Dissertations / Theses on the topic 'Plant biology not elsewhere classified'

The primary aim of the thesis is to provide a comprehensive investigation of the osmotic dehydration processes in plant tissue. Effort has been concentrated on the modelling for simulating the processes. Two mathematical models for simulating the mass transfer during osmotic dehydration processes in plant tissues are developed and verified using existing experimental data. Both models are based on the mechanism of diffusion and convection of any mobile material that can transport in plant tissues. The mass balance equation for the transport of each constituent is established separately for intracellular and extra-cellular volumes with taking into account the mass transfer across the cell membrane the intracellular and extra-cellular volumes and the shrinkage of the whole tissue. The contribution from turgor pressure is considered in both models. Model two uses Darcy’s law to build the relation between shrinkage velocity and hydrostatic pressure in each volume because the plant tissue can be considered as the porous medium. Moreover, it has been extended to solve the multi-dimensional problems. A lot of efforts have been made to the parameter study and the sensitivity analyses. The parameters investigated including the concentration of the osmotic solution, diffusion coefficient, permeability of the cell membrane, elastic modulus of the cell wall, critical cell volume etc. The models allow us to quantitatively simulate the time evolution of intracellular and extra-cellular volumes as well as the time evolution of concentrations in each cross-section.

Breast cancer (BC) is the most common and most lethal cancer among women worldwide. More than a million and a half are diagnosed every year with more than 600,000 deaths among women worldwide. It is estimated than 1 in every 7 women will develop breast cancer in their life time. It is a major public health concern with high economic cost as well. BC is a multidimensional construct. Several dimensions of this construct have never been examined before in the United Arab Emirates (UAE). This study investigated major facets of the Quality of life (QOL) among women with BC in the UAE, compared it with a sample of age matched healthy group of women without any neoplastic background, changes in serum biomarkers of women with BC and to detect the impact of the disease on these biomarkers at the beginning of the disease before treatment started and then again 12 months later following treatment for the cancer and the role of ghrelin hormone in BC and depression at a tissue level and at serum level. In order to examine QOL with its all dimensions among women with BC, an epidemiological case-control study was conducted recruiting a sample of 300 women, 155 women with BC and 145 age-matched healthy women without any neoplastic background as a control group. This was carried out by using a series of standardized psychometric tools in addition to conducting a psychiatric diagnostic interview. Moreover, blood biomarker results were reviewed retrospectively for cases and controls at the beginning and then 12 months following treatment for BC. In relation to the histopathological characteristics and treatment modalities for BC, all pathology, medical and oncology data for 155 women with BC was retrieved from the computer system and analyzed retrospectively. Finally, in relation to ghrelin hormone, all mammary morphological types, normal, benign and malignant were examined with immunohistochemistry for the expression of ghrelin and its functioning receptor (GHS-R1a). Serum of the same women, whose mammary tissue sections were examined by IHC, was tested for ghrelin serum level to find out its link to BC and depression. This was carried out by Enzyme-Linked Immunosorbent Assay (ELISA). The results have demonstrated that women with BC had poor QOL in comparison to the control group. They had poor view of their body image and sexuality and moreover physical disability rate was high. They also tended to suppress negative emotions to a great extent. Anxiety symptoms were also high. Major depressive disorders and post traumatic disorders were lower among women with BC compared to healthy controls. Several risk factors turned to be linked to BC. These included age, having night shift work, hypertension, diabetes mellitus, oral contraceptive pills, hormonal replacement therapy and not breast feeding. In terms of significant traumatic life events, the Arabic version of the CESC English scale showed to have high validity and reliability among women with BC in the UAE. The results also showed that the levels of several serum haematological and biochemical markers seemed to be abnormal among women with BC compared to healthy control. These included elevated levels of platelet, basophils, liver enzymes, lactate dehydrogenase and tumour serum markers. On the other hand, they were low levels of serum magnesium, C-reactive protein and creatinine. Analysis of histopathological characteristics indicated that the aggressive biological nature of the disease was at the late stage and presentation to medical services for treatment. Clinically, women with BC seemed to have all treatment modalities for BC with high rate of mastectomy and axillary clearance. Regarding ghrelin hormone and it relation to BC, the results showed that malignant mammary tissues had an exclusive and differential immune-reactivity to ghrelin hormone, whereas its receptor, the GHS-R1a, was immune-reactive all mammary tissue morphological types. In addition, more metastasis to the lymph nodes was significantly correlated with more immune-reactivity to ghrelin receptor. The results for gene expression for pro-ghrelin, ghrelin and its receptors were inconclusive It is concluded that breast cancer is the most common cancer among women in the UAE. It attacks women at an earlier age than their counterparts in the West. More attention should to be allocated to the QOL and the unmet psychosocial needs of women with BC. This in turn would improve compliance to treatment and prognosis as well. It is also recommended that awareness campaigns and early screening should be applied for early detection of the disease to prevent late presentation to the medical services and other complications.

