Molecular Biology: Principles and Practice 2nd Edition

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Molecular Biology: Principles and Practice 2nd Edition

By Michael M. Cox, Jennifer Doudna, and Michael O’Donnell

Molecular Biology: Principles and Practice 2nd Edition PDF. Learn how science is done and get excited about scientific discovery. Molecular Biology takes you through the fundamental concepts of science by sharing the work of researchers who have shaped, and who continue to shape the field today.

Table of Contents

I. Foundations

1. Evolution, Science, and Molecular Biology

2. DNA: The Repository of Biological Information

3. Chemical Basis of Information Molecules

4. Protein Structure

5. Protein Function

II. Nucleic Acid Structure and Methods

6. DNA and RNA Structure

7. Studying Genes

8. Genomes, Transcriptomes, and Proteomes

9. Topology: Functional Deformations of DNA

10. Nucleosomes, Chromatin, and Chromosome Structure

III. Information Transfer

11. DNA Replication

12. DNA Mutation and Repair

13. Recombinational DNA Repair and Homologous Recombination

14. Site-Specific Recombination and Transposition

15. Transcription: DNA-Dependent Synthesis of RNA

16. RNA Processing

17. The Genetic Code

18. Protein Synthesis

IV. Regulation

19. Regulating the Flow of Information

20. The Regulation of Gene Expression in Bacteria

21. The Transcriptional Regulation of Gene Expression in Eukaryotes

22. The Posttranscriptional Regulation of Gene Expression in Eukaryotes

Appendix: Model Organisms

Glossary

Solutions to Problems

Index

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Molecular Biology 2nd Edition – David P. Clark

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Molecular Biology 2nd Edition

By David P. Clark and Nanette J. Pazdernik

Molecular Biology 2nd Edition PDF examines the basic concepts of molecular biology while incorporating primary literature from today’s leading researchers. This updated edition includes Focuses on Relevant Research sections that integrate primary literature from Cell Press and focus on helping the student learn how to read and understand research to prepare them for the scientific world.

The new Academic Cell Study Guide features all the articles from the text with concurrent case studies to help students build foundations in the content while allowing them to make the appropriate connections to the text. Animations provided deal with topics such as protein purification, transcription, splicing reactions, cell division and DNA replication and SDS-PAGE. The text also includes updated chapters on Genomics and Systems Biology, Proteomics, Bacterial Genetics and Molecular Evolution and RNA. An updated ancillary package includes flashcards, online self quizzing, references with links to outside content and PowerPoint slides with images.

This text is designed for undergraduate students taking a course in Molecular Biology and upper-level students studying Cell Biology, Microbiology, Genetics, Biology, Pharmacology, Biotechnology, Biochemistry, and Agriculture.

NEW: “Focus On Relevant Research” sections integrate primary literature from Cell Press and focus on helping the student learn how to read and understand research to prepare them for the scientific world.
NEW: Academic Cell Study Guide features all articles from the text with concurrent case studies to help students build foundations in the content while allowing them to make the appropriate connections to the text.
NEW: Animations provided include topics in protein purification, transcription, splicing reactions, cell division and DNA replication and SDS-PAGE
Updated chapters on Genomics and Systems Biology, Proteomics, Bacterial Genetics and Molecular Evolution and RNA
Updated ancillary package includes flashcards, online self quizzing, references with links to outside content and PowerPoint slides with images.
Fully revised art program

