Microbial Interactions at Nanobiotechnology Interfaces
Description
This book covers a wide range of topics including synthesis of nanomaterials with specific size, shape, and properties, structure-function relationships, tailoring the surface of nanomaterials for improving the properties, interaction of nanomaterials with proteins/microorganism/eukaryotic cells, and applications in different sectors.
This book also provides a strong foundation for researchers who are interested to venture into developing functionalized nanomaterials for any biological applications in their research. Practical concepts such as modelling nanomaterials, and simulating the molecular interactions with biomolecules, transcriptomic or genomic approaches, advanced imaging techniques to investigate the functionalization of nanomaterials/interaction of nanomaterials with biomolecules and microorganisms are some of the chapters that offer significant benefits to the researchers.
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Persons
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.
Content
Preface xi
List of Contributors xiii
1 Shape- and Size-Dependent Antibacterial Activity of Nanomaterials 1
Senthilguru Kulanthaivel and Prashant Mishra
1.1 Introduction 1
1.2 Synthesis of Nanomaterials 3
1.3 Classification of NMs 4
1.3.1 Classification Based on Dimensions 5
1.3.1.1 Zero-Dimensional NMs 5
1.3.1.2 One-Dimensional NMs 6
1.3.1.3 Two-Dimensional NMs 6
1.3.1.4 Three-Dimensional NMs 6
1.3.2 Classification Based on Chemical Compositions 7
1.3.2.1 Carbon-Based NMs 7
1.3.2.2 Organic-Based NMs 7
1.3.2.3 Inorganic-Based NMs 8
1.3.3 Classification Based on Origin 9
1.4 Application of NMs 9
1.4.1 Advanced Application of NMs as Antimicrobial Agents 9
1.5 Bacterial Resistance to Antibiotics 10
1.5.1 Mechanism of Antibiotic Resistance 10
1.5.1.1 Antibiotics Modification 11
1.5.1.2 Antibiotic Efflux 12
1.5.1.3 Target Modification or Bypass or Protection 12
1.6 Microbial Resistance: Role of NMs 12
1.6.1 Overcoming the Existing Antibiotic Resistance Mechanisms 13
1.6.1.1 Combating Microbes Using Multiple Mechanisms Simultaneously 13
1.6.1.2 Acting as Good Carriers of Antibiotics 13
1.7 Antibacterial Application of NMs 15
1.7.1 Nanometals 16
1.7.2 Metal Oxides 17
1.7.3 Carbonaceous NMs 18
1.7.4 Cationic Polymer NMs 19
1.8 Interaction of NMs with Bacteria 19
1.9 Antibacterial Mechanism of NMs 20
1.10 Factors Affecting the Antibacterial Activity of NMs 22
1.10.1 Size 22
1.10.2 Shape 23
1.10.3 Zeta Potential 24
1.10.4 Roughness 24
1.10.5 Synthesis Methods and Stabilizing Agents 25
1.10.6 Environmental Conditions 26
1.11 Influence of Size on the Antibacterial Activity and Mechanism of Action of Nanomaterials 27
1.12 Influence of Shape on the Antibacterial Activity and Mechanism of Action of Nanomaterials 30
1.13 Effects of Functionalization on the Antimicrobial Property of Nanomaterials 34
1.14 Conclusion and Future Perspectives 35
Questions and Answers 36
References 38
2 Size- and Shape-Selective Synthesis of DNA-Based Nanomaterials and Their Application in Surface-Enhanced Raman Scattering 53
K. Karthick and Subrata Kundu
2.1 Introduction 53
2.2 Mechanism of Surface-Enhanced Raman Scattering (SERS) 55
2.2.1 Significance of Nano-Bio Interfaces and Role of DNA in Enhancing SERS Activity 56
2.3 Size- and Shape-Selective Synthesis of Metal NPs with DNA for SERS Studies 57
2.3.1 Metal NP Assemblies on DNA Using Photochemical Route for SERS Studies 58
2.3.2 Metal NP Assemblies on DNA Using Chemical Reduction Process as Aquasol for SERS Studies 69
2.3.3 Metal NP Assemblies on DNA Using Chemical Reduction as Organosol for SERS Studies 77
2.3.4 Metal NP Assemblies on DNA Prepared Using Microwave Heating for SERS Studies 79
2.3.5 Conclusions and Outcomes of DNA-Based Metal Nanostructures for SERS Studies 83
Take Home Message 85
