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  • Image from http://www.epa.gov/airdata/ad_maps.html

    Air Quality Data Mining: Mining the US EPA AirData website for student-led evaluation of air quality issues

    Learning Objectives
    Students 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.
  • Students participating in the peer review process. Practicing the writing of scientific manuscripts prepares students to understand and engage in the primary literature they encounter.
  • Adult female Daphnia dentifera. Daphnia spp. make a great study system due to their transparent body and their ease of upkeep in a lab.

    Dynamic Daphnia: An inquiry-based research experience in ecology that teaches the scientific process to first-year...

    Learning Objectives
    Students 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.
  • Using Undergraduate Molecular Biology Labs to Discover Targets of miRNAs in Humans

    Learning Objectives
    • Use biological databases to generate and compare lists of predicted miR targets, and obtain the mRNA sequence of their selected candidate gene
    • Use bioinformatics tools to design and optimize primer sets for qPCR
  • A three-dimensional model of methionine is superimposed on a phase contrast micrograph of Saccharomyces cerevisiae from a log phase culture.

    Follow the Sulfur: Using Yeast Mutants to Study a Metabolic Pathway

    Learning Objectives
    At 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.
  • pClone Red Makes Research Look Easy

    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.
  • 3D Print Models: A collection of 3D models printed from online repository files.
  • Normal Arabidopsis plants (A) have flat, spatula shaped leaves. asymmetric leaves2 (as2) mutant plants (B) have leaves that are curled under and slightly twisted. asymmetric leaves1(as1) mutant plants (C) have leaves that are curled under and twisted but also have reduced petioles.  In the laboratory activities I present, students analyze the sequence of the as1 and as2 alleles and computationally model the wild-type and mutant proteins. Visualizing the 3-D structure of the proteins helps students understan

    Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes

    Learning Objectives
    Students successfully completing this lesson will:
    1. Practice basic molecular biology laboratory skills such as DNA isolation, PCR, and gel electrophoresis.
    2. Gather and analyze quantitative and qualitative scientific data and present it in figures.
    3. Use bioinformatics to analyze DNA sequences and obtain protein sequences for molecular modeling.
    4. Make and analyze three-dimensional (3-D) protein models using molecular modeling software.
    5. 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.
  • CRISPR/Cas9 in yeast experimental overview

    CRISPR/Cas9 in yeast: a multi-week laboratory exercise for undergraduate students

    Learning Objectives
    Week 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.
    Week 3-4: Cloning
    • 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.
    Week 5: Screening clones
    • 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.  
    Week 6: Selection of clones and transformation of yeast
    • 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. 
    Week 7: Phenotyping
    • Design an experiment to determine auxotrophic phenotypes.
    • Predict the outcome of multi-step experiments.
    Multiweek
    • 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.
    Alignment with Society-Generated Learning Objectives - From Biochemistry and Molecular Biology, and Genetics Learning Frameworks
    • 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.
  • Bacteria growing on petri dish

    You and Your Oral Microflora: Introducing non-biology majors to their “forgotten organ”

    Learning Objectives
    Students 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
  • Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course

    Learning Objectives
    Students 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.
  • DNA

    Using CRISPR-Cas9 to teach the fundamentals of molecular biology and experimental design

    Learning Objectives
    Module 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.
    Module 2
    • 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.
    Module 3
    • 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.
    Module 4
    • Design and implement an experiment that tests the CRISPR-Cas9 principle.
    • Predict the outcome of a successful in vitro Cas9 digest.
    Presentation of Data Post Lesson
    • 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.
  • pClone Red Makes Research Look Easy

    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.  
  • Abelson kinase signaling network. The image shows many connections between genes and illustrates that signaling molecules and pathways function within networks. It emphasizes the indispensability of computational tools in understanding the molecular functioning of cells. The image was generated with Cytoscape from publicly accessible protein-protein interactions databases.

    Investigating Cell Signaling with Gene Expression Datasets

    Learning Objectives
    Students will be able to:
    • Explain the hierarchical organization of signal transduction pathways.
    • Explain the role of enzymes in signal propagation and amplification.
    • Recognize the centrality of signaling pathways in cellular processes, such as metabolism, cell division, or cell motility.
    • Rationalize the etiologic basis of disease in terms of deranged signaling pathways.
    • Use software to analyze and interpret gene expression data.
    • Use an appropriate statistical method for hypotheses testing.
    • Produce reports that are written in scientific style.
  • SNP model by David Eccles (gringer) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY 4.0 (http://creativecommons.org/licenses/by/4.0)], via Wikimedia Commons

    Exploration of the Human Genome by Investigation of Personalized SNPs

    Learning Objectives
    Students successfully completing this lesson will be able to:
    • Effectively use the bioinformatics databases (SNPedia, the UCSC Genome Browser, and NCBI) to explore SNPs of interest within the human genome.
    • Identify three health-related SNPs of personal interest and use the UCSC Genome Browser to define their precise chromosomal locations and determine whether they lie within a gene or are intergenic.
    • Establish a list of all genome-wide association studies correlated with a particular health-related SNP.
    • Predict which model organism would be most appropriate for conducting further research on a human disease.