Note: Front Cover -- Aquaporins -- Copyright Page -- Contents -- Contributors -- Preface -- Previous Volumes In Series -- Chapter 1. Discovery of the Aquaporins and Their Impact on Basic and Clinical Physiology -- I. Pre-Aquaporin Era -- II. The First Recognized Water Channel Protein -- III. Other Mammalian Aquaporins -- IV. Nonmammalian Homologs -- V. Perspective -- References -- Chapter 2. The Aquaporin Superfamily: Structure and Function -- I. Introduction -- II. Two-Dimensional Crystallization of Membrane Proteins -- III. Electron Crystallography -- IV. Atomic Force Microscopy -- V. AQP1, The Erythrocyte Water Channel -- VI. AQP0: The Major Intrinsic Protein of Lens Fiber Cells -- VII. Water Channel of Escherichia Coli: Aqpz -- VIII. Glycerol Channel of Escherichia Coli: Glpf -- IX. Comparison of the High-Resolution Projection Structures of Glpf and AQP1 -- X. Conclusion and Perspectives -- References -- Chapter 3. Physiological Roles of Aquaporins in the Kidney -- I. Introduction -- II. Water Transport along The Renal Tubule -- III. Water Permeability along the Renal Tubule -- IV. Aquaporin-1 Facilitates Isoosmotic Fluid Transport in Proximal Tubule -- V. Aquaporin-1 Allows Osmotic Equilibration In the Thin Descending Limb Of Henle Despite Rapid Flow Of Tubule Fluid -- VI. Aquaporin-1 Allows Osmotic Equilibration in the Descending Vasa Recta -- VII. Aquaporins Provide Molecular Targets For Regulation of Water Transport in the Renal Collecting Duct -- References -- Chapter 4. Pathophysiology of Renal Aquaporins -- I. Introduction -- II. Pathophysiology of Renal Aquaporins -- III. Inherited NDI and CDI -- IV. Acquired NDI -- V. Urinary Concentrating Defects -- VI. States of Water Retention -- VII. Conclusions -- References -- Chapter 5. Genetic and Biophysical Approaches to Study Water Channel Biology -- I. Introduction. , II. Lessons from Aquaporin Knockout Mice -- III. Biophysical Analysis of Aquaporin Function -- IV. Aquaporin Structure and Function -- V. New Directions in Aquaporin Physiology and Biophysics -- References -- Chapter 6. Trafficking of Native and Mutant Mammalian MIP Proteins -- I. Normal Routing of MIP Proteins -- II. Disturbed Trafficking of MIP Proteins -- References -- Chapter 7. Aquaporins Of Plants: Structure, Function, Regulation, and Role in Plant Water Relations -- I. The Transpiration Stream -- II. Water Movement in and Between Living Tissues -- III. Molecular Characteristics and Transport Properties Of Plant Aquaporins -- IV. Subcellular Location of Plant Aquaporins -- V. What Do The Water and Solute Transport Properties Of Membranes Tell Us about the Aquaporins In Those Membranes? -- VI. The Multiple Roles of Aquaporins: How to Link Water Transport Properties to Functions at the Cellular and Tissue Level -- VII. Regulation of Aquaporin Expression and Water Transport Activity -- References -- Chapter 8. Microbial Water Channels and Glycerol Facilitators -- I. Introduction -- II. Microbial Aquaporins and Glycerol Facilitators -- III. Transport Properties and Channel Selectivity of Microbial MIP Channels -- IV. From Primary to Quaternary Structure in Microbial MIPs -- V. Physiological Roles -- VI. Microbial MIP Channels in Osmoregulation -- VII. Control of the Function of Microbial MIP Channels -- VIII. Conclusions and Future Perspectives -- References -- Chapter 9. Future Directions Of Aquaporin Research -- I. Identification And Characterization of New MIP Channels -- II. Why Have So Many MIP Channels? -- III. Analysis of the Physiological Roles of Aquaporins -- IV. Structure and Function -- V. Aquaporins as Targets for Treatment of Human Disease -- VI. Aquaporins as Possible Targets for Genetic Engineering and Crop Improvement. , VII. Metabolic Engineering With Aquaporins -- VIII. The Aquaporin Research Community -- References -- Index.

