Dissertations / Theses on the topic 'Soil sciences not elsewhere classified'

Irish agriculture is becoming increasingly regulated, with restrictions on fertiliser application rates and stocking rates to reduce nitrate (NO₀⁻) leaching losses. However these regulations have been, to date, based on minimal field research. The purpose of this study was to determine the actual leaching losses of nitrate from Irish dairy pasture at a range of stocking rates, and to investigate the effectiveness of the nitrification inhibitor DCD at reducing nitrate leaching losses where these are deemed excessive. In grazed pastures, a major source of leached nitrate is the urine patch, where a high rate of N is applied in one application. This trial recorded the losses from urine and non-urine areas of pasture separately. Nitrate leaching losses from three soils were recorded using lysimeters at Johnstown Castle, Co. Wexford, over two years. Total nitrate losses were higher from the freely drained Clonakilty and Elton soils than from the heavy Rathangan soil. Mean nitrate losses from urine patches ranged from 16 - 233 kg nitrate-N / ha⁻¹, and were reduced by up to 53% when DCD was applied. DCD also reduced peak and mean nitrate-N concentrations in many cases. In addition, DCD halved the nitrous oxide (N₂O) emission factor on the Rathangan soil, caused increases in pasture N content, and increased herbage yield in some treatments. The distribution of urine patches under dairy grazing was recorded using GPS at Kilworth, Co. Cork. Cows were also found to deposit 0.359 urine patches per grazing hour. A model was produced to predict field-scale nitrate leaching losses from dairy pasture at a range of stocking rates. At 2.94 cows per hectare, the highest stocking rate, annual field N loss was below 34 kg nitrate-N ha⁻¹, mean drainage N concentrations were below 5.65 mg nitrate-N L⁻¹ (the EU drinking water guideline value), and the worst-case-scenario autumn peak concentration did not exceed 21.55 mg nitrate-N L⁻¹ (above the EU Maximum Allowable Concentration (MAC) but below the World Health Organisation (WHO) drinking water limit). DCD reduced total annual field N loss by 21% (a conservative estimate), and also reduced mean and peak nitrate concentrations. Provided fertiliser application rates are at or below 291 kg N ha⁻¹, and based on current legislative values for drinking water quality, this trial does not support any blanket restrictions on the stocking rate of Irish dairy farms. However where particularly high water quality is required, DCD shows potential as a useful tool to achieve low nitrate concentrations.

In today’s world, antimicrobial resistance is one of the biggest global health issues that mankind is facing. This most effective way to ensure a wound does not become infected is through cleanliness and continued disinfection of the wound site. There is a lack of new antimicrobial drugs coming to the market due to economical and clinical reasons, this is evident in Lord O’Neill’s 2016 report and is addressed by Professor Dame Sally Davies in Parliament, (“We have reached a critical point and must act now on a global scale to slow down antimicrobial resistance”2). Prescription drugs have led to this epidemic that was highlighted by O’Neill. The latest report (2016) by O’Neill states, it is critical to improve sanitation and hygiene, refrain from overusing antibiotics in agriculture and the environment as well as introducing rapid diagnostics and vaccines3. This is leading to the need for photodynamic antimicrobial chemotherapy (PACT) that involves the use of a reactive oxygen species (ROS), photosensitiser, and light to cause microbial death. PACT is a treatment for resistant and non-resistant pathogens that is included in the treatment of multidrug resistant infections. The approach is to use novel antimicrobial drugs topically, avoiding systemic photo-toxicity, thus leading itself towards topical infection control. Herein, we report the development of a range of novel photosensitisers based on the second generation photodynamic therapeutic dyes (PDT) that are based on the tricyclic isoalloxazine structure of riboflavin, vitamin B2. Photosensitisers were synthesised using similar strategies to the isoalloxazine for a number of reasons: e.g. photoactivity and capability of degradation. In order to investigate which photosensitisers gave the highest reactive oxygen yield, functional group changes were made on the N-phenyl ring by substituting a range of electron withdrawing/donating substituents at different positions (ortho, meta, para). The free amide moiety was used to attach the photosensitiser to a solid support that would act as proof of principal of a photosensitiser attached to a bandage. These dyes show a phototherapeutic response via a Type I and II mechanism upon illumination by light of a selected wavelength. The mechanisms produce highly toxic oxygen-species, such as radical production via Type I pathway and singlet oxygen generation by Type II, thus causing terminal damage to microbes in a short time period. The synthesised photosensitisers are illuminated using blue light (440 - 490 nm) and white light in order to monitor and compare the singlet oxygen and radical yields generated as they absorb approximately at 440 nm, thus blue light being ideal for irradiation. The outstanding singlet oxygen result generated by compound 12c of 172% and a radical production by 11c of 227% show promising generators of cytotoxic species, resulting in microbial death. The synthesised photosensitisers have been tested against two opportunistic microbes (Gram positive and Gram negative bacteria; Staphylococcus aureus (S. aureus), and Escherichia coli (E.coli). They have proven to be problematic from its presence within the healthcare system especially when found on surgical site infections. From the statistics generated for the National Health Service (NHS) in the UK we can see that 52.4 % of S. aureus, and 43.1 % E.coli originates within the hospital environment. Antimicrobial activity was observed for several compounds under different light regimes on and off the solid support. As a result, the best observed MIC value of 0.25 mM/mL was achieved for S. aureus in darkness and in blue light without the polymer support. Additionally, when these compounds were linked to a polymer support (mimicking a bandage), antimicrobial activity was retained when irradiated using blue light at 1.0 mM/mL. These results show potential towards the next generation of antimicrobial disinfection agents. In time, these compounds could be integrated into the healthcare system for use as a new generation of self- cleaning bandages towards post-operative wound disinfection rather than employing front line antimicrobials. This is a moot subject under review in parliament and former UK prime minister has highlighted the concern. In a statement recently released, he states “If we fail to act, we are looking at an almost unthinkable scenario where antibiotics no longer work and we are cast back into the dark ages of medicine" – David Cameron, UK Prime Minister2.

