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Biotechnology Course Outline

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					                                      Biotechnology Course Outline
                                              Ms. Lawson
                                               2009-2010

**Microbiology Labs: Some microbiology lab procedures and results will be discussed only in this
classroom. The microorganisms required for these lab activities are potentially pathogenic and cannot be
handled safely in a high school environment.

**Biotechnology Labs: Biotechnology labs do not contain any pathogenic microorganisms or
human/animal products. Simulated materials are used to demonstrate certain biotechnology procedures that
would involve the use of potential pathogens.

Introduction to Biotechnology
Course Introduction
- Course description
- Course outline
- New Hampshire Community Technical College credit option
- General classroom policies
- Materials needed
Defining Microbiology
Defining Biotechnology
- Ancient biotechnology
   Domestication
   Food
- Classical biotechnology
   Fermentation control
- Antibiotics
- Modern biotechnology
Safety
- Safety contract
   Heat and fire safety
   Chemical safety
   Laboratory equipment safety
   Specimen safety
    Electrical equipment safety
   Field study/trip safety
   Reporting accidents
- Safety violation cards
- Laboratory waste disposal
- Working with Escherichia coli
- National Institute of Health (NIH) guidelines
- Standard microbiological practices
Inventory of Biotechnology Course Materials, Chemical
Identification and Chemical Storage Check
Biotechnology Equipment Standard Operating Procedures (SOPs)
Measurements, Micropipetting and Sterile Techniques
- Metric measurement
- Scientific method
- Digital micropipettors
                                                                                                           1
- Microcapillary pipettes
- Transfer pipettes
- 10 ml. Pipettes
- To flame of not to flame?
- Microcentrifuge (microfuge)
- Lab: Measurements, Micropipetting and Sterile Techniques
Aseptic Environments “People vs. Germs”
- Aseptic Technique
   Sterilization
   Disinfection
   Sanitization
- Lab: How Effective is Your Disinfectant? (Smith)
- Worker protection
- Environment protection
- Experiment or product protection
- Creating aseptic environments
   Washing surfaces
   Autoclave instruments
   Laminar flow hoods
   Flaming
***Classroom decontamination to occur frequently throughout the
year to minimize equipment contamination of microbes and DNA




                                                                  2
Chapter 1 – The Microbial World and You
Microbes in our lives
Naming and classifying microorganisms
- Nomenclature
Types of Microorganisms
- Bacteria
- Archae
- Fungi
- Protozoa
- Algae
- Viruses
- Multicellular Animal Parasites
- Classification of Microorganisms
A brief history of microbiology
- The first observations
- The debate over spontaneous generation
    Evidence pro and con
    The theory of biogenesis
- The golden age of microbiology
    Fermentation and pasteurization
    The germ theory of disease
    Vaccination
- The birth of modern chemotherapy
    The first synthetic drugs
    A fortunate accident – antibiotics
- Modern developments in microbiology
    Bacteriology, mycology and parasitology
    Immunology
    Virology
    Recombinant DNA technology
Microbes and human welfare
- Recycling vital elements
- Sewage treatment: using microbes to recycle water
- Bioremediation: using microbes to clean pollutants
- Insect pest control by microorganisms
- Modern biotechnology and genetic engineering
Microbes and human disease
- Normal microbiota
- Infectious disease
- Emerging infectious disease
Chapter 10 – Classification of Microorganisms
The study of phylogenic relationships
- Whittaker’s five kingdoms
- Woese’s three domains
- A phylogenic hierarchy
Classification of organisms
- Scientific nomenclature
- The taxonomic hierarchy
- Classification of prokaryotes
                                                       3
- Classification of eukaryotes
- Classification of viruses
Methods of classifying and identifying microorganisms
- Morphological characteristics
- Differential staining
- Biochemical tests
- Serology
- Phage typing
- Fatty acid profiles
- Flow cytometry
- DNA base composition
- DNA fingerprinting
- Ribosomal RNA sequencing
- The polymerase chain reaction
- Nucleic acid hybridization
- Putting classification methods together
   Dichotomous keys
   Cladograms
Chapter 11 – The Prokaryotes: Domains Bacteria and Archaea
Prokaryotic groups
Domain bacteria
The proteobacteria
- The  (alpha) proteobacteria
- The  (beta) proteobacteria
- The  (gamma) proteobacteria
   Pseudomonadales
   Legionellales
   Vibrionales
   Enterobacteriales
   Pasteurellales
- Purple and green photosynthetic bacteria
- The  (delta) proteobacteria
   Desulfovibrionales
   Myxococcales
- The  (epsilon) proteobacteria
The nonproteobacteria gram-negative bacteria
- Cyanobacteria
- Chylamydiales
   Spirochetes
- Bacteroides
- Fusobacteria
- Sphingobacteria
The gram-positive bacteria
- Low G + C gram-positive bacteria
    Mycoplasmatales
   Clostridiales
   Lactobacillales
- High G + C gram-positive bacteria
                                                             4
   Actinomycetes
Domain Archaea
Microbial Diversity
Basic Laboratory Techniques for Isolation, Cultivation, and Cultural
Characterization of Microorganisms
- Lab: Isolating Bacterial Cultures (Smith)
- Lab: Bacterial Identification (Smith)
