Teaching

BIOL 371 - Microbial Genetics

Evaluation of bacteria and their genetic systems at the molecular and cellular level, including discussion of bacterial genome organization and regulation, mechanisms of genetic variation and horizontal gene transfer, and experimental approaches used to investigate gene function. Recent advances in microbial genetics are emphasized alongside applications to antibiotic resistance, virulence, biotechnology, and microbial evolution.

Course Learning Outcomes

  • Define and describe bacterial genomes in terms of overall organization, including chromosomes and plasmids, gene content, and common regulatory architectures such as operons, regulons, and global regulators.
  • Explain core mechanisms of bacterial gene regulation, including transcriptional control, post transcriptional regulation through small RNAs, and regulatory responses to environmental cues such as stress, nutrient availability, and quorum sensing.
  • Describe and compare the mechanisms that generate genetic variation in bacteria, including mutation, recombination, gene duplication, and genome rearrangements.
  • Explain horizontal gene transfer processes, including transformation, transduction, and conjugation, and connect these mechanisms to adaptation and clinically relevant phenomena such as antibiotic resistance and virulence.
  • Apply common genetic tools and experimental approaches used in microbial genetics, including selection and screening, genetic mapping, polymerase chain reaction strategies, cloning, and CRISPR based editing or perturbation, to design and interpret experiments.
  • Analyze and interpret microbial genetics data, including mutant phenotypes, gene expression readouts, and sequence variants, to draw evidence-based conclusions about gene function and regulation.
  • Evaluate recent advances in microbial genetics, including high throughput sequencing, comparative genomics, transposon insertion sequencing, single cell approaches, CRISPR technologies, and metagenomics, and discuss how these approaches are applied in research, biotechnology, and medicine.
  • Discuss how bacterial genetics shapes microbial evolution, ecology, and host microbe interactions, including the roles of mobile genetic elements such as plasmids, bacteriophages, and transposons in shaping genomes.
  • Build skills to assess the accuracy of microbial genetics information in public sources such as news, social media, and popular science, including identifying misleading claims and distinguishing correlation from causation.
  • Evaluate peer reviewed primary literature in microbial genetics by summarizing key questions, methods, results, and limitations, and proposing logical next experiments.

BIOL 372 - Methods in Microbial Genetics

Methods in Microbial Genetics (BIOL 372) is an in-person laboratory course that builds practical skills in microbiology and microbial genetics methods. Students culture, isolate, and characterize bacteria using aseptic technique, microscopy, and differential staining, then carry out molecular workflows such as plasmid design, plasmid extraction and quantification, restriction digestion, agarose gel electrophoresis, DNA ligation, and chemical transformation to generate recombinant Escherichia coli that express a fluorescent reporter protein. The course emphasizes experimental design, appropriate controls, accurate documentation, and troubleshooting, and it includes applied investigations of bacterial growth dynamics and the chemical and physical control of microbial populations relevant to infection control and antibiotic susceptibility.

Course Learning Outcomes

  • Apply biosafety, aseptic technique, and contamination control practices to safely handle microorganisms, cultures, and waste, including proper labeling, incubation, disinfection, and sterile transfers.
  • Use the compound brightfield microscope correctly (10×, 40×, 100× oil), optimize illumination (condenser/iris), and explain how magnification, numerical aperture, and wavelength determine resolution.
  • Record accurate microbiological observations (tables, drawings, and narratives) that document morphology, staining results, colony characteristics, and experimental outcomes in a reproducible format.
  • Culture microorganisms using appropriate media formats (broth, plates, slants, deeps), and isolate and maintain pure cultures using streak/spread plating and colony-based subculturing.
  • Characterize microorganisms using macroscopic culture features (growth patterns, pigmentation, colony form/margin/elevation) and microscopic traits (cell shape, arrangement) and distinguish contamination from expected growth.
  • Prepare bacterial smears and perform staining workflows linking reagent function and cell envelope structure to observed staining outcomes (Gram-positive vs Gram-negative).
  • Design and conduct a restriction–ligation cloning workflow: plasmid design, plasmid preparation and quantification, restriction digestion, and ligation setup.
  • Analyze DNA using agarose gel electrophoresis to verify fragment size and reaction success (PCR/digests) and apply gel-based evidence to troubleshoot failures (e.g., partial digestion, contamination, incorrect banding).
  • Transform E. coli chemically, select transformants using antibiotics, screen clones using fluorescence reporters, and interpret colony-level phenotypes as evidence of plasmid uptake and gene expression.
  • Quantify and interpret microbial growth and control: generate bacterial growth curves from OD600 data and evaluate chemical/physical antimicrobial effectiveness using zone-of-inhibition assays and moist-heat survival tests.
  • Demonstrate increasing independence as a researcher by preparing for lab, executing multi-step workflows efficiently, using controls to diagnose problems, and drawing evidence-based conclusions from experimental data.

Resources on Bacteria and Microbes

Books

  1. . Authored by Larry Snyder, Joseph E. Peters, Tina M. Henkin and Wendy Champness.
  2. Madigan, M. T., Bender, K. S., Buckley, D. H., Sattley, W. M., & Stahl, D. A. (2021). . Pearson.
  3. by: Gerard J. Tortora, Berdell R. Funke and Christine L. Case. Pearson 2020.
  4. by: Joanne Willey, Linda Sherwood, Chris Woolverton. McGraw-Hill Higher Education, 2013.

Podcasts

  • : "TWiM is for everyone who wants to learn about the science of microbiology in a casual way."
  • : "Meet the Microbiologist is a podcast hosted by Ashley Hagen, that showcases the people behind the scientific discoveries. Each guest introduces their research in one of the cutting-edge areas of the microbial sciences: genomics, antibiotic resistance, synthetic biology, emerging infectious diseases, microbial ecology, public health, probiotics and more!"
  • : "Get updates on new episodes, video snippets from interviews, little blurbs on recent science discoveries we can’t stop thinking about, and more."
  • : "An informative, lighthearted podcast hosted by epidemiologists and disease ecologists Erin Welsh and Erin Allmann Updyke. They explore the biology, history, and impact of infectious diseases, chronic conditions, and, more recently, topics like, for example, nutrition and environmental toxins, making complex science accessible to the public."