As far back as the 1920s, Otto Warburg observed that cancerous cells display an altered state of metabolism surrounding lipid biosynthesis. However, only until recently has metabolic reprogramming been a recognised hallmark of the disease. The number of cancer cases diagnosed is set to triple by 2030, demonstrating the need for disease prevention, improved diagnostic testing and personalised treatment therapies. However, with some cancers occurring in the brain and spinal cord, the type of treatment available can become challenging due to their locality. Such cancer types include meningioma and glioma which are the most common brain tumours diagnosed. An initial study involving human meningioma tissue revealed unusually high levels of the phosphatidylserine enriched with docosahexaenoic acid (DHA). In this study, the metabolism surrounding lipid biosynthesis was examined to establish if such alterations in lipid profiles were related to an altered state of metabolism. From the results gained, it can be suggested that meningioma does have an altered state of metabolism, evolving around serine as opposed to DHA. From the grade I and grade II meningioma tissues immunochemically examined, positive expressions of pyruvate kinase isoform 2 (PKM2) and phosphoglycerate dehydrogenase (PHGDH) were shown. Therefore, the results demonstrated that within meningioma tissues, serine can allosterically regulate the flux through glycolysis. The association that serine presence alone can alter the metabolic flux was demonstrated in the model organism, Lipomyces starkeyi. Those L. starkeyi cells supplemented with serine, displayed a 50% reduction in the amount of radiolabelled acetate taken up during exponential and stationary growth phases. The radiolabelled study also highlighted that with serine presence, de novo lipid biosynthesis was altered. Once synthesised, these neutral lipids go on to be 4 stored in membrane bound organelles. Within the phenotype of cancerous cells, such storage of neutral lipids into lipid droplets prevent lipotoxicity. The light microscopy study of L. starkeyi cells supplemented with serine demonstrated that the formation of such lipid droplets was enhanced during lipid accumulation. These findings suggest that the production, storage and mobilisation of lipids within serine supplemented cells are adapted to cellular requirements, promoting a cancerous phenotype. In order to gain an insight into the potential impact that an altered metabolic state may give to meningioma, a liposomal study was developed. Supplementation of both phosphatidylserine-consisting liposomes, as well as tumour-derived liposomes, enhanced the cellular viability of the non-cancerous cell line, SVG, during exponential phase. The supplementation of meningioma-derived liposomes also increased the viability of the non-cancerous human fetal glial SVG cell line, similar to that observed with phosphatidylserine containing liposomal preparations. Therefore, the data suggest that in fact, the phospholipid (phosphatidylserine), rather than the fatty acid (DHA) plays a role in cellular viability. It is concluded that the results gained from this study can be used clinically in the diagnosis and management of meningioma as well as other diseased cells displaying ectopic lipid accumulation. The observation that meningioma has an altered biochemistry may provide guidance when histologically grading meningioma tumours. For those tumours expressing the enzymes involved in serine biosynthesis, such as PKM2 and PHGDH, a targeted treatment therapy surrounding enzyme inhibitors can be examined. By targeting serine biosynthesis, the resources needed to enable a cancerous phenotype are depleted. Future research can examine such targeted therapies utilizing either the developed model organism, L. starkeyi or the conventional SVG and U87 cell lines.

A low technology fermentation system for biodegradation of cellulose based waste material is described. Using a substrate of thermally bonded paper plastic laminate in a defined mineral salts medium the cellulolytic nicrofungus Trichoderma viride XXI 2% 458 was shown to effect the separation of the laminate into its components by enzymic degradation of the paper. This aerobically induced separation occurred within 14 days compared to upto 90 days by purely physical means. Growth of the fungus within the fermentation system was found to provide conditions that control the growth of contaminating microorganisms. Carbonolytic enzyme activity of Trichoderma viride was investigated by measurenent of substrate weight loss and by reduction in the viscosity of soluble substrate analogues when acted upon by filtrate front-the fermentation systais. An investigation of the effect of changes in carbon to nitrogen ratios during fermentation indicated that maximum carbonolytic enzyme activity occurred at a carbon to nitrogen ratio of 0.6:1 within this system. An examination of three other cellulolytic fungi in order to assess their potential as biodegradative organisms within the fermentation system showed that under microthermophilic conditions only Acrenonium stricturn approached the biodegradative activity of Trichoderma viride at mesophilic temperatures. The products of fermentation by Trichoderma viride were examined; protein levels in the residual cellulolytic substrate following biodegradation of paper plastic laminate were determined and found to reach levels of up to 9% following 35 days fermentation. The amino acid composition of protein produced by Trichoderma viride when grown on a range of substrates was determined and found to contain a wide range of essential and non essential amino acids. An investigation of mycotoxins both in the culture medium and residual paper component was undertaken. Comparisons with eleven common mycotoxin standards revealed no positive identifications under the conditions investigated.

"The hypothesis that primary C and N (sucrose and ureides) transport solutes may play a role as osmotica in the control of oxygen diffusion into the infected zone of the legume nodule was considered" -- p. i.

Industrial hemp (Cannabis sativa L.) production is experiencing a significant increase in worldwide production since regaining popularity in many countries since the 1990's. Currently, production in Australia is very limited, and no major grain or fibre processing facilities yet exist, owing to the lack of suitable low THC (A9-tetrahydrocannibinol) varieties. Hemp production in subtropical regions of Australia is particularly limited as short day lengths (photoperiods) result in early plant maturity, and thus, poor yielding crops. The aim of this research is to determine the viability of a new variety of hemp, bred specifically for subtropical production whilst determining the effects of day length and plant density on yield and flowering time. Trials were conducted in Bundaberg, QLD in 2010-2012 in both field and controlled environment (plastic house) settings. Plant densities of 100, 200, 300 and 400 plants m-2 were compared for fibre production and densities of 50, 80, 100 and 150 plants m2 were compared for grain production to assist in the establishment of appropriate commercial sowing rates. Harvested fibre yields were greatest at 300 plants m2 whereas grain yields were greatest at 150 plants m2, with the potential of even higher yields at densities greater than 150 plants m2. Photoperiod experiments were conducted in a controlled plastic house evaluating plant responses to varying photoperiods. Treatments comparing ambient day length, 13 hour 40 minute fixed photoperiod and 14 hour 40 minute fixed photoperiod determined that a 13 hour 40 minute photoperiod did not significantly prolong vegetative growth compared to natural day lengths in the hemp variety BundyGem but at 14 hours 40 minutes maturity times were significantly delayed, thereby contributing to greater plant height and fibre yield. Previous research also suggests that a critical photoperiod of between 14 and 16 hours is required before flowering is delayed in hemp. This theory was supported by a field experiment whereby successive plantings of BundyGem throughout the spring/summer period of 2011/2012, flowered at the same age despite subtle changes in day length for the growing period (never exceeding 13 hours 40 minutes). This research confirms that subtropical fibre hemp is not yet suitable for subtropical production in Australia with existing varieties due to the limitation of photoperiod on yield. Grain production may still be viable despite early plant maturity with yields comparable with those produced in Europe and Canada.

