Crystallization of Escherichia coli Catabolite Gene Activator Protein with its DNA Binding Site: The use of Modular DNA

To obtain crystals of the Escherichia coli catabolite gene activator protein (CAP) complexed with its DNA-binding site, we have searched for crystallization conditions with 26 different DNA segments ≥28 base-pairs in length that explore a variety of nucleotide sequences, lengths, and extended 5′ or 3′ termini. In addition to utilizing uninterrupted asymmetric lac site sequences, we devised a novel approach of synthesizing half-sites that allowed us to efficiently generate symmetric DNA segments with a wide variety of extended termini and lengths in the large size range (≥28 bp) required by this protein. We report three crystal forms that are suitable for X-ray analysis, one of which (crystal form III) gives measurable diffraction amplitudes to 3 Å resolution. Additives such as calcium, n-octyl-β-d-glucopyranoside and spermine produce modest improvements in the quality of diffraction from crystal form III. Adequate stabilization of crystal form III is unexpectedly complex, requiring a greater than tenfold reduction in the salt concentration followed by addition of 2-methyl-2,4-pentanediol and then an increase in the concentration of polyethylene glycol.

Repression of common bull sperm flora and in vitro impairment of sperm motility with Pseudomonas aeruginosa introduced by contaminated lubricant

Semen collected from clinically healthy bulls at an artificial insemination centre was examined for bacterial diversity. While bacteria that are normally present in the common flora of bovine semen were absent, such as Mycoplasma sp., Proteus sp. and Corynebacterium sp., all semen samples contained an unusually high number of Pseudomonas aeruginosa strains. Analysis via pulsed field gel electrophoresis demonstrated that one particular P. aeruginosa strain, present in a sealed bottle of lubricant, was widespread in bull semen. This strain was shown to secrete substances that inhibited both the growth of bacteria constituting the normal bull sperm flora and the motility of spermatozoa in vitro. This study demonstrated that commercially available lubricants might contain bacteria that can spread amongst breeding bulls and affect the quality of semen. Bacteriological controls and species' identification are necessary at several production levels, including lubricants and extenders, to ensure high semen quality and avoid the spread of pathogens.

Sugar modification as a means to increase the biological performance of oligonucleotides

Modification of the ribose unit in DNA and RNA profoundly influences the self-rcognition and the biological properties of the nucleic acids. Conformational restriction of the ribose units, as in LNA and tricyclo-DNA, has been identified as a powerful tool to increase DNA and RNA affinity as well as biological stability and antisense properties. Apart from that sugar modified DNA analogues, as homo-DNA, have shown to be orthogonal base-pairing systems which by virtue of non-crosscommunicating with the natural nucleic acids open novel applications in biotechnology.

The effects of a changing climate on root respiration of woody plants in sugar maple forests and northern peatlands

Global climate change might significantly impact future ecosystems. The purpose of this thesis was to investigate potential changes in woody plant fine root respiration in response to a changing climate. In a sugar maple dominated northern hardwood forest, the soil was experimentally warmed (+4 °C) to determine if the tree roots could metabolically acclimate to warmer soil conditions. After one and a half years of soil warming, there was an indication of slight acclimation in the fine roots of sugar maple, helping the ecosystem avoid excessive C loss to the atmosphere. In a poor fen northern peatland in northern Michigan, the impacts of water level changes on woody plant fine root respiration were investigated. In areas of increased and also decreased water levels, there were increases in the CO2 efflux from ecosystem fine root respiration. These studies show the importance of investigating further the impacts climate change may have on C balance in northern ecosystems.

Investigating within-canopy variation of functional traits and cellular structure of sugar maple (Acer saccharum) leaves

Patterns of increasing leaf mass per area (LMA), area-based leaf nitrogen (Narea), and carbon isotope composition (δ13C) with increasing height in the canopy have been attributed to light gradients or hydraulic limitation in tall trees. Theoretical optimal distributions of LMA and Narea that scale with light maximize canopy photosynthesis; however, sub-optimal distributions are often observed due to hydraulic constraints on leaf development. Using observational, experimental, and modeling approaches, we investigated the response of leaf functional traits (LMA, density, thickness, and leaf nitrogen), leaf carbon isotope composition (δ13C), and cellular structure to light availability, height, and leaf water potential (Ψl) in an Acer saccharum forest to tease apart the influence of light and hydraulic limitations. LMA, leaf and palisade layer thickness, and leaf density were greater at greater light availability but similar heights, highlighting the strong control of light on leaf morphology and cellular structure. Experimental shading decreased both LMA and area-based leaf nitrogen (Narea) and revealed that LMA and Narea were more strongly correlated with height earlier in the growing season and with light later in the growing season. The supply of CO2 to leaves at higher heights appeared to be constrained by stomatal sensitivity to vapor pressure deficit (VPD) or midday leaf water potential, as indicated by increasing δ13C and VPD and decreasing midday Ψl with height. Model simulations showed that daily canopy photosynthesis was biased during the early growing season when seasonality was not accounted for, and was biased throughout the growing season when vertical gradients in LMA and Narea were not accounted for. Overall, our results suggest that leaves acclimate to light soon after leaf expansion, through an accumulation of leaf carbon, thickening of palisade layers and increased LMA, and reduction in stomatal sensitivity to Ψl or VPD. This period of light acclimation in leaves appears to optimize leaf function over time, despite height-related constraints early in the growing season. Our results imply that vertical gradients in leaf functional traits and leaf acclimation to light should be incorporated in canopy function models in order to refine estimates of canopy photosynthesis.

