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  • “Phenology of a Dawn Redwood” – Images collected by students for this lesson pieced together illustrating a Metasequoia glyptostroboides changing color and dropping its leaves in the fall of 2017 on Michigan State University campus.

    Quantifying and Visualizing Campus Tree Phenology

    Learning Objectives
    The Learning Objectives of this lesson span across the entire semester.
    • Observe and collect information on phenological changes in local trees.
    • Become familiar with a database and how to work with large datasets.
    • Analyze and visualize data from the database to test their hypotheses and questions.
    • Develop a research proposal including empirically-driven questions and hypotheses.
    • Synthesize the results of their analysis in the context of plant biodiversity and local environmental conditions.
  • 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.
  • Image of tick from US Department of Agriculture_ARS photo by Scott Bauer

    Mice, Acorns, and Lyme Disease: a Case Study to Teach the Ecology of Emerging Infectious Diseases.

    Learning Objectives
    Students will be able to...
    • outline the life cycle of ticks and explain the transmission cycle of Lyme disease.
    • describe factors that make mice a competent reservoir for Borrelia burgdorferi.
    • analyze and interpret line and bar graphs of data on the effects of changes to ecological communities on the risk of human exposure to Lyme disease.
    • explain how the incidence of Lyme disease is determined by interactions between bacteria, animals, humans and the environment.
    • predict how changes in the ecosystem affect Borrelia burgdorferi transmission.
    • explain how human activities affect biodiversity and the consequences of those actions on disease outbreaks.
  • 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.
  • 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.
  • 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.
  • 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
  • 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
  • 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)
  • Peterson MP, Rosvall KA, Choi J-H, Ziegenfus C, Tang H, Colbourne JK, et al. (2013) Testosterone Affects Neural Gene Expression Differently in Male and Female Juncos: A Role for Hormones in Mediating Sexual Dimorphism and Conflict. PLoS ONE 8(4): e61784. doi:10.1371/journal.pone.0061784

    Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

    Learning Objectives
    • From raw RNAseq data, run a basic analysis culminating in a list of differentially expressed genes.
    • Explain and evaluate statistical tests in RNAseq data. Specifically, given the output of a particular test, students should be able to interpret and explain the result.
    • Use the Linux command line to complete specified objectives in an RNAseq workflow.
    • Generate meaningful visualizations of results from new data in R.
    • (In addition, each chapter of this lesson plan contains more specific learning objectives, such as “Students will demonstrate their ability to map reads to a reference.”)
  • 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.
  • 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.
  • 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 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.
  • Using Place-Based Economically Relevant Organisms to Improve Student Understanding of the Roles of Carbon Dioxide,...

    Learning Objectives
    At the end of this lesson, students will be able to:
    • Describe the roles of light energy and carbon dioxide in photosynthetic organisms.
    • Identify the effect of nutrients on the growth of photosynthetic organisms.
    • Describe global cycles in atmospheric carbon dioxide levels and how they relate to photosynthetic organisms.
  • photo credit John Friedlein. Author (SRB) helps a student troubleshooting RStudio in the workshop session of class.
  • “The outcome of the Central Dogma is not always intuitive” Variation in gene size does not necessarily correlate with variation in protein size. Here, two related genes differ in length due to a deletion mutation that removes four nucleotides. Many students do not predict that the smaller gene, after transcription and translation, would produce a larger protein.

    Predicting and classifying effects of insertion and deletion mutations on protein coding regions

    Learning Objectives
    Students will be able to:
    • accurately predict effects of frameshift mutations in protein coding regions
    • conduct statistical analysis to compare expected and observed values
    • become familiar with accessing and using DNA sequence databases and analysis tools
  • Monarch larvae

    Does it pose a threat? Investigating the impact of Bt corn on monarch butterflies

    Learning Objectives
    Students will be able to:
    • Apply genetics concepts to a relevant case study of Bt corn and monarch butterflies
    • Read figures and text from primary literature
    • Identify claims presented in scientific studies
    • Evaluate data presented in scientific studies
    • Critically reason using data
    • Evaluate the consequences of GM technology on non-target organisms
    • Communicate scientific data orally
  • 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
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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 Undergraduate Molecular Biology Labs to Discover Targets of miRNAs in Humans

    Learning Objectives
    • Use biological databases to generate and compare lists of predicted miR targets, and obtain the mRNA sequence of their selected candidate gene
    • Use bioinformatics tools to design and optimize primer sets for qPCR
  • 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.
  • MA plot of RNA-seq data. An MA plot is a visual summary of gene expression data which identifies genes showing differential expression between two treatments.

    Tackling "Big Data" with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy

    Learning Objectives
    • Students will locate and download high-throughput sequence data and genome annotation files from publically available data repositories.
    • Students will use Galaxy to create an automated computational workflow that performs sequence quality assessment, trimming, and mapping of RNA-seq data.
    • Students will analyze and interpret the outputs of RNA-seq analysis programs.
    • Students will identify a group of genes that is differentially expressed between treatment and control samples, and interpret the biological significance of this list of differentially expressed 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
  • 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.
  • Using phylogenetics to make inferences about historical biogeographic patterns of evolution.

    Building Trees: Introducing evolutionary concepts by exploring Crassulaceae phylogeny and biogeography

    Learning Objectives
    Students will be able to:
    • Estimate phylogenetic trees using diverse data types and phylogenetic models.
    • Correctly make inferences about evolutionary history and relatedness from the tree diagrams obtained.
    • Use selected computer programs for phylogenetic analysis.
    • Use bootstrapping to assess the statistical support for a phylogeny.
    • Use phylogenetic data to construct, compare, and evaluate the role of geologic processes in shaping the historical and current geographic distributions of a group of organisms.
  • 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)
  • Simplified Representation of the Global Carbon Cycle, https://earthobservatory.nasa.gov/Features/CarbonCycle/images/carbon_cycle.jpg

    Promoting Climate Change Literacy for Non-majors: Implementation of an atmospheric carbon dioxide modeling activity as...

    Learning Objectives
    • Students will be able to manipulate and produce data and graphs.
    • Students will be able to design a simple mathematical model of atmospheric CO2 that can be used to make predictions.
    • Students will be able to conduct simulations, analyze, interpret, and draw conclusions about atmospheric CO2 levels from their own computer generated simulated data.
     
  • Results formula questions. Shows the five questions that comprise the formula for writing a scientific Results section.
  • 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.
  • 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.
  • Strawberries

    The Case of the Missing Strawberries: RFLP analysis

    Learning Objectives
    Students will be able to:
    • Describe the relationship of cells, chromosomes, and DNA.
    • Isolate DNA from strawberries.
    • Digest DNA with restriction enzymes.
    • Perform gel electrophoresis.
    • Design an experiment to compare DNAs by RFLP analysis.
    • Predict results of RFLP analysis.
    • Interpret results of RFLP analysis.
    • Use appropriate safety procedures in the lab.
  • Format of a typical course meeting
  • The MAP Kinase signal transduction pathway

    Cell Signaling Pathways - a Case Study Approach

    Learning Objectives
    • Use knowledge of positive and negative regulation of signaling pathways to predict the outcome of genetic modifications or pharmaceutical manipulation.
    • From phenotypic data, predict whether a mutation is in a coding or a regulatory region of a gene involved in signaling.
    • Use data, combined with knowledge of pathways, to make reasonable predictions about the genetic basis of altered signaling pathways.
    • Interpret and use pathway diagrams.
    • Synthesize information by applying prior knowledge on gene expression when considering congenital syndromes.
  • 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
  • Arabidopsis Seedling

    Linking Genotype to Phenotype: The Effect of a Mutation in Gibberellic Acid Production on Plant Germination

    Learning Objectives
    Students will be able to:
    • identify when germination occurs.
    • score germination in the presence and absence of GA to construct graphs of collated class data of wild-type and mutant specimens.
    • identify the genotype of an unknown sample based on the analysis of their graphical data.
    • organize data and perform quantitative data analysis.
    • explain the importance of GA for plant germination.
    • connect the inheritance of a mutation with the observed phenotype.
  • Pipets - photo by Magnus Manske

    Learning to Pipet Correctly by Pipetting Incorrectly?

    Learning Objectives
    • Students will be able to use analytical balances and micropipettes.
    • Students will be able to calculate averages and standard deviations.
    • Students will be able to use t-tests to compare two independent samples.
    • Students will be able to justify accepting or rejecting a null hypothesis based on an interpretation of p-values.
    • Students will learn to use spreadsheet software such as Microsoft Excel and/or Google Sheets
    • Students will be able to explain how pipetting incorrectly leads to errors.
  • 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.
  • Multiple sequence alignment of homologous cytochrome C protein sequences using Jalview viewer.

    Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence...

    Learning Objectives
    At the end of this lesson, students will be able to:
    • Define similarity in a non-biological and biological sense when provided with two strings of letters.
    • Quantify the similarity between two gene/protein sequences.
    • Explain how a substitution matrix is used to quantify similarity.
    • Calculate amino acid similarity scores using a scoring matrix.
    • Demonstrate how to access genomic data (e.g., from NCBI nucleotide and protein databases).
    • Demonstrate how to use bioinformatics tools to analyze genomic data (e.g., BLASTP), explain a simplified BLAST search algorithm including how similarity is used to perform a BLAST search, and how to evaluate the results of a BLAST search.
    • Create a nearest-neighbor distance matrix.
    • Create a multiple sequence alignment using a nearest-neighbor distance matrix and a phylogram based on similarity of amino acid sequences.
    • Use appropriate bioinformatics sequence alignment tools to investigate a biological question.
  • American coot (Fulica Americana) family at the Cloisters City Park pond in Morrow Bay, CA. "Mike" Michael L. Baird [CC BY 2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons, https://upload.wikimedia.org/wikipedia/commons/d/db/Fulica_americana3.jpg

    Knowing your own: A classroom case study using the scientific method to investigate how birds learn to recognize their...

    Learning Objectives
    • Students will be able to identify and describe the steps of the scientific method.
    • Students will be able to develop hypotheses and predictions.
    • Students will be able to construct and interpret bar graphs based on data and predictions.
    • Students will be able to draw conclusions from data presented in graphical form.
  • 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.
  • Human karyotype

    Homologous chromosomes? Exploring human sex chromosomes, sex determination and sex reversal using bioinformatics...

    Learning Objectives
    Students successfully completing this lesson will:
    • Practice navigating an online bioinformatics resource and identify evidence relevant to solving investigation questions
    • Contrast the array of genes expected on homologous autosomal chromosomes pairs with the array of genes expected on sex chromosome pairs
    • Use bioinformatics evidence to defend the definition of homologous chromosomes
    • Define chromosomal sex and defend the definition using experimental data
    • Investigate the genetic basis of human chromosomal sex determination
    • Identify at least two genetic mutations can lead to sex reversal

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