Southern University and A&M College Interns Conduct Bioinformatics Research

By Wesley Gray posted 10-22-2020 15:41


The Science Research Education Program (SREP) at Southern University and A&M College in Baton Rouge (SUBR), Louisiana, aims to enhance the academic and research preparedness of SUBR STEM students, ultimately increasing the number of underrepresented minorities in the biomedical fields. The program is designed to impact the students’ academic and research training by providing them with the necessary skills and expertise to complete a rigorous STEM program after graduating from college.

Our SREP 2020 virtual summer research science camp for undergraduate students was a partnership with SOT and the Louisiana Biomedical Research Network (LBRN) program. Because of the COVID-19 pandemic crisis, the 2020 program’s goals were shifted from a practical training experience to a virtual training space. The aims of the SREP 2020 virtual summer training are to expose students to data science through the analysis of COVID-19 genomic data from the towns and cities where the participants lived and to explore the area of natural product research as a treatment for COVID-19.

The camp’s main focus was for students to learn the basics of bioinformatics analysis, prepare a bioinformatic pipeline for data analysis of COVID-19’s DNA, and generate a white paper for use as a senior research project in the fall. Furthermore, it was to prepare them for online synchronous instruction in the fall 2020 semester.

The virtual camp activity was divided into three parts, and the participants were engaged via synchronous online activities for three to four hours per day. During the six weeks, LBRN provided online guest lectures covering the current scientific information on the crisis. The camp activities that ran concurrently were as follows:

Activity One

This involved asynchronous and synchronous instruction in fundamental bioinformatics and DNA sequencing. These activities were delivered using subject-specific videos lasting 10–15 minutes, PowerPoint presentations, group discussions, and professional lectures from Pine-Biotech, a bioinformatics research group.

Activity Two

This involved developing a bioinformatic pipeline to analyze COVID-19 genomic DNA. The participants used the bioinformatic tools to determine the correlation between COVID-19 infection and ACE spike glycoprotein in patients’ samples from different regions in the country. Participants obtained COVID-19 DNA genomic samples from positive cases in their area (Louisiana, Michigan, and Jamaica). They then developed a bioinformatic pipeline and utilized multiple sequence alignment and phylogenetic analysis to determine if mutations in the spike glycoprotein were responsible for different infection rates noted in their region of study. At the end of each stage of the pipeline development, the student presented their data to the group and, at the program conclusion, received a certificate of completion in bioinformatic skills.

Activity Three

This activity involved student professional development and the integration of toxicological concepts. During this phase of the camp, students were introduced to toxicology and its implication in the current coronavirus crisis. Several guest speakers spoke candidly about the pros and cons of a career in toxicology. Dr. Christopher Bradfield from the Molecular Toxicology program at University of Wisconsin–Madison and Dr. Russell Ledet, a SUBR graduate and 2011 SOT Undergraduate Diversity Program participant, presented their experience and advice to the students.

Overall, the participants appreciated the opportunity to work with faculty-/researcher-led small virtual groups. They enjoyed the chance to work on the COVID-19 issues with faculty mentors whose research goals and interests included the intersection of community-driven/-based research.

The specific outcomes of the summer camp are as follows:

  • The group generated and presented a poster entitled “The Effect of SARS-COV-2 Spike Glycoprotein Mutation on Infection Rate in Louisiana and Jamaica”; and
  • Each member received an Omics Logic Certification from Pine-Biotech for completing three units of a Bioinformatic and a SARS-Cov-2 Genomics Data Analysis.

This blog is one of a series highlighting 2020 undergraduate intern research activities that were supported by SOT with funds administered by the Faculty United for Toxicology Undergraduate Recruitment and Education (FUTURE) Committee. Internship hosts can apply for matching funding for up to one-half of the cost for a summer undergraduate research position. The application deadline for next year is January 8. Relevant intern positions are listed on the “Internship Resources” web page of the SOT website whether or not they receive SOT support. Please send internship opportunity information to SOT Headquarters.