 2560y x 2560z, 16 bits) sur des segments d’artère de souris de plusieurs mm de long permettent de reconstruire le volume artériel et révèlent, au sein des parois, des détails ultra-structuraux jusque-là inconnus. Nous avons développé un premier programme d’analyse d’image (script Matlab) qui permet d’isoler les structures élastiques contenues dans les parois artérielles en vue de les analyser qualitativement et quantitativement en 3D.
Travail de thèse
Le travail à réaliser dans le cadre de ce projet de thèse comporte deux grands axes ; une partie analyse d’image visant à développer et améliorer l’outil logiciel déjà présent ; une partie imagerie haute résolution qui sera réalisée en étroite collaboration avec nos collègues anglais.
A – Analyse d’image
Le principal objectif de ce projet sera d’améliorer le système d’analyse d’image afin de le rendre plus efficace dans la détection des structures et des modifications structurales des échantillons. Il faudra ensuite rendre la détection du logiciel moins sensible aux variations de l’échantillon afin que la méthode d’analyse d’image puisse être généralisée afin de simplifier la démarche d’analyse. En effet, des échantillons à comparer peuvent donner lieu à des images ayant une luminosité ou un contraste différent. Le logiciel devra pouvoir s’affranchir de ces différences pour faciliter la comparaison des échantillons entre eux. Le logiciel développé sera mis en oeuvre sur les données d’imagerie haute résolution déjà disponible dans l’équipe, celles qui seront générées lors durant la thèse, mais aussi sur celles obtenues par nos collaborateurs (Angleterre, Espagne, Suisse).
B – Imagerie Synchrotron
Au cours de la thèse, l’étudiant-e sera amené-e à préparer des échantillons en vue de les imager par microtomographie X sur un synchrotron. Il lui appartiendra en particulier d’améliorer la méthode de préparation des échantillons (murins voire humains), afin d’obtenir des échantillons dans un contexte physiologique le plus proche possible des conditions in vivo et d’obtenir la meilleure qualité d’image possible sans utiliser d’agents de contraste. Ce travail sera principalement réalisé à Reims mais l’étudiant-e recruté-e devra également se rendre en France ou à l’étranger pour acquérir des images sur synchrotron ou réaliser des expériences en lien avec le sujet proposé. Il pourra s’agir de séjours courts (moins d’une semaine) ou plus longs.
Profil recherché
Le-la doctorant-e, biologiste ou bio-informaticien(ne), devra impérativement avoir des connaissances en programmation informatique (exemple : langage orienté objet) et/ou traitement d’image/du signal. Idéalement, la personne aura de plus une première expérience de Matlab et d’ImageJ, mais des compétences en d’autres langages (Python, etc…) peuvent aussi convenir. L’étudiant-e devra également être capable de préparer les échantillons d’origine animale. Idéalement, la personne aura une première expérience en expérimentation animale. La personne intègrera une équipe de biologistes, bio-informaticiens et biophysiciens d’une dizaine de personnes.
Caractéristiques du poste
Durée : 3 ans à compter du 1er octobre 2018
UMR CNRS 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)
Équipe Modélisation Moléculaire et Imagerie Multi-échelle (MIME)
Université de Reims Champagne Ardenne, UFR Sciences Exactes et Naturelles
Moulin de la Housse, Bât. 18, 51687 Reims cedex 2
Directeur de thèse : Pr. Laurent Debelle
Co-encadrant : Dr. Sébastien Almagro
Contact
laurent.debelle@univ-reims.fr et sebastien.almagro@univ-reims.fr
Tél : 03.26.91.35.02 et 03.26.91.81.94
Les personnes intéressées par ce sujet sont invitées à envoyer les éléments suivants.
• CV et lettre de motivation
• Relevés de notes L, M1, M2 + attestation de réussite de Master si déjà disponible

2018-07-Montpellier

Offre de Thèse CIFRE : Etude des interactions fonctionnelles entre la signalisation inflammatoire et la polarisation macrophagique dans la tumorigénèse
Contexte
Dans le cadre d'un projet portant sur l’étude des interactions fonctionnelles entre la signalisation inflammatoire et la polarisation macrophagique dans la tumorigénèse, la société de biotechnologie AZELEAD (http://www.azelead.com/) et l’équipe de recherche du Dr. Nadine Laguette (https://www.igh.cnrs.fr/fr/recherche/departements/bases-moleculaires-de-pathologies-humaines/2-bases-moleculaires-de-l-inflammation) recrutent un(e) étudiant(e) en thèse.
Description du projet
A ce jour, une inflammation résiduelle a été détectée chez tous les patients cancéreux et cette inflammation chronique corrèle avec un mauvais pronostic. Par leur présence massive au sein des tumeurs, les macrophages contribuent de façon importante à la production de cytokines inflammatoires et facteurs de croissance dans le microenvironnement tumoral. Les recherches récentes et la littérature mettent en évidence que les macrophages peuvent se différencier en plusieurs sous-types distincts enréponse aux stimuli extérieurs : principalement les macrophages M1 dits « classiques » et les macrophages M2 dits « alternatifs ». L’infiltration des tumeurs par les macrophages M1 corrèle avec une meilleure survie des patients tandis que les macrophages M2 favorisent le développement tumoral, l’angiogenèse et la dissémination métastatique. Les mécanismes moléculaires conduisant à la polarisation M1 ou M2 ont été largement étudiés dans différents contextes mais le rôle joué par le microenvironnement demeure peu connu. En particulier, le rôle de la voie cGAS-STING, de reconnaissance des acides nucléiques cytosoliques dans la polarisation macrophagique demeure mal établi. Or, cette voie apparaît comme jouant un rôle déterminant dans l’inflammation associée au cancer. Dans ce contexte, le but de ce projet de thèse est d’étudier les interactions entre les cellules tumorales et les macrophages. Ce projet vise à explorer les voies récemment décrites de l’immunité innée (voie STING-cGAS) dans la polarisation macrophagique et le devenir tumoral.
Pour mener à bien ce projet, intégrant le microenvironnement tumoral, nous utiliserons des modèles in vitro (développés par l’équipe de recherche du Dr. Nadine Laguette) et in vivo chez le poisson zèbre (développés par AZELEAD). Le poisson zèbre est est un modèle de choix pour l'étude de nombreuses pathologies, notamment en raison de sa transparence à l'état embryonnaire qui permet une imagerie in vivo des processus biologiques à haute résolution. De plus il est aujourd’hui reconnu comme étant un excellent modèle d’étude pour l’immunité innée.
Le projet s’articulera autour des 3 axes de recherche suivants :
- Caractérisation des acides nucléiques et étude de leur impact sur la polarisation des macrophages.
- Modélisation des mécanismes de détection des acides nucléiques dans les différents sous-types de macrophage.
- Analyse des conséquences de la détection des acides nucléiques cytosoliques sur la tumorigénèse dans le modèle zebrafish.
A terme, ce projet permettra de déterminer les mécanismes moléculaires de la réponse immunitaire innée liée aux acides nucléiques inflammatoires au sein de microenvironnements complexes afin de permettre l’identification de nouvelles cibles pharmacologiques pour prévenir l’inflammation.
Missions
--- L’étudiant participera à la mise en oeuvre et à la mise au point de protocoles expérimentaux nécessaires à la réalisation de son projet de recherche.
--- Techniques utilisées : L’étudiant utilisera des approches de biochimie (Western Blot, Immunoprécipitation), de biologie moléculaire (clonage, PCR, RT-qPCR) et de biologie cellulaire (immunofluorescence, cytométrie en flux, live imaging, micro-injection). L’étudiant réalisera ses expériences ex vivo, in vitroet in vivo (sur le zebrafish).
--- Compétences attendues : L’étudiant sera organisé, rigoureux et motivé. Des connaissances en immunologie sont attendues.
- Une expérience en expérimentation animale sera appréciée).
Caractéristiques du poste
--‐ CDD de 3 ans
--‐ Niveau exigé : Bac + 5
--‐ Expérience du travail en laboratoire de recherche
--‐ Début de la mission : Octobre 2018
Environnement et contexte de travail
--‐ Lieu:
(1) AZELEAD : 377 rue du professeur Blayac, 34080 MONTPELLIER
(2) Equipe du Dr N. Laguette : « Bases Moléculaires de l’Inflammation », Institut de Génétique Humaine (UMR 9002) ; 141 rue de la Cardonille ; 34396 Montpellier
Le candidat retenu sera responsable des expériences permettant le bon déroulement de son projet de recherche. Il participera activement à la conception et à la réalisation des expériences. Son travail sera réparti sur les sites de l’IGH et du laboratoire de recherche d’AZELEAD où il sera encadré respectivement par le Dr. Kissa et le Dr. Laguette. Il devra faire des comptes-rendus réguliers au cours de réunions conjointes entre AZELEAD et l’équipe de recherche. La personne recrutée sera en contact direct avec les différents membres des deux équipes.
2018-07-Nantes

