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Follow the Sulfur: Using Yeast Mutants to Study a Metabolic Pathway
Learning ObjectivesAt 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.
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Visits to the writing center and office hours provide students structured reflection and low-stakes feedback on...
Learning Objectives- Students will be able to write a lab report that contains a descriptive title, complete and concise abstract, substantive and relevant introduction that includes a testable hypothesis, descriptive methods, description and comparison of results of various testable groups, biological explanation of the results that reflect the testable hypothesis, a conclusion that contains societal implications or scientific impact, and references cited in the document.
- Students will be able to self-identify weaknesses and strengths of their writing.
- Students will understand how to utilize office hours and the writing center to receive feedback on their lab reports.
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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.
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The ACTN3 Polymorphism: Applications in Genetics and Physiology Teaching Laboratories
Learning Objectives- Test hypotheses related to the role of ACTN3 in skeletal muscle function.
- Explain how polymorphic variants of the ACTN3 gene affect protein structure and function.
- List and explain the differences between fast twitch and slow twitch muscle fibers.
- List and explain possible roles of the ACTN3 protein in skeletal muscle function.
- Find and analyze relevant scientific publications about the relationship between ACTN3 genotype and muscle function.
- Formulate hypotheses related to the relationship between ACTN3 genotype and skeletal muscle function.
- Design experiments to test hypotheses about the role of ACTN3 in skeletal muscle function.
- Statistically analyze experimental results using relevant software.
- Present experimental results in writing.
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You and Your Oral Microflora: Introducing non-biology majors to their “forgotten organ”
Learning ObjectivesStudents 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
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A Short Laboratory Module to Help Infuse Metacognition during an Introductory Course-based Research Experience
Learning 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.
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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.
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Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes
Learning ObjectivesStudents successfully completing this lesson will:- Practice basic molecular biology laboratory skills such as DNA isolation, PCR, and gel electrophoresis.
- Gather and analyze quantitative and qualitative scientific data and present it in figures.
- Use bioinformatics to analyze DNA sequences and obtain protein sequences for molecular modeling.
- Make and analyze three-dimensional (3-D) protein models using molecular modeling software.
- 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.
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Air Quality Data Mining: Mining the US EPA AirData website for student-led evaluation of air quality issues
Learning ObjectivesStudents will be able to:- Describe various parameters of air quality that can negatively impact human health, list priority air pollutants, and interpret the EPA Air Quality Index as it relates to human health.
- Identify an air quality problem that varies on spatial and/or temporal scales that can be addressed using publicly available U.S. EPA air data.
- Collect appropriate U.S. EPA Airdata information needed to answer that/those questions, using the U.S. EPA Airdata website data mining tools.
- Analyze the data as needed to address or answer their question(s).
- Interpret data and draw conclusions regarding air quality levels and/or impacts on human and public health.
- Communicate results in the form of a scientific paper.
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Antibiotic Resistance Genes Detection in Environmental Samples
Learning 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.
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Homologous chromosomes? Exploring human sex chromosomes, sex determination and sex reversal using bioinformatics...
Learning ObjectivesStudents 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
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The Case of the Missing Strawberries: RFLP analysis
Learning ObjectivesStudents 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.
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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.
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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.
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An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure
Learning 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:
- pre-mRNA
- 5' capping
- 3' polyadenylation
- splicing
- mRNA
- 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.