Skip to main content

You are here

Filters

Search

  • Starting Conversations About Discrimination Against Women in STEM

    Learning Objectives
    After the discussion, each attendee will be able to:
    • identify common forms of discrimination that women in academic STEM positions experience.
    • begin supporting women while and after they experience discrimination.
    • implement institutional change at a scale that is appropriate for them.
  • Understanding Host-Pathogen Interactions With the Use of <em>Galleria mellonella</em>

    Learning Objectives
    Students will be able to:
    • Describe at least two innate physical defenses in the human body that are used to fend off an infection.
    • Describe how bacterial structures stimulate a non-specific immune response.
    • Describe innate immune responses used against bacterial pathogens.
    • Describe how animal models can be used in the study of bacterial virulence.
    • Identify innate immune responses in G. mellonella and how these can be used for virulence studies.
    • Define pathogenic behavior.
    • Compare and contrast the virulence of various microbes.
    • Collect and accurately report survival data using a Kaplan-Meier plot.
    • Evaluate survival data to determine virulence properties of a given microbe.
  • Phylogeny of HIV1 pol genes sequenced anonymously from viral pools of six victims and the defendant (CCO1-CCO7), plus control samples. Used with permission from Proceedings of the National Academy of Sciences of the United States of America.

    Forensic Phylogenetics: Implementing Tree-thinking in a Court of Law

    Learning Objectives
     
    • Students will be able to infer the topological and temporal relationships expected in an evolutionary tree (phylogeny) of a pathogen in the case of transmission from one host to the next.
    • Students will be able to draw trees representing the transmission events from one host (patient zero) to multiple secondary patients.
  • Using Current Events to Teach Written, Visual, and Oral Science Communication

    Learning Objectives
    Students will be able to:
    • Identify scientific themes in local and global current events
    • Identify when scientific information is or is not communicated in a manner accessible to a general audience
    • Evaluate scientific information to distinguish evidence-based statements from statements not based on evidence
    • Explore the use of written, visual, and auditory methods of communicating scientific messages from local current events
    • Explain the importance of translating a scientific message for a general audience
  • Teaching Genetic Linkage and Recombination through Mapping with Molecular Markers

    Learning Objectives
    Students 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.
  • A three-dimensional model of methionine is superimposed on a phase contrast micrograph of Saccharomyces cerevisiae from a log phase culture.

    Follow the Sulfur: Using Yeast Mutants to Study a Metabolic Pathway

    Learning Objectives
    At 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.
  • Building a Model of Tumorigenesis: A small group activity for a cancer biology/cell biology course

    Learning Objectives
    At the end of the activity, students will be able to:
    • Analyze data from a retrospective clinical study uncovering genetic alterations in colorectal cancer.
    • Draw conclusions about human tumorigenesis using data from a retrospective clinical study.
    • Present scientific data in an appropriate and accurate way.
    • Discuss why modeling is an important practice of science.
    • Create a simple model of the genetic changes associated with a particular human cancer.
  • Student-Driven Design-and-Improve Modules to Explore the Effect of Plant Bioactive Compounds in Three Model Organisms

    Learning Objectives
    Students will be able to:
    • Perform background research of peer-reviewed literature to make informed hypotheses.
    • Design a controlled experiment and write a protocol.
    • Conduct laboratory investigations from a written protocol.
    • Perform laboratory tasks such as pipetting and dissecting microscope work.
    • Record data in a table in Excel.
    • Calculate means and standard deviations.
    • Perform & correctly interpret statistical significance testing (chi-square and t-test) in Excel.
    • Graph data in Excel to include error bars.
    • Evaluate experimental results to suggest improvements to the experimental design or to answer further questions stemming from the results.
    • Perform further experiments based on the evaluation of a previous experiment.
    • Work in groups to design and perform experiments.
    • Write a guided lab report, a modified traditional lab report that is broken down into questions with embedded specific instructions.
    • Present with their research group to the whole class using PowerPoint (or equivalent).
    • Compare the advantages and limitations of different model organisms to answer scientific questions.
    • Propose a plan for an ecologically-sound habitat to address a current environmental problem.
  • Human karyotype

