Overview

The Ciliate Genome Consortium is an NSF funded collaborative research initiative that involves undergraduate students in the functional annotation of genes from Tetrahymena thermophila. The recently completed sequencing of the Tetrahymena genome revealed ~28,000 genes, but only ~200 have been functionally characterized. Exploring the remaining genes through localization, expression, and gene knockout or over-expression studies will provide valuable information on gene function to the research community.

The research activities are packaged as modules for integration into existing undergraduate laboratory curricula in molecular or cell biology. Each module exposes student to basic molecular techniques in the context of a real research problem. Through these modules, students engage original research and produce novel results that may then be published and disseminated through the gene database contained within this website, which is also linked with the official Tetrahymena Genome Database (TGD).

The consortium is based at the Joint Science Department of Claremont McKenna, Pitzer, and Scripps Colleges in Claremont, CA. Any interested institution, class, or individual student is encouraged to join the consortium and participate in these research projects. For information on how to get involved, please go to Getting Involved on this site.

Research Modules - short descriptions:

Bioinformatics Module (3-4 hours)
This module guides students through identification of a gene(s) of interest that belongs to a particular gene family, or that may be a homolog of a specific gene in another organism. It is used as a precursor to the other modules.

Students learn: how to retrieve gene information from various databases, the difference between genomic and coding sequences, gene structure (start and stop codons, introns and exons), gene translation tools, organism-specific codon usage, BLAST searching, sequence alignments, functional domain concepts, evolutionary sequence conservation.

Gene Expression Profiling (5 x 4-hour laboratory periods)
In this module students assess the relative amount of expression of a gene of interest throughout different stages in the Tetrahymena life cycle. The life cycle is complex and involves a number of physiological changes and DNA processing events (see Tetrahymena Facts). Gene expression is evaluated through assessing the relative production of gene transcripts at different time points in the life cycle by reverse transcriptase PCR, yielding an "expression profile".

Students learn: Standard molecular techniques (genomic DNA isolation, RNA isolation, cDNA synthesis, PCR, primer design, agarose gel electrophoresis, nucleic acid quantification), cytological analysis by fluorescence microscopy, effective data presentation, use of graphics software.

Coding Sequence Determination (5 x 4 hour laboratory periods)
The coding sequences of all putative Tetrahymena genes have been computationally predicted. These predictions now require experimental testing. In this module, students work in teams to identify introns, exons, and the 5' and 3' termini of gene transcripts and coding sequences by PCR.

Students learn: Standard molecular techniques (primer design, PCR, agarose gel electrophoresis, genomic DNA isolation, RNA isolation, cDNA synthesis, nucleic acid quantification), difference between genomic and coding sequences, introns vs. exons, basic gene structure, concept of 3' and 5' untranslated regions, effective data presentation, and use of graphics software.

GFP Tagging Module (9 x 4 hour laboratory periods)
This module was developed by Douglas Chalker, Washington University, MO. Students engineer genetic constructs for the tagging and expression of a Tetrahymena protein of interest. Fluorescence microscopy is used to determine localization of the tagged protein.

Students learn: Standard molecular techniques (primer design, PCR, agarose gel electrophoresis, genomic DNA isolation, DNA quantification, basic cloning into vectors, recombination concepts, plasmid isolation, restriction enzyme analysis, bacterial and Tetrahymena transformation, DNA sequencing, Southern blotting), fluorescence microscopy, gene induction, expression cloning concepts, use of selectable markers, effective data presentation, and use of graphics software.

Gene Knockout Construction (10 x 4 hour laboratory periods)
In this module students engineer genetic constructs to delete individual genes from the Tetrahymena genome.

Students learn: Standard molecular techniques (primer design, PCR, agarose gel electrophoresis, DNA quantification, genomic DNA isolation, restriction enzyme analysis, bacterial transformation, cloning into vectors, plasmid isolation, DNA sequencing), site-directed mutagenesis, gene organization concepts, effective data presentation, and use of graphics software.

Gene Over-expression (under development)
Students engineer genetic constructs to over-express genes of interest.