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E-raamat: Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria [Wiley Online]

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  • Formaat: 440 pages
  • Ilmumisaeg: 01-Sep-2017
  • Kirjastus: John Wiley & Sons Inc
  • ISBN-10: 1119332168
  • ISBN-13: 9781119332169
Teised raamatud teemal:
  • Wiley Online
  • Hind: 153,31 €*
  • * hind, mis tagab piiramatu üheaegsete kasutajate arvuga ligipääsu piiramatuks ajaks
Molecular Tools for the Detection and Quantification of Toxigenic CyanobacteriaSuurem pilt
  • Formaat: 440 pages
  • Ilmumisaeg: 01-Sep-2017
  • Kirjastus: John Wiley & Sons Inc
  • ISBN-10: 1119332168
  • ISBN-13: 9781119332169
Teised raamatud teemal:
Wiley Online e-raamatudRohkem infot Wiley Online kohta
Raamatu kodulehekülg: https://onlinelibrary.wiley.com/doi/book/10.1002/9781119332169

A guide to state-of-the-art molecular tools for monitoring and managing the toxigenicity of cyanobacteria

Runaway eutrophication and climate change has made the monitoring and management of toxigenic organisms in the world’s bodies of water more urgent than ever. In order to influence public policy regarding the detection and quantification of those organisms, it is incumbent upon scientists to raise the awareness of policy makers concerning the increased occurrence of toxigenic cyanobacteria and the threats they pose. As molecular methods can handle many samples in short time and help identify toxigenic organisms, they are reliable, cost-effective tools available for tracking toxigenic cyanobacteria worldwide. This volume arms scientists with the tools they need to track toxigenicity in surface waters and food supplies and, hopefully, to develop new techniques for managing the spread of toxic cyanobacteria.

This handbook offers the first comprehensive treatment of molecular tools for monitoring toxigenic cyanobacteria. Growing out of the findings of the landmark European Cooperation in Science and Technology Cyanobacteria project (CYANOCOST), it provides detailed, practical coverage of the full array of available molecular tools and protocols, from water sampling, nucleic acid extraction, and downstream analysis—including PCR and qPCR based methods—to  genotyping (DGGE), diagnostic microarrays, and community characterization using next-gen sequencing techniques.

  • Offers an overview of the latest trends in the field, while providing a foundation for understanding and applying the tools and techniques described
  • Provides detailed coverage of the full range of molecular tools currently available, with expert guidance on the analysis and interpretation of results
  • Includes step-by-step guidance on standard operational procedures, including molecular tests used in environmental monitoring, with individual chapters devoted to each procedure
  • Complements the published Handbook of Cyanobacterial Monitoring and Cyanotoxin Analysis from the CyanoCOST project

This handbook is an indispensable working resource for scientists, lab technicians, and water management professionals and an excellent text/reference for graduate students and supervisors who use molecular tools. It will also be of great value to environmental health and protection officials and policy makers.

