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Ongoing Research at the BRL

Ahner Group
  • Research on-going in the Ahner laboratory is focused broadly on how organisms adapt to environmental stress such as trace metal toxicity and how organisms can be harnessed to produce raw materials in a sustainable manner. Modern molecular biology can be used to generate new plants and algae that can be used directly to make specialty enzymes or medicines such as in biomolecular farming or that can be used in feedstocks to promote processing or increase the value of residue materials. We also are working on projects to improve and enable biofuel production from aquatic microalgae.
Bergstom Group
  • Epidemiology and sustainable management of diseases affecting bioenergy feedstocks.
    Infectious diseases are a potential threat to sustainable production of perennial grasses as biofuel feedstock crops. Lab members study the etiology, epidemiology and integrated management of diseases affecting warm season and cool season grasses with potential as biofuel feedstock crops in the Northeast. We are conducting surveys of diseases in perennial grasses, and assessing disease resistance in cultivars of switchgrass and other grass species to prevalent rusts, fungal leaf blights, and smuts. Clean seed programs, seed treatment, and crop polyculture are also being investigated as components of integrated disease management for feedstock crops.
  • Lignocellulose degrading capabilities of plant pathogens.
    During bioconversion, the carbohydrate polymers that form lignocellulose undergo hydrolysis, which is typically catalyzed by mixtures of enzymes including cellulases, hemicellulases and other accessory enzymes that target and degrade specific constituents of the plant cell wall. Along with colleagues, we have demonstrated that plant pathogenic microbes possess a diverse and largely unexplored array of plant cell-wall degrading enzymes of potential application to lignocellulosic digestion. For example, upon screening libraries of plant pathogenic fungi for cellulase- and xylanase-mediated degradation of pre-treated switchgrass, we identified multiple isolates with gross enzymatic activities equivalent to or in excess of an established industrial strain, Trichoderma reesei Rut-C30. Among our top performing strains are representatives of the genus Fusarium, whose hosts span a range of cultivated species and many of which are also relevant to bioenergy (e.g. corn, wheat, tomato, potato, sugarcane, bean, cowpea, date and oil palm), and Colletotrichum navitas, the causal agent of anthracnose disease of switchgrass.
  • Evaluation and improvement of plant pathogenic filamentous fungi for biotechnological applications.
    To achieve the full potential of the "integrated biorefinery" operational model, there is a pressing need to discover and improve upon novel microbes (and their associated enzyme arsenals) whose activities rival or surpass current industrial options such as Trichoderma reesei and Aspergillus niger. Therefore, we are working with colleagues toward identifying strains of plant pathogenic filamentous fungi that have enhanced capabilities to thrive on and degrade specific lignocellulosic substrates such as pretreated switchgrass. We are experimenting with a range of bioinformatic, genetic, genomic and metabolic approaches for distinguishing and optimizing strains in the laboratory. With a comprehensive understanding of these strains - in terms of enzymatic capabilities, metabolic processes, and regulatory and secretory mechanisms - we can then evaluate promising candidates for subsequent scale-up applications to large-scale industrial biotechnology.
Gibson Group
  • The major thrust of Dr. Gibson's research program is the discovery of new natural products (small molecules and enzymes) that have high intrinsic value for the public benefit. The Gibson Group searchs for naturally occurring compounds produced in plants, fungi, or bacteria that are capable of protecting crops from pests, and possess high target selectivity, environmental compatibility, and novel modes of action. The potential of the microbes as biological control agents for pest species is also a thrust of the overall research program. The Gibson Group haa a strong interest in the potential of plant pathogenic fungi and bacteria to contribute accessory enzymes for optimizing treatment processes for optimal hydrolysis of lignocellulosic biomass. The Group's search strategies include traditional methods of solid and liquid culture manipulations, molecular screening of genomic DNA for presence of key biosynthetic enzymes for secondary metabolites of interest, and the use of knockout or expression strategies in order to link a specific metabolite to the biosynthetic gene cluster. For the enzyme screening studies, we combine traditional biochemical screening with molecular evolution strategies to improve selected accessory enzymes for optimized industrial characteristics.
Tester Group

  • Two alternative techniques for the mid-stream processing of microalgae for biofuel applications.
    Harvesting biomass and extraction of lipids have been an understudied, yet critical portion of the process chain for algae based fuels. Most plans for microalgae apply soybean-type biodiesel processing to a very different feed stock, unique in its dilute growth media, single cell structure, rigorous cell walls, and thin sustainability criteria. For microalgae to be viable as a fuel source, they must be grown and processed efficiently, or they will not be a sustainable source of biofuel.