Implementation of a 3D-printed model of human mucosa to study virus/host interactions
Context
The 3D printing of living cells / tissues is one of the last revolutions in the field of biological engineering and regenerative medicine. We propose to use this automated, reliable and reproducible technology to develop a unique experimental model of immunocompetent human mucosa and explore, for the first time, the entry into the mucosa of species-specific viruses. Our primary objective through this collaborative project is the development of an immuno-competent human mucosal equivalent, that is to say containing the major dendritic cell subpopulations of the mucous membranes, Langerhans cells (CL) in the body. epithelium and interstitial dendritic cells (DCs) in the underlying connective tissue. By development, we mean the development of all manufacturing processes as well as the characterization of biomaterials and cells used to achieve our goal. Thus we plan to carry out on this first phase of the tender (i) the identification of the biomaterials of natural or synthetic origins used to form the model, (ii) the choice of the primary human cells used, ( iii) analysis of cell viability over time (impact of biomaterials used, availability of nutrients, oxygen, etc.), (iv) analysis of the macrostructural evolution of the reconstructed tissue as a function of time (Phenotypic / functional stability, absence of surface keratinization), (v) phenotypic-functional monitoring of integrated dendritic cells (ability to interact with epithelial / stromal cells, permissiveness to CMV infection in a complex environment, presentation of antigen, modulation of the transcriptome, etc.).
Working hypothesis and aims
The objective is to fabricate a vascularized human mucosa using 3D bioprinting and to use it to set up an innovative model to study human/transplant-related viruses interactions.
WP2 : 4D bioprinting of the connective tissue with or without the epithelial layer. A subsequent addition of immune cells will be addressed in this package. Extrusion and sprayning cells are two deposition mthods that will be used here.
WP3 : Validation of the model, ie cell viability phenotypes over time will be assessed.
WP4 : Macrostructural evolution of the 3D-printed model follow-up, ie variability assessment over time (hours to 21 days).
WP5 : Does this model support viral infections (HCMV for instance) ? Do immune cells play a role in the viral infection, either deleterious or beneficial for the virus ? Testing blocking agents, ie antiviral compounds.
This project relies mainly on cutting-edge tissue engineering/3D bioprinting techniques as well as on imaging techniques for the analysis part.
Main milestones of the thesis
Milestone 1: Getting a model of mucosa (malphigian epithelium relying on a 3D-printed connective tissue) resembling a native human genital mucosa. The validation phase will lie on the use of imaging, (RT-)qPCR, cytometry, RNAseq (single cell and bulk) (collaboration with Centrale Nantes).
Milestone 2: Set up insertion of immune cells (ie myeloid DC).
Milestone 3: The model recapitulates viral infections (HCMV) in a native tissue. Immune cells play a role in the various parameters like the viral spreading.
Milestone 4: Identification of new antiviral compounds.
Scientific and technical skills required by the candidate
The candidate must be interested in immunology, virology and bio-engineering. (S)He must be enthusiastic, conscientious, hard-worker, prone to teamworking but independent. Speaking/writting english fluently is suitable.
Keywords
3D bioprinting
Mucosa/skin equivalent
Host/pathogen interactions
Unit / team / Supervisor’s name:
UMR1064 INSERM/CRTI - HALARY

