Physics-Biology interface seminar – archives


Investigating embryogenesis using numerical simulations of biophysics

Ivo Sbalzarini (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany)

Abstract:

Development and morphogenesis of tissues, organs, and embryos emerges from the collective self-organization of cells that communicate though chemical and mechanical signals. Decisions about growth, division, and migration are taken locally by each cell based on the collective information. In this sense, a developing tissue is akin to a massively parallel computer system, where each cell or processor computes robust local decisions, integrating communication with other cells/processors. Mechanistically understanding and reprogramming this system is a grand challenge. Our vision is to develop a virtual computer model of a developing embryo, incorporating the known biochemistry and biophysics into a computational model in 3D-space and time, in order to understand the information-processing aspects of development on an algorithmic basis. While the “hardware” (proteins, lipids, etc.) and the “source code” (genome) are increasingly known, we known virtually nothing about the algorithms that this code implements on this hardware. Using examples from our work, I outline our roadmap toward a virtual embryo, and highlight challenges along the way. These range from globally optimal approaches to image analysis, to novel languages for parallel high-performance computing, to virtual reality and real-time graphics for 3D microscopy and numerical simulations of biochemical and biomechanical models. This cooperative interdisciplinary effort contributes to all involved disciplines.

Bio:

Ivo Sbalzarini is the Chair of Scientific Computing for Systems Biology on the faculty of computer science of TU Dresden, and director of the TUD-Department in the Center for Systems Biology Dresden. He also is a permanent Senior Research Group Leader with the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden. He graduated in Mechanical Engineering from ETH Zurich in 2002 (Willi Studer Award). He completed his doctorate in computer science in 2006 at ETH Zurich (Chorafas Award, Weizmann Institute of Science), where he formed a close collaboration between biology and computer science. In 2006, he was named Assistant Professor for Computational Science in the Department of Computer Science of ETH Zurich. In 2012, Ivo and his group moved to Dresden, where he became one of the founding members of the new Max Planck Center for Systems Biology and the TU-Dresden Chair of Scientific Computing for Systems Biology. He also serves as a co-leader of the biological systems path of the Center for Advancing Electronics Dresden, Dean of the International Max Planck Research School in Cell, Developmental, and Systems Biology, and Vice-Dean of the Faculty of Computer Science.


Ribosome assembly studied by single-molecule force measurements

Thierry Bizebard (IBPC, Paris)

Ribosomes belong to the most complicated structures in biology. Their assembly is a question of fundamental interest, but is still poorly understood. In vitro reconstitution studies have shown that the ribosome assembly process is highly cooperative and starts with the binding of a few ribosomal (r-) proteins to rRNA, but how these early binders act is unknown. Our work focuses on the initial phase of the assembly of the large subunit (50S) of the E. coli ribosome, which involves 23S rRNA, five r-proteins and a selection of assembly “helper” proteins. Our force measurements on single RNA molecules have allowed us to pinpoint several important properties of the early-binding r-proteins we have studied:

- These proteins bind with high cooperativity to the rRNA (as would be expected to obtain a high yield of fully assembled and active ribosomes).
- The r-proteins act as molecular clamps, stabilising the RNA 3D structure.
- As such, they afford a strong mechanical and energetical stabilisation of the ribonucleoprotein structure (which is also probably necessary for optimum activity).

In the near future, we intend to further improve the potential of our single-molecule measurements by implementing combined force/fluorescence manipulations, and apply this methodology to our study of the early phase of E. coli large ribosomal subunit assembly.


