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Unravelling Single Cell Genomics: Micro and Nanotools [Kietas viršelis]

Contributions by , Edited by (CNRS, France), Series edited by (University of Manchester, UK), Contributions by , Edited by , Edited by (Agilent Technologies, France), Contributions by , Contributions by , Series edited by (Cornell University, USA), Series edited by (Florida State University, USA)
  • Formatas: Hardback, 336 pages, aukštis x plotis: 234x156 mm, weight: 1421 g, No
  • Serija: Nanoscience & Nanotechnology Series Volume 15
  • Išleidimo metai: 18-Oct-2010
  • Leidėjas: Royal Society of Chemistry
  • ISBN-10: 1847559115
  • ISBN-13: 9781847559111
Kitos knygos pagal šią temą:
Unravelling Single Cell Genomics: Micro and NanotoolsDidesnis paveikslėlis
  • Formatas: Hardback, 336 pages, aukštis x plotis: 234x156 mm, weight: 1421 g, No
  • Serija: Nanoscience & Nanotechnology Series Volume 15
  • Išleidimo metai: 18-Oct-2010
  • Leidėjas: Royal Society of Chemistry
  • ISBN-10: 1847559115
  • ISBN-13: 9781847559111
Kitos knygos pagal šią temą:
Pastovi nuoroda: https://www.kriso.lt/db/9781847559111.html
Raktažodžiai:
Aimed predominantly at graduate students, this book provides all the necessary information to conduct experiments in microfluidics and molecular biology.


This unique introduction to the growing field of microfluidics applied to genomics provides an overview of the latest technologies and emphasizes its potential in answering important biological questions. Written by a physicist and a biologist, it offers a more comprehensive view than the previous literature. The book starts with key ideas in molecular biology, developmental biology and microtechnology before going on to cover the specifics of single cell analysis and microfluidic devices for single cell molecular analysis. Review chapters discuss the state-of-the art and will prove invaluable to all those planning to develop microdevices for molecular analysis of single cells. Methods allowing complete analysis of gene expression in the single cell are stressed - as opposed the more commonly used techniques that allow analysis of only a few genes at a time. As pioneers in the field, the authors understand how critical it is for a physicist to understand the biological issues and questions related to single cell analysis, as well for biologists to understand what microfluidics is all about. Aimed predominantly at graduate students, this book will also be of significant interest to scientists working in or affiliated with this field.

Recenzijos

"Initial chapters are based on the basics of cell biology, followed by a discussion of the need for single cell analysis and developments in this area."



"This book will benefit students and specialists alike..." * Materials World Magazine *

Chapter 1 An Introduction to Molecular Biology
1(14)
Luce Dauphinot
Abstract
1(1)
1.1 DNA Structure and Gene Expression
1(5)
1.2 Molecular Biology Tools for Nucleic Acid Studies
6(7)
1.2.1 DNA Engineering
6(1)
1.2.2 Polymerase Chain Reaction
7(3)
1.2.3 DNA Microarrays
10(3)
References
13(2)
Chapter 2 The Central Dogma in Molecular Biology
15(11)
Laili Mahmoudian
Abstract
15(1)
2.1 Replication
15(2)
2.2 Transcription
17(1)
2.3 Translation
18(1)
2.4 Regulation of Gene Expression
18(5)
2.4.1 Transcriptional Control
19(2)
2.4.2 Post-transcriptional Modifications
21(1)
2.4.3 Translational Control
21(1)
2.4.4 Post-translational Control
22(1)
2.5 Limitations of the Central Dogma
23(1)
2.6 Single Cells and their Complexity
24(1)
References
24(2)
Chapter 3 From Unicellular to Multicellular Organisms: Tells from Evolution and from Development
26(10)
Tania Vitalis
Abstract
26(1)
3.1 Cells from Evolution
26(6)
3.2 Cells from Development
32(3)
References
35(1)
Chapter 4 Understanding Cellular Differentiation
36(9)
Tania Vitalis
Abstract
36(1)
4.1 Development of the Cerebral Cortex
36(1)
4.2 Neuronal Differentiation
37(2)
4.3 Single Cell Analysis in Differentiation Processes
39(4)
References
43(2)
Chapter 5 Realistic Models of Neurons Require Quantitative Information at the Single-cell Level
45(9)
Nicolas Le Novere
Abstract
45(1)
5.1 Introduction
45(4)
5.2 The Importance of Precise Neuronal Morphology
49(1)
5.3 Each Neuron has a Unique Neurochemistry
50(1)
5.4 Conclusions
51(1)
References
51(3)
Chapter 6 Application to Cancerogenesis: Towards Targeted Cancer Therapies?
