Foreword xv
Preface xvii
Part I Hydrodynamic Flow Confinement (HFC) 1
1 Hydrodynamic Flow Confinement Using a Microfluidic Probe 3
Emmanuel Delamarche, Robert D. Lovchik, Julien F. Cors, and Govind V. Kaigala
1.1 Introduction 3
1.2 HFC Principle 4
1.3 MFP Heads 7
1.4 Vertical MFP 8
1.5 Advanced MFP Heads and Holders 9
1.6 Surface Processing Using an MFP 11
1.7 MFP Components 15
1.8 Outlook 16
Acknowledgments 17
References 17
2 Hierarchical Hydrodynamic Flow Confinement (hHFC) and Recirculation for Performing Microscale Chemistry on Surfaces 21
Julien F. Cors, Julien Autebert, Aditya Kashyap, David P. Taylor, Robert D. Lovchik, Emmanuel Delamarche, and Govind V. Kaigala
2.1 Introduction 21
2.2 Hierarchical HFC 22
2.2.1 Minimal Dilution of the Processing Liquid 22
2.2.2 Numerical Simulations of Hierarchical HFC 22
2.2.3 Dilution Measurement of hHFC 25
2.2.4 Microscale Chemistry Using hHFC 26
2.3 Recirculation 28
2.3.1 Recirculation of Small Volumes of Liquids within an MFP Head 28
2.3.2 AnalyticalModel: Diffusive Transport between Two Laminar Flows in hHFC 30
2.4 Microscale Deposition 33
2.4.1 Patterning Proteins on Surfaces 33
2.4.2 Protein Deposition Using hHFC and Recirculation 35
2.4.3 AnalyticalModel: Convective Transport between Two Laminar Flows in hHFC 39
2.4.4 Conclusion and Outlook 42
Acknowledgments 43
References 43
3 Design of Hydrodynamically ConfinedMicroflow Devices with Numerical Modeling: Controlling Flow Envelope, Pressure, and Shear Stress 47
Choongbae Park, Kevin V. Christ, and Kevin T. Turner
3.1 Introduction 47
3.2 Theory 48
3.2.1 Pressure, Velocity Distribution, and Nondimensional Quantities 48
3.2.2 Shear Stress 50
3.3 Device and ExperimentalMethods for CFD Validation 50
3.4 Numerical Modeling of HCM devices 52
3.5 Envelope Size and Pressure Drop Across HCMs 54
3.6 Hydrodynamic Loads Generated by HCM Devices 58
3.7 Concluding Remarks 60
References 60
4 Hele-Shaw Flow Theory in the Context of Open Microfluidics: From Dipoles to Quadrupoles 63
Etienne Boulais and Thomas Gervais
4.1 Introduction 63
4.2 Fundamentals of Hele-Shaw Flows 64
4.2.1 Derivation of Hele-Shaw Equation from the Navier-Stokes Equation 64
4.2.2 Hele-Shaw Point Sources, Round Monopoles, and Square Monopoles 68
4.3 Applications to Microfluidic Dipoles and Quadrupoles 69
4.3.1 Velocity Potentials for Dipoles and Quadrupoles 70
4.3.2 Deriving Key Operation Characteristics for Dipoles and Quadrupoles 71
4.3.2.1 Stagnation Points and the Hydrodynamic Flow Confinement Zone 71
4.3.3 Numerical Investigation of Model Accuracy 74
4.4 Diffusion in Hele-Shaw Flows 76
4.4.1 Advection-Diffusion Transport Equations 76
4.4.2 High Peclet Number Asymptotic Solutions Near Stagnation Points 77
4.4.2.1 Floating Gradient Along the Central Line in a Microfluidic Quadrupole 78
4.4.2.2 Diffusion Broadening in the HFC Envelope for Dipoles and Quadrupoles 80
4.4.3 Numerical Investigation of Model Accuracy 80
4.5 Conclusion 81
References 82
5 Implementation and Applications of Microfluidic Quadrupoles 83
Ayoola T. Brimmo andMohammad A. Qasaimeh
5.1 Introduction 83
5.2 Principles and Configurations of MQs 85
5.3 Implementation of MQs 87
5.4 MQ Analysis and Characterization 88
5.4.1 Stagnation Point Visualization 88
5.4.2 Hydrodynamic Flow Confinement 90
5.4.3 Concentration Gradient Measurement 91
5.4.4 Stagnation Point Hydrodynamic Manipulation 92
5.5 Application of MQs in Biology and Life Sciences 94
