Bioinformatics Lab: A Course-Based Undergraduate Research Experience Curriculum
Kristen M. DeAngelis, Mallory Choudoir, Ashley Eng, and Maureen A. Morrow
This is a computer lab course intended to give students technical and practical experience in analyzing sequencing data. We focus on bacterial genomes from recently isolated bacteria, so there is a possibility of discovery of new microbial diversity. Collaborative learning will be encouraged, but students will work individually to assemble, annotate, and analyze a bacterial genome.
Each week will begin with a review on the topic to be covered for that week. When applicable, there will be pre-recorded lectures to introduce lab topics, and students are expected to have watched these before coming to class. Our time in class will be spent as a computer lab, where students will work collaboratively and at their own pace to complete their genome sequencing and analysis. The guided analysis will transition into independent study. Students will produce a final capstone report in the style of the Microbiology Resource Announcements published by the American Society of Microbiology.
This course fulfils the Microbiology Major requirement as a Major Laboratory Elective, and the Microbiology Graduate requirement as a core graduate-level course in microbial science.
Integrative Experience: Soil Microbes and the Sustainability of Organic Agriculture
Kristen DeAngelis and Luiz Domeignoz Horta
This curriculum describes a one-unit course designed to fulfill the University of Massachusetts requirement for Integrative Experience as part of the Gen Ed curriculum for undergraduates.
Microbiology 562: D. Batch Fermentation Module
Kristen DeAngelis and Cecilia Prado
In this module, we set up a fermentation of grains by yeast with hops to brew beer (D1). We make media and pour plates to grow and identify microbial contaminants (D2). Two weeks after setting up the primary fermentation, we prime and condition the fermentation (D3). While we wait for the priming and conditioning to finish, we do a bioinformatics analysis of microbial communities turning ethanol (a product of fermentation) to n-caproic acid, (D4), to illustrate the power of metagenomic sequencing in resolving microorganisms and their potential physiology. Then we identify and examine the microbial contaminants cultured in the primary fermentation (D5). When the beer is finished, we perform a sensory analysis (D6) followed by a field trip to the Berkshire Brewing Company in South Deerfield, MA, where we will tour their brewing facilities and microbiology lab.
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