54(7)
Bernhard Polzer
Christoph A. Klein
Abstract
54(1)
6.1 Molecular Diagnosis in Cancer
54(1)
6.2 Detection and Malignant Origin of Disseminated Cancer Cells
55(2)
6.3 Genomic Studies of Single Disseminated Cancer Cells
57(1)
6.4 Oncogene Dependence and Tumor Suppressor Sensitivity in Metastasis Founder Cells
58(2)
References
60(1)
Chapter 7 Capturing a Single Cell
61(12)
Catherine Rey
Anne Wierinckx
Severine Croze
Catherine Legras-Lachuer
Joel Lachuer
Abstract
61(1)
7.1 Introduction
61(1)
7.2 Overview of Cell Sorting Technologies
62(1)
7.3 Laser Capture Microdissection Technologies
63(3)
7.3.1 Infrared Laser Capture Systems
63(3)
7.3.2 Ultraviolet Cutting Systems
66(1)
7.4 Protocols Before Laser Microdissection (Tissue Sampling and Preparation)
66(4)
7.4.1 Dissection from Fresh Frozen Tissue
67(1)
7.4.2 Dissection from Formalin-fixed Paraffin-embedded Tissue
67(2)
7.4.3 Immuno Laser Capture Microdissection
69(1)
7.4.4 Other Cell-labeling Methods
70(1)
7.5 Conclusion
70(1)
References
70(3)
Chapter 8 Looking at the DNA of a Single Cell
73(8)
Bernhard Polzer
Christoph A. Klein
Abstract
73(1)
8.1 Challenges of Single Cell DNA Amplification
73(1)
8.2 Methods for Amplifying Genomic DNA of Single Cells
74(2)
8.3 Array Comparative Genomic Hybridization of Single Cells
76(1)
8.4 Combined Genome and Transcriptome Analysis of Single Cells
77(1)
8.5 Perspective on Single Cell DNA Analysis
78(1)
References
78(3)
Chapter 9 Gene Analysis of Single Cells
81(12)
Bruno Cauli
Bertrand Lambolez
Abstract
81(1)
9.1 Single Cell RT-PCR After Patch Clamp
81(2)
9.2 Correlating mRNA Expression and Functional Properties of Single Cells
83(1)
9.3 Quantitative Analyses by scPCR
84(1)
9.4 Molecular and Functional Phenotyping of Neuronal Types
84(2)
9.5 Patch-clamp Harvesting of Single Cells
86(3)
9.6 Sensitivity Limits
89(1)
9.7 Controls
89(1)
9.8 Interpretation of scPCR Results
90(1)
Conclusion
91(1)
Acknowledgement
91(1)
References
91(2)
Chapter 10 Proteomics
93(18)
Anne-Marie Hesse
Joelle Vinh
Abstract
93(1)
10.1 Motivation to Study Proteins at the Single Cell Level
93(4)
10.1.1 Proteins, mRNAs and DNA
94(1)
10.1.2 Sample Preparation
95(1)
10.1.3 Sub-proteome Analysis
96(1)
10.2 Analytical Strategies
97(8)
10.2.1 Mass Spectrometry
98(4)
10.2.2 Coupling Separation Techniques and Mass Spectrometry
102(3)
10.3 Strategies for Studying Proteins in Low Amounts of Samples
105(2)
10.3.1 How to Enhance the Sensitivity: Miniaturization, Integration, and Automation
105(1)
10.3.2 MALDI Interfaces
106(1)
Conclusion
107(1)
References
107(4)
Chapter 11 Microfluidics: Basic Concepts and Microchip Fabrication
111(39)
Conni Vollrath
Petra S. Dittrich
Abstract
111(1)
11.1 Size Matters: An Introduction
111(2)
11.2 A Short Chronology of Microfluidics Research
113(3)
11.3 Microfluidics: Some Basics
116(9)
11.3.1 Flow Generation
117(2)
11.3.2 Laminar Flow
119(4)
11.3.3 Digital Microfluidics: Segmented Flow
123(2)
11.4 Fabrication Techniques and Materials
125(18)
11.4.1 Photolithography
125(3)
11.4.2 Soft Lithography
128(3)
11.4.3 Microchip Materials
131(10)
11.4.4 From Fabrication to Application
141(2)
11.5 Concluding Remarks
143(1)
References
144(6)
Chapter 12 Cell Capture and Lysis on a Chip
150(35)
Severine Le Gac
Albert van den Berg
Abstract
150(1)
12.1 Introduction
150(1)
12.2 Cell Capture on a Chip
151(12)
