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  • 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
  • Students working with fruit flies in the classroom.

    Fruit Fly Genetics in a Day: A Guided Exploration to Help Many Large Sections of Beginning Students Uncover the Secrets...

    Learning Objectives
    • Students will be able to handle and anesthetize Drosophila fruit flies.
    • Students will be able to use a dissecting microscope to sex Drosophila fruit flies.
    • Students will implement some steps of the scientific method.
    • Students will successfully predict the results of sex-linked genetics crosses.
    • Students will interpret genetic data.
  • 3D Print Models: A collection of 3D models printed from online repository files.
  • Students present their posters to classmates and instructors during a poster fair.

    Discovery Poster Project

    Learning Objectives
    Students will be able to:
    • identify and learn about a scientific research discovery of interest to them using popular press articles and the primary literature
    • find a group on campus doing research that aligns with their interests and communicate with the faculty leader of that group
    • create and present a poster that synthesizes their knowledge of the research beyond the discovery
  • DNA

    Why do Some People Inherit a Predisposition to Cancer? A small group activity on cancer genetics

    Learning Objectives
    At the end of this activity, we expect students will be able to:
    1. Use family pedigrees and additional genetic information to determine inheritance patterns for hereditary forms of cancer
    2. Explain why a person with or without cancer can pass on a mutant allele to the next generation and how that impacts probability calculations
    3. Distinguish between proto-oncogenes and tumor suppressor genes
  • 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.
  • Science press release cartoon.  Cartoon of a newspaper with the headline “Extra Extra! Cell Biology Makes Headlines!”

    Teaching students to read, interpret, and write about scientific research: A press release assignment in a large, lower...

    Learning Objectives
    Students will:
    • interpret the main conclusions and their supporting evidence in a primary research article.
    • concisely communicate the significance of scientific findings to an educated nonspecialist audience.
    • identify the components of a primary research article and the components of the "inverted pyramid" press release structure.
    • identify the central figure in a primary research paper and describe its key finding.
    • demonstrate an understanding of intellectual property by giving appropriate credit to other people's original work.
  • Snake

    Why Meiosis Matters: The case of the fatherless snake

    Learning Objectives
    Students will be able to:
    • Compare and contrast the process and outcomes of mitosis & meiosis
    • Predict consequences of abnormal meiosis including
      • The potential genotype and/or phenotypes of offspring produced when meiosis does not occur properly
      • The stage(s) of meiosis that could have been abnormal given an offspring’s genotype and/or phenotype
  • Students at Century College use gel electrophoresis to analyze PCR samples in order to detect a group of ampicillin-resistance genes.

    Antibiotic Resistance Genes Detection in Environmental Samples

    Learning Objectives
    After 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.
  • DNA Detective: Genotype to Phenotype. A Bioinformatics Workshop for Middle School to College. In this image, students are selecting the mutant Arabidopsis plant defective for the “mystery” gene that they identified and annotated through the DNA Subway Red Line.
  • Set Up Fly Traps: The photo is of the fly traps after being set up for the experiment

    Gotcha! Which fly trap is the best? An introduction to experimental data collection and analysis

    Learning Objectives
    Students will:
    • design and execute an experiment
    • collect, organize, and summarize data
    • analyze and interpret data and make inferences
  • Image from a clicker-based case study on muscular dystrophy and the effect of mutations on the processes in the central dogma.

    A clicker-based case study that untangles student thinking about the processes in the central dogma

    Learning Objectives
    Students will be able to:
    • explain the differences between silent (no change in the resulting amino acid sequence), missense (a change in the amino acid sequence), and nonsense (a change resulting in a premature stop codon) mutations.
    • differentiate between how information is encoded during DNA replication, transcription, and translation.
    • evaluate how different types of mutations (silent, missense, and nonsense) and the location of those mutations (intron, exon, and promoter) differentially affect the processes in the central dogma.
    • predict the molecular (DNA size, mRNA length, mRNA abundance, and protein length) and/or phenotypic consequences of mutations.
  • 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.