The phenylpropanoid pathway gives rise to a wide variety of specialized metabolites, but the majority of carbon flux going through this pathway is directed towards the synthesis of the lignin monomers: p-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol. Lignin is a major impediment in biomass saccharification, which negatively affects animal feed and biofuel production. In an effort to improve biomass for the latter purposes, researchers have altered the polymer through genetic manipulations and generated biomass with lower recalcitrance to saccharification; however, in many cases these efforts have resulted in plant dwarfism. To date, we do not have a full understanding of the extent of lignin modifications a plant is able to tolerate without affecting its growth. More importantly, the mechanism that links dwarfism and modifications in lignin content and composition remains unknown. To contribute to answering these questions, we designed a strategy to incorporate a novel monomer into the lignin of Arabidopsis thaliana. We used mutants in genes that code for enzymes and regulators of the phenylpropanoid pathway to redirect the pathway’s flux towards the synthesis of p-coumaraldehyde and prevent the incorporation of p-coumaryl alcohol. Despite being mutated for the genes typically considered to be required for monolignol biosynthesis, the plants we generated continue to incorporate p-coumaryl alcohol into their lignin. This result suggests that the pathway’s architecture has not been completely elucidated and that there are more enzymes involved in lignification than previously thought. Additionally, we explored the connection between perturbations in phenylpropanoid metabolism and plant growth, by using an inducible system to track the changes in gene expression and metabolism that occur when phenylpropanoid metabolism is restored in a lignin biosynthetic mutant. The use of an inducible system allowed us to not only determine the metabolic processes affected in this mutant, but the proximal sequence of events that lead to restored growth when a functional copy of the mutant gene is induced. Finally, we redirected the flux through the pathway to assess the effects of simultaneously modulating lignin content and composition. Through this project we discovered that redirecting phenylpropanoid flux towards the synthesis of sinapyl alcohol in lignin-deficient mutant backgrounds, results in plant dwarfism. The growth impairment of these mutants can be overcome by providing exogenous coniferyl alcohol, suggesting that dwarfism in these mutants is caused by deficiency in coniferyl alcohol and/or derivatives thereof and not lignin alone. Altogether these projects allowed us to define the cellular processes affected by perturbations in phenylpropanoid homeostasis and the role of other phenylpropanoids besides lignin in this process.