2018-05-Reims

Approche multi-échelle du suivi dynamique de la déconstruction de la biomasse lignocellulosique (DYNADECOL)
CONTEXTE
La transformation de la biomasse lignocellulosique pour l’obtention de produits chimiques, de matériaux et de carburants à travers les bio-raffineries est en plein développement. En effet, cette ressource qui peut être issue de résidus agricoles, forestiers ou de cultures dédiées, est considérée comme un moyen de contribuer à limiter notre dépendance vis-à-vis du carbone fossile et donc de limiter les rejets de gaz à effet de serre. De plus, son utilisation permet de s’affranchir de la compétition avec l’usage alimentaire dans le cas des plantes de grande culture.
La difficulté dans la valorisation de cette biomasse lignocellulosique réside dans sa complexité chimique et physique. Les polymères qui la constituent (cellulose, hémicellulose, lignine) sont présents dans des proportions variables, varient en terme de structure chimique et interagissent pour former un maillage tridimensionnel.
L’utilisation d’agents biologiques comme les enzymes est aujourd’hui considérée comme essentielle dans la déconstruction de la biomasse lignocellulosique, puisque ce sont des catalyseurs spécifiques et verts qui agissent dans des conditions douces, ce qui limite la consommation d’énergie. Mais la résistance à la dégradation de la biomasse lignocellulosique, appelée plus communément récalcitrance, nécessite d’effectuer un pré-traitement physico-chimique pour faciliter la progression et l’hydrolyse des enzymes dans la matrice lignocellulosique.
Afin de déterminer les facteurs chimiques et structuraux qui gouvernent l’hydrolyse, la caractérisation des substrats à différentes échelles spatiales s’avère nécessaire en combinaison avec un suivi en temps réel des modifications survenant au cours de la réaction enzymatique. En effet, la récalcitrance de la lignocellulose s’établit au niveau tissus, des cellules et des polymères, avec une variabilité importante.
PROJET
L’approche du projet consiste en la sélection d’échantillons contrastés d’une graminée modèle (tige de maïs) pré-traités ou non par un procédé hydrothermique standard hydrolysant les hémicelluloses. Les échantillons natifs et prétraités seront caractérisés par différents approches. La composition chimique à l’échelle de l’échantillon sera déterminée par des méthodes de chimie humide. La variabilité à différentes échelles d’organisation sera étudiée par différentes techniques d’imagerie ou de microspectroscopie (macro/microscopie de fluorescence, microspectroscopie vibrationnelle, imagerie MALDI, IRM). Une cartographie de la variabilité de composition chimique en fonction des tissus, types cellulaires pourra être dressée qui sera mise en regard de la réactivité vis-à-vis du traitement hydrothermique. Ces échantillons seront ensuite hydrolysés par des cocktails cellulasiques commerciaux complétés ou non avec des enzymes oxydatives ciblant la cellulose agissant en synergie avec les cellulases. L’hydrolyse des différentstissus, types cellulaires sera suivi en temps réel par des approches d’imagerie ou de microspectroscopie. Des profils de dégradation des différents tissus ou types cellulaires seront extraits et interprétés en fonction des connaissances générés sur les tissus ou types cellulaires.
Ce projet de thèse sera réalisé sous la co-tutelle du laboratoire FARE à Reims et du laboratoire BIA à Nantes (le doctorant passera 50% de son temps dans chaque laboratoire). Ces laboratoires travaillent sur la déconstruction de la biomasse lignocellulosique et son aptitude aux transformations biotechnologiques avec des outils et approches de pointe et complémentaires en microscopies, spectroscopies, biochimie et physico-chimie. Ils ont participé et sont impliqués dans différentes projets nationaux dédiés à la caractérisation de la biomasse lignocellulosiques (projets ANR Funlock 2014-2018, Lignoprog 2015-2018, HiSolids 2015-2019, projet FUTUROL 2009-2017,). Le projet de thèse s’appuie donc sur une expertise reconnue et unique en France, ce qui est une vraie opportunité pour le doctorant de réaliser une thèse de doctorat de haut niveau tout en tissant un réseau de compétences d’excellence.
MOTS CLES : lignocellulose, microscopie, enzyme, imagerie, modélisation
FORMATION ET COMPETENCES REQUISES
Le projet de thèse est par définition pluridisciplinaire. Le/la candidat(e) sera issu(e) d’un Master 2 ou équivalent, et aura reçu des enseignements dans au moins deux modules en biochimie végétale, biochimie des enzymes, physico-chimie des biopolymères, imagerie de microscopie. La connaissance théorique et pratique des outils et techniques de microscopie (fluorescence) et/ou de spectroscopie est un plus.
Rigueur et organisation, écoute, capacités à travailler en équipe et en interactions avec plusieurs personnes et à s’intégrer rapidement dans un collectif de recherche sont des compétences nécessaires pour réaliser les travaux de thèse dans les meilleures conditions.
INFORMATIONS PRATIQUES
Adresse des laboratoires d’accueil :
Laboratoire FARE, 2 esplanade Roland Garros, 51100 Reims, https://www6.nancy.inra.fr/fare/
Laboratoire BIA, rue de la Géraudière, 44300 Nantes, https://www6.angers-nantes.inra.fr/bia
Durée du contrat : 36 mois à partir du 1er octobre 2018, à partager entre Reims et Nantes
Salaire : environ 1400 € nets/mois
Référence de l’annonce : 2018-DYNADECOL
Responsables et contacts de la thèse :
Dr Gabriel Paës, gabriel.paes@inra.fr, 03.26.77.36.25
Dr Fabienne Guillon, fabienne.guillon@inra.fr, 02.40.67.50.16
Pour candidater : prendre tout d’abord contact avec les responsables de la thèse en envoyant votre CV et lettre de motivation. Consignes détaillées prochainement disponibles sur le site de l’école doctorale ABIES de l’Université de Reims Champagne-Ardenne à l’adresse :
http://www.univ-reims.fr/recherche-et-valorisation/ecoles-doctorales/offres-de-these-abies/offres-de-these-abies,22325,37043.html

2018-05-Louvain

The Laboratory of Enteric NeuroScience (LENS) and Cell and Tissue Imaging Cluster, University of Leuven, Belgium is currently hiring : a PhD student in Neuroimaging – Neurophotonics
PROJECT
In this project, we will explore the full extent of second-harmonic and fluorescence imaging techniques to investigate microtubular structures in neurons. Using non-linear optical approaches, structural information of specific biomolecules can be revealed in a label-free way. In combination with calcium imaging, electrical and optogenetic technology, we aim to investigate the relation between neuronal activity, axonal transport and microtubule structure.
PROFILE and REQUIREMENTS
- You received basic or advanced training in optics and have a keen interest in (neuro)biology or vice versa.
- You are a strong team player and motivated to become part of a multidisciplinary research group.
- You communicate well in English and have experience writing scientific papers in English
- You are passionate about (optical) technology, as well as neurosciences.
- You hold a master’s degree in optics/physics/technology or in the domain of life sciences (biotechnology, biology, biochemistry; bio-engineering (bio)medical sciences).
- You have a keen interest in (optical) microscopy and a good understanding of (neuro) biology (or vice versa)
- You have a critical scientific and quantitative attitude.
- Students who are eligible for a Chinese Student Council (CSC) fellowship are encouraged to apply.
OFFER
We offer:
- A position as a full-time (100%) postdoctoral fellow/researcher on an annual contract basis with the possibility of renewal within the budgetary limits of the project and depending on a positive evaluation.
- A dynamic and international research environment with access to multiple advanced imaging systems (confocal, multiphoton, intravital, super resolution) set in a vast neuroscience community.
- Salary scales are set according to university regulations within the available budget of the research project and depending on the candidate’s relevant former professional experience.
- Starting date: as soon as possible
Living in Leuven:
http://www.kuleuven.be/english/living
INTERESTED ?
Send your CV and a letter of interest (including one or two references) via the job site of the KU Leuven or directly to Prof. Dr. Pieter Vanden Berghe (pieter.vandenberghe@kuleuven.be) For further information, you can send an email to the same address. Feedback: Only candidates who make it to the 2nd selection round will be notified by July 15th 2018 at the latest. You can apply for this job no later than June 30, 2018 via the online application tool KU Leuven seeks to foster an environment where all talents can flourish, regardless of gender, age, cultural background, nationality or impairments. If you have any questions relating to accessibility or support, please contact us at diversiteit.HR@kuleuven.be….

