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  • Image from http://www.epa.gov/airdata/ad_maps.html

    Air Quality Data Mining: Mining the US EPA AirData website for student-led evaluation of air quality issues

    Learning Objectives
    Students will be able to:
    • Describe various parameters of air quality that can negatively impact human health, list priority air pollutants, and interpret the EPA Air Quality Index as it relates to human health.
    • Identify an air quality problem that varies on spatial and/or temporal scales that can be addressed using publicly available U.S. EPA air data.
    • Collect appropriate U.S. EPA Airdata information needed to answer that/those questions, using the U.S. EPA Airdata website data mining tools.
    • Analyze the data as needed to address or answer their question(s).
    • Interpret data and draw conclusions regarding air quality levels and/or impacts on human and public health.
    • Communicate results in the form of a scientific paper.
  • 3D Print Model of the Mars Curiosity Rover, printed from NASA 3D Resources (https://nasa3d.arc.nasa.gov/detail/mars-rover-curiosity)

    Exploring the March to Mars Using 3D Print Models

    Learning Objectives
    • Students will be able to describe the major aspects of the Mars Curiosity Rover missions.
    • Students will be able to synthesize information learned from a classroom jigsaw activity on the Mars Curiosity Rover missions.
    • Students will be able to work in teams to plan a future manned mission to Mars.
    • Students will be able to summarize their reports to the class.
  • 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.
  • 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)
  • pClone Red Makes Research Look Easy

    Using Synthetic Biology and pClone Red for Authentic Research on Promoter Function: Introductory Biology (identifying...

    Learning Objectives
    • Describe how cells can produce proteins at the right time and correct amount.
    • Diagram how a repressor works to reduce transcription.
    • Diagram how an activator works to increase transcription.
    • Identify a new promoter from literature and design a method to clone it and test its function.
    • Successfully and safely manipulate DNA and Escherichia coli for ligation and transformation experiments.
    • Design an experiment to verify a new 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.
  • Adult female Daphnia dentifera. Daphnia spp. make a great study system due to their transparent body and their ease of upkeep in a lab.

    Dynamic Daphnia: An inquiry-based research experience in ecology that teaches the scientific process to first-year...

    Learning Objectives
    Students will be able to:
    • Construct written predictions about 1 factor experiments.
    • Interpret simple (2 variables) figures.
    • Construct simple (2 variables) figures from data.
    • Design simple 1 factor experiments with appropriate controls.
    • Demonstrate proper use of standard laboratory items, including a two-stop pipette, stereomicroscope, and laboratory notebook.
    • Calculate means and standard deviations.
    • Given some scaffolding (instructions), select the correct statistical test for a data set, be able to run a t-test, ANOVA, chi-squared test, and linear regression in Microsoft Excel, and be able to correctly interpret their results.
    • Construct and present a scientific poster.
  • Memory Helper is an illustration of a made up dietary supplement. Because the supplement is named Memory Helper, and because a picture of a brain is placed on the label, consumers might believe that the supplement is a memory aid. We add the footnote “tested?” to suggest that consumers should take a closer look.

    Bad Science: Exploring the unethical research behind a putative memory supplement

    Learning Objectives
    Students will be able to:
    • create criteria for evaluating information that is touted as scientific.
    • apply those criteria to evaluate the claim that Prevagen® enhances memory.
    • identify the misleading tactics used on the Prevagen® website and in their self-published reporting.
    • decide whether to recommend taking Prevagen® and explain their decisions.
  • Hydrozoan polyps on a hermit-crab shell (photo by Tiffany Galush)

    A new approach to course-based research using a hermit crab-hydrozoan symbiosis

    Learning Objectives
    Students will be able to:
    • define different types of symbiotic interactions, with specific examples.
    • summarize and critically evaluate contemporary primary literature relevant to ecological symbioses, in particular that between hermit crabs and Hydractinia spp.
    • articulate a question, based on observations of a natural phenomenon (in this example, the hermit crab-Hydractinia interaction).
    • articulate a testable hypothesis, based on their own observations and read of the literature.
    • design appropriate experimental or observational studies to address their hypotheses.
    • collect and interpret data in light of their hypotheses.
    • problem-solve and troubleshoot issues that arise during their experiment.
    • communicate scientific results, both orally and in written form.
  • blind cave fish
  • ACTN3 from https://upload.wikimedia.org/wikipedia/commons/3/33/Protein_ACTN3_PDB_1tjt.png

