Highly active antiretroviral therapy (HAART) is currently the only treatment that effectively reduces the morbidity and mortality of individuals infected with Human Immunodeficiency Virus-1 (HIV-1). Standard HAART regimens typically comprise 2 nucleoside reverse transcriptase inhibitors and either one non-nucleoside reverse transcriptase inhibitor or a protease inhibitor. These drugs bind to and inhibit the HIV-1 Reverse Transcriptase and Protease enzymes respectively, thereby suppressing viral replication. The nucleoside reverse transcriptase inhibitors promote mitochondrial (mt) dysfunction by strongly inhibiting mt polymerase gamma (Pol-y) and subsequently, mtDNA replication. In contrast, the non-nucleoside reverse transcriptase inhibitors, efavirenz (EFV) and nevirapine (NVP) do not inhibit Pol-y although EFV has been shown to induce mt depolarisation ( mlow) in vitro at supra-therapeutic concentrations. However, the capacity of non-nucleoside reverse transcriptase inhibitor drugs to induce mt toxicity in vivo previously remained undetermined. The objective of this study was to determine the influence of EFV and NVP on peripheral lymphocyte mt transmembrane potential (Avj/m) and apoptosis in HIV-1-infected patients treated with these non-nucleoside reverse transcriptase inhibitors. Thirty-two HIV-1-infected patients on HAART between 4 and 24 months (12 on EFV, 20 on NVP) and 16 HAART-naive HIV-1-infected patients were enrolled into this study. All participants were black South African patients. Spontaneous peripheral lymphocyte apoptosis and mlow were measured ex vivo by flow cytometry for all patients. CD4 T-helper apoptosis for the EFV and NVP cohorts was 19.38% ± 2.62% and 23.35% ± 1.51% (mean ± SEM), respectively, whereas total lymphocyte mlow was 27.25% ± 5.05% and 17.04% ± 2.98%, respectively. Both parameters for each cohort were significantly lower (P < 0.05) than that of the HAART-naive patients. The NVP cohort exhibited both a significant time dependent increase in peripheral lymphocyte ö¿mlow (P = 0.038) and correlation between Thelper apoptosis and low (P = 0.0005). These trends were not observed in the EFV cohort. This study provides evidence that both EFV and NVP induce peripheral lymphocyte ö¿ m low in HIV-1-infected patients on non-nucleoside reverse transcriptase inhibitor-based HAART, which in the case of NVP is sufficient to induce the apoptosis cascade. / Thesis (M.Med.Sci.)--University of KwaZulu-Natal, 2008.

The medicinal plant Sutherlandia frutescens (SF) is commonly consumed in South Africa, and is traditionally applied to a range of ailments. Yet its popularity stems from the use of SF as a cancer treatment. This plant contains a range of active compounds including L-canavanine (L-CAV), D-pinitol and gamma (γ)-aminobutyric acid, all of which contribute to the therapeutic properties of SF. It is also endorsed by the South African Ministry of Health as a supplementary treatment for HIV/AIDS. Maize is the staple crop of South Africa, and can be frequently contaminated by the mycotoxin fumonisin B1 (FB1). The mycotoxin is linked to an extensive list of livestock diseases. Although little is known about its role in human disease, FB1 has been epidemiologically linked to oesophageal cancer in South Africa. Both SF and FB1 have been shown to promote apoptosis, and the effect(s) of consuming both in combination is currently unknown. The principle aim of this study was to determine whether SF and FB1 had either synergistic or antagonising effects in combination, by investigating immune cell toxicity Jurkat cells. Apoptotic parameters such as caspase activation, mitochondrial depolarisation, phosphatidylserine (PS) externalisation and ATP quantification were analysed. Levels of caspase activation were highest in cells treated with SF only (caspase-3: 86.79 RLU, no