List of Contributors
xix
About the Editors xxiii
About the Book xxvii
Preface xxix
Acknowledgments xxxi
1 Introduction
1(18)
Rainer Kurmayer
Kaarina Sivonen
Nico Salmaso
1.1 A Brief Historical Overview
1(1)
1.2 The Genetic Basis of Toxin Production
2(6)
1.2.1 Microcystin and Nodularin
2(3)
1.2.2 Cylindrospermopsin
5(1)
1.2.3 Saxitoxin
6(2)
1.2.4 Anatoxin
8(1)
1.3 Application of Molecular Tools
8(5)
1.4 Laboratory Safety Issues
13(1)
1.5 References
14(5)
2 Sampling and Metadata
19(24)
Rainer Kurmayer
Guntram Christiansen
Konstantinos Kormas
Wim Vyverman
Elie Verleyen
Vitor Ramos
Vitor Vasconcelos
Nico Salmaso
2.1 Introduction
19(1)
2.2 Handling of Samples
20(1)
2.3 Sample Contamination
21(1)
2.4 Sampling
21(2)
2.4.1 Quantitative Depth-Integrated and Discrete Sampling
21(1)
2.4.2 Qualitative Plankton Net Sampling
22(1)
2.4.3 Surface (Scum Material) Sampling
22(1)
2.4.4 Benthic (Terrestrial) Cyanobacteria Sampling
22(1)
2.4.5 Food Supplement Sampling
22(1)
2.4.6 Isolation of Single Colonies/Filaments
22(1)
2.5 Subsampling Food Supplement Samples
23(1)
2.6 Sampling of Nucleic Acids
23(1)
2.7 General Conclusions
24(1)
2.8 References
24(19)
SOP 2.1 Sampling and Filtration (DNA)
26(1)
Rainer Kurmayer
Konstantinos Kormas
SOP 2.1.1 Introduction
26(1)
SOP 2.1.2 Experimental
26(1)
SOP 2.1.3 Procedure
27(1)
SOP 2.1.4 Notes
28(1)
SOP 2.1.5 References
29(1)
SOP 2.2 Sampling of Benthic Cyanobacteria
29(1)
Wim Vyverman
Elie Verleyen
SOP 2.2.1 Introduction
29(1)
SOP 2.2.2 Experimental
30(1)
SOP 2.2.3 Procedure
30(1)
SOP 2.2.4 Notes
31(1)
SOP 2.2.5 References
31(1)
SOP 2.3 Isolation of Single Cyanobacteria Colonies/Filaments
32(1)
Rainer Kurmayer
SOP 2.3.1 Introduction
32(1)
SOP 2.3.2 Experimental
32(1)
SOP 2.3.3 Procedure
33(1)
SOP 2.3.4 Notes
33(1)
SOP 2.3.5 References
33(1)
SOP 2.4 Sampling Food Supplements
34(1)
Vitor Ramos
Cristiana Moreira
Vitor Vasconcelos
SOP 2.4.1 Introduction
34(1)
SOP 2.4.2 Experimental
35(1)
SOP 2.4.3 Procedure (Fig. 8.3)
35(1)
SOP 2.4.4 Notes
36(1)
SOP 2.4.5 References
36(1)
SOP 2.5 Sampling and Filtration (RNA)
37(1)
Rainer Kurmayer
Guntram Christiansen
SOP 2.5.1 Introduction
37(1)
SOP 2.5.2 Experimental
37(1)
SOP 2.5.3 Procedure
38(1)
SOP 2.5.4 Notes
38(1)
SOP 2.5.5 References
38(1)
SOP 2.6 Sampling of Abiotic and Biotic Data and Recording Metadata
39(1)
Elie Verleyen
Maxime Sweetlove
Dagmar Ohbels
Wim Vyverman
SOP 2.6.1 Introduction
39(1)
SOP 2.6.2 Experimental
39(1)
SOP 2.6.3 Type of Metadata and Additional Biotic and Abiotic Data
40(1)
SOP 2.6.4 Notes
41(1)
SOP 2.6.5 References
42(1)
3 Isolation, Purification, and Cultivation of Toxigenic Cyflnobacteria
43(36)
Sigrid Haande
Iwonu Jasser
