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E-grāmata: DNA Techniques to Verify Food Authenticity: Applications in Food Fraud

Edited by (LGC Limited, UK), Edited by (Department for the Environment, Food and Rural Affairs, UK), Edited by (Michael Walker Consulting Ltd, UK)
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DNA Techniques to Verify Food Authenticity: Applications in Food FraudPalielināt
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Describing the science behind DNA as a target analyte, its extraction, amplification, detection and quantitation as applied to the detection of food fraud and food crime, this book covers this topical and growing area post the horsemeat scandal. Worldwide authorities in the area have been bought together to provide comprehensive coverage of all issues ranging from sampling of DNA through to emerging techniques such as next generation sequencing. It will appeal to a two-fold market – food-testing laboratories worldwide and food policy professionals and regulatory organisations who use these techniques to back up legislation. The food supply chain needs to reassure consumers and businesses about the safety and standards of food. Global estimates of the cost of food fraud to economies run into billions of dollars hence a huge surge in interest in food authenticity and means of detecting and preventing food fraud and food crime. Approaches targeting DNA markers have assumed a pre-eminence.
This book is the most comprehensive and timely collection of material from those working at the forefront of DNA techniques applied to food authenticity. Addressing the new field of analytical molecular biology as it combines the quality assurance rigour of analytical chemistry with DNA techniques, it introduces the science behind DNA as a target analyte, its extraction, amplification, detection and quantitation as applied to the detection of food fraud and food crime. Making the link with traditional forensic DNA profiling and describing emerging and cutting-edge techniques such as next generation sequencing, this book presents real-world case studies from a wide perspective including from analytical service providers, industry, enforcement agencies and academics. It will appeal to food testing laboratories worldwide, who are just starting to use these techniques and students of molecular biology, food science and food integrity. Food policy professionals and regulatory organisations who will be using these techniques to back up legislation and regulation will find the text invaluable. Those in the food industry in regulatory and technical roles will want to have this book on their desks.

Providing the most comprehensive and timely collection of material from those working at the forefront of DNA techniques applied to food authenticity, this book will appeal to food testing laboratories worldwide and food policy professionals and regulatory organisations who will be using these techniques to back up legislation and regulation.

Describing the science behind DNA as a target analyte, its extraction, amplification, detection and quantitation as applied to the detection of food fraud and food crime, this book covers this topical and growing area post the horsemeat scandal. Worldwide authorities in the area have been bought together to provide comprehensive coverage of all issues ranging from sampling of DNA through to emerging techniques such as next generation sequencing. It will appeal to a two-fold market – food-testing laboratories worldwide and food policy professionals and regulatory organisations who use these techniques to back up legislation.

Recenzijas

This is an ambitious book. The scope ranges from the basic science and history of DNA testing to cuttingedge techniques and case studies. It aims to be the goto reference for testing laboratories new to the DNA field, for people in food industry technical roles, for students and for regulators; it is likely to be a wellthumbed fixture on their desk. The book achieves its aim of providing something for everyone, over a very wide target audience.Throughout the book, the underlying theme is consistently stressed: that the rigour traditionally applied to analytical quality control must equally be applied to DNAbased methods. * https://doi.org/10.1002/fsat.3401_16.x *

