Biology 241: Introduction to Applied Microbiology

Dr. B.J. Butler, B1 Rm 279 ext. 35081, bjbutler@uwaterloo.ca

IN1

textbook:
Madigan, M.T., Martinko, J.M., Stahl, D.A., Clark, D.P. 2012. Brock Biology of Microorganisms, 13th ed. Pearson Benjamin Cummings. available at UW bookstore (12th ed is fine)

lab sessions: begin the week of January 14th

instructor: Dr. C. Duxbury, ESC Rm 357F, ext. 36450, cduxbury@uwaterloo.ca Lab Manual available at UW bookstore WHMIS required

course web page: on LEARN (D2L)

course syllabus (incl textbook page references), .ppt slides, course news (announcements, up-dates, corrections), Laboratory module, links to outside info check the Biol 241 web page regularly

mark distribution:
lecture component: midterm exam 20% final exam 50% laboratory component: 30% (lab reports, quizzes, lab exam; further breakdown provided in lab)

IN2

exams:
midterm exam: Wed Feb 27th, 5:45-6:45 p.m. (rooms TBA) lab exam: Wed Mar 27th, 5:45-6:45 p.m. (rooms TBA) final exam: to be scheduled by Registrar (2.5 h) exam format: multiple choice, matching, true-or-false questions

other resources (will put some on reserve Davis):

Prescott, L.M., Harley, J.P., Klein, D.A. 2005. Microbiology, 6th ed. McGraw-Hill. Black, J.G. 2002. Microbiology: principles and explorations. 5th ed. Wiley. Perry, J.J., Staley, J.T., Lory, S. 2002. Microbial life. Sinauer Associates. also copy of Madigan et al.

Academic discipline and integrity:

Policy 71 (Student Discipline), Policy 70 (Student Grievances & Petitions) https://uwaterloo.ca/secretariat/policies-procedures-guidelines Biology Departments policies: see your lab manual

IN3

issues:
infringing unreasonably on the work of others cheating on exams, assignments, work term reports, or any other work impersonating another student/being impersonated for exam, assignments plagiarism - presenting ideas, words, other intellectual property of another as one's own; others work must be properly acknowledged & referenced obtaining by improper means exams, similar materials; using, distributing to others falsifying academic records, or submitting false credentials oral/written misrepresentations which may affect academic evaluations fraudulent health claims, obtaining medical/other certificates under false pretenses, altering certificates for purposes of misrepresentation. submitting an essay, report, or assignment when a major portion has been previously submitted/being submitted for another course without express permission of all instructors involved

Disciplinary Penalties: one or more of the following may be imposed

reprimand submission of a failing grade in an examination, test, assignment, or course; or, where applicable, failed standing in a term. disciplinary probation for the balance of the period of registration at the University... restraining orders in the case of threats to individuals; restitution for property or other damages expunging grades or revoking degrees. suspension of a student from the University; shall not exceed three years... expulsion shall be permanent and a statement of such action shall be part of the student's permanent academic record... such other penalty or order as appropriate in the circumstances.

IN4

uWaterloo Office of Academic Integrity:

(https://uwaterloo.ca/academic-integrity/ ) "To create and promote a culture of academic integrity, the behaviour of all members of the University of Waterloo is based on honesty, trust, fairness, respect and responsibility."

IN5

Verification of Illness Forms:

your original VIF document must be certified by Science Undergraduate Office (ESC 253) they provide copies for profs, instructors inform Butler/Duxbury promptly if you miss midterm or final exam/lab exam, lab session (e-mail, phone message - on day of, if possible) must submit VIF in timely manner (within one week) provided info must be equivalent to UWaterloos VIF see Biol 241 course syllabus (LEARN website) for instructions if needed I didnt know that is not acceptable. Your responsibility is to be aware of the uWaterloo, Faculty of Science, Dept of Biology regulations as they apply to you!