Buffel grass (Cenchrus ciliaris) is an introduced, summer growing, perennial tufted tussock grass which is used extensively in improved pastures in the grazing industry. Since 1993 there has been an increasing level of dieback in buffel grass in districts of Central Queensland districts, involving red leaf symptoms and occurring in roughly circular patches. There is a potential for this condition to destroy large areas, ultimately resulting in loss of production for beef, dairy and sheep farmers who use this grass in improved pastures. This is the first multifaceted study of buffel grass dieback (BGD). Areas showing signs of dieback have previously been the subject of extensive testing for soil fertility factors, soil chemistry, nematodes and phytoplasmas, with few conclusive results. Therefore, one of the aims of this project was to find the cause of buffel grass dieback. Specific objectives included describing the plant and field symptoms, determining factors responsible for plant death, and determining the method of spread. A complete description of the symptoms was made at plant, patch and paddock levels. Symptoms of Buffel Grass Dieback (BGD) presented as a reddening of the leaves starting from the tip and progressively moving towards the ligule. The red symptoms range from bright red, to dark red, to bronze (RHSPCC red group 45: A, B; 46: A, B; greyed-orange group 166: A; 177; A) (The Royal Horticultural Society, 2001). Symptoms first appeared on the tips of the older leaves and progressively moved down the leaf. The next oldest leaf then showed symptoms, and so on, with the youngest leaf showing symptoms last. Any tillers followed the same pattern, regardless of whether symptoms on the primary shoot had progressed past the point at which the tiller was produced. The amount of time from new growth to the appearance of the red symptoms seemed to be directly proportional to the amount of rainfall. That is, the more rain, the longer it took for symptoms to develop. The amount of subsequent rainfall seemed to influence the time it took for plants to succumb to the condition. That is, when there was adequate water and lush growth plants grew faster than the spread of the condition. When plants became water stressed, the condition overtook growth and the plants succumbed. Symptomatic leaves did not always have a clear red-green boundary. Occasionally, BGD symptoms progressed faster down one half of the leaf. Red symptoms were invariably more vivid on the adaxial surface of the leaves than on the abaxial surface. Roots of affected plants appeared stunted compared to roots of unaffected plants. Roots of affected plants often displayed soft, darker, ovoid sunken regions, which were possibly lesions. The BGD condition appeared to become dormant as buffel grass became dormant. That is, if the dieback condition killed the plant before the onset of dormancy, no new shoots were produced subsequent to a rainfall event. However, if dormancy occurred before the plant succumbed to the condition, new shoots were produced after rain, and the cycle repeated with symptoms first appearing in the oldest leaf. Patches were roughly circular and ranged from 2 m diameter to over 60 m diameter. Adjacent patches often coalesced and further enlarged. Symptoms first appeared on the periphery of an existing patch, where during the last cycle the plants had become dormant before succumbing to the condition. Symptoms progressively moved outwards from the periphery of the patch, at a rate of approximately 5 cm per week. Patch spread was irregular and did not correspond with soil compaction or land slope, though the condition may spread more rapidly downhill due to runoff. BGD affected plants weighed approximately two thirds that of unaffected plants. They were noticeably shorter and had shorter leaves and internodes, with the difference in height attributed to internodes rather than leaf length. BGD affected plants also had fewer tillers than unaffected plants of the same age. Although the numbers of leaves per tiller were the same as un-affected plants, the overall result was a decreased amount of foliage available for grazing, thereby decreasing productivity of livestock. In fact, the loss of productivity was twofold, since cattle had been observed to selectively graze unaffected plants. BGD affected plants had fewer seed heads, shorter seed fascicles, and a higher proportion of non-viable embryos compared to unaffected plants. Therefore, not only did BGD affected plants succumb and die, but there were fewer seedlings to replace them. This could have detrimental consequences for the sustainability of an improved pasture. At the cellular level, there was no discernable difference in cell size between BGD affected plants and unaffected plants in either roots or leaves. However, the roots of BGD affected plants were more damaged at the cellular level, with the cortex mostly sloughed off and the mesophyll cells disrupted. The bulliform and mesophyll cells of BGD affected leaves were more irregular in shape. The bundle sheath cells of BGD affected leaves appeared disrupted, with chloroplasts not in their usual alignment. There also seemed to be a breakdown of chloroplasts. The leaf pigment data concurred with the premise of a breakdown of chloroplasts. Red symptomatic leaves had lower concentrations of chlorophylls a and b compared to green leaves on the same plant. Red symptomatic leaves also had higher concentrations of anthocyanins and carotenoids. It appears that, in red symptomatic leaves, chlorophylls were being destroyed and anthocyanins were being excessively produced. There was no discernible difference in the phloem vessels of BGD affected and unaffected plants, both in the roots and the leaves. However, the xylem of both roots and leaves was partially occluded by structures tentatively identified as tyloses. These structures could also have been local accumulations of phenols or polyphenols, or in some cases the remnants of partially decomposed cells. These occlusions seemed more severe in the roots than in the leaves. Possible inclusion bodies were also found in the mesophyll cells of BGD affected leaves. Inclusion bodies are usually a sign of pathogen infection. However, there were no pathogens detected in the histology work. Chemical analyses were made of BGD affected plants, as well as of the soil in which they were growing, concluding that both plants and soil in the BGD affected paddock surveyed were deficient in nitrogen, phosphorus, sulfur and zinc. A survey was made of other plant species present in the vicinity of the dieback condition, with particular attention given to those species which have reported allelopathic effects. In addition, a study was made on other plant species which also appear to be affected by the dieback condition. Microbial isolations were regularly made from both plant and soil material. The isolates obtained were tested for proof of pathogenicity using Kochs Postulates, but none proved to be the causal agent of BGD. The mode of transmission of the condition was studied, and BGD was found to be soilborne. Whether root contact is necessary for successful transmission was not established. Possible methods of controlling the condition were investigated. While none of the treatments successfully controlled the condition, one of the treatments investigated, Amistar (a systemic fungicide), greatly reduced symptom severity. Although the cause of BGD was not found, several important discoveries were made concerning its effect and spread, and many possible causes of the condition were eliminated. It is likely that BGD is caused by a disease complex, with potential pathogens including soilborne fungi and/or viruses. Several abiotic factors such as water and nutritional stress may be contributing causal agents, weakening the plants and making them more susceptible to a pathogen. . More work is needed to conclusively identify the primary causal agent of this potentially costly condition.

"Pisonia grands R. Br. (Nyctaginaceae) is a large tropical tree whose distribution is restricted to coral cays, in particular those with high seasonal nesting seabird populations. These trees are often the dominant plant species found on coral cays. This is the case for the chosen study site on North West Island, a coral cay which lies off the Central Queensland coast within the Mackay Capricorn section of the Great Barrier Reef. Coral cays are almost entirely composed of coral rubble and sand and as a result the substrate pH (c. 9.0) and many ions are found as insoluble salts. The high pH, abundance of calcium, lack of water and high seasonal input of nitrates from nesting seabirds, are possible influences on the biosynthesis of oxalates which are found in high concentrations in P. grandis. The aims of this study are twofold. The first aim was to investigate the influence of environmental factors, such as pH and nitrate concentration, on the biosynthesis of oxalate in Pisonia grandis leaf. The second aim was to purify and characterise the enzyme glycolic acid oxidase (E.C. 1.1.3.1) (GAO), an enzyme involved in the biosynthesis of oxalate..." --abstract.. Pisonia grandis R. Br. (Nyctaginaceae) is a large tropical tree whose distribution is restricted to coral cays, in particular those with high seasonal nesting seabird populations. These trees are often the most dominant plant species found on coral cays. This is the case for the chosen study site on North West Island, a coral cay which lies off the Central Queensland coast within the Mackay Capricorn section of the Great Barrier Reef. Coral cays are almost entirely composed of coral rubble and sand and as a result the substrate pH is high (c. 9.0) and many ions are found as insoluble salts. The high pH, abundance of calcium, lack of water and high seasonal input of nitrates from nesting seabirds, are possible influences on the biosynthesis of oxalates which are found in high concentrations in P. grandis. The aims of this study were twofold. The first aim was to investigate the influence of environmental factors, such as pH and nitrate concentration, on the biosynthesis of oxalate in Pisonia grandis leaf. The second aim was to purify and characterise the enzyme glycolic acid oxidase (E.C. 1.1 .3.1) (GAO), an enzyme involved in the biosynthesis of oxalate. P. grandis was grown in a hydroponic system which was constructed in a glasshouse. The effect of variations in light intensity, pH and the concentrations of nitrate, calcium and sodium chloride in the nutrient sol ution on leaf oxalate concentration was investigated. A small diurnal variation in leaf soluble oxalate concentration was observed (O.5mmol/g DW at 07:00hrs and 0.62 mmol/g/DW at 19:00hrs) which was consistent with the notion that an intermediate in the formation of oxalate was derived from photosynthesis or photorespiration. In all other experimental regimes leaf oxalate concentrations were shown to vary in response to changes in the excess cation content of the leaves. These hydroponic studies suggested that changes in leaf excess cation concentration, and associated changes in intracellular pH, stimulate changes in the biosynthesis of oxalate in Pisonia. GAO was isolated to purity from the leaves of P. grandis and was found to be similar to GAO from other sources. The holoenzyme was found to be a hexamer (M.Wt. 250000) of subunits with molecular weight 44000. In vitro, with glycolate substrate, GAO had a pH optima of 7.0 and a Km of O.4mM. The enzyme exhibited partial competitive inhibition by oxalate (Ki 2.75mM) and was irreversibly inhibited by phydroxymercuribenzoate. Phenyllactate and iodoacetate did not inhibitthe enzyme preparation. These studies were repeated for glyoxylate and lactate as the enzyme substrates. The pH optima determined for GAO in vitro with glycolate and glyoxylate substrates, in conjunction with the pH optima reported for aminotransferase enzymes, supports the notion that leaf oxalate participates in a biochemical pH stat within the leaves of Pisonia grandis.