Note: Intro -- Related Titles -- Title Page -- Copyright -- Table of Contents -- List of Contributors -- About the Series Editors -- Chapter 1: Integrative Analysis of Omics Data -- Summary -- 1.1 Introduction -- 1.2 Omics Data and Their Measurement Platforms -- 1.3 Data Processing: Quality Assessment, Quantification, Normalization, and Statistical Analysis -- 1.4 Data Integration: From a List of Genes to Biological Meaning -- 1.5 Outlook and Perspectives -- References -- Chapter 2: 13C Flux Analysis in Biotechnology and Medicine -- 2.1 Introduction -- 2.2 Theoretical Foundations of 13C MFA -- 2.3 Metabolic Flux Analysis in Biotechnology -- 2.4 Metabolic Flux Analysis in Medicine -- 2.5 Emerging Challenges for 13C MFA -- 2.6 Conclusion -- Acknowledgments -- Disclosure -- References -- Chapter 3: Metabolic Modeling for Design of Cell Factories -- Summary -- 3.1 Introduction -- 3.2 Building and Refining Genome-Scale Metabolic Models -- 3.3 Strain Design Algorithms -- 3.4 Case Studies -- 3.5 Conclusions -- Acknowledgments -- References -- Chapter 4: Genome-Scale Metabolic Modeling and In silico Strain Design of Escherichia coli -- 4.1 Introduction -- 4.2 The COBRA Approach -- 4.3 History of E. coli Metabolic Modeling -- 4.4 In silico Model-Based Strain Design of E. coli Cell Factories -- 4.5 Future Directions of Model-Guided Strain Design in E. coli -- References -- Chapter 5: Accelerating the Drug Development Pipeline with Genome-Scale Metabolic Network Reconstructions -- Summary -- 5.1 Introduction -- 5.2 Metabolic Reconstructions in the Drug Development Pipeline -- 5.3 Species-Level Microbial Reconstructions -- 5.4 The Human Reconstruction -- 5.5 Community Models -- 5.6 Personalized Medicine -- 5.7 Conclusion -- References -- Chapter 6: Computational Modeling of Microbial Communities -- Summary -- 6.1 Introduction -- 6.2 Ecological Models. , 6.3 Genome-Scale Metabolic Models -- 6.4 Concluding Remarks -- References -- Chapter 7: Drug Targeting of the Human Microbiome -- Summary -- 7.1 Introduction -- 7.2 The Human Microbiome -- 7.3 Association of the Human Microbiome with Human Diseases -- 7.4 Drug Targeting of the Human Microbiome -- 7.5 Future Perspectives -- 7.6 Concluding Remarks -- Acknowledgments -- References -- Chapter 8: Toward Genome-Scale Models of Signal Transduction Networks -- 8.1 Introduction -- 8.2 The Potential of Network Reconstruction -- 8.3 Information Transfer Networks -- 8.4 Approaches to Reconstruction of ITNs -- 8.5 The rxncon Approach to ITNWR -- 8.6 Toward Quantitative Analysis and Modeling of Large ITNs -- 8.7 Conclusion and Outlook -- Acknowledgments -- References -- Chapter 9: Systems Biology of Aging -- Summary -- 9.1 Introduction -- 9.2 The Biology of Aging -- 9.3 The Mathematics of Aging -- 9.4 Future Challenges -- Conflict of Interest -- References -- Chapter 10: Modeling the Dynamics of the Immune Response -- 10.1 Background -- 10.2 Dynamics of NF-κB Signaling -- 10.3 JAK/STAT Signaling -- 10.4 Conclusions -- Acknowledgments -- References -- Chapter 11: Dynamics of Signal Transduction in Single Cells Quantified by Microscopy -- 11.1 Introduction -- 11.2 Single-Cell Measurement Techniques -- 11.3 Microscopy -- 11.4 Imaging Signal Transduction -- 11.5 Conclusions -- References -- Chapter 12: Image-Based In silico Models of Organogenesis -- Summary -- 12.1 Introduction -- 12.2 Typical Workflow of Image-Based In silico Modeling Experiments -- 12.3 Application: Image-Based Modeling of Branching Morphogenesis -- 12.4 Future Avenues -- References -- Chapter 13: Progress toward Quantitative Design Principles of Multicellular Systems -- Summary -- 13.1 Toward Quantitative Design Principles of Multicellular Systems. , 13.2 Breaking Multicellular Systems into Distinct Functional and Spatial Modules May Be Possible -- 13.3 Communication among Cells as a Means of Cell-Cell Interaction -- 13.4 Making Sense of the Combinatorial Possibilities Due to Many Ways that Cells Can Be Arranged in Space -- 13.5 From Individual Cells to Collective Behaviors of Cell Populations -- 13.6 Tuning Multicellular Behaviors -- 13.7 A New Framework for Quantitatively Understanding Multicellular Systems -- Acknowledgments -- References -- Chapter 14: Precision Genome Editing for Systems Biology - A Temporal Perspective -- Summary -- 14.1 Early Techniques in DNA Alterations -- 14.2 Zinc-Finger Nucleases -- 14.3 TALENs -- 14.4 CRISPR-Cas9 -- 14.5 Considerations of Gene-Editing Nuclease Technologies -- 14.6 Applications -- 14.7 A Focus on the Application of Genome-Engineering Nucleases on Chromosomal Rearrangements -- 14.8 Future Perspectives -- References -- Index -- End User License Agreement.

