Workshop Announcement
Travel Directions

Blue, blue, my world is blue
Authors          Audiences          Overview           Materials          Resources           Future Directions



Kathleen Duncan
Foothill College



Possible Audiences:

Freshman biology majors in an ecology, evolution, and systematics course (Biology 1C at Foothill College). This course is the third in a series and thus students should have completed a course in cell biology (Biology 1A) and a course in anatomy and physiology of plants and animals (Biology 1C). Additionally some students may have complete a lower division course in molecular genetics (Biology 1D).



Brief Overview

Develop two new laboratory modules and integrate three existing modules to introduce students to the the field of phylogenetic systematics and the tools available in the field of bioinformatics. These labs would be used after studying the basic principles of evolutionary theory.

Secondary goals include:

  1. Give a thorough introduction to the concept of model organisms in general and Arabidopsis in particular.
  2. Make connections between topics covered in all four courses (Biol 1A - 1D).

    Laboratory modules:

    Module 1 = Chemicules - fictitious organisms used to give students experience in building cladograms
    Module 2 = Patterns of HIV evolution
    Module 3 = Explore the phylogeny of the cryptochrome gene family in Arabidopsis
    Module 4 = Explore the phylogeny of the PAS domain (part of the blue light receptor) across diverse taxa including bacteria, fungi, animals, and other eukaryotes.
    Module 5 = One organisms, three genomes

General format of lab:

  • Students will be working in groups of 4 with six to eight groups/lab
  • During the first hour three of the groups will report on work from the previous lab. Each group alotted 5-10 min for presentation and 10 minutes of brainstorming with the class.
  • Instructor introduces next problem (15-30min)
  • Students work collaborativly in groups for 1.5 hours.
  • Students complete their work before the next lab period.

Background information on the cryptochrome gene family:

Plants have an extensive and complex network of responses to their environment (can't run, can't hide, can't pick up and move to a better neighborhood). Adaptation to light environment requires the ability to receive a light signal and translate that to a cellular and ultimately a developmental response. Plants have different responses to different wavelengths and intensities of light.

By analyzing mutations in Arabidopsis that affect the response of plants to blue light genetic elements of the response network were identified including blue light photoreceptors. Members of the cryptochrome gene family have diverse roles such as DNA repair, blue light phototransduction and circadian rhythm. (Note: in the plant blue light receptors there is no photolyase activity.)

Students will be asked to first explore the gene duplication and divergence events that have occurred in Arabidopsis. In the following lab, students will be asked to explore the phylogeny of this gene family in diverse taxa and speculate on the role of blue light receptors in bacteria, flowering plants, and animals (eg: what is a blue light receptor doing in the pineal gland?)



Project Materials

Existing resources:

  • Chemicules protocol and data set
  • HIV data set
  • Rubisco data set
  • McClade
  • Workbench

New resources that must be developed:

  • NA sequence data set for Arabidopsis cryptochromes
  • protein sequence data set for Arabidopsis cryptochromes
  • NA sequence data set for cryptochrome gene family in diverse taxa
  • protein sequence data set for cryptochrome gene family in diverse taxa
  • domain annotations for Arabidopsis protein sequence
  • entries for lab manual introducing Arabidopsis and blue light receptors

Resources and References


Future Directions

Module 6 = Two organisms, a shared genome - the story of leghemoglobin
Module 7 = The phylogeny of hemoglobins and the geography of hemoglobinopathies - the sickle cell and thalassemia stories
Module 8 = Photorespiration and global warming - the vulnerability of rubisco, global warming, and the related issues regarding human quality of life