The Mediator (Med) complex comprises about 30 subunits and is a transcriptional co-regulator in eukaryotic systems. The core Mediator complex, consisting of the head, middle and tail modules, functions as a bridge between transcription factors and basal transcription machinery, whereas the CDK8 kinase module can attenuate Mediator’s ability to function as either a co-activator or co-repressor. Many Arabidopsis Mediator subunit has been functionally characterized, which reveals critical roles of Mediator in many aspects of plant growth and development, responses to biotic and abiotic stimuli, and metabolic homeostasis. Traditional genetic and biochemical approaches laid the foundation for our understanding of Mediator function, but recent transcriptomic and metabolomic studies have provided deeper insights into how specific subunits cooperate in the regulation of plant metabolism. In Chapter 1, we highlight recent developments in the investigation of Mediator and plant metabolism, with emphasis on the large-scale biology studies of med mutants.

We previously found that MED5, an Arabidopsis Mediator tail subunit, is required for maintaining phenylpropanoid homeostasis. A semi-dominant mutation (reduced epidermal fluorescence 4-3, ref4-3) that causes a single amino acid substitution in MED5b functions as a strong suppressor of the pathway, leading to decreased soluble phenylpropanoid accumulation, reduced lignin content and dwarfism. In contrast, loss of MED5a and MED5b (med5) results in increased levels of phenylpropanoids. In Chapter 2, we present our finding that ref4-3 requires CDK8, a Mediator kinase module subunit, to repress plant growth even though the repression of phenylpropanoid metabolism in ref4-3 is CDK8-independent. Transcriptome profiling revealed that salicylic acid (SA) biosynthesis genes are up-regulated in a CDK8-dependent manner in ref4-3, resulting in hyper-accumulation of SA and up-regulation of SA response genes. Both growth repression and hyper-accumulation of SA in ref4-3 require CDK8 with intact kinase activity, but these SA phenotypes are not connected with dwarfing. In contrast, mRNA-sequencing (RNA-seq) analysis revealed the up-regulation of a DNA J protein-encoding gene in ref4-3, the elimination of which partially suppresses dwarfing. Together, our study reveals genetic interactions between Mediator tail and kinase module subunits and enhances our understanding of dwarfing in phenylpropanoid pathway mutants.

In Chapter 3, we characterize other phenotypes of med5 and ref4-3, and find that in addition to the up-regulated phenylpropanoid metabolism, med5 show other interesting phenotypes including hypocotyl and petiole elongation as well as accelerated flowering, all of which are known collectively as the shade avoidance syndrome (SAS), suggesting that MED5 antagonize shade avoidance in wild-type plants. In contrast, the constitutive ref4-3 mutant protein inhibits the process, and the stunted growth of ref4-3 mutants is substantially alleviated by the light treatment that triggers SAS. Moreover, ref4-3 mimics the loss-of-function med5 mutants in maintaining abscisic acid (ABA) levels under both normal and drought growth conditions. The phenotypic characterization of med5 mutants extend our understanding of the role of Mediator in SAS and ABA signaling, providing further insight into the physiological and metabolic responses that require MED5.

In Chapter 4, we explore the function of MED5 and CDK8 in gene expression regulation by investigating the effect of mutations in Mediator including med5, ref4-3, cdk8-1 and ref4-3 cdk8-1 on genome-wide Pol II distribution. We find that loss of MED5 results in loss of Pol II occupancy at many target genes. In contrast, many genes show enriched Pol II levels in ref4-3, some of which overlap with those showing reduced Pol II occupancy in med5. In addition, Pol II occupancy is significantly reduced when CDK8 is disrupted in ref4-3. Our results help to narrow down the direct gene targets of MED5 and identify genes that may be closely related to the growth deficiency observed in ref4-3 plants, providing a critical foundation to elucidate the molecular function of Mediator in transcription regulation.

Amur honeysuckle (Lonicera maackii) is a shrub endemic to East Asia which has become invasive and nearly ubiquitous to the forest ecosystems of eastern North America. Through its extended growing season, competitive ability, and potential allelopathy, Amur honeysuckle alters native herbaceous-layer plant communities and inhibits the regeneration of native tree species. As such, it is representative of a range of invasive shrub species imported from East Asia. My thesis contributes to questions fundamental to the understanding this and other invasive shrubs: 1) How do species become invasive? 2) How can the invasions of the species be effectively controlled? 3) How does the ecosystem respond to treatment of the invasive species?

