The NF-κB transcription factor is expressed in the majority of mammalian cells and regulates a large number of genes with important functions in a variety of cellular processes including cell growth, division, apoptosis and inflammatory responses. Perturbation of NF-κB response has been implicated in a variety of diseases such as asthma and inflammatory bowel disease, in addition to various forms of cancer. Through experiments at the single cell level it has been shown that NF-κB displays complex temporal activation, notably including nucleo-cytoplasmic oscillations. It has been observed that these oscillations occur in a heterogeneous manner; as such they are masked when measured at the population level. In contrast, pulsed TNFα treatment at 100 min intervals produces regular and synchronous nuclear peaks of NF-κB. Such pulsatile stimulation may reflect more accurately physiological conditions. The work in this project uses a Systems Biology approach consisting of bioinformatic, mathematical, and experimental methodologies to investigate how NF-κB can regulate such a diverse set of gene responses. Previously published studies have proposed that target gene expression levels following NF-κB activation (continuous TNFα) can be explained by a combination of key parameters, including transcript degradation rate, transcript structure, and transcription initiation rate. Initial work in this project highlighted that these explanatory factors are not sufficient to describe the observed temporal order of gene transcription. The roles of miRNAs and NF-κB subunit phosphorylation in regulation were additionally explored. A large set of genes was identified that are activated more strongly by pulsed TNFα than by continuous TNFα treatment. This suggests a new unreported mechanism of gene regulation, the possible causes of which are examined in this thesis. The gene list was refined by altering pulse frequency, which revealed an enrichment of NF-κB targets correlated with the regularity of these pulses. Temperature shift and anti-inflammatory drug treatment (Diclofenac) were shown to have a profound effect on NF-κB oscillation frequency. These perturbations provide an alternative method to study the effects of NF-κB oscillation frequency on specific target genes, independent of a pulse regime. Integration and analysis of these datasets suggested that a core, frequency-encoded set of genes regulated by NF-κB might exist. It is proposed that such genes may respond optimally to specific frequencies of NF-κB activation, implying a potential frequency threshold. The presence of such genes may explain the need for the complex systems that control NF-κB timing. It was noted that there was an enrichment of genes encoding transcription factors within the frequency encoding set, in addition to proteins which are known to be involved in the control of inflammation.

Wnt signalling is a critical cellular communication pathway controlling cell fate in all metazoan organisms. Timely activation of this pathway is crucial to coordinate development, control homeostasis of adult tissues, and to avoid cancer. Wnt signal transduction depends primarily on the activities of three multiprotein complexes; the 'degradasome', which targets the central effector β-catenin for degradation in the absence of Wnt; the 'signalosome', which is assembled by Dishevelled upon Wnt-receptor binding to inactivate the degradasome, thus allowing β-catenin to accumulate; and the 'enhanceosome', which captures β-catenin, granting it access to target genes and relieving their transcriptional repression by Gro/TLE. Many of the components of these complexes have now been identified, but details of their regulation, and in particular the mechanisms by which they are switched on and off, remain poorly understood. The majority of this thesis is concerned with the mechanism by which β-catenin relieves the transcriptional repression imposed upon Wnt target genes, and thereby activates the Wnt 'transcriptional switch'. In Chapter 2, I present data showing that apposition of Gro/TLE and UBR5, a HECT E3 ubiquitin ligase, by β-catenin promotes Gro/TLE ubiquitylation, earmarking it for extraction by the VCP/p97 ATPase and ultimately leading to inactivation of its repressive function. In Chapter 3, I present the results of a different, ongoing study to identify the mechanism by which a cytoplasmic negative regulator, Naked, acts to interfere with the function of Dishevelled, promoting the switching of signalosomes and the termination of canonical Wnt signalling. These findings advance our understanding of the mechanisms by which the Wnt signalling pathway is switched on and off, and suggest new targets for therapeutic intervention in Wnt- driven cancers.

