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  • 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)
  • Neutrophils in a Danio rerio Embryo. Student-generated picture of a wounded zebrafish embryo that was stained to show the neutrophils (small black dots) that had migrated toward the wound site on the fin.

    Inexpensive Cell Migration Inquiry Lab using Zebrafish

    Learning Objectives
    Students will:
    • formulate a hypothesis and design an experiment with the proper controls.
    • describe the steps involved in the zebrafish wounding assay (treating zebrafish embryos with drugs or control substances, wounding the embryo, staining the embryo, and counting neutrophils near the wound).
    • summarize results into a figure and write a descriptive figure legend.
    • perform appropriate statistical analysis.
    • interpret results in a discussion that draws connections between the cytoskeleton and cell migration.
    • put data into context by appropriately using information from journal articles in the introduction and discussion of a lab report.
  • Possible implementations of a short research module

    A Short Laboratory Module to Help Infuse Metacognition during an Introductory Course-based Research Experience

    Learning Objectives
    • Students will be able to evaluate the strengths and weaknesses of data.
    • Students will be able to employ prior knowledge in formulating a biological research question or hypothesis.
    • Students will be able to distinguish a research question from a testable hypothesis.
    • Students will recognize that the following are essential elements in experimental design: identifying gaps in prior knowledge, picking an appropriate approach (ex. experimental tools and controls) for testing a hypothesis, and reproducibility and repeatability.
    • Students will be able to identify appropriate experimental tools, approaches and controls to use in testing a hypothesis.
    • Students will be able to accurately explain why an experimental approach they have selected is a good choice for testing a particular hypothesis.
    • Students will be able to discuss whether experimental outcomes support or fail to support a particular hypothesis, and in the case of the latter, discuss possible reasons why.
  • 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)
  • How Silly Putty® is like bone

    What do Bone and Silly Putty® have in Common?: A Lesson on Bone Viscoelasticity

    Learning Objectives
    • Students will be able to explain how the anatomical structure of long bones relates to their function.
    • Students will be able to define viscoelasticity, hysteresis, anisotropy, stiffness, strength, ductility, and toughness.
    • Students will be able to identify the elastic and plastic regions of a stress-strain curve. They will be able to correlate each phase of the stress-strain curve with physical changes to bone.
    • Students will be able to predict how a bone would respond to changes in the magnitude of an applied force, and to variations in the speed or angle at which a force is applied.
    • Students will be able to determine the reason(s) why bone injuries occur more frequently during athletic events than during normal everyday use.
  • Structure of protein ADA2

    Understanding Protein Domains: A Modular Approach

    Learning Objectives
    • Students will be able to compare protein sequences and identify conserved regions and putative domains.
    • Students will be able to obtain, examine, and compare structural models of protein domains.
    • Students will be able to interpret data on protein interactions (in vitro pull-down and in vitro and in vivo functional assays)
    • Students will be able to propose experiments to test protein interactions.
  • A photo of grizzly bears fishing in the McNeil Falls in Alaska, taken using BearCam by Lawrence Griffing.

    Authentic Ecological Inquiries Using BearCam Archives

    Learning Objectives
    Students will be able to:
    • conduct an authentic ecological inquiry including
      • generate a testable hypothesis based on observations,
      • design investigation with appropriate sampling selection and variables,
      • collect and analyze data following the design, and
      • interpret results and draw conclusions based on the evidence.
    • write a research report with appropriate structure and style.
    • evaluate the quality of inquiry reports using a rubric.
    • conduct peer review to evaluate and provide feedback to others' work.
    • revise the inquiry report based on peer feedback and self-assessment.
  • CRISPR/Cas9 in yeast experimental overview

    CRISPR/Cas9 in yeast: a multi-week laboratory exercise for undergraduate students

