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Submit a ProposalDiatom Morphogenesis
 | Edited by Vadim V. Annenkov, Joseph Seckbach, and Richard Gordon Series: Diatoms: Biology and Applications Copyright: 2022 | Status: Published ISBN: 9781119487951 | Hardcover | 438 pages | 163 illustrations Price: $249 USD  |
One Line Description
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.
Audience
Researchers, scientists, and graduate students in the fields of phycology, general biology, marine sciences, the chemistry of silica, materials science, and ecology.
Researchers, scientists, and graduate students in the fields of phycology, general biology, marine sciences, the chemistry of silica, materials science, and ecology.
Description
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.
Back to Top
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.
Back to Top
Author / Editor Details
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 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).
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Table of Contents
Preface
Part 1: General Issues
1. Introduction for a Tutorial on Diatom Morphology
Kalina Manoylov and Mohamed Ghobara
1.1 Diatoms in Brief
1.2 Tools to Explore Diatom Frustule Morphology
1.3 Diatom Frustule 3D Reconstruction
1.3.1 Recommended Steps to Understand the Complex Diatom Morphology: A Guide for Beginners
1.4 Conclusion
Acknowledgements
References
2. The Uncanny Symmetry of Some Diatoms and Not of Others: A Multi-Scale Morphological Characteristic and a Puzzle for Morphogenesis