2018-04-Lille

Doctoral grant (funded by I-SITE ULNE) : Synchronization of the mammalian circadian clock with metabolism: biophotonic approaches coupled with mathematical modeling
CONTEXT The team of Marc Lefranc at PhLAM develops data-driven mathematical models to describe the dynamics of the circadian clock, which synchronizes to the day/night cycle and orchestrates many biological functions. The team of Laurent Héliot at PhLAM has leading expertise in tracking the dynamics of molecules and their interactions using real-time biophotonic approaches in living cells.
SUBJECT There is increasing evidence that disruption of the circadian clock in metabolic organs plays a key role in pathologies such as obesity or diabetes. To clarify the mechanisms involved, we have designed a mathematical model of the mammalian liver clock synchronized to feeding/fasting cycles via the intracellular factors NAD+ and AMP (Woller et al, Cell Rep 17, 1087, 2016). We seek a PhD student to develop biophotonic experiments with cell cultures to obtain data for validating and extending this model. Using reporters for key metabolic actors such as SIRT1 or AMPK, as well as for core clock genes, we will quantify how various factors reset the circadian clock of hepatocytes and compare measurements with model predictions, but also validate molecular interactions playing a central role in the model. There will be a strong interaction with the modeling part of the project, to which the candidate is also welcome to contribute.
PROFILE Candidates should have a strong motivation for quantitative approaches to biological systems, combining biophotonic experiments with mathematical modeling. Since the student will interact closely with experts in microscopy and biophotonics, mathematical modeling, and biology, excellent communication skills and a capacity to work in an interdisciplinary environment are required. Applicants with a physics/optics or a biological background will be both considered, however some familiarity with complementary expertises, in particular modeling, will be appreciated.
APPLICATION The contract is for 3 years. Funding is already secured from the University of Lille Nord Europe ISITE project. Candidates should send as soon as possible a cover letter stating their motivations and curriculum vitae to Marc Lefranc (marc.lefranc@univ-lille1.fr).
WHERE On the Science and Technology campus of the University of Lille, in northern France. Lille is the core of the 4th French urban area (1.2 M people) and is connected by high-speed trains to Brussels (40 min), Roissy airport (50 min.), Paris (60 min), and London (80 min). With a lively atmosphere and a reasonable cost of living, Lille is an attractive place to stay.

2018-02-Rennes

High-content multiplex FRET biosensors to simultaneously monitor mitochondrial functions in cancer cells
3 keywords : cancer / mitochondria / FRET biosensors ; ACRONYM mitoFRET ; Unit/Team of supervising099ff> : IGDR/team « Quantitative Fluorescence Microscopy » ; Name of the scientific director and co-director : Marc Tramier / Giulia Bertolin ; Contact : giulia.bertolin@univ-rennes1.fr, marc.tramier@univ-rennes1.fr

Socio-economic and scientific context : This project is proposed by the “Quantitative Fluorescence Microscopy” team. The goal of the team is to develop novel technologies and applied methodologies in fluorescence microscopy to study protein-protien interactions, protein dynamics and catalytic activities in living samples. Giulia Bertolin, recently recruited in the team (CR2 CNRS) is an expert in mitochondria and focus its research in the link between mitochondria and cancer.
The projects benefits from an exceptional environment in terms of equipment – with a fastFLIM prototype microscope developed within the team and co-founded by IBiSA, Rennes Métropole and Région Bretagne, and complementary tools within the team such as multiplex FRET and HCS-FLIM. The project also benefits from the collaboration with the GEO team of Marie-Dominique Galibert, whose expertise in the field of melanoma and the mechanisms of resistance in BRAF mutant melanoma.

Open questions : Taking into account our current knowledge on mitochondrial physiology, one fundamental question remains unanswered: how are ATP production, mitochondrial turnover and oxidative stress simultaneously regulated, both in physiological and in cancer conditions? To answer this extremely multifaceted issue, multiple FRET biosensors of mitochondrial functions will be used simultaneously. For this project FRET biosensors will be used in conjunction with high-content screening procedures to monitor the global mitochondrial activity, potentially leading to the integration of FRET-based assays to develop innovative strategies of personalised medicine. This innovative approach will be applied to cancer cells of melanoma to underline the contribution of mitochondrial functions to the pathology.

Thesis milestones : During his/her PhD internship, the selected candidate will develop three main axes:
1. Validation of multiplex FRET approaches applied to mitochondrial biosensors. We propose to apply our validated multiplex approach to determine how three mitochondrial functions are intertwined: ATP production, ROS production and the NAD+/NADH ratio.
2. Development of new FRET biosensors of mitophagy and ATP production to be used with multiplex approaches. The aim is to characterize a new FRET biosensor based on the mitophagy marker LC3 relying on the conformational changes of LC3 observed in vitro. A second biosensor we are currently building is based on the ATP5B subunit of complex V of the mitochondrial respiratory chain
3. Adapt the multiplex FRET approaches to high content screening (HCS) methodologies to analyse mitochondrial biosensors in cancer cells. This screening will be performed in melanoma cancer cells, currently used in the first phases of pharmacological trials. Our screening will be useful to understand the existence of such mitochondrial signatures in a biological context closer to the patient.

Methodological and technical approaches :  Development of methods and techniques of quantitative microscopy, multiplex FRET by FLIM in HCS mode. Development of new FRET biosensors for mitophagy and for ATP production. Cell biology approaches in cancer cell line paradigm (melanoma) to unveil the existence of mitochondrial signatures in this biological context.

Scientific and technical skills required by the candidate : The candidate must have a strong competence in microscopy applied to biology (M2 in biological-health sciences or physics-bio interface), with complementary skills in cell culture and molecular biology. Knowledge of mitochondrial physiology would be a plus.

