Instructor: Stjepko Golubic,
Tel. 3-2436,
Prerequisite: Core biology courses, chemistry, cell biology, consent.
Objectives: The course promotes an understanding of microbial structures, functions and diversity. It reviews the basic biological principles as applied to microorganisms, and emphasizes the phylogenetic and metabolic diversity among them. The course exploits new advances in molecular research in dealing with microbial diversity, ecology and niche differentiation. It stresses microbial roles in biogeochemical cycling of elements in nature, and global importance of microorganisms. It deals with interactions among viruses, bacteria and macroorganisms and promotes a balanced view of beneficial vs. harmful effects of microorganisms on environmental and human health and society. The first part of the course introduces the subject and reviews basic structural and functional properties of microorganisms, microbiological methods of study and viruses. The second part deals with genetic basis, evolutionary history, and phylogenetic and metabolic diversity of microorganisms. The last part deals with the interrelations between microorganisms and humans as their hosts. Laboratory sessions are run independently. They provide hand-on experience in growing and observing microorganisms.
Evaluation: Best 3 of 4 exams (3+final): 75%; no makeups; Lab: 25% - must be passed to pass the course.
Textbook: Madigan, M.T, Martinko, J.M., Stahl, D.A. & Clark, D.P., 2012. Brock Biology of Microorganisms, 13th edition, Benjamin Cummings, Pearson 1043pp.+ Appendices. Older issues have different chapter schedule, but 11th and 12th Edition are accepted.
January
1.
17-19. Introduction to Microbiology
Microbiology as basic and applied science - The importance of
the microbial world - Microorganisms as cells and organisms - Microorganisms in
their environment - Microbiology in historic perspective - Prokaryotic and
eukaryotic cellular organization - Diversity of microorganisms - Microorganisms
seen at the level of macromolecules. Chapters 1 – 3.
2. 24-26. Microbial
Cells and their Interaction with the Environment
Microscopy - transmitted light, dark field, phase contrast
and fluorescence microscopy. - Differential (Nomarski)
interference contrast, atomic force and confocal scanning laser light
microscopy - Scanning and transmission electron microscopy – Structure and
functions of the plasma membrane - Cell wall: gram-positive, gram-negative
bacteria, archaea - Microbial locomotion: Bacteria Flagellar motion and gliding movement - Behavioral
responses: taxes - Cellular inclusions - Endospores - Eukaryotic organelles.
February
3. 31-02. Microbial
Nutrition and Energy Generation
Nutrition and culturing - Culture media - Aseptic procedures
- Energy generation and biocatalysis - Enzyme
structure and function - Oxidation-Reduction - NAD as redox carrier -
Phosphorylation - Electron carriers and electron transport systems - Proton
motive force: chemiosmosis - Carbon flow - Energy yielding metabolic systems -
Biosynthesis. Ch. 5.
4. 07-09. Microbial
Growth and Control
Cell growth and binary fission - Peptidoglycan biosynthesis
in cell division. - Growth of microbial populations - Growth cycle - Growth
measurements: direct and indirect - Batch and continuous cultures - Factors
influencing microbial growth - Heat: cardinal points, thermophily,
psychrophyly - Osmotic effects - Oxygen. - Microbial
growth control: heat, radiation and filter sterilization - Disinfectants -
Antiseptics - Antibiotics and sulfa drugs - Antibiotic resistance - Fungal and
viral control. Ch. 6, 20.
5. 14-16. Viruses
Properties and types - The virion -
The virus host - Virus replication - DNA and RNA, Double and single stranded,
Positive and negative strand viruses - Viral proteins - Viral diversity -
Virulent bacteriophages - Lysogenic and temperate bacteriophages - Animal
viruses - Plant viruses - Viruses and cancer - Retroviruses - Vectors - Viroids and prions. Ch. 9, 16.
-----------------------EXAM-1: Feb. 23
March
6. 28-01. Elements of
Bacterial Genetics and Engineering
Replication, Transcription, Translaton
(Review) - Gene expression - Mutation and recombination - Types of mutation -
Mutagenesis - Genetic recombination - Genetic techniques in vivo: Transformation
- Transduction - Plasmids - Genetic elements - Conjugation - Complementation -
Transposition. - Genetic techniques in vitro: Restriction enzymes - DNA
sequencing - DNA synthesizing - Molecular cloning - Cloning vectors -
Polymerase Chain Reaction (PCR) - The bacterial chromosome. - Principles of
genetic engineering - Expression of foreign genes - Practical applications.
