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  • Students participating in the peer review process. Practicing the writing of scientific manuscripts prepares students to understand and engage in the primary literature they encounter.
  • Fully annotated mitochondrial genome of a lichenized fungal species (Cladonia subtenuis).  This represents a visual representation of the final project result of the lesson plan. Students will submit their annotation to NCBI (GenBank) and upon acceptance of their annotation, they typically add this publicly available resource into their resume.

    A CURE-based approach to teaching genomics using mitochondrial genomes

    Learning Objectives
    • Install the appropriate programs such as Putty and WinSCP.
    • Navigate NCBI's website including their different BLAST programs (e.g., blastn, tblastx, blastp and blastx)
    • Use command-line BLAST to identify mitochondrial contigs within a whole genome assembly
    • Filter the desired sequence (using grep) and move the assembled mitochondrial genome onto your own computer (using FTP or SCP)
    • Error-correct contigs (bwa mem, samtools tview), connect and circularize organellar contigs (extending from filtered reads)
    • Transform assembled sequences into annotated genomes
    • Orient to canonical start locations in the mitochondrial genome (cox1)
    • Identify the boundaries of all coding components of the mitochondrial genome using BLAST, including: Protein coding genes (BLASTx and tBLASTX), tRNAs (proprietary programs such as tRNAscan), rRNAs (BLASTn, Chlorobox), ORFs (NCBI's ORFFinder)
    • Deposit annotation onto genome repository (NCBI)
    • Update CV/resume to reflect bioinformatics skills learned in this lesson
  • 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
  • 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.
  • 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.
  • 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)
  • 3D Print Models: A collection of 3D models printed from online repository files.
  • 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.
  • Image from a clicker-based case study on muscular dystrophy and the effect of mutations on the processes in the central dogma.

    A clicker-based case study that untangles student thinking about the processes in the central dogma

    Learning Objectives
    Students will be able to:
    • explain the differences between silent (no change in the resulting amino acid sequence), missense (a change in the amino acid sequence), and nonsense (a change resulting in a premature stop codon) mutations.
    • differentiate between how information is encoded during DNA replication, transcription, and translation.
    • evaluate how different types of mutations (silent, missense, and nonsense) and the location of those mutations (intron, exon, and promoter) differentially affect the processes in the central dogma.
    • predict the molecular (DNA size, mRNA length, mRNA abundance, and protein length) and/or phenotypic consequences of mutations.
  • Bacteria growing on petri dish

    You and Your Oral Microflora: Introducing non-biology majors to their “forgotten organ”

    Learning Objectives
    Students will be able to:
    • Explain both beneficial and detrimental roles of microbes in human health.
    • Compare and contrast DNA replication as it occurs inside a cell versus in a test tube
    • Identify an unknown sequence of DNA by performing a BLAST search
    • Navigate sources of scientific information to assess the accuracy of their experimental techniques
  • This is a representation of what might happen during peer discussion.

    In-class peer grading of daily quizzes increases feedback opportunities

    Learning Objectives
    Each of these objectives are illustrated with a succinct slide presentation or other supplemental material available ahead of class time through the course administration system. Learners found it particularly helpful to have video clips that remind them of mathematical manipulations available (in the above example objective c). Students understand that foundational objectives tend to be the focus of the quiz (objectives a-d) and that others will be given more time to work on together in class (objectives e-g), but I don't specify this exactly to reduce temptation that 'gamers' take a shortcut that would impact their group work negatively later on. However, the assignment for a focused graded group activity is posted as well, so it is clear what we are working towards; if desired individuals could prepare ahead of the class.
  • 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.
  • Science press release cartoon.  Cartoon of a newspaper with the headline “Extra Extra! Cell Biology Makes Headlines!”

    Teaching students to read, interpret, and write about scientific research: A press release assignment in a large, lower...

    Learning Objectives
    Students will:
    • interpret the main conclusions and their supporting evidence in a primary research article.
    • concisely communicate the significance of scientific findings to an educated nonspecialist audience.
    • identify the components of a primary research article and the components of the "inverted pyramid" press release structure.
    • identify the central figure in a primary research paper and describe its key finding.
    • demonstrate an understanding of intellectual property by giving appropriate credit to other people's original work.
  • 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.
  • DNA Detective: Genotype to Phenotype. A Bioinformatics Workshop for Middle School to College. In this image, students are selecting the mutant Arabidopsis plant defective for the “mystery” gene that they identified and annotated through the DNA Subway Red Line.
  • A crossbill feeds on a pinecone

    Coevolution or not? Crossbills, squirrels and pinecones

    Learning Objectives
    1. Define coevolution.
    2. Identify types of evidence that would help determine whether two species are currently in a coevolutionary relationship.
    3. Interpret graphs.
    4. Evaluate evidence about whether two species are coevolving and use evidence to make a scientific argument.
    5. Describe what evidence of a coevolutionary relationship might look like.
    6. Distinguish between coadaptation and coevolution.
  • Confocal microscope image of a mouse egg that is arrested at metaphase of meiosis II. Green, tubulin staining of meiotic spindle; red, actin staining of egg membrane; blue, DNA. This image was obtained on a Zeiss 510 Meta confocal microscope in the Department of Genetics at Rutgers University

    Sex-specific differences in Meiosis: Real-world applications

    Learning Objectives
    After completion of the lesson students will be able to:
    1. Describe the differences between female and male meiosis.
    2. Interpret graphical data to make decisions relevant to medical practices.
    3. Develop a hypothesis that explains the difference in incidence of aneuploidy in gametes between males and females.
  • 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.
  • DNA

    Why do Some People Inherit a Predisposition to Cancer? A small group activity on cancer genetics

    Learning Objectives
    At the end of this activity, we expect students will be able to:
    1. Use family pedigrees and additional genetic information to determine inheritance patterns for hereditary forms of cancer
    2. Explain why a person with or without cancer can pass on a mutant allele to the next generation and how that impacts probability calculations
    3. Distinguish between proto-oncogenes and tumor suppressor genes
  • Modeling the Research Process: Authentic human physiology research in a large non-majors course

    Learning Objectives
    Students will be able to:
    • Read current scientific literature
    • Formulate testable hypotheses
    • Design an experimental procedure to test their hypothesis
    • Make scientific observations
    • Analyze and interpret data
    • Communicate results visually and orally
  • Using the Cell Engineer/Detective Approach to Explore Cell Structure and Function

    Learning Objectives
    Students will be able to:
    • Identify the major cell organelles
    • List the major functions of the organelles
    • Predict how changes in organelle/cell structure could alter cellular function
    • Explain how overall cellular function is dependent upon organelles/cell structure
    • Relate cell structure to everyday contexts