Chapter 1 The Role of DNA Analysis in the Determination of Food Authenticity 1(11)
S.B. Primrose
1.1 A Brief History of Food Adulteration
1(1)
1.2 Food Fraud in the 21st Century
2(2)
1.3 Challenges in Detecting Food Misdescription and Fraud
4(1)
1.4 The Role of DNA in Food Authenticity Determination
5(1)
1.5 Application of DNA-based Analytical Methods to Different Commodities and Food Authenticity Problems
6(2)
1.6 Pushing the Boundaries: Specialist Techniques for Breed or Variety Identification and Determination of Geographical Origin
8(1)
1.7 Fitness for Purpose
9(1)
1.8 Final Comments
9(1)
References
9(3)
Chapter 2 Forensic DNA - Criminal and Paternity Methods and Applications - How Can This Help in Verifying Food Authenticity? 12(17)
Victoria Moore
2.1 Some History
12(2)
2.2 Applying the Forensic Code of Conduct
14(2)
2.3 Key Issues - Complexities Within Forensic Regulatory Bodies and Associations
16(2)
2.4 Key Issues - Databases and Communication
18(3)
2.5 Document Recording
21(3)
2.5.1 Receipt of Materials
21(1)
2.5.2 Examination, Standard Operating Procedures and Quality Control
22(2)
2.6 Conclusion
24(1)
References
25(4)
Chapter 3 DNA Extraction from Food Matrices 29(21)
Timothy Wilkes
3.1 Introduction
29(1)
3.2 Factors Influencing the Choice of Extraction Methodology
30(3)
3.2.1 Sample Source and Processing
30(1)
3.2.2 Sample Collection and Storage
30(1)
3.2.3 Homogenisation
30(1)
3.2.4 Presence of Contaminants
31(2)
3.3 General DNA Extraction Methods
33(4)
3.3.1 Phenol-Chloroform Extractions
34(1)
3.3.2 Detergent and Protease-based Extractions
34(1)
3.3.3 Solid-phase Extraction Methods
35(1)
3.3.4 Concentrating DNA Post-extraction
36(1)
3.4 DNA Extraction Methods Frequently Employed with Food and Feed Samples
37(2)
3.5 Determining DNA Quantity and Purity
39(7)
3.5.1 Quantification of DNA
39(3)
3.5.2 Evaluation of DNA Purity
42(2)
3.5.3 RNA Contamination
44(1)
3.5.4 Non-nucleic-acid Contamination
44(1)
3.5.5 Evaluation of a DNA Sample's Integrity
44(1)
3.5.6 Determining the Presence of Inhibitory Compounds
45(1)
3.6 Concluding Remarks
46(1)
Acknowledgements
47(1)
References
47(3)
Chapter 4 "DNA Techniques" Case Study: Isothermal Approaches 50(13)
G. Nixon
4.1 Introduction
50(1)
4.2 Main Isothermal NAA Technologies
51(4)
4.2.1 Cross Priming Amplification (CPA)
51(1)
4.2.2 Helicase-dependent Amplification (HDA)
51(1)
4.2.3 Loop-mediated Isothermal Amplification (LAMP)
52(2)
4.2.4 Recombinase Polymerase Amplification (RPA)
54(1)
4.3 PCR vs. Isothermal Technologies
55(1)
4.4 Food Applications
55(2)
4.4.1 Meat Speciation
55(2)
4.4.2 GMOs
57(1)
4.4.3 Allergens
57(1)
4.5 Future View
57(1)
4.6 Conclusion
58(1)
Acknowledgements
58(1)
References
59(4)
Chapter 5 Digital Polymerase Chain Reaction (dPCR) - General Aspects and Applications 63(7)
S. Pecoraro
5.1 Introduction
63(1)
5.2 General Properties of dPCR
64(1)
5.3 dPCR Platforms
65(1)
5.4 Assumptions for Absolute DNA Quantification with dPCR
66(1)
5.5 Applications of dPCR in Food Analysis
67(1)
5.6 Future Aspects
67(1)
References
68(2)
Chapter 6 UK Food Authenticity Programme - The Analytical Tool Box 70(16)
L.H. Foster
S.B. Primrose
6.1 Introduction: Drivers and Rationale for the Programme
70(1)
6.2 Policy Context: Industry, Enforcement and Consumer Trust
71(3)
6.3 Technical Challenges Affecting Policy Development and Food Law Enforcement
74(1)
6.4 The Analytical Toolbox
74(5)
6.4.1 Chemical Methods
75(1)
6.4.2 Physical Methods
76(1)
6.4.3 Proteomic-based Methods
76(1)
6.4.4 DNA-based Methods
77(2)
6.5 Upskilling: Knowledge Transfer of Government-funded DNA Techniques to Support Food Law Enforcement
79(1)
6.6 Forward Look and Future Challenges
79(2)
6.6.1 Collaboration - a Global Response to Food Fraud
80(1)
6.6.2 Future Tools to Tackle Food Fraud
80(1)
6.6.3 Food Labelling and Informed Choice
81(1)
6.7 Conclusion
81(1)
Acknowledgement
82(1)
References
82(4)
Chapter 7 Fitness for Purpose of DNA-based Analytical Methods 86(10)
S.B. Primrose
L.H. Foster
7.1 Introduction
86(1)
7.2 Fitness for Purpose
87(1)