significance compared to other treatments; caspase-8: 40.1 RLU, significance compared to other treatments [p<0.05]; caspase-9: 11.07 RLU, significance compared to FB1 and control treatments [p<0.05]). ATP levels were significantly highest in SF-treated cells compared to other treatments (8.17 RLU, [p<0.05]). Mitochondrial depolarisation was also highest in SF-treated Jurkat cells at 18.5% depolarisation with no significance compared to other treatments, however PS externalisation were significantly lower in SF-treated cells compared with other treatments (3.69% [p<0.05]). Oxidative stress parameters were also investigated, including thiobutyric acid reactive species (TBARS), Glutathione (GSH) and Reactive Nitrogen Species (RNS) assays. TBARS levels were significantly higher in FB1 treated cells (OD 1.95, [p<0.05]) compared to SF and control. Glutathione and RNS levels were also lowest in FB1-treated cells. The data suggests that SF induces apoptosis, characteristic of its nature as an anti-cancer treatment, and FB1 induces oxidative stress, which is characteristic of its carcinogenic properties. Based on this preliminary study, it appears that FB1 and SF both synergises and antagonises the other in combination, yet further investigation is needed into its effects in vivo. / Thesis (M.Med.Sc.)-University of KwaZulu-Natal, 2011.

The use of antibiotics and antimicrobial drugs has played a large role in the elimination of many infectious diseases, however the wide spread use of such drugs has given rise to the phenomenon of antimicrobial resistance and has rendered antibiotics ineffective to a broad range of bacteria. The aim of the study was to ascertain the differences if any in the phenotypic and genotypic resistance profiles of K. pneumoniae isolated from a single tertiary hospital in two surveillance studies undertaken at different times, viz., 2001 and 2007 with special emphasis on ESBLs. A correlation with antibiotic use was also undertaken. ESBL positives were identified and phenotypic resistance profiles were generated based on the resistance profiles of individual isolates by means of their MIC data. The molecular detection of ESBLs was carried out using representative isolates and sequencing was based on the phenotypic expression of the most common ESBL genes. The data was summarized using median values and interquartile ranges. Antibiotic use and susceptibility in 2000 was compared to that in 2007 using a Wilcoxon signed rank test for paired data since the same drugs were tested in both years. Of the isolates that were tested, sequencing revealed that TEM – 1 was identified in all isolates and SHV-1 and SHV-2 were identified in 60 % in the isolates collected in 2000 and 77 % and 11 % respectively in the isolates collected in 2007. SHV – 11 was present in 67% of isolates from 2007 and 55% of those were in combination with SHV – 1. Sequencing also revealed CTXM-15 present in one of the isolates collected in 2007. There was 100% susceptibility to cefoxitin and only one isolate in 2007 showing an intermediate result to imipenem. No novel β-lactamases were identified in this study; however the decrease in susceptibility over time is proof of bacterial evolution. The variety of β-lactamases and diversity of plasmid profiles in these two small populations provides proof to the claim that dissemination of resistance in Klebsiella pneumonia is effortless. Statistical analysis showed an increase in resistance from the year 2000 to 2007 however the correlation between overall antibiotic use and the increase in resistance did not reach statistical significance. It was observed that resistance increased despite only a slight increase in the use of a few antibiotics to which we attributed co-carriage of resistance genes. / Thesis (M.Med.Sc.)-University of KwaZulu-Natal, Westville, 2012.

