Volume 1 |
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xvii | |
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xxix | |
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xxxi | |
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Part I Industrial Biotechnology: From Pioneers to Visionary |
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1 | (148) |
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1 History of Industrial Biotechnology |
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3 | (82) |
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1.1 The Beginning of Industrial Microbiology |
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3 | (4) |
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1.2 Primary Metabolites and Enzymes |
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7 | (1) |
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1.2.1 Birth, Rise, and Decline of the Term "Biotechnology" in the Period 1900 - 1940 |
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7 | (1) |
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1.2.2 Influential Scholars Boosting Industrial Fermentation from 1900 to 1940 |
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8 | (1) |
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1.2.3 Milestone Achievements in Industrial Fermentation Technology |
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10 | (1) |
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1.2.3.1 The Acetone- Butanol-Ethanol (ABE) Fermentation Process |
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10 | (1) |
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1.2.3.2 A Novel Vitamin C Fermentation Process |
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11 | (1) |
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1.2.3.3 The Lactic Acid Fermentation Process |
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11 | (1) |
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1.2.3.4 Fermentative Production of Glycerol |
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12 | (1) |
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1.2.3.5 L-(-)-Ephedrine by Fermentation |
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12 | (1) |
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1.2.3.6 Steroid Transformations |
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13 | (1) |
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1.2.3.7 The Citric Acid Fermentation Process |
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13 | (1) |
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1.2.3.8 Gluconic Acid Process |
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13 | (1) |
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1.2.3.9 Other Important Fermentation Processes and Products |
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14 | (1) |
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1.2.3.10 Applied Biocatalysis and Industrial Enzymes |
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14 | (2) |
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16 | (1) |
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16 | (1) |
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20 | (1) |
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23 | (1) |
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1.3.4 Mutagenesis and Strain Improvement |
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24 | (1) |
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1.3.5 Semisynthetic Antibiotics to Combat Resistant Microbes |
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26 | (1) |
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1.4 The Biotechnology Era Between 1970 and 2015 |
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27 | (1) |
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1.4.1 Biotechnology in the 1960s and 1970s; Governmental and Political Initiatives |
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27 | (1) |
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1.4.2 The Development of New Biotechnology Companies |
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29 | (1) |
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1.4.3 New Bioengineering Tools |
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35 | (1) |
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39 | (1) |
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1.4.4.1 Food, Feed, Industrial Commodities, and Specialties |
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39 | (1) |
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1.4.4.2 Biopharmaceuticals |
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43 | (1) |
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1.4.4.3 Plant Products, Seeds |
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46 | (1) |
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47 | (1) |
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1.4.5.1 Scientific Status |
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47 | (1) |
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1.4.5.2 Political, Institutional, and Socioeconomic Conditions |
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47 | (1) |
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47 | (1) |
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48 | (1) |
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1.5 How Pioneering Developments Led to Genetic Engineering |
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48 | (1) |
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1.5.1 Preamble: People and Principles in Developing Enabling Technologies |
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48 | (1) |
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1.5.2 Academic Freedom and Patenting: Hindrance to Science or Lever for Innovation? |
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49 | (1) |
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1.5.3 Conceptual Leaps and Jumps |
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50 | (1) |
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1.5.4 Surprise Discoveries Initiate Novel Areas/Methods of Research |
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51 | (1) |
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1.5.5 Methodology Without Which Gene Technology Would Not Have Been Possible |
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52 | (1) |
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1.5.5.1 Centrifugation: Preparation of Molecules of Different Sizes, Shapes, and/or Densities: Velocity Gradient Centrifugation |