    Learning Objectives
    Week 1: CRISPR design
    • Locate the coding sequence, flanking sequence, protein product, and characteristics of a given gene from the Saccharomyces Genome Database (https://www.yeastgenome.org/).
    • Design and defend the design of guide RNA and single stranded template for DNA repair in CRISPR/Cas9 gene editing studies to generate Saccharomyces cerevisiae auxotrophic mutants.
    Week 3-4: Cloning
    • Describe the qualities of the vector, pML104, that allow replication and selection in bacteria and yeast as well as allow expression of necessary factors in CRISPR/Cas9 genome editing, including Cas9 and sgRNA.
    • Describe the rationale of and perform procedures necessary for cloning a small cassette (i.e., sgRNA gene) into a vector (i.e., pML104) including; restriction digest, annealing of DNA strands, removal of 5’ phosphates, ligation, and transformation.
    • Recognize and design appropriate controls for cloning procedures such as ligation and transformation.
    Week 5: Screening clones
    • Describe the method of polymerase chain reaction (PCR), including the rationale for essential components of a reaction mixture and thermal-cycling conditions.
    • Locate the binding sites of and design primers for PCR, then report the expected size of the amplification product.
    • Describe and perform isolation of plasmid DNA from E. coli.  
    Week 6: Selection of clones and transformation of yeast
    • Describe the rationale for and perform procedures to transform yeast, including the essential components of a transformation mixture and conditions necessary for transformation.
    • Describe the basic conditions required for cultivating yeast.
    • Describe the rationale for and perform agarose gel electrophoresis of a given size of DNA.
    • Analyze DNA separated by agarose gel electrophoresis, including size estimation.
    • Recognize and describe the qualities of a template for DNA repair that allows efficient DNA repair. 
    Week 7: Phenotyping
    • Design an experiment to determine auxotrophic phenotypes.
    • Predict the outcome of multi-step experiments.
    Multiweek
    • Recognize and describe conditions necessary for growth of E. coli and S. cerevisiae.
    • Qualitatively and quantitatively analyze scientific data from scientific experiments, including bacterial and yeast transformation, agarose gel electrophoresis, extraction of plasmid DNA from bacteria, PCR, and auxotroph phenotypic analysis.
    • Communicate science to peers through maintenance of a laboratory notebook, verbal communication with group members, and writing of a formal laboratory report written in a format acceptable for journal publication.
    • Troubleshoot scientific protocols by identifying procedures that are prone to error, comparing recommended protocols to actual procedure, and using positive and negative controls to narrow the location of a potential error.
    • Communicate specific potential or actual uses of CRISPR/Cas9 in science and/or medicine.
    Alignment with Society-Generated Learning Objectives - From Biochemistry and Molecular Biology, and Genetics Learning Frameworks
    • Use various bioinformatics approaches to analyze macromolecular primary sequence and structure.
    • Illustrate how DNA is replicated and genes are transmitted from one generation to the next in multiple types of organisms including bacteria, eukaryotes, viruses, and retroviruses.
    • Define what a genome consists of and how the information in various genes and other sequence classes within each genome are used to store and express genetic information.
    • Explain the meaning of ploidy (haploid, diploid, aneuploid etc.) and how it relates to the number of homologues of each chromosome. 
    • Predict the effects of mutations on the activity, structure, or stability of a protein and design appropriate experiments to assess the effects of mutations.
    • Predict the growth behavior of microbes based on their growth conditions, e.g., temperature, available nutrient, aeration level, etc.
    • Discuss the benefits of specific tools of modern biotechnology that are derived from naturally occurring microbes (e.g. cloning vectors, restriction enzymes, Taq polymerase, etc.)
    • Accurately prepare and use reagents and perform experiments.
    • When presented with an observation, develop a testable and falsifiable hypothesis.
    • When provided with a hypothesis, identify the appropriate experimental observations and controllable variables.
  • ACTN3 from https://upload.wikimedia.org/wikipedia/commons/3/33/Protein_ACTN3_PDB_1tjt.png

    The Science Behind the ACTN3 Polymorphism

    Learning Objectives
    This article accompanies the lesson "The ACTN3 Polymorphism: Applications in Genetics and Physiology Teaching Laboratories." Learning objectives for the lesson include:
    1. Test hypotheses related to the role of ACTN3 in skeletal muscle function.
    2. Explain how polymorphic variants of the ACTN3 gene affect protein structure and function.
    3. List and explain the differences between fast twitch and slow twitch muscle fibers.
    4. List and explain possible roles of the ACTN3 protein in skeletal muscle function.
    5. Find and analyze relevant scientific publications about the relationship between ACTN3 genotype and muscle function.
    6. Formulate hypotheses related to the relationship between ACTN3 genotype and skeletal muscle function.
    7. Design experiments to test hypotheses about the role of ACTN3 in skeletal muscle function.
    8. Statistically analyze experimental results using relevant software.
    9. Present experimental results in writing.
  • Students preforming the leaky neuron activity.

    The Leaky Neuron: Understanding synaptic integration using an analogy involving leaky cups

    Learning Objectives
    Students will able to:
    • compare and contrast spatial and temporal summation in terms of the number of presynaptic events and the timing of these events
    • predict the relative contribution to reaching threshold and firing an action potential as a function of distance from the axon hillock
    • predict how the frequency of incoming presynaptic action potentials effects the success of temporal summation of resultant postsynaptic potentials
  • Example image of dividing cells obtained from the Allen Institute for Cell Science 3D Cell Viewer.

    A virtual laboratory on cell division using a publicly-available image database

    Learning Objectives
    • Students will name and describe the salient features and cellular tasks for each stage of cell division.
    • Students will predict the relative durations of the stages of cell division using prior knowledge and facts from assigned readings.
    • Students will describe the relationship between duration of each stage of cell division and the frequency of cells present in each stage of cell division counted in a random sample of images of pluripotent stem cells.
    • Students will identify the stages of cell division present in research-quality images of human pluripotent stem cells in various stages of cell division.
    • Students will quantify, analyze and summarize data on the prevalence of cells at different stages of cell division in randomly sampled cell populations.
    • Students will use data to reflect on and revise predictions.