Table of Contents

Title

Copyright

Dedication

Acknowledgements

UNIT 1. Basic Chemical and Biological Principles

Chapter 1. Cells and Organisms

1 What Is Life?

2 Living Creatures Are Made of Cells

3 Eubacteria and Archaea Are Genetically Distinct

4 Eukaryotic Cells Are Subdivided into Compartments

5 The Diversity of Eukaryotes

6 Haploidy, Diploidy, and the Eukaryote Cell Cycle

7 Organisms Are Classified

8 Some Widely-Studied Organisms Serve as Models

9 Basic Characteristics of a Model Organism

10 Purifying DNA from Model Organisms

11 Viruses Are Not Living Cells

12 Bacterial Viruses Infect Bacteria

13 Human Viral Diseases Are Common

14 A Variety of Subcellular Genetic Entities Exist

Chapter 2. Basic Genetics

1 Gregor Mendel, The Father of Classical Genetics

2 Genes Determine Each Step in Biochemical Pathways

3 Mutants Result from Alterations in Genes

4 Phenotypes and Genotypes

5 Chromosomes Are Long, Thin Molecules That Carry Genes

6 Dominant and Recessive Alleles

7 Genes from Both Parents Are Mixed by Sexual Reproduction

8 Neighboring Genes Are Linked During Inheritance Unless the DNA Recombines

9 Identifying Genes that Cause Human Diseases

Chapter 3. DNA, RNA, and Protein

1 History of DNA as the Genetic Material

2 Nucleic Acid Molecules Carry Genetic Information

3 Chemical Structure of Nucleic Acids

4 Double-Stranded DNA Forms a Double Helix

5 Constituents of Chromosomes

6 The Central Dogma Outlines the Flow of Genetic Information

7 Ribosomes Read the Genetic Code

8 Various Classes of RNA Have Different Functions

9 Proteins Carry Out Many Cell Functions

Chapter 4. Genomes and DNA

1 Genome Organization

2 Repeated Sequences Are a Feature of Eukaryotic DNA

3 Palindromes, Inverted Repeats, and Stem and Loop Structures

4 Multiple A-Tracts Cause DNA to Bend

5 Supercoiling Is Necessary for Packaging of Bacterial DNA

6 Separation of DNA Fragments by Electrophoresis

7 Alternative Helical Structures of DNA Occur

8 Packaging DNA in Eukaryotic Nuclei

Chapter 5. Manipulation of Nucleic Acids

1 Manipulating DNA

2 Chemical Synthesis of DNA

3 Measuring the Concentration of DNA and RNA with Ultraviolet Light

4 Radioactive Labeling of Nucleic Acids

5 Fluorescence in the Detection of DNA and RNA

6 The Electron Microscope

7 Hybridization of DNA and RNA

UNIT 2. The Genome

Chapter 6. Polymerase Chain Reaction

1 Fundamentals of the Polymerase Chain Reaction

2 Inverse PCR

3 Randomly Amplified Polymorphic DNA (RAPD)

4 Reverse Transcriptase PCR

5 Differential Display PCR

6 Rapid Amplification of cDNA Ends (RACE)

7 PCR in Genetic Engineering

8 Directed Mutagenesis

9 Engineering Deletions and Insertions by PCR

10 Real-Time Fluorescent PCR

11 Molecular Beacons and Scorpion Primers

12 Use of PCR in Medical Diagnosis

13 Environmental Analysis by PCR

14 Rescuing DNA from Extinct Life Forms by PCR

Chapter 7. Cloning Genes for Analysis

1 Properties of Cloning Vectors

2 Detecting Insertions in Vectors

3 Moving Genes Between Organisms: Shuttle Vectors

4 Bacteriophage Lambda Vectors

5 Cosmid Vectors

6 Yeast Artificial Chromosomes

7 Bacterial and P1 Artificial Chromosomes

8 Recombineering Increases the Speed of Gene Cloning

9 A DNA Library is a Collection of Genes from One Source

10 Cloning Complementary DNA Avoids Introns

11 Chromosome Walking

12 Cloning by Subtractive Hybridization

13 Expression Vectors

Chapter 8. DNA Sequencing

1 DNA Sequencing—General Principles for Chain Termination Sequencing

2 Primer Walking Along a Strand of DNA

3 Automated Sequencing

4 Cycle Sequencing

5 The Emergence of DNA Chip Technology

6 Pyrosequencing

7 Second-Generation Sequencing

8 Third-Generation Sequencing

9 Nanopore Detectors for DNA

Chapter 9. Genomics & Systems Biology

1 Large-Scale Mapping with Sequence Tags

2 Assembling Small Genomes by Shotgun Sequencing

3 Race for the Human Genome

4 Survey of the Human Genome

5 Pharmacogenomics—Genetically-Individualized Drug Treatment

6 Personal Genomics and Comparative Genomics

7 Bioinformatics and Computer Analysis

8 Systems Biology

9 Metagenomics and Community Sampling

10 Epigenetics and Epigenomics

UNIT 3. The Central Dogma of Molecular Biology

Chapter 10. Cell Division and DNA Replication

1 Cell Division and Reproduction Are Not Always Identical

2 DNA Replication Occurs at the Replication Fork

3 Properties of DNA Polymerase

4 Nucleotides Are the Precursors for DNA Synthesis

5 DNA Polymerase Elongates DNA Strands

6 The Complete Replication Fork Is Complex

7 Discontinuous Synthesis of the Lagging Strand

8 Chromosome Replication Initiates at oriC

9 Chromosome Replication Terminates at terC

10 Cell Division in Bacteria Occurs after Replication of Chromosomes

11 The Concept of the Replicon

12 Replicating Linear DNA in Eukaryotes

13 Cell Division in Higher Organisms

Chapter 11. Transcription of Genes

1 Genes Are Expressed by Making RNA

2 How Is the Beginning of a Gene Recognized?

3 Manufacturing the Message

4 RNA Polymerase Knows Where to Stop

5 How Does the Cell Know Which Genes to Turn On?

6 Transcription in Eukaryotes Is More Complex

Chapter 12. Processing of RNA

1 RNA Is Processed in Several Ways

2 Coding and Non-Coding RNA

3 Processing of Ribosomal and Transfer RNA

4 Eukaryotic Messenger RNA Contains a Cap and a Tail

5 Introns Are Removed from RNA by Splicing

6 Alternative Splicing Produces Multiple Forms of RNA

7 Inteins and Protein Splicing

8 Base Modification of rRNA Requires Guide RNA

9 RNA Editing Alters the Base Sequence

10 Transport of RNA out of the Nucleus

11 Degradation of mRNA

Chapter 13. Protein Synthesis

1 Overview of Protein Synthesis

2 Proteins Are Chains of Amino Acids

3 Decoding the Genetic Information

4 The Ribosome: The Cell’s Decoding Machine

5 Three Possible Reading Frames Exist

6 The tRNA Occupies Three Sites During Elongation of the Polypeptide

7 Bacterial mRNA Can Code for Several Proteins

8 Some Ribosomes Become Stalled and Are Rescued

9 Differences between Eukaryotic and Prokaryotic Protein Synthesis

10 Protein Synthesis Is Halted When Resources Are Scarce

11 A Signal Sequence Marks a Protein for Export from the Cell

12 Protein Synthesis Occurs in Mitochondria and Chloroplasts

13 Mistranslation Usually Results in Mistakes in Protein Synthesis

14 Many Antibiotics Work by Inhibiting Protein Synthesis

15 Post-Translational Modifications of Proteins

16 Selenocysteine and Pyrrolysine: Rare Amino Acids

17 Degradation of Proteins

Chapter 14. Protein Structure and Function