Muriel Gugger
Camilla H.C. Hagman
Annick Wilmotte
Andreas Ballot
3.1 Introduction
43(1)
3.2 Methodical Principles for Cyanobacterial Isolation, Purification, and Cultivation
44(5)
3.2.1 Sampling, Identification, and Treatments Prior to the Isolation of Cyanobacteria
44(1)
3.2.2 Traditional Techniques for the Isolation and Purification of Cyanobacteria
45(2)
3.2.3 Culture Media Preparation
47(1)
3.2.4 Cultivation Conditions
48(1)
3.3 General Conclusions
49(1)
3.4 References
49(30)
SOP 3.1 Isolation, Purification, and Clonal Isolate Testing
51(1)
Sigrid Haande
Camilla H.C. Hagman
Andreas Ballot
SOP 3.1.1 Introduction
51(1)
SOP 3.1.2 Experimental
51(1)
SOP 3.1.3 Procedure
52(2)
SOP 3.1.4 Notes
54(1)
SOP 3.1.5 References
54(1)
SOP 3.2 Isolation of Picocyanobacterial Cells by Flow Cytometer (FCM) Sorting
55(1)
Ewa Kozlowska
Hvona Jasser
SOP 3.2.1 Introduction
55(1)
SOP 3.2.2 Experimental
56(1)
SOP 3.2.3 Procedure
56(2)
SOP 3.2.4 Notes
58(1)
SOP 3.2.5 References
59(1)
SOP 3.3 Axenizalion
60(1)
Muriel Digger
SOP 3.3.1 Introduction
60(1)
SOP 3.3.2 Experimental
60(1)
SOP 3.3.3 Procedure
61(2)
SOP 3.3.4 Notes
63(1)
SOP 3.3.5 References
63(1)
SOP 3.4 Culture Media (Solid and Liquid)
64(1)
Sigrid Haande
Camilla H.C. Hagman
Andreas Ballot
SOP 3.4.1 Introduction
64(1)
SOP 3.4.2 Experimental
64(1)
SOP 3.4.3 Procedure
65(3)
SOP 3.4.4 Notes
68(1)
SOP 3.4.5 References
68(1)
SOP 3.5 Strain Maintenance (Living Cultures)
69(1)
Sigrid Haande
Camilla H.C. Hagman
Andreas Ballot
SOP 3.5.1 Introduction
69(1)
SOP 3.5.2 Experimental
69(1)
SOP 3.5.3 Procedure
70(2)
SOP 3.5.4 Notes
72(1)
SOP 3.5.5 References
73(1)
SOP 3.6 Cryopreservation and Recovery
73(1)
Muriel Gugger
SOP 3.6.1 Introduction
73(1)
SOP 3.6.2 Experimental
74(1)
SOP 3.6.3 Procedure
75(3)
SOP 3.6.4 Notes
78(1)
SOP 3.6.5 References
78(1)
4 Taxonomic Identification of Cyanobacteria by a Polyphasic Approach
79(56)
Annick Wilmotte
H. Dail Laughinghouse
Camilla Capelli
Rosmarie Rippka
Nico Salmaso
4.1 Introduction
79(3)
4.2 Nomenclature and Classification of Cyanobacteria
82(2)
4.3 Microscopy
84(3)
4.3.1 Light Microscopy
84(2)
4.3.2 Autofluorescence Microscopy
86(1)
4.4 Molecular Markers: Single Loci
87(7)
4.5 Molecular Markers: Multiple Loci
94(2)
4.5.1 Multilocus Sequence Typing (MLST) and Multilocus Sequence Analysis (MLSA)
94(2)
4.5.2 Genome-Based Extension of MLST and MLSA
96(1)
4.6 Molecular Typing Methods Based on Gel Electrophoresis
96(1)
4.7 Denaturing Gradient Gel Electrophoresis (DGGE)
97(1)
4.8 Taxonomic and Molecular Databases
97(1)
4.9 The Polyphasic Approach
98(7)
4.10 Final Considerations
105(1)
4.11 References
106(29)
SOP 4.1 Taxonomic Identification by Light Microscopy