First, I examined the role of self-compatibility within Amur honeysuckle. I compared the berry production, seed production, and germination rates between closed-pollinated and open-pollinated flowering branches of Amur honeysuckle individuals across multiple types of invasions (heavy, light, and sprouting). I found that Amur honeysuckle not only possesses the ability to self-pollinate, but that it can produce viable self-pollinated seed sets. This ability may help explain how Amur honeysuckle able to invade isolated forest patches far removed from the main invasion.

Second, I evaluated the effectiveness of a novel herbicide adjuvant in reducing the amount of herbicide needed in the ‘cut-stump’ method of controlling Amur honeysuckle. Combining various concentrations of the most common herbicide in the world, glyphosate, with concentrations of cellulases derived from fungi, 2XL, I examined whether the cellulases improved the effectiveness of glyphosate, potentially by increasing glyphosate movement into the vascular tissue of Amur honeysuckle through the degradation of cell walls. While 2XL was not an effective adjuvant, glyphosate concentrations of less than half the recommended dosages were equally effective as higher concentrations in preventing sprouting of treated stumps. The ineffectiveness of 2XL may imply a need for protein-mitigated diffusion of glyphosate across cell walls and into the vascular tissue of the plant, which would be inhibited by the breakdown of cell walls.

Finally, I tested how deeper intensities of mulching-head treatments affected the sprouting response of Amur honeysuckle and the response of the herbaceous-layer plant community after treatment. I found a negative relationship between the volume of sprouting Amur honeysuckle and increasing depth of mulching-head treatment. Additionally, increasing mulching-head intensities were correlated with increased herbaceous layer diversity and conservation value as represented by Floristic Quality Index. Mulching-head treatments are a promising tool in controlling heavy invasions of non-native shrubs.

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.

Phenotypic data is of crucial importance for plant breeding in estimating a plant's biomass. Traits such as leaf area and plant height are known to be correlated with biomass. Image analysis and computer vision methods can automate data analysis for high-throughput phenotyping. Many methods have been proposed for plant phenotyping in controlled environments such as greenhouses. In this thesis, we present multiple methods to estimate traits of the plant crop sorghum from images acquired from UAV and field-based sensors. We describe machine learning techniques to extract the plots of a crop field, a method for leaf counting from low-resolution images, and a statistical model that uses prior information about the field structure to estimate the center of each plant. We also develop a new loss function to train Convolutional Neural Networks (CNNs) to count and locate objects of any type and use it to estimate plant centers. Our methods are evaluated with ground truth of sorghum fields and publicly available datasets and are shown to outperform the state of the art in generic object detection and domain-specific tasks.

This thesis also examines the use of crowdsourcing information in video analytics. The large number of cameras deployed for public safety surveillance systems requires intelligent processing capable of automatically analyzing video in real time. We incorporate crowdsourcing in an online basis to improve a crowdflow estimation method. We present various approaches to characterize this uncertainty and to aggregate crowdsourcing results. Our techniques are evaluated using publicly available datasets.

T-cells are present in the immune system to fight against invaders. Once their job is done, suppressing their activity is an important step in maintaining a proper immune response. Myeloid derived suppressor cells (MDSCs) are immune cells that suppress T-cell activity. Currently, MDSCs are defined as a heterogeneous population of immature cells that are derived in the bone marrow and travel to the site of inflammation or cancer. Two major subtypes of MDSCs have been identified in mice and humans, monocyte-like MDSCs (M-MDSC) and granulocyte MDSCs (G-MDSC). G-MDSCs typically make up the majority of the total population of MDSCs but are less T-cell suppressive than M-MDSCs. One of the major problems in the study of MDSCs is that the current marker system for subtypes does not differentiate between precursor MDSCs (lacking suppressive ability) and functional MDSCs (those with suppressive ability). Therefore, using cancer models in mice, we investigated the development and potential to classify precursor MDSCs from functional MDSCs. While MDSCs have been highlighted as a target cell to inhibit in cancer, in other conditions, such as pregnancy, MDSCs have been shown to be beneficial in maintaining a normal pregnancy. Therefore, targeting the increase of MDSCs in abnormal pregnancy conditions like pre-eclampsia may act as a prevention or therapeutic strategy. Finally, it is known that many dietary components can act as modulators of immune cells. Specifically, the polyphenol like phytochemical, curcumin has been shown to act as an anti-inflammatory agent with the potential to modulate multiple immune cells. Therefore, we propose two different studies to investigate the potential of curcumin as either an inhibitor and/or promotor of MDSCs in a disease-specific context. Together the role of phytochemicals as immunomodulators of MDSCs is still very young, in part due to the complexity of phytochemicals themselves, but the studies cited here provide evidence that the field is ripe for additional questions to be asked.