7.2.1 What is 'Fitness for Purpose?'
87(1)
7.3 Challenges for Fitness for Purpose for Authenticity
88(1)
7.4 Sampling and Extraction
88(1)
7.5 Qualitative Versus Quantitative Analysis
89(2)
7.6 Reference Materials
91(1)
7.7 Validation
91(1)
7.8 Measurement Uncertainty
91(1)
7.9 How is Fitness for Purpose Achieved?
92(2)
7.10 Full Validation
94(1)
7.11 Conclusions
94(1)
References
94(2)
Chapter 8 GMO Detection and Identification Using Next-generation Sequencing 96(11)
Marie-Alice Fraiture
Nina Papazova
Kevin Vanneste
Sigrid C.J. de Keersmaecker
Nancy H. Roosens
8.1 The Current Landscape of GMO Detection
96(1)
8.2 Applying NGS to GMO Detection: Current Approaches
97(5)
8.3 Challenges for the Detection and Characterization of GMOs Using NGS Related to the Host
102(1)
8.4 Conclusion and Perspectives
103(1)
References
103(4)
Chapter 9 A Perspective on Quantitative DNA Approaches 107(13)
Malcolm Burns
9.1 Introduction: The Requirement for Accurate Quantitation of Food Samples
107(2)
9.2 Recommendations for Methods for Accurate Quantitation of Food Samples
109(2)
9.3 Approaches for Quantitative Estimation of Food Samples Using DNA
111(4)
9.3.1 Choice of Target for Quantitative Estimation
111(1)
9.3.2 Choice of Method for Quantitative Estimation
111(2)
9.3.3 Expression Units and Measurement Scales
113(2)
9.4 Ensuring Fitness for Purpose for Accurate Quantitation of Food Samples
115(1)
9.5 Summary and Future Perspectives on Quantitative DNA Approaches
116(1)
Acknowledgements
117(1)
References
117(3)
Chapter 10 DNA in Food and Feed Law 120(21)
Nigel Payne
10.1 Introduction
120(1)
10.2 Food
121(4)
10.2.1 Framework Law
121(3)
10.2.2 Food - Subordinate Law
124(1)
10.2.3 Protected Designations
124(1)
10.3 Other Authenticity Issues
125(1)
10.3.1 Honey
125(1)
10.3.2 Herbs and Spices
125(1)
10.4 Allergens in Food
126(1)
10.5 Microbiological Safety of Food
127(1)
10.6 Genetically Modified Organisms - GMOs
128(2)
10.6.1 GM Rice and Rice Products
129(1)
10.7 Organic Food and Feed
130(1)
10.8 Protection of Vegan, Halal and Kosher Food
130(1)
10.9 Investigation of Food "Complaints"
130(1)
10.10 Animal Feeding Stuffs
131(1)
10.11 Legal Provisions for Official Controls of Food and Feed
131(1)
10.12 Taking of Samples
132(1)
10.13 Interpreting Results in a Legal Context
133(1)
10.14 EU Exit
134(1)
References
134(5)
Case Studies
139(2)
Chapter 11 Harmonising DNA Methods - The GMO Story 141(6)
Hendrik Emons
11.1 Introduction
141(1)
11.2 The Harmonisation Challenge
142(1)
11.3 The Network Approach
143(1)
11.4 Achievements and Current Status
144(1)
Acknowledgements
145(1)
References
145(2)
Chapter 12 Metrology of DNA Approaches 147(7)
Mojca Milavec
David Dobnik
Alexandra Bogozalec Kosir
Jana Zel
12.1 Introduction
147(1)
12.2 Key Comparison Studies
148(2)
