Perface -- Contents -- Section A-Introduction -- 1. Introduction: Scope of Biotechnology and Industrial Microbiology -- 1.1 NATURE OF BIOTECHNOLOGY ANDINDUSTRIAL MICROBIOLOGY -- 1.2 CHARACTERISTICS OF INDUSTRIAL MICROBIOLOGY -- 1.2.1 Industrial vs Medical Microbiology -- 1.2.2 Multi-disciplinary or Team-work Nature of Industrial Microbiology -- 1.2.3 Obsolescence in Industrial Microbiology -- 1.2.4 Free Communication of Procedures in Industrial Microbiology -- 1.3 PATENTS AND INTELLECTUAL PROPERTY RIGHTS IN INDUSTRIAL MICROBIOLOGY AND BIOTECHNOLOGY -- 1.4 THE USE OF THE WORD 'FERMENTATION' IN INDUSTRIAL MICROBIOLOGY -- 1.5 ORGANIZATIONAL SET-UP IN AN INDUSTRIAL MICROBIOLOGY ESTABLISHMENT -- SUGGESTED READINGS -- Section B-Biological Basis of Productivity in Industrial Microbiology and Biotechnology -- 2. Some Microorganisms Commonly Used in Industrial Microbiology and Biotechnology -- 2.1 BASIC NATURE OF CELLS OF LIVING THINGS -- 2.2 CLASSIFICATION OF LIVING THINGS: THREE DOMAINS OF LIVING THINGS -- 2.3 TAXONOMIC GROUPING OF MICRO-ORGANISMS IMPORTANT IN INDUSTRIAL MICROBIOLOGY AND BIOTECHNOLOGY -- 2.3.1 Bacteria -- 2.3.1.1 The Proteobacteria -- 2.3.1.1.1 The Acetic Acid Bacteria -- 2.3.1.2 The Firmicutes -- 2.3.1.2.1 Spore forming firmicutes -- 2.3.1.2.2 Non-spore forming firmicutes -- 2.3.1.3 The Actinobacteria -- 2.3.1.3.1 The Actinomycetes -- 2.3.2 Eucarya: Fungi -- 2.4 CHARACTERISTICS IMPORTANT IN MICROBES USED IN INDUSTRIAL MICROBIOLOGY AND BIOTECHNOLGY -- SUGGESTED READINGS -- 3. Aspects of Molecular Biology and Bioinformatics of Relevance in Industrial Microbiology and Biotechnology -- 3.1 PROTEIN SYNTHESIS -- 3.2 THE POLYMERASE CHAIN REACTION -- 3.2.1 Some Applications of PCR in Industrial Microbiology and Biotechnology -- 3.3 MICROARRAYS -- 3.3.1 Applications of Microarray Technology -- 3.4 SEQUENCING OF DNA.

3.4.1 Sequencing of Short DNA Fragments -- 3.4.2 Sequencing of Genomes or Large DNA fragments -- 3.4.2.1 Use of bacterial artificial chromosomes (BACs) -- 3.4.2.2 Use of the shot-gun approach -- 3.5 THE OPEN READING FRAME AND THE IDENTIFICATION OF GENES -- 3.6 METAGENOMICS -- 3.7 NATURE OF BIOINFORMATICS -- 3.7.1 Some Contributions of Bioinformatics to Biotechnology -- SUGGESTED READINGS -- 4. Industrial Media and the Nutrition of Industrial Organisms -- 4.1 THE BASIC NUTRIENT REQUIREMENTS OF INDUSTRIAL MEDIA -- 4.2 CRITERIA FOR THE CHOICE OF RAW MATERIALS USED IN INDUSTRIAL MEDIA -- 4.3 SOME RAW MATERIALS USED IN COMPOUNDING INDUSTRIAL MEDIA -- 4.4 GROWTH FACTORS -- 4.5 WATER -- 4.6 SOME POTENTIAL SOURCES OF COMPONENTS OF INDUSTRIAL MEDIA -- 4.6.1 Carbohydrate Sources -- 4.6.2 Protein Sources -- 4.7 THE USE OF PLANT WASTE MATERIALS IN INDUSTRIAL MICROBIOLOGY MEDIA: SACCHARIFICATION OF POLYSACCHARIDES -- 4.7.1 Starch -- 4.7.1.1 Saccharification of starch -- 4.7.1.1.1 Saccharification of starch with acid -- 4.7.1.1.2 Use of enzymes -- 4.7.1.1.3 Enzymes involved in the hydrolysis of starch -- 4.7.1.1.4 Industrial saccharification of starch by enzymes -- 4.7.2 Cellulose, Hemi-celluloses and Lignin in Plant Materials -- 4.7.2.1 Cellulose -- 4.7.2.2 Hemicelluloses -- 4.7.2.3 Lignin -- 4.7.2.4 Pretreatment of cellulose-containing materials before saccharification -- 4.7.2.5 Hydrolysis of cellulose -- 4.7.2.5.1 Molecular structure of cellulose -- SUGGESTED READINGS -- 5. Metabolic Pathways for the Biosynthesis of Industrial Microbiology Products -- 5.1 THE NATURE OF METABOLIC PATHWAYS -- 5.2 INDUSTRIAL MICROBIOLOGICAL PRODUCTS AS PRIMARY AND SECONDARY METABOLITES -- 5.2.1 Products of Primary Metabolism -- 5.2.2 Products of Secondary Metabolism -- 5.3 TROPHOPHASE-IDIOPHASE RELATIONSHIPS IN THE PRODUCTION OF SECONDARY PRODUCTS.

