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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.
• ### 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.
• ### Discovery Poster Project

Learning Objectives
Students will be able to:
• identify and learn about a scientific research discovery of interest to them using popular press articles and the primary literature
• find a group on campus doing research that aligns with their interests and communicate with the faculty leader of that group
• create and present a poster that synthesizes their knowledge of the research beyond the discovery
• ### 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 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.
• ### 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
• ### 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.
• ### 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.
• ### 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.
• ### 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