BMS 640 - Experimental Methods in Cell & Molecular Biology

Course Overview

Successful biomedical research requires proposing and testing a novel hypothesis, and the ability to apply the scientific method and implement the appropriate scientific methods to address the biological question. This course focuses on common techniques used in cell and molecular biology. By the end of the course, students will be expected to understand principals, assays, methods, and interpretation of data generated using these techniques. This course is designed for first and second year Ph.D. students or M.S. students. The format of this course will be student-led presentations and discussion of weekly topics, including analysis of published data from the literature. In addition, students will complete short problem sets during the semester. There will be a final written assignment to test the students’ mastery of the principles covered during the semester.

This class is offered in the Fall.

Topics Covered

  • Orientation, Scientific Method and Lab Fundamentals of
    experimental design
  • DNA methods I (DNA extraction, gels and restriction
    enzymes and mapping, Southern blots, sequencing, next gen)
  • DNA methods II (Primer design, DNA polymerases, real
    time quantitative PCR, cDNA methods, nucleotide BLAST)
  • DNA methods III (Bacterial transformation and plasmid
    purification, vectors for recombinant protein production,
    vectors for eukaryotic gene expression, viral expression
    vectors, DNA cloning
  • RNA methods (Total RNA extraction, polyA RNA purification,
    Northern blot analysis)
  • RNA methods II (siRNA, shRNA, microRNAs, RNA-seq)
  • Gene regulation and expression methods (RNase protection
    assay, promoter reporter assay, gene chip microarray)
  • Cell cycle analysis (flow cytometry, measurement of DNA
    synthesis, senescence, and apoptosis)
  • Protein methods I (Protein extraction, SDS-PAGE,
    antibodies, western blotting, immunoprecipitation)
  • Proteins methods II (translational assays, posttranslational
    modification, subcellular protein trafficking, secretion)
  • Protein methods III (immunofluorescence/confocal
    microscopy, mass spec, proteomics)
  • Cell signaling pathway methods (ligand-receptor
    interactions, detecting activation of receptors, detecting
    activation of signaling pathways)
  • DNA-protein interaction methods (EMSA, ChIP, DNA
    reporter assays)
  • Tissue culture methods (normal and transformed cell
    characteristics, tissue culture, gene delivery – lentivirus,
    adenovirus, retrovirus, and plasmid transfection)
  • Mouse genetic models overview