Microbial Interactions at Nanobiotechnology Interfaces

Navanietha Rathinam is a Research Scientist in the Composite and Nanocomposite Advanced Manufacturing-Biomaterials Center, Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD. His research activities are focused on bio-electrochemical interface technologies, biomaterials, and biofilm engineering. He received the Young Faculty Award for his accomplishments in teaching and research. In 2016, he received the Award for Cutting Edge Research (Fulbright Faculty Award). He has been a PI/Co-I for 4 research grants and served as a panelist for NASA and National Science Foundation. He is currently serving as an Ambassador to the American Society for Microbiology. He also serves as an editor for books on Bioelectrochemical Interface Engineering (WILEY), Biofilm engineering (American Chemical Society), and Biomanufacturing (American Chemical Society). He is an Associate editor for IEEE Access and an editorial board member for a few reputed journals.Rajesh Sani is a Professor in the Departments of Chemical and Biological Engineering and Applied Biological Sciences at South Dakota School of Mines and Technology, South Dakota, USA. His research expertise includes Extremophilic Bioprocessing, Biocatalysis, Rules of Life in Biofilms, Biomaterials, Gas to Liquid Fuels, Genome Editing of Extremophiles and Space Biology. Over the past 14 years, he has been the PI or co-PI on over $44.45 million in funded research. He has one patent, seven invention disclosures, and published over 94 peer-reviewed articles in high impact factor journals and have contributed to over 24 book chapters. In addition, he has edited eight books and one Proceedings for Springer International Publishing AG, Wiley, and ACS publications. Dr Sani has been leading a research consortium funded by the NSF with the aid of 84 scientists and engineers.

• Preface xiList of Contributors xiii1 Shape- and Size-Dependent Antibacterial Activity of Nanomaterials 1Senthilguru Kulanthaivel and Prashant Mishra1.1 Introduction 11.2 Synthesis of Nanomaterials 31.3 Classification of NMs 41.3.1 Classification Based on Dimensions 51.3.1.1 Zero-Dimensional NMs 51.3.1.2 One-Dimensional NMs 61.3.1.3 Two-Dimensional NMs 61.3.1.4 Three-Dimensional NMs 61.3.2 Classification Based on Chemical Compositions 71.3.2.1 Carbon-Based NMs 71.3.2.2 Organic-Based NMs 71.3.2.3 Inorganic-Based NMs 81.3.3 Classification Based on Origin 91.4 Application of NMs 91.4.1 Advanced Application of NMs as Antimicrobial Agents 91.5 Bacterial Resistance to Antibiotics 101.5.1 Mechanism of Antibiotic Resistance 101.5.1.1 Antibiotics Modification 111.5.1.2 Antibiotic Efflux 121.5.1.3 Target Modification or Bypass or Protection 121.6 Microbial Resistance: Role of NMs 121.6.1 Overcoming the Existing Antibiotic Resistance Mechanisms 131.6.1.1 Combating Microbes Using Multiple Mechanisms Simultaneously 131.6.1.2 Acting as Good Carriers of Antibiotics 131.7 Antibacterial Application of NMs 151.7.1 Nanometals 161.7.2 Metal Oxides 171.7.3 Carbonaceous NMs 181.7.4 Cationic Polymer NMs 191.8 Interaction of NMs with Bacteria 191.9 Antibacterial Mechanism of NMs 201.10 Factors Affecting the Antibacterial Activity of NMs 221.10.1 Size 221.10.2 Shape 231.10.3 Zeta Potential 241.10.4 Roughness 241.10.5 Synthesis Methods and Stabilizing Agents 251.10.6 Environmental Conditions 261.11 Influence of Size on the Antibacterial Activity and Mechanism of Action of Nanomaterials 271.12 Influence of Shape on the Antibacterial Activity and Mechanism of Action of Nanomaterials 301.13 Effects of Functionalization on the Antimicrobial Property of Nanomaterials 341.14 Conclusion and Future Perspectives 35Questions and Answers 36References 382 Size- and Shape-Selective Synthesis of DNA-Based Nanomaterials and Their Application in Surface-Enhanced Raman Scattering 53K. Karthick and Subrata Kundu2.1 Introduction 532.2 Mechanism of Surface-Enhanced Raman Scattering (SERS) 552.2.1 Significance of Nano-Bio Interfaces and Role of DNA in Enhancing SERS Activity 562.3 Size- and Shape-Selective Synthesis of Metal NPs with DNA for SERS Studies 572.3.1 Metal NP Assemblies on DNA Using Photochemical Route for SERS Studies 582.3.2 Metal NP Assemblies on