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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.”)
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.
My Dog IS My Homework: Exploring Canine Genetics to Understand Genotype-Phenotype RelationshipsLearning ObjectivesStudents will be able to:
- Interpret selected articles from scientific journals and synthesize relevant information related to canine genetics and coat inheritance.
- Work together as a team to conduct experiments following strict protocols that produce usable results.
- Keep a detailed laboratory notebook.
- Collaboratively create a research poster and participate in a poster session mimicking a scientific conference.
- Explain the difference between genotype and phenotype; describe the consequences of gene mutations on protein structure and function; articulate the combinatory effects of three specific genes on dog coat phenotypes.
- Perform the following skills in a laboratory setting: isolate DNA, amplify DNA using PCR, analyze DNA sample using gel electrophoresis, use basic bioinformatic tools to analyze DNA sequence data.
A Quick and Simple Natural Selection Role PlayLearning ObjectivesAfter completing of this activity, students will be able to:
- Explain how natural selection impacts allele frequency in a population
- List and describe the four requirements for natural selection to occur in a population
- Refute common misconceptions regarding evolution and natural selection
Out of Your Seat and on Your Feet! An adaptable course-based research project in plant ecology for advanced studentsLearning ObjectivesStudents 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)
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
Predicting and classifying effects of insertion and deletion mutations on protein coding regionsLearning ObjectivesStudents will be able to:
- accurately predict effects of frameshift mutations in protein coding regions
- conduct statistical analysis to compare expected and observed values
- become familiar with accessing and using DNA sequence databases and analysis tools
Chilling in the Cold: Using Thermal Acclimation to Demonstrate Phenotypic Plasticity in AnimalsLearning ObjectivesStudents will be able to:
- Describe how the scientific method can be used to answer real-world problems.
- Define the basic components of an experiment.
- Predict how tolerance of extreme temperatures and phenotypic plasticity may influence individual fitness and ultimately shape the evolution of organisms.
- Understand the basic principles of climate change and evaluate how these changes in temperature regimes will impact organisms.
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
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.
A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!Learning ObjectivesStudents will be able to...
- Write basic command line scripts and use simple command-line bioinformatics tools.
- Explain how next generation sequencing data is used to generate and address hypotheses in biological research.
- Discuss the importance of assessing the quality of sequencing data.
- Identify the components of a FASTQ file.
- Assess sequencing read quality using command-line to generate FASTQE and FASTP reports.
- Trim and filter low quality reads in a FASTQ file.
- Compare and contrast FASTQE and FASTP tools.
The impact of diet and antibiotics on the gut microbiomeLearning ObjectivesAfter completing the exercise, students will be able to:
- Identify several of the nine phyla that contribute to the gut microbiome and name the two predominant ones;
- Describe how diet impacts the gut microbiome and compare the composition of the gut microbiome between different diets;
- Describe how antibiotic treatment impacts the gut microbiome and understand how this leads to infection, for example by Clostridium difficile;
- Trace the response to a change in diet, starting with i) changes in the composition of the microbiome, followed by ii) changes in the bacterial metabolic pathways and the respective excreted metabolic products, resulting in iii) a molecular response in the host intestinal cells, and eventually iv) resulting in human disease;
- Improve their ability to read scientific literature;
- Express themselves orally and in writing;
- Develop team working skill
Exploring the Lytic and Lysogenic Life Cycles of BacteriophagesLearning ObjectivesStudents will be able to:
- Label the key parts of a bacteriophage.
- Arrange the steps of lytic and lysogenic viral infections by bacteriophage.
- Predict the replication cycle of a virus based on the genes it carries.
- Compare and contrast the replication cycles of bacteriophages T4 and lambda.
- Compare and contrast the differences between lysogenic and latent viral infections.
- Interpret and analyze graphical representations of qPCR and plaque assay data.
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
The Inside and Outside the BodyLearning ObjectivesStudents will be able to:
- correctly identify when a substance (e.g. fetus, bacteria, toxins) is inside or outside the body.
- recognize the point at which a substance transitions from the inside to the outside of the body and vice versa.
- apply the concept of inside and outside the body to both normal events, such as the movement of oxygen from the alveolus to the blood, and abnormal events, such as the presence of blood in the urine.
Cell Signaling Pathways - a Case Study ApproachLearning Objectives
- Use knowledge of positive and negative regulation of signaling pathways to predict the outcome of genetic modifications or pharmaceutical manipulation.
- From phenotypic data, predict whether a mutation is in a coding or a regulatory region of a gene involved in signaling.
- Use data, combined with knowledge of pathways, to make reasonable predictions about the genetic basis of altered signaling pathways.
- Interpret and use pathway diagrams.
- Synthesize information by applying prior knowledge on gene expression when considering congenital syndromes.
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 CRISPR-Cas9 to teach the fundamentals of molecular biology and experimental designLearning ObjectivesModule 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.
- 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.
- 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.
- Design and implement an experiment that tests the CRISPR-Cas9 principle.
- Predict the outcome of a successful in vitro Cas9 digest.