5.4 ROLE OF SECONDARY METABOLITES IN THE PHYSIOLOGY OF ORGANISMS PRODUCING THEM -- 5.5 PATHWAYS FOR THE SYNTHESIS OF PRIMARY AND SECONDARY METABOLITES OF INDUSTRIAL IMPORTANCE -- 5.5.1 Catabolism of Carbohydrates -- 5.5.2 The Catabolism of Hydrocarbons -- 5.6 CARBON PATHWAYS FOR THE FORMATION OF SOME INDUSTRIAL PRODUCTS DERIVED FROM PRIMARY METABOLISM -- 5.6.1 Catabolic Products -- 5.6.2 Anabolic Products -- 5.7 CARBON PATHWAYS FOR THE FORMATION OF SOME PRODUCTS OF MICROBIAL SECONDARY METABOLISM OF INDUSTRIAL IMPORTANCE -- SUGGESTED READINGS -- 6. Overproduction of Metabolites of Industrial Microoganisms -- 6.1 MECHANISMS ENABLING MICROORGANISMS TO AVOID OVERPRODUCTION OF PRIMARY METABOLIC PRODUCTS THROUGH ENZYME REGULATION -- 6.1.1 Substrate Induction -- 6.1.1.1 The Jacob-Monod Model of the (negative) control of protein synthesis -- 6.1.1.2 Positive control of protein synthesis -- 6.1.2 Catabolite Regulation -- 6.1.3 Feedback Regulation -- 6.1.3.1 Feedback inhibition -- 6.1.3.2 Feedback Repression -- 6.1.3.3 Regulation in branched pathway -- 6.1.4 Amino Acid Regulation of RNA Synthesis -- 6.1.5 Energy Charge Regulation -- 6.1.6 Permeability Control -- 6.1.6.1 Passive transport -- 6.1.6.2 Transportation via specific carriers -- 6.2 DERANGEMENT OR BYPASSING OF REGULATORY MECHANISMS FOR THE OVER-PRODUCTION OF PRIMARY METABOLITES -- 6.2.1 Metabolic Control -- 6.2.1.1 Feedback control -- 6.2.1.2 Restriction of enzyme activity -- 6.2.2 Permeability -- 6.3 REGULATION OF OVERPRODUCTION IN SECONDARY METABOLITES -- 6.3.1 Induction -- 6.3.2 Catabolite Regulation -- 6.3.2.1 Carbon catabolite regulation -- 6.3.2.2 Nitrogen catabolite regulation -- 6.3.3 Feedback Regulation -- 6.3.4 ATP or Energy Charge Regulation of Secondary Metabolites -- 6.4 EMPIRICAL METHODS EMPLOYED TO DISORGANIZE REGULATORY MECHANISMS IN SECONDARY METABOLITE PRODUCTION.

