Systems Biology of Bacteria

Series Page

Series Advisors

Contributors

Chapter 1. High-resolution temporal analysis of global promoter activity in Bacillus subtilis

1. Introduction

2. Gene Fusion Technology

3. Reporter proteins

4. Cellular Placement of Transcriptional Fusions

5. Choice of System

6. Use of Promoter Fusions to Study Biological Processes at High Temporal Resolution in Bacteria

7. Methodology for High-throughput Analysis of Promoter Activity with Fine Temporal Resolution in B. subtilis

8. Conclusions

References

Chapter 2. Data mining for microbiologists

1. Introduction

2. What is Data Mining?

3. The Data Mining Process

4. Inferential Techniques

5. Machine Learning Techniques

6. The Role of eScience

7. Case Study: Data Mining for Protein Function Prediction

8. Data Mining with Microbial Data: Practical Issues

9. Conclusions

References

Chapter 3. Proteomics

Abbreviations

1. Introduction

2. Absolute Quantification Workflows in Proteomics

3. The Proteomics Workflow

4. Generation of Absolute Quantitative Data by Targeted Mass Spectrometry

5. Generation of Large-Scale Relative Proteomics Data: Differential 2D Gel Image Analysis

6. Large-Scale Absolute Quantitative Proteomics with SRM-Calibrated 2D PAGE

References

Chapter 4. Imaging fluorescent protein fusions in live bacteria

1. Introduction

2. Molecular Toolkits

3. Functional Analysis

4. Growth Conditions

5. Agarose Slide Preparation

6. Imaging Hardware

7. Imaging Software

8. Image Processing

9. Concluding Remarks

References

Chapter 5. Targeted and quantitative metabolomics in bacteria

1. Introduction

2. Cultivation of Bacteria for Metabolome Analysis

3. Sampling Bacterial Cultures for Metabolome Analysis

4. Extraction of Metabolites from Bacteria

5. Analysis by Mass Spectrometry

6. Interpretation of Metabolite Data

7. Outlook

References

Chapter 6. Array-based approaches to bacterial transcriptome analysis

1. Introduction

2. Prior Considerations

3. Performing the Experiments

4. Data Analysis

5. Final Comments

References

Index