Research - Physiology and Biochemistry

The Feldman Lab researches plant development e.g. how the populations of cells in and around the meristem interact to control root development. We've shown that quiescent center formation precedes organization of a root meristem, and that high levels of enzyme ascorbic acid oxidase occur within the quiescent center. We use microarrays to characterize quiescent center expression profiles, and to study the many original and unique differentiation events occurring in the root cap as it perceives and transduces environmental stimuli.

The circadian clock is a key adaptation for life on earth, since it lets organisms coordinate internal physiological activities with daily and seasonal environmental changes. The Harmon lab investigates the plant circadian oscillator's molecular mechanism, using Arabidopsis as a model system. We apply genetic, biochemical, molecular, and genomic approaches to identify and characterize proteins contributing the plant clockworks. We seek to integrate their function into current clock models.

Organisms respond to environmental signals including light, temperature, and water supply and endogenous signals such as hormones, metabolites and other regulatory molecules. Cells transduce these signals into a specific response using signal transduction pathways. Our research focuses on the mechanisms of hormonal signaling in plant cells. Using the cereal aleurone as a model system, we research the signal transduction pathway regulated by the antagonistic plant hormones gibberellic acid (GA) and abscisic acid (ABA).

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

Prokaryotes are highly organized cells with many ultrastructural similarities to eukaryotes. In addition to a highly dynamic cytoskeleton composed of homologues of actin, tubulin and intermediate filaments, many prokaryotes possess intracellular membranous organelles. My lab uses bacterial magnetosomes as a model system to study the molecular mechanisms governing the biogenesis and maintenance of prokaryotic organelles. Using a variety of approaches, we identify and investigate key genes involved in controlling magnetosome formation and function.

We study Amt and Rh proteins, which appear to be membrane channels for hydrated gases. They are the only two members of their superfamily. The Amt proteins are channels for ammonium. The Rh proteins, of Rh blood group substance fame, appear to be channels for carbon dioxide (probably H2CO3). We focus on the physiological roles of Rh and Amt proteins in the green alga Chlamydomonas reinhardtii. We continue collaborations to determine the structures of bacterial enhancer-binding proteins, which regulate transcription by the sigma54 holoenzyme form of RNA polymerase.

We study how plants perceive and respond to extracellular signals by modifying their developmental and physiological programs. Our studies have identified a new molecular network for calcium signal transduction in plants. Downstream of these early signaling events, plants respond to environmental signals by regulating the biochemical processes including those in the chloroplasts. We focus on the new regulators for the biogenesis of the photosynthetic complexes (bioenergy conversion) and for starch metabolism (biomass production).

We study the photosynthesis of plants, microalgae, cyanobacteria, and photosynthetic bacteria. Approaches include biophysics and biochemistry of the process, molecular biology and genetics of the organisms, and scale ups for product generation. Applied aspects include diverting the flow of photosynthesis to generate high-value compounds instead of the normally produced sugars. Products of interest are biofuels, feedstock for the synthetic chemistry industry and neutraceuticals. Our trademark is product generation directly from photosynthesis, bypassing the need to harvest and process the respective biomass.

Photosynthetic organisms have evolved multiple mechanisms to cope with excessive light. We seek to identify and dissect these processes by isolating algal and plant mutants. We use a diverse set of techniques, including genetics, physiology, biochemistry, and molecular biology, focused on one particular species, Chlamydomonas reinhardtii, a unicellular green alga. We study the cellular processes involved in coping with reactive oxygen species produced in excessive light.

The cells of higher plants are encased by a wall, a sophisticated, highly complex material consisting mainly of various polysaccharides and polyphenols. The Pauly lab uses a synthetic biology approach whereby all necessary components of the biosynthetic machinery of cross-linking glycans and pectins are identified. To achieve this goal we use various genetic approaches including forward, reverse, and chemical genetics with the model organism Arabidopsis, but also maize as a grass species.

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 isolate pure populations of Caulobacter swarmer cells and observe many parameters during their synchronous cell cycle progress including fluorescent protein localization, DNA content, and global transcriptional patterns. The sequenced Caulobacter genome expedites genetic manipulations and lets us search comprehensively for genes affecting processes of interest. We also pursue in vitro studies to determine how biochemical properties of individual regulatory proteins contribute to cell cycle progression and cellular asymmetry.

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.

We study plant-pathogen interactions, especially the host's active, if unwitting, role in disease development. We work with powdery mildew disease on model plant Arabidopsis thaliana, using mutational analysis to identify host factors required for successful disease development. We also study a new area of plant-pathogen biology, non-host resistance that protects all members of a plant species from all members of a pathogen species. Results from both these projects highlight the importance of both active and passive defenses operating in the host cell wall.

We seek to obtain a genetic, bio-chemical, and cell biological understanding of the mechanisms that enable gram-negative plant pathogens to cause disease on plants, and that allow plants to counteract bacterial pathogens.

Vitamin B12 is essential to most animals but is synthesized only by certain prokaryotes. Using genetic, biochemical, and bioinformatics approaches, we are investigating three areas related to vitamin B12 in bacteria: 1) the biosynthesis of 5,6-dimethylbenzimidazole (DMB), the least understood component of B12; 2) the function of B12 in the symbiotic interaction between the nitrogen-fixing bacterium Sinorhizobium meliloti and its plant host, alfalfa, and 3) the structure and function of novel B12-like compounds found in nature

The Terry Lab researches how to improve the efficiency with which plants remove and detoxify toxic metals and metalloids like Arsenic, Chromium, Lead, Selenium, Mercury, and Cadmium from contaminated soil, sediments, and water. For example, many plant species detoxify Chromium (VI), a very toxic form of the element, to essentially non-toxic Chromium (III). Some plants can also convert toxic forms of Selenium, e.g., selenate and selenite, to volatile but non-toxic dimethylselenide.

My Lab couples predictive biochemistry and analytical chemistry with forward and reverse genetics and genomics to discover small molecules and their biosynthetic pathways which alter defense-related regulatory pathways resulting in large-scale transcriptional changes and redirection of plant cellular metabolism. We use biochemical, molecular, theoretical and informatic approaches to analyze these molecules at cellular and organismic levels. We study the evolution of their biosynthesis, their regulation, and functional roles.

My Lab has two projects underway 1) studying Agrobacterium-specific proteins and their molecular mechanisms responsible for producing a DNA-protein complex capable of plant cell transformation, and 2) researching Plasmodesmata structure.