Experimental microbial genetics

Lectures: 5 sessions / week, 4 hours / session

Before taking this course, students are expected to have completed: Introduction to Experimental Biology and Communication (7.02), Genetics (7.03), and General Biochemistry (7.05).

Individual research projects in Project Lab will center on using molecular genetics to examine the biology of the bacterium Pseudomonas aeruginosa, an opportunistic pathogen often found in the lungs of cystic fibrosis patients. Students will engage in independent projects to probe various aspects of P. aeruginosa physiology such as antibiotic resistance, phase variation, toxin production, secondary metabolite production, twitching motility, swarming behaviors, and more. Projects will aim to discover the molecular basis for these processes using both classical and new, cutting-edge techniques. These include plasmid manipulation, genetic complementation, mutagenesis, PCR, DNA sequencing, enzyme assays, and gene expression studies.

The course consists of these three key components: laboratory work, oral presentations, and writing requirements. Because communication is an especially important component of scientific research, this course aims to improve your written and oral communication skills. Research "at the bench" will occupy the bulk of your time; however, you are also responsible for making oral presentations to the class and for writing up your research results in a format suitable for publication in The Journal of Bacteriology.

The first two weeks of the course will be a Molecular Biology "Boot Camp" in which the whole class will conduct a short project designed to help master some basic techniques. Following that, students will pursue an independent research project with a partner. The instructors and TAs work with students to choose a project and will then coach each team through its execution over the course of the semester, including the initial planning, the design of individual experiments, data interpretation, and technical troubleshooting.

Once each week we will begin class with a group meeting during which we will discuss issues of general or specific concern, explain protocols, and plan experimental strategies. During these meetings you will have the opportunity to hone your presentation skills through progress reports, journal club, and other presentations.

Written communication has been the standard for disseminating scientific achievements and new knowledge for centuries. Developing good scientific writing skills is thus a critical component of this course. You will be required to fulfill a number of writing assignments, culminating in a final paper (~15 pages) that describes your own research.

To give you some background on how Pseudomonas aeruginosa acts in vitro and in vivo, a list of relevant journal articles is provided.

Grading will be based on your performance in the areas summarized below. Although students in this course will typically work in groups of two, students are graded independently.

You are expected to attend class every day during the regular lab hours. You will receive a lower grade in this class if you do not show up on time.

You may find a need to stay late on occasion. With a prior notice, the TAs can stick around so that students may complete the day's experiments. However, the TAs will not look favorably upon you if you need to work late because you did not arrive on time or wasted time during the normal hours. If this is repeatedly the case, it will affect your final grade. Occasionally you may need plates taken out of the incubator or cultures started over the weekend. A member of the teaching staff can do these things for you at their discretion. The more organized you are about your request the more likely we are to say yes (e.g. prepare tubes with medium for us and label them clearly). Under no circumstances will you be allowed to work in the lab when no member of teaching staff is present.

At mid-term, we will hand out a written evaluation of your progress to date. The evaluation will give you an idea of your strengths and weaknesses. For some, the evaluation will be a "wake up call" which will identify deficiencies in experimental, technical, or communication skills. The grade will not be recorded; it serves to provide you with an opportunity to improve going into the second part of the term.

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