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 xv Part 1: General Issues 1 1 Introduction for a Tutorial on Diatom Morphology 3 Kalina Manoylov and Mohamed Ghobara 1.1 Diatoms in Brief 3 1.2 Tools to Explore Diatom Frustule Morphology 7 1.3 Diatom Frustule 3D Reconstruction 12 1.3.1 Recommended Steps to Understand the Complex Diatom Morphology: A Guide for Beginners 13 1.4 Conclusion 15 Acknowledgements 15 References 15 2 The Uncanny Symmetry of Some Diatoms and Not of Others: A Multi-Scale Morphological Characteristic and a Puzzle for Morphogenesis 19 Janice L. Pappas, Mary Ann Tiffany and Richard Gordon 2.1 Introduction 20 2.1.1 Recognition and Symmetry 21 2.1.2 Symmetry and Growth 24 2.1.3 Diatom Pattern Formation, Growth, and Symmetry 25 2.1.4 Diatoms and Uncanny Symmetry 27 2.1.5 Purpose of This Study 28 2.2 Methods 28 2.2.1 Centric Diatom Images Used for Analysis 28 2.2.2 Centric Diatoms, Morphology, and Valve Formation 34 2.2.3 Image Entropy and Symmetry Measurement 36 2.2.4 Image Preparation for Measurement 37 2.2.5 Image Tilt and Slant Measurement Correction for Entropy Values 38 2.2.6 Symmetry Analysis 39 2.2.7 Entropy, Symmetry, and Stability 40 2.2.8 Randomness and Instability 42 2.3 Results 43 2.3.1 Symmetry Analysis 43 2.3.2 Valve Formation-Stability and Instability Analyses 49 2.4 Discussion 51 2.4.1 Symmetry and Scale in Diatoms 55 2.4.2 Valve Formation and Stability 56 2.4.3 Symmetry, Stability and Diatom Morphogenesis 57 2.4.4 Future Research-Symmetry, Stability and Directionality in Diatom Morphogenesis 58 References 59 3 On the Size Sequence of Diatoms in Clonal Chains 69 Thomas Harbich 3.1 Introduction 70 3.2 Mathematical Analysis of t he Size Sequence 73 3.2.1 Alternative Method for Calculating the Size Sequence 73 3.2.2 Self-Similarity and Fractal Structure 75 3.2.3 Matching Fragments to a Generation Based on Known Size Indices of the Fragment 76 3.2.4 Sequence of the Differences of the Size Indices 78 3.2.5 Matching Fragments to a Generation Based on Unknown Size Indices of the Fragment 80 3.2.6 Synchronicity of Cell Divisions 81 3.3 Observations 82 3.3.1 Challenges in Verifying the Sequence of Sizes 82 3.3.2 Materials and Methods 83 3.3.3 Investigation of the Size Sequence of a Eunotia sp. 84 3.3.4 Synchronicity 86 3.4 Conclusions 87 Acknowledgements 88 Appendix 3A L-System for the Generation of the Sequence of Differences in Size Indices of Adjacent Diatoms 88 Appendix 3B Probability Consideration for Loss of Synchronicity 89 References 91 4 Valve Morphogenesis in Amphitetras antediluviana Ehrenburg 93 Mary A. Tiffany and Bonnie L. Hurwitz 4.1 Introduction 93 4.2 Material and Methods 94 4.3 Observations 94 4.3.1 Amphitetras antediluviana Mature Valves 94 4.3.2 Amphitetras antediluviana Forming Valves 96 4.3.3 Amphitetras antediluviana Girdle Band Formation 101 4.4 Conclusion 101 Acknowledgments 102 References 102 Glossary 104 Part 2: Simulation 105 5 Geometric Models of Concentric and Spiral Areola Patterns of Centric Diatoms 107 Anton M. Lyakh 5.1 Introduction 107 5.2 Set of Common Rules Used in the Models 109 5.3 Concentric Pattern of Areolae 109 5.4 Spiral Patterns of Areolae 110 5.4.1 Unidirectional Spiral Pattern 111 5.4.2 Bidirectional Spiral Pattern 113 5.4.3 Common Genesis of Unidirectional and Bidirectional Spiral Patterns 113 5.5 Conversion of an Areolae-Based Model Into a Frame-Based Model 114 5.6 Conclusion 114 Acknowledgements 114 References 115 6 Diatom Pore Arrays' Periodicities and Symmetries in the Euclidean Plane: Nature Between Perfection and Imperfection 117 Mohamed M. Ghobara, Mary Ann Tiffany, Richard Gordon and Louisa Reissig 6.1 Introduction 118 6.2 Materials and Methods 122 6.2.1 Micrograph Segmentation 123 6.2.2 Two-Dimensional Fast Fourier Analysis and Autocorrelation Function Analysis 123 6.2.3 Lattice Measurements and Recognition 123 6.2.4 Accu