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Sampling and Analysis of Indoor Microorganisms by Chin S. Yang, and Patricia Heinsohn Hardcover - 273 pages Shipped in CLICK HERE Cat.# JW-MBIO1 $ 93.60 BUY Published:  2007   ISBN:  9780471730934

Investigation techniques and analytical methodologies for addressing microbial contamination indoors

Microbial contamination indoors is a significant environmental and occupational health and safety problem. This book provides fundamental background information on fungal and bacterial growth indoors as well as in-depth, practical approaches to analyzing and remedying problems. The information helps investigators, laboratory managers, and environmental health professionals properly use state-of-the-science methods and correctly interpret the results. With chapters by expert microbiologists, mycologists, environmental professionals, and industrial hygienists, Sampling and Analysis of Indoor Microorganisms is a multidisciplinary, comprehensive reference on advanced approaches, covering:

• Microbiological problems in a water-damaged environment
• Indoor construction techniques and materials that impact environmental microbiology
• Microbial ecology indoors, airborne bacteria, genetic-based analytical methods, and statistical tools for microorganism analysis
• Microbiological sampling approaches
• Mold removal principles and methods, including specialized microbial remediation techniques for HVAC systems, legionellas and biofilms, and sewage contamination
• A forensic approach toward the assessment of fungal growth in the indoor environment

A must-have guide for practicing professionals, including environmental health and safety personnel, public health officials, and building and construction engineers and architects, this is also a valuable reference for attorneys, home inspectors, water restoration personnel, mold remediation contractors, insurance adjusters, and others.

Soil Microbiology, Ecology and Biochemistry 3e by Paul Eldor Hardcover - 400 pages Shipped in CLICK HERE Cat.# EL-MBIO1 $100.90 BUY Published:  2006   ISBN:  9780125468077

This revised and updated edition guides students through biochemical and microbial processes in soils and introduces them to microbial processes in water and sediments. This classic book includes basic concepts and applications in agriculture, forestry, ecology, and environmental science. It is also an invaluable resource for research in biogeochemistry, microbiology, sustainable agriculture, and environmental amelioration. The Third Edition has been expanded from 13 to 19 chapters including such topics as bioremediation, molecular biology of soil, biodiversity of soil organisms, and the impact of global climate change on soil microhabitats. Furthermore, the lead author has decided to recruit contibuted chapters from leading soil microbiologists and agronomists.

Modern Multidisciplinary Applied Microbiology: Exploiting Microbes and Their Interactions by Antonio Mendez-Vilas Hardcover - 820 pages Shipped in CLICK HERE Cat.# JW-MBIO2 $272.70 BUY Published:  2006   ISBN:  9783527316113

Indexed and cross-referenced interdisciplinary contributions provide an integrated view of the this thriving and important field, with reports on key research from the frontiers of applied microbiology. Topics include food, environmental, industrial, pharmaceutical, medical, bioinformatics and education sciences.

Table of Contents:

1. Environmental Microbiology, Marine Microbiology, Water/Aquatic Microbiology, Geomicrobiology
2. Industrial Microbiology - Future Bioindustries
3. Food Microbiology
4. Agriculture, Soil, Forest Microbiology
5. Bioremediation
6. Microbial Biotechnology
7. Microfactories - Microbial Production of Chemicals, Pharmaceuticals and Biopolymers
8. Medical Microbiology
9. Microbial Physiology, Metabolism and Gene Expression
10. Analytical Techniques, Imaging Techniques, Microscopy
11. Methods in Basic and Applied Microbiology. Microbiology Education
 

Pathogenomics, Genome Analysis of Pathogenic Microbes by Jörg Hacker, Ulrich Dobrindt, and Werner Göbel Hardcover - 616 pages Shipped in CLICK HERE Cat.# JW-MBIO3 $259.05 BUY Published:  2006   ISBN:  9783527312658

The first book on this young, highly dynamic, and expanding field.

This comprehensive, interdisciplinary text focuses on those pathogenic bacteria that are of high scientific and public health interest, yet which also display great potential for the development of new diagnostic, prophylactic and therapeutic procedures.

The authors cover all aspects of pathogenomics, including methods, genomics and applications. In addition, the ongoing development of genome, transcriptome, proteome and bioinformatic analyses of pathogenic microorganisms and their host interactions makes for a comprehensive introduction to the field of modern genomic analysis.

This result is invaluable to researchers and students wishing to gain a general overview of microbial functional genome analysis and pathogenesis, while also representing a good starting point for those new to the area.

