Infusing Bioinformatics and Research-Like Experience into a Molecular Biology Laboratory Course

Oct 15, 2026

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A nine-week, sophomore-level molecular biology laboratory project integrates research-like bioinformatics and cloning into a course experience. Students in small groups choose a tumor suppressor gene or an oncogene, mine primary literature and bioinformatics engines for gene and promoter sequences, and design PCR primers. They then amplify, clone promoter regions, perform diagnostic restriction digests to confirm results, and present findings. Each student submits an individual report, learning to read primary literature, use bioinformatics tools, clone DNA sequences, and communicate results orally and in writing.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages6

Reading Time15 min

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Abstract

Introduction

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Course schedule and experimental details

ARTICLES Infusing Bioinformatics and Research-Like Experience into a Molecular Biology Laboratory Course Luiza A. Nogaj Department of Biological Sciences, Mount St. Mary’s College, 12001 Chalon Rd, Los Angeles, California 90049 [lnogaj@msmc.la.edu](lnogaj@msmc.la.edu) Abstract: A nine-week laboratory project designed for a sophomore level molecular biology course is described. Small groups of students (3-4 per group) choose a tumor suppressor gene (TSG) or an oncogene for this project. Each group researches the role of their TSG/oncogene from primary literature articles and uses bioinformatics engines to find the gene and promoter sequence of their TSG/oncogene. Based on the promoter sequences, students design appropriate primers for the PCR amplification and cloning of the promoter of the gene of interest and perform a diagnostic digest to confirm the results. Finally, each student writes an individual report about his or her findings and results and each group presents the results to the class. This laboratory sequence teaches students how to read primary literature, use common bioinformatics engines, clone a DNA sequence, and present the results in an oral and written format. Key words: project-based learning, molecular biology laboratory, bioinformatics, molecular cloning INTRODUCTION Traditional molecular biology and biochemistry laboratory courses are composed of individual and very prescriptive exercises. Those exercises teach students techniques but they do not show the scientific process or excite the students to continue doing research (Burnette & Wessler, 2003) . Students performing those laboratory exercises do not design experiments or develop the critical thinking skills so crucial in undergraduate education (Glidon and Rosengren, 2012; Knutson et al, 2010; Coil et al, 2010) . Evidence suggests that research-focused instruction is more effective for developing those skills (Vision and Change in Undergraduate Biology Education, 2011; Anderson et al, 2005; Treacy et al, 2011) . In addition to implementing active learning and problem solving approaches into the biology and biochemistry curriculum, it is also important to integrate modern computational skills and bioinformatics (Badotti et al, 2014; Honts, 2003; Voet, 2003; Voet, 2004) . Numerous institutions are introducing bioinformatics into existing biology and biochemistry curricula at multiple levels (Wightamand Hark, 2012; Hydorn et al, 2005; Furge et al, 2009) . In an effort to engage students in an authentic research experience and to bring a sophomore level molecular biology laboratory curriculum into the 21st century, a nine-week laboratory project was developed. Students enrolled in the course meet once a week for three hours and are simultaneously taking a molecular biology lecture (3 hours per week for 16 weeks) . Students taking molecular biology – lecture and laboratory-have already completed two semesters of general biology and general chemistry courses. The total number of students taking the laboratory course varied between 30 and 50 people. During the nine-week project students examine primary literature, mine bioinformatics engines for gene and promoter sequences, and clone promoter sequences into vectors. Additionally, students present the results to the class and write individual laboratory reports about the project. The goal of this student-centered adventure is to combine computational skills, bioinformatics, and molecular cloning techniques into one cohesive whole. It also gives students the freedom to choose a gene and its promoter, learn about it from primary literature and then present the findings in an oral and written format. METHODS The project begins with a short introduction to bioinformatics and the structure of a typical gene and its promoter. During the first session students complete an activity that familiarizes them with different search engines (Bioinformatics Resource Portal ExPASy, National Center fo

FAQs

What is the nine-week laboratory project for?

It is a sophomore-level molecular biology laboratory project designed to provide students with an authentic, research-like experience that combines bioinformatics, molecular cloning, and scientific communication.

How do students choose their gene targets and sequence information?

Students work in groups of 3–4 and choose either a tumor suppressor gene (TSG) or an oncogene, then research its role using primary literature and use bioinformatics engines to identify gene and promoter sequences.

What experimental steps do students perform after obtaining promoter sequences?

Based on the promoter sequences, students design PCR primers, run PCR and cloning procedures, and use diagnostic restriction digests to confirm the cloning results.

Oct 15, 2026

Upload by Ben