Diatom Morphogenesis

Professor Vadim V. Annenkov earned his PhD from Irkutsk Institute of Organic Chemistry Siberian Branch of Russian Academy of Sciences in 1989 and Doctor of Science (Doctor Habilitation) in Polymer Chemistry from Irkutsk State University in 2002. He has worked in the Limnological Institute (Siberian Branch of RAS) since 2004. He is the author of about 150 scientific papers, 18 patents, 120 abstracts of conferences. Citation Index according to WOS is 824, H-index is 15.Professor J. Seckbach is a retired senior academician at The Hebrew University of Jerusalem, Israel. He earned his PhD from the University of Chicago and did a post-doctorate in the Division of Biology at Caltech, in Pasadena, CA. He served at Louisiana State University (LSU), Baton Rouge, LA, USA, as the first selected Chair for the Louisiana Sea Grant and Technology transfer. Professor Joseph Seckbach has edited over 40 scientific books and authored about 140 scientific articles. Richard Gordon’s involvement with diatoms goes back to 1970 with his capillarity model for their gliding motility, published in the Proceedings of the National Academy of Sciences of the United States of America. He later worked on a diffusion-limited aggregation model for diatom morphogenesis, which led to the first paper ever published on diatom nanotechnology in 1988. He organized the first workshop on diatom nanotech in 2003. His other research is on computed tomography algorithms, HIV/AIDS prevention, and embryogenesis. See: https://en.wikipedia.org/wiki/Richard_Gordon_(theoretical_biologist).

• Preface xvPart 1: General Issues 11 Introduction for a Tutorial on Diatom Morphology 3Kalina Manoylov and Mohamed Ghobara1.1 Diatoms in Brief 31.2 Tools to Explore Diatom Frustule Morphology 71.3 Diatom Frustule 3D Reconstruction 121.3.1 Recommended Steps to Understand the Complex Diatom Morphology: A Guide for Beginners 131.4 Conclusion 15Acknowledgements 15References 152 The Uncanny Symmetry of Some Diatoms and Not of Others: A Multi-Scale Morphological Characteristic and a Puzzle for Morphogenesis 19Janice L. Pappas, Mary Ann Tiffany and Richard Gordon2.1 Introduction 202.1.1 Recognition and Symmetry 212.1.2 Symmetry and Growth 242.1.3 Diatom Pattern Formation, Growth, and Symmetry 252.1.4 Diatoms and Uncanny Symmetry 272.1.5 Purpose of This Study 282.2 Methods 282.2.1 Centric Diatom Images Used for Analysis 282.2.2 Centric Diatoms, Morphology, and Valve Formation 342.2.3 Image Entropy and Symmetry Measurement 362.2.4 Image Preparation for Measurement 372.2.5 Image Tilt and Slant Measurement Correction for Entropy Values 382.2.6 Symmetry Analysis 392.2.7 Entropy, Symmetry, and Stability 402.2.8 Randomness and Instability 422.3 Results 432.3.1 Symmetry Analysis 432.3.2 Valve Formation—Stability and Instability Analyses 492.4 Discussion 512.4.1 Symmetry and Scale in Diatoms 552.4.2 Valve Formation and Stability 562.4.3 Symmetry, Stability and Diatom Morphogenesis 572.4.4 Future Research—Symmetry, Stability and Directionality in DiatomMorphogenesis 58References 593 On the Size Sequence of Diatoms in Clonal Chains 69Thomas Harbich3.1 Introduction 703.2 Mathematical Analysis of t he Size Sequence 733.2.1 Alternative Method for Calculating the Size Sequence 733.2.2 Self-Similarity and Fractal Structure 753.2.3 Matching Fragments to a Generation Based on Known Size Indices of the Fragment 763.2.4 Sequence of the Differences of the Size Indices 783.2.5 Matching Fragments to a Generation Based on Unknown Size Indices of the Fragment 803.2.6 Synchronicity of Cell Divisions 813.3 Observations 823.3.1 Challenges in Verifying the Sequence of Sizes 823.3.2 Materials and Methods 833.3.3 Investigation of the Size Sequence of a Eunotia sp. 843.3.4 Synchronicity 863.4 Conclusions 87Acknowledgements 88Appendix 3A L-System for the Generation of the Sequence of Differences in Size Indices of Adjacent Diatoms 88Appendix 3B Probability Consideration