Table of Contents:

Foreword
Preface
List of Contributors
Color Plates

I. Methods

1. Bioinformatics: Data Mining Among Genome Sequences

1.1 Systematic Genome Analysis of Pathogens as a Basis for Pharmacogenomic Strategies
1.2 Direct Sequence Annotation Tools for Functional Genomics
1.3 Identification of Protein Function
1.4 Obtaining Protein Information from a Domain Server
1.5 Pathway Analysis
1.6 Network Analysis
1.7 Adaptation in Time and to Stimuli
1.8 Pathogen-Specific Challenges
1.9 Pathogen Adaptation Potential
1.10 The Fight Against Resistance
1.11 Drug Design and Antibiotics
1.12 Annotation Platforms Suitable for Pathogenomics
1.13 Conclusions

2. Transcriptome Analysis: Towards a Comprehensive Understanding of Global Transcription Activity

2.1 Introduction
2.2 Development of Transcriptomics
2.3 Introducing the Microarray
2.4 Microarray Methods
2.5 Data Normalization and Analysis
2.6 Transcriptomics: Where We Are Now and What’s to Come

3. Physiological Proteomics of Bacillus subtilis and Staphylococcus aureus: Towards a Comprehensive Understanding of Cell Physiology and Pathogenicity

3.1 Introduction
3.2 Proteomics of Bacillus subtilis: The Gram-positive Model Organism
3.3 Physiological Proteomics of Staphylococcus aureus
3.4 Outlook: Second Generation Proteomics and New Fields in S. aureus Physiology and Infection Biology

4. Impact of Genome Sequences on Mutational Analysis of Fungal and Bacterial Pathogens

4.1 The Long Road from Sequence to Function
4.2 Classical Genetics Still at the Forefront in the Postgenome Era
4.3 Genome-Scale Mutational Analyses
4.4 Conclusion

II Genomics of Pathogenic Bacteria

5. Pathogenomics of Escherichia coli and Shigella Species

5.1 Introduction
5.2 Comparative Genomics of Shigella
5.3 Comparative Genomics of Escherichia coli
5.4 Conclusions

6. Pathogenomics of Salmonella Species

6.1 Introduction
6.2 Salmonella Signature Genes
6.3 Subspecies I Signature Genes
6.4 Host Restriction

7. Pathogenomics of Enterococcus faecalis

7.1 Introduction
7.2 Enterococcal Pathogenesis
7.3 Genome Sequence of E. faecalis
7.4 Conclusions and Future Perspectives

8. Genomics of Streptococci

8.1 Introduction
8.2 Bacterial Genomes
8.3 Streptococcal Genomic Bacteriophages

9. Pathogenic Staphylococci: Lessons from Comparative Genomics

9.1 Introduction
9.2 Comparative Genomics of S. aureus
9.3 Staphylococcus epidermidis
9.4 Concluding Remarks

10. Pathogenomics: Insights into Tuberculosis and Related Mycobacterial Diseases

10.1 Introduction
10.2 Molecular Basis of Pathogenicity
10.3 Evolution of the M. tuberculosis Complex
10.4 Some Metabolic Insight from the Genome Sequences
10.5 Other Major Mycobacterial Human Pathogens
10.6 Concluding Remarks

11. Genomes of Pathogenic Neisseria Species

11.1 Introduction
11.2 Genomes of Pathogenic Neisseria Species
11.3 Future Perspectives

12. Genomics of Pathogenic Clostridia and Bacilli

12.1 Genomics of Pathogenic Clostridia spp.
12.2 Genomics of Pathogenic Bacilli

13. The Genomes of Pathogenic Bartonella Species

13.1 Introduction
13.2 Bartonella Species and Pathogenicity
13.3 The Bartonella Genomes
13.4 Genomic Islands and Phages
13.5 Genomic Islands and Phages in Bartonella Species
13.6 The Chromosome II-Like Segment in Bartonella
13.7 B. quintana’s Evolution into a Human Pathogen
13.8 Conclusions and Future Perspectives

14. Pathogenomics of Gastric and Enterohepatic Helicobacter Species

14.1 Introduction
14.2 Helicobacter pylori
14.3 Helicobacter hepaticus
14.4 Genome Comparisons of Gastric and Enterohepatic Helicobacter Species with Related Bacteria
14.5 Outlook

15. Genomics of the Opportunistic Pathogen Legionella pneumophila

15.1 The Genus Legionella: Epidemiology, Life Cycle, and Pathogenesis
15.2 Genomics of Legionella pneumophila
15.3 Specific Features of the Legionella Genomes
15.4 Conclusions

16. Genomics of Listeria monocytogenes

16.1 Introduction: From Pregenomics to Postgenomics
16.2 Listeria monocytogenes: A Facultative Intracellular Pathogen
16.3 Listeria monocytogenes Genetics in the Pregenomic Era: Identification and Characterization of Important Virulence Factors
16.4 Genome Sequence of L. monocytogenes and Its Comparison with the Closely Related L. innocua
16.5 Genomic Approaches to Studying the other Members of the Genus Listeria
16.6 Evolutionary Aspects
16.7 Identification of Listerial Virulence Factors in the Postgenomic Era
16.8 Proteomics
16.9 Transcriptomics
16.10 Conclusions

