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Quantifying above-ground biomass (AGB) and carbon sequestration has been a significant focus of attention within the UNFCCC and Kyoto Protocol for improvement of national carbon accounting systems (IPCC, 2007; UNFCCC, 2011). A multitude of research has been carried out in relatively flat and homogeneous forests (Ranson & Sun, 1994; Beaudoin et al.,1994; Kurvonen et al., 1999; Austin et al., 2003; Dimitris et al., 2005), yet forests in the highlands, which generally form heterogeneous forest cover and sparse woodlands with mountainous terrain have been largely neglected in AGB studies (Cloude et al., 2001; 2008; Lumsdon et al., 2005; 2008; Erxue et al., 2009, Tan et al., 2010; 2011a; 2011b; 2011c; 2011d). Since mountain forests constitute approximately 28% of the total global forest area (Price and Butt, 2000), a better understanding of the slope effects is of primary importance in AGB estimation. The main objective of this research is to estimate AGB in the aforementioned forest in Glen Affric, Scotland using both SAR and LiDAR data. Two types of Synthetic Aperture Radar (SAR) data were used in this research: TerraSAR-X, operating at X-band and ALOS PALSAR, operating at L-band, both are fully polarimetric. The former data was acquired on 13 April 2010 and of the latter, two scenes were acquired on 17 April 2007 and 08 June 2009. Airborne LiDAR data were acquired on 09 June 2007. Two field measurement campaigns were carried out, one of which was done from winter 2006 to spring 2007 where physical parameters of trees in 170 circular plots were measured by the Forestry Commission team. Another intensive fieldwork was organised by myself with the help of my fellow colleagues and it comprised of tree measurement in two transects of 200m x 50m at a relatively flat and dense plantation forest and 400m x 50m at hilly and sparse semi-natural forest. AGB is estimated for both the transects to investigate the effectiveness of the proposed method at plot-level. This thesis evaluates the capability of polarimetric Synthetic Aperture Radar data for AGB estimation by investigating the relationship between the SAR backscattering coefficient and AGB and also the relationship between the decomposed scattering mechanisms and AGB. Due to the terrain and heterogeneous nature of the forests, the result from the backscatter-AGB analysis show that these forests present a challenge for simple AGB estimation. As an alternative, polarimetric techniques were applied to the problem by decomposing the backscattering information into scattering mechanisms based on the approach by Yamaguchi (2005; 2006), which are then regressed to the field measured AGB. Of the two data sets, ALOS PALSAR demonstrates a better estimation capacity for AGB estimation than TerraSAR-X. The AGB estimated results from SAR data are compared with AGB derived from LiDAR data. Since tree height is often correlated with AGB (Onge et al., 2008; Gang et al., 2010), the effectiveness of the tree height retrieval from LiDAR is evaluated as an indicator of AGB. Tree delineation was performed before AGB of individual trees were calculated allometrically. Results were validated by comparison to the fieldwork data. The amount of overestimation varies across the different canopy conditions. These results give some indication of when to use LiDAR or SAR to retrieve forest AGB. LiDAR is able to estimate AGB with good accuracy and the R2 value obtained is 0.97 with RMSE of 14.81 ton/ha. The R2 and RMSE obtained for TerraSAR-X are 0.41 and 28.5 ton/ha, respectively while for ALOS PALSAR data are 0.70 and 23.6 ton/ha, respectively. While airborne LiDAR data with very accurate height measurement and consequent three-dimensional (3D) stand profiles which allows investigation into the relationship between height, number density and AGB, it's limited to small coverage area, or large areas but at large cost. ALOS PALSAR, on the other hand, can cover big coverage area but it provide a lower resolution, hence, lower estimation accuracy.

