Programme DutchBiophysics

Online programma

You can view the online programme here (possibly subject to change).

Confirmed invited speakers

Keynote speaker

Matthieu Piel (Centre de recherche de l’Institut Curie)

Matthieu PielMatthieu Piel

Matthieu Piel is leading the team ‘Systems biology of cell polarity and cell division’ at Institut Curie/Institut Pierre Gilles de Gennes in Paris. Trained as a physicist at Ecole Polytechnique and Université Pierre and Marie Curie, he did his PhD in a cell biology lab, working on the centrosome with Michel Bornens. During his post-doctoral stay at Harvard University with Andrew Murray, working on yeast mating and chemotropism, thanks to a collaboration with the lab of George Whitesides, he learned the basics of microfabrication and microfluidics. Back in France to start his lab at Institut Curie in 2007, he adapted these methods to study fundamental questions in cell biology, focusing on cell division and cell migration. The team main discoveries are related to how forces affect the cell division axis, spindle assembly and cytokinesis, the importance of ESCRT III complex in plasma and nuclear envelope repair, and the impact of confinement on cancer and immune cell migration and nuclear integrity. The work of the team resulted in above 80 articles cited about 10 000 times.

Abstract

Dynamics and mechanics of the acto-myosin cortex in immune cells
The acto-myosin cortex controls cell shape and cell motility. Despite decades of studies, it remains a fascinating, far from being understood. I will first present results we obtained on migratory cancer and immune cells, which show that acto-myosin can adapt rapidly to the migration environment when cells face various types of constrains. I will then show results we obtained with a new tool which allows for the first time to directly measure the physical properties of the cell cortex in live cells. I will conclude with perspectives on acto-myosin dynamics in cells migrating through complex environments, and the potential function of the microtubule cytoskeleton.

International speakers

Maria Garcia-Parajo (Instituto de Ciencias Fotónicas)

Maria Garcia-ParajoMaria Garcia-Parajo

Maria Garcia-Parajo received her PhD in Physical Electronics in 1993 at Imperial College, London, UK. After a two-years postdoc at the L2M-CNRS, Bagneux, France she obtained a permanent position in the Applied Optics group of the University of Twente from 1998 to 2005. In 2005 she moved to Barcelona as ICREA Research Professor, first hosted at the IBEC - Institute for Bioengineering of Catalonia and since July 2011 at ICFO-Institute of Photonic Sciences, leading the Single Molecule Biophotonics group. Her research focuses on the development of advanced optical techniques to the study of biological processes at the single molecular level on living cells. She has co-authored more than 150 publications in peer-reviewed international Journals and delivered more than 170 talks at international conferences and workshops upon invitation. She coordinates several international research projects and has been a member of the executive board of the Spanish Biophysical and the International Fluorescence Societies. She has received several prestigious awards including the Young Academy fellowship of the Netherlands Royal Academy of Sciences (1999), the Advanced grant of the Human Frontiers Science Program (2012), Bruker National Prize in Biophysics given by the Spanish Biophysical Society (2017) and Advanced ERC grant 2017. She is currently part of the Gender Committee at ICFO and actively involved in (inter)national actions to promote gender equality in Science.

Abstract

Linking nano- and meso-scale compartmentalization of the plasma membrane using high density single particle tracking tools
In the last decade, compartmentalization of the plasma membrane has emerged as a dominant feature regulating key functions. Here, I will focus on recent studies aiming at linking compartmentalization of the cell membrane at multiple spatiotemporal scales. For this, we combine multi-color single particle tracking approaches at different labelling densities. I will show data on CD44, a highly glycosylated adhesion receptor that connects the extracellular glycocalyx matrix to the intracellular actin cytoskeleton. Our results reveal a hierarchical spatiotemporal organization of CD44 which is dependent on the dynamic turnover of the underlying cortical actin cytoskeleton and regulates the function of other receptors by acting as transmembrane fence.

Bart Hoogenboom (University College London)

Bart HoogenboomBart Hoogenboom

Bart Hoogenboom is a Professor of Biophysics at the Department of Physics and Astronomy (UCL) and the London Centre for Nanotechnology, where he is also lead scientist for its atomic force microscopy facilities. He was initially trained as a solid-state physicist, working on correlated-electron systems and scanning probe microscopy. Since his PhD, he has gradually shifted his focus to nanoscale biological structures and processes, and currently leads a nanoscale biophysics research group.