2018-01-Birmingham/Nottingham

Investigating the role of actin dynamics on receptor clustering and oligomerisation
Project Description
Project Overview and Aims : One of the major ways in which cell-cell communication is mediated is through the binding of chemical messengers to cell surface proteins, called receptors. The way in which receptors relay their signals to the cell cytoplasm and nucleus is highly dependent on how they are organised within the cell membrane. The actin cytoskeleton is critical for this organisation and plays a key role in receptor clustering and oligomerisation, as well as potentially in the organisation of how receptors interact with their signalling proteins. Recently a very dynamic fine F-actin network has been identified at the cell cortex which allows for rapid movement of receptors and actively drives receptor clustering, with actin polymerisation regulated by the Arp2/3 and formin proteins. This project will use a combination of advanced microscopy techniques such as single molecule localisation microscopy (SMLM), live cell super-resolution imaging and fluorescence correlation spectroscopy (FCS) to visualise this F actin and it’s dynamics with high-resolution. Alongside this we will monitor receptor dynamics and diffusion to describe how the cytoskeleton influences receptor behaviour and to investigate the receptor specific actin binding proteins and signalling pathways that drive this behaviour. In this work we will focus on two major classes of receptors: G protein coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs).
Project Plan : The project will use gene editing techniques (CRISPR-Cas9) to fluorescently tag receptors at natural levels of expression in a Jurkat T cell line which naturally express several cell surface receptors linked to the cytoskeleton (GPCRs – CXCR4 chemokine, Adenosine- A2A and -A2B; RTKs – EGFR). By expressing fluorescent versions of these receptors along with a fluorescent actin the interaction between the receptors and cytoskeleton can be visualised. The study will also utilise small molecule inhibitors of actin polymerisation and fluorescent receptor ligands to understand how this interaction is modified by ligand binding or cytoskeletal disruption.
Techniques and project organisation This will be a multi-disciplinary project giving the student experience over a wide number of techniques including cell culture, molecular biology, CRISPR-Cas9 and standard biochemical pharmacological techniques. However, the main focus will be on microscopy and advanced imaging approaches to looking at cytoskeletal and
receptor organisation in the cell. The project will be split between the Medical School in Birmingham and the School of Life Sciences in Nottingham and will take advantage of state of the art systems and imaging expertise. Both sites have newly refurbished imaging facilities with Nottingham having expertise in FCS and receptor dynamics and Birmingham in SMLM and actin dynamics. Both imaging facilities are supported by microscope and image analyst specialists and have access to advanced computing facilities. The project will be initially based mainly in Birmingham, but with increasing periods of time spent in Nottingham for the pharmacological and FCS-based aspects in years 2 and 3. However, the student will meet with both supervisors on a regular basis to ensure that the project is successful.

The project is one of six that has been funded through the Centre of Membrane Proteins and Receptors (COMPARE: http://www.birmingham-nottingham.ac.uk/compare/index.aspx) that focus on receptor clustering. The six studentships will form a doctoral training programme that will provide additional training and opportunities for collaboration.
Applications should include a letter explaining why this project is of interest to the applicant along with a CV and the names of two referees. They should be sent to BR-BN-COMPARE BR-BNCOMPARE@ exmail.nottingham.ac.uk by 31 January.
Funding Notes Funded by COMPARE, fees and stipend at UK rates for UK and EU nationals.

2017-10-Rennes

Création d’un automate d’analyse d’images et d’un prototype de microscope automatisé
Offre de Thèse CIFRE (Informatique/Electronique)
Le laboratoire : L'Institut de Génétique et Développement de Rennes (IGDR) est un laboratoire de recherche académique en biologie cellulaire, sous tutelle du CNRS et de l'Université de Rennes 1. L’équipe « Une ingénierie inverse de la division cellulaire » (CeDRE, Resp. J. Pécréaux) vise à comprendre les aspects physiques et mécaniques de la division cellulaire par une approche interdisciplinaire : elle combine biologie, microscopie, modélisation biophysique basée sur une quantification des expériences par la physique expérimentale et les statistiques, analyse d’image et du signal. Son activité requiert l’utilisation et le développement d’approches de microscopie innovantes et quantitatives.
L’équipe « Microscopie de Fluorescence Quantitative » (Resp. M. Tramier) est directement adossée à la plateforme de microscopie MRic et collabore étroitement avec les biologistes de la communauté rennaise. Sa vocation est de développer des techniques et des méthodologies en microscopie de fluorescence pour étudier la dynamique des interactions protéiques et des activités biochimiques sur échantillon vivant. Son activité se situe à l’interface entre cette recherche méthodologique et son application en biologie pour répondre à de nouvelles questions d’intérêt.

L’entreprise : Combo Microtech, spin-off de l’Institut de Développement et Génétique de Rennes, a développé une technologie de rupture qui améliore considérablement la performance des microscopes et rend leur utilisation aisée. Son potentiel peut lui permettre de s’affirmer comme la plateforme universelle pour interfacer et piloter les microscopes utilisés dans la recherche en sciences du vivant.
A partir de sa technologie-socle, le programme d’innovation “Combo-smart” a pour objectif de rendre les microscopes capables d’acquérir les images de façon intelligente et autonome. Précisément il s’agit de détecter les événements d’intérêt pour automatiser la prise d’image afin d’en maximiser la qualité et éliminer les données inutiles.

Contexte : La thèse s’effectuera au sein de l'équipe de Jacques Pécréaux, en lien étroit avec celle de Marc Tramier et l’équipe R&D de Combo Microtech. La microscopie de fluorescence est un outil central dans la compréhension du vivant. Elle permet de suivre la localisation d’un ou plusieurs composants de la cellule au cours du temps. Afin d’étudier des événements rares ou de tester des banques de molécules sur des échantillons vivants (crible), il est souhaitable d’automatiser l’acquisition des images. Nous avons récemment breveté une approche innovante du pilotage des périphériques utilisant un microcontrôleur programmable. Cette approche permet des gains entre 3x et 10x en vitesse d’acquisition. Ce travail est valorisé par la startup Combo Microtech récemment créée. En lien avec cette entreprise, les équipes de l’IGDR mettent en oeuvre un nouveau programme de recherche visant à réaliser une analyse à la volée des images acquises afin de modifier le pilotage de l’expérience en fonction de mesures réalisées sur l’image. A terme, nous souhaitons créer un automate de microscopie.

Objectifs : Lors de cette thèse nous souhaitons ainsi concevoir et développer un prototype de système embarqué, appelé smart-cam, capable d’analyser à la volée des images de microscopie du vivant en utilisant des algorithmes bâtis sur des librairies d’analyse d’image classique en vision industrielle (type openCV) afin d’assurer des performances optimales et utilisant un système d’exploitation embarqué type linux. Ce système embarqué pilotera donc une caméra scientifique, réalisera l’analyse, retournera des informations de pilotage au microcontrôleur en charge du pilotage de l’expérience. Ce dernier, programmé selon un paradigme « machine d’états » orchestre les différents périphériques afin d’optimiser l’acquisition des images. Cela impliquera donc une évolution des firmwares de ce composant. Enfin, la smart-cam retournera à l’ordinateur les images analysées comme intéressantes afin de les stocker via un logiciel adéquat, dans un soucis de stockage parcimonieux. Ce prototype a vocation à démontrer la technologie et à constituer une étape vers le marché. Ainsi, une attention particulière sera portée à l’expérience utilisateur. Afin de parfaire ces aspects, deux applications seront poursuivies durant ce travail :
● l’acquisition à haut débit en utilisant une modalité particulière appelée imagerie en durée
de vie de fluorescence ;
● le suivi automatique de division cellulaire (un évènement rare sur des cellules humaines), sur
un grand champ avec passage à haute cadence d’acquisition lors des évènements de mitose,
dans la perspective de recherche en cancérologie fondamentale.