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53 | (1) |
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1.5.5.2 X-ray Crystallography: Understanding Molecular Structure at the Atomic Level |
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54 | (1) |
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1.5.5.3 Chromatography with Solvent Motion or Electric Charge: Detection of Mutant Gene Products |
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55 | (1) |
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1.5.5.4 Protein Sequencing |
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55 | (1) |
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1.5.5.5 Nucleic Acid Sequencing - the Prelude: Phage + Bacterial Genetics and Biochemistry, the Gene Concept |
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56 | (3) |
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1.5.6 DNA: Its Transfer to and Selection in Living Cells |
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59 | (1) |
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1.5.7 Gene Cloning (1971-1982) the Era of Modern Biotechnology Based on Molecular Biology Begins |
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60 | (1) |
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1.5.7.1 A Prerequisite for Cloning: Nucleic Acid, Biochemistry, and Enzymology |
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60 | (1) |
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1.5.7.2 Applying Known Methods or a Conceptual Jump: the Details |
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61 | (3) |
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1.5.8 Genome Mapping: Clone Libraries, Restriction Maps, and RFLPs |
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64 | (1) |
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1.5.8.1 Prelude: Human Genetics before Genome Sequencing |
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64 | (1) |
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1.5.8.2 Important Ideas on Gene Mapping in the DNA Age |
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64 | (1) |
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1.5.8.3 DNA Hybridization Chip Sequencing and More |
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69 | (1) |
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1.5.8.4 Mega Sequencing: Impact on Biotechnology |
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69 | (2) |
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1.5.9 Expressing Genes in Other Organisms: Transgenic Animals Carrying rDNA |
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71 | (1) |
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72 | (1) |
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73 | (12) |
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2 Synthetic Biology: An Emerging Approach for Strain Engineering |
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85 | (26) |
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85 | (1) |
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86 | (1) |
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87 | (1) |
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2.2.2 Transcriptional Control |
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89 | (1) |
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2.2.2.1 Promoter Engineering |
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89 | (1) |
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2.2.2.2 Optimization of Gene Expression Vectors |
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94 | (2) |
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2.3 Functional and Robust Modules |
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96 | (1) |
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2.3.1 Synthetic Pathway Modules |
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96 | (1) |
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2.3.1.1 Pathway Assembly Tools |
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97 | (1) |
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2.3.1.2 Pathway Metabolic Flux Optimization Approaches |
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97 | (2) |
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2.3.2 Synthetic Circuit Modules |
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99 | (1) |
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2.3.2.1 Examples of Synthetic Circuits |
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99 | (1) |
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2.3.2.2 Synthetic Circuit Design |
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100 | (1) |
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2.3.2.3 Next-Generation Synthetic Circuits |
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102 | (1) |
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2.4 Microbial Communities |
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102 | (2) |
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2.5 Conclusions and Future Prospects |
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104 | (1) |
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104 | (1) |
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104 | (7) |
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3 Toward Genome-Scale Metabolic Pathway Analysis |
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111 | (14) |
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111 | (3) |
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114 | (2) |
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3.3 Calculating Short EFMs in Genome-Scale Metabolic Networks |
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116 | (4) |
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120 | (1) |
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121 | (1) |
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121 | (4) |
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4 Cell-Free Synthetic Systems for Metabolic Engineering and Biosynthetic Pathway Prototyping |
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125 | (24) |
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125 | (2) |
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127 | (1) |
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4.2.1 Purified Enzyme Systems |
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128 | (1) |
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4.2.2 Crude Cell Lysate Systems |
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128 | (1) |
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4.3 The Benefits of Cell-Free Systems |
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129 | (1) |
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4.3.1 Purified Enzyme Systems |
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130 | (1) |
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4.3.2 Crude Cell Lysate Systems |
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133 | (1) |
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4.3.3 Variations of Cell-Free Systems |
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134 | (1) |
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4.4 Challenges and Opportunities in Cell-Free Systems |
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135 | (1) |
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136 | (1) |
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4.4.2 Spatial Organization |
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137 | (1) |
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4.4.3 Cell-Free System Stability |
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138 | (1) |
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139 | (1) |
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140 | (1) |
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141 | (1) |
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141 | (1) |
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142 | (7) |
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Part II Multipurpose Bacterial Cell Factories |
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149 | (178) |
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5 Industrial Biotechnology: Escherichia coil as a Host |
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151 | (32) |
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151 | (1) |
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151 | (1) |
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152 | (1) |
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152 | (1) |
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152 | (1) |
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156 | (1) |
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157 | (1) |
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159 | (1) |
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5.2.5 Hydrogen and Alkanes |
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160 | (1) |
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160 | (1) |
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161 | (1) |
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161 | (1) |
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162 | (1) |
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163 | (1) |
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5.2.11 Protein as Product |
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164 | (1) |
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5.3 Rewiring Central Metabolism |
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165 | (1) |
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5.3.1 NOG and Carbon Efficiency |
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165 | (1) |
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5.3.2 Methanol and CO2 Utilization |
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165 | (1) |
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5.3.3 Advancing Analytical Techniques |
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166 | (1) |
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5.4 Alternative Carbon Sources |
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167 | (1) |
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5.4.1 Complex Carbohydrates |
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167 | (1) |
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168 | (1) |
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169 | (1) |
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5.5 E. coli Techniques and Concerns |
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169 | (1) |
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5.5.1 Genetic Manipulation |
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169 | (1) |
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5.5.2 Phage Contamination |
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169 | (1) |
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170 | (1) |
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171 | (12) |
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6 Industrial Microorganisms: Corynebacterium glutamicum |
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183 | (38) |
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183 | (2) |
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6.2 Physiology and Metabolism |
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185 | (1) |
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6.2.1 Substrate Assimilation, Catabolic Pathways, and Gluconeogenesis |
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186 | (1) |
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6.2.2 Tricarboxylic Acid Cycle and Glyoxylate Shunt |
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187 | (1) |
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6.2.3 Reactions of the Pyruvate Node |
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189 | (1) |
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192 | (1) |
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6.3 Genetic Manipulation of Corynebacterium glutamicum |
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192 | (1) |
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192 | (1) |
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6.3.2 Transformation Methods |
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194 | (1) |
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6.3.3 Engineering Gene Expression |
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195 | (1) |
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6.4 Systems Biology of Corynebacterium glutamicum |
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196 | (1) |
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196 | (1) |
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6.4.2 Transcriptome Analysis |
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197 | (1) |
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198 | (1) |
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6.4.4 Metabolome Analysis |
