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Genetics

  • Arabidopsis Seedling

    Linking Genotype to Phenotype: The Effect of a Mutation in Gibberellic Acid Production on Plant Germination

    Learning Objectives
    Students 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.
  • Medical students at a fair. Credit: Danieladelrio

    Casting a Wide Net via Case Studies: Educating across the undergraduate to medical school continuum in the biological...

    Learning Objectives
    At 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.
  • Students using the Understanding Eukaryotic Genes curriculum to construct a gene model. Students are working as a pair to complete each Module using classroom computers.

    An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

    Learning Objectives
    Module 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.
    Module 2
    • 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.
    Module 3
    • 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:
    • pre-mRNA
    • 5' capping
    • 3' polyadenylation
    • splicing
    • mRNA
    Module 4
    • 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.
    Module 5
    • 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.
    Module 6
    • 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.
  • A pair of homologous chromosomes.

    Meiosis: A Play in Three Acts, Starring DNA Sequence

    Learning Objectives
    • Students will be able to identify sister chromatids and homologous chromosomes at different stages of meiosis.
    • Students will be able to identify haploid and diploid cells, whether or not the chromosomes are replicated.
    • Students will be able to explain why homologous chromosomes must pair during meiosis.
    • Students will be able to relate DNA sequence similarity to chromosomal structures.
    • Students will be able to identify crossing over as the key to proper pairing of homologous chromosomes during meiosis.
    • Students will be able to predict the outcomes of meiosis for a particular individual or cell.
  • 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.
  • 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.
  • 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.
  • “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
  • A A student assists Colorado Parks & Wildlife employees spawning greenback cutthroat trout at the Leadville National Fish Hatchery; B greenback cutthroat trout adults in a hatchery raceway; C tissue samples collected by students to be used for genetic analysis (images taken by S. Love Stowell)

    Cutthroat trout in Colorado: A case study connecting evolution and conservation

    Learning Objectives
    Students will be able to:
    • interpret figures such as maps, phylogenies, STRUCTURE plots, and networks for species delimitation
    • identify sources of uncertainty and disagreement in real data sets
    • propose research to address or remedy uncertainty
    • construct an evidence-based argument for the management of a rare taxon
  • 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.
  • Normal Arabidopsis plants (A) have flat, spatula shaped leaves. asymmetric leaves2 (as2) mutant plants (B) have leaves that are curled under and slightly twisted. asymmetric leaves1(as1) mutant plants (C) have leaves that are curled under and twisted but also have reduced petioles.  In the laboratory activities I present, students analyze the sequence of the as1 and as2 alleles and computationally model the wild-type and mutant proteins. Visualizing the 3-D structure of the proteins helps students understan

    Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes

    Learning Objectives
    Students successfully completing this lesson will:
    1. Practice basic molecular biology laboratory skills such as DNA isolation, PCR, and gel electrophoresis.
    2. Gather and analyze quantitative and qualitative scientific data and present it in figures.
    3. Use bioinformatics to analyze DNA sequences and obtain protein sequences for molecular modeling.
    4. Make and analyze three-dimensional (3-D) protein models using molecular modeling software.
    5. 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.
  • blind cave fish
  • 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.
  • pClone Red Makes Research Look Easy

    Using Synthetic Biology and pClone Red for Authentic Research on Promoter Function: Genetics (analyzing mutant...

    Learning Objectives
    • Describe how cells can produce proteins at the right time and correct amount. 
    • Diagram a bacterial promoter with −35 and −10 elements and the transcription start site.
    • Describe how mutational analysis can be used to study promoter sequence requirements.
    • Develop a promoter mutation hypothesis and design an experiment to test it.
    • Successfully and safely manipulate DNA and Escherichia coli for ligation and transformation experiments. 
    • Design an experiment to verify a mutated 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.  
  • pClone Red Makes Research Look Easy

    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.
  • 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.
  • 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.
  • Using Undergraduate Molecular Biology Labs to Discover Targets of miRNAs in Humans

    Learning 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
  • Double-stranded, supercoiled yarn. Intertwined, supercoiled, and double-stranded yarn, representing chromosomal template DNA, with a section marked with black stripes to represent the DNA fragment for modeling PCR fundamentals.

    A Kinesthetic Modeling Activity to Teach PCR Fundamentals

    Learning Objectives
    Students will be able to:
    • Draw or model the first three cycles of PCR, including the correct directionality (5’- and 3’-ends) of the primers and single-stranded PCR products.
    • Diagram how single-stranded products from the first cycle of PCR are used as templates for subsequent PCR cycles.
    • Demonstrate which parts of the primers will anneal to the original DNA template and subsequent PCR products.
    • Model and demonstrate when the primer restriction enzyme sites are incorporated into double-stranded PCR products.
    • Calculate the number of desired-length PCR products and long PCR products for each amplification cycle.
    • Demonstrate how the incorporation of primer restriction enzyme sites into PCR products is a useful tool for subsequent cloning of the product into a vector.
  • Strawberries

    The Case of the Missing Strawberries: RFLP analysis

    Learning Objectives
    Students 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.
  • Monarch larvae

    Does it pose a threat? Investigating the impact of Bt corn on monarch butterflies

    Learning Objectives
    Students 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
  • 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
  • Green Snake

    Why Meiosis Matters: The case of the fatherless snake

    Learning Objectives
    Students 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
  • Confocal microscope image of a mouse egg that is arrested at metaphase of meiosis II. Green, tubulin staining of meiotic spindle; red, actin staining of egg membrane; blue, DNA. This image was obtained on a Zeiss 510 Meta confocal microscope in the Department of Genetics at Rutgers University

    Sex-specific differences in Meiosis: Real-world applications

    Learning Objectives
    After completion of the lesson students will be able to:
    1. Describe the differences between female and male meiosis.
    2. Interpret graphical data to make decisions relevant to medical practices.
    3. Develop a hypothesis that explains the difference in incidence of aneuploidy in gametes between males and females.
  • Bacteria growing on petri dish

    You and Your Oral Microflora: Introducing non-biology majors to their “forgotten organ”

    Learning Objectives
    Students 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
  • 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
  • Green snake curled up on ground