Molecular tools for the detection and quantification of toxigenic cyanobacteria. (2017)

• Record Type: Book
• Further Information: Note: Edited by Rainer Kurmayer, Kaarina Sivonen, Annick Wilmotte, Nico Salmaso.
• Editors: Kurmayer, Rainer, 1969-; Sivonen, Kaarina, 1954-; Wilmotte, Annick, 1960-; Salmaso, Nico
• Contents: List of Contributors xix About the Editors xxiii About the Book xxvii Preface xxix Acknowledgments xxxi 1 Introduction 1; Rainer Kurmayer, Kaarina Sivonen, and Nico Salmaso 1.1 A Brief Historical Overview 1 1.2 The Genetic Basis of Toxin Production 2 1.2.1 Microcystin and Nodularin 2 1.2.2 Cylindrospermopsin 5 1.2.3 Saxitoxin 6 1.2.4 Anatoxin 8 1.3 Application of Molecular Tools 8 1.4 Laboratory Safety Issues 13 1.5 References 14 2 Sampling and Metadata 19; Rainer Kurmayer, Guntram Christiansen, Konstantinos Kormas, Wim Vyverman, Elie Verleyen, Vitor Ramos, Vitor Vasconcelos, and Nico Salmaso 2.1 Introduction 19 2.2 Handling of Samples 20 2.3 Sample Contamination 21 2.4 Sampling 21 2.4.1 Quantitative Depth-Integrated and Discrete Sampling 21 2.4.2 Qualitative Plankton Net Sampling 22 2.4.3 Surface (Scum Material) Sampling 22 2.4.4 Benthic (Terrestrial) Cyanobacteria Sampling 22 2.4.5 Food Supplement Sampling 22 2.4.6 Isolation of Single Colonies/Filaments 22 2.5 Subsampling Food Supplement Samples 23 2.6 Sampling of Nucleic Acids 23 2.7 General Conclusions 24 2.8 References 24 SOP 2.1 Sampling and Filtration (DNA) 26; Rainer Kurmayer and Konstantinos Kormas SOP 2.1.1 Introduction 26 SOP 2.1.2 Experimental 26 SOP 2.1.3 Procedure 27 SOP 2.1.4 Notes 28 SOP 2.1.5 References 29 SOP 2.2 Sampling of Benthic Cyanobacteria 29; Wim Vyverman and Elie Verleyen SOP 2.2.1 Introduction 29 SOP 2.2.2 Experimental 30 SOP 2.2.3 Procedure 30 SOP 2.2.4 Notes 31 SOP 2.2.5 References 31 SOP 2.3 Isolation of Single Cyanobacteria Colonies/Filaments 32 Rainer Kurmayer SOP 2.3.1 Introduction 32 SOP 2.3.2 Experimental 32 SOP 2.3.3 Procedure 33 SOP 2.3.4 Notes 33 SOP 2.3.5 References 33 SOP 2.4 Sampling Food Supplements 34; Vitor Ramos, Cristiana Moreira, and Vitor Vasconcelos SOP 2.4.1 Introduction 34 SOP 2.4.2 Experimental 35 SOP 2.4.3 Procedure (Fig. 8.3) 35 SOP 2.4.4 Notes 36 SOP 2.4.5 References 36 SOP 2.5 Sampling and Filtration (RNA) 37; Rainer Kurmayer and Guntram Christiansen SOP 2.5.1 Introduction 37 SOP 2.5.2 Experimental 37 SOP 2.5.3 Procedure 38 SOP 2.5.4 Notes 38 SOP 2.5.5 References 38 SOP 2.6 Sampling of Abiotic and Biotic Data and Recording Metadata 39; Elie Verleyen, Maxime Sweetlove, Dagmar Obbels, and Wim Vyverman SOP 2.6.1 Introduction 39 SOP 2.6.2 Experimental 39 SOP 2.6.3 Type of Metadata and Additional Biotic and Abiotic Data 40 SOP 2.6.4 Notes 41 SOP 2.6.5 References 42 3 Isolation, Purification, and Cultivation of Toxigenic Cyanobacteria 43; Sigrid Haande, Iwona Jasser, Muriel Gugger, Camilla H.C. Hagman, Annick Wilmotte, and Andreas Ballot 3.1 Introduction 43 3.2 Methodical Principles for Cyanobacterial Isolation, Purification, and Cultivation 44 3.2.1 Sampling, Identification, and Treatments Prior to the Isolation of Cyanobacteria 44 3.2.2 Traditional Techniques for the Isolation and Purification of Cyanobacteria 45 3.2.3 Culture Media Preparation 47 3.2.4 Cultivation Conditions 48 3.3 General Conclusions 49 3.4 References 49 SOP 3.1 Isolation, Purification, and Clonal Isolate Testing 51; Sigrid Haande, Camilla H.C. Hagman, and Andreas Ballot SOP 3.1.1 Introduction 51 SOP 3.1.2 Experimental 51 SOP 3.1.3 Procedure 52 SOP 3.1.4 Notes 54 SOP 3.1.5 References 54 SOP 3.2 Isolation of