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Multiple Sclerosis
Assembling DNA Barcodes
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Author(s):
Jeremy R. deWaard
,
Natalia V. Ivanova
,
Mehrdad Hajibabaei
,
Paul D. N. Hebert
Publication date
(Print):
2008
Publisher:
Humana Press
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Book Chapter
Publication date (Print):
2008
Pages
: 275-294
DOI:
10.1007/978-1-59745-548-0_15
PubMed ID:
18642605
SO-VID:
815bfbd0-bd9f-446b-8127-7aa6a65e9c8d
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Book chapters
pp. 1
RNA Interference: Mechanisms, Technical Challenges, and Therapeutic Opportunities
pp. 1
The Evolution of Mass Spectrometry in the Clinical Laboratory
pp. 1
A Historical Overview of RNAi in Plants
pp. 1
Knock-in and Knock-out: The Use of Reverse Genetics in Somatic Cells to Dissect Mitotic Pathways
pp. 1
Methods of Telomerase Inhibition
pp. 1
Histological Analysis of the Embryonic and Adult Tooth
pp. 1
Digital Images Are Data: And Should Be Treated as Such
pp. 1
MicroRNAs, Long Noncoding RNAs, and Their Functions in Human Disease
pp. 1
Piecing the Puzzle Together: Genetic Requirements for miRNA Biogenesis in Arabidopsis thaliana
pp. 1
High-Throughput Protein Production (HTPP): A Review of Enabling Technologies to Expedite Protein Production
pp. 1
Genetic Terminology
pp. 3
Biophysical and Spectroscopic Methods for Monitoring Protein Misfolding and Amyloid Aggregation
pp. 3
Measuring Plant Root Traits Under Controlled and Field Conditions: Step-by-Step Procedures
pp. 3
Muscle Stem Cells: A Model System for Adult Stem Cell Biology
pp. 3
Structural Basis of Protein-Protein Interactions
pp. 3
Enabling Molecular Technologies for Trait Improvement in Wheat
pp. 3
Alzheimer’s as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks
pp. 3
Design and Validation of CRISPR/Cas9 Systems for Targeted Gene Modification in Induced Pluripotent Stem Cells
pp. 3
Novel Insights/Translational Implication from the Emerging Biology of Melanoma
pp. 3
Re-Factoring Glycolytic Genes for Targeted Engineering of Catabolism in Gram-Negative Bacteria
pp. 3
Structural Biology of Nonribosomal Peptide Synthetases
pp. 3
What Is Synthetic Biology?
pp. 3
Positional Gene Cloning in Experimental Populations
pp. 3
Plasmid DNA Isolation and Visualization: Isolation and Characterization of Plasmids from Clinical Samples
pp. 7
RNA-Seq and Expression Arrays: Selection Guidelines for Genome-Wide Expression Profiling
pp. 11
Comparative Genomics as a Foundation for Evo-Devo Studies in Birds
pp. 11
Emerging Clinical Issues in Melanoma in the Molecularly Targeted Era
pp. 13
Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies
pp. 15
Determination of Gene Expression Patterns by Whole-Mount In Situ Hybridization
pp. 15
Quality Control and Validation Issues in LC-MS Metabolomics
pp. 17
Nanostructured RNAs for RNA Interference
pp. 19
Ultrasensitive RT-QuIC Seed Amplification Assays for Disease-Associated Tau, α-Synuclein, and Prion Aggregates
pp. 19
Designing Experiments for High-Throughput Protein Expression
pp. 19
Prediction of Plant miRNA Genes
pp. 21
Isolation and Visualization of Plasmids from Gram-Positive Bacteria of Interest in Public Health
pp. 21
Investigation of PrPC Metabolism and Function in Live Cells
pp. 23
Quantitative Analysis of Protein-Protein Interactions
pp. 23
Unveiling Brain Aβ Heterogeneity Through Targeted Proteomic Analysis
pp. 23
Construction and Screening of Marine Metagenomic Large Insert Libraries
pp. 23
Determination of Gene Expression Patterns by In Situ Hybridization in Sections
pp. 25
What Will Be the Benefits of Biotech Wheat for European Agriculture?
