Progress in DNA sequencing of plant genomes has revealed that, in addition to microorganisms, a number of plants contain genes which share similarity to microbial 1-aminocyclopropane-1-carboxylate (ACC) deaminases. ACC deaminases break down ACC, the immediate precursor of ethylene in plants, into ammonia and α-ketobutyrate. We therefore sought to isolate putative ACC deaminase cDNAs from tomato plants with the objective of establishing whether the product of this gene is a functional ACC deaminase. It was demonstrated that the enzyme encoded by the putative ACC deaminase cDNA does not have the ability to break the cyclopropane ring of ACC, but rather that it utilizes D-cysteine as a substrate, and in fact encodes a D-cysteine desulfhydrase. Kinetic characterization of the enzyme has shown that it is similar to other previously characterized D-cysteine desulfhydrases. Using site-directed mutagenesis, it was shown that altering two amino acid residues within the predicted active site changed the enzyme from D-cysteine desulfhydrase to ACC deaminase. Concomitantly, it was shown that by altering two amino acids residues at the same position within the active site of ACC deaminase from Pseudomonas putida UW4 changed this enzyme into D-cysteine desulfhydrase.

The present elemental analysis workhorse worldwide is Inductively Coupled Plasma (ICP) Atomic Emission Spectrometry (AES) and Mass Spectrometry (MS). Due to the high power requirements, large gas consumption and the more obvious attribute, size, the ICP is tethered to the lab. Usually, samples must be collected, bottled, sometimes stabilized by acids and then shipped back to the lab for analysis (hours to days to weeks turnover rate). Due to the demand for a portable analyzer this thesis will focus on further development of microplasma devices (MPDs) for portable on-site analysis, in (near) real-time. Mini-In-Torch Vapourization (mini-ITV) is the sample introduction method for MPDs which removes the need for sample preparation (further necessitates portability). Mini-ITV introduces the sample into the MPD via electrothermal vapourization of a dry (water-free) nano- to micro- volume sample. Pneumatic nebulization, the commercially available ICP sample introduction method would extinguish the microplasma. Microplasma stability is the first issue addressed by confining the microplasma to a quartz tube (“wall-stabilized”) in hopes of a more stable MPD background emission. Once stabilized MPD conditions were found key microplasma parameters were studied including MPD power, HVac frequency, operating mode, inter-electrode distance (IED) and observation location, in hopes of improved MPD analytical performance. Microplasma excitation mechanism and maximum energy available in the microplasma for analyte are discussed. Some fundamental characteristics such as excitation temperature (Texc) and changes in atom/ion population with variation in some of the key MPD parameters were also determined.

Needle trap device (NTD) is a technique that is useful for a wide variety of applications involving the sample preparation of compounds with a wide range of chemico-physico properties, and varying volatilities. A newly designed NTD that improves the performance relative to previous NTD designs is simple to produce is developed. The NTD utilizes a side-hole needle with a modified tip to improve the sealing between the NTD and narrow neck liner of the GC injector, thereby increasing the desorption efficiency. The slurry packing method was applied, evaluated, and NTDs prepared by this method were compared to NTDs prepared using the vacuum aspiration method. NTD geometries including blunt tip with a side-hole needle, tapered tip with side-hole needle, dome tapered tip with side-hole, sliding tip with side-hole and blunt tip with no side-hole needle (expanded desorptive flow) were prepared and evaluated. Sampling performance and desorption efficiency were investigated using automated headspace extraction of benzene, toluene, ethylbenzene, p¬-xylene (BTEX), anthracene and pyrene. The tapered tip and sliding tip NTDs were found to have increased desorption efficiency. SPME and NTDs are valuable sample preparation tools for on-site analysis. Combining both extraction techniques allows for the differentiation of free and particle-bound compounds in a sample matrix. Portable GC/MS instrumentation can achieve fast separation, identification, and quantitation of samples prepared by the above techniques on-site without the need for transport to the laboratory. This minimizes the effects of volatiles lost and sample degradation during storage time. Here, SPME and tapered tip NTDs combined with portable GC/MS are used to investigate free and total emissions of BTEX and select PAHs from gasoline and diesel exhaust. Using the above optimized technologies, cigarette smoke in a smoking area where people were actively smoking and inside a smoker’s car were also investigated. Target contaminants were found in the investigated matrices at ng/mL levels.

