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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.
Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence...Learning ObjectivesAt 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.
Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active TeachingLearning Objectives
- From raw RNAseq data, run a basic analysis culminating in a list of differentially expressed genes.
- Explain and evaluate statistical tests in RNAseq data. Specifically, given the output of a particular test, students should be able to interpret and explain the result.
- Use the Linux command line to complete specified objectives in an RNAseq workflow.
- Generate meaningful visualizations of results from new data in R.
- (In addition, each chapter of this lesson plan contains more specific learning objectives, such as “Students will demonstrate their ability to map reads to a reference.”)
A first lesson in mathematical modeling for biologists: RocsLearning 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.
Does it pose a threat? Investigating the impact of Bt corn on monarch butterfliesLearning ObjectivesStudents will be able to:
- Apply genetics concepts to a relevant case study of Bt corn and monarch butterflies
- Read figures and text from primary literature
- Identify claims presented in scientific studies
- Evaluate data presented in scientific studies
- Critically reason using data
- Evaluate the consequences of GM technology on non-target organisms
- Communicate scientific data orally
BioMap Degree Plan: A project to guide students in exploring, defining, and building a plan to achieve career goalsLearning ObjectivesStudents will be able to...
- Identify their values and interests.
- Identify careers that align with their values and interests.
- Identify academic programs and co-curricular experiences that will prepare them for a career.
- Create the first draft of a BioMap Degree Plan to support achievement of their career goals.
- Articulate how their undergraduate academic experience will prepare them for their future career.
- Use professional communication skills
Exploring the March to Mars Using 3D Print ModelsLearning Objectives
- Students will be able to describe the major aspects of the Mars Curiosity Rover missions.
- Students will be able to synthesize information learned from a classroom jigsaw activity on the Mars Curiosity Rover missions.
- Students will be able to work in teams to plan a future manned mission to Mars.
- Students will be able to summarize their reports to the class.
Visits to the writing center and office hours provide students structured reflection and low-stakes feedback on...Learning Objectives
- Students will be able to write a lab report that contains a descriptive title, complete and concise abstract, substantive and relevant introduction that includes a testable hypothesis, descriptive methods, description and comparison of results of various testable groups, biological explanation of the results that reflect the testable hypothesis, a conclusion that contains societal implications or scientific impact, and references cited in the document.
- Students will be able to self-identify weaknesses and strengths of their writing.
- Students will understand how to utilize office hours and the writing center to receive feedback on their lab reports.
Linking Genotype to Phenotype: The Effect of a Mutation in Gibberellic Acid Production on Plant GerminationLearning ObjectivesStudents 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.
Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypesLearning ObjectivesStudents successfully completing this lesson will:
- Practice basic molecular biology laboratory skills such as DNA isolation, PCR, and gel electrophoresis.
- Gather and analyze quantitative and qualitative scientific data and present it in figures.
- Use bioinformatics to analyze DNA sequences and obtain protein sequences for molecular modeling.
- Make and analyze three-dimensional (3-D) protein models using molecular modeling software.
- 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 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 Short Laboratory Module to Help Infuse Metacognition during an Introductory Course-based Research ExperienceLearning 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.
Using Structured Decision Making to Explore Complex Environmental IssuesLearning ObjectivesStudents will be able to:
- Describe the process, challenges, and benefits of structured decision making for natural resource management decisions.
- Explain and reflect on the role of science and scientists in structured decision making and how those roles interact and compare to the roles of other stakeholders.
- Assess scientific evidence for a given management or policy action to resolve an environmental issue.
An undergraduate bioinformatics curriculum that teaches eukaryotic gene structureLearning ObjectivesModule 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.
- 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.
- 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:
- 5' capping
- 3' polyadenylation
- 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.
- 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.
- 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.
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
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
Dynamic Daphnia: An inquiry-based research experience in ecology that teaches the scientific process to first-year...Learning ObjectivesStudents 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.
Mice, Acorns, and Lyme Disease: a Case Study to Teach the Ecology of Emerging Infectious Diseases.Learning ObjectivesStudents will be able to...
- outline the life cycle of ticks and explain the transmission cycle of Lyme disease.
- describe factors that make mice a competent reservoir for Borrelia burgdorferi.
- analyze and interpret line and bar graphs of data on the effects of changes to ecological communities on the risk of human exposure to Lyme disease.
- explain how the incidence of Lyme disease is determined by interactions between bacteria, animals, humans and the environment.
- predict how changes in the ecosystem affect Borrelia burgdorferi transmission.
- explain how human activities affect biodiversity and the consequences of those actions on disease outbreaks.
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).
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 PathwayLearning ObjectivesAt 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.
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
Building Trees: Introducing evolutionary concepts by exploring Crassulaceae phylogeny and biogeographyLearning ObjectivesStudents 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.
Homologous chromosomes? Exploring human sex chromosomes, sex determination and sex reversal using bioinformatics...Learning ObjectivesStudents 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
Using Yeast to Make Scientists: A Six-Week Student-Driven Research Project for the Cell Biology LaboratoryLearning 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
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.
Why Meiosis Matters: The case of the fatherless snakeLearning ObjectivesStudents 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
Teaching Genetic Linkage and Recombination through Mapping with Molecular MarkersLearning ObjectivesStudents will be able to:
- Explain how recombination can lead to new combinations of linked alleles.
- Explain how molecular markers (such as microsatellites) can be used to map the location of genes/loci, including what crosses would be informative and why.
- Explain how banding patterns on an electrophoresis gel represent the segregation of alleles during meiosis.
- Predict how recombination frequency between two linked loci affects the genotype frequencies of the products of meiosis compared to loci that are unlinked (or very tightly linked).
- Analyze data from a cross (phenotypes and/or genotypes) to determine if the cross involves linked genes.
- Calculate the map distance between linked genes using data from genetic crosses, such as gel electrophoresis banding patterns.
- Justify conclusions about genetic linkage by describing the information in the data that allows you to determine genes are linked.
Antibiotic Resistance Genes Detection in Environmental SamplesLearning ObjectivesAfter 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.
The Case of the Missing Strawberries: RFLP analysisLearning ObjectivesStudents will be able to:
- Describe the relationship of cells, chromosomes, and DNA.
- Isolate DNA from strawberries.
- Digest DNA with restriction enzymes.
- Perform gel electrophoresis.
- Design an experiment to compare DNAs by RFLP analysis.
- Predict results of RFLP analysis.
- Interpret results of RFLP analysis.
- Use appropriate safety procedures in the lab.