The hydrolysis of urea by the widely distributed enzyme urease is special in that it is one of the few biologically occurring reactions that can generate carbonate ions without an associated production of protons. When this hydrolysis occurs in a calcium-rich environment, calcite (calcium carbonate) precipitates from solution forming a solid-crystalline material. The binding strength of the precipitated crystals is highly dependent on the rate of carbonate formation and under suitable conditions it is possible to control the reaction to generate hard binding calcite cement (or Biocement). The objective of this thesis was to develop an industrially suitable cost-effective microbial process for the production of urease active cells and investigate the potential for urease active cells to act as a catalyst for the production of Biocement. The biocementation capability of two suitable strains was compared. Sporosarcina pasteurii (formally Bacillus pasteurii) produced significantly higher levels of urease activity compared to Proteus vulgaris, however the level of urease activity was variable with respect to biomass suggesting that the enzyme was not constitutive as indicated by the literature, but subject to regulation. The environmental and physiological conditions for maximum urease activity in S. pasteurii were investigated and it was found that the potential urease capacity of the organism was very high (29 mM urea.min-1.OD-1) and sufficient for biocementation without additional processing (e.g. concentration, cell lysis). The regulation mechanism for S. pasteurii urease was not fully elucidated in this study, however it was shown that low specific urease activity was not due to depletion of urea nor due to the high concentrations of the main reaction product, ammonium. pH conditions were shown to have a regulatory effect on urease but it was evident that another co-regulating mechanism existed. Despite not fully exploiting the urease capability of S. pasteurii, sufficient urease activity to allow direct application of the enzyme without additional processing could still be achieved and the organism was considered suitable for biocementation. Urease was the most expensive component of the cementation process and cost-efficient production was desired, thus an economic growth procedure was developed for large-scale cultivation of S. pasteurii. The organism is a moderate alkaliphile (growth optimum pH 9.25) and it was shown that sufficient activity for biocementation could be cultivated in non-sterile conditions with a minimum of upstream and downstream processing. The cultivation medium was economised and expensive components were replace with a food-grade protein source and acetate, which lowered production costs by 95%. A high level of urease activity (21 mM urea hydrolysed.min-1) was produced in the new medium at a low cost ($0.20 (AUD) per L). The performance of urease in whole S. pasteurii cells was evaluated under biocementation conditions (i.e. presence of high concentrations of urea, Ca2+, NH4 +/NH3, NO3 - and Cl- ions). It was established that the rate of urea hydrolysis was not constant during cementation, but largely controlled by the external concentrations of urea and calcium, which constantly changed during cementation due to precipitation of solid calcium carbonate from the system. A simple model was generated that predicted the change in urea hydrolysis rate over the course of cementation. It was shown that whole cell S. pasteurii urease was tolerant to concentrations of up to 3 M urea and 2 M calcium, and the rate of urea hydrolysis was unaffected up to by 3 M ammonium. This allowed the controlled precipitation of up to 1.5 M CaCO3 within one treatment, and indicated that the enzyme was very stable inspite of extreme chemical conditions. A cost-efficient cementation procedure for the production of high cementation strength was developed. Several biocementation trials were conducted into order to optimise the imparted cementation strength by determining the effect of urea hydrolysis rate on the development of strength. It was shown that high cementation strength was produced at low urea hydrolysis rates and that the development of cementation strength was not linear over the course of the reaction but mostly occurred in the first few hours of the reaction. In addition, the whole cell bacterial enzyme had capacity to be immobilised in the cementation material and re-used to subsequent applications, offering a significant cost-saving to the process. An industry-sponsored trial was undertaken to investigate the effectiveness of Biocement for increasing in-situ strength and stiffness of two different sandy soils; (a) Koolschijn sand and (b) 90% Koolschijn sand mixed with 10% peat (Holland Veen). After biocementation treatment, Koolschijn sand indicated a shear strength of 1.8 MPa and a stiffness of 250 MPa, which represents an 8-fold and 3-fold respective improvement in strength compared to unconsolidated sand. Significantly lower strength improvements were observed in sand mixed with peat. In combination, trials of producing bacteria under economically acceptable conditions and cementation trials support the possibility of on-site production and in-situ application of large field applications.

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (p. 63-69).

