Molecular and Cellular Bacteriology
Spring 2016
Instructors: Bryan Bellaire
Office: 1136 Vet Med
Contact Information: 294-1006 bbella@iastate.edu
Office hours: by appointment
Thomas Bobik
Office: 2152 MBB
Contact Information: 294-8247 bobik@iastate.edu
WRF 11AM-12:00 Noon, right after class.
Nancy Cornick
Office: 2130 Vet Med
Contact Information: 294-6499 ncornick@iastate.edu
Office hours: by appointment
Chris Minion
Office: 1130 Vet Med
Contact Information: 294-6347 fcminion@iastate.edu
Office hours: by appointment
Greg Phillips
Office: VMRI Building 6
Contact Information: 294-1525 gregory@iastate.edu
Office hours: by appointment
Credits:
4
Lectures:
MWRF 10-11 AM, 1420 Molecular Biology Bldg.
Textbooks (none are required): Microbial Physiology 4th ed. Moat, Foster, and Spector, Wiley-Liss,
New York, 2002
Microbiology: An Evolving Science 2nd ed. Norton 2010
Class website: Blackboard and Dr. Bobik's web site.
Course description and objectives: The focus of this class is on microbial molecular,
physiological, genetic, cellular, and development biology using bacteria as models. Students will
learn relationships between bacterial structure and function, energy generation mechanisms,
biosynthesis, stress adaptation, virulence and how they are regulated. Emphasis will be placed on
the integration of the various levels of biological processes to develop a systems biology
perspective on bacterial development, interactions with hosts, and metabolic engineering. The
second half of the course will place particular emphasis on bacterial pathogens and how the host
environment influences microbial behavior and on how this information is relevant to solving
current medical problems or concerns. The course emphasizes active learning, i.e. weekly
discussions and projects.
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Learning objectives include:
-promote the integration of concepts in microbial physiology, biochemistry, genetics, and
pathogenesis
-integrate concepts of molecular and cellular biology into developmental biology & bacterial-host
interactions
-encourage students to relate basic and fundamental knowledge to solving real-world problems
-expose students to a specialized area of microbiology in great depth
-improve writing skills for the clear communication of scientific concepts
-promote skills in both formal and informal scientific interaction and generate enthusiasm toward
sharing and defending ideas
Assessments: We provide a variety of experiences to assess your conceptual understanding of
course content. There are 4 exams including the final. Each exam is worth 100 points toward your
final grade. Special assignments may also be utilized to test writing and analytical skills.
Assessments for Unit 1 and 2 (first ½ of semester with Dr. Bobik as instructor)
The total points for unit 1 and 2 will be 250 pts
Two exams 250 pts (125 pts each). Essay, short answer and multiple choice.
Two exams 200 pts (100 pts each). Essay, short answer and multiple choice.Assessments for
Unit 3 and 4 (last ½ of the class with Drs. Cornick, Bellaire, Phillips and Minion )
The total points for units 3 and 4 will be 250 pts
Two exams 250 pts (125 pts each), Short answer, multiple choice, essay
Grading: Letter grades are based on the standard distribution: 90% (A), 80% (B), 70% (C), 60%
(D), and <60% (F). The curve may be adjusted downward to better reflect student performance
and fairness.
Assigned readings: Students are strongly encouraged to read the assigned readings prior to the
class for which they are assigned. The textbook does not cover all material adequately,
particularly for the second half of the class, and consequently there will be supplemental reading
assignments provided by the instructor.
Makeup exam and late assignment policy: Special arrangements may be made for students who
must be away for professional or personal reasons (University-sponsored activities, National
Guard, interviews, illness, family or personal emergencies, etc.). Approval must be obtained from
the Instructors prior to the activity if possible. Appropriate documentation will be required.
Contact the instructor about scheduling makeup exams or timelines for completion of late
assignments.
Dead Week: This class follows the ISU Dead Week policy as noted in section 10.6.4 of the
Faculty Handbook
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Lectures, notes, movies, and articles will be available on Blackboard. THESE MATERIALS ARE
COPYRIGHTED AND CAN ONLY BE USED FOR CLASS PURPOSES! It is likely that not all
lectures will be made available depending on the individual instructor.
Course Policies
1. Class attendance: Class attendance is optional, but all lecture material is examinable. Lecture
PowerPoint files and/or notes will usually be made available for download.
2. Credit for late work: Late submissions are NOT acceptable. If a student is unable to
complete any of the exams at the appointed time, you must contact the instructor
immediately. The instructor will decide the format of the make-up exam; either a new written
or an “oral exam” of 2-3 hours duration will be conducted.