    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
  • Engaging Undergraduates in Mechanisms of Tubular Reabsorption and Secretion in the Mammalian Kidney

    Learning Objectives
    Students will be able to:
    • Describe the process by which substances are reabsorbed or secreted in the nephron by passive diffusion, primary active transport, and secondary active transport.
    • Explain what causes the transport maximum for certain substances in the renal tubule.
    • Explain how water is reabsorbed in the renal tubule.
    • Describe the characteristics of the different segments of the nephron. List, in general, what is reabsorbed/secreted by each.
    • Describe mechanisms for reabsorption and secretion in a particular segment of the nephron given a figure.
    • Predict how changes to the hydrostatic and colloid osmotic forces in the kidney will affect tubular reabsorption.
    • Define the molecular function of aldosterone, angiotensin II, and anti-diuretic hormone on the renal tubule and the overall effect on water and sodium reabsorption.
  • MA plot of RNA-seq data. An MA plot is a visual summary of gene expression data which identifies genes showing differential expression between two treatments.

    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.
  • A CRISPR/Cas Guide RNA Design In Silico Activity

    Learning Objectives
    After the lesson, students should be able to:
    • Explain why each of the following are required for CRISPR/Cas9 genome engineering: (1) gene and genome sequences, (2) gRNA targeting the genome, (3) source of Cas9, and (4) endogenous DNA repair machinery.
    • Devise a strategy to approach a genome-editing goal.
    • Use genome databases to identify the genome sequence of a target gene.
    • Read and interpret the graphical summary of a gene in a genome browser.
    • Explain how the CRISPOR algorithm identifies optimal gRNA target sites in a sequence by predicting on- and off-target effects.
    • Justify selection of a CRISPR/Cas9 target sequence based on gene structure and gRNA characteristics.
    • Diagram gene structure, target region and gRNA target site.
  • :  Illustration of protein colocalization. This image shows two different color schemes that can be used to visualize immunofluorescence data and analyze colocalization.

    Learning About Protein Localization: A Lesson for Analyzing Figures in a Scientific Publication

    Learning Objectives
    At the end of this activity students will be able to:
    • Explain how eukaryotic cells "know" where a particular protein should be located.
    • Analyze immunofluorescence data to determine protein localization within a cell.
    • Analyze a western blot with subcellular fractions to determine protein localization within a cell.
    • Describe an experiment that can be used to analyze the subcellular localization of a specific protein.
    • Describe an experiment that can be used to determine the signal sequence of a protein.
  • Data Analysis Recitation Activities Support Better Understanding in SEA-PHAGES CURE

    Learning Objectives
    Overall Broadly, following these activities, students will be able to:
    • Explain the goals, procedures, and outcomes of the experiments they perform
    • Analyze and interpret the data they generate
    • Apply the methods they use to real-world situations
    Direct Isolation Following this activity, students will be able to:
    • Describe how to isolate a novel phage from a soil sample using different protocols
    • Compare and contrast direct and enriched isolation protocols
    • Critically analyze plaque assay results and explain experimental shortfalls
    Three-Phase Streak Following this activity, students will be able to:
    • Describe the procedures associated with isolation and purification of a phage from an environmental sample
    • Compare and contrast example three-streak plates to critically analyze varying results
    • Rationalize differences in three-streak plates and next step procedures
    Serial Dilution Following this activity, students will be able to:
    • Calculate PFU titer
    • Explain the meaning of PFU
    • Differentiate between the serial dilution and titer experiments
    DNA Extraction Following this activity, students will be able to:
    • Detail the contents of phage MTL (medium titer lysate)
    • Explain the purpose of adding nuclease and resin to the MTL
    • Explain the contents of their sample at various stages of the DNA isolation protocol
    • Explain the function of resin in the protocol
    • Differentiate between filters and columns
    • Read a spectrophotometer spectrum
    • Explain the significance of the 260/280 ratio in DNA isolations
    • Calculate how much DNA to add to a restriction digest reaction based on its concentration
    Restriction Enzymes and Gels Following this activity, students will be able to:
    • Explain how restriction enzymes work.
    • Identify restriction enzyme cutting sequences within a DNA fragment.
    • Differentiate between the number of cutting sites for a restriction enzyme and the number of fragments it creates.
    • Explain why and how gel electrophoresis works
    • Analyze a gel by determining whether and how many times a restriction enzyme has cut a fragment of phage DNA
    • Create a hypothetical gel based on a given sequence or set of fragments
    • Compare their gel to known phage samples based on the number and size of DNA fragments generated by restriction enzyme digestion
  • Clock
  • Grow the Gradient game board. A student moves game pieces on the game board as they learn how the loop of Henle creates a salt concentration gradient in the medulla.