Étapes de la thèse :
● Réaliser un prototype v1 dont les algorithmes sont programmés “à la main” pour affermir les choix technologiques : OS embarqué, type de système, cadre de développement, modalité de dialogue avec les autres composants, etc. Cela se basera sur la preuve de concept en cours de développement. (6 mois)
● Réaliser une interface minimale permettant le transcodage. Concevoir ainsi le prototype v2 dont le code embarqué sera auto-généré sur la base de l’algorithme fourni par l’utilisateur dans 90 % des cas. Proposer une interface simple et ergonomique permettant de démontrer le système. (1 an)
● Tester et améliorer le prototype sur les deux applications proposées. Ces deux cas permettront de démontrer l’intérêt de l’innovation proposée en plus de permettre aux équipes de recherche de poursuivre leur travaux. (1 an)
● Rédaction, valorisation et publication (6 mois)

Compétences recherchées :
● Une formation typiquement en science de l’ingénieur ou en électronique, avec une bonne connaissance des systèmes embarqués.
● Maîtrise de java ou d’un langage orienté objet. Une expérience de développement d’un algorithme d’analyse d’image sera un plus.
● Programmation en C et/ou C++.
● Connaissance génériques des OS et systèmes embarqués. Familiarité avec Linux et sa gestion de périphériques.
● Motivation pour travailler dans un environnement multidisciplinaire (mathématiques appliqués, physique de la matière molle, optique, biologie cellulaire), en équipe, et capable de communiquer professionnellement en anglais.

Détails de l’offre :
Date : à partir de l’automne 2017 pour une durée de 3 ans.
Lieu : IGDR -> 2 Avenue du Professeur Léon Bernard, 35000 Rennes
Combo Microtech -> 1137 A avenue des Champs-Blancs, 35510 Cesson-Sévigné
Rémunération : 30.000€ bruts annuel
Contact : jacques.pecreaux@univ-rennes1.fr
marc.tramier@univ-rennes1.fr

2017-09-Bordeaux

Thesis Project
Host Laboratory : Interdisciplinary Institute for Neuroscience (IINS), UMR5297, Bordeaux – France
In the team “Quantitative Imaging of the Cell” directed by Jean-Baptiste Sibarita.
Start : PhD start will be beginning of 2017 academic year. Possibility to perform a Master 2 internship or a last year of engineer school internship during 2016-2017 academic year.
The PhD financing will be done through the ANR project “soLIVE” granted in 2016.
Keywords : Light-sheet microscopy; Super-resolution; Single Particle Tracking; Structured Illumination Microscopy;
Drosophila embryos.
Project description : A PhD position is currently available at the Interdisciplinary Institute for Neuroscience (IINS) at Bordeaux to develop new super-resolution approaches for probing the fast and long-term dynamics of proteins in depth within complex tissues at high spatial resolution. This work will be based on a light-sheet microscope recently developed in the team and named soSPIM, which combines a single-objective with micro-fabricated chips featuring 45° mirrors1. We already demonstrated the capabilities of this systems to perform multi-scale 3D imaging from the whole drosophila embryos scale down to the single cell scale. In addition, we have shown that the combination of the optical sectioning provided by the light sheet excitation with a high numerical objective enables to perform single molecule based super-resolution up to 30 μm deep above the coverslip. The aim of the project will be to improve the imaging capabilities of the soSPIM system to probe the various dynamics of adhesion proteins during the development of drosophila embryos at high spatial resolution. It will consist of implementing on the soSPIM system single particle tracking approaches and structured illumination microscopy methods2 to probe the fast and long-term dynamics of proteins respectively. To achieve this goal, we will implement both excitation beam shaping3 and adaptive optics4 in order to optimize the excitation and detection paths, respectively, and implement specific micro-fabrication processes to create devices dedicated to the imaging of drosophila embryos. In collaboration with G. Giannone team (IINS, Bordeaux) and N. Brown team (Gurdon Institute, Cambridge), we will then study the formation and maturation of adhesion sites during drosophila embryos development and their role in muscle tissue formation.
Required skills : The candidate should be highly motivated and should show a strong interest in the development of imaging tools for biology. Prior knowledge in optical microscopy and interest in micro-fabrication processes and biology would be preferred. The candidate is strongly encouraged to perform his Master 2 internship or last year of engineer school internship on this subject before the thesis.
Contact : To apply, candidates should email a CV and a motivation letter to :  Rémi Galland (remi.galland@u-bordeaux.fr)
References :
1. Galland, R. et al. 3D high- and super-resolution imaging using single-objective SPIM. Nat. Methods 12, 641–644 (2015).
2. Gustafsson, M. G. L. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc. 198, 82–87 (2000).
3. Chen, B.-C. et al. Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution. Science (80-. ). 346, 1257998–1257998 (2014).
4. Izeddin, I. et al. PSF shaping using adaptive optics for three-dimensional single-molecule superresolution imaging and tracking. Opt. Express 20, 4957–67 (2012).

2017-09-Strasbourg

Site-selective faithful monitoring at the single molecule level of local changes in nucleic acids
UMR 7213 CNRS, Laboratoire de Biophotonique et Pharmacologie
Faculté de Pharmacie
74 route du Rhin
F - 67401 Illkirch
http://www-lbp.u-strasbg.fr

Applications are being sought for a 3 years PhD position in the Laboratory of Biophotonics and Pharmacology in Strasbourg, France (http://www-lbp.unistra.fr/). The project is funded by The French National Research Agency and will be carried out under the supervision of Pr Yves Mély and Pascal Didier.
We are seeking a highly motivated student with expertise in fluorescence and microscopy, with a keen interest in applying this knowledge to biology and notably nucleic acids. Fluorescent labelling of nucleic acids has been revolutionized by the introduction of deoxythienoguanosine, thG, a truly faithful surrogate for G, which reproduces the structural context and dynamics of the native nucleotide and remains well fluorescent in nucleic acids. Moreover, thG exhibits an environment sensitive emission that opens a fantastic range of applications. In this project, our ambition is to apply this outstanding probe in single molecule measurements, in order to faithfully monitor for the first time local changes in nucleic acids on a single molecule level. To reach this challenging aim, we will enhance thG emission and photostability using surface plasmon resonance together with DNA origamis to precisely control the metal/fluorophore distance. The developed system will be used to characterize the poorly understood dynamics of the successive molecular steps involved in the replication of the DNA methylation pattern by the UHRF1/DNMT1 tandem. This thGbased single molecule fluorescence approach will help solving a large range of biological questions involving local and transient structural nucleic acid changes. Moreover, the deciphering of the molecular mechanism of the base flipping steps in DNA methylation replication by the UHRF1/DNMT1 tandem should provide new clues on its possible blockage and thus, lead to major therapeutic applications in pathologies, such as cancers and neurodegenerative diseases, where the methylation profile is modified. We are looking for creative students that can contribute with their own ideas and proposals.
Candidates having a master of physics or biophysics or physicochemistry should send a detailed CV to yves.mely@unistra.fr or pascal.didier@unistra.fr.
Deadline for application : September 30, 2017

