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Experimental Genetic Analysis
Biology 256
Fall 2001

Dr. Karen Hicks
Higley 102
PBX 5379
office hours: MWF 11-12, R 2-4, and by appointment

Course Description

This laboratory course will introduce both genetic concepts and genetic approaches commonly used to understand biological processes. We will cover fundamental techniques in "forward" genetics including mutant screens, double mutant analysis, linkage mapping, and map-based cloning of genetic loci. We will also cover "reverse" genetic techniques including the identification and isolation of knock-out alleles in specific genes. We will use the model plant Arabidopsis thaliana as our experimental organism, although the approaches taken in this course can be applied to any organism amenable to genetic analysis. As your major course assignment, you will propose a genetic approach to understand a biological process (of your choice) in an organism OTHER than Arabidopsis.

Prerequisite: BIOL114 (7, 14) and either BIOL 109-110 (9-10) or BIOL 109-111 (9-11).


Lab handouts, journal articles and appropriate background reading will be assigned throughout the semester. A textbook is not required for this course, although many of my genetics textbooks will be available in the laboratory (on a "reserve" basis). You may find LIFE: The Science of Biology (Purves et al) and The Cartoon Guide to Genetics (Gonick and Wheeler) to be useful "refresher" texts.
Course requirements and grading scheme
Laboratory notebook. Keeping a thorough and organized lab notebook is essential for any scientist. Your notebook should be thorough enough that another individual could repeat or continue your study. Notebooks will be handed in to be graded on a regular basis. Note that the notebook grade is a substantial portion of your course grade - your notebook should reflect everything that you accomplish in this class. Most of your lab notebook will be produced in class, although your notebook should also include all other notes you take relevant to the course, including notes on library research you carry out, class discussions, ideas, etc. Keeping your notebook up to date at all times will likely improve your grade. At a minimum, your notebook should include:
the date, time, and place (lab, library, growth room, greenhouse, etc.)
the purpose of your experiment
a thorough description of the protocol you used (you may refer to the lab handout, but describe exactly what you did)
your original data and observations
your analysis and calculations
a display of the data in tables, graphs, figures, pictures
a summary/conclusion of the findings
a discussion of the problems you encountered
your plans/suggestions for future experiments
Problem sets. Problem sets will be assigned in order for you to further practice the genetic concepts and approaches covered in this course.

Project proposal. As a culmination of your work, you will propose a genetic approach to understand a biological process of your choice, and present this is both written and oral form. You must choose a model genetic organism OTHER than Arabidopsis for your project proposal.

Participation. Attendance and thoughtful participation in all laboratory activities/experiments and class discussions is mandatory, including periodic brief oral reports on your experiments. You will receive a zero for any lab period that is missed. Make-up labs will not be possible. You must let me know by the third week of class if you will miss more than one Tuesday afternoon lab session (i.e. because of sporting events). In addition, many of the experiments will require additional time than is allotted in the three hour laboratory session.  Students are expected to do the work necessary to complete all the experiments. When a lab exercise needs to be completed outside of the scheduled class period (before or after the scheduled class time), I will be available to assist.

  • Laboratory notebook                                                     40%

  • Problem sets                                                                  20%
  • Project proposal                                                             20%
  • Attendance, participation in discussions,                        20%

  •         brief oral reports, and performance in lab
    Late penalties
    A penalty of 1/3 of a grade per day will be exacted for any written assignment turned in late (that is, an "A" will become an "A-" if it is turned in one day late, etc.). Oral presentations may only be given on the assigned date (no late presentations will be accepted).
    Advice on how to do well in this course
    Complete any assigned reading (including lab handouts) BEFORE coming to class.
    Attend every class. Ask questions. Participate in discussion. Pay attention to details.

    Keep a thorough and detailed lab notebook. Keep your lab notebook up to date at all times.

    Turn in all assignments on time.

    Ask for help when you need it.


    You are responsible for your own safety during laboratory classes. The most important safety rule is to think before acting. Wear protective devices whenever needed including eye protection, lab coats, and gloves. If you have a question about a safety issue, stop the experiment and ask.
    Laboratory practice
    You are responsible for the equipment and space that you use - please leave the equipment and laboratory/plant growth spaces in the same (or better!) condition than you found them. Clean all glassware, potting supplies, benchtops, and instruments thoroughly.
    Academic honesty
    I strongly encourage you to exchange information, discuss class material, and bounce ideas off of one another (and me).  However, all work submitted for evaluation must be your own, and all contributions from others must be explicitly acknowledged (state who you worked with and the nature of the interaction). This class will follow the official Kenyon College position on academic honesty. It is your responsibility to review the official College policy on academic honesty and adhere to this policy. If you have questions or are unsure, please ask!
    The college will make reasonable accommodations for persons with documented disabilities. Students should notify the Coordinator for Students with Disabilities, Erin Salva, located in the Office of Academic Advising and their instructors of any special needs. Instructors should be notified sometime during the first two weeks of class.
    Lab schedule
    ** This schedule may be updated during the semester. **
    Date Topic Major assignments due
    8/28 Introduction  
    9/4 Activation tagging, transgenic organisms  
    9/11 EMS mutant hunt  
    9/18 Genetic analysis of new mutants, genetic crosses  Lab notebooks due 9/20
    9/25 No new topics  Genetic crosses problem set due 9/27
    10/4 Reverse genetic approaches, RNA interference  
    10/9 No class  
    10/16 Linkage mapping Lab notebooks due 10/18
    10/23 No new topics Linkage analysis problem set due 10/25
    10/30 No new topics  
    11/6 Quantitative trait analysis, use of naturally occuring variation  
    11/13 Map-based cloning Preliminary project proposal due 11/14 or 11/16
    Lab notebooks due 11/15
    11/20 Thanksgiving break  
    11/27 No new topics Map-based cloning problem set due 11/29
    12/4 No new topics  
    12/11 Project proposal powerpoint presentations Lab notebooks due 12/11 
    Final (written) project proposal due 12/14
    Useful links


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