The organic electronic ion pump (OEIP) is an electrically controlled polymer-based device that has the capability to interact with biological systems down to a single cell level by mimicking neural signalling. This is accomplished by translation of an electrical signal into a chemical output, such as ions and neurotransmitters. Because of the combined spatial and temporal precision, this is a technology with a promising future as an advanced therapeutic device. Depending on the application, the OEIP requires different geometries. Implants that will be used to control on a single cell level require very small dimensions, while for example extracorporeal mounted OIEPs, with only the delivery channel penetrating the skin, require much longer channels. Despite the application, it is necessary to have a good knowledge about the transport and delivery properties and how they change due to the geometry. These properties have been observed as very varying and unstable in early unpublished results, and these findings motivate this project. This project includes photolithographic fabrication and investigation of transport and delivery properties such as effective resistance, efficiency and stability of OEIPs with varying delivery channel lengths and widths. Shorter delivery channels show a consistent but relatively low efficiency. Delamination between different layers of the device is suspected as the cause. Initially, the longer delivery channels show a low functionality, most probably due to poor encapsulation. It is suggested that a soft, water-permeable plastic best encapsulates OEIPs that will be used as a medical implant, while a material impermeable to water, for example a metal, could successfully encapsulate OEIPs operating in air.

Activated receptor tyrosine kinase (RTK), such as the epidermal growth factor (EGF) receptor (EGFR) and the platelet-derived growth factor (PDGF) receptor (PDGFR), recruit downstream signalling proteins, including phosphatidylinositol 3-kinase (PI3K). PI3K, composed of a regulatory p85 subunit and a catalytic p110 subunit, phosphorylates phosphatidylinositol 4,5-bisphosphate at the 3 position to generate phosphatidylinositol 3,4,5-trisphosphate. This lipid second messenger activates Akt, which promotes cell growth, cell cycle entry and progression, as well as cell survival and cellular migration. PTEN, a tumor suppressor protein, dephosphorylates phosphatidylinositol 3,4,5-trisphosphate at the 3 position, turning off Akt signalling. PTEN contains a C-terminal PDZ binding motif that binds to the PDZ2 domain of MAGI-2, a scaffolding protein that localizes signalling molecules to the plasma membrane. MAGI-2 has ten domains that potentially mediate multiple protein-protein interactions simultaneously. A PTEN associated-complex (PAC) has been described and may contain MAGI-2, PTEN and p85. The PAC is hypothesized to form at the plasma membrane at appropriate sites for PTEN to gain access to its lipid substrates, since the binding of PTEN to MAGI-2 has been shown to enhance the suppression of PI3K-mediated Akt signalling. In order to better understand the role of the PAC in attenuation of the Akt signalling pathway, regions of the MAGI-2 scaffolding protein were mapped to identify the interactions taking place in the PAC. MAGI-2, and its individual domains, were expressed as GST fusion proteins. These were immobilized onto beads and allowed to bind to cellular proteins including PTEN, p85, PDGFR and EGFR using a GST pull-down experiment. The proteins bound to GST-MAGI-2 were identified using an immunoblot analysis. In vitro pull-down experiments revealed that MAGI-2 PDZ2 and PDZ5 domains bind to PTEN, and both MAGI-2 WW domains were shown to bind to p85. EGFR and PDGFR did not bind to the PDZ domains of MAGI-2 under the conditions studied. In order to study protein-protein interactions in cells, immunoprecipitation assays were also performed. Full length MAGI-2 was expressed tagged to a Myc epitope. This was used in immunoprecipitation assays to determine if MAGI-2 could co-immunoprecipitate with proteins involved in the Akt signalling pathway, such as PTEN, p85, PDGFR and EGFR. MAGI-2 can co-immunoprecipitate with PTEN upon 5 min EGF stimulation however, this result was inconclusive because replicate experiments did not verify this initial observation. MAGI-2 does not co-immunoprecipitate with the EGFR nor p85, under the conditions tested. We examined for these interactions after 5 min of growth factor stimulation and more experiments that test different time points after growth factor stimulation would reveal if these interactions are present at shorter time points. MAGI-2 has been shown to bind to PTEN and p85 in vitro and therefore has the potential to regulate the attenuation of the PI3K/Akt signalling pathway in response to activated EGFR and/or PDGFR.