2017-09-Paris

PhD position in the mechanics of neuronal development
A 3-year funded PhD position is available at the Institut de Biologie Paris Seine to investigate the role of mechanical forces in the construction of a neuronal circuit in vivo. During neuronal circuit formation, neurons move towards their final location while growing axons towards their target. While the biochemical guidance cues involved in neuronal migration and axon elongation are extensively studied, the contribution of mechanical forces in these processes remains largely unexplored in vivo. In the lab we address this question using the zebrafish olfactory circuit as a model system. Its location underneath the skin of the embryo makes it amenable to live imaging and mechanical perturbation. We already obtained imaging and functional data suggesting an important function for mechanical cues in the formation of the circuit: olfactory axons extend through the effect of extrinsic mechanical forces that drive the passive displacement of neuronal cell bodies away from their axon tips (Breau et al., Nat Comm, in press). The purpose of the PhD project is to further identify the origin and contribution of mechanical forces in the construction of the circuit, and the molecular mechanisms involved in force propagation and sensing. To achieve this goal, the student will use a pluridisciplinary strategy combining multiscale live imaging, genetic/optogenetic tools and physical approaches to measure and perturb forces in vivo. We are looking for a highly motivated student willing to join an interdisciplinary environment involving strong interactions between biologists and physicists.
Requirements :
- Master degree in cell/developmental biology or in biophysics
- Strong interest towards interdisciplinary work
Additional beneficial skills :
- Experience with zebrafish
- Skills in confocal, biphoton or light sheet microscopy
- Experience in image analysis (Image J, Matlab)
Starting date : between October 2017 and January 2018. To apply, please send your CV and references to Marie Breau, Institut de Biologie Paris Seine : marie.breau@upmc.fr

2017-09-Strasbourg-Karlsruhe

Study of the organization and dynamics of CD44 / MET complexes at the plasma membrane stimulated by endogenous (HGF) and bacterial ligands (Internalin B) by advanced microscopy techniques
Laboratoire de Biophotonique et Pharmacologie
(LBP) UMR 7213 CNRS
Faculté de Pharmacie
74 route du Rhin
F - 67401 Illkirch
http://www-lbp.unistra.fr/rubrique3.html

Institute of Toxicology and Genetics
Karlsruhe Institute of Technology (KIT)
Postfach 3640
D-70621 Karlsruhe
http://www.itg.kit.edu/orian-rousseau.php

We are looking for a young scientist willing to work on an interdisciplinary project in cell biology using advanced fluorescence microscopy techniques. The aim of this project is to characterize the organization and dynamics of CD44 transmembrane glycoproteins that play an essential role in cell migration and proliferation in physiological and pathological situations. The variety of CD44 functions is related to their ability to associate with ligands such as MET (receptor tyrosine kinase (RTK)) and HGF (human growth factor). Moreover, Listeria monocytogenes through its protein Internalin B (InlB) uses also this MET pathway to infect host cells. As these processes take place at the plasma membrane, the membrane organization plays a crucial role, in particular the lipid rafts, which are small and dynamic membrane domains enriched with sphingolipids and cholesterol. The objective of this PhD thesis will be to investigate the interplay between CD44v6, MET and the lipid domains on HGF and InlB stimulation. The PhD student will first quantitatively characterize the interaction of CD44v6 with MET promoted by HGF and InlB by FLIM-FRET in live HEK-293 cells. The amounts of CD44v6/MET complexes and MET dimers will be determined in non-activated cells and compared to those in the presence of HGF or InlB. Further information will be obtained by using downregulated CD44v6 (siRNA and specific Crispr/cas constructs) and primary cells isolated from a Cd44v6 floxed mouse. Quantitative data on MET dimerization in cells in which the expression of CD44v6 can be manipulated will provide valuable insights into the role of CD44v6 in MET dimerization. In parallel, deletion mutants of InlB will be used to analyze the contribution of the different InlB domains in the recruitment of CD44v6. These investigations will be completed by solution measurements to characterize the interaction of wild-type and mutant InlB with the purified CD44v6 ectodomain. The comparison with HGF data will shed light on how L. monocytogenes takes advantage of the MET/CD44v6 pair to interact with and then enter non phagocytic cells. In a second task, the phD student will investigate by two-color super-resolution localization microscopy the role of lipid rafts in the CD44v6/MET complex formation upon HGF and InlB activation. Localizations of membrane proteins fused to photoactivable proteins or organic fluorescent dyes will be pinpointed and their spatial distribution analyzed relative to those of lipid rafts. Treated cells with altered cell membrane organization will also be measured. This will provide an extensive view of the distribution of CD44v6 or MET in and out of the raft domains. Complementary information in live cells will be obtained by single particle tracking (sPT). This should help to further decipher the mechanism of CD44/MET complex formation upon HGF- and InlB-activation. Taken together, these data will give a better understanding of the interaction between CD44v6 and MET and its connection with the lipid domains, as well as its stimulation by HGF and InlB. Comparison of HGF and InlB stimulations should also give a clearer picture of how InlB hijacks the MET-related pathway to prompt bacterial invasion.

This project is funded for a 3 years PhD position by the French-German University and will be carried out under the double supervision of Pr. Yves Mély (Strasbourg) and Pr. Veronique Orian-Rousseau (Karlsruhe).
The student should have a background in biophysics with interest for biology or a background in biology with interest for biophysical techniques. Excellent communication skills in spoken and written English are expected.
Interested individuals should send a curriculum vitae, a motivation letter, and recommendation letter(s) (or contact details of at least one referee) by e-mail to yves.mely@unistra.fr or veronique.orian-rousseau@kit.edu.
Deadline for application : September 30, 2017

2017-08-Gand (Belgique)

