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  • Reprinted by permission from Macmillan Publishers Ltd.

    A Hands-on Introduction to Hidden Markov Models

    Learning Objectives
    • Students will be able to process unannotated genomic data using ab initio gene finders as well as other inputs.
    • Students will be able to defend the proposed gene annotation.
    • Students will reflect on the other uses for HMMs.
  • Students using the Understanding Eukaryotic Genes curriculum to construct a gene model. Students are working as a pair to complete each Module using classroom computers.

    An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

    Learning Objectives
    Module 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.
    Module 2
    • 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.
    Module 3
    • 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
    Module 4
    • 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.
    Module 5
    • 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.
    Module 6
    • 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.
  • 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
  • DNA barcoding research in first-year biology curriculum

    CURE-all: Large Scale Implementation of Authentic DNA Barcoding Research into First-Year Biology Curriculum

    Learning Objectives
    Students will be able to: Week 1-4: Fundamentals of Science and Biology
    • List the major processes involved in scientific discovery
    • List the different types of scientific studies and which types can establish causation
    • Design experiments with appropriate controls
    • Create and evaluate phylogenetic trees
    • Define taxonomy and phylogeny and explain their relationship to each other
    • Explain DNA sequence divergence and how it applies to evolutionary relationships and DNA barcoding
    Week 5-6: Ecology
    • Define and measure biodiversity and explain its importance
    • Catalog organisms using the morphospecies concept
    • Geographically map organisms using smartphones and an online mapping program
    • Calculate metrics of species diversity using spreadsheet software
    • Use spreadsheet software to quantify and graph biodiversity at forest edges vs. interiors
    • Write a formal lab report
    Week 7-11: Cellular and Molecular Biology
    • Extract, amplify, visualize and sequence DNA using standard molecular techniques (PCR, gel electrophoresis, Sanger sequencing)
    • Explain how DNA extraction, PCR, gel electrophoresis, and Sanger sequencing work at the molecular level
    Week 12-13: Bioinformatics
    • Trim and assemble raw DNA sequence data
    • Taxonomically identify DNA sequences isolated from unknown organisms using BLAST
    • Visualize sequence data relationships using sequence alignments and gene-based phylogenetic trees
    • Map and report data in a publicly available online database
    • Share data in a formal scientific poster