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RESEARCH PROJECTS

Cameron Currie
Bacteriology Department

Our  research focus is on the ecology and evolution of symbiotic associations between animals and microbes. We utilize a cross-disciplinary approach incorporating ecological, evolutionary, behavioral, and microbiological approaches and employ molecular ecology and phylogenetic techniques to examine how microbes shape the biology of higher organisms. Our main study system is the quadripartite association between fungus-growing ants, their fungal cultivars, mutualistic bacteria, and specialized pathogens.  Current studies include sequencing the genome of the mutualistic bacteria associated with the ants and isolating microorganisms that are successful at  degrading cellulose material for possible use improving biofuel production.

Timothy Donohue
Department of Bacteriology

Research interests: harvesting the power of biological energy generation

We analyze how cells generate biomass or biofuels from sunlight or other renewable energy sources. To do this, we study metabolic pathways and regulatory networks of the photosynthetic bacterium Rhodobacter sphaeroides. We take advantage of the R. sphaeroides genome sequence, microarrays, proteomics and molecular techniques to decipher how the energy in sunlight or renewable nutrients is funneled into cell material or biofuel formation.

Our long range goals are to identify metabolic and regulatory activities that are critical to bioenergy formation, to obtain a thorough understanding of energy-generating pathways of agricultural, environmental and medical importance, and to use computational models to increase the ability of microbes to utilize sunlight, generate renewable sources of energy, remove greenhouse gases or other toxic compounds, and synthesize compounds that reduce our dependence on fossil fuels.

Randy Jackson
Department of Agronomy

Many types of high yielding crops have been proposed to supply feedstock to the latent cellulosic ethanol industry.  While these systems are well known for producing large quantities of aboveground biomass, an important consideration is their relative sustainability in a variety of agroecological settings.  Sustainability must be grounded by asking: sustainable for what, for whom, at what cost, and for how long? These are social and political considerations that will vary with time and place.  Integral to most formulations, however, is the concept of ecosystem services, which have been defined in the Millennium Ecosystem Assessment as: provisioning (e.g. food, fuel, and fiber), supporting (e.g. soil building and water availability), regulating (e.g. climate stabilization and water quality),  and cultural (e.g. spirituality, aesthetics, and educational) elements of ecosystems that promote human well-being.  Ignoring these dimensions may make biofuel production incompatible with other sustainability goals that society has deemed important (e.g. Clean Water Act, Endangered Species Act, climate stabilization).

We are using a subset of the Wisconsin Integrated Cropping Systems Trial (WICST), agronomic plots established at Arlington Agricultural Research Station (AARS) in 1992, to assess tradeoffs in ecosystem services under alternative cropping systems by measuring things such as greenhouse gas fluxes, soil C changes, biomass production, and biodiversity. In addition to the WICST plots, in spring 2008 we installed a new cropping systems experiment at AARS.  This experiment is an exact replica of an experiment also started in spring 2008 at Michigan State University’s Kellogg Biological Station (KBS).

Shawn Kaeppler, Heidi Kaeppler, Natalia de Leon
Department of Agronomy

Research Interests: corn genes and genotypes

Our primary research approach utilizes genetic and genomic technologies to understand genes in corn important for productivity, and to develop useful corn germplasm. Our research related to biofuels is designed to understand the genes and genotypes that maximize the amount and efficiency of ethanol production per unit of land and per unit of energy input. This research utilizes genetic approaches to identify genes underlying complex phenotypes. Genomic technologies used in this research include microarrays, transformation, and sequence analysis. Summer students who work with our project participate in molecular studies in the laboratory as well as have the opportunity to measure and pollinate plants in the field. An overarching objective of our research is to apply laboratory research to solving practical and important problems in agriculture.