Single-cell leukocyte mechanics: force generation, viscoelasticity, and rupture mechanics

Julien Husson (LadHyX, École polytechnique, France)

Leukocytes are very soft cells that perform many diverse functions: they adhere, crawl, transmigrate, kill, phagocytose or interact with other cells. During their activation, leukocytes both generate mechanical forces and change their viscoelastic properties (i.e. they stiffen/soften, get more or less viscous). We have developed micropipette-based setups to quantify single-leukocyte mechanical properties and monitor them over time while a leukocytes gets activated by a relevant stimulus. We further quantify rupture properties of cell membrane, as these help us to better understand cell structure and dynamics. We use this approach in diverse contexts involving leukocytes: activation of T lymphocytes, phagocytosis of a target by a neutrophil, or transmigration of a lymphoblast across an endothelial monolayer. We perform microrheology experiments with a profile microindentation setup [1,2], measure forces generated by T lymphocytes [3,4], characterize cell-substrate adhesion [5] or establish a rupture criteria for membrane rupture [2,6] (Figure 1). These mechanical measurements shed a new light on how cell mechanical properties evolve over a short period of time (seconds), how they adapt to the stiffness of their environment, and how intracellular signaling is involved.

170517_Husson T-lymphocytes in the human body routinely undergo large deformations, both passively when going through narrow capillaries and actively when transmigrating across endothelial cells or squeezing through tissue. In this artistic rendering, a T-lymphocyte is aspirated in a micropipette to mimic passive deformations that occur when squeezing through narrow capillaries. The fluorescent signal is due to the entry of propidium iodide into the cell and indicates membrane rupture (Image: Julien Husson, LadHyX, Ecole polytechnique, cellmechanics.jimdo.com/galleries)

1. Guillou, L., Babataheri, A., Puech, P.-H., Barakat, A.I. & Husson, J. Dynamic monitoring of cell mechanical properties using profile microindentation. Scientific Reports 6:21529 (2016). 2. Guillou, L., Babataheri, A., Saitakis, M., Bohineust, A., Dogniaux, S., Hivroz, C., Barakat, A.I. & Husson, J. T lymphocyte passive deformation is controlled by unfolding of membrane surface reservoirs. Molecular Biology of the Cell 27(22): 3574-3582. (2016, journal cover). 3. Husson, J., Chemin, K., Bohineust, A., Hivroz, C. & Henry, N. Force Generation upon T Cell Receptor Engagement. PLoS One 6(5):e19680 (2011). 4. Basu, R.*, Whitlock, B.M.*, Husson, J.*, Le Floc’h, A., Jin, W., Dotiwala, F., Giannone, G., Hivroz, C., Lieberman, J., Kam, L.C. & Huse, M. Cytotoxic T Cells Use Mechanical Force to Potentiate Target Cell Killing. Cell 165(1):100–110 (2016). 5. Hogan, B., Babataheri, A., Hwang, Y., Barakat, A.I. & Husson, J. Characterizing Cell Adhesion by Using Micropipette Aspiration. Biophysical Journal 109(2):209-19 (2015). 6. Gonzalez-Rodriguez, D., L. Guillou, F. Cornat, J. Lafaurie-Janvore, A. Babataheri, E. de Langre, A.I. Barakat, and J. Husson. Mechanical Criterion for the Rupture of a Cell Membrane under Compression. Biophys. J. 111: 2711–2721 (2016).

Whole-brain imaging during vestibular stimulation in zebrafish with a novel rotatable light-sheet microscope

Volker Bormuth (Laboratoire Jean Perrin, Université Pierre et Marie Curie)

Light-sheet microscopy allows cell resolved whole-brain calcium imaging at several brain scans per second in zebrafish larvae. Currently this technique is not compatible with dynamic stimulation of the vestibular system. We developed an ultra-stable miniaturized light-sheet microscope that can be rotated while performing whole-brain recordings. Rotating the microscope rotates the fish and stimulates the vestibular system while imaging always the same plane in the brain. We demonstrate volumetric whole-brain neuronal activity recordings during vestibular stimulation. We mapped the brain activity with cellular resolution of the vestibule-ocular reflex (VOR) which drives compensatory eyes movements to maintain clear vision during body rotation. Our long-term goal is study with this system multisensory signal processing by the vertebrate brain by combining visual with vestibular stimuli.


Molecular chaperones as cellular non-equilibrium machines.