Questions and Answers 85
References 86
Academic Profile 90
3 Surface Modification Strategies to Control the Nanomaterial-Microbe Interplay 93
T. K. Vasudha, R. Akhil, W. Aadinath, and Vignesh Muthuvijayan
3.1 Introduction 93
3.2 Factors Influencing NM-Microbe Cross talk 96
3.2.1 Surface Features of Microbes 96
3.2.2 Physicochemical Properties of NMs 97
3.3 Surface Functionalization 100
3.3.1 Techniques Used for Surface Functionalization 101
3.3.1.1 Self-Assembled Monolayers 102
3.3.1.2 Layer-by-Layer Technique 102
3.3.2 Surface Functionalization Strategies 103
3.3.2.1 Physicochemical Modifications 103
3.3.2.2 Biofunctionalization 105
3.4 Characterization of NM-Microbe Interactions 106
3.4.1 Microbe Parameters 107
3.4.2 NM Parameters 108
3.5 Toxicity of the Surface-Modified NMs 109
3.6 Challenges and Future Perspectives 110
Questions and Answers 111
Take Home Message 112
References 112
4 Surface Functionalization of Nanoparticles for Stability in Biological Systems 129
Srishti Agarwal and D. Sakthi Kumar
4.1 Introduction 129
4.2 Major Processes Affecting NP Stability in Biological Media 130
4.2.1 Aggregation 130
4.2.2 Nanoparticle Design and Properties 131
4.2.3 Hydrophobicity/Hydrophilicity Effects 133
4.2.4 Effect of Protein Corona 134
4.2.4.1 Effect of Protein Corona on Active Targeting 134
4.2.5 External Factors 135
4.3 Measures to Enhance NP Stability in Biological Systems 135
4.3.1 Stabilization Against Aggregation 135
4.3.2 Ligand Exchange 136
4.3.3 Coating with Additional Layers 136
4.3.3.1 Silica Coating 137
4.3.3.2 PEG Coating 138
4.3.3.3 Lipid Bilayer Coating 141
4.3.3.4 Zwitterionic Coating 141
4.3.3.5 Protein Coating 143
4.3.3.6 Aptamer Coating 144
4.3.4 Subsiding the Nonspecific Protein Interaction 146
4.3.5 Nanoparticle Design 146
4.3.5.1 Particle Functionalization 147
4.3.6 Influence of NM Physicochemical Properties on Microbe-NM Interaction 149
4.4 Conclusion and Future Perspectives 151
4.5 Summary 152
Questions and Answers 152
References 153
5 Molecular Mechanisms Behind Nano-Cancer Therapeutics 167
Surya Prakash Singh and Aravind Kumar Rengan
5.1 Nanotechnology at Nano-Bio Interfaces 167
5.2 Armory of Nanomedicine at Nano-Bio Interfaces 168
5.3 Nanoparticle Edge in Modulating Biological Process 170
5.4 Intracellular Uptake and Trafficking of Nanoparticle 173
5.5 Challenges in Clinical Applications 176
5.6 Conclusion 177
Take Home Message 177
Questions and Answers 178
References 179
6 Protein Nanoparticle Interactions and Factors Influencing These Interactions 187
R. Mala and R. Keerthana
6.1 Introduction 187
6.2 Types and Biomedical Application of Nanoparticles 188
6.3 Methods and Mechanisms of Nanomaterials Synthesis 189
6.4 Routes of Entry of Nanoparticles into Biological System 190
6.5 Rationale for Studying Nanoparticles-Protein Interactions 191
6.6 Formation of Protein Corona 191
6.6.1 Structure and Composition of Corona 191
6.6.2 Kinetics of Formation of Nanoparticles-Corona 193
6.7 Nanoparticles-Induced Structural Changes in Proteins 195
6.7.1 Reversible 195
6.7.2 Irreversible 195
6.8 Factors Influencing Corona Formation 196
6.8.1 Properties of Nanoparticles 196
6.8.1.1 Size 196
6.8.1.2 Shape 198
6.8.1.3 Charge 198
6.8.1.4 Surface Functionalization 198
6.8.1.5 Surface Reactivity 199
6.8.1.6 Solubility 199
6.8.2 Properties of Protein 199
6.8.3 Effect of Surrounding Environment 201
6.8.3.1 Effect of Media Composition on Corona Formation 201
6.8.3.2 Effect of Temperature 201
6.8.3.3 Static In Vitro Model Vs. Dynamic In Vivo System 201
6.9 Interaction of Nanoparticles with Cells and Their Uptake 202
6.10 Pleiotrophic Effect of Nanoparticles 204
6.11 Analytical Methods to Study Nanoparticles-Protein Interaction 204
6.11.1 Spectral Properties 204
6.11.1.1 UV-Vis Spectroscopy 204
6.11.1.2 FTIR 205
6.11.1.3 Raman Spectroscopy 205
6.11.1.4 Fluorescence Spectroscopy 206