pp. 27
Integrating Molecular Biomarkers into Current Clinical Management in Melanoma
pp. 27
Bacterial Genome Editing Strategy for Control of Transcription and Protein Stability
pp. 29
Bioinformatics: Identification of Markers from Next-Generation Sequence Data
pp. 31
Gateway Cloning for Protein Expression
pp. 31
Methods for Isolation of Total RNA to Recover miRNAs and Other Small RNAs from Diverse Species
pp. 33
Immunohistochemistry and Detection of Proliferating Cells by BrdU
pp. 33
Protein Structure Prediction
pp. 35
A Guide for Designing and Analyzing RNA-Seq Data
pp. 37
One Long Oligonucleotide or Two Short Oligonucleotides Based shRNA Construction and Expression
pp. 37
Crystallographic Analysis of MATE-Type Multidrug Exporter with Its Inhibitors
pp. 39
Detection, Isolation, and Characterization of Plasmids in the Environment
pp. 39
Protein-Protein Interaction Databases
pp. 41
Detection of Apoptosis by TUNEL Assay
pp. 41
Detecting Phenotypically Resistant Mycobacterium tuberculosis Using Wavelength Modulated Raman Spectroscopy
pp. 43
PLGA Microspheres Encapsulating siRNA
pp. 43
Imaging and Quantification of Extracellular Vesicles by Transmission Electron Microscopy
pp. 45
Advances in Adjuvant Therapy: Potential for Prognostic and Predictive Biomarkers
pp. 49
Solubilization of Proteins: The Importance of Lysis Buffer Choice
pp. 49
Application of Systems Theory in Longitudinal Studies on the Origin and Progression of Alzheimer’s Disease
pp. 49
Use of siRNA in Dental Tissue-Derived Cell Cultures: Integrin Knockdown in Fibroblasts
pp. 51
miRNA Target Prediction in Plants
pp. 51
Introduction to Bioinformatics
pp. 53
Magnetic Nanoparticle and Magnetic Field Assisted siRNA Delivery In Vitro
pp. 53
Expansion of Human Induced Pluripotent Stem Cells in Stirred Suspension Bioreactors
pp. 55
Exercising Bioengineered Skeletal Muscle In Vitro: Biopsy to Bioreactor
pp. 55
Flexi Vector Cloning
pp. 57
QuickRNASeq: Guide for Pipeline Implementation and for Interactive Results Visualization
pp. 57
Computational Prediction of Protein-Protein Interactions
pp. 59
Organ Cultures and Kidney-Capsule Grafting of Tooth Germs
pp. 59
A Method to Discover Phased siRNA Loci
pp. 59
Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment
pp. 61
Bacteriophage Isolation and Characterization: Phages of Escherichia coli
pp. 63
Fabrication of DNA Microarray
pp. 63
Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design
pp. 67
Fluorescence Resonance Energy Transfer Microscopy (FRET)
pp. 69
Toward a Resilient, Functional Microbiome: Drought Tolerance-Alleviating Microbes for Sustainable Agriculture
pp. 69
Multiplex Droplet Digital PCR Protocols for Quantification of GM Maize Events
pp. 69
Evaluation of Skull and Tooth Morphology and Mineralization Using High-Resolution X-Ray Tomography
pp. 71
Directed Gene Silencing with Artificial MicroRNAs
pp. 71
Immunologic Monitoring of Cancer Vaccine Trials Using the ELISPOT Assay
pp. 73
Carbon–Carbon Bond-Forming Enzymes for the Synthesis of Non-natural Amino Acids
pp. 75
The Precise Engineering of Expression Vectors Using High-Throughput In-Fusion™ PCR Cloning
pp. 75
Site Identification by Ligand Competitive Saturation (SILCS) Simulations for Fragment-Based Drug Design
pp. 77
Structure-Based Computational Approaches for Small-Molecule Modulation of Protein-Protein Interactions
pp. 81
Small Molecule Recognition of Poly(A)
pp. 81
Detection and Characterization of Transposons in Bacteria
pp. 81
Electron Microscopy
pp. 81
RNAi-Mediated Resistance to Viruses in Genetically Engineered Plants
pp. 83
Markers for Anti-cytotoxic T-lymphocyte Antigen 4 (CTLA-4) Therapy in Melanoma
pp. 83
Extended Metabolic Space Modeling
pp. 85
NetoVIR: Modular Approach to Customize Sample Preparation Procedures for Viral Metagenomics
pp. 85
MitoPho8Δ60 Assay as a Tool to Quantitatively Measure Mitophagy Activity
pp. 89
Bioinformatics Analysis of Small RNAs in Plants Using Next Generation Sequencing Technologies
pp. 89
