Bioinformatics Workshops Further Educates PCCC Students
In February, Microbiology Professor Foote, and CIS Professor Rodrigues teamed up to host the first Bioinformatics Workshop of the new year! The workshop was designed to bring awareness to the world of science and allow students to have a first-hand experience with the future of science and technology. Although this workshop focused on scientific work, students from all degree programs were encouraged to participate and learn the basics of Bioinformatics: the science of analyzing complex, biological information (such as genetic codes).
Wednesday, February 20, 2019- DNA Extraction
The students that participated in this session were instructed to extract DNA from several plants, including herbs, to determine if the different plants shared similar characteristics within their DNA. In order to extract the DNA, the students were instructed to grind small amounts of a plant lead in a tube with a pestle (used for muddling) and a lysis buffer, which is a buffer solution that “breaks open” cells. More specifically, it breaks the cell wall, cell membrane, and the chloroplast membrane.
This allows for the release of DNA into the solution. Once the DNA was collected, students were instructed to attach the DNA to a piece of filter paper, which was afterwards washed in order to remove any debris. Once the paper was removed, the paper was placed in an elution buffer, used to dismiss unwanted proteins, so the DNA would be able to float off of the paper. This was completed in the lab by Professor Foote.
Professor Foote stated, “The prep continued in the lab with myself and a student worker, Eric Mendoza, who helped to prepare the PCR reactions for each sample, do the PCR, and run gel electrophoresis to ensure we had pure DNA. This PCR product was sent to a commercial company Genewiz, that give us the a special rate.”
Wednesday, February 27, 2019- DNA Bioinformatics
Professor Foote received the DNA sequences that were posted by the company Genewiz. In this session, students were guided through a web-based interface called the DNA Subway, allowing students to perform DNA analysis, such as polishing sequences, making a consensus sequence, and searching a large database for potential matches. Finally, students used the sequences from their samples and other sequences from the database to make phylogenetic trees to show the relationship between other plants’ DNA sequences.
Wednesday, March 6, 2019- Python Coding
Professor Rodrigues led this session by using Python Programming. Python is known as a language used for high- level programming. This language can be used for the development of applications, website applications and other programming tasks. Although it may seem intimidating, Professor Rodrigues led the students through basic Python coding that brought the gathered codes and DNA’s to life. Python is also considered one of the easiest programming languages in the field of bioinformatics.
Professor Foote stated, “The reason I asked Professor Rodrigues to help me run these 3 workshops was because I realized that we needed to have a collaborative action plan to bring together Biology and CIS majors so that all the students could become more familiar with the booming field of bioinformatics. It is absolutely necessary to prepare our students for their future jobs and there is significant demand for individuals that have programming savvy and a biological background. The opportunities are tremendous and he was completely thrilled to be able to do this with me."