Convective clouds in the tropics can be grouped into three categories: shallow clouds with cloud-top heights near 2 km above the surface, mid-level congestus clouds with tops near the 0°C level, and deep convective clouds capped by the tropopause. This trimodal distribution is visible in cloud data from the Geoscience Laser Altimeter System (GLAS), carried aboard the Ice, Cloud, and land Elevation Satellite (ICESat), as well as in precipitation data from the Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR). Fractional areal coverage (FAC) data is calculated at each of the three levels to describe how often optically thick clouds or precipitation are seen at each level. By dividing the FAC of TRMM PR-observed precipitation by the FAC of thick GLAS/ICESat-observed clouds, the fraction of clouds that are precipitating is derived. The tropical mean precipitating cloud fraction is low: 3.7% for shallow clouds, 6.5% for mid-level clouds, and 24.1% for deep clouds. On a regional basis, the FAC maps created in this study show interesting trends. The presence of nonphysical answers in the PCF graphs, however, suggest that greater study with more precise instruments is needed to properly understand the true precipitating cloud fraction of the tropical atmosphere.

The semi-arid regions of the Pacific Northwest are characterized by a high degree of annual temperature and precipitation variation. As a result of this climatic variation, dryland nitrogen fertilizer trials on fallow- ,wheat rotations typically demonstrate a variable response. Wheat growers in the area must not only cope with this climatic variation and its sundry effects upon their livelihood, they must also make decisions regarding the future level of anticipated climatic variation. The specific objectives were to: 1) develop a climatically responsive yield potential prediction model for soft white winter wheat from historical data at the Sherman Branch Experiment Station (Moro, OR); 2) modify this model for use on commercial fields; 3) field simulate five fallow-crop precipitation patterns characteristic of the variation found in the Sherman county area of eastern Oregon in order to test the yield potential model: 4) examine the effects of precipitation variation on nitrogen fertilizer responses, moisture storage and depletion and nitrogen mineralization; and 5) establish a quantitative relationship between precipitation/ soil moisture and nitrate accumulation in both the fallow and crop seasons. Two interacting regression models were developed to estimate grain yield levels in the 250-350 mm precipitation zone of eastern Oregon. The first model estimates yield potential from monthly precipitation and temperature values. The second model estimates the percent grain reduction due to delayed crop emergence. The grain yield model was adapted to commercial fields using a Productivity Index factor (PI). The PI is a measure of the productivity of other locations in relation to the Sherman Branch Experiment Station, using water-use-efficiency (WUE) as the basis of comparison. The field simulation of five fallow-crop precipitation patterns demonstrated that the maximum grain yield response occurred at 40 kg N (soil + fertilizer)/metric ton. The grain yield model demonstrated a 15% level of accuracy on a commercial field basis in both field trials and a survey of past production levels (1972-1980). It was hypothesized that the distribution of precipitation in the fallow and crop periods had an effect on both the amount and distribution of stored soil moisture. The field simulation demonstrated that more soil moisture was stored at the 90-240 cm depths by the patterns with more fallow season precipitation when measured in March of the crop year. Soil moisture storage and storage efficiencies fluctuated throughout the fallow and crop periods. At the cessation of the winter precipitation season in both the fallow and crop periods (March), the storage efficiency was highest when low levels of precipitation occurred. At this point in time, the mean crop period storage efficiency was 10% below the mean fallow period storage efficiency (34 and 44%, respectively) in both simulation studies. Soil moisture, temperature and immobilization requirements of crop residues interact to affect the net amount of nitrogen mineralization. The mineralization model proposed by Stanford and Smith (1972) was tested under field conditions. When the nitrogen immobilization requirement of the crop residues was included, the actual and predicted values were in agreement at the close of the 1978 fallow period. A nitrogen deficit was predicted at the 0-30 cm depth at the close of the 1980 fallow; however, the actual levels indicated a net accumulation of nitrate-nitrogen. Crop season mineralization, inferred from Mitscherlick and a-value extrapolations, in 1979 demonstrated that there was a decreasing amount of net mineralization during the crop season with increasing amounts of both fallow and crop season precipitation. Crop season mineralization in 1980 indicated that there was no net accumulation of nitrogen, rather a tie-up of 14 kg N/ha. This result reflects both the unsatisfied immobilization requirement predicted for the 1979 fallow season and crop season denitrification. / Graduation date: 1981