Electrostatic Precipitators (ESPs) are widely used to capture particulate matter from flue gas. In coal-based power stations, they are used for capturing fly ash before the flue gas is released to the environment. Coal-based power plants are still one of the major suppliers of energy because they are more reliable and have lower unit cost of power generation. Under the current environmental protection regulation controlled by the Environment Protection Agency (EPA), only the finer particles can be released to the environment. However, this is likely to change and coal-based power plants will then have to face stricter rules about permissible size limits for particulate matter (PM) discharged in flue gas, namely the particle size of PM 2.5 (micron) or less. It is therefore required that the capabilities of ESPs are enhanced so that they will be able to capture these finer particles. The main aim of the research is to investigate the micro-size particulate matter capture ability of existing ESPs and determine the operational parameter relationships to improve the collection efficiency of ESPs. In particular, this research focuses specifically on the flow phenomena of the finer fly ash particles inside the ESP model and how they are impacted by the changed geometries and varied electric fields. This involves studying the flow velocity and forces associated with the flow and the electric field and the relevant parameters affecting the dust collection and thus establishing and validating a relationship between the interaction of two phase flow and electric field to reveal the underlying physics for collecting finer particles. To achieve the aim, a laboratory scale ESP was constructed for undertaking various tests and measurements using a novel method. This method involved flow measurement in the ESP chamber using a pitot tube and a cobra tube, whilst employing different shaped baffles in the chamber, varying production of electrostatic field in the ESP model and testing its capturing capacity. This research investigated the influence of internal geometry of the ESP on the flow in the ESP chamber. Two different shaped baffles – semicircular and arrow shaped - were designed, fabricated and inserted in the ESP chamber to effect changes to the flue gas pathway to enhance collection efficiency and collection capability of submicron particles. The flow measurements and experimental results were compared and validated with the 2D ii simulation results. Results using baffles indicate that internal geometry of the ESP has an influence on collection efficiency and changing the internal shape produces swirling flow inside ESP, which, in turn, improves collection efficiency. In addition, baffles increase residence time, which allows capture of sub-micron particles. A high voltage transformer and associated electrode plates and rods were designed, constructed and fitted into the model ESP for measuring and investigating particle collection efficiency under various velocities and electric/voltage characteristics. Production of electric field in a lab model ESP of this type and its testing constitutes a novel approach as such work is not found in the public domain. The experimental results show that ESP collection efficiency is higher at high voltages and at low fly ash velocity and the collection efficiency rapidly decreases when voltage reduces. A mathematical model was developed and validated with the experimental measurements to confirm the collection efficiency. By analysing the various conditions and scenarios, an optimum operational condition within an operational range were developed and recommended for future ESP operation. By implementing a TR (Transformer–Rectifier) in different collection chambers, power consumption of the ESP can be reduced. The research also revealed new information on the particulate matter size distribution and the collection of submicron particles from flue gas of coal-fired power plants. Particle size distribution analysis was conducted using a Mastersizer and the morphology of the particles was analysed using a Scanning Electron Microscope (SEM). Size distribution analysis suggested that higher voltage and lower flue gas velocity will be more suitable to capture submicron particles. The morphology study indicated that smaller particles have a tendency to agglomerate with bigger particles. Overall, this thesis provides new knowledge about Electrostatic Precipitator operation with new geometries and under various electric field conditions at a laboratory scale, whilst achieving operational efficiency improvement and improving the capture of sub-micron particulate matter. The knowledge obtained from this research would be a good basis to operate industrial ESPs for future sustainable coal-fired power generation.

A survey of the community of helminths in Emydura krefftii Gray in central and northern Queensland was undertaken. Then a detailed study of Sychnocotyle kholo Ferguson, Cribb and Smales, 1999, a newly described aspidogastrean parasite of E. krefftii, was conducted. The principal aim of this study was to examine the life history, fine morphology and phylogenetic relationships of this species. Specimens of Emydura krefftii were sampled from six coastal catchments from Cooktown to Bundaberg in northern and central Queensland. Concurrently data were collated on the community structure of helminths of E. krefftii. To examine the life history of S. kholo, molluscs were collected and examined for juvenile aspidogastreans from areas sampled for turtles and S. kholo eggs were collected from the faeces of collected turtles. The study of morphology of this helminth involved staining whole mounts and sections for light microscopy for gross morphology and examination of organ systems. Scanning electron microscopy was used to examine the outer surface of the worm in detail. For fine morphology of organs, transmission electron microscopy and confocal microscopy were applied. Finally characters were identified for a phylogenetic analysis and a data matrix was constructed and executed with Phylogenetic Analysis Using Parsimony (PAUP) software.

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.

Regulation of metabolism in mammalian cells is achieved through a complex interplay between cellular signaling, metabolic reactions, and transcriptional changes. The modeling of metabolic fluxes in a cell requires the knowledge of all these mechanisms, some of which may be unknown. A cybernetic approach provides a framework to model these complex interactions through the implicit accounting of such regulatory mechanisms, assuming a biological “goal”. The goal-oriented control policies of cybernetic models have been used to predict metabolic phenomena ranging from complex substrate uptake patterns and dynamic metabolic flux distributions to the behavior of gene knockout strains. The premise underlying the cybernetic framework is that the regulatory processes affecting metabolism can be mathematically formulated as a cybernetic objective through variables that constrain the network to achieve a specified biological “goal”.

Cybernetic theory builds on the perspective that regulation is organized towards achieving goals relevant to an organism’s survival or displaying a specific phenotype in response to a stimulus. While cybernetic models have been established by prior work carried out in bacterial systems, we show its applicability to more complex biological systems with a predefined goal. We have modeled eicosanoid, a well-characterized set of inflammatory lipids derived from arachidonic acid, metabolism in mouse bone marrow derived macrophage (BMDM) cells stimulated by Kdo2-Lipid A (KLA, a chemical analogue of Lipopolysaccharide found on the surface of bacterial cells) and adenosine triphosphate (ATP, a danger signal released in response to surrounding cell death) using cybernetic control variables. Here, the cybernetic goal is inflammation; the hallmark of inflammation is the expression of cytokines which act as autocrine signals to stimulate a pro-inflammatory response. Tumor necrosis factor (TNF)-α is an exemplary pro-inflammatory marker and can be designated as a cybernetic objective for modeling eicosanoid—prostaglandin (PG) and leukotriene (LK)—metabolism. Transcriptomic and lipidomic data for eicosanoid biosynthesis and conversion were obtained from the LIPID Maps database. We show that the cybernetic model captures the complex regulation of PG metabolism and provides a reliable description of PG formation using the treatment ATP stimulation. We then validated our model by predicting an independent data set, the PG response of KLA primed ATP stimulated BMDM cells.

