The roux Lab

Aurélien Roux

Professor, Principal Investigator

My research focus is on the mechanical and dynamic properties of lipids and proteins involved in membrane traffic. Specifically, how do these properties produce efficient membrane deformation, lipid and protein sorting within traffic intermediates, and fission of separating membranes?

My research focus is on the mechanical and dynamic properties of lipids and proteins involved in membrane traffic. Specifically, how do these properties produce efficient membrane deformation, lipid and protein sorting within traffic intermediates, and fission of separating membranes? I have previously shown that:

  1. Specific lipid species can be segregated into areas of different within membranes, depending on how they affect membrane rigidity,

  2. Induction of lipid phase separation along tubules leads to membrane fission,

  3. Dynamin has a new kind of mechano-enzymatic activity that twists the membrane to generate both constriction and tension for membrane fission.

  4. Nucleation of dynamin polymerization onto a tubule is membrane-curvature dependent, and its polymerization free energy is compatible with its deforming activity.

As a Ph.D student, I worked in collaboration with cell biologists (Bruno Goud’s lab, Curie Institute, Paris) and physicists (Patricia Bassereau’s lab, Curie Institute, Paris) in order to understand how membrane properties (e.g. bending rigidity, tension, and composition) facilitate or interfere with various stages of membrane traffic within cells. My main findings during this period can be summarized as follows:

a) I developed a minimal assay to study the formation of membrane tubules using the force generated by molecular motors. I coupled biotinylated kinesins with Giant Unilammellar Vesicles (GUVs) via streptavidin beads. Then, by allowing the GUVs and kinesins to sediment on a network of microtubules, I observed the generation of tubules growing at the speed of kinesin translocation (Roux et al. 2002).

b) Some lipids will spontaneously sequester into liquid-ordered (Lo) domains. These domains are characterized by an increased bending rigidity compared to liquid-disordered (Ld) domains. By fluorescent labeling of one such lipid species, I found that these lipids were partially excluded from membrane tubules pulled from GUVs by molecular motors (Roux et al. 2005).

c) I developed a method to induce lipid phase separation along lipid tubules. I showed that bleaching of a particular fluorescent lipid could oxidize 5 percent of the cholesterol present in GUVs, and that the oxidation of cholesterol induces phase separation of previously miscible lipids. Further, by bleaching fluorescent lipids in tubules, I induced phase separation along their length, and observed that membrane fission occurred at the boundary between domains of different composition (Roux et al. 2005).

My continuing interest in membrane fission led me to pursue post-doctoral work in Pietro de Camilli’s laboratory. In order to study the mechanism of membrane tubule formation and fission by dynamin, I created an assay utilizing membrane sheets on which I could monitor the activity of dynamin-induced tubulation. After the addition of GTP, I observed the contraction of the tubules and the formation of super-coiled membrane loops. This suggested a twisting activity of dynamin that I confirmed by attaching a small bead to the tubules and quantifying the rotation of these beads caused by dynamin-mediated GTP hydrolysis (Roux et al. 2006).

From July 2007 to April 2010, as a Chargé de Recherche in the CNRS, France, I have been interested in how membrane properties affect the polymerization of dynamin onto a template. An essential question about dynamin is how it is recruited to the neck of endocytic buds. By using a combination of micropipette and optical tweezers to extract tubules out of Giant Unilamellar liposomes, I could study the nucleation of dynamin polymerization onto tubules of radii ranging from 10 to 100 nm. I found that at a physiological concentration of 250 nM, dynamin is able to polymerize only on tubules comprised between 10 and 35 nm (19 nm in average) (Roux et al. 2010). This supports the idea that the build-up of membrane curvature during the formation of endocytic buds could spontaneously recruit dynamin at their neck.

From my earliest academic studies, I have been convinced that soft-matter physics could provide interesting tools and concepts for the understanding of living cell processes. Thus, I always tried to be at the interface between physics and biology. For my Ph.D. work, I chose to work in both cell biology and physics labs on the theme of membrane intracellular traffic.

Thirty years of membrane physics has led to reliable models and data describing the fundamental mechanical properties of pure lipid membranes. In contrast, intracellular traffic is a cell process that requires a great variety of mechano-enzymes to remodel, cut and transport membranes within cells.

My view is that the tools and concepts from membrane physics can fruitfully be applied to study membranes interacting with proteins involved in membrane traffic:

  • Technically, membranes can be used as force and deformation probes for the study of the mechanical properties of proteins involved in membrane traffic

  • Conceptually, membranes have very special properties and proteins interacting with bilayers must have evolved to exploit these properties

If physics is crucial for the understanding of membrane traffic, membrane traffic provides interesting objects for the discovery of new physics:

  • Most of these objects are working at the mesoscale, where physics laws are constrained by a small number (ten to several hundred) of molecules in interaction.

