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Detection of Pathogens in Water Using Micro and Nano-Technology

BOOK

Detection of Pathogens in Water Using Micro and Nano-Technology

Giampaolo Zuccheri | Nikolaos Asproulis

(2012)

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Additional Information

Book Details

ISBN
978-1-78040-109-6
Edition
1
Language
English
Pages
313
Subjects
The environment
Environmental science, engineering & technology
Water supply & treatment

Abstract

Detection of Pathogens in Water Using Micro and Nano-Technology aims to promote the uptake of innovative micro and nano-technological approaches towards the development of an integrated, cost-effective nano-biological sensor useful for security and environmental assays. 
The book describes the concerted efforts of a large European research project and the achievements of additional leading research groups. The reported knowledge and expertise should support in the innovation and integration of often separated unitary processes. Sampling, cell lysis and DNA/RNA extraction, DNA hybridisation detection micro- and nanosensors, microfluidics, together also with computational modelling and risk assessment can be integrated in the framework of the current and evolving European regulations and needs. The development and uptake of molecular methods is revolutionizing the field of waterborne pathogens detection, commonly performed with time-consuming cultural methods. The molecular detection methods are enabling the development of integrated instruments based on biosensor that will ultimately automate the full pathway of the microbiological analysis of water. 
Editors: Giampaolo Zuccheri, University of Bologna, Italy and Nikolaos Asproulis, Cranfield University, UK 

