Syllabus for Advanced Bacteriology MICRO 225
Li Shen MEB6217 568-4076
Joy Sturtevant MEB6207 568-6116
Major objectives: introduce core Knowledge:
1) Overview of disease(s) associated with bacterial family (pathogens and microflora)
2) Genome, structure, physiology, and environmental requirements of bacteria.
3) Antibacterial reagents and drug resistance
3) Mechanism of pathogenesis
4) Techniques used in Bacteriology Research
5) Applications of bioinformatics in basic bacterial research
6) Discussion of current literature relevant to topics presented
Articles will be chosen that focus on bacteria pathogen and host interaction
Part I Principles and basic concepts of Medical Bacteriology
This section will focus on basic characteristics of bacteria and overall themes that are shared by bacteria with regard to initiating pathogenesis and survival strategies in the host. Problem Sets will reinforce concepts taught in lectures and test the students on ability to apply concepts to solving theoretical experimental problems focusing on bacteria-host interactions.
Part II Advanced topics in Bacterial Pathogenesis.
Classes in part II will focus in detail upon specific examples of bacterial pathogenesis related attributes and the experimental approaches which have been used to study them. This section will focus on how the concepts and techniques presented in Part I are applied.
Each section will consist of two days. On day one the general topic will be introduced and then the focus will usually be on one or two organisms which will be covered in more detail. On day two students will participate in discussion and presentation of journal article(s). *For each section in Part II, a short answer question or problem set will be assigned to the students either prior or after the lectures/discussions. They will answer, individually, and email their responses. These will be graded and constitute part of the problem sets percentage for overall grade.
Part III Metagenomics, Microbiome, Bioinformatics
This section will focus on application of bioinformatics to bacterial disease. It will showcase new technology that can provide more effective methods to provide information about the microbiome. This will include current methodologies of deep sequencing and corresponding data analysis.
Resources:
1) Schaechter’s Mechanisms of Microbial Disease
2) http://www.textbookofbacteriology.net/
EVALUATION
Participation in class discussions and journal article discussion/ critiques 15%
Problem sets* 25%
Midterm exam covering material presented in Part I: short answer 20%
Final Exam: 2 sessions during the week of Dec 3 40%
EVALUATION AND GRADING
In-class participation (15%)
Each student will be scored as follows:
0-5% Little or no contribution to in class discussions
6-10% Infrequent and/or poorly considered contributions to in class discussions
10-15% Frequent and well considered in class contributions
Performance in problem solving assignments (25%)
Specific requirements for each problem set will be included in the assignment. In general, performance will be evaluated as follows:
0-5% Little evidence that the problem has been considered or is poorly understood
6-10% Some understanding of the problem in hand but inadequate consideration given to
possible solutions
11-15% Good understanding of problem and some evidence of viable explanation or resolution
16-20% Excellent grasp of problem in hand and well considered and viable solutions provided
0-5% Discretionary: dependent on individual problems
Midterm Exam – short answer (20%)
Final Exam –
Each student will be scored by attending faculty according to the following criteria:
0-10% Poor presentation, lacking an organized structure and/or poor understanding of the issues under consideration
11-20% Acceptable presentation/organization with evidence of understanding of the topic, but lacking in content or else impractical approaches offered
21-30% Clear presentation with some evidence of a reasoned approach and some potentially
viable approaches offered
31-35% Clear and well - structured presentation, well defined goals, with carefully rationalized
and practical approaches presented
0 – 5% Visual presentation of powerpoint
Final grades will be calculated from the overall % as determined above according to the following scale:
A = 80 -100% (as long as 80% in each category is achieved)
B = 70-79% (as long as 60% in each category is achieved)
C = 60 -69%
Fail <60%
CLASSES: TUES/ THURS 9 - 11:00, SMALL MIP CONFERENCE ROOM
PART 1
Thu Aug 15 Overview of Course; Establishment of Infectious Diseases Li Shen
Tue Aug 20 Biology of Bacteria Ken Johnston
Thu Aug 22 Microbiome Chris McGowin
Tue Aug 27 Approaches to Study Bacterial Pathogenesis (Classical) Ken Johnston
Thu Aug 29 Approaches to Study Bacterial Pathogenesis (Genetics/ Gene expression) Li Shen
Tue Sep 3 Problem Day * STAFF
Thu Sep 5 Bacterial Toxins and Secretion Systems Li Shen
Tue Sep 10 Strategies to Fight Bacterial Infections Joy Sturtevant
Thu Sep 11 Bacterial Survival Strategies Joy Sturtevant
Tue Sep 17 Antibiotics and Antibiotic Drug Resistance Jeff Hobden
Thu Sep 19 Resistant / susceptibility testing/ clinical implications Jeff Hobden
Tue Sep 24 Determinants of Bacterial Pathogenesis Chris McGowin
Thu Sep 26 Midterm exam* (in class)
PART 2 Advanced Topics: Bacterial Pathogenesis
Examples of Types of Bacterial Infections
Tue Oct 1 Bacterial Infections I: Streptococci (pyogenes) Ken Johnston
Thu Oct 3 Bacterial Infections II: Neisseria, Hemophilus, Bordatella Ken Johnston
Tue Oct 8 Bacterial Infections III: Nosocomial Infections Jeff Hobden
Thu Oct 10 Bacterial Infections IV: Toxigenic Enterics Jeff Hobden
Tue Oct 15 Bacterial Infections V: Chlamydia I Li Shen
Thu Oct 17 Bacterial Infections V: Chlamydia II Li Shen
Tue Oct 22 Bacterial Infections VI: Mycoplasmas I Chris McGowin
Thu Oct 24 Bacterial Infections VI: Mycoplasmas II Chris McGowin
Tues Oct 29 Bacterial Infections VII: Mycobacteria Arnold Zea
Thu Oct 31 Bacterial Infections VII: Mycobacteria Arnold Zea
Tue Nov 5 Consequences of Infections: Biofilms I Tom Wen
Thu Nov 7 Consequences of Infections: Biofilms I I Tom Wen
Tue Nov 12 Metagenomics, Microbiome, Bioinformatics Chris McGowin, Chris Taylor
Thu Nov 14 Metagenomics, Microbiome, Bioinformatics Chris McGowin, Chris Taylor
Tue Nov 19 Metagenomics, Microbiome, Bioinformatics Chris McGowin, Chris Taylor
Thu Nov 21 Metagenomics, Microbiome, Bioinformatics Chris McGowin, Chris Taylor
Tue Nov 26 Metagenomics, Microbiome, Bioinformatics Chris McGowin, Chris Taylor
Thu Nov 28 Thanksgiving