Determination of Evolutionary Relationships Using

Introduction

This activity introduces students to molecular biology software tools which allow scientists rapid access to protein and genetic sequence databases and sequence analysis tools which reside on numerous remote machines located throughout the world, via a web browser such as Netscape or Microsoft Explorer. Developed to facilitate the work of scientists well familiar with the myriad of established protein and DNA sequence databases which often differ significantly in communication syntax, Biology Workbench possesses a fairly high learning curve and appears quite foreign to anyone unacquainted with the databases or analysis tools made more accessible through the Biology Workbench interface.

In December, 1997, as part of its charge and in response to recent reports on the need for expansion of technological efforts to achieve the goals of current education reform, the Education Division of NCSA began efforts toward development of an Education Version of Biology Workbench, presently known as Biology Workbench Education Enhancements. Scaled-down from the full professional version, Biology Workbench Education Enhancements provides a more limited menu of databases and fewer options for database query, effectively leading new users to more successful early use experiences. You will not only be using this software tool over the next several class periods, you will be playing a role in critiquing it in its current form and shaping its future direction.

Activity #1 Instructions

1. Begin by obtaining an evaluation form from your teacher or print a copy of the online evaluation form.
2. Working either individually or with a partner, go to the Biology Workbench Education Enhancements Home Page (http://bioweb.ncsa.uiuc.edu/educwb/). Read that page and jot down any impressions you'd like to share with the developers.
3. Read the section entitled Introduction to the Biology Workbench (http://glycine.ncsa.uiuc.edu/educwb/introtobwb.html). Jot down any impressions you'd like to share with the developers.
4. Press the "Home" button in the bottom left corner of that page, which will return you to the Biology Workbench Education Enhancements Home Page. Select the "Tutorials" option and click to bring you to our project of major focus, Ajit Chary's "Myoglobin as a Probe for Understanding Molecular Evolution" (http://glycine.ncsa.uiuc.edu/educwb/tutorials/myoglobin/myoglobinintro.html).
5. Examine the page, jotting down any comments you deem appropriate for the developers of the page.
6. Move to the next page (http://glycine.ncsa.uiuc.edu/educwb/tutorials/myoglobin/myoglobin01.html ) by clicking the "Next" button. Jot down any comments you deem appropriate.
7. Continue this effort for each of the pages in the tutorial. Follow the directions, being certain to jot down your thoughts as they occur for each of the pages with URLs ranging from myoglobin01.html through myoglobin14.html. If you attempt an action which causes difficulties or is unclear, be certain to state so on your evaluation sheet.
8. Turn in the completed evaluation form once completed.

Activity #2 Instructions

1. Working either individually or with a partner, go to the Biology Workbench Education Enhancements Home Page (http://bioweb.ncsa.uiuc.edu/educwb/).
2. Using the protein of your choice, select ten species of your own choosing (a minimum of five should be arthropods).
3. Perform a protein comparison following the entry procedure you learned during Activity #1.
4. Print your resulting similarity tree. Did the comparison yield any surprises? If so, what were they? How can you explain them?
5. Write up this activity using your standard classroom lab report format or an alternate format suggested by your teacher.