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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.

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 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.
• ### 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
• ### 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
• ### 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.