Studies have shown that the traditional healers have used Tulbaghia violacea (TV) (also known as ‘wild garlic’) for the treatment of a number of ailments including fever, tuberculosis, stomach problems, and oesophageal cancer. However, little is known with regards to the anticancer and antiproliferative properties of this plant. Therefore, this study investigated the effects of TV and domesticated garlic extracts on Jurkat cells, in order to determine whether or not these extracts possess anti-proliferative properties. Cultured Jurkat cells were treated with IC50 concentrations of garlic (14μg/ml), TV leaf (256μg/ml), TV bulb (225μg/ml) and TV stalk (216μg/ml) extracts as determined by the methylthiazol tetrazolium assay. Free radical production was measured using the thiobarbituric acid reactive substance (TBARS) and nitric oxide (NO) assays, while glutathione (GSH) concentration was measured using the GSH-Glo™ assay. The apoptosis inducing properties of each extract were measured using flow cytometry (Annexin V- Fluos and JC-1 assays) and luminometry (caspases 3/7, 8, 9 and ATP). Western blots were run to determine protein expression, while comet and DNA fragmentation assays were used to determine the level of DNA damage induced. Wild and domesticated garlic extracts induced a significant increase in malondialdehyde concentration ([MDA]), with TV bulb extract inducing the highest concentration (p<0.0001). A significant increase in NO concentration was observed in the bulb (p<0.0001) and stalk (p<0.001) extracts, and leaf (p<0.05) and stalk (p<0.05) TV extracts significantly increasing GSH concentration. The longest comet tails were observed in TV bulb extracts (p<0.0001) and comprised mainly of single strand breaks, while the comets induced following garlic exposure contained double strand breaks. All extracts, except TV leaf, increased the percentage of cells undergoing apoptosis. Tulbaghia violacea leaf induced a significant (p<0.0001) increase in percentage of cells undergoing necrosis, whereas TV bulb resulted in a significant (p<0.0001) decrease. All TV extracts induced caspase 3/7 and 9 activity, with the most significant increase in caspase 9 activity observed for TV leaf and bulb. No significant change in caspase 3/7 activity was evident for domesticated garlic. Cleavage of PARP and expression of NF B and HSP 70 occured for all extracts. However, HSP 70 was not differentially expressed. Exposure to wild and domesticated garlic extracts induced peroxidative lipid and DNA damage within the cells, indicating oxidative stress. This damage occurred in conjunction with increased percentage of cells undergoing apoptosis and expression of caspase 3/7. Therefore, these findings suggest that TV is inducing cell death through apoptosis in Jurkat cells using a number of mechanisms, including the induction of oxidative stress. This is of clinical significance, as cell death through apoptosis is the preferred method of action for anti-cancer drugs. / Thesis (M.Med.)-University of KwaZulu-Natal, Durban, 2012.

Ethnopharmacological relevance: Indigenous plants such as Tulbaghia violacea(TV) and Allium sativum (garlic) are traditionally used as natural remedies to treat a variety of ailments, including cancer. This study investigated the effects of TV leaf and bulb extracts and garlic extract on a cancerous oesophageal cell line (SNO). Materials and methods: The methylthiazoltetrazolium (MTT) assay was used to determine the IC50 of TV leaf (TVL) (250μg/ml) and TV bulb extracts (TVB) (25μg/ml) and garlic (500μg/ml). Extracts were treated individually and in combination for a period of 24 hours. Oxidative damage and intracellular glutathione levels were assessed using the Thiobarbituric Acid Reactive Substances (TBARS) Assay and GSH-Glo™ Luminometry Assay, respectively. The CellTiter-Glo® Luminescent Cell Viability Assay was used to assess ATP activity. Induction of apoptosis and mitochondrial membrane potential were determined via the Caspase-Glo® 3/7 Assay, Caspase-Glo® 8 Assay, Caspase-Glo® 9 Assay and JC-1 Mitoscreen Assay, respectively. Morphological apoptotic changes were determined using the Hoechst 33342 stain. Expressions of p53, PARP and NFKB activities were determined by western blotting. Results: Bulb and leaf extracts of TV increased lipid peroxidation compared to the control (p>0.05), whilst garlic and combination of TV leaf and bulb (TVB + TVL) extracts significantly decreased lipid peroxidation relative to the control (p< 0.05). Endogenous glutathione levels significantly decreased in all TV treatments compared to the control (p<0.05).However, garlic was accompanied by insignificantly increased intracellular glutathione levels compared to the control (p> 0.05). The percentages of depolarised mitochondria in all treated cells were significantly decreased compared to untreated cells (p< 0.05). ATP levels increased