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  • Using phylogenetics to make inferences about historical biogeographic patterns of evolution.

    Building Trees: Introducing evolutionary concepts by exploring Crassulaceae phylogeny and biogeography

    Learning Objectives
    Students will be able to:
    • Estimate phylogenetic trees using diverse data types and phylogenetic models.
    • Correctly make inferences about evolutionary history and relatedness from the tree diagrams obtained.
    • Use selected computer programs for phylogenetic analysis.
    • Use bootstrapping to assess the statistical support for a phylogeny.
    • Use phylogenetic data to construct, compare, and evaluate the role of geologic processes in shaping the historical and current geographic distributions of a group of organisms.
  • DNA barcoding research in first-year biology curriculum

    CURE-all: Large Scale Implementation of Authentic DNA Barcoding Research into First-Year Biology Curriculum

    Learning Objectives
    Students 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
    Week 5-6: Ecology
    • 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
    Week 7-11: Cellular and Molecular Biology
    • 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
    Week 12-13: Bioinformatics
    • 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
  • “The outcome of the Central Dogma is not always intuitive” Variation in gene size does not necessarily correlate with variation in protein size. Here, two related genes differ in length due to a deletion mutation that removes four nucleotides. Many students do not predict that the smaller gene, after transcription and translation, would produce a larger protein.

    Predicting and classifying effects of insertion and deletion mutations on protein coding regions

    Learning Objectives
    Students will be able to:
    • accurately predict effects of frameshift mutations in protein coding regions
    • conduct statistical analysis to compare expected and observed values
    • become familiar with accessing and using DNA sequence databases and analysis tools
  • pClone Red Makes Research Look Easy

    Using Synthetic Biology and pClone Red for Authentic Research on Promoter Function: Genetics (analyzing mutant...

    Learning Objectives
    • Describe how cells can produce proteins at the right time and correct amount. 
    • Diagram a bacterial promoter with −35 and −10 elements and the transcription start site.
    • Describe how mutational analysis can be used to study promoter sequence requirements.
    • Develop a promoter mutation hypothesis and design an experiment to test it.
    • Successfully and safely manipulate DNA and Escherichia coli for ligation and transformation experiments. 
    • Design an experiment to verify a mutated promoter has been cloned into a destination vector. 
    • Design an experiment to measure the strength of a promoter. 
    • Analyze data showing reporter protein produced and use the data to assess promoter strength. 
    • Define type IIs restriction enzymes.
    • Distinguish between type II and type IIs restriction enzymes.
    • Explain how Golden Gate Assembly (GGA) works.
    • Measure the relative strength of a promoter compared to a standard promoter.