PROGRESS IN ANALYTICAL ATOMIC SPECTROSCOPY
CONTENTS 1 BIOCHEMICAL AND MOLECULAR BIOLOGICAL METHODS IN LIFE SCIENCES STUDIES 1 1 FROM BIOCHEMISTRY AND MOLECULAR BIOLOGY TO THE LIFE SCIENCES 1 2 THE EDUCATION OF LIFE SCIENTISTS 1 3 AIMS OF LIFE SCIENCE STUDIES 1 4 PERSONAL QUALITIES AND SCIENTI? C CONDUCT 1 5 SUGGESTIONS FOR FURTHER READING 2 BASIC PRINCIPLES 2 1 BIOLOGICALLY IMPORTANT MOLECULES 2 2 THE IMPORTANCE OF STRUCTURE 2 3 PARAMETERS OF BIOLOGICAL SAMPLES 2 4 MEASUREMENT OF THE PH: THE PH ELECTRODE 2 5 BUFFERS 2 6 IONISATION PROPERTIES OF AMINO ACIDS 2 7 QUANTITATIVE BIOCHEMICAL MEASUREMENTS 2 8 EXPERIMENT DESIGN AND RESEARCH CONDUCT 2 9 SUGGESTIONS FOR FURTHER READING 3 CELL CULTURE TECHNIQUES 3 1 INTRODUCTION 3 2 THE CELL CULTURE LABORATORY AND EQUIPMENT 3 3 SAFETY CONSIDERATIONS IN CELL CULTURE 3 4 ASEPTIC TECHNIQUES AND GOOD CELL CULTURE PRACTICE 3 5 TYPES OF ANIMAL CELLS, CHARACTERISTICS AND MAINTENANCE IN CULTURE 3 6 STEM CELL CULTURE 3 7 BACTERIAL CELL CULTURE 3 8 POTENTIAL USE OF CELL CULTURES CONTENTS 3 9 ACKNOWLEDGEMENTS 3 10 SUGGESTIONS FOR FURTHER READING 4 RECOMBINANT DNA TECHNIQUES AND MOLECULAR CLONING 4 1 INTRODUCTION 4 2 STRUCTURE OF NUCLEIC ACIDS 4 3 GENES AND GENOME COMPLEXITY 4 4 LOCATION AND PACKAGING OF NUCLEIC ACIDS 4 5 FUNCTIONS OF NUCLEIC ACIDS 4 6 THE MANIPULATION OF NUCLEIC ACIDS: BASIC TOOLS AND TECHNIQUES 4 7 ISOLATION AND SEPARATION OF NUCLEIC ACIDS 4 8 AUTOMATED ANALYSIS OF NUCLEIC ACID FRAGMENTS 4 9 MOLECULAR ANALYSIS OF NUCLEIC ACID SEQUENCES 4 10 THE POLYMERASE CHAIN REACTION (PCR) 4 11 CONSTRUCTING GENE LIBRARIES 4 12 CLONING VECTORS 4 13 HYBRIDISATION AND GENE PROBES 4 14 SCREENING GENE LIBRARIES 4 15 APPLICATIONS OF GENE CLONING 4 16 EXPRESSION OF FOREIGN GENES 4 17 ANALYSING GENES AND GENE EXPRESSION 4 18 ANALYSING GENETIC MUTATIONS AND POLYMORPHISMS 4 19 MOLECULAR BIOTECHNOLOGY AND APPLICATIONS 4 20 PHARMACOGENOMICS 4 21 SUGGESTIONS FOR FURTHER READING 5 PREPARATIVE PROTEIN BIOCHEMISTRY 5 1 INTRODUCTION 5 2 DETERMINATION OF PROTEIN CONCENTRATIONS 5 3 ENGINEERING PROTEINS FOR PURI? CATION 5 4 PRODUCING RECOMBINANT PROTEIN 5 5 CELL-DISRUPTION METHODS 5 6 PRELIMINARY PURI? CATION STEPS 5 7 PRINCIPLES OF LIQUID CHROMATOGRAPHY 5 8 CHROMATOGRAPHIC METHODS FOR PROTEIN PURI? CATION 5 9 OTHER METHODS OF PROTEIN PURI? CATION 5 10 MONITORING PROTEIN PURI? CATION 5 11 STORAGE 5 12 SUGGESTIONS FOR FURTHER READING 6 ELECTROPHORETIC TECHNIQUES 6 1 GENERAL PRINCIPLES 6 2 SUPPORT MEDIA AND BUFFERS 6 3 ELECTROPHORESIS OF PROTEINS 6 4 ELECTROPHORESIS OF NUCLEIC ACIDS 6 5 CAPILLARY ELECTROPHORESIS 