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• ### 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.
• ### 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.
• ### 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.
• ### Your Tax Dollars at Work: A mock grant writing experience centered on scientific process skills

Learning Objectives
Students will be able to:
• Propose a testable, novel question contributing to a biological field of study.
• Formulate a study rationale.
• Describe relevant background information on a topic using the primary literature.
• Choose appropriate scientific, mathematical, and statistical methods to analyze a research question.
• Determine the financial costs of a research project.
• Present a proposal for peer review and compose a constructive peer review.
• Collaborate as a member of a scientific team.
• Articulate the review criteria and process used in NSF-style proposal review.
• ### 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.
• ### 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
• ### A Hands-on Introduction to Hidden Markov Models

Learning Objectives
• Students will be able to process unannotated genomic data using ab initio gene finders as well as other inputs.
• Students will be able to defend the proposed gene annotation.
• Students will reflect on the other uses for HMMs.
• ### 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 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
• ### 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.
• ### 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.
• ### Why Meiosis Matters: The case of the fatherless snake

Learning Objectives
Students will be able to:
• Compare and contrast the process and outcomes of mitosis & meiosis
• Predict consequences of abnormal meiosis including
• The potential genotype and/or phenotypes of offspring produced when meiosis does not occur properly
• The stage(s) of meiosis that could have been abnormal given an offspring’s genotype and/or phenotype
• ### 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.
• ### 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.
• ### 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.
• ### 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.
• ### Infectious Chocolate Joy with a Side of Poissonian Statistics: An activity connecting life science students with subtle...

Learning Objectives
• Students will define a Poisson distribution.
• Students will generate a data set on the probability of a T cell being infected with a virus(es).
• Students will predict the likelihood of one observing the mean value of viruses occurring.
• Students will evaluate the outcomes of a random process.
• Students will hypothesize whether a process is Poissonian and design a test for that hypothesis.
• Students will collect data and create a histogram from their data.
• ### A 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)
• ### 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.
• ### The ACTN3 Polymorphism: Applications in Genetics and Physiology Teaching Laboratories

Learning Objectives
1. Test hypotheses related to the role of ACTN3 in skeletal muscle function.
2. Explain how polymorphic variants of the ACTN3 gene affect protein structure and function.
3. List and explain the differences between fast twitch and slow twitch muscle fibers.
4. List and explain possible roles of the ACTN3 protein in skeletal muscle function.
5. Find and analyze relevant scientific publications about the relationship between ACTN3 genotype and muscle function.
6. Formulate hypotheses related to the relationship between ACTN3 genotype and skeletal muscle function.
7. Design experiments to test hypotheses about the role of ACTN3 in skeletal muscle function.
8. Statistically analyze experimental results using relevant software.
9. Present experimental results in writing.
• ### 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.
• ### 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
• ### Using Pathway Maps to Link Concepts, Peer Review, Primary Literature Searches and Data Assessment in Large Enrollment...

Learning Objectives
• Define basic concepts and terminology of Ecosystem Ecology
• Link biological processes that affect each other
• Evaluate whether the link causes a positive, negative, or neutral effect
• Find primary literature
• Identify data that correctly supports or refutes an hypothesis
• ### 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.
• ### 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.
• ### 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.
• ### 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.
• ### 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
• ### Bad Cell Reception? Using a cell part activity to help students appreciate cell biology, with an improved data plan and...

Learning Objectives
• Identify cell parts and explain their function
• Explain how defects in a cell part can result in human disease
• Generate thought-provoking questions that expand upon existing knowledge
• Create a hypothesis and plan an experiment to answer a cell part question
• Find and reference relevant cell biology journal articles
• ### 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
• ### 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.
• ### 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.
• ### 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.
• ### A Short Laboratory Module to Help Infuse Metacognition during an Introductory Course-based Research Experience

Learning Objectives
• Students will be able to evaluate the strengths and weaknesses of data.
• Students will be able to employ prior knowledge in formulating a biological research question or hypothesis.
• Students will be able to distinguish a research question from a testable hypothesis.
• Students will recognize that the following are essential elements in experimental design: identifying gaps in prior knowledge, picking an appropriate approach (ex. experimental tools and controls) for testing a hypothesis, and reproducibility and repeatability.
• Students will be able to identify appropriate experimental tools, approaches and controls to use in testing a hypothesis.
• Students will be able to accurately explain why an experimental approach they have selected is a good choice for testing a particular hypothesis.
• Students will be able to discuss whether experimental outcomes support or fail to support a particular hypothesis, and in the case of the latter, discuss possible reasons why.

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)
• ### 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