7. 06-08. Microbial
evolution, Phylogeny and Classification
Early life on Earth - RNA-life - Primitive metabolism -
Cyanobacteria: Impact of oxygenic photosynthesis - Microbial fossil record -
Origins of eukaryotic cellular organization - Evolutionary chronometer
molecules - Ribosomal RNA sequences and cellular evolution - The tree of life -
Phylogenetic probes - Characteristics of the primary Domains and prokaryotic
Kingdoms - Conventional and molecular taxonomy - Bacterial species concept.
------------------ SPRING
RECESS: March 10-18.
8. 20-22. Microbial
Ecology and Metabolic Diversity
Microbial communities - Aquatic habitats, BOD - Terrestrial
environments - Extreme environments - Deep sea hydrothermal vents and seeps -
Biodegradation - Microbial integration with plants and animals. - Global
cycling of elements. - Genetic stains, group specific probes, PCR, DGGE, FISH.
- Microelectrode measure of microbial activity - Stable isotopes. Phototrophic
way of life: Anoxygenic and oxygenic phototrophy - Autotrophic C-fixation - Chemotrophic way
of life: organotrophs vs. lithotrophs - H-, S- and Fe2+-oxidation,
Nitrification & methane oxidation - Anaerobic way of life: Aerobic
vs. anaerobic respiration - Sulfate-reduction - Acetogenesis
- Methanogenesis - Fermentations - N-fixation. - Ch.
17 – 19.
9. 27-29. Microbial
Diversity
Phylogeny of Bacteria: 1 Proteobacteria,
2. Gram-Positives, 3. Cyanobacteria, 4.
Chlamydia, 5. Planctomyces, 6. Verrucomicrobia, 7. Flavobacteria,
8. Cytophaga, 9. Green Sulfur Bacteria,
10.Spirochetes, 11. Deinococci, 12.
Green Non-Sulfur Bacteria, 13. Thermotoga, Thermodesulfobacterium, 14. Aquifex.
Phylogeny of Archaea: 1. Euryarchaeota:
Halophiles, Methanogens, Thermoplasmas, Hyperthermophiles, 2. Crenarchaeota:
Sulfolobales, Thermoproteales,
Desulfurococcales,Hyperthermophiles, 3. Korarchaeota. Phylogeny of Eucaryotes:
Protozoa, Fungi, Slime Molds, Algae.
April
10. 03. Human Host -
Parasite Interactions
Humans as microbial hosts - Microflora
of a healthy body - Pathogen exposure, adherence, invasion and growth - Tissue
specificity - Virulence: Exotoxins incl. Enterotoxins - Endotoxins -
Nonspecific defense responses - Age, stress and diet Compromised host - Inflamation and fever.
-----------------------
EXAM-2: Apr. 05
11. 10-12. Immune
Response
Cells and organs of the Immune system - Nonspecific immunity:
Phagocytosis. The immune system and specific immunity - Antigens and antibodies
- Antigen presentation system - Lymphocytes and cell mediated immunity -
T-cytotoxic and natural killer cells - T-helper cells - macrophage activation -
B-cell activation. Antibodies and immunity - Immunoglobulin formation -
Complement system - Immunization - Vaccination. - Autoimmunity -
Molecular immunology. Ch. 22, 23.
12. 17-19. Clinical
Diagnostics
Pathogen isolation and identification - Growth-dependent
identification - Antibiogram - Immunodiagnostics -
Polyclonal and monoclonal antibodies - Serology - Fluorescent antibodies -
ELISA - Radioimmunoassay - Immunoblot - DNA and RNA
probes - Diagnostic virology. Ch. 23, 24.
13. 24-26. Microbial
Diseases
Epidemiologic approaches to public health - Mortality and
morbidity - The course of a disease - Reservoirs and epidemics - Infectious
disease transmission - Herd immunity - Epidemiology of AIDS - Nosocomial infections
- Epidemiology and public health - Common diseases and their transmission.
May
14. 1-3.
Industrial Microbiology
Microbial
products and food industry - Biotechnology and genetic engineering -Wastewater
treatment, Water Purification.
----------------------- EXAM-3: May, 01
FINAL EXAM TBA
The background color approximates
that of purple sulfur bacteria
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Updated 01/13/2012