1 The Structure of Proteins Reflects Four Levels of Organization

2 Determining Protein Structures

3 Nucleoproteins, Lipoproteins, and Glycoproteins Are Conjugated Proteins

4 Proteins Serve Numerous Cellular Functions

5 Protein (Nano)-Machines

6 Enzymes Catalyze Metabolic Reactions

7 Binding of Proteins to DNA Occurs in Several Different Ways

8 Denaturation of Proteins

Chapter 15. Proteomics

1 The Proteome

2 Antibodies Are Essential Proteomics Tools

3 Western Blotting of Proteins

4 Isolating Proteins with Chromatography

5 Mass Spectrometry for Protein Identification

6 Protein-Tagging Systems

7 Selection by Phage Display

8 Protein Interactions: The Yeast Two-Hybrid System

9 Protein Interaction by Co-Immunoprecipitation

10 Protein Arrays

11 Metabolomics

UNIT 4. Regulating Gene Expression

Chapter 16. Regulation of Transcription in Prokaryotes

1 Gene Regulation Ensures a Physiological Response

2 Regulation at the Level of Transcription Involves Several Steps

3 Alternative Sigma Factors in Prokaryotes Recognize Different Sets of Genes

4 Activators and Repressors Participate in Positive and Negative Regulation

5 Two-Component Regulatory Systems

6 Specific versus Global Control

7 Accessory Factors and Nucleoid-Binding Proteins

8 Anti-Termination as a Control Mechanism

Chapter 17. Regulation of Transcription in Eukaryotes

1 Transcriptional Regulation in Eukaryotes Is More Complex Than in Prokaryotes

2 Specific Transcription Factors Regulate Protein-Encoding Genes

3 Negative Regulation of Transcription Occurs in Eukaryotes

4 Heterochromatin Blocks Access to DNA in Eukaryotes

5 Methylation of Eukaryotic DNA Controls Gene Expression

6 X-Chromosome Inactivation Occurs in Female XX Animals

Chapter 18. Regulation at the RNA Level

1 Regulation at the Level of mRNA

2 Basic Principles of RNA Interference (RNAi)

3 Long Non-coding Regulatory RNA

4 CRISPR: Anti-Viral Defense in Bacteria

5 Premature Termination Causes Attenuation of RNA Transcription

6 Riboswitches—RNA Acting Directly As a Control Mechanism

Chapter 19. Analysis of Gene Expression

1 Monitoring Gene Expression

2 Reporter Genes for Monitoring Gene Expression

3 Deletion Analysis of the Upstream Region

4 DNA-Protein Complexes Can Be Isolated by Chromatin Immunoprecipitation

5 Location of the Start of Transcription by Primer Extension

6 Transcriptome Analysis

7 DNA Microarrays for Gene Expression

8 TaqMan Quantitative PCR to Assay Gene Expression

9 Serial Analysis of Gene Expression (SAGE)

UNIT 5. Subcellular Life Forms

Chapter 20. Plasmids

1 Plasmids as Replicons

2 General Properties of Plasmids

3 Plasmid DNA Replicates by Two Alternative Methods

4 Many Plasmids Help Their Host Cells

5 Plasmids May Provide Aggressive Characters

6 Ti Plasmids Are Transferred from Bacteria to Plants

7 The 2μ Plasmid of Yeast

8 Certain DNA Molecules May Behave as Viruses or Plasmids

Chapter 21. Viruses

1 Viruses Are Infectious Packages of Genetic Information

2 The Great Diversity of Viruses

3 Viruses with RNA Genomes Have Very Few Genes

4 Retroviruses Use Both RNA and DNA

5 Subviral Infectious Agents

Chapter 22. Mobile DNA

1 Subcellular Genetic Elements as Gene Creatures

2 Most Mobile DNA Consists of Transposable Elements

3 Retroelements Make an RNA Copy

4 The Multitude of Transposable Elements

5 Junk DNA and Selfish DNA

UNIT 6. Changing the DNA Blueprint

Chapter 23. Mutations and Repair

1 Mutations Alter the DNA Sequence

2 The Major Types of Mutation

3 Chemical Mutagens Damage DNA

4 Overview of DNA Repair

5 Mutations Occur More Frequently at Hotspots

6 Reversions Are Genetic Alterations That Change the Phenotype Back to Wild-Type

7 Site-Directed Mutagenesis

Chapter 24. Recombination

1 Overview of Recombination

2 Molecular Basis of Homologous Recombination

3 Site-Specific Recombination

4 Recombination in Higher Organisms

5 Gene Conversion

Chapter 25. Bacterial Genetics

1 Reproduction versus Gene Transfer

2 Fate of the Incoming DNA after Uptake

3 Transformation Is Gene Transfer by Naked DNA

4 Gene Transfer by Virus—Transduction

5 Transfer of Plasmids between Bacteria

6 Gene Transfer among Gram-Positive Bacteria

7 Archaeal Genetics

8 Whole-Genome Sequencing

Chapter 26. Molecular Evolution

1 Getting Started—Formation of the Earth

2 Oparin’s Theory of the Origin of Life

3 Origin of Informational Macromolecules

4 The Autotrophic Theory of the Origin of Metabolism

5 Evolution of DNA, RNA, and Protein Sequences

6 Different Proteins Evolve at Very Different Rates

7 Symbiotic Origin of Eukaryotic Cells

8 DNA Sequencing and Biological Classification

9 Evolving Sideways: Horizontal Gene Transfer

Glossary

Index

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Molecular Diagnostics George Patrinos PDF

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Molecular Diagnostics George Patrinos

By George Patrinos, Wilhelm Ansorge and Phillip B. Danielson

Molecular Diagnostics 3rd Edition PDF focuses on the technologies and applications that professionals need to work in, develop, and manage a clinical diagnostic laboratory. Each chapter contains an expert introduction to each subject that is next to technical details and many applications for molecular genetic testing that can be found in comprehensive reference lists at the end of each chapter. Contents are divided into three parts, technologies, application of those technologies, and related issues. The first part is dedicated to the battery of the most widely used molecular pathology techniques. New chapters have been added, including the various new technologies involved in next-generation sequencing (mutation detection, gene expression, etc.), mass spectrometry, and protein-specific methodologies. All revised chapters have been completely updated, to include not only technology innovations, but also novel diagnostic applications. As with previous editions, each of the chapters in this section includes a brief description of the technique followed by examples from the area of expertise from the selected contributor. The second part of the book attempts to integrate previously analyzed technologies into the different aspects of molecular diagnostics, such as identification of genetically modified organisms, stem cells, pharmacogenomics, modern forensic science, molecular microbiology, and genetic diagnosis. Part three focuses on various everyday issues in a diagnostic laboratory, from genetic counseling and related ethical and psychological issues, to safety and quality management.