Activated receptor tyrosine kinase (RTK), such as the epidermal growth factor (EGF) receptor (EGFR) and the platelet-derived growth factor (PDGF) receptor (PDGFR), recruit downstream signalling proteins, including phosphatidylinositol 3-kinase (PI3K). PI3K, composed of a regulatory p85 subunit and a catalytic p110 subunit, phosphorylates phosphatidylinositol 4,5-bisphosphate at the 3 position to generate phosphatidylinositol 3,4,5-trisphosphate. This lipid second messenger activates Akt, which promotes cell growth, cell cycle entry and progression, as well as cell survival and cellular migration. PTEN, a tumor suppressor protein, dephosphorylates phosphatidylinositol 3,4,5-trisphosphate at the 3 position, turning off Akt signalling. PTEN contains a C-terminal PDZ binding motif that binds to the PDZ2 domain of MAGI-2, a scaffolding protein that localizes signalling molecules to the plasma membrane. MAGI-2 has ten domains that potentially mediate multiple protein-protein interactions simultaneously. A PTEN associated-complex (PAC) has been described and may contain MAGI-2, PTEN and p85. The PAC is hypothesized to form at the plasma membrane at appropriate sites for PTEN to gain access to its lipid substrates, since the binding of PTEN to MAGI-2 has been shown to enhance the suppression of PI3K-mediated Akt signalling. In order to better understand the role of the PAC in attenuation of the Akt signalling pathway, regions of the MAGI-2 scaffolding protein were mapped to identify the interactions taking place in the PAC. MAGI-2, and its individual domains, were expressed as GST fusion proteins. These were immobilized onto beads and allowed to bind to cellular proteins including PTEN, p85, PDGFR and EGFR using a GST pull-down experiment. The proteins bound to GST-MAGI-2 were identified using an immunoblot analysis. In vitro pull-down experiments revealed that MAGI-2 PDZ2 and PDZ5 domains bind to PTEN, and both MAGI-2 WW domains were shown to bind to p85. EGFR and PDGFR did not bind to the PDZ domains of MAGI-2 under the conditions studied. In order to study protein-protein interactions in cells, immunoprecipitation assays were also performed. Full length MAGI-2 was expressed tagged to a Myc epitope. This was used in immunoprecipitation assays to determine if MAGI-2 could co-immunoprecipitate with proteins involved in the Akt signalling pathway, such as PTEN, p85, PDGFR and EGFR. MAGI-2 can co-immunoprecipitate with PTEN upon 5 min EGF stimulation however, this result was inconclusive because replicate experiments did not verify this initial observation. MAGI-2 does not co-immunoprecipitate with the EGFR nor p85, under the conditions tested. We examined for these interactions after 5 min of growth factor stimulation and more experiments that test different time points after growth factor stimulation would reveal if these interactions are present at shorter time points. MAGI-2 has been shown to bind to PTEN and p85 in vitro and therefore has the potential to regulate the attenuation of the PI3K/Akt signalling pathway in response to activated EGFR and/or PDGFR.

Following the discovery of the DISC1 gene in 2000, subsequent research has led to DISC1 becoming one of the most promising candidate genes for psychiatric disorders. Acting as a scaffold protein, DISC1 has a large number of interacting proteins and is involved in a series of intracellular signalling pathways. Amongst these binding proteins are two enzymes, PDE4 and GSK3β, that were originally implicated in psychiatric disease by virtue of their inhibition by psychoactive drugs. PDE4 enzymes are inhibited by rolipram, which possesses anti-depressant and anti-psychotic activity, while GSK3β is one of the major targets of lithium, a potent mood stabiliser. Both these enzymes are intricately involved in the PI3K/AKT, cAMP, and MAPK signalling pathways, all of which have a number of downstream outcomes with potential relevance to psychiatric disorders. The Millar and Porteous laboratory had established that DISC1 modulates PDE4 activity, but this predated awareness of GSK3 as another DISC1 interactor whose binding site overlapped with that of PDE4. Since cAMP is a key regulator of signalling pathways in the brain, I hypothesised that not only DISC1, but also GSK3β may be involved in the regulation of PDE4 activity to control local cAMP levels and gradients. To investigate this hypothesis, I characterised SHSY5Y cells as a model for measuring PDE4 activity, and performed a series of genetic and pharmacological manipulations on this system. Inhibition of GSK3β resulted in a decrease of basal PDE4 activity that was amplified by DISC1 overexpression. Wild type cells that were treated with forskolin exhibited a significant increase in PDE4 activity, which was suppressed by GSK3β inhibition and both overexpression and knockdown of DISC1. Further experiments confirmed that none of these changes were a result of differences in PDE4 mRNA or protein expression. Thus I have provided evidence that suggests tonic activation of PDE4 by GSK3β and evidence for modulation of PDE4 activity by DISC1. I provide evidence for the localisation of PDE4B & PDE4D with key psychiatric associated receptors in structures resembling developing dendritic spines; furthermore, agonism of NMDA receptors results in a significant increase in PDE4 activity in primary neurons. These results are a simple demonstration of an emerging principle in psychiatric research: that none of the signalling pathways implicated in psychiatric disease are acting in isolation. There are likely to be multiple points of integration between these pathways, with the demonstrated DISC1-GSK3β-PDE4 interaction forming one of these points. My results add an important new element to the understanding of how the DISC1 complex may regulate intracellular signalling in response to extracellular cues.

