It is well established that high impact practices such as course-based undergraduate research (CUREs), promote higher retention, increased self-efficacy and higher sense of community for undergraduate STEM majors1,2, and for Professor Richard Pollenz from the Department of Cell Biology, Microbiology and Molecular Biology (CMMB) at the University of South Florida (USF), that experience comes to life in his labs.
Under the direction of Dr. Pollenz, who has run the Science Education Alliance Phage Hunters and Advancing Genomics and Evolutionary Science (SEA PHAGES) program since 2017, a diverse group of 32 first-year students are exposed to an authentic undergraduate research experience each Fall through enrollment in Introductory Biology Laboratory.
The SEA PHAGES program is a world-wide program with support from the Howard Hughes Medical Institute (HHMI), and the University of Pittsburgh. During this program students isolate and characterize their own novel bacteriophages (viruses that can kill bacteria) from soil samples that they collect. Since there are estimated to be 1 x 1032 different phage across the biosphere – enough that if laid end to end would create a line longer than the width of the Milky Way galaxy – every phage that is found is unique, thus each student has the opportunity to name the phage and they are ultimately archived in a national database for global scientific use. Since bacteriophages infect and kill very specific strains of bacteria, the phages that the students contribute to the database each year may be important in the development of new therapies that can be used to fight the increasing number of antibiotic resistant bacterial strains (such as tuberculosis) that have become one of the top health issues of our time.
Students in this course master fundamental processes such as aseptic technique, plating of bacteria, DNA extraction, and phage purification. They also evaluate their phages using electron microscopy, so they can see the morphology of the phage that they have isolated.
Since 2017, USF undergraduates have placed 107 novel phages into The Actinobacteriophage Database. In addition, a subset of the students from the SEA PHAGES discovery lab also enroll in an additional semester of research through the SEA PHAGES bioinformatics course, to complete the annotation of several genomes that are then published in the Genbank database through the National Center for Biological Information (NCBI).
During the SEA PHAGES bioinformatics course, the undergraduate cohort work as a team to analyze in detail all of the genes that constitute the phage genome. Phages have tremendous genetic diversity and the entire phage population evolves on a daily basis. To put that in perspective, consider that the ability of humans to walk evolved over millions of years, thus, phages represent a tremendous reservoir of novels genes. Nearly 70% of the genes within a specific phage genome have never been observed before and do not match to any known genes in any genetic database and many of the techniques that are now used for genetic engineering and gene therapy were found in phages and bacteria.
Students evaluate the genes and develop independent research projects and then complete presentations at the USF Undergraduate Research Symposium and the USF-hosted Pholoria Phage Phest, which is intended to further develop communication and public speaking skills. The Spring 2021 cohort also completed a manuscript that will be published as a Genome Resource Announcement.
To begin to analyze the function of the phage genes, USF became one of only eight institutions in the 2nd cohort of the HHMI SEA GENES initiative in 2020. SEA GENES is an upper level lab that acts as a continuation of the SEA PHAGES work, and in Spring 2021, 15 students completed the first semester of this initiative.
SEA GENES is designed to provide students an authentic research experience using upper level Cell Biology and Genetics labs. In GENES students clone the genes from one of their isolated phages and carry out advanced cell biology and genetics experiments to determine if expression of the different genes results in cytotoxicity (death) to the host bacteria or the expression can actually save the bacteria from phage infection (provide immunity). These findings may be important in the development of new antibiotics or in finding new tools that can be used in genetic engineering and health.
In Spring 2021, the SEA GENES students evaluated 62 genes from the phage Girr and found 13 genes that conferred toxicity and 1 that conferred immunity. This data has now been placed in a public database and subsequent cohorts of USF undergraduates will further analyze these genes and others from Girr to determine how and why they kill the bacteria or confer immunity.
The addition of the SEA GENES program means that an incoming first-year student will have the opportunity to complete up to two years of undergraduate research, all while taking their normal course load. Thus, students will gain key research skills but still maintain the ability to work or engage in other co-curricular activities.
Since 2017, many of the SEA PHAGES students have leveraged the experience they gained in the program to earn scholarships, research internships and admission to medical and graduate schools. Nearly all students who have engaged in the program have remained in their STEM major and enrolled at USF. CMMB is hoping to expand these programs over the next several years and continue growth in this area of research.
1Findley-Van Nostrand D. Pollenz, RS. 2017. Evaluating Psychosocial Mechanisms Underlying STEM Persistence in Undergraduates: Evidence of Impact from a Six-Day Pre-College Engagement STEM Academy Program. CBE: Life Sci. Edu. 16:ar36 2
2Kuchynka, S, Findley-Van Nostrand D and Pollenz, RS. 2019. Evaluating Psychosocial Mechanisms Underlying STEM Persistence in Undergraduates: Scalability and Longitudinal Analysis of Three Cohorts of a pre-entry STEM Academy Program. CBE: Life Sci. Edu. 18:ar41 3. Science Education Alliance.
Example publication with student authors from 2021:
Vanessa Franco, Kaylee Barnhill, Abbigail Biggs, Jackson Bland, Harris Choudhary, Trey Crogan, Alyssa Finocchiaro, Thomas Fuller, Christopher Handwacker, Zoe Howar, Mohammed Iqbal, Ann Matthew, Sydney Miller, Shivani Padhye, Emily Rainey, Arianna Rodriguez, Emma Stewart, Michael Chase, Louis Otero, Richard S Pollenz. 2021. Genome Sequence of VanLee a Novel Lysogenic Bacteriophage that infects multiple Gordonia strains, Microbacterium foliorum. Microbiology Resource Announcement, Jul 29;10(30):e0051921. doi: 10.1128/MRA.00519-21.