Presents a comprehensive account of all new technologies and applications used in clinical diagnostic laboratories
Explores a wide range of molecular-based tests that are available to assess DNA variation and changes in gene expression
Offers clear translational presentations by the top molecular pathologists, clinical chemists, and molecular geneticists in the field

Table of Contents

List of Contributors
Preface, Third Edition
Chapter 1. Molecular Diagnostics: Past, Present, and Future
- 1.1. Introduction
- 1.2. History of Molecular Diagnostics: Inventing the Wheel
- 1.3. The Post-Polymerase Chain Reaction Revolution
- 1.4. Molecular Diagnostics in the Post-Genomic Era
- 1.5. Future Perspectives: What Lies Beyond
- 1.6. Conclusions
Chapter 2. Describing DNA Variants (Mutation Nomenclature)
- 2.1. Introduction
- 2.2. History
- 2.3. Authorization
- 2.4. Definitions
- 2.5. Variant Descriptions
- 2.6. Mutalyzer
- 2.7. Concluding Remarks
Chapter 3. Low- and Medium-Throughput Variant Detection Methods: A Historical Perspective
- 3.1. Introduction
- 3.2. Genetic Screening Methods
- 3.3. Genetic Scanning Methods
- 3.4. Conclusions
Chapter 4. Quantitative Polymerase Chain Reaction
- 4.1. History of the Polymerase Chain Reaction
- 4.2. Principle of Real-Time Polymerase Chain Reaction
- 4.3. Real-Time Thermal Cyclers
- 4.4. How Data Are Obtained
- 4.5. How Data Are Quantified
- 4.6. Multiplex Quantitative Polymerase Chain Reaction
- 4.7. Applications of Quantitative Polymerase Chain Reaction and Reverse Transcriptase-Quantitative Polymerase Chain Reaction
- 4.8. Criteria for Optimizing Quantitative Polymerase Chain Reaction Assays
- 4.9. Conclusions
Chapter 5. Integrated Polymerase Chain Reaction Technologies (Sample-to-Answer Technologies)
- 5.1. Introduction
- 5.2. Commercial Sample-to-Answer Assay Systems
- 5.3. Clinical Applications: Performance for Infectious Pathogen Diagnostics
- 5.4. Forensic Applications: Performance for Human Identity Testing
- 5.5. Continuing Evolution of Sample-to-Answer Technologies
Chapter 6. High-Resolution Melting Curve Analysis for Molecular Diagnostics
- 6.1. Introduction to Melting Analysis
- 6.2. Genotyping of Known Variants by High-Resolution Melting
- 6.3. Variant Scanning by High-Resolution Melting
- 6.4. Specific Examples of High-Resolution Melting in Clinical Diagnostics
- 6.5. Other Applications of High-Resolution Melting in Molecular Diagnostics
- 6.6. Melting Curve Prediction and Assay Design Tools
- 6.7. Conclusions
Chapter 7. Molecular Techniques for DNA Methylation Studies
- 7.1. Introduction
- 7.2. Clinical Applications of DNA Methylation Analysis
- 7.3. Methods for DNA Methylation Analysis
- 7.4. Single-Cell DNA Methylation Analysis
- 7.5. Conclusions
Chapter 8. Perspectives for Future DNA Sequencing Techniques and Applications
- 8.1. Introduction
- 8.2. Commercially Available Analysis Platforms
- 8.3. Techniques/Systems in Development
- 8.4. Potential Future Techniques/Systems/Analysis Platforms
- 8.5. Perspectives for Future Applications and Diagnostics Techniques
- 8.6. Conclusions
Chapter 9. Advanced Personal Genome Sequencing as the Ultimate Diagnostic Test
- 9.1. Introduction
- 9.2. Advanced Whole-Genome Sequencing
- 9.3. What Is Needed to Implement This Vision of Genomic Precision Health Care Fully?
- 9.4. Conclusion
Chapter 10. Application of Padlock and Selector Probes in Molecular Medicine
- 10.1. Introduction
- 10.2. Padlock and Selector Probes
- 10.3. Application of Padlock and Molecular Inversion Probes for Genotyping
- 10.4. Biosensor Approaches Based on Rolling Circle–Amplified Padlock Probes
- 10.5. Application of Padlock Probes for Infectious Disease Diagnostics
- 10.6. Targeted Multiplex Copy Number Variation Analysis Using Selector Probes
- 10.7. High-Throughput Targeted Sequencing Using Selectors and Gap-Fill Padlock Probes
- 10.8. In Situ Nucleic Acid Detection Using Padlock Probes
- 10.9. Automation and Miniaturization of Padlock Probe/Rolling Circle Amplification Assays
- 10.10. Conclusions
Chapter 11. Advances in Microfluidics and Lab-on-a-Chip Technologies
- 11.1. Overview
- 11.2. Microfluidics for DNA Amplification and Analysis
- 11.3. Microfluidics for High-Resolution Melting Analysis
- 11.4. Microfluidics in Cytogenetics
- 11.5. Microfluidics for Protein Detection and Analysis
- 11.6. Microfluidic Sample Preparation
- 11.7. Microfluidics in Cell Sorting
- 11.8. Future of Microfluidics for Medical Diagnostics
Chapter 12. Protein Diagnostics by Proximity Ligation: Combining Multiple Recognition and DNA Amplification for Improved Protein Analyses
- 12.1. Introduction
- 12.2. Binding the Proteome
- 12.3. Current Affinity-Based Protein Detection Assays
- 12.4. Proximity-Dependent Nucleic Acid–Based Assays
- 12.5. Conclusion and Future Perspectives
Chapter 13. Application of Proteomics to Medical Diagnostics
- 13.1. Introduction
- 13.2. Clinical Impact and “Proteomics” Potential
- 13.3. Strategies for Mass Spectrometry–Based Proteomics: Discovery and Verification
- 13.4. Bioinformatics
- 13.5. Examples of Discovery and Verification Proteomics
- 13.6. Examples of Protein-Based Diagnostics Assays
- 13.7. Challenges in Clinical Proteomics
- 13.8. Future Advances and Concluding Remarks
Chapter 14. Molecular Cytogenetics in Molecular Diagnostics
- 14.1. Introduction
- 14.2. From Conventional to Molecular Cytogenetics
- 14.3. Fluorescence In Situ Hybridization
- 14.4. Basic Technical Elements and Materials
- 14.5. Types of Fluorescence In Situ Hybridization Probes and Fluorescence In Situ Hybridization Approaches for Metaphase and Interphase Fluorescence In situ Hybridization
- 14.6. Multicolor Fluorescence In Situ Hybridization Screening Assays
- 14.7. Multicolor Whole-Metaphase Scanning Techniques
- 14.8. Multicolor Chromosome Banding Techniques
- 14.9. Whole-Genome Scanning and Comparative Genomic Hybridization
- 14.10. Array-Based Techniques (Microarray)
- 14.11. Conclusions and Future Perspectives
- Glossary
Chapter 15. Cytogenomics of Solid Tumors by Next-Generation Sequencing: A Clinical Perspective