5.5.1 MQs for Biochemical Concentration Gradient Assays 94
5.5.2 Studying Neutrophil Chemotaxis Using the Lateral MQ 95
5.6 Summary and Outlook 95
References 98
6 Hydrodynamic Flow Confinement-Assisted Immunohistochemistry from Micrometer to Millimeter Scale 101
Robert D. Lovchik, David P. Taylor, Emmanuel Delamarche, And Govind V. Kaigala
6.1 Immunohistochemical Analysis of Tissue Sections 101
6.2 Probe Heads for Multiscale Surface Interactions 102
6.2.1 Probe Design and Operating Conditions for Millimeter-Scale HFCs 103
6.2.2 Slit-Aperture Probes 105
6.2.3 Aperture-Array Probes 105
6.3 Immunohistochemistry with Microfluidic Probes 107
6.4 Micro-IHC on Human Tissue Sections 108
6.4.1 Micro-IHC on Tissue Microarrays 109
6.5 Millimeter-Scale Immunohistochemistry 109
6.6 Outlook 112
Acknowledgments 113
References 113
7 Local Nucleic Acid Analysis of Adherent Cells 115
Aditya Kashyap, Deborah Huber, Julien Autebert, and Govind V. Kaigala
7.1 Introduction 115
7.1.1 Heterogeneity in Cells and Their Microenvironments 115
7.1.2 State of the Art: Microfluidic Devices for Nucleic Acid Analysis 116
7.1.3 Microfluidic Probe for Spatial Probing of Standard Biological Substrates 119
7.2 Methods 121
7.2.1 MFP Platform, Head, and Handling 121
7.2.2 Cell Handling 122
7.2.3 ?FISH Protocol 123
7.2.4 Local Lysis and Sample Retrieval Protocol 123
7.2.5 DNA and RNA Quantification 124
7.3 Results 124
7.3.1 Genomic Analysis 126
7.3.1.1 Study of Chromosomal Characteristics of Adherent Cells Using ?FISH 124
7.3.1.2 Operational Parameterization for ?FISH 126
7.3.1.3 Improved Probe Incubation and Consumption Using ?FISH 126
7.3.1.4 ?FISH Allows for SpatialMultiplexing of Probes 127
7.3.1.5 Selective Local Lysis for DNA Analysis Using the MFP (Spatialyse) 127
7.3.1.6 Operational Parameterization and Liquid Handling for Spatialyse 127
7.3.1.7 Quantitation of DNA in Local Lysate 129
7.3.2 Transcriptomic Analysis 130
7.3.2.1 Spatially Resolved Probing of Gene Expression in Adherent Cocultures 130
7.4 Discussion 131
7.5 Concluding Remarks 133
Acknowledgments 134
References 134
8 Microfluidic Probe for Neural Organotypic Brain Tissue and Cell Perfusion 139
Donald MacNearney, Mohammad A. Qasaimeh, and David Juncker
8.1 Introduction 139
8.2 Microperfusion of Organotypic Brain Slices Using the Microfluidic Probe 141
8.2.1 Design of Perfusion Chamber for Organotypic Brain Slice Culture 141
8.2.2 Design of PDMS MFP 143
8.2.3 Microscope Setup 147
8.2.4 Microperfusion of Organotypic Brain Slices 148
8.3 Microperfusion of Live Dissociated Neural Cell Cultures Using the Microfluidic Probe 148
8.4 Conclusion 152
Acknowledgments 153
References 153
9 The Multifunctional Pipette 155
Aldo Jesorka and Irep Gozen
9.1 Introduction 155
9.2 Open Volume Probes 157
9.3 Detailed View on the Multifunctional Pipette 159
9.3.1 Chip Concept 159
9.3.2 Device Design and Function 161
9.3.3 Fabrication 165
9.4 Integrated Functions 167
9.4.1 Valveless Switching 168
9.4.2 Control Schematics 169
9.4.3 Operation 170
9.5 Functional Extensions and Applications 172
9.5.1 In-Channel Electrodes 172
9.5.2 Single-Cell Superfusion 173
9.5.3 Optofluidic Thermometer 173
9.5.4 Multiprobe Operation 175
9.5.5 Lab-on-a-Membrane 176
9.6 Future Technology 178
9.6.1 Materials and Fabrication 179
9.6.2 Collection and Integration of Assays and Sensors 181
9.6.3 Automation 182
Acknowledgments 183
References 183
