FlyBase for Undergrads
Dr. Hui-Min Chung (University of West Florida) and her students have developed an instructional video aimed at introducing undergraduate students to the research tools available at FlyBase.
Bioinformatics Tools Tutorial Project – KRas
This lab is an updated, stand-alone version of the bioinformatics exercise originally developed for Bio 3055 at Washington University. This exercise introduces students to the genetic basis of disease using the KRas protein.
Investigating Gene Flow in Grasshopper Populations
Students use grasshoppers collected from glades in the Missouri Ozarks to generate and analyze sequence data to determine if the grasshopper populations are becoming fragmented due to the suppression of forest fires. Sequence data are provided here so students who do not have access to grasshoppers can still perform the sequence analysis portion of the lab.
Identifying Unknown Bacteria Using Biochemical and Molecular Methods
Students use two different protocols, one based on sequence analysis and one based on biochemistry, to determine the identity of an unknown bacterial strain.
Investigating a Eukaryotic Genome: Cloning and Sequencing a Fragment of Yeast DNA
This lab provides an opportunity for students to randomly clone a fragment of the yeast genome into E. coli and then investigate what part of the genome they have cloned through sequence analysis.
RNA-Seq Primer
This PowerPoint presentation provides a brief introduction to the different types of RNA-Seq evidence tracks (e.g. Bowtie, TopHat, Cufflinks) that are on the GEP UCSC Genome Browser.
Sequencing Workshop
Dr. Justin R. DiAngelo (Penn State Berks) has developed an exercise for the Sanger Sequencing and Next Generation Sequencing video tours.
Introduction to the Complete GEP Gene Annotation Process
Developed by Dr. Ken Saville (Albion College) and Dr. Gerard McNeil (York College, City University of New York), this walkthrough provides a comprehensive overview of the entire GEP gene annotation process. This walkthrough includes a brief description of the research problem and step-by-step instructions on how to use the UCSC Genome Browser, FlyBase, the Gene Record Finder and NCBI BLAST to investigate a feature in a Drosophila erecta Muller F element annotation project. The walkthrough then shows how students can use the Gene Model Checker to verify a gene model; it also includes a sample GEP Annotation Report.
Using BLAST and ExPASy for Genetic and Protein Analysis of H1N1 Variability
Ms. Julie Ertmann (University City High School, MO) has designed a standalone activity using BLAST for AP or second year high school biology students. This exercise uses BLAST and ExPASy for genetic and protein analysis of H1N1 variability, including mutations that confer resistance to antiviral medications. Development of this exercise was supported by an NSF Mathematics and Science Partnership grant #06344780, to B Schaal, Washington University in St. Louis. If you have questions about this activity, please email the author at: jertmann@ucityschools.org.
Investigating a Mutation in HIV-1
Students use the HIV Problem Space on the BioQuest BEDROCK Website to investigate whether a specific HIV mutation can be correlated with a decline in immune system function. In order to perform this analysis, students must generate and analyze multiple sequence alignments of HIV sequences generated from the ALIVE study.