This dissertation focuses on examining the relationship between antecedent soil moisture and summer precipitation in the U.S. Great Plains (GP). The influence of Nino sea surface temperatures (SSTs) on summer precipitation has also been investigated to compare their relative contributions to those from local moisture recycling. Both observational data and model simulations have been used to investigate how and why soil moisture can affect subsequent summer precipitation in the GP. Observational analysis indicates that spring (May 1st) soil moisture is significantly correlated with summer precipitation only during periods when Nino SSTs are not strongly correlated with summer precipitation (e.g. 1925-1936). During periods when Nino SSTs are strongly correlated with summer precipitation (e.g. 1940-1970), spring soil moisture is not a good predictor of summer precipitation in the GP. The periods of strong correlation between Nino SSTs and summer precipitation are associated with strong SST persistence. This study suggests that both local soil moisture and remote SST anomalies (deviation from SST climatology) influence summer precipitation in the GP. The soil moisture anomalies are of greatest importance during years when Nino SST persistence is low. Model results have demonstrated that there are significant differences in precipitation response to soil moisture anomalies depending on their sign (+/-), timing and persistence. The influence of dry soil moisture anomalies on subsequent precipitation tends to last longer than wet soil moisture anomalies when initialized on May 1st. Dry soils can influence summer precipitation in the subsequent 2-3 months. However, the precipitation response to wet soil moisture anomalies is faster and greater in magnitude than the response to dry soil moisture anomalies. Persistent soil moisture anomalies that are sustained for an entire month produced larger precipitation changes than soil moisture anomalies only applied on the first day of the month. It appears that the length of soil moisture memory also depends on the sign of soil moisture anomaly. The results of this study may be model-dependent due to the significant inter-model variations in land surface parameterizations. This may restrict the potential for drawing general conclusions.

Convective clouds in the tropics can be grouped into three categories: shallow clouds with cloud-top heights near 2 km above the surface, mid-level congestus clouds with tops near the 0°C level, and deep convective clouds capped by the tropopause. This trimodal distribution is visible in cloud data from the Geoscience Laser Altimeter System (GLAS), carried aboard the Ice, Cloud, and land Elevation Satellite (ICESat), as well as in precipitation data from the Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR). Fractional areal coverage (FAC) data is calculated at each of the three levels to describe how often optically thick clouds or precipitation are seen at each level. By dividing the FAC of TRMM PR-observed precipitation by the FAC of thick GLAS/ICESat-observed clouds, the fraction of clouds that are precipitating is derived. The tropical mean precipitating cloud fraction is low: 3.7% for shallow clouds, 6.5% for mid-level clouds, and 24.1% for deep clouds. On a regional basis, the FAC maps created in this study show interesting trends. The presence of nonphysical answers in the PCF graphs, however, suggest that greater study with more precise instruments is needed to properly understand the true precipitating cloud fraction of the tropical atmosphere.

The relationship between precipitation and large-flow is important to understand and characterize in the climate system. We examine statistical relationships between the Tropical Rainfall Measurement Mission (TRMM) 3B42 gridded precipitation and large-scale ow variables in the Tropics for 2000{2007. These variables include NCEP/NCAR Re-analysis sea surface temperatures (SSTs), vertical temperature pro files, omega, and moist static energy, as well as Atmospheric Infrared Sounder (AIRS) vertical temperatures and QuikSCAT surface divergence. We perform correlation analysis, empirical orthogonal function analysis, and logistic regression analysis on monthly, pentad, daily and near-instantaneous time scales. Logistic regression analysis is able to incorporate the non-linear nature of precipitation in the relation- ship. Flow variables are interpolated to the 0.25 degrees TRMM 3B42 grid and examined separately for each month to o set the effects of the seasonal cycle. January correlations of NCEP/NCAR Re-analysis SSTs and TRMM 3B42 precipitation have a coherent area of positive correlations in the Western and Central Tropical Pacific on all time scales. These areas correspond with the South Pacific Convergence Zone (SPCZ) and the Inter Tropical Convergence Zone (ITCZ). 500mb omega is negatively correlated with TRMM 3B42 precipitation across the Tropics on all time scales. QuikSCAT divergence correlations with precipitation have a band of weak and noisy correlations along the ITCZ on monthly time scales in January. Moist static energy, calculated from NCEP/NCAR Re-analysis has a large area of negative correlations with precipitation in the Central Tropical Pacific on all four time scales. The first few Empirical Orthogonal Functions (EOFs) of vertical temperature profiles in the Tropical Pacific have similar structure on monthly, pentad, and daily timescales. Logistic regression fit coefficients are large for SST and precipitation in four regions located across the Tropical Pacific. These areas show clear thresholded behavior. Logistic regression results for other variables and precipitation are less clear. The results from SST and precipitation logistic regression analysis indicate the potential usefulness of logistic regression as a non-linear statistic relating precipitation and certain ow variables.

