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# Introductory Biology

• ### 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.
• ### 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.
• ### 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 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.
• ### 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.
• ### 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.

• ### 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.
• ### 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.
• ### 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
• ### 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.
• ### 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
• ### 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.
• ### Modeling the Research Process: Authentic human physiology research in a large non-majors course

Learning Objectives
Students will be able to:
• Formulate testable hypotheses
• Design an experimental procedure to test their hypothesis
• Make scientific observations
• Analyze and interpret data
• Communicate results visually and orally
• ### 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
• ### 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.
• ### 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.”)
• ### 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.
• ### 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.
• ### 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.
• ### An active-learning lesson that targets student understanding of population growth in ecology

Learning Objectives
Students will be able to:
• Calculate and compare population density and abundance.
• Identify whether a growth curve describes exponential, linear, and/or logistic growth.
• Describe and calculate a population's growth rate using linear, exponential, and logistic models.
• Explain the influence of carrying capacity and population density on growth rate.
• ### 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
• ### 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)