Stroke is the third leading cause of death in the western world, and the primary cause of adult disability. There is a great need for methods to identify patients at risk of stroke and decide appropriate treatment. The main criterion for identifying patients at risk of stroke is the percentage of the narrowing in the carotid arteries, which lead blood from the heart to the brain, which currently is quantified manually. This project is in collaboration with Blackpool Victoria Hospital and Christies Hospital in Manchester. The aim of this project is to develop software methods to improve computer-assisted carotid artery stenosis measurement based on Magnetic Resonance Images. A methodology is therefore presented, based on 3D geometry extracted from Contract-Enhanced MR Angiograms, to identify and segment the internal carotid arteries for stenosis quantification. The MRA data volume is initially automatically reduced, by locating the carotid arteries and creating two volumes of interest, each including a single set of carotids (either left or right). The artery of interest (Internal Carotid Artery - ICA) is identified in each sub-volume automatically, by tracking the carotid bifurcation and selecting the artery branch with no further arterial branches. The central axis of the ICA is consequently determined by calculating and connecting together the centres of gravity (centroids) of the 2D contours of the carotid in the axial plane. Segmentation of the ICA is carried out, perpendicular to the central axis, by applying adaptive thresholds along the ICA central axis based on local image characteristics. Hence, the cross-sectional area of the segmented ICA is then measured at different points along the vessel. The most stenotic area is identified, and a reference region is manually selected. The degree of stenosis is then quantified based on the reference and stenosed area measurements, according to the NASCET criterion. This provides a fully automated methodology to locate, identify, and measure the internal carotid stenosis. It is the first time that such complete methodology that covers the processing of the MRI data until the stenosis measurement is taken is developed and is fully automatic. The segmentation results are thoroughly evaluated against the manual delineations of two clinical experts (each performed the delineations twice), and against two popular segmentation techniques. The results were found successful and perform better than manual measurements and other current techniques. They present smaller variability than manual measurements and are able to deal with irregularities in the arterial structure, where other computerised techniques fail. The suggested methodologies seem promising and able to improve considerably both current clinical practice and other existing methodologies.

There are currently several evaluation methods suited to children within the Child-Computer Interaction (CCI) community. However, these methods are user based leaving a gap in inspection method suited to children, that is, where children will act as the inspection method evaluators. This research focused on how to design an effective and easy to use inspection method where children will perform the evaluation based on their values. To ensure that the above is met, a user centred approach and a mixed methodology was explored and finally resulted in the creation of the Inspection Method for Children (IMCH) with an accompanying guideline. This six stages method could be used by CCI researchers as a guide to develop similar methods for children, by industries to perform inspection method evaluation with children on technologies designed for children and could be used by designers to gather design criteria for children’s technology. The process undertaken within this research to develop the new method is also novel and could be adapted by new and old researchers when adapting method to suit children. Future work will focus on carrying out evaluation with wider age range of children in the method to ensure suitability of the method for more children. Comparative studies of the method with other usability method to determine the effectiveness of the method and as a refinement process to produce a validated and refined IMCH method.

The use of lipid profiles from the immobilised alga Selenastrum capricornuizim was investigated as a potential indicator of heavy metal pollution in freshwater environments. The toxicity of Cu", Zn 2 and Cd2t on algal growth was determined and the effective concentration inhibiting specific growth rate by 50 % (EC5 0) for each metal was found to be 124 pM Cu, 20 pM Zn and 5.7 pM Cd respectively. The Cu 24 EC50 value for immobilised cells was also shown to be 124 j.tM, suggesting that Cu exhibits similar toxic effects on growth in both free and immobilised cells. Studies of the effects of temperature and heavy metal exposure (Cu21, Zn 2 and Cd2 +) on S. caprzcornutum demonstrated that these factors altered the fatty acid and free sterol composition of free algal cells in batch culture. A shift in temperature from 25°C to 10°C led to an increase in the relative proportion of oleate and decrease in linoleate and parinate (18:4), together with a significant increase in the composition of ergostenol. Exposure to heavy metal ions led to an increase in oleate (with all three metals) and altered relative proportions of linoleate and parinate (changes being metal specific). Metal ion treatment also increased a22 desaturation of chondrillasterol. This characteristic lipid signature when S. capricornutum was exposed to heavy metal ions was significantly different from changes associated with other environmental factors. These changes in lipid composition upon heavy metal treatment were also observed during exposure of S. capricornuiwn to lower metal concentrations typically found in polluted environments. Studies of cells immobilised within alginate beads showed that gel confinement significantly affected the biochemistry and physiology of algal cells, with a reduction in growth rate and final cells numbers. Scanning electron microscopy demonstrated that growth was mainly limited to the bead periphery. Immobilisation altered the lipid of composition of cells as a consequence of alterations in membrane fluidity and membrane disruption. The Cu uptake from solution was greater in immobilised cells than free cells, thus gel confinement did not confer any protection to cells. The characteristic and significant changes within the lipid composition of free cells with Cu treatment were similarly observed in immobilised cells but were only apparent at 124 pM Cu. Thus lipid profiles, especially sterol composition of immobilised algal cells, may potentially be utilised as sensitive and novel indicators of heavy metal pollution in freshwater environments.

Despite improved knowledge and advanced treatments of high-grade gliomas, the overall survival rate of glioma patients remains low due to the recurrences and locations of the tumour. Evidence shows that the existence of a subpopulation of cells - cancer stem cells (CSCs) may be the major obstacle in treating gliomas. CD133 and nestin have been suggested as the markers of CSCs and natural stem cells. The primary focus of this study was to identify CD133+/nestin+ stem-like cells and discover their association with multidrug resistance (MDR) related genes, i.e. multiple drug resistance I (mdrl) gene and anti-apoptotic gene (bcl-2) in human glioma compared to normal brain tissues and cell lines. Glioma and normal astrocyte cell lines have been employed for CD133 isolating purposes to characterise the association with MDR related genotype and phenotype. The chemosensitivity of the isolated CD 133 population was investigated using chemosensitivity assay. Meanwhile, a serum deprivation method was established in this study to enrich and select CD 133+ CSCs in a glioma (GOS-3) cell line. As a secondary focus of this project, the possibility of immortalisation enzyme hTERT being a discriminative masker between normal and cancer brain stem cells and the transcriptional correlation between cd133 and bmi-lIc-myc oncogenes were investigated. For the first time, findings of the current study demonstrated that 1) there was an evident increase of CD133 gene expression in glioma compared to normal brain tissues where the latter expressed low levels of CD133, P-gp and Bcl-2 than glioma tissues, with an exception of nestin expression, 2) serum deprivation enriched CD133 expression and demonstrated a direct coexpression between CD133 and drug resistance in GOS-3 cells, 3) hTERT may not be a discriminative marker for normal and cancer brain stem cells, 4) although there was a strong transcriptional association between bmil and cmyc, there was an inverse transcriptional association between these genes and cd133 in serum deprived glioma cells, suggesting that bmil may not be essential for the maintenance of glioma stem cells, and 5) CD133+ glioma and normal brain cells showed a significantly high resistance towards chemotherapeutic drugs compared to the autologous CD133- cells. In conclusion, an improved understanding of molecules contributing to the maintenance of CSCs may lead to a combined treatment, targeting both CSCs and their protective MDR phenotypes leading eventually to attractive strategies for the treatment of gliomas.

