Characterization of phosphoproteins-including detection, identification of phosphoproteins and identification of phosphorylation sites-is mostly done with radiolabeling and proteomic techniques. Three main topics related to phosphoprotein characterization are included in this dissertation. First, large-scale characterization of the CHO (Chinese hamster ovary) cell phosphoproteome was done using two dimensional gel electrophoresis (2DE) separation, visualization of phosphoproteins by radiolabeling or a phosphoprotein specific dye, followed by MALDI-TOF identification. Because radiolabeling of phosphoproteins is very sensitive and straightforward to quantify, such analysis can give a clear picture of the relative phosphosphorylation of proteins present in a sample. But there are also limitations to this approach, such as the inability of 2DE to separate hydrophobic, acidic and large proteins and the poor detection limits of common protein stains such as Coomassie stain. Additionally, it is difficulty to excise the right spots for identification because of the low abundance of phosphoproteins which have been visualized by radiolabeling. Furthermore, there are problems associated with metabolic radiolabeling. A second topic of the dissertation is the development of a novel strong cation exchange monolithic column for MudPIT (multidimensional protein identification technology) and phosphopeptide isolation. This column, a poly(AMPS-co-PEGDA) monolith containing as high as 40% AMPS, has several favorable features, such as high binding capacity, extraordinarily high resolution, and high peak capacity, making it ideal for resolving complex peptide samples. Application of this novel column to isolate model phosphopeptides was shown. More general use of this column in MudPIT (strong cation exchange column followed by reverse-phased MS/MS) is probably somewhat limited, due to the hydrophobicity of the AMPS monomer. A better monolith could be obtained if a more hydrophilic monomer was used. In the third area of the dissertation, several individual protein phosphorylation sites were analyzed, employing different strategies. Phosphorylation sites of one multiply phosphorylated tryptic peptide from CK2-phosphorylated phosducin-like protein (PhLP) was well characterized using enrichment with a MonoTip® TiO Pipette Tip. Analysis of syntaxin 1a phosphorylation by AMPK (AMP-activated protein kinase) was done by peptide level mapping for potential phosphopeptides after its unsuccessful trial with enrichment using the MonoTip® TiO Pipette Tip. Several criteria such as existence of non-phosphorylated forms of potential phosphopeptides, controls and reasonable retention times were used to rule out false positives. Phosphorylation of syntaxin 1a by AMPK was narrowed down to tryptic peptide T32 with evidence from different sources. Three phosphorylation sites of syntaxin 4 by AMPK were identified within the same peptide (Q65QVTILATPLPEESMK80). Further pinpointing of phosphorylation site(s) for syntaxin 1a by AMPK and further confirmation of these phosphorylation sites in syntaxin 4 by AMPK are required in vivo. The role of phosphorylation in syntaxin 4 by AMPK is the next step toward elucidation of AMPK activation and regulation of the glucose uptake mechanism.