Alessandro Barducci (Centre de Biochimie Structurale-INSERM, Montpellier)

Molecular chaperones are a vast class of proteins that maintain protein homeostasis in the cell and are thus essential for cell viability. In order to assist protein folding and prevent misfolding, most chaperones proceed through conformational cycles that are regulated by complex interaction networks and fueled by ATP-hydrolysis. A remarkable example are the 70-kDalton heat shock proteins (Hsp70s), which are essential in prokaryotes and eukaryotes and are involved in co-translational folding, refolding of misfolded and aggregated proteins, protein translocation, and protein degradation. While the investigation of Hsp70 cycle has attracted great attention in the last decades, the actual role of ATP-hydrolysis and, thus of energy consumption, in the chaperone function has been long unaddressed. Here we will prove how biochemical data, recent single-molecule fluorescence experiments and molecular simulations can be combined into an appropriate theoretical framework to show that: i) ATP hydrolysis allows Hsp70 chaperones to increase their affinity for the client proteins beyond the bounds imposed by equilibrium thermodynamics ii) This ultra-affinity can be exploited to perform mechanical work on client proteins thus avoiding the formation of misfolded and potentially cytotoxic species.


Block Copolymer Assemblies Beneath the Surface: Modeling Intra-Domain Textures and Chirality Transfer to Mesodomains

Greg Grason (U. of Massachussets, Amherst)

This seminar replaces that of Thierry Bizebard, was rescheduled to May 31st. Please note the more soft matter focus. Self-assembled block copolymer (BCP) melts are a chemically-versatile platform for generating a rich spectrum of periodically-ordered nanostructures of various morphologies, from arrays of layers and columns to cubic arrays of spheres and bicontinuous networks. They are also a model system for understanding processes and properties of self-assemblies, more broadly. Decades of study of BCP assembly have uncovered the principles that connect molecular BCP structure to the translational order of the (scalar) composition profiles in the ordered states. In this talk, I will describe recent efforts to understand the generic, yet poorly known, patterns of orientational ordering of constituent chain segments that underlie the otherwise well-known “standard” BCP morphologies1. From generic properties of the random-walk statistics in BCPs, we show that the direction and degree of alignment of segments varies non-trivially from place-to-place in self-organized domains, and from one morphology to another, leading to new opportunities to manipulate and harness the physics sub-domain textures. Specifically, I will discuss how our efforts to model chiral BCPs2 which have been observed to transfer handedness of chain chemistry to the chiral symmetry of mesodomain shapes that are not formed in achiral BCPs. Our generalized orientational self-consistent field (oSCF) theory framework3 shows that the thermodynamic drive for twisted, or cholesteric, packings of segments of chiral blocks stabilizes observed helical cylinder morphologies, and suggests new mechanisms for driving formation as of yet, unobserved mesochiral domain symmetries4. References
  1. I. Prasad, Y. Seo, L. Hall and G. M. Grason arxiv.org/1612.07994 (2016)
  2. G. M. Grason ACS MacroLetters 4, 526 (2015). Front Cover Story
  3. W. Zhao, T. Russell and G. M. Grason, J. Chem. Phys. 137, 104911 (2012).
  4. W. Zhao, T. Russell and G. M. Grason, Phys. Rev. Lett. 110, 058301 (2013).

Physical biology of chromatin: understanding the functional role of 3D chromosome folding using polymer physics

Daniel Jost (Université Grenoble Alpes)

Cellular differentiation occurs during the development of multicellular organisms and leads to the formation of many different tissues where gene expression is modulated without modification of the genetic information. These modulations are in part encoded by chromatin-associated proteins or biochemical tags that are set down at the chromatin level directly on DNA or on histone tails. These markers are directly or indirectly involved in the local organization and structure of the chromatin fiber, and therefore may modulate the accessibility of DNA to transcription factors or enzymatic complexes, playing a fundamental role in the transcriptional regulation of gene expression. Propagation, maintenance and inheritance of these epigenetic marks are crucial mechanisms in development, phenotype stabilization and disease. Experimental evidence have shown that the pattern of chromatin markers along chromosomes is strongly correlated with the 3D chromatin organization ins