Picocyanobacterial Cells by Flow Cytometer (FCM) Sorting 55; Ewa Koz³owska and Iwona Jasser SOP 3.2.1 Introduction 55 SOP 3.2.2 Experimental 56 SOP 3.2.3 Procedure 56 SOP 3.2.4 Notes 58 SOP 3.2.5 References 59 SOP 3.3 Axenization 60; Muriel Gugger SOP 3.3.1 Introduction 60 SOP 3.3.2 Experimental 60 SOP 3.3.3 Procedure 61 SOP 3.3.4 Notes 63 SOP 3.3.5 References 63 SOP 3.4 Culture Media (Solid and Liquid) 64; Sigrid Haande, Camilla H.C. Hagman, and Andreas Ballot SOP 3.4.1 Introduction 64 SOP 3.4.2 Experimental 64 SOP 3.4.3 Procedure 65 SOP 3.4.4 Notes 68 SOP 3.4.5 References 68 SOP 3.5 Strain Maintenance (Living Cultures) 69; Sigrid Haande, Camilla H.C. Hagman, and Andreas Ballot SOP 3.5.1 Introduction 69 SOP 3.5.2 Experimental 69 SOP 3.5.3 Procedure 70 SOP 3.5.4 Notes 72 SOP 3.5.5 References 73 SOP 3.6 Cryopreservation and Recovery 73; Muriel Gugger SOP 3.6.1 Introduction 73 SOP 3.6.2 Experimental 74 SOP 3.6.3 Procedure 75 SOP 3.6.4 Notes 78 SOP 3.6.5 References 78 4 Taxonomic Identification of Cyanobacteria by a Polyphasic Approach 79; Annick Wilmotte, H. Dail Laughinghouse IV, Camilla Capelli, Rosmarie Rippka, and Nico Salmaso 4.1 Introduction 79 4.2 Nomenclature and Classification of Cyanobacteria 82 4.3 Microscopy 84 4.3.1 Light Microscopy 84 4.3.2 Autofluorescence Microscopy 86 4.4 Molecular Markers: Single Loci 87 4.5 Molecular Markers: Multiple Loci 94 4.5.1 Multilocus Sequence Typing (MLST) and Multilocus Sequence Analysis (MLSA) 94 4.5.2 Genome-Based Extension of MLST and MLSA 96 4.6 Molecular Typing Methods Based on Gel Electrophoresis 96 4.7 Denaturing Gradient Gel Electrophoresis (DGGE) 97 4.8 Taxonomic and Molecular Databases 97 4.9 The Polyphasic Approach 98 4.10 Final Considerations 105 4.11 References 106 SOP 4.1 Taxonomic Identification by Light Microscopy 120; Nico Salmaso, Rosmarie Rippka, and Annick Wilmotte SOP 4.1.1 Introduction 120 SOP 4.1.2 Experimental 121 SOP 4.1.3 References 124 SOP 4.2 Polyphasic Approach on Cyanobacterial Strains 125; Nico Salmaso, Camilla Capelli, Rosmarie Rippka, and Annick Wilmotte SOP 4.2.1 Introduction 125 SOP 4.2.2 Experimental 126 SOP 4.2.3 References 131 5 Nucleic Acid Extraction 135; Elke Dittmann, Anne Rantala-Ylinen, Vitor Ramos, Vitor Vasconcelos, Guntram Christiansen, and Rainer Kurmayer 5.1 Introduction 135 5.2 Specific Extraction Procedures and Storage 137 5.2.1 DNA Extraction from Laboratory Strains 137 5.2.2 DNA Extraction from Field Samples 137 5.2.3 DNA Extraction from Food Supplements 137 5.2.4 RNA Extraction from Laboratory Strains 138 5.2.5 RNA Extraction from Field Samples 138 5.2.6 Single Colony and Filament Analysis 138 5.2.7 Whole Genome Amplification 139 5.2.8 Nucleic Acid Storage 139 5.3 References 139 SOP 5.1 Standard DNA Isolation Technique for Cyanobacteria 140; Elke Dittmann SOP 5.1.1 Introduction 140 SOP 5.1.2 Experimental 140 SOP 5.1.3 Procedure 141 SOP 5.1.4 Notes 141 SOP 5.1.5 References 142 SOP 5.2 DNA Isolation Protocol for Cyanobacteria with Extensive Mucilage 143; Guntram Christiansen, Elisabeth Entfellner, and Rainer Kurmayer SOP 5.2.1 Introduction 143 SOP 5.2.2 Experimental 143 SOP 5.2.3 Procedure 144 SOP 5.2.4 Notes 145</p&
• Edition: 1st
• Publisher Details: Hoboken, New Jersey : John Wiley & Sons, Inc
• Publication Date: 2017
• Extent: 1 online resource
• Subjects: 579.39; Cyanobacteria; Cyanobacterial toxins
• Languages: English
• ISBNs: 9781119332145; 9781119332121
• Related ISBNs: 9781119332107
• Notes: Note: Description based on CIP data; resource not viewed.
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