In the mammal, anaesthetics are known to act via two distinct mechanisms, either increasing inhibition via GABAA receptors (eg. Na-thiopentone) or decreasing excitation via NIvIDA receptors (eg. ketamine). The aim of this thesis is to investigate the effects of both increased inhibition and decreased excitation at the synaptic level within an invertebrate model system, something which cannot readily be done in vertebrate systems. This was achieved by carrying out experiments using both the above mentioned anaesthetics on the whole animal, isolated brain and cultured neurons. In invertebrates it has been shown that GABA and Glutamate can be both excitatory and inhibitory, and injection of GABA into Lymnaea has been shown to result in behavioural changes in feeding, locomotion, escape reactions, male mating and respiration. Injection of Na-thiopentone into the whole animal was carried out in this investigation, in order to establish the anaesthetic response of the animal model to this barbiturate. The presence of gamma-aminobutyric acid (GABA) receptors has been demonstrated in a respiratory interneuron (RPeD1) both electrophysiologically and via molecular techniques, however inmiunostaining has proved negative in RPeD1 and follower cells VD2/3 (unidirectional excitatory synapse) and VD4 (mutual inhibitory synapse). This suggests that these neurons are not themselves GABAergic, although this investigation shows the responses of these neurons to bath and direct application of GABA. Na-thiopentone did not reliably anaesthetise Lymnaea upon injection into the sole of the foot, suggesting that Na-thiopentone binds to proteins within the snail, andlor has a low affininty for the GABAA receptor in Lymnaea. Other anaesthetic studies using propofol and ketaniine have also demonstrated a lack of anaesthetic response. RPeD1 hyperpolarised and became quiescent in response to the application of high concentrations of GABA (10 3-104M), however at lower doses (1O 8-1O 5M), no effect was observed (p < 0.05). Under these conditions simultaneous recordings from VD4 showed hyperpolarisation in response to the application of GABA, whereas VD2 and VD3 exhibited excitatory responses. Presynaptic picoinjection of GABA also resulted in hyperpolarisation and quiescence in RJeD1, but the simultaneous response in VD3 was not observed. Postsynaptic application of GABA directly to 'VD2, and VD4 however, resulted in responses similar to those seen in the whole brain. VD2 and 3 also receive input 2, which hyperpolarises RPeD1 and elicits an excitatory EPSP in VD2 and 3 as this is similar to the response observed in this experiment it is possible that the effects of input 2 on RPeD1 and VD2 & 3 are mediated by GABA. As RPeDI does not stain positively for GABA and hyperpolarises in response to the drug, it seems unlikely that the postsynaptie effects are due to presynaptic release of GABA. RPeD1 has been shown to form reciprocal synapses with VD4 both in vivo and in vitro. When perfused with GABA (lmJ'i4), both cells hyperpolarised reversibly. The postsynaptic response could be due to the action of GABA presynaptically inhibiting RPeDI, or directly on postsynaptic GABA receptors. However VD4 forms connections with other cells in the brain such as input 3 which may also have resulted in this inhibitory response. RPeD1 would however have received a simultaneous excitatory input from this interneuron. Attempts were made to establish the nature of the RPeD1JVD4 synapse in these experiments, but no synapses were evident. These experiments therefore confirm the presence of GABA receptors in RPeD1 and suggest theft presence in VD2, and VD4. This investigation confirms the findings of previous studies, that injection and bath perfusion of barbiturates does not lead to responses in Lymnaea comparable to that of the mammal. In addition to it's main target site, ketamine (a frequently used intravenous anaesthetic) has also been shown to act at cholinergic receptors. The effects of ketamine on learning and memory and apoptosis in the mammalian CNS are well recognised. Within the Lymnaea CNS, VD4 and LPeD1 form a unidirectional excitatory cholinergic synapse, and this was chosen to investigate the effects of ketamine on excitatory synaptic transmission, short term potentiation and synapse formation in the invertebrate animal model. Ketamine decreased synaptic transmission between VD4 and LPeD1 in a concentration dependent manner, but did not significantly affect short term synaptic plasticity (pc0.05). While neurite outgrowth remained extensive, actual sprouting was diminished by all doses of ketamine. Cells exhibited extensive veiling, which was not present in control cells. Percentage chemical synapse formation was reduced by all doses of ketamine, and in some cases inappropriate inhibitory chemical synapses were formed. Furthermore acute, clinically relevant levels of ketamine reduce excitatory cholinergic transmission between VD4 and LPeD1, but short term plasticity is unaffected. Nerve regeneration was seriously compromised, and formation of appropriate chemical synapses greatly reduced. This data has serious implications for the clinical - use of ketamine, particularly in pregnant women, children or critical care patients where nerve regeneration and synapse formation are of great importance and long term exposure common practice. In conclusion, this work supports that of other studies which have showed that invertebrates appear to be relatively insensitive to barbiturates, whereas ketamine appears to effect excitation in a manner similar to that in the mammal.

Antiulcer agents, notably inhibitors of gastric acid secretion, have been the most successful category of drugs to be discovered in recent years; and moreover, there are currently four such agents in the world list of top 25 best selling drugs. Histamine H2 antagonists have been the number one selling pharmaceutical product for more than a decade and inhibitors of the parietal cell HIC-ATPase, so called "proton pump inhibitors" (PPI), look set to continue this success. The proposed study was designed to establish the relative efficacy and mechanisms of action of three novel agents using both in vitro and in vivo models. The three compounds namely AG-1749 (Lansoprazole), PD-136450 and transforming growth factor alpha (TGF(x) were studied to evaluate their antisecretory and antiulccr activities. Lansoprazole, the second PPI to be developed for clinical use, is a non-competitive inhibitor of the H1C-ATPase and has recently been launched in a number of countries. PD-136450 is a competitive antagonist of central and peripheral cholecystokinin-B (CCK-B) receptors (gastrin receptor) and it under clinical development as an anxiolytic but which has actions on the stomach and pancreas. Anxiolytic drug is otherwise known as anti-anxiety drugs, which are used to treat anxiety disorders, like depression, panic disorders, phobias and many personality disorders. TOFu is a polypeptide growth factor, which acts at the EGF receptor and displays potent mitogenic and antisecretory activity. The initial study deals with the comparison of the three compounds with omeprazole and ranitidine in terms of their ability to inhibit acid secretion and their activity in a range of experimental ulcer models. Potency, duration of action and activity against a range of stimulants of acid secretion (histamine, pentagastrin and basal) was determined in anaesthetized rat models by establishing dose-response relationships. The compounds represent a spectrum of activities in as much as lansoprazole is a potent, long acting inhibitor, PD-136450 is an orally active but selective inhibitor, while TOFu has a very short duration and is only active after parenteral administration. In a view to find out the mechanism of action of these drugs on gastric acid secretion, isolated gastric glands from rabbits were employed as an in vitro technique using radiolabeled 14C-aminopyrine as a marker. The results show that lansoprazole was the most potent antisecretory agent compared to other two drugs. The second phase of the study deals with the activity of the three compounds against gastric ulcers induced by acid hypersecretion, indomethacin and stress. This study enabled us to assess the extent to which antisecretory activity per se compared with other actions such as wound healing (TGFa) or anxiolytic activity (PD-136450) contribute to ulcer healing. As other workers already established that prostaglandins and nitric oxide are involved in the cytoprotective activity, the present study investigated the influence of prostaglandin and nitric oxide by using indomethacin and L-NAME pretreatment on the cytoprotective activity of lansoprazole, PD-136450 and TGFcz. Moreover, the three drugs were tested for their activities on the mucus and bicarbonate production in the stomach. It was found that lansoprazole and TGFc increased the gastric mucus secretion while PD-136450 did not show any change. Moreover it was evidenced from this study that the protective activity of PD-136450 is associated with the influence of bicarbonate secretion from the pancreas. In conclusion, the results of this study have indicated that lansoprazole, PD- 136450 and TGFct are potent antisecretory and antiulcer agents which have great therapeutic importance.

