Saturday, April 5, 2008

Genomics of Disease


Product Details

  • Hardcover: 240 pages
  • Publisher: Springer; 1 edition (March 19, 2008)
  • Language: English
  • ISBN-10: 0387767223
  • ISBN-13: 978-0387767222
  • Product Dimensions: 9.3 x 6.2 x 0.7 inches

· Product Description

The title will develop from the 24th Stadler symposium. It will explore the general theme "GENOME EXPLOITATION: Data Mining the Genomes". The idea behind the theme is to discuss and illustrate how scientists are going to characterize and make use of the massive amount of information being accumulated about plant and animal genomes. The book will present a state-of-the-art picture on mining the Genome databases. This will be one of the few times that researchers in both plants and animals will be working together to create a seminal data resource.

Contents

Roles of Plant Hormones in Plant Resistance

and Susceptibility to Pathogens

Lionel Navarro, Rajendra Bari, Alexandre Seilaniantz, Adnane Nemri,

and Jonathan D.G. Jones

Canine Genetics Facilitates Understanding of Human Biology

Elaine A. Ostrander, Heidi G. Parker, and Nathan B. Sutter

Xanthomonas oryzae pv. oryzae AvrXA21 Activity Is Dependent

on a Type One Secretion System, Is Regulated by a Two-Component

Regulatory System that Responds to Cell Population Density,

and Is Conserved in Other Xanthomonas spp.

Sang-Won Lee, Sang-Wook Han, Laura E. Bartley, and Pamela C. Ronald

Unraveling the Genetic Mysteries of the Cat: New Discoveries

in Feline-Inherited Diseases and Traits

Leslie A. Lyons

Variation in Chicken Gene Structure and Expression Associated

with Food-Safety Pathogen Resistance: Integrated Approaches

to Salmonella Resistance

S.J. Lamont

Functional Genomics and Bioinformatics of the Phytophthora sojae

Soybean Interaction

Brett M. Tyler, Rays H.Y. Jiang, Lecong Zhou, Sucheta Tripathy,

Daolong Dou, Trudy Torto-Alalibo, Hua Li, Yongcai Mao, Bing Liu,

Miguel Vega-Sanchez, Santiago X. Mideros, Regina Hanlon, BrianM. Smith,

Konstantinos Krampis, Keying Ye, Steven St. Martin, Anne E. Dorrance,

Ina Hoeschele, and M.A. Saghai Maroof

Canine SINEs and Their Effects on Phenotypes of the Domestic Dog

Leigh Anne Clark, Jacquelyn M. Wahl, Christine A. Rees, George M. Strain,

Edward J. Cargill, Sharon L. Vanderlip, and Keith E. Murphy

Ovine Disease Resistance: Integrating Comparative and Functional

Genomics Approaches in a Genome Information-Poor Species

H.W. Raadsma, K.J. Fullard, N.M. Kingsford, E.T. Margawati,

E. Estuningsih, S. Widjayanti, Subandriyo, N. Clairoux, T.W. Spithill,

and D. Piedrafita

Integrating Genomics to Understand the Mareks Disease

Virus Chicken HostPathogen Interaction

Hans H. Cheng

Combining Genomic Tools to Dissect Multifactorial Virulence

in Pseudomonas aeruginosa

Daniel G. Lee, Jonathan M. Urbach, Gang Wu, Nicole T. Liberati,

Rhonda L. Feinbaum, and Frederick M. Ausubel

Genetic Dissection of the Interaction Between the Plant Pathogen

Xanthomonas campestris pv. vesicatoria and Its Host Plants

Ulla Bonas, Doreen G¨urlebeck, Daniela B¨uttner, Monique Egler,

Simone Hahn, Sabine Kay, Antje Kr¨uger, Christian Lorenz, Robert Szczesny,

and Frank Thieme

Structure and Function of RXLR Effectors

of Plant Pathogenic Oomycetes William Morgan, Jorunn Bos, Catherine Bruce, Minkyoung Lee,