    Grow the Gradient: An interactive countercurrent multiplier game

    Learning Objectives
    • Students will be able to simulate the movement of water and sodium at each region of the loop of Henle.
    • Students will be able to associate osmosis and active transport with movement of water/solutes at each region of the loop of Henle.
    • Students will be able to model how the descending and ascending limbs of the loop of Henle maintain a concentration gradient within the medulla.
    • Students will be able to predict the effects of altering normal water and salt movement out of the loop of Henle on the salt concentration of the medulla, urine concentration, and urine volume.
    Advanced Learning Objectives for Extensions
    • Students will be able to predict the impact of the length of the loop of Henle on the magnitude of the concentration gradient within the medulla.
    • Students will be able to predict the length of the loop of Henle in organisms from different habitats.
  • Students working with fruit flies in the classroom.

    Fruit Fly Genetics in a Day: A Guided Exploration to Help Many Large Sections of Beginning Students Uncover the Secrets...

    Learning Objectives
    • Students will be able to handle and anesthetize Drosophila fruit flies.
    • Students will be able to use a dissecting microscope to sex Drosophila fruit flies.
    • Students will implement some steps of the scientific method.
    • Students will successfully predict the results of sex-linked genetics crosses.
    • Students will interpret genetic data.
  • SNP model by David Eccles (gringer) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY 4.0 (http://creativecommons.org/licenses/by/4.0)], via Wikimedia Commons

    Exploration of the Human Genome by Investigation of Personalized SNPs

    Learning Objectives
    Students successfully completing this lesson will be able to:
    • Effectively use the bioinformatics databases (SNPedia, the UCSC Genome Browser, and NCBI) to explore SNPs of interest within the human genome.
    • Identify three health-related SNPs of personal interest and use the UCSC Genome Browser to define their precise chromosomal locations and determine whether they lie within a gene or are intergenic.
    • Establish a list of all genome-wide association studies correlated with a particular health-related SNP.
    • Predict which model organism would be most appropriate for conducting further research on a human disease.
  • Using Immunocytochemistry and Fluorescence Microscopy Imaging to Explore the Mechanism of Action of Anti-Cancer Drugs...

    Learning Objectives
    Students will:
    • name and describe the changes to chromosomes and cytoskeleton during each stage of mitosis.
    • compare the usefulness and limitations of information obtained by light microscopy and fluorescence microscopy.
    • quantify, analyze and summarize their data on the prevalence of cells at different stages of cell division in randomly sampled cell populations.
    • describe how cell imaging is used to collect and analyze data on dynamic cellular events.
    • present their scientific data in an appropriate and accurate way to an audience.
  • Exploring Species Interactions with "Snapshot Serengeti"

    Learning Objectives
    Students will:
    • Engage in meta-cognitive learning.
    • Develop and conduct an authentic scientific inquiry.
    • Generate a testable research question based on observations.
    • Evaluate different methods of visualizing data.
    • Generate and interpret graphs to answer questions.
    • Communicate the results of research and the nature of science in oral and written form.
    • Place exploratory research into a larger context of the scientific process.
    • Participate in citizen science initiatives.
    • Collaborate with peers on a scientific task.
  • Interactive Video Vignettes (IVVs) to Help Students Learn Genetics Concepts

