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

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.

Loop-Mediated Isothermal Amplification (LAMP) Assay for Detecting Burkholderia cepacia Complex in Non-Sterile Pharmaceutical Products

“…The cost-efficiency (250 reactions (10 μL) = about USD 250; approx. USD 1/reaction) of LAMP assays makes it acceptable to use even in resource-limited laboratories of smaller pharmaceutical manufacturers [ 38 ]. Furthermore, LAMP can be carried out by trained undergraduate students in an unclassified environment, without the need for specialized equipment and/or expensive supplies [ 38 ].…”

Dual-Functional Tetrahedron Multivalent Aptamer Assisted Amplification-Free CRISPR/Cas12a Assay for Sensitive Detection of Salmonella

“…Even sensitive enough, the nucleic acid amplification techniques require professional operations and expensive instruments. 8 On the other hand, ELISA gains much attention due to their high throughput, high specificity, rapid detection, and automatic operation. 9,10 However, its insufficient sensitivity (detection limit: ∼10 4 cfu mL −1 ) and the high price and instability of antibody limit the application in Salmonella determination.…”

“…Alternatively, nucleic acid amplification techniques (e.g., polymerization chain reaction, PCR) and immunologically based methods (e.g., enzyme-linked immunosorbent assay, ELISA) are the common methods for rapid screening bacteria in the laboratory. Even sensitive enough, the nucleic acid amplification techniques require professional operations and expensive instruments . On the other hand, ELISA gains much attention due to their high throughput, high specificity, rapid detection, and automatic operation. , However, its insufficient sensitivity (detection limit: ∼10 4 cfu mL –1 ) and the high price and instability of antibody limit the application in Salmonella determination .…”

Evaluation of the loop-mediated isothermal amplification assay for Staphylococcus aureus detection: a systematic review and meta-analysis

“…Compared with the traditional culture, it is simpler and more efficient with higher sensitivity. At present, LAMP is more suitable for clinical diagnosis, laboratories, and fields with limited resources [ 3 , 10 ]. In recent years, the commonly used versions used to detect S. aureus are eazyplex ® MRSAplus (Amplex BioSystems, Giessen, Germany), eazyplex ® MRSA (Amplex BioSystems, Giessen, Germany), Loopamp DNA amplification kit (Eiken Chemical Co. Ltd., Tokyo, Japan), LAMP-LFD and m-LAMP-LFB [ 3 ].…”