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198 | (1) |
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199 | (1) |
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6.5 Application in Biotechnology |
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200 | (1) |
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6.5.1 Wild-Type Producers and Classical Mutants |
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200 | (1) |
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6.5.2 Top-Selling Amino Acids |
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200 | (1) |
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6.5.2.1 Glutamate Biosynthesis |
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201 | (1) |
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6.5.2.2 L-Lysine Biosynthesis |
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201 | (1) |
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6.5.2.3 Biosynthesis of Aromatic Amino Acids |
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202 | (1) |
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6.5.3 Tailoied Strains by Recombinant DNA Technology |
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202 | (1) |
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6.6 Conclusions and Perspectives |
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202 | (1) |
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203 | (18) |
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7 Host Organisms: Bacillus subtilis |
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221 | (78) |
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7.1 Introduction and Scope |
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221 | (1) |
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7.2 Identification of Genetic Traits Pertinent to Enhanced Biosynthesis of a Value Product |
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222 | (3) |
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7.3 Traits to Be Engineered for Enhanced Synthesis and Secretion of Proteinaceous Products |
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225 | (1) |
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7.3.1 Signal Peptides and Signal Peptidases |
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225 | (1) |
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7.3.2 Protein Transport Pathways |
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226 | (1) |
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226 | (1) |
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228 | (1) |
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7.3.2.3 Extracellular and Membrane-Bound Proteases of B. subtilis |
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229 | (2) |
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7.4 Engineering of Genetic Traits in Bacillus subtilis |
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231 | (1) |
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7.4.1 Natural Competence and Double Crossover Integration |
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232 | (1) |
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7.4.2 Tools to Modify Protein Expression Levels in B. subtilis Production Strains |
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233 | (1) |
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7.4.2.1 Promoters of Various Strength for Customized mRNA Synthesis |
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233 | (1) |
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7.4.2.2 Gene Amplification and Plasmid Vectors |
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234 | (1) |
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7.4.2.3 mRNA-Stabilizing Elements and Transcriptional Terminators |
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234 | (1) |
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235 | (1) |
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236 | (1) |
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7.4.3 Modification of the Amino Acid Sequence of an Enzyme |
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237 | (1) |
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7.4.4 Transforming DNA Constructs Obtained by Template-Free Synthesis or by PCR |
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237 | (1) |
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7.4.5 Production Strains Devoid of Antibiotic Resistance Markers |
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238 | (1) |
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7.4.5.1 Chromosomal Modification with Transiently Employed Selection Markers |
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238 | (1) |
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7.4.5.2 Counterselection Strategies to Force the Deletion of Dominant Markers |
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239 | (1) |
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7.4.5.3 Removal of the Selection Marker by Cre/loxP Site-Specific Recombination |
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240 | (1) |
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241 | (1) |
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7.4.6 Introduction of Exogenous DNA into Bacillus Strains Incapable of Developing Natural Competence |
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242 | (1) |
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7.4.6.1 Phage Transduction |
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242 | (1) |
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7.4.6.2 Protoplast Transformation and Protoplast Fusion |
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243 | (1) |
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7.4.6.3 Electrotransformation |
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243 | (1) |
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7.4.7 Lysed Protoplast Transformation |
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244 | (1) |
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245 | (2) |
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7.6 Significance of Classical Strain Improvement in Times of Synthetic Biology |
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247 | (1) |
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7.6.1 Generation of Genetic Diversity in Random Fashion |
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248 | (1) |
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7.6.2 Screening Platforms |
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249 | (1) |
