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Transcript
BIO 338 MICROBIOLOGY
Spring Term.
Instructor: Walter J. Bruyninckx
Office:
Phone:
Science Center, Room 217
- office: 866-7242
- home: 866-4522
Office Hours: MTWRF ... 8:00 - 5:00 pm
You can talk to me whenever you meet me, or find me in my office. Alternatively, set
up an appointment.
Textbook: Madigan Michael T., Martinko John M., Dunlap Paul V., and Clark David C. (2009,
2012, or 2014) Brock biology of microorganisms. 12th or 13th or 14th edition. Prentice Hall. Upper
Saddle River, NJ.
Goal.
The microbiology course will help you to (1) acquire basic knowledge and understanding of
prokaryotes (Bacteria and Archaea), and (2) give you a sense of their metabolic and ecological
diversity. In addition, the course will introduce you to (3) microbial pathogenesis, the central topic
of medical microbiology, and (4) teach you the fundamentals of and skills to identify and
differentiate bacteria of medical importance. Finally, the course seeks (5) to introduce you to
primary microbiological literature.
This knowledge base should be sufficient for you to read and understand articles such as published
in Infection and Immunity, Microbial Pathogenesis, Applied and Environmental Microbiology,
Journal of Bacteriology, Microbiology, Journal of Systematic Bacteriology, and Microbiological
Reviews. Specifically, you will be able to:
(1) use an article's introduction to relate the published work to one or more lecture topics of
microbiology,
(2) identify the main results/conclusions of an article,
(3) explain how the conclusions/results confirm, extent or contradict the information presented in
lecture or textbook,
(4) understand the principles of the methods encountered in class or laboratory,
(5) be able to verbally describe the results presented in an article's tables and figures,
(6) draw conclusions from a set of tables, figures and verbal descriptions of results.
(7) Although you are not held responsible for the technical aspects of the papers' discussions, you
will be able to paraphrase meaningfully the implications of the published findings as set out by the
authors.
(Although the course will provide you with an introduction to the pathogenesis of bacterial
diseases, this area of the life sciences evolves rapidly. Thus, this course is but meaningful if it will
foster a life-long interest in and study of (medical) microbiology. To accomplish this you need to
acquire the skills to consult, read, and study the primary literature. This cannot be viewed a
separate goal of the course but is the logical consequence of the fulfillment of its primary task, the
study of microbiology.)
Activities.
To accomplish the goals of this course, you should be prepared for MICROBIOLOGY to occupy a
considerable amount of your time, activities, and thoughts. YOU SHOULD BE PREPARED TO
PARTICIPATE IN ALL LECTURES AND LABS; EXCEPT FOR MEDICAL EMERGENCIES
OF YOURSELF OR OF DIRECT FAMILY MEMBERS THERE ARE NO EXCUSABLE
ABSENCES FROM COURSE ACTIVITIES. The following activities are organized:
1. Lectures. Lectures are primarily designed to help you acquire the major microbiological concepts
(i.e., mental pictures). You should stop a lecture until all of us clearly understand how a specific
lecture topic relates to the course as a whole. This may mean that we run out of time to cover all
of the lecture material. You may be expected to make up this time on your own (= self study).
Alternatively, some of the lab time may be used for this, or we use our microbiology evenings.
Your schedule, social agenda, and priorities at Hanover College should be sufficiently flexible to
permit this! Lectures are not intended to and cannot be the sole or principal source of your
(factual) information. Your chief sources of information are your textbook and hand-out notes,
and other microbiology articles. NOTE: You should do every effort to use class/lecture time as a
time of study and learning. As such, it should be possible for you to take an exam immediately
after lecture!
2. Laboratory. The microbiology laboratory is an important part of the course. Foremost, it aims to
introduce you to the basic skills and techniques used to identify bacteria of medical importance.
Simultaneously, it allows you to 'get to know' bacteria, appreciate their morphological and
metabolic differences, and provide real images to the plethora of disease-causing agents. Finally,
some quantitative tests will be introduced.
