Dissertations / Theses on the topic 'Biological psychology not elsewhere classified'

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.

Research has consistently demonstrated that exposure to nature, as opposed to urban environments, can be beneficial to health and wellbeing. Among natural landscapes, aquatic (blue space) scenes are among the most preferred and psychologically restorative. Since such landscapes face an increasing range of demands, there is a need to understand how their restorative qualities arise and might be preserved, both in terms of the content of a scene and the psychological processes involved in its interpretation. This thesis examines the cognitive impact of placing artificial (human-made) objects in natural landscapes with and without water. It reports new findings regarding the importance of specific scene content for the restorative potential of blue space. The research also explores some of the underlying psychological processes, addressing novel questions about implicit (subconscious) attitudes towards natural landscapes. It compares implicit and explicit attitudes for the first time in this context. In four studies, methods from social and experimental psychology were used to investigate attitudes towards blue and green space with and without artificial objects. To examine the issues of both artificial objects and implicit attitudes, Study 1 used the Affect Misattribution Procedure (which measures implicit attitudes towards images) to assess whether implicit affect (subconscious positive or negative emotion) differed when the same natural scene was viewed with and without artificial objects. Results showed that introducing objects into natural scenes had a negative impact on implicit affect, particularly when the scene contained water. In order to be able to compare implicit and explicit attitudes, Study 2 examined explicit affective reactions to the images from Study 1 using questions adapted from the Perceived Restorativeness Scale (a measure of the restorative potential of environments). Blue space scenes were rated more highly than green space scenes on all components except aesthetics. The presence of artificial objects resulted in lower ratings on all measures for both blue and green scenes. Study 3 was motivated by an indication in the results from Study 1 that implicit attitudes towards blue and green space may differ. The Affect Misattribution Procedure was used to investigate this for natural landscapes without artificial objects. The study also examined whether implicit attitudes differ according to the type of blue or green environment. Viewing blue space scenes resulted in more positive implicit affect than green space, with sea views generating the most positive implicit affect of all. Following the discovery that artificial objects had a more negative impact on implicit attitudes to blue space than green space, Study 4 tested the possibility that this could be due to such objects being more disruptive to the conceptual coherence of aquatic scenes. The conceptual-semantic congruence of artificial objects was assessed using a lexical decision task, in which participants reacted to object words superimposed on scenes. Results did not support the hypothesis that artificial objects are less congruent in blue space than green space. Overall, the studies provide evidence that placing artificial objects in natural landscapes, particularly aquatic landscapes, adversely affects both implicit and explicit attitudes towards the scenes and may reduce their restorative potential. By successfully combining methods from social and experimental psychology, this research validates novel ways of formulating and addressing questions about why some environments have a more positive psychological impact than others. The new results reported here are not easily explained by current restorative theory, therefore might contribute to refining the theoretical framework within which restorative environments are studied.

Rapid growth of energy consumption and greenhouse gas emissions from fossil fuels have promoted extensive research on biofuels. Algal biofuels have been considered as a promising and environmentally friendly renewable energy source. However, several limitations have inhibited the development of cost-effective biofuel production, which includes unstable cultivation caused by invading organisms and high cost of lipid extraction. This dissertation aims to investigate photochemical approaches to prevent culture collapse caused by invading organisms and biological approaches for the development of cost-effective lipid extraction methods.

As a chemical-free water treatment technology, ultraviolet (UV) irradiation has been widely applied to inactivate pathogens but has not been used in algal cultivation to control invading organisms. To evaluate the potential of using UV irradiation to control invading algal species and minimize virus predation, Tetraselmis sp. and Paramecium bursaria Chlorella virus 1 (PBCV-1) were examined as challenge organisms to evaluate effectiveness of UV disinfection. The concentration of viable (reproductively/infectively active) cells and viruses were quantified by a most probable number (MPN) assay and a plaque assay. A low-pressure collimated-beam reactor was used to investigate UV₂₅₄ dose-response behavior of both challenge organisms. A medium-pressure collimated-beam reactor equipped with a series of narrow bandpass optical filters was used to investigate the action spectra of both challenge organisms. Both challenge organisms showed roughly five log₁₀ units of inactivation for UV₂₅₄ doses over 120 mJ/cm². the most effective wavelengths for inactivation of Tetraselmis were from 254 nm to 280 nm, in which the inactivation was mainly attributed to UV-induced DNA damage. On the contrary, the most effective wavelength for inactivation of PBCV-1 was observed at 214 nm, where the loss of infectivity was mainly attributed to protein damage. These results provide important information for design of UV reactors to minimize the impact of invading organisms in algal cultivation systems.

Additionally, a virus-assisted cell disruption method was developed for cost-effective lipid extraction from algal biomass. Detailed mechanistic studies were conducted to evaluate infection behavior of Chlorovirus PBCV-1 on Chlorella sp., impact of infection on mechanical strength of algal cell wall, lipid yield, and lipid distribution. Viral disruption with multiplicity of infection (MOI) of 10^-8 completely disrupted concentrated algal biomass in six days. Viral disruption significantly reduced the mechanical strength of algal cells for lipid extraction. Lipid yield with viral disruption increased more than three times compared with no disruption control and was similar to that of ultrasonic disruption. Moreover, lipid composition analysis showed that the quality of extracted lipids was not affected by viral infection. The results showed that viral infection is a cost-effective process for lipid extraction from algal cells as extensive energy input and chemicals required by existing disruption methods are no longer needed.

Overall, this dissertation provides innovative approaches for the development of cost-efficient algal biofuels. Application of UV disinfection and viral disruption significantly reduces chemical consumption and improves sustainability of algal biofuel production.

The goal of my dissertation is to take a step toward shifting the narrative in engineering from “surviving” to “thriving” so that more engineering students can reach their full potential in college and beyond. Many engineering students experience barriers such as the hardships of engineering culture, which are exacerbated for women and underrepresented racial/ethnic minorities(such as Black, Latinx, and Indigenous students). These barriers are well documented in research and well discussed in interventions to support engineering student success, under the assumption that helping students cope with these cultural and systemic barriers will, by itself, lead to their success. My research on engineering thriving challenges this assumption by asserting that the skills engineering students need to succeed academically, socially, and personally differ from the skills they need to “survive” cultural and systemic barriers.

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.

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.

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.

Osteoarthritis (OA) is a leading cause of disability globally, with higher incidence in older people and lower socioeconomic status populations. The challenges health care systems face with management of the disease highlights the importance of OA research. Many studies examine possible risk factors of knee and hip OA including obesity, smoking, and alcohol consumption. Findings support that while obesity increases risk of knee OA, smoking is not a major risk factor. These extrinsic factors are, however, associated with lower socioeconomic status, and also with anxiety and depression disorders. Up to 30% of patients with chronic knee OA have described psychological stress and decreased quality of life due to debilitating pain, but the effects of psychological stress on development of knee OA has not been described.

At the cellular level, mechanosensitive cation channels in cartilage and bone, are involved with OA, but studies looking specifically at synovium and joint capsule are limited. Transient receptor potential (TRP) channels are upregulated in joint capsule in end-stage primary shoulder OA. We were unable to identify any previous studies evaluating Piezo channel expression in musculoskeletal soft tissues, but Piezo channel antagonism reduces chondrocyte death after mechanical injury. These findings suggest channels may help regulate joint responses to repetitive loading during training or work while also contributing to protective mechanisms within the musculoskeletal system. The overall objective of this research was to investigate factors that impact OA development or the disease phenotype. Two studies evaluated the following aims: 1) demonstrate the influence of chronic psychological stress on knee OA and overall systemic health, and 2) characterize the role of mechanosensitive channels in the joint capsule in OA. The first study used a mouse chronic social defeat model paired with destabilization of the medial meniscus (DMM) surgery to create a social stress scenario during OA development. We hypothesized chronic social defeat would exacerbate knee OA structural changes and systemic inflammation. The second study aimed to explore the role of mechanosensitive channels in joint capsule during OA development in the equine. Immunohistochemistry was performed on forelimb fetlock joint capsule from horses with varying degrees of lameness to first identify TRP and Piezo channel expression. Next, fibroblasts were isolated from the tissue to determine channel activity. We hypothesized that TRP and Piezo channels are required for normal homeostasis, but are dysregulated in OA and dysregulation contributes to fibrosis of the joint capsule. Joint capsule fibrosis leads to joint stiffening and reduced range of motion, two of the cardinal signs of OA.

The results of the first study showed OA was induced to a similar extent in both groups of mice that underwent DMM surgery. While anxiety- and depressive-like behaviors were exhibited by mice that underwent chronic social defeat episodes, unexpectedly, the majority of systemic inflammatory markers were not worse in mice with DMM and chronic social defeat compared to DMM alone. We were also able to show TRP and Piezo channel expression in one normal dorsal and palmar fetlock joint capsule sample, however, COVID-19 prevented further investigation. With our results we were able to conclude that while chronic social stress influences development of OA, in the current experiments, neither systemic inflammation nor structural signs of knee OA were worse with chronic social stress. We hope that exploration of OA through these two studies will help us understand how the disease contributes to overall systemic dysfunction while also providing a baseline for future development of TRP and Piezo channel modulators to prevent joint pathologies.

The methylotrophic yeast, Pichia pastoris (recently reclassified as spp. Komagatella) has long been regarded as a useful host organism for the production of recombinant proteins, particularly when using the AOX system which utilizes methanol as both the inducing agent as well as the primary carbon source for growth and energy. Significant historical work has shown that growth rate and protein productivity can be correlated to methanol concentration. However, the relationship between oxygen and protein productivity are less consistent. While with many variations models having been developed and used for analyzing culture kinetics, these models have only been applied to methanol concentration. Furthermore, while results for methanol are fairly consistent, oxygen considerations have been far less consistent.

