Instructor Interview
Below, Dr. Vanessa Cheung describes various aspects of how she and her colleagues teach 7.003 Applied Molecular Biology Lab:
OCW: Who takes 7.003, and how much background do they typically have in the topic of the course?
Vanessa Cheung: All 7.003 students have previously completed 7.002 as a prerequisite, which is an introductory biology lab course. So at the very least we know all of our students have been exposed to the basic fundamentals of working in a molecular biology lab. Most of our students have some additional prior biology research experience, since the majority of them are upperclassmen (juniors/seniors) and are in bio-related majors. (There are occasionally physics and engineering majors in the course, but they’re typically also double-majoring in biology or computational biology.) For example, in the fall of 2022, 34 of the 40 students had previously done a UROP research project in a biology- or chemistry-related lab. This can make it challenging to teach 7.003, since there can be a wide range of lab experience in the students coming into the class, but even the most experienced researcher can always find something new to learn when working in the lab—e.g., our graduate TAs often remark about how much they themselves learn from teaching the class!
OCW: The heart of the course is the lab manual, which lays out step-by-step instructions for completing a series of experiments over 23 laboratory sessions. Does the series form a progressive sequence, with each experiment drawing on skills students have developed in the previous experiments? Or are the experiments more freestanding, each being designed to develop mastery of a different set of skills and techniques?
Vanessa Cheung: The lab sessions in 7.003 are designed to be a progressive series of experiments, instead of 23 separate unrelated lab protocols. We want the course to feel as much like a real-life research project as possible, something similar to the progression of experiments one might follow when working in an actual molecular biology lab. The main project in 7.003 is a genetic screen to identify genes involved in the yeast mating pathway, and each individual lab day works in sequence toward fulfilling the main project goal. The samples created in one lab session are directly used in the experiments in the following lab session, which we find helps give students a greater sense of ownership and involvement in their work throughout the class. Students often comment that their favorite lab days are the ones where they can finally see the results of a procedure or assay after they have first spent several weeks laying the experimental groundwork for that assay.
Teaching a lab course where the lab sessions are based on a series of experiments does have some extra challenges. Our students are usually very detail-oriented and tend to hyper-focus just on what they’re doing in lab on that particular day. It’s easy for them to get caught up in the details and forget about the “big picture,” so we often have to remind students how the experiments they’re performing in lab one day relate to what they’ve already done, and to what they will do in the future lab sessions. Having all the lab sessions be sequential also makes it difficult to manage from a practical standpoint. We have to follow a tight time schedule; if a student’s experiment doesn’t work one day, there’s no time for them to redo that experiment and thus they won’t have the samples necessary to perform the experiments for the next lab day. We try to avoid this by doing extensive test-runs of all the experimental procedures in advance and having multitudes of back-up samples available for students at every step of the project. It requires a lot of extra prep work every semester, but it helps to maximize the students’ success in the lab.
OCW: What are the advantages to using the model organism Saccharomyces cerevisiae for a lab course in molecular biology? (In the lab manual you say that S. cerevisiae has “many similarities to humans”—can you describe those similarities in a way that would make sense to a nonspecialist?)
Vanessa Cheung: As the name implies, a model organism is a species we study that serves as a model for something else that we actually care about, where that “something else” usually is human biology or disease. Aside from the obvious ethical reasons, humans just aren’t good genetic subjects for studying biological processes. Humans are expensive to grow and maintain, their genome is huge and complex, and editing the genome in humans is very complicated. Scientists instead study model organisms that have similar biological processes or behaviors to humans but are smaller, cheaper, and easier to perform research on. The general public is usually familiar with the lab mouse as a model organism, but there are many other less well-known but equally effective model organisms like yeast, worms, and flies.
The budding yeast Saccharomyces cerevisiae, the same yeast used in baking bread or brewing beer, is an excellent model organism because it is a single-cell organism, so it is easy to maintain and quick to grow—a single yeast cell can divide into two cells in just about 90 minutes. Yeasts have a small, compact genome, so if you mutate yeast, you are very likely to disrupt an actual gene and see an effect in the mutated yeast cell’s properties. It is also ridiculously easy to edit and manipulate the genome in yeast cells, in comparison to the genomes of most other species. Our 7.003 class project takes advantage of these characteristics to perform a mutagenesis screen in yeast, where we introduce foreign pieces of DNA into the yeast genome to disrupt genes and then look for those mutated yeasts in which the mating signaling pathway has been broken. Performing a similar type of screen in human cells (or any other model organism cell type) would be much more expensive and time-consuming. It would take weeks to perform the necessary experiments and would require screening through hundreds of thousands of human cells and the use of expensive specialized equipment—it could never be done in just one semester-long lab class. Working with yeast however, our 7.003 students only need to screen through several hundred yeast cells and can perform the initial mutagenesis screen in just a few lab days with some nutrient media plates and toothpicks.