    The ACTN3 Polymorphism: Applications in Genetics and Physiology Teaching Laboratories

    Learning Objectives
    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.
  • Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course

    Learning Objectives
    Students 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.
  • Your Tax Dollars at Work: A mock grant writing experience centered on scientific process skills

    Learning Objectives
    Students will be able to:
    • Propose a testable, novel question contributing to a biological field of study.
    • Formulate a study rationale.
    • Describe relevant background information on a topic using the primary literature.
    • Choose appropriate scientific, mathematical, and statistical methods to analyze a research question.
    • Determine the financial costs of a research project.
    • Present a proposal for peer review and compose a constructive peer review.
    • Collaborate as a member of a scientific team.
    • Articulate the review criteria and process used in NSF-style proposal review.
  • 3D Print Models: A collection of 3D models printed from online repository files.
  • The Roc is a mythical giant bird of prey, first conceived during the Islamic Golden Age (~8th to 13th centuries CE), popularized in folk tales gathered in One Thousand One Nights. Rocs figured prominently in tales of Sinbad the Sailor. In this 1898 illustration by René Bull, the Roc is harassing two of Sinbad’s small fleet of ships. Illustration by René Bull is licensed under CC BY 2.0. (Source: https://en.wikipedia.org/wiki/Roc_(mythology)#mediaviewer/File:Rocweb.jpg)

    A first lesson in mathematical modeling for biologists: Rocs

    Learning Objectives
    • Systematically develop a functioning, discrete, single-species model of an exponentially-growing or -declining population.
    • Use the model to recommend appropriate action for population management.
    • Communicate model output and recommendations to non-expert audiences.
    • Generate a collaborative work product that most individuals could not generate on their own, given time and resource constraints.
  • Structure of protein ABCB6

    Investigating the Function of a Transport Protein: Where is ABCB6 Located in Human Cells?

    Learning Objectives
    At the end of this activity students will be able to:
    • describe the use of two common research techniques for studying proteins: SDS-PAGE and immunoblot analysis.
    • determine a protein’s subcellular location based on results from: 1) immunoblotting after differential centrifugation, and 2) immunofluorescence microscopy.
    • analyze protein localization data based on the limitations of differential centrifugation and immunofluorescence microscopy.
  • Format of a typical course meeting
  • 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
  • Medical students at a fair. Credit: Danieladelrio

    Casting a Wide Net via Case Studies: Educating across the undergraduate to medical school continuum in the biological...

    Learning Objectives
    At the end of this lesson, the student should be able to:
    • Consider the potential advantages and disadvantages of widespread use of whole genome sequencing and direct-to-consumer genetic testing.
    • Explore the critical need to maintain privacy of individual genetic test results to protect patient interests.
    • Dissect the nuances of reporting whole genome sequencing results.
    • Recognize the economic ramifications of precision medicine strategies.
    • Formulate a deeper understanding of the ethical dimensions of emerging genetic testing technologies.
  • Enzymatic avocado browning is driven by polyphenol oxidase. Mashed avocado pulp is bright green but turns dark brown over the course of two hours at room temperature in the presence of air and salt. This reaction can be accelerated or inhibited by more than 20 different testable reagents, allowing students to explore experimental design.

    The Avocado Lab: An Inquiry-Driven Exploration of an Enzymatic Browning Reaction

    Learning Objectives
    Students will be able to:
    • develop a testable research question and supportive hypothesis regarding the browning of damaged avocado flesh caused by the activity of avocado polyphenol oxidase (aPPO).
    • design and execute a well-controlled experiment to test aPPO hypotheses.
    • evaluate qualitative enzyme activity data.
    • create a figure and legend to present qualitative data that tests multiple hypotheses and variables.
    • search for and correctly cite primary literature to support or refute hypotheses.
    • know the role of reducing reagents, pH, chelators, and temperature in reactions catalyzed by aPPO.
    • explain why the effects of salt and detergent differ for aPPO experiments conducted in situ
    • (in mashed avocado flesh) as compared to in vitro (on purified protein).
    • discuss how substrate and cofactor availability affect aPPO reactions.
    • describe how endogenous subcellular organization restricts aPPO reactions in a healthy avocado.
    • evaluate food handling practices for fruits expressing PPO.
  • 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.
  • 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
  • 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
  • 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.  
  • Abelson kinase signaling network. The image shows many connections between genes and illustrates that signaling molecules and pathways function within networks. It emphasizes the indispensability of computational tools in understanding the molecular functioning of cells. The image was generated with Cytoscape from publicly accessible protein-protein interactions databases.