The plant hormone salicylic acid (SA) is an essential activator of plant immune responses directed against biotrophic pathogens. The transcription cofactor NPR1 (Nonexpressor of pathogenesis- related (PR) genes 1) functions to transduce the SA signal into an operational response directed to limited pathogen damage. In the absence of pathogen, NPR1 protein resides in the cytoplasm as a large molecular weight oligomer held together by disulphide bonding. Initiation of defence signalling leads to changes in intracellular redox conditions that promote NPR1 momomer release. Translocation of monomeric NPR1 to the nucleus results in the activation of over 2200 immune-related genes in Arabidopsis. NPR1 lacks a canonical DNA-binding domain but is known to perform part of its regulatory function through engagement of TGA factors (bZIP transcription factor). Induction of SA-dependent signalling is invariably associated with PR-1 gene expression and accumulation of mRNA for this gene serves as a useful marker of defence activation. However, both functional redundancy and stochastic factors limit the effectiveness of standard genetic approaches used in plant research, and thus much of the hierarchal processes surrounding NPR1-dependent gene activation are not fully understood. Using a synthetic biology approach we aim to complete exploratory work and set the foundations for the development of a yeast tool that can be used to manipulate and subsequently understand NPR1 function in relation to interacting partners and gene activation. Accordingly, using this tool we sought to create a conceptual protein circuit based on theoretical plant immunity. In completing this work we have developed a Saccharomyces cerevisiae strain that exhibits a highly oxidising intracellular redox environment. This was achieved by knocking out genes encoding S-nitrosoglutathione reductase (SFA1), flavohemoglobin (YHB1) and YAP1 (bZIP transcription factor), all important components in regulating cellular redox homeostasis and protein S-nitrosylation state in S. cerevisiae. Characterisation of this cell (designated Δsfa1yap1yhb1) reveals a high tolerance to such redox perturbations. Importantly, NPR1 is by default, assembled predominantly in the oligomeric form in this biological chassis. By activating two inducible inputs in the form of Arabidopsis S-nitrosoglutathione reductase (AtGSNOR) and Thioredoxin (AtTRXh5) which both function to promote NPR1 monomerisation, we have created a switch to selectively control NPR1 oligomer-monomer equilibrium. To complete the synthetic circuit, TGA3 was included, along with a modified yeast MEL1 promoter that has been customised to contain the TGA-responsive upstream activation sequence (termed the as-1 element) present in the promoter region of the PR-1 gene. Using FRET tools we were able to confirm nuclear interaction between monomeric NPR1 and TGA3, with this association appearing to induce as-1 element binding. However this process is not sufficient to activate a Luciferase (LUC) reporter gene, even when the GAL4 activation domain (GAL4 AD) is fused to NPR1. Ordinarily, a CUL3-dependent proteolysis-coupled transcription cycle is necessary to maintain efficient NPR1-dependent gene transcription in Arabidopsis. Although S. cerevisiae encodes an evolutionarily related CUL3 ortholog, examination by western blot demonstrates that NPR1 protein is stable in this cell, indicating an endogenous mechanism to degrade NPR1 is either not present or not functional in yeast. As such, this synthetic yeast tool represents a completely novel approach to identify missing components functioning in NPR1-mediated transcriptional regulation. Furthermore, in collaboration with a skilled bioinformatician, and using a rule-based stochastic modeling tool known as Kappa, we have been able to develop, for the first time, a preliminary mathematical simulation representative of NPR1-dependent gene activation that can be used as a foundation for future works.

