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• ### 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 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.

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)
• ### 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.
• ### 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
• ### An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

Learning Objectives
Module 1
• Demonstrate basic skills in using the UCSC Genome Browser to navigate to a genomic region and to control the display settings for different evidence tracks.
• Explain the relationships among DNA, pre-mRNA, mRNA, and protein.
Module 2
• Describe how a primary transcript (pre-mRNA) can be synthesized using a DNA molecule as the template.
• Explain the importance of the 5' and 3' regions of the gene for initiation and termination of transcription by RNA polymerase II.
• Identify the beginning and the end of a transcript using the capabilities of the genome browser.
Module 3
• Explain how the primary transcript generated by RNA polymerase II is processed to become a mature mRNA, using the sequence signals identified in Module 2.
• Use the genome browser to analyze the relationships among:
• pre-mRNA
• 5' capping
• splicing
• mRNA
Module 4
• Identify splice donor and acceptor sites that are best supported by RNA-Seq data and TopHat splice junction predictions.
• Utilize the canonical splice donor and splice acceptor sequences to identify intron-exon boundaries.
Module 5
• Determine the codons for specific amino acids and identify reading frames by examining the Base Position track in the genome browser.
• Assemble exons to maintain the open reading frame (ORF) for a given gene.
• Define the phases of the splice donor and acceptor sites and describe how they impact the maintenance of the ORF.
• Identify the start and stop codons of an assembled ORF.
Module 6
• Demonstrate how alternative splicing of a gene can lead to different mRNAs.
• Show how alternative splicing can lead to the production of different polypeptides and result in drastic changes in phenotype.
• ### 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.
• ### 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
• ### 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.
• ### 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.
• ### 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.

• ### 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.
• ### Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes

Learning Objectives
Students successfully completing this lesson will:
1. Practice basic molecular biology laboratory skills such as DNA isolation, PCR, and gel electrophoresis.
2. Gather and analyze quantitative and qualitative scientific data and present it in figures.
3. Use bioinformatics to analyze DNA sequences and obtain protein sequences for molecular modeling.
4. Make and analyze three-dimensional (3-D) protein models using molecular modeling software.
5. Write a laboratory report using the collected data to explain how mutations in the DNA cause changes in protein structure/function which lead to mutant phenotypes.
• ### 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.
• ### 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.