Site quality, or the ability of land to grow trees, is an important component for identifying the most appropriate locations for establishing plantations of fast growing tree species to meet societys demands for timber and other environmental benefits. The goal of this thesis project was to predict site quality for poplars using soil and site information in Saskatchewan, Alberta and Quebec and to examine the effect of site quality on competition control in hybrid poplar plantations in Saskatchewan.<p>The first study examined factors affecting trembling aspen productivity in the boreal shield ecozone of Quebec on till and fluvial parent materials using general map data and measured soil and site information. Relationships with productivity were stronger using measured soil and site variables for individual parent materials (R2>0.6) than using general map data only (R2<0.25). Including biological variables, such as overstory species composition, had a major impact on site quality with conifer dominance negatively impacting the growth of trembling aspen.<p>The second study examined the factors affecting trembling aspen productivity in the boreal transition ecoregion of Saskatchewan on three different soil parent materials: fluvial, lacustrine and till. Relationships with productivity were stronger using soil and site variables for individual parent materials (R2 0.48-0.58) than using agricultural capability classes or other soil properties for all plots combined (R2<0.2). For fluvial and lacustrine sites, increasing clay content and nutrient availability (e.g. pH and total N) were positively related to productivity while tree productivity was negatively related to poor drainage for till sites. <p>The third study examined the factors affecting site quality for a single hybrid poplar clone in industrial plantations in Alberta at both the local scale (between plantations) and the microsite scale (within plantations). At the local scale, foliar P and Cu concentrations, soil water availability and drainage, and Ca and Mn in the C horizon were related to hybrid poplar productivity. There were also curved relationships with productivity and soil texture in the B horizon and pH of the A horizon, indicating an optimal range for poplar growth. At the microsite scale, soil texture was the best predictor of productivity with different relationships at each site depending on where the sites were in relation to the optimal soil texture.<p>The final study examined the response of hybrid poplar plantations in Saskatchewan to interspecific competition control on a range of site productivities. Competition control greatly increased tree growth with the greatest benefit being on the best quality sites. Both water and nutrients were highly competed for between trees and weeds. In the weed-free plots, tree growth was positively related to the amount of silt and clay in the soil and foliar P concentrations. This series of studies has demonstrated that it should be possible to predict poplar productivity reasonably well using only soil and site information within limited areas across Canada. However, the important drivers of productivity varied between the regions studied and between site groupings, such as by parent material, within local areas. This information can now be used to help land managers make better decisions regarding the establishment and management of plantations of fast growing tree species, notably hybrid poplar plantations.

Soil and groundwater is the final receptor environment of contamination on land, especially easy to contaminate groundwater aquifers, because of the underground environment often obscure, it is difficult to clarify the scope of pollution, in addition, the transport and chemical transformation process are also difficult to evaluate. Resulting that although consumes on huge cost and materials, and times on oil contaminated site investigation and remediation, obtaining the solution of the problem is still hard. In this study, it combines with the environmental site assessment and the triad rapid investigation, the establishment of site contamination conceptual model, the key designated contaminated area, collect samples of the implementation for laboratory analysis, Moreover, use cyclic evaluation process, continuously updated site conceptual model, to clarify the distribution of contaminated sites, impact of pollution, hydro-geological characteristics and pollution sources. It also discussed the effective reduction of pollution critical area, to obtain high-density results, in order to improve sampling and analysis to make the efficiency of the case of site investigation, and using environmental forensic techniques to determine and provide the evidence of pollution sources. ESA phase I implements the key results of the preliminary delineation of contaminated areas, soil and groundwater pollution concerns and possible sources of material. ESA phase II evaluates preliminary assessment of sites contaminated soil contamination is a high carbon number of oil and contaminants move to the surface to deeper soil 9 m at the lower, deeper pollution range is unknown. Groundwater test results garnered less than control standards, but the detection of trace gas station in MTBE, it is included in the possible sources of pollution. Taking ESA phase II assessment in a further analysis, the soil contaminants are TPHC10-C40 based, contamination depth of 8m, gas station area within the tank and pipeline testing values are low, there is no sign of oil leakage. Pollution more than 5m in depth the most serious, TPH concentrations in general are 10,000 mg/kg or more, the depth of 5m and the following have been significantly reduced, TPH concentrations than in the 5,000 mg/kg or less. Interviews showed that the specific relationship between the people, suspected underground oil refining line set 40 years ago, suspected of shipping oil from the waste obtained after the hull, after the system by then resold for profit. Identification of pollution sources than the results, TPHC10-C40 carbon number distribution or pattern of the peak are more similar to diesel. TIC illustration showed that the distillate oil mixture for two, than the peak apex, suggesting that the low-carbon should be diesel fuel, and the high-carbon would be fuel. Pr/Ph ratio than, presumably with the CPC diesel from different sources. Alkyl bicyclic sesquiterpene class fingerprint comparison results, the shape of the fingerprint sample slightly different, but the main features of the same types of compounds. Analysis of aromatic compounds, indicators showed that the samples compound ratio of methyl phenanthrene and methyl dibenzothiophene isomers, dibenzothiophene, and phenanthrene isomers are closer. Integrated fingerprint analysis (fingerprinting) results, similar to the site characteristics of pollutants, for the same pollution source. The site is semi-volatile pollutants, substances insoluble in water, more stored in the main pollution silt/clay layer, subject to geological conditions, ground remediation techniques are more difficult to grasp in the transmission path, remediation systems that require high density, break through the bottleneck transmission path, but a majority of sites on private land, during the remediation process it is difficult to obtain the burgage, therefore, it would be fit the inappropriate comprehensive ground handling. Subsequent remediation plan can be removed towards the high pollution of soil pollution, and long-term monitoring of permeable reactive barrier type with natural degradation. Recommendations for the future studies can be dust inhalation and skin contact with soil, groundwater ingestion, inhalation and skin contact exposure pathways for risk assessment, site management provided a basis for administrative control.

