Bioinformatics is commonly defined as computational molecular biology. In other words, bioinformatics makes use of technology to analyze nucleic acids (DNA and RNA) and proteins. Before getting to the fundamentals of bioinformatics, this course will begin with a general overview of how genetic information is encoded and used by cells. The course will then transition to exploring some of the common databases used when performing biological research. Specific emphasis will be put on the National Center for Biotechnology Information (NCBI) database. Once students learn to use these databases, they will look at an application of bioinformatics. Students will learn what bioengineering is and how researchers can manipulate the genome of an organism in the laboratory.
By the end of the course, students can describe the general structures of DNA and RNA and the central dogma of molecular biology. The student will also be able to perform searches on NCBI and will be familiar with common analysis tools on NCBI. The student will understand what bioengineering is and the methods by which it is done in the laboratory.
Week 1- The Central Dogma of Molecular Biology
Module 1.1: DNA and RNA Basics
Module 1.2: DNA Replication
Module 1.3: Transcription
Module 1.4: Translation
Week 2- Introduction to Bioinformatics
Module 2.1: What is Bioinformatics?
Module 2.2: Genomics versus Transcriptomics versus Proteomics
Module 2.4: Sequencing
Module 2.5: Alignment
Week 3- Bioinformatics Databases
Module 3.1: Introduction to Bioinformatics Databases
Module 3.2: NCBI Entrez Search
Module 3.3: NCBI Protein Visualizer
Module 3.4: NCBI BLAST
Week 4- Bioengineering Applications
Module 4.1: What is Genetic Engineering?
Module 4.2: CRISPR-Cas9
Module 4.3: Genetic Engineering Applications
For this case study, students will analyze the sequence of COVID-19. Students will perform searches on NCBI to access the sequences identified in the case study. Students
will then determine how the sequence of COVID-19 compares to these other sequences by using a bioinformatics tool called the Basic Local Alignment Search Tool (BLAST).
From this exercise, students will learn how bioinformatics databases can be used to elucidate key information about a virus as well as provide clues on how a virus becomes more infectious, thus suggesting potential new targets for therapeutics.
To begin, students will be given a recorded video lecture and written notes on the fundamentals of viruses. Then, students will be given a worksheet with questions to guide
them through the case study. Students will be given a week to respond to these questions.
Students will determine a gene of interest and propose a plan on how they would genetically engineer cells to change gene expression for the potential treatment of a disease. In order to do so, students should consider different enhancers, promoters, and terminators as well as the annotations of different genes. Students will choose a method to genetically engineer cells in the laboratory. Students will describe their method and explain their choice.
Students will be given two weeks to prepare a paper on their design.