Deep slurry injection is a process of solid waste disposal that involves grinding the solid waste to a relatively fine-grained consistency, mixing the ground waste with water and/or other liquids to form slurry, and disposing of the slurry by pumping it down a well at a high enough pressure that fractures are created within the target formation. This thesis describes the site assessment criteria involved in selecting a suitable target reservoir for deep slurry injection. The main goals of this study are the follows: <ul> <li>Identify the geological parameters important for a prospective injection site</li> <li>Recognize the role of each parameter</li> <li>Determine the relationships among different parameters</li> <li>Design and develop a model which can assemble all the parameters into a semi-quantitative evaluation process that could allow site ranking and elimination of sites that are not suitable</li> <li>Evaluate the model against several real slurry injection cases and several prospective cases where slurry injection may take place in future</li> </ul> The quantitative and qualitative parameters that are recognized as important for making a decision regarding a target reservoir for deep slurry injection operations are permeability, porosity, depth, areal extent, thickness, mechanical strength, and compressibility of a reservoir; thickness and flow properties of the cap rock; geographical distance between an injection well and a waste source or collection centre; and, regional and detailed structural and tectonic setup of an area. Additional factors affecting the security level of a site include the details of the lithostratigraphic column overlying the target reservoir and the presence of overlying fracture blunting horizons. Each parameter is discussed in detail to determine its role in site assessment and also its relationship with other parameters. A geological assessment model is developed and is divided into two components; a decision tree and a numerical calculation system. The decision tree deals with the most critical parameters, those that render a site unsuitable or suitable, but of unspecified quality. The numerical calculation gives a score to a prospective injection site based on the rank numbers and weighting factors for the various parameters. The score for a particular site shows its favourability for the injection operation, and allows a direct comparison with other available sites. Three categories have been defined for this purpose, i. e. average, below average, and above average. A score range of 85 to 99 of 125 places a site in the ?average? category; a site will be unsuitable for injection if it belongs to the ?below average? category, i. e. if the total score is less than 85, and the best sites will generally have scores that are in the ?above average? category, with a score of 100 or higher. One may assume that for sites that fall in the ?average? category there will have to be more detailed tests and assessments. The geological assessment model is evaluated using original geological data from North America and Indonesia for sites that already have undergone deep slurry injection operations and also for some possible prospective sites. The results obtained from the model are satisfactory as they are in agreement with the empirical observations. Areas for future work consist of the writing of a computer program for the geological model, and further evaluation of the model using original data from more areas representing more diverse geology from around the world.

Deep slurry injection is a process of solid waste disposal that involves grinding the solid waste to a relatively fine-grained consistency, mixing the ground waste with water and/or other liquids to form slurry, and disposing of the slurry by pumping it down a well at a high enough pressure that fractures are created within the target formation. This thesis describes the site assessment criteria involved in selecting a suitable target reservoir for deep slurry injection. The main goals of this study are the follows: <ul> <li>Identify the geological parameters important for a prospective injection site</li> <li>Recognize the role of each parameter</li> <li>Determine the relationships among different parameters</li> <li>Design and develop a model which can assemble all the parameters into a semi-quantitative evaluation process that could allow site ranking and elimination of sites that are not suitable</li> <li>Evaluate the model against several real slurry injection cases and several prospective cases where slurry injection may take place in future</li> </ul> The quantitative and qualitative parameters that are recognized as important for making a decision regarding a target reservoir for deep slurry injection operations are permeability, porosity, depth, areal extent, thickness, mechanical strength, and compressibility of a reservoir; thickness and flow properties of the cap rock; geographical distance between an injection well and a waste source or collection centre; and, regional and detailed structural and tectonic setup of an area. Additional factors affecting the security level of a site include the details of the lithostratigraphic column overlying the target reservoir and the presence of overlying fracture blunting horizons. Each parameter is discussed in detail to determine its role in site assessment and also its relationship with other parameters. A geological assessment model is developed and is divided into two components; a decision tree and a numerical calculation system. The decision tree deals with the most critical parameters, those that render a site unsuitable or suitable, but of unspecified quality. The numerical calculation gives a score to a prospective injection site based on the rank numbers and weighting factors for the various parameters. The score for a particular site shows its favourability for the injection operation, and allows a direct comparison with other available sites. Three categories have been defined for this purpose, i. e. average, below average, and above average. A score range of 85 to 99 of 125 places a site in the ?average? category; a site will be unsuitable for injection if it belongs to the ?below average? category, i. e. if the total score is less than 85, and the best sites will generally have scores that are in the ?above average? category, with a score of 100 or higher. One may assume that for sites that fall in the ?average? category there will have to be more detailed tests and assessments. The geological assessment model is evaluated using original geological data from North America and Indonesia for sites that already have undergone deep slurry injection operations and also for some possible prospective sites. The results obtained from the model are satisfactory as they are in agreement with the empirical observations. Areas for future work consist of the writing of a computer program for the geological model, and further evaluation of the model using original data from more areas representing more diverse geology from around the world.

"SELECT CD is a site-specific, decision-support tool for selecting ecologically viable tree species, reproduction cuttings, and regeneration methods in the coastal forest (CDF, CWH, and MH zones). SELECT CD integrates information from several existing guides with new information from literature and recent research into a single, user-friendly resource. SELECT CD also includes a rich library of visuals and an illustrated glossary of technical terms."