A Computational Fragment-Based De Novo Design Protocol Guided by Ligand Efficiency Indices (LEI)
pp. 91
The Polymerase Incomplete Primer Extension (PIPE) Method Applied to High-Throughput Cloning and Site-Directed Mutagenesis
pp. 93
Measuring Plasmid Conjugation Using Antibiotic Selection
pp. 93
Targeting Protein-Protein Interactions for Drug Discovery
pp. 95
Deoxyoligonucleotide Microarrays for Gene Expression Profiling in Murine Tooth Germs
pp. 95
Clinical Studies of Methionine-Restricted Diets for Cancer Patients
pp. 95
Capillary Blotting of Glycosaminoglycans on Nitrocellulose Membranes After Agarose-Gel Electrophoresis Separation
pp. 97
Marker Utility for Combination Therapy
pp. 97
Identification of HR-Inducing cDNAs from Plant Pathogens via a Gateway®-Compatible Binary Potato Virus X-Expression Vector
pp. 97
Solution-State Nuclear Magnetic Resonance Spectroscopy and Protein Folding
pp. 99
Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Subsequent Fermentation for Optimized Production
pp. 99
Measuring Plasmid Conjugation Using Fluorescent Reporters
pp. 101
Effects of Mild and Severe Oxidative Stress on BACE1 Expression and APP Amyloidogenic Processing
pp. 103
A Mouse Model of Permanent Focal Ischemia: Distal Middle Cerebral Artery Occlusion
pp. 105
A Family of LIC Vectors for High-Throughput Cloning and Purification of Proteins
pp. 105
Analysis of Mass Spectrometry Data in Proteomics
pp. 107
Cytoplasmic Delivery of siRNAs to Monocytes and Dendritic Cells via Electroporation
pp. 107
High-Throughput Approaches for miRNA Expression Analysis
pp. 109
Studying Protein-Protein Interactions Using Surface Plasmon Resonance
pp. 109
Ex Vivo Megakaryocyte Expansion and Platelet Production from Human Cord Blood Stem Cells
pp. 111
Methods to Quantify DNA Transfer in Enterococcus
pp. 111
Biomarkers in Cerebrospinal Fluid: Analysis of Cell-Free Circulating Mitochondrial DNA by Digital PCR
pp. 111
Lineage Differentiation of Mesenchymal Stem Cells from Dental Pulp, Apical Papilla, and Periodontal Ligament
pp. 113
16S rRNA Gene Analysis with QIIME2
pp. 115
RNA Preparation and Characterization for Gene Expression Studies
pp. 117
Assaying for BRAF V600E in Tissue and Blood in Melanoma
pp. 117
Delivery of siRNAs to Cancer Cells via Bacteria
pp. 117
“System 48” High-Throughput Cloning and Protein Expression Analysis
pp. 117
A Guide to Genome-Wide In Vivo RNAi Applications in Drosophila
pp. 119
Machine Learning Methods in Computational Toxicology
pp. 119
CRISPR/Cas-Mediated Knockin in Human Pluripotent Stem Cells
pp. 121
Transcript Profiling Using Long-Read Sequencing Technologies
pp. 123
Quantifying and Characterizing Distributive Conjugal Transfer in Mycobacterium smegmatis
pp. 123
In Vivo Transplantation and Tooth Repair
pp. 123
The Classification of Protein Domains
pp. 127
AMMOS Software: Method and Application
pp. 127
In Situ Detection of miRNAs Using LNA Probes
pp. 129
Validated Capillary Electrophoretic Assays for Disaccharide Composition Analysis of Galactosaminoglycans in Biologic Samples and Drugs/Nutraceuticals
pp. 129
Molecular Mechanisms and Signaling Pathways Involved in the Nutritional Support of Spermatogenesis by Sertoli Cells
pp. 129
Automated 96-Well Purification of Hexahistidine-Tagged Recombinant Proteins on MagneHis Ni2+-Particles
pp. 129
Extraction Protocol for Nontargeted NMR and LC-MS Metabolomics-Based Analysis of Hard Coral and Their Algal Symbionts
pp. 129
Agrobacterium-Mediated Transformation of Wheat Using Immature Embryos
pp. 131
Microwell Array-Mediated Delivery of Lipoplexes Containing Nucleic Acids for Enhanced Therapeutic Efficacy
pp. 135
Methods to Validate Tooth-Supporting Regenerative Therapies
pp. 135
Spectrophotometric Assays to Quantify the Activity of T4SS ATPases
pp. 137
Analysis of miRNA Modifications
pp. 137
Selecting Patients for KIT Inhibition in Melanoma
pp. 139
Resonant Waveguide Grating for Monitoring Biomolecular Interactions
pp. 139
2in1 Vectors Improve In Planta BiFC and FRET Analyses