Table of Contents

Section Title Page Action Price
Cover page 1
Half-title page 2
Title page 3
Copyright page 4
Contents 5
Preface 13
Contributors 16
Chapter 1 21
Overview of European regulation and standards on microbiological water analysis 21
1.1 INTRODUCTION 21
1.2 EUROPEAN REGULATION ON MICROBIOLOGICAL ANALYSIS OF DRINKING WATER 21
1.3 EUROPEAN REGULATION ON MICROBIOLOGICAL ANALYSIS OF RECREATIONALWATER 22
1.3.1 Case of non-treated recreational water (seas, rivers, coastal water…) 22
1.3.2 Case of treated recreational water (swimming & spa pools etc.) 23
1.4 EUROPEAN AND INTERNATIONAL STANDARDS FOR MICROBIOLOGICALWATER ANALYSIS 23
ABBREVIATIONS 26
REFERENCES 26
Chapter 2 27
Risk analysis of bio-terroristic attacks on drinking water systems 27
2.1 INTRODUCTION 27
2.2 DEFINITIONS 28
2.3 RISK ANALYSIS FOR TERRORISM 29
2.3.1 Critical infrastructure and key asset inventory 30
2.3.2 Criticality assessment 30
2.3.3 Threat assessment 30
2.3.4 Vulnerability assessment 32
2.3.5 Risk evaluation 32
2.4 RISK ANALYSIS OF BIO-TERRORISTIC ATTACKS ON DRINKING WATER SYSTEMS 32
2.4.1 Threat assessment 32
2.4.2 Criticality assessment 41
2.4.3 Vulnerability assessment 41
2.5 RISK ESTIMATION 42
2.5.1 Hierarchical risk estimation 42
2.5.2 Quantitative microbial risk assessment 45
2.5.3 Data sources 46
REFERENCES 47
Chapter 3 53
Sample collection procedures for Online Contaminant Monitoring System 53
3.1 INTRODUCTION 53
3.2 MICROBIAL MONITORING OF DRINKING WATER 54
3.3 SAMPLING PLAN 56
3.3.1 What should the sampling plan include? 57
3.4 NEW SECURITY APPROACHES FOR DRINKING WATER 60
3.4.1 Water sources 61
3.4.2 Raw water transport 62
3.4.3 Treatment plants 62
3.4.4 Service reservoirs and distribution 62
3.5 NEW APPROACH OF ONLINE CONTAMINATION MONITORING DEVICE (OCMD) 63
3.5.1 Location of OCMD in water system 64
REFERENCES 65
Chapter 4 67
A device to extract highly diluted specimens out of large volumes of water for analysis in lab-on-a-chip detection systems 67
4.1 THE NEED FOR A MACRO-TO-MICRO-FLUIDIC INTERFACE 67
4.1.1 The DINAMICS EU research project\r 67
4.1.2 Device needed for generating input for analytics 67
4.2 PRINCIPLES OF SEPARATION 68
4.2.1 Survey of concentration methods 68
4.3 THE NEEDLE IN THE HAYSTACK 72
4.4 TECHNICAL DESCRIPTION OF THE DINAMICS CONCENTRATION APPARATUS 73
4.4.1 First draft of the dead-end filtration system 74
4.4.2 Tangential (cross-flow) filtration system 76
4.4.3 Steps towards a continuous working device 76
4.5 CONCLUSIONS 79
REFERENCES 79
Chapter 5 80
Sustainable DNA/RNA release methods for in-line waterborne pathogen screening devices 80
DEFINITIONS AND GLOSSARY 80
5.1 INTRODUCTION 80
5.2 SURVEY ON PATHOGEN-LYSIS/CELL-DISRUPTION METHODS 82
5.2.1 Examples for devices utilizing electric field 84
5.2.2 Examples for devices harnessing mechanical impact 86
5.2.3 Chemical impact based methods (i.e. no Cell-Wall digestive enzymes added) 91
5.3 CONSIDERATIONS FOR WATER SAMPLES AND IN-LINE (QUASI CONTINUOUS) OPERATION 91
5.4 THE REALISED CASE IN THE DINAMICS PROJECT 95
REFERENCES 98
Chapter 6 100
The microsystem based core of the DINAMICS water testing system: Design considerations and realization of the chip units 100
6.1 MICROFLUIDICS IN DINAMICS 100
6.2 LAYOUT OF THE FLUIDIC PARTS OF DINAMICS 100
6.3 MICROFLUIDIC COMPONENTS IN DINAMICS 102
6.3.1 The valve component 102
6.3.2 The mixer component 103
6.3.3 The DNA isolation component 105
6.3.4 The PCR reaction component 107
6.3.5 The hybridization chamber component 109
6.3.6 Fabrication – Technology platform 109
6.4 CURRENT STATUS 111
6.5 CONCLUSION 112
REFERENCES 112
Chapter 7 113
Electrochemical biosensor strategies for pathogen detection in water security 113
7.1 INTRODUCTION 113
7.2 BIOSENSOR STRATEGIES FOR PATHOGEN DETECTION IN WATER SECURITY 113
7.2.1 Conventional laboratory analysis 114
7.2.2 Biosensor analysis 115