3. Reading assignments. 4 recent papers will be discussed on Friday afternoon.
4. Participation. It is expected that you have a genuine interest and passion for Microbiology
and that you show that interest by your ACTIVE participation in the course. You
demonstrate this by being ready for class at 8:00 AM (NOT: walking and starting your
breakfast at 8:00 AM), asking serious questions, and, at least, volunteering answers when
questions are being asked.
5. EXAMS. There will be four exams (Friday morning) and one lab exam (multiple choice) in this
course. The Friday morning exams will be focused on the materials covered that week.
LAB SCHEDULE.
WEEK
SUBJECT.
______________________________________________________________________
week 1
Introduction to basic media, microscope
Inoculation techniques
Differentiation of gram-positives
(KOH reaction, Gram-stain, Acid fast stain, TSI slant,
urease slant, motility deep, catalase test, coagulase
test, hyaluronidase test)
Enumeration bacteria: filter method drinking water
week 2
Differentiation of non-enteric gram-negatives.
(MacConkey plates, O/F medium, oxidase-, indole test)
Enumeration of total and coliform bacteria in surface water:
ready gel (total count, coliscan), dilution tubes.
Petrifilm, swabbing, and handwashing and dilutions.
week 3
Differentiation of enterobacteria.
(carbohydrate fermentation, API-20E strips,
anti-salmonella tests, HektoenEnteric plates)
Petrifilm, swabbing, and handwashing and dilutions.
week 4
Identification of unknown bacteria.
Antibiotic sensitivity test
Anaerobic jars
SlimPlate total count
Antibiotic sensitivity test.
________________________________________________________________________
MICROBIOLOGY: LECTURE OVERVIEW (12th Edition)
LESSON 1: Structure of prokaryotic cell.
- overview, shape, size
- cytoplasmic membrane: composition (Function: see BIO 120)
- Cell wall of bacteria: peptidoglycan, protoplast, lysozyme, penicillin
- Cell wall of gram-positive bacteria: teichoic acid.
- Cell wall of gram-negative bacteria: LPS, periplasmic space
- Cell wall of bacteria: Gram-stain and KOH-reaction
- Flagella and motility
- Pili, fimbriae, and attachment
- Glycocalyx, capsule, slime layer, paracrystalline surface layer (S-layer)
- Cytoplasmic inclusions: storage polymers and gasvesicles.
- Endospores
LESSON 2: Microbial growth.
- Microbial nutrition and culture media
- Population growth, generation time, and growth cycle.
- Measurement of population growth
- Continuous cultures
- Effect of environmental factors on growth: temperature, pH, water, Oxygen
- Microbial growth control: heat, radiation, filter, chemical
(p22-34, 63-66)
(p66-69).
(p74-81)
(p74-81)
(p74-81)
(p58-59.)
(p92-97)
(p82-83)
(p82-83)
(p83-87)
(p87-91)
(p102-108)
(p136-142)
(p142-144)
(p144-148)
(p148-151).
(p151-165)
(p670-681)
LESSON 3: Overview of energy metabolism, Gram-positive bacteria of medical importance.
- Energy metabolism: overview (see: BIO120),
(p112-119)
- Energy metabolism of chemoorganotrophs
(p119-134)
- glycolysis: Embden-Meyerhof, Entner-Douderoff, and
(p119-134, p345)
phosphoketolase pathway
(p376-377)
- Citric acid cycle and Hexose Monophosphate Shunt.
(p127-129)
- Fermentation: homolactic vs. heterolactic fermentation
(p376-377).
- Gram-positive bactera (Chapter 12)
(p374-394)
LESSON 4: Bacterial attachment and competiton for iron.
LESSON 5: Photosynthesis and phototrophs.
- Photosynthesis: anoxygenix and oxygenix photosynthesis
- Carbon dioxide fixation: Calvin cycle.
- Purple phototrophic bacteria
- Green sulfur bacteria
- Green nonsulfur bacteria
- Cyanobacteria and Prochlorophytes
(p533-544)
(p545-548)
(p332-335)
(p405-407)
(p412-414)
(p394-399)
LESSON 6: Chemolithotrophs.