10 Single-Cell Analysis with the BioPen 187
Irep Gozen, Gavin Jeffries, Tatsiana Lobovkina, Emanuele Celauro, Mehrnaz Shaali, Baharan Ali Doosti, and Aldo Jesorka
10.1 Introduction 187
10.2 The Single-Cell Challenge 189
10.2.1 Single-Cell Analysis 189
10.2.2 Technology Overview 190
10.2.3 Adherent Cells 191
10.3 Superfusion Techniques 192
10.3.1 Hydrodynamic Confinement 192
10.4 The BioPen 193
10.5 Application Areas 194
10.5.1 Cell Zeiosis and Ion Channel Activation 194
10.5.2 Single Cell Enzymology 196
10.5.3 Local Temperature Adjustment and Measurement in a Single-Cell Environment 199
10.5.4 Intercellular Communication 202
10.5.5 Single-Cell Viability Test 203
10.5.6 Single Muscle Fiber Physiology 205
10.5.7 Single-Cell Electroporation 208
10.5.8 Local Superfusion of Tissue Slices 210
10.6 Future Technology 213
Acknowledgments 215
References 215
11 Microfluidic Probes for Single-Cell Proteomic Analysis 221
Aniruddh Sarkar, LidanWu, and Jongyoon Han
11.1 Introduction 221
11.2 Technical Requirements of Single-Cell Proteomic Analysis 223
11.3 Methods for Single-Cell Proteomic Analysis 225
11.4 Microfluidics Enabling Next-Generation Single-Cell Proteomics 229
11.5 Open-Ended Microwells for Proteomic and Multiparameter Single-Cell Studies 231
11.6 Microfluidic Probes in In Situ Single-Cell Proteomic Measurement 231
11.7 Outlook for FutureWork with Microfluidic Single-Cell Proteomic Assay 236
11.7.1 Sensitivity 236
11.7.2 Throughput 238
11.7.3 Porting Other Assays to the Microfluidic Probe 240
11.7.4 Applications in Single-Cell Biology 241
11.8 Conclusion 242
References 242
Part II Localized Chemistry 249
12 Aqueous Two-Phase Systems for Micropatterning of Cells and Biomolecules 251
Stephanie L. Ham and Hossein Tavana
12.1 Introduction 251
12.2 Small Molecules Applications 253
12.2.1 Bioreagent Patterning 253
12.2.2 Antibody Assays 253
12.2.3 Collagen Microgels 256
12.3 Cell Patterning 258
12.3.1 Bacterial Cells 258
12.3.2 Mammalian Cells 260
12.3.2.1 Cell Exclusion and Cell Island Patterning 260
12.3.2.2 Cell Co-Culturing 262
12.3.2.3 Heterocellular Stem Cell Niche Engineering 264
12.3.2.4 Skin Tissue Engineering 265
12.3.2.5 Three-Dimensional Cellular Models 266
12.4 Conclusions 269
Acknowledgments 269
References 269
13 Development of Pipettes as Mobile Nanofluidic Devices for Mass Spectrometric Analysis 273
Anumita Saha-Shah and Lane A. Baker
13.1 Introduction 273
13.2 Segmented Flow Analysis 275
13.3 Utility of Nano- and Micropipettes in Mass Spectrometry 276
13.4 Development of Nanopipette Probes for Local Sampling 276
13.5 MALDI-MS Analysis of Analyte Post-Nanopipette Sampling 278
13.5.1 Single Allium cepa Cell Analysis 279
13.5.2 Lipid Analysis in Mouse Brain 280
13.6 Development of Segmented Flow Sampling 282
13.7 Study of Intercellular Heterogeneity 286
13.8 Conclusion and Outlook 288
Acknowledgments 290
References 290
14 FluidFM: Development of the Instrument as well as Its Applications for 2D and 3D Lithography 295
Tomaso Zambelli, Mathias J. Aebersold, Pascal Behr, Hana Han, Luca Hirt, VincentMartinez, Orane Guillaume-Gentil, and Janos Voros
14.1 Microchanneled AFM Cantilevers 296
14.1.1 Silicon-Based Hollow Probes 296
14.1.2 Polymer-Based Hollow Probes 297
14.2 Development of the FluidFM 300
14.3 Calibration of Hollow Probes: Stiffness and Flow 303
14.3.1 Stiffness 303
14.3.2 Flow 305
14.4 FluidFM as Lithography Tool in Liquid 308