DNA Using Chemical Reduction Process as Aquasol for SERS Studies 692.3.3 Metal NP Assemblies on DNA Using Chemical Reduction as Organosol for SERS Studies 772.3.4 Metal NP Assemblies on DNA Prepared Using Microwave Heating for SERS Studies 792.3.5 Conclusions and Outcomes of DNA-Based Metal Nanostructures for SERS Studies 83Take Home Message 85Questions and Answers 85References 86Academic Profile 903 Surface Modification Strategies to Control the Nanomaterial–Microbe Interplay 93T. K. Vasudha, R. Akhil, W. Aadinath, and Vignesh Muthuvijayan3.1 Introduction 933.2 Factors Influencing NM–Microbe Cross talk 963.2.1 Surface Features of Microbes 963.2.2 Physicochemical Properties of NMs 973.3 Surface Functionalization 1003.3.1 Techniques Used for Surface Functionalization 1013.3.1.1 Self-Assembled Monolayers 1023.3.1.2 Layer-by-Layer Technique 1023.3.2 Surface Functionalization Strategies 1033.3.2.1 Physicochemical Modifications 1033.3.2.2 Biofunctionalization 1053.4 Characterization of NM–Microbe Interactions 1063.4.1 Microbe Parameters 1073.4.2 NM Parameters 1083.5 Toxicity of the Surface-Modified NMs 1093.6 Challenges and Future Perspectives 110Questions and Answers 111Take Home Message 112References 1124 Surface Functionalization of Nanoparticles for Stability in Biological Systems 129Srishti Agarwal and D. Sakthi Kumar4.1 Introduction 1294.2 Major Processes Affecting NP Stability in Biological Media 1304.2.1 Aggregation 1304.2.2 Nanoparticle Design and Properties 1314.2.3 Hydrophobicity/Hydrophilicity Effects 1334.2.4 Effect of Protein Corona 1344.2.4.1 Effect of Protein Corona on Active Targeting 1344.2.5 External Factors 1354.3 Measures to Enhance NP Stability in Biological Systems 1354.3.1 Stabilization Against Aggregation 1354.3.2 Ligand Exchange 1364.3.3 Coating with Additional Layers 1364.3.3.1 Silica Coating 1374.3.3.2 PEG Coating 1384.3.3.3 Lipid Bilayer Coating 1414.3.3.4 Zwitterionic Coating 1414.3.3.5 Protein Coating 1434.3.3.6 Aptamer Coating 1444.3.4 Subsiding the Nonspecific Protein Interaction 1464.3.5 Nanoparticle Design 1464.3.5.1 Particle Functionalization 1474.3.6 Influence of NM Physicochemical Properties on Microbe–NM Interaction 1494.4 Conclusion and Future Perspectives 1514.5 Summary 152Questions and Answers 152References 1535 Molecular Mechanisms Behind Nano-Cancer Therapeutics 167Surya Prakash Singh and Aravind Kumar Rengan5.1 Nanotechnology at Nano–Bio Interfaces 1675.2 Armory of Nanomedicine at Nano–Bio Interfaces 1685.3 Nanoparticle Edge in Modulating Biological Process 1705.4 Intracellular Uptake and Trafficking of Nanoparticle 1735.5 Challenges in Clinical Applications 1765.6 Conclusion 177Take Home Message 177Questions and Answers 178References 1796 Protein Nanoparticle Interactions and Factors Influencing These Interactions 187R. Mala and R. Keerthana6.1 Introduction 1876.2 Types and Biomedical Application of Nanoparticles 1886.3 Methods and Mechanisms of Nanomaterials Synthesis 1896.4 Routes of Entry of Nanoparticles into Biological System 1906.5 Rationale for Studying Nanoparticles–Protein Interactions 1916.6 Formation of Protein Corona 1916.6.1 Structure and Composition of Corona 1916.6.2 Kinetics of Formation of Nanoparticles–Corona 1936.7 Nanoparticles-Induced Structural Changes in Proteins 1956.7.1 Reversible 1956.7.2 Irreversible 1956.8 Factors Influencing Corona Formation 1966.8.1 Properties of Nanoparticles 1966.8.1.1 Size 1966.8.1.2 Shape 1986.8.1.3 Charge 1986.8.1.4 Surface Functionalization 1986.8.1.5 Surface Reactivity 1996.8.1.6 Solubility 1996.8.2 Properties of Protein 1996.8.3 Effect of Surrounding Environment 2016.8.3.1 Effect of Media Composition on Corona Formation 2016.8.3.2 Effect of Temperature 2016.8.3.3 Static In Vitro Model Vs. Dynamic In Vivo System 2016.9 Interaction of Nanoparticles with Cells and Their Uptake 2026.10 Pleiotrophic Effect of Nanoparticles 2046.11 Analytical Methods to Study Nanoparticles–Protein Interaction 2046.11.1 Spectral Properties 2046.11.1.1 UV–Vis Spectroscopy 2046.11.1.2 FTIR 2056.11.1.3 Raman Spectroscopy 2056.11.1.4 Fluorescence Spectroscopy 2066.11.2 Surface Plasmon Resonance 2086.11.3 Cellular Uptake of Nanoparticles–Protein 2086.11.3.1 Flow Cytometry 2086.11.3.2 Confocal Microscopy 