This project was prepared as part of a BioQUEST faculty development workshop entitled ASM/BioQUEST Bioinformatics Institute at American Society for Microbiology in March 2006. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

Upcoming events               BEDROCK Problem Spaces

Bad Hygiene or Bad Bug? (Investigation of C. difficile outbreak and toxicity using bioinformatics tools, case-based approach, and molecular genetics simulation using CaseIt software; linked with Project 2 above)
Authors          Audiences          Overview           Materials          Resources           Future Directions



Ruth A. Gyure
Western Connecticut State University

Karen Klyczek
University of Wisconsin-River Falls

Mark Bergland
University of Wisconsin-River Falls

Susan Godfrey
University of Pittsburgh


Possible Audiences:

Entry level courses in biology or microbiology  


Brief Overview:

Investigation of the molecular basis for strain differences in Clostridium difficile pathovars associated with recent outbreaks of severe C. difficile-associated disease in North America.  


Project Materials:

Currently a few tcdC sequences from outbreak-related and historical C. difficile strains, obtained from GenBank (NCBI).  


Resources and References:

(1) McDonald et al, New England Journal of Medicine 353(23): 2433-41, Dec. 2005. This paper presents evidence that outbreak-associated strains have a deletion in the gene for a down-regulating protein that controls expression of a pair of toxin genes, and share also antibiotic resistance and other features. (2) Case It!, a source of software that provides simulation of restriction digestion, PCR, Southern blotting, and PFGE (in silico performance of experiments that were used to generate data relevant to the case). These methods are currently prominent in epidemiological investigations involving C. difficile. (3) Biology Workbench Biology Workbench This resource facilitates use by novices of DNA and protein sequence analysis tools for generating multiple sequence alignments, rooted & unrooted trees, and other goodies. (4) NCBI, resources such as BLAST & PubMed for finding and downloading DNA sequence data and related materials and locating relevant journal articles.  


Future Directions:

Write a finished case incorporating these materials to be used in classroom settings and for dissemination to interested teachers. This includes generating text for background and other support documents, identifying additional print resources students can use, collecting a dataset of sequences of relevant C. difficile genes from various sources, both historical and outbreak-related, and fleshing out the interfaces between the case documents and the Case It! and Biology Workbench tool collections.  



- Bad hygiene or bad bug.ppt