- Lab: Culture Transfer Techniques (Cappuccino + Sherman)
- Lab: Techniques for Isolation of Pure Cultures (Cappuccino +
Sherman)
- Lab Cultural Characteristics of Microorganisms (Cappuccino +
Sherman)
Chapter 12 – The Eukaryotes: Fungi, Algae, Protozoa and
Helminths
Fungi
- Characteristics of fungi
   Vegetative structures
   Life cycle
   Nutritional adaptations
- Medically important phyla of fungi
   Zygomycota
   Ascomycota
   Basidiomycota
- Fungal diseases
- Economic effects of fungi
- Lab: Cultivation and Morphology of Molds (Cappuccino + Sherman)
- Lab: Yeast Morphology (Cappuccino + Sherman)
- Lab: Identification of Unknown Fungi (Cappuccino + Sherman)
Lichens
Algae
- Characteristics of algae
   Vegetative structures
   Life cycle
   Nutrition
- Selected phyla of algae
- Roles of algae in nature
Protozoa
- Characteristics of protozoa
   Life cycle
   Nutrition
- Medically important phyla of protozoa
   Archaezoa
   Microsporidia
   Rhizopoda
   Apicomplexan
   Ciliophora
   Euglenozoa
- Lab: Free-Living Protozoa (Cappuccino + Sherman)
- Lab: Parasitic Protozoa (Cappuccino + Sherman)
                                                                       5
Slime molds
Helminthes
- Characteristics of helminthes
   Life cycle
- Platyhelminthes
   Trematodes
   Cestodes
   Humans as definitive hosts
   Humans as intermediate hosts
- Nematodes
   Eggs infective for humans
Arthropods as vectors
Chapter 3 – Observing Microorganisms Through a Microscope
Units of measurement
Microscopy: the instruments
- Light microscope
   Compound light microscope
   Resolution
   Dark field microscopy
   Phase-contrast microscopy
   Differential inference contrast (DIC) microscopy
   Fluorescence microscopy
   Confocal microscopy
- Lab: Microscopic Examination of Stained Cell Preparations
(Cappuccino + Sherman)
- Lab: Microscopic Examination of Living Bacterial Preparations
(Cappuccino + Sherman)
- Lab: The Microscopic Measurement of Microorganisms
Chapter 4 – Functional Anatomy of Prokaryotic and Eukaryotic
Cells
Comparing prokaryotic and eukaryotic cells
The prokaryotic cell structure
The size, shape and arrangement of bacterial cells
Structures external to the cell wall
- Glycolyx
- Flagella
- Axial filaments
- Fimbriae and pili
The cell wall
- Composition and characteristics
   Gram-positive walls
   Gram-negative walls
- Cell walls and the gram stain mechanisms
- Atypical cell walls
- Damage to the cell wall
Structures internal to the cell wall
- The plasma (cytoplasmic) membrane
       Structure
       Functions
                                                                  6
    Destruction of the plasma membrane by antimicrobial agents
    The movement of materials across membranes
       Passive processes
       Osmosis
       Active processes
- Cytoplasm
- The nuclear area
- Inclusions
    Metachromatic granules
    Polysaccharide granules
    Lipid inclusions
    Sulfur granules
    Carboxysomes
    Gas vacuoles
    Magnetosomes
- Endospores
- Lab: Bacterial Staining (Cappuccino + Sherman)
- Lab: Preparation of Bacterial Smears (Cappuccino + Sherman)
- Lab: Simple Staining (Cappuccino + Sherman)
- Lab: Negative Staining (Cappuccino + Sherman)
- Lab: Gram Stain (Cappuccino + Sherman)
- Lab Acid-Fast Stain (Ziehl Neelsen Method) (Cappuccino +
Sherman)
- Lab: Differential Staining for Visualization of Bacterial Cell
Structures (Cappuccino + Sherman)
The eukaryotic cell
- Flagella and cilia
- The cell wall and glycocalyx
- The plasma (cytoplasmic) membrane
- Cytoplasm
- Organelles
    The nucleus
    Endoplasmic reticulum
    Ribosomes
    Golgi complex
    Lysosomes
    Vacuoles
    Mitochondria
    Chloroplasts
    Peroxisomes
    Centrosomes
The evolution of eukaryotes
Chapter 5 – Microbial Metabolism
Catabolic and anabolic reactions
Enzymes
- Naming enzymes
- Enzyme components
- The mechanism of enzyme action
- Factors influencing enzymatic activity
                                                                   7
   Temperature
   pH
   Substrate concentration
   Inhibitors
- Feedback inhibition
- Ribozymes
- Lab: Extracellular Enzymatic Activities of Microorganisms
(Cappuccino + Sherman)
Energy production
- Oxidation-reduction reactions
- The generation of ATP
   Substrate-level phosphorylation
   Oxidative phosphorylation
   Photophosphorylation
- Metabolic pathways of energy production
Carbohydrate metabolism
- Glycolysis
- Alternatives to glycolysis
   The pentose phosphate pathway
   The Entner-Doudoroff pathway
- Cellular respiration
   Aerobic respiration
   The electron transport chain (system)
   The chemiosmotic mechanisms of ATP generation
   A summary of aerobic respiration
   Anaerobic respiration
- Fermentation
   Lactic acid fermentation
   Alcohol fermentation
- Lab: Carbohydrate Metabolism (Cappuccino + Sherman)
Lipid and protein catabolism
Biochemical tests and bacterial identification
Photosynthesis
- The light reactions: photophosphorylation
- The dark reactions: the Calvin-Benson cycle
A summary of energy production mechanisms
Metabolic diversity among organisms
- Photoautotrophs
- Photoheterotrophs
- Chemoautotrophs
- Chemoheterotrophs
Metabolic pathways of energy use
- Polysaccharide biosynthesis
- Lipid biosynthesis
- Amino acid and protein biosynthesis
- Purine and pyrimidine biosynthesis



                                                              8
The integration of metabolism
Chapter 6 – Microbial Growth
The requirements for growth
- Physical requirements
    Temperature
    pH
    Osmotic pressure
- Lab: Physical Factors: Temperature (Cappuccino + Sherman)