for Loss of Synchronicity 89References 914 Valve Morphogenesis in Amphitetras antediluviana Ehrenburg 93Mary A. Tiffany and Bonnie L. Hurwitz4.1 Introduction 934.2 Material and Methods 944.3 Observations 944.3.1 Amphitetras antediluviana Mature Valves 944.3.2 Amphitetras antediluviana Forming Valves 964.3.3 Amphitetras antediluviana Girdle Band Formation 1014.4 Conclusion 101Acknowledgments 102References 102Glossary 104Part 2: Simulation 1055 Geometric Models of Concentric and Spiral Areola Patterns of Centric Diatoms 107Anton M. Lyakh5.1 Introduction 1075.2 Set of Common Rules Used in the Models 1095.3 Concentric Pattern of Areolae 1095.4 Spiral Patterns of Areolae 1105.4.1 Unidirectional Spiral Pattern 1115.4.2 Bidirectional Spiral Pattern 1135.4.3 Common Genesis of Unidirectional and Bidirectional Spiral Patterns 1135.5 Conversion of an Areolae-Based Model Into a Frame-Based Model 1145.6 Conclusion 114Acknowledgements 114References 1156 Diatom Pore Arrays’ Periodicities and Symmetries in the Euclidean Plane: Nature Between Perfection and Imperfection 117Mohamed M. Ghobara, Mary Ann Tiffany, Richard Gordon and Louisa Reissig6.1 Introduction 1186.2 Materials and Methods 1226.2.1 Micrograph Segmentation 1236.2.2 Two-Dimensional Fast Fourier Analysis and Autocorrelation Function Analysis 1236.2.3 Lattice Measurements and Recognition 1236.2.4 Accuracy of 2D ACF-Based Calculations 1256.2.5 The Perfection of the Unit Cell Parameters Between Different Parts (Groups of Pore Arrays) of the Same Valve and the Same Micrograph 1266.3 Results and Discussion 1266.3.1 Toward Standardization of the Methodology for the Recognition of 2D Periodicities of Pore Arrays in Diatom Micrographs 1266.3.1.1 Using Two-Dimensional Fast Fourier Transform Analysis 1266.3.1.2 Using Two-Dimensional Autocorrelation Function 1316.3.1.3 The Accuracy of Lattice Parameters’ Measurements Using the Proposed 2D ACF Analysis 1346.3.2 Exploring the Periodicity in Our Studied Micrographs and the Possible Presence of Different Types of 2D Lattices in Diatoms 1376.3.2.1 Irregular Pore Scattering (Non-Periodic Pores) 1376.3.2.2 Linear Periodicity of Pores in Striae (1D Periodicity) 1386.3.2.3 The Different 2D Lattices in Diatom Pore Arrays 1406.3.3 How Perfectly Can Diatoms Build Their 2D Pore Arrays? 1466.3.3.1 Variation of the 2D Lattice Within the Connected Pore Array of the Valve 1466.3.3.2 Comparison of 2D Lattice Parameters and Degree of Perfection of Distinct Pore Array Groups in the Same Micrograph and Valve but With Different Rotational or Reflection Symmetry 1486.3.3.3 The Perfection of 2D Lattices of Diatom Pore Arrays Compared to Perfect (Non-Oblique) 2D Bravais Lattices 1486.3.4 Planar Symmetry Groups to Describe the Whole Diatom Valve Symmetries and Additionally Describe the Complicated 2D Periodic Pore Arrays’ Symmetries 1496.3.4.1 Rosette Groups 1506.3.4.2 Frieze Groups 1516.3.4.3 Wallpaper Groups 1536.4 Conclusion 153Acknowledgment 154Glossary 154References 1557 Quantified Ensemble 3D Surface Features Modeled as a Window on Centric Diatom Valve Morphogenesis 159Janice L. Pappas7.1 Introduction 1597.1.1 From 3D Surface Morphology to Morphogenesis 1607.1.2 Geometric Basis of 3D Surface Models and Analysis 1637.1.3 Differential Geometry of 3D Surface 1637.1.4 3D Surface Feature Geometry and Morphological Attributes 1657.1.5 Centric Diatom Taxa Used as Exemplars in 3D Surface Models for Morphogenetic Analysis 1667.1.6 Morphogenetic Descriptors of Centric Diatoms in Valve Formation as Sequential Change in 3D Surface Morphology 1667.1.7 Purposes of This Study 1677.2 Methods 1687.2.1 Measurement of Ensemble Surface Features and 3D Surface Morphology: Derivation and Solution of the Jacobian, Hessian, Laplacian, and Christoffel Symbols 1687.2.1.1 The Jacobian of 3D Surface Morphology 1687.2.1.2 Monge Patch 1697.2.1.3 First and Second Fundamental Forms and Surface Characterization of the Monge Patch 1697.2.1.4 3D Surface