Hsin-Yen Liu, Sang-Keun Oh, Jing Song, Joe Win, Carolyn Young,

and Sophien Kamoun

The Biotrophic Phase of Ustilago maydis: Novel Determinants

for Compatibility

Thomas Brefort, Kerstin Schipper, Gunther D¨ohlemann,

and Regine Kahmann

Virulence Evolution in Malaria

M.J. Mackinnon

The Ins and Outs of Host Recognition of Magnaporthe oryzae

Sally A. Leong

Index

Friday, April 4, 2008

Color Atlas of Genetics 3rd

Product Details

# Paperback: 496 pages

# Publisher: Thieme Medical Publishers; 3rd edition (January 6, 2006)

# Language: English

# ISBN-10: 1588903362

# ISBN-13: 978-1588903365

American Journal of Medical Genetics

A remarkable achievement...concise but informative...No geneticist or
physician should be without a copy of this remarkable edition. --This
text refers to the Paperback edition.

Book Description

A remarkable achievement by a single author...concise but
informative...No geneticist or physician interested in genetic diseases
should be without a copy of this remarkable edition." --American
Journal of Medical Genetics understanding of genetics is a fundamental element of all medical and
scientific educational programs, across virtually all disciplines. And
the applications--and implications--of genetic research are at the
heart of current medical scientific debates. Completely updated and
revised, The Color Atlas of Genetics is an invaluable guide for
students of medicine and biology, clinicians, and anyone else
interested in this rapidly evolving field.

With more than 200
absorbing full-color plates concisely explained on facing pages, the
atlas offers readers an easy-to-use, yet remarkably detailed guide to
key molecular, theoretical, and medical aspects of genetics and
genomics. Brief descriptions of numerous genetic diseases are included,
with references for more detailed information.

Readers will find
that this incomparable book presents a comprehensive picture of the
field from its fascinating history to its most advanced applications.

Introduction

Chronology

Important Advances that Contributed

to the Development of Genetics

Part I. Fundamentals

Prologue

Taxonomy of Living Organisms:

The Tree of Life

Human Evolution

The Cell and Its Components

Molecular Basis of Genetics

Some Types of Chemical Bonds

Carbohydrates

Lipids (Fats)

Nucleotides and Nucleic Acids

Amino Acids

Proteins

DNA as a Carrier of Genetic

Information

DNA and Its Components

DNA Structure

Alternative DNA Structures

DNA Replication

The Flow of Genetic Information:

Transcription and Translation

Genes and Mutation

Genetic Code

Processing of RNA

DNA Amplification by Polymerase

Chain Reaction (PCR)

DNA Sequencing

Automated DNA Sequencing

Restriction Mapping

DNA Cloning

cDNA Cloning

DNA Libraries

Southern Blot Hybridization

Detection of Mutations

without Sequencing

DNA Polymorphism

Mutations

Mutations Due to Different Base

Modifications

Recombination

Transposition

Trinucleotide Repeat Expansion

DNA Repair

Xeroderma Pigmentosum

Prokaryotic Cells and Viruses

Bacteria in the Study of Genetics

Recombination in Bacteria

Bacteriophages

DNA Transfer between Cells

Classification of Viruses

Replication of Viruses

Retroviruses

Retrovirus Integration and

Transcription

Eukaryotic Cells

Cell Communication

Yeast: Eukaryotic Cells with a Diploid

and a Haploid Phase

Mating Type Determination in

Yeast Cells and Yeast Two-Hybrid

System

Cell Division: Mitosis

Meiosis in Germ Cells

Meiosis Prophase I

Formation of Gametes

Cell Cycle Control

Programmed Cell Death

Cell Culture

Mitochondrial Genetics

Mitochondria: Energy Conversion

Chloroplasts and Mitochondria

The Mitochondrial Genome

of Man

Mitochondrial Diseases

Formal Genetics

The Mendelian Traits

Segregation of Mendelian Traits

Independent Distribution of Two

Different Traits

Phenotype and Genotype

Segregation of Parental Genotypes

Monogenic Inheritance

Linkage and Recombination

Estimating Genetic Distance

Segregation Analysis with Linked

Genetic Markers

Linkage Analysis

Quantitative Differences in Genetic

Traits

Normal Distribution and Polygenic

Threshold Model

Distribution of Genes in a

Population

HardyWeinberg Equilibrium

Principle

Consanguinity and Inbreeding

Twins

Polymorphism

Biochemical Polymorphism

Differences in Geographical

Distribution of Some Alleles

Chromosomes

Chromosomes in Metaphase

Visible Functional Structures

of Chromosomes

Chromosome Organization

Functional Elements of

Chromosomes

DNA and Nucleosomes

DNA in Chromosomes

The Telomere

The Banding Patterns of

Human Chromosomes

Karyotypes of Man and Mouse

Preparation of Metaphase

Chromosomes for Analysis

Fluorescence In-Situ Hybridization

(FISH)

