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Molec Biol of Model Systems (Module 3)
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Molecular Biology of Model Systems

Molecular Biology of Model Systems - module 3

Biology 491H

Spring 2007


Class meeting

Thursday and Friday: 1:25 pm-4:25 pm


Morrill 107


Ana L. Caicedo

Office:Morrill 420G

Office hours available by appointment.


Phone: 545-0975

Teaching Assistant

Alicja Bledzka



Welcome to module 3 of the Molecular Biology of Model Systems class! In this unit we will examine how touch stresses can affect gene expression in the model plant A. thaliana. You will learn how to extract and quantify RNA, use web resources to design primers, and evaluate patterns of gene expression by using RT-PCR. You will design your own experiment to assess the expression of genes responsive to touch. This means that the research you will be performing will be novel and original. As with all scientific research, there is a small chance that your experiment may not succeed; we will, of course, do everything possible to carry out successful experiments, but you will also find that there is much to be learned from occasional failures.

For this unit you will need to have a bound lab notebook (you can continue using the one you used for module 1). You will also find it helpful to have a binder, where you can keep your background readings and protocols, and a USB flash drive, to store your presentation and the data you get off the web. Below is an overview of what we will be doing in each lab session. You should check the course website ( often to download protocols and required background reading for each class. Each day of class will have its own preparation page.


In this module you will be evaluated on:

  • maintenance of a well-organized lab notebook (20%)
  • a written assignment related to the genes you will be studying and the primers you design (20%)
  • an oral presentation of your experimental results (60% of grade)

The written assignment and oral presentation will be carried out with your lab partner or group, but each person should turn in an individual lab notebook. Details about the expectations and grading will be provided with each assignment link.


The class schedule can also be viewed by clicking on the link in the Navigation Tree. Be sure to check the preparation page for each day of class, for the material you will need.

March 29, Lab 1: Introduction to plant stress, gene expression, and the TCH genes. Introduction to experimental design. Student teams design the experiments they will carry out.

March 30, Lab 2: Review of PCR and introduction to primer design. And the TAIR online databases (TAIR). Student teams design the primers they will use. First assignment due.

April 5, Lab 3: In class PCR and agarose gel electrophoresis; student teams check their primers. Review of RNA extraction and experimental protocol.

April 6, Lab 4: Plant stimulation, tissue harvest, and RNA extraction. UV spectrophotometry and quantification of RNA.

April 12, Lab 5: Introduction to reverse transcription and quantification of RT-PCR products. Normalizing reactions to a housekeeping gene. Student teams set up RT-PCR of extracted RNA.

April 13, Lab 6: Agarose gel electrophoresis of RT-PCR products; interpretation of expression results.

April 19, Lab 7: Oral presentation of experimental results; lab notebooks due.


There is no text book for this course. ALL reading materials can be found on the course website on the preparation page for the given day of class.

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Ana Caicedo --