John Markley
Department of Biochemistry

Students will join our “Team Metabolon”, which consists of undergraduates, graduate students, and postdocs. This group analyzes mixtures of metabolites from biomass to identify and quantify the most abundant soluble constituents. We work with researchers developing improved methods for breaking down biomass and enriching the product with compounds on pathways to biofuels. Our approach is to carry out extractions and to use two-dimensional nuclear magnetic resonance spectroscopy to identify the molecules present. Students will learn how to perform extractions and make up solutions of standard compounds used for quantitative analysis. They will participate in NMR data collection and analysis and learn to use our computerized tools that automate these processes. Students with particular interest in bioinformatics and computer science can participate in developing our database of NMR spectra and the tools that use this database. For more information, see http://mmcd.nmrfam.wisc.edu/.

Patrick Masson
Department of Genetics

The cytoskeletal microtubular network plays critical roles in plant morphogenesis and biomass production by mediating cell division and modulating the anisotropic expansion of interphase cells. In turn, the latter process governs guided organs growth (“tropism”) toward sites within their direct environment that are better suited for optimal performance of their primary functions. The Masson laboratory has used the complex root growth behaviors displayed by Arabidopsis seedlings growing on tilted hard-agar surfaces as a phenotype to uncover mutations that affect genes involved in the regulation of the dynamic instability of cortical microtubules in expanding interphase cells. Recent work has focused on a family of plant-specific proteins that appear to modulate the bundling of cortical microtubules in expanding cells of the plant. Undergraduate Summer Research projects will be aimed at further characterizing the root-growth behavioral and hormonal-response phenotypes associated with single, double and multiple mutations in these genes.

David Mead, President
Lucigen Corporation

Having the correct enzymes for biomass degradation, at a low enough price to be affordable, is a major goal of biofuels research. Currently, the biomass-degrading enzyme products that are commercially available are too expensive for practical use in the production of biofuels.  The discovery of new high specific activity biomass active enzymes for evaluation in degradation studies is the focus of this research. An improved pipeline for enzyme discovery specific to the problems unique to this field was developed and validated, and a number of new carbohydrases with high specific activity and broad specificity have been produced. The next step is to develop a minimal set of biomass active enzymes that eliminates the bottleneck in cellulose degradation, in conjunction with research scientists at the Great Lakes Bioenergy Research Center.

Brian F. Pfleger
Department of Chemical and Biological Engineering

My research interests lie in developing microorganisms capable of producing small molecules of significant social, economic, and scientific value from renewable resources.  In the coming decades, our economy will need to be based on such resources in order to sustain itself.   To reach such ends, my research group will develop new tools for engineering biological systems and explore the world of protein engineering in order to develop new biological catalysts for essential chemical reactions. It is my goal to develop a leading laboratory in the field of Synthetic Biology in order to harness the growing database of biological parts for use in developing novel technologies for chemical synthesis.  This research includes the production of biofuels, and related organic building blocks, from biomass such as cellulose.

Michael Sussman
Department of Biochemistry

Systems biology describes a new means of studying a specific aspect of biology using a genome wide profiling method to determine how changes in the transcriptome, proteome and metabolome are engaged with each other, to elicit the phenotype or developmental and environmental change under study. Thrust 5 is in charge of creating and providing enabling technologies that allow each of the other thrusts to use this powerful new tool for understanding and manipulating the metabolic pathways that underlie the use of plants and microbes for biofuel applications. A critical aspect of this approach is a QUANTITATIVE approach to profiling changes in the RNA, proteins and small molecules and examining how these changes are affected by each other in response to any particular perturbation under study. For example, one can use reverse genetics to ‘knockout’ one or more genes and study how the absence of the proteins encoded by those genes (or RNA’s for genes that act without coding for proteins) perturbs the system. Similarly, drugs or environmental perturbations can be used to create quantitative changes in the transcriptome, proteome and metabolome whose measurements reveal how the various molecular components of cells create the amazing varieties of phenotypes that allow us to harness plants and microbes for our own benefit. Synthetic biology (gene synthesis), protein engineering and computational modeling are also important areas of research.