Biology 365 Microbial Genomics Laboratory Conducts Research on Enterococcus

Velina Batchvarov | December 17, 2015
Two students use pipettes in the Sandbox Lab

Two students use pipettes in the Sandbox Lab
Image by: Anna Pinkert

Over the past semester, 15 senior biology students have been spending their Wednesday afternoons at the new Sandbox Laboratory in the Integrated Sciences Complex working with bacteria.

As part of the Microbial Genomics Laboratory, students isolate and analyze bacteria from the environment, using basic microbiological methods as well as molecular biology methods. The class is particularly focused on enterococcus, a common human intestinal bacterium.

The experience is designed so that the students can conduct a research project from start to finish. This type of hands-on work is at the core of the Sandbox concept: Each student creates his or her own learning experience within a team framework.

In order to scale up and enhance research opportunities for undergraduate students, College of Science and Mathematics Dean Andrew Grosovsky is using the Sandbox Lab as a model to promote team-based undergraduate research. The activities are supported through the generous funding that the college has received from Sanofi Genzyme to increase student success in STEM. The Sandbox Lab mimics the environment of a federally funded research lab and gives students the feel of working in a real research lab.

The enterococcus research students have been conducting this semester has real world applications. Some strains are serious human pathogens. High-level counts of the bacteria are the second leading cause for hospital infections. Students address questions about the bacteria’s ecology and how they may become disease-causing organisms.

Professor Mike Shiaris and his teaching assistant Casandra (Casey) Lyons challenged the students who signed up for the Microbial Genomics Laboratory to push themselves to work hard and try new approaches to problem solving.

The first part of the course consists of hands-on wet lab experiment. Students have been working on isolating bacteria, obtaining pure cultures, extracting genomic DNA from microbial isolates, PCR-amplifying target genes, cloning the PCR products, and sending out the cloned DNA for sequencing.

During the second part, which is a dry lab, students have been using computer-based bioinformatics methods to analyze DNA sequences and test hypotheses. They have been collaborating on data analysis by combining their data to analyze diversity using a visualization method known as a phylogenetic tree. They then compiled a research paper of their findings.

Lyons, who is a PhD student in biology, has noticed that the students have gradually become more confident in their ability to ask critical questions, to complete their work and interpret their results. When students finished their experiments, she shared a job posting for an entry-level bench scientist in molecular biology and asked what they thought of the job requirements. Students were excited to match most of the skills that they have learned in the Sandbox Lab with the job requirements.

Shiaris, who developed the Microbial Genomics Laboratory experience for the students, has designed the class so that the principles that students have been using in their own research are applicable to the biological research in general.

“They have the opportunity to deal with real science research in a simulated research environment,” Shiaris said.

Moreover, the students develop competency in both independent thinking and team interactions. Most of the students in Shiaris’ class enroll at a graduate school or become employed in biotechnology or biomedical research companies in the Boston metro area.

The cutting edge concept of the Sandbox Lab is its multi-functionality. It is designed to provide interactive experiences for various groups of students. Current projects include: The School for the Environment’s “Science and Service in the Park,” engaging undergraduates through doctoral-level students, and the Biology’s Department’s Lego Robotics class for students who are learning computer programming. To read more about the current projects, visit the Sandbox Lab page.  

Tags: csm , isc , microbiology , research , sandbox , science , shiaris , undergraduate

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