6 6 MICROCHIP ELECTROPHORESIS 6 7 SUGGESTIONS FOR FURTHER READING 7 IMMUNOCHEMICAL TECHNIQUES 7 1 INTRODUCTION 7 2 ANTIBODY PREPARATION 7 3 IMMUNOASSAY FORMATS 7 4 IMMUNO MICROSCOPY 7 5 LATERAL FLOW DEVICES 7 6 EPITOPE MAPPING 7 7 IMMUNOBLOTTING 7 8 FLUORESCENCE-ACTIVATED CELL SORTING (FACS) 7 9 CELL AND TISSUE STAINING TECHNIQUES 7 10 IMMUNOCAPTURE POLYMERASE CHAIN REACTION (PCR) 7 11 IMMUNOAF? NITY CHROMATOGRAPHY 7 12 ANTIBODY-BASED BIOSENSORS 7 13 LUMINEX ® TECHNOLOGY 7 14 THERAPEUTIC ANTIBODIES 7 15 SUGGESTIONS FOR FURTHER READING 8 FLOW CYTOMETRY 8 1 INTRODUCTION 8 2 INSTRUMENTATION 8 3 FLUORESCENCE-ACTIVATED CELL SORTING (FACS) 8 4 FLUORESCENCE LABELS 8 5 PRACTICAL CONSIDERATIONS 8 6 APPLICATIONS 8 7 SUGGESTIONS FOR FURTHER READING 9 RADIOISOTOPE TECHNIQUES 9 1 WHY USE A RADIOISOTOPE? 9 2 THE NATURE OF RADIOACTIVITY 9 3 DETECTION AND MEASUREMENT OF RADIOACTIVITY 9 4 OTHER PRACTICAL ASPECTS OF COUNTING RADIOACTIVITY AND ANALYSIS OF DATA 9 5 SAFETY ASPECTS 9 6 SUGGESTIONS FOR FURTHER READING 10 PRINCIPLES OF CLINICAL BIOCHEMISTRY GILL RUMSBY 10 1 PRINCIPLES OF CLINICAL BIOCHEMICAL ANALYSIS 10 2 CLINICAL MEASUREMENTS AND QUALITY CONTROL 10 3 EXAMPLES OF BIOCHEMICAL AIDS TO CLINICAL DIAGNOSIS 10 4 SUGGESTIONS FOR FURTHER READING 11 MICROSCOPY 11 1 INTRODUCTION 11 2 THE LIGHT MICROSCOPE 11 3 OPTICAL SECTIONING 11 4 IMAGING LIVE CELLS AND TISSUES 11 5 MEASURING CELLULAR DYNAMICS 11 6 THE ELECTRON MICROSCOPE 11 7 IMAGE MANAGEMENT 11 8 SUGGESTIONS FOR FURTHER READING 12 CENTRIFUGATION AND ULTRACENTRIFUGATION 12 1 INTRODUCTION 12 2 BASIC PRINCIPLES OF SEDIMENTATION 12 3 TYPES, CARE AND SAFETY ASPECTS OF CENTRIFUGES 12 4 PREPARATIVE CENTRIFUGATION 12 5 ANALYTICAL ULTRACENTRIFUGATION 12 6 SUGGESTIONS FOR FURTHER READING 13 SPECTROSCOPIC TECHNIQUES 13 1 INTRODUCTION 13 2 ULTRAVIOLET AND VISIBLE LIGHT SPECTROSCOPY 13 3 CIRCULAR DICHROISM SPECTROSCOPY 13 4 INFRARED AND RAMAN SPECTROSCOPY 13 5 FLUORESCENCE SPECTROSCOPY 13 6 LUMINOMETRY 13 7 ATOMIC SPECTROSCOPY 13 8 RAPID MIXING TECHNIQUES FOR KINETICS 13 9 SUGGESTIONS FOR FURTHER READING 14 BASIC TECHNIQUES PROBING MOLECULAR STRUCTURE AND INTERACTIONS 14 1 INTRODUCTION 14 2 ISOTHERMAL TITRATION CALORIMETRY 14 3 TECHNIQUES TO INVESTIGATE THE THREE-DIMENSIONAL STRUCTURE 14 4 SWITCH TECHNIQUES 14 5 SOLID-PHASE BINDING TECHNIQUES WITH WASHING STEPS 14 6 SOLID-PHASE BINDING TECHNIQUES COMBINED WITH FLOW 14 7 SUGGESTIONS FOR FURTHER READING 15 MASS SPECTROMETRIC TECHNIQUES 15 1 INTRODUCTION 15 2 IONISATION 15 3 MASS ANALYSERS 15 4 DETECTORS 15 5 OTHER COMPONENTS 15 6 