III Genomics of Pathogens and Their Hosts: Applications

17. Genomics of Viruses

17.1 Introduction: Wide Scope of Virogenomics
17.2 Retrieving Information
17.3 Applications of Data Banks to Virology
17.4 Beyond Reference Strains: Towards a Second-Generation Virogenomics?
17.5 Virogenomics Through Microarrays

18. Genomics of Pathogenic Fungi

18.1 Introduction
18.2 Genomics of Primary Fungal Pathogens.
18.3 Genomics of Opportunistic Fungal Pathogens
18.4 The Tool Box for Functional Genomics
18.5 Fungal Virulence – From the Genomic Point of View
18.6 Conclusion

19. Genomics of Pathogenic Parasites

19.1 Exploring the Genomes of Pathogenic Protozoans
19.2 The Shaping of the Proteomes of the Pathogenic Protists
19.3 Role of Horizontal Gene Transfer in Protozoan Genome Plasticity
19.4 The Apicomplexa
19.5 The Pathogenic Kinetoplastids
19.6 The Pathogenic Diplomanad Giardia and the Parabasalid Trichomonas
19.7 Postgenomic Strategies and the Search for Cure

20. Model Host Systems: Tools for Comprehensive Analysis of Host–Pathogen Interactions

20.1 Introduction
20.2 Host–Pathogen Interactions
20.3 Arabidopsis thaliana: A Plant as a Model for Human Disease
20.4 Dictyostelium discoideum: Perspectives from a Social Amoeba
20.5 Caenorhabditis elegans: Answers from a Worm
20.6 Drosophila melanogaster: A Fruitful Model
20.7 Danio rerio: Fishing for Knowledge
20.8 Mus musculus: Of Mice and Men
20.9 Clean Models and Dirty Reality

21. Expression Analysis of Human Genes During Infection

21.1 Introduction
21.2 Comparison of Gene Expression Profiles of Macrophages and Dendritic Cells In Vitro Upon Infection with Different Pathogens
21.3 Septicemia
21.4 Gene Expression in Epithelial Cells Modulated by Bacteria
21.5 Common Signatures
21.6 Genetic Polymorphisms and Mutations Affect Gene Expression: Impact on Infection Susceptibility and Infection Course
21.7 Concluding Remarks

22. Pathogenomics: Application and New Diagnostic Tools

22.1 Introduction: “In Our Hands”
22.2 Microbiological Diagnostics of Bacterial Pathogens: Aims, Tasks, and Current Limitations
22.3 The Pregenomic Era: Conventional and Molecular Methods in Microbiological Diagnostics
22.4 The Postgenomic Era: Use of DNA Microarrays in the Diagnosis of Infectious Diseases in Humans and Animals
22.5 Microarray Technology in Bacteria: Further Areas of Applications
22.6 Current Limitations on the Use of DNA Microarrays in Diagnostics in Medical Microbiological Laboratories
22.7 Final Remarks

23. The Search for New Antibiotics

23.1 The Need for Novel Antibiotics
23.2 Where Will the New Antibiotics Come From?
23.3 Contributions of Genomic Technologies to Antibacterial Research
23.4 Alternative Approaches in Antibacterial Drug Discovery

24. Reverse Vaccinology: Revolutionizing the Approach to Vaccine Design

24.1 Impact of Genomics on Vaccine Design
24.2 MenB Vaccine Approach by Reverse Vaccinology
24.3 Following the MenB Experience: Other Pathogens
24.4 Functional Genomics
24.5 Gene Expression In Vivo: IVET and STM
24.6 Transcriptome Analysis and Comparative Genomics
24.7 Proteomics and Vaccine Design

24.8 Conclusions
Index

Wastewater Microbiology (Ed.3) by Gabriel Bitton Hardcover - 768 pages Shipped in CLICK HERE Cat.# JW-MBIO4 $122.70 BUY Published:  2006   ISBN:  9780471650713

The new edition of a classic reference incorporating the latest findings and discoveries

The Third Edition of this classic reference provides readers with concise, up-to-the-moment coverage of the role of microorganisms in water and wastewater treatment. By providing a solid foundation in microbiology, microbial growth, metabolism, and nutrient cycling, the text gives readers the tools they need to make critical decisions that affect public health, as well as the practical aspects of treatment, disinfection, water distribution, bioremediation, and water and wastewater reuse.

The publication begins a discussion of microbiology principles, followed by a discussion of public health issues and concerns. Next, the core of the text is dedicated to a thorough examination of wastewater and drinking water treatment, biosolids, pollution-control biotechnology, and drinking water distribution. The remainder of the text discusses toxicity testing in wastewater treatment plants, and the public health aspects of wastewater disposal and reuse.