Abstract

Polymer physics goes nuclear
To enter and exit the nucleus, macromolecular cargoes cross a selective barrier located in large protein assemblies called nuclear pore complexes (NPCs). This selective barrier consist to a significant extent of natively unfolded proteins in condensed, disordered arrangements, in a nanopore confinement shaped by the NPC scaffold structure. By numerical simulations based on polymer physics, it has been demonstrated that there is a large qualitative variability in the arrangements that these proteins could adopt. The important biological question is which or these arrangements apply in the NPC and how they give rise to a transport selectivity that is literally vital for the cell. We use a range of approaches to answer this question, from nanoscale characterisation by atomic force microscopy, via the use of reductionist mimics of the NPC, to numerical simulations. Interestingly, we find that many key characteristics of the NPC and its transport functionality can be understood based on conceptually simple models from polymer physics, providing new insights as well as indicating avenues to gain a comprehensive understanding of transport between the cell nucleus and the cytoplasm.

Jennifer L. RossJennifer L. Ross

Jennifer Ross (Department of Physics at Syracuse University)

Ross an award-winning biophysicist studying the self-organization of the microtubule cytoskeleton and microtubule-based enzymes using high-resolution single-molecule imaging techniques. She has her Ph.D. in Physics, is a Fellow of the American Physical Society, and is currently serving on the Biophysical Society Council and the past chair of the Division of Biological Physics in the American Physical Society. As a Cottrell Scholar, Ross has pioneered innovative teaching techniques to train students in the optics concepts needed to understand microscopy. Her engaging and active learning style has been adopted at microscopy short courses around the world. She is also an advocate for women and under-represented groups and has a blog to help others make it in academics.

Abstract

Biological active matter of enzymes
The cell is a complex autonomous machine taking in information, performing computations, and responding to the environment. Much of the internal structure and architecture is transient and created through active processes. Recent advances in active matter physics with biological elements are opening new insights into the physics behind how cellular organizations are generated, maintained, and destroyed. I will present two short stories with enzymes at the heart of the activity driving organization and transport. The first will discuss self-organization of microtubules in the presence of “weakly interacting” crosslinkers. The second will discuss possible mechanisms for the cell to mix itself using self-propelled single molecule enzymes. These works illustrate the importance of the fundamental physics to build structures and propel matter inside living cells while informing on new physics we can learn from biological elements and materials.

 

National speakers

Daniela Kraft (Leiden University)

Daniela KraftDaniela Kraft

Daniela Kraft is an associate professor in Soft Matter Physics at the Huygens-Kamerlingh Onnes Laboratory at Leiden University, The Netherlands. She obtained her Ph.D. cum laude from the University of Utrecht, The Netherlands, under supervision of Willem Kegel. Supported by a Rubicon grant, she then joined the Center for Soft Matter Research at New York University, USA, as a postdoctoral researcher. In 2013, she moved to Leiden, where she established her own group. Her research focuses on self-assembly in biological and soft matter systems, ranging from anisotropic colloidal particles to lipid membranes, emulsions, and viruses. Dr. Kraft has been awarded a VENI fellowship from the Netherlands Organisation for Scientific Research, an ERC starting grant and the paper of the year award 2017 from Biophysical Journal.

Abstract

Lipid demixing on curved surfaces
Phase-separation studies in artificial lipid membranes have unveiled a coupling between membrane geometry and position of different lipid domains. However, a lack of independent experimental control over membrane geometry and composition has precluded a complete understanding of the process.
I will show how we overcome this limitation by fabricating multicomponent lipid bilayers supported by colloidal and 3D printed scaffolds. Thanks to a combination of experiments and theoretical modeling, we obtained key insights into how local curvature and composition determine the spatial arrangement and the degree of demixing of the lipid domains. Our results provide key insights into phase separation in lipid membranes and complex fluids in general.