LIFE CYCLE ASSESSMENTS (LCAs) OF PYROLYSIS-BASED GASOLINE AND DIESEL FROM DIFFERENT REGIONAL FEEDSTOCKS: CORN STOVER, SWITCHGRASS, SUGAR CANE BAGASSE, WASTE WOOD, GUINEA GRASS, ALGAE, AND ALBIZIA

Renewable hydrocarbon biofuels are being investigated as possible alternatives to conventional liquid transportation fossil fuels like gasoline, kerosene (aviation fuel), and diesel. A diverse range of biomass feedstocks such as corn stover, sugarcane bagasse, switchgrass, waste wood, and algae, are being evaluated as candidates for pyrolysis and catalytic upgrading to produce drop-in hydrocarbon fuels. This research has developed preliminary life cycle assessments (LCA) for each feedstock-specific pathway and compared the greenhouse gas (GHG) emissions of the hydrocarbon biofuels to current fossil fuels. As a comprehensive study, this analysis attempts to account for all of the GHG emissions associated with each feedstock pathway through the entire life cycle. Emissions from all stages including feedstock production, land use change, pyrolysis, stabilizing the pyrolysis oil for transport and storage, and upgrading the stabilized pyrolysis oil to a hydrocarbon fuel are included. In addition to GHG emissions, the energy requirements and water use have been evaluated over the entire life cycle. The goal of this research is to help understand the relative advantages and disadvantages of the feedstocks and the resultant hydrocarbon biofuels based on three environmental indicators; GHG emissions, energy demand, and water utilization. Results indicate that liquid hydrocarbon biofuels produced through this pyrolysis-based pathway can achieve greenhouse gas emission savings of greater than 50% compared to petroleum fuels, thus potentially qualifying these biofuels under the US EPA RFS2 program. GHG emissions from biofuels ranged from 10.7-74.3 g/MJ from biofuels derived from sugarcane bagasse and wild algae at the extremes of this range, respectively. The cumulative energy demand (CED) shows that energy in every biofuel process is primarily from renewable biomass and the remaining energy demand is mostly from fossil fuels. The CED for biofuel range from 1.25-3.25 MJ/MJ from biofuels derived from sugarcane bagasse to wild algae respectively, while the other feedstock-derived biofuels are around 2 MJ/MJ. Water utilization is primarily from cooling water use during the pyrolysis stage if irrigation is not used during the feedstock production stage. Water use ranges from 1.7 - 17.2 gallons of water per kg of biofuel from sugarcane bagasse to open pond algae, respectively.

Evaluation of sugar maple dieback in the Upper Great Lakes region and development of a forest health youth education program

Acer saccharum Marsh., is one of the most valuable trees in the northern hardwood forests. Severe dieback was recently reported by area foresters in the western Upper Great Lakes Region. Sugar Maple has had a history of dieback over the last 100 years throughout its range and different variables have been identified as being the predisposing and inciting factors in different regions at different times. Some of the most common factors attributed to previous maple dieback episodes were insect defoliation outbreaks, inadequate precipitation, poor soils, atmospheric deposition, fungal pathogens, poor management, or a combination of these. The current sugar maple dieback was evaluated to determine the etiology, severity, and change in dieback on both industry and public lands. A network of 120 sugar maple health evaluation plots was established in the Upper Peninsula, Michigan, northern Wisconsin, and eastern Minnesota and evaluated annually from 2009-2012. Mean sugar maple crown dieback between 2009-2012 was 12.4% (ranging from 0.8-75.5%) across the region. Overall, during the sampling period, mean dieback decreased by 5% but individual plots and trees continued to decline. Relationships were examined between sugar maple dieback and growth, habitat conditions, ownership, climate, soil, foliage nutrients, and the maple pathogen sapstreak. The only statistically significant factor was found to be a high level of forest floor impacts due to exotic earthworm activity. Sugar maple on soils with lower pH had less earthworm impacts, less dieback, and higher growth rates than those on soils more favorable to earthworms. Nutritional status of foliage and soil was correlated with dieback and growth suggesting perturbation of nutrient cycling may be predisposing or contributing to dieback. The previous winter's snowfall totals, length of stay on the ground, and number of days with freezing temperatures had a significant positive relationship to sugar maple growth rates. Sapstreak disease, Ceratocystis virescens, may be contributing to dieback in some stands but was not related to the amount of dieback in the region. The ultimate goal of this research is to help forest managers in the Great Lakes Region prevent, anticipate, reduce, and/or salvage stands with dieback and loss in the future. An improved understanding of the complex etiology associated with sugar maple dieback in the Upper Great Lakes Region is necessary to make appropriate silvicultural decisions. Forest Health education helps increase awareness and proactive forest management in the face of changing forest ecosystems. Lessons are included to assist educators in incorporating forest health into standard biological disciplines at the secondary school curricula.