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CURE-all: Large Scale Implementation of Authentic DNA Barcoding Research into First-Year Biology CurriculumLearning ObjectivesStudents 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
- 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
- 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
- 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
Sex-specific differences in Meiosis: Real-world applicationsLearning ObjectivesAfter completion of the lesson students will be able to:
- Describe the differences between female and male meiosis.
- Interpret graphical data to make decisions relevant to medical practices.
- Develop a hypothesis that explains the difference in incidence of aneuploidy in gametes between males and females.
Authentic Ecological Inquiries Using BearCam ArchivesLearning ObjectivesStudents will be able to:
- conduct an authentic ecological inquiry including
- generate a testable hypothesis based on observations,
- design investigation with appropriate sampling selection and variables,
- 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.
- conduct an authentic ecological inquiry including
A flexible, multi-week approach to plant biology - How will plants respond to higher levels of CO2?Learning ObjectivesStudents 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).
Modeling the Research Process: Authentic human physiology research in a large non-majors courseLearning ObjectivesStudents will be able to:
- Read current scientific literature
- Formulate testable hypotheses
- Design an experimental procedure to test their hypothesis
- Make scientific observations
- Analyze and interpret data
- Communicate results visually and orally
Discovery Poster ProjectLearning ObjectivesStudents 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
The Avocado Lab: An Inquiry-Driven Exploration of an Enzymatic Browning ReactionLearning ObjectivesStudents will be able to:
- develop a testable research question and supportive hypothesis regarding the browning of damaged avocado flesh caused by the activity of avocado polyphenol oxidase (aPPO).
- design and execute a well-controlled experiment to test aPPO hypotheses.
- evaluate qualitative enzyme activity data.
- create a figure and legend to present qualitative data that tests multiple hypotheses and variables.
- search for and correctly cite primary literature to support or refute hypotheses.
- know the role of reducing reagents, pH, chelators, and temperature in reactions catalyzed by aPPO.
- explain why the effects of salt and detergent differ for aPPO experiments conducted in situ
- (in mashed avocado flesh) as compared to in vitro (on purified protein).
- discuss how substrate and cofactor availability affect aPPO reactions.
- describe how endogenous subcellular organization restricts aPPO reactions in a healthy avocado.
- evaluate food handling practices for fruits expressing PPO.
Bad Science: Exploring the unethical research behind a putative memory supplementLearning ObjectivesStudents will be able to:
- create criteria for evaluating information that is touted as scientific.
- apply those criteria to evaluate the claim that Prevagen® enhances memory.
- identify the misleading tactics used on the Prevagen® website and in their self-published reporting.
- decide whether to recommend taking Prevagen® and explain their decisions.
You and Your Oral Microflora: Introducing non-biology majors to their “forgotten organ”Learning ObjectivesStudents 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
Why do Some People Inherit a Predisposition to Cancer? A small group activity on cancer geneticsLearning ObjectivesAt the end of this activity, we expect students will be able to:
- Use family pedigrees and additional genetic information to determine inheritance patterns for hereditary forms of cancer
- Explain why a person with or without cancer can pass on a mutant allele to the next generation and how that impacts probability calculations
- Distinguish between proto-oncogenes and tumor suppressor genes
Casting a Wide Net via Case Studies: Educating across the undergraduate to medical school continuum in the biological...Learning ObjectivesAt the end of this lesson, the student should be able to:
- Consider the potential advantages and disadvantages of widespread use of whole genome sequencing and direct-to-consumer genetic testing.
- Explore the critical need to maintain privacy of individual genetic test results to protect patient interests.
- Dissect the nuances of reporting whole genome sequencing results.
- Recognize the economic ramifications of precision medicine strategies.
- Formulate a deeper understanding of the ethical dimensions of emerging genetic testing technologies.
A new approach to course-based research using a hermit crab-hydrozoan symbiosisLearning ObjectivesStudents 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.
Coevolution or not? Crossbills, squirrels and pineconesLearning Objectives
- Define coevolution.
- Identify types of evidence that would help determine whether two species are currently in a coevolutionary relationship.
- Interpret graphs.
- Evaluate evidence about whether two species are coevolving and use evidence to make a scientific argument.
- Describe what evidence of a coevolutionary relationship might look like.
- Distinguish between coadaptation and coevolution.
A virtual laboratory on cell division using a publicly-available image databaseLearning 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.
A CURE-based approach to teaching genomics using mitochondrial genomesLearning Objectives
- Install the appropriate programs such as Putty and WinSCP.
- Navigate NCBI's website including their different BLAST programs (e.g., blastn, tblastx, blastp and blastx)
- Use command-line BLAST to identify mitochondrial contigs within a whole genome assembly
- Filter the desired sequence (using grep) and move the assembled mitochondrial genome onto your own computer (using FTP or SCP)
- Error-correct contigs (bwa mem, samtools tview), connect and circularize organellar contigs (extending from filtered reads)
- Transform assembled sequences into annotated genomes
- Orient to canonical start locations in the mitochondrial genome (cox1)
- Identify the boundaries of all coding components of the mitochondrial genome using BLAST, including: Protein coding genes (BLASTx and tBLASTX), tRNAs (proprietary programs such as tRNAscan), rRNAs (BLASTn, Chlorobox), ORFs (NCBI's ORFFinder)
- Deposit annotation onto genome repository (NCBI)
- Update CV/resume to reflect bioinformatics skills learned in this lesson
A clicker-based case study that untangles student thinking about the processes in the central dogmaLearning ObjectivesStudents 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.
Teaching students to read, interpret, and write about scientific research: A press release assignment in a large, lower...Learning ObjectivesStudents will:
- interpret the main conclusions and their supporting evidence in a primary research article.
- concisely communicate the significance of scientific findings to an educated nonspecialist audience.
- identify the components of a primary research article and the components of the "inverted pyramid" press release structure.
- identify the central figure in a primary research paper and describe its key finding.
- demonstrate an understanding of intellectual property by giving appropriate credit to other people's original work.