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Cutthroat trout in Colorado: A case study connecting evolution and conservationLearning ObjectivesStudents 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
Fly Exercise: A Simple Experiment to Test the Physiological Effects of Exercise on a Model OrganismLearning ObjectivesStudents will:
- demonstrate understanding of the concept and details of experimental design.
- perform an organic lipid extraction to determine total lipid content.
- quantify enzyme activity, as well as triglyceride, glucose, and glycogen concentrations.
- organize their collected data into spreadsheets for statistical analyses.
- interpret the results to gain insight on the varying effects exercise has on an organism's physiology.
- graphically present their results so that trends can be easily identified.
Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics CourseLearning ObjectivesStudents will be able to:
- list and perform the steps of sequence processing and taxonomic inference.
- interpret microbial community diversity from metagenomic sequence datasets.
- compare microbial diversity within and between samples or treatments.
A CURE-based approach to teaching genomics using mitochondrial genomesLearning Objectives
- Install the appropriate programs such as Putty and WinSCP.
- Navigate NCBI's website including their different BLAST programs (e.g., blastn, tblastx, blastp and blastx)
- Use command-line BLAST to identify mitochondrial contigs within a whole genome assembly
- Filter the desired sequence (using grep) and move the assembled mitochondrial genome onto your own computer (using FTP or SCP)
- Error-correct contigs (bwa mem, samtools tview), connect and circularize organellar contigs (extending from filtered reads)
- Transform assembled sequences into annotated genomes
- Orient to canonical start locations in the mitochondrial genome (cox1)
- Identify the boundaries of all coding components of the mitochondrial genome using BLAST, including: Protein coding genes (BLASTx and tBLASTX), tRNAs (proprietary programs such as tRNAscan), rRNAs (BLASTn, Chlorobox), ORFs (NCBI's ORFFinder)
- Deposit annotation onto genome repository (NCBI)
- Update CV/resume to reflect bioinformatics skills learned in this lesson
Understanding Protein Domains: A Modular ApproachLearning Objectives
- Students will be able to compare protein sequences and identify conserved regions and putative domains.
- Students will be able to obtain, examine, and compare structural models of protein domains.
- Students will be able to interpret data on protein interactions (in vitro pull-down and in vitro and in vivo functional assays)
- Students will be able to propose experiments to test protein interactions.
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.