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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)
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.
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.
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.
Discovering Cellular Respiration with Computational Modeling and SimulationsLearning ObjectivesStudents 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.