pp. 143
Analyzing Copy Number Variation with Droplet Digital PCR
pp. 143
E. coli and Insect Cell Expression, Automated Purification and Quantitative Analysis
pp. 143
Modulating the Tumor Microenvironment with RNA Interference as a Cancer Treatment Strategy
pp. 145
Identification of Relaxase-DNA Covalent Complexes and DNA Strand Transfer Reaction Products by Polyacrylamide Gel Electrophoresis
pp. 147
Target Preparation for Genotyping Specific Genes or Gene Segments
pp. 149
MicroRNA Promoter Analysis
pp. 149
Determination of Absolute Configuration Using Single Crystal X-Ray Diffraction
pp. 149
Live-Cell High Content Screening in Drug Development
pp. 149
Generation of a Bioengineered Tooth by Using a Three-Dimensional Cell Manipulation Method (Organ Germ Method)
pp. 153
Reverse Phase Protein Arrays and Drug Discovery
pp. 153
Quartz Microbalance Technology for Probing Biomolecular Interactions
pp. 157
Hexahistidine-Tagged Maltose-Binding Protein as a Fusion Partner for the Production of Soluble Recombinant Proteins in Escherichia coli
pp. 157
Genotyping of Mutations in the Beta-Globin Gene Using Allele Specific Hybridization
pp. 157
First Biochemical Steps on Bacterial Transposition Pathways
pp. 159
Plasma Polymer and PEG-Based Coatings for DNA, Protein and Cell Microarrays
pp. 159
Defining the Structure and Function of Acyl-Homoserine Lactone Autoinducers
pp. 161
RNAi-Based Techniques for the Analysis of Gene Function in Drosophila Germline Stem Cells
pp. 163
Analyzing Tandem Mass Spectra Using the DRIP Toolkit: Training, Searching, and Post-Processing
pp. 163
Detecting Mechanisms of Acquired BRAF Inhibitor Resistance in Melanoma
pp. 163
Targeted In Vivo Delivery of siRNA and an Endosome-Releasing Agent to Hepatocytes
pp. 163
Computational Methods for Comparative Analysis of Plant Small RNAs
pp. 165
Label-Free Kinetic Analysis of an Antibody–Antigen Interaction Using Biolayer Interferometry
pp. 165
Genome Editing in Human Pluripotent Stem Cells
pp. 167
In Vitro Studies on Odontogenic Tumors
pp. 167
Preparation of Frozen Liver Tissues for Integrated Omics Analysis
pp. 167
Preparation of Barley Pollen Mother Cells for Confocal and Super Resolution Microscopy
pp. 169
A Bioinformatics Pipeline for the Identification of CHO Cell Differential Gene Expression from RNA-Seq Data
pp. 169
Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt
pp. 171
Advanced Mitochondrial Respiration Assay for Evaluation of Mitochondrial Dysfunction in Alzheimer’s Disease
pp. 173
PHB-Intein-Mediated Protein Purification Strategy
pp. 177
deGradFP: A System to Knockdown GFP-Tagged Proteins
pp. 177
Current Status of Diagnostic and Prognostic Markers in Melanoma
pp. 179
Generation of a Three-Dimensional Kidney Structure from Pluripotent Stem Cells
pp. 179
Rapid miRNA Imaging in Cells Using Fluorogenic Templated Staudinger Reaction Between PNA-Based Probes
pp. 179
Whole Mount Immunohistochemistry and In Situ Hybridization of Larval and Adult Zebrafish Dental Tissues
pp. 179
Natural Transformation in Escherichia coli
pp. 181
Simple and Effective Affinity Purification Procedures for Mass Spectrometry-Based Identification of Protein-Protein Interactions in Cell Signaling Pathways
pp. 183
Rapid Phenotyping Adult Plant Resistance to Stem Rust in Wheat Grown under Controlled Conditions
pp. 183
Melanoblasts as Multipotent Cells in Murine Skin
pp. 183
Biotic Stress-Associated microRNAs: Identification, Detection, Regulation, and Functional Analysis
pp. 183
Characterization of Protein-Protein Interactions by Isothermal Titration Calorimetry
pp. 185
Liposome-Enhanced Lateral-Flow Assays for the Sandwich-Hybridization Detection of RNA
pp. 185
High-Throughput Biotinylation of Proteins
pp. 187
Cell-Internalization SELEX: Method for Identifying Cell-Internalizing RNA Aptamers for Delivering siRNAs to Target Cells
pp. 189
Integron Identification in Bacterial Genomes and Cassette Recombination Assays
pp. 191
ER Membrane Protein Interactions Using the Split-Ubiquitin System (SUS)