6.11.2 Surface Plasmon Resonance 208
6.11.3 Cellular Uptake of Nanoparticles-Protein 208
6.11.3.1 Flow Cytometry 208
6.11.3.2 Confocal Microscopy 208
6.11.4 Binding Affinity 209
6.11.4.1 Differential Scanning Calorimetry and Isothermal Calorimetry 209
6.11.4.2 Isothermal Titration Calorimetry 209
Questions and Answers 209
References 210
7 Interaction Effects of Nanoparticles with Microorganisms Employed in the Remediation of Nitrogen-Rich Wastewater 225
Parmita Chawley and Sheeja Jagadevan
7.1 Introduction 225
7.2 Bacterial Nitrification Process 227
7.2.1 Effect of NPs on Functional Gene Abundance and Transcriptional Response 227
7.2.2 Effect of NPs on Enzyme Activity 229
7.2.3 Effect on Cellular Morphology 230
7.3 Effect of NPs on Denitrifying Bacteria 231
7.3.1 Effect on Functional Gene Abundance and Transcriptional Response 232
7.3.2 Enzymatic Response 234
7.4 Impact of Nanoparticles on Nitrogen Removal 236
7.5 Conclusion 236
Take Home Message 236
Questions and Answers 237
References 238
8 Silver-Based Nanoparticles for Antibacterial Activity: Recent Development and Mechanistic Approaches 245
Arpita Roy, Papia Basuthakur, Shagufta Haque, and Chitta Ranjan Patra
8.1 Introduction 245
8.2 Historical Background of Silver 246
8.3 Synthesis Procedures of Silver Nanoparticles 247
8.3.1 Chemical Synthesis 247
8.3.2 Physical Methods 249
8.3.3 Biological Methods 249
8.4 Biological Application of Silver Nanoparticles 251
8.5 Bacterial Infection and Antibiotic Resistance 251
8.6 Nanosilver for Antibacterial Therapy 254
8.6.1 Metallic Silver Nanoparticles 254
8.6.2 Biosynthesized Silver Nanoparticles 254
8.6.3 Silver Nanocomposites 257
8.6.4 Silver Nanoscaffolds 260
8.7 Influence of Size and Shape of Silver Nanoparticles as Antibacterial Agents 260
8.8 Nanosilver and Its Mechanism of Action for Antibacterial Therapy 261
8.9 Application of Silver Nanoparticle in Commercial Products 266
8.9.1 Silver Nanoparticles in Wound Dressing Materials and Devices 266
8.9.2 Silver Nanoparticles in Soaps and Detergents 268
8.9.3 Silver Nanoparticles in Fabrics 269
8.9.4 Silver Nanoparticles in Cosmetics 271
8.9.5 Silver Nanoparticles in Food Packaging 271
8.9.6 Silver Nanoparticles in Paints 273
8.10 Toxicity of Silver Nanoparticles 273
8.11 Future Prospective and Challenges 275
8.12 Conclusion 276
Take Home Message 276
Questions and Answers 277
Abbreviation 278
References 280
9 Microbial Gold Nanoparticles and Their Biomedical Applications 303
Dindyal Mandal, Rohit Kumar Singh, Uday Suryakant Maharana, Bijayananda Panigrahi, and Sourav Mishra
9.1 Introduction 303
9.2 Microbial Gold Nanoparticles Synthesis 304
9.2.1 Bacteria-Mediated Gold Nanoparticles 306
9.2.2 Algae-Mediated Gold Nanoparticles 308
9.2.3 Fungi-Mediated Gold Nanoparticles 311
9.2.4 Yeast-Mediated Gold Nanoparticles 315
9.2.5 Mechanism Involved in Microbial Nanoparticles Synthesis 315
9.3 Applications of Microbial Gold Nanoparticles 317
9.3.1 Biosensing 317
9.3.2 Antibacterial Activity of Au NPs 318
9.3.3 Anticancer Activity of Microbial Gold Nanoparticles 321
9.4 Conclusion 322
Take Home Message 323
Questions and Answers 323
References 325
10 Nano-Bio Interactions and Their Practical Implications in Agriculture 337
Achintya N. Bezbaruah and Ann-Marie Fortuna
10.1 Introduction 337
10.1.1 Agriculturally Beneficial Soil Microorganisms 339
10.2 Engineered Nanomaterials and Agriculture 340
10.2.1 Pathways for ENM to Soil 340
10.2.2 Fate of ENMs in Soil 340
10.2.3 Chemical Interactions of ENM in Soil 343
10.2.4 Mechanisms Controlling Heteroaggregation 344
10.2.5 Mobility of Colloids and ENMs in Soil 344
10.2.6 Nanoagriculture 345
10.2.7 Nanopesticides 348
10.2.8 ENMs and Agriculturally Beneficial Microorganisms 349
10.3 Summary 352
References 353
11 Biogeochemical Interactions of Bioreduced Uranium Nanoparticles 359