The process of inflammation is mediated by the production of multiple cytokines, chemokines, and lipid mediators each of which contribute to specific individual objectives. For such complex processes in mammalian systems, a cybernetic objective based on a single protein/component may not be sufficient to capture all the biological processes thereby necessitating the use of multiple objectives. The choice of the objective function has been made by intuitive considerations in this thesis. If objectives are conjectured, an argument can be made for numerous alternatives. Since regulatory effects are estimated from unregulated kinetics, one encounters the risk of multiplicity in this regard giving rise to multiple models. The best model is of course that which is able to predict a comprehensive set of perturbations. Here, we have extended our above model to also capture the dynamics of LKs. We have used migration as a biological goal for LK using the chemoattractant CCL2 as a key representative molecule describing cell activation leading to an inflammatory response where a goal composed of multiple cybernetic objectives is warranted. Alternative model objectives included relating both branches of the eicosanoid metabolic network to the inflammatory cytokine TNF-α, as well as the simple maximization of all metabolic products such that each equally contributes to the inflammatory system outcome. We were again able to show that all three cybernetic objectives describing the LK and PG branches for eicosanoid metabolism capture the complex regulation and provide a reliable description of eicosanoid formation. We performed simulated drug and gene perturbation analyses on the system to identify differences between the models and propose additional experiments to select the best cybernetic model.

The advantage to using cybernetic modeling is in its ability to capture system behavior without the same level of detail required for these interactions as standard kinetic modeling. Given the complexity of mammalian systems, the cybernetic goal for mammalian cells may not be based solely on survival or growth but on specific context dependent cellular responses. In this thesis, we have laid the groundwork for the application of cybernetic modeling in complex mammalian systems through a specific example case of eicosanoid metabolism in BMDM cells, illustrated the case for multiple objectives, and highlighted the extensibility of the cybernetic framework to other complex biological systems.

Environmental DNA (eDNA) is being used increasingly for biomonitoring of communities (e.g., microbes, macroinvertebrates, fish species) across terrestrial and aquatic ecosystems. Developing methods that combine eDNA approaches with metagenomic barcoded amplicon sequencing (eDNA-metabarcoding) are now providing a powerful noninvasive and cost-effective means for comprehensively surveying biodiversity in a wide range of habitats. Invasive species have a substantial impact on the ecology and economics of the Great Lakes region, and eDNAmetabarcoding methods have recently been applied in monitoring non-native, as well as native, fish populations in the freshwater systems there. In this research, we validated an eDNAmetabarcoding approach that uses established platforms, the MiFish/MitoFish pipeline, for fish community monitoring on Lake Michigan. For validation, we compared survey results from our eDNA-metabarcoding approach to those obtained using traditional surveys (e.g., electrofishing and seining). We also sampled a closed 180,000-gallon freshwater fish tank system to see how well our methods characterized a known native fish population that resided in the tank. Finally, we applied the approach to monitoring invasive and native fish populations in southern Lake Michigan at a site that is currently undergoing restoration to improve the aquatic habitats.. We were able to reliably capture the fish community structure of the native fish tank as well as those of open waters on the lake using our methods. Diversity patterns detected at the restoration site using our eDNA-metabarcoding approach accurately reflected those of the historical record, which have taken many years to establish by conventional means. Overall, this study suggests eDNAmetabarcoding is an efficient, credible, and powerful approach to biomonitoring.

Worldwide, as many as 1 billion people suffer from neurological disorders. Fundamentally, neurological disorders are caused by dysregulation of biochemical signaling within neurons, leading to deficits in learning and memory formation. To identify better preventative and therapeutic strategies for patients of neurological disorders, we require a better understanding of how biochemical signaling is regulated within neurons.

Biochemical signaling at the connections between neurons, called synapses, regulates dynamic shifts in a synapse’s size and connective strength. Called synaptic plasticity, these shifts are initiated by calcium ion (Ca²⁺) flux into message-receiving structures called dendritic spines. Within dendritic spines, Ca²⁺ binds sensor proteins such as calmodulin (CaM). Importantly, Ca²⁺/CaM may bind and activate a wide variety of proteins, which subsequently facilitate signaling pathways regulating the dendritic spine’s size and connective strength.

In this thesis, I use computational models to characterize molecular mechanisms regulating Ca²⁺-dependent protein signaling within the dendritic spine. Specifically, I explore how Ca²⁺/CaM differentially activates binding partners and how these binding partners transduce signals downstream. For this, I present deterministic models of Ca²⁺, CaM, and CaM-dependent proteins, and in analyzing model output I demonstrate in-part that competition for CaM-binding alone may be sufficient to set the Ca²⁺ frequency-dependence of protein activation. Subsequently, I adapt my deterministic models into particle-based, spatial-stochastic frameworks to quantify how spatial effects influence model output, showing evidence that spatial gradients of Ca²⁺/CaM may set spatial gradients of activated proteins downstream. Additionally, I incorporate into my models the most detailed model to-date of Ca²⁺/CaM-dependent protein kinase II (CaMKII), a multi-subunit protein essential to synaptic plasticity. With this detailed model of CaMKII, my analysis suggests that the many subunits of CaMKII provide avidity effects that significantly increase the protein’s effective affinity for binding partners, particularly Ca²⁺/CaM. Altogether, this thesis provides a detailed analysis of Ca²⁺-dependent signaling within dendritic spines, characterizing molecular mechanisms that may be useful for the development of novel therapeutics for patients of neurological disorders.