Janice L. Pappas, Mary Ann Tiffany and Richard Gordon
2.1 Introduction
2.1.1 Recognition and Symmetry
2.1.2 Symmetry and Growth
2.1.3 Diatom Pattern Formation, Growth, and Symmetry
2.1.4 Diatoms and Uncanny Symmetry
2.1.5 Purpose of This Study
2.2 Methods
2.2.1 Centric Diatom Images Used for Analysis
2.2.2 Centric Diatoms, Morphology, and Valve Formation
2.2.3 Image Entropy and Symmetry Measurement
2.2.4 Image Preparation for Measurement
2.2.5 Image Tilt and Slant Measurement Correction for Entropy Values
2.2.6 Symmetry Analysis
2.2.7 Entropy, Symmetry, and Stability
2.2.8 Randomness and Instability
2.3 Results
2.3.1 Symmetry Analysis
2.3.2 Valve Formation—Stability and Instability Analyses
2.4 Discussion
2.4.1 Symmetry and Scale in Diatoms
2.4.2 Valve Formation and Stability
2.4.3 Symmetry, Stability and Diatom Morphogenesis
2.4.4 Future Research—Symmetry, Stability and Directionality in Diatom Morphogenesis 58 References
3. On the Size Sequence of Diatoms in Clonal Chains
Thomas Harbich
3.1 Introduction
3.2 Mathematical Analysis of the Size Sequence
3.2.1 Alternative Method for Calculating the Size Sequence
3.2.2 Self-Similarity and Fractal Structure
3.2.3 Matching Fragments to a Generation Based on Known Size Indices of the Fragment
3.2.4 Sequence of the Differences of the Size Indices
3.2.5 Matching Fragments to a Generation Based on Unknown Size Indices of the Fragment
3.2.6 Synchronicity of Cell Divisions
3.3 Observations
3.3.1 Challenges in Verifying the Sequence of Sizes
3.3.2 Materials and Methods
3.3.3 Investigation of the Size Sequence of a Eunotia sp.
3.3.4 Synchronicity
3.4 Conclusions
Acknowledgements
Appendix 3A L-System for the Generation of the Sequence of Differences
in Size Indices of Adjacent Diatoms
Appendix 3B Probability Consideration for Loss of Synchronicity
References
4. Valve Morphogenesis in Amphitetras antediluviana Ehrenburg
Mary A. Tiffany and Bonnie L. Hurwitz
4.1 Introduction
4.2 Material and Methods
4.3 Observations
4.3.1 Amphitetras antediluviana Mature Valves
4.3.2 Amphitetras antediluviana Forming Valves
4.3.3 Amphitetras antediluviana Girdle Band Formation
4.4 Conclusion
Acknowledgments
References
Glossary
Part 2: Simulation
5. Geometric Models of Concentric and Spiral Areola Patterns of Centric Diatoms
Anton M. Lyakh
5.1 Introduction
5.2 Set of Common Rules Used in the Models
5.3 Concentric Pattern of Areolae
5.4 Spiral Patterns of Areolae
5.4.1 Unidirectional Spiral Pattern
5.4.2 Bidirectional Spiral Pattern
5.4.3 Common Genesis of Unidirectional and Bidirectional Spiral Patterns
5.5 Conversion of an Areolae-Based Model Into a Frame-Based Model
5.6 Conclusion
Acknowledgements
References
6. Diatom Pore Arrays’ Periodicities and Symmetries in the Euclidean Plane:
Nature Between Perfection and Imperfection
Mohamed M. Ghobara, Mary Ann Tiffany, Richard Gordon and Louisa Reissig
6.1 Introduction
6.2 Materials and Methods
6.2.1 Micrograph Segmentation
6.2.2 Two-Dimensional Fast Fourier Analysis and Autocorrelation Function Analysis 6.2.3 Lattice Measurements and Recognition
6.2.4 Accuracy of 2D ACF-Based Calculations
6.2.5 The Perfection of the Unit Cell Parameters Between Different Parts (Groups of Pore Arrays) of the Same Valve and the Same Micrograph
6.3 Results and Discussion
6.3.1 Toward Standardization of the Methodology for the Recognition of 2D Periodicities of Pore Arrays in Diatom Micrographs
6.3.1.1 Using Two-Dimensional Fast Fourier Transform Analysis
6.3.1.2 Using Two-Dimensional Autocorrelation Function
6.3.1.3 The Accuracy of Lattice Parameters’ Measurements Using the Proposed 2D ACF Analysis
6.3.2 Exploring the Periodicity in Our Studied Micrographs and the Possible Presence of Different Types of 2D Lattices in Diatoms
6.3.2.1 Irregular Pore Scattering (Non-Periodic Pores)
6.3.2.2 Linear Periodicity of Pores in Striae (1D Periodicity)
6.3.2.3 The Different 2D Lattices in Diatom Pore Arrays
6.3.3 How Perfectly Can Diatoms Build Their 2D Pore Arrays?
6.3.3.1 Variation of the 2D Lattice Within the Connected. Pore Array of the Valve
6.3.3.2 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
6.3.3.3 The Perfection of 2D Lattices of Diatom Pore Arrays Compared to Perfect (Non-Oblique) 2D Bravais Lattices
6.3.4 Planar Symmetry Groups to Describe the Whole Diatom Valve Symmetries and Additionally Describe the Complicated 2D Periodic Pore Arrays’ Symmetries
6.3.4.1 Rosette Groups
6.3.4.2 Frieze Groups
6.3.4.3 Wallpaper Groups
6.4 Conclusion
Acknowledgment
Glossary
References
7. Quantified Ensemble 3D Surface Features Modeled as a Window on Centric Diatom Valve Morphogenesis
Janice L. Pappas
7.1 Introduction
7.1.1 From 3D Surface Morphology to Morphogenesis
7.1.2 Geometric Basis of 3D Surface Models and Analysis
7.1.3 Differential Geometry of 3D Surface
7.1.4 3D Surface Feature Geometry and Morphological Attributes
7.1.5 Centric Diatom Taxa Used as Exemplars in 3D Surface Models for Morphogenetic Analysis
7.1.6 Morphogenetic Descriptors of Centric Diatoms in Valve Formation as Sequential Change in 3D Surface Morphology
7.1.7 Purposes of This Study
7.2 Methods
7.2.1 Measurement of Ensemble Surface Features and 3D Surface Morphology: Derivation and Solution of the Jacobian, Hessian, Laplacian, and Christoffel Symbols
7.2.1.1 The Jacobian of 3D Surface Morphology
7.2.1.2 Monge Patch
7.2.1.3 First and Second Fundamental Forms and Surface Characterization of the Monge Patch
7.2.1.4 3D Surface Characterization via Gauss and Weingarten Maps and the Fundamental Forms
7.2.1.5 Peaks, Valleys, and Saddles of Surface Morphology and the Hessian
7.2.1.6 Smoothness as a Characterization of Surface Morphology and the Laplacian
7.2.1.7 Point Connections of 3D Surface Morphology and Christoffel Symbols
7.2.1.8 Protocol for Using Centric Diatom 3D Surface Models and Their Ensemble Surface Features in Valve Formation Analysis