3. Extensions for late work: N/A
4. Reporting illness: Every attempt should be made to contact the instructor whose lecture you
are going to miss. Email is the best way.
5. Classroom behavior: Professional behavior that is conducive to a learning environment is
required. Professional behavior includes but is not limited to being on time and being prepared
for class. Students must not behave in such as way to interfere with others learning.
Students should treat every member of the class with respect and listen to all ideas.
The professional behavior conduct in the CVM Honor Code and ISU Policy on student
classroom disruption apply at all times
http://www.dso.iastate.edu/sa/issuesconcerns/disruption
Students are not permitted to have on their person or bring unauthorized written materials or
electronic devices of any type into the examination room during written examinations without
permission of the instructor. If a student is observed to have an unauthorized electronic
device during an examination or any unauthorized materials, the student will be quietly asked
or given a written statement to stop their examination and be escorted from the room. At
that point, the examination will be retained by the instructor or proctor. The event will
trigger a thorough investigation of a possible academic dishonesty violation.
6. Reading material: Students are expected to have read the assigned material before class.
You can expect to be called on to answer questions over the assigned reading. Most of the
assignments will be posted on Blackboard.
7. Academic Dishonesty and the Honor Code: Student conduct follows Iowa State University’s
policy on academic dishonesty. The instructor/instructor-in-charge observing academic
dishonesty reports the student suspected of academic dishonesty to the appropriate office.
Campus- wide policies regarding academic misconduct are found at:
http://www.dso.iastate.edu/ja/academic/misconduct.html.
Forms of academic dishonesty:
Obtaining unauthorized information. Information obtained dishonestly, for example, by copying
graded homework assignments from another student, working with another student on a takehome test or homework when not specifically permitted to do so by the instructor.
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Tendering of information. Students may not give or sell their work to another person who plans
to submit it as his or her own. This includes giving their work to another student to be copied,
giving someone answers to exam questions during the exam, taking an exam and discussing its
contents with students who will be taking the same exam, or giving or selling a term paper to
another student.
Misrepresentation. Students misrepresent their work by handing in the work of someone else.
The following are examples: purchasing a paper from a term paper service; reproducing another
person’s paper (even with modifications) and submitting it as their own; having another student
take their exam.
Plagiarism. Unacknowledged use of the information, ideas, or phrasing of other writers is an
offense comparable with theft and fraud, and it is so recognized by the copyright and patent
laws.
8. Disability Accommodation: Iowa State University is committed to assuring that all
educational activities are free from discrimination and harassment based on disability status.
All students requesting accommodations are required to meet with staff in Student Disability
Resources (SDR) to establish eligibility. A Student Academic Accommodation Request (SAAR)
form will be provided to eligible students. The provision of reasonable accommodations in this
course will be arranged after timely delivery of the SAAR form to the instructor. Students
are encouraged to deliver completed SAAR forms as early in the semester as possible. SDR, a
unit in the Dean of Students Office, is located in room 1076, Student Services Building or
online at www.dso.iastate.edu/dr/. Contact SDR by e-mail at
disabilityresources@iastate.edu or by phone at 515-294-7220 for additional
information. Students with SAAR forms who need accommodations for a distraction free
room and/or more time for testing need to contact Ms. Chris Trower (cctrower@iastate.edu)
and Ms. Dai Nguyen (dna112@iastate.edu) in the Microbiology Program Office to arrange a
time and place for the exam.
9. Harassment and Discrimination: Iowa State University strives to maintain our campus as a
place of work and study for faculty, staff, and students that is free of all forms of
prohibited discrimination and harassment. For more information, or if you believe you are a
victim of discrimination or harassment, please visit the following URL for additional guidance:
http://policy.iastate.edu/policy/discrimination/ .
10. Religious, Civic, and Military Accommodations: There may be times when an academic
requirement conflicts with religious observances and practices, or required civic or military
duty. If that happens, students may request reasonable accommodation of their religious
practices http://www.eoc.iastate.edu/discrimination/religious
Civic http://www.dso.iastate.edu/sa/juryduty
Military http://www.veterans.iastate.edu/active-duty#leave
11. Unforeseen Circumstances and Adaptation of the Syllabus: Note: Information in the
syllabus is subject to change. Changes will be announced in class and posted on the course site
on Blackboard Learn or the appropriate Learning Management System.
