Diatom Microscopy

Nirmal Mazumder obtained his PhD degree in 2013 from National Yang-Ming University, Taiwan. He has two years of post-doctoral research experience. In 2016, he joined the Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India as an assistant professor. His research interests relate to the development of Stokes-Mueller-based light microscopy for tissue characterization and deep learning. He also investigates the photonics properties of diatoms as well as frustules for bio-photonics applications. He has published several peer-reviewed journal articles and book chapters. 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.

Preface xi

1 Investigation of Diatoms with Optical Microscopy 1
Shih-Ting Lin, Ming-Xin Lee and Guan-Yu Zhuo

1.1 Introduction 2

1.2 Light Microscopy 4

1.2.1 Phase Contrast Microscopy 4

1.2.2 Differential Interference Contrast (DIC) Microscopy 6

1.2.3 Darkfield Microscopy 9

1.3 Fluorescence Microscopy 10

1.4 Confocal Laser Scanning Microscopy 12

1.5 Multiphoton Microscopy 19

1.6 Super-Resolution Optical Microscopy 22

1.7 Conclusion 25

Acknowledgement 25

References 25

2 Nanobioscience Studies of Living Diatoms Using Unique Optical Microscopy Systems 33
Kazuo Umemura

Abbreviations 33

2.1 Trajectory Analysis of Gliding Among Individual Diatom Cells Using Microchamber Systems 35

2.2 Direct Observation of Floating Phenomena of Individual Diatoms Using a “Tumbled” Microscope System 40

2.3 Three-Dimensional Physical Imaging of Living Diatom Cells Using a Holographic Microscope System 44

Acknowledgements 47

References 47

3 Recent Insights Into the Ultrastructure of Diatoms Using Scanning and Transmission Electron-Microscopy 57
Dharshini Gopal, Shweta Chakrabarti, Dataram Venkata Srikar Keshav, Richard Gordon and Nirmal Mazumder

3.1 Introduction 58

3.2 Scanning Electron Microscopy (SEM) of Diatoms 58

3.3 Transmission Electron Microscopy (TEM) of Diatoms 65

3.3.1 Limitations 69

3.4 Conclusion 73

References 73

4 Atomic Force Microscopy Study of Diatoms 81
Ishita Chakraborty, Shweta Chakrabarti, Vishwanath Managuli and Nirmal Mazumder

4.1 Introduction 82

4.2 Types of AFM Modes 86

4.3 Sample Preparation and Methods 88

4.4 Study of Diatom Ultrastructure Under AFM 88

4.5 Conclusion 102

Glossary 104

Acknowledgement 104

References 105

5 Refractive Index Tomography for Diatom Analysis 111
Juan M. Soto, José A. Rodrigo and Tatiana Alieva

5.1 Introduction 112

5.2 Fundamentals of PC-ODT 113

5.3 Experimental Setup for PC-ODT 117

5.4 Diatom RI Reconstructions with Bright-Field Illumination 120

5.5 Illumination Impact on PC-ODT Performance 126

5.6 Concluding Remarks 131

Acknowledgement 134

References 134

6 Luminescent Diatom Frustules: A Review on the Key Research Applications 139
Jayur Tisso, Shruthi Shetty, Nirmal Mazumder, Ankur Gogoi and Gazi A. Ahmed

6.1 Introduction 140

6.2 Key Research Applications of Luminescence Properties of Diatom Frustules 141

6.2.1 Novel Nanophotonic and Optoelectronic Applications of Luminescent Diatom Frustules 142

6.2.2 Applications of Diatom Luminescence in Sensing 145

6.2.3 Biomedical Applications of Diatom Luminescence 149

6.2.4 Other Studies on Diatom Luminescence 151

6.3 Future Perspectives 167

6.4 Conclusion 168

Acknowledgement 168

References 168

7 Micro to Nano Ornateness of Diatoms from Geographically Distant Origins of the Globe 179
Mohd Jahir Khan, Daniel Mathys and Vandana Vinayak