The thesis summarizes a selection of my research within Synthetic Aperture Radar (SAR). Mainly the research is aimed at applying and developing signal processing methods to single channel and multi channel SAR for wideband systems. SAR systems can generate images looking very similar to optical pictures, i.e. photos, and sometimes with much finer resolution compared to optical systems orbiting Earth. SAR has also for instance been used to obtain fine resolution images of the moon, Venus and the satellites of Saturn. Other applications for SAR has is to detect changes in ice sheets and deforestation. In this thesis, SAR systems capable of very high resolution imaging are con- sidered, and data from such systems, namely the VHF system CARABAS-II and the UHF system LORA, is used. High resolution imaging in this thesis refers to high resolution with regard to wavelength, this independent of system operating frequency. Two of the topics in this thesis are related to detection and parameter estimation of moving objects in SAR, the first one using CARABAS-II data and the second with LORA data. On the CARABAS-II data, a speed estimation and refocusing method is introduced and applied to single channel CARABAS-II data. The results show good estimation accuracy as well as good ability to focus the object and suppress forest clutter by ap- plying the refocusing algorithm. The results on LORA data are satisfactory especially with regard to forest clutter suppression. The ability to detect and focus images of ships allow for surveillance of coastal areas and help in rescue of ships lost at sea. Detection and location of cars and trucks allow for traffic monitoring to obtain statistics of how many cars travel the roads and their speed. In the thesis, two more important aspects for SAR processing is presented. One paper presents windowing of UWB SAR images. A strong object such as a power line in a SAR image cause ringing on both sides of the power line. This ringing can cause a small house to be covered by these so called side lobes. Applying a window can make these side lobes in the image much suppressed, however if windowing too much, the power line will smear over the image, covering the small house. The last topic in the thesis concern with theoretical limits for measurement accuracy of parameters for a moving object in a SAR image. These parameters are position, velocity, radar cross section and phase. The theoretical expressions are verified using simulations for a single channel system for estimation accuracy of target speed and relative speed.

Class of 2012 Abstract / Specific Aims: The purpose of this study is to identify the incidence of symptoms associated after exposure to “bath salts,” a term for synthetic cathinones in Arizona. Methods: This is a retrospective chart review of reported exposures to synthetic cathinones to the Arizona Poison and Drug Information Center and the Banner Good Samaritan Poison and Drug Information Center. Main Results: There were 306 cases of synthetic cathinone exposures reviewed and 76.5% were males (n=234) and 23.5% were females (n=72). They were ingested, inhaled, snorted, or injected. The mean age of exposure to synthetic cathinones was 29 years old. The most common symptoms included agitation (48.7%), hallucinations (27.1%), confusion (17.6%), hypertension (21.9%), tachycardia (50.6%), CK elevation (17.3%) and chest pain (9.5%). Less frequent symptoms exhibited in synthetic cathinone abuse included other CNS effects, gastrointestinal symptoms, muscular dysfunction, visual disturbances, and respiratory issues. Conclusions: The symptoms exhibited after exposure to synthetic cathinones were mainly neurologic and cardiovascular. In most cases, symptoms were effectively resolved within 24 to 48 hours after treatment with intravenous fluids and benzodiazepines. In some reports, patients were also given oxygen, anti-emetics, sedatives and anti-psychotic medications. Medical outcomes included major (1.6%), moderate (42.2%) and minor effects (26.1%) while 92 patients were lost to follow-up.

The purpose of this research has been to explore the native monorhamnolipid (mRL) mixture produced by Pseudomonas aeruginosa ATCC 9027, as well as newly- synthesized monorhamnolipid diastereomers (R,R)-Rha-C10-C10, (R,S)-Rha-C10-C10, (S,S)-Rha-C10-C10 and (S,R)-Rha-C10-C10, to understand their aggregation and phase behavior in aqueous solution. This work is in response to the consideration that biosurfactants offer a "greener" alternative to conventional surfactants. Relationships between chemical structure of the diastereomers and surface activity were studied using surface tension measurements. It was found that the critical aggregation concentration (CAC) values are lower for deprotonated (R,S)-Rha-C10-C10 and higher for protonated (R,S)-Rha-C10-C10 compared to the other diastereomers or the native mRL mixture. Furthermore, the 1:1:1:1 diastereomeric mixture has the overall lowest cross-sectional area for deprotonated rhamnolipids. Dynamic light scattering (DLS) was used to study the hydrodynamic radii (Rh) of the mRL aggregates and the four diastereomers in aqueous solution. In all five surfactants studied, each observed at pH 8.0 and 4.0, three aggregate populations were observed. For all deprotonated rhamnolipids the micelle, at a hydrodynamic radius of ~2 nm, was found to be in the highest abundance where the two lower abundant other population take on a lamellar aggregate structure. Data to support this were collected using fluorescence probing techniques. For the surfactants in the protonated state, pH 4.0, it was found that all form primarily lamellar structures, also confirmed using fluorescence probing. The average aggregation numbers (Nagg) of the micelles for the deprotonated native mRL mixture and the four diastereomers were studied using steady-state and time-resolved fluorescence quenching measurements. Somewhat unexpectedly, the Nagg values were observed to be a strong function of the rhamnolipid concentration for all systems. At low concentrations, pre-micellar aggregates with aggregation numbers too small for micelles were observed. A critical concentration is identified at which a critical aggregation number is defined; this is proposed to be the smallest fully-formed micelle in solution with values of ~25-30 molecules/micelle for the native mRL mixture and all four diastereomers. Thus, the aggregation properties of the native mRL mixture and the four diastereomers are generally similar at this critical concentration. However, the increase in aggregation number above this critical point varies for all the surfactants, where the (R,R)-Rha-C10-C10 diastereomer has the greatest increase in monomers with concentration and the (S,S) and (R,S) diastereomers have the lowest. The increased observed aggregation number is consistent with the computational work showing increased growth with concentration for the deprotonated rhamnolipid micelles. Furthermore, these computations have confirmed the ability of protonated rhamnolipids to form lamellar structures in solution. Fluorescence probing work was also used to study rhamnolipid phase behavior as a function of varying solution conditions, such as ionic strength, solution pH, surfactant concentration, and temperature. Steady-state fluorescence methods are utilized to probe the surfactant microenvironment using the polarity-sensitive dyes prodan and laurdan. By dissolving the dye within the rhamnolipid aggregates and observing their solvatochromic behavior, all surfactants studied are known to form more micellar aggregates at high pH and low surfactant concentration, whereas elongation of the micelle is observed at low pH and moderate to high surfactant concentration.

Two highly homologous synthetic peptides MLC(3-13) (K-R-A-K-A-K-T-TK-K-R-G) and MLC(5-13) (A-K-A-K-T-T-K-K-R-G) corresponding to the amino terminal amino acid sequence of smooth muscle myosin light chain were utilized as substrates for protein kinase C purified from murine lymphosarcoma tumors to determine the role of the primary amino acid sequence of protein kinase C substrates in defining the lipid (phosphatidyl serine and diacylglycerol) requirements for the activation of the enzyme. Removal of the basic residues lysine and arginine from the amino terminus of MLC(3-13) did not have a significant effect on the Ka value of diacylglycerol. The binding of effector to calcium-protein kinase C appears to be random since binding of one effector did not block the binding of the other.

Current biofuel production methods use engineered bacteria to break down cellulose and convert it to biofuel. However, this production is limited by the toxicity of the biofuel to the organism that is producing it. Therefore, to increase yields, microbial biofuel tolerance must be increased. Tolerant strains of bacteria use a wide range of mechanisms to counteract the detrimental effects of toxic solvents. Previous research demonstrates that efflux pumps are effective at increasing tolerance to various biofuels. However, when overexpressed, efflux pumps burden cells, which hinders growth and slows biofuel production. Therefore, the toxicity of the biofuel must be balanced with the toxicity of pump overexpression. We have developed a mathematical model and experimentally characterized parts for a synthetic feedback loop to control efflux pump expression so that it is proportional to the concentration of biofuel present. In this way, the biofuel production rate will be maximal when the concentration of biofuel is low because the cell does not expend energy expressing efflux pumps when they are not needed. Additionally, the microbe is able to adapt to toxic conditions by triggering the expression of efflux pumps, which allows it to continue biofuel production. The mathematical model shows that this feedback loop increases biofuel production relative to a model that expresses efflux pumps at a constant level by delaying pump expression until it is needed. This result is more pronounced when there is variability in biofuel production rates because the system can use feedback to adjust to the actual production rate. To complement the mathematical model, we also constructed a whole cell biosensor that responds to biofuel by expressing a fluorescent reporter protein from a promoter under the control of the sensor.

In the past ten years, synthetic cannabinoids (SC) have emerged as drugs of abuse. Unlike D9-tetrahydrocannabinol (THC), many SCs are associated with serious health complications and death. One way in which THC and SCs differ lies with their enhanced potency and efficacy at the CB1 receptor. No current methods exist to measure efficacy at the CB1 receptor in vivo, and the abuse-related properties of SC cannabinoids are not well explored. Here, we utilized CB1 wild type (WT), heterozygous (HET), and knockout (KO) mice. By employing CB1 ligands which differ in efficacy we have developed a method to explore the relationship between efficacy and the ability to produce cannabimimetic (catalepsy, hypothermia, and antinociception) effects when CB1 expression was reduced by half. Additionally, the intracranial self-stimulation procedure (ICSS) was utilized to investigate the effects of enhanced efficacy at CB1 upon reward processes using representative SC CP55,940. As predicted, the potency shift between WT and HET mice inversely correlated with the efficacy of the test drug for both hypothermia and antinociception, but not catalepsy. This efficacy stratification was correlated with the agonist-stimulated [35S]GTPgS binding assay, demonstrating this model as an effective tool to ascertain in vivo efficacy differences at CB1. In ICSS, CP55,940 elicited only rate-decreasing effects acutely, although tolerance developed following repeated dosing, with no evidence for spontaneous or rimonabant-precipitated withdrawal. Together, these data indicate that highly efficacious cannabinoid ligands require few receptors to produce cannabimimetic effects, and that the model provides an effective means to quickly ascertain differences in efficacy.

A variety of novel cage-functionalized pyridyl containing crown ethers have been prepared for use in selective alkali metal complexation studies. A highly preorganized, cage-functionalized cryptand also has been designed and has been synthesized for use as a selective Li+ complexant. The alkali metal picrate extraction profiles of these cage-functionalized crown ethers also have been studied. Novel cage-functionalized diazacrown ethers have been prepared for selective alkali metal complexation studies. Alkali metal picrate extraction experiments have been performed by using this new class of synthetic ionophores to investigate the effects of cage-annulation and the influence of N-pivot lariat sidearms upon their resulting complexation properties. Novel pyridyl containing calix[4]arene receptors were prepared. Analysis of their respective 1H NMR and 13C NMR spectra suggests that calix[4]arene moieties in the ligand occupy the cone conformation. The complexation properties of these host molecules were estimated by performing a series of alkali metal picrate extraction experiments. An optically active cage-functionalized crown ether which contains a binaphthyl moiety as the chiral unit was prepared. The ability of the resulting optically active crown ether to distinguish between enantiomers of guest ammonium ions (i.e., phenylethylamonium and phenylglycinate salts) in transport experiments was investigated. Hexacyclo[11.2.1.02,12.05,10.05,15.010,14]hexadeca-6,8-diene-4,11-dione was prepared from hexacyclo[7.4.2.01,9.03,7.04,14.06,15] pentadeca-10,12-diene-2,8-dione. Unanticipated but remarkable acid and base promoted rearrangements of this new cage dione to novel polycyclic systems were observed and subsequently were investigated. The structures of the new systems thereby obtained were determined unequivocally by application of X-ray crystallographic methods. It is noteworthy that the reactions reported herein each provide the corresponding rearranged product in high yield in a single synthetic step. Pi-facial and regioselectivity in the thermal Diels-Alder cycloaddition between hexacyclo[11.2.1.02,12.05,10.05,15.010,14]hexadeca-6,8-diene- 4,11-dione and ethyl propiolate have been explored. This reaction proceeds via stereospecific approach of the dienophile toward the syn face of the diene p -system. However, [4+2]cycloaddition proceeds with only modest proximal/distal regioselectivity. The structure of the minor reaction product was established unequivocally via application of X-ray crystallographic techniques.