The many advances in wastewater and drinking water microbiology have all been thoroughly integrated into the publication, including:

• A new chapter on bioterrorism and drinking water safety
• The latest developments in biofilm microbial ecology and biofilm impact on drinking water quality
• New, state-of-the-art detection techniques
• Expanded and revised treatment of toxicity testing, including new testing methods and studies on endocrine disrupters in wastewater
• Alternatives to conventional wastewater treatment

New problem sets, which test readers' knowledge, as well as a list of Internet resources have been added to each chapter. In addition, the publication's extensive references have been thoroughly revised for readers who would like to learn more about the latest findings and discoveries on specialized topics. Finally, the color plate section has been expanded and contains many new illustrations and tables.

An authoritative guide for all researchers, administrators, and engineers in the field of microbiology, Wastewater Microbiology, Third Edition is also a valuable reference for civil and environmental engineers, public health officials, and students involved in environmental engineering and science.

Table of Contents:

Preface
Preface to the First Edition
Preface to the Second Edition

PART A. FUNDAMENTALS OF MICROBIOLOGY

1. The Microbial World
2. Microbial Metabolism and Growth
3. Role of Microorganisms in Biogeochemical Cycles

PART B. PUBLIC HEALTH MICROBIOLOGY

4. Pathogens and Parasites in Domestic Wastewater
5. Microbial Indicators of Fecal Contamination
6. Water and Wastewater Disinfection

PART C. MICROBIOLOGY OF WASTEWATER TREATMENT

7. Introduction to Wastewater Treatment
8. Activated Sludge Process
9. Bulking and Foaming in Activated Sludge Plants
10. Processes Based on Attached Microbial Growth
11. Waste Stabilizations Ponds
12. Sludge Microbiology
13. Anaerobic Digestion of Wastewater and Biosolids
14. Bioaerosols and Bioodors from Wastewater Treatment Plants

PART D. MICROBIOLOGY OF DRINKING WATER TREATMENT

15. Microbiological Aspects of Drinking Water Treatment
16. Microbiological Aspects if Drinking Water Distribution
17. Bioterrorism and Drinking Water Safety

PART E. BIOTECHNOLOGY IN WASTEWATER TREATMENT

18. Pollution Control Biotechnology.

PART F. FATE AND TOXICITY OF CHEMICALS IN WASTEWATER TREATMENT PLANTS

19. Fate of Xenobiotics and Toxic Metals in Wastewater Treatment Plants
20. Toxicity Testing in Wastewater Treatment Plants Using Microorganisms

PART G. MICROBIOLOGY AND PUBLIC HEALTH ASPECTS OF WASTEWATER EFFLUENTS AND BIOSOLIDS DISPOSAL AND REUSE

21. Public Health Aspects of Wastewater and Biosolids Disposal on Land
22. Public Health Aspects of Wastewater and Biosolids Disposal in the Marine Environment
23. Wastewater Reuse

References
Index

Microbial Proteomics, Functional Biology of Whole Organisms by Ian Humphery-Smith, and Michael Hecker Hardcover - 512 pages Shipped in CLICK HERE Cat.# JW-MBIO5 $159.05 BUY Published:  2006   ISBN:  9780471699750

Discover important lessons learned about whole organism biology via microbial proteomics

This text provides an exhaustive analysis and presentation of current research in the field of microbial proteomics, with an emphasis on new developments and applications and future directions in research. The editors and authors show how and why the relative simplicity of microbes has made them attractive targets for extensive experimental manipulation in a quest for both improved disease prevention and treatment and an improved understanding of whole organism functional biology. In particular, the text demonstrates how microbial proteomic analyses can aid in drug discovery, including identification of new targets, novel diagnostic markers, and lead optimization.

Each chapter is written by one or more leading experts in the field and carefully edited to ensure a consistent and thorough approach throughout. Methods, technologies, and tools associated with the most promising approaches are stressed. Key topics covered include:

• Microbial pathogenesis at the proteome level
• Whole cell modelling
• Structural proteomics and computational analysis
• Biomolecular interactions
• Physiological proteomics
• Metabolic reconstruction using proteomics data

While presenting the practical utility of proteomics data, the text is also clear on the field's current limitations, pointing to areas where further investigation is needed.

Offering a state-of-the-art perspective from internationally recognized experts, this text is ideally suited for researchers and students across the gamut of genomic sciences, including biochemistry, microbiology, molecular biology, genetics, biomedical and pharmaceutical sciences, biotechnology, and veterinary science.