7.3 Results
7.4 Discussion
7.4.1 Ensemble Surface Features and Physical Characteristics of Valve Morphogenesis
7.4.2 Factors Affecting Valve Formation
7.4.3 Diatom Growth Patterns—Buckling and Wave Fronts
7.4.4 Valve Formation, Ensemble Surface Features, and Self-Similarity
7.4.5 Diatom Morphogenesis: Cytoplasmic Inheritance and Phenotypic Plasticity
7.4.6 Phenotypic Variation and Ensemble Surface Features: Epistasis and Canalization
7.5 Conclusions
Acknowledgment
References
8. Buckling: A Geometric and Biophysical Multiscale Feature of Centric Diatom Valve Morphogenesis
Janice L. Pappas and Richard Gordon
8.1 Introduction
8.2 Purpose of Study
8.3 Background: Multiscale Diatom Morphogenesis
8.3.1 Valve Morphogenesis—Schemata of Schmid and Volcani and of Hildebrand, Lerch, and Shrestha
8.3.2 Valve Formation—An Overview at the Microscale
8.3.3 Valve Formation—An Overview at the Meso- and Microscale
8.3.4 Valve Formation—An Overview at the Meso- and Nanoscale
8.4 Biophysics of Diatom Valve Formation and Buckling
8.4.1 Buckling as a Multiscale Measure of Valve Formation
8.4.2 Valve Formation—Cytoplasmic Features and Buckling
8.4.3 Buckling: Microtubule Filaments and Bundles
8.4.4 Buckling: Actin Filament Ring
8.5 Geometrical and Biophysical Aspects of Buckling and Valve Formation
8.5.1 Buckling: Geometry of Valve Formation as a Multiscale Wave Front
8.5.2 Buckling: Valve Formation and Hamiltonian Biophysics
8.5.3 Buckling: Valve Formation and Deformation Gradients
8.5.4 Buckling: Multiscale Measurement With Respect to Valve Formation
8.5.5 Buckling: Krylov Methods and Association of Valve Surface Buckling With Microtubule and Actin Buckling
8.6 Methods
8.6.1 Constructing and Analyzing 3D Valve Surface and 2D Microtubule and Actin Filament Models
8.6.2 Krylov Methods: Associating Valve Surface With Microtubule and Actin Filament Buckling
8.7 Results
8.8 Conclusion
References
9. Are Mantle Profiles of Circular Centric Diatoms a Measure of Buckling Forces During Valve Morphogenesis?
Janice L. Pappas and Richard Gordon
9.1 Introduction
9.2 Methods
9.2.1 Background: Circular Centric 2D Profiles and 3D Surfaces of Revolution
9.3 Results
9.3.1 Approximate Constant Profile Length Representing Approximate Same Sized Valves
9.3.2 Change in Profile Length Representing Size Reduction During Valve Morphogenesis
9.3.2.1 Inferences About Complementarity and Heterovalvy
9.3.3 Are Profiles Measures of Buckling Forces During Valve Morphogenesis?
9.4 Discussion
9.4.1 Laminated Structures and Mantle Buckling Forces Affecting the Valve Profile 9.5 Conclusion
Acknowledgement
References
Part 3: Physiology, Biochemistry and Applications
10. The Effect of the Silica Cell Wall on Diatom Transport and Metabolism
Mark Hildebrand
Publications by and about Mark Hildebrand
11. Diatom Plasticity: Trends, Issues, and Applications on Modern and Classical Taxonomy, Eco-Evolutionary Dynamics, and Climate Change
Lawrence Victor D. Vitug
11.1 Introduction
11.2 Model Species: Phaeodactylum tricornutum
11.3 Transformation Mechanisms of P. tricornutum
11.4 Future Advances in the Phenotypic Plasticity on P. tricornutum
11.4.1 Genomic and Molecular Mechanisms in Diatom Phenotypic Plasticity
11.4.2 Biogeography of Diatoms
11.4.3 Eco-Evolutionary Dynamics Approach on Diatoms Phenotypic Plasticity
11.4.4 Adaptive Behavior and Evolutionary Changes in Diatoms Linking to Diatom Plasticity