S. Sevinç Sengör and Rajesh K. Sani
11.1 Introduction 359
11.2 Coupled Biogeochemical Mechanisms and Interactions of U in the Subsurface 361
11.3 Biogenic Uraninite Precipitation and Its Nanoparticulate Forms 367
11.4 Re-oxidation and Stability of Bioreduced Uranium 371
11.5 Summary and Conclusions 373
Questions and Answers 374
References 376
12 Characterization and Quantification of Mobile Bioreduced Uranium Phases 383
S. Sevinç Sengör and Rajesh K. Sani
12.1 Introduction 383
12.2 Characterization of Biogenic U(IV) 384
12.3 Quantification of Mobile Bioreduced U(IV) Nanoparticles 386
12.4 Summary and Conclusions 388
Questions and Answers 389
References 391
Index 395
1
Shape- and Size-Dependent Antibacterial Activity of Nanomaterials
Senthilguru Kulanthaivel and Prashant Mishra
Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
Objectives
- To understand the importance of studying nanomaterials-bio interface and the factors that dictate it.
- To understand the current situation of antibiotic resistance of microbes and their effect on worldwide healthcare.
- To know the strategies to overcome the antibiotic resistance mechanism and role of nanomaterials in combatting it.
- To understand the mechanism of action of antimicrobial nanomaterials and the factors that influence their antimicrobial properties.
- To understand the key role of size and shape of the nanomaterials on the antimicrobial properties of nanomaterials.
1.1 Introduction
Over the past three decades "Nanotechnology" has emerged as a promising strategy to overcome impasses that have accumulated in various fields of science and technology (Albanese, Tang, & Chan, 2012). Nanomaterials (NMs) are defined as minuscule structures having at least one of their dimensions equal to or between 1 and 100 nm. Since there is no single universally accepted definition, so far various organizations have given their own definition to the term "NMs" (Boverhof et al., 2015). US Food and Drug Administration (USFDA) defines nanomaterial as "materials that have at least one dimension in the range of approximately 1-100 nm and exhibit dimension dependent phenomena" (Bleeker et al., 2012). As per Environmental Protection Agency (EPA) definition, "NMs can exhibit unique properties dissimilar than the equivalent chemical compound in a larger dimension." Similarly, the International Organization for Standardization (ISO) defines it as "material with any external nanoscale dimension or having internal nanoscale surface structure." EU Commission has described it as "a manufactured or natural material that possesses unbound, aggregated or agglomerated particles where external dimensions are between 1-100 nm size range" (Jeevanandam et al., 2018).
NMs generally exist in the shape of spheres, cubes, rods, tubes, flowers, and platelets (Machado et al., 2015). NMs in the nanoscale dimensions possess a high surface area-to-volume ratio and also a high number of atoms/molecules present on the surface rather than the interior of the materials. These are the properties that majorly contribute to the unique functionality of the nanoscale materials, which vary from the bulk of the same material. Therefore, modulation in their structural properties such as change of size or shape will significantly affect their optical, electrical, magnetic, and biological activity (He et al., 2010; Machado et al., 2015). This is one of the distinct advantages of nanotechnology where by engineering the design or production parameters we can modulate the functionality of the NMs specific to particular application (Machado et al., 2015). Hence, the recent studies in nanotechnology are majorly focused on understanding the effect of physicochemical properties such as size, shape, and surface chemistry of the material on the optical, electrical, magnetic, and biological activities.