Table of Contents:

PREFACE
ACKNOWLEDGMENTS
CONTRIBUTORS

PART I: GENERAL PROTEOMICS OF MICROORGANISMS/MODEL ORGANISMS

1. Holistic Biology of Microorganisms: Genomics, Transcriptomics, and Proteomics
2. Strategies for Measuring Dynamics: The Temporal Component of Proteomics
3. Quest for Complete Proteome Coverage
4. Proteome of Mycoplasma pneumoniae
5. Proteomics of Archaea

PART II: PROTEOMICS AND CELL PHYSIOLOGY

6. Elucidation of Mechanisms of Acid Stress in Listeria monocytogenes by Proteomic Analysis
7. Oxidation of Bacterial Proteome in Response to Starvation
8. Tale of Two Metal Reducers: Comparative Proteome Analysis of Geobacter sulferreducens PCA and Shewanella oneidensis MR-1
9. AMT Tag Approach to Proteomic Characterization of Deinococcus radiodurans and Shewanella oneidensis

PART III: PHYSIOLOGICAL PROTEOMICS OF INDUSTRIAL BACTERIA

10. Proteomics of Corynebacterium glutamicum: Essential Industrial Bacterium
11. Proteomics of Lactococcus lactis: Phenotypes for a Domestic Bacterium
12. Proteomic Survey through Secretome of Bacillus subtilis

PART IV: PROTEOMICS OF PATHOGENIC MICROORGANISMS

13. Analyzing Bacterial Pathogenesis at Level of Proteome
14. Unraveling Edwardsiella tarda Pathogenesis Using the Proteomics Approach

15. Structural Proteomics and Computational Analysis of a Deadly Pathogen: Combating Mycobacterium tuberculosis from Multiple Fronts

16. Proteomic Studies of Plant-Pathogenic Oomycetes and Fungi
17. Candida albicans Biology and Pathogenicity: Insights from Proteomics
18. Contributions of Proteomics to Diagnosis, Treatment, and Prevention of Candidiasis
19. Identification of Protein Candidates for Developing Bacterial Ghost Vaccines against Brucella
20. Genomics and Proteomics in Reverse Vaccines

PART V: PROTEOME DATABASES, BIOINFORMATICS, AND BIOCHEMICAL MODELING

21. Databases and Resources for in silico Proteome Analysis
22. Interspecies and Intraspecies Comparison of Microbial Proteins: Learning about Gene Ancestry, Protein Function, and Species Life Style
23. Cellular Kinetic Modeling of the Microbial Metabolism

INDEX

Proteomics of Microbial Pathogens by Peter R. Jungblut, and Michael Hecker Hardcover - 343 pages Shipped in CLICK HERE Cat.# JW-MBIO6 $233.60 BUY Published:  2006   ISBN:  9783527317592

Containing proven, high-quality research articles selected from the popular Proteomics journal, this is a current overview of the latest research into the proteomics analysis of microbial pathogens as well as several review articles.

Table of Contents:

1. Proteomics of microbial pathogens
2. Genome and proteome analysis of Chlamydia
3. Helicobacter pylori vaccine development based on combined subproteome analysis
4. A comprehensive proteome map of growing Bacillus subtilis cells
5. A targeted proteomics approach to the rapid identification of bacterial cell mixtures by matrix-assisted laser desorption/ionization mass spectrometry
6. Proteome analysis of Neisseria meningitidis serogroup A
7. Protein identification and tracking in two-dimensional electrophoretic gels by minimal protein identifiers
8. Continued proteomic analysis of Mycobacterium leprae subcellular fractions
9. CFP10 discriminates between nonacetylated and acetylated ESAT-6 of Mycobacterium tuberculosis by differential interaction
10. The Helicobacter pylori CagA protein induces tyrosine dephosphorylation of ezrin
11. Action and Reaction: Chlamydophila pneumoniae proteome alteration in a persistent infection induced by iron deficiency
12. Assessment of protein spot components applying correspondence analysis for peptide mass fingerprint data
13. Presentation of differentially regulated proteins within a web-accessible proteome database system of microorganisms
14. The cell wall subproteome of Listeria monocytogenes
15. Low virulent strains of Candida albicans: Unravelling the antigens for a future vaccine
16. Proteomic analysis of the sarcosine-insoluble outer membrane fraction of the bacterial pathogen Bartonella henselae
17. The influence of agr and B in growth phase dependent regulation of virulence factors in Staphylococcus aureus
18. Comparative proteome analysis of cellular proteins extracted from highly virulent Francisella tularensis ssp. tularensis and less virulent F. tularensis ssp. holarctica and F. tularensis ssp. mediaasiatica
19. Proteome comparison of Vibrio cholerae cultured in aerobic and anaerobic conditions
20. Highly phosphorylated bacterial proteins
21. Induction of Mycobacterium avium proteins upon infection of human macrophages
22. Proteomics-based identification of novel Candida albicans antigens for diagnosis of systemic candidiasis in patients with underlying hematological malignancies

Microbial Functional Genomics by Jizhong Zhou, Dorothea K. Thompson, Ying Xu, and James M. Tiedje Hardcover - 624 pages Shipped in CLICK HERE Cat.# JW-MBIO7 $138.15 BUY Published:  2004   ISBN:  9780471071907

Microbial Functional Genomics offers a timely summary of the principles, approaches, and applications. It presents a comprehensive review of microbial functional genomics, covering microbial diversity, microbial genome sequencing, genomic technologies, genome-wide functional analysis, applied functional genomics, and future directions. An introduction will offer a definition of the field and an overview of the historical and comparative genomics aspects.

