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• ### 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.
• ### 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.
• ### Teaching the Biological Relevance of Chemical Kinetics Using Cold-Blooded Animal Biology

Learning Objectives
Students will be able to:
• Predict the effect of reaction temperature on the rate of a chemical reaction
• Interpret a graph plotted between rate of a chemical reaction and temperature
• Discuss chemical kinetics utilizing case studies of cold-blooded animals
• ### 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.

• ### 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.
• ### 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.

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)
• ### 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.
• ### 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.
• ### 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)
• ### 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.
• ### 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
• ### 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.
• ### 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.
• ### 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.
• ### 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.
• ### 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
• ### 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.
• ### Using CRISPR-Cas9 to teach the fundamentals of molecular biology and experimental design

Learning Objectives
Module 1
• Generate a testable hypothesis that requires a creative design of reagents based on critical reading of and review of prior research.
• Demonstrate proficiency in using molecular cloning software to analyze, manipulate and verify DNA sequences.
• Predict the downstream effect on the mRNA and protein after successfully inserting a DNA repair template into the genome of a cell/organism.
• Compare and contrast the processes of DNA duplication and PCR.
• Demonstrate the ability to design primers to amplify a nucleotide sequence.
• Analyze and evaluate the results of DNA agarose gel electrophoresis.
Module 2
• Identify the key features in genomic DNA, specifically those required for CRISPR-Cas9 mediated gene edits.
• Explain how compatible ends of DNA are used to produce recombinant DNA in a ligation reaction.
• Explain the chemical principles behind plasmid DNA purification from bacterial cultures.
• Devise a strategy to screen clones based on antibiotic selection and the mechanism of digestion by DNA endonucleases.
• Predict and evaluate the results of a diagnostic digest.
Module 3
• Explain the chemical principles behind DNA purification using phenol-chloroform extraction and ethanol precipitation.
• Explain the key differences between DNA duplication and transcription.
• Demonstrate the ability to perform lab work with sterile technique.
• Compare and contrast the results of a non-denaturing vs. denaturing agarose gel.
• Evaluate the results of a denaturing agarose gel.
Module 4
• Design and implement an experiment that tests the CRISPR-Cas9 principle.
• Predict the outcome of a successful in vitro Cas9 digest.
Presentation of Data Post Lesson
• Summarize important background information on gene of interest from analysis of primary literature.
• Produce figures and figure legends that clearly indicate results.
• Organize and construct a poster that clearly and professionally displays the important aspects of the lesson.
• Demonstrate understanding of the lesson by presenting a poster to an audience in lay terms, mid-level terms, or at an expert level.
• Demonstrate understanding of procedures by writing a formal materials and methods paper.
• ### Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course

Learning Objectives
Students will be able to:
• list and perform the steps of sequence processing and taxonomic inference.
• interpret microbial community diversity from metagenomic sequence datasets.
• compare microbial diversity within and between samples or treatments.
• ### 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
• ### 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,
• 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 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.
• ### 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.
• ### 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
• ### A virtual laboratory on cell division using a publicly-available image database

Learning Objectives
• Students will name and describe the salient features and cellular tasks for each stage of cell division.
• Students will predict the relative durations of the stages of cell division using prior knowledge and facts from assigned readings.
• Students will describe the relationship between duration of each stage of cell division and the frequency of cells present in each stage of cell division counted in a random sample of images of pluripotent stem cells.
• Students will identify the stages of cell division present in research-quality images of human pluripotent stem cells in various stages of cell division.
• Students will quantify, analyze and summarize data on the prevalence of cells at different stages of cell division in randomly sampled cell populations.
• Students will use data to reflect on and revise predictions.
• ### 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.