- 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.
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.
Data, Distributions, and Hypotheses: Exploring Diversity and Disturbance in the Tallgrass PrairieLearning ObjectivesStudents will be able to:
- present and interpret data in a graphical format using an existing long-term data set from a published manuscript.
- identify different sources of variation within a data set and the consequences of grouping biological units into larger entities for the interpretation of results.
- apply transect-based vegetation sampling to estimate plant community composition, richness, and diversity in two different prairie restoration parcels with different burn regimes.
- summarize the transect-based vegetation data in graphs and figures to make comparisons that align with hypotheses and predictions.
- conduct simple statistical analyses to test explicit hypotheses and predictions.
- interpret statistical outputs and infer the biological implications of their results.
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
To Vaccinate or Not to VaccinateLearning ObjectivesStudents will be able to:
- Describe the effect of exposure frequency on disease transmission
- Explain the concept of herd immunity
- Defend the importance of vaccines
- Describe the role of vaccination in immunity
- Explain what a direct ELISA is and how it can be used to diagnose infection
Unwrapping Enzyme KineticsLearning ObjectivesStudents will be able to:
- calculate an initial rate from plotted data.
- describe the effect of substrate concentration and product inhibition on the behavior of enzymes.
- understand why enzymes saturate resulting in hyperbolic rate vs. substrate concentration plots.
- estimate the kinetic parameters Vmax and KM from enzyme saturation data.
- calculate the kinetic parameters Vmax and KM from enzyme saturation data using direct fitting and Lineweaver-Burk methods.
An active-learning lesson that targets student understanding of population growth in ecologyLearning ObjectivesStudents will be able to:
- Calculate and compare population density and abundance.
- Identify whether a growth curve describes exponential, linear, and/or logistic growth.
- Describe and calculate a population's growth rate using linear, exponential, and logistic models.
- Explain the influence of carrying capacity and population density on growth rate.
Evaluating the Quick Fix: Weight Loss Drugs and Cellular RespirationLearning Objectives
- Students will be able to explain how the energy from sugars is transformed into ATP via cellular respiration.
- Students will be able to predict an outcome if there is a perturbation in the cellular respiration pathway.
- Students will be able to state and evaluate a hypothesis.
- Students will be able to interpret data from a graph, and use that data to make inferences about the action of a drug.
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).
Green Design: How do Leaf Structures Optimize Photosynthesis and Promote Survival?Learning ObjectivesStudents will be able to:
- Analyze structural and anatomical features that optimize photosynthesis under various environmental conditions such as shading, water deficit, or high temperature. (ASPB-BSA Learning Objective)
- Identify & draw the cellular anatomy of a typical monocot and dicot leaf
- Describe the internal structure of a monocot and dicot leaf and how those structures contribute to the main functions of the leaf
- Apply the core concept of Structure & Function to plant leaves
The ACTN3 Polymorphism: Applications in Genetics and Physiology Teaching LaboratoriesLearning Objectives
- Test hypotheses related to the role of ACTN3 in skeletal muscle function.
- Explain how polymorphic variants of the ACTN3 gene affect protein structure and function.
- List and explain the differences between fast twitch and slow twitch muscle fibers.
- List and explain possible roles of the ACTN3 protein in skeletal muscle function.
- Find and analyze relevant scientific publications about the relationship between ACTN3 genotype and muscle function.
- Formulate hypotheses related to the relationship between ACTN3 genotype and skeletal muscle function.
- Design experiments to test hypotheses about the role of ACTN3 in skeletal muscle function.
- Statistically analyze experimental results using relevant software.
- Present experimental results in writing.
Using the Cell Engineer/Detective Approach to Explore Cell Structure and FunctionLearning ObjectivesStudents will be able to:
- Identify the major cell organelles
- List the major functions of the organelles
- Predict how changes in organelle/cell structure could alter cellular function
- Explain how overall cellular function is dependent upon organelles/cell structure
- Relate cell structure to everyday contexts
CRISPR/Cas9 in yeast: a multi-week laboratory exercise for undergraduate studentsLearning ObjectivesWeek 1: CRISPR design
- Locate the coding sequence, flanking sequence, protein product, and characteristics of a given gene from the Saccharomyces Genome Database (https://www.yeastgenome.org/).
- Design and defend the design of guide RNA and single stranded template for DNA repair in CRISPR/Cas9 gene editing studies to generate Saccharomyces cerevisiae auxotrophic mutants.
- Describe the qualities of the vector, pML104, that allow replication and selection in bacteria and yeast as well as allow expression of necessary factors in CRISPR/Cas9 genome editing, including Cas9 and sgRNA.
- Describe the rationale of and perform procedures necessary for cloning a small cassette (i.e., sgRNA gene) into a vector (i.e., pML104) including; restriction digest, annealing of DNA strands, removal of 5’ phosphates, ligation, and transformation.
- Recognize and design appropriate controls for cloning procedures such as ligation and transformation.
- Describe the method of polymerase chain reaction (PCR), including the rationale for essential components of a reaction mixture and thermal-cycling conditions.
