Unravelling single cell genomics : micro and nanotools

Description

Content: Machine generated contents note: ch. 1 An Introduction to Molecular Biology / Luce Dauphinot -- Abstract -- 1.1. DNA Structure and Gene Expression -- 1.2. Molecular Biology Tools for Nucleic Acid Studies -- 1.2.1. DNA Engineering -- 1.2.2. Polymerase Chain Reaction -- 1.2.3. DNA Microarrays -- References -- ch. 2 The Central Dogma in Molecular Biology / Laili Mahmoudian -- Abstract -- 2.1. Replication -- 2.2. Transcription -- 2.3. Translation -- 2.4. Regulation of Gene Expression -- 2.4.1. Transcriptional Control -- 2.4.2. Post-transcriptional Modifications -- 2.4.3. Translational Control -- 2.4.4. Post-translational Control -- 2.5. Limitations of the Central Dogma -- 2.6. Single Cells and their Complexity -- References -- ch. 3 From Unicellular to Multicellular Organisms: Tells from Evolution and from Development / Tania Vitalis -- Abstract -- 3.1. Cells from Evolution -- 3.2. Cells from Development -- References -- ch. 4 Understanding Cellular Differentiation / Tania Vitalis -- Abstract 4.1. Development of the Cerebral Cortex -- 4.2. Neuronal Differentiation -- 4.3. Single Cell Analysis in Differentiation Processes -- References -- ch. 5 Realistic Models of Neurons Require Quantitative Information at the Single-cell Level / Nicolas Le Novere -- Abstract -- 5.1. Introduction -- 5.2. The Importance of Precise Neuronal Morphology -- 5.3. Each Neuron has a Unique Neurochemistry -- 5.4. Conclusions -- References -- ch. 6 Application to Cancerogenesis: Towards Targeted Cancer Therapies? / Christoph A. Klein -- Abstract -- 6.1. Molecular Diagnosis in Cancer -- 6.2. Detection and Malignant Origin of Disseminated Cancer Cells -- 6.3. Genomic Studies of Single Disseminated Cancer Cells -- 6.4. Oncogene Dependence and Tumor Suppressor Sensitivity in Metastasis Founder Cells -- References -- ch. 7 Capturing a Single Cell / Joel Lachuer -- Abstract -- 7.1. Introduction -- 7.2. Overview of Cell Sorting Technologies -- 7.3. Laser Capture Microdissection Technologies -- 7.3.1. Infrared Laser Capture Systems -- 7.3.2. Ultraviolet Cutting Systems 7.4. Protocols Before Laser Microdissection (Tissue Sampling and Preparation) -- 7.4.1. Dissection from Fresh Frozen Tissue -- 7.4.2. Dissection from Formalin-fixed Paraffin-embedded Tissue -- 7.4.3. Immuno Laser Capture Microdissection -- 7.4.4. Other Cell-labeling Methods -- 7.5. Conclusion -- References -- ch. 8 Looking at the DNA of a Single Cell / Christoph A. Klein -- Abstract -- 8.1. Challenges of Single Cell DNA Amplification -- 8.2. Methods for Amplifying Genomic DNA of Single Cells -- 8.3. Array Comparative Genomic Hybridization of Single Cells -- 8.4. Combined Genome and Transcriptome Analysis of Single Cells -- 8.5. Perspective on Single Cell DNA Analysis -- References -- ch. 9 Gene Analysis of Single Cells / Bertrand Lambolez -- Abstract -- 9.1. Single Cell RT-PCR After Patch Clamp -- 9.2. Correlating mRNA Expression and Functional Properties of Single Cells -- 9.3. Quantitative Analyses by scPCR -- 9.4. Molecular and Functional Phenotyping of Neuronal Types -- 9.5. Patch-clamp Harvesting of Single Cells 9.6. Sensitivity Limits -- 9.7. Controls -- 9.8. Interpretation of scPCR Results -- Conclusion -- Acknowledgement -- References -- ch. 10 Proteomics / Joelle Vinh -- Abstract -- 10.1. Motivation to Study Proteins at the Single Cell Level -- 10.1.1. Proteins, mRNAs and DNA -- 10.1.2. Sample Preparation -- 10.1.3. Sub-proteome Analysis -- 10.2. Analytical Strategies -- 10.2.1. Mass Spectrometry -- 10.2.2. Coupling Separation Techniques and Mass Spectrometry -- 10.3. Strategies for Studying Proteins in Low Amounts of Samples -- 10.3.1. How to Enhance the Sensitivity: Miniaturization, Integration, and Automation -- 10.3.2. MALDI Interfaces -- Conclusion -- References -- ch. 11 Microfluidics: Basic Concepts and Microchip Fabrication / Petra S. Dittrich -- Abstract -- 11.1. Size Matters: An Introduction -- 11.2. A Short Chronology of Microfluidics Research -- 11.3. Microfluidics: Some Basics -- 11.3.1. Flow Generation -- 11.3.2. Laminar Flow -- 11.3.3. Digital Microfluidics: Segmented Flow -- 11.4. Fabrication Techniques and Materials 11.4.1. Photolithography -- 11.4.2. Soft Lithography -- 11.4.3. Microchip Materials -- 11.4.4. From Fabrication to Application -- 11.5. Concluding Remarks -- References -- ch. 12 Cell Capture and Lysis on a Chip / Albert van den Berg -- Abstract -- 12.1. Introduction -- 12.2. Cell Capture on a Chip -- 12.2.1. Mechanical Trapping -- 12.2.2. Electrical Trapping -- 12.2.3. Fluidic Trapping -- 12.2.4. Alternative