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7.6.3 High-Throughput, Low-Intensity Fed-Batch Cultivation |
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250 | (1) |
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7.6.4 Medium-Throughput, High-Intensity Fed-Batch Cultivation |
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251 | (1) |
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7.7 Resource-Efficient B. subtilis Fermentation Processes |
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252 | (2) |
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7.8 Safety of Bacillus subtilis |
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254 | (1) |
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7.8.1 Absence of Acquired Added Antimicrobial Resistance Genes |
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255 | (1) |
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7.8.2 Safety of Surfactin |
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256 | (1) |
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7.8.3 Absence of Toxin Production |
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257 | (1) |
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7.8.4 Absence of Sporulation |
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258 | (1) |
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7.9 Bacillus Production Strains on the Factory Floor: Some Examples |
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258 | (1) |
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258 | (1) |
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263 | (1) |
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7.9.3 (R)-Pantothenic Acid |
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267 | (1) |
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7.9.4 Production Strains for Metabolites with Unusual Biochemistry |
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271 | (1) |
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7.9.4.1 Biotin (Vitamin B7) |
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271 | (1) |
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7.9.4.2 Thiamine (Vitamin B1) |
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273 | (1) |
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7.9.4.3 Pyridoxine (Vitamin B6) |
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275 | (3) |
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278 | (2) |
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280 | (1) |
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280 | (19) |
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8 Host Organism: Pseudomonas putida |
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299 | (28) |
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Jose M. Borrero-de Acuria |
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299 | (1) |
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8.2 Physiology and Metabolism |
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300 | (1) |
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300 | (1) |
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8.2.2 Major Catabolic Pathways |
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300 | (1) |
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8.2.3 Degradation of Xenobiotics |
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302 | (1) |
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8.2.4 Regulation of Core Carbon and Energy Metabolism |
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303 | (1) |
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304 | (1) |
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304 | (1) |
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8.3.2 Engineering Gene Expression |
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304 | (3) |
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307 | (1) |
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8.4.1 Genomics and Genome Scale-Modeling |
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308 | (1) |
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308 | (1) |
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309 | (1) |
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8.4.4 Metabolomics and Fluxomics |
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310 | (1) |
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311 | (1) |
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8.5 Application in Biotechnology |
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311 | (1) |
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8.5.1 Biopolymers and Advanced Materials |
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312 | (1) |
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8.5.2 High-Value Chemicals |
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314 | (1) |
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315 | (1) |
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315 | (12) |
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Part III Exploiting Anaerobic Biosynthetic Power |
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327 | (126) |
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9 Host Organisms: Clostridium acetobutylicum/Clostridium beijerinckii and Related Organisms |
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329 | (36) |
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Bettina Schiel-Bengelsdorf |
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329 | (1) |
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330 | (1) |
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330 | (1) |
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331 | (1) |
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9.2.3 C. saccharobutylicum |
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331 | (1) |
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9.2.4 C. saccharoperbutylacetonicum |
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332 | (1) |
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332 | (1) |
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9.3.1 History of Bacteriophages Infecting Solventogenic Clostridia |
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332 | (1) |
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335 | (1) |
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335 | (1) |
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9.4 ABE Fermentation of Solvent-Producing Clostridium Strains |
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336 | (6) |