- Locate the binding sites of and design primers for PCR, then report the expected size of the amplification product.
- Describe and perform isolation of plasmid DNA from E. coli.
- Describe the rationale for and perform procedures to transform yeast, including the essential components of a transformation mixture and conditions necessary for transformation.
- Describe the basic conditions required for cultivating yeast.
- Describe the rationale for and perform agarose gel electrophoresis of a given size of DNA.
- Analyze DNA separated by agarose gel electrophoresis, including size estimation.
- Recognize and describe the qualities of a template for DNA repair that allows efficient DNA repair.
- Design an experiment to determine auxotrophic phenotypes.
- Predict the outcome of multi-step experiments.
- Recognize and describe conditions necessary for growth of E. coli and S. cerevisiae.
- Qualitatively and quantitatively analyze scientific data from scientific experiments, including bacterial and yeast transformation, agarose gel electrophoresis, extraction of plasmid DNA from bacteria, PCR, and auxotroph phenotypic analysis.
- Communicate science to peers through maintenance of a laboratory notebook, verbal communication with group members, and writing of a formal laboratory report written in a format acceptable for journal publication.
- Troubleshoot scientific protocols by identifying procedures that are prone to error, comparing recommended protocols to actual procedure, and using positive and negative controls to narrow the location of a potential error.
- Communicate specific potential or actual uses of CRISPR/Cas9 in science and/or medicine.
- Use various bioinformatics approaches to analyze macromolecular primary sequence and structure.
- Illustrate how DNA is replicated and genes are transmitted from one generation to the next in multiple types of organisms including bacteria, eukaryotes, viruses, and retroviruses.
- Define what a genome consists of and how the information in various genes and other sequence classes within each genome are used to store and express genetic information.
- Explain the meaning of ploidy (haploid, diploid, aneuploid etc.) and how it relates to the number of homologues of each chromosome.
- Predict the effects of mutations on the activity, structure, or stability of a protein and design appropriate experiments to assess the effects of mutations.
- Predict the growth behavior of microbes based on their growth conditions, e.g., temperature, available nutrient, aeration level, etc.
- Discuss the benefits of specific tools of modern biotechnology that are derived from naturally occurring microbes (e.g. cloning vectors, restriction enzymes, Taq polymerase, etc.)
- Accurately prepare and use reagents and perform experiments.
- When presented with an observation, develop a testable and falsifiable hypothesis.
- When provided with a hypothesis, identify the appropriate experimental observations and controllable variables.
Using Student Perceptions and Cooperative Learning to Unpack Primary Literature on Global ChangeLearning Objectives
- Students will be able to identify key points and define key terms (e.g., planetary boundary, threshold, Anthropocene) established in the primary literature.
- Students will be able to predict consequences of human activities on key earth system processes relevant to global environmental change.
- Students will be able to identify processes for which human activity has caused changes that exceed the proposed planetary boundary.
- Students will be able to evaluate and summarize evidence used to define thresholds for key earth systems processes and discuss and evaluate variation and uncertainty in data.
Investigating Cell Signaling with Gene Expression DatasetsLearning ObjectivesStudents 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.
Using Undergraduate Molecular Biology Labs to Discover Targets of miRNAs in HumansLearning Objectives
- Use biological databases to generate and compare lists of predicted miR targets, and obtain the mRNA sequence of their selected candidate gene
- Use bioinformatics tools to design and optimize primer sets for qPCR
Biodiversity Show and Tell: An Accessible Activity to Encourage Students to Explore the Tree of LifeLearning ObjectivesStudents will be able to
- describe the ecology and natural history of their chosen species.
- describe human effects on their species and its habitat.
- share interesting facts about a wide variety of species with friends and family outside the class.
- stay engaged during readings and whole-class lectures on the topic of organismal diversity.
Understanding Gastric Acid Secretion: An Active Learning ApproachLearning Objectives
- List the channels, transporters, and receptors found on each membrane face of parietal cells.
- Explain the mechanism through which the proton pump is regulated by gastrin, histamine, somatostatin, and acetylcholine.
- Predict the effects of pharmaceuticals that are active in the stomach and their impact on GI function.
- Justify H. pylori as the cause of gastric ulcers.
The Comics Project: Synthesizing and Communicating Science with ComicsLearning Objectives
- Students will be able to use the CRAAP Test to evaluate the quality of various sources of scientific information.
- Students will be able to discuss the relationship between science and society.
- Students will be able to draw simple comics to communicate scientific information.
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.
Using Zebrafish in a Developmental Biology Lab Course to Explore Interactions Between Development and the EnvironmentLearning ObjectivesAt the end of this lesson, students will be able to:
- Design, execute, and analyze a novel, controlled experiment to examine how environmental conditions affect developmental outcomes.
- Apply quantitative reasoning skills (e.g. data analysis, serial dilutions, generating data tables and/or graphs, etc.).
- Perform basic morphometric analysis.
- Present experimental findings orally in the form of a scientific meeting presentation.
- Present findings using standard scientific writing conventions.