About the Author:
Jizhong Zhou is a Staff Scientist and science leader for the Microbial Genomics and Ecology section in the Environmental Sciences Division of Oak Ridge National Laboratory. He is the author of more than 50 publications on molecular biology, microbial genomics, molecular evolution, microbial ecology, bioremediation, and theoretical ecology.

Ying Xu is the group leader of the computational protein structure group of Life Sciences Division of Oak Ridge National Laboratory. He serves on a number of scientific review committees including the NIH review panel on structural genomics.

James M. Tiedje is University Distinguished Professor of Microbial Ecology and Director of the National Science Foundation Center for Microbial Ecology at Michigan State University. He is a Fellow of ASA, SSSA, AAAS, the International Institute of Biotechnology and a Fellow of the American Academy of Microbiology.

Dorothea Thompson is currently a Research Staff Scientist in the Environmental Sciences Division at Oak Ridge National Laborat ory (ORNL), working in the area of microbial functional genomics. She received her Ph.D. in molecular microbiology from The Ohio State University (Columbus, OH) and master’s degrees from Virginia Tech and the Pennsylvania State University. Dr. Thompson pursued postdoctoral training in bacterial pathogen typing and vaccine development at the U. S. Food and Drug Administration in Bethesda, Maryland, and in DNA microarray-based gene expression analysis at ORNL before becoming a staff member in 2002. Her research interests and expertise focus on the mechanisms of transcription regulation in prokaryotic systems and the use of genomic technologies, specifically DNA microarrays, to describe the molecular basis underlying cellular adaptation to environmental stresses.

Table of Contents:

Foreword
Preface
Acknowledgments

1. Genomics: Toward a Genome-level Understanding of the Structure, Functions, and Evolution of Biological Systems

1.1 Introduction
1.2 Definitions and Classifications
1.2.1 Classification based on system attributes
1.2.2 Classification based on relationships to other scientific disciplines
1.2.3 Classification based on types of organisms studied
1.3 Historical Perspective of Genomics
1.4 Challenges of Studying Functional Genomics
1.4.1 Defining gene function
1.4.2 Identifying and characterizing the molecular machines of life
1.4.3 Delineating gene regulatory networks
1.4.4 System-level understanding of biological systems beyond individual cells
1.4.5 Computational challenges
1.4.6 Multidisciplinary collaborations
1.5 Scope and General Approaches
1.5.1 Structural Genomics
1.5.2 Transcriptomics
1.5.3 Proteomics
1.6 Importance of Microbial Functional Genomics to the Study of Eukaryotes
1.7 Summary

2. Microbial Diversity and Genomics

2.1 Introduction
2.2 Biochemical Diversity
2.3 Genetic Diversity
2.3.1 The unseen majority
2.3.2 How many prokaryotic species are there?
2.4 The Challenge of Describing Prokaryotic Diversity
2.4.1 Methods to study microbial diversity
2.4.2 Limitations of culture-independent methods
2.4.3 Interesting findings from culture-independent approaches
2.5 Diversity of Microbial Genomes and Whole-Genome Sequencing
2.5.1 Genomic diversity within species
2.5.2 Genome structure and its relation to the ecological niche
2.5.3 General trends in genome functional content
2.5.4 Biases in the collection of sequenced species: a limit to understanding
2.6 Summary

3. Computational Genome Annotation

3.1 Introduction
3.2 Prediction of Protein-Coding Genes
3.2.1 Evaluation of coding potential
3.2.2 Identification of translation start
3.2.3 Ab initio gene prediction through information fusion
3.2.4 Gene identification through comparative analysis
3.2.5 Interpretation of gene prediction
3.3 Prediction of RNA-Coding Genes
3.4 Identification of Promoters
3.4.1 Promoter prediction through feature recognition
3.5 Operon Identification
3.6 Functional Categories of Genes
3.7 Characterization of Other Features in a Genome
3.8 Genome-Scale Gene Mapping
3.9 Existing Genome Annotation Systems
3.10 Summary