7.2.3 Conclusions 119
7.3 COMMON ELECTROCHEMICAL DETECTION SYSTEMS FOR DNA BIOSENSORS 119
7.4 THE ON-CHIP SIMPLIFIED ELECTROCHEMICAL TECHNIQUE DEVELOPED IN THE DINAMICS PROJECT 124
7.4.1 On-chip voltammetry 124
7.4.2 Electrochemical reporter 125
7.4.3 Measurement principle 125
7.4.4 Interpretation of the measurements 126
7.4.5 Results 127
7.4.6 Conclusions 129
Acknowledgements 129
REFERENCES 129
Chapter 8 131
Biochemical and nanotechnological strategies for signal enhancement in the detection of nucleic acids with biosensors 131
8.1 INTRODUCTION 131
8.1.1 Rationale of the classification 132
8.2 ENHANCEMENT METHODS BASED ON ENZYMATIC (OR CATALYZED) REACTIONS 133
8.2.1 Peroxidase to enhance the signal of nucleic acids detection 134
8.2.2 One to several instances of alkaline phosphatase for the electrochemical detection of nucleic acids 134
8.2.3 Terminal transferase to grow DNA at the recognition site 136
8.2.4 Signal enhancement of fluorescence through the use of a nickase 136
8.2.5 RNase H as a target recycling operator for RNA-based sensors 137
8.2.6 Nucleic acid sequence-based amplification (NASBA) 138
8.2.7 Strand displacement amplification 139
8.2.8 Loop mediated isothermal amplification (LAMP) 139
8.2.9 Metal nanoparticles as active enhancer labels 140
8.3 ENHANCEMENT METHODS BASED ON NANOPARTICLES OR NANOSTRUCTURES\r 140
8.3.1 Methods that employ liposomes 140
8.3.2 Fluorescent nanoparticle labels 141
8.3.3 Colorimetric assays with metal nanoparticles 141
8.3.4 Signal amplification by conjugate breakdown: the bio-barcode assay 142
8.3.5 Quantum dots instead of organic dyes 142
8.4 METHOD BASED ON DNA NANOSTRUCTURES 142
8.4.1 Cascade signal amplification by the combined use of rolling circle amplification 143
8.4.2 Branched DNA signal amplification 144
8.4.3 Aptamers and DNAzymes 145
8.4.4 Hybridization chain reaction and surface-initiated DNA polymerization 145
8.5 CONCLUSIONS AND PERSPECTIVES 148
REFERENCES 148
Chapter 9 153
Computational modelling of aqueous environments in micro and nanochannels 153
9.1 INTRODUCTION 153
9.2 EFFECTS OF PHYSICAL CHARACTERISTICS\r 155
9.2.1 Surface roughness 155
9.2.2 Surface stiffness 155
9.2.3 Wetting – surface energy – contact angle 156
9.2.4 Shear rate – pressure 156
9.3 COMPUTATIONAL APPROACHES\r 157
9.3.1 Atomistic modelling 157
9.3.2 Continuum modelling 159
9.4 LIQUID FLOW IN CONFINED GEOMETRIES 9.4.1 Flow behaviour in nanochannels 168
9.5 MOLECULAR MODELLING OF WATER 175
REFERENCES 176
Chapter 10 180
Computational recipes of transport phenomena in micro and nanofluidics 180
10.1 INTRODUCTION 180
10.2 MODELLING APPROACHES 181
10.2.1 Modelling multiple scales 181
10.2.2 Brownian motion 182
10.2.4 Continuum scale diffusion 184
10.3 META-MODELLING FOR MACROMOLECULES 186
10.4 HYBRID CONTINUUM-MOLECULAR MODELS 187
REFERENCES 188
Chapter 11 190
Multi-detection of waterborne pathogens in raw and treated water samples by using ultrafiltration concentration and DNA array te 190
11.1 INTRODUCTION 190
11.2 IMPROVED AND SIMPLIFIED METHOD FOR CONCENTRATING VIRAL, BACTERIAL, AND PROTOZOAN PATHOGENS 191
11.2.1 Technical challenges for a universal concentration protocol 191
11.2.2 Protocol 194
11.3 INTEGRATED PROTOCOL FOR NUCLEIC ACID EXTRACTION, AMPLIFICATION AND SEQUENCE IDENTIFICATION THROUGH HIGH DENSITY MICROARRAY 195
11.4 RESULTS 198
11.4.1 Recovery from 30 L-initial volume to final concentrate 198
11.4.2 Impact of BSA blocking and elution agents on waterborne pathogen recovery using two-step ultrafiltration protocol from 30 199
11.4.3 Back volume calculation and comparison with other available detection methods 201
11.4.4 Multi-detection of waterborne pathogens by DNA Chip hybridization 201
11.5 CONCLUSIONS 203
Acknowledgements 204
REFERENCES 204
Chapter 12 207
Detection and enumeration of waterborne mycobacteria 207