    Learning Objectives
    Learning Objectives that align with the Marfamily IVV
    • Define the term "trait" in terms of genetic and environmental influences.
    • Recognize that negative traits/disorders can be encoded by dominant alleles.
    • Correctly interpret a pedigree.
    • Determine the probability of inheritance of a single gene, autosomal trait.
    • Use both phenotype and relationship data to assign genotypes within a family.
    Learning Ojectives that align with the Matter of Taste IVV
    • Describe the relationships between a gene and its alleles.
    • Describe potential relationships between alleles of the same gene.
    • Explain how each allele for a gene contributes to the organism's phenotype.
    • Describe dominance purely as the allele whose associated phenotype is observed regardless of the sequence of the second allele.
    • Calculate allele frequency using the Hardy-Weinberg equations.
  • Genome view obtained from the integrated genome viewer: screenshot of Illumina 75bp single-end reads from two rockfishes Sebastes chrysomelas (top) and S. carnatus (bottom) aligned to a closely related reference genome (S. rubrivinctus).  Reads shown are within the coding region of a gene that was located in an island of genomic divergence between the two species.  The CT mutation within S. carnatus is predicted to cause an amino acid substitution from Lysine to Phenylalanine in a taste receptor gene.  This

    An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome...

    Learning Objectives
    At the end of the activity, students will be able to:
    • Explain the steps involved in genome assembly, annotation, and variant detection to other students and instructors.
    • Create meaningful visualizations of their data using the integrated genome viewer.
    • Use the Linux command line and web-based tools to answer research questions.
    • Produce annotated genomes and call variants from raw sequencing reads in non-model species.
  • Students engaged in building the PCR model

    A Close-Up Look at PCR

    Learning Objectives
    At the end of this lesson students will be able to...
    • Describe the role of a primer in PCR
    • Predict sequence and length of PCR product based on primer sequences
    • Recognize that primers are incorporated into the final PCR products and explain why
    • Identify covalent and hydrogen bonds formed and broken during PCR
    • Predict the structure of PCR products after each cycle of the reaction
    • Explain why amplification proceeds exponentially
  • 3D Print Models: A collection of 3D models printed from online repository files.
  • Assessing <em>in vivo </em> Antimicrobial Activity Through the Analysis of <em>Galleria mellonella...

    Learning Objectives
    After completing this lesson, students will be able to:
    • Describe how G. mellonella can be used in antimicrobial testing.
    • Evaluate in vivo survival data from publications.
    • Compare and contrast the data derived from in vitro and in vivo testing methods.
    • Interpret survival curve data for specific microorganism in the presence of an antimicrobial compound both in vivo and in vitro.
    • Analyze quantitative data in the form of a Kaplan-Meier Plot (survival curve) to determine the effectiveness of an antimicrobial drug in the form of a Case Study.
    • Synthesize ideas in the form of a short lab report.
  • The mechanisms regulating the cellular respiration system.

    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.
  • Sodium-Potassium pump

    Lights, Camera, Acting Transport! Using role-play to teach membrane transport

    Learning Objectives
    At the end of this activity, students should be able to:
    • Compare and contrast the mechanisms of simple diffusion, facilitated diffusion, and active transport (both primary and secondary).
    • Identify, and provide a rationale for, the mechanism(s) by which various substances cross the plasma membrane.
    • Describe the steps involved in the transport of ions by the Na+/K+ pump, and explain the importance of electrogenic pumps to the generation and maintenance of membrane potentials.
    • Explain the function of electrochemical gradients as potential energy sources specifically used in secondary active transport.
    • Relate each molecule or ion transported by the Na+/glucose cotransporter (SGLT1) to its own concentration or electrochemical gradient, and describe which molecules travel with and against these gradients.
  • Mapping a Mutation to its Gene: The "Fly Lab" as a Modern Research Experience