11.4.5 Climate Change and Phenotypic Plasticity
11.5 Conclusion
References
12. Frustule Photonics and Light Harvesting Strategies in Diatoms
Johannes W. Goessling, Yanyan Su, Michael Kühl and Marianne Ellegaard
12.1 Introduction
12.2 Light Spectral Characteristics and Signaling
12.2.1 Variation of Light Regimes
12.2.2 Light Perception and Signaling
12.3 Photosynthesis and Photo-Protection in Diatoms
12.3.1 Pigment-Based Light Absorption
12.3.2 Molecular Photo-Protection Mechanisms
12.3.3 Intracellular Structural Adaptation in Response to Light
12.3.4 Motility as a Unique Photo-Protection Mechanism
12.4 Frustule Photonics Related to Diatom Photobiology
12.4.1 An Extracellular Structure With Optical Properties
12.4.2 Intraspecific and Intra-Individual Variation of Frustule Periodicity
12.4.3 Photonic Crystal Properties
12.4.4 Light Confinement and Focusing
12.4.5 Scattering and Dispersion of Light
12.4.6 Attenuation of UV Light for Photo-Protection
12.5 Frustule Photonics in Light of Niche Differentiation
12.6 Conclusion
References
13. Steps of Silicic Acid Transformation to Siliceous Frustules: Main Hypotheses and Discoveries
Vadim V. Annenkov, Elena N. Danilovtseva and Richard Gordon
13.1 Introduction
13.2 Penetration of the Boundary Layer: The Diatom as an Antenna for Silica
13.3 Getting Past the Cloud of Extracellular Material
13.4 Adsorption of Silica Onto the Outer Organic Coat of the Diatom
13.5 Getting Past the Silica Frustule or Through Its Pores
13.6 Getting Past the Inner Organic Coat, the Diatotepum
13.7 Transport of Silica Across the Cell Membrane
13.8 Cytoplasm Storage and Trafficking of Silica to the Places of Synthesis of the Frustule Parts
13.9 Transport and Patterning of Silica Across the Silicalemma
13.10 Precipitation and Morphogenesis of the Nascent Valve Within the Silicalemma
13.11 Thickening of the Valve Within the Silicalemma
13.12 Exteriorization of the Valve
13.13 Future Work Needed
13.14 Conclusion
References
14. The Effects of Cytoskeletal Inhibitors on Diatom Valve Morphogenesis
Yekaterina D. Bedoshvili and Yelena V. Likhoshway
14.1 Introduction
14.2 Cytoskeleton and Its Role in Cell Morphogenesis
14.3 Abnormalities of Diatom Valve Morphogenesis Induced by Cytoskeleton Inhibitors
14.4 Conclusion
Acknowledgment
References
15. Modeling Silicon Pools in Diatoms Using the Chemistry Toolbox
Argyro Spinthaki and Konstantinos D. Demadis
15.1 Diatoms
15.2 “Silicon Pools” Biology
15.3 Silica Particle Formation From Silicic Acid
15.4 Stabilization of “Soluble” Silica Species (Monosilicic and Disilicic Acids)
15.4.1 Cationic Polymers
15.4.2 Neutral (Uncharged) Polymers
15.4.3 Zwitterionic Polymers
15.4.4 Blends of Cationic/Anionic Polymers
15.5 Chemical Mechanisms
15.6 Conclusions/Perspectives
Acknowledgments
References
16. The Mesopores of Raphid Pennate Diatoms: Toward Natural Controllable Anisotropic Mesoporous Silica Microparticles
Mohamed M. Ghobara, Richard Gordon and Louisa Reissig
16.1 Introduction
16.2 Morphology and Very Fine Ultrastructure of Diatom Frustules
16.3 Synthetic Mesoporous Silica
16.4 The Potential of Raphid Pennates’ Mesoporous Bio-Silica, Similarities,
and Dissimilarities Compared With Synthetic MSM/Ns
16.4.1 The Current Potential of Diatom Porous Silica in Applications
16.4.2 Why Should We Be Interested in the Mesoporous Silica of Raphid Pennate Frustules if the Frustules of Other Species With Larger Pores Work?