- Lab: Physcial Factors: pH of the Extracellular Environment
(Cappuccino + Sherman)
- Chemical requirements
    Carbon
    Nitrogen, sulfur and phosphorous
- Trace elements
- Oxygen
- Lab: Physical Factors: Atmospheric Oxygen Requirements
(Cappuccino + Sherman)
- Organic Growth Factors
Culture media
- Chemically defined media
- Complex media
- Anaerobic growth media
- Special culture techniques
 - Selective and differential media
- Enrichment culture
- Lab: Nutritional Requirements: Media for the Routine Cultivation of
Bacteria (Cappuccino + Sherman)
- Lab: Use of Differential and Selective Media (Cappuccino +
Sherman)
- Lab: Techniques for the Cultivation of Anaerobic Microorganisms
(Cappuccino + Sherman)
- Lab: Triple Sugar-Iron Agar Test
- Lab: Iambic Test (Cappuccino + Sherman)
- Lab: Hydrogen Sulfide Test (Cappuccino + Sherman)
- Lab: Urease Test (Cappuccino + Sherman)
- Lab: Litmus Milk Reactions (Cappuccino + Sherman)
- Lab: Nitrate Reduction Test (Cappuccino + Sherman)
- Lab: Catalase Test (Cappuccino + Sherman)
- Lab: Oxidase Test (Cappuccino + Sherman)
- Lab: Utilization of Amino Acids (Cappuccino + Sherman)
- Generation time
- Logarithmic representation of bacterial populations
- Phases of growth
    The lag phase
    The log phase
    The stationary phase
    The death phase
- Lab: The Bacterial Growth Curve (Cappuccino + Sherman)
- Direct measurement of microbial growth
                                                                        9
   Plate counts
   Serial dilutions
   Pour plates and spread plates
   Filtration
   The most probable number method
   Direct microscopic count
- Lab: Serial Dilution – Agar Plate Procedure to Quantitate Viable Cells
(Cappuccino + Sherman)
- Estimation bacterial numbers by indirect methods
   Turbidity
   Metabolic activity
   Dry weight
- Lab: Genus Identification of Unknown Bacterial Cultures
(Cappuccino + Sherman)
Chapter 7 – The Control of Microbial Growth
The terminology of microbial control
The rate of microbial death
Actions of microbial control agents
- Alteration of membrane permeability
- Damage to proteins and nucleic acids
Physical methods of microbial control
- Heat
   Moist heat
   Pasteurization
   Filtration
   Low temperatures
   Osmotic pressure
   Radiation
- Lab: Physical Agents of Control: Moist Heat (Cappuccino +
Sherman)
- Lab: Physical Agents of Control: Environmental Osmotic Pressure
(Cappuccino + Sherman)
- Lab: Physical Agents of Control: Electromagnetic Radiations
(Cappuccino + Sherman)
Chemical methods of microbial control
- Principles of effective disinfection
- Evaluation a disinfectant
   Use-dilution tests
   The disk-diffusion method
- Types of disinfectants
   Phenol and phenolics
   Bisphenols
   Biguarides
   Halogens
   Alcohols
   Heavy metals and their compounds
   Sulfur-active agents
   Quaternary ammonium compounds (QUATS)
   Chemical food preservatives
                                                                           10
Antibiotics
Aldehydes
Gaseous chemosterilizers
Peroxygens (oxidizing agents)




                                11
Microbial Characteristics and Microbial Control
Chapter 13 – Viruses, Viroids and Prions
General characteristics of viruses
- Host range
- Viral size
Viral Structure
- Nucleic acid
- Capsid and envelope
- General morphology
   Helical viruses
   Polyhedral viruses
   Enveloped viruses
   Complex viruses
Taxonomy of viruses
The isolation, cultivation and identification of viruses
- Growing bacteriophages in the laboratory
- Growing animal viruses in the laboratory
   In living animals
   In embryonated eggs
   In cell cultures
- Viral identification
Viral multiplication
- Multiplication of bacteriophages
   T-even bacteriophages: the lytic-cycle
   A one-step growth experiment
   Bacteriophage lambda: the lysogenic cycle
- Multiplication of animal viruses
   Attachment
   Penetration
   Uncoating
   The biosynthesis of DNA viruses
   The biosynthesis of RNA viruses
- Latent viral infections
- Persistent viral infections
- Prions
- Plant viruses and viroids
- Lab: Cultivation and Enumeration of Bacteriophages (Cappuccino +
Sherman)
- Lab: Isolation of Coliphages from Raw Sewage (Cappuccino +
Sherman)
Chapter 8 – Microbial Genetics + DNA Science
Structure and function of the genetic material
How we learned that DNA is the genetic material
- Molecular biology and the nature of heredity
- Diversity and similarity of species
- The passing of traits from one generation to the next
- Where are genes located
- The link between evolution and genetics
- Genes as physical entities
                                                                     12
- The job of the gene
- Structure of the DNA molecule
- Lab: What Does DNA Look Like? (Edvotek #S-10)
How we learned the function of DNA
- Genotype and phenotype
- DNA and chromosomes
- The flow of genetic information
- DNA replication
   DNA polymerase
   DNA synthesis
- Replication of chromosomal ends
- RNA and protein synthesis
   Transcription
   Translation
- Protein modification
- Protein degradation
- The Central Dogma
How we learned how genes are regulated
- Repression and induction
   Repression
   Induction
- The lac operon model
- Gene regulation in Eukaryotes
   Initiation of transcription
   Transcriptional regulation
   Enhancers
   Signal integration at enhancers
- RNA processing
   Creating a 5’ cap structure
   Creating a poly(A) tail
   MRNA stability and turnover
   RNA splicing
- Alternative splicing
- Translational control
- Transposable elements
- Gene rearrangements
   Simple switches in salmonella, trypanosomes and yeast
