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  • A schematic of the relationship between the different types of pasta or beans and the respective gut and environmental bacteria

    The impact of diet and antibiotics on the gut microbiome

    Learning Objectives
    After completing the exercise, students will be able to:
    • Identify several of the nine phyla that contribute to the gut microbiome and name the two predominant ones;
    • Describe how diet impacts the gut microbiome and compare the composition of the gut microbiome between different diets;
    • Describe how antibiotic treatment impacts the gut microbiome and understand how this leads to infection, for example by Clostridium difficile;
    • Trace the response to a change in diet, starting with i) changes in the composition of the microbiome, followed by ii) changes in the bacterial metabolic pathways and the respective excreted metabolic products, resulting in iii) a molecular response in the host intestinal cells, and eventually iv) resulting in human disease;
    • Improve their ability to read scientific literature;
    • Express themselves orally and in writing;
    • Develop team working skill
  • A three-dimensional model of methionine is superimposed on a phase contrast micrograph of Saccharomyces cerevisiae from a log phase culture.

    Follow the Sulfur: Using Yeast Mutants to Study a Metabolic Pathway

    Learning Objectives
    At the end of this lesson, students will be able to:
    • use spot plating techniques to compare the growth of yeast strains on solid culture media.
    • predict the ability of specific met deletion strains to grow on media containing various sulfur sources.
    • predict how mutations in specific genes will affect the concentrations of metabolites in the pathways involved in methionine biosynthesis.
  • Plant ecology students surveying vegetation at Red Hills, CA, spring 2012.  From left to right are G.L, F.D, A.M., and R.P.  Photo used with permission from all students.

    Out of Your Seat and on Your Feet! An adaptable course-based research project in plant ecology for advanced students

    Learning Objectives
    Students 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)
  • The mechanisms regulating the cellular respiration system.

    Discovering Cellular Respiration with Computational Modeling and Simulations

    Learning Objectives
    Students will be able to:
    • Describe how changes in cellular homeostasis affect metabolic intermediates.
    • Perturb and interpret a simulation of cellular respiration.
    • Describe cellular mechanisms regulating cellular respiration.
    • Describe how glucose, oxygen, and coenzymes affect cellular respiration.
    • Describe the interconnectedness of cellular respiration.
    • Identify and describe the inputs and outputs of cellular respiration, glycolysis, pyruvate processing, citric acid cycle, and the electron transport chain.
    • Describe how different energy sources are used in cellular respiration.
    • Trace carbon through cellular respiration from glucose to carbon dioxide.
  • 3D Print Models: A collection of 3D models printed from online repository files.
  • This collage contains original images taken by the course instructor. The images show a microscopic view of stomata on the underside of a Brassica rapa leaf (A), B. rapa plants in their growth trays (B), a flowering B. rapa plant (C), and different concentrations of foliar protein (D). Photos edited via Microsoft Windows Photo Editor and Phototastic Collage Maker.

    A flexible, multi-week approach to plant biology - How will plants respond to higher levels of CO2?

    Learning Objectives
    Students will be able to:
    • Apply findings from each week's lesson to make predictions and informed hypotheses about the next week's lesson.
    • Keep a detailed laboratory notebook.
    • Write and peer-edit the sections of a scientific paper, and collaboratively write an entire lab report in the form of a scientific research paper.
    • Search for, find, and read scientific research papers.
    • Work together as a team to conduct experiments.
    • Connect findings and ideas from each week's lesson to get a broader understanding of how plants will respond to higher levels of CO2 (e.g., stomatal density, photosynthetic/respiratory rates, foliar protein concentrations, growth, and resource allocation).
    Note: Additional, more specific objectives are included with each of the four lessons (Supporting Files S1-S4)