120(1)
Nico Salmaso
Rosmarie Rippka
Annick Wilmotte
SOP 4.1.1 Introduction
120(1)
SOP 4.1.2 Experimental
121(3)
SOP 4.1.3 References
124(1)
SOP 4.2 Polyphasic Approach on Cyanobacterial Strains
125(1)
Nico Salmaso
Camilla Capelli
Rosmarie Rippka
Annick Wilmotte
SOP 4.2.1 Introduction
125(1)
SOP 4.2.2 Experimental
126(5)
SOP 4.2.3 References
131(4)
5 Nucleic Acid Extraction
135(28)
Elke Dittmann
Anne Rantala-Ylinen
Vitor Ramos
Vitor Vasconcelos
Guntram Christiansen
Rainer Kurmayer
5.1 Introduction
135(2)
5.2 Specific Extraction Procedures and Storage
137(2)
5.2.1 DNA Extraction from Laboratory Strains
137(1)
5.2.2 DNA Extraction from Field Samples
137(1)
5.2.3 DNA Extraction from Food Supplements
137(1)
5.2.4 RNA Extraction from Laboratory Strains
138(1)
5.2.5 RNA Extraction from Field Samples
138(1)
5.2.6 Single Colony and Filament Analysis
138(1)
5.2.7 Whole Genome Amplification
139(1)
5.2.8 Nucleic Acid Storage
139(1)
5.3 References
139(24)
SOP 5.1 Standard DNA Isolation Technique for Cyanobacteria
140(1)
Elke Dittmann
SOP 5.1.1 Introduction
140(1)
SOP 5.1.2 Experimental
140(1)
SOP 5.1.3 Procedure
141(1)
SOP 5.1.4 Notes
141(1)
SOP 5.1.5 References
142(1)
SOP 5.2 DNA Isolation Protocol for Cyanobacteria with Extensive Mucilage
143(1)
Guntram Christiansen
Elisabeth Entfellnei
Rainer Kurmayer
SOP 5.2.1 Introduction
143(1)
SOP 5.2.2 Experimental
143(1)
SOP 5.2.3 Procedure
144(1)
SOP 5.2.4 Notes
145(1)
SOP 5.2.5 References
145(1)
SOP 5.3 Quantitative DNA Isolation from Filters
145(1)
Rainer Kurmayer
SOP 5.3.1 Introduction
146(1)
SOP 5.3.2 Experimental
146(1)
SOP 5.3.3 Procedure
147(1)
SOP 5.3.4 Notes
148(1)
SOP 5.3.5 References
148(1)
SOP 5.4 Genomic DNA Extraction from Single Filaments/Colonies for Multiple PCR Analyses
149(1)
Guntram Christiansen
Chen Qin
Rainer Kurmayer
SOP 5.4.1 Introduction
149(1)
SOP 5.4.2 Experimental
149(1)
SOP 5.4.3 Procedure
150(1)
SOP 5.4.4 Notes
151(1)
SOP 5.4.5 References
151(1)
SOP 5.5 "Whole Genome Amplification Using Bacteriophage Phi29 DNA Polymerase
151(1)
Guntram Christiansen
Rainer Kurmayer
SOP 5.5.1 Introduction
151(1)
SOP 5.5.2 Experimental
152(1)
SOP 5.5.3 Procedure
152(1)
SOP 5.5.4 Notes
152(1)
SOP 5.5.5 Reference
153(1)
SOP 5.6 DNA Extraction from Food Supplements
153(1)
Vitor Ramos
Cristiana Moreira
Vitor Vasconcelos
SOP 5.6.1 Introduction
153(1)
SOP 5.6.2 Experimental
153(1)
SOP 5.6.3 Procedure
154(1)
SOP 5.6.4 Notes
155(1)
SOP 5.6.5 References
156(1)
SOP 5.7 RNA Extraction from Cyanobacteria
156(1)
Guntram Christiansen
Rainer Kurmayer
SOP 5.7.1 Introduction
156(1)
SOP 5.7.2 Experimental
156(2)
SOP 5.7.3 Procedure
158(1)
SOP 5.7.4 Notes
158(1)
SOP 5.7.5 References