   Antibody diversity
- Tissue specific gene regulation
- Coordinate expression of genes
   The cell cycle
   Apoptosis
   Body axis formation
Microbial mutation: change in the genetic material
- Types of mutations
- Mutagens
   Chemical mutagens
   Radiation
- The frequency of mutation
                                                           13
- Identifying mutants
- Identifying chemical carcinogens
Microbial genetic transfer and recombination
- Transformation in bacteria
- Conjugation in bacteria
- Transduction in bacteria
- Plasmids and transposons
    Plasmids
    Transposons
Microbial genes and evolution
- Lab: Enzyme Induction (Cappuccino + Sherman)
- Lab: Bacterial Conjugation (Cappuccino + Sherman)
- Lab: Isolation of a Streptomycin-Resistant Mutant (Cappuccino +
Sherman)
- Lab: The Ames Test: A Bacterial Test System for Chemical
Carcinogenicity (Cappuccino + Sherman)
Chapter 9 – Biotechnology and Recombinant DNA + DNA Science
Basic tools and techniques of DNA science
- Restriction endonucleases
- Gel electrophoresis
    Horizontal gel electrophoresis
    Vertical gel electrophoresis
- Lab: Principles of Gel Filtration Chromatography (Edvotek #108)
- Lab: Principles + Practice of Agarose Gel Electrophoresis (Edvotek
#101)
- Lab: Whose DNA Was Left Behind? (Edvotek #S-51)
- Lab: Gel Analysis of DNA from Plants (Edvotek #907)
- The plasmid vector
    Propagation of plasmid
    Selectable markers
    Inserting new genes into plasmids
- The host cell: Escherichia coli
- Lab: Isolation of E. coli Chromosomal DNA (Edvotek #203)
- Transformation
- Lab: Transformation of E. coli with pGAL (Edvotek #221)
- Lab: EZ Gene Splicer DNA Recombination + Transformation Kit
(Carolina Biotechnology)
- Electroporation
- Isolation and analysis of recombinant plasmids
    DNA miniprep procedure
- Lab: Mini-prep Isolation of Plasmid DNA (Edvotek #202)
- The first recombinant DNA molecule
- Model systems
    Escherichia coli
    Yeast
    Nematode worms
    Fruit fly
    Zebrafish
    Amphibians
                                                                       14
   Chicken
   Mouse
   Human cell culture
   Plants
- Lab: Isolation of Chloroplasts, Mitochondria and Extraction of Plant
Genomic DNA (Edvotek #910)
Methods for finding and expressing important genes
- The biochemist’s and molecular geneticist’s problem
- Creating and screening library
   The DNA library
   Vectors and libraries
       Bacteriophage 
       Cosmids
       BACs and PACs
   Screening DNA libraries
   Identifying specific DNA sequences
- Lab: Analysis of Eco RI Cleavage Patterns of Lambda DNA (Edvotek
#112)
- Lab: Analysis of Restriction Enzyme Cleavage Patterns of DNA
(Edvotek #102)
- Lab: Cleavage of DNA with Restriction Enzymes (Edvotek #213)
- Lab: DNA Restriction Analysis Kit (Carolina Biotechnology)
- Lab: Restriction Enzyme cleavage of DNA Kit (Carolina
Biotechnology)
   Making a probe for -globin
       Isolating globin mRNA
       Making a cDNA probe from mRNA
   Screening
   Other screening strategies
      Synthetic oligonucleotides
       BAC and PAC library screening
       cDNA libraries
       Computer-based screening
- Working with cloned genes
   Southern Hybridization
- Lab: Southern Blot Analysis (Edvotek #207)
-mRNA analysis
   Northern hybridization
   In situ hybridization
- Protein analysis
   Making proteins by expressing foreign genes in Escherichia coli and
   systems
- Lab: Molecular Weight Determination of Proteins (Edvotek #110)
- Lab: DNA/RNA Microarrays (Edvotek #235)
- Lab: Ion Exchange Chromatography (Edvotek #243)
- Lab: Diversity of Fish Proteins (Edvotek #253)
- Using antibodies and marker proteins
   Uses for antibodies
   Methods for studying proteins
                                                                         15
       Western blot
       Immunocytochemistry
      Green fluorescent protein (GFP)
- Lab: Transformation with Green Fluorescent Protein (Edvotek #223)
- Lab: Purification and Size Determination of Green and Blue
Fluorescent Proteins (Edvotek #255)
- Putting it all together: transgenic animals
    Transgenic mice
    Chimeras, ES cells and homologous recombination
    Making a knock-out mouse
    Example of a knock-out mouse study
Modern methods for analyzing whole genomes
- Genesis of the Human Genome Project
- Chromosomes maps and markers
   Polymerase chain reaction
       Denaturing
       Annealing
       Extension
    DNA sequencing
- Lab: PCR – Polymerase Chain Reaction (Edvotek #103)
- Lab: Size Determination of DNA Restriction Fragments (Edvotek
#104)
- Lab: Mapping of Restriction Sites on Plasmid DNA (Edvotek #105)
- Hierarchical shotgun clone libraries
- Expressed sequence tags
- Whole-genome shotgun sequence
- Finishing the human genome sequence
- Bioinformatics: finding the information in our genes
- Lab: Sequencing the Human Genome (Edvotek #339)
- Lab: DNA Bioinformatics (Edvotek #340)
- Lab: Carolina Webcutter Kit (Carolina Biotechnology)
- Beyond the Human Genome
    DNA microarrays
    Functional analysis
- The structure and meaning of the human genome
- Junk DNA
The DNA science of cancer
- Defining cancer
    Lung cancer
    Liver cancer
    Stomach cancer
    Cervical cancer
    Skin cancer
    Breast cancer
- Tumor viruses as cancer models
    Flattened morphology
    Anchorage-dependent growth
    Growth in confluent monolayer
    Contact inhibition
                                                                      16
- The origin of viral oncogenes: transduction
- Viruses and human cancer
- Mammalian cell transfection
- Human oncogenes