- 15.1. A Tumor Presents
- 15.2. From Microscopic Examination to Molecular Cytogenomics
- 15.3. The Promise of Liquid Biopsy for Cancer Diagnostics
- 15.4. Cytogenomic Applications
- 15.5. Implementation of Cytogenomics in the Clinic
- 15.6. Bioinformatics and Data Analysis
- 15.7. Concluding Remarks
Chapter 16. Pharmacogenomics in Clinical Care and Drug Discovery
- 16.1. Introduction
- 16.2. Pharmacogenetics Versus Pharmacogenomics
- 16.3. History of Pharmacogenomics
- 16.4. Analytical Methods in Pharmacogenomics
- 16.5. Pharmacogenomics in Clinical Settings
- 16.6. Population Differences in Pharmacogenomics
- 16.7. Complex Phenotypes
- 16.8. Pharmacogenomics and Regulatory Agencies
- 16.9. Pharmacogenomics in Drug Development
- 16.10. Useful Resources in Pharmacogenomics
- 16.11. New Trends in Pharmacogenomics
- 16.12. Ethical Implications
- 16.13. Public Health Pharmacogenomics
- 16.14. Conclusions and Future Perspectives
Chapter 17. Nutrigenomics: Integrating Genomic Approaches Into Nutrition Research
- 17.1. Introduction
- 17.2. Nature of Genetic Variation
- 17.3. Nutritional Epidemiology
- 17.4. Experimental Models
- 17.5. Defining the Phenotype
- 17.6. Integrating Complex Data Sets: Data Management, Bioinformatics, and Statistics
- 17.7. Conclusions
Chapter 18. DNA Microarrays and Genetic Testing
- 18.1. Introduction
- 18.2. DNA Microarrays
- 18.3. New Developments in DNA Microarrays and Genetic Testing
Chapter 19. Bioinformatics Tools for Data Analysis
- 19.1. Introduction
- 19.2. Next-Generation Sequencing Pipelines
- 19.3. Molecular Pathway Analysis: Why and What?
- 19.4. Conclusions
Chapter 20. Genomic Databases: Emerging Tools for Molecular Diagnostics
- 20.1. Introduction
- 20.2. Historical Overview of Genetic Databases
- 20.3. Models for Database Management
- 20.4. Mutation Database Types
- 20.5. Locus-Specific Databases in Molecular Genetic Testing
- 20.6. National/Ethnic Mutation Databases: Archiving the Genomic Basis of Human Disorders on a Population Basis
- 20.7. Database Management Systems for Locus-Specific Databases and National/Ethnic Mutation Databases
- 20.8. Incentivizing Data Sharing: The Microattribution Approach
- 20.9. Future Challenges
- 20.10. Conclusions
Chapter 21. Molecular Diagnostic Applications in Forensic Science
- 21.1. Introduction
- 21.2. Genetic Markers Commonly Used for Forensic Analysis
- 21.3. DNA Extraction Methodologies
- 21.4. DNA Quantitation
- 21.5. Capillary Electrophoresis and Data Interpretation
- 21.6. Statistical Calculations
- 21.7. Next Generation of Forensic DNA Technologies
- 21.8. Conclusions
Chapter 22. New Perspectives in Mass Disaster Victim Identification Assisted by DNA Typing and Forensic Genomics
- 22.1. Introduction
- 22.2. Classification of Mass Fatalities and Diverse Scenarios for Human Remains Retrieval
- 22.3. Conventional Identification Criteria Routinely Used for Human Identification
- 22.4. Criteria for the Preservation of Remains
- 22.5. DNA Polymorphisms Used for Tracing Kinship Between Fragmentary Human Remains and the Relatives Claiming Them
- 22.6. Challenges Concerning DNA Degradation and Contamination
- 22.7. Criteria Evolution and Technical Approaches Applied to DNA-Based Victim Identification in Mass Disasters From the Early 1990s to Date
- 22.8. Description of Analyzed Cases
- 22.9. From Forensic Genetics to Forensic Genomics: The Change of a Paradigm Driven by Technology
- 22.10. Future Perspectives
Chapter 23. Preimplantation Genetic Diagnosis
- 23.1. Introduction
- 23.2. Assisted Reproductive Technology and Biopsy
- 23.3. Preimplantation Genetic Diagnosis for Monogenic Disorders
- 23.4. Preimplantation Genetic Diagnosis for Chromosomal Aberrations
- 23.5. Emerging Technologies
- 23.6. Clinical Outcome of Preimplantation Genetic Diagnosis
- 23.7. Accuracy and Quality Control
- 23.8. Conclusions and Future Perspectives
- Web Resources
Chapter 24. Noninvasive Cell-Free DNA Prenatal Testing for Fetal Aneuploidy in Maternal Blood
- 24.1. Introduction
- 24.2. Established Prenatal Screening and Diagnosis Practices
- 24.3. Historical Background of Noninvasive Prenatal Testing
- 24.4. Origin of Cell-Free Fetal DNA
- 24.5. Noninvasive Prenatal Testing Methodologies
- 24.6. Biological and Technical Factors That Affect Noninvasive Prenatal Testing Results
- 24.7. Noninvasive Prenatal Testing in Clinical Trials
- 24.8. Noninvasive Prenatal Testing in the Clinical Setting
- 24.9. Counseling and Ethical Issues
- 24.10. Future Applications of Noninvasive Prenatal Testing
- 24.11. Conclusions
Chapter 25. Genetic Testing and Psychology
- 25.1. Introduction
- 25.2. Getting to the Test: Awareness, Access, and Advertising
- 25.3. Individual Factors Influencing the Utilization of Genetic Testing
- 25.4. Getting the Genetic Test Results: Personal Impact and Professional Communication
- 25.5. Family Communication
- 25.6. Future Challenges: Complexity and Diversity
Chapter 26. Genomic Medicine in Developing Countries and Resource-Limited Environments
- 26.1. Introduction
- 26.2. Conclusions and Future Perspectives
Chapter 27. Public Understanding of Genetic Testing and Obstacles to Genetics Literacy
- 27.1. Genetics Literacy and the Public Understanding of Genetic Testing
- 27.2. Obstacles to Genetics Literacy and How These Might Be Overcome
- 27.3. Conclusions and Suggestions
Chapter 28. Safety and the Biorepository
- 28.1. Introduction
- 28.2. Understanding Regulatory and Other Safety Issues Relevant to Biorepositories
- 28.3. Individuals Involved in Oversight of a Biorepository
- 28.4. Safety Training/Employee Education in a Biorepository
- 28.5. Biorepository Safety Areas
- 28.6. Conclusions
Chapter 29. Quality Assurance in Genetic Laboratories
- 29.1. Introduction
- 29.2. International Standards
- 29.3. Accreditation and Certification
- 29.4. Elements of a Quality Management System
- 29.5. Quality Control
- 29.6. Quality Assessment
- 29.7. Diagnostic Validation
- 29.8. Quality Improvement
- 29.9. Conclusions
Index