Atherogenesis is the leading cause of death in the developed world, and is putting considerable monetary pressure on health systems the world over. Although the risk factors are well understood, unfortunately, the initiation and development of this disease still remains relatively poorly understood, but it is becoming increasingly identifiable as a dysfunction of the endothelial cells that line the walls of arteries. The prevailing haemodynamic environment plays an important role in the focal nature of atherosclerosis to very specific regions of the human vasculature. Disturbed haemodynamics lead to very low wall shear stress, and inhibit the transport of important blood borne chemicals. The present study models, both computationally and mathematically, the transport and hydrolysis of important blood borne adneosine nucleotides in physiologically relevant arterial geometries. In depth analysis into the factors that affect the transport of these low diffusion coefficient species is undertaken. A mathematical model of the complex underlying endothelial cell dynamics is utilised to model production of key intracellular molecules that have been implicated into the complex initiation processes of atherosclerosis; hence regions of the vasculature can be identified as being 'hot spots' for atherogenesis. This model is linked into CFD software allowing for the assessment of how 3D low yields and mass transfer affect the underlying cell signalling. Three studies are undertaken to further understand nucleotide variations at the endothelium and to understand factors involved in determining the underlying cell dynamics. The major focus of the first two studies is geometric variations. This is primarily due to the plethora of evidence implicating the geometry of the human vasculature, hence the haemodynamics, as an influential factor in atherosclerosis initiation. The final model looks at a physiologically realistic geometry to provide a more realistic reproduction of the in vivo environment.

No description available.

Abstract Acinetobacter baumannii is a prevalent nosocomial where infections are typically secondary infections to patients that already have an infection or other source of being immunocompromised. Like many other infectious bacteria, A. baumannii is increasingly considered a multi-drug resistant pathogen. This eliminates the ability to treat A. baumannii infections with traditional antibiotics, hence the need for another method of treating A. baumannii. This research study was designed to find a way to affect the survival of A. baumannii such that it can be applied to a hospital setting to prevent further infections to immunocompromised patients. One mechanism potentially used by A. baumannii to persist on hospital surfaces is through the use of the bacterial second messenger cyclic-di-GMP (c-di-GMP). This nucleotide signal is regulated in response to environmental conditions, and then activates c-di-GMP-binding proteins that induce phenotypic changes. I hypothesized that by deleting these c-di-GMP-binding proteins that it will produce measurable differences in phenotype like biofilm formation, motility, and desiccation survival. Reducing phenotypes such as these may alter A. baumannii’s ability to persist on hospital surfaces, and potentially lead to future surface eradication. A. baumannii encodes two potential c-di-GMP-binding proteins of particular interest, one that contains a sole PilZ domain and another that pairs a PilZ domain with a hydrolase domain. PilZ domains bind c-di-GMP within a conserved binding site, regulating the conformational structure of the protein, and are named for the first studied PilZ domain within the pilus-associated PilZ protein. Pili are used in pilus-mediated motility and surface attachment, and they are A. baumannii’s primary method of motility due to not having flagellum. I hypothesized that by removing these c-di-GMP-binding proteins, I would interrupt the c-di-GMP signaling that might regulate motility. I am testing two A. baumannii strains: 5075, a recent military hospital isolate and 17978, an older lab strain. A notable difference between these two strains is that 5075 demonstrates twitching motility where it utilizes type IV pili, but 17978 demonstrates swarming motility that has unknown mechanisms. Both c-di-GMP-binding proteins were tested for their role in twitching or swarming motility of the respective strains. I found that swarming motility of 17978 is regulated by both c-di-GMP-binding proteins. While I am still generating the deletion strain for the c-di-GMP-binding hydrolase enzyme, the sole PilZ domain protein is also required for twitching motility in the 5075 strain. These results suggest c-di-GMP regulates both forms of motility in A. baumannii. Future plans include determining the role of the c-di-GMP-binding hydrolase enzyme in twitching motility and identifying the role that these proteins play through binding of c-di-GMP.

No description available.