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A Course-Based Undergraduate Research Experience (CURE) Using Transposon-directed insertion sequencing (TraDIS) to Identify Genes Required for Bacteriophage P1 Propagation in Escherichia coli

ABSTRACT: Understanding gene function through forward genetic screens remains foundational to microbial genetics. Here, we describe the design and implementation of a multi-week course-based undergraduate research experience (CURE) embedded within a third-year Microbial Genetics course. In this CURE, students construct a high-density Tn5 transposon insertion library in Escherichia coli, challenge the library with bacteriophage P1, and use Transposon-Directed Insertion-site Sequencing (TraDIS) coupled with statistical analysis (edgeR) to identify genes required for phage propagation. Students perform transposome electroporation, phage infection assays, genomic DNA extraction, high-throughput sequencing data processing in Galaxy, differential insertion analysis, visualization in Artemis, and Gene Ontology enrichment analysis. The project integrates wet-lab microbiology, molecular genetics, and bioinformatics while modeling an authentic forward genetic screen. This CURE emphasizes experimental design, genome-wide functional analysis, statistical reasoning, and interpretation of large-scale sequencing data. The curriculum is adaptable to other bacterial species, phage systems, or selective pressures and provides a scalable framework for integrating authentic genomics research into upper-level microbiology courses.

ORGANISM(S): Escherichia coli BW25113

PROVIDER: GSE319528 | GEO | 2026/09/09

REPOSITORIES: GEO

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Project description:Bioinformatics, a discipline at the crossroads of Biology and Computational Sciences, also referred to as Computational Biology, is nowadays widely spread in research programs. However, implementing any Bioinformatics projects requires the ability to comprehend biological concepts and apply computational approaches, and rare are the undergraduate programs offering such multi-disciplinary training. In addition, understanding the dynamic between Biology research projects and Bioinformatics analyses is challenging with no real-life experience. Course-based undergraduate research experience (CURE) courses are innovative programs that allow more students to acquire research experience and provide the perfect setting to introduce students to applied bioinformatics. As a part of the Bachelor of Health Sciences of the Cumming School of Medicine at the University of Calgary (Canada), a CURE applied bioinformatics was implemented in the Winter of 2023 to 2025. Students investigated the effect of structural variants (SVs, genetic variants larger than 50 bp) on gene expression in the model organism Caenorhabditis elegans (a hermaphrodite 1-mm long roundworm). The students detected and characterized SVs by analyzing genome and transcriptome sequencing data of C. elegans strains called balancers, as they are known to carry large genomic variations balancing regions of the genome by limiting recombination and allowing maintenance of lethal mutations. They used Galaxy, a public web-based supercomputing resource, but also a local High-Performance computing system, and R, to report different effects of SVs on gene expression and splicing. Students’ research explained the molecular mechanism behind the uncoordinated phenotype caused by the reciprocal translocation eT1(III;V) and uncovered unexpected effects on gene expression on an understudied gene. We evaluated the course’s impact on student learning journeys and showed that the CURE favored students’ understanding of the Bioinformatics field and fostered their research interest. We provide here guidelines to facilitate the CURE implementations to improve access for undergraduate students to bioinformatics research experiences.

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A Course-Based Undergraduate Research Experience (CURE) Using Transposon-directed insertion sequencing (TraDIS) to Identify Genes Required for Bacteriophage P1 Propagation in Escherichia coli

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