Moreover, many of the proteins use chemical energy to perform their tasks so equilibrium physics does not apply. Thus, understanding cellular trafficking requires the development of new theoretical tools and is a growing field of physics.

My long-term goal is to understand how protein and lipid assemblies coordinate to perform cell functions involving membranes: endocytosis, cell division, cell migration and others. These functions are based on essential physico-chemical abilities of membranes: deformation, fusion, fission, fluidity and permeability. I intend to understand how proteins exploit the peculiar physical properties of lipid membranes in order to proceed with their function.

Frédéric Humbert

Lab Technician

I joined Aurélien's lab when he started his lab at the University of Geneva in 2010. I work in his lab since then as a technician specialized in biochemistry.

Paulina Nowak

PhD Student

My PhD project is focused on mTOR complex 2 signalling and its interaction with the plasma membrane. I combine genetic, biochemical and biophysical approaches to study how membrane stresses, such as tension and lipid packing defects, impact cellular signalling pathways. These interactions are particularly interesting in the context of mTOR, as it is the main regulator of cellular growth and metabolism, and its dysregulation leads to cancer and other diseases.

I started my PhD in September 2018. Before that, I obtained my MSc in Biophysics at the Jagiellonian University in Cracow, Poland, where I worked in the group of Prof. Pyrc on the internalisation of human respiratory viruses to the host cell. I also worked in the group of Prof. Miaczynska at the International Institute of Molecular and Cell Biology in Warsaw, Poland, on the role of ESCRT proteins in cancer biology.

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Guillaume Pernollet

PhD Student

Mechanosensing, the recognition that cells are sensitive and responsive to their mechanical environment, emerged over the nineties and allowed breakthroughs in fields like Morphogenesis and Stem cells differentiation. However, the range of mechanical factors cells are sensitive to and how these factors, either individually or via their combined effect, impact tissues organization is not completely understood yet.

The goal of my PhD in the Roux lab at UNIGE is therefore to examine how tissue organization is impacted by mechanical and geometrical cues such as substrate rigidity, curvature or confinement. To achieve this, I culture epithelial tissues on hydrogel patterns and in hollow alginate capsules, which allow me to apply wide ranges of mechanical cues.

My PhD started at the Roux lab in January 2020. I studied at EPFL, Lausanne where I obtained a bachelor's degree and then a master's degree in Physics and a minor in Biotechnology.

Markku Hakala

Post-Doctoral Researcher

I am fascinated by complex cellular protein machineries that maintain cell morphology and provide force for cellular processes. During my PhD, I studied assembly and disassembly of actin filament networks in migrating mammalian cells. By using in vitro reconstitution and mammalian cells as a model system, I’m currently studying membrane invagination process in clathrin-mediated endocytosis. I’m focusing on how clathrin coat assembles on membrane and how it deforms membrane to promote endocytosis.

I did my PhD at University of Helsinki, Finland, under supervision of Pekka Lappalainen. During this time, I concentrated on how the turnover of dendritic actin networks is regulated in migrating cells by actin-binding proteins twinfilins and GMF. I joined groups of Aurélien Roux and Marko Kaksonen at University of Geneva in 2020.

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Anne-Laure Boinet

PhD Student

The aim of my PhD project is to further our understanding of the dynamics of coat formation and evolution in clathrin-mediated endocytosis. To this end I am using genetic engineering and microscopy techniques in live cells, using S. cerevisiae as a model.

This project is a joint PhD between the Roux and Kaksonen labs.

I started my PhD in November 2020. Prior to that, I worked for 1.5 years as a Research Associate in a biotech startup based in Oxford, UK, after obtaining my master’s degree in Biotechnology Engineering from the ENSTBB (Bordeaux, France) in 2018.

Maria Tettamanti

PhD Student

Marine Luciano

Post-Doctoral Researcher

Javier Espadas

Post-Doctoral Researcher

Living matter is compartmentalized at all organizational scales. But while this is so, it is the ability to adapt, connect and disconnect these compartments that makes life so unexpected and dynamic. Eukaryotic cells are also compartmentalized, first with respect to their environment, but also elegantly segmented within it. The barrier function of each compartment is achieved by unique fluid membranes with molecular machineries acting to transiently allow communication across the membrane. However, the ESCRT-III complex is the only machinery capable of adapting to and remodeling all membranes across the cell. Furthermore, the ESCRT-III complex was carefully designed during evolution as it is the only protein machinery related to membrane remodeling in the common eukaryotic ancestor of the Asgard archaea. In my postdoc, I am currently working on the biophysical and biochemical characterization of membrane remodeling by Asgard ESCRT-III proteins. I am trying to understand how these proteins have functionally evolved and identify the original mechanism of action of this machinery.