12.3 Partition Volume Variability - a Critical Factor Influencing the Accuracy of Absolute Quantification by Digital PCR
150(1)
12.4 Conclusions
151(1)
References
152(2)
Chapter 13 The Almond and Mahaleb Allergen Story - PCR Resolution of Live Incident Investigations 154(8)
Michael Walker
Malcolm Burns
13.1 Introduction
154(1)
13.2 Almond and the Prunus Family
155(1)
13.3 Sample Authentication
155(2)
13.3.1 Real Time PCR Assay Development
156(1)
13.4 Results
157(1)
13.4.1 Referred Cumin Sample
157(1)
13.4.2 Referred Paprika Sample
157(1)
13.5 Conclusions
158(1)
Acknowledgements
159(1)
References
159(3)
Chapter 14 Food Fraud Prevention - Selecting the Right Test, Method, and Sampling Plan 162(7)
John Spink
14.1 Introduction
162(1)
14.2 Food Fraud Overview
163(1)
14.3 Criminology and Food Fraud Prevention
163(1)
14.4 Case Study: Horsemeat Incident
164(2)
14.5 Conclusion
166(1)
References
166(3)
Chapter 15 Meat Speciation 169(8)
Maria Karczmarczyk
15.1 Comparison Between PCR and ELISA
169(1)
15.2 Qualitative PCR Testing
170(1)
15.3 Quantitative PCR Testing
170(3)
15.3.1 Low DNA Content Samples - Dairy, Gelatine
171(1)
15.3.2 Effects of Food Processing
171(1)
15.3.3 Interference - Inhibition
171(1)
15.3.4 Limit of Detection (LOD)
172(1)
15.4 Proprietary Methods - Considerations and Validation Approaches
173(1)
15.5 Reporting
174(1)
15.6 New Developments
174(1)
References
175(2)
Chapter 16 The Horse Meat Scandal - The European Analytical Response 177(12)
Marien Aline
Fumiere Olivier
Debode Frederic
Hulin Julie
Berben Gilbert
16.1 Introduction
177(1)
16.2 Material and Methods
178(3)
16.2.1 Real-time PCR Analysis
178(1)
16.2.2 Specificity of the Horse PCR Method
179(1)
16.2.3 Sensitivity of the Horse PCR Method
180(1)
16.2.4 Robustness of the Horse PCR Method
180(1)
16.2.5 Development of a Semi-quantitative Method for the Detection of Horse Meat
181(1)
16.3 Results
181(4)
16.3.1 Evaluation of the Performance of the Horse PCR Method
181(1)
16.3.2 Development of a Semi-quantitative Method for the Detection of Horse Meat
182(3)
Acknowledgements
185(1)
References
185(4)
Chapter 17 Horse Meat: Technical Appeals and Court Action 189(11)
Michael Walker
17.1 Introduction
189(1)
17.2 Technical Appeals
190(4)
17.2.1 Technical Approach
190(1)
17.2.2 DNA
191(1)
17.2.3 ELISA
192(1)
17.2.4 Interpretation
192(2)
17.3 Prosecutions
194(3)
17.3.1 Bulgarian Sausage
194(1)
17.3.2 Abattoir with no Horse Traceability
194(1)
17.3.3 Frozen Blocks of Meat and 'Bargain' Beef Burgers with Horse
195(1)
17.3.4 Heart in Burgers
196(1)
17.3.5 The Netherlands
196(1)
17.3.6 France
196(1)
17.4 Conclusions
197(1)
References
197(3)
Chapter 18 Durum Wheat and Pasta Authenticity 200(7)
Gordon Wiseman
18.1 Introduction and Regulations
200(1)
18.2 Case Study
201(4)