14.4.1 Patterning Nanoparticles 308
14.4.2 Electrochemical 2D Patterning and 3D Printing 312
14.5 Conclusions and Outlook 316
Acknowledgments 317
References 317
15 FluidFM Applications in Single-Cell Biology 325
Orane Guillaume-Gentil,MaximilianMittelviefhaus, Livie Dorwling-Carter, Tomaso Zambelli and Julia A. Vorholt
15.1 Introduction 325
15.2 Nondestructive Cell Manipulations 326
15.3 Spatial Cell Manipulation 327
15.3.1 Substrate Micropatterning 327
15.3.2 Pick and Place 329
15.3.3 Cell Dispensing/Removal 330
15.4 Controlled Fluid Delivery 331
15.4.1 Extracellular Fluid Delivery 332
15.4.2 Intracellular Fluid Delivery 333
15.5 Mechanical Measurements 335
15.5.1 Quantification of Cell Elasticity 336
15.5.2 Quantification of Single-Cell Adhesion Forces 337
15.6 Ionic Current Measurements 341
15.6.1 Adaptation of the FluidFM Setup for Picoampere Current Measurements 342
15.6.2 Force-Controlled Patch Clamp with the FluidFM 343
15.6.3 Scanning Ion Conductance Microscopy with the FluidFM 346
15.7 Molecular Analyses 348
15.8 Conclusion and Future Perspectives 349
References 350
16 Soft Probes for Scanning ElectrochemicalMicroscopy 355
Tzu-En Lin, Andreas Lesch, Alexandra Bondarenko, Fernando Cortes-Salazar, and Hubert H. Girault
16.1 Introduction 355
16.2 Principles of Scanning Electrochemical Microscopy (SECM) 356
16.2.1 SECM Feedback Mode 356
16.2.2 SECM Generation/Collection Modes 358
16.3 Soft Probes for SECM 358
16.3.1 Fabrication and Characterization 359
16.3.2 Operation Principles 360
16.4 Applications of Soft SECM Probes 360
16.4.1 Reactivity Imaging of Extended Three-Dimensional Samples 362
16.4.2 High-Throughput Patterning and Imaging of Delicate Surfaces 362
16.4.3 Detection of Cancer Biomarkers in Skin Biopsy Sections 364
16.5 Conclusions and Future Perspectives 368
References 368
17 Microfluidic Probes for Scanning Electrochemical Microscopy 373
Alexandra Bondarenko, Fernando Cortes-Salazar, Tzu-En Lin, Andreas Lesch, and Hubert H. Girault
17.1 Introduction 373
17.2 Combining Microfluidics with SECM 374
17.2.1 Fountain Pen Probe 374
17.2.2 Electrochemical Push-Pull Probes 375
17.3 Electrochemical Characterization 377
17.3.1 Cyclic Voltammetry 377
17.3.2 SECM Experiments 378
17.4 Applications 382
17.4.1 SECM Imaging of Human Fingerprints Contaminated with Explosive Traces 382
17.4.2 Monitoring Enzymatic Reactions 384
17.4.3 Local Manipulation of Adherent Live Cell Microenvironments 385
17.5 Conclusions and Outlook 389
References 389
18 Chemistrode for High Temporal- and Spatial-Resolution Chemical Analysis 391
Alexander J. Donovan and Ying Liu
18.1 Introduction 391
18.2 Chemistrode Design and Operation 394
18.2.1 Chemistrode Design and Fabrication 394
18.2.2 Chemistrode Operation 394
18.3 Physical Principles Governing the Transport Processes 395
18.3.1 Non-dimensional Groups 395
18.3.2 Coalescence Dynamics of Incoming Plugs with the Hydrophilic Substrate 396
18.3.3 Mass Transfer at the Hydrophilic Substrate 398
18.4 Multiform Chemical Analysis Independent in Space and Time from Data Acquisition 400
18.4.1 Online Analysis 400
18.4.2 Parallel Offline Analysis 401
18.5 Applicability for Stimuli-Response Surfaces 403
18.5.1 Single Islet Cell Stimulation and Response Analysis 403
18.5.2 Isolation and Incubation of Individual Cells from Multispecies Mixtures 405
18.6 Challenges and Future Directions 406
Acknowledgments 407
References 407
Index 411