pp. 191
Energy Intake, Physical Activity, Energy Balance, and Cancer: Epidemiologic Evidence
pp. 195
Making a Kidney Organoid Using the Directed Differentiation of Human Pluripotent Stem Cells
pp. 195
An Electrical Impedance-Based Method for Quantitative Real-Time Analysis of Semaphorin-Elicited Endothelial Cell Collapse
pp. 197
5-Fluoro-d,l-Tryptophan as a Dual NMR and Fluorescent Probe of α-Synuclein
pp. 199
High-Throughput Insect Cell Protein Expression Applications
pp. 199
Chromosomal Copy Number Analysis in Melanoma Diagnostics
pp. 201
Strategies for siRNA Navigation to Desired Cells
pp. 203
Methods to Study Antagonistic Activities Among Oral Bacteria
pp. 203
Abiotic Stress-Associated miRNAs: Detection and Functional Analysis
pp. 203
Antibody Epitope Mapping Using De Novo Generated Synthetic Peptide Libraries
pp. 203
β-Amyloid Protein Aggregation
pp. 203
Pharmacology of Mammalian Olfactory Receptors
pp. 205
Cellular Expression of A20 and ABIN-3 in Response to Toll-Like Receptor-4 Stimulation
pp. 205
Sedimentation Equilibrium Studies
pp. 207
Isolation of Carotenoid Hyperproducing Mutants of Xanthophyllomyces dendrorhous (Phaffia rhodozyma) by Flow Cytometry and Cell Sorting
pp. 209
Methods to Identify and Analyze Vesicle-Protected DNA Transfer
pp. 215
Kinase Activity Determination of Specific AMPK Complexes/Heterotrimers in the Skeletal Muscle
pp. 217
Use of Guanidinopropyl-Modified siRNAs to Silence Gene Expression
pp. 219
Generating Sample-Specific Databases for Mass Spectrometry-Based Proteomic Analysis by Using RNA Sequencing
pp. 219
Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME
pp. 219
Fluorescence Resonance Energy Transfer Techniques to Study Ligand-Mediated Interactions of PPARs with Coregulators
pp. 223
Detecting Protein-Protein Interactions by Gel Filtration Chromatography
pp. 223
Measuring Plasmid Stability in Gram-Negative Bacteria
pp. 223
An In Vitro Model of the Human Colon: Studies of Intestinal Biofilms and Clostridium difficile Infection
pp. 227
BUSCO: Assessing Genome Assembly and Annotation Completeness
pp. 227
Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host–Microbiota Interactions
pp. 227
Construction and Analysis of Multiparameter Prognostic Models for Melanoma Outcome
pp. 229
High-Throughput Protein Expression Using Cell-Free System
pp. 231
Processing of miRNA Precursors
pp. 231
Capillary Electrophoresis Analysis of a 9-plex STR Assay for Canine Genotyping
pp. 231
Analysis of Epigenetic Alterations to Proprotein Convertase Genes in Disease
pp. 233
Using Light Scattering to Determine the Stoichiometry of Protein Complexes
pp. 233
Prediction of Interacting Protein Residues Using Sequence and Structure Data
pp. 233
Targeted Gene Knock Out Using Nuclease-Assisted Vector Integration: Hemi- and Homozygous Deletion of JAG1
pp. 235
MiniBioReactor Arrays (MBRAs) as a Tool for Studying C. difficile Physiology in the Presence of a Complex Community
pp. 235
Databases and Associated Tools for Glycomics and Glycoproteomics
pp. 235
Functional Interaction Network Construction and Analysis for Disease Discovery
pp. 235
Methods for the Analysis and Characterization of Defense Mechanisms Against Horizontal Gene Transfer: CRISPR Systems
pp. 235
Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies
pp. 237
Production of O-GlcNAc Modified Recombinant Tau in E. coli and Detection of Ser400 O-GlcNAc Tau In Vivo
pp. 237
Human Papillomavirus Testing in Head and Neck Squamous Cell Carcinoma: Best Practice for Diagnosis
pp. 239
Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development
pp. 239
Circular Dichroism (CD) Analyses of Protein-Protein Interactions
pp. 241
Extensive Phenotypic Analysis, Transcription Factor Profiling, and Effector Cytokine Production of Human MAIT Cells by Flow Cytometry
pp. 243
Profiling Tumor Infiltrating Immune Cells with CIBERSORT
pp. 243
Purification of Arabidopsis Argonaute Complexes and Associated Small RNAs
pp. 243