159(1)
SOP 5.8 cDNA Synthesis
159(1)
Guntram Christiansen
Rainer Kurmayer
SOP 5.8.1 Introduction
159(1)
SOP 5.8.2 Experimental
159(1)
SOP 5.8.3 Procedure
160(1)
SOP 5.8.4 Notes
161(1)
SOP 5.8.5 References
161(2)
6 Conventional PCR
163(42)
Elke Dittmann
Anne Rantala-Ylinen
Kaarina Sivonen
Ilona Gagala
Joanna Mankiewicz-Boczek
Samuel Cires
Andreas Ballot
Guntram Christiansen
Rainer Kurmayer
Vitor Ramos
Vitor Vasconcelos
Martin Saker
6.1 Introduction
163(1)
6.2 Principle of PCR and Available Enzymes
164(6)
6.2.1 Primer Development
165(3)
6.2.2 Setup of PCR Conditions for DNA and Single Colony Analysis
168(1)
6.2.3 Gel Electrophoresis and Documentation
168(1)
6.2.4 Troubleshooting of PCR Results
168(1)
6.2.5 PCR Product Downstream Processing (RFLP, Cloning, Sequencing)
169(1)
6.3 Special Notes
170(1)
6.4 References
170(35)
SOP 6.1 PCR Detection of Microcystin Biosynthesis Genes Combined with RFLP Differentiation of the Producing Genus
172(1)
Elke Dittmann
SOP 6.1.1 Introduction
172(1)
SOP 6.1.2 Experimental
172(1)
SOP 6.1.3 Procedure
173(1)
SOP 6.1.4 Notes
174(1)
SOP 6.1.5 Reference
174(1)
SOP 6.2 PCR Detection of Microcystin and Nodularin Biosynthesis Genes in the Cyanobacterial Orders Oscillatoriales, Chroococcales, Stigonematales, and Nostocales
175(1)
Elke Dittmann
Joanna Mankiewicz-Boczek
Ilona Gagala
SOP 6.2.1 Introduction
175(1)
SOP 6.2.2 Experimental
175(2)
SOP 6.2.3 Procedure
177(1)
SOP 6.2.4 Notes
177(1)
SOP 6.2.5 References
178(1)
SOP 6.3 Genus-Specific PCR Detection of Microcystin Biosynthesis Genes in Anabaena/Nodularia and Microcystis and Planktothrix, Respectively
179(1)
Anne Rantala-Ylinen
Kaarina Sivonen
SOP 6.3.1 Introduction
179(1)
SOP 6.3.2 Experimental
179(2)
SOP 6.3.3 Procedure
181(1)
SOP 6.3.4 Notes
181(1)
SOP 6.3.5 References
181(1)
SOP 6.4 PCR Detection of Anatoxin Biosynthesis Genes Combined with RFLP Differentiation of the Producing Genus
182(1)
Anne Rantala-Ylinen
Kaarina Sivonen
SOP 6.4.1 Introduction
182(1)
SOP 6.4.2 Experimental
182(1)
SOP 6.4.3 Procedure
183(1)
SOP 6.4.4 Notes
184(1)
SOP 6.4.5 Reference
184(1)
SOP 6.5 PCR Detection of the Saxitoxin Biosynthesis Genes, sxtA, sxtX, sxtR, sxtG, and sxtI
185(1)
Andreas Ballot
Samuel Cires
SOP 6.5.1 Introduction
185(2)
SOP 6.5.2 Experimental
187(1)
SOP 6.5.3 Procedure
187(1)
SOP 6.5.4 Notes
188(1)
SOP 6.5.5 References
189(1)
SOP 6.6 PCR Detection of the Cylindrospermopsin Biosynthesis Gene cyrJ
189(1)
Samuel Cires
Andreas Ballot
SOP 6.6.1 Introduction
189(1)
SOP 6.6.2 Experimental
190(1)
SOP 6.6.3 Procedure
191(1)
SOP 6.6.4 Notes
191(1)
SOP 6.6.5 References
192(1)
SOP 6.7 PCR from Single Filament of Toxigenic Planktothrix
193(1)