significantly in garlic and combination (TVB + TVL) treated cells as compared to the control (p< 0.05), yet no significant differences were noted in TVL and TVB treatments (p> 0.05). Caspase8 and caspase 9 activities significantly increased in garlic and combination treated cells relative to the control (p<0.05). A similar trend was noted for caspase 3/7 activity in garlic and combination treatments (p< 0.05). However, initiator and executioner activities in TVL (p> 0.05) and TVB (p> 0.05) treatments did not significantly differ from the control (p> 0.05). All treatments (including garlic) resulted in increased DNA fragmentation and condensation. All treatments decreased p53 expression (p< 0.05), PARP expression (p< 0.05) and NFK B expression (p>0.05) compared to the control. Conclusions: All TV extracts and garlic induces apoptosis in the oesophageal cancerous SNO cell line through changes in oxidative stress, antioxidant systems, and nuclear chromatin condensation, as well as through induction of nuclear genes and signalling pathways. Since inhibition of apoptosis is a principal alteration in cancer, induction of apoptosis would result in a decrease in cancer cell growth. Thus, TV could be exploited as a potential anti-cancer agent. / Thesis (M.Med.Sc.)-University of KwaZulu-Natal, Durban, 2012.

Consistently high levels of air pollutants such as sulphur dioxide, particle matter and nitric oxides have been observed in the Durban South (DS) industrial basin. The adverse health outcomes associated with ambient air pollution (AAP) exposure have underlying molecular mechanisms. Oxidative stress is a known outcome of AAP exposure and contributes to the exacerbation of adverse AAP related outcomes such as chronic obstructive pulmonary disorder (COPD) and asthma. Pregnant women are at increased risk of developing oxidative stress due to increased energy expenditure. Oxidative stress during pregnancy is linked to adverse birth outcomes such as intrauterine growth retardation and low birth weight. The mitochondria are the most abundant source of endogenous reactive oxygen species (ROS), making these organelles extremely susceptible to oxidative damage. Alterations in mitochondrial function by air pollutants can contribute to oxidative stress. Uncoupling protein2 (UCP2) is an anion carrier located on the inner mitochondrial membrane that regulates mitochondrial ROS production by reducing mitochondrial membrane potential (Δψm) through mild uncoupling. Genetic variation in genes that play a role in oxidative stress response is likely to influence susceptibility to oxidative stress related health outcomes. The aim of this study was to evaluate air pollution associated oxidative stress response in women from the DS industrial basin and determine the functional relevance of a common -866G/A promoter polymorphism in the UCP2 gene. Fifty pregnant women from DS and 50 from north Durban (DN; control) were recruited. The thiobarbituric acid assay (TBARS) and comet assay were performed to measure oxidative stress and DNA fragmentation. Mitochondrial function was evaluated by JC-1 Mitoscreen and ATP luminometry. Quantitative PCR (qPCR) was performed to measure mitochondrial DNA (mtDNA) damage. Antioxidant response was determined by qPCR to measure mRNA expression of superoxide dismutase 2 (SOD2), nuclear factor erythroid 2-related factor 2 (Nrf2) and UCP2 mRNA expression. Western blots were performed to quantify UCP2 and Nrf2 protein expression. The samples were genotyped using PCR - restriction fragment length polymorphism. Results from the TBARS assay showed women from DS displayed elevated levels of MDA, a marker for oxidative stress (0.07±0.06μM; p = 0.56). ATP (1.89 fold) and Δψm (45.3±17.2%; p = 0.8) were also elevated in women from DS, favouring free radical production. DNA fragmentation, as indicated by comet tail length was also higher in DS when compared to the control group (0.57±0.16μm; p = 0.037). Analysis of mtDNA viability showed a 0.49 fold change in mtDNA amplification in women from the industrialized DS. All antioxidant genes, i.e. Nrf2 (0.73 fold), UCP2 (1.58 fold), SOD2 (1.23 fold), were up regulated in women from DS. Analysis of protein expression showed a significant increase in UCP2 expression (0.08±0.03RBI; p = 0.049) and a significant decline in Nrf2 levels (1.68±0.84RBI; p = 0.03). The homozygous G genotype was significantly more frequent in DS (37.5%) than in DN (18.6%; p = 0.047; OR: 2.57; 95% CI: 1.353 to 4.885). This genotype exhibited higher MDA levels, comet tail length, Δψm, SOD2, Nrf2, and UCP2 expression than the AA/GA in genotype in women from DS (p > 0.05). This study found that pregnant women from a more industrialized area exhibit higher markers for oxidative stress and conditions that favour mitochondrial free radical production. / Thesis (M.Med.Sc.)-University of KwaZulu-Natal, Durban, 2012.

