SEA-PHAGES: A nation-wide and collaborative discovery-based laboratory course for undergraduates on bacteriophage diversity

Project Location

MD
US
The PHAGES course engages undergraduates with little or no background in college-level biology in authentic research, providing them opportunities for significant contributions to the field of genomics as they learn to think like scientists.

Student Audience

Introductory, Major, Non-major

Scientific Domain

  • Bioinformatics/Computational biology
  • Evolution
  • Genetics/Genomics
  • Microbiology
  • Molecular and cellular biology

Nature of the Research

  • Wet lab/bench research
  • Informatics/computational research
  • Basic research

Core Concepts

  • Evolution: The diversity of life evolved over time by process of mutation, selection, and genetic change.
  • Structure and Function: Basic units of structure define the function of all living things.
  • Information Flow and Exchange: The growth and behavior of organisms are activated through the expression of genetic information in context.
  • Systems: Living systems are interconnected and interacting.

Core Competencies

  • Applying the process of science
  • Using quantitative reasoning
  • Communicating and collaborating

Guiding Questions

  • How diverse is the viral population for a given bacterial strain, species, or phylum?
  • How has the viral population evolved?

Learning Objectives

  • Aseptic Technique
  • Culturing bacteria
  • Isolating bacteriophages
  • DNA extraction and manipulation
  • Genome annotation

Overview

The PHAGES course is a year-long discovery-based laboratory course.
In the first semester, students isolate bacteriophages from local environmental samples, purify and characterize their phages, and extract DNA for further analysis. By the end of the first semester, the students will have selected phages for whole genome sequencing. During the break between semesters, the DNA is sequenced and the sequence is then returned to the students.
In the second semester, the students employ bioinformatics methods to annotate their phage’s genome sequence. After quality control checks, the students’ annotated sequence is submitted to the National Center for Biotechnology Information GenBank database.
At the end of the school year, a student and a faculty member from each SEA school will be invited to the annual SEA‐PHAGES Symposium, which is a student‐centered scientific meeting

References

Pope et al. 2015. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife. doi: 10.7554/eLife.06416.

Getting Started

For an up-to-date list of resources required to offer the PHAGES course, please review the SEA-PHAGES Program Announcement at https://www.hhmi.org/programs/science-education-alliance