Biotechnology Course Outline - Londonderry School District

concernedimpartialBiotechnology

Dec 3, 2012 (4 years and 9 months ago)

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1

Biotechnology Course Outline

Ms. Lawson

2012
-
2013


**
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
h
andled 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 th
e 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 M
icrobiology



Defining Biotechnology



-

Ancient biotechnology




Domestication




Food



-

Classical biotechnology




Fermentation control



-

Antibiotics



-

Modern biotechnology



Safety



-

Safety contract




Heat and fire sa
fety




Chemical safety




Laboratory equipment safety




Specimen safety




Electrical equipment safety




Field study/trip safety




Reporting accidents



-

Safety violation cards



-

Laboratory waste disposal



-

Workin
g 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 Opera
ting Procedures (SOPs)



Measurements, Micropipetting and Sterile Techniques



-

Metric measurement



-

Scientific method



-

Digital micropipettors




2

-

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 You
r Disinfectant? (Smith)



-

Worker protection



-

Environment protection



-

Experiment or product protection



-

Creating aseptic environments




Washing surfaces




Autoclave instruments




Laminar flow hoods




Flaming



***
Clas
sroom decontamination to occur frequently throughout the
year

to minimize equipment contamination of microbes and DNA




3

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 spon
taneous 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 we
lfare



-

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 phyloge
nic hierarchy



Classification of organisms



-

Scientific nomenclature



-

The taxonomic hierarchy



-

Classification of prokaryotes




4

-

Classification of eukaryotes



-

Classification of viruses



Methods of classifying and identifying microorgani
sms



-

Morphological characteristics



-

Differential staining



-

Biochemical tests



-

Serology



-

Phage typing



-

Fatty acid profiles



-

Flow cytometry



-

DNA base composition



-

DNA fingerprinting



-

Ribosomal RNA sequencing



-

The p
olymerase 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 pho
tosynthetic bacteria



-

The


(delta) proteobacteria




Desulfovibrionales




Myxococcales



-

The


(epsilon) proteobacteria



The nonproteobacteria gram
-
negative bacteria



-

Cyanobacteria



-

Chylamydiales




Spirochetes



-

Bacter
oides



-

Fusobacteria



-

Sphingobacteria



The gram
-
positive bacteria



-

Low G + C gram
-
positive bacteria




Mycoplasmatales




Clostridiales




Lactobacillales



-

High G + C gram
-
positive bacteria




5


Actinomycetes



Domain A
rchaea



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 Te
chniques (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



F
ungi



-

Characteristics of fungi




Vegetative structures




Life cycle




Nutritional adaptations



-

Medically important phyla of fungi




Zygomycota




Ascomycota




Basidiomycota



-

Fungal diseases



-

Economic effec
ts 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




Ve
getative 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




Archaez
oa




Microsporidia




Rhizopoda




Apicomplexan




Ciliophora




Euglenozoa



-

Lab: Free
-
Living Protozoa (Cappuccino + Sherman)



-

Lab: Parasitic Protozoa (Cappuccino + Sherman)




6

Slime molds



Helminthes



-

Characteristic
s 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


Obs
erving Microorganisms Through a Microscope



Units of measurement



Microscopy: the instruments



-

Light microscope




Compound light microscope




Resolution




Dark field microscopy




Phase
-
contrast microscopy




Differentia
l inference contrast (DIC) microscopy




Fluorescence microscopy




Confocal microscopy



-

Lab: Microscopic Examination of Stained Cell Preparations
(Cappuccino + Sherman)



-

Lab: Microscopic Examination of Living Bacterial Preparations
(Capp
uccino + 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 arrangeme
nt 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 wa
lls 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




7


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




Polysac
charide granules




Lipid inclusions




Sulfur granules




Carboxysomes




Gas vacuoles




Magnetosomes



-

Endospores



-

Lab: Bacterial Staining (Cappuccino + Sherman)



-

Lab: Preparation of Bacterial Smears (Cappuccino + She
rman)



-

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




Endoplasmi
c reticulum




Ribosomes




Golgi complex




Lysosomes




Vacuoles




Mitochondria




Chloroplasts




Peroxisomes




Centrosomes



The evolution of eukaryotes



Chapter 5


Microbial Metabolism



Catabolic and ana
bolic reactions



Enzymes



-

Naming enzymes



-

Enzyme components



-

The mechanism of enzyme action



-

Factors influencing enzymatic activity




8


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 phosphorylati
on




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




A
lcohol fermentation



-

Lab: Carbohydrate Metabolism (Cappuccino + Sherman)