7.1 Introduction 180

7.2 Materials and Methods 183

7.2.1 Diatom Samples and Microscopy 183

7.2.1.1 By Michael J. Stringer 183

7.2.1.2 Diatom Oamaru Slides by Diane Winter 184

7.2.1.3 By Daniel Mathys 184

7.2.1.4 Diatom Sampling, Slide Preparation and Imaging from Himalayas, Plains and Arabian Sea, India 185

7.3 Diatoms from Different Geographical Origins of the World 185

7.3.1 Oamaru Diatoms 185

7.3.2 Diatom Images Gifted by Michael J. Stringer 186

7.3.3 Diatoms from Natural History Museum Basel, Switzerland a Piece of Art by Daniel Mathys 190

7.3.4 Diatoms from India 193

7.4 Conclusion 216

7.5 Acknowledgements 216

References 216

8 Types of X-Ray Techniques for Diatom Research 221
Mridula Sunder, Neha Acharya, Smitha Nayak, Richard Gordon and Nirmal Mazumder

8.1 Introduction 221

8.2 Applications 222

8.2.1 Synchrotron Radiation-Based X-Ray Techniques 222

8.2.2 X-Ray Computed Tomography 224

8.2.3 X-Ray Fluorescence-Based Techniques 226

8.2.4 X-Ray Microanalysis 227

8.2.5 X-Ray Absorption-Based Techniques 228

8.2.6 X-Ray Diffraction 229

8.2.7 Other X-Ray-Based Techniques 230

8.3 Conclusions 233

Glossary 233

References 234

9 Diatom Assisted SERS 237
Rajib Biswas and Sankar Biswas

9.1 Introduction 237

9.2 Diatom 239

9.2.1 Basic Overview 239

9.2.2 Physiological Characteristics 239

9.2.3 Optical and Relevant Properties 240

9.3 Raman Scattering 241

9.3.1 Basics 241

9.3.2 Surface Enhanced Raman Scattering 242

9.3.3 Optoelectronic Investigations 242

9.4 SERS Through Diatom: Fundamentals and Application Overview 243

9.5 Conclusion and Future Outlook 245

References 246

10 Diatoms as Sensors and Their Applications 251
Priyasha De and Nirmal Mazumder

10.1 Introduction 251

10.2 Diatoms as Biosensors 255

10.2.1 Electrochemical Sensors 260

10.2.2 Plasmonic Sensors 261

10.2.3 Immunoassay Sensors 264

10.2.4 Optical and Optofluidic Sensors 268

10.2.5 Biochemical Sensors 271

10.2.6 FRET-Based Sensors 273

10.2.7 Microfluidics-Based Sensors 274

10.3 Conclusion 276

Acknowledgments 276

References 277

11 Diatom Frustules: A Transducer Platform for Optical Detection of Molecules 283
Viji S., Ponpandian N. and Viswanathan C.

11.1 Introduction 284

11.2 Optical Properties of Diatom Frustules 285

11.2.1 Diatom as a Photoluminescent Materials 285

11.2.2 Diatom as a Photonic Crystal 287

11.2.3 Diatoms as a SERS Substrate 288

11.3 Methods Involved in Thin Film Deposition of Diatom Frustules 290

11.4 Diatom as an Optical Transducer for Biosensors 294

11.5 Diatom as an Optical Transducer for Gas/Chemical Sensors 297

11.6 Conclusion 300

References 301

12 Effects of Light on Physico-Chemical Properties of Diatoms 307
Janardan Sen, Priyal Dhawan, Priyasha De and Nirmal Mazumder

12.1 Introduction 308

12.2 Effect of Light on Diatom Function and Morphology 310

12.2.1 Effect of Light Intensity on Diatom Morphology 310

12.2.2 Effect of Light Intensity on Diatom Growth 313

12.2.3 Effect of Light Intensity on Photosynthesis in Diatoms 318

12.2.4 Effect of Wavelength of Light on Diatom Pigment System 321

12.2.5 Effect of Light Intensity on the Physiology of Diatoms 327

12.3 Conclusion 330

Acknowledgment 330

References 330

Index 335