Qin Chen
Guntram Christiansen
Rainer Kurmayer
SOP 6.7.1 Introduction
193(1)
SOP 6.7.2 Experimental
193(1)
SOP 6.7.3 Procedure
194(1)
SOP 6.7.4 Notes
195(1)
SOP 6.7.5 References
195(1)
SOP 6.8 Analysis of Microcystin Biosynthesis Gene Subpopulation Variability in Planktothrix
196(1)
Rentier Kurmayer
SOP 6.8.1 Introduction
196(1)
SOP 6.8.2 Experimental
196(1)
SOP 6.8.3 Procedure
197(1)
SOP 6.8.4 Notes
197(1)
SOP 6.8.5 References
198(1)
SOP 6.9 PCR Detection of Microcystin Biosynthesis Genes from Food Supplements
199(1)
Vitor Ramos
Cristiana Moreira
Vitor Vasconcelos
SOP 6.9.1 Introduction
199(1)
SOP 6.9.2 Experimental
199(2)
SOP 6.9.3 Procedure
201(1)
SOP 6.9.4 Notes
202(1)
SOP 6.9.5 References
203(2)
7 Quantitative PCR
205(36)
Anne Rantala-Ylinen
Henna Savela
Kaarina Sivonen
Rainer Kurmayer
7.1 Introduction
205(1)
7.2 Primer/Probe Design
206(2)
7.3 Optimization
208(1)
7.4 Absolute Quantification
208(1)
7.5 Relative Quantification
209(1)
7.6 Calibration of qPCR Results
209(1)
7.7 General Conclusions
210(1)
7.8 References
210(31)
SOP 7.1 Optimization of qPCR Assays
211(1)
Rainer Kurmayer
SOP 7.1.1 Introduction
211(1)
SOP 7.1.2 Experimental
211(1)
SOP 7.1.3 Procedure
212(1)
SOP 7.1.4 Notes
213(1)
SOP 7.1.5 References
213(1)
SOP 7.2 Calibration of qPCR Results
214(1)
Rainer Kurmayer
SOP 7.2.1 Introduction
214(1)
SOP 7.2.2 Experimental
214(1)
SOP 7.2.3 Procedure
215(2)
SOP 7.2.4 Notes
217(1)
SOP 7.2.5 References
217(1)
SOP 7.3 Quantification of Potentially Microcystin/Nodularin-Producing
218(1)
Anabaena
Microcystis
Planktothrix
Nodularis Anne Rantala-Ylinen
Kaarina Sivonen
Rainer Kurmayer
SOP 7.3.1 Introduction
218(1)
SOP 7.3.2 Experimental
219(1)
SOP 7.3.3 Procedure
219(2)
SOP 7.3.4 Notes
221(1)
SOP 7.3.5 References
221(1)
SOP 7.4 Relative Quantification of Microcystis or Planktothrix mcy Genotypes Using qPCR
222(1)
Rainer Kurmayer
SOP 7.4.1 Introduction
222(1)
SOP 7.4.2 Experimental
222(2)
SOP 7.4.3 Procedure
224(1)
SOP 7.4.4 Notes
225(1)
SOP 7.4.5 References
225(1)
SOP 7.5 Quantification of Transcript Amounts of mcy Genes in Planktothrix
226(1)
Guntram Christiansen
Rainer Kurmayer
SOP 7.5.1 Introduction
226(1)
SOP 7.5.2 Experimental
226(1)
SOP 7.5.3 Procedure
227(1)
SOP 7.5.4 Notes
228(1)
SOP 7.5.5 References
228(1)
SOP 7.6 Quantification of Potentially Cylindrospermopsin-Producing Chrysosporum ovalisporum
229(1)
Rehab El-Shehawy
Antonio Quesada
SOP 7.6.1 Introduction
229(1)
SOP 7.6.2 Experimental
229(1)
SOP 7.6.3 Procedure
230(1)
SOP 7.6.4 Notes
231(1)
SOP 7.6.5 References
231(1)
SOP 7.7 qPCR Detection of the Paralytic Shellfish Toxin Biosynthesis Gene sxtB
231(1)
Henna Savela
SOP 7.7.1 Introduction
231(1)