- Lab: Morphology of Cancer Cells (Edvotek #990)
- Tumor suppressor genes
- Uniting oncogenes and tumor suppressors
- Cooperative transformation and “multi-hit” oncogenesis
- Carcinogens, point mutations and individuals at risk
- Chromosome abnormalities and gene amplification
- Signal transduction: cancer as a disease of communication
- The cell cycle and apoptosis
- Improving cancer diagnosis and treatment
Applying DNA science to human genetics and evolution
- Charles Davenport and the eugenics record office
- The construction of genetic blame
   Eugenic social engineering
   Opposition and the end of eugenics
- Problems on the road to modern human genetics
- Determining the chromosomal basis of human disease
   Sickle cell brings human genetics into the molecular era
- Lab: In Search of the Sickle Cell Gene (Edvotek #315)
   Making therapeutics from cloned genes
   Expressing insulin and growth hormone in Escherichia coli
   Expressing t-PA, erythropoietin and interferons in mammalian
   systems
- The importance of DNA polymorphisms
   DNA polymorphisms and human identity
   Variable number of tandem repeats
   Short tandem repeats
- Lab: DNA Fingerprinting – Amplification of DNA for Fingerprinting
(Edvotek #130)
- Lab: PCR-Based DNA Fingerprinting (Edvotek #371)
- Lab: Paternity Testing Simulation (Edvotek #114)
- Lab: Cancer Gene Detection (Edvotek #115)
- Gene cloning: from linkage to DNA diagnosis
   The triumph of cloning the Huntington’s disease gene
   Cloning the Duchenne muscular dystrophy gene
   Cloning the cystic fibrosis gene
- Finding genes behind complex disorders
   Single-nucleotide polymorphisms
   Pharmacogenetics
- Human history and populations
- The biological concept of race
- Fossil records and human evolution
- The DNA molecular clock
- DNA and human evolution
   Neandertal
   “Bushy” evolution
                                                                      17
   Climate changes and population bottlenecks
   The hunter-gatherer remains
Chapter 14 – Principles of Disease and Epidemiology
Pathology, infection and disease
Normal microbiota
- Relationships between the normal microbiota and the host
- Opportunistic microorganisms
- cooperation among microorganisms
The etiology of infectious disease
- Koch’s postulates
- Exceptions to Koch’s postulates
Classifying infectious diseases
- Predisposing factors
- The development of disease
   The incubation period
   The prodromal period
   The period of illness
   The period of decline
   The period of convalescence
The spread of infection
- Reservoirs of infection
   Human reservoirs
   Animal reservoirs
   Nonliving reservoirs
- The transmission of disease
   Contact transmission
   Vehicle transmission
   Vectors
- Portals of exit
Nosocomial (Hospital-Acquired) Infections
- Microorganisms in the hospital
- The compromised host
- The chain of transmission
- The control of nosocomial infections
Emerging infectious diseases
Epidemiology
- Descriptive epidemiology
- Analytical epidemiology
- Experimental epidemiology
- Case reporting
- The Centers for Disease Control and Prevention (CDC)
Chapter 15 – Microbial Mechanisms of Pathogenicity
How microorganisms enter a host
- Portals of entry
   Mucous membranes
   Skin
   The parenteral route
- The preferred portal of entry
- Numbers of invading microbes
                                                             18
- Adherence
How bacterial pathogens penetrate host defenses
- Capsules
- Components of the cell wall
- Enzymes
- Penetration into the host cell cytoskeleton
How bacterial pathogens damage host cells
- Direct damage
- The production of toxins
    Exotoxins
    Endotoxins
- Plasmids, lysogeny and pathogenicity
Pathogenic properties of nonbacterial microorganisms
- Viruses
    Viral mechanisms for evading host defenses
    Cytopathic effects of viruses
- Fungi, protozoa, helminthes and algae
Chapter 16 – Nonspecific Defenses of the Host
The skin and mucous membranes
- Mechanical factors
- Chemical factors
- Normal microbiota and nonspecific resistance
Phagocytosis
- Formed elements in blood
- Actions of phagocytic cells
- The mechanism of phagocytosis
    Chemotaxis
    Adherence
    Ingestion
    Digestion
Inflammation
- Vasodilation and increase permeability of blood vessels
- Phagocyte migration and phagocytosis
- Tissue repair
Fever
Antimicrobial substances
- The complement system
    Components
    Pathways of activation
    Consequences of complement activation
    Complement and disease
- Interferons
Chapter 17 – Specific Defenses of the Host: The Immune Response
Immunity
- Types of acquired immunity
    Naturally acquired immunity
    Artificially acquired immunity
- The duality of the immune system
    Humoral (antibody-mediated) immunity
                                                                  19
   Cell-mediated immunity
Antigens and Antibodies
- The nature of antigens
- The nature of antibodies
   Antibody-structure
   Immunoglobin classes
B cells and humoral immunity
- Apoptosis
- Activation of antibody-producing cells by clonal selection
- Antigen-antibody binding and its results
- Monoclonal antibodies and their uses
T cells and cell-mediated immunity
- Chemical messengers of immune cells: cytokines
- Cellular components of immunity
   Types of T cells
   Nonspecific cellular components
The interrelationship of cell-mediated and humoral immunity
- The production of antibodies
- Antibody-dependent cell-mediated cytotoxicity
Chapter 18 – Practical Applications of Immunology
Vaccines
- Principles and effects of vaccination
