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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)
Predicting and classifying effects of insertion and deletion mutations on protein coding regionsLearning ObjectivesStudents 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
Dynamic Daphnia: An inquiry-based research experience in ecology that teaches the scientific process to first-year...Learning ObjectivesStudents will be able to:
- Construct written predictions about 1 factor experiments.
- Interpret simple (2 variables) figures.
- Construct simple (2 variables) figures from data.
- Design simple 1 factor experiments with appropriate controls.
- Demonstrate proper use of standard laboratory items, including a two-stop pipette, stereomicroscope, and laboratory notebook.
- Calculate means and standard deviations.
- Given some scaffolding (instructions), select the correct statistical test for a data set, be able to run a t-test, ANOVA, chi-squared test, and linear regression in Microsoft Excel, and be able to correctly interpret their results.
- Construct and present a scientific poster.
Investigating the Function of a Transport Protein: Where is ABCB6 Located in Human Cells?Learning ObjectivesAt the end of this activity students will be able to:
- describe the use of two common research techniques for studying proteins: SDS-PAGE and immunoblot analysis.
- determine a protein’s subcellular location based on results from: 1) immunoblotting after differential centrifugation, and 2) immunofluorescence microscopy.
- analyze protein localization data based on the limitations of differential centrifugation and immunofluorescence microscopy.
Building Trees: Introducing evolutionary concepts by exploring Crassulaceae phylogeny and biogeographyLearning ObjectivesStudents will be able to:
- Estimate phylogenetic trees using diverse data types and phylogenetic models.
- Correctly make inferences about evolutionary history and relatedness from the tree diagrams obtained.
- Use selected computer programs for phylogenetic analysis.
- Use bootstrapping to assess the statistical support for a phylogeny.
- Use phylogenetic data to construct, compare, and evaluate the role of geologic processes in shaping the historical and current geographic distributions of a group of organisms.
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.
An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome...Learning ObjectivesAt 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.
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.
Using Yeast to Make Scientists: A Six-Week Student-Driven Research Project for the Cell Biology LaboratoryLearning Objectives
- Learn about basic S. cerevisiae biology
- Use sterile technique
- Perform a yeast viability assay
- Use a spectrophotometer to measure growth of S. cerevisiae
- Perform a literature search
- Calculate concentrations of chemicals appropriate for S. cerevisiae
- Generate S. cerevisiae growth curves
- Troubleshoot experimental difficulties
- Perform statistical analysis
- Present findings to an audience
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.
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.