18.2.1 Is T. aestivum Present in the Pasta?
201(1)
18.2.2 qPCR Confirmation and Quantification of the T. aestivum
202(2)
18.2.3 Analytical Uncertainty
204(1)
18.3 Conclusions
205(1)
Acknowledgement
205(1)
References
206(1)
Chapter 19 The Authenticity of Basmati Rice - A Case Study 207(12)
Mark Woolfe
Katherine Steele
19.1 Introduction
207(1)
19.2 Methodology Development to Authenticate Basmati Rice
208(1)
19.2.1 Basmati Rice Variety Authentication and Quantification
208(1)
19.3 Food Standards Agency's Basmati Rice Survey
209(2)
19.3.1 Basmati Rice Variety Identification
209(1)
19.3.2 Quantitative Measurement of Non-basmati Varieties
209(2)
19.3.3 Follow-up Action of the Survey
211(1)
19.4 Further Development of the Methodology
211(5)
19.4.1 Basmati Variety Identification
211(2)
19.4.2 Quantitative Determination of Non-basmati Varieties in Basmati Rice
213(1)
19.4.3 Lab-on-a-chip Approach to Basmati Rice Authenticity
214(2)
19.5 Postscript to Basmati Rice Methodology
216(1)
Acknowledgements
216(1)
References
217(2)
Chapter 20 Horse Meat: The International Collaborative Trial of the Real-time PCR Method for the Quantitation of Horse DNA 219(8)
Malcolm Burns
Lucy Foster
20.1 Food Fraud
219(1)
20.2 The 2013 Horse Meat Issue
220(1)
20.3 Challenges in Meat Quantitation
220(1)
20.4 Development of a Real-time PCR Method for the Quantitation of Horse DNA
221(1)
20.5 International Collaborative Trial of the Real-time PCR Method for the Quantitation of Horse DNA
222(2)
20.6 Summary
224(1)
Acknowledgements
224(1)
References
225(2)
Chapter 21 Standardization of DNA-based Methods for Food Authenticity Testing 227(8)
L. Grohmann
C. Seiler
21.1 Introduction
227(1)
21.2 CEN and ISO - Activities and Projects
228(5)
21.2.1 CEN WS/86 - Authenticity in the Feed and Food Chain - General Principles and Basic Requirements
228(1)
21.2.2 CEN Food Authenticity Coordination Group (FACG) and a New Technical Committee on Food Authenticity
229(1)
21.2.3 CEN/TC 275/WG 11 'Genetically Modified Organisms and Species Analysis'
229(3)
21.2.4 ISO/TC 34/SC 16 'Horizontal Biomarker Analysis'
232(1)
21.3 Discussion and Outlook
233(1)
21.4 Conclusion
233(1)
Acknowledgement
234(1)
References
234(1)
Chapter 22 Authentication of Chinese Traditional Medicine by DNA Analysis 235(20)
Foo Wing Lee
Olive Tin Wai Li
Winnie Wing Yan Chum
22.1 Introduction
235(1)
22.2 Reliability of DNA Methods for Species Identification
236(1)
22.3 Selection of DNA Markers
237(1)
22.4 Bioinformatics Analysis
238(5)
22.5 Demo Analysis
243(2)
22.6 Example Cases
245(6)
22.6.1 Authentication of Cordyceps
247(3)
22.6.2 Authentication of Oviductus Ranae
250(1)
22.7 Conclusion
251(1)
Acknowledgements
251(1)
References
251(4)
Chapter 23 DNA Point of Use Applications 255(9)
Michael Walker
Malcolm Burns
Lucy Foster
23.1 Introduction
255(1)
23.2 PoU in Criminal DNA Profiling
256(1)
23.2.1 ParaDNA™
256(1)
23.2.2 RapidHIT by IntegenX
257(1)
23.3 PoU in Point of Care Diagnostics
257(2)
23.3.1 Genie II/III™ by OptiGene
257(1)
23.3.2 QuantuMDx Q-POC™
258(1)
23.3.3 Biocartis Idylla™
258(1)
23.4 Discussion
259(2)
23.5 Conclusions
261(1)
Acknowledgements
261(1)
References
261(3)
Chapter 24 Commercial DNA Testing 264(19)
Barbara Hirst
Lourdes Fernandez-Calvino
Thomas Weiss
24.1 Introduction
264(1)
24.2 Expectations from Commercial Clients
265(1)