    Learning Objectives
    After analysis of multiple datasets and cross-examining their findings with bioinformatic resources, students will be able to map a mutation to a single gene conclusively. During this process, students will:
    • handle adult Drosophila and score their phenotypes
    • use Punnett squares and cross diagrams to predict outcomes of genetic crosses and compare these predictions to their data
    • determine the mode of inheritance of a mutant trait
    • use chi-square tests to determine whether the data from genetic crosses fit with the predictions of Mendel's First Law (Equal Segregation) and Second Law (Independent Assortment)
    • three-point map an unknown mutation relative to known loci (a known gene and several transposable element insertions at known genomic locations)
    • interpret complementation tests between the unknown mutation and deletions and duplications of known genomic segments
    • demonstrate their ability to gather bioinformatics data from a model organism database (Flybase), genome browser (GBrowse), and search tool (BLAST)
    • critically evaluate their data and hypothesize the identity of the unknown gene in a written lab report
    • design experiments to further confirm or extend their findings
  • Reprinted by permission from Macmillan Publishers Ltd.

    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.
  • Image from a clicker-based case study on muscular dystrophy and the effect of mutations on the processes in the central dogma.

    A clicker-based case study that untangles student thinking about the processes in the central dogma

    Learning Objectives
    Students 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.
  • “Phenology of a Dawn Redwood” – Images collected by students for this lesson pieced together illustrating a Metasequoia glyptostroboides changing color and dropping its leaves in the fall of 2017 on Michigan State University campus.

    Quantifying and Visualizing Campus Tree Phenology

    Learning Objectives
    The Learning Objectives of this lesson span across the entire semester.
    • Observe and collect information on phenological changes in local trees.
    • Become familiar with a database and how to work with large datasets.
    • Analyze and visualize data from the database to test their hypotheses and questions.
    • Develop a research proposal including empirically-driven questions and hypotheses.
    • Synthesize the results of their analysis in the context of plant biodiversity and local environmental conditions.
  • Picture of three popular graphic memoirs, which we used in our class.

    Using Comics to Make Science Come Alive

    Learning Objectives
    Students will
    • be motivated to learn science related to specific socio-scientific issues.
    • learn science that applies to specific socio-scientific issues.
    • be able to discuss the relationship between science and society, as well as the biology behind the issue, related to specific socio-scientific issues.
  • Format of a typical course meeting
  • Ain't No Mountain Pine Enough: A Case Study of How Mountain Pine Beetles are Affecting Ecosystem Processes

    Learning Objectives
    Students will be able to
    • describe fluxes of carbon and reservoirs of carbon in the terrestrial carbon cycle.
    • describe ways in which biota influence the carbon cycle and vice versa.
    • describe factors that influence Mountain Pine Beetle population dynamics.
    • generate hypotheses and predictions about how Mountain Pine Beetle might impact the carbon cycle and design experiments to test their hypotheses.
    • calculate effect sizes and standard deviations in R, generate figures in R, and interpret the result.
    • evaluate the quality of data and experimental design.
    • brainstorm experimental factors that contribute to contrasting scientific results.
    • summarize complex and context-dependent results in a way that is communicable to public audiences.
  • 	http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=TCA. Image adapted from :Image:Citric acid cycle noi.svg| (uploaded to Commons by wadester16)

    A simple way for students to visualize cellular respiration: adapting the board game MousetrapTM to model complexity

    Learning Objectives
    • Students will be able to describe the three stages of cellular respiration.
    • Students will be able to identify the reactants entering and the products formed during each stage of cellular respiration.
    • Students will be able to explain how chemical energy in carbohydrates is transferred to ATP through the stages of cellular respiration.
    • Students will be able to explain the effects of compartmentalization of cellular respiration reactions in different cellular spaces.
    • Students will be able to predict biological outcomes when a specific stage(s) of cellular respiration is altered. 
  • From Cre/LoxP to Fate Maps: Inclusive and Equitable Approaches for Engaging Developmental Biology Students in...