Aneuploidy

Chromosome Translocation

Structural Chromosomal

Aberrations

Multicolor FISH Identification of

Chromosomes

Comparative Genomic

Hybridization

Regulation of Gene Function

Ribosomes and Protein Assembly

Transcription

Prokaryotic Repressor and Activator:

the lac Operon

Genetic Control by Alternative RNA

Structure

Basic Mechanisms of

Gene Control

Regulation of Gene Expression in

Eukaryotes

DNA-Binding Proteins, I

DNA-Binding Proteins, II

RNA Interference (RNAi)

Targeted Gene Disruption

Epigenetic Modifications

DNA Methylation

Reversible Changes in Chromatin

Structure

Genomic Imprinting

Mammalian X Chromosome

Inactivation

Part II. Genomics

Genomics, the Study of the

Organization of Genomes

Gene Identification

Identification of Expressed DNA

Approaches to Genome Analysis

Genomes of Microorganisms

The Complete Sequence of the

Escherichia coli Genome

The Genome of a Multiresistant

Plasmid

Architecture of the Human Genome

The Human Genome Project

Genomic Structure of the Human X

and Y Chromosomes

Genome Analysis with DNA

Microarrays

Genome Scan and Array CGH

The Dynamic Genome: Mobile

Genetic Elements

Evolution of Genes and Genomes

Comparative Genomics

Part III. Genetics and

Medicine

Cell-to-Cell Interactions .

Intracellular Signal Transduction

Signal Transduction Pathways

TGF-_ and Wnt/_-Catenin Signaling

Pathways

The Hedgehog and TNF-α Signal

Transduction Pathways

The Notch/Delta Signaling Pathway

Neurotransmitter Receptors and Ion

Channels

Genetic Defects in Ion Channels:

LQT Syndromes

Chloride Channel Defects: Cystic

Fibrosis

Sensory Perception

Rhodopsin, a Photoreceptor

Mutations in Rhodopsin: Pigmentary

Retinal Degeneration

Color Vision

Auditory System

Odorant Receptors

Mammalian Taste Receptors

Genes in Embryonic Development

Genetic Determination of Embryonic

Development in Drosophila

Cell Lineage in a Nematode,

C. elegans

Developmental Genes in a Plant,

Arabidopsis

Immune System

Components of the Immune

System

Immunoglobulin Molecules

Genetic Diversity Generated by

Somatic Recombination

Mechanisms in Immunoglobulin

Gene Rearrangement

The T-Cell Receptor

Genes of the MHC Region

Evolution of the Immunoglobulin

Supergene Family

Hereditary Immunodeficiencies

Origins of Cancer

Genetic Causes of Cancer:

Background

Categories of Cancer Genes

The p53 Tumor Suppressor Gene

The APC Gene and Polyposis coli

Breast Cancer Susceptibility Genes

Retinoblastoma

The BCR/ABL Fusion Protein

in CML

Neurofibromatosis

Genomic Instability Diseases

Hemoglobin

Hemoglobin

Hemoglobin Genes

Sickle Cell Anemia

Mutations in Globin Genes

The Thalassemias

Hereditary Persistence of Fetal

Hemoglobin (HPFH)

DNA Analysis in Hemoglobin

Disorders

Lysosomes and Peroxisomes

Lysosomes

Diseases Due to Lysosomal Enzyme

Defects

Mucopolysaccharide Storage

Diseases

Peroxisomal Biogenesis Diseases

Cholesterol Metabolism

Cholesterol Biosynthesis Pathway

Distal Cholesterol Biosynthesis

Pathway

Familial Hypercholesterolemia

LDL Receptor Mutations

Homeostasis

Diabetes Mellitus

Protease Inhibitor α1-Antitrypsin

Blood Coagulation Factor VIII

(Hemophilia A)

