Research - Fundamental Science

The Baker Lab seeks understanding of the molecular, genetic and biochemical bases of host-microbe interactions, and investigates mechanisms of pathogen-induced host disease and disease resistance. Our experimental system to study plant-pathogen recognition and signal transduction includes a diverse plant pathogen set and Solanaceae plant hosts. We anticipate our studies will lead to new, environmentally benign strategies for durable, broad-spectrum disease resistant crops.

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.

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.

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.

The research objectives of the Lemaux Lab include the development and use of genetic transformation systems for monocotyledonous species, such as Triticum aestivum, Zea mays, Avena sativa, Hordeum vulgare, Oryzae sativa, Festuca spp., Dactylis glomerata, and Poa pratensis. Our long-term objective is to use transformed cereals to explore basic biological questions as well as to understand and improve crop characteristics.

Our research group studies aspects of epiphytic bacteria that live on healthy plants' surfaces, emphasizing bacteria active in ice nucleation, causing frost damage to plants. We also study plant pathogenic bacteria that inhabit plant surfaces before infection. We use molecular genetic and ecological approaches to study how epiphytic bacteria interact with other microorganisms on plants, and with the plants on which they live. We seek to better understand adaptations epiphytic bacteria have evolved to exploit this unique habitat.

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).

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.

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 study the pattern and process of fungal evolution, both to understand the process and to make fungi the best models for evolutionary biology. We focus on the key evolutionary event that forms the tree of life: speciation. Recently we have documented species divergences, compared phylogenetic and biological species recognition, addressed the timing of species divergence, and evaluated selection acting on potentially adaptive genes. Now, we are using genetics and genomics to find genes that maintain species and facilitate adaptation.

Our goal is to understand how components of eukaryotic chromatin interrelate and integrate to regulate transcriptional activity. We combine genetics and biochemistry with genomics and computational analysis to study DNA methylation, deposition of histone variants, chromatin associated proteins and nucleosome remodeling.