Exercises

From Computational Cell Biology

Contents 1 Modeling the Cell Cycle Exercise 1.1 A. Draw flow diagrams or concept map for the statements provided below. 1.2 B. Create the same concept maps in Stella. 1.3 C. What goes in the boxes? Reaction rates Exercise rationale 2 Virtual Cell Exercises 2.1 Virtual Cell and Key Concepts 2.2 Relevance of FRAP to courses 2.3 Experimental principle 2.3.1 Learning Goals 2.3.2 Materials Needed 2.3.3 BLG Tasks 2.4 Evaluation Forms

Modeling the Cell Cycle Exercise

Work in groups of 3. Work with people from different discipline. The goal of the lab is to become familiar with the software and the process of constructing a model.

A. Draw flow diagrams or concept map for the statements provided below.

1.Create a concept map of the following:

• inactive MPF becomes active MPF
• Active MPF becomes inactive MPF

2.Concept map the following:

• Cyclin is synthesized and degraded
• Cyclin stimulates inactive MPF to become active MPF

B. Create the same concept maps in Stella.

Intro to Stella Controls

How do we create a reaction in Stella? What are the factors in a reaction?

C. What goes in the boxes? Reaction rates Exercise rationale

1. Consider all reactions to be linear and based on the law of mass action (rate constant x substrate).

2. Use two of following set of rate constants in the rate equation: 0.05, 0.1, 1.0

3. Select initial concentration values for cyclin and MPF stocks in a range from 0.1 to 1. Choose at least three values to examine.

Write a notes (report) containing the following:

1. Describe the characteristics of one set of simulation results. 2. Describe briefly why you think you obtained the results you did? 3. What questions came up if any?

Exercise version 7/30/07

For additional work, try entering additional kinetic reactions and paramter values from the table

Virtual Cell Exercises

Virtual Cell and Key Concepts

This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [1]

The first tutorial is based on FRAP. We use the FRAP Tutorial to become familiar with the Virtual Cell user interface and commands. What is outlined below is the experimental context and homework assignment that accompanies the tutorial.

Relevance of FRAP to courses

Course Relevance: Cell Biology, Biochemistry

Concepts

• Biology: diffusion, compartments

• Experiments: time series, fluorescent microscopy, wave lengths, lasers

• Data Analysis: image capture, image analysis

Experimental principle

Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

Learning Goals

Basic learning goals (BLG):

• To have students do data analysis
• To become familiar with constructing a simple model in Virtual Cell.

Advanced learning goals (ALG):

• extract data values from image files
• compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

Materials Needed

ALG: Image stack, image analysis data

• To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

• Image stack for extracting values using Image J:
  • Download and unzip image stack (Coming Soon).
    • Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

• Image analysis:
  • Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data [email Dr.Holmes].

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See spreadsheet of FRAP Homework obtained from [Dr.Holmes].

BLG Tasks

1. In excel, plot the data as a time series. Compare the plots, normalize based on t/msqi.

• To normalize data across images vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation created in Tutorial

What is needed in the simulation for an accurate comparison to experiment?

Evaluation Forms

Evaluation Tool for Cell Cycle and Modeling Course Module