Mature skeletal muscle fibres can be classified as type I, type IIa, type IIx or type IIb fibres according to the myosin heavy chain (MHC) isoform that they express. More broadly, type I fibres are classified as slow fibres and type IIa, IIx and IIb fibres as fast fibres. However, the phenotype of an adult skeletal muscle fibre is not fixed: it displays plasticity being capable of adapting to changing activity and loading levels by either transition towards a slower phenotype or transition towards a faster phenotype. Overall, the aims of these studies were to further investigate and define the signal transduction pathways implicated in the control of skeletal muscle fibre phenotype. The ability of a fast muscle to undergo a transition towards a slower phenotype in response to chronic low-frequency stimulation (CLFS) was assessed, via metabolic enzyme activity assays and NADH-TR staining, following blockade of the calcineurin signalling pathway. Metabolic enzyme assays and northern blots were employed to assess the changes in enzyme activities and MEC isoform expression levels following blockade of the calcineurin and ERK1/2 signalling pathways in primary cultures of rat myotubes. Differences in the levels of various signal transduction proteins/transcription factors between slow and fast muscle were investigated using western blotting. The nuclear translocation kinetics of NFAT and NF-κB in response to treatment with the calcium ionophore A23187 were investigated in L6 myotubes using immunocytochernistry. Calcineurin blockade using cyclosporin A failed to prevent a decrease in lactate dehydrogenase activity and an increase in NADH-TR staining intensity, both characteristics of a transition towards a slower phenotype, following CLFS of the fast rat tibialis anterior muscle. Blockade of the ERK1/2 pathway in primary cultures of rat myotubes using U0126 significantly decreased MHC Iβ mRNA levels and significantly increased MIHC IIx, MEC IIb and perinatal MHC mRNA levels. Calcineurin blockade significantly decreased MHC Iβ and embryonal mRNA levels and significantly increased MHC IIx mRNA levels. Calcineurin blockade also significantly increased the activities of lactate dehydrogenase and creatine kinase while ERK1/2 blockade significantly increased the activities of lactate dehydrogenase, creatine kinase, hexokinase, malate dehydrogenase and β-hydroxyacyl-CoA deydrogenase. ERK1/2 and NF-κB levels were found to be higher in slow muscle compared to fast muscle while calcineurin and p38α,β levels were higher in fast muscle compared to slow muscle. No nuclear translocation of NF-κB and only limited evidence for NFAT nuclear translocation was seen in L6 myotubes following treatment with A23187. Overall these studies further characterize the roles of the ERK1/2 and calcineurin pathways in the regulation of muscle phenotype suggesting that each pathway controls some, but not all, of the genes that are differentially expressed between slow and fast muscle fibres. Western blotting suggests further signal transduction protein/transcription factor targets, the functions of which may be explored in the future.

The problem of sediment transport and sedimentation in estuaries is examined in relation to the Boyne Estuary situated on the Central Queensland Coast. Bottom material characteristics are examined and the most appropriate formulae for prediction of sediment transport are identified.. Estuaries are natural resources that play an important role in the economic and social development of nations. They offer habitat for fish, sites for harbours, industries, and recreational activities. Sediment transport into estuaries, and the subsequent shoaling of estuaries are important estuarine processes that impact upon the physical condition (shape, depth etc) of the estuary, and therefore the uses to which the estuary can be put. As such, estuaries represent important and complex engineering problems. The sediment transport aspect of these estuarine processes is examined in this thesis with a view to quantifying the sediment transport rate in the Boyne Estuary on the Central Queensland coast of Australia. The estuary was characterised into five distinct zones using the particle size distribution of the bottom materiaL A null point, at which the velocity of the river current is effectively balanced by the velocity of the incoming tidal and coastal current was identified in one of the five zones. Analyses of the sediment transport rate were carried out using the depth of flow, mean velocity of flow, bottom roughness and characteristics of the bottom material ofthe Boyne Estuary. Sediment transport formulae reported in the literature are reviewed for this purpose with six formulae, namely, the Ackers-White formula, the Engelund-Hansen formula, the Inglis-Lacey formula, the Van Rijn formula, the Ranga Raju formula, and the Zanke formula, being selected for detailed study. Three of the six formulae (the Van Rijn formula, the Ranga Raju formula, and the Zanke formula) predict the components of the total sediment transport, namely, the bed load transport, and suspended load transport separately. The other three formulae predict the total sediment transport without any detail on the components. Wash load transport is not considered in any of the formulae. The Van Rijn formula was selected as the reference sediment transport formula and three other sediment transport formulae, namely, the Ackers-White, the Engelund-Hansen, and the Inglis-Lacey, that predict close results with the reference formula were found to be suitable for the evaluation of sedimenttransport rate in the Boyne Estuary.

In this thesis we investigate how modern artificial intelligent techniques, namely the genetic algorithm /evolutionary algorithm can be applied to find irrigation strategies for a cropped soil. We begin by providing an introductory chapter detailing the work that is to be carried out and the results obtained from research. In Chapter 2 we introduce some basic concepts of soil physics in order to give an understanding of the nature of soil composition and the movement of water within a cropped soil. We then summarise background research undertaken by Terry Janz in his Masters Thesis which shows how an irrigation schedule can be obtained using classical methods to solve the Richards' flow equation with realistic parameters and field data. Genetic and evolutionary algorithms are introduced in Chapter 3; their algorithmic structure is defined and contrasted with classic search techniques. In Chapter 4 we apply a genetic algorithm to the problem posed in Chapter 2 to obtain a schedule of irrigation defined as a sequence of irrigation on and irrigation off switches, to control moisture content at specific levels at certain depths within the soil, so that "nutrient uptake" by the root can be maximised. The problem posed is the classical optimal control problem in which the tracking of a desired set of final states is to be achieved. Finally in Chapter 5, we undertake an initial research study into how an evolutionary algorithm can be applied to solve the tracking problem associated with boundary control of a parabolic distributed process. The problem is first transformed into a classical optimal control problem with ordinary differential equations as differential constraints, by using the method of semi-discretisation, or method of lines. Our results are compared with classical techniques commonly used to solve this type of problem, including the finite element method which uses full discretisation of both the state and time variables. It is shown that it is feasible to apply evolutionary learning to problems of boundary control which arise in determining realistic irrigation strategies.

