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Experimental Genetic Analysis
Biology 256
Fall 2005

Dr. Karen Hicks
Fischman 102
PBX 5379
office hours: TR 9-11 AM, W 12-1 PM, 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 mutant alleles in specific genes of interest. 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 (of your choice) OTHER than Arabidopsis.

Prerequisites: BIOL114 and either BIOL 109-110 or BIOL 109-111.


Required textbook: Advanced Genetic Analysis; Hawley and Walker, 2003. This book covers the principles of modern genetic analysis and provides excellent background reading for the projects we will be undertaking in this course.

Lab handouts. I will be distributing lab handouts that absolutely MUST be read prior to coming to class in order for us to make the most effective use of our time.

Additional required readings.
Additional readings in the form of primary and secondary journal articles will be assigned throughout the semester and will be available in the library, on the web, and/or on the P drive.
Again, assigned readings MUST be read prior to coming to class.

Suggested readings.
I will make available many of my genetics textbooks in the laboratory on a "reserve" basis - these textbooks are not to leave the lab. In addition, you may find Biological Science (Freeman) and The Cartoon Guide to Genetics (Gonick and Wheeler) to be useful "refresher" texts. These are available in the bookstore. In addition, I have a number of copies of each of these and will lend them out on a first-come first-served basis.

 Course assignments and evaluation

Each student's work will be evaluated based on written accounts of experimental work as well as laboratory participation and performance.  The final grade will be based on the following components:

Laboratory notebook.  40%
Keeping a neat, organized, and detailed lab notebook is essential for any scientist. It should be thorough enough that another individual could repeat or continue your study. 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
Keep your notebook up to date as you work; never re-copy your notes later, as you could make an error while re-copying.  Before leaving lab, you must meet with me to show me your notebook.  At that time I will mark each notebook to indicate that I have reviewed it, and point out any problems that I see at that time.  In addition, notebooks will be handed in to be graded on a regular basis (see schedule). The notebook grade is a substantial portion of your course grade.  
I recommend that you use a three-ring binder for your laboratory notebook, as we will be simultaneously carrying out a number of projects during the semester.

Problem sets.  15%
Problem sets will be assigned in order for you to further practice the genetic concepts and approaches covered in this course. You are expected to work on these independently.

Project proposal.  25%

As a culmination of your work, you will propose a genetic approach to understand a biological process of your choice. You must choose a model genetic organism OTHER than Arabidopsis for your project proposal.

Participation (attendance, participation, and performance in lab).  20%

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.
General Policies and Expectations

Attendance. Attendance is mandatory for all fourteen scheduled laboratory sessions.  Make-up labs will not be possible.  If you know that you will miss a Tuesday afternoon lab session (i.e. because of sporting events), see me as soon as possible. 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, usually at their convenience. Each student will be issued a key to the lab for this purpose.

Preparation. Proper preparation will be essential for completing the exercises in a safe and timely fashion.  Assigned reading material is to be completed before coming to class.  You should be familiar with the protocols to be used before class time.  Handouts and protocols will be distributed in class over the course of the semester.

Safety. 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.

Cleanliness. 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.

Late penalties.  A penalty of 5% per day will be exacted for any written assignment turned in late.

Advice on how to do well in this course
Complete all 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.

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!


For assistance related to a physical, psychological or learning disability that may impact your ability to participate fully in the course, please speak with me and with Erin Salva, Coordinator of Disability Services (PBX5453;  All information and documentation of disability is confidential.

Lab schedule
In this course we will experience all the uncertainties associated with doing real science.  This schedule may need to be amended, especially as much of what we will do depends on having living organisms at the right developmental stage.  Announcements of changes will be made in class or via email.  However, deadlines for assignments will be consistently enforced
Date Topic  Reading assignments
Major assignments due
8/30 Introduction
Initiate EMS mutant hunt
H&W pp. xiv - xvi, 27-28, 31-42, 46-51
9/6 Continue EMS mutant hunt
Genetic analysis of new mutants
Design of genetic crosses
H&W 1-14, 55-60
9/13 Genetic crosses
Analysis of cross-progeny

H&W 60-79
PS 1 (genetic crosses) due 9/16
9/20 Linkage mapping I
H&W 151-169; EMBO workshop handout
Lab notebooks due 9/23
Linkage mapping II
H&W 168-193; PNAS (1991) 88:9828-9832

10/4 Linkage mapping III

10/11 October break - no class   PS2 (linkage) due 10/14
10/18 Linkage mapping IV
TIPS (2003) 8:413-416


Linkage mapping V

Plant Phys. (2000) 123:795–805; H&W 15-30, 51-54

Lab notebooks due 10/28
11/1 Linkage mapping VI
Map-based cloning

 PS3 (map-based cloning) due 11/4

Insertional mutagenesis & activation tagging Construction of transgenic organisms

Locating an insertion I

H&W 42-44, 82 - 106; Plant Phys. (2000) 122:1003–1013
Preliminary project proposal due 11/11

Locating an insertion II

Reverse genetic approaches

H&W 44-45; Plant Cell (1999) 11:2283–2290; PNAS (2000) 97:4985–4990
Lab notebooks due 11/18
11/22 Thanksgiving break
11/29 Locating an insertion III
H&W 107-118
12/6 No new topics / catch-up

12/13 Phenotypic analysis of TILLING-derived alleles Plant Phys. (2001) 126:480–484
Lab notebooks due 12/13 at end of class  
Final project proposal due 12/19 at noon.
Useful links


last updated 110705