16.4.3 Similarities and Dissimilarities Compared With Synthetic MSM/Ns
16.5 Our Ability to Control the Diatom Frustule’s Ultrastructure
16.5.1 Physicochemical Parameters Alteration Approach
16.5.2 Genetic Engineering Approach
16.6 Conclusion
Acknowledgment
References
Glossary
Index
Back to Top
Preface
Part 1: General Issues
1. Introduction for a Tutorial on Diatom Morphology
Kalina Manoylov and Mohamed Ghobara
1.1 Diatoms in Brief
1.2 Tools to Explore Diatom Frustule Morphology
1.3 Diatom Frustule 3D Reconstruction
1.3.1 Recommended Steps to Understand the Complex Diatom Morphology: A Guide for Beginners
1.4 Conclusion
Acknowledgements
References
2. The Uncanny Symmetry of Some Diatoms and Not of Others: A Multi-Scale Morphological Characteristic and a Puzzle for Morphogenesis
Janice L. Pappas, Mary Ann Tiffany and Richard Gordon
2.1 Introduction
2.1.1 Recognition and Symmetry
2.1.2 Symmetry and Growth
2.1.3 Diatom Pattern Formation, Growth, and Symmetry
2.1.4 Diatoms and Uncanny Symmetry
2.1.5 Purpose of This Study
2.2 Methods
2.2.1 Centric Diatom Images Used for Analysis
2.2.2 Centric Diatoms, Morphology, and Valve Formation
2.2.3 Image Entropy and Symmetry Measurement
2.2.4 Image Preparation for Measurement
2.2.5 Image Tilt and Slant Measurement Correction for Entropy Values
2.2.6 Symmetry Analysis
2.2.7 Entropy, Symmetry, and Stability
2.2.8 Randomness and Instability
2.3 Results
2.3.1 Symmetry Analysis
2.3.2 Valve Formation—Stability and Instability Analyses
2.4 Discussion
2.4.1 Symmetry and Scale in Diatoms
2.4.2 Valve Formation and Stability
2.4.3 Symmetry, Stability and Diatom Morphogenesis
2.4.4 Future Research—Symmetry, Stability and Directionality in Diatom Morphogenesis 58 References
3. On the Size Sequence of Diatoms in Clonal Chains
Thomas Harbich
3.1 Introduction
3.2 Mathematical Analysis of the Size Sequence
3.2.1 Alternative Method for Calculating the Size Sequence
3.2.2 Self-Similarity and Fractal Structure
3.2.3 Matching Fragments to a Generation Based on Known Size Indices of the Fragment
3.2.4 Sequence of the Differences of the Size Indices
3.2.5 Matching Fragments to a Generation Based on Unknown Size Indices of the Fragment
3.2.6 Synchronicity of Cell Divisions
3.3 Observations
3.3.1 Challenges in Verifying the Sequence of Sizes
3.3.2 Materials and Methods
3.3.3 Investigation of the Size Sequence of a Eunotia sp.
3.3.4 Synchronicity
3.4 Conclusions
Acknowledgements
Appendix 3A L-System for the Generation of the Sequence of Differences
in Size Indices of Adjacent Diatoms
Appendix 3B Probability Consideration for Loss of Synchronicity
References
4. Valve Morphogenesis in Amphitetras antediluviana Ehrenburg
Mary A. Tiffany and Bonnie L. Hurwitz
4.1 Introduction
4.2 Material and Methods
4.3 Observations
4.3.1 Amphitetras antediluviana Mature Valves
4.3.2 Amphitetras antediluviana Forming Valves
4.3.3 Amphitetras antediluviana Girdle Band Formation
4.4 Conclusion
Acknowledgments
References
Glossary
Part 2: Simulation
5. Geometric Models of Concentric and Spiral Areola Patterns of Centric Diatoms
Anton M. Lyakh
5.1 Introduction
5.2 Set of Common Rules Used in the Models
5.3 Concentric Pattern of Areolae
5.4 Spiral Patterns of Areolae
5.4.1 Unidirectional Spiral Pattern
5.4.2 Bidirectional Spiral Pattern
5.4.3 Common Genesis of Unidirectional and Bidirectional Spiral Patterns
5.5 Conversion of an Areolae-Based Model Into a Frame-Based Model
5.6 Conclusion
Acknowledgements