The land ecosystems in northern high latitudes (>45° N) occupy 22% of the global surface and store more than 1600 Pg soil organic carbon. Warming in this region has been documented during the past decades. Warming-induced changes in regional carbon dynamics are expected to loom large in the global carbon cycle and exert large feedbacks to the global climate system. Numerous Earth System Models have been widely used to quantify the response of terrestrial ecosystem carbon dynamics to climatic changes. However, predictions of terrestrial ecosystem carbon responses to increasing levels of atmospheric carbon dioxide (CO2) and climate change is still uncertain due to model limitations. The limitations include relatively low levels of representation of ecosystem processes that determine the exchanges of water, energy, and carbon between land ecosystems and the atmosphere and omitting some key biogeochemical mechanisms. To improve model realism and provide a better projection of the Arctic carbon dynamics, this dissertation developed three new versions of a process-based biogeochemistry models that involve more fundamental processes of terrestrial ecosystems. First, microbial dynamics and enzyme kinetics that catalyze soil carbon decomposition have been incorporated into the extant terrestrial ecosystem model TEM to remedy the inadequate representation of soil decomposition process. Furthermore, a vital microbial life-history trait, microbial dormancy, has been implemented into previous microbial-based model to consider the impacts of microbial dormancy in modeling. Additionally, the role of moss in the Arctic terrestrial ecosystem carbon quantification was also demonstrated by incorporating moss and higher plant interactions in modelling.

The East Barmoya and adjoining catchments in coastal central Queensland are suffering classic symptoms of dryland salinity, brought on by clearing of dry-rainforests in their upper catchments. The problem became manifest in the 1920-30s, expanded rapidly in the 1950s and has intermittently increased until the present, lagging some 20 to 30 years behind the period of large scale clearing in the catchment. Plant succession onto the new saline environment is considered, and a production system involving marine couch (Sporobolus virginicus) and swamp-oak (Casuarina glauca) is advocated. The role of soil mounding and mulching for the establishment of Casuarina glauca onto waterlogged, salinized land (water-table within 1 m of soil surface, surface soil EC1:5 0.0-0.1 m c. 10 dS.m -1) in Central Queensland was investigated in a factorial experiment involving two levels of soil mounding (0.05 and 0.15 m) and four mulch conditions (no mulch, hay, black and white plastic). Mounding was of little effect on plant survival, growth, soil pH or conductivity, however mulching greatly influenced these parameters, with the exception of soil pH. Plastic mulch is recommended over hay mulch. Installation of the plastic mulch was mechanized, involving cultivation of the soil to mix surface salts, mounding of soil into an M cross-section to harvest rain water to the seedling, and use of a commercial mulchlayer for plastic film installation. An established individual swamp-oak was found to use 8-11 L.d-1 of groundwater. Using a steady state model for the water-table depression due to water extraction from a well and assuming that the tree used only groundwater, the depression was calculated to be c. 1 m (steady state) for the low hydraulic conductivity soils (clays) that typify dryland salinity discharge sites. During a forty day period, the tree caused a water-table depression of 10 cm, relative to a reference point 10 m from the tree. Further, a diurnal oscillation of 1 cm occurred in the water-table under the tree. With water use by the single tree considered to be sufficient to cause localized inhibition of the unsaturated flow of groundwater to the soil surface, an estimation was made of the density of trees required to lower the water-table beyond the capillary fringe and thereby reverse the salinization process.

Methane (CH₄) is the second most powerful greenhouse gas (GHG) behind carbon dioxide (CO₂), and is able to trap a large amount of long-wave radiation, leading to surface warming. Carbon monoxide (CO) plays an important role in controlling the oxidizing capacity of the atmosphere by reacting with OH radicals that affect atmospheric CH₄ dynamics. Terrestrial ecosystems play an important role in determining the amount of these gases into the atmosphere. However, global quantifications of CH₄ emissions from wetlands and its sinks from uplands, and CO exchanges between land and the atmosphere are still fraught with large uncertainties, presenting a big challenge to interpret complex atmospheric CH₄ dynamics in recent decades. In this dissertation, I apply modeling approaches to estimate the global CH₄ and CO exchanges between land ecosystems and the atmosphere and analyze how they respond to contemporary and future climate change.

Firstly, I develop a process-based biogeochemistry model embedded in Terrestrial Ecosystem Model (TEM) to quantify the CO exchange between soils and the atmosphere at the global scale (Chapter 2). Parameterizations were conducted by using the CO in situ data for eleven representative ecosystem types. The model is then extrapolated to global terrestrial ecosystems. Globally soils act as a sink of atmospheric CO. Areas near the equator, Eastern US, Europe and eastern Asia will be the largest sink regions due to their optimum soil moisture and high temperature. The annual global soil net flux of atmospheric CO is primarily controlled by air temperature, soil temperature, SOC and atmospheric CO concentrations, while its monthly variation is mainly determined by air temperature, precipitation, soil temperature and soil moisture.

Secondly, to better quantify the global CH₄ emissions from wetlands and their uncertainties, I revise, parameterize and verify a process-based biogeochemical model for methane for various wetland ecosystems (Chapter 3). The model is then extrapolated to the global scale to quantify the uncertainty induced from four different types of uncertainty sources including parameterization, wetland type distribution, wetland area distribution and meteorological input. Spatially, the northeast US and Amazon are two hotspots of CH₄ emissions, while consumption hotspots are in the eastern US and eastern China. The relationships between both wetland emissions and upland consumption and El Niño and La Niña events are analyzed. This study highlights the need for more in situ methane flux data, more accurate wetland type and area distribution information to better constrain the model uncertainty.

Thirdly, to further constrain the global wetland CH₄ emissions, I develop a predictive model of CH₄ emissions using an artificial neural network (ANN) approach and available field observations of CH₄ fluxes (Chapter 4). Eleven explanatory variables including three transient climate variables (precipitation, air temperature and solar radiation) and eight static soil property variables are considered in developing the ANN models. The models are then extrapolated to the global scale to estimate monthly CH₄ emissions from 1979 to 2099. Significant interannual and seasonal variations of wetland CH₄ emissions exist in the past four decades, and the emissions in this period are most sensitive to variations in solar radiation and air temperature. This study reduced the uncertainty in global CH₄ emissions from wetlands and called for better characterizing variations of wetland areas and water table position and more long-term observations of CH₄ fluxes in tropical regions.

Finally, in order to study a new pathway of CH₄ emissions from palm tree stem, I develop a two-dimensional diffusion model. The model is optimized using field data of methane emissions from palm tree stems (Chapter 5). The model is then extrapolated to Pastaza-Marañón foreland basin (PMFB) in Peru by using a process-based biogeochemical model. To our knowledge, this is among the first efforts to quantify regional CH₄ emissions through this pathway. The estimates can be improved by considering the effects of changes in temperature, precipitation and radiation and using long-period continuous flux observations. Regional and global estimates of CH₄ emissions through this pathway can be further constrained using more accurate palm swamp classification and spatial distribution data of palm trees at the global scale.

"The Central Queensland University developed an on-site wastewater treatment and reuse technology. Septic tanks were used for primary treatment and the discharged effluent was then pumped though a series of contained channels. The channels were designed to be a modified evapotranspiration trench; they were comprised of an aggregate layer and a soil layer in which were planted a variety of plants. The aggregate and the soil provided physical filtration, the microorganisms within the effluent, aggregate and soil provided nutrient reuse and transformation and the plants also used the nutrients and reused the treated effluent through evapotranspiration. Any effluent that was not transpired was returned to a holding tank and pumped through the evapotranspiration again. The treatment technology was assessed in relation to its ability to treat effluent in a sustainable manner. The water and soil was examined for concentrations of nutrients, heavy metals, salts, sodium, and organic carbon %. The pH, temperature and number of colony forming units of certain microorganism potential pathogens were also inspected in the soil and the water. The plants grown within the evapotranspiration channels were assessed in regards to their health, water usage, and in some cases potential pathogens on fruit. The infrastructure that was used to construct the wastewater treatment and reuse system was also evaluated in regards to reliability and maintenance. Certain limiting factors, in particular sodicity and salinity were identified, but the trial was successful and a sustainable form of on-site wastewater treatment and reuse technology was developed." --abstract

Food insecurity and nutrition are two of the biggest challenges facing our society. Urban agriculture can help address these challenges, though lack of awareness about opportunities for engagement and degraded soils are two barriers that could prevent people from realizing the benefits that these operations can provide. Soils in urban areas are often highly degraded due to development activities and lack the structure and microbial life needed to sustain healthy, productive plants. Many lifelong habits such as healthy eating and engagement in community gardening are best established during young adulthood. Graduate school is a particularly unique time period, as many students are living on their own for the first time with modest incomes and some have young families that are particularly vulnerable to food insecurity. Consequently, the first objective of this project was to identify which barriers, if any, Purdue graduate students face when purchasing and consuming fresh produce and participating in local urban agriculture initiatives as Purdue’s campus and much of the surrounding area are characterized as food deserts by the USDA. We also sought to determine how the COVID-19 pandemic influenced food access and motivations for healthy eating and community garden engagement. To answer these questions, we distributed a voluntary 33 question online Qualtrics® survey to all Purdue graduate students via mass email blast. Results indicate that many Purdue graduate students face individual and structural barriers to accessing fresh fruits and vegetables. International respondents, in particular, were particularly vulnerable to structural barriers. Not having access to a personal vehicle appears to be the primary predictor of who was most vulnerable, especially during the pandemic. Results also indicate that students are interested in participating in local urban agriculture initiatives, but most are unaware of their existence. Students indicated that e-mails were the best method for increasing awareness and engagement. The second objective of this study was to determine whether leaf mold compost could improve the health and productivity of degraded urban soils. In addition, we aimed to determine whether the leaf compost could better support a beneficial microbial inoculant to further enhance crop productivity, as well as the extent to which plant genotype moderates these beneficial plant-soil-microbial relationships. To answer these questions, leaf compost was obtained from a local grower and applied to experimental plots at the Purdue University Farm. Two tomato varieties, Wisconsin 55 and Corbarino, were inoculated with Trichoderma harzianum T-22 or a sterile water control, and transplanted into the field trials. 15 Survival following transplanting, vigor, disease ratings and the yield and quality of tomato fruit were quantified over the course of two growing seasons. Results indicated that several measures of soil health were significantly increased in compost-amended soils and the health and productivity of tomato plants greatly improved. The microbial inoculant dramatically reduced transplant stress, especially in Wisconsin 55. Other more subtle differences among the tomato varieties indicated that urban agriculture systems could be improved through varietal selection. These studies highlight the fact that graduate students are not immune to food insecurity and proper nutrition and they are interested in connecting with urban agriculture initiatives to address these challenges. Pairing of the two groups could prove to be a successful mutualistic symbiosis as graduate students provide the enthusiasm and manpower that urban gardens need while urban gardens offer access to low-cost fresh produce that many graduate students desire. Leaf mold compost can aid in these initiatives by providing a cost-effective approach to improve the health and productivity of urban soils and crops, while at the same time providing further benefits such as reduced accumulation of valuable carbon sources in municipal landfills. Results like these provide stark evidence that agriculture, particularly urban agriculture, can continue to improve access to nutritious foods through green initiatives and innovations.

Variations in stable isotope abundances of nitrogen (δ¹⁵N) and oxygen (δ¹⁸O) of nitrate are a useful tool for determining sources of nitrate as well as understanding the transformations of nitrogen within soil (Chapter 2). Various sources of nitrate are known to display distinctive isotopic compositions, while nitrogen transformation processes fractionate both N and O isotopes and can reveal the reaction pathways of nitrogen compounds. However, to fully understand the δ¹⁵N and δ¹⁸O values of nitrate sources, we must understand the chemistry and the isotopic fractionations that occur during inorganic and biochemical reactions. Among all N cycle processes, nitrification and denitrification displayed some of the largest and most variable isotope enrichment factors, ranging from -35 to 0‰ for nitrification, and -40 to -5‰ for denitrification. In this dissertation, I will first characterize the isotopic enrichment factors of ¹⁵N during nitrification and denitrification in a Midwestern agricultural soil, two important microbial processes in the soil nitrogen cycle. Nitrification incubations found that a large enrichment factor of -25.5‰ occurs during nitrification NH₄⁺ è NO₃^-, which agrees well with previous studies (Chapter 3). Additionally, oxygen isotopic exchange that occurs between nitrite and water during nitrification was also quantified and found that 82% of oxygen in NO₃^- are derived from H₂O, much greater than the 66% predicted by the biochemical steps of nitrification. The isotopic enrichment that occurs during denitrification was assessed by measuring the change in δ¹⁵N as the reactant NO₃^- was reduced to N₂ gas (Chapter 4). The incubations and kinetic models showed that denitrification can causes large isotopic enrichment in the δ¹⁵N of remaining NO₃^-. The enrichment factor for NO₂^- è gaseous N was -9.1‰, while the enrichment factors for NO₃^- è NO₂^- were between -17 to -10‰, both of which were within the range of values report in literature. The results demonstrated that nitrification and denitrification caused large isotope fractionation and can alter the presumed δ¹⁵N and δ¹⁸O values of nitrate sources, potentially leading to incorrect apportionment of nitrate sources.

