Diatom Morphogenesis

DIATOM MORPHOGENESIS

A unique book presenting the range of silica structures formed by diatoms, theories and hypotheses of how they are made, and applications to nanotechnology by use or imitation of diatom morphogenesis.

There are up to 200,000 species of diatoms, each species of these algal cells bearing an ornate, amorphous silica glass shell. The silica is structured at 7 orders of magnitude size range and is thus the most complex multiscalar solid structure known. Recent research is beginning to unravel how a single cell marshals chemical, physical, biochemical, genetic, and cytoskeletal processes to produce these single-cell marvels. The field of diatom nanotechnology is advancing as this understanding matures.

Diatoms have been actively studied over the recent 10-20 years with various modern equipment, experimental and computer simulation approaches, including molecular biology, fluorescence-based methods, electron, confocal, and AFM microscopy. This has resulted in a huge amount of information but the key stages of their silica morphogenesis are still not clear. This is the time to reconsider and consolidate the work performed so far and to understand how we can go ahead.

The main objective of this book is to describe the actual situation in the science of diatom morphogenesis, to specify the most important unresolved questions, and to present the corresponding hypotheses. The following areas are discussed:

• A tutorial chapter, with a glossary for newcomers to the field, who are often from outside of biology, let alone phycology;

• Diatom Morphogenesis: general issues, including symmetry and size issues;

• Diatom Morphogenesis: simulation, including analytical and numerical methods for description of the diatom valve shape and pore structure;

• Diatom Morphogenesis: physiology, biochemistry, and applications, including the relationship between taxonomy and physiology, biosilicification hypotheses, and ideas about applications of diatoms.

Audience

Researchers, scientists, and graduate students in the fields of phycology, general biology, marine sciences, the chemistry of silica, materials science, and ecology.

Autorentext

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).

Zusammenfassung
DIATOM MORPHOGENESIS A unique book presenting the range of silica structures formed by diatoms, theories and hypotheses of how they are made, and applications to nanotechnology by use or imitation of diatom morphogenesis. There are up to 200,000 species of diatoms, each species of these algal cells bearing an ornate, amorphous silica glass shell. The silica is structured at 7 orders of magnitude size range and is thus the most complex multiscalar solid structure known. Recent research is beginning to unravel how a single cell marshals chemical, physical, biochemical, genetic, and cytoskeletal processes to produce these single-cell marvels. The field of diatom nanotechnology is advancing as this understanding matures. Diatoms have been actively studied over the recent 10-20 years with various modern equipment, experimental and computer simulation approaches, including molecular biology, fluorescence-based methods, electron, confocal, and AFM microscopy. This has resulted in a huge amount of information but the key stages of their silica morphogenesis are still not clear. This is the time to reconsider and consolidate the work performed so far and to understand how we can go ahead. The main objective of this book is to describe the actual situation in the science of diatom morphogenesis, to specify the most important unresolved questions, and to present the corresponding hypotheses. The following areas are discussed:

• A tutorial chapter, with a glossary for newcomers to the field, who are often from outside of biology, let alone phycology;
• Diatom Morphogenesis: general issues, including symmetry and size issues;
• Diatom Morphogenesis: simulation, including analytical and numerical methods for description of the diatom valve shape and pore structure;
• Diatom Morphogenesis: physiology, biochemistry, and applications, including the relationship between taxonomy and physiology, biosilicification hypotheses, and ideas about applications of diatoms. Audience Researchers, scientists, and graduate students in the fields of phycology, general biology, marine sciences, the chemistry of silica, materials science, and ecology.

Inhalt
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 FormationStability 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 ResearchSymmetry, 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 …