SUGGESTIONS FOR FURTHER READING 16 FUNDAMENTALS OF BIOINFORMATICS 16 1 INTRODUCTION 16 2 BIOLOGICAL DATABASES 16 3 BIOLOGICAL DATA FORMATS 16 4 SEQUENCE ALIGNMENT AND TOOLS 16 5 ANNOTATION OF PREDICTED PEPTIDES 16 6 PRINCIPLES OF PHYLOGENETICS 16 7 SUGGESTIONS FOR FURTHER READING 17 FUNDAMENTALS OF CHEMOINFORMATICS 17 1 INTRODUCTION 17 2 COMPUTER REPRESENTATIONS OF CHEMICAL STRUCTURE 17 3 CALCULATION OF COMPOUND PROPERTIES 17 4 MOLECULAR MECHANICS 17 5 DATABASES 17 6 SUGGESTIONS FOR FURTHER READING 18 THE PYTHON PROGRAMMING LANGUAGE 18 1 INTRODUCTION 18 2 GETTING STARTED 18 3 EXAMPLES 18 4 SUGGESTIONS FOR FURTHER READING 19 DATA ANALYSIS 19 1 INTRODUCTION 19 2 DATA REPRESENTATIONS 19 3 DATA ANALYSIS 19 4 CONCLUSION 19 5 SUGGESTIONS FOR FURTHER READING 20 FUNDAMENTALS OF GENOME SEQUENCING AND ANNOTATION 20 1 INTRODUCTION 20 2 GENOMIC SEQUENCING 20 3 ASSEMBLY OF GENOMIC INFORMATION 20 4 PREDICTION OF GENES 20 5 FUNCTIONAL ANNOTATION 20 6 POST-GENOMIC ANALYSES 20 7 FACTORS AFFECTING THE SEQUENCING, ANNOTATION AND ASSEMBLY OF EUKARYOTIC GENOMES, AND SUBSEQUENT ANALYSES 20 8 CONCLUDING REMARKS 20 9 SUGGESTIONS FOR FURTHER READING 21 FUNDAMENTALS OF PROTEOMICS SONJA HESS AND MICHAEL WEISS 21 1 INTRODUCTION: FROM EDMAN SEQUENCING TO MASS SPECTROMETRY 21 2 DIGESTION 21 3 TANDEM MASS SPECTROMETRY 21 4 THE IMPORTANCE OF ISOTOPES FOR FINDING THE CHARGE STATE OF A PEPTIDE 21 5 SAMPLE PREPARATION AND HANDLING 21 6 POST-TRANSLATIONAL MODI? CATION OF PROTEINS 21 7 ANALYSING PROTEIN COMPLEXES 21 8 COMPUTING AND DATABASE ANALYSIS 21 9 SUGGESTIONS FOR FURTHER READING 22 FUNDAMENTALS OF METABOLOMICS JAMES I MACRAE 22 1 INTRODUCTION: WHAT IS METABOLOMICS? 22 2 SAMPLE PREPARATION 22 3 DATA ACQUISITION 22 4 UNTARGETED AND TARGETED METABOLOMICS 22 5 CHEMOMETRICS AND DATA ANALYSIS 22 6 FURTHER METABOLOMICS TECHNIQUES AND TERMINOLOGY 22 7 SUGGESTIONS FOR FURTHER READING 23 ENZYMES AND RECEPTORS MEGAN CROSS AND ANDREAS HOFMANN 23 1 DE? NITION AND CLASSI? CATION OF ENZYMES 23 2 ENZYME KINETICS 23 3 ANALYTICAL METHODS TO INVESTIGATE ENZYME KINETICS 23 4 MOLECULAR MECHANISMS OF ENZYMES 23 5 REGULATION OF ENZYME ACTIVITY 23 6 RECEPTORS 23 7 CHARACTERISATION OF RECEPTOR–LIGAND BINDING 23 8 SUGGESTIONS FOR FURTHER READING 24 DRUG DISCOVERY AND DEVELOPMENT 24 1 INTRODUCTION 24 2 MOLECULAR LIBRARIES AND DRUG-DISCOVERY STRATEGIES 24 3 ASSEMBLING A MOLECULAR LIBRARY 24 4 COMPOUND MANAGEMENT 24 5 SCREENING STRATEGIES USED IN HIT DISCOVERY 24 6 ACTIVE-TO-HIT PHASE 24 7 HIT-TO-LEAD PHASE 24 8 ADMET 24 9 LEAD OPTIMISATION 24 10 SUGGESTIONS FOR FURTHER READING