Research - Biophysics

The Brenner Lab develops methods to characterize macromolecular function and relationships using protein and RNA sequence information, evolutionary principles, and computational methods. We also investigate how many natural mRNA transcripts are apparent targets of the nonsense-mediated mRNA decay pathway for RNA surveillance. In many instances, alternative splicing induces NMD for gene regulation.

We study structural and functional characterization of bacterial microcompartments and of proteins involved in photoprotection in photosynthetic organisms.

We research molecular mechanisms by which light regulates gene expression in plants, focusing on the phytochromes family of photoreceptors. The photoreceptor molecule acts as a biological switch that upon perception of the light signal, triggers changes in transcription detectable within 5 minutes of stimulus. We recently developed a novel light-switchable gene promoter system potentially usable in any light-accessible eukaryotic cell system for rapid, conditional induction or repression of expression.

We work on algorithm development for homolog identification, multiple sequence alignment, phylogenetic tree construction, protein fold prediction, identification of domain boundaries (and novel domains), and detection of key amino acids, such as catalytic or binding pocket residues. We integrate phylogenetic tree construction and subfamily identification into our protein structure and function prediction methods, to enable us to infer the changes produced in protein function and structure over the evolution of a protein superfamily.

The research program in my lab is largely directed toward understanding how plant cell wall polysaccharides are synthesized, how the structures relate to the functions of the cell wall, and how the system is regulated. A major focus is in understanding how cellulose is made and deposited. Most of our experimental work employs Arabidopsis as a model organism, and uses a variety of experimental approaches ranging from analytical biochemistry to genetics and cell biology.