Course objectives

The goal of this course is for students to gain experience in common techniques of DNA manipulation and analysis. To achieve this goal, we will spend the first 3 - 4 weeks demonstrating commonly used molecular techniques, such as DNA extraction, PCR, cloning, sequencing, and microsatellite analysis. Subsequently, each student will pursue a research project of her/his own choosing, subject to approval by the instructor. These research project will usually be part of students' thesis projects, and should be designed to be doable within the time-frame of the course and should not involve unreasonable consumption of expensive consumables (see also course fees). Sometimes, this project will be preliminary work for a more extensive research project, which can be carried out in MMBL or elsewhere.

Prerequisites and textbook

As Fish 542 / Ocean 574 was not offered this year, there are no specific pre-requisites for the course. However, some knowledge of genetics will be expected - check out the Fish 542 website (ask Lorenz for password) and / or the Fish 444 website (ask Kerry Naish for password). I will select class participants primarily based on previous experience with genetics, both theoretical and practical, and the value and feasibility of their project. Priority will be given to students from the School of Aquatic and Fishery Sciences and the School of Oceanography, who may register in Period I of the registration period. Students from all other departments may register in Period II. You will need an access code to register, so come to see me to discuss things.

There is no specific textbook. I will provide my own personal copy of the three volume Sambrook & Russell laboratory manual on Molecular Cloning, which also has a website. I also have a copy of Hillis et al. (1996) Molecular Systematics, which is slightly out of date, but still useful. Please do not take these books home - use them in the lab or in the conference room, and return them to the assigned shelf. In addition, there are a lot of resources on the internet - links to some of those are provided on the links pages (protocols and software).

Format

There are lab sections on Tuesday and Thursday afternoons, when the whole class will work in the laboratory. Tuesday at 13:30 we will meet in the conference room down the corridor from the lab (room FTR 103) to discuss progress of projects and to answer any questions. After the initial training period, the laboratory will be accessible to students daily for the duration of building access (7:30 - 17:30). In fact, some overnight experiments will require that you also attend on other days - if this only can happen after hours, please come and talk to me.

Research Project

Each student will choose a research project in consultation with the instructor, and prepare a written research proposal (~5 pages) that outlines the project design, major methods to be used, and experimental goals. Many will have a project proposal already, and it will be ok to use that, as long as it follows the guidelines below (i.e. don't give me a 20 page proposal, and do present molecular methodology). See the proposal guidelines on the Grading page.

Each student should keep a lab notebook that records each day's activities. The lab notebook should be well organized and neat enough that someone else (not previously familiar with the work) could interpret what was done. See lab notebook section on the Grading page.

At some point around the middle of the quarter, we will hold a lab meeting in room FTR 103, in which each student will present his/her project and progress to date. At the end of quarter students will submit short written reports based on their proposals and lab notebooks, and will present their projects to the class for discussion.

Laboratory and Facilities

Please take note of rules on safety and equipment use.

Most of the labwork will be carried out in room FTR 129, including DNA extraction, setting up restriction digests, PCR and gel electrophoresis. You will each be assigned bench space, and will also be allotted space in a refrigerator to store samples or solutions that need to be refrigerated. You will keep all reagents/solutions that you make up for your personal research at your bench spot. All solutions and personal consumables should be clearly labeled and dated. Each pair of students will be assigned a set of pipettors. These are expensive, delicate pieces of equipment and need to be guarded and handled carefully - see the rules page..

Some other activities need to be carried out in MMBL in the Marine Studies Building. The following list gives you some activities and room numbers: