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7.341 | Fall 2022 | Undergraduate

# Microbes at War: The Mechanisms That Drive Infectious Diseases

### Course Meeting Times

Lectures: 1 session / week, 2 hours / session

### Prerequisites

There are no absolute prerequisites. However, a background knowledge of genetics, biochemistry, and cell biology is expected. Ideally, students have successfully taken at least one of the following classes: 7.03 Genetics, 7.05 General Biochemistry, 7.06 Cell Biology, 7.08 Fundamentals of Chemical Biology, 7.21 Microbial Physiology, or 7.28 Molecular Biology.

### Course Description

Your war against pathogenic microbes has begun. It started with a urinary tract infection that you countered by drinking lots of cranberry juice. The second attack was directed at your sense of smell and taste. Your body was in a fight with COVID-19 which was won by your body’s immunity T cells. You celebrate your victory over COVID-19 with a hike and a steak dinner with friends. However, due to a tick bite you received on the hike, you had a severe allergic reaction to the beef! You have had a streak of extremely bad luck: Why did you lose your sense of smell? How can a tick bite cause a meat allergy? And did the cranberry juice do anything to help cure your urinary tract infection? To answer these and other questions, we are going to take a dive into the molecular world of microbes.

In this class, we will use the primary research literature to explore the molecular interactions between pathogens and their hosts that allow microbes to cause infectious diseases. We will examine the factors that pathogens use to colonize a host and how the host response can impact the outcome of the infection. During this course, students will learn (1) how various microbes interact with their hosts to cause diseases; (2) how the host responds in an attempt to stay healthy (and how this sometimes backfires!); (3) the methods researchers use to study these processes; and (4) how to critically read, evaluate, and discuss the primary research literature.

We will highlight how microbes are important for and utilized in both academic and industrial biomedical careers. This will include a field trip to a commercial laboratory that develops exciting new microbial products to better human health. By the end of the class, students will have both developed critical scientific skills in evaluating scientific literature and an appreciation of the microbes influencing our lives and health every day.

### Intended Learning Outcomes

By the end of this course, students will be able to do the following:

- Identify mechanisms by which microbes shape human health
- Appreciate both the historical background and the modern-day status of host-pathogen interactions
- Understand and articulate how microbes interact with their hosts to cause various infectious diseases
- Navigate primary research articles, quickly identifying and summarizing the key points and experiments
- Critically analyze the experimental design, results, and conclusions of primary research articles
- Interpret data from a variety of different experimental systems, model organisms, and data types
- Design rigorous follow-up experiments to test the authors’ conclusions
- Recognize that an understanding of microbiology is important for both academic and industrial biomedical careers

### Course Expectations

- During the first class, we will introduce ourselves, discuss the course logistics, and introduce some of the broad, overreaching concepts to be covered. We will discuss how to critically read scientific journal articles to provide a basis for the rest of the class. We will also discuss ways to search and access the primary literature using PubMed, Google Scholar, and MIT library resources. All subsequent class meetings will involve active discussions of two related assigned papers, as outlined in the Course Calendar section below.
- The primary objective is for students to learn to read and critically discuss primary scientific literature. Students should understand how to effectively and quickly dissect a scientific paper. Other important skills include understanding experimental design, identifying appropriate experimental controls, interpreting data, and designing the next steps.
- To be successful in this course, students should come to class prepared to discuss the content of the assigned papers, including the main question addressed in the paper, the figures (main and supplementary), tables, methods used, and the main conclusions.
- To ensure everyone is prepared for class discussions, each student will send the instructor brief written answers to a few basic questions about each article. Details are explained on the Assignments page.
- Over the semester, there will be two longer assignments, one written and one oral, described on the Assignments page.
- To assist you with understanding new experimental methods and concepts, at the end of each class the instructor will briefly introduce key topics and methods required to understand the papers assigned for the following class.
- This class is for you!!! To get the most out of class, engaging in the discussions during class is essential. Engaging in critical analysis of articles can be intimidating, but we will improve these skills together. Therefore, ask questions, share your thoughts, and engage in (kind and thoughtful) debate and discussion with your classmates. We are here to learn together. Please reach out if there is a way the instructor can help you reach your full potential in this class.

