PARE-Seq

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

Background Videos

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.

Understanding Antibiotics and Antibiotic Resistance

  • 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.)

>> Transcript

Antimicrobial Resistant Bacteria Spread: Through the Environment and Human Exposure

  • Introduction of One Health concept 
  • Bacterial/organismal spread (through water, food, soil, animals, etc.) 
  • Molecular spread (transmission of resistance genes from bacterium to bacterium) 

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Why Is Antimicrobial Resistance a Public Health Issue?

  • 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)

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Spotlight on Antibiotic Resistance Genes of Clinical Significance

  • 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 

>> Transcript

Tools of Bioinformatics

  • 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 

>> Transcript


Bioinformatics Activity

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.


Galaxy Tutorial

This video provides step-by-step instructions on how to use the Galaxy bioinformatics workflow in the PARE-Seq module.


Assessments

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.


Resources (Downloads)

Video Transcripts

  • Background Videos 1-5
  • PARE-Seq sequence analysis

Final Assignments

  • Lab Report Assignment
  • Poster Assignment

Galaxy Bioinformatics Activity

  • Step-by-Step Instructions

Instructor Materials

  • Instructor Manual
  • Discussion Toolkit