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9.5 Genome-Based Comparison of Solvent-Producing Clostridium Strains |
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342 | (3) |
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9.6 Regulation of Solvent Formation in C. acetobutylicum |
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345 | (1) |
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9.7 Genetic Tools for Clostridial Species |
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346 | (7) |
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9.8 Industrial Application of ABE Fermentation |
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353 | (2) |
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355 | (1) |
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355 | (10) |
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10 Advances in Consolidated Bioprocessing Using Clostridium thermocellum and Thermoanaerobacter saccharolyticum |
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365 | (30) |
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365 | (1) |
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10.2 CBP Organism Development Strategies |
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366 | (1) |
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10.3 Plant Cell Wall Solubilization by C. thermocellum |
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367 | (1) |
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10.3.1 Understanding and Describing Solubilization |
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367 | (1) |
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10.3.2 Comparative Solubilization Effectiveness |
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368 | (4) |
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10.4 Bioenergetics of C. thermocellum Cellulose Fermentation |
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372 | (1) |
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10.4.1 Membrane Energetics |
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372 | (1) |
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10.4.2 Sugar Conversion to Pyruvate |
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374 | (1) |
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10.4.3 End-Product Formation |
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376 | (2) |
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10.5 Metabolic Engineering |
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378 | (1) |
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10.5.1 Transformation and Genetic Tool Development |
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378 | (1) |
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10.5.2 Ethanol Tolerance and Titer |
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378 | (1) |
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10.5.3 Metabolic Engineering for High Ethanol Yield |
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380 | (1) |
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10.5.3.1 Metabolic Engineering of T saccharolyticum |
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381 | (1) |
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382 | (1) |
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10.5.3.3 The Pyruvate to Ethanol Pathway in T saccharolyticum |
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382 | (1) |
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10.5.3.4 Engineering C. thermocellum and Comparison with T saccharolyticum |
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383 | (1) |
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10.5.3.5 Current State of Strain Development |
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386 | (1) |
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10.6 Summary and Future Directions |
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386 | (2) |
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388 | (1) |
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388 | (7) |
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395 | (58) |
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395 | (3) |
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398 | (1) |
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400 | (1) |
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403 | (1) |
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403 | (1) |
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11.2.4 Nondairy Drinks and Foods |
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404 | (1) |
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404 | (1) |
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11.2.4.2 Fruits and Legumes |
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405 | (1) |
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11.2.4.3 Gluten-Free Foods |
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406 | (1) |
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11.3 Industrially Relevant Compounds |
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406 | (1) |
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406 | (1) |
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11.3.1.1 Antimicrobial Compounds |
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406 | (1) |
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414 | (1) |
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416 | (4) |
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420 | (1) |
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11.3.2.1 Low-Calorie Sugars |
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420 | (1) |
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423 | (1) |
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11.3.2.3 Conjugated Linoleic Acids |
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|
426 | (1) |
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11.3.2.4 gamma-Aminobutyric Acid |
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|
427 | (1) |
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|
428 | (1) |
|
11.3.2.6 Exopolysaccharides |
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429 | (1) |
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430 | (1) |
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|
430 | (1) |
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|
433 | (1) |
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|
434 | (1) |
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|
435 | (1) |
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|
