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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.
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.
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.
What do Bone and Silly Putty® have in Common?: A Lesson on Bone ViscoelasticityLearning Objectives
- Students will be able to explain how the anatomical structure of long bones relates to their function.
- Students will be able to define viscoelasticity, hysteresis, anisotropy, stiffness, strength, ductility, and toughness.
- Students will be able to identify the elastic and plastic regions of a stress-strain curve. They will be able to correlate each phase of the stress-strain curve with physical changes to bone.
- Students will be able to predict how a bone would respond to changes in the magnitude of an applied force, and to variations in the speed or angle at which a force is applied.
- Students will be able to determine the reason(s) why bone injuries occur more frequently during athletic events than during normal everyday use.
A Close-Up Look at PCRLearning ObjectivesAt 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
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.
Differential Gene Expression during Xenopus laevis DevelopmentLearning ObjectivesStudents 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
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.
Plotting Cranial and Spinal Nerve Pathways in a Human Anatomy LabLearning Objectives
- Identify and describe the functions of cranial and spinal nerves
- Identify cranial and spinal nerve origination points and what structures they innervate
- Trace the routes that cranial and spinal nerves take throughout the body
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.
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.
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.
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.
Meiosis: A Play in Three Acts, Starring DNA SequenceLearning 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.