Characterization via Gauss and Weingarten Maps and the Fundamental Forms 1707.2.1.5 Peaks, Valleys, and Saddles of Surface Morphology and the Hessian 1707.2.1.6 Smoothness as a Characterization of Surface Morphology and the Laplacian 1717.2.1.7 Point Connections of 3D Surface Morphology and Christoffel Symbols 1717.2.1.8 Protocol for Using Centric Diatom 3D Surface Models and Their Ensemble Surface Features in Valve Formation Analysis 1737.3 Results 1747.4 Discussion 1847.4.1 Ensemble Surface Features and Physical Characteristics of Valve Morphogenesis 1867.4.2 Factors Affecting Valve Formation 1877.4.3 Diatom Growth Patterns—Buckling and Wave Fronts 1877.4.4 Valve Formation, Ensemble Surface Features, and Self-Similarity 1897.4.5 Diatom Morphogenesis: Cytoplasmic Inheritance and Phenotypic Plasticity 1897.4.6 Phenotypic Variation and Ensemble Surface Features: Epistasis and Canalization 1907.5 Conclusions 190Acknowledgment 191References 1918 Buckling: A Geometric and Biophysical Multiscale Feature of Centric Diatom Valve Morphogenesis 195Janice L. Pappas and Richard Gordon8.1 Introduction 1968.2 Purpose of Study 1978.3 Background: Multiscale Diatom Morphogenesis 1988.3.1 Valve Morphogenesis—Schemata of Schmid and Volcani and of Hildebrand, Lerch, and Shrestha 1988.3.2 Valve Formation—An Overview at the Microscale 1998.3.3 Valve Formation—An Overview at the Meso- and Microscale 2008.3.4 Valve Formation—An Overview at the Meso- and Nanoscale 2008.4 Biophysics of Diatom Valve Formation and Buckling 2018.4.1 Buckling as a Multiscale Measure of Valve Formation 2018.4.2 Valve Formation—Cytoplasmic Features and Buckling 2028.4.3 Buckling: Microtubule Filaments and Bundles 2038.4.4 Buckling: Actin Filament Ring 2048.5 Geometrical and Biophysical Aspects of Buckling and Valve Formation 2058.5.1 Buckling: Geometry of Valve Formation as a Multiscale Wave Front 2058.5.2 Buckling: Valve Formation and Hamiltonian Biophysics 2078.5.3 Buckling: Valve Formation and Deformation Gradients 2088.5.4 Buckling: Multiscale Measurement With Respect to Valve Formation 2108.5.5 Buckling: Krylov Methods and Association of Valve Surface Buckling With Microtubule and Actin Buckling 2108.6 Methods 2118.6.1 Constructing and Analyzing 3D Valve Surface and 2D Microtubule and Actin Filament Models 2118.6.2 Krylov Methods: Associating Valve Surface With Microtubule and Actin Filament Buckling 2128.7 Results 2128.8 Conclusion 216References 2239 Are Mantle Profiles of Circular Centric Diatoms a Measure of Buckling Forces During Valve Morphogenesis? 231Janice L. Pappas and Richard Gordon9.1 Introduction 2319.2 Methods 2339.2.1 Background: Circular Centric 2D Profiles and 3D Surfaces of Revolution 2369.3 Results 2389.3.1 Approximate Constant Profile Length Representing Approximate Same Sized Valves 2399.3.2 Change in Profile Length Representing Size Reduction During Valve Morphogenesis 2409.3.2.1 Inferences About Complementarity and Heterovalvy 2429.3.3 Are Profiles Measures of Buckling Forces During Valve Morphogenesis? 2439.4 Discussion 2459.4.1 Laminated Structures and Mantle Buckling Forces Affecting the Valve Profile 2479.5 Conclusion 248Acknowledgement 248References 248Part 3: Physiology, Biochemistry and Applications 25110 The Effect of the Silica Cell Wall on Diatom Transport and Metabolism 253Mark HildebrandPublications by and about Mark Hildebrand 25411 Diatom Plasticity: Trends, Issues, and Applications on Modern and Classical Taxonomy, Eco‑Evolutionary Dynamics, and Climate Change 261Lawrence Victor D. Vitug11.1 Introduction 26111.2 Model Species: Phaeodactylum tricornutum 26211.3 Transformation Mechanisms of P. tricornutum 26311.4 Future Advances in the Phenotypic Plasticity on P. tricornutum 26311.4.1 Genomic and Molecular Mechanisms in Diatom Phenotypic Plasticity 26311.4.2 Biogeography of Diatoms 26311.4.3 Eco-Evolutionary Dynamics Approach on Diatoms Phenotypic Plasticity 26411.4.4 Adaptive Behavior and Evolutionary