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Bioprocess Engineering Principles 2nd Edition

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Bioprocess Engineering Principles 2nd Edition

By Pauline M. Doran

Bioprocess Engineering Principles 2nd Edition PDF discusses bioprocess engineering from the perspective of biology students. It includes a great deal of new material and has been extensively revised and expanded. These updates strengthen the book and maintain its position as the book of choice for senior undergraduates and graduates seeking to move from biochemistry/microbiology/molecular biology to bioprocess engineering.

All chapters thoroughly revised for current developments, with over 200 pgs of new material, including significant new content in: Metabolic Engineering, Sustainable Bioprocessing, Membrane Filtration, Turbulence and Impeller Design, Downstream Processing, Oxygen Transfer Systems
Over 150 new problems and worked examples
More than 100 new illustrations

Table of Contents

Part 1: Introduction

Chapter 1 – Bioprocess Development: An Interdisciplinary Challenge

Chapter 2 – Introduction to Engineering Calculations

Chapter 3 – Presentation and Analysis of Data

Part 2: Material and Energy Balances

Chapter 5 – Energy Balances

Chapter 6 – Unsteady-State Material and Energy Balances

Part 3: Physical Processes

Chapter 7 – Fluid Flow

Chapter 8 – Mixing

Chapter 9 – Heat Transfer

Chapter 10 – Mass Transfer

Chapter 11 – Unit Operations

Chapter 12 – Homogeneous Reactions

Chapter 13 – Heterogeneous Reactions

Chapter 14 – Reactor Engineering

Appendix A – Conversion Factors

Appendix B – Ideal Gas Constant

Appendix C – Physical and Chemical Property Data

Appendix D – Steam Tables

Appendix E – Mathematical Rules

Appendix F – U.S. Sieve and Tyler Standard Screen Series

Index

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Biotechnology Academic Cell Update

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Biotechnology Academic Cell Update

By David P. Clark and Nanette Pazdernik

Biotechnology Academic Cell Update PDF. It’s now available with the most current and relevant journal articles from Cell Press, Biotechnology Academic Cell Update Edition approaches modern biotechnology from a molecular basis, which grew out of the increasing biochemical understanding of physiology. Using straightforward, less-technical jargon, Clark and Pazdernik manage to introduce each chapter with a basic concept that ultimately evolves into a more specific detailed principle. This up-to-date text covers a wide realm of topics, including the forensics used in crime scene investigations, the burgeoning field of nanobiotechnology, bioethics and other cutting edge topics in today’s world of biotechnology.