- Types of vaccines and their characteristics
- The development of new vaccines
- Safety of vaccines
Diagnostic Immunology
- Precipitation reactions
- Lab: Precipitin Reaction: The Ring Test (Cappuccino + Sherman)
- Lab: Antigen-Antibody Interaction: The Ouchterlony Procedure
(Edvotek #270)
- Lab: Immunoelectrophoresis (Edvotek #272)
- Lab: Precipitin Reaction: Immunodiffusion (Cappuccino + Sherman)
- Agglutination reactions
   Direct agglutination tests
   Indirect (passive) agglutination tests
   Hemagglutination
- Lab: Agglutination Reaction: The Febrile Antibody Test (Cappuccino
+ Sherman)
- Lab: Latex Agglutination Test (Cappuccino + Sherman)
- Lab: Agglutination Reaction: Mono-Test for Infectious
Mononucleosis (Cappuccino + Sherman)
- Neutralization reactions
- Complement-fixation reactions
- Fluorescent-antibody techniques
- Lab: Immunofluorescence (Cappuccino + Sherman)
- Enzyme-Linked Immunoabsorbent Assay (ELISA)
- Lab: Introduction to ELISA Reactions (Edvotek #269)
- Lab: Quantitative ELISA Laboratory Activity (Edvotek #278)
- Lab: Enzyme-Linked Immunoabsorbent Assay (Cappuccino +
                                                                       20
Sherman)
- Lab: Clinical Diagnostic Immunoblot (Edvotek #276)
- Radioimmunology
- The future of diagnostic immunology
Chapter 19 – Disorders Associated with the Immune System
Hypersensitivity
- Type I (anaphylactic) reactions
   Systemic anaphylaxis
   Localized anaphylaxis
   Prevention of anaphylactic reactions
- Type II (cytotoxic) reactions
   The ABO blood group system
   The Rh blood group system
   Drug-induced cytotoxic reactions
- Type III (immune complex) reactions
- Type IV (cell-mediated) reactions
   Causes of type IV reactions
   Cell-mediated hypersensitivity reactions of the skin
Autoimmune Diseases
- Type I autoimmunity
- Type II (cytotoxic) autoimmune reactions
- Type III (immune complex) autoimmune reactions
- Type IV (cell-mediated) autoimmune reactions
Reactions related to the human leukocyte antigen (HLA) complex
- Reactions to transplantation
   Privileged sites and privileged tissue
   Grafts
   Bone marrow transplants
- Immunosuppression
Immune Deficiencies
- Congenital immune deficiencies
- Acquired immune deficiencies
The immune system and cancer
- Immunotherapy
Acquired Immunodeficiency Syndrome (AIDS)
- The origin of AIDS
-HIV infection
   The structure of HIV
   The infectiveness and pathogenicity of HIV
   Clades (subtypes) of HIV
   Survival with HIV
- Diagnostic methods
- Lab: How Does a Doctor Test for AIDS? (Edvotek #S-70)
- Lab: AIDS Kit: Simulation of HIV Detection by Western Blot
(Edvotek #275)
- HIV transmission
- AIDS worldwide
- The prevention and treatment of AIDS
   HIV vaccines
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    Chemotherapy
- The AIDS epidemic and the importance of scientific research
Chapter 20 – Antimicrobial Drugs
The history of chemotherapy
The spectrum of antimicrobial activity
The action of antimicrobial drugs
- The inhibition of the cell wall synthesis
- The inhibition of protein synthesis
- Injury to the plasma membrane
- The inhibition of nucleic acid synthesis
- Inhibiting the synthesis of essential metabolites
A survey of commonly used antimicrobial drugs
- Antibacterial antibiotics: inhibitors of cell wall synthesis
    Penicillin
    Cephalosporins
    Carbapenems
    Bacitracin
    Vanomycin
    Isoniazid (INH)
    Ethambutol
- Inhibitors of protein synthesis
    Aminoglycosides
    Tetracycline
    Chloramphenicol
    Macrolides
- Injury to the plasma membrane
- Inhibitors of nucleic acid (DNA?RNA) synthesis
    Rifamycins
    Quinolones and fluoroquinolones
- Competitive inhibitors of the synthesis of essential metabolites
    Sulfonamides
- Lab: Chemical Agents of Control: Chemotherapeutic Agents
(Cappuccino + Sherman)
- Lab: Determination of Penicillin Activity in the Presence and
Absence of Penicillinase (Cappuccino + Sherman)
- Lab: Chemical Agents of Control: Disinfectants and Antiseptics
(Cappuccino + Sherman)
    Azoles
    Griseofulvin
    Other antifungal drugs
- Antiviral Drugs
    Nucleoside and nucleotide analogs
    Other enzyme inhibitors
    Interferons
- Antiprotozoan and antihelminthic drugs
    Antiprozoan drugs
    Antihelminthic drugs
Tests to guide chemotherapy
- The diffusion methods
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- Broth dilution tests
The effectiveness of chemotherapeutic agents
- Antibiotic Safety
- Lab: Assay for Antibiotic Resistance Enzyme (Carolina
Biotechnology)
- Effects of combinations of drugs
- The future of chemotherapeutic agents
*Chapter 21, 22, 23, 24, 25 and 26 Student Projects: Research paper
and presentation of human system diseases
Chapter 21 – Microbial Diseases of the Skin and Eyes
Structure and function of the skin
- Mucous Membranes
Normal microbiota of the skin
Microbial diseases of the skin
- Bacterial diseases of the skin
    Staphylococcal skin infections
    Streptococcus skin infections
    Infections by pseudomonads
    Acne
- Lab: Identification of Human Staphylococcal Pathogens (Cappuccino
+ Sherman)
- Viral diseases of the skin
    Warts
    Smallpox (variola)
    Chickenpox (varicella) and shingles (Herpes zoster)
    Herpes simplex
    Measles (rubeola)
    Rubella
    Other viral rashes
- Fungal diseases of the skin
    Cutaneous mycoses
    Subcutaneous mycoses
    Candidiasis
- Parasitic infestation of the skin
    Scabies
Microbial diseases of the eye
- Inflammation of the eye membranes: conjunctivitis
- Bacterial diseases of the eye
    Neonatal gonorrheal opthalmia
    Inclusion conjunctivitis
