Biotechnology: A Laboratory Skills Course, Second Edition Detailed Chapter Outlines Below is a chapter-by-chapter outline of the student edition of Biotechnology: A Laboratory Skills Course, second edition. The vignettes and student activities are listed at the end of each chapter outline. Please visit bio-rad.com/textbook for more information. Chapter 1: Biotechnology Industry 1.5 Industry Practices ■■ Good Laboratory Practice 1.1 What Is Biotechnology? ■■ Good Manufacturing Practice ■■ The Biotechnology Toolkit 1.6 Biotechnology Company Structure 1.2 Who Uses Biotechnology? ■■ Life Science Research 1.7 Careers in Biotechnology — -Omics and Systems Biology ■■ Careers in the Laboratory — Laboratory Technician ■■ Healthcare — Quality Assurance Technician — Drug Discovery, Development, and Testing — Research Associate — Protein-Based Drug Production — Research and Development Scientist — Personalized Medicine — Clinical Scientist — Clinical Diagnostics — Engineer ■■ Agriculture ■■ Non-Laboratory Career ■■ Food ■■ Industrial Manufacturing Chapter 1 Vignettes ■■ Biofuels Bioethics — Biotechnology: Good or Bad? ■■ Mining Biotech in the Real World — Affecting Government Policy ■■ Pollution Monitoring and Waste Management ■■ Conservation Biotech in the Real World — Bio-Rad: Then and Now ■■ Biodefense Careers in Biotech — Timothy Balmorez, Chemist, Bio-Rad ■■ Forensics Laboratories, Inc. ■■ Human Origins ■■ Nanotechnology How To… Write an SOP 1.3 The Biotechnology Industry ■■ What Is a Biotechnology Company? Chapter 2: Laboratory Skills ■■ Biotechnology Product Development 2.1 Laboratory Safety ■■ Funding Biotechnological Advancement ■■ Operating Safely in a Laboratory ■■ Patents ■■ Safety Training 1.4 Governmental Regulation of Biotechnology ■■ Personal Protective Equipment ■■ Regulation of Genetically Modified Organisms ■■ Chemical Safety ■■ Regulation of Products in Healthcare ■■ Biological Safety ■■ Preclinical Research ■■ General Laboratory Safety ■■ Clinical Trials ■■ Waste Disposal ■■ Regulation of Animal Research ■■ Cleanrooms ■■ Regulation of Human Research 2.2 Laboratory Notebooks ■■ Regulation of Waste Disposal ■■ Laboratory Notebook Structure ■■ Regulation of Nanotechnology ■■ Components of a Laboratory Notebook Entry ■■ Workplace Safety Regulation Biotechnology: A Laboratory Skills Course, Second Edition 2.3 Laboratory Equipment Chapter 2 Vignettes ■■ Measuring volumes Bioethics — Waste Disposal — Graduated Cylinders Biotech in the Real World — Who Invented Claritin? How — Volumetric Flasks Laboratory Notebooks Played Their Part — Vacuum-Assisted Pipetts — Micropipets Careers in Biotech — Joshua Moore, Bio-Containment — Burettes Protocol Support Supervisor, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) ■■ Liquid Containers — Erlenmeyer Flasks How To… Use an Adjustable-Volume Micropipet — Reagent Bottles Chapter 2 Activities ■■ Measuring Mass 2.A DNA Extraction and Precipitation — Balances 2.B Pipetting ■■ Measuring Temperature — Thermometers 2.C Kool-Aid Column Chromatography ■■ Measuring pH 2.D Making Solutions — pH Meters 2.E Titration ■■ Calibration 2.F Writing a Standard Operating Procedure ■■ Washing Glassware ■■ Disinfecting and Sterilizing — Autoclaving Chapter 3: Microbiology and Cell Culture — Disinfecting Surfaces with Bleach 3.1 Microbiology and Cell Biology — Disinfecting Surfaces with Alcohol ■■ Three Domains of Life — Disinfecting Using a Microwave Oven ■■ Microorganisms and History — Disinfecting with Germicidal UV Light — Sterilizing Solutions 3.2 Bacteria ■■ Names and Shapes of Bacteria ■■ Labeling ■■ Bacterial Environments 2.4 Numerical Data 3.3 Uses of Bacteria in Biotechnology ■■ Significant Figures ■■ Food Production ■■ Scientific Notation ■■ Protein Production ■■ Units of Measure — Metric Prefixes 3.4 Culturing Bacteria in the Laboratory ■■ Growth Media 2.5 Preparing Solutions — Solid Media ■■ Percent Solutions — Antibiotic Selection — Mass per Volume Percent Solutions — Liquid Media — Volume per Volume Percent Solutions — Percentages, Ratios, and Proportions 3.5 Microbiological Techniques — Diluting Percent Solutions ■■ Tools ■■ Aseptic Technique ■■ Using Stock Solutions Given in Terms of “x” ■■ Using Streak Plate Technique to Isolate ■■ Molar Solutions — The Mole Single Colonies ■■ — Molarity Labeling Media ■■ — Making Molar Solutions Quantifying Bacteria a. Proportional Method — Serial Dilution and Plate Counts b. Unit Cancellation Method — Optical Density of Bacteria ■■ Identification of Bacteria ■■ Making Compound Molar Solutions ■■ Diluting Molar Solutions 3.6 Eukaryotic Cells ■■ Preparing Small Volume Dilutions ■■ Organelles ■■ Normality ■■ Other Eukaryotic Cells © 2018 Bio-Rad Laboratories, Inc. 2 Bulletin 7123 Biotechnology: A Laboratory Skills Course, Second