Methods in bioengineering : systems analysis of biological networks

• Other Authors: Jayaraman, Arul, Hahn, Juergen
• Format: Electronic eBook
• Language: English
• Published: Boston [Mass.] : Artech House, ©2009.
• Series: Artech House methods in bioengineering series.
• Subjects: Bioengineering.; Biotechnology.; Biological models.; System analysis.; elektronické knihy; electronic books
• ISBN: 9781596934078; 1596934077; 9781596934061; 1596934069
• Physical Description: 1 online resource (xii, 316 pages) : illustrations

Table of Contents:

• Methods in Bioengineering: Systems Analysis of Biological Networks; Contents; Chapter 1 Quantitative Immunofluorescence for Measuring Spatial Compartmentation of Covalently Modified Signaling Proteins; 1.1 Introduction; 1.2 Experimental Design; 1.3 Materials; 1.3.1 Cell culture; 1.3.2 Buffers/reagents; 1.3.3 Immunofluorescence reagents; 1.4 Methods; 1.4.1 Cell culture and stimulation for phospho-ERK measurements; 1.4.2 Antibody labeling of phosphorylated ERK (ppERK); 1.4.3 Fluorescence microscopy imaging of ppERK and automated imageanalysis
• 1.5 Data Acquisition, Anticipated Results, and Interpretation1.6 Statistical Guidelines; 1.7 Discussion and Commentary; 1.8 Application Notes; 1.9 Summary Points; Acknowledgments; References; Chapter 2 Development of Green Fluorescent Protein-Based Reporter Cell Lines for Dynamic Profiling of Transcription Factor and Kinase Activation; 2.1 Introduction; 2.2 Materials; 2.2.1 Cell and bacterial culture; 2.2.2 Buffers and reagents; 2.2.3 Cloning; 2.2.4 Microscopy; 2.3 Methods; 2.3.1 3T3-L1 cell culture; 2.3.2 Transcription factor reporter development; 2.3.3 Kinase reporter development
• 2.4 Application Notes2.4.1 Electroporation of TF reporter plasmids into 3T3-L1 preadipocytes; 2.4.2 Monitoring activation of ERK in HepG2 cells; 2.5 Data Acquisition, Anticipated Results, and Interpretation; 2.6 Discussion and Commentary; 2.7 Summary Points; Acknowledgments; References; Chapter 3 Comparison of Algorithms for Analyzing Fluorescent Microscopy Images and Computation of Transcription Factor Profiles; 3.1 Introduction; 3.2 Preliminaries; 3.2.1 Principles of GFP reporter systems; 3.2.2 Wavelets; 3.2.3 K-means clustering; 3.2.4 Principal component analysis
• 3.2.5 Mathematical description of digital images and image analysis3.3 Methods; 3.3.1 Image analysis based on wavelets and a bidirectional search; 3.3.2 Image analysis based on K-means clustering and PCA; 3.3.3 Determining fluorescence intensity of an image; 3.3.4 Comparison of the two image analysis procedures; 3.4 Data Acquisition, Anticipated Results, and Interpretation; 3.4.1 Developing a model describing the relationship between the transcription factor concentration and the observed fluorescence intensity
• 3.4.2 Solution of an inverse problem for determining transcription factor concentrations3.5 Application Notes; 3.6 Summary and Conclusions; Acknowledgments; References; Chapter 4 Data-Driven, Mechanistic Modeling of Biochemical Reaction Networks; 4.1 Introduction; 4.2 Principles of Data-Driven Modeling; 4.2.1 Types of experimental data; 4.2.2 Data processing and normalization; 4.2.3 Suitability of models used in conjunction with quantitative data; 4.2.4 Issues related to parameter specification and estimation; 4.3 Examples of Data-Driven Modeling