4. Microbial Evolution from a Genomics Perspective

4.1 Introduction
4.2 Identification of Orthologous Genes
4.3 Genome Perspectives on Molecular Clock
4.3.1 Historical overview
4.3.2 Current genomic view on molecular evolutionary clock
4.3.3 Timing genome divergence
4.4 Genome Perspectives on Horizontal Gene Transfer
4.4.1 Historical overview of horizontal gene transfer
4.4.2 Identification of HGT
4.4.3 Mechanisms underlying HGT
4.4.4 Types of genes subjected to HGT
4.4.5 Classification and scope of HGT
4.4.6 Evolutionary impact of HGT
4.5 Genomic Perspectives on Gene Duplication, Gene Loss, and Other Evolutionary Processes
4.5.1 Gene and genome duplication
4.5.2 Genomic perspectives on gene loss
4.5.3 Genomic perspectives on other evolutionary processes
4.6 Universal Tree of Life
4.6.1 Establishment of a universal tree of life
4.6.2 Challenges and current view of the universal tree
4.6.3 Genome-based phylogenetic analysis
4.7 Minimal Genomes
4.8 Genomic Insights into Lifestyle Evolution
4.9 Genome Perspective of Mitochondrial Evolution
4.10 Summary

5. Computational Methods for Functional Prediction of Genes

5.1 Introduction
5.2 Methods for Gene Function Inference
5.2.1 Gene functions at different levels
5.2.2 Searching for clues to gene function
5.3 From Gene Sequence to Function
5.3.1 Hierarchies of protein families
5.3.2 Searching family trees
5.3.3 Orthologous vs. paralogous genes
5.3.4 Genes with multiple domains
5.4 Identification of Sequence Motifs
5.5 Structure-Based Function Prediction
5.5.1 Protein fold recognition through protein threading
5.5.2 From structure to function
5.5.3 Disordered vs. ordered regions in proteins
5.6 Nonhomologous Approaches to Functional Inference
5.7 Functional Inference at a Systems Level
5.8 Summary

6. DNA Microarray Technology

6.1 Introduction
6.2 Types of Microarrays and Advantages
6.2.1 Concepts, principles, and history
6.2.2 Microarray types and their advantages
6.3 Microarray Fabrication
6.3.1 Microarray fabrication substrates and modification
6.3.2 Arraying technology
6.3.3 Critical issues for microarray fabrication
6.4 Microarray Hybridization and Detection
6.4.1 Probe design, target preparation, and quality
6.4.2 Hybridization
6.4.3 Detection
6.4.4 Critical issues in hybridization and detection
6.5 Microarray Image Processing
6.5.1 Data acquisition
6.5.2 Assessment of spot quality and reliability, and background subtraction
6.6 Using Microarrays to Monitor Gene Expression
6.6.1 General approaches to revealing differences in gene expression
6.6.2 Specificity, sensitivity, reproducibility, and quantitation of microarray-based detection for monitoring gene expression
6.6.3 Microarray experimental design for monitoring gene expression
6.7 Summary

7. Microarray Gene Expression Data Analysis

7.1 Introduction
7.2 Normalization of Microarray Gene Expression Data
7.2.1 Sources of systematic errors
7.2.2 Experimental design to minimize systematic variations
7.2.3 Selection of reference points for data normalization
7.2.4 Normalization methods
7.3 Data Analysis
7.3.1 Data transformation
7.3.2 Principle component analysis
7.4 Identification of Differentially Expressed Genes
7.5 Identification of Coexpressed Genes
7.5.1 Basics of gene expression data clustering
7.5.2 Clustering of gene expression data
7.5.3 Cluster identification from noisy background
7.5.4 EXCAVATOR: a software for gene expression data analysis
7.5.5 Discovering subtypes through data clustering
7.6 Applications of Gene Expression Data Analysis for Pathway Inference
7.6.1 Data-constrained pathway construction
7.7 Summary

8. Mutagenesis as a Genomic Tool for Studying Gene Function

8.1 Introduction
8.2 Transposon Mutagenesis
8.2.1 Overview of transposition in bacteria
8.2.2 Transposons as tools for mutagenesis
8.2.3 Transposon-based approaches for identification of essential genes
8.2.4 Signature-tagged mutagenesis for studying bacterial pathogenicity
8.3 Targeted Mutagenesis Through Allelic Exchange
8.3.1 Suicide vector systems for allelic exchange
8.3.2 Strategies commonly utilized for targeted mutagenesis by allelic exchange
8.3.3 Application of allele exchange approach in functional genomic studies for sequenced microorganisms
8.4 Gene Silencing Using Antisense mRNA Molecules
8.4.1 Antisense RNA regulation in vivo
8.4.2 Antisense approach to large-scale functional genomic studies
8.5 Summary

9. Mass Spectrometry

9.1 Introduction
9.2 Fundamentals of Mass Spectrometry
9.2.1 Basic components of any mass spectrometer
9.2.2 Ionization methods
9.2.3 Mass analyzers
9.2.4 Coupling separation methods with mass spectrometry
9.2.5 Ion structural characterization
9.3 Fundamentals of Protein and Peptide Mass Spectrometry
9.3.1 Protein measurements
9.3.2 Peptide measurements
9.4 Mass Spectrometry for Protein and Proteome Characterization
9.4.1 Overview of mass spectrometry approaches for protein studies
9.4.2 Bottom-up mass spectrometry proteomics
9.4.3 Top-down mass spectrometry proteomics
9.4.4 Relating mass spectrometry proteomic data to biological information
9.5 Summary

