Title Quantitative Biology of Endocytosis
Subtitle (Colloquium Lectures on Quantitative Cell Biology)
Author Julien Berro, Michael M. Lacy
ISBN 9781615047840
List price USD 39.95
Price outside India Available on Request
Original price
Binding Paperback
No of pages 74
Book size 153 x 229 mm
Publishing year 2018
Original publisher Morgan & Claypool Publishers (Eurospan Group)
Published in India by .
Exclusive distributors Viva Books Private Limited
Sales territory India, Sri Lanka, Bangladesh, Pakistan, Nepal, .
Status New Arrival
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Description:

Clathrin-mediated endocytosis (CME) is a ubiquitous internalization process in eukaryotic cells. It consists of the formation of an approximately 50-nm diameter vesicle out of a flat membrane. Genetics, biochemistry, and microscopy experiments performed in the last four decades have been instrumental to discover and characterize major endocytic proteins in yeast and mammals. However, due to the highly dynamic nature of the endocytic assembly and its small size, many questions remain unresolved: how are endocytic proteins organized spatially and dynamically? How are forces produced and how are their directions controlled? How do the biochemical activities of endocytic proteins and the membrane shape and mechanics regulate each other? These questions are virtually impossible to visualize or measure directly with conventional approaches but thanks to new quantitative biology methods, it is now possible to infer the mechanisms of endocytosis in exquisite detail. This book introduces quantitative microscopy and mathematical modeling approaches that have been used to count the copy number of endocytic proteins, infer their localization with nanometer precision, and infer molecular and physical mechanisms that are involved in the robust formation of endocytic vesicles.

Contents:

Abstract

Chapter 1. Introduction to Clathrin-Mediated Endocytosis • Proteins Involved in CME • Membrane Coat Proteins • Endocytic Actin Meshwork • Membrane Scission and Late Regulation • Membrane in CME • Forces in CME • Comparison of CME in Yeast and Mammals • CME in Human Health and Disease • Understanding CME Requires Quantitative Approaches • Conclusions

Chapter 2. Collecting Quantitative Data • Using Fluorescence Microscopy to Obtain Quantitative Data About Endocytosis • Overview of Fluorescence Microscopes That Can Be Used for Quantitative Analysis of Endmytosis • Comparison of Different Fluorescence Microscopy Systems • General Considerations About Fluorescent Tags • Practical Considerations for Counting Molecules Using a Fluorescence Microscope • Tag a Protein of Interest at its Genomic Locus • Limit Photobleaching • Limit Uneven Illumination of the Field of View • Ensure the Microscopy System Is Used in Conditions Where the Signal Is Linear • Calibrate the Microscope Using Flexible Settings to Avoid Calibrating Too Often • Best Practices to Limit Sources of Variability • Electron Microscopy and Correlative Light and Electron Microscopy (CLEM) • Super-Resolution Microscopy

Chapter 3. From Raw Images to Quantitative Measurements: Extracting, Correcting, and Aligning the Fluorescence Microscopy Data • Tracking Endocytic Events • Challenges in Tracking Endorytic Events • Tracking and Track Curation • Best Practice in Tracking and Curating Tracks • Processing the Data to Count Molecules • Pre-Processing of the Movies • Correcting for Cytoplasmic Background • Aligning the Tracking Data Simple but Biased Alignment Methods • Advanced and More Accurate Alignment Methods • Counting the Number of Endocytic Events

Chapter 4. Using Quantitative Microscopy Data to Infer the Molecular Mechanisms of Endocytosis • How are Endocytic Proteins Organized? • The Protein Copy Numbers and Their Stoichiometries Constrain Possible Molecular Organizations and Mechanisms • High-Resolution Track Alignment Can Infer the Organization of Endogtic Proteins • The Organization of the Actin Meshwork Around the Endocytic Vesicle Can Be Inferred from the Vesicle’s Movements • What are the Molecular Mechanisms of Actin Dynamics During Endocytosis? • Inferring Mechanisms by Comparing Numbers and Stoichiometries • Mathematical Modeling Constrained by Quantitative Data Allows One to Test Different Mechanisms and Make Testable Predictions • What are the Mechanical Properties of the Membrane and the Forces Involved in Membrane Deformations? • Modeling of Membrane Shapes Can Elucidate Mechanical Properties and Forces Involved During CME • Simulations to Test Possible Force Distributions to Elongate the CCP and Propose New Mechanisms

Chapter 5. Perspectives and Future of Quantitative Biology of Endocytosis • Open Questions in CME Quantities That are Not (Yet?) Measurable • Advances in Microscopy Techniques • Advances in Computational Tools • Applications to Other Systems

References

Author Biographies 

About the Authors:

Julien Berro, Ph.D., is an assistant professor of Molecular Biophysics and Biochemistry, and of Cell Biology at Yale University. He initially trained in Physics, Applied Mathematics and Computer Sciences at the Institut National Polytechnique of Grenoble, France. He obtained his Ph.D. in Mathematical Modeling in Biology at Université Joseph Fourier, Grenoble, France, where he worked with Jean-Louis Martiel and Laurent Blanchoin on mathematical models for actin filament biochemistry and mechanics. After a brief tenure as an assistant professor in the department of Mathematics at Université Claude Bernard, Lyon, France, he decided to further his training by learning cell biology and quantitative microscopy in the laboratory of Tom Pollard at Yale University. Since he started his own laboratory in 2013, he has combined experimental, computational, and theoretical approaches to uncover the mechanisms of molecular machineries that produce forces in the cell, with a particular focus on the actin cytoskeleton and endocytosis.

Michael M. Lacy, Ph.D., completed his dissertation research in the laboratory of Prof. Julien Berro at Yale University. He earned his B.S. degree in Biochemistry at Tufts University in 2012 and his Ph.D. in Molecular Biophysics and Biochemistry at Yale in 2018, and he is now a postdoctoral researcher in the Berro laboratory before he leaves to launch his career in scientific editing and communication. Mike began the first stage of his Ph.D. research in the laboratory of Prof. Elizabeth Rhoades where he studied intrinsically disordered proteins. Mike’s research in the Berro laboratory has developed and used single-molecule fluorescence microscopy to study membrane remodeling, focusing on the actin cytoskeleton and endocytosis in yeast. Mike was an editor for the Yale Journal of Biology and Medicine from 2014 to 2018, and he has been a member of the Biophysical Society since 2013. In his spare time, he enjoys bicycling, playing softball, and homebrewing beer.

Target Audience:

Students majoring in Biochemistry and Cell Biology.

 

 
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