References
6. Diatom Pore Arrays’ Periodicities and Symmetries in the Euclidean Plane:
Nature Between Perfection and Imperfection
Mohamed M. Ghobara, Mary Ann Tiffany, Richard Gordon and Louisa Reissig
6.1 Introduction
6.2 Materials and Methods
6.2.1 Micrograph Segmentation
6.2.2 Two-Dimensional Fast Fourier Analysis and Autocorrelation Function Analysis 6.2.3 Lattice Measurements and Recognition
6.2.4 Accuracy of 2D ACF-Based Calculations
6.2.5 The Perfection of the Unit Cell Parameters Between Different Parts (Groups of Pore Arrays) of the Same Valve and the Same Micrograph
6.3 Results and Discussion
6.3.1 Toward Standardization of the Methodology for the Recognition of 2D Periodicities of Pore Arrays in Diatom Micrographs
6.3.1.1 Using Two-Dimensional Fast Fourier Transform Analysis
6.3.1.2 Using Two-Dimensional Autocorrelation Function
6.3.1.3 The Accuracy of Lattice Parameters’ Measurements Using the Proposed 2D ACF Analysis
6.3.2 Exploring the Periodicity in Our Studied Micrographs and the Possible Presence of Different Types of 2D Lattices in Diatoms
6.3.2.1 Irregular Pore Scattering (Non-Periodic Pores)
6.3.2.2 Linear Periodicity of Pores in Striae (1D Periodicity)
6.3.2.3 The Different 2D Lattices in Diatom Pore Arrays
6.3.3 How Perfectly Can Diatoms Build Their 2D Pore Arrays?
6.3.3.1 Variation of the 2D Lattice Within the Connected. Pore Array of the Valve
6.3.3.2 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
6.3.3.3 The Perfection of 2D Lattices of Diatom Pore Arrays Compared to Perfect (Non-Oblique) 2D Bravais Lattices
6.3.4 Planar Symmetry Groups to Describe the Whole Diatom Valve Symmetries and Additionally Describe the Complicated 2D Periodic Pore Arrays’ Symmetries
6.3.4.1 Rosette Groups
6.3.4.2 Frieze Groups
6.3.4.3 Wallpaper Groups
6.4 Conclusion
Acknowledgment
Glossary
References
7. Quantified Ensemble 3D Surface Features Modeled as a Window on Centric Diatom Valve Morphogenesis
Janice L. Pappas
7.1 Introduction
7.1.1 From 3D Surface Morphology to Morphogenesis
7.1.2 Geometric Basis of 3D Surface Models and Analysis
7.1.3 Differential Geometry of 3D Surface
7.1.4 3D Surface Feature Geometry and Morphological Attributes
7.1.5 Centric Diatom Taxa Used as Exemplars in 3D Surface Models for Morphogenetic Analysis
7.1.6 Morphogenetic Descriptors of Centric Diatoms in Valve Formation as Sequential Change in 3D Surface Morphology
7.1.7 Purposes of This Study
7.2 Methods
7.2.1 Measurement of Ensemble Surface Features and 3D Surface Morphology: Derivation and Solution of the Jacobian, Hessian, Laplacian, and Christoffel Symbols
7.2.1.1 The Jacobian of 3D Surface Morphology
7.2.1.2 Monge Patch
7.2.1.3 First and Second Fundamental Forms and Surface Characterization of the Monge Patch
7.2.1.4 3D Surface Characterization via Gauss and Weingarten Maps and the Fundamental Forms
7.2.1.5 Peaks, Valleys, and Saddles of Surface Morphology and the Hessian
7.2.1.6 Smoothness as a Characterization of Surface Morphology and the Laplacian
7.2.1.7 Point Connections of 3D Surface Morphology and Christoffel Symbols
7.2.1.8 Protocol for Using Centric Diatom 3D Surface Models and Their Ensemble Surface Features in Valve Formation Analysis
7.3 Results
7.4 Discussion
7.4.1 Ensemble Surface Features and Physical Characteristics of Valve Morphogenesis
7.4.2 Factors Affecting Valve Formation
7.4.3 Diatom Growth Patterns—Buckling and Wave Fronts
7.4.4 Valve Formation, Ensemble Surface Features, and Self-Similarity