Edition 3.7 Uses of Eukaryotic Cells in Biotechnology 4.4 DNA Analysis Techniques ■■ Fermentation ■■ Horizontal Agarose Gel Electrophoresis ■■ Protein Production ■■ Agarose Gels and Running Buffer ■■ Stem Cells ■■ Standards for DNA Electrophoresis ■■ Equipment 3.8 Eukaryotic Cell Culture — Horizontal Gel Electrophoresis Chambers ■■ Growth Media — Power Supplies ■■ Environment ■■ Sterility ■■ Running an Agarose Gel ■■ Visualization ■■ Agarose Gel Staining and Imaging Chapter 3 Vignettes 4.5 Restriction Enzymes as Forensic Tools Bioethics — Should Human Embryos Be Used for Research? ■■ Restriction Fragment Length Polymorphisms ■■ Southern Blotting Biotech in the Real World — Artificial Life! Chapter 4 Vignettes Careers in Biotech — Katie Dalpozzo, Laboratory Research Bioethics — Personal Genetic Information Associate, Bavarian Nordic Biotech in the Real World — Fighting Crime with DNA How To… Use Aseptic Technique to Transfer Bacteria Careers in Biotech — Elisa Ciullo, Sr. Supervisor, Clinical Chapter 3 Activities Filing Operations, Genentech 3.A Making Microbiology Media How To... Set Up a Restriction Digest 3.B Disk Diffusion Test (Modified Kirby-Bauer Test) Chapter 4 Activities 3.C Microbes and Health: An Illustration of Koch’s Postulates 4.A Restriction Site Prediction Using NEBcutter 3.D Gram Staining 4.B Casting Agarose Gels 3.E Quantifying Bacterial Numbers 4.C Dye Electrophoresis 3.F Staining Eukaryotic Cells 4.D Restriction Digestion and Analysis of Lambda DNA Chapter 4: DNA Structure and Analysis 4.E Forensic DNA Fingerprinting 4.F Plasmid Mapping 4.1 Molecular Biology ■■ The Central Dogma of Molecular Biology Chapter 5: Bacterial Transformation 4.2 DNA Structure and Plasmid Purification 4.3 Recombinant DNA Technology 5.1 History of Bacterial Transformation and ■■ Restriction Enzymes Plasmids Bacteria ■■ Ligases ■■ Plasmid Structure ■■ Nontraditional Cloning Techniques ■■ Features of Plasmids — Golden Gate Assembly ■■ Using Plasmids in Biotechnology — Gibson Assembly ■■ Transcriptional Regulation of Plasmids — TOPO (TA) Cloning ■■ Genetically Engineering the pGLO Plasmid ■■ Using Enzymes in the Laboratory ■■ Plasmids for Eukaryotic Expression ■■ CRISPR-Cas9 Technology — How CRISPR works 5.2 Transforming Cells ■■ — Applications of CRISPR Technology Selection of Transformed Cells ■■ a. Agriculture Transformation Efficiency b. Industry 5.3 Plasmid Purification and Quantitation c. Public Health ■■ Growing Bacteria in a Liquid Culture d. Medicine ■■ Purifying Plasmid DNA from a Culture ■■ DNA Quantitation — Gel Quantitation — Spectrophotometric Quantitation — Quantitation of DNA with a Fluorometer © 2018 Bio-Rad Laboratories, Inc. 3 Bulletin 7123 Biotechnology: A Laboratory Skills Course, Second Edition Chapter 5 Vignettes 6.6 Techniques Based on PCR Bioethics — A World without Antibiotics? ■■ DNA Microarrays ■■ DNA Sequencing Biotech in the Real World — Biotech on the Pharm — Primer Sequences Careers in Biotech — Denise Gangadharan, PhD, Associate ■■ Next-Generation Sequencing Director for Science, Centers for Disease Control and — Sequencing by Synthesis Prevention — Pyrosequencing How To... Transform E. coli Using Electroporation — Ion Semiconductor Sequencing — Sequencing by Ligation How To… Use a Microcentrifuge ■■ Sequence Data Analysis Using Bioinformatics Chapter 5 Activities 5.A Bacterial Transformation with S3 Plasmid 6.7 Real-World Applications of PCR ■■ PCR in Medicine 5.B Bacterial Transformation with pGLO Plasmid ■■ PCR in Agriculture 5.C Purification of S3 and pGLO Plasmids ■■ PCR in Forensics ■■ PCR in Paternity Testing 5.D DNA Quantitation ■■ PCR in Human Migration ■■ PCR in Wildlife Conservation Chapter 6: The Polymerase Chain Reaction Chapter 6 Vignettes 6.1 Invention of PCR Bioethics — Forensic DNA Databases — Is Your Privacy Protected? 6.2 What Is PCR? ■■ Three Stages of PCR Biotech in the Real World — A Universe of Viruses — Denaturation Careers in Biotech — Dora Barbosa, Research Associate, — Annealing University of California San Francisco — Extension How To... Program a Thermal Cycler ■■ PCR and DNA Replication ■■ Components of a PCR Reaction Chapter 6 Activities ■■ Setting Up a PCR Reaction 6.A STR PCR Analysis — Master Mixes 6.B GMO Detection by PCR ■■ Analysis of PCR Products 6.C Detection of the Human PV92 Alu Insertion 6.3 Thermal Cyclers 6.D Fish DNA Barcoding 6.4 Types of PCR ■■ Real-Time, or Quantitative, PCR Chapter 7: Protein Structure and Analysis ■■ Digital PCR ■■ Reverse Transcription PCR 7.1 Protein Synthesis ■■ Multiplex PCR ■■ Bacterial Transcription ■■ Degenerate PCR ■■ Eukaryotic Transcription ■■ Nested PCR ■■ Translation ■■ Fast PCR ■■ Posttranslational Modifications ■■ Isothermal PCR 7.2 Protein Structure ■■ Random Amplification of Polymorphic DNA ■■ Amino