    Trachoma
- Other infectious diseases of the eye
    Herpetic keratitis
    Acanthamoeba keratitis




                                                                      23
Chapter 22 – Microbial Diseases of the Nervous System
Structure and function of the nervous system
- Bacterial diseases of the nervous system
   Bacterial meningitis
   Haemophilus influnzae meningitis
   Neisseria meningitis (meningococcal meningitis)
   Streptococcus pneumoniae meningitis (pneumococcal meningitis)
   Diagnosis and treatment of the most common types of bacterial
   meningitis
   Listeriosis
   Tetanus
   Botulism
       Botulinal types
       Incidence and treatment of botulism
   Leprosy
- Viral diseases of the nervous system
   Poliomyelitis
   Rabies
       Rabies treatment
   Arboviral encephalitis
- Fungal diseases of the nervous system
   Cryptococcus neoformans meningitis (cryptococcosis)
- Protozoan diseases of the nervous system
   African trypanosomiasis
   Naegleria meningoencephalitis
- Nervous system diseases caused by prions
- Lab: Detection of Mad Cow Disease (Edvotek #117)
Chapter 23 – Microbial Diseases of the Cardiovascular and
Lymphatic Systems
Structure and function of the cardiovascular and lymphatic system
- Bacterial diseases of the cardiovascular and lymphatic systems
   Puerperal sepsis
   Bacterial infections of the heart
   Rheumatic fever
   Tularemia
   Brucellosis (undulant fever)
   Anthrax
   Gangrene
   Systemic diseases caused by bites and scratches
       Cat-scratch disease
   Vector-transmitted diseases
       Plague
       Relapsing
       Lyme disease (lyme borreliosis)
       Other tick borne diseases
       Epidemic typhus
       Endemic murine typhus
       Spotted fevers
- Lab: Microbiological Analysis of Blood Specimens (Cappuccino +
                                                                    24
Sherman)
- Viral diseases of the cardiovascular and lymphatic systems
   Burkitt’s lymphoma
   Infectious mononucleosis
   Classic viral hemorrhagic fevers
Emerging viral hemorrhagic fevers
- Protozoan diseases of the cardiovascular and lymphatic systems
   American trypanosomiasis (Chaga’s disease)
   Toxoplasmosis
   Malaria
   Leishmaniasis
       Leishmania donovani infection
       Leishmania tropica infection
       Leishmania braziliensis infection
   Babesiosis
- Helminthic diseases of the cardiovascular and lymphatic systems
   Schistosomiasis
    Swimmer’s itch
Chapter 24 – Microbial Diseases of the Respiratory System
Structure and function of the respiratory system
Normal microbiota of the respiratory system
Microbial diseases of the upper respiratory system
- Bacterial diseases of the upper respiratory system
   Streptococcal pharyngitis (strep throat)
   Scarlet fever
    Diphtheria
   Otitis media
- Lab: Normal Microbial Flora of the Throat and Skin (Cappuccino +
Sherman)
- Lab: Identification of Human Streptococcal Pathogens (Cappuccino +
Sherman)
- Viral disease of the upper respiratory system
   The common cold
- Bacterial diseases of the lower respiratory system
   Pertusis (whooping cough)
   Tuberculosis
       Pathogenesis of tuberculosis
       Diagnosis and treatment of tuberculosis
   Bacterial pneumonia
       Pneumococcal pneumonia
       Haemophilus influenzae pneumonia
       Mycoplasmal pneumonia
       Legionellosis
       Psittacosis (ornithosis)
       Chlamydial pneumonia
       Q fever
       Other bacterial pneumonias
- Lab: Identification of Streptococcus pneumoniae (Cappuccino +
Sherman)
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- Viral diseases of the lower respiratory system
   Viral pneumonia
       Respiratory syncytial virus (RSV)
   Influenza flu
       The influenza virus
       Epidemiology of influenza
- Fungal diseases of the lower respiratory system
   Histoplasmosis
   Coccidiomycosis
   Pneumocystis pneumonia
   Blastomycosis (North African blastomycosis)
   Other fungi involved in respiratory disease
Chapter 25 – Microbial Diseases of the Digestive System
Structure and function of the digestive system
Normal microbiota of the digestive system
- Bacterial diseases of the mouth
   Dental caries (tooth decay)
   Periodontal disease
       Gingivitis
       Periodonitis
- Lab: Microbial Flora of the Mouth: Determination of Susceptibility to
Dental Caries (Cappuccino + Sherman)
- Bacterial diseases of the lower digestive system
   Staphylococcal food poisoning (staphylococcal enterotoxicosis)
   Shigelosis (bacillary dysentery)
   Salmonellosis (salmonella gastroenteritis)
   Typhoid fever
   Cholera
   Vibrio gastroenteritis
   Escherichia coli gastroenteritis
   Campylobacter gastroenteritis
   Helicobacter peptic ulcer disease
   Yersinia gastroenteritis
   Clostridium perfringens gastroenteritis
   Bacillus cereus gastroenteritis
- Lab: Identification of Enteric Microorganisms Using Computer-
Assisted Multitest Microsystems (Cappuccino + Sherman)
- Lab: Isolation and Presumptive Identification of Campylobacter
(Cappuccino + Sherman)
- Viral diseases of the digestive system
   Mumps
   Cytomegalovirus (CMV) inclusion disease
   Hepatitis
       Hepatitis A
       Hepatitis B
       Hepatitis C
       Hepatitis D (delta hepatitis)
       Hepatitis E
       Other types of hepatitis
                                                                          26
   Viral gastroenteritis
- Fungal diseases
   Ergot poisoning
    Aflatoxin poisoning
- Protozoan diseases of the digestive system
   Giardiasis
   Cryptosporidiosis
   Cyclospora diarrheal infection
   Amoebic dysentery
- Helminthic diseases of the digestive system
