BISC 219/F10

Fall 2010

Lecturing Faculty: Martina Koniger and Drew Webb

Laboratory Instructors: Melissa Beers and Tucker Crum
Study Group Leader/Course Peer Mentor: Catherine Cheng

Lecture: T/F 11:10-12:20
Lab: M 1:30-5; T 12:30-4; W 2:15-5:45; Th 1-4:30; F 1-4:30

Welcome to BISC 219!
Please complete two brief surveys BEFORE attending your first lab and lecture about interest and concept familiarity with genetics. These surveys are found at: [1] and at [2] (http://www.surveymonkey.com/s/5XPB32W and at http://www.surveymonkey.com/s/TYS8CTH)
The password for both surveys is posted to the welcome email message in your First Class Lab conference. Thank you for your participation. You will get a few bonus points at the end of the semester for completing the entry and the exit versions of these surveys.

Over the course of the semester you will perform experiments that encompass both forward and reverse genetics approaches to answer complex questions about gene structure and function using the nematode worm, Caenorhabditis elegans, as a model organism. You will gain familiarity with sophisticated molecular tools that are widely used to study gene location, regulation and expression.

The success of your experiments is largely in your own hands. Please read through the entire set of experiments before beginning a lab series and read again, carefully, the portion to be done in lab that day before starting your work. Try to avoid the “hands-on- brain-off” pitfall common to lab students; instead, think as well as do. Be aware of what is actually happening in your tube during each step of a protocol. Know where you are in the stepwise progression toward answering your experimental questions as you complete each part of an experiment or series. Success in these labs will depend on paying meticulous attention to detail and on following instructions precisely. It is equally important to understand the conceptual basis of your experimental design and its goals. By doing all this, you will eventually see the results of your faith and hard work: you will have modeled the way science is done by scientists.

Many of the reagents used in these experiments are expensive and they require many hours of preparation. In using them, please exercise care and common sense to avoid contaminating reagent stocks and to make sure you don’t “hord” shared reagents. A considerable amount of money has been spent to provide enough equipment of adequate sophistication so that each student will have “hands-on” experience. For example, you will be using micropipets for dispensing tiny quantities of solution very accurately. These micropipets cost approximately $250 each. Please treat all of the equipment with care so that many classes of genetics students can use them.

You will be required to follow specific instructions concerning the handling or disposal of materials. Please obey these instructions precisely, both for your own protection and to comply with established guidelines for use of these reagents. You should read the Wellesley College Safety Information at: Wellesley Safety. This site has specific safety information related to the type of experiments you will perform. There are times when you should wear gloves in lab to prevent contaminating your samples and also to prevent your samples from contaminating you. Please remember, however, that your gloves can be easily contaminated if you touch your face, hair, etc. and that you can contaminate door-knobs, computer keyboards, phones or other non-lab equipment with your gloves. Change your gloves often and never touch non-lab equipment (such as computer key boards) with gloved hands unless specifically directed to do so.

Be forewarned that you will be expected to come into lab outside of normal hours to collect data or to continue an experiment. We have tried to keep the extra time to a minimum, but please understand that BISC219 lab is an ambitious program in genetics requiring your full commitment and cooperation.

The three series of experiments you will perform during the semester are:
Series 1: Autosome or Sex Chromosome?

Series 2: Classical (Forward) Genetics: Locating & Characterizing a Gene Mutation Associated with a Abnormal Phenotype in C. elegans

Series 3: Reverse Genetics using RNA interference (RNAi)

You will be expected to keep a lab notebook of all the work done in these experiments. This notebook should be useful to you when you write your scientific paper on your work at the conclusion of each series of experiments. Protocols are provided in this wiki, but an outline or flow chart should be written by you before lab in your notebook. Do not just print and attach the directions found in the wiki. Prepare tables for results and do all calculations in your notebook.

Acquisition of scientific writing skills is a primary goal of the lab experience; therefore, writing about your experiments in the form of scientific research reports will constitute the bulk of your lab grade. The process of learning scientific writing will be aided through small practice assignments before you write a complete paper. There is a 5% per day penalty for late work. Unless there are exceptional circumstances, no work will be accepted for point credit more than one week after the due date.

Another good way to learn to write effectively about your work is to read well constructed research reports. Therefore, during the semester you will read and discuss several primary research articles that are related to your experiments.

We sincerely hope that you find your introduction to the world of genetics both exciting and intellectually stimulating. As always, we appreciate comments and suggestions for improving the program. Good luck and have fun!

Links to Labs& Project Info

Series1:
Worm Info
Lab 1: Worm Boot Camp & Sex-Linked or Autosomal Start
Lab 2: Sex-Linked or Autosomal Finale
Series2:
Background: Classical Forward Genetics and Gene Mapping
Lab 2: Mutant Hunt
Lab 3: Linkage Test Part 1
Lab 4: Linkage Test Part 2, Mapping and Complementation
Lab 5: Mapping Con't
Lab 6: Finish Complementation; Mapping Con't
Lab 7: Complete Mapping: Score
Series3:
Schedule of Reverse Genetics Project
RNAi General Information
Media Recipes
Lab 5: Picking your gene to RNAi
Lab 6: Cloning your gene of interest
Lab 7: Picking your transformant
Lab 8: Plasmid purification and transformation
Lab 9: Induction of bacteria for RNAi
Lab 10: Scoring your worms and RNA purification
Lab 11: RT PCR reactions