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# Introductory Biology

• ### Antibiotic Resistance Genes Detection in Environmental Samples

Learning Objectives
After completing this laboratory series, students will be able to:
• apply the scientific method in formulating a hypothesis, designing a controlled experiment using appropriate molecular biology techniques, and analyzing experimental results;
• conduct a molecular biology experiment and explain the principles behind methodologies, such as accurate use of micropipettes, PCR (polymerase chain reaction), and gel electrophoresis;
• determine the presence of antibiotic-resistance genes in environmental samples by analyzing PCR products using gel electrophoresis;
• explain mechanisms of microbial antibiotic resistance;
• contribute data to the Antibiotic Resistance Genes Network;
• define and apply key concepts of antibiotic resistance and gene identification via PCR fragment size.
• ### 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.
• ### 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.
• ### 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.
• ### 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.
• ### 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.
• ### 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
• ### 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.
• ### 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.
• ### Evaluating the Quick Fix: Weight Loss Drugs and Cellular Respiration

Learning Objectives
• Students will be able to explain how the energy from sugars is transformed into ATP via cellular respiration.
• Students will be able to predict an outcome if there is a perturbation in the cellular respiration pathway.
• Students will be able to state and evaluate a hypothesis.
• Students will be able to interpret data from a graph, and use that data to make inferences about the action of a drug.
• ### 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.
• ### 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
• ### Sex and gender: What does it mean to be female or male?

Learning Objectives
• Students will be able to distinguish between sex and gender, and apply each term appropriately.
• Students will be able to compare and contrast levels of sexual determination.
• Students will be able to critique societal misrepresentations surrounding sex, gender, and gender identity.
• ### 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.
• ### 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.
• ### 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.
• ### Meiosis: A Play in Three Acts, Starring DNA Sequence

Learning Objectives
• Students will be able to identify sister chromatids and homologous chromosomes at different stages of meiosis.
• Students will be able to identify haploid and diploid cells, whether or not the chromosomes are replicated.
• Students will be able to explain why homologous chromosomes must pair during meiosis.
• Students will be able to relate DNA sequence similarity to chromosomal structures.
• Students will be able to identify crossing over as the key to proper pairing of homologous chromosomes during meiosis.
• Students will be able to predict the outcomes of meiosis for a particular individual or cell.
• ### 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.”)
• ### 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
• ### Grow the Gradient: An interactive countercurrent multiplier game

Learning Objectives
• Students will be able to simulate the movement of water and sodium at each region of the loop of Henle.
• Students will be able to associate osmosis and active transport with movement of water/solutes at each region of the loop of Henle.
• Students will be able to model how the descending and ascending limbs of the loop of Henle maintain a concentration gradient within the medulla.
• Students will be able to predict the effects of altering normal water and salt movement out of the loop of Henle on the salt concentration of the medulla, urine concentration, and urine volume.
Advanced Learning Objectives for Extensions
• Students will be able to predict the impact of the length of the loop of Henle on the magnitude of the concentration gradient within the medulla.
• Students will be able to predict the length of the loop of Henle in organisms from different habitats.
• ### 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.
• ### 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)
• ### 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 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
• ### 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.
• ### Teaching Cell Structures through Games

Learning Objectives
• Students will identify cell structures when viewing an image or diagram of a cell.
• Students will define the function of eukaryotic organelles and structures, including describing the processes and conditions related to transmembrane transport
• Students will differentiate between prokaryotic and eukaryotic cells, plant and animal cells according to their structural organization.
• ### 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
• ### 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
• ### 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.
• ### 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 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.
• ### A simple way for students to visualize cellular respiration: adapting the board game MousetrapTM to model complexity

Learning Objectives
• Students will be able to describe the three stages of cellular respiration.
• Students will be able to identify the reactants entering and the products formed during each stage of cellular respiration.
• Students will be able to explain how chemical energy in carbohydrates is transferred to ATP through the stages of cellular respiration.
• Students will be able to explain the effects of compartmentalization of cellular respiration reactions in different cellular spaces.
• Students will be able to predict biological outcomes when a specific stage(s) of cellular respiration is altered.
• ### 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.
• ### 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.