12.1 ECOLOGY OF WATERBORNE MYCOBACTERIA 207
12.1.1 Mycobacterial diseases 207
12.1.2 Mycobacterial habitats 208
12.1.3 Transmission of mycobacteria 208
12.2 PHYSIOLOGICAL ECOLOGY OF WATERBORNE MYCOBACTERIA 208
12.2.1 The lipid-rich mycobacterial envelope 209
12.2.2 Consequences of the slow growth of mycobacteria 209
12.2.3 Viable but unculturable mycobacteria 210
12.3 RISK ANALYSIS AND SOURCE-TRACKING ENVIRONMENTAL MYCOBACTERIA 210
12.3.1 Mycobacterium avium and the candidate contaminant list 210
12.3.2 Risk analysis for mycobacteria 211
12.3.3 Source-tracking and DNA fingerprinting 211
12.4 SAMPLING AND SAMPLE TREATMENT STRATEGIES FOR MYCOBACTERIAL DETECTION AND ENUMERATION 211
12.4.1 Sampling strategies 211
12.4.2 Sample treatment 212
12.4.3 Sample concentration methods 212
12.5 MYCOBACTERIAL DETECTION OR ENUMERATION 213
12.5.1 Detection or enumeration 213
12.5.2 Culture, PCR, or qPCR 213
12.5.3 Culture of mycobacteria 213
12.5.4 PCR-detection and qPCR enumeration of mycobacteria 214
REFERENCES 214
Chapter 13 219
New molecular technologies for the rapid detection of Legionella in water 219
13.1 INTRODUCTION 219
13.2 IMMUNODETECTION AND FAST DETECTION\r 220
13.3 LEGIONELLA DETECTION USING MICROFLUIDICS 221
13.3.1 Microarray platforms using antibodies 221
13.3.2 Microarray platforms using DNA 223
13.4 FUTURE RESEARCH DIRECTIONS 227
REFERENCES 228
Chapter 14 229
Detection of virus in the water environment 229
14.1 INTRODUCTION 229
14.1.1 The waterborne viruses 229
14.1.2 Transmission of virus in the water environment 231
14.1.3 Virus in wastewater treatment plants 234
14.1.4 Monitoring of virus in sewage water – an epidemiological tool 234
14.2 CONCENTRATION OF VIRUS FROM WATER SAMPLES 235
14.2.1 Concentration based on ionic charge (electrostatic adsorption/elution) 235
14.2.2 Concentration based on particle size separation (ultrafiltration) 238
14.2.3 Other concentration techniques 239
14.3 DETECTION AND QUANTIFICATION METHODS 241
14.3.1 Cell culture assays 241
14.3.2 Molecular assays (PCR and real-time PCR) 243
14.3.3 ICC-PCR and detection of viral mRNA 244
14.4 PERSPECTIVES 244
Acknowledgements 245
REFERENCES 245
Chapter 15 252
Design of PCR primers for the detection of waterborne bacteria 252
15.1 INTRODUCTION 252
15.2 THE TARGET GENES 252
15.2.1 rRNA genes 253
15.2.2 Housekeeping genes 253
15.2.3 Pathogenicity genes 253
15.2.4 Deep sequencing 253
15.3 DESIGN OF PCR PRIMERS 254
15.3.1 The features of PCR primers 254
15.3.2 The softwares for designing PCR primers 255
15.4 DNA-BASED DETECTION TECHNOLOGIES\r 258
15.4.1 Specific detection 258
15.4.2 Global detection: the sequencing 265
15.5 CONCLUSIONS 266
REFERENCES 267
Chapter 16 270
Fluid structure and boundary slippage in nanoscale liquid films 270
16.1 ABSTRACT 270
16.2 INTRODUCTION 270
16.3 MOLECULAR DYNAMICS SIMULATION MODEL 272
16.4 RESULTS\r 275
16.4.1 Fluid density, velocity, and temperature profiles 275
16.4.2 Shear viscosity and slip length 277
16.4.3 Friction coefficient versus slip velocity 279
16.4.4 Friction coefficient and induced fluid structure 282
16.5 CONCLUSIONS 287
Acknowledgments 288
REFERENCES 288
Chapter 17 291
Understanding slip at the nanoscale in fluid flows using atomistic simulations 291
17.1 INTRODUCTION – DEFINITION OF SLIP\r 291
17.1.1 Continuum theory and slip 291
17.1.2 Incorporating velocity slip in continuum models 292
17.2 IMPORTANCE OF SLIP 292
17.3 EXPERIMENTAL MEASUREMENT OF SLIP 294
17.4 ATOMISTIC SIMULATIONS 294
17.4.1 Methodological issues 295
17.4.2 Property calculations 298
17.4.3 Transport properties 298
17.4.4 Slip velocity/length calculation 299
17.5 ATOMISTIC SIMULATIONS RESULTS ABOUT SLIP 300
17.5.1 Wall roughness effects 302
17.5.2 Effect of periodic wall patterns 303
17.5.3 Effect of nanostripes 306
17.6 CONCLUSIONS 308
REFERENCES 308

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