Background videos produced by undergraduates provide students with the context necessary to understand the Galaxy-based bioinformatics activity. In the bioinformatics workflow, students analyze authentic soil and water metagenomic sequence files for the presence of antibiotic resistance genes.
Meet the PARE-Seq undergraduate developers
It is recommended that students watch all five background videos here prior to the bioinformatics activity (also available on the Background page). In particular, we suggest they focus on video 4 (Spotlight on Antibiotic Resistance Genes of Clinical Significance) and 5 (Tools of Bioinformatics) below.
- Basic overview of bacterial targets of antimicrobial compounds
- Antibiotics as providing selective pressure for natural selection
- Mechanisms of resistance (e.g. efflux, pumps, inactivation of the antibiotic, etc.)
- Introduction of One Health concept
- Bacterial/organismal spread (through water, food, soil, animals, etc.)
- Molecular spread (transmission of resistance genes from bacterium to bacterium)
- Explanation of how antibiotic resistance in the environment is linked to human health
- Conditions in low income countries that contribute to resistance
- Conditions in high income countries that contribute to resistance
- Interview with Dr. Maya Nadimpalli (environmental resistance in low income countries)
- Why the genes studied in PARE are of interest to clinicians (blaNDM-1, blaCTX-M-15, tetA, tetO, tetM, armA, and mcr-1
- What antibiotic is inhibited by each gene product
- Mechanism of resistance for each
- Molecular vs. culture-based approaches to environmental surveillance
- PCR-based vs. sequenced based molecular approaches
- The advantage of long-read, Nanopore sequencing technology for our work
- Interview with Dr. Amy Pickering
Analyzing a Metagenomic Sample in Galaxy
This video covers the concepts of evolutionary conservation and homology that underlie bioinformatics research. We discuss the Bioinformatics workflow in the Galaxy online platform and interpreting the key outputs of Galaxy workflow.
This video provides step-by-step instructions on how to use the Galaxy bioinformatics workflow in the PARE-Seq module.
Please complete the following Quiz and Post-Assessment surveys as instructed within the course curriculum. More information can be found in the materials at the start of each survey.
- Background Videos 1-5
- PARE-Seq sequence analysis
- Lab Report Assignment
- Poster Assignment
- Step-by-Step Instructions
- Instructor Manual
- Discussion Toolkit
- Webinar for instructors (YouTube)