24.3 Are Expectations Always Deliverable?
266(1)
24.4 DNA Approaches
267(1)
24.5 Overview of Commercial DNA Tests
268(8)
24.5.1 DNA Detection Methods
268(8)
24.6 Comparison of Commercial DNA Tests and In-house Methods
276(1)
24.7 Challenges in the Development of In-house DNA Test Methods
277(1)
24.8 Reporting PCR Results
278(2)
References
280(3)
Chapter 25 EU Food Integrity and Joining up the Landscape (EU Perspective) 283(13)
Elena Maestri
Nelson Marmiroli
25.1 The Turning Point in EU Food Studies
283(1)
25.2 Research on Food in the EU
284(10)
25.2.1 The Beginning
285(4)
25.2.2 Research at the Turn of the Century
289(3)
25.2.3 The Advent of Food Integrity
292(1)
25.2.4 Research in FP7
293(1)
25.2.5 Horizon 2020
294(1)
Acknowledgements
294(1)
References
294(2)
Chapter 26 The Food Authenticity Network 296(15)
Selvarani Elahi
Stephen Ellison
Mark Woolfe
26.1 Background
296(1)
26.2 Creation of the Food Authenticity Network
297(2)
26.2.1 Network Structure
298(1)
26.3 Centres of Expertise (CoE) for Food Authenticity Testing
299(1)
26.4 Authenticity Research and Methods
300(1)
26.5 Training
300(1)
26.6 Discussions and Forums
300(1)
26.7 Policy and Law
301(1)
26.8 Quality
301(1)
26.9 Relevant Organisations
301(1)
26.10 Latest News and Events
301(1)
26.11 Food Fraud Mitigation
302(1)
26.12 Social Media Platforms
302(1)
26.12.1 Twitter
302(1)
26.12.2 LinkedIn
303(1)
26.13 Growth
303(1)
26.14 Impact
303(4)
26.14.1 Membership
303(2)
26.14.2 Member Surveys
305(2)
26.14.3 Analytics Data
307(1)
26.15 International Recognition
307(2)
26.16 Global Network
309(1)
26.17 Conclusions
309(1)
References
310(1)
Chapter 27 A Vision for the Future 311(7)
L.H. Foster
M. Burns
M. Walker
27.1 Introduction
311(1)
27.2 Changing World
312(1)
27.3 Food Fraud Prevention - Technological Opportunities
312(1)
27.4 Analytical Developments and Future Needs
313(2)
27.5 Labelling and the Consumer
315(1)
27.6 Conclusions
315(1)
References
316(2)
Subject Index 318
The editors possess unrivalled expertise and are keen to describe and foster advances in the key area of DNA techniques applied to food authenticity. Dr Lucy Foster is an experienced food scientist, and head of food research including authenticity research at Defra, for many years commissioning studies of global reach. Dr Malcolm Burns is an internationally recognised molecular biologist and expert in DNA quantitation. Dr Michael Walker was a founder board member of the Food Standards Agency, a subject matter expert to the Elliott Review, is Head of the Office of the Government Chemist, and, with a thriving consulting practice, is an experienced expert witness.
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