Changes in Diatoms Linking to Diatom Plasticity 26511.4.5 Climate Change and Phenotypic Plasticity 26511.5 Conclusion 265References 26512 Frustule Photonics and Light Harvesting Strategies in Diatoms 269Johannes W. Goessling, Yanyan Su, Michael Kühl and Marianne Ellegaard12.1 Introduction 27012.2 Light Spectral Characteristics and Signaling 27412.2.1 Variation of Light Regimes 27412.2.2 Light Perception and Signaling 27512.3 Photosynthesis and Photo-Protection in Diatoms 27612.3.1 Pigment-Based Light Absorption 27612.3.2 Molecular Photo-Protection Mechanisms 27612.3.3 Intracellular Structural Adaptation in Response to Light 27712.3.4 Motility as a Unique Photo-Protection Mechanism 27812.4 Frustule Photonics Related to Diatom Photobiology 27912.4.1 An Extracellular Structure With Optical Properties 27912.4.2 Intraspecific and Intra-Individual Variation of Frustule Periodicity 28112.4.3 Photonic Crystal Properties 28112.4.4 Light Confinement and Focusing 28212.4.5 Scattering and Dispersion of Light 28312.4.6 Attenuation of UV Light for Photo-Protection 28312.5 Frustule Photonics in Light of Niche Differentiation 28512.6 Conclusion 291References 29213 Steps of Silicic Acid Transformation to Siliceous Frustules: Main Hypotheses and Discoveries 301Vadim V. Annenkov, Elena N. Danilovtseva and Richard Gordon13.1 Introduction 30113.2 Penetration of the Boundary Layer: The Diatom as an Antenna for Silica 30313.3 Getting Past the Cloud of Extracellular Material 30413.4 Adsorption of Silica Onto the Outer Organic Coat of the Diatom 30513.5 Getting Past the Silica Frustule or Through Its Pores 30613.6 Getting Past the Inner Organic Coat, the Diatotepum 30613.7 Transport of Silica Across the Cell Membrane 30713.8 Cytoplasm Storage and Trafficking of Silica to the Places of Synthesis of the Frustule Parts 30913.9 Transport and Patterning of Silica Across the Silicalemma 31113.10 Precipitation and Morphogenesis of the Nascent Valve Within the Silicalemma 31413.11 Thickening of the Valve Within the Silicalemma 31913.12 Exteriorization of the Valve 32113.13 Future Work Needed 32113.14 Conclusion 323References 32614 The Effects of Cytoskeletal Inhibitors on Diatom Valve Morphogenesis 349Yekaterina D. Bedoshvili and Yelena V. Likhoshway14.1 Introduction 34914.2 Cytoskeleton and Its Role in Cell Morphogenesis 35014.3 Abnormalities of Diatom Valve Morphogenesis Induced by Cytoskeleton Inhibitors 35214.4 Conclusion 358Acknowledgment 360References 36015 Modeling Silicon Pools in Diatoms Using the Chemistry Toolbox 365Argyro Spinthaki and Konstantinos D. Demadis15.1 Diatoms 36515.2 “Silicon Pools” Biology 36615.3 Silica Particle Formation From Silicic Acid 36615.4 Stabilization of “Soluble” Silica Species (Monosilicic and Disilicic Acids) 37015.4.1 Cationic Polymers 37015.4.2 Neutral (Uncharged) Polymers 37215.4.3 Zwitterionic Polymers 37315.4.4 Blends of Cationic/Anionic Polymers 37515.5 Chemical Mechanisms 37615.6 Conclusions/Perspectives 377Acknowledgments 378References 37816 The Mesopores of Raphid Pennate Diatoms: Toward Natural Controllable Anisotropic Mesoporous Silica Microparticles 383Mohamed M. Ghobara, Richard Gordon and Louisa Reissig16.1 Introduction 38416.2 Morphology and Very Fine Ultrastructure of Diatom Frustules 38616.3 Synthetic Mesoporous Silica 39116.4 The Potential of Raphid Pennates’ Mesoporous Bio-Silica, Similarities, and Dissimilarities Compared With Synthetic MSM/Ns 39316.4.1 The Current Potential of Diatom Porous Silica in Applications 39316.4.2 Why Should We Be Interested in the Mesoporous Silica of Raphid Pennate Frustules if the Frustules of Other Species With Larger Pores Work? 39316.4.3 Similarities and Dissimilarities Compared With Synthetic MSM/Ns 39416.5 Our Ability to Control the Diatom Frustule’s Ultrastructure 39616.5.1 Physicochemical Parameters Alteration Approach 39716.5.2 Genetic Engineering Approach 39816.6 Conclusion 399Acknowledgment 399References 399Glossary 408Index 411