2086.11.4 Binding Affinity 2096.11.4.1 Differential Scanning Calorimetry and Isothermal Calorimetry 2096.11.4.2 Isothermal Titration Calorimetry 209Questions and Answers 209References 2107 Interaction Effects of Nanoparticles with Microorganisms Employed in the Remediation of Nitrogen-Rich Wastewater 225Parmita Chawley and Sheeja Jagadevan7.1 Introduction 2257.2 Bacterial Nitrification Process 2277.2.1 Effect of NPs on Functional Gene Abundance and Transcriptional Response 2277.2.2 Effect of NPs on Enzyme Activity 2297.2.3 Effect on Cellular Morphology 2307.3 Effect of NPs on Denitrifying Bacteria 2317.3.1 Effect on Functional Gene Abundance and Transcriptional Response 2327.3.2 Enzymatic Response 2347.4 Impact of Nanoparticles on Nitrogen Removal 2367.5 Conclusion 236Take Home Message 236Questions and Answers 237References 2388 Silver-Based Nanoparticles for Antibacterial Activity: Recent Development and Mechanistic Approaches 245Arpita Roy, Papia Basuthakur, Shagufta Haque, and Chitta Ranjan Patra8.1 Introduction 2458.2 Historical Background of Silver 2468.3 Synthesis Procedures of Silver Nanoparticles 2478.3.1 Chemical Synthesis 2478.3.2 Physical Methods 2498.3.3 Biological Methods 2498.4 Biological Application of Silver Nanoparticles 2518.5 Bacterial Infection and Antibiotic Resistance 2518.6 Nanosilver for Antibacterial Therapy 2548.6.1 Metallic Silver Nanoparticles 2548.6.2 Biosynthesized Silver Nanoparticles 2548.6.3 Silver Nanocomposites 2578.6.4 Silver Nanoscaffolds 2608.7 Influence of Size and Shape of Silver Nanoparticles as Antibacterial Agents 2608.8 Nanosilver and Its Mechanism of Action for Antibacterial Therapy 2618.9 Application of Silver Nanoparticle in Commercial Products 2668.9.1 Silver Nanoparticles in Wound Dressing Materials and Devices 2668.9.2 Silver Nanoparticles in Soaps and Detergents 2688.9.3 Silver Nanoparticles in Fabrics 2698.9.4 Silver Nanoparticles in Cosmetics 2718.9.5 Silver Nanoparticles in Food Packaging 2718.9.6 Silver Nanoparticles in Paints 2738.10 Toxicity of Silver Nanoparticles 2738.11 Future Prospective and Challenges 2758.12 Conclusion 276Take Home Message 276Questions and Answers 277Abbreviation 278References 2809 Microbial Gold Nanoparticles and Their Biomedical Applications 303Dindyal Mandal, Rohit Kumar Singh, Uday Suryakant Maharana, Bijayananda Panigrahi, and Sourav Mishra9.1 Introduction 3039.2 Microbial Gold Nanoparticles Synthesis 3049.2.1 Bacteria-Mediated Gold Nanoparticles 3069.2.2 Algae-Mediated Gold Nanoparticles 3089.2.3 Fungi-Mediated Gold Nanoparticles 3119.2.4 Yeast-Mediated Gold Nanoparticles 3159.2.5 Mechanism Involved in Microbial Nanoparticles Synthesis 3159.3 Applications of Microbial Gold Nanoparticles 3179.3.1 Biosensing 3179.3.2 Antibacterial Activity of Au NPs 3189.3.3 Anticancer Activity of Microbial Gold Nanoparticles 3219.4 Conclusion 322Take Home Message 323Questions and Answers 323References 32510 Nano-Bio Interactions and Their Practical Implications in Agriculture 337Achintya N. Bezbaruah and Ann-Marie Fortuna10.1 Introduction 33710.1.1 Agriculturally Beneficial Soil Microorganisms 33910.2 Engineered Nanomaterials and Agriculture 34010.2.1 Pathways for ENM to Soil 34010.2.2 Fate of ENMs in Soil 34010.2.3 Chemical Interactions of ENM in Soil 34310.2.4 Mechanisms Controlling Heteroaggregation 34410.2.5 Mobility of Colloids and ENMs in Soil 34410.2.6 Nanoagriculture 34510.2.7 Nanopesticides 34810.2.8 ENMs and Agriculturally Beneficial Microorganisms 34910.3 Summary 352References 35311 Biogeochemical Interactions of Bioreduced Uranium Nanoparticles 359S. Sevinç Şengör and Rajesh K. Sani11.1 Introduction 35911.2 Coupled Biogeochemical Mechanisms and Interactions of U in the Subsurface 36111.3 Biogenic Uraninite Precipitation and Its Nanoparticulate Forms 36711.4 Re-oxidation and Stability of Bioreduced Uranium 37111.5 Summary and Conclusions 373Questions and Answers 374References 37612 Characterization and Quantification of Mobile Bioreduced Uranium Phases 383S. Sevinç Şengör and Rajesh K. Sani12.1 Introduction 38312.2 Characterization of Biogenic U(IV) 38412.3 Quantification of Mobile Bioreduced U(IV) Nanoparticles 38612.4 Summary and Conclusions 388Questions and Answers 389References 391Index 395