IN6

course outline: more detail, page #s in syllabus file (LEARN website)

Lecture Topics
1. 2. 3. 4. 5. 6. 7. Microbial Ecology Bacteria-Bacteriophage Interactions Soil and Aquatic Environments Biogeochemical Cycling Biodegradation & Bioremediation Sewage Treatment Water Treatment & Quality

chpts in Madigan et al., 13th; 12th ed

23, parts of 22; 23, parts of 22 part of 9; part of 10 23; 23 24, parts of 25, with ref to 14, 13; 24, parts of 21, with ref to 15, 16, 17 24, parts of 14, with reference to 15; 24, parts of 21, with ref to 15, 16 35; 36 35; 36

8.
9. 10. 11. 12.

Food Microbiology, Industrial Microbiology

Biotechnology Host-Parasite Relationships Pathogenicity Immunology Epidemiology

36, 26, 15; 37, 25

parts of 11, 15; parts of 11, 26 27; 28 28, 29; 29, 30 32; 33

13.
14.

Infectious Disease Transmission

Antimicrobial Agents

parts of 33, 35, 36; parts of 34, 35, 36, 37

part of 26; part of 27

The invisible world of microorganisms underlies and shapes what we call the visible world. microbes possess extraordinary genetic and physiological diversity anoxic environments may arise as a result of aerobic microbial metabolism anaerobic microbes can exploit these environments different microorganisms are adapted to survive in and exploit an enormous range of environments, inanimate and animate among all life forms on earth, microorganisms have widest range of genetic and evolutionary diversity There are no such things as pure and applied science there are only science, and the application of science. L. Pasteur

IN7

Butlers philosophy for the teaching, learning, and application of microbiology: if one understands how the microorganisms work, then, through this understanding, one can devise ways in which the benefits of microorganisms can be increased, in which the damage incurred by microorganisms can be decreased

IN8a

(Fig 1.8 12th ed; 13th ed)

Applied microbiology: medical

(i) infectious and non-infectious disease and pathogenesis cholera (Vibrio cholerae) emerging infections Staphylococcus, Streptococcus, Pseudomonas foodborne, waterborne illnesses Helicobacter pylori (ulcers) malaria prions (mad cow or BSE, CJ) hepatitis, influenza viruses, oncogenic viruses sexually transmitted diseases (ii) immunology antibodies and B cells antigenic variation cellular immunity T lymphocytes immune diseases
(Fig 1.7, 12th ed)

IN8

Applied microbiology: agriculture

Agrobacterium & plant cell transformation biocontrol e.g., weeds, microbial insecticides nitrogen cycle; nodule formation in legumes plant pathogens plant disease resistance natural, engineered pesticide biodegradation methane production, agricultural waste management rumen fermentation (ruminants: cattle, sheep)

IN9

Applied microbiology: environmental

aquatic, soil microbiology biodegradation, bioremediation treatment of effluents, municipal wastewaters biofilms, biofouling, biodeterioration biomonitoring of environmental contaminants low-nutrient environments drinking water microbiology extremophiles (pH, temperature, pressure) microbial ore leaching space flight, life on Mars?

(Fig 1.9 13th ed; 1.7, 12th ed)

IN10

Applied microbiology: industry

brewing, wine making fermented dairy, vegetable products food spoilage and preservation quality control in food industry lactic acid bacteria enzyme, amino acid production biocatalysis

Applied microbiology: genetics

DNA restriction, modification & sequencing recombinant DNA procedures site-directed mutagenesis genetic transformation
(Fig 1.7, 12th ed)

microbial fermentations virus vaccines mammalian proteins transgenic plants & animals environmental biotechnology gene regulation & gene therapy

IN11

Biol 240/Biol 240L Biol 241 (Intro to Applied Microbiology) Biol 345
(Microorgs in Foods)

Biol 431
(Bacterial Molec Genetics)

Biol 346
(Microb Ecol & Div)

Biol 442 (Virology) Biol 443

(Fermentation Biotech)

Biol 348L
(Lab Methods in Microbiol)

Biol 444
(Microorgs & Disease)

Biol 475

Biol 474
(Bioprocessing)

(Curr Topics in Appl Microbiol)

Biol 447
(Environ Microbiol)

Biol 466
(Adv Biogeochem Microbiol)

Biol 449

Biol 448

(Public Health Micro) (Microb Physiol & Biochem)