SOP 7.7.2 Experimental
232(1)
SOP 7.7.3 Procedure
233(1)
SOP 7.7.4 Notes
234(1)
SOP 7.7.5 References
234(1)
SOP 7.8 Application of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) Guidelines to Quantitative Analysis of Toxic Cyanobacteria
234(1)
Henna Savela
SOP 7.8.1 Introduction
234(1)
SOP 7.8.2 Sampling
235(1)
SOP 7.8.3 Sample Preparation and DNA Extraction
235(1)
SOP 7.8.4 Target Information and Oligonucleotide Design
235(3)
SOP 7.8.5 qPCR Protocol
238(1)
SOP 7.8.6 qPCR Validation
239(1)
SOP 7.8.7 Data Analysis
239(1)
SOP 7.8.8 Reference
239(2)
8 DNA (Diagnostic) and cDNA Microarray
241(22)
Anne Rantula-Ylinen
Kaarina Sivonen
Annick Wilmotte
8.1 DNA (Diagnostic) Microarray
241(3)
8.1.1 Introduction
241(1)
8.1.2 Methodological Principles
242(1)
8.1.3 General Conclusions
243(1)
8.1.4 References
243(1)
8.2 cDNA Microarray for Cyanobacteria
244(19)
Hans C.P. Matthijs
J. Merijn Schuurmans
8.2.1 Introduction
244(1)
8.2.2 Principles of Microarray Use
244(1)
8.2.3 Considerations for Experimental Design
245(1)
8.2.4 Microarray: Practical Approach
246(1)
8.2.5 Microarray: Data Analysis
246(1)
8.2.6 References
246(2)
SOP 8.1 DNA-Chip Detection of Potential Microcystin and Nodularin Producing Cyanobacteria in Environmental Water Samples
248(1)
Anne Rantala-Ylinen
Kaarina Sivonen
SOP 8.1.1 Introduction
248(1)
SOP 8.1.2 Experimental
249(1)
SOP 8.1.3 Procedure
250(3)
SOP 8.1.4 Notes
253(1)
SOP 8.1.5 References
253(1)
SOP 8.2 cDNA Microarrays for Cyanobacteria
254(1)
J. Merijn Schuurmans
Hans C.P. Matthijs
SOP 8.2.1 Introduction
254(1)
SOP 8.2.2 Experimental
254(2)
SOP 8.2.3 Procedure
256(3)
SOP 8.2.4 Notes
259(2)
SOP 8.2.5 Reference
261(2)
9 Analysis of Toxigenic Cyanobacterial Communities through Denaturing Gradient Gel Electrophoresis
263(14)
Iwona Jasser
Aleksandra Bukowska
Jean-Francois Humbert
Kaisa Haukka
David P. Fewer
9.1 Introduction
263(1)
9.2 Main Applications of the Method
264(1)
9.3 Possible Applications
264(1)
9.4 DGGE Procedure
265(2)
9.5 General Conclusions Including Pros and Cons of the Method
267(1)
9.6 Optimization of the Method and Troubleshooting
267(1)
9.7 References
268(9)
SOP 9.1 DGGE-mryA Conditions
270(1)
Aleksandra Bukowska
Iwona Jasser
SOP 9.1.1 Introduction
270(1)
SOP 9.1.2 Experimental
270(2)
SOP 9.1.3 Procedure
272(3)
SOP 9.1.4 Notes
275(1)
SOP 9.1.5 References
275(2)
10 Monitoring of Toxigenic Cyanobacteria Using Next-Generation Sequencing Techniques
277(24)
Li Deng
Maxiine Sweetlove
Stephan Blank
Dagmar Obbels
Elie Verleyen
Wim Vyverman
Rainer Kurmayer
10.1 Introduction
277(2)
10.2 Specific Procedures
279(4)
10.2.1 16S rRNA Gene Amplicon Library Preparation
279(1)