A chemist by training, I did my PhD in the laboratory of Vadim Frolov and Anna Shnyrova in the Membrane Nanomechanics group in the Biofisika Institute in Bilbao, Spain. During this time, I developed model membrane systems to reconstitute membrane fission and fusion processes by membrane remodeling proteins such as dynamin, atlastin and reticulon. I identified the mechanism of membrane fragmentation in the endoplasmic reticulum mediated by reticulon, counterbalancing membrane fusion by atlastin, both in vitro and in cellulo. Moreover, I also identified how membrane composition triggers the expected functionality of dynamin and dynamin-related proteins, and how changes in composition lead to functional promiscuity catastrophy to cell maintenance.

Yamini Ravichandran

Post-Doctoral Researcher

Self-organization is a fascinating process observed during various biological process and one such fascination is morphogenesis. Where biochemical signaling driven symmetry breaking events and physical processes such as cellular rearrangements, tissue folding work synergistically to pattern and mold tissues in a spatio-temporal manner. Mishaps in this process give rise to morphogenetic mutants and variable developmental phenotypes in a diverse range of organisms.

My project explores the interplay between long range cytoskeletal elements during morphogenesis observed in small organisms and deriving analogies from the physics of liquid crystals.

My previous scientific research focused on understanding intracellular components driving intracellular symmetry breaking events during cell-migration.

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Juan Manuel García Arcos

Post-Doctoral Researcher

My project in the team of Pr. Roux is to understand the relationship between cytoskeletal dynamics and membrane tension, with a focus on the establishment of membrane tension gradient by actin dynamics. I am generally interested in cell dynamics during cell migration, by using microscopy to describe quantitatively physical processes in cells.

I started my postdoc in the Roux lab in November 2021, after doing a PhD in the lab of Matthieu Piel at Institut Curie (France). During my PhD, I studied actin dynamics in confined amoeboid cells (see thesis link). I hold a bachelors degree in Biotecnology from the University Pablo de Olavide (Sevilla, my hometown), a masters degreee in Interdisciplinary Life Sciences from Paris Diderot University and a maters in Pedagogy and EdTech from Paris Descartes University.

Link to Juan Ma Thesis

Juan Ma's Google Scholar

Juan Ma's ORCID

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Claire Dessalles

Post-Doctoral Researcher

Morphogenesis, a central event in the embryo development, hinges on a finely orchestrated collective motion of cells, with protrusions and invaginations happening at well-defined positions. Topological defects, a small region where cellular alignment is perturbed, have been identified as organizers of these morphogenic events in vitro in 2D (Guillamat P. et al., 2022). During my postdoc, I am studying the coupling between topological defects, stress fields and morphogenesis in vitro, in and on 3D structures of various topologies. To quantitatively investigate this phenomena, I grow epithelia and myofibroblasts inside alginate microcapsules, which I produce using a 3D printed microfluidic device (Alessandri K. et al., 2016). Because shell thickness and diameter can be tuned, I can quantify cell motion, collective alignment and stress fields as a response to topology, curvature and rigidity. Using this controled model system, I hope to uncover the link between active matter, mechanics and morphogenesis.

I started my postdoc in January 2022 in the Roux lab. Prior to coming to Geneva, I did my PhD in the Hydrodynamics laboratory at Ecole Polytechnique (France). My thesis is entitled Forces in a microvessel-on-chip: system development, poroelasticity mechanics and cellular response (see link below). I hold a Mechanical Engineering degree from Ecole Polytechnique in France (2016) and an MSc in Bioengineering from EPFL in Switzerland (2018). I did my first master thesis in the Biophysics group at FAU in Erlangen (Germany) on cardiomyocytes mechanics and my second master thesis in the Microbs group at EPFL in Lausanne (Switzerland) on microactuators mechanics.

Claire's Google Scholar

Claire's Thesis

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César Bernat Silvestre

Post-Doctoral Researcher

ESCRT-III complex has emerged as a key player for deforming and breaking membranes. These processes are essential for many cellular functions, including biogenesis of MVBs, cytokinetic abscission, nuclear envelope sealing and exosome shedding among others. My aim is to understand the dynamics of the ESCRT-III complex in the different ESCRT-III cellular functions, and resolve what controls the time of the sequence recruitment of ESCRT-III machinery. Moreover, I am also interested in studying the function of CHMP1 and IST1 proteins, two ESCRT-III subunits, which form the fission complex and their role is understudied in vivo. For these purposes, I combine cell and molecular biology and biochemistry techniques.