435 | (18) |
Volume 2 |
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xv | |
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xxvii | |
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xxix | |
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Part IV Microbial Treasure Chests for High-Value Natural Compounds |
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453 | (52) |
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12 Host Organisms: Myxobacterium |
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455 | (32) |
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12.1 Introduction into the Myxobacteria |
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455 | (2) |
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12.2 Phylogeny and Classification |
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457 | (2) |
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|
459 | (1) |
|
12.4 Growth and Nutritional Requirements |
|
|
460 | (2) |
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12.5 Genetics and Genomics |
|
|
462 | (2) |
|
12.6 Secondary Metabolism |
|
|
464 | (4) |
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|
468 | (1) |
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|
468 | (1) |
|
12.7.2 Secondary Metabolism of Myxococcus xanthus |
|
|
469 | (1) |
|
12.7.3 Myxococcus xanthus as Expression Host |
|
|
470 | (1) |
|
12.7.4 Heterologous Expression of the Epothilone Gene Cluster from Sorangium cellulosum in Myxococcus xanthus |
|
|
471 | (1) |
|
12.7.5 Production of Myxovirescin by Fermentation of Myxococcus virescens |
|
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472 | (1) |
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|
472 | (1) |
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|
472 | (1) |
|
12.8.2 Sorangium cellulosum So ce56 |
|
|
472 | (1) |
|
12.8.3 The Anticancer Drug Ixabepilone is a Derivative of Epothilone from Sorangium cellulosum So ce90 |
|
|
474 | (1) |
|
12.8.4 Other Sorangium Secondary Metabolites Holding Promise for Future Application |
|
|
475 | (1) |
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|
476 | (1) |
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|
476 | (11) |
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13 Host Organism: Streptomyces |
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487 | (18) |
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487 | (2) |
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13.2 Streptomyces Genome Manipulation Toolkits |
|
|
489 | (1) |
|
13.2.1 Site-Specific Recombinases |
|
|
490 | (1) |
|
|
491 | (1) |
|
13.2.3 I-Scel Endonuclease and CRISPR/Cas9 |
|
|
492 | (1) |
|
13.2.4 Reporter Genes for Streptomycetes |
|
|
492 | (1) |
|
13.2.5 Genetic Controlling Elements for Streptomycetes |
|
|
493 | (2) |
|
13.3 Hots for Heterologous Production of Natural Products |
|
|
495 | (1) |
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|
496 | (1) |
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|
497 | (1) |
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|
497 | (2) |
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|
499 | (1) |
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|
499 | (6) |
|
Part V Extending the Raw Material Basis for Bioproduction |
|
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505 | (138) |
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14 Extreme Thermophiles as Metabolic Engineering Platforms: Strategies and Current Perspective |
|
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507 | (74) |
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|
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|
|
|
|
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|
|
507 | (2) |
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14.2 Bioprocessing Advantages for Extremely Thermophilic Hosts |
|
|
509 | (1) |
|
14.3 Biobased Chemicals and Fuels: Targets and Opportunities |
|
|
510 | (2) |
|
14.4 Considerations for Selecting an Extremely Thermophilic Host |
|
|
512 | (1) |
|
14.5 General Strategies for Genetic Manipulation of Extreme Thermophiles |
|
|
513 | (8) |
|
14.6 Limitations and Barriers to Genetic Modification of Extreme Thermophiles |
|
|
521 | (2) |
|
14.7 Current Status of Metabolic Engineering Efforts and Prospects in Extreme Thermophiles |
|
|
523 | (1) |
|
14.7.1 Pyrococcus furiosus |
|
|
523 | (1) |
|
14.7.1.1 Genetic Tools - R furiosus |
|
|
523 | (1) |
|
14.7.1.2 Metabolic Engineering - P. furiosus |
|
|
528 | (9) |
|
14.7.2 Thermococcus Species |
|
|
537 | (1) |
|
14.7.2.1 Genetic Tools - Thermococcus Species |
|
|
537 | (1) |
|
14.7.2.2 Metabolic Engineering - Thermococcus Species |
|
|
538 | (1) |
|
14.7.3 Sulfolobus Species |
|
|
538 | (1) |
|
14.7.3.1 Genetics Tools - Sulfolobus Species |
|
|
539 | (1) |
|
14.7.3.2 Metabolic Engineering - Sulfolobus Species |
|
|
541 | (1) |
|
14.7.4 Thermotoga maritima |
|
|
541 | (1) |
|
14.7.4.1 Genetic Tools - Thermotoga Species |
|
|
542 | (1) |
|
14.7.4.2 Metabolic Engineering - Thermotoga Species |
|
|
544 | (1) |
|
|
544 | (1) |
|
14.7.5.1 Genetic Tools - Thermus Species |
|
|
545 | (1) |
|
14.7.5.2 Metabolic Engineering - Thermus Species |
|
|
547 | (1) |
|
14.7.6 Caldicellulosiruptor bescii |
|
|
548 | (1) |
|
14.7.6.1 Genetics Tools - Caldicellulosiruptor bescii |
|
|
548 | (1) |
|
14.7.6.2 Metabolic Engineering - Caldicellulosiruptor bescii |
|
|
550 | (2) |
|
14.7.7 Thermoanaerobacter Species |
|
|
552 | (1) |
|
14.7.7.1 Genetic Tools - Thermoanaerobacter Species |
|
|
552 | (1) |
|
14.7.7.2 Metabolic Engineering - Thermoanaerobacter Species |
|
|
553 | (2) |
|
14.7.8 Caldanaerobacter subterraneus subsp. tengcongensis |
|
|
555 | (1) |
|
14.7.8.1 Genetics Tools - Caldanaerobacter subterraneus subsp. tengcongensis |
|
|
555 | (1) |
|
14.7.8.2 Metabolic Engineering - Caldanaerobacter subterraneus subsp. tengcongensis |
|
|
556 | (1) |
|
14.8 Metabolic Engineering of Extreme Thermophiles - Tool Kit Needs |
|
|
556 | (1) |
|
|
556 | (1) |
|
14.8.2 Ribosomal Binding Sites |
|
|
557 | (1) |
|
|
558 | (1) |
|
14.9 Conclusions and Future Perspectives |
|
|
558 | (2) |
|
|
560 | (1) |
|
|
560 | (21) |
|
15 Cyanobacteria as a Host Organism |
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|
581 | (24) |
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|
|
15.1 Introduction and Relevance: Cyanobacteria as a Host Organism |
|
|
581 | (1) |
|
15.2 General Description of Cyanobacteria |
|
|
582 | (1) |
|
15.2.1 A Diverse Bacterial Group and Its Metabolisms |
|
|
582 | (1) |
|
|
583 | (1) |
|
|
584 | (1) |
|
15.2.4 Light/Dark Regulation |
|
|