The development of internet is creating intense competition in social network sites nowadays. How to conduct users¡¦ loyalty to social network sites gradually becomes an important issue to operate long-term social network sites. The study attempts to examine how consumers¡¦ utilitarian value, hedonic value and social value affect their loyalty. Furthermore, this study examines whether the relationship is mediated by gender difference. The model and relationship are tested and validated by using PLS and data collected from 200 people having facebook accounts in Taiwan. The results shows that loyalty is strongly affected by utilitarian value, hedonic value and social value. We also find that the difference of gender has positive influence on hedonic value and loyalty and negative influence on social value and loyalty. The implication for research and practice are also discussed.

The objective of this longitudinal study was to study the relationship between changes in prevalence of resistant enteric bacteria associated with mean monthly doses (MMD) of various antibiotics used in each of two host species. From January 2004 – January 2007, monthly composite swine fecal samples and human wastewater samples representing various production and occupational cohorts, respectively, were collected from 19 geographically unique locations in east- and south-central Texas. Bacterial isolates cultivated on CHROMagar-E.coliTM and DifcoTM mEnterococcus (ME) were tested for susceptibility to multiple antibiotics by microbroth dilution using the SensititreTM system. The relationship between the prevalence of resistant bacteria, sampling period, and antibiotic use within each host species was assessed in a generalized linear model adjusted for the dependence of responses within location using a binomial distribution and logit link function in STATA® ver. 9.2. For the swine E. coli isolates, the relationship between tetracycline resistance and level of chlortetracycline (CTC) use in swine illustrated a dose-response relationship, with odds ratios (OR) of 1.20 and 1.81 (P < 0.05) for second- and third-level categories of MMD relative to baseline (zero-use) respectively. When considered by swine production groups, intake boar isolates had an elevated relative odds of resistance to tetracycline (OR = 1.51, P < 0.05), and the nursery units had an elevated odds (OR = 2.61, P < 0.05) of exhibiting resistance to ceftiofur, relative to pigs housed in the farrowing barns. Regarding swine Enterococci isolates, those swine from locations that utilized tylosin had an elevated OR of 3.54 (P < 0.05) of exhibiting resistance to tylosin, relative to those locations that used no tylosin. At this juncture, an apparent occupational risk of harboring tetracycline-resistant E. coli, and the apparent sparing effect (Enterococcus spp.) associated with exposure to swine production, remain unexplained. This study demonstrated that the prevalences of tetracycline- and tylosin-resistant enteric bacteria swine were dependent on CTC and tylosin use in feed, respectively. Swine production group-effects on the prevalence of tetracycline, ceftiofur, and erythromycin resistance were also important. This study provides a better understanding of the relationships between antibiotic prescribing practices at the ecologic level and the relative odds of carriage of resistant bacteria within two host species in a vertically integrated agri-food system.

Phosphotriesterase (PTE) from Pseudomonas diminuta is a zinc metalloenzyme found in soil bacteria capable of organophosphate hydrolysis at rates approaching the diffusion controlled limit. Interest in PTE for degradation of chemical warfare agents and disposal of pesticides supports the need to understand the mechanism by which it performs hydrolysis. For further mechanistic clarity, this work will provide direct confirmation of the solvent bridge identity and the protonated species resulting in loss of catalytic identity. Inhibitor and product binding to the metal center will also be addressed; as well as the evaluation of the catalytic activity of Fe(II)-substituted PTE. This work has determined that the Mn/Mn-PTE electron paramagnetic resonance (EPR) spectrum exhibits exchange coupling that is facilitated through a hydroxide bridge. Protonation of the bridging hydroxide results in the loss of the exchange coupling between the two divalent cations and the loss of catalytic activity. The reversible protonation of the bridging hydroxide has an apparent pKa of 7.3 based upon changes in the EPR spectrum of Mn/Mn-PTE with alterations in pH. The pH-rate profile for the hydrolysis of paraoxon by Mn/Mn-PTE shows the requirement of a single function group that must be unprotonated with a pKa of 7.1. The comparable pKa values are proposed to result from the protonation of the same ionizable species. The effects of inhibitor and product binding on the magnetic properties of the metal center and the hydroxyl bridge are investigated by accessing new EPR spectral features. This work concludes that the binding of inhibitor occurs at the metal center and results in an increase of non-bridged hydroxyl species. These results, in conjunction with kinetic and crystallographic data, suggest that substrate binding via the phosphoryl oxygen at the ?-metal weakens the hydroxyl bridge coordination to the ?-metal. This loss of coordination would increase the nucleophilic character of the bridge, and binding of the substrate to the metal center would result in a stronger nucleophile for hydrolysis. Lastly, Fe(II) binding and activation of apoenzyme is evaluated under anaerobic conditions. This work concludes Fe/Fe-PTE is not catalytically active, but can bind up to 2 equivalent Fe(II) ions per active site.

Recent improvements in structural genomics efforts have greatly increased the number of hypothetical proteins in the Protein Data Bank. Several computational methodologies have been developed to determine the function of these proteins but none of these methods have been able to account successfully for the diversity in the sequence and structural conformations observed in proteins that have the same function. An additional complication is the flexibility in both the protein active site and the ligand. In this dissertation, novel approaches to deal with both the ligand flexibility and the diversity in stereochemistry have been proposed. The active site analysis problem is formalized as a classification problem in which, for a given test protein, the goal is to predict the class of ligand most likely to bind the active site based on its stereochemical nature and thereby define its function. Traditional methods that have adapted a similar methodology have struggled to account for the flexibility observed in large ligands. Therefore, I propose a novel fragment-based approach to dealing with larger ligands. The advantage of the fragment-based methodology is that considering the protein-ligand interactions in a piecewise manner does not affect the active site patterns, and it also provides for a way to account for the problems associated with flexible ligands. I also propose two feature-based methodologies to account for the diversity observed in sequences and structural conformations among proteins with the same function. The feature-based methodologies provide detailed descriptions of the active site stereochemistry and are capable of identifying stereochemical patterns within the active site despite the diversity. Finally, I propose a Markov Random Field approach to combine the individual ligand fragment classifications (based on the stereochemical descriptors) into a single multi-fragment ligand class. This probabilistic framework combines the information provided by stereochemical features with the information regarding geometric constraints between ligand fragments to make a final ligand class prediction. The feature-based fragment identification methodology had an accuracy of 84% across a diverse set of ligand fragments and the mrf analysis was able to succesfully combine the various ligand fragments (identified by feature-based analysis) into one final ligand based on statistical models of ligand fragment distances. This novel approach to protein active site analysis was additionally tested on 3 proteins with very low sequence and structural similarity to other proteins in the PDB (a challenge for traditional methods) and in each of these cases, this approach successfully identified the cognate ligand. This approach addresses the two main issues that affect the accuracy of current automated methodologies in protein function assignment.

The primary objectives of this research are to identify the relation between Leadership in Energy and Environmental Design (LEED) criteria regarding sustainable site credits and the appraised value of land parcels in the City of Houston, and additionally to analyze the effects of detail components which leverage the sustainable credits regarding the Public Transportation Access (PTA) in terms of economic issues. To accomplish these objectives, the approach to estimate sustainable ratings of specific parcels using Geographic Information Systems (GIS) was established. Green construction must be one of the most powerful trends in the construction industry. One of the main concepts to underlie the basis of this green construction is sustainability. This sustainability has to be considered in the process of the site selection prior to the actual activities to construct a building. Recently, the U.S. Green Building Council (USGBC) has suggested the modified guideline with "LEED 2009 for New Construction and Major Renovations". According to this metric, it is clear that this principle endeavors to block environmental abuses related to land development or restoration projects. On the other hand, it is not easy to check the serviceability of these rules to guarantee continuous economic merit through sustainable land development or restoration encouraged by these criteria. The criteria regarding the sustainable site selection in this LEED metric are Sustainable Site Credit (SSC) #1: Site Selection, SSC #3: Brownfield, and SSC #4.1: Public Transportation Access. Linear regression methods were used for predictive analysis. In this model, the unit appraisal value of the land was used as the dependent variable to reflect the economic values of the land, and LEED-sustainable-site criteria were used as the categorical independent variables. According to statistical results, the models to predict the appraisal parcel value using sustainable site components have relatively low R-square. Moreover, SSC #1 and SSC #3 were not significant factors affecting the unit value of land. This outcome means that there are no statistically significant effects of SSC #1 and SSC #3 on parcel value. On the other hand, SSC #4.1 was highly significant. Furthermore, the detail components of SSC #4.1 regarding the bus stops and railroad stations were also significant. These results can lead to improved environmental preservation by avoiding development which is far from the PTA as well as increasing economic value while enhancing the development density near the PTA corridors. Finally, GIS was used to determine the LEED ratings of individual parcels. The methods established to do this can be applied to other projects for the other regions, or the same region at different times.