    Learning Objectives
    • Create genetic methods to determine the fate map of cardiac muscle cells during mouse and zebrafish development.
    • Distinguish between gene knockout and fate mapping experimental approaches using Cre/LoxP technology.
    • Grasp the significance of how fate mapping methods are applied to answer important questions in developmental biology.
  • Students participating in the peer review process. Practicing the writing of scientific manuscripts prepares students to understand and engage in the primary literature they encounter.
  • Aldh1a2 expression in Stage 33 Xenopus laevis embryo: In this lab exercise, students visualize differential gene expression in Xenopus embryos using in situ hybridization.

    Differential Gene Expression during Xenopus laevis Development

    Learning Objectives
    Students will be able to:
    • identify different stages of Xenopus development
    • contrast the strengths and limitations of the Xenopus model organism
    • explain the process and purpose of in situ hybridization
    • compare gene expression patterns from different germ layers or organ domains
    • compare gene expression patterns from different developmental stages
  • Multiple sequence alignment of homologous cytochrome C protein sequences using Jalview viewer.

    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.
  • Many colorful hand prints
  • A tuco-tuco in South America (photo credit: Jeremy Hsu)

    Furry with a chance of evolution: Exploring genetic drift with tuco-tucos

    Learning Objectives
    • Students will be able to explain how genetic drift leads to allelic changes over generations.
    • Students will be able to demonstrate that sampling error can affect every generation, which can result in random changes in allelic frequency.
    • Students will be able to explore and evaluate the effect of population size on the strength of genetic drift.
    • Students will be able to analyze quantitative data associated with genetic drift.
  • A Remote Introductory Biology Lab Using Backyard Birdwatching to Teach Data Analysis and Communication

    Learning Objectives
    Students will:
    • Develop a prediction and a testable hypothesis based on class-collected data
    • Use a PivotTable to summarize a complex dataset to address the specific question
    • Interpret results of the experiment and summarize the findings in an engaging way
  • Peterson MP, Rosvall KA, Choi J-H, Ziegenfus C, Tang H, Colbourne JK, et al. (2013) Testosterone Affects Neural Gene Expression Differently in Male and Female Juncos: A Role for Hormones in Mediating Sexual Dimorphism and Conflict. PLoS ONE 8(4): e61784. doi:10.1371/journal.pone.0061784

    Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

    Learning 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.”)
  • Simplified Representation of the Global Carbon Cycle, https://earthobservatory.nasa.gov/Features/CarbonCycle/images/carbon_cycle.jpg

    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 Relationships

    Learning Objectives
    Students 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.
    Note: Additional, more specific objectives and goals are included with each of the lessons.
  • Plant ecology students surveying vegetation at Red Hills, CA, spring 2012.  From left to right are G.L, F.D, A.M., and R.P.  Photo used with permission from all students.

    Out of Your Seat and on Your Feet! An adaptable course-based research project in plant ecology for advanced students

    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)
  • DNA

    Why do Some People Inherit a Predisposition to Cancer? A small group activity on cancer genetics

    Learning Objectives
    At the end of this activity, we expect students will be able to:
    1. Use family pedigrees and additional genetic information to determine inheritance patterns for hereditary forms of cancer
    2. Explain why a person with or without cancer can pass on a mutant allele to the next generation and how that impacts probability calculations
    3. Distinguish between proto-oncogenes and tumor suppressor genes
  • “The outcome of the Central Dogma is not always intuitive” Variation in gene size does not necessarily correlate with variation in protein size. Here, two related genes differ in length due to a deletion mutation that removes four nucleotides. Many students do not predict that the smaller gene, after transcription and translation, would produce a larger protein.

    Predicting and classifying effects of insertion and deletion mutations on protein coding regions

    Learning Objectives
    Students 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

Pages