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  • A A student assists Colorado Parks & Wildlife employees spawning greenback cutthroat trout at the Leadville National Fish Hatchery; B greenback cutthroat trout adults in a hatchery raceway; C tissue samples collected by students to be used for genetic analysis (images taken by S. Love Stowell)

    Cutthroat trout in Colorado: A case study connecting evolution and conservation

    Learning Objectives
    Students will be able to:
    • interpret figures such as maps, phylogenies, STRUCTURE plots, and networks for species delimitation
    • identify sources of uncertainty and disagreement in real data sets
    • propose research to address or remedy uncertainty
    • construct an evidence-based argument for the management of a rare taxon
  • Images of students participating in the SIDE activity

    Using a Sequential Interpretation of Data in Envelopes (SIDE) approach to identify a mystery TRP channel

    Learning Objectives
    • Students will be able to analyze data from multiple experimental methodologies to determine the identity of their "mystery" TRP channel.
    • Students will be able to interpret the results of individual experiments and from multiple experiments simultaneously to identify their "mystery" TRP channel.
    • Students will be able to evaluate the advantages and limitations of experimental methodologies presented in this lesson.
  • photo credit John Friedlein. Author (SRB) helps a student troubleshooting RStudio in the workshop session of 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.
  • Format of a typical course meeting
  • 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.
  • 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.
  • Students using the Understanding Eukaryotic Genes curriculum to construct a gene model. Students are working as a pair to complete each Module using classroom computers.

    An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

    Learning Objectives
    Module 1
    • Demonstrate basic skills in using the UCSC Genome Browser to navigate to a genomic region and to control the display settings for different evidence tracks.
    • Explain the relationships among DNA, pre-mRNA, mRNA, and protein.
    Module 2
    • Describe how a primary transcript (pre-mRNA) can be synthesized using a DNA molecule as the template.
    • Explain the importance of the 5' and 3' regions of the gene for initiation and termination of transcription by RNA polymerase II.
    • Identify the beginning and the end of a transcript using the capabilities of the genome browser.
    Module 3
    • Explain how the primary transcript generated by RNA polymerase II is processed to become a mature mRNA, using the sequence signals identified in Module 2.
    • Use the genome browser to analyze the relationships among:
    • pre-mRNA
    • 5' capping
    • 3' polyadenylation
    • splicing
    • mRNA
    Module 4
    • Identify splice donor and acceptor sites that are best supported by RNA-Seq data and TopHat splice junction predictions.
    • Utilize the canonical splice donor and splice acceptor sequences to identify intron-exon boundaries.
    Module 5
    • Determine the codons for specific amino acids and identify reading frames by examining the Base Position track in the genome browser.
    • Assemble exons to maintain the open reading frame (ORF) for a given gene.
    • Define the phases of the splice donor and acceptor sites and describe how they impact the maintenance of the ORF.
    • Identify the start and stop codons of an assembled ORF.
    Module 6
    • Demonstrate how alternative splicing of a gene can lead to different mRNAs.
    • Show how alternative splicing can lead to the production of different polypeptides and result in drastic changes in phenotype.
  • 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.
  • Mechanisms regulating the lac operon system

    Discovering Prokaryotic Gene Regulation by Building and Investigating a Computational Model of the lac Operon

    Learning Objectives
    Students will be able to:
    • model how the components of the lac operon contribute to gene regulation and expression.
    • generate and test predictions using computational modeling and simulations.
    • interpret and record graphs displaying simulation results.
    • relate simulation results to cellular events.
    • describe how changes in environmental glucose and lactose levels impact regulation of the lac operon.
    • predict, test, and explain how mutations in specific elements in the lac operon affect their protein product and other elements within the operon.
  • 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.
  • Graphic of structured decision making process

    Using Structured Decision Making to Explore Complex Environmental Issues

    Learning Objectives
    Students will be able to:
    1. Describe the process, challenges, and benefits of structured decision making for natural resource management decisions.
    2. Explain and reflect on the role of science and scientists in structured decision making and how those roles interact and compare to the roles of other stakeholders.
    3. Assess scientific evidence for a given management or policy action to resolve an environmental issue.
  • Students engaged in building the PCR model

    A Close-Up Look at PCR

    Learning Objectives
    At the end of this lesson students will be able to...
    • Describe the role of a primer in PCR
    • Predict sequence and length of PCR product based on primer sequences
    • Recognize that primers are incorporated into the final PCR products and explain why
    • Identify covalent and hydrogen bonds formed and broken during PCR
    • Predict the structure of PCR products after each cycle of the reaction
    • Explain why amplification proceeds exponentially
  • The mechanisms regulating the trp operon system.

    Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon

    Learning Objectives
    Students will be able to:
    • Perturb and interpret simulations of the trp operon.
    • Define how simulation results relate to cellular events.
    • Describe the biological role of the trp operon.
    • Describe cellular mechanisms regulating the trp operon.
    • Explain mechanistically how changes in the extracellular environment affect the trp operon.
    • Define the impact of mutations on trp operon expression and regulation.