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Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics CourseLearning ObjectivesStudents will be able to:
- list and perform the steps of sequence processing and taxonomic inference.
- interpret microbial community diversity from metagenomic sequence datasets.
- compare microbial diversity within and between samples or treatments.
Out of Your Seat and on Your Feet! An adaptable course-based research project in plant ecology for advanced studentsLearning ObjectivesStudents will:
- Articulate testable hypotheses. (Lab 8, final presentation/paper, in-class exercises)
- Analyze data to determine the level of support for articulated hypotheses. (Labs 4-7, final presentation/paper)
- Identify multiple species of plants in the field quickly and accurately. (Labs 2-3, field trip)
- Measure environmental variables and sample vegetation in the field. (Labs 2-3, field trip)
- Analyze soil samples using a variety of low-tech lab techniques. (Open labs after field trip)
- Use multiple statistical techniques to analyze data for patterns. (Labs 4-8, final presentation/paper)
- Interpret statistical analyses to distinguish between strong and weak interactions in a biological system. (Labs 4-7, final presentation/paper)
- Develop and present a conference-style presentation in a public forum. (Lab 8, final presentation/paper)
- Write a publication-ready research paper communicating findings and displaying data. (Lab 8, final presentation/paper)
CURE-all: Large Scale Implementation of Authentic DNA Barcoding Research into First-Year Biology CurriculumLearning ObjectivesStudents will be able to: Week 1-4: Fundamentals of Science and Biology
- List the major processes involved in scientific discovery
- List the different types of scientific studies and which types can establish causation
- Design experiments with appropriate controls
- Create and evaluate phylogenetic trees
- Define taxonomy and phylogeny and explain their relationship to each other
- Explain DNA sequence divergence and how it applies to evolutionary relationships and DNA barcoding
- Define and measure biodiversity and explain its importance
- Catalog organisms using the morphospecies concept
- Geographically map organisms using smartphones and an online mapping program
- Calculate metrics of species diversity using spreadsheet software
- Use spreadsheet software to quantify and graph biodiversity at forest edges vs. interiors
- Write a formal lab report
- Extract, amplify, visualize and sequence DNA using standard molecular techniques (PCR, gel electrophoresis, Sanger sequencing)
- Explain how DNA extraction, PCR, gel electrophoresis, and Sanger sequencing work at the molecular level
- Trim and assemble raw DNA sequence data
- Taxonomically identify DNA sequences isolated from unknown organisms using BLAST
- Visualize sequence data relationships using sequence alignments and gene-based phylogenetic trees
- Map and report data in a publicly available online database
- Share data in a formal scientific poster
Teaching Biodiversity with Museum Specimens in an Inquiry-Based LabLearning ObjectivesStudents completing this lab module will:
- Learn how to appropriately handle and measure museum specimens.
- Develop the necessary statistical skills to analyze museum specimen data.
- Become familiar with how to search an online museum database and integrate supplemental data with their own dataset.
- Strengthen scientific communication skills by presenting research to their peers.
- Demonstrate ability to investigate scientific questions and address obstacles that occur during data collection and integration.
- Increase proficiency in managing and using large datasets for scientific research.
- Make connections between natural history knowledge and morphology of organisms in developing and testing hypotheses.