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Mapping the Mechanobiome: Novel Mathematically-Derived 3D Visualization of the Cellular Mechanoresponsive System for Interactive Publication

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Mapping the Mechanobiome: Novel Mathematically-Derived 3D Visualization of the Cellular Mechanoresponsive System for Interactive Publication Mapping the Mechanobiome: Novel mathematically-derived 3D visualization of the cellular mechanoresponsive system for interactive publication by Cecilia C. Johnson A thesis submitted to Johns Hopkins University in conformity with the requirements for the degree of Master of Arts. Baltimore, Maryland March, 2019 © 2019 Cecilia Johnson All Rights Reserved Abstract Mechanical forces, ubiquitous in biological settings, are major determinants of cell fate; they should not be considered a detail applicable to specialized circumstances but rather a vital component of cell biology. To sense, respond, and generate both intracellular and extracellular mechanical forces, cells contain a highly integrated and dynamic network of macromolecules throughout the cell. The Robinson Lab at the Johns Hopkins School of Medicine developed the term “mechanobiome,” to describe and categorize that network of macromolecules. At the interface of cell biology, physics, and engineering, the concept of the mechanobiome provides researchers a systems-level understanding of the extensive contributions of physical force and mechanical cell properties on cell morphology, differentiation, physiology, and disease. Although numerous diseases, including cancer, cardiovascular disease, and chronic obstructive pulmonary disease, develop from abnormal cell mechanics, the mechanobiome is rarely explored as a novel source of therapeutic targets. Increased understanding of the mechanobiome will enhance understanding of normal biological machinery and ultimately lead to new pathways for targeting disease. To address the lack of comprehensive, accurate visualizations of the mechanobiome, two novel theoretical 3D models of the mechanobiome were developed: one at the cellular level and one at the nanoscale level. By integrating published data on components of the mechanobiome, such as crystal structures, macromolecule concentrations, and polymer dissociation constants, a proportionately accurate visualization of the cell’s mechanical system was produced. A platform was prototyped to present these novel 3D visuals as interactives on an accessible web-based educational resource, “Mapping the Mechanobiome.” The resource also provides review-style descriptions of fundamental ii concepts in mechanobiome research with accompanying visual media generated from the mathematically-derived models. This resource will contribute to discussions on the forefront of mechanobiome research, provide a comprehensive understanding for new researchers in the field, and advance research efforts by highlighting the significance of fundamental mechanical properties. The novel, mathematically-derived models have the potential to reveal aspects of the mechanobiome not previously considered due to the lack of accurate visualization of the full working system. This resource provides a platform to further enhance our understanding of the role of mechanics in health and disease. Cecilia C. Johnson, Author Douglas N. Robinson, Ph.D., Preceptor Professor, Departments of Cell Biology, Pharmacology and Molecular Sciences, Medicine, Oncology, and Chemical and Biomolecular Engineering Johns Hopkins University School of Medicine Corinne Sandone, M.A., C.M.I., Thesis Advisor Professor and Director, Department of Art as Applied to Medicine Johns Hopkins University School of Medicine iii Acknowledgements I extend endless gratitude to Cory Sandone, my department advisor. Thank you for your wisdom, guidance, and support, and for never losing faith in me or my project. Your encouragement has kept me sane, and your insight taught me how to be a better communicator. To Douglas Robinson and Priyanka Kothari: thank you for helping me navigate through such a complex and all-encompassing topic. Thank you for understanding the breadth of my project and helping to keep everything ambitious, but manageable. Finally, thank you for dedicating your time to providing me feedback, resources, and assistance with math. I would like to thank David Rini, Jennifer Fairman, Veronica Falconieri, Graham Johnson, Li Yao, and Sandra Gabelli for answering technical questions throughout my thesis and providing resources whenever I hit roadblocks. Additional thank you to the above names plus Tim Phelps, Gary Lees, Juan Garcia, Lydia Gregg, Norman Barker, Ian Suk, Anne Altemus, Donald Bliss, Mike Linkinhoker and Sarah Poynton, for teaching me the lessons and skills necessary to complete this project. I am not the same artist I was before I started at Johns Hopkins, and that is thanks to your guidance. So long as I am an artist, scientist, or communicator, I will carry your lessons with me. Thank you to Dacia Balch and Carol Pfeffer for consistently checking in on me and my classmate’s sanity and mental health, for many pats on the back, and for that foot massage that one time. To my loving family, thank you for supporting my every move and for always believing in me. You are always there for me, from my most anxious to my most excited iv moments. Extra thank you to my brothers for spoiling me with computer equipment I needed to work on my thesis at home. Un-acknowledgement to Emily and Will, who stole my bedroom when I left for school. Additional appreciation must be given to Gina Martucci and Gregory Freideman, whose friendship and love define such a large part of who I am. Enough thanks can never be given to you and your endless amounts of patience. Special thanks are extended to Gregory’s cooking skills, for without them, I would have survived only on chocolates and coffee. A huge thank you to my classmates, including those graduating in 2020, for your encouragement, laughter, support, silliness, dinners, Mario party breaks, late night studio companionship, love, and mug cakes. Finally, thank you to The Vesalius Trust for Visual Communication in the Health Sciences for their generous support of this project. v Table of Contents Abstract ......................................................................................... Error! Bookmark not defined. Acknowledgements ......................................................................................................................... iv Introduction ........................................................................................................................................ 1 Content Background .................................................................................................................... 1 The “Ome” in Mechanobiome .......................................................................................................... 1 Building Blocks of the Mechanobiome ............................................................................................... 2 Actin .......................................................................................................................................... 2 Actin Regulatory Proteins ...................................................................................................... 3 Crosslinkers and Stabilizing Proteins ................................................................................... 4 Myosin-II .................................................................................................................................. 5 Microtubules ............................................................................................................................ 7 Intermediate Filaments ........................................................................................................... 7 Physiological Relevance of the Mechanobiome ..................................................................................... 8 Implications in Health and Medicine .............................................................................................. 10 Model Organism Dictyostelium discoideum ............................................................................. 11 Visualization Considerations................................................................................................... 13 Difficulties of Visualizing “Omes” ................................................................................................. 13 Existing Visuals of the Mechanobiome........................................................................................... 17 Learning Theories .......................................................................................................................... 19 Audience ........................................................................................................................................ 20 Materials and Methods .................................................................................................................. 21 Defining the Need ...................................................................................................................... 21 Project Development ................................................................................................................. 23 Literature Review ........................................................................................................................ 26 Interactive Development .......................................................................................................... 29 Production Workflow ................................................................................................................. 31 Interactive 3D Models ...................................................................................................................
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