One challenge when teaching 7.003 is convincing the students the importance or relevance of the class research project (partly because students have to write a paper about their project and partly to keep students interested in the course material!). Having studied yeast genetics for my own PhD, I find the yeast mating signaling pathway inherently interesting to learn about, but I often joke with my students that there are only about five people in the entire world who truly care about yeast mating. However, biological pathways and processes usually consist of fundamental components that are conserved throughout species. Humans, yeast, mice, and flies don’t look at all alike to the naked eye, but on the molecular level, there are lots of similarities. Similar genes in all those species’ genomes encode similar protein molecules that have similar structures and perform similar functions that all cells need to do in order to survive, like cellular division or constructing new proteins. The yeast genome only has about 6000 different genes (compared to approximately 20,000 genes in the human genome), but about 2000 of those yeast genes (or around a third of the entire yeast genome) are conserved in humans. The yeast mating pathway we study in 7.003 in particular has strong similarity to signaling pathways in human cells that are involved in regulating how cells divide—as such, these related signaling pathways are often mutated in the tumor cells of many human cancer patients. Studying how the mating pathway works in yeast can provide insight into similar pathways in humans and how they might affect processes like cancer development.
OCW: How closely is the SciComm (scientific communication) content of the course integrated with the lab content?
Vanessa Cheung: 7.003 is a CI-M (Communication Intensive) course, so there is a significant scientific communication component that is closely integrated with the lab content. We think it is important for our students to learn not just how to do great science but also how to effectively tell everyone about the great science they did. The 7.003 teaching staff includes a team of writing instructors who meet with the students every other week to discuss scientific writing. Students work on writing a publication-ready scientific manuscript of their yeast mutagenesis screen class project. They have to explain the rationale for the project in the paper’s “Introduction” section, describe the experimental protocols in the “Methods” section, present data and figures in the “Results” section, and finally explain the significance of their findings in the “Discussion” section. Students write drafts of these individual paper sections throughout the semester and work through multiple rounds of revisions for each section, with the writing instructors giving feedback on the writing, formatting, and organization of the drafts, while the lab instructors and TAs give technical feedback on the drafts to make sure the scientific content is accurate and comprehensive. Most teachers will agree that being able to clearly explain a topic to others is one way to demonstrate understanding of that topic, and our students often say that they appreciate the SciComm component of 7.003 for making them really think about their class project and experimental analysis to understand it a level deep enough to write an entire paper about it.
OCW: What would you like to share about teaching 7.003 that we haven’t yet addressed?
Vanessa Cheung: One of the key strengths of 7.003 as a class is its emphasis on students being active participants in their own learning. There’s always the hands-on, practical aspect from being a lab class, of course, but we also encourage students to be actively involved in the class beyond just physically performing the experiments. One of the benefits of the 7.003 lab class format is it’s very conducive for small-group discussions and informal question-and-answer sessions. We’re lucky to have a good teacher-student ratio, where each graduate TA manages a small group of about 8–10 students. While we do have weekly lectures in 7.003, a lot of the course content is covered in the daily “in-lab questions” (ILQs). During the lab class sessions (e.g. either during incubation wait times or after the experiments are finished), students work on the ILQs with their lab partners and classmates, and then they discuss the ILQs together as a group with their TA. We find this small-group discussion format is really effective in teaching concepts to the students, as they’re encouraged to talk to each other and the TAs about the question answers and actively think through the ILQ problems themselves, as opposed to passively listening to material in a lecture. Likewise, we also always encourage students to work on their post-lab notebook assignments in lab before they leave class, so that they can benefit from discussing their experimental data with their lab partner and also ask their TA questions—and get answers in real time!—if they’re confused about any of the data analysis.
Curriculum Information
Prerequisites
- 7.01x Introductory Biology (7.012, 7.013, 7.014, 7.015, or 7.016)
- 7.002 Fundamentals of Experimental Molecular Biology
Requirements Satisfied
- General Institute Requirement (GIR): Laboratory Requirement
- Communication Intensive in the Major
- 7.003 is a required subject for the Bachelor of Science in Biology and for the Bachelor of Science in Chemical-Biological Engineering.
- 7.003 can be applied toward the departmental laboratory requirement for the Bachelor of Science in Chemistry and Biology or the Bachelor of Science in Computer Science and Biology, but is not required.
Offered
Every semester
Assessment and Grading
Students’ grades were based on the following activities:
- 40% Laboratory notebooks
- 10% Laboratory participation
- 15% Problem sets
- 35% Scientific communication work
Student Information
Enrollment
Typically around 30 students
Student Background
Most of the students in 7.003 are juniors or seniors and are majoring in biology, biochemistry, computational biology, or chemical or biochemical engineering; a few come from other scientific disciplines. All 7.003 students have previously completed 7.002 as a prerequisite, which is an introductory biology lab course, so they are familiar with the basic fundamentals of working in a molecular biology lab.
How Student Time Was Spent
During an average week, students were expected to spend 12 hours on the course, roughly divided as follows:
Lectures
- Met once per week for 1 hour per session; 13 sessions total; mandatory attendance.
Lab Sessions
- Met twice per week for 3 or 4 hours per session; 23 sessions total; mandatory attendance.
Out of Class
- Outside of class, students completed two problem sets and worked on their lab notebooks.