This work presents various bi-variate models which includes considerations for growth and inhibition for both methanol and oxygen with this expanded model showing strong alignment to previous works to both oxygen and methanol data. While more work is necessary to fully confirm and validate which form of the bivariate model is most appropriate, this work provides a framework necessary to expand analysis to include oxygen considerations. This framework has the potential to be used to further inform selection of feeding methodology as well as direct investigations into metabolic studies.

This dissertation reports a study of the dissolution mechanism which governs the leaching of Cu from chalcopyrite (CuFeS2) in acidic media at atmospheric pressure and examines the differences between chemical (abiotic), leaching and bioleaching. An array of solution, solid surface and bulk speciation studies were used to make a comprehensive study of the CuFeS2 leaching process(es).
Thesis (PhD)--University of South Australia, 2008.

In 2018, the World Health Organization (WHO) reported approximately 37 million people are living with the Human Immunodeficiency Virus (HIV). Suppressing replication of the virus down to undetectable levels was achieved by combination antiretroviral therapy (cART) which effectively reduced the mortality and morbidity rates of HIV positive individuals. Despite the improvements towards combatting HIV/AIDS, no successful treatment exists to eradicate the virus from an infected individual. Treatment regimens are lifelong and prompt less than desirable side effects including but not limited to; drug-drug interactions, toxicity, systemic organ complications, central nervous system HIV triggered disorders and most importantly, drug resistance. Current therapies are becoming ineffective against highly resistant HIV strains making the ability to treat long-term viral suppression a growing issue. Therefore, potent and more effective HIV inhibitors provide the best chance for long-term successful cART.

HIV-1 protease (PR) enzyme plays a critical role in the life cycle and replication of HIV. Significant advancements were achieved through structure-based design and X-ray crystallographic analysis of protease-bound to HIV-1 and brought about several FDA protease inhibitors (PI). Highly mutated HIV-1 variants create a challenge for current and future treatment regimens. This thesis work focuses on the design, synthesis, and evaluation of two new classes of potent HIV-1 PIs that exhibit a novel bicyclic oxazolidinone feature as the P2 ligand and a novel bis squaramide scaffold as the P2/P3 ligand. Several inhibitors displayed good to excellent activity toward HIV-1 protease and significant antiviral activity in MT-4 cells. Inhibitors 1.65g and 1.65h were further evaluated against a panel of highly resistant multidrug-resistant HIV-1 variants and displayed antiviral activity similar to Darunavir. X-ray crystal structures of inhibitor 1.65a and inhibitor 1.65i were co-crystallized with wild type HIV-1 protease and solved at a 1.22 Å and 1.30 Å resolution and maintained strong hydrogen bond with the backbone of the PR enzyme.

Cognitive control is accomplished by a set of higher-order cognitive processes that are recruited to aid in the completion of various tasks. A popular proposed mechanism is the Dual Mechanisms of Control (Braver, Gray, & Burgess, 2007), proposing proactive and reactive mechanisms. While neuroscience studies provide evidence that these are two distinct processes, it remains unclear whether the processes are competing, or whether they can be used together. That is, are the two processes able to both be enacted to some degree? Further, whether these mechanisms can be titrated to produce a gradient-like use of control on a trial-level basis is unknown. These are the two primary pursuits of this dissertation. Experiment 1 shows the titrated pattern of control use, indicating (a) sensitivity to task demands, and (b) dynamic use of proactive and reactive control at the trial level, in a new task. Further, a novel contribution is the observation of ability to titrate the use of control. Additional experiments relate performance on this task to working memory (Experiment 2), replicate the findings in an online format (Experiment 3), and differentiate performance from distance effects commonly seen in relative judgment tasks (Experiment 4). This work has implications for the understanding of how cognitive control functions and how dynamically the use of these mechanisms can be adjusted.

Many animal species invest in extended parental care for their offspring. Parental care is costly, and natural selection favors investment strategies which maximize reproductive success. Biparental care is relatively rare, but when it does occur it has been found to increase success in terms of offspring survival and growth and in terms of future reproductive opportunities. In burying beetles (Nicrophorus spp.), both male and female participate in extended parental care. However, the fitness benefits of biparental care in burying beetles have been difficult to establish, with some studies reporting significantly smaller broods produced when both male and female are present. Variation in environmental conditions, such as temperature, is an important part of the context in which biparental care evolves. I hypothesize that biparental care acts as a buffer against environmental variation. This hypothesis predicts that biparental care will lead to greater reproductive success compared to uniparental care when temperature is increased during a reproductive attempt. I also tested the load-lightening hypothesis, which holds that biparental care benefits future reproduction by lowering the costs of reproduction. This predicts that the additional care by the other parent will allow females to rear higher quality second broods. I conducted a male removal experiment at two temperature treatments, using the species Nicrophorus orbicollis. I measured reproductive success during manipulated first brood and during second broods which females reared without a male, regardless of prior experience. I found that, contrary to my hypothesis, biparental care at the higher temperature resulted in reduced reproductive success compared to uniparental care. I found no effect of biparental care on the success of second broods. Instead, I found evidence of reproductive restraint associated with the higher temperature treatment in delayed egg-laying and increased feeding during second broods.