12.2.1 Mechanical Trapping
152(3)
12.2.2 Electrical Trapping
155(2)
12.2.3 Fluidic Trapping
157(1)
12.2.4 Alternative Trapping Techniques
158(3)
12.2.5 Conclusion on Cell Trapping
161(2)
12.3 Cell Lysis in a Chip
163(16)
12.3.1 Thermal Lysis
164(1)
12.3.2 Chemical Lysis
165(4)
12.3.3 "Alkaline" or Electrochemical Lysis
169(2)
12.3.4 Electrical Lysis
171(3)
12.3.5 Mechanical Lysis
174(2)
12.3.6 Alternative Mechanical Lysis: Acoustic Lysis
176(1)
12.3.7 Optical Lysis
176(3)
12.3.8 Conclusion on Cell Lysis
179(1)
12.4 Conclusion
179(3)
References
182(3)
Chapter 13 DNA Analysis in Microfluidic Devices and their Application to Single Cell Analysis
185(11)
Yann Marcy
Angelique Le Bras
Abstract
185(1)
13.1 Amplification on a Chip
186(4)
13.1.1 Polymerase Chain Reaction
186(3)
13.1.2 Isothermal Techniques
189(1)
13.2 DNA Analysis
190(1)
13.2.1 Real-time PCR Detection
190(1)
13.2.2 Capillary Electrophoresis
191(1)
13.3 Why and When Smaller is Better
191(1)
13.4 Applications of Microfluidic Single Cell Genetic Analysis in Microbial Ecology
192(1)
13.5 Conclusion
193(1)
References
194(2)
Chapter 14 Gene Expression Analysis on Microchips
196(13)
Max Chahert
Abstract
196(1)
14.1 Introduction
197(3)
14.2 Multi-step Microfluidic RT-PCR
200(2)
14.3 One-step Microfluidic RNA Analysis
202(1)
14.4 Microfluidic cDNA Analysis
203(2)
14.5 Single Cell RNA Analysis
205(1)
14.6 Conclusion
206(1)
Acknowledgement
207(1)
References
207(2)
Chapter 15 Analysis of Proteins at the Single Cell Level
209(34)
Severine Le Gac
Abstract
209(1)
15.1 Introduction
210(3)
15.1.1 Protein Analysis: The Challenge
210(1)
15.1.2 Why Microfluidics?
211(1)
15.1.3 Microfluidics and Protein Analysis
212(1)
15.2 Electrospray Ionization Mass Spectrometry
213(8)
15.2.1 Connections and Coupling
214(1)
15.2.2 Sample Processing: Purification and Digestion
215(5)
15.2.3 Integrated Systems
220(1)
15.3 MALDI-MS
221(4)
15.3.1 Microfabricated MALDI Targets
222(1)
15.3.2 Off-line Sample Preparation
222(2)
15.3.3 Integrated Microsystems
224(1)
15.4 Innovative Approaches for Protein Analysis at the Single Cell Level
225(13)
15.4.1 Invasive Analysis
225(5)
15.4.2 Partially Invasive Analysis
230(4)
15.4.3 Non-invasive Analysis
234(4)
15.5 Conclusion and Perspectives
238(1)
References
238(5)
Chapter 16 A Concrete Case: A Microfluidic Device for Single Cell Whole Transcriptome Analysis
243(18)
Nathalie Bontoux
Luce Dauphinot
Marie-Claude Potier
Abstract
243(1)
16.1 Introduction
244(1)
16.2 Choice of Biological Protocol, Material and Fabrication Technique
245(3)
16.2.1 Protocols for Single Cell Whole Transcriptome Analysis
245(1)
16.2.2 Miniaturizing Reactions: Continuous Flows, Reaction Chambers or Droplet Micro-fluidic Reactions
245(1)
16.2.3 Choosing the Microchip Material
246(1)
16.2.4 Microchip Fabrication
246(2)
16.3 Integrating Reverse Transcription on a Chip
248(4)
16.3.1 Gene Expression Profiling of Single-Cell Scale Amounts of RNA
249(2)
16.3.2 Gene Expression Profiling of Single Cells
251(1)
16.4 Amplifying the Transcriptome on a Chip
252(3)
16.5 Detecting the Transcriptome on a Chip
255(3)
16.5.1 Microfluidics and Conventional Microarrays
255(1)
16.5.2 Microarray Development Using DNA Immobilization onto Microchannels
256(1)
16.5.3 Towards Transcriptome Analysis in the Liquid Phase
257(1)
16.6 Some Practical Conclusions
258(1)
References
258(3)
