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Current Protocols in Microbiology

Current Protocols in Microbiology

Online ISBN: 9780471729259

DOI: 10.1002/9780471729259

Browse by Table of Contents

Foreword
Preface
Selected Suppliers of Reagents and Equipment
Chapter 1 Technologies
1. Introduction
2. Section A Safety
3. Section B Biofilms
4. Section C Quorum Sensing
5. Section D PCR Techniques
6. Section E Genomic Methods
7. Section F Protein and Proteomic Methods
8. Section G Bioremediation
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    UNIT 1G.1 Biological Sand Filters: Low-Cost Bioremediation Technique for Production of Clean Drinking Water
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    UNIT 1G.2 Bioremediation of Turbid Surface Water Using Seed Extract from the Moringa oleifera Lam. (Drumstick) Tree
Chapter 2 Microscopy and Imaging
1. Introduction
2. Section A Light Microscopy
  1. UNIT 2A.1 Proper Alignment and Adjustment of the Light Microscope
  2. UNIT 2A.2 Total Internal Reflection Fluorescence (TIRF) Microscopy
3. Section B Electron Microscopy
  1. UNIT 2B.1 Transmission Electron Microscopy
  2. UNIT 2B.2 Scanning Electron Microscopy
4. Section C Other Imaging Methods
Chapter 3 Alpha Proteobacteria
1. Introduction
2. Section A Rickettsiales
3. Section B Brucella
  1. UNIT 3B.1 Laboratory Maintenance of Brucella abortus
4. Section C Bartonella
  1. UNIT 3C.1 Laboratory Maintenance of Bartonella quintana
5. Section D Rhizobiales
Chapter 4 Beta Proteobacteria
1. Introduction
2. Section A Neisseria gonorrhoeae
3. Section B Bordetella
  1. UNIT 4B.1 Laboratory Maintenance of Bordetella pertussis
4. Section C Burkholderia
  1. UNIT 4C.1 Burkholderia thailandensis: Growth and Laboratory Maintenance
  2. UNIT 4C.2 Burkholderia thailandensis: Genetic Manipulation
Chapter 5 Enteric Gamma Proteobacteria
1. Introduction
2. Section A Escherichia coli
3. Section B Yersinia
Chapter 6 Nonenteric Gamma Proteobacteria
1. Introduction
2. Section A Vibrionales
3. Section B Moraxella
  1. UNIT 6B.1 Laboratory Maintenance of Moraxella catarrhalis
4. Section C Coxiella
  1. UNIT 6C.1 Laboratory Maintenance of Coxiella burnetii
5. Section D Pasturella
  1. UNIT 6D.1 Laboratory Growth and Maintenance of Haemophilus influenzae
6. Section E Pseudomonas
  1. UNIT 6E.1 Growth and Laboratory Maintenance of Pseudomonas aeruginosa
7. Section F Stenotrophomonas
  1. UNIT 6F.1 Laboratory Culture and Maintenance of Stenotrophomonas maltophilia
  2. UNIT 6F.2 Genetic Manipulation of Stenotrophomonas maltophilia
8. Section G Acinetobacter
  1. UNIT 6G.1 Laboratory Maintenance of Acinetobacter baumannii
  2. UNIT 6G.2 Genetic Manipulation of Acinetobacter baumannii
Chapter 7 Delta Proteobacteria
1. Introduction
2. Section A Myxococcaceae
  1. UNIT 7A.1 Myxococcus xanthus Growth, Development, and Isolation
3. Section B Bdellovibrionales
Chapter 8 Epsilon Proteobacteria
1. Introduction
2. Section A Campylobacter
3. Section B Helicobacter
  1. UNIT 8B.1 Laboratory Maintenance of Helicobacter Species
Chapter 9 Firmicutes (Low G+C Gram Positive)
1. Introduction
2. Section A Clostridiae
3. Section B Listeria
4. Section C Staphylococcus
5. Section D Streptococcus
Chapter 10 Actinobacteria (High G+C Gram Positive)
1. Introduction
2. Section A Mycobacterium tuberculosis
3. Section B Mycobacterium marinum
  1. UNIT 10B.1 Laboratory Maintenance of Mycobacterium marinum
  2. UNIT 10B.2 Zebrafish and Frog Models of Mycobacterium marinum Infection
4. Section C Mycobacterium smegmatis
  1. UNIT 10C.1 Laboratory Maintenance of Mycobacterium smegmatis
5. Section D Mycobacterium abscessus
  1. UNIT 10D.1 Laboratory Maintenance of Mycobacterium abscessus
  2. UNIT 10D.2 Genetic Manipulation of Mycobacterium abscessus
6. Section E Streptomyces
7. Section F Nocardia Species
  1. UNIT 10F.1 Laboratory Maintenance of Nocardia Species
  2. UNIT 10F.2 Genetic Manipulation of Nocardia Species
8. Section G Micromonosporaceae Species
  1. UNIT 10G.1 Actinomadura Species: Laboratory Maintenance and Ribosome Engineering
9. Section H Pseudonocardiaceae Species
  1. UNIT 10H.1 Saccharopolyspora Species: Laboratory Maintenance and Enhanced Production of Secondary Metabolites
Chapter 11 Chlamydiae
1. Introduction
2. Section A Chlamydia trachomatis
3. Section B Chlamydia pneumoniae
  1. UNIT 11B.1 Cultivation and Laboratory Maintenance of Chlamydia pneumoniae
Chapter 12 Spirochetes
1. Introduction
2. UNIT 12.1 Analysis of Bacterial Membrane Proteins Produced During Mammalian Infection Using Hydrophobic Antigen Tissue Triton Extraction (HATTREX)
3. Section A Treponema pallidum and Related Treponemes
  1. UNIT 12A.1 Isolation and Laboratory Maintenance of Treponema pallidum
4. Section B Oral Treponemes
  1. UNIT 12B.1 Laboratory Maintenance of Treponema denticola
  2. UNIT 12B.2 Genetic Manipulation of Treponema denticola
5. Section C Lyme Disease Borrelia
6. Section D Brachyspira
  1. UNIT 12D.1 Isolation and Maintenance of Brachyspira Species
7. Section E Leptospira
8. Section F Hard Tick Relapsing Fever Borrelia
  1. UNIT 12F.1 Laboratory Cultivation and Maintenance of Borrelia miyamotoi
Chapter 13 Other Eubacteria
1. Introduction
2. Section A Fusobacteria
  1. UNIT 13A.1 Laboratory Maintenance of Fusobacteria
3. Section B Flavobacterium
  1. UNIT 13B.1 Laboratory Maintenance of Flavobacterium psychrophilum and Flavobacterium columnare
4. Section C Bacteroides
  1. UNIT 13C.1 Laboratory Maintenance and Cultivation of Bacteroides Species
  2. UNIT 13C.2 Genetic Manipulation of Porphyromonas gingivalis
Chapter 14 DNA Viruses
1. Introduction
2. Section A Pox Viruses
3. Section B Papillomaviruses
4. Section C Adenoviruses
  1. UNIT 14C.1 Human Adenoviruses: Propagation, Purification, Quantification, and Storage
5. Section D Adeno-Associated Viruses
6. Section E Herpesviruses
7. Section F Polyoma Viruses
  1. UNIT 14F.1 Mouse Polyomavirus: Propagation, Purification, Quantification, and Storage
  2. UNIT 14F.2 In Vitro Replication Assay for Merkel Cell Polyomavirus (MCPyV)
8. Section G Mimiviridae
  1. UNIT 14G.1 Mimiviruses: Replication, Purification, and Quantification
Chapter 15 RNA Viruses
1. Introduction
2. Section A Arenaviruses
  1. UNIT 15A.1 Lymphocytic Choriomeningitis Virus (LCMV): Propagation, Quantitation, and Storage
3. Section B Alphaviruses
  1. UNIT 15B.1 Sindbis Virus: Propagation, Quantification, and Storage
4. Section C Reoviruses
5. Section D Flaviviruses
6. Section E Coronaviruses
  1. UNIT 15E.1 Coronaviruses: Propagation, Quantification, Storage, and Construction of Recombinant Mouse Hepatitis Virus
  2. UNIT 15E.2 Growth and Quantification of MERS-CoV Infection
7. Section F Paramyxoviruses
  1. UNIT 15F.1 Human Parainfluenza Virus Type 3 (HPIV-3): Construction and Rescue of an Infectious, Recombinant Virus Expressing the Enhanced Green Fluorescent Protein (EGFP)
  2. UNIT 15F.2 Newcastle Disease Virus: Propagation, Quantification, and Storage
8. Section G Orthomyxoviruses
9. Section H Picornaviruses
10. Section I Bornaviruses
  1. UNIT 15I.1 Avian Bornaviruses: Diagnosis, Isolation, and Genotyping
11. Section J Retroviruses
  1. UNIT 15J.1 Human Immunodeficiency Viruses: Propagation, Quantification, and Storage
12. Section K Caliciviruses
  1. UNIT 15K.1 Human Norovirus Detection and Production, Quantification, and Storage of Virus-Like Particles
  2. UNIT 15K.2 Murine Norovirus: Propagation, Quantification, and Genetic Manipulation
Chapter 16 Plant Viruses
1. Introduction
2. Section A Plant Propagation for Virus Infection
  1. UNIT 16A.1 Growth Conditions for Plant Virus–Host Studies
  2. UNIT 16A.2 Propagation of Major Plant-Virus Hosts
3. Section B Plant Inoculation Methods
4. Section C Methods of Virus Detection
  1. UNIT 16C.1 Reverse Transcription-Polymerase Chain Reaction-Based Detection of Plant Viruses
5. Section D Preparation and Inoculation of Protoplasts
6. Section E Methodologies to Extract and Study Viral RNA
  1. UNIT 16E.1 Extracting Viral RNAs from Plant Protoplasts
  2. UNIT 16E.3 Northern Analysis of Viral Plus- and Minus-Strand RNAs
7. Section F Cloning Full-Length RNA Viruses
  1. UNIT 16F.1 Cloning of Large Positive-Strand RNA Viruses
  2. UNIT 16F.3 Rapid Full-Length Cloning of Nonpolyadenylated RNA Virus Genomes
8. Section G Viroids
  1. UNIT 16G.1 Identification of Viroids by Gel Electrophoresis
9. Section H RNA Silencing
  1. UNIT 16H.2 Isolation and Cloning of Small RNAs from Virus-Infected Plants
10. Section I Viral Vector Methodologies
11. Section J Expression of Viruses in Yeast
  1. UNIT 16J.1 A High-Throughput Approach for Studying Virus Replication in Yeast
12. Section K Translation of Plant Viral RNA
  1. UNIT 16K.1 In Vitro Translation of Plant Viral RNA
  2. UNIT 16K.2 In Vivo Translation Studies of Plant Viral RNAs Using Reporter Genes
Chapter 17 Anti-Infectives
1. Introduction
2. UNIT 17.1 Characterization of the In Vitro Activity of Novel Lipoglycopeptide Antibiotics
3. UNIT 17.2 Structure-Based Approaches to Antibiotic Drug Discovery
4. UNIT 17.3 Novel Approaches to Bacterial Infection Therapy by Interfering with Cell-to-Cell Signaling
5. UNIT 17.4 Identification of Small-Molecule Scaffolds for P450 Inhibitors
6. UNIT 17.5 Cell-Based Hepatitis C Virus Infection Fluorescence Resonance Energy Transfer (FRET) Assay for Antiviral Compound Screening
7. UNIT 17.6 Laboratory Detection of Vancomycin Nonsusceptible Staphylococcus aureus
8. UNIT 17.7 Screening of Hepatitis C Virus Inhibitors Using Genotype 1a HCV Replicon Cell Lines
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  UNIT 17.8 HT-SPOTi: A Rapid Drug Susceptibility Test (DST) to Evaluate Antibiotic Resistance Profiles and Novel Chemicals for Anti-Infective Drug Discovery
10. UNIT 17.9 Aminoglycoside-Enabled Elucidation of Bacterial Persister Metabolism
Chapter 18 Vaccines
1. UNIT 18.1 Progress in Vaccine Development
2. UNIT 18.2 Newcastle Disease Virus-Like Particles: Preparation, Purification, Quantification, and Incorporation of Foreign Glycoproteins
3. UNIT 18.3 DNA Immunization
4. UNIT 18.4 Western Blot Assay for Quantitative and Qualitative Antigen Detection in Vaccine Development
Chapter 19 Mycology
1. Section A Mycology
  1. UNIT 19A.1 Detection and Isolation of Epichloë Species, Fungal Endophytes of Grasses
Chapter 20 Parasitic Protozoa
1. Section A Blastocystis
  1. UNIT 20A.1 Blastocystis: Isolation, Xenic Cultivation, and Cryopreservation
  2. UNIT 20A.2 Molecular Identification and Subtype Analysis of Blastocystis
2. Section B Cryptosporidium
  1. UNIT 20B.1 Cryptosporidium: Identification and Genetic Typing
3. Section C Toxoplasma
  1. UNIT 20C.1 Toxoplasma gondii: Laboratory Maintenance and Growth
  2. UNIT 20C.2 Purification Toxoplasma gondii Tissue Cysts Using Percoll Gradients
4. Section D Sarcocystis
  1. UNIT 20D.1 Isolation, Culture and Cryopreservation of Sarcocystis species
Chapter 21 Protists
1. Section A Oomycetes
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    UNIT 21A.1 Efficient Genome Editing in the Oomycete Phytophthora sojae Using CRISPR/Cas9
Appendix 1 Useful Information and Data
1. APPENDIX 1A Abbreviations Used in this Manual
2. APPENDIX 1B Resources for International Biosafety Guidelines and Regulations
Appendix 2 Commonly Used Reagents and Equipment
1. APPENDIX 2A Commonly Used Reagents
2. APPENDIX 2B Standard Laboratory Equipment
3. APPENDIX 2C Where to Find Recipes for Media
Appendix 3 Commonly Used Techniques
1. APPENDIX 3A Assays for Total Protein
2. APPENDIX 3B Diagnosis and Treatment of Mycoplasma-Contaminated Cell Cultures
3. APPENDIX 3C Differential Staining of Bacteria: Gram Stain
4. APPENDIX 3D Direct PCR of Intact Bacteria (Colony PCR)
5. APPENDIX 3E Preliminary Staining of Bacteria: Simple Stains
6. APPENDIX 3F Preliminary Staining of Bacteria: Negative Stain
7. APPENDIX 3G Differential Staining of Bacteria: Flagella Stain
8. APPENDIX 3H Differential Staining of Bacteria: Acid Fast Stain
9. APPENDIX 3I Differential Staining of Bacteria: Capsule Stain
10. APPENDIX 3J Differential Staining of Bacteria: Endospore Stain
11. APPENDIX 3K Fluorescent Staining of Bacteria: Viability and Antibody Labeling
12. APPENDIX 3L Generation of Transformation Competent E. coli
13. APPENDIX 3M SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) of Proteins
14. APPENDIX A.3N Care and Handling of Laboratory Mice
Appendix 4 Commonly Used Methods for Cell Culture
1. APPENDIX 4A Common Bacterial Culture Techniques and Media
2. APPENDIX 4B Isolation and Culture of Human Umbilical Vein Endothelial Cells (HUVEC)
3. APPENDIX 4C Isolation of Human Peripheral Blood Mononuclear Cells (PBMCs)
4. APPENDIX 4D Aseptic Technique
5. APPENDIX 4E Growth and Maintenance of Vero Cell Lines
6. APPENDIX 4F Anaerobic Cell Culture
7. APPENDIX 4G Growth and Maintenance of Quail Fibrosarcoma QM5 Cells
8. APPENDIX 4H Growth and Maintenance of Baby Hamster Kidney (BHK) Cells
9. APPENDIX 4I Growth and Maintenance of Chick Embryo Fibroblasts (CEF)
10. APPENDIX 4J Growth and Maintenance of Mosquito Cell Lines
11. APPENDIX A.4K A Simple and Low-Cost Procedure for Growing Geobacter sulfurreducens Cell Cultures and Biofilms in Bioelectrochemical Systems