Loop-Mediated Isothermal Amplification (LAMP) as a Rapid, Affordable and Effective Tool to Involve Students in Undergraduate Research

Andrew V Nguyen; Amos Orlofsky; Kaylynn Pubill; Mangala Tawde; Gaozhen Li; Diana Mata; Oscar Bermudes; Miguel Fernandez; Jonathan Santana; Woochul Kim; Enzon Chimbay; Yeeun Kim; Trieu Nguyen; Malcolm Fox; Janelly Eralte; Molly Metz; Davida S Smyth; Caterina Panzeca; Mazhar I Khan

doi:10.3389/fmicb.2020.603381

Loop-Mediated Isothermal Amplification (LAMP) as a Rapid, Affordable and Effective Tool to Involve Students in Undergraduate Research

Front Microbiol. 2020 Dec 9:11:603381. doi: 10.3389/fmicb.2020.603381. eCollection 2020.

Authors

Andrew V Nguyen¹, Amos Orlofsky¹, Kaylynn Pubill¹, Mangala Tawde¹, Gaozhen Li¹, Diana Mata¹, Oscar Bermudes¹, Miguel Fernandez¹, Jonathan Santana¹, Woochul Kim¹, Enzon Chimbay¹, Yeeun Kim¹, Trieu Nguyen¹, Malcolm Fox¹, Janelly Eralte², Molly Metz³, Davida S Smyth³, Caterina Panzeca⁴, Mazhar I Khan⁵

Affiliations

¹ Department of Biological Sciences and Geology, The City University of New York, Queensborough Community College, Bayside, NY, United States.
² Department of Natural Sciences, Mercy College, Dobbs Ferry, NY, United States.
³ Department of Natural Sciences and Mathematics, Eugene Lang College of Liberal Arts of the New School, New York, NY, United States.
⁴ Department of Science, SUNY Maritime College, New York, NY, United States.
⁵ Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, Storrs, CT, United States.

Abstract

Undergraduate research (UR) is a high-impact practice (HIP) to engage undergraduate student in science, technology, engineering and mathematics (STEM), especially from underrepresented groups. UR experiences (UREs) can be integrated into the classroom, making authentic research experiences inclusive and available to all students. However, developing UR pedagogy can be challenging for faculty in resource-limited labs, such as community colleges and small liberal arts colleges. Often molecular biology research methods are expensive, time-consuming and need equipment not readily available or affordable in small schools. Polymerase chain reaction (PCR) is one of the most commonly used techniques in research labs and many UREs. We have investigated loop-mediated isothermal amplification (LAMP) as an inexpensive, accessible alternative to PCR for DNA amplification enabling the identification of microorganisms in the context of UREs. LAMP does not require expensive instrumentation or reagents and uses equipment commonly found in teaching labs. By performing the technique, students learn several key scientific skills that will be useful in their undergraduate or graduate STEM careers. We designed guided independent research experiences for several undergraduates that included the use of LAMP. Students successfully applied the technique to culture samples of common environmental bacteria, including Escherichia coli, Salmonella spp., Staphylococcus aureus, and Enterococcus, and were in addition, able to detect both Salmonella and Enterococcus in directly sampled environmental waters. To highlight the accessibility and affordability of this URE, a simple boiling method was used for DNA preparation from environmental samples. Student response data show positive attitudes toward UR when LAMP is utilized as a research tool to tackle relevant biological questions. The feasibility of using simplified LAMP in UREs points to a potential, more expanded application to public engagement with science and broader and more inclusive interactions with the research community.

Keywords: HIP’s; LAMP; research tool; stem education; undergraduate research (UR).