Transfection-Based Genomic Readout for Identifying Rare Transcriptional Splice Variants
pp. 245
Immune Monitoring Using mRNA-Transfected Dendritic Cells
pp. 245
Expression and Microarrays
pp. 245
The Production of Glycoproteins by Transient Expression in Mammalian Cells
pp. 247
GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples
pp. 249
Quantification of Small Molecules Using Microarray Technology
pp. 251
Therapy of Respiratory Viral Infections with Intranasal siRNAs
pp. 253
The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements
pp. 253
Quantification of Mitotic Chromosome Alignment
pp. 255
Metagenomics and CAZyme Discovery
pp. 255
Transient Assays for the Analysis of miRNA Processing and Function
pp. 257
Identifying Components of Complexes
pp. 257
High-Throughput Single-Cell RNA Sequencing and Data Analysis
pp. 259
Immunohistochemical Diagnostic and Prognostic Markers for Melanoma
pp. 263
Engineering Therapeutic Cancer Vaccines That Activate Antitumor Immunity
pp. 265
High-Throughput Expression and Detergent Screening of Integral Membrane Proteins
pp. 265
Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan
pp. 267
Protein-Protein Interaction Analysis by Nuclear Magnetic Resonance Spectroscopy
pp. 267
Bacterial Amyloids
pp. 269
Immunosuppressive Factor Blockade in Dendritic Cells via siRNAs Results in Objective Clinical Responses
pp. 269
Experimental Model for Studying the Involvement of Regulatory Cytotoxic T Cells in Bone Resorption
pp. 271
Predicting Transcription Factor Binding Sites and Their Cognate Transcription Factors Using Gene Expression Data
pp. 273
Cell-Free Expression for Nanolipoprotein Particles: Building a High-Throughput Membrane Protein Solubility Platform
pp. 273
Flow Cytometry Analysis and Quantitative Characterization of Tau in Synaptosomes from Alzheimer’s Disease Brains
pp. 275
Assembling DNA Barcodes
pp. 275
Lymphatic Invasion as a Prognostic Biomarker in Primary Cutaneous Melanoma
pp. 275
Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data
pp. 277
A Weighted SNP Correlation Network Method for Estimating Polygenic Risk Scores
pp. 277
Targeting bcr-abl Transcripts with siRNAs in an Imatinib-Resistant Chronic Myeloid Leukemia Patient: Challenges and Future Directions
pp. 277
Identifying Intracellular Sites of Eicosanoid Lipid Mediator Synthesis with EicosaCell Assays
pp. 277
Pressure Myography to Study the Function and Structure of Isolated Small Arteries
pp. 279
Deciphering Metatranscriptomic Data
pp. 281
Quantitative Protein Analysis by Mass Spectrometry
pp. 281
Computational Diagnostics with Gene Expression Profiles
pp. 285
PlasmidFinder and In Silico pMLST: Identification and Typing of Plasmid Replicons in Whole-Genome Sequencing (WGS)
pp. 287
Assessing Carbon Source-Dependent Phenotypic Variability in Pseudomonas putida
pp. 287
Tumor-Infiltrating Lymphocytes and Their Significance in Melanoma Prognosis
pp. 289
Addressing Intracellular Amyloidosis in Bacteria with RepA-WH1, a Prion-Like Protein
pp. 291
Whole Genome Duplication in Plants: Implications for Evolutionary Analysis
pp. 291
High-Throughput Screening to Identify Chemoreceptor Ligands
pp. 291
Cell Models to Study Cell-to-Cell Transmission of α-Synuclein
pp. 293
A Facile Method for Interfering with Off-Target Silencing Mediated by the Sense Strand
pp. 295
MOBscan: Automated Annotation of MOB Relaxases
pp. 297
Analysis of Quantitative Trait Loci
pp. 297
Expression and Purification of Soluble His6-Tagged TEV Protease
pp. 299
A “Living Bioreactor” for the Production of Tissue-Engineered Small Intestine
pp. 299
Self-Assembly of PNA-Encoded Peptides into Microarrays
pp. 301
Overcoming the Challenges of siRNA Activation of Innate Immunity: Design Better Therapeutic siRNAs
pp. 301
Synthesis, Mass Spectrometric Characterization, and Analysis of the PPARδ Agonist GW1516 and Its Major Human Metabolites: Targets in Sports Drug Testing
pp. 305
Quantitative Modeling and Automated Analysis of Meiotic Recombination
pp. 307
