I teach courses both in the lower and upper division, primarily related to microbiology. Although some of my research is carried out by students in my research lab, much of it is embedded in the laboratory courses I teach as Course-based Undergraduate Research Experiences (CUREs). Beginning in BIOL112, which Biology majors (and others) typically take in Spring of their 1st year, students begin with the isolation and characterization of bacteria associated with plants. A subset of these bacterial isolates are further analyzed in the upper division General Microbiology Lab (BIOL362) and Microbial Genomics Lab (BIOL363).
BIOL112: General Biology II Lab
The goal of this course is to provide students with an authentic course-based research experience. The research project, in collaboration with The Bay Foundation, is on the identification of microbes that associate with California native plants, with the ultimate goal to find bacterial strains that can be used as seed inoculants to enhance plant restoration efforts at local sites. The most recent focus has been on the El Segundo sand dunes. Students are not only immersed in a research project, but work on a variety of scientific presentation skills throughout the course by participating in lab meetings, journal clubs, and giving a formal oral presentation, with the class culminating in presentation of their results during a poster session and the formal writing of a scientific paper.
BIOL311: Plant Interactions
Plant Interactions is an upper division course that meets the biology major’s requirement for a course in Plant Biology and Organismal Diversity. Topics range from plant-microbe interactions, both pathogenic and symbiotic, plant interactions with herbivores, plant phytochemicals, to agriculture and biofuels. The goal of the course is to teach students biological principals particularly in relationship to molecular biology and biochemistry, experimental design and analysis, and critical thinking, while using as a backdrop the fundamental interactions that occur with plants.
BIOL362: General Microbiology Lab
My goal for this course is to maintain all the core skills and understandings important for a Microbiology lab while providing an “authentic” research experience for students. The analysis of the bacterial strains isolated in BIOL112 has shown that there are certain species that appear more abundant but also some that have the potential to be novel species. Students learn fundamental techniques in microbiology which involve phenotypic, biochemical, and molecular approaches to bacterial analysis to make precise species identification or determine whether they may be working with a novel species. Properties such as biofilm formation and motility are assessed, as well as the role plant exudates may have in regulating these processes. Students apply the skills they’ve learned in a final project of their design.
BIOL363: Microbial Genomics Lab
Microbial genomics is an upper division laboratory that involves a semester-long project related to microbial functional genomics The project involves bacterial genome analysis and mutagenesis of beneficial plant-associated bacteria that were originally isolated in BIOL112 and further analyzed in BIOL361. Students analyze the sequenced genomes as well as generate transposon mutants, screening them for alterations in properties these bacterial strains are known to have and have implications in plant microbe interactions, including exopolysaccharide production, motility, auxin production, cellulase production and phosphate solubilization. Molecular techniques are used to identify the mutated genes based on their findings, students then design and carry out further experiments to characterize these mutants.
BIOL460: Environmental Microbiology
The Environmental Microbiology lecture fulfills the Biology major’s UD Organismal Diversity requirement as well as the UD Microbiology requirement for Environmental Science majors. Core themes in the course include the central role of microbes in biogeochemical cycling, the diversity of microbes in different environments, syntrophic interactions between microbes, microbes in bioremediation, the use of metagenomic analyses to assess microbes in the environment, and the role of microbes in climate change, both as far as their contributing and alleviating it.
BIOL394, 494, 399, 499, 562: Independent Research
I have a number of students that are engaged in independent research with me during the academic year. We have weekly lab meetings, where lab members give updates to the group on their projects, have journal clubs to discuss the primary literature, and end each semester with formal presentations. Students also regularly present their work on conferences.