In this study, the space-time relationship of precipitation fields is examined by testing the Taylor's "frozen field" hypothesis (TH). Specifically, the hypothesis supposes that if a spatio-temporal precipitation field with a stationary covariance Cov(r,tau) in both space r and time tau, moves with a constant velocity v, then the temporal covariance at time lag tau is equal to the spatial covariance at space lag v tau, that is, Cov(0;tau) = Cov(v tau, 0). Of specific interest is whether there is a cut-off or decorrelation time scale for which the TH holds for a given mean flow velocity v. The validity of the TH is tested for precipitation fields using high-resolution gridded NEXRAD radar reflectivity data over southeastern United States by employing two different statistical approaches. The first method is based upon rigorous hypothesis testing while the second is based on a simple correlation analysis, which neglects possible dependencies in the correlation estimates. The data-set has an approximate horizontal resolution of 4 km x 4 km and a temporal resolution of 15 minutes, while the time period of study is 4 days. The results of both statistical methods suggest that the TH might hold for the shortest space and time scales resolved by the data (4 km and 15 minutes), but that it does not hold for longer periods or larger spatial scales. The fidelity of global climate models in accurately simulating seasonal mean precipitation in the tropics is investigated by comparisons with satellite observations. Specifically, six-year long (2000-2005) simulations are performed using a high-resolution (36-km) Weather Research Forecast (WRF) model and the Community Atmosphere Model (CAM) at T85 spatial resolution and the results are compared with satellite observations from the Tropical Rainfall Measuring Mission (TRMM). The primary goal is to study the annual cycle of rainfall over four land regions of the tropics namely, the Indian monsoon, the Amazon, tropical Africa and the North American monsoon. The results indicate that the WRF model systematically underestimates the magnitude of monthly mean rainfall over most Tropical land regions but gets the seasonal timing right. On the other hand, CAM produces rainfall magnitudes that are closer to the observations but the rainfall peak leads or lags the observations by a month or two. Some of these regional biases can be attributed to erroneous circulation and moisture surpluses/deficits in the lower troposphere in both models. Overall, the results seem to indicate that employing a higher spatial resolution (36 km) does not significantly improve simulation of precipitation. We speculate that a combination of several physics parameterizations and lack of model tuning gives rise to the observed differences between the models and the observations.

Isolated from marine sponges, many bromopyrrole alkaloids have become natural products of intense scientific interest. The oroidin-derived class of dimeric bromopyrrole alkaloids that include ageliferin, bromoageliferin, and dibromoageliferin exhibit interesting biological properties, including actomycin ATPase, antiviral and antibacterial activities. As a prelude to the total synthesis of ageliferin, an intramolecular Diels-Alder (IMDA) reaction was explored as a means to introduce the three contiguous stereocenters. Toward this end, various IMDA precursors were synthesized, and several strategies for the synthesis of IMDA substrates were devised and explored. Affinity chromatography is a powerful technique that enables the purification of a specific protein from a complex mixture. However, traditional affinity chromatography techniques are somewhat limited due to the solid state of the matrix. To overcome these limitations, the utility of a soluble polymer as an alternative affinity matrix was explored for the isolation of natural product receptors. This polymer displays physical properties that make it an ideal matrix for protein isolation and purification. The parent polymer is soluble in aqueous solution at 4 °C and precipitates once the mixture reaches 32 °C. Furthermore, employing this polymer for affinity chromatography may limit the nonspecific binding of proteins. It is also possible to determine the ligand loading using standard analytical techniques such as 1H and 13C NMR. For proof of concept, a dexamethasone-containing macroligand was synthesized to isolate the known glucocorticoid receptor. In addition, a cyclosporin A-containing macroligand was synthesized and employed to isolate the well known and more robust cyclophilins. In this work, it was demonstrated that indeed the ligand loading can be determined by 1H NMR technique. In addition, it was established, as expected, that the water solubility of the macroligands varies based on the hydrophilicity and hydrophobicity of the ligand and degree of ligand loading.

Thesis (Ph. D.)--Florida State University, 2003. / Advisor: Dr. Eric A. Smith, Florida State University, College of Arts and Sciences, Dept. of Meteorology. Title and description from dissertation home page (viewed Mar. 02, 2003). Includes bibliographical references.