- Chemolithotrophy: hydrogen, sulfur, iron, and ammonium oxidation
- Nitrifying bacteria
- Sulfur and iron-oxidizing bacteria
- Hydrogen-oxidizing bacteria
(p548-557)
(p335-337)
(p337-340)
(p340-342)
LESSON 7: Industrial and food, microbiology.
- Large-scale fermentation
- Production of antibiotics, vitamins, steroids and enzymes
- Production of organic acids
- Alcohol and alcoholic beverages
- Fermentation: dairy, bread, meat, vegetables and silage.
- Food preservation and foodborne microbiological diseases
- Sewage and wastewater microbiology
(p942-947)
(p947-958)
(p964-965)
(p958-964)
(p965-996)
(p923-939)
(p906-921)
LESSON 8: Concepts of Immunology.
- Nonspecific immunity: complement
- Nonspecific immunity: phagocytosis
- T-lymphocytes, TCR, MHC molecules, antigen presentation
- B-lymphocytes, antibodies, humoral immunity
(p750-751)
(p732-735, 767)
(p739-743, 765)
(p743-749, 767)
LESSON 9: Anaerobic respiration and fermentation.
- Anaerobic respiration: nitrate reduction and sulfur reduction
- Ferric iron, manganese, chlorate, and organic e-acceptors
- Fermentations
- Methanotrophs, methylotrophs
- sulfate-reducing
- homoacetogenic bacteria (p563-564) and Acetic acid bacteria
(p557-564)
(p568-570)
(p571-577)
(p579-581, 342-344)
(p371-373)
(p348, 963-964)
LESSON 10: Plant-microbial interactions and Bioremediation.
- Nitrogen fixation
- Lichens and mycorrhizae
- Crown gall and Hairy Root
- Root nodule bacteria and symbiosis with legumes
- Free-living, aerobic nitrogen-fixing bacteria
- Bioremediation: hydrocarbon transformations
- Bioremediation: petroleum biodegradations
- Bioremediation: biodegradation of xenobiotics
(p586-591)
(p656-658)
(p659-660)
(p661-666)
(p348-350)
(p577-579, 584-586)
(p651-653)
(p653-655)
LESSON 11: Gram-negative bacteria of medical importance.
- Budding and appendaged bacteris
- Gliding and Sheathed bacteria
- helical bacteria: Spirilla and Spirochetes
- Pseudomonads, Zymomonas and Chromobacterium
- Vibrio and related genera
- Facultative aerobic gram-negative Rods
(p363-367)
(p362-363, 367-371)
(p355-361, 407-411)
(p345-348)
(p355-356)
(p351-355)
- Neisseria and other gram-negative cocci
(p350-351)
LESSON 12: Bacterial Infection: bacterial toxins.
- Extracellularly-acting toxins: enzymes.
- Membrane-acting toxins: porins and hemolysins.
- Intracellularly-acting enzymes: ADP-ribosylating enzymes.
- Intracellularly-acting enzymes: neurotoxins.
- Systemically-acting toxins: Endotoxin and Superantigens.
(p716-721)
LESSON 13: Antibiotic sensitivity
- Antimetabolites: folic acid antagonists.
- Interference with peptidoglycan synthesis: penicillins, cephalosporins
- Interference with DNA replication:
- Interference with transcription:
- Interference with protein synthesis:
- Other antimicrobials.
(p681-692)
LESSON 14: Microbial ecology.
- Microbial ecosystems
- Aquatic, terrestrial, deep-sea and hydrothermal vent habitats
- Carbon cycle
- Biogeochemical cycles: nitrogen, sulfur, iron
- Microbial leaching
- Mercury and Heavy metal transformations
LESSON 15: The Archaea.
- Phylogeny and general metabolism
- Extreme halophiles
- Methanogens
- Extreme thermophiles: Euryarchaeota and Crenarchaeota
LESSON 16: Bacterial infection: intracellular parasites.
- Listeria, Yersinia, Legionella, Brucella, Mycobacterium.
- Rickettsia
- Chlamydia
(p593-617)
(p619-630)
(p632-640)
(p640-646)
(p647-649)
(p649-651)
(p420-422)
(p422-426)
(p426-430, 564-568)
(p430-446)
(p388-390)
(p357-359)
(p399-401)