This project was prepared as part of a BioQUEST faculty development workshop entitled Implementing Bioinformatics in Introductory Undergraduate Biology Courses:
Exploring Microbiology, Molecular Data and Visualization
at San Diego Supercomputing Center in January 2007. 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:

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Escherichia coli O157:H7 Outbreak from Fresh Spinach
Authors          Audiences          Overview           Materials          Resources           Future Directions



Jianmin Zhong
Humboldt State University

H. Neval Erturk
Converse College

Juanita Quevedo
Sweetwater Union High School District


Possible Audiences:

Students in High School and College Biology, Microbiology, General Biology, Medical Microbiology, Bioinformatics, Genetics, Molecular Biology, Evolution

Learning Goals
* Investigate the origin of virulence genes
* Understand the factors that contribute to virulence
* Demonstrate proficiency in using bioinformatics tools
* Identify protein functions based on homology searches


Brief Overview:

* Infection with E. coli O157:H7 is a public health problem of serious concern. As of 1 PM (ET) October 12, 2006, 199 persons infected with the outbreak strain of E. coli O157:H7 had been reported to the CDC from 26 states.
* The 2006 North American E. coli outbreak was linked to a large quantity of bagged spinach contaminated with the E. coli O157:H7 strain.
* E. coli O157:H7 is an enterohemorrhagic strain of the bacterium E. coli and an emerging cause of foodborne illness.
* Infection leads to diarrhea, bloody diarrhea, and haemorrhagic uraemic syndrome (HUS).
* Most illnesses have been associated with eating undercooked, contaminated ground beef, although, it is also transmitted via person-to-person contact, eating produce, drinking unpasteurized milk or swimming in or drinking contaminated water.  


Project Materials:

Microbial Genome Resources
Biology WorkBench
Protein Data Bank



Resources and References:

• Virulence gene sequences associated with E. coli O157
• Verocytotoxin (VT)
• Intimin (eaeA)
• EHEC-haemolysin E (hly)
• Type II secretion (etpD)
• Catalase-peroxidase (katP)
• Serine protease (espP)
• Fimbriae (fimA)
• Virulence protein sequences associated with E. coli
• Enterohemorrhagic E. coli (EHEC). Welinder-Olsson C, Kaijser B. Scand J Infect Dis. 2005;37(6-7):405-16.
FDA October 2006


Future Directions:

Learning outcomes

• Obtain nucleotide sequences of given virulence factors using NCBI or PDB
• Find homologous sequences using Biology Workbench
• Perform a multiple sequence alignment of homologous sequences using ClustalW
• Create a rooted or unrooted phylogenetic tree
• Develop a theory of virulence factor origin using generated phylogenetic tree
• Identify functions for virulence factors given (hint: use BLAST)



- 1gg9_pdb_catalase.txt
- 1jqt_pdb_type_II_secretion.txt
- 1mt0_pdb_haemolysin.txt
- 2ane_pdb_protease.txt
- E[1]._coli_O157_review_1.pdf
- Fimbrea_1o9z_pdb.txt
- Intimin_1f02_pdb.txt
- Verocytotoxin_1qoh_pdb.txt
- Verocytotoxinprotein.txt