The results of the denitrification incubation experiments were applied to a field study, where the measured enrichment factor was utilized to quantify loss of N by field-scale denitrification (Chapter 5). Field-based estimates of total denitrification have long been a challenge and only limited success has been found using N mass balance, N₂O gas flux, or isotope labeling techniques. Here, the flux of nitrate and chloride from tile drain discharge from a small field was determined by measuring both dissolved ions (ion chromatography) and monitoring water discharge. The δ¹⁵N and δ¹⁸O of tile nitrate was also measured at a high temporal resolution. Fluxes of all N inputs, which included N wet and dry deposition, fertilizer application, and soil mineralization were determined. The d¹⁵N and d¹⁸O values of these nitrate sources was also determined. Using this data, I first detected shifts in δ¹⁵N and δ¹⁸O values in the tile drain nitrate, which indicated variable amounts of denitrification. Next, a Rayleigh distillation model was used to determine the fraction of NO₃^- loss by field scale denitrification. This natural abundance isotope method was able to account for the spatial and temporal variability of denitrification by integrating it across the field scale. Overall, I found only 3.3% of applied N was denitrified. Furthermore, this study emphasized the importance of complementary information (e.g. soil moisture, soil temperature, precipitation, isotopic composition of H₂O, etc.), and the evidence it can provide to nitrogen inputs and processes within the soil.

The poultry industry has rapidly grown in the last few years with a focus in improving growth and productivity of broiler chickens, with performance assessed on measures such as feed conversion ratio, body weight gain and good immunity. The incorporation of antibiotics and feed additives in poultry diets, have been implemented for years to ensure the maintenance of poultry health with a focus on the control and reduction of zoonotic pathogens. In the last few years, however, key issues surrounding the antimicrobial resistance of antibiotics have urged for alternative supplementations. Nanoparticles (NPs) of silver and other metals have been heavily used in the poultry industry to improve the growth and performance of birds. Whilst successful, metal NPs exhibited higher toxicity at the higher surface to volume ratio, especially with the use of silver. This study proposes the use of NPs of essential metals and natural compounds to safely deliver nutrients, resulting in positive impacts on health and productivity with little to no toxic effects. Selenium is an essential mineral, required for the proper functioning of the immunity and is an important element in the first cell line of defence in the body. The work described in this thesis explores the ability of selenium NPs to improve the health and growth of broiler chickens by modulating their gut microbiome and metabolome, without the toxic effects observed with silver. Selenium NPs were synthesised using a simple chemical reduction method and a full characterisation was performed, assessing the physicochemical properties of the NP. Selenium NPs were then compared in an animal trial against two commonly used selenium additives in the poultry industry, sodium selenite (inorganic selenium) and selenomethionine (organic selenium). The performance of the birds was assessed based on body weight gain, the gut microbial composition and metabolite production. The toxicity of NPs was further investigated by quantifying selenium concentration in various tissues, along with a detailed histopathological assessment. Results show selenium NPs completely altered the gut microbial ecology at high concentration, with a strong correlation observed between Faecalibacterium prausnitzii abundance and increasing concentration of selenium NPs. Selenium NPs additionally increased villus height/crypt ratio associated with enhanced absorption in the small intestine and an overall increase of healthy colonic metabolites. Finally, an in vitro study demonstrated the ability of selenium NPs to reduce emerging pathogenic Enterococcus cecorum species. This thesis demonstrates the prospective ability of selenium NPs as alternatives to antibiotics and bulk supplementation, resulting in an improvement of health and performance of broiler chickens in the poultry industry.

The behaviour of waste biomass materials, specifically bagasse* and sawdust, in deep fluidized beds was investigated. The bagasse used was dry (less than 1% moisture by mass). Sawdust was from mixed eucalyptus hardwoods with moisture contents up to 25% by mass. A series of cold flow visualisation tests were completed in a bed of 190mm diameter using graded river sand of surface mean particle diameters of 180 and 490 microns. Bagasse was added to the bed in various quantities and the ingestion and mixing phenomena observed. The influence of distributor design, cones, and draft tubes on mixing rates were investigated for use in the combustor design. Combustion Tests using Sawdust and Bagasse were completed in a Combustor of 489mm diameter with graded river sands of surface mean particle diameters of 300,490 and 530 microns. Various configurations were tested including a shallow bed of depth 130mm, deep beds of depths up to 460mm, a Reverse Circulation Bed, and Modified Spouted Beds of depths up to 740mm. Fuel feeding systems included above bed chutes, an ingestor tube, a direct bed wall screw feeder, and a pressurised screw feeder fitted to the air supply of a Modified Spouted Bed. Bagasse was not successfully fed through the screw feeder systems used. Sawdust, which has similar fluidized bed combustion characteristics to bagasse, was used in screw feeders to indicate the possible results that could be obtained from bagasse using below bed feed systems. Configurations utilising direct below bed surface screw feed, Ingestor tube feed, and pressurised screw feed to the fluidizing air were all successful in increasing the percentage of combustion occurring below the bed surface. The best results were obtained from pre-mixed air and fuel particles entering the modified spouted bed giving combustion efficiencies of up to 60% comparable to coal. Higher efficiencies would be possible with further optimisation of the design. The results of the investigation open several avenues of development including partial gasification/combustion systems and further development of the ingestor tube, reverse circulation bed and modified spouted bed concepts. The problems encountered with the combustion of lightweight, particulate biomass fuels are now reduced to finding practical methods of fuel feeding and rate control. *Bagasse is the cellulose residue from sugar cane stalks which remains after crushing.It is particulate, fibrous, tangled and irregular in size, length and aspect ratio.

The research presented here analyses and compares textual narratives generated within policy, scholarly and popular media to discern how the sexuality or intimacy needs of people categorised as ‘learning disabled’ have been historically and more recently managed in Australia and the United Kingdom. The research uses a modified critical discourse analytical approach which, in order to clarify the distinct role of power in the construction of discourses of sexuality, is mediated by the more recent ideas of progressive phronesis offered by Flyvbjerg (1998a; 2001). The analysis identifies three broad stages in the historical development of the discourses about the sexuality of learning disabled people. The first phase was prior to the 1800s, when these people were labelled non-derogatorily as ‘idiots’, and perceived as childlike, innocent and asexual. The second stage was in the 1800s when, with the emergence of scientific rationality and medicalisation, so-called idiots became medicalised and categorised as ‘feeble-minded’ or ‘moral imbeciles’. This thesis demonstrates that, during this period, an emphasis on sexual self-denial, anxieties about venereal disease and non-procreative erotic pleasure helped to inform discourses of eugenics and learning disabled people became perceived as a sexual threat to the society. This underpinned policies of sexual control through institutionalisation, gender segregation and sterilisation. The third period in the development of discourses relating to the sexuality of learning disabled people paralleled the ‘sexual revolution’ of the late- 1900s and the move towards deinstitutionalisation and human rights. This analysis shows that, although the principle of ‘sexual freedom’ was ostensibly incorporated in modern policy discourse, the sexuality of learning disabled people continues to be influenced by significant barriers of sexual intolerance, demonstrated by continuing practices of sexual segregation, sterilisation, criminal labelling and imprisonment. The analysis indicates that a discourse of sexuality, which has legitimised the control and management of learning disabled people in varying forms since the Enlightenment, continues to be encountered in policy and popular narratives. Robust sexuality awareness and education programs for carers of these people, and society in general, are necessary so that intimacy and/or sexual desires are accepted as a normal need for all human beings.