10. Identification of Protein–Ligand Interactions

10.1 Introduction
10.2 High-Throughput Cloning of Open Reading Frames
10.2.1 Bacteriophage l att recombination-based cloning
10.2.2 Topoisomerase-based cloning
10.2.3 In vivo recombination-based cloning in yeast
10.2.4 Advantages and disadvantages of recombinational cloning systems
10.3 Yeast Two-Hybrid Selection System
10.3.1 Analysis of genome-wide protein–protein interactions in yeast
10.3.2 Genome-wide yeast two-hybrid analysis of other organisms
10.4 Use of Phage Display to Detect Protein–Ligand Interactions
10.4.1 Display of proteins on M13 filamentous phage
10.4.2 Display of proteins on the T7 bacteriophage
10.4.3 Combining yeast two-hybrid and phage display data
10.5 Detecting Interactions with Protein Fragment Complementation Assays
10.5.1 Overview
10.5.2 Protein fragment complementation using dihydrofolate reductase
10.5.3 Monitoring protein interactions by intracistronic b-galactosidase complementation
10.6 Use of Mass Spectrometry for Protein–Protein Interaction Mapping
10.6.1 Overview
10.6.2 Identification of substrates for E. coli GroEL
10.6.3 Identification of protein complexes in Saccharomyces cerevisiae
10.7 Protein Assays for Protein Expression Profiling and Interactions
10.7.1 Antibody arrays for protein expression profiling
10.7.2 Functional analysis using peptide, protein, and small-molecule arrays
10.8 Surface Plasmon Resonance Biosensor Analysis
10.8.1 Measuring interactions of biomolecules with SPR
10.8.2 Integration of SPR biosensors with mass spectrometry
10.9 Summary

11. The Functional Genomics of Model Organisms: Addressing Old Questions from a New Perspective

11.1 Introduction
11.2 Escherichia coli: A Model Eubacterium
11.2.1 E. coli genome
11.2.2 E. coli transcriptomics
11.2.3 E. coli proteomics
11.2.4 Modeling E. coli metabolism: in silico metabolomics
11.3 Bacillus subtilis: A Paradigm for Gram-Positive Bacteria
11.3.1 B. subtilis genome
11.3.2 B. subtilis transcriptomics
11.3.3 B. subtilis proteomics
11.4 Saccharomyces cerevisiae: A Model for Higher Eukaryotes
11.4.1 Yeast genome
11.4.2 Yeast transcriptomics
11.4.3 Yeast proteomics
11.4.4 Yeast interactome: mapping protein–protein interactions
11.5 Comparative Genomics of Model Eukaryotic Organisms
11.6 Summary

12. Functional Genomic Analysis of Bacterial Pathogens and Environmentally Significant Microorganisms

12.1 Introduction
12.2 Advancing Knowledge of Bacterial Pathogenesis through Genome Sequence and Function Annotation
12.2.1 Predicting virulence genes from sequence homology
12.2.2 Repeated DNA elements indicate potential virulence factors
12.2.3 Evolution of bacterial pathogens: gene acquisition and loss
12.3 Comparative Genomics: Clues to Bacterial Pathogenicity
12.3.1 The genomics of Mycobacterium tuberculosis: virulence gene identification and genome plasticity
12.3.2 Microarray-based comparative genomics of Helicobacter pylori
12.3.3 Comparative analysis of the Borrelia burgdorferi and Treponema pallidum genomes
12.3.4 Sequence comparison of pathogenic and nonpathogenic species of Listeria
12.3.5 Comparative genomics of Chlamydia pneumoniae and Chlamydia trachomatis: two closely related obligate intracellular pathogens
12.4 Discovery of Novel Infection-Related Genes Using Signature-Tagged Mutagenesis
12.4.1 Vibrio cholerae genes critical for colonization
12.4.2 Virulence genes of Staphylococcus aureus infection
12.4.3 Escherichia coli K1: identification of invasion genes
12.4.4 Diverse genes implicated in Streptococcus pneumoniae virulence
12.5 Application of Microarrays to Delineating Gene Function and Interaction
12.5.1 Exploring the transcriptome of bacterial pathogens
12.5.2 Elucidating the molecular intricacies of host–pathogen interactions
12.5.3 Identification of antimicrobial drug targets
12.6 The Proteomics of Bacterial Pathogenesis
12.6.1 Comparative proteomics
12.6.2 Defining the proteome of individual bacterial pathogens
12.6.3 Proteomic approach to host–pathogen interactions
12.7 Genome Sequence and Functional Analysis of Environmentally Important Microorganisms
12.7.1 Dissimilatory metal ion-reducing bacterium Shewanella oneidensis
12.7.2 Extreme radiation-resistant bacteri