I studied Pharmacy in Valencia (Spain) before joining the Biochemistry and Molecular Biology department for my PhD in Valencia. For my thesis, supervised by Fernando Aniento and María Jesús Marcote, I studied the transport of GPI-anchored proteins along the early secretory pathway in Arabidopsis, focusing on the role of GPI-anchor remodeling and p24 proteins as cargo receptors. Then, I joined the Roux’s lab in Geneva (Switzerland) in January 2022 for investigating the dynamics of the ESCRT-III complex assembly and fission in different cellular processes.

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Cesar’s Thesis

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Oriol Mane Benach

PhD Student

Morphogenesis consists of a series of complex events, including symmetry breaking, cell differentiation and shape changes. The intrinsic capacity of stem cells to self-organize into functional tissues has enabled the development of in vitro biomimetic structures such as organoids and gastruloids. These approaches have improved the understanding of the mechanisms by which signaling pathways pattern tissues, but the role of tissue mechanics in cell fate patterning remains poorly understood. Differentiation patterns require the apparition of locations with strong expression of genetic markers previously homogeneously expressed, a process called symmetry breaking. Furthermore, fate is coupled to shape, as highly curved areas contain specific cell types. During my PhD I will explore the mechanical cues regulating stem cells morphogenesis in 3D. We aim at understanding how symmetry breaking and coupling between curvature and cell fate are controlled by mechanics of the growing tissue.

In 2021 I obtained my B.Sc. program in Biology at the University of Barcelona with a specific focus on Molecular, Cell and Systems biology. I combined my bachelor’s degree with working as laboratory technician in the Cellular and Molecular mechanobiology group led by Prof. Pere Roca-Cusachs at Institut de Bioenginyeria de Catalunya (IBEC). After two years, I became research assistant at the Integrative cell and tissue Dynamics group led by Prof. Xavier Trepat, again at IBEC. The project was focused on the development of an in vitro model for studying the role of the tumor microenvironment in cancer immunotherapies outcomes In 2022 I obtained the Interdisciplinary Master in Life Sciences (IMaLiS) at École Normale Supérieure (ENS) in Paris, thanks to a Labec Memolife fellowship. As part of my master's degree, I am did my internship in the Oocyte Mechanics and Morphogenesis group, led by Marie Emilie Terret & Marie-Hélene Verlhac at Collège de France. I started my PhD in Roux lab September 2022.

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Joshua Tran

PhD Student

In cells, the Endosomal Sorting Complex Required for Transport (ESCRT) Complexes are involved in membrane remodeling and scission. An ancient and evolutionarily conserved system, the ESCRTs are found to cluster cargoes, such as transmembrane proteins, and deform endosomal membranes away from the cystosol into cargo-containing intraluminal vesicles (ILVs). In my PhD, I want to uncover the mechanism of ESCRT-dependent ILV formation and in particular, focus on the impact of cargo clustering on ESCRT recruitment and subsequent membrane deformation and scission. I will be using in vitro reconstitution to investigate mechanism and complement this with cryo-electron microscopy to add structural context.

I started my PhD in the Roux Lab in September 2022. Prior to joining, I did my studies at the University of California, Berkeley where I earned a Bachelors in Biochemistry and Molecular Biology in May 2022. My research journey began at the Scripps Research Insitute (La Jolla, CA) where I trained in the lab of Prof. Ian Macrae in x-ray crystallography for structure-based drug discovery. I continued my training in x-ray crystallography in the lab of Prof. James Hurley at UC Berkeley and investigated protein-protein interactions in the autophagy pathway.

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Roux Lab Alumni & Current Position

Post-Doctoral scientist, Diana Pinheiro group, IST Austria, Vienna, Austria.

Post-Doctoral Fellow (SNF and EMBO), Rapoport's lab, Harvard Medical School, Cambridge, MA, USA.

Scientific Communication Officer, Cytosurge Inc., Zurich and City Cancer Challenge, Geneva, Switzerland.

Staff Scientist, ACCESS Geneva, Platform of high throughput microscopy, University of Geneva, Geneva, Switzerland.

Group Leader, Emmy Noether Fellow (DFG), Department of Biochemistry, University of Heidelberg, Germany.

Chargé de Recherche 2ième Classe CNRS, Institut Nanotechnologie de Lyon, UMR 5270, Lyon, France.

Associate Professor, non-tenured, University of Barcelona, Barcelona, Spain.

Laura Houzet

Post-Doctoral fellow (EMBO fellowship), Janet Iwasa’s lab, University of Utah, Salt-Lake City, USA

Data Safety manager, United Biosource LLC (UBC Pharmaceutical services), Geneva.

Staff Scientist, Novartis, Basel, Switzerland.

Group Leader at Biofisika Institute in Bilbao, Spain, recipient of the Ramon y Cajal fellowship and of the Ikerbasque fellowship.

Scientific Engineer, Microscopy Platform for Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland.