Automation and basic techniques in medical microbiology / / Santi M. Mandal and Debarati Paul

• Record Nr.: UNINA9910561300603321
• Autore: Mandal Santi M.
• Pubbl/distr/stampa: Gateway East, Singapore : , : Springer, , [2022]; ©2022
• ISBN: 1-0716-2372-9
• Descrizione fisica: 1 online resource (213 pages)
• Disciplina: 616.9041
• Soggetti: Medical microbiology; Microbiology - Technique; Microbiologia mèdica; Metodologia de la ciència; Llibres electrònics
• Lingua di pubblicazione: Inglese
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Nota di bibliografia: Includes bibliographical references and index.
• Nota di contenuto: Intro -- Preface -- Acknowledgements -- Contents -- About the Authors -- 1: Good Laboratory Practices -- 1.1 Introduction -- 1.2 Basic Record and Lab Note Book -- 1.3 Laboratory Safety Equipment -- 1.4 Biosafety Levels and Practices -- 2: Automation in Medical Microbiology -- 2.1 Introduction -- 2.2 Applications of Automation -- 2.3 Advantages and Disadvantages -- 2.3.1 Advantages of Using Auto-analysers -- 2.3.2 Disadvantages of Automation -- 2.4 Types of Auto-analysers -- 2.5 History of Auto-analysers -- 2.6 Laboratory Automation and Total Laboratory Automation -- 2.7 Types and Applications of Auto-analysers in Microbiology -- 2.7.1 Microbiological Specimen Processor -- 2.7.2 Routine Biochemistry Analysers -- 2.7.3 Immunology-Based Analysers -- 2.7.4 Haematology Analysers -- 2.7.5 Cell Counter -- 2.7.6 Coagulometer(s) -- 2.7.7 Additional Instrument for Haematology-Based Methods -- 2.7.8 Other Miscellaneous Analysers -- References -- 3: Manual and Automated Characterization of Multi-antibiotic-Resistant (MAR) Bacteria -- 3.1 Introduction -- 3.2 Types of Antibiotic Sensitivity Tests -- 3.2.1 Kirby-Bauer Disc Diffusion Method -- 3.2.2 The Minimum Inhibitory Concentration (MIC) Method ; -- 3.2.3 RAPD PCR Analysis -- 3.2.4 Multiplex PCR -- 3.2.5 Padlock PCR and Microarray Analysis -- 3.2.6 Real-Time PCR for Quantitative Data -- References -- 4: Rapid Microbial Genome Sequencing Techniques and Applications -- 4.1 Introduction -- 4.2 WGS Techniques -- 4.3 Data Analysis -- Protocol for WGS (adapted from Gautam et al. 2019) -- 4.4 Applications -- 4.5 Challenges -- References -- 5: Spectroscopy: Principle, Types and Microbiological Applications -- 5.1 Introduction -- 5.2 General Types of Spectra -- 5.2.1 Continuous Spectra -- 5.2.2 Discrete Spectra -- 5.2.2.1 Emission Line Spectra -- 5.2.2.2 Absorption Line Spectra -- 5.3 Principle of Spectroscopy.; 5.4 Optical Instruments in Spectroscopy -- 5.5 Is Spectroscopy Different from Spectrometry? -- 5.6 Uses of Spectroscopy -- 5.7 Types of Spectroscopy -- 5.7.1 Ultraviolet and Visible Spectroscopy -- 5.7.1.1 Background -- 5.7.1.2 Principle -- 5.7.1.3 Applications of UV-Vis Spectroscopy -- 5.7.1.3.1 Spectroscopy in Environmental Analysis -- 5.7.1.3.2 UV-Vis Spectroscopy for Water Analysis and Environmental Applications -- 5.7.1.3.3 Spectrophotometric Analysis of Bacterial Water Contaminants -- 5.7.1.3.4 Spectrophotometers for Chlorine and Flouride Quantification -- 5.7.1.3.5 UV-Vis Spectroscopy for Geological Studies Linked to Water Contamination -- 5.7.1.3.6 Other Applications -- 5.7.2 Infrared Spectroscopy -- 5.7.2.1 Introduction -- 5.7.2.1.1 Molecular Vibrations and Vibrational Frequency -- 5.7.2.1.1.1 Vibration of Diatomic Molecules -- 5.7.2.1.1.2 Vibrational Transitions -- 5.7.2.1.1.3 Types of Vibrations (Sharma 2007) -- 5.7.2.2 Instrumentation -- 5.7.2.2.1 Source -- 5.7.2.2.2 Sample Types and Preparation -- 5.7.2.2.3 Various Types of Detectors Used -- 5.7.2.3 FTIR (Fourier Transform IR Spectrometers) -- 5.7.2.4 Advantages of FTIR -- 5.7.2.5 Applications of IR Spectroscopy -- 5.7.3 Mass Spectrometry -- 5.7.3.1 The Mass Spectrometer -- 5.7.3.2 The Nature of Mass Spectra -- 5.7.3.3 The Working Principle of a Mass Spectrometer -- 5.7.3.4 Applications of Mass Spectrometry -- 5.7.3.4.1 Analysis of Biomolecules -- 5.7.3.4.2 Analysis of Glycans -- 5.7.3.4.3 Analysis of Lipids -- 5.7.3.4.4 Analysis of Proteins and Peptides -- 5.7.3.4.5 Analysis of Oligonucleotides -- 5.7.4 Nuclear Magnetic Resonance (NMR) Spectroscopy -- 5.7.4.1 NMR Spectrum -- 5.7.4.2 NMR Spectrometers -- 5.7.4.3 Applications of NMR -- 5.8 Applications of Spectroscopy in Microbiology -- References -- 6: MALDI-TOF MS for Bacterial Identification -- 6.1 Introduction.; 6.2 MALDI: Sample Preparation and Analysis -- 6.2.1 Sample Preparation -- 6.2.2 Protein Digestion -- 6.2.3 MALDI/MS Analysis -- 6.3 Uses of MALDI-TOF -- 6.4 MALDI-TOF MS-Based Antimicrobial Susceptibility Testing -- 6.4.1 Detection of Antibiotic Degradation -- 6.4.2 Identification of Biomarker for Detecting Antibiotic-Resistant Strains -- 6.4.3 Phenotypic Antibiotic Resistance Analysis of Bacterial Strains -- 6.5 Advantages and Limitations -- 6.6 Challenges -- References -- 7: Enzyme-Linked Immunosorbent Assay (ELISA) -- 7.1 Introduction -- 7.2 Indirect ELISA -- 7.2.1 Steps of Indirect ELISA -- 7.3 Direct or Sandwich ELISA -- 7.3.1 Steps of Double Antibody Sandwich (DAS) ELISA -- 7.3.2 Steps of Triple Antibody Sandwich (TAS) ELISA -- 7.4 Competitive ELISA -- 7.5 Radioimmunoassay (RIA) -- 7.5.1 Steps of RIA -- 7.6 Automated ELISA -- References -- 8: Isolation of Normal Microbiota from the Human Body and Microbial Identification -- 8.1 Introduction -- 8.2 Collection of Samples from Various Parts of the Body -- 8.3 Biochemical Tests for Identification of Bacteria -- 8.3.1 Carbohydrate Fermentation -- 8.3.2 Indole Production Test -- 8.3.3 Methyl Red Test -- 8.3.4 Voges-Proskauer Test -- 8.3.5 Citrate Utilization -- 8.3.6 Urease Test -- 8.3.7 Catalase Test -- 8.3.8 ; Coagulase Test -- 8.3.9 Lactophenol Cotton Blue -- 8.4 Rapid Multitest Systems -- 8.4.1 Automated Validation of Every Result (VITEK) System for Microbial Identification -- 8.4.2 Biolog: Phenotype Microarrays -- 8.4.3 Electromigration Techniques -- 8.4.4 MIDI Sherlock System for FAME Analysis -- 8.5 Computer-Aided Gene Analysis for Identification of Microbes -- 8.5.1 Ribosomal RNA Gene Sequencing -- 8.5.2 Phylogenetic Analysis -- 8.5.3 Generating Multiple Sequence Alignments -- 8.6 Conclusion -- References -- 9: Microarrays and Its Application in Medical Microbiology -- 9.1 Introduction.; 9.2 Basic Principle -- 9.3 Immobilization Strategies Used for Preparing Microarrays -- 9.4 Manufacture of the Different Components of Microarrays -- 9.4.1 Oligonucleotide Synthesis -- 9.5 Properties of Fluorescence and Fluorophores -- 9.6 Measuring Fluorescence -- 9.7 Labelling Samples for Analysis of Gene Expressions -- 9.8 Labelling Strategies -- 9.8.1 Labelling Bacterial Transcripts -- 9.9 Labelling Samples for Gene Expression Microarray -- 9.10 Calculating Label Density in Probe -- 9.11 Steps for Microarray Hybridization -- 9.12 Different Slide Types for Microarray -- 9.13 Comparing Automated and Manual Hybridization (Table 9.2) -- 9.14 Imaging for Microarray System -- 9.15 Optical System for Imaging in Microarray -- 9.16 Detector System, Amplifier System and Digital Resolution for Imaging in Microarray -- 9.17 Scanners and Excitation Light System for Microarray -- 9.18 Data Analysis in Microarray -- 9.19 Normalization of Data for Correcting Experimental Variation Between Slides -- 9.20 Visualizing of Data and Clustering -- 9.21 Troubleshooting During Microarray-Based Experiments -- 9.22 Applications of Microarrays -- 9.23 Limitations of Microarray Technique -- 9.24 Conclusion and Future Direction -- References -- 10: Immunotechnology -- 10.1 Introduction -- 10.1.1 Monoclonal Antibodies: Purification and Concentrate -- 10.1.1.1 Principle -- 10.1.1.2 Method -- 10.1.2 Concentrate the Purified Antibody -- 10.1.3 Analysis and Quality Assurance -- 10.1.4 Preparation of Separation Gel -- 10.1.5 Preparation of Protein Sample and Loading -- 10.1.6 Staining and Distaining of the Gel -- 10.1.7 Quality Assurance -- 10.2 Immunoelectrophoresis -- 10.2.1 Protocol -- 10.3 Western Blotting -- 10.3.1 Required Material -- 10.3.2 Protocol -- 10.3.3 Blocking of Membrane -- 10.3.4 Binding of Primary Antibody -- 10.3.5 Binding of Secondary Antibody.; 10.4 Determination of Cell Number -- 10.4.1 Required Material -- 10.4.2 Method -- 10.5 Immunofluorescence Assay -- 10.5.1 Principle -- 10.5.2 Immunofluorescence Technique -- 10.5.3 Labelling of Antibodies with Fluorochromes -- 10.5.4 Detection of Fluorochrome-Labelled Reagent -- 10.5.5 Selection of Fluorochrome -- 10.5.6 Materials -- 10.5.7 Blocking Buffer -- 10.5.8 Dilution Buffer -- 10.5.9 Fixative Solution -- 10.5.10 Immunostaining -- 10.5.11 Immunofluorescence Staining Method -- 10.5.12 Uses -- References -- 11: Advances in Microscopy -- 11.1 Introduction -- 11.2 Light Microscopy -- 11.2.1 Physical Properties of Light -- 11.2.2 Reflection -- 11.2.3 Transmission -- 11.2.4 Absorption -- 11.2.5 Refraction -- 11.2.6 Diffraction -- 11.2.7 The Human Eye -- 11.2.8 Polarization -- 11.2.9 Fluorescence -- 11.2.10 Important Concepts in Microscopy -- 11.2.11 Contrast -- 11.2.12 Magnification -- 11.2.13 Sensitivity -- 11.2.14 Simple Theory of Microscopy -- 11.2.15 Metric Units Used in Microscopy -- 11.2.16 Light Microscopes -- 11.2.16.1 The Compound Light Microscope -- 11.2.16.2 Inverted Microscope -- 11.3 Dark Field Microscope -- 11.4 Phase Contrast Microscopy -- 11.5 Differential Interference Contrast Microscopy (DIC) -- 11.6 Fluorescence Microscopy -- 11.6.1 Fluorescent Antibody Technique or Immunofluorescence -- 11.6.2 Identification of Chromosome -- ; 11.6.2.1 Fluorescence In Situ Hybridization (FISH) -- 11.7 Polarization Microscopy -- 11.8 Confocal Microscopy -- 11.9 Electron Microscopy -- 11.9.1 Introduction -- 11.9.2 Transmission Electron Microscope (TEM) -- 11.9.3 Scanning Electron Microscope -- 11.9.4 Scanning Tunneling Microscope (STM) -- 11.9.5 Atomic Force Microscope -- 11.9.6 Sample Preparation for Light Microscope -- 11.9.6.1 Wet Mount Method -- 11.9.7 Histological Techniques -- 11.9.8 Sample Preparation for Electron Microscope.; 11.9.9 Sample Preparation of TEM and SEM.