Chapter 17 Tiny Droplets for High-throughput Cell-based Assays
261(24)
J.-C. Baret
V. Taly
Abstract
261(1)
17.1 Introduction
262(1)
17.2 Droplet-based Microfluidics
263(2)
17.2.1 EWOD and "Digital Microfluidics": Tools for High-content Screening
263(2)
17.2.2 Droplet-based Microfluidics: Tools for High-throughput Screening
265(1)
17.3 Generating and Manipulating Droplets
265(5)
17.3.1 Droplet Production
265(2)
17.3.2 Droplet Division
267(1)
17.3.3 Droplet Flow, Droplet Synchronization, and Droplet Incubation
267(2)
17.3.4 Droplet Content Detection and Droplet Sorting
269(1)
17.4 In Vitro Compartmentalization of Biological Reactions
270(5)
17.4.1 Cell Compartmentalization in Aqueous Droplets
271(1)
17.4.2 Incubation and Cell Viability in Droplets
271(1)
17.4.3 Cell-based Assays and Cell Manipulation
272(3)
17.5 Towards Integrated Platforms for Cell-based Assays
275(3)
17.6 Conclusions
278(1)
References
279(6)
Chapter 18 New Detection Methods for Single Cells
285(25)
Emmanuel Fort
Abstract
285(1)
18.1 Introduction
286(1)
18.2 Bio-barcode Strategy
287(1)
18.2.1 Principle
287(1)
18.2.2 An Example: DNA Origami
287(1)
18.3 Imaging Gene Expression in Living Cells
288(5)
18.3.1 Motivations
288(1)
18.3.2 Improvements in Photonic Microscopy
288(2)
18.3.3 Improvements in Fluorophore Design
290(3)
18.4 Quantum Dots-based Techniques
293(2)
18.4.1 Quantum Dots Bead-based Assays
294(1)
18.4.2 Single Quantum Dots-based DNA Nanosensors
294(1)
18.4.3 Quantum Dots for Super-resolution Microscopy
295(1)
18.5 Gold Nanoparticle-based Detection Methods
295(8)
18.5.1 Resonant Light Scattering Detection
298(1)
18.5.2 Molecular Beacons with Gold Nanoparticles
298(1)
18.5.3 Molecular Plasmonic Rulers
299(1)
18.5.4 Surface-enhanced Raman Scattering Detection
300(3)
18.6 Electrochemical Sensors
303(1)
18.7 Concluding Remarks
304(1)
References
304(6)
Subject Index 310
After graduating from the Ecole Polytechnique, Nathalie Bontoux completed her MSc and PhD at the Paris VI University. She also carried out graduate research at the Laboratory of Photonics and Nanostructures, in Marcoussis and the Laboratory of Neurobiology at the ESPCI in Paris. In addition to her research, she has also held teaching posts at the LycŚe Saint Louis, Ecole Polytechnique and Orsay University. Currently, she is working as a product specialist on bioconsumables, including Lab-on-a-Chip kits, at Agilent Technologies. Marie-Claude Potier is recognized as a world expert in Down's syndrome and gene expression. She started as a Staff Scientist CNRS in 1991 before completing a PhD in Molecular Neuropharmacology and three years postdoctoral research at the Laboratory of Molecular Biology of the MRC in Cambridge. Her work focuses on the characterization of Down's syndrome phenotypes and the development of therapeutic approaches in mouse models. For the past decade, she has also been working on high throughput gene expression technologies using microarrays which have revealed gene expression modifications in Down's syndrome. More recently, using microfluidics, she has been involved in the development of a breakthrough method for gene expression profiling in single cells that has been used to study specific neuronal populations in the brain. For the past 6 years, she has led a research team and is currently the Vice Director of the CNRS unit.