SUGGESTED READINGS -- 7. Screening for Productive Strains and Strain Improvement in Biotechnological Organisms -- 7.1 SOURCES OF MICROORGANISMS USED IN BIOTECHNOLOGY -- 7.1.1 Literature Search and Culture Collection Supply -- 7.1.2 Isolation de novo of Organisms Producing Metabolites of Economic Importance -- 7.1.2.1 Enrichment with the substrate utilized by the organism being sought -- 7.1.2.2 Enrichment with toxic analogues of the substrate utilized by the organism being sought -- 7.1.2.3 Testing microbial metabolites for bioactive activity -- 7.2 STRAIN IMPROVEMENT -- 7.2.1 Selection from Naturally Occurring Variants -- 7.2.2 Manipulation of the Genome of Industrial Organisms in Strain Improvement -- 7.2.2.1 Genome manipulations not involving Foreign DNA or Bases: Conventional Mutation -- 7.2.2.1.1 Physical agents -- 7.2.2.1.2 Chemical mutagens -- 7.2.2.1.3 Choice of mutagen -- 7.2.2.1.4 The practical isolation of mutants -- 7.2.2.2 Strain Improvement Methods Involving Foreign DNA or Bases -- 7.2.2.2.1 Transduction -- 7.2.2.2.2 Transformation -- 7.2.2.2.3 Conjugation -- 7.2.2.2.4 Parasexual recombination -- 7.2.2.2.5 Protoplast fusion -- 7.2.2.2.6 Site-directed mutation -- 7.2.2.2.7 Metabolic engineering -- 7.2.2.2.8 Genetic engineering -- 7.2.2.2.8.1 Dissection of a portion of the DNA of the donor organism -- 7.2.2.2.8.2 The attachment of the spliced piece of DNA to a vector -- 7.2.2.2.8.3 Plasmids -- 7.2.2.2.8.4 Phages -- 7.2.2.2.8.5 Cosmids -- 7.2.2.2.8.6 Transfer of the vector along with the attached DNA into the host all -- 7.2.2.2.8.7 Recognizing the transformed cell -- 7.2.2.2.8.8 Gene transfer into organisms other than E. coli, including plants and animals -- 7.2.2.2.8.9 Application of genetic engineering in industrial microbiology and biotechnology in general -- 7.2.2.2.8.10 Genetically engineered plants.

7.2.2.2.8.11 Transgenic animals and plants as biological fermentors (or Bioreactors) -- SUGGESTED READINGS -- 8. The Preservation of the Gene Pool in Industrial Organisms: Culture Collections -- 8.1 THE PLACE OF CULTURE COLLECTIONS IN INDUSTRIAL MICROBIOLOGY AND BIOTECHNOLOGY -- 8.2 TYPES OF CULTURE COLLECTIONS -- 8.3 HANDLING CULTURE COLLECTIONS -- 8.4 METHODS OF PRESERVING MICROORGANISMS -- 8.4.1 Microbial Preservation Methods Based on the Reduction of the Temperature of Growth -- 8.4.1.1 Preservation on agar with ordinary refrigeration (4 - 10°C) -- 8.4.1.2 Preservation in Deep Freezers at about -20°C, or between -60°C and -80°C -- 8.4.1.3 Storage in low temperature liquid or vapor phase nitrogen (-156°C to -196°C) -- 8.4.2 Microbial Preservation Methods Based on Dehydration -- 8.4.2.1 Drying on sterile silica gel -- 8.4.2.2 Preservation on sterile filter paper -- 8.4.2.3 Preservation in sterile dry soil -- 8.4.2.4 Freeze-drying (drying with freezing), lyophilization -- 8.4.2.5 L-drying (liquid drying, drying without refrigeration) -- 8.4.3 Microbial Preservation Methods Based on the Reduction of Nutrients -- 8.4.3.1 Storage in distilled water -- 8.4.4 The Need for Experimentation to Determine the Most Appropriate Method of Preserving an Organism -- SUGGESTED READINGS -- Section C-Basic Operations in Industrial Fermentations -- 9. Fermentors and Fermentor Operation -- 9.1 DEFINITION OF A FERMENTOR -- 9.2 THE AERATED STIRRED TANK BATCH FERMENTOR -- 9.2.1 Construction Materials for Fermentors -- 9.2.2 Aeration and Agitation in a Fermentor -- 9.2.3 Temperature Control in a Fermentor -- 9.2.4 Foam Production and Control -- 9.2.4.1 Foaming patterns -- 9.2.4.2 Foam control -- 9.2.5 Process Control in a Fermentor -- 9.2.5.1 pH measurement and control -- 9.2.5.2 Carbon dioxide measurement -- 9.2.5.3 Oxygen determination and control -- 9.2.5.4 Pressure.

9.2.5.5 Computer control.