7.4.5 Diatom Morphogenesis: Cytoplasmic Inheritance and Phenotypic Plasticity
7.4.6 Phenotypic Variation and Ensemble Surface Features: Epistasis and Canalization
7.5 Conclusions
Acknowledgment
References
8. Buckling: A Geometric and Biophysical Multiscale Feature of Centric Diatom Valve Morphogenesis
Janice L. Pappas and Richard Gordon
8.1 Introduction
8.2 Purpose of Study
8.3 Background: Multiscale Diatom Morphogenesis
8.3.1 Valve Morphogenesis—Schemata of Schmid and Volcani and of Hildebrand, Lerch, and Shrestha
8.3.2 Valve Formation—An Overview at the Microscale
8.3.3 Valve Formation—An Overview at the Meso- and Microscale
8.3.4 Valve Formation—An Overview at the Meso- and Nanoscale
8.4 Biophysics of Diatom Valve Formation and Buckling
8.4.1 Buckling as a Multiscale Measure of Valve Formation
8.4.2 Valve Formation—Cytoplasmic Features and Buckling
8.4.3 Buckling: Microtubule Filaments and Bundles
8.4.4 Buckling: Actin Filament Ring
8.5 Geometrical and Biophysical Aspects of Buckling and Valve Formation
8.5.1 Buckling: Geometry of Valve Formation as a Multiscale Wave Front
8.5.2 Buckling: Valve Formation and Hamiltonian Biophysics
8.5.3 Buckling: Valve Formation and Deformation Gradients
8.5.4 Buckling: Multiscale Measurement With Respect to Valve Formation
8.5.5 Buckling: Krylov Methods and Association of Valve Surface Buckling With Microtubule and Actin Buckling
8.6 Methods
8.6.1 Constructing and Analyzing 3D Valve Surface and 2D Microtubule and Actin Filament Models
8.6.2 Krylov Methods: Associating Valve Surface With Microtubule and Actin Filament Buckling
8.7 Results
8.8 Conclusion
References
9. Are Mantle Profiles of Circular Centric Diatoms a Measure of Buckling Forces During Valve Morphogenesis?
Janice L. Pappas and Richard Gordon
9.1 Introduction
9.2 Methods
9.2.1 Background: Circular Centric 2D Profiles and 3D Surfaces of Revolution
9.3 Results
9.3.1 Approximate Constant Profile Length Representing Approximate Same Sized Valves
9.3.2 Change in Profile Length Representing Size Reduction During Valve Morphogenesis
9.3.2.1 Inferences About Complementarity and Heterovalvy
9.3.3 Are Profiles Measures of Buckling Forces During Valve Morphogenesis?
9.4 Discussion
9.4.1 Laminated Structures and Mantle Buckling Forces Affecting the Valve Profile 9.5 Conclusion
Acknowledgement
References
Part 3: Physiology, Biochemistry and Applications
10. The Effect of the Silica Cell Wall on Diatom Transport and Metabolism
Mark Hildebrand
Publications by and about Mark Hildebrand
11. Diatom Plasticity: Trends, Issues, and Applications on Modern and Classical Taxonomy, Eco-Evolutionary Dynamics, and Climate Change
Lawrence Victor D. Vitug
11.1 Introduction
11.2 Model Species: Phaeodactylum tricornutum
11.3 Transformation Mechanisms of P. tricornutum
11.4 Future Advances in the Phenotypic Plasticity on P. tricornutum
11.4.1 Genomic and Molecular Mechanisms in Diatom Phenotypic Plasticity
11.4.2 Biogeography of Diatoms
11.4.3 Eco-Evolutionary Dynamics Approach on Diatoms Phenotypic Plasticity
11.4.4 Adaptive Behavior and Evolutionary Changes in Diatoms Linking to Diatom Plasticity
11.4.5 Climate Change and Phenotypic Plasticity
11.5 Conclusion
References
12. Frustule Photonics and Light Harvesting Strategies in Diatoms
Johannes W. Goessling, Yanyan Su, Michael Kühl and Marianne Ellegaard
12.1 Introduction
12.2 Light Spectral Characteristics and Signaling
12.2.1 Variation of Light Regimes
