Advanced Bioinformatics: Genetic Research

In this lesson, students are introduced to the process of genetic research. The lesson begins with a Think-Pair-Share activity designed to introduce students to the types of research questions people in different career fields might answer using bioinformatics tools. After a short background explanation provided by the teacher about how genetic research is done, students make their own hypotheses and predictions about the relatedness of canine species, and align paper DNA sequences to evaluate their hypotheses. The lesson concludes with a group activity introducing students to pairwise comparisons of DNA sequences, which will be explored more fully in later lessons. In Lesson One, students learn how DNA sequencing core lab managers might use bioinformatics tools in their career.

In this lesson, students will receive an “unknown” DNA sequence and use the bioinformatics tool Basic Local Alignment Search Tool (BLAST) to identify the species from which the sequence came. Students then visit the Barcode of Life Database (BOLD) to obtain taxonomic information about their species and form taxonomic groups for scientific collaboration. The lesson ends with each student generating a hypothesis about the relatedness of the species within each group. In Lesson Two, students learn how postdoctoral scientists in DNA and history might use bioinformatics tools in their career.

In this lesson, students learn how to use bioinformatics tools to analyze DNA sequence data and draw conclusions about evolutionary relationships. Students collaborate with their group members by pooling their DNA sequences from Lesson Two: DNA Barcoding and the Barcode of Life Database (BOLD) to perform and analyze multiple sequence alignments using the computer programs ClustalW2 and JalView. After comparing relatedness among and between the species within their group, students use their sequence alignment to generate a phylogenetic tree, which is a graphical representation of inferred evolutionary relationships. This tree is used to draw conclusions about their research question and hypothesis. In Lesson Three, students learn how microbiologists might use bioinformatics tools in their career.

In this lesson, students perform a paper exercise designed to reinforce student understanding of the complementary nature of DNA and how that complementarity leads to six potential protein reading frames in any given DNA sequence. They also gain familiarity with the circular format codon table. Students then use the bioinformatics tool ORFinder to identify the reading frames in their DNA sequence from Lesson Two and Lesson Three, and to select the proper open reading frame to use in a multiple sequence alignment using their protein sequences. In Lesson Four, students learn how biological anthropologists might use bioinformatics tools in their career.

Prior to this lesson, students learned how the cytochrome c oxidase subunit 1 (COI) gene is used to barcode animals. In this lesson, students learn more about the cytochrome c oxidase protein and its three-dimensional structure. In particular, students learn how to identify the active site in cytochrome c oxidase. Once they can find this site, they look at aligned structures (one of which contains a poison) and then determine the identity of a foreign substance that acts as a poison by binding to the active site. This lesson allows students to explore the use of the molecular visualization program Cn3D to learn more about cytochrome c oxidase, a ubiquitous and important protein. In Lesson Five, students learn how molecular diagnostics researchers might use bioinformatics tools in their career.

In this lesson, students compile and synthesize what they have learned in the preceding lessons by writing a research report. The research report includes Introduction, Methods, Results, Discussion, andReferences sections. Emphasis is placed on relating previous lesson activities to the original research question and hypothesis. Extensions and lesson alternatives include instructions for creating a scientific poster, writing a scientific abstract, or writing a science-related magazine article. In Lesson Six, students learn how science and technical writers might use bioinformatics tools in their career.

In this lesson, students learn about Leigh’s disease, a rare form of Subacute Necrotizing Encephalomyelopathy (SNEM) that can be caused by a deficiency in cytochrome c oxidase (complex IV). Deficiencies in the large, 13-subunit cytochrome c oxidase complex can result from defects in one of several proteins, including cytochrome c oxidase subunit 1, the protein encoded by the DNA barcoding gene, and examined in Lesson 5. Without the COI protein, cells are unable to harness usable energy from glucose. This is a jigsaw exercise. Students are assigned or choose one of four stakeholder parties. They meet in “like” interest groups to become more familiar with that stakeholder’s position and concerns. Afterwards, they meet in “mixed” groups with a representative from each of the stakeholder groups. Students identify areas of agreement and disagreement, and propose a compromise to recommend to Congress regarding funding for rare disease research. In Lesson Seven, students learn how pediatric neurologists might use bioinformatics tools in their career.

In this lesson, students synthesize the information they have learned throughout the unit about people in various careers who use bioinformatics. Students then have the opportunity to perform independent research about a career of interest before developing a resume to use when applying for a bioinformatics-related job. Students also learn about writing cover letters. Optional extensions include peer-editing of resumes and a mock interview for a job related to a career of interest.

DNA sequencing is performed by scientists in many different fields of biology. Many bioinformatics programs are used during the process of analyzing DNA sequences. In this lesson, students learn how to analyze DNA sequence data from chromatograms using the bioinformatics tools FinchTV and BLAST. Using data generated by students in class or data supplied by the Bio-ITEST project, students learn what DNA chromatogram files look like, learn about the significance of the four differently-colored peaks, learn about data quality, and learn how data from multiple samples are used in combination with quality values to identify and correct errors. Students use their edited data in BLAST searches at the NCBI and the Barcode of Life Database (BOLD) to identify and confirm the source of their original DNA. Students then use the bioinformatics resources at BOLD to place their data in a phylogenetic tree and see how phylogenetic trees can be used to support sample identification. Learning these techniques will provide students with the basic tools for inquiry-driven research.

In this lesson, students perform the wet lab experiments necessary for DNA barcoding. Beginning with a small tissue sample, students purify the DNA, perform the polymerase chain reaction (PCR) using COI-specific primer pools, and analyze their PCR products by agarose gel electrophoresis. PCR reactions that result in products of the correct size are purified and submitted for DNA sequencing. This DNA sequence data can be used in Lesson Nine, or as part of an independent project.