VonWillebrand Bleeding Disease

Pharmacogenetics

Cytochrome P450 (CYP) Genes

Amino Acid Degradation and Urea

Cycle Disorders

Maintaining Cell and Tissue Shape

Cytoskeletal Proteins in

Erythrocytes

Hereditary Muscle Diseases

Duchenne Muscular Dystrophy

Collagen Molecules

Osteogenesis Imperfecta

Molecular Basis of Bone

Development

Sex Determination and Differentiation

Mammalian Sex Determination

Sex Differentiation

Disorders of Sexual Development

Congenital Adrenal Hyperplasia

Atypical Patterns of Genetic

Transmission

Diseases of Unstable Repeat

Expansion

Fragile X Syndrome

KaryotypePhenotype Relationship

Autosomal Trisomies

Other Numerical Chromosomal

Deviation

Autosomal Deletion Syndromes

A Brief Guide to Genetic Diagnosis

Principles of Genetic Diagnostics

Gene and Stem Cell Therapy

Morbid Anatomy of the Human

Genome

Chromosomal Location of Human

Genetic Diseases

Chromosomal LocationAlphabetical

List

AppendixSupplementary

Data

Glossary

Index

Principles and Technical Aspects of PCR Amplification


Principles and Technical Aspects of PCR Amplification
by Elizabeth van Pelt-Verkuil (Author), Alexander van Belkum (Author), John P. Hays (Author)

Product Details
* Hardcover: 339 pages
* Publisher: Springer; 1 edition (April 2008)
* Language: English
* ISBN-10: 1402062400


Book Description
Kary Mullis was awarded a Nobel Prize for inventing the PCR technique more than 15 years ago in 1993. Since its "discovery", multiple adaptations and variations of the standard PCR technique have been described, with many of these adaptations and variations currently being used in clinical, diagnostic and academic laboratories across the world. Further, these techniques are being applied at the diagnostic level (e.g. as high throughput testing methodologies to detect minimum residual disease, the presence/absence of specific pathogens etc), as well as to increase our understanding of fundamental disease processes.
Frequently, PCR technicians and specialists limit their understanding of PCR to one particular methodology. However, this approach limits their appreciation of the range of versatile PCR techniques currently available, techniques that may be applicable and indeed more suitable to their own laboratory situation.
This manual aims to provide the reader with a guide to the standard PCR technique and its many available modifications, with particular emphasis on the role of PCR techniques in the diagnostic laboratory (the central theme of this manual). Further, many important technical issues have been addressed, including types of PCR template material, PCR optimization, the analysis of PCR products, quality control and quality assurance, variants and adaptations of the standard PCR protocol, quantitative PCR and in situ PCR. The reader of this manual will be excellently informed about the fundamental principles of PCR and the true potential of PCR within clinical laboratory practice.

