Biological Physics of the Developing Embryo pptx

Biological Physics of the Developing Embryo During development, cells and tissues undergo dynamic changes in pattern and form that employ a wider range of physical mechanisms than at any other time during an organism’s life. Biological Physics of the Developing Embryo presents a framework within which physics can be used to analyze these biological phenomena. Written to be accessible to both biologists and physicists, major stages and components of biological development are introduced and then analyzed from the viewpoint of physics. The presentation of physical models requires no mathematics beyond basic calculus. Physical concepts introduced include dif- fusion, viscosity and elasticity, adhesion, dynamical systems, electrical poten- tial, percolation, fractals, reaction diffusion systems, and cellular automata. With full-color figures throughout, this comprehensive textbook teaches biophysics by application to developmental biology and is suitable for graduate and upper-undergraduate courses in physics and biology. Gabor Forgacs is George H. Vineyard Professor of Biological Physics at the University of Missouri, Columbia. He received his Ph.D. in condensed matter physics from the Roland Eötvös University in Budapest. He made contributions to the physics of phase transitions, surface and interfacial phenomena and to statistical mechanics before moving to biological physics, where he has stud- ied the biomechanical properties of living materials and has modeled early developmental phenomena. His recent research on constructing models of liv- ing structures of prescribed geometry using automated printing technology has been the topic of numerous articles in the international press. Professor Forgacs has held positions at the Central Research Institute for Physics, Budapest, at the French Atomic Energy Agency, Saclay, and at Clark- son University, Potsdam. He has been a Fulbright Fellow at the Institute of Bio- physics of the Budapest Medical University and has organized several meetings on the frontiers between physics and biology at the Les Houches Center for Physics. He has also served as advisor to several federal agencies of the USA on the promotion of interdisciplinary researc h, in particular at the interface of physics and biology. He is a member of a number of professional associations, such as The Biophysical Society, The American Society for Cell Biology, and The American Physical Society. Stuart A. Newman is Professor of Cell Biology and Anatomy at New York Medical College, Valhalla, New York. He received an A.B. from Columbia Uni- versity and a Ph.D. in Chemical Physics from the University of Chicago. He has contributed to several scientific fields, including developmental pattern formation and morphogenesis, cell differentiation, the theory of biochemical networks, protein folding and assembly, and mechanisms of morphological evolution. He has also written on the philosophy, cultural background and social implications of biological research. Professor Newman has been an INSERM Fellow at the Pasteur Institute, Paris, and a Fogarty Senior International Fellow at Monash University, Aus- tralia. He is a co-editor (with Brian K. Hall) of Cartilage: Molecular Aspects (CRC Press, 1991) and (with Gerd B. Müller) of Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology (MIT Press, 2003). He has tes- tified before US Congressional committees on cloning, stem cells, and the patenting of organisms and has served as a consultant to the US National Institutes of Health on both technical and societal issues. Biological Physics of the Developing Embryo Gabor Forgacs University of Missouri and Stuart A. Newman New York Medical College cambridge university press Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, São Paulo Cambridge University Press The Edinburgh Building, Cambridge cb2 2ru,UK First published in print format isbn-13 978-0-521-78337-8 isbn-13 978-0-521-78946-2 isbn-13 978-0-511-13689-4 © G. Forgacs and S. A. Newman 2005 2005 Informationonthistitle:www.cambrid g e.or g /9780521783378 This publication is in copyright. Subject to statutory exception and to the provision of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. isbn-10 0-511-13689-7 isbn-10 0-521-78337-2 isbn-10 0-521-78946-x Cambridge University Press has no responsibility for the persistence or accuracy of urls for external or third-party internet websites referred to in this publication, and does not guarantee that any content on such websites is, or will remain, accurate or appropriate. Published in the United States of America by Cambridge University Press, New York www.cambridge.org hardback p a p erback p a p erback eBook (NetLibrary) eBook (NetLibrary) hardback Contents Acknowledgments pagevii Introduction:Biologyandphysics 1 1Thecell:fundamentalunitofdevelopmentalsystems 6 Theeukaryoticcell6 Diffusion8 Osmosis15 Viscosity16 Elasticityandviscoelasticity21 Perspective22 2Cleavageandblastulaformation 24 The cell biology of early cleavage and blastula formation24 Physicalprocessesinthecleavingblastula29 Physicalmodelsofcleavageandblastulaformation39 Perspective50 3Cellstates:stability,oscillation,differentiation 51 Geneexpressionandbiochemicalstate52 Howphysicsdescribesthebehaviorofacomplexsystem53 Oscillatoryprocessesinearlydevelopment57 Multistabilityincell-typediversification63 Perspective76 4 Cell adhesion, compartmentalization, and lumen formation 77 Adhesionanddifferentialadhesionindevelopment78 Thecellsurface80 Celladhesion:specificandnonspecificaspects81 Thekineticsofcelladhesion84 Differentialadhesionofembryonictissues90 Thephysicsofcellsorting95 Perspective97 5 Epithelial morphogenesis: gastrulation and neurulation 99 Physicalpropertiesofepithelia100 