    Ultrasonic cavitation for cell disruption and partitioning of cell content is one facet of our work. Conventional large scale algae production systems (for nutrient supplements, animal feed, and specialty proteins) rely on energy intensive harvesting and copious amounts of solvents for extraction of targeted cell contents. Cavitation may offer benefits of easier processing and downstream separations of cell matter and protein, lipids, and recyclable water. In this way, the use of operations like centrifugation, filtration, and organic solvent extraction can be mitigated or avoided and the overall sustainability of the algae to biofuel process could be increased by alleviating the key bottleneck of harvesting and extraction. We are performing ultrasound experiments which explore the range of conditions under which this technique may be useful for algal fuel applications, including a variety of cell densities, added gases, and algae species.

    A second option for efficient processing involves hot, pressurized water. By going above the normal boiling point (100 ºC) and pressurizing to maintain a liquid phase, unique chemical reactions are possible. This temperature region, using a dense phase water, is referred to as hydrothermal media. Reactions of biomass feed stocks in hydrothermal media have yielded upgraded oil and gaseous products. In this work, hydrothermal conversion is performed on two species of whole microalgae. The products are measured and analyzed to determine the quality and quantity of product oil. As part of this analysis, carbon and nitrogen are measured in the product phases, and the lipid profile of the oil is determined. Model compound studies also shed light on the reactions that occur in hydrothermal processing of algae which are critical to further development.

Walker Group
  • Biomass pretreatment

    Producing a concentrated solution of Monosaccharides from biomass is a key bottleneck in the selective production of materials or fuels from biomass. This process is generally constituted of a thermo-chemical or pretreatment stage followed by a biologically catalyzed stage. Read more...

  • Enzyme discovery and characterization

    Releasing fermentable sugars from plant biomass is a process called enzymatic hydrolysis. This is a critical step in the production of ethanol from lignocellulosic biomass. This step generally follows a pretreatment step, which increases the surface area accessible to the hydrolytic enzymes. The sugars released from the biomass can then be fermented to ethanol. Read more...

  • Fermentation

    In the context of industrial biotechnology, "fermentation" is a general term referring to processes which may utilize a variety of different microorganisms to transform different substrates to a wide variety of products, ranging from commodity chemicals and raw materials for industrial processing to value-added pharmaceuticals. Fermentations utilize a variety of different microorganisms, and may be anaerobic or aerobic. Read more...

  • Systems Biology

    Although experimentation is key for the development of novel fermentation processes and organisms to economically produce bioproducts from biomass, significant resources (time and cost) can be saved through computational modeling. Computational models of metabolic, transcriptional regulatory, and signaling networks can predict environmental or genetic parameters which can be manipulated to achieve optimal fermentation performance. Read more...

  • Composting & molecular ecology

    In composting, heterotrophic microbial activity and growth lead to the degradation of organic material. This degradation occurs via the formation of complex microbial communities that work in a delicate balance to drive changes in the temperature and pH of the compost pile. Although composting is an ancient method, it has evolved as a useful method for the reduction of municipal solid wastes and for the destruction of potentially hazardous pathogenic organisms. Read more...

  • Nanoscale enzyme imaging

    Fluorescence spectroscopy techniques allow the visualization of molecular events that are not readily accessible through other methods. Fluorescence emission enhances the detection and spatial and temporal resolution of binding and molecular displacements. In this area, we are exploiting the advantages offered by fluorescence spectroscopy to study the interactions between cellulases and cellulose fibrils at the most fundamental scales spanning the micro to nanometer range. Read more...

  • Biomass characterization and analytical systems

    The characterization of the conversion processes of lignocellulosic biomass to biofuels requires a large array of methods and analytical systems to extract the meaningful parameters necessary to describe the solid materials and the conversion liquors. The crucial point is also to develop robust, reliable and high-throughput methods that allow the analysis of large number of samples of various sizes (from mg to kg) and of high heterogeneity. Read more...

  • Industrial Ecology

    Our lab is involved in different aspects of industrial ecology, which is the integration an entire industrial process to maximize resource use, minimize waste generation and maximize its re-use. Indeed, we study the impact of biomass processing and logistics prior to its conversion. We also study the environmental impact of the technologies we develop and how they compare to other technologies from a life cycle perspective. Read more...

Wilson Group
  • Our research focus is to determine the mechanism of plant cell wall degrading enzymes, especially cellulases. Our long term goal is to engineer proteins with higher activity on pretreated biomass substrates. We have been studying the proteins required to degrade cellulose produced by the thermophilic soil bacterium, Thermobifida fusca for many years. At this time we are focusing on two proteins: the exocellulase Cel48A and a novel cellulase, E7, which is a member of CBM family 33 that can cleave both cellulose and chitin to produce a range of oligosaccharides. Using site directed mutagenesis, four Cel48A residues have been identified that are require only for crystalline cellulose hydrolysis and thus probably function to move a cellulose molecule from crystalline cellulose into the enzymes active site tunnel. We are trying to understand the mechanism that E7 uses to degrade cellulose and its ability to synergize with other cellulases.