Lipid and protein catabolism



Biochemical tests and bacterial identification



Photosynthesis



-

The light reactions: photophosphorylation



-

The dark reactions: the Cal
vin
-
Benson cycle



A summary of energy production mechanisms



Metabolic diversity among organisms



-

Photoautotrophs



-

Photoheterotrophs



-

Chemoautotrophs



-

Chemoheterotrophs



Metabolic pathways of energy use



-

Polysaccharide biosynthesi
s



-

Lipid biosynthesis



-

Amino acid and protein biosynthesis



-

Purine and pyrimidine biosynthesis




9

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 phosp
horous



-

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 +
Sher
man)



-

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 Ami
no 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 Gro
wth Curve (Cappuccino + Sherman)



-

Direct measurement of microbial growth




10


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 p
roteins 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



-

Principl
es 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




11


Antibiotics




Aldehydes




Gaseous chemosterilizers




Peroxygens (oxidizing agents)




12

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 t
he 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 ex
periment




Bacteriophage lambda: the lysogenic cycle



-

Multiplication of animal viruses




Attachment




Penetration




Uncoating




The biosynthesis of DNA viruses




The biosynthesis of RNA viruses



-

Latent viral infe
ctions



-

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


Microb
ial 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 g
eneration to the next



-

Where are genes located



-

The link between evolution and genetics



-

Genes as physical entities




13

-

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




Tran
scription




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 regulat
ion 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 stabilit
y 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




14

-

Identifying mutants



-

Identifying chemical carcinogens



Microbial genetic transfer and recombination



-

Transformation in bacteria



-

Conjugation in bacteria



-

Transduction in bacteria



-

Plasmids and transposo
ns




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 electro
phoresis




Horizontal gel electrophoresis




Vertical gel electrophoresis



-

Lab: Principles of Gel Filtration Chromatography (Edvotek #108)



-

Lab: Principles + Practices 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



-

Isola
tion 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




15


Chicken




Mouse




Human cell culture




Plants



-

Lab: Isolation of Chloroplasts, Mitochondria and Extraction of Plant
Genomic DNA (Edvotek #910)



Methods for finding and ex
pressing 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 co
li

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 antibo
dies and marker proteins




Uses for antibodies




Methods for studying proteins




16


Western blot




Immunocytochemistry




Green fluorescent protein (GFP)



-

Lab: Transformation with Green Fluorescent Protein (Edvot
ek #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




Anneal
ing




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)



-

Hi
erarchical 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 sc
ience of cancer



-

Defining cancer




Lung cancer




Liver cancer




Stomach cancer




Cervical cancer




Skin cancer




Breast cancer



-

Tumor viruses as cancer models




Flattened morphology




Anchorage
-
depend
ent growth




Growth in confluent monolayer




Contact inhibition




17

-

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



-

Si
gnal 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 c
onstruction 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 mam
malian


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: PCR
-
Based Identification of Genetically Modified Foods and
Plants (Edvotek #962)



-

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




Si
ngle
-
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




18


Climate changes and popu
lation 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 microorg
anisms



-

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 incubati
on 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




Nonliv
ing reservoirs



-

The transmission of disease




Contact transmission




Vehicle transmission




Vectors



-

Portals of exit



Nosocomial (Hospital
-
Acquired) Infections



-

Microorganisms in the hospital



-

The compromised host



-

T
he chain of transmission



-

The control of nosocomial infections



Emerging infectious diseases



Epidemiology



-

Descriptive epidemiology



-

Analytical epidemiology



-

Experimental epidemiology



-

Case reporting



-

The Centers for Disease C
ontrol 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 o
f invading microbes




19

-

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 dama
ge



-

The production of toxins




Exotoxins




Endotoxins



-

Plasmids, lysogeny and pathogenicity



Pathogenic properties of nonbacterial microorganisms



-

Viruses




Viral mechanisms for evading host defenses




Cytopathic effec
ts 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



-

Phagocyt
e 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
-
mediat
ed) immunity




20


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 antib
ody
-
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 Im
munology



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 Reactio
n: 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 + Sherma
n)



-

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 +



21

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




Lo
calized 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 tra
nsplants



-

Immunosuppression



Immune Deficiencies



-

Congenital immune deficiencies



-

Acquired immune deficiencies



The immune system and cancer



-

Immunotherapy



Acquired Immunodeficiency Syndrome (AIDS)



-

The origin of AIDS



-
HIV inf
ection




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: Simulat
ion of HIV Detection by Western Blot
(Edvotek #275)



-

HIV transmission



-

AIDS worldwide



-

The prevention and treatment of AIDS




HIV vaccines




22


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




Cephalosporin
s




Carbapenems




Bacitracin




Vanomycin




Isoniazid (INH)




Ethambutol



-

Inhibitors of protein synthesis




Aminoglycosides




Tetracycline




Chloramphenicol




Macrolides



-

Injury to the plasma mem
brane



-

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: Chemothera
peutic 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)




Azol
es




Griseofulvin




Other antifungal drugs



-

Antiviral Drugs




Nucleoside and nucleotide analogs




Other enzyme inhibitors




Interferons



-

Antiprotozoan and antihelminthic drugs




Antiprozoan drugs




Antihelm
inthic drugs



Tests to guide chemotherapy



-

The diffusion methods




23

-

Broth dilution tests



The effectiveness of chemotherapeutic agents



-

Antibiotic Safety



-

Lab: Assay for Antibiotic Resistance Enzyme (Carolina
Biotechnology)



-

Effects o
f 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 fun
ction 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 e
ye



-

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




24

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




Ne
isseria 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 o
f the nervous system




Cryptococcus neoformans meningitis (cryptococcosis)



-

Protozoan diseases of the nervous system




African trypanosomiasis




Naegleria meningoencephalitis



-

Nervous system diseases caused by prions



-

Lab: Det
ection 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
-
scr
atch disease




Vector
-
transmitted diseases




Plague




Relapsing




Lyme disease (lyme borreliosis)




Other tick borne diseases




Epidemic typhus




Endemic murine typhus




Spo
tted fevers



-

Lab: Microbiological Analysis of Blood Specimens (Cappuccino +



25

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 Dise
ases 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




Streptoc
occal 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 tr
eatment of tuberculosis




Bacterial pneumonia




Pneumococcal pneumonia




Haemophilus influenzae pneumonia




Mycoplasmal pneumonia




Legionellosis




Psittacosis (ornithosis)




Chlamydia
l pneumonia




Q fever




Other bacterial pneumonias



-

Lab: Identification of Streptococcus pneumoniae (Cappuccino +
Sherman)




26

-

Viral diseases of the lower respiratory system




Viral pneumonia




Respiratory syncyt
ial virus (RSV)




Influenza flu




The influenza virus




Epidemiology of influenza



-

Fungal diseases of the lower respiratory system




Histoplasmosis




Coccidiomycosis




Pneumocystis pneumonia




Blastom
ycosis (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



-

Bacteria
l 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)



-

B
acterial 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

gastro
enteritis



-

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 digesti
ve system




Mumps




Cytomegalovirus (CMV) inclusion disease




Hepatitis




Hepatitis A




Hepatitis B




Hepatitis C




Hepatitis D (delta hepatitis)




Hepatitis E




Other typ
es of hepatitis




27


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 Dis
eases 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 dis
eases 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 Imm
unodiagnostic
Procedures (Cappuccino + Sherman)



-

Lab: Species Identification of Unknown Bacterial Cultures



28

(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 decom
position



-

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 (C
appuccino +
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



Aquati
c 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 (wastewa
ter) treatment




Primary sewage treatment




Biochemical oxygen demand (BOD)




Secondary sewage treatment




Disinfection and release




Sludge digestion




Septic tanks




Oxidation ponds




29


Tertiary sewage treatm
ent



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 product
ion




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)



-

La
b: Microbiological Analysis of Food Products: Bacterial Count
(Cappuccino + Sherman)



-

Lab: Sauerkraut Production (Cappuccino + Sherman)



Industrial microbiology



-

Fermentation technology




Immobilized enzymes and microorganisms



-

Industri
al products




Amino acids




Citric acid




Enzymes




Vitamins




Pharmaceuticals




Copper extraction by leaching




Microorganisms and industrial products



-

Good manufacturing practices



Alternative energy sourc
es 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




30

-

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 Depa
rtment 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 Organiza
tion (BIO)



-

The Council of Biotechnology Centers (CBC)



Ethics and regulations



-

International perspective




-

Free enterprise



-

Confidentiality