Using Comparative Genomics for Inquiry-Based Learning to Dissect Virulence of Escherichia coli O157:H7 and Yersinia pestis

Abstract

Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of Genomes database. In the second module, students use an alignment of five Yersinia pestis genomes to analyze single-nucleotide polymorphisms of three genes to classify strains into biovar groups. Students are then given sequences of bacterial DNA amplified from the teeth of corpses from the first and second pandemics of the bubonic plague and asked to classify these new samples. Learning-assessment results reveal student improvement in self-efficacy and content knowledge, as well as students' ability to use BLAST to identify genomic islands and conduct analyses of virulence factors from E. coli O157:H7 or Y. pestis. Each of these educational modules offers educators new ready-to-implement resources for integrating comparative genomic topics into their curricula.

Engaging Students in Authentic Microbiology Research in an Introductory Biology Laboratory Course is Correlated with Gains in Student Understanding of the Nature of Authentic Research and Critical Thinking

“…Open-ended investigations allow students to learn how science is performed by allowing them to do real research projects (17, 37, 44). Students learn more when they are given the freedom and opportunity to actively discover why and how things are the way they are (5, 33), and the earlier students get involved in research, the more benefits they will receive (9, 38). …”

“…Because involvement in this type of course can improve critical thinking skills and increase students’ enthusiasm for science and belief in their ability to perform scientific research (19, 21, 22), we created a novel microbiology research-based module that involves second semester freshman Biology majors at Purdue University in research early in their academic careers, similar to modules that have been described recently (5, 6, 13, 20). Within this module, we provided students with the same laboratory skills they would learn in traditional lab classes (pipetting, spectrophotometry, use of balance, preparation of dilutions, and basic statistics), but within the context of an actual research project.…”

A Survey of <i>Escherichia coli</i> O157:H7 Virulence Factors: The First 25 Years and 13 Genomes

“…The gene espP produces a protein that contributes to the bloody diarrhea in many patients suffering from E. coli O157:H7 infections through its role as a serine protease that may degrade host protein [62]. sapB predicted antimicrobial peptide transporter subunit; membrane component of ABC superfamily [68] sapC predicted antimicrobial peptide transporter subunit; membrane component of ABC superfamily [68] sapD peptide transport system ATP-binding protein [68] sapF peptide transport system ATP-binding protein [68] afuABC afuA periplasmic ferric iron-binding protein [64] afuB putative permease component of transport system for ferric iron [109] afuC putative ATP-binding component of a transport system [109] L7004 putative hemolysin expression modulating protein [5] kdtA 3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase) endotoxin system [105] Island with iron transport cluster Z4382 putative iron compound-binding protein of ABC transporter family [5] Z4383 putative iron compound permease protein of ABC transporter family [5] Z4384 putative iron compound permease protein of ABC transporter family [5] Z4385 putative ATP-binding protein of ABC transporter family [5] Z4386 putative iron compound receptor [5] Survival through host defense barriers katP bifunctional catalase/peroxidase [80] terZABCDEF terZ putative phage inhibition, colicin resistance and tellurite resistance protein [78] terA putative phage inhibition, colicin resistance and tellurite resistance protein [78] terB putative phage inhibition, colicin resistance and tellurite resistance protein [78] terC putative phage inhibition, colicin resistance and tellurite resistance protein [78] Continued terD putative phage inhibition, colicin resistance and tellurite resistance protein [78] terE putative phage inhibition, colicin resistance and tellurite resistance protein [78] terF putative phage inhibition, colicin resistance and tellurite resistance protein [78] ureABCDEFG ureA putative urease structural subunit A (gamma) [74] ureB putative urease structural subunit B (beta) [74] ureC putative urease structural subunit C (alpha) [74] ureD putative urease accessory protein D (p...…”

“…The strains used in this study for the lineage I sample set were all clinical isolates from humans and were composed of strain EDL933 from the 1982 Michigan ground beef outbreak [6], FRIK 533 a patient isolate from a Milwaukee outbreak from the Wisconsin state hygiene lab harbored in the culture collection of Dr. Charles W. Kaspar (Food Research Institute Kaspar), and fda518 a strain presumably from the Food and Drug Administration. The strains of bovine origin representing the lineage II sample set were farm isolates ne037 presumably from Nebraska, FRIK 2000 also referred to as strain 767-8-1 [94], FRIK 1985 also referred to as strain 396-2-2 [95]- [105].…”

Strategies for Using Peer‐assisted Learning Effectively in an Undergraduate Bioinformatics Course

“…Such inquiries result in the discovery of novel genes or new functional properties previously not known or attributed to particular organisms . Exposure to databases and various online computational resources can begin at the undergraduate level (, and references therein). The in silico nature of this undertaking may trigger unease among biology majors with little to no experience in bioinformatics.…”