Liedewij Laan (Delft University of Technology)

Liedewij LaanLiedewij Laan

Liedewij Laan is an associate professor at the Bionanoscience department at Delft University of Technology. Her group focusses on evolutionary cell biophysics and is fascinated by how the physical and chemical properties of the building blocks of life (such as proteins, DNA, lipids etc.) constrain and facilitate evolution of cellular functions. The function she focusses on is symmetry breaking in budding yeast, and she uses a broad range of techniques such as live cell microscopy, experimental evolution, in vitro reconstitutions and modelling. She received an honorary mention for the Christiaan Huygens Prize for Physics 2011. From 2017 Laan is a recipient of a Starting grant from the European Research Council (ERC) and a VIDI grant from NWO.

Abstract

Evolutionary cell biophysics: predicting evolutionary trajectories bottom-up
How new functions evolve is one of the fascinating questions in biology. As pioneers of the emerging field of evolutionary cell biophysics, we study how the physical and chemical properties of the building blocks of a cell (such as proteins, DNA, lipids etc. that need to obey physical and chemical laws) constrain and facilitate evolution of cellular functions. The cellular function my lab focusses on is pattern formation in budding yeast, which is the first step in polarity establishment and essential for proliferation. Our previous experimental evolution study showed that the polarity network can, by evolution, recover from the deletion of an important component. Here I will present, using a combined (bottom-up) modelling and experimental approach, how this remarkable adaptability emerges from noise and the molecular interaction in the network. As a next step I will discuss how we use our multi-scale model to predict future evolutionary steps.

Tineke Lenstra (Netherlands Cancer Institute)

Tineke LenstraTineke Lenstra

Tineke Lenstra received her Bachelor's and Master's degree in biomedical sciences cum laude from Utrecht University. In 2008, she joined the laboratory of Frank Holstege at University Medical Centre Utrecht, where she used genome-wide expression analysis to study transcription regulatory complexes. She was awarded a cum laude PhD in 2012. As a postdoc in laboratory of Dan Larson at the National Cancer Institute in Bethesda, USA, she used cutting-edge single-molecule techniques to study transcription dynamics in single cells. In 2016, she established an independent group at the Netherlands Cancer Institute (NKI) in Amsterdam, where her lab focuses on the regulatory mechanisms of stochastic transcription in eukaryotic cells.

For her work, Tineke has received a number of awards, including the NVBMB prize, the Fellows Award for Research Excellence, the NCI Director's Innovation Award and the “Cancer Genomics and Developmental Biology” PhD Student Award. Her research was supported by the ERC starting grant, CancerGenomics.nl, EMBO long-term fellowships, KWF fellowship for basic research, the NWO Toptalent Program and Huygens Scholarship Talent Program.

Abstract

A single-molecule understanding of transcriptional bursting
Transcriptional in single cells is a stochastic process, which arises from the random collision of molecules. This stochastic behavior results in variability in gene activity between cells, and as well as within a cell over time. In our lab, we use single-molecule imaging techniques to visualize the dynamics of transcription in living cells. We and others have shown that genes are often transcribed in bursts, with periods of activity followed by periods of inactivity. Transcriptional bursting is observed from bacteria to yeast to human cells, but the origin and regulators of bursting are still largely unknown. In this talk, I will focus on how transcriptional bursting in yeast is regulated by transcriptional activators and nucleosomes.

Marvin Tanenbaum (Hubrecht Institute)

Marvin TanenbaumMarvin Tanenbaum

Marvin Tanenbaum is group leader at the Hubrecht Institute and investigator at Oncode Institute. His group studies the molecular mechanisms of gene expression control at the single cell level and aims to understand how control of gene expression affects important cellular decisions. The Tanenbaum group has developed several new imaging techniques, including the SunTag fluorescence imaging system. Using the SunTag system they can directly visualize and quantify translation of single mRNA molecules in living cells to study the dynamics and regulation of each individual mRNA in real time.

Abstract

Multi-color single molecule imaging uncovers extensive heterogeneity in mRNA decoding
mRNA translation is a key step in decoding genetic information and is surprisingly heterogeneous; multiple distinct proteins can be produced from a single mRNA. Studying translation heterogeneity is challenging, as current methods require averaging of thousands of mRNAs. We developed a new approach to visualize translation of individual mRNA molecules in real-time in live cells using fluorescence microscopy. We find that mRNA decoding choices are largely stochastic, but that the probability of synthesizing a particular protein differs among mRNA molecules, and can be dynamically regulated over time. This study provides key insights into mRNA decoding heterogeneity, and provides powerful tools to visualize complex translation heterogeneity.