Considering the aforementioned advantages, NMs have found enormous applications in various fields and products such as cosmetics, catalysts, fillers, biomedical devices, and semiconductors. As per data report from 2015, approximately more than 1800 products from 622 companies in 32 countries contain engineered NMs. In summary, 762 (i.e. around 42%) of the total products are used in the health and fitness category where silver is the most predominantly used NM, in almost 435 products, which are around 24% of the total. Further, about 528 products (i.e. 29% of total) contain NMs as liquid suspension where dermal contact is highly possible. Hence, the abundant application of these materials is leading towards a long-term co-existence of such NMs with living systems which may result in adverse toxicological effects to the living bodies. In this context, it is necessary to study the effect of these materials on biological entities such as proteins, DNA, RNA, cell membranes, cell organelles, cells, tissues, and organs. The interactions between the biological system and NMs strongly depend upon the environment and the biophysico-chemical property of the nano-bio interface (Nel et al., 2009). As discussed, size, shape, and surface chemistry are the most important factors that govern the physicochemical properties of the NM that in turn throws light at the nano-bio interface. Understanding the effect of these physicochemical factors and extrapolating them toward the interactions at the nano-bio interface would help us to design or engineer NMs for specific applications with an added advantage of minimal toxicity to living bodies. There are a number of analytical tools to study the interaction of nano-biomolecules/proteins. Among them the most employed are mass spectroscopy, Fourier transform infrared spectroscopy, circular dichroism spectroscopy, Raman spectroscopy, nuclear magnetic resonance, UV-vis spectroscopy, surface plasma resonance, quartz crystal balance, atomic force microscopy, fluorescence correlation spectroscopy, fluorescence spectroscopy, and isothermal calorimetry (Saptarshi, Duschl, & Lopata, 2013). Among the different strategies, mass spectroscopy-based proteomics is the most preferred. Even though the technique is a qualitative measure of proteins bound to NMs, such as nanoparticles (NPs), it can be applied over a wide range of NMs. UV-vis spectroscopy is employed to measure changes observed in the adsorption spectrum caused by NM-protein interaction. Similar to UV-vis spectroscopy, fluorescence spectroscopy is employed to measure changes in the fluorescence spectra caused by the binding of protein on to NMs. Surface plasma resonance is used to study changes in electrons' oscillation on the surface of metal NMs as a result of protein interaction with NM. Isothermal calorimetry analysis is employed to determine the binding constant and other thermodynamic parameters of the nano/bio interface (Saptarshi et al., 2013). Quartz crystal balance is used to measure changes in mass on the surface of oscillating quartz caused by the NM-protein interaction. In a study, adsorption of proteins myoglobin, bovine serum albumin, and cytochrome over the surface of gold NPs was studied using quartz crystal balance (Kaufman et al., 2007). Confocal Raman spectroscopy and confocal spectroscopy can be employed to study and visualize NM-protein interaction and intake of NMs into cells by fluorescent labeling of NPs. In recent times, a combination of these techniques has been strategically employed to study the different aspects of NM-protein/biomolecule interaction. NMs can be synthesized through different routes such as chemical, physical, and green methods. Changes in the synthesis methods, concentration of reactants, and conditions can definitely modulate the morphological parameters (size and shape) of NMs. Taking this into account, the selection of synthesis route also plays an important role in governing NMs' morphological features and their functions. Keeping the aforementioned perspectives in mind, this chapter describes the effects of size and shape of NMs on their biological activity.
1.2 Synthesis of Nanomaterials
NMs can be synthesized by a number of methods that are grouped into two different categories: (i) bottom-up and (ii) top-down method. Schematics of typical methods for synthesis of NMs are given in Figure 1.1 as described by Ealias and Saravanakumar (2017).
Figure 1.1 Schematics of typical methods for synthesis of NMs.
- Bottom-up method: It is a constructive method wherein the atoms build up clusters that in turn form the NMs. This category includes methods such as sol-gel, spinning, chemical vapor deposition, pyrolysis, and biosynthesis.
- Top-down method: On the contrary, the top-down method is a destructive method where the bulk materials are reduced into nanoscale materials. It includes methods such as mechanical milling, nanolithography, laser ablation, sputtering, and thermal decomposition. The typical method of synthesis for various NMs is given in Table 1.1.
1.3 Classification of NMs
In nature, NMs are built by nanoscale or submicron-sized blocks that exhibit size-dependent effects. Over the last two decades, a number of NMs or nanostructured materials have been developed and a lot of new developments are underway. The abundant increase in the number of NMs has set forth the need for the classification of these materials. An understanding of the classification would give insight into the interaction of NMs with various surfaces and resultant functionality of the NMs. The first classification of NMs was given by Gleiter (2000) in which the materials were classified on the basis of crystalline forms and chemical compositions. The scheme subdivided the materials into three classes where each class has four kinds of materials (Gleiter, 2000). However, the list of Gleiter was not considered complete as it failed to take account of...