Gastrulation108 Convergenceandextension117 Neurulation122 vi Contents Perspective128 Appendix:Linearstabilityanalysis 128 6Mesenchymalmorphogenesis 131 Developmentoftheneuralcrest134 The extracellular matrix: networks and phase transformations138 Mesenchymalcondensation149 Perspective 154 7 Pattern formation: segmentation, axes, and asymmetry 155 Basicmechanismsofcellpatternformation157 Segmentation162 Epithelialpatterningbyjuxtacrinesignaling168 Mesoderminductionbydiffusiongradients171 Reaction diffusionsystems173 Controlofaxisformationandleft rightasymmetry177 Perspective 187 8Organogenesis 188 Developmentofthecardiovascularsystem190 Fractalsandtheirbiologicalsignificance197 Branching morphogenesis: development of the salivarygland203 Vertebratelimbdevelopment210 Perspective 222 9 Fertilization: generating one living dynamical system fromtwo 223 Developmentoftheeggandsperm224 Interactionoftheeggandsperm233 Propagation of calcium waves: spatiotemporal encodingofpostfertilizationevents236 Surface contraction waves and the initiation of development242 Perspective 247 10Evolutionofdevelopmentalmechanisms 248 Thephysicaloriginsofdevelopmentalsystems249 Analyzing an evolutionary transition using physical concepts:segmentationininsects256 Theevolutionofdevelopmentalrobustness262 Perspective272 Glossary 273 References 291 Index 327 Acknowledgments The writing of this text, addressed simultaneously to biologists and physicists, presented us with many challenges. Without the help of colleagues in both fields the book would still be on the drawing board. Of the many who advised us, made constructive remarks, and pro- vided suggestions on the presentation of complex issues, we wish to thank particularly Mark Alber, Daniel Ben-Avraham, Andras Czirók, Scott Gilbert, James Glazier, Tilmann Glimm, Michel Grandbois, George Hentschel, Kunihiko Kaneko, Ioan Kosztin, Roeland Merks, Gerd M ¨ uller, Vidyanand Nanjundiah, Adrian Neagu, Olivier Pourquié, Diego Rasskin-Gutman and Isaac Salazar-Ciudad. Commentary from students was indispensable; in this regard we received invaluable help from Richard Jamison, an undergraduate at Clemson University, and Yvonne Solbrekken, an undergraduate at the University of Missouri, Columbia, who read most of the chapters. We thank the members of our laboratories for their patience with us during the last five years. Their capabilities and independence have made it possible for us to pursue our research programs while writing this book. Gabor Forgacs was on the faculty of Clarkson University, Potsdam, NY, when this project was initiated, and some of the writ- ing was done while he was a visiting scholar at the Institute for Ad- vanced Study of the Collegium Budapest. Stuart Newman benefited from study visits to the Indian Institute of Science, Bangalore, the Konrad Lorenz Institute, Vienna, and the University of Tokyo-Komaba, in the course of this work. In a cross-disciplinary text such as this one, graphic materials are an essential element. Sue Seif, an experienced medical illustrator, was, like us, new to the world of textbook writing. Our interactions with her in the design of the figures in many instances deepened our understanding of the material presented here. Any reader who accompanies us across this difficult terrain will appreciate the fresh- ness and clarity of Sue’s visual imagination. Harry Frisch introduced the authors to one another more than a quarter century ago and thought that we had things to teach each other. Malcolm Steinberg, a valued colleague of both of us, showed the way to an integration of biological and physical ideas. Judith Plesset, our program officer at the National Science Foundation, was instrumental in fostering our scientific collaboration during much of the intervening period, when many of the ideas in this book were gestated. We are grateful to each of them and for the support of our families. Introduction: Biology and physics Physics deals with natural phenomena and their explanations. Biolo- gical systems are part of nature and as such should obey the laws of physics. However correct this statement may be, it is of limited value when the question is how physics can help unravel the complexity of life. Physicists are intellectual idealists, drawing on a tradition that ex- tends back more than 2000 years to Plato. They try to model the sys- tems they study in terms of a minimal number of ‘‘relevant” features. What is relevant depends on the question of interest and is typically arrived at by intuition. This approach is justified (or abandoned) after the fact, by comparing the results obtained using the model system with experiments performed on the ‘‘real” system. As an example, consider the trajectory of the Earth around the Sun. Its precise de- tails can be derived from Newton’s law of gravity, in which the two extensive bodies are each reduced to a point particle characterized by a single quantity, its mass. If one is interested in the pattern of earth- quakes, however, the point-particle description is totally inadequate and knowledge of the Earth’s inner structure is needed. An idealized approach to living systems has several pitfalls some- thing recognized by Plato’s student Aristotle, perhaps the first to at- tempt a scientific analysis of living systems. In the first place, intu- ition helps little in determining what is relevant. The functions of an organism’s many components, and the interactions among them in its overall economy, are complex and highly integrated. Organ- isms and their cells may act in a goal-directed fashion, but how the various parts and pathways serve these goals is often obscure. And because of the enormous degree of evolutionary refinement behind every modern-day organism, eliminating