CSB350: Laboratory methods in plant molecular biology research (Undergraduate course)
Topics in this course include vector construction, CRISPR-Cas mediated mutagenesis, plant transformations, PCR, genetic mapping, and bioinformatics analyses. This course introduces students to current recombinant, molecular and biochemical techniques and covers some of the basic ethical issues in recombinant DNA Technology. The adopted techniques are important for us to study the biological functions of proteins from various sequenced genomes. These techniques will include, analysis of CRISPR-Cas system for plants, CRISPR-Cas mediated gene deletion in Arabidopsis, Agrobacterium-mediated transformation of Arabidopsis, extraction of genomic DNA from Arabidopsis, PCR analysis of Arabidopsis CRISPR-Cas deletion lines, phenotypic analysis of Arabidopsis gene deletion lines, construction of protein expression vectors, design of functional mutants, analysis of protein expression, purification, and crystallization. Enzymes of the shikimate pathway will be the subjects for our studies. The shikimate pathway plays an important role in the biosynthesis of secondary metabolites and plant hormones. In Arabidopsis, perturbations of the pathway result in distinct and visible phenotypes, some of which will be the focus of this course. Furthermore, some of the enzymes can easily be studied because their catalyzed reaction is monitored calorimetrically.
CSB450: Proteomics in Systems Biology (Graduate course)
This course will cover current approaches that promise to unravel the mystery of proteomes. These approaches include, 2D-gel electrophoresis, protein-protein interactions, structural biology, enzyme kinetics, and mass spectrometry. We will look at proteome dynamics, regulations, and products under different cellular conditions. Relevant topics include: Enabling technologies in proteomics, Protein separation, identification, mass spectrometry, Quantitative proteomics, Phospho and Glyco proteomics, Protein-protein interactions, Structural biology in proteomics.
CSB490: Team Based Learning (Graduate course)
This is a team-based learning course in the classroom (CSB490H1). Typically, we will have 4 to 6 groups of students working on a specific subject assigned in the previous lecture session. There will be a minimal number of very short lectures that will be used to introduce new concepts, as the focus in this course is on self-directed learning and research within a team environment. We will deal with team constructions, discussion of team development, and strategies on how to function within a team throughout the course as required. Students will learn that the team will be dependent on each member for it to be successful and that the team-based learning is a relevant model for future activities in professional school, graduate school, or the work place. We will provide several examples of scientific questions in the field of biology and protein biochemistry, with a particular focus on protein-protein interaction.
The overall theme for the course is “Regulatory Mechanisms in Plants”. Protein-protein interaction lies at the heart of biological processes including regulated networks and protein turnover. We have established a large repertoire of protein-protein interaction data through the process of interrogating biological systems with synergistic approaches: Y2H, TAP-tagging, CoIP analysis. Through the analysis of this data, we have started to understand how protein domains have evolved to participate in specific regulated processes, including signaling networks, and regulation of metabolic pathways. In this course, we will look at some examples to understand the complexity of these regulatory processes. We will focus on the role of the shikimate pathway in metabolic regulation and in particular, the role of key cell signalling and regulatory proteins in plants. The examples we will explore include: the 14-3-3 proteins in the flowering response, retrograde signalling and inter-organellar communication, transcription factors in metabolic networks, and HSP90 proteins in the stress response.
CSB1020: Protein-Protein interaction in complex regulatory processes in plants (Graduate Course)
Protein-protein interaction lies at the heart of many biological processes, including network regulation and protein turnover. We have established a large repertoire of protein-protein interaction data by interrogating biological systems with synergistic approaches: Y2H, TAP-tagging, CoiP analysis. Through the analysis of these data, we have started to understand how protein domains have evolved to participate in specific processes, such as signal transduction and metabolic pathway regulation. In this course we will look at select examples that highlight the diversity of some of the key molecular players involved, such as 14-3-3 proteins, calmodulins, ubiquitin, and kinases, and we will explore how these proteins have evolved to participate in complex regulatory processes.