Using Peptide Arrays Created by the SPOT Method for Defining Protein-Protein Interactions
pp. 309
High-Throughput Protein Concentration and Buffer Exchange: Comparison of Ultrafiltration and Ammonium Sulfate Precipitation
pp. 309
Plasmid Typing and Classification
pp. 311
Protocols for Developing Novel Chikungunya Virus DNA Vaccines
pp. 311
Better Utilization of Mouse Models of Neurodegenerative Diseases in Preclinical Studies: From the Bench to the Clinic
pp. 311
Gas Exchange Measurements for the Determination of Photosynthetic Efficiency in Arabidopsis Leaves
pp. 313
Biosensors for d-Amino Acid Detection
pp. 317
NMR Analysis of Fecal Samples
pp. 321
Gene Silencing In Vitro and In Vivo Using Intronic MicroRNAs
pp. 321
Preparation and Characterization of Biocompatible Chitosan Nanoparticles for Targeted Brain Delivery of Peptides
pp. 323
Plasmid Reconstruction from Next-Gen Data: A Detailed Protocol for the Use of PLACNETw for the Reconstruction of Plasmids from WGS Datasets
pp. 323
Fluorescence Polarization Assay to Quantify Protein-Protein Interactions: An Update
pp. 325
Pathological Staging of Melanoma
pp. 327
Molecular Similarity Concepts and Search Calculations
pp. 329
Förster Resonance Energy Transfer (FRET) Microscopy for Monitoring Biomolecular Interactions
pp. 331
Applications of ApoB LDLR-Binding Domain Approach for the Development of CNS-Penetrating Peptides for Alzheimer’s Disease
pp. 335
Chromatin Immunoprecipitation for Identification of Protein–DNA Interactions in Human Cells
pp. 335
Agent-Based Modeling of Cancer Stem Cell Driven Solid Tumor Growth
pp. 337
Use of Inosine Monophosphate Dehydrogenase Activity Assay to Determine the Specificity of PARP-1 Inhibitors
pp. 339
Data Conversion with ProteoWizard msConvert
pp. 339
A Protocol for Top-Down Proteomics Using HPLC and ETD/PTR-MS
pp. 341
In Silico Identification of Novel Endo-siRNAs
pp. 341
Statistical Analysis of Accessory Genome
pp. 341
Utilizing ELISA to Monitor Protein-Protein Interaction
pp. 343
Analysis of Vesicular Trafficking in Primary Neurons by Live Imaging
pp. 349
Rhizosphere Sampling Protocols for Microbiome (16S/18S/ITS rRNA) Library Preparation and Enrichment for the Isolation of Drought Tolerance-Promoting Microbes
pp. 349
Optimization of the MAD Algorithm for Virtual Screening
pp. 349
Seamless Ligation Cloning Extract (SLiCE) Method Using Cell Lysates from Laboratory Escherichia coli Strains and its Application to SLiP Site-Directed Mutagenesis
pp. 353
Computer-Assisted Annotation of Small RNA Transcriptomes
pp. 353
Genotyping of Human Leukocyte Antigen (HLA) Ancestral Haplotypes as Prognostic Marker in Cancer Using PCR Analysis
pp. 353
Glutathione-S-Transferase (GST)-Fusion Based Assays for Studying Protein-Protein Interactions
pp. 355
Identification of Transcriptional Regulators of Psoriasis from RNA-Seq Experiments
pp. 355
Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits
pp. 363
Gene Targeting MRI: Nucleic Acid-Based Imaging and Applications
pp. 365
Hexahistidine (6xHis) Fusion-Based Assays for Protein-Protein Interactions
pp. 365
miR-CATCH: MicroRNA Capture Affinity Technology
pp. 367
B7-H Abnormalities in Melanoma and Clinical Relevance
pp. 367
A Computational Method to Search for DNA Structural Motifs in Functional Genomic Elements
pp. 369
LC/MS Data Processing for Label-Free Quantitative Analysis
pp. 371
Electrospun Nanofiber Scaffolds for Investigating Cell–Matrix Adhesion
pp. 371
Studying Protein-Protein Interactions via Blot Overlay/Far Western Blot
pp. 371
Methods to Study Fitness and Compensatory Adaptation in Plasmid-Carrying Bacteria
pp. 375
Roles of MicroRNAs in Cancers and Development
pp. 377
Detecting Structural Invariants in Biological Reaction Networks
pp. 381
Co-immunoprecipitation from Transfected Cells
pp. 381
Melanoma Susceptibility Genes and Risk Assessment
pp. 383
A Broad Host Range Plasmid-Based Roadmap for ssDNA-Based Recombineering in Gram-Negative Bacteria
pp. 391
In Vivo Protein Cross-Linking
pp. 395