Examines the flow characterisation of molasses in four different pipe fittings at low Reynolds number.. This thesis examines the flow characterisation of molasses, a highly viscous non-Newtonian fluid, in four different pipe fittings at low Reynolds number. This flow condition of low Reynolds is typically encountered in sugar mills. The experimental results reveal that the current 2K method in use in the sugar industry substantially overestimates the actual losses at very low Reynolds number. New experimental data for these flows, are presented in this thesis to predict the head loss accurately and to improve design of pipework in sugar mills . Chapter 1 discusses the basic theory and constitutive equations to define Newtonian and non-Newtonian fluids and their flows. The aims and plans for this study are also laid out here. Chapter 2 gives the details on selection of the fittings, the design and construction of the test rigs, experimental set up and the other technical details related to the equipment used in the experiment. Chapter 3 discusses experimental and test.procedure. It presents fluid preparation, fluid characterisation, flow induction, measurement of the flow rate. Chapter 4 presents calculation procedure and results of the experiments conducted on various fittings with molasses of different viscosity. Chapter 5 gives analysis and correlation of the experimental data. Chapter 6 presents the major conclusion drawn from this project and makes suggestions and proposals for further work in this area.

Plantation forests are susceptible to many pests, which can reduce the quality and value of the wood products they source. Certain species of the fungal genus Mycosphaerella are a concern in eucalyptus plantations around the world. Mycosphaerella leaf disease (referred to as MLD from here in) can cause significant leaf necrosis, discolouration and defoliation. In Australia severe outbreaks of MLD have been observed in various eucalyptus plantations. The three aspects of MLD research targeted in this Thesis were factors influencing its atmospheric ascospore concentrations, the effect of its symptoms on leaf spectral properties, and the use of remote sensing to detect MLD’s symptom distribution and severity.

New synthetic methods are explored for the synthesis of protoberberines using carbanionimine (CAI) cycloaddition, aza Diels-Alder (DA) cycloaddition.. Protoberberine alkaloids are widely distributed in numerous plant families, and commonly found as active components in many folklore medicines in Asia, Europe and North America. Due to their broad diversity of biological activities, there are great efforts about chemical, biogenetic and enzymatic synthesis, transformation, pharmacology, and culture development studies of these alkaloids. In this thesis, new synthetic methods are explored for the synthesis of protoberberines using the following approaches a) carbanionimine (CAI) cycloaddition, b) aza Diels-Alder (DA) cycloaddition. The structure elucidation of products using various analytical techniques, such as IR, UV-vis., MS, NMR and X-ray, are broadly discussed. Detailed stereostructure and conformation analysis have been studied using various one and two dimensional NMR techniques, which show great advantage for structure analysis in the liquid state, and give the consistent conclusion as the solid state structure as determined by the single crystal X-ray diffraction method. The carbanion-cyclic imine approach has been most successful in the synthesis of protoberberines, which contain a four-ring system (ABCD). Cycloaddition of 3,4-dihydroisoquinoline (DHIQ, eg A-I) with phthalide anion (eg A-2) gives stereo and regia selective 13-hydroxy protoberberines (eg A-3) with single diastereomers observed and isolated, which are transformed to various functionalised derivatives. The novel reaction of 3-methoxyphthalide anion (A-4) with DHIQ, where a 2+1 adduct (A-6) is formed, is broadly studied. The mechanisms are studied in details and highly suggestive via tandem nucleophilic condensation of the anion, in which the 8,13-dioxo intermediate (eg A-5) plays an important role. The geometry change due to the replace of angular 13a-H with methyl group accounts for the different facial selectivity of 13-keto to nucleophiles in A-5a A-5b. These are supported by theoretical AMl calculation and Surface Probe Analysis on model compounds (A-8). The phthalide anion-acyclic imine approach has been used to provide open chain products (eg A-10 and A-11). NMR and AMl calculation prove trans stereochemistry of major isomers (eg A-10). The conclusion is in contrast to previous assignments by MacLean, Cushman, and Prager on similar compounds. The direct asymmetric synthesis is also explored by using a chiral o-toluamide anion (eg A-12) instead of a phthalide counterpart. A series of chiral amine auxiliary agents have been studied and the tertiary o-toluamide with a bulky cyclohexyl group in addition to the chiral substituent on the amide nitrogen atom (A-12) gives the highest enantioselectivity (>96% ee). This approach established a new, fast entry to both enantiomers of protoberberines and exhibits predictable regiochemistry. This is an obvious advantage in all anion-imine cycloaddition reactions in our study and others. DA methodology is also studied, however only the reaction between DHIQ (AB synthon) and phthalazine (A-14, CD synthon) works. This reaction is the first example of aza DA reaction with phthalazine as an aza diene with an aza dienophile. The other AB+CD approaches with DHIQ (AB) as dienophile allowed to react with different dienes (CD), such as isobenzofuran and cyclopentadienone, do not give any adducts under thermal, Lewis acid catalyst or high pressure conditions. While the first step of an AB+C+D approach which involves sequential DA reaction of DHIQ with s-tetrazine (A-16) was successful, the second step involving benzyne or cyclic enamine cycloaddition failed.

Utilizing environmental DNA (eDNA) for the detection of species in the field is a potentially cost-effective and time-saving technology that may be useful in understanding the distribution and abundance of threatened or endangered species such as the Eastern Massasauga (Sistrurus catenatus). I describe the development of an eDNA assay for the species and evaluate its ability to detect eDNA in laboratory and field conditions. In the field samples, I also investigated the potential for abiotic conditions to influence eDNA detection. Species-specific primers and probe were designed to amplify a 152 bp segment of the massasauga COI gene. Target eDNA could be detected in samples containing as little as 100 copies of target DNA/μL. Water samples collected from laboratory housed snakes indicated that eDNA can be detected in water 56 days after massasauga removal. Field samples were taken from crayfish burrows, known overwintering habitat for the species, from four sites that vary in snake use as ascertained by traditional visual surveys. Of the 60 burrows sampled, seven had a positive detection for massasauga eDNA with no difference in detection rate between DNA extracted from burrow water and burrow sediment. Occupancy models fitted to burrow water indicated that larger amounts of total DNA in a sample may increase the probability of detection of a massasauga eDNA. Large confidence intervals in site occupancy (ѱ) and burrow detection (Θ) values suggest that a larger sample size is needed for more reliable occupancy models. Abiotic conditions within crayfish burrows varied among sites but correlation with eDNA detection was not supported. Estimates of qPCR detection within a burrow with eDNA (ρ) suggest that up to 10 qPCR replicates per burrow sample may be necessary. Further studies need to examine eDNA degradation in the field, improve upon the limit of detection, and sample a larger number of sites for eDNA sampling to be a stand-alone survey method for Eastern Massasaugas.