Course Syllabus
Bacterial Virulence Mechanisms
BIOMDSCI 556
Fall, 2025
Meets M, W, F at (10:00) (Location TBD)
Course director:
Jason Park Office ADBF 4043 Phone 509-335-6066
Schedule: Block 23 (3rd 5 week module of semester; October 27th through December 5th).
Class meets in person Mondays, Wednesdays, and Fridays from 10:00 to 11:00 in TBD.
Class attendance is mandatory (real-time discussions). Contact course instructor if you miss a class – make-up work will be assigned.
Contributing Faculty Instructors: Week 1 – Jason Park (jpark12@wsu.edu; 5-6066)
Week 2 – TBD
Week 3 – Viveka Vadyvaloo
Week 4 – Arden Baylink
Week 5 – Anders Omsland
Prerequisites:
Enrolled in Multidisciplinary Program in Infectious Disease PhD program, or by approval of course director.
Credits: 1
Required textbooks: None. Readings vary yearly and will be assigned by instructors.
Course Overview: Bacterial Virulence Mechanisms (BIOMDSCI ###) is a 1-credit short course intended to introduce students to the diversity of molecular bacterial mechanisms that contribute to virulence in human and/or veterinary diseases. Each week we will read, present, and discuss papers covering a different theme of bacterial virulence mechanisms. Themes will be chosen by faculty from the WSU Multidisciplinary Program in Infectious Disease PhD program to highlight the diversity of bacterial pathogen research at WSU. Each Monday faculty or post-doc will give an overview of a theme in bacterial virulence. Students will be assigned journal articles within that theme to present on Wednesday and Friday of that week. Presenting students will lead the class in discussion of the article emphasizing framing of the research question, hypothesis testing, data interpretation, and remaining questions. Students not assigned to present on a given are also required to read the paper and write a brief outline detailing the rational of each experiment from the paper. The last part of the course will be the Design a Better Pathogen competition held during finals week at the end of the semester.
Learning outcomes:
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Perspective on the diversity of molecular mechanisms utilized by bacteria to facilitate disease. |
Instructor lead overview of themes among bacterial virulence mechanisms followed by student lead paper discussions. |
Quality of student lead presentation, group discussion of research articles, and individual written outlines. |
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Demonstrated ability to accurately interpret results of scientific papers on infectious diseases |
Written paper outlines and related oral presentations class on assigned papers |
Quality of written outline and scholarly nature of in class discussions |
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Ability to frame background knowledge leading to scientific question, and identify sub-aims tested by individual experiment. |
Student lead discussion of assigned papers and design a better pathogen |
Presentation of assigned research articles and their Design a Better Pathogen presentation. |
Expectations of Student Effort: For each hour of lecture equivalent, students should expect to have a minimum of two hours of work outside class.
Grading
40% of your grade for this section will be:
Presentation of the assigned papers background - 10 points
Discussion of conclusions and resulting model of pathogen strategy - 10 points
Presentation of assigned figure- 20 points
20% of your grade: Paper outlines for papers not assigned to you that week
40% of grade for final “better” pathogen presentation
Organization and logic 10
Sufficient framing of background 10
Explanation of key virulence mechanism 10
Presentation of research question about your organism 10
Calculation of final grade is as follows: Sum of points earned up to 100/100 x 100 = percentage of points earned (normal rounding conventions will be followed).
If your final % is: Your final grade will be:
93 or above A
90-92 A-
88-89 B+
83-87 B
80-82 B-
78-79 C+
73-77 C
70-72 C-
68-69 D+
63-67 D
Below 63 F
Assignments
- Paper outlines: For all papers that you are not assigned to present, you are to fill out a paper outline highlighting key aspects of the paper. These are meant to be accurate, but concise bullet point dissections of the paper to demonstrate you have read the paper and are prepared to participate in class discussion. A template will be given out at the beginning of this section.
- Paper presentations and discussions: The entire class is still responsible for reading the paper and be ready to discuss the figures. For each paper, a pair of students will be assigned to lead the paper discussion. One presenter will present an intro and conclusion to their paper. The other student will be lead discussion of the figures/figure-panels.
- Intro – Aim to be a ~10 minutes max PowerPoint presentation. Briefly cover the background of the pathogen including; disease, lifecycle, general epidemiology, and core virulence mechanisms relevant to the paper. Introduce any cellular/molecular processes that are necessary to understanding the paper. Most of this information will be mentioned in the introduction section of the paper, but external diagrams and references are encouraged to flesh out discussion. This intro should end by emphasizing the studies scientific questions, hypotheses being tested, or discovery goals.
- Figure discussion – Approach each figure in the context of the question being asked. Briefly describe the method used and results of the figure. Then state what the results answer and what question remains leading to the next figure.
- Conclusions – At the end of discussion of the paper, go beyond just a bullet list of conclusions. Revisit the questions from the intro and how the findings of the paper refine our understanding of pathogen. Also discuss what it left unanswered or things that could complicate the papers conclusions.
- Design a “better” pathogen presentation. Tentatively scheduled for classes assigned date and time in the finals week schedule. Date time TBD. Schedule will be adjusted if conflicts arise.
