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In Silico Phage‐Hunting in Sinorhizobium Genomes: Incorporating Original Research in Undergraduate Molecular Biology and Microbiology Courses
Author(s) -
MartinezVaz Betsy,
Jensen Autumn,
Vang Mandy
Publication year - 2016
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.30.1_supplement.662.20
Subject(s) - in silico , biology , genome , computational biology , bacteriophage , bacterial genome size , sinorhizobium , microbiology and biotechnology , bacteria , genetics , rhizobia , nitrogen fixation , gene , escherichia coli
The study of bacterial viruses (bacteriophages) is an excellent tool to teach basic principles of molecular biology and microbiology. The availability of numerous complete bacterial genome sequences in public databases provides a unique opportunity for in‐silico ‐phage hunting. This approach consists of identifying and characterizing bacteriophages integrated in bacterial chromosomes using computational analyses. The objective of this project was to develop a set of investigative laboratory exercises to allow undergraduate students to participate in a study about the prevalence of bacteriophages in bacteria of the genus Sinorhizobium. These bacteria play a critical role in agriculture due their ability to form nitrogen‐fixing symbioses with alfalfa and related legumes. The role of bacteriophages in N 2 fixation and on the physiology of rhizobia remains largely unexplored. The first part of the project consisted of searching Sinorhizobium genomes for the presence of bacteriophages using PHAST, a bioinformatics tool that identifies viral sequences integrated in bacterial chromosomes. Further bioinformatics analyzes were conducted to determine the numbers and types of proteins encoded by the viruses. The students then designed several procedures to activate and excise the predicted bacteriophages out of the Sinorhizobium genomes. Exposure to UV light and Mitomycin treatments led to the successful isolation and molecular characterization of three novel bacteriophages. This set of laboratory exercises was field tested in two undergraduate molecular biology and microbiology courses. The learning objectives of the project were assessed by comparing the scores of pre and post‐tests and by evaluating the bacteriophage characterization protocols designed by the students. Post‐tests were higher than pre‐test scores at or below p=0.005 . Normalized learning gains showed improvement in the student's of bioinformatics analyzes skills, basic virology concepts and the structure and function of proteins encoded by bacteriophage genomes. Support or Funding Information This project was supported by a grant of the National Science Foundation.