Laboratory Introduction [ .pdf ] [ Course Home ]

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Class Structure:
We will be characterizing the ru5 mutation, which occurs in an unknown gene in C. elegans, using a number of cell biology techniques. For the first half of the class, we will be performing three sets of experiments I have devised. In the second half of the course, each of you will chose and design an independent project.

Lab Schedule: (Attendance in the laboratory is mandatory on Thursdays).
8/30 No lab
9/6 Lab safety. Lab 1: Mapping mutations.
9/13 Lab 1 continued. Begin Lab 2: pick worms for PCR
9/20 Finish Lab 1. Continue Lab 2: Lysis and PCR reactions
9/27 Finish Lab 2: Run Gels. Lab 3: collect eggs for antibody stain
10/4 Lab 3 continue antibody stain.
10/11 Lab 3 complete antibody stain. Work on independent research proposals
10/16 (Tuesday) Independent project proposal due
10/18 Meet to discuss proposal.
10/25 BREAK
11/1 Begin independent projects
11/8 Independent projects continue. Lab research paper 1 due.
11/15 Independent projects continue
11/22 Thanksgiving
11/29 Analyze results; Complete Projects
12/6 Oral Presentation of independent project results.
12/14 Lab notebooks due. Lab Research paper 2 due.

Many of the experiments we will be doing in this laboratory have never been done before and the outcomes of the experiments are unknown. Since we will be working with live animals, we may have to come to the laboratory on days other than the scheduled lab day. If we are doing an experiment that requires you to come to lab on a day other than Thursday and you have a scheduling conflict, please let me know ahead of time.

Keeping a laboratory notebook:
Keeping a laboratory notebook is required for the class. Please refer the Investigations manual for specifics on keeping a laboratory notebook (see pages 16-17, keeping a record).

Since the laboratory involves an independent research project, it is critical that you come prepared for each laboratory session. Prior to coming to lab, write out the general and specific objectives at the top of each lab page. To save time during the lab, include a step-by-step protocol for each lab in your notebook. As we perform the experiment, it is simple to indicate any changes from the standard protocol. You can also add volumes, numbers, times, dates, etc as you go along. When the lab is finished, be sure to include a summary of the results.

A laboratory notebook should be a record of the things you do during the lab. It should not be a record of the way things should have gone. The notebook should include details, so that someone else can understand what you did and repeat the experiment. For example, if you add twice as much buffer as the protocol says, put that in your notebook. These details can be critical for understanding why an experiment did or didn’t work.

• You will be required to turn in your laboratory notebook at the end of the term.
  

Writing a scientific paper:
Two scientific papers based on your laboratory work will be required for the class. Please refer the Investigations manual for specifics on writing a scientific paper (see pages 18-27). A scientific paper is a formal presentation of your laboratory work. Each paper will include an abstract, introduction, materials and methods, results, discussion, and bibliography. You are expected to do some research on the topic and should include relevant citations in each section.

• A write up of the first 3 laboratory projects will be due at 5 pm Thursday 11/8.
• A write up of your independent projects will be due at 5 pm Friday 12/14.
  

Oral Presentation of Independent Research
Each of us will be required to do a 12-minute oral presentation of the data gathered from the independent research projects. (Please refer to Investigations (p. 34) for information on what to include in an oral presentation). The purpose of this presentation is to discuss your actual data (whether the experiments worked the way you expected or not).

Laboratory Grading:

40% of your final grade for the course is based on your work in the lab.

• 10% of Final Grade: Laboratory Notebook
• 10% of Final Grade: Participation and Oral Presentations
• 10% of Final Grade: Scientific Paper 1
• 10% of Final Grade: Scientific Paper 2Independent Projects:
  

At the beginning of the Advanced Cell Biology labs we will do several types of experiments to introduce you to C. elegans, cell biology, and the ru5 mutation. In the second half of the course, you will design and work on an independent project. The independent project should focus on some aspect of C. elegans biology specifically related to the ru5 mutation or pharyngeal development.

The independent project should be fairly simple in design, similar to the experiments we do in the first three weeks of the laboratory. You should be able to complete the project in approximately 3 weeks of experimentation.

I recommend you talk to me about your ideas for a project well before the due date for the proposal. I am happy to discuss your ideas for experiments, help you focus your ideas into something feasible in 3 or 4 weeks of lab, and provide technical assistance. I also have several books on C. elegans biology and techniques that you may find useful for your project. If you are having trouble coming up with a simple project, please see me as soon as possible.

A written proposal will be due on October 16, 2001. This proposal should include a description of the hypothesis you are testing, references, an experimental design, a step-by-step outline of the experiment, and a complete list of strains, reagents, and equipment you will require. I have included a template for you to follow for your project.

I will meet with each of you individually on October 18 to discuss and finalize your projects. A project must be finalized before the Fall Break, to permit me to order strains, reagents, etc, that you will require for your experiments.