Note: Intro -- Yeast Stress Responses -- Table of Contents -- List of contributors -- 1 Introduction -- What is stress? -- Studies of stress responses -- Cell proliferation and stress -- Aim of the stress response -- Phases of the stress response -- Sensing and signalling -- Adaptation to stress -- Yeast as a model -- 2The environmental stress response: a common yeast response to diverse environmental stresses -- 2.1 Introduction -- 2.2 The environmental stress response -- 2.3 Responsiveness of ESR gene expression -- 2.4 Transcript levels versus protein synthesis levels -- 2.5 Functions represented by genes repressed in the ESR -- 2.5.1 Ribosome synthesis -- 2.5.2 tRNA synthesis -- 2.5.3 General transcription -- 2.5.4 RNA splicing and export -- 2.5.5 Translation -- 2.6 Functions represented by genes induced in the ESR -- 2.6.1 Carbohydrate metabolism -- 2.6.2 Fatty acid metabolism -- 2.6.3 Respiration -- 2.6.4 Oxidative stress defense -- 2.6.5 Autophagy and vacuolar functions -- 2.6.6 Protein folding and degradation -- 2.6.7 Cytoskeletal reorganization -- 2.6.8 Signaling -- 2.7 Functional themes in the ESR -- 2.7.1 Differential expression of isozymes -- 2.7.2 Coinduction of genes with counterproductive functions -- 2.7.3 Regulation of control steps of metabolic processes -- 2.8 The role of the ESR -- 2.9 Regulation of ESR gene expression -- 2.9.1 Rap1p -- 2.9.2 Chromatin remodeling -- 2.9.3 Regulated mRNA turnover -- 2.9.4 Msn2p and Msn4p -- 2.9.5 Condition-specific transcriptional induction -- 2.9.6 Condition-specific cellular signaling -- 2.9.7 Advantages of the complex regulation of ESR gene expression -- 2.10 Orchestration of cellular responses to stress -- 2.11 Conclusions -- 3 The yeast response to heat shock -- 3.1 Introduction -- 3.2 The heat shock and environmental stress responses. , 3.2.1 Transcriptional regulators of heat shock gene induction -- 3.2.2 Delineation of the Hsf1p and Msn2p/Msn4p heat shock regulons -- 3.2.3 The role of trehalose in thermotolerance -- 3.2.4 Thermal stress phenotypes in yeast -- 3.3 Regulation of the heat shock factor Hsf1p -- 3.3.1 Regulation of Hsf1p transcriptional activation -- 3.3.2 The role of phosphorylation in Hsf1p regulation -- 3.3.3 Genetic and structural insights into DNA binding and regulation -- 3.3.4 Sensing the proteome: regulation by protein chaperones -- 3.3.5 Hsf1p-like proteins in yeast -- 3.3.6 Hsf1p and the cell cycle -- 3.4 New directions in protein chaperone biology -- 3.4.1 Hsp90 chaperone complex subunits in yeast -- 3.4.2 Endogenous yeast Hsp90 substrates -- 3.4.3 Protein chaperones and yeast prion propagation -- 3.5 Stress and aging -- 3.6 Conclusions -- 4 The osmotic stress response of Saccharomyces cerevisiae -- 4.1 Introduction -- 4.2 Structural and morphological effects caused by osmotic stress -- 4.3 Glycerol and glycerol metabolism -- 4.3.1 Glycerol metabolic pathways -- 4.3.2 Glycerol transport -- 4.3.3 Glycerol accumulation under osmotic stress: multiple levels of control -- 4.4 Transport processes affected by osmotic stress -- 4.4.1 MIP channels: aquaporins and glycerol channels -- 4.4.2 Osmolyte uptake systems -- 4.4.3 Ion channels -- 4.5 Perception of and response to osmotic stress: the role of signalling pathways -- 4.5.1 S. cerevisise MAPK pathways -- 4.5.2 The HOG MAPK pathway in Saccharomyces cerevisise -- 4.5.3 Control of gene expression -- 4.5.4 The cell integrity pathway -- 4.5.5 Skn7p: a putative link between osmosensing pathways -- 4.5.6 Additional systems involved in osmotic stress signalling -- 4.5.7 Mechanisms of osmosensing -- 4.6 Metabolic adjustments -- 4.7 Osmotic signalling in other yeasts: the S. pombe Sty1 pathway -- 4.8 Conclusions. , 5 Ion homeostasis in Saccharomyces cerevisiae under NaCl stress -- 5.1 Introduction -- 5.2 Yeast Na+ and K+ relations -- 5.2.1 Growth and intracellular ion levels -- 5.2.2 Why is K but not Na a preferred intracellular cation? -- 5.2.3 Na toxicity -- 5.3 Adaptation to high concentrations of salt: role of ion transporters -- 5.3.1 The plasma membrane H -ATPase -- 5.3.2 K transport systems -- 5.3.3 The Pmr2Ap/Ena1p sodium transporter -- 5.3.4 The Nha1p Na /H antiporter -- 5.3.5 Compartmentalization of Na -- 5.4 Regulation of ion homeostasis -- 5.4.1 Control at transcriptional level: ENA1 -- 5.4.2 Control on protein level -- 5.4.3 Regulation of the Trk1/2p system -- 5.5 Ion transporters and membrane targeting -- 5.5.1 Targeting of P-type ATPases to the plasma membrane -- 5.5.2 Nhx1p is involved in membrane traffic out of the prevacuolar compartment -- 5.6 The genome-wide transcriptional response -- 5.7 Conclusions -- 6 Oxidative stress responses in yeast -- 6.1 Introduction -- 6.2 Effects of oxygen free radicals on biological molecules -- 6.2.1 Some concepts of free radical chemistry -- 6.3 Biological effects of oxygen free radicals in yeast -- 6.3.1 Methods for measuring the cellular toxicity of ROS -- 6.3.2 Cellular effects of ROS in S. cerevisiae -- 6.4 Antioxidant defenses and thiol redox homeostasis -- 6.4.1 Metal containing antioxidants -- 6.4.2 Thiol redox control pathways and peroxidase systems -- 6.5 Adaptive oxidative stress responses -- 6.5.1 S. cerevisiae adaptive responses to oxidative stress -- 6.5.2 The genomic response underlying oxidative stress adapted states -- 6.6 Control of S. cerevisiae oxidative stress responses -- 6.6.1 The Yap1 pathway -- 6.6.2 Skn7 as a stress response coordinator -- 6.6.3 An H2O2-inducible Msn2/4 pathway -- 6.5.4 Other regulators of the oxidative stress response in S. cerevisiae. , 6.7 Control of S. pombe oxidative stress responses -- 6.7.1 The stress-activated MAP kinase pathway -- 6.7.2 Atf1, a bZip transcription factor substrate of Spc1/Sty1 -- 6.7.3 The S. pombe Yap1 homologue Pap1 -- 6.7.4 The response regulator Prr1, a homologue of Skn7 -- 6.7.5 Two two-component phosphorelay systems contribute to the H2O2 response -- 6.8 Regulators of the oxidative stress response in other yeasts -- 6.9 Conclusions -- 7 From feast to famine -- adaptation to nutrient availability in yeast -- 7.1 Introduction -- 7.2 Setting the stage: limitation, starvation, and cell cycle checkpoints -- 7.3 Specific responses to nutrient depletion -- 7.3.1 Carbon Source Signalling -- 7.3.2 Nitrogen Source Signalling -- 7.3.3 Phosphor Limitation and Starvation -- 7.3.4 Sulphur Limitation and Starvation -- 7.4 Common responses to nutrient depletion -- 7.4.1 General Concepts -- 7.4.2 Nutrient signal integration and the control of metabolism and growth -- 7.4.3 The FGM pathway -- an integrator of responses to nutrient availability -- 7.4.4 Nutritional control by targets of rapamycin (Tor) proteins -- 7.4.5 Glycogen and Trehalose metabolism -- 7.4.6 Morphological differentiation as a response to nutrient limitation -- 7.5 Conclusions -- Index.