some features to produce a simplified model risks throwing the baby out with the bath water. Analyzing the role of any component of a living system is made all the more difficult by the fact that whereas many cellular and or- ganismal features are functional adaptations resulting from natural selection, some of these may no longer serve the same function in the modern-day organism. Still others are ‘‘side effects” or are charac- teristic (‘‘generic”) properties of all such material systems. To a major extent, therefore, living systems have to be treated ‘‘as is”, with com- plexity as a fundamental and irreducible property. One property of a living organism that sets it apart from other physical systems is its ability and drive to reproduce. When physics is used to understand biological systems it must be kept in mind that many of the physical processes taking place in the body will be organized to serve this goal, and all others must at least be consistent with it. The notion of goal-directed behavior is totally irrelevant for the inanimate world. [...]... (in the figure their concentration in R is zero), the pressures they exert on the movable walls are not equal: their difference is called the osmotic pressure In particular, if the two springs are made of the same material, the one attached to L will be more compressed, corresponding to the membrane of “cell” L being more stretched 15 16 BIOLOGICAL PHYSICS OF THE DEVELOPING EMBRYO pressure due to the. .. such as the frog, the ball is of nonuniform thickness as a result of different rates of cleavage at opposite poles of the zygote In mammals, such as the mouse and human, the outer surface of the ball consists of a layer of flat cells (the ‘‘trophoblast”), which gives rise to the extraembryonic membranes that attach to and communicate with the mother’s uterus A cluster of about 30 cells termed the ‘‘inner... be required of the scientist of tomorrow is the ability to speak the language of other disciplines The present book attempts to help the reader to become at least bilingual 5 Chapter 1 The cell: fundamental unit of developmental systems For the biologist the cell is the basic unit of life Its functions may depend on physics and chemistry but it is the functions themselves -DNA replication, the transcription...2 BIOLOGICAL PHYSICS OF THE DEVELOPING EMBRYO Physics and biology differ not only in their objects of study but also in their methods Physics seeks to discover universal laws, valid everywhere in time and space (e.g., Newton’s laws of motion, the laws of thermodynamics) Theory expresses these general laws in mathematical form and provides ‘‘models” for complex processes in terms of simpler... x in the x direction (see Fig 1.5) For it to move, the plate has to displace the liquid molecules it encounters The state of the liquid is thus perturbed This perturbation in the state of the liquid is called shear and leads to friction, i.e., viscous drag, acting on the plate (Howard, 2001) A measure of the shear, or rather the rate of shearing, is the modification of the liquid’s velocity in the vicinity... time The role and importance of physics in the study of biological systems at various levels of complexity (the operation of molecular motors, the architectural organization of the cell, the biomechanical properties of tissues, and so forth) is being recognized to an increasing extent by biologists The objective of the book is to present a framework within which physics can be used to analyze biological. .. small region of space (A) diffuse symmetrically outward in the absence of forces (B) or, when an external force is present, preferentially in the direction of the force (C) 11 12 BIOLOGICAL PHYSICS OF THE DEVELOPING EMBRYO dimension, if all the particles are initially at the origin with concentration c 0 then after time t their concentration at x is 2 c(x, t) = c 0 e−x /4D t (4π D t)1/2 (The mathematically... velocity in the vicinity of the plate For forces that are not too strong, the shear rate is proportional to F x The proportionality constant between F x and the shear rate is the viscosity η, obviously a property of the liquid (for the precise definition of viscosity see Box 1.1) The customary unit of η is the Pa s (pascal second) The viscosity of water is 0.001 Pa s The viscosity of the cytoplasm varies... connection with Eq 1.2), the ratio of the inertial term (proportional to the mass) and the frictional term contains the expression ρvL /η We can now plug in known values of these factors The typical size L of a cell is of order 10 micrometers and the cellular density is of order that of water A characteristic time T could be identified with the early -embryo cell cycle time For the sea urchin embryo, which we... abruptly The spindle then forms from the microtubules that extend from the centrosomes and attach to the kinetochores of the chromosomes The chromosomes then begin to move toward the cell equator, defined by the location of the centrosomes, which are now at opposite poles of the cell At metaphase (C), the chromosomes are aligned at the equator and sister chromatids are attached by microtubules to the opposite . it. The notion of goal-directed behavior is totally irrelevant for the inanimate world. 2 BIOLOGICAL PHYSICS OF THE DEVELOPING EMBRYO Physics and biology differ not only in their objects of study. are examples of morphogenesis, the set of mechanisms that create complex 4 BIOLOGICAL PHYSICS OF THE DEVELOPING EMBRYO biological forms out of simpler structures. While each episode of de- velopmental. lyse. If the voltage across the membrane is not appropriate, a voltage-gated ion channel will not function. If the viscosity of the cytoplasm is too 8 BIOLOGICAL PHYSICS OF THE DEVELOPING EMBRYO large,