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  • 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.
  • 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
  • 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.
  • blind cave fish
  • 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.
  • 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.
  • 3D Print Models: A collection of 3D models printed from online repository files.
  • 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 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.
  • Format of a typical course meeting
  • 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.
  • 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.
  • 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
  • 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.
  • 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.
  • Figure 2. ICB-Students come to class prepared to discuss the text
  • Results formula questions. Shows the five questions that comprise the formula for writing a scientific Results section.
  • SNP model by David Eccles (gringer) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY 4.0 (http://creativecommons.org/licenses/by/4.0)], via Wikimedia Commons

    Exploration of the Human Genome by Investigation of Personalized SNPs

    Learning Objectives
    Students successfully completing this lesson will be able to:
    • Effectively use the bioinformatics databases (SNPedia, the UCSC Genome Browser, and NCBI) to explore SNPs of interest within the human genome.
    • Identify three health-related SNPs of personal interest and use the UCSC Genome Browser to define their precise chromosomal locations and determine whether they lie within a gene or are intergenic.
    • Establish a list of all genome-wide association studies correlated with a particular health-related SNP.
    • Predict which model organism would be most appropriate for conducting further research on a human disease.
  • Playon Words Title Screen

    Using Gamification to Teach Undergraduate Students about Scientific Writing

    Learning Objectives
    Topics within Playon Words are grouped into “mini-games.” The Learning Objectives for each mini-game are as follows: Sentence Sensei
    • Identify the best sentence variant from a list of options
    • Identify and eliminate needless words
    • Identify where and when to use different types of punctuation marks
    • Identify and correct common grammar mistakes
    Organization Optimizer
    • Organize sentences in a logical order
    • Describe the components of different sections of a scientific paper
    • Identify the section of a scientific paper where a given sentence belongs
    • Eliminate sentences which do not belong in a given writing sample
    Science Officer Training
    • Classify statements as scientific or non-scientific
    • Identify which statements support a particular hypothesis or position
    • Classify provided sentences (e.g. hypotheses vs. predictions, problems vs. experiments, results vs. discussion)
    Reference Referee
    • Compare and contrast different types (e.g. primary literature, review articles, popular literature etc.) and sources (PubMed, Web of Science, Google Scholar etc.) of scientific information
    • Identify locations in texts where citations are needed
    • Identify citations and/or references that are incorrect or missing key information
    • Identify information that does not belong in the reference list (e.g. vendor information)
  • Two cells stained

    Bad Cell Reception? Using a cell part activity to help students appreciate cell biology, with an improved data plan and...

    Learning Objectives
    • Identify cell parts and explain their function
    • Explain how defects in a cell part can result in human disease
    • Generate thought-provoking questions that expand upon existing knowledge
    • Create a hypothesis and plan an experiment to answer a cell part question
    • Find and reference relevant cell biology journal articles
  • Students use plastic Easter eggs and chocolate pieces to simulate the distribution of HIV in T lymphocytes.

    Infectious Chocolate Joy with a Side of Poissonian Statistics: An activity connecting life science students with subtle...

    Learning Objectives
    • Students will define a Poisson distribution.
    • Students will generate a data set on the probability of a T cell being infected with a virus(es).
    • Students will predict the likelihood of one observing the mean value of viruses occurring.
    • Students will evaluate the outcomes of a random process.
    • Students will hypothesize whether a process is Poissonian and design a test for that hypothesis.
    • Students will collect data and create a histogram from their data.
  • 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)
  • 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.
  • 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.  
  • Sodium-Potassium pump

    Lights, Camera, Acting Transport! Using role-play to teach membrane transport

    Learning Objectives
    At the end of this activity, students should be able to:
    • Compare and contrast the mechanisms of simple diffusion, facilitated diffusion, and active transport (both primary and secondary).
    • Identify, and provide a rationale for, the mechanism(s) by which various substances cross the plasma membrane.
    • Describe the steps involved in the transport of ions by the Na+/K+ pump, and explain the importance of electrogenic pumps to the generation and maintenance of membrane potentials.
    • Explain the function of electrochemical gradients as potential energy sources specifically used in secondary active transport.
    • Relate each molecule or ion transported by the Na+/glucose cotransporter (SGLT1) to its own concentration or electrochemical gradient, and describe which molecules travel with and against these gradients.
  • 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.
  • 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
  • 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