12.2.2 Light Perception and Signaling
12.3 Photosynthesis and Photo-Protection in Diatoms
12.3.1 Pigment-Based Light Absorption
12.3.2 Molecular Photo-Protection Mechanisms
12.3.3 Intracellular Structural Adaptation in Response to Light
12.3.4 Motility as a Unique Photo-Protection Mechanism
12.4 Frustule Photonics Related to Diatom Photobiology
12.4.1 An Extracellular Structure With Optical Properties
12.4.2 Intraspecific and Intra-Individual Variation of Frustule Periodicity
12.4.3 Photonic Crystal Properties
12.4.4 Light Confinement and Focusing
12.4.5 Scattering and Dispersion of Light
12.4.6 Attenuation of UV Light for Photo-Protection
12.5 Frustule Photonics in Light of Niche Differentiation
12.6 Conclusion
References
13. Steps of Silicic Acid Transformation to Siliceous Frustules: Main Hypotheses and Discoveries
Vadim V. Annenkov, Elena N. Danilovtseva and Richard Gordon
13.1 Introduction
13.2 Penetration of the Boundary Layer: The Diatom as an Antenna for Silica
13.3 Getting Past the Cloud of Extracellular Material
13.4 Adsorption of Silica Onto the Outer Organic Coat of the Diatom
13.5 Getting Past the Silica Frustule or Through Its Pores
13.6 Getting Past the Inner Organic Coat, the Diatotepum
13.7 Transport of Silica Across the Cell Membrane
13.8 Cytoplasm Storage and Trafficking of Silica to the Places of Synthesis of the Frustule Parts
13.9 Transport and Patterning of Silica Across the Silicalemma
13.10 Precipitation and Morphogenesis of the Nascent Valve Within the Silicalemma
13.11 Thickening of the Valve Within the Silicalemma
13.12 Exteriorization of the Valve
13.13 Future Work Needed
13.14 Conclusion
References
14. The Effects of Cytoskeletal Inhibitors on Diatom Valve Morphogenesis
Yekaterina D. Bedoshvili and Yelena V. Likhoshway
14.1 Introduction
14.2 Cytoskeleton and Its Role in Cell Morphogenesis
14.3 Abnormalities of Diatom Valve Morphogenesis Induced by Cytoskeleton Inhibitors
14.4 Conclusion
Acknowledgment
References
15. Modeling Silicon Pools in Diatoms Using the Chemistry Toolbox
Argyro Spinthaki and Konstantinos D. Demadis
15.1 Diatoms
15.2 “Silicon Pools” Biology
15.3 Silica Particle Formation From Silicic Acid
15.4 Stabilization of “Soluble” Silica Species (Monosilicic and Disilicic Acids)
15.4.1 Cationic Polymers
15.4.2 Neutral (Uncharged) Polymers
15.4.3 Zwitterionic Polymers
15.4.4 Blends of Cationic/Anionic Polymers
15.5 Chemical Mechanisms
15.6 Conclusions/Perspectives
Acknowledgments
References
16. The Mesopores of Raphid Pennate Diatoms: Toward Natural Controllable Anisotropic Mesoporous Silica Microparticles
Mohamed M. Ghobara, Richard Gordon and Louisa Reissig
16.1 Introduction
16.2 Morphology and Very Fine Ultrastructure of Diatom Frustules
16.3 Synthetic Mesoporous Silica
16.4 The Potential of Raphid Pennates’ Mesoporous Bio-Silica, Similarities,
and Dissimilarities Compared With Synthetic MSM/Ns
16.4.1 The Current Potential of Diatom Porous Silica in Applications
16.4.2 Why Should We Be Interested in the Mesoporous Silica of Raphid Pennate Frustules if the Frustules of Other Species With Larger Pores Work?
16.4.3 Similarities and Dissimilarities Compared With Synthetic MSM/Ns
16.5 Our Ability to Control the Diatom Frustule’s Ultrastructure
16.5.1 Physicochemical Parameters Alteration Approach
16.5.2 Genetic Engineering Approach
16.6 Conclusion
Acknowledgment
References
Glossary
Index
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