   Tapeworms
   Hydatid disease
    Nematodes
       Pinworms
       Hookworms
       Ascariasis
       Trichinosis
Chapter 26 – Microbial Diseases of the Urinary and Reproductive
Systems
Structure and function of the urinary system
Structure and function of the nervous system
Normal microbiota of the urinary and reproductive systems
Diseases of the urinary system,
- Bacterial diseases of the urinary system
   Cystitis
   Pyelonephritis
   Leptospirosis
- Lab: Microbiological Analysis of Urine Specimens (Cappuccino +
Sherman)
Diseases of the reproductive system
- Bacterial diseases of the reproductive system
   Gonorrhea
   Nongonococcal urethritis (NGU)
   Pelvic inflammatory disease (PID)
   Syphilis
   Lymphogranuloma venereum (LGV)
   Chancroid (soft chancre)
   Bacterial vaginitis
- Viral diseases of the reproductive system
   Genital herpes
   Genital warts
   AIDS
- Fungal disease of the reproductive system
   Candidiasis
- Protozoan disease of the reproductive system
   Trichomoniasis
- Lab: Sexually Transmitted Diseases: Rapid Immunodiagnostic
Procedures (Cappuccino + Sherman)
- Lab: Species Identification of Unknown Bacterial Cultures
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(Cappuccino + Sherman)
Chapter 27 – Environmental Microbiology
Metabolic Diversity
- Habitat variety
- Symbiosis
Soil microbiology and biogeochemical cycles
- The carbon cycle
- The nitrogen cycle
   Ammonification
   Nitrification
   Denitrification
   Nitrogen fixation
- Lab: Nitrogen Cycle (Cappuccino + Sherman)
- The sulfur cycle
   Acid decomposition
- Life without sunshine
- The phosphorous cycle
- Lab: Microbial Populations in Soil: Enumeration (Cappuccino +
Sherman)
- Lab: Isolation of Antibiotic-Producing Microorganisms and
Determination of Antimicrobial Spectrum of Isolates (Cappuccino +
Sherman)
- Lab: Isolation of Pseudomonas Species by Means of the Enrichment
Culture Technique (Cappuccino + Sherman)
- The degradation of synthetic chemicals in soil and water
   Bioremediation
   Solid municipal waste
Aquatic microbiology and sewage treatment
- Biofilms
- Aquatic microorganisms
   Freshwater microbiota
   Seawater microbiota
- The role of microorganisms in water quality
   Water pollution
   Water purity tests
- Lab: How Clean is the Water We Drink + Air We Breath? (Edvotek
#S-30)
- Lab: Standard Qualitative Analysis of Water (Cappuccino + Sherman)
- Lab: Quantitative Analysis of Water: Membrane Filter Method
(Cappuccino + Sherman)
- Water treatment
- Sewage (wastewater) treatment
   Primary sewage treatment
   Biochemical oxygen demand (BOD)
   Secondary sewage treatment
   Disinfection and release
   Sludge digestion
   Septic tanks
   Oxidation ponds
                                                                       28
    Tertiary sewage treatment
Chapter 28 – Applied and Industrial Microbiology
Food microbiology
- Industrial food canning
    Spoilage of canned food
- Aseptic packaging
- Radiation and industrial food preservation
- The role of microorganisms in food production
    Cheese
    Other dairy products
    Nondairy fermentations
    Alcoholic beverages and vinegar
- Lab: Do Microbes Help Make or Spoil our Food? (Edvotek #S-31)
- Lab: Methylene Blue Reductase Test (Cappuccino + Sherman)
- Lab: Microbiological Analysis of Food Products: Bacterial Count
(Cappuccino + Sherman)
- Lab: Sauerkraut Production (Cappuccino + Sherman)
Industrial microbiology
- Fermentation technology
    Immobilized enzymes and microorganisms
- Industrial products
    Amino acids
    Citric acid
    Enzymes
    Vitamins
    Pharmaceuticals
    Copper extraction by leaching
    Microorganisms and industrial products
- Good manufacturing practices
Alternative energy sources using microorganisms
Industrial microbiology and the future
Conclusion to Biotechnology
*Student Projects: Research papers, presentations and debates
related to social. legal and ethical issues related to biotechnology.
Using Biotechnology: Social and Environmental Impacts
Biotechnology as innovation
- Types of innovations
- Sources of innovation
Considering technology
- Decision-making
- What to consider
    Agriculture and horticulture producers
    Food products
    Health care
Social impact
- Selectivity
- Quality of life
The environment
- Sustaining the environment
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- Biotechnology and the environment
    Negative impacts
       Herbicide resistance
       Insect resistance
    Positive impacts
       Reduce pesticide use
      Waste disposal
       Human activity
Issues and Ethics
Issues and biotechnology
- Identifying an issue
- Action plans
Ethics and biotechnology
- Ethics in science
    Bioethics and the legal system
- Religion and biotechnology
- Ethics and the future of biotechnology
Specific ethical issues
- The Human Genome Project
    The Ethical, Legal and Social Implications Program (ELSI)
- Cloning
- Genetic engineering
Regulations in Biotechnology
Nature and purposes of regulations
- Nature of regulation
- Purpose of regulations
Agencies and responsibilities
- Who makes regulations
- Responsible agencies
    United States Department of Agriculture (USDA)
    United States Environmental Protection Agency (EPA)
    U.S. Food and Drug Administration (FDA)
- Getting a new product approved
- The federal register
Organizations
- The Biotechnology Industry Organization (BIO)
- The Council of Biotechnology Centers (CBC)
Ethics and regulations
- International perspective
 - Free enterprise
- Confidentiality




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