    Investigating Cell Signaling with Gene Expression Datasets

    Learning Objectives
    Students will be able to:
    • Explain the hierarchical organization of signal transduction pathways.
    • Explain the role of enzymes in signal propagation and amplification.
    • Recognize the centrality of signaling pathways in cellular processes, such as metabolism, cell division, or cell motility.
    • Rationalize the etiologic basis of disease in terms of deranged signaling pathways.
    • Use software to analyze and interpret gene expression data.
    • Use an appropriate statistical method for hypotheses testing.
    • Produce reports that are written in scientific style.
  • 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)
  • Sample Student Growth Curve. This image shows a yeast growth curve generated by a student in our lab, superimposed on an image of Saccharomyces cerevisiae cells.

    Using Yeast to Make Scientists: A Six-Week Student-Driven Research Project for the Cell Biology Laboratory

    Learning Objectives
    • Learn about basic S. cerevisiae biology
    • Use sterile technique
    • Perform a yeast viability assay
    • Use a spectrophotometer to measure growth of S. cerevisiae
    • Perform a literature search
    • Calculate concentrations of chemicals appropriate for S. cerevisiae
    • Generate S. cerevisiae growth curves
    • Troubleshoot experimental difficulties
    • Perform statistical analysis
    • Present findings to an audience
  • Building a Model of Tumorigenesis: A small group activity for a cancer biology/cell biology course

    Learning Objectives
    At the end of the activity, students will be able to:
    • Analyze data from a retrospective clinical study uncovering genetic alterations in colorectal cancer.
    • Draw conclusions about human tumorigenesis using data from a retrospective clinical study.
    • Present scientific data in an appropriate and accurate way.
    • Discuss why modeling is an important practice of science.
    • Create a simple model of the genetic changes associated with a particular human cancer.
  • DNA

    Using CRISPR-Cas9 to teach the fundamentals of molecular biology and experimental design

    Learning Objectives
    Module 1
    • Generate a testable hypothesis that requires a creative design of reagents based on critical reading of and review of prior research.
    • Demonstrate proficiency in using molecular cloning software to analyze, manipulate and verify DNA sequences.
    • Predict the downstream effect on the mRNA and protein after successfully inserting a DNA repair template into the genome of a cell/organism.
    • Compare and contrast the processes of DNA duplication and PCR.
    • Demonstrate the ability to design primers to amplify a nucleotide sequence.
    • Analyze and evaluate the results of DNA agarose gel electrophoresis.
    Module 2
    • Identify the key features in genomic DNA, specifically those required for CRISPR-Cas9 mediated gene edits.
    • Explain how compatible ends of DNA are used to produce recombinant DNA in a ligation reaction.
    • Explain the chemical principles behind plasmid DNA purification from bacterial cultures.
    • Devise a strategy to screen clones based on antibiotic selection and the mechanism of digestion by DNA endonucleases.
    • Predict and evaluate the results of a diagnostic digest.
    Module 3
    • Explain the chemical principles behind DNA purification using phenol-chloroform extraction and ethanol precipitation.
    • Explain the key differences between DNA duplication and transcription.
    • Demonstrate the ability to perform lab work with sterile technique.
    • Compare and contrast the results of a non-denaturing vs. denaturing agarose gel.
    • Evaluate the results of a denaturing agarose gel.
    Module 4
    • Design and implement an experiment that tests the CRISPR-Cas9 principle.
    • Predict the outcome of a successful in vitro Cas9 digest.
    Presentation of Data Post Lesson
    • Summarize important background information on gene of interest from analysis of primary literature.
    • Produce figures and figure legends that clearly indicate results.
    • Organize and construct a poster that clearly and professionally displays the important aspects of the lesson.
    • Demonstrate understanding of the lesson by presenting a poster to an audience in lay terms, mid-level terms, or at an expert level.
    • Demonstrate understanding of procedures by writing a formal materials and methods paper.