Table of Contents

PREFACE
ACKNOWLEDGMENTS
INTRODUCTION
CHAPTER 1 Basics of biotechnology

CHAPTER 2 DNA, RNA, and protein

CHAPTER 3 Recombinant DNA technology

CHAPTER 4 DNA synthesis in vivo and in vitro

CHAPTER 5 RNA-based technologies

CHAPTER 6 Immune technology

CHAPTER 7 Nanobiotechnology

CHAPTER 8 Genomics and gene expression

CHAPTER 9 Proteomics

CHAPTER 10 Recombinant proteins

CHAPTER 11 Protein engineering

CHAPTER 12 Environmental biotechnology

CHAPTER 13 Pathway engineering

CHAPTER 14 Transgenic plants and plant biotechnology

CHAPTER 15 Transgenic animals

CHAPTER 16 Inherited defects

CHAPTER 17 Gene therapy

CHAPTER 18 Molecular biology of cancer

CHAPTER 19 Noninfectious diseases

CHAPTER 20 Aging and apoptosis

CHAPTER 21 Bacterial infections

CHAPTER 22 Viral and prion infections

CHAPTER 23 Biowarfare and bioterrorism

CHAPTER 24 Forensic molecular biology

CHAPTER 25 Bioethics in biotechnology

BIOTECHNOLOGY Multiple-choice answer key

GLOSSARY

INDEX

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Biotechnology Entrepreneurship: Starting, Managing, and Leading Biotech Companies

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Biotechnology Entrepreneurship: Starting, Managing, and Leading Biotech Companies

By Craig Shimasaki

Biotechnology Entrepreneurship: Starting, Managing, and Leading Biotech Companies PDF. As an authoritative guide to biotechnology enterprise and entrepreneurship, Biotechnology Entrepreneurship and Management supports the international community in training the biotechnology leaders of tomorrow.

Outlining fundamental concepts vital to graduate students and practitioners entering the biotech industry in management or in any entrepreneurial capacity, Biotechnology Entrepreneurship and Management provides tested strategies and hard-won lessons from a leading board of educators and practitioners.

It provides a ‘how-to’ for individuals training at any level for the biotech industry, from macro to micro. Coverage ranges from the initial challenge of translating a technology idea into a working business case, through securing angel investment, and in managing all aspects of the result: business valuation, business development, partnering, biological manufacturing, FDA approvals and regulatory requirements.

An engaging and user-friendly style is complemented by diverse diagrams, graphics and business flow charts with decision trees to support effective management and decision making.

Provides tested strategies and lessons in an engaging and user-friendly style supplemented by tailored pedagogy, training tips and overview sidebars
Case studies are interspersed throughout each chapter to support key concepts and best practices.
Enhanced by use of numerous detailed graphics, tables and flow charts

Table of Contents

Front Matter

Copyright

Dedication

Preface

Foreword

Acknowledgements

Contributors

Section I: Biotechnology Entrepreneurship

Section II: The Human Capital

Section III: The Technology

Section IV: The Emerging-Stage Biotechnology Company

Section V: Biotechnology Market Development

Section VI: The Financial Capital

Section VII: Biotechnology Product Development

Section VIII: The Later-Stage Biotechnology Company

Index

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Biotechnology in Animal Husbandry

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Biotechnology in Animal Husbandry

By Various

Biotechnology in Animal Husbandry PDF. Animal biotechnology is a broad umbrella encompassing the polarities of fundamental and applied research including molecular modelling, molecular and quantitative genetics, gene manipulation, development of diagnostics and vaccines and manipulation of tissue or digestion metabolism by growth promoters. Although animal biotechnology in the broadest sense is not new, what is new is the level of complexity and precision involved in scientists’ current ability to manipulate living organisms.
This new book sets out to show that the important ideas in animal biotechnology are exciting and relevant to everyday experience. It represents an important update of the literature for research workers, lecturers, and advisers in animal science, but is also a core text for advanced undergraduate courses in animal science and biotechnology. It will be an essential acquisition for librarians in agriculture and veterinary science.

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Cell and Molecular Biology and Imaging of Stem Cells

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Cell and Molecular Biology and Imaging of Stem Cells

By Heide Schatten

Cell and Molecular Biology and Imaging of Stem Cells PDF features original and review articles written by experts who have made significant contributions to stem cell biology and imaging. Chapters cover a broad spectrum of aspects of the field, including Stem cells from the Amniotic Fluid and Placenta, Biomaterials as Artificial Niches for Pluripotent Stem Cell Engineering, Low-Intensity Ultrasound in Stem Cells and Tissue Engineering, Mammalian Neo-Oogenesis from Ovarian Stem Cells, Oct4-EGFP Transgenic Pigs as a New Tool for Visualization of Pluripotent and Reprogrammed Cells, Regulation of Adult Intestinal Stem Cells, Stem Cell Therapy for Veterinary Orthopedic Lesions, Sex Steroid Combinations in Regenerative Medicine for Brain and Heart Diseases, Hair Follicle Stem Cells, The Potential of Using Induced Pluripotent Stem Cells in Skin Diseases, Mitochondrial Differentiation in Early Embryo Cells and Pluripotent Stem Cells, and The Role of Centrosomes in Cancer Stem Cell Functions.

Cell and Molecular Biology and Imaging of Stem Cells addresses a wide variety of cell and molecular topics in unprecedented detail, and is a must-read for graduate students and academic and industry professionals in the expanding field of stem cell biology.