Contents

Foreword

Chapter 1 The Polymerase Chain Reaction

1.1 An Overview of the PCR Process

1.2 Before PCR and Beyond

Chapter 2 A Brief Comparison Between In Vivo DNA Replication

and In Vitro PCR Amplifi cation

2.1 Nucleic Acid Targets

2.1.1 DNA

2.1.2 RNA

2.2 Target DNA Strand Separation and Primer Annealing

2.3 DNA Dependent DNA Polymerase and Oligonucleotide

Primers

2.4 Deoxyribonucleotides and Additional Factors

Chapter 3 The PCR in Practice

3.1 Brief Overview of PCR Requirements

3.1.1 The PCR Reaction Mix

3.1.2 The PCR Thermocycling Regime

3.1.3 Analysis of PCR Amplifi cation Products

3.1.4 Miscellaneous Considerations

Chapter 4 The Different Types and Varieties of Nucleic Acid

Target Molecules

4.1 General Features

4.2 A Brief Description of In Vivo DNA and RNA Targets

4.3 DNA Samples

4.3.1 DNA Isolation Procedures

4.3.2 Comments on Nucleic Acids in Specifi c

Sample Types

4.4 RNA Samples

4.4.1 Working Free of RNase Contamination

4.4.2 RNA Isolation for RT-PCR

4.5 Reverse Transcription and RT-PCR

4.5.1 cDNA Synthesis

4.5.2 cDNA Synthesis Using RACE

4.5.3 RNA Extraction and cDNA

Synthesis Controls

Chapter 5 PCR Primers

5.1 PCR Primer Design and Quality Requirements

5.1.1 Different Primer Species

5.2 Primer Hybridisation (Annealing)

5.3 Thermodynamic Approach of Tm Calculations

5.4 Primer Synthesis

5.5 Non-radioactive Primer Labelling

5.6 The Effect of Mismatches Between PCR

Primer and Target

5.7 Primer Concentration

Chapter 6 Deoxynucleotide Triphosphates and Buffer Components

6.1 Factors Affecting the Choice of dNTP Concentration

6.2 Modifi ed dNTPs and Their Applications

6.3 The PCR Buffer

6.3.1 Monovalent Ions

6.3.2 Magnesium Ions

Chapter 7 Taq and Other Thermostable DNA Polymerases

7.1 The Advantages and Disadvantages of Taq over

Klenow Fragment DNA Polymerase

7.2 Misincorporation of Nucleotides and Fidelity

of DNA Synthesis by Taq Polymerase

7.3 Taq DNA Polymerase and Its Modifi cations

7.4 Taq Polymerase Unit Defi nition and Working

Concentrations

7.5 Other Thermostable Polymerases

and Their Applications

7.6 Mixtures of Thermostable Polymerases

Chapter 8 Important Considerations for Typical, Quantitative

and Real-Time PCR Protocols

8.1 The Typical PCR Amplifi cation Protocol

8.1.1 Denaturation (Melting) of the Template DNA

8.1.2 Annealing (Hybridisation) of PCR Primers

8.1.3 Calculating the Primer Annealing

Temperature (Tm)