Students will each construct presentation introducing a fictional pathogen of their own design. This is intended to be lighthearted and entirely fictional. This is not intended to dream up how to make a superbug. Examples will be giving in the course. While you better-pathogen is fictional, try to root it believable details and mechanisms. The presentation should include details we would expect from a normal research presentation of a real pathogen. Aspects of presentation should include;
- Disease history, epidemiology, susceptible population (human or animal), geography…
- Disease; symptoms, progression, outcomes, current treatment…
- Define the organism; Phylogeny among related pathogens or non-pathogens, Evolutionarily roots, Defining characteristics
- Lifecycle; Examples - Hosts, vectors, reservoirs, co-infections, transmission …
- Highlight a mechanism critical to your pathogen.
- Examples: effectors, toxins, pathogen specific adaptations, interactions with immune system, metabolic interactions,
- Steps in the lifecycle that need more research.
- Be creative but link it to something plausible.
- Propose a scientific question and/or hypothesis that should be prioritized for testing.
This presentation will be given to the class and all instructors. It will be graded by the instructors on organization, framing of background, explanation of key mechanism, presentation of research question about your organism. You will also be judged by your peers to determine the courses Best Pathogen of 2025.
Schedule
Theme 1: Secreted Bacterial Toxins and Effectors
In week 1 we will introduce the format and expectations of the class. We will cover how to present background framework leading to hypothesis or scientific question, identifying the sub-aims or questions addressed by individual experiments, and then reviewing how findings contribute to our models of a pathogens virulence strategy.
Paper topics in this week will cover examples of secreted virulence proteins (“toxins” vs “effectors”) utilized by pathogenic bacteria. Example papers will highlight how pathogens overcome different hurdles during infection by targeting host cell pathways.
October 27 – Course introduction, introduction to secreted bacterial toxins and effectors, guidance on paper presentation assignments, overview of outline assignments, overview of design a better pathogen assignment, and example better-pathogen presentation.
Assigned reading ahead of class:
- Green ER, Mecsas J. Bacterial Secretion Systems: An Overview. Microbiol Spectr. 2016 Feb;4(1):10.1128/microbiolspec. VMBF-0012-2015. PMID: 26999395
- Galán JE. Common themes in the design and function of bacterial effectors. Cell Host Microbe. 2009 Jun 18;5(6):571-9. PMID: 19527884
October 29 – Ledvina, H. E. et al. A Phosphatidylinositol 3-Kinase Effector Alters Phagosomal Maturation to Promote Intracellular Growth of Francisella. Cell Host Microbe 24, 285-295.e8 (2018).
- Example presentation given by Jason Park
October 31 – Du, J. et al. The type III secretion system apparatus determines the intracellular niche of bacterial pathogens. PNAS 113, 4794–4799 (2016)
- Intro / discussion presenter __ ___
- Data presenter __ ___
Theme 2: Mechanisms of Immune Evasion
Papers will cover example of bacterial mechanisms to evade the mammalian immune system. This is an extremely broad subject, but we will highlight a few example strategies used by pathogens well adapted to evading immune responses.
November 3 – Presentation by guest instructor TBD overview of mechanisms used by bacteria to evade mammalian immune responses.
Assigned reading before class:
- TBD review articles covering active mechanisms for evasion of the mammalian immune system.
November 5 – TBD, Staphylococcus and protein A
- Intro / discussion presenter __ ___
- Data presenter __ ___
November 7 – TBD, Antigen switching through recombination
- Intro / discussion presenter __ ___
- Data presenter __ ___
Theme 3: Biofilms and bacterial virulence.
Papers in this section will consider how biofilm formation contributes to the persistence, spread, and virulence of some bacterial pathogens.
Assigned reading before class:
- TBD review articles.
November 10 – Presentation by Dr. Viveka Vadyvaloo discussing biofilm formation in human pathogens
November 12– TBD, Paper highlighting how biofilms contribute to persistence and spread
- Intro / discussion presenter __ ___
- Data presenter __ ___
November 14 – TBD, Paper on pathogen biofilm in the human body.
- Intro / discussion presenter __ ___
- Data presenter __ ___
Theme 4: Bacterial movement and chemotaxis in bacterial pathogens
We will cover how bacterial movement contributes to bacterial infection, dissemination, and virulence in human or veterinary disease.
Assigned reading before class:
- TBD review articles.
November 17 – Introduction by Dr. Arden Baylink on bacterial chemo-sensing, chemotaxis, and motility.
- Intro / discussion presenter __ ___
- Data presenter __ __
November 19 – TBD, Paper about how chemotaxis contributes to bacterial dissemination in the body.
- Intro / discussion presenter __ ___
- Data presenter __ ___
November 21 – TBD, Other examples of motility in disease. Maybe some drawbacks of the flagella.
- Intro / discussion presenter __ ___
- Data presenter __ ___
Theme 5: Bacterial metabolism and nutritional virulence.
This section will consider how the metabolism of the bacteria can interface with that of their host and how metabolic biproducts of the bacteria can affect the host or microbiome.
Assigned reading before class:
- TBD review articles.
December 1 –Presentation by Dr. Anders Omsland introducing to metabolic host-microbe interactions and the concept of nutritional virulence.
December 3 – TBD. Paper focused on nutrient harvesting by the pathogen from the host
- Intro / discussion presenter __ ___
- Data presenter __ __
December 5 – TBD. Paper focused on how metabolic products of bacteria can impact the host to cause disease.
- Intro / discussion presenter __ ___
- Data presenter __ __
TBA - Design a better pathogen presentation.
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