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Molecular and Cellular Bacteriology Schedule (2016)
Lecturer code
Bobik
Cornick
Bellaire
Phillips
Minion
Putative schedule
Date
Class
1
M Jan. 11
2
3
4
5
6
W Jan. 13
R Jan. 14
F Jan. 15
M Jan. 18
W Jan. 20
R Jan. 21
7
8
F Jan. 22
M Jan. 25
9
10
11
12
W Jan. 27
R Jan. 28
F Jan. 20
M Feb. 1
13
W Feb. 3
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
R Feb. 4
F Feb. 5
M Feb. 8
W Feb. 10
R Feb. 11
F Feb. 12
M Feb.15
W Feb. 17
R Feb. 18
F Feb. 19
M Feb. 22
W Feb. 24
R Feb. 25
F Feb. 26
M Feb.29
W Mar. 2
R Mar. 3
F Mar. 4
M Mar. 7
W Mar. 9
R Mar. 10
F Mar. 11
Topic (Tentative)
Introduction to Molecular and Cellular
Bacteriology
Growth & Factors Affecting Growth
DNA Replication/transcription
Transcription/translation
No Class- University Holiday, MLK day
Translation/Protein folding
Protein folding, trafficking, degradation,
secretion
Recombination
Mutation/DNA repair
Plasmids/DNA exchange
DNA exchange
Discussion/Catch up day
Bacteriophage, T4, Lambda, CRISPRS
Regulation of Gene Expression 1
Global regulation and 2-component systems
Regulation of Gene Expression 2, Pho regulon,
Quorum sensing and alternative sigmas
Discussion/catch-up
Exam I (Lectures 1-14)
Genome sequencing
Genome analysis
Methods for determining gene function
Methods for determining gene function
Genomics/ Bacterial cell wall
Bacterial cell wall
Discussion/Catch up day
LPS/Outer Membranes/periplasm
Cytoplasmic Membrane/lipids and phospholipids
Cell division/cytoskeleton
Cytoskeleton/metabolite transport
Metabolite transport
Discussion/Catch up day
Exam II (Lectures 16-28)
Glucose catabolism
TCA cycle/electron transport
Anaerobic respiration
Biosynthesis CO2 fixation
Biosynthesis: Amino Acids
Degradation of polysaccharides, lipids
Moat, Foster, Spector
Readings pp.
1-7;12-18
Slonczewski 2nd
ed Readings pp.
19-24, handout
31-44
47-57
(234-41)
261-64; 269-72
57-73
74-88
(275-83)
(284-92)
127-32,
145-67
101-27
138-140
315-18
(326-31)
245-50, 256-63,
194-95; 201-04, 22327
232-36
197-200; 386-92
342-56
171-192
250-54; 292-97
373-81; 428-45
289-310
(88-91)
289-310
310-15; 450-66
561-70
(93-98)
(82-86)
101-06
383-90
120-26
(302-12)
361-63
Chapt 13
Chapt 13 – 14
Chapt 14
Chapt 15
Chapt 15
Supplemental
reading
5
36
M Mar. 21
Spring Break March 14-18
Motility, Chemotaxis, surface motility
37
W Mar. 23
Bacterial Differentiation-Endospores
38
R Mar. 24
Metabolism at host-pathogen interface
39
F Mar. 25
Host-pathogen Interactions- Toxins
40
41
42
43
44
45
46
47
48
49
M Mar. 28
W Mar. 30
R Mar. 31
F Ap. 1
M Apr. 4
W Ap. 6
R Ap. 7
F Ap. 8
M Ap. 11
W Ap. 13
Catch-up/discussion
Virulence regulation-General schemes
Mycoplasmas – pathogenic mechanisms
Iron uptake
Exam III (Lectures 30-41)
How do antibiotics really kill bacteria
Nutrient deprivation-Stringent response
Protein secretion
Microbiomes, commensals
Oxidative stress, cell death
50
R Ap. 14
Osmoregulation/Stress tolerance
51
F Ap. 15
52
M Ap. 18
Host-pathogen interactions, Adherence &
colonization
Host-pathogen interactions, Tissue and cell
invasion
Intracellular Pathogens
Biofilms
Antigenic variation in Neisseria and Borrelia
Gram negative pathogens
Gram positive pathogens
Circumventing the immune response
Catch-up/discussion
Final Exam (Lectures 42-59)
53
W Ap. 20
54
R Ap. 21
55
F Ap. 22
56
M Ap. 25
57
W Ap. 27
58
R Ap. 28
59
F Ap. 29
MAY 2-6
Supplemental
reading
Supplemental
reading
Supplemental
reading
Supplemental
reading
Supplemental reading
Supplemental reading
Supplemental reading
88-100
164-66
601-05; Supplemental reading
77-81
591-601;
Supplemental reading
582-590;
Supplemental reading
648-655
950-952
657-672
1033-1047
Supplemental reading
Supplemental reading
Supplemental reading
Supplemental reading
Supplemental reading
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