“Ocean viruses: From isolates to genomes” — A laboratory course

Taught Spring 2009, 2010, 2011 at Tucson High Magnet School. Supported by NSF grant (DBI-0850105) and NSF-funded UA K-12 BioME graduate fellowship program.


Matt Sullivan, Margaret Wilch, (pictured at left), Tucson High School science teacher and 2008 Arizona Bioeducator of the Year, Bonnie Poulos, Assistant Staff Scientist, collaborated in developing the original curriculum and lab protocols. Jennifer Brum, post-doc, assisted with their revision in 2010. Graduate student Matt Herron assisted with the class as a BioME fellow in 2009. Graduate student Bonnie Hurwitz contributed the section on genome assembly and annotation. In 2011, Natalie Solonenko, research assistant, worked on the lab protocols, and undergraduates Ryan Schenck and Eric Andersen assisted in the lab and classroom.


Outline of 2010 curriculum

Presentations and protocols for download

    1. Isolation of cyanophages
      • Isolate oceanic viruses from the Tara Oceans expedition that infect oceanic cyanobacteria (Prochlorococcus and Synechococcus)


    1. PCR screen for and sequence diagnostic genes in the resulting isolates
      • Use pcr (polymerase chain reaction) primers to screen isolated viruses for 3 genes:
        • psbA (photosynthesis gene) – all isolated viruses should have this
        • g20 (viral capsid assembly gene) – only myoviruses should have this
        • DNA pol (DNA polymerase gene) – only podoviruses should have this
      • Use sequences of these genes to phylogenetically characterize the isolated viruses
      • Develop hypotheses about what types of viruses have been isolated based on results from pcr and sequencing


    1. TEM analysis of isolated viruses
      • Use TEM (transmission electron microscopy) to look at the isolated viruses and test hypotheses
    2. Assemble, annotate, and analyze genomes of viruses isolated in last year’s class
      • Use cutting-edge bioinformatic analyses to gain information about the isolated viruses from their sequenced genomes

  1. Trip to Biosphere 2
    • Use a newly-developed method to collect samples for analysis of viruses at the Biosphere 2 Ocean habitat