8.1.4 DNA Chain Extension/Elongation

8.1.5 PCR Cycle Number

8.1.6 The “Plateau Phase” and Final Stages of PCR

Thermocycling

8.1.7 PCR Sensitivity

8.2 Quantitative PCR Protocols

8.2.1 Quantitative PCR Controls

8.3 Real-Time PCR Protocols

8.4 RNA Extraction and Treatment

Chapter 9 Analysis of PCR Amplifi cation Products

9.1 Visualizing PCR Amplifi cation Products

9.1.1 Intercalating Chemical Dyes and Silver Ions

9.1.2 Fluorescent or Hapten Labelled Amplimers

9.2 Post-PCR Electrophoretic Analysis of Amplimers

9.2.1 Gel Electrophoresis Methodologies

9.2.2 Probe Hybridisation Methodologies

9.3 Real-Time Analysis of PCR Amplimers

9.3.1 In vitro Analysis Using Intercalating

Chemical Dyes

9.3.2 FRET Quenching Assays

9.3.3 TaqMan Probes

9.3.4 FRET Enhancement Reactions

9.4 Nucleic Acid Sequencing

9.4.1 DNA Sequencing Using Non-thermostable

DNA Polymerases

9.4.2 PCR Sequencing Using Thermostable

DNA Polymerases

9.4.3 The Fidelity of PCR Sequencing Reactions

Chapter 10 Ensuring PCR Quality Laboratory Organisation, PCR

Optimization and Controls

10.1 The Primary Level of Quality Control – Laboratory

Organization and the Prevention of PCR

Contamination

10.1.1 Sources and Routes of Contamination

10.1.2 PCR Contamination Issues Within

Individual PCR Laboratories

10.1.3 Detecting and Preventing PCR

Contamination

10.2 The Secondary Level of PCR Quality Control – PCR

Design and Optimization

10.2.1 Extrinsic and Intrinsic Factors

10.2.2 The Developmental Steps Needed

to Achieve High Quality PCR Results

10.2.3 The Use of Positive and Negative Controls

in PCR Quality

10.2.4 Causes and Solutions for False Positive

and False Negative PCR Results

10.3 Quality Considerations Specifi c for RT-PCR

Methodologies

10.3.1 Problems Likely to Cause False Positive

Results in RT-PCR Assays

10.3.2 Problems Likely to Cause False Negative

Results in RT-PCR Assays

Chapter 11 Ensuring PCR Quality Quality Criteria and Quality

Assurance

11.1 Quality Control Criteria and PCR

11.1.1 Sensitivity and Diagnostic Sensitivity

11.1.2 Specifi city and Diagnostic Specifi city

11.1.3 Reference and Threshold Values

11.1.4 The Predictive Value

11.1.5 Effi ciency

11.1.6 Error and Accuracy

11.1.7 Precision and Correctness

11.1.8 Defi ning the Analytical or Quantifi cation

Range and Sensitivity

11.1.9 Recovery, Reproducibility and Quality

Assurance

11.2 Quality Assurance and Multicenter Studies

Chapter 12 Variants and Adaptations of the Standard PCR Protocol

12.1 Generating Labelled PCR Amplimers for PCR

Product Visualization, DNA Probes and Cloning

12.2 Two-Step PCR Protocol

12.3 Booster PCR

12.4 Hot-Start and Time-Release PCR Protocols

12.5 Inverse PCR

12.6 Asymmetric PCR

12.7 PCR Mediated DNA Sequencing Strategies

12.7.1 Generating Single-Stranded DNA

for Sanger Sequencing Reactions

12.7.2 Classical Sanger Sequencing

of Single-Stranded PCR Products

12.7.3 Direct PCR Sequencing

12.7.4 Four-Tube Cycle Sequencing

12.7.5 One-Tube Cycle Sequencing

12.7.6 Diffi cult to Sequence Templates

12.8 Touchdown and Touch-Up PCR

12.9 Multiplex PCR

12.10 PCR Using Degenerate Primers

12.11 Repeat and Inter-repeat PCR

12.11.1 Repeat PCR

12.11.2 Inter-repeat PCR and Random Amplifi cation

of Polymorphic DNA (RAPD)

12.12 AFLP Fingerprinting

12.13 Base Excision Sequence Scanning (BESS-T-Scan)

for Mutation Detection

12.14 Differential Display RT-PCR (DD-PCR)

12.15 The Protein Truncation Test (PTT)

12.16 Methylation Specifi c PCR and PCR in the Detection

of Mutagens

12.17 Breakpoint PCR

12.18 Site Directed Mutagenesis by PCR

12.19 PCR Amplimers for Cloning and Expression

12.20 SAGE

12.21 PCR Inhibition by DNA Specifi c Antibiotics

and Mutagens

Chapter 13 In Situ PCR Amplifi cation (ISA) Major Considerations,

Sample Processing and Applications

13.1 Tissue Processing – Nucleic Acid Fixation/Extraction

13.1.1 Fixation

13.1.2 Type of Nucleic Acid

13.1.3 Detrimental Effects of Various Fixatives

on Nucleic Acids

13.1.4 Effects of Tissue Processing Steps

(Decalcifi cation, Dehydration, Intermedium

Application, Embedding) and Storage

of Paraffi n Blocks

13.1.5 Effects of Histological and Histochemical

Staining

13.2 Differences in Approach for ISH, ISA and

Standard PCR

13.2.1 Different Types of Tissue Preparations .

13.2.2 DNA and RT-PCR on Paraffi n-Embedded

Tissue Sections

13.2.3 Improvement of PCR Effi ciency Using

Fixed Tissue Sections

13.3 An Introduction to In Situ Amplifi cation (ISA)

13.4 Considerations in the Development of ISA Protocols

13.4.1 IS-PCR or PCR-ISH

13.4.2 Diffusion of Nucleic Acids

13.4.3 The Correct Fixative

13.4.4 Damage Caused by Paraffi n Embedding

13.4.5 Detachment of Cells and Tissue Sections

13.4.6 Specimen Proteolysis

13.4.7 Acetylation and Other Forms of Tissue

Section Pre-treatment

13.4.8 Pre-treatment of Preparations for IS-PCR

13.4.9 Testing for Loss of Amplimers Due

to Leakage from Their Site of Production

13.4.10 Miscellaneous IS-PCR Considerations

13.4.11 Mispriming

13.4.12 Primer Independent Non-specifi c

DNA Synthesis

13.4.13 Evaporation of Reactants During IS-PCR/

Wet Hot Start Procedure

13.4.14 Cell Thickness and ISA

13.4.15 Choosing a Hybridisation Control

for Testing Amplimer Specifi city

13.4.16 Choice of the PCR Processor

13.4.17 Choice of the Final Detection Method

13.5 ISA Optimisation

13.6 ISA Controls

Index

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