Bioinformatics

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

• Students will locate and download high-throughput sequence data and genome annotation files from publically available data repositories.

• Students will use Galaxy to create an automated computational workflow that performs sequence quality assessment, trimming, and mapping of RNA-seq data.

• Students will analyze and interpret the outputs of RNA-seq analysis programs.

• Students will identify a group of genes that is differentially expressed between treatment and control samples, and interpret the biological significance of this list of differentially expressed genes.

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

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.

• 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.”)

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.

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.