584 | (1) |
|
|
585 | (1) |
|
|
585 | (1) |
|
|
586 | (1) |
|
|
587 | (1) |
|
15.3.4 Ribosome Binding Sites |
|
|
588 | (1) |
|
15.4 Improving Photosynthetic Efficiency |
|
|
588 | (1) |
|
15.4.1 Improving Light Harvesting |
|
|
588 | (1) |
|
15.4.2 Improving Carbon Fixation |
|
|
589 | (1) |
|
15.5 Direct Conversion of CO2 into Biofuels and Chemicals |
|
|
590 | (1) |
|
15.5.1 Fuels and Chemicals from Acetyl-CoA |
|
|
590 | (1) |
|
15.5.2 Fuels and Chemicals from Keto Acids |
|
|
594 | (1) |
|
15.5.3 Chemicals from TCA Cycle Intermediates |
|
|
596 | (1) |
|
|
596 | (1) |
|
|
597 | (1) |
|
|
597 | (8) |
|
|
605 | (38) |
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|
|
|
|
|
16.1 Introduction to Algae as an Industrial Organism |
|
|
605 | (1) |
|
|
605 | (1) |
|
16.1.2 Scalability and Growth Rate |
|
|
606 | (1) |
|
16.1.3 Genetic Malleability |
|
|
606 | (1) |
|
16.2 Algal Genetic Engineering |
|
|
606 | (1) |
|
16.2.1 Nuclear Genetic Engineering |
|
|
607 | (1) |
|
16.2.1.1 Nuclear Transformation Methods |
|
|
607 | (1) |
|
16.2.1.2 Regulation of Nuclear Transgene Expression |
|
|
607 | (1) |
|
16.2.1.3 Tools for Increased Nuclear Gene Expression |
|
|
608 | (1) |
|
16.2.1.4 Selection and Screening Methods |
|
|
608 | (1) |
|
16.2.1.5 Gene Targeting and Genome Editing |
|
|
609 | (1) |
|
16.2.2 Chloroplast Genetic Engineering |
|
|
610 | (1) |
|
16.2.2.1 Chloroplast Transformation Methods |
|
|
610 | (1) |
|
16.2.2.2 Gene Regulation in the Chloroplast |
|
|
611 | (1) |
|
16.2.2.3 Chloroplast Selection and Reporters |
|
|
611 | (1) |
|
16.2.3 Other Transformable Species |
|
|
612 | (1) |
|
16.2.3.1 Parameters for Transformation Optimization |
|
|
612 | (1) |
|
16.2.3.2 Species Successfully Transformed |
|
|
613 | (1) |
|
16.3 Therapeutic and Nutraceutical Applications |
|
|
613 | (1) |
|
16.3.1 Protein Therapeutics |
|
|
614 | (1) |
|
16.3.1.1 Human Antibodies and Antibody-Drug Conjugates |
|
|
614 | (1) |
|
16.3.1.2 Other Chloroplast-Produced Protein Therapeutics |
|
|
615 | (1) |
|
16.3.1.3 Nuclear-Expressed Protein Therapeutics |
|
|
615 | (1) |
|
16.3.2 Nutraceuticals and Nutritional Supplements |
|
|
616 | (1) |
|
16.3.2.1 Omega-3 Fatty Acids |
|
|
616 | (1) |
|
16.3.2.2 Source of Organic Selenium |
|
|
616 | (1) |
|
16.3.2.3 Carotenoids from Wild-Type and Engineered Algae |
|
|
616 | (1) |
|
16.3.3 Recombinant Vaccines |
|
|
617 | (1) |
|
16.3.3.1 Vaccine Antigens Produced in Algae |
|
|
617 | (1) |
|
16.3.3.2 Animal Efficacy Studies |
|
|
618 | (1) |
|
16.3.3.3 Recombinant Oral Vaccines |
|
|
619 | (1) |
|
16.4 Bioenergy Applications |
|
|
619 | (1) |
|
16.4.1 Altering Lipid Metabolism |
|
|
620 | (1) |
|
16.4.1.1 Changes in Nutrient Availability |
|
|
620 | (1) |
|
16.4.1.2 Changes in Temperature |
|
|
621 | (1) |
|
16.4.1.3 Changes in Light Intensity |
|
|
621 | (1) |
|
16.4.1.4 Genetic Manipulation of Lipid C9ntent |
|
|
621 | (1) |
|
16.4.2 Increasing Photosynthetic Efficiency |
|
|
622 | (1) |
|
16.4.2.1 Improving Light Utilization |
|
|
622 | (1) |
|
16.4.2.2 Improving Photosynthetic Efficiency |
|
|
622 | (1) |
|
16.4.2.3 Expanding the Photosynthetically Active Spectrum |
|
|
623 | (1) |
|
16.4.3 Modifying Carbon Assimilation |
|
|
623 | (1) |
|
16.4.3.1 Engineering RuBisCO |
|
|
624 | (1) |
|
16.5 Other Industrial Applications |
|
|
624 | (1) |
|
|
625 | (1) |
|
16.5.1.1 Algal Protein Extracts as Animal Feedstocks |
|
|
625 | (1) |
|
16.5.1.2 Engineered Algae to Enhance Immune Function |
|
|
625 | (1) |
|
16.5.2 Industrial Enzymes |
|
|
626 | (1) |
|
16.5.2.1 Enzymes for Processing Cellulosic Biofuels |
|
|
626 | (1) |
|
16.5.2.2 Enzymes for Food Processing |
|
|
626 | (1) |
|
16.6 Industrial-Scale Algal Production |
|
|
627 | (1) |
|
16.6.1 Enclosed Photobioreactors and Fermenters |
|
|
627 | (1) |
|
16.6.1.1 Optimizing Photobioreactor Design |
|
|
628 | (1) |
|
16.6.1.2 Modifying Trophic Conversion Pathways for Heterotrophic Growth |
|
|
628 | (1) |
|
|
629 | (1) |
|
16.6.2.1 Media and Water Optimization |
|
|
629 | (1) |
|
16.6.2.2 Efficient Harvesting Methods |
|
|
629 | (1) |
|
16.7 Conclusions and Potential of Algal Platforms |
|
|
630 | (1) |
|
|
630 | (13) |
|
Part VI Eukaryotic Workhorses: Complex Cells Enable Complex Products |
|
|
643 | (72) |
|
17 Host Organisms: Mammalian Cells |
|
|
645 | (28) |
|
|
|
|
645 | (1) |
|
17.2 Basics of Cellular Structure and Metabolism |
|
|
646 | (1) |
|
17.2.1 Cellular Structure |
|
|
646 | (1) |
|
|
650 | (1) |
|
17.3 The Genome of CHO Cells |
|
|
651 | (1) |
|
17.4 Molecular Biology Tools |
|
|
652 | (2) |
|
17.5 Kinetics of Growth and Product Formation |
|
|
654 | (2) |
|
17.6 Intracellular Metabolome Analysis |
|
|
656 | (5) |
|
17.7 Proteome and Gene Expression Analysis |
|
|
661 | (1) |
|
17.8 Improving Cellular Performance by Genetic and Metabolic Engineering |
|
|
662 | (2) |
|
|
664 | (1) |
|
|
664 | (9) |
|
18 Industrial Microorganisms: Saccharomyces cerevisiae and other Yeasts |
|
|
673 | (14) |
|
|
|
|
|
|
18.1 Industrial Application of Yeasts |
|
|
673 | (2) |
|
18.2 Baker's Yeast as Versatile Host for Metabolic Engineering |
|
|
675 | (2) |
|
18.3 Protein Production in Yeasts |
|
|
677 | (1) |
|
18.4 Lipid Production in Yeasts |
|
|
678 | (2) |
|
18.5 Pentose-Utilizing Yeasts |
|
|
680 | (1) |
|
18.5.1 Engineered S. cerevisiae |
|
|
680 | (1) |
|
18.5.2 Yeasts that Naturally Utilize Xylose and Other Pentoses |
|
|
681 | (1) |
|
|
681 | (1) |
|
|
682 | (1) |
|
|
682 | (5) |
|
19 Industrial Microorganisms: Pichia pastoris |
|
|
687 | (28) |
|
|
|
|
19.1 Physiology and Genetics of Pichia pastoris |
|
|
687 | (1) |
|
19.1.1 Methylotrophic Yeasts |
|
|
687 | (1) |
|
19.1.2 Taxonomy and Natural Isolates |
|
|
688 | (1) |
|
|
689 | (1) |
|
|
689 | (2) |
|
19.2 Methylotrophic Metabolism |
|
|
691 | (1) |
|
19.2.1 Dissimilation of Methanol to Generate Energy |
|
|
692 | (1) |
|
19.2.2 Assimilation of Methanol to Form Biomass |
|
|
692 | (1) |
|
19.2.3 Implications for Production Processes |
|
|
693 | (1) |
|
19.3 Application for the Production of Recombinant Proteins |
|
|
693 | (1) |
|
|
693 | (1) |
|
|
695 | (1) |
|
19.3.3 Vectors and Selection Markers |
|
|
696 | (1) |
|
19.3.4 Integration of Multiple Gene Copies |
|
|
698 | (1) |
|
19.3.5 Metabolic Engineering to Enhance Productivity of Recombinant Proteins |
|
|
700 | (1) |
|
19.3.6 Engineering Protein Folding and Secretion Pathways to Enhance Productivity |
|
|
701 | (1) |
|
19.3.7 Protein Glycosylation and Glycoengineering |
|
|
703 | (1) |
|
19.3.8 Recombinant Proteins on the Market |
|
|
703 | (1) |
|
19.4 Application of P pastoris for Metabolite Production |
|
|
703 | (2) |
|
|
705 | (1) |
|
|
705 | (10) |
Index |
|
715 | |