### Grading

This course will be graded as pass/fail (6 units). To earn a passing grade, students are expected to a) attend all class sessions and participate actively (and fulfill any make-up assignments) and b) appropriately complete both the written and oral assignments.

### Inclusivity Statement by the Instructor

As the instructor, I value an inclusive environment and community within my classroom. I will treat all students in my classroom with the utmost dignity and respect. I welcome individuals of all backgrounds, beliefs, ethnicities, national origins, gender identities, sexual orientations, religious and political affiliations, and other visible and non-visible differences. All members of this class are expected to contribute to a respectful, welcoming, and inclusive environment for every other member of the class. This is a learning environment; therefore, all should feel comfortable contributing to the discussion and asking questions. If this standard is not being upheld, please feel free to speak with me.

### Other Tools/Resources/Tips

- You may want to download a citation manager, such as Mendeley or Zotero, to keep track of the papers you read and to help insert citations into your written assignment. I recommend Zotero. However, if you work in a research laboratory, ask what others in your lab are using. Lab members typically use the same program, allowing them to easily share papers across the lab.
- If you are struggling to understand a method or topic, check out iBiology, YouTube, or JoVE. iBiology and YouTube have some good videos about scientific content. JoVE has videos about experimental methods to help you understand practically what is going on.
- If you want to learn more about why critically reading journal articles is important check out Retraction Watch and MicrobiomDigest on X (Twitter).

#### If you just love microbes and want to learn more…

##### For an engaging read:

Strathdee, Steffanie A., Teresa Barker, and Thomas L. Patterson. 2020. The Perfect Predator : A Scientist’s Race to Save Her Husband from a Deadly Superbug : A Memoir. First trade paperback ed. Hachette Books. ISBN: 9780316418119.

##### For the podcast lovers:

This Week in Microbiology (TWiM) podcast. Hosted by Vincent Racaniello, with co-hosts Elio Schaechter, Michael Schmidt, Michele Swanson and Petra Levin. American Society for Microbiology (ASM).

This Week in Parasitology (TWiP) podcast. Hosted by Vincent Racaniello, Dick Despommier, and Daniel Griffin, MD. American Society for Microbiology (ASM).

This Week in Virology (TWiP) podcast. Hosted by Vincent Racaniello, Dick Despommier, Alan Dove, Rich Condit, Kathy Spindler, and Brianne Barker. American Society for Microbiology (ASM).

### Calendar

Week | Topics
--- | ---
1 | Welcome to the “Battlefield”—Introduction to Host-Pathogen Interactions and How to Effectively Read Journal Articles
2 | Identify the Enemy—Koch’s Postulates
3 | The World’s Deadliest Infectious Disease—Tuberculosis
4 | On the Front Lines—How Bacteria Can Stake Their Claim on the Battlefield Paper for Midterm assignment will be provided.
5 | Not All Microbes Are Bad—Field Trip Preparation
6 | Field Trip!!! Concerto Biosciences Written Assignment Due
7 | Preprint Week—and the Mysterious Hepatitis Outbreak
8 | Illness Is Sweeping through the Ranks—Norovirus (Winter Vomiting Bug)
9 | Biological Sex, Pregnancy, and Infectious Diseases—Malaria
10 | Friendly Fire—How the Immune System Can Go Awry, and a Tick Bite Can Lead to Allergic Reactions to Meat Final Presentation Topic Due
11 | A Battle You Have Been a Part of—The Global Fight Against COVID-19
12 | What Is Your Favorite (or Least Favorite) Microbe?
13 | The Final Battle—Oral Presentations

## Course Info

##### Instructor

- Dr. Lisa McLellan

##### Departments

- Biology

##### As Taught In

Fall 2022

##### Level

Undergraduate

##### Topics

- Health and Medicine
  - Immunology
- Science
  - Biology
    - Biochemistry
    - Cell Biology
    - Genetics
    - Microbiology

##### Learning Resource Types

assignment Written Assignments
assignment Presentation Assignments
co_present Instructor Insights

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