Visualization of molecular dynamics of necroptosis
Location : VIB-UGent, Center for Inflammation Research (IRC)
Lab : Molecular Signalling and Cell Death unit
Position : PhD – SB application
About the lab : The Molecular Signalling and Cell Death Unit (MSCDU) of Prof. Peter Vandenabeele performs innovative research in molecular signalling of different cell death modalities and inflammation at three major levels: molecules, cells, and organisms. Several research projects translate fundamental knowledge into potential clinical applications, while other research projects are more explorative starting from simple biological questions. The team supervised by Prof. Franck Riquet unravels necroptosis based on advanced microscopy and biosensor constructs to visualize the dynamics of molecular events.
Your job : The death dynamics team of Franck Riquet consists of ~ 5 people and is embedded in Vandenabeele Lab, which consists of around 35 people that perform research in the field of cell death and inflammation. We are looking for an enthusiastic scientist/student to start a PhD in our team. When TNF is binding to TNF receptor 1 (TNFR1), the cellular outcomes can be fundamentally different: survival and pro-inflammatory signaling versus cell death signaling by apoptosis or necroptosis. The former outcomes are initiated by receptor-associated complex I formation, while the latter outcomes are a consequence of a cytosolic complex II. In this project we want to visualize the dynamics of this complexes, especially complex II by using cellular biosensor constructs. These will be used to identify and validate the biochemical and cellular processes (Ca++, ROS, metabolism, pHi, RIPK1 complex formation) that are crucial in the propagation of necroptosis. If we can successfully visualize these cellular outcomes, we also want to develop transgenic models in which we can score the dynamics of these processes in vivo or ex vivo. Fundamental insight in the cell biology of necroptosis regulation has important biomedical implications on the long term, to examine which pathophysiological conditions are associated with necroptosis and to develop strategies to modulate cell death outcomes by cellular and metabolic conditions rather than targeting the process itself. The position is expected to be funded by an SB PhD grant (Strategic basic research, FWO), which should be defended by the candidate.
Profile :
• The candidate should have a Master degree in the field of biomedical sciences, biotechnology and biochemistry, or bioengineering.
• The candidate should be able to work independently and at the same time be a team-player
• The candidate should have excellent communication skills and a strong passion for scientific research in general
• The candidate is expected to have strong hands-on experience in molecular and cell biology techniques (the project involves mainly in vitro work).
We offer : An excellent and international research environment with young and motivated people. Great expertize in field of cell death and inflammation, (inter)national collaborations, close guidance, and the availability of several core facilities with high-tech equipment.
Contact person : Prof. Franck Riquet, Prof. Peter Vandenabeele
Deadline of application : 15/08/2017 – you will be invited for an intake interview.

2017-05-Rennes

PHD POSITION IN BIOMECHANICS AND MORPHOGENESIS IN C. ELEGANS, IGDR, Rennes, France
Animal development requires the coordination of growth which controls cell proliferation, and morphogenesis which controls the acquisition of a particular shape. Coordinated morphogenesis between different organs and tissues is usually controlled by classical biochemical signalling pathways (Notch, Hedgehog, Wnt etc). However morphogenesis can also be controlled by a biomechanical rather than a biochemical signal. It is particularly the case for the elongation step of C. elegans embryonic morphogenesis. This signalling pathway covers three tissues of different developmental origins: a mechanical signal generated by muscle contractions is received by the dorsoventral epidermis. It is then transmitted to the lateral epidermis where it controls the establishment of a planar polarity required for elongation (Gillard et al, in prep).
The purpose of the PhD project is to decipher the last step of this biomechanical transtissular signalling pathway which controls embryonic morphogenesis. Using state-of-the-art gene editing and quantitative live imaging techniques you will identify and characterise the molecular mechanisms allowing signal transduction between the dorsoventral and lateral epidermis.
Key words: Biomechanics/ Signalling/ Morphogenesis/ Development/ C. elegans
Techniques: Imaging / Genetics / Gene editing / Biochemistry
Position taken: October 2017
Assignment: Molecular mechanisms of epithelial polarity maintenance - Institute of Genetics and Development of Rennes
Founding: Fully founded 3-year PhD fellowship
Deadline: 22-05-2017
To apply please send a CV, a cover letter and the name of 2-3 referees to: gmichaux@univ-rennes1.fr

2017-05-Lille-Leuven

Improved methods for spatial-temporal fluorescence imaging of cell activity
Supervisors Cyril Ruckebusch (LASIR CNRS U. de Lille) Peter Dedecker (Department of Chemistry, KU Leuven)
Keywords Super-resolution, Fluorescence, Imaging, Living cell, Chemometrics, Data analysis, Image processing
Summary The PhD projects aim to develop a new methodology -from cell preparation to data analysis- to extract superresolution spatial-temporal information on cell activity in response to some external stress. Ultimately this work aims to provide new insights into how biological systems are structured at the nanoscale, and how this structures provides e.g. signaling specificity, using the latest methodologies in imaging and data analysis.
Context Fluorescence microscopy is about the only technique that can provide structural and dynamic information on selected components in live cells while only minimally interfering with the chemical or biological system under study. Previously limited to a spatial resolution of a few hundred nanometers due to diffraction, the recent development of super-resolution fluorescence imaging, which is one of the major technological advances of the last decade, has allowed direct access to the tens of nanometers length scale. To achieve such super-resolution in wide-field the key is the use of smart fluorophores that display fluorescence dynamics in combination with tailored data analysis and image processing techniques. However, simply visualizing the spatial distribution of molecules is not sufficient to understand biological issues occurring in living cells. In particular, improved superresolution fluorescence imaging techniques are required to follow and investigate biological dynamics.
Research project One of the most important issues in biology is understanding signaling activities in living cells. How does the cell transfer specific signals through a complex interaction network in order to trigger an action in response to a stressing event? To achieve this transduction, the cell must regulate its response by managing the spatial temporal organization of its constituents. This means that a given molecule not only has to be present in the cell but has to be there in the right place at a particular time. Advances in biosensor technology (chemically smart labels) have made possible to visualize and quantify the cellular activation dynamics in living cells. Information about when and where activity arises is assessed following how the fluorescence emission of the probe changes conditional on some aspects of the environment. One approach consists of mapping Forster Resonant Energy Transfer activity at an interesting spatial and temporal resolution. However, the construction of diffraction unlimited and high-sensitivity superresolution FRET activity maps requires acquiring and interpreted multicolor donor acceptor data, as well as developing specific data analysis methods. On top of that, several side issues complicating the development of robust models have to be solved such as handling stationary signals, dealing with strong photobleaching and low S/N to noise ratio or unraveling signal multiplexing when several biosensors are present in the same cell.
Application The candidate should be highly motivated, enthusiastic and opened to interdisciplinary science and international collaborations. The position is administratively based in Lille but work will be equally shared between U. de Lille and KU Leuven both offering an ideal environment and top-level equipments. The PhD applicant will join a 36 months bi-national (“cotutelle internationale”) PhD Program and will get diploma from both universities. Candidates should hold a master in physics, (bio-)chemistry or equivalent, and ideally have experience or have shown a strong interest in optical microscopy and data/image analysis. To apply, please send a CV and the name of 2 references to Cyril Ruckebusch (Cyril.ruckebusch@univ-lille1.fr) and Peter Dedecker (peter.dedecker@chem.kuleuven.be).