10.2.2 Amplicon Purification, Quantification and Pooling
280(1)
10.2.3 Sequencing
280(1)
10.2.4 Bioinformatic Exploration of Sequencing Results
281(1)
10.2.5 General Conclusions Including Pros and Cons of the Method
281(1)
10.2.6 References
281(2)
10.3 Bioinformatic Processing of Amplicon Sequencing Datasets
283(3)
Maxime Sweetlove
Dagmar Obbels
Elie Verleyen
Igor S. Pessi
Annick Wilmotte
Wim Vyverman
10.3.1 Introduction
283(1)
10.3.2 Sequencing Platforms
283(1)
10.3.3 Data Formats
284(1)
10.3.4 Error Associated with NGS Data
285(1)
10.3.5 OTU Delineation: Choosing a Similarity Threshold
286(1)
10.3.6 Conclusions
286(1)
10.4 References
286(15)
SOP 10.1 Standard Technique to Generating 16S rRNA PCR Amplicons for NGS
288(1)
Li Deng
Stephan Blank
Guntram Christiansen
Rainer Kurmayer
SOP 10.1.1 Introduction
288(1)
SOP 10.1.2 Experimental
288(1)
SOP 10.1.3 Procedure
289(1)
SOP 10.1.4 Notes
290(1)
SOP 10.1.5 References
290(1)
SOP 10.2 Bioinformatics Analysis for NGS Amplicon Sequencing
291(1)
Maxime Sweetlove
Dagmar Obbels
Elie Verleyen
Igor S. Pessi
Annick Wilmotte
Wim Vyverman
SOP 10.2.1 Introduction
291(1)
SOP 10.2.2 Experimental
291(7)
SOP 10.2.3 Practical Tips and Alternatives for Quality Filtering
298(1)
SOP 10.2.4 References
298(3)
11 Application of Molecular Tools in Monitoring Cyanobacteria and Their Potential Toxin Production
301(34)
Vitor Ramos
Cristiana Moreira
Joanna Mankiewicz-Boczek
Vitor Vasconcelos
11.1 Introduction
301(2)
11.2 Possible Applications
303(12)
11.3 Checklist of Publications, Applications and Lessons from Practice
315(6)
11.3.1 Molecular-Based Studies on (Toxic) Cyanobacteria: Overview of Methods Being Used, and Generic Findings and Concerns
315(1)
11.3.2 The Need for Complementary Approaches
316(1)
11.3.3 Interpreting Results
316(1)
11.3.4 Choice of Molecular Tools for Toxigenicity Assessment
317(1)
11.3.5 Common and Possible Applications of Molecular Tools
318(3)
11.4 General Conclusions
321(3)
11.5 Acknowledgments
324(1)
11.6 References
324(11)
Appendix: Supplementary Tables 335(41)
Cyanobacterial Species Cited in the Book 376(3)
Glossary 379(14)
Index 393
EDITED BY RAINER KURMAYER, PhD, is an Associate Professor at the University of Innsbruck, Research Institute for Limnology, Mondsee, Austria.

KAARINA SIVONEN, PhD, is a Professor of Microbiology at the University of Helsinki, Finland.

ANNICK WILMOTTE, PhD, is a FRS-FNRS Research Associate at InBios Center for Protein Engineering, University of Liège, Belgium.

NICO SALMASO, PhD, is Head of the Hydrobiology Unit of the Istituto Agrario di S. Michele All'Adige, Fondazione E. Mach (FEM), Trento, Italy.
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