Peptide and Protein Ion/Ion Reactions in Electrodynamic Ion Traps: Tools and Methods
pp. 395
Developing Fixed-Parameter Algorithms to Solve Combinatorially Explosive Biological Problems
pp. 397
Clinical, Pathologic, and Imaging Features and Biological Markers of Uveal Melanoma
pp. 399
Conjugative Assembly Genome Engineering (CAGE)
pp. 409
Identification of Protein-Protein Interactions by Standard Gal4p-Based Yeast Two-Hybrid Screening
pp. 409
Robust Multiparametric Assessment of Cellular Senescence
pp. 415
Targeting MicroRNAs to Withstand Cancer Metastasis
pp. 427
A Prognostic Test to Predict the Risk of Metastasis in Uveal Melanoma Based on a 15-Gene Expression Profile
pp. 433
Reverse Two-Hybrid Techniques in the Yeast Saccharomyces cerevisiae
pp. 439
Urinary MicroRNAs as a New Class of Noninvasive Biomarkers in Oncology, Nephrology, and Cardiology
pp. 441
Visualization
pp. 441
Molecular Karyotyping for Detection of Prognostic Markers in Fine Needle Aspiration Biopsy Samples of Uveal Melanoma
pp. 447
MAPPIT, a Mammalian Two-Hybrid Method for In-Cell Detection of Protein-Protein Interactions
pp. 451
Genetic Engineering of Industrial Strains of Saccharomyces cerevisiae
pp. 457
Bioluminescence Resonance Energy Transfer to Detect Protein-Protein Interactions in Live Cells
pp. 459
Characterization of Genetic Networks Associated with Alzheimer’s Disease
pp. 461
ERBB4 Mutation Analysis: Emerging Molecular Target for Melanoma Treatment
pp. 465
Magnetic Bead-Based Isolation of Exosomes
pp. 467
Mapping Biochemical Networks with Protein Fragment Complementation Assays
pp. 481
Epigenetic Markers of Prognosis in Melanoma
pp. 483
Detection of Protein-Protein Interaction Using Bimolecular Fluorescence Complementation Assay
pp. 483
Modified 2′-Ribose Small RNAs Function as Toll-Like Receptor-7/8 Antagonists
pp. 487
Systematic Methods for Structurally Consistent Coarse-Grained Models
pp. 497
Split-Luciferase Complementation Assay to Detect Channel–Protein Interactions in Live Cells
pp. 497
Translating Antisense Technology into a Treatment for Huntington’s Disease
pp. 501
Isolation of Melanoma Cell Subpopulations Using Negative Selection
pp. 509
Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles
pp. 513
Circulating Tumor Cells as Prognostic Biomarkers in Cutaneous Melanoma Patients
pp. 515
Confocal Microscopy for Intracellular Co-localization of Proteins
pp. 523
Detection of Chondroitin Sulfate Proteoglycan 4 (CSPG4) in Melanoma
pp. 529
Fluorescence Polarization Assay to Quantify Protein-Protein Interactions in an HTS Format
pp. 537
Targeting Damage-Associated Molecular Pattern Molecules (DAMPs) and DAMP Receptors in Melanoma
pp. 541
Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy
pp. 545
Estrogen Receptor Alpha/Co-activator Interaction Assay: TR-FRET
pp. 553
The Clinical Use of PET/CT in the Evaluation of Melanoma
pp. 555
High Content Screening Biosensor Assay to Identify Disruptors of p53–hDM2 Protein-Protein Interactions
pp. 567
Case Study: Discovery of Inhibitors of the MDM2–p53 Protein-Protein Interaction
pp. 583
Co-immunoprecipitation: Protein–RNA and Protein–DNA Interaction
pp. 583
Immune System Functional Pathway Analysis Using Single Cell Network Profiling (SCNP): A Novel Tool in Cancer Immunotherapy
pp. 587
Biophysical Methods for Identifying Fragment-Based Inhibitors of Protein-Protein Interactions
pp. 601
Quantitative and Spatial Image Analysis of Tumor and Draining Lymph Nodes Using Immunohistochemistry and High-Resolution Multispectral Imaging to Predict Metastasis
pp. 623
COLD-PCR Enriches Low-Level Variant DNA Sequences and Increases the Sensitivity of Genetic Testing
pp. 641
Isolation of Circulating MicroRNAs from Microvesicles Found in Human Plasma
pp. 655
Detection of Circulating Tumor Cells by Photoacoustic Flowmetry
pp. 667
Statistical Design and Evaluation of Biomarker Studies
pp. 679
Tissue Resources for Clinical Use and Marker Studies in Melanoma
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