Trapping Techniques -- 12.2.5. Conclusion on Cell Trapping -- 12.3. Cell Lysis in a Chip -- 12.3.1. Thermal Lysis -- 12.3.2. Chemical Lysis -- 12.3.3. "Alkaline" or Electrochemical Lysis -- 12.3.4. Electrical Lysis -- 12.3.5. Mechanical Lysis -- 12.3.6. Alternative Mechanical Lysis: Acoustic Lysis -- 12.3.7. Optical Lysis -- 12.3.8. Conclusion on Cell Lysis -- 12.4. Conclusion -- References -- ch. 13 DNA Analysis in Microfluidic Devices and their Application to Single Cell Analysis / Angelique Le Bras -- Abstract -- 13.1. Amplification on a Chip -- 13.1.1. Polymerase Chain Reaction -- 13.1.2. Isothermal Techniques 13.2. DNA Analysis -- 13.2.1. Real-time PCR Detection -- 13.2.2. Capillary Electrophoresis -- 13.3. Why and When Smaller is Better -- 13.4. Applications of Microfluidic Single Cell Genetic Analysis in Microbial Ecology -- 13.5. Conclusion -- References -- ch. 14 Gene Expression Analysis on Microchips / Max Chahert -- Abstract -- 14.1. Introduction -- 14.2. Multi-step Microfluidic RT-PCR -- 14.3. One-step Microfluidic RNA Analysis -- 14.4. Microfluidic cDNA Analysis -- 14.5. Single Cell RNA Analysis -- 14.6. Conclusion -- Acknowledgement -- References -- ch. 15 Analysis of Proteins at the Single Cell Level / Severine Le Gac -- Abstract -- 15.1. Introduction -- 15.1.1. Protein Analysis: The Challenge -- 15.1.2. Why Microfluidics? -- 15.1.3. Microfluidics and Protein Analysis -- 15.2. Electrospray Ionization Mass Spectrometry -- 15.2.1. Connections and Coupling -- 15.2.2. Sample Processing: Purification and Digestion -- 15.2.3. Integrated Systems -- 15.3. MALDI-MS -- 15.3.1. Microfabricated MALDI Targets 15.3.2. Off-line Sample Preparation -- 15.3.3. Integrated Microsystems -- 15.4. Innovative Approaches for Protein Analysis at the Single Cell Level -- 15.4.1. Invasive Analysis -- 15.4.2. Partially Invasive Analysis -- 15.4.3. Non-invasive Analysis -- 15.5. Conclusion and Perspectives -- References -- ch. 16 A Concrete Case: A Microfluidic Device for Single Cell Whole Transcriptome Analysis / Marie-Claude Potier -- Abstract -- 16.1. Introduction -- 16.2. Choice of Biological Protocol, Material and Fabrication Technique -- 16.2.1. Protocols for Single Cell Whole Transcriptome Analysis -- 16.2.2. Miniaturizing Reactions: Continuous Flows, Reaction Chambers or Droplet Micro-fluidic Reactions -- 16.2.3. Choosing the Microchip Material -- 16.2.4. Microchip Fabrication -- 16.3. Integrating Reverse Transcription on a Chip -- 16.3.1. Gene Expression Profiling of Single-Cell Scale Amounts of RNA -- 16.3.2. Gene Expression Profiling of Single Cells -- 16.4. Amplifying the Transcriptome on a Chip -- 16.5. Detecting the Transcriptome on a Chip 16.5.1. Microfluidics and Conventional Microarrays -- 16.5.2. Microarray Development Using DNA Immobilization onto Microchannels -- 16.5.3. Towards Transcriptome Analysis in the Liquid Phase -- 16.6. Some Practical Conclusions -- References -- ch. 17 Tiny Droplets for High-throughput Cell-based Assays / V. Taly -- Abstract -- 17.1. Introduction -- 17.2. Droplet-based Microfluidics -- 17.2.1. EWOD and "Digital Microfluidics": Tools for High-content Screening -- 17.2.2. Droplet-based Microfluidics: Tools for High-throughput Screening -- 17.3. Generating and Manipulating Droplets -- 17.3.1. Droplet Production -- 17.3.2. Droplet Division -- 17.3.3. Droplet Flow, Droplet Synchronization, and Droplet Incubation -- 17.3.4. Droplet Content Detection and Droplet Sorting -- 17.4. In Vitro Compartmentalization of Biological Reactions -- 17.4.1. Cell Compartmentalization in Aqueous Droplets -- 17.4.2. Incubation and Cell Viability in Droplets -- 17.4.3. Cell-based Assays and Cell Manipulation -- 17.5. Towards Integrated Platforms for Cell-based Assays 17.6. Conclusions -- References -- ch. 18 New Detection Methods for Single Cells / Emmanuel Fort -- Abstract -- 18.1. Introduction -- 18.2. Bio-barcode Strategy -- 18.2.1. Principle -- 18.2.2. An Example: DNA Origami -- 18.3. Imaging Gene Expression in Living Cells -- 18.3.1. Motivations -- 18.3.2. Improvements in Photonic Microscopy -- 18.3.3. Improvements in Fluorophore Design -- 18.4. Quantum Dots-based Techniques -- 18.4.1. Quantum Dots Bead-based Assays -- 18.4.2. Single Quantum Dots-based DNA Nanosensors -- 18.4.3. Quantum Dots for Super-resolution Microscopy -- 18.5. Gold Nanoparticle-based Detection Methods -- 18.5.1. Resonant Light Scattering Detection -- 18.5.2. Molecular Beacons with Gold Nanoparticles -- 18.5.3. Molecular Plasmonic Rulers -- 18.5.4. Surface-enhanced Raman Scattering Detection -- 18.6. Electrochemical Sensors -- 18.7. Concluding Remarks -- References