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  • A schematic of the relationship between the different types of pasta or beans and the respective gut and environmental bacteria

    The impact of diet and antibiotics on the gut microbiome

    Learning Objectives
    After completing the exercise, students will be able to:
    • Identify several of the nine phyla that contribute to the gut microbiome and name the two predominant ones;
    • Describe how diet impacts the gut microbiome and compare the composition of the gut microbiome between different diets;
    • Describe how antibiotic treatment impacts the gut microbiome and understand how this leads to infection, for example by Clostridium difficile;
    • Trace the response to a change in diet, starting with i) changes in the composition of the microbiome, followed by ii) changes in the bacterial metabolic pathways and the respective excreted metabolic products, resulting in iii) a molecular response in the host intestinal cells, and eventually iv) resulting in human disease;
    • Improve their ability to read scientific literature;
    • Express themselves orally and in writing;
    • Develop team working skill
  • Fully annotated mitochondrial genome of a lichenized fungal species (Cladonia subtenuis).  This represents a visual representation of the final project result of the lesson plan. Students will submit their annotation to NCBI (GenBank) and upon acceptance of their annotation, they typically add this publicly available resource into their resume.

    A CURE-based approach to teaching genomics using mitochondrial genomes

    Learning 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
  • Peterson MP, Rosvall KA, Choi J-H, Ziegenfus C, Tang H, Colbourne JK, et al. (2013) Testosterone Affects Neural Gene Expression Differently in Male and Female Juncos: A Role for Hormones in Mediating Sexual Dimorphism and Conflict. PLoS ONE 8(4): e61784. doi:10.1371/journal.pone.0061784

    Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

    Learning Objectives
    • From raw RNAseq data, run a basic analysis culminating in a list of differentially expressed genes.
    • Explain and evaluate statistical tests in RNAseq data. Specifically, given the output of a particular test, students should be able to interpret and explain the result.
    • Use the Linux command line to complete specified objectives in an RNAseq workflow.
    • Generate meaningful visualizations of results from new data in R.
    • (In addition, each chapter of this lesson plan contains more specific learning objectives, such as “Students will demonstrate their ability to map reads to a reference.”)
  • Training future faculty map

    Training future faculty in 30 minutes a week: A modular framework to provide just-in-time professional development to...

    Learning Objectives
    TAs will be able to:
    • design small classroom activities
    • design fair quiz and exam questions
    • use rubrics to grade assignments fairly and in a timely manner
    • offer constructive, actionable feedback on student written work
    • compare and contrast context-specific strategies for dealing with student problems
    • compare and contrast context-specific time management strategies
    • discuss the importance of diversity, evaluate their own implicit biases, and discuss how these could impact their teaching
    • compare and contrast different methods of summarizing teaching experience on job application materials
    • evaluate their teaching in a reflective manner to develop future teaching goals