Reviews new imaging tools and markers for cell and molecular imaging in stem cell biology.
Covers novel aspects of stem cell imaging in reproductive biology and stem cell niches
Includes chapters on the developing area of centrosome biology as it applies to embryonic and adult stem differentiation

Table of Contents

Contributors vii

Preface xi

1 Cell and Molecular Biology and Imaging of Stem Cells: Stem Cells from the Amniotic Fluid and Placenta 1
Amritha Kidiyoor, Sean V. Murphy, and Anthony Atala

2 Biomaterials as Artificial Niches for Pluripotent Stem Cell Engineering 21
Kyung Min Park and Sharon Gerecht

3 Low-Intensity Ultrasound in Stem Cells and Tissue Engineering 45
Byung Hyune Choi, Kil Hwan Kim, Mrigendra Bir Karmacharya, Byoung-Hyun Min and So Ra Park

4 Mammalian Neo-Oogenesis from Ovarian Stem Cells In Vivo and In Vitro 67
Antonin Bukovsky and Michael R. Caudle

5 Oct4-EGFP Transgenic Pigs as a New Tool for Visualization of Pluripotent and Reprogrammed Cells 137
Monika Nowak-Imialek and Heiner Niemann

6 Regulation of Adult Intestinal Stem Cells through Thyroid Hormone-Induced Tissue Interactions during Amphibian Metamorphosis 153
Atsuko Ishizuya-Oka

7 Stem Cell Therapy for Veterinary Orthopedic Lesions 173
Anna Paula Balesdent Barreira and Ana Liz Garcia Alves

8 Sex Steroid Combinations in Regenerative Medicine for Brain and Heart Diseases: The Vascular Stem Cell Niche and a Clinical Proposal 193
Antonin Bukovsky and Michael R. Caudle

9 Hair Follicle Stem Cells 211
Hilda Amalia Pasolli

10 The Potential of Using Induced Pluripotent Stem Cells in Skin Diseases 223
Shigeki Ohta, Ophelia Veraitch, Hideyuki Okano, Manabu Ohyama, and Yutaka Kawakami

11 Mitochondrial Differentiation in Early Embryo Cells and Pluripotent Stem Cells 247
Heide Schatten, Qing-Yuan Sun, and Randall S. Prather

12 The Role of Centrosomes in Cancer Stem Cell Functions 259
Heide Schatten

Index 281

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Cell and Molecular Biology of the Cytoskeleton

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Cell and Molecular Biology of the Cytoskeleton

By J.W. Shay

Cell and Molecular Biology of the Cytoskeleton PDF focuses on the three major fibrous proteins in the cytoplasm that are collectively known as the cytoskeletal sys tem. These polymorphic cytoskeletal proteins are microtubules (25-nm diam eter), microfilaments (6-nm diameter), and intermediate filaments (l O-nm diameter). Microtubules consist of tubulin and several well-characterized mi crotubule-associated proteins (MAPs) such as MAPl, MAP2, and tau. Micro filaments consist of actin and associate with actin-binding proteins, including alpha-actinin, filamin, myosin, tropomyosin, vinculin, and others. Intermedi ate filaments consist of at least five different tissue-specific classes, including desmin or skeletin (muscle), prekeratin (epithelial), vimentin (mesenchymal), neurofilament (nerve), and glial acidic fibrillary protein (astrocytes). In this volume distinguished researchers in the field cover the interaction of these fibrous proteins, not only with each other and other cytoplasmic components, but also with such biological processes as cell shape changes, growth, motility, secretion, and division. These comprehensive reviews ex plore the cytoskeleton’s molecular, biochemical, and structural properties with an emphasis on their manifestation in the living cell.

Table of Contents

Front Matter

Probing the Cytoskeleton by Microinjection

Structural Aspects of Intermediate Filaments

The Structure and Evolution of Intermediate Filament Genes

Differential Expression of the Genes Encoding the Keratins of Cultured Human Epidermal Cells

Organization and Expression of the Vimentin and Desmin Genes

Actin

The Actin Genes in Caenorhabditis elegans

Implications of Microtubule Polarity for Microtubule Function

Molecular Mechanisms Controlling Tubulin Synthesis

Regulation of Tubulin Expression in Brain

Tubulins from Plants, Fungi, and Protists

Back Matter

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Confocal Microscopy for Biologists

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Confocal Microscopy for Biologists

By Alan R. Hibbs

Confocal Microscopy for Biologists PDF. There has been a great upsurge in interest in light microscopy in recent years due to the advent of a number of significant advances in microscopy, one of the most important of which is confocal microscopy. Confocal microscopy has now become an important research tool, with a large number of new fluorescent dyes becoming available in the past few years, for probing your pet structure or molecule within fixed or living cell or tissue sampies. Many of the people interested in using confocal microscopy to further their research do not have a background in microscopy or even cell biology and so not only do they find considerable difficulty in obtaining satisfactory results with a confocal microscope, but they may be mislead by how data is being presented. This book is intended to teach you the basic concepts ofmicroscopy, fluorescence, digital imaging and the principles of confocal microscopy so that you may take full advantage ofthe excellent confocal microscopes now available. This book is also an excellent reference source for information related to confocal microscopy for both beginners and the more advanced users. For example, do you need to know the optimal pinhole size for a 63x 1. 4 NA lens? Do you need to know the fluorescence emission spectrum of Alexa 568? Access to the wealth of practical information in this book is made easier by using both the detailed index and the extensive glossary.

Table of Contents

1. WHAT IS CONFOCAL MICROSCOPY

2. UNDERSTANDING MICROSCOPY

3. CONFOCAL MICROSCOPY HARDWARE

4. IMAGE COLLECTION

5. DIGITAL IMAGES IN MICROSCOPY

6. IMAGING SOFTWARE

7. PRESENTATION AND PUBLICATION

8. WHAT IS FLUORESCENCE

9. FLUORESCENT PROBES

10. CONFOCAL MICROSCOPY TECHNIQUES

11. FLUORESCENCE IMMUNOLABELLING

12. IMAGING LIVE CELLS

13. THE INTERNET

14. TECHNICAL SUPPLIES

15. FURTHER READING

APPENDIX 1: CONFOCAL MICROSCOPES

A. BIO-RAD CELL SCIENCE DIVISION

CARL ZEISS MICROSCOPY

LEICA MICROSYSTEMS

NIKON INSTRUMENTS

OL YMPUS CORPORATION

ATTO BIOSCIENCE

YOKOGAWA ELECTRIC CORPORATION

PERKINELMER LIFE SCIENCES

VISITECH INTERNATIONAL

GLOSSARY

INDEX

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