Thesis (MScMedSc (Biomedical Sciences. Molecular Biology and Human Genetics. Medical Biochemistry))--University of Stellenbosch, 2009. / The mammalian neocortex contributes to the increasing functional complexity of the mammalian brain, partly because of its striking organisation into distinct neuronal layers. The development of the neocortex has been well studied because disrupted neurodevelopment results in several human diseases. The basic principles of neocortical development have been well established for some time; however the molecular mechanisms have only recently been identified. One major advance in our understanding of these molecular mechanisms was the discovery of Reelin, an extracellular matrix protein that directs the migration of neurons to their final positions in the developing neocortex. Reelin is a large multi-domain protein that exerts its functions by binding to its ligands on the cell surface and initiating a signal transduction cascade that ultimately results in cytoskeletal rearrangements. Several investigations have been undertaken to elucidate the functions of each of these domains to gain a better understanding reelin’s functions. We have previously identified the WR40 repeat protein 47 (WDR47), a protein of unknown function, as a novel putative ligand for the N-terminal reeler domain of reelin. To gain better understanding into the functional significance of this interaction, the present study sought to identify novel WDR47- interacting proteins. In order to achieve this, a cDNA encoding a polypeptide that contains the two N-terminal domains of WDR47, i.e. the Lis homology and the C-terminal Lis homology domain (CTLH) was used as bait in a Y2H screen of a foetal brain cDNA library. Putative WDR47 ligands were subsequently verified using 3D in vivo co-localisation. Results of these analyses showed that SCG10, a microtubule destabilizing protein belonging to the stathmin family of proteins, interacted with the N-terminal of WDR47. The identification of SCG10 as a novel WDR47 interacting protein not only sheds some light on the role and function of WDR47 but also aids in a better understanding of the reelin pathway and cortical lamination. Moreover, the data presented here, may also provide researchers with new avenues of research into molecular mechanisms involved in neuronal migration disorders.

Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2007. / Tuberculosis (TB) is a global health problem and demands rigorous control management efforts. A dramatic increase in the acquisition and spread of drug resistant TB globally has been observed in recent years. A grim picture has emerged for the control program with the discovery of extreme drug-resistant TB, which is virtually untreatable and is of immense concern for the future of TB control. In the last decade strain-specific genetic markers have been identified to examine the molecular epidemiology and spread of TB, including IS6110 DNA-fingerprinting and spoligotyping. Although spoligotyping has less discriminatory power than the gold standard, IS6110 DNA-fingerprinting, it is simpler, faster and less expensive, as it is PCR-based. Spoligotyping has been applied to enhance our understanding of the dynamics of drug susceptible and drug resistant strains of Mycobacterium tuberculosis in high incidence communities, by studying 3 aspects of the TB epidemic: molecular epidemiology of drug resistant TB, recurrent TB and the evolution of M. tuberculosis. By using spoligotyping and other genotypic and phenotypic analysis of drug-resistant M. tuberculosis isolates from the Western Cape Province of South Africa showed that drug resistance is widespread and recently transmitted. An emerging drug resistant M. tuberculosis outbreak has been identified, termed DRF150, which has specific genotypic characteristics and is resistant to 5 first-line drugs in 45% of the cases. Inappropriate chemotherapy; poor adherence to treatment and prolonged periods of infectiousness due to the delay in susceptibility testing has led to the development and spread of this drug resistant genotype. The study demonstrates the ability of the spoligotyping technique to accurately determine the pathogenic mechanism of recurrent disease by spoligotyping, making it useful in large-scale intervention studies. Application of spoligotyping and a newly developed PCR-method showed that the occurrence of multiple infections was higher than what was previously assumed and also more frequent in retreatment cases than new cases. These findings have important implications for the understanding of protective immunity, and the development and testing of new vaccines and drugs. Various different molecular markers including spoligotyping has been used to reconstruct the evolutionary history of isolates with less than 6 copies of IS6110 element (termed Low Copy Clade (LCC)), which were previously poor defined. It was also shown that LCC is widely disseminated and play an important role in the global tuberculosis epidemic. Reconstruction of the evolutionary relationship of M. tuberculosis Principal Genetic Group 2 strains, identified previously unknown genetic relationships between strain families and laid the foundation to establish correlations between genotype and phenotype. Spoligotyping signatures, created by evolution of the Direct Repeat region in M. tuberculosis, were identified, which will enable the analysis of the strain population structure in different settings and will also enable the rapid identification of strain families that acquire drug-resistance or escape protective immunity in drug and vaccine trials. This study contributed to our understanding of the molecular epidemiology of drug resistant TB, recurrent TB and the evolution of M. tuberculosis in high incidence communities.

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: The investigation was aimed to improve the understanding of the binding interactions between DevS and DevR that are implicated in the regulation of the dormancy response in Mycobacterium tuberculosis. These binding interactions could provide good drug targets for the treatment of persistent tuberculosis, the mechanistic understanding of their binding interactions is important for the development of a validated inhibitor screen. A detailed in silico analysis of the amino acid residues that play a role in the binding of receptor DevR to both kinase DevS and the target DNA was undertaken. A reasonable approximation of the DevS structure was produced using homologous protein structures. In silico docking of DevS to DevR merely produced a set of probable candidate structures, since more than one conformation with similar docked energies was observed. The decision on which one is the more correct form can only be estimated by crystallization of this complex. Therefore, the functional expression and purification of the Dev TCS components were pursued. Denaturing HIS™-select nickel affinity gel purification in the form of matrix-assisted refolding led to the production of functional Dev TCS proteins. To understand the binding of DevR to DNA consensus sequences, as well as the nature of these interactions, a model was built of the full length DevR dimer binding to DNA consensus sequences. Based on this model, single mutations were made to DevR in vitro and their effects assessed in order to validate the model built. During Electrophoretic Mobility Shift Assay (EMSA) analysis, it was found that K179I and N183L mutants prevented the binding of DevR to the DNA consensus sequences. If DevR and DevS binding are to be used in a drug development program, it is essential to have the protocols to accurately measure their interaction, in addition to developing a fundamental understanding of how their interactions occur. The binding affinity of DevR to both DevS and the truncated soluble fragment of DevS (DevS201) were explored, using the BIAcore instrument, an SPR-based biosensor. For sufficiently strong binding between a histidine kinase and a response regulator, the KD needs to be in the nM range. The KD was calculated to be 255 nM for DevS201 and 184 nM for DevS. Therefore it can be concluded that DevS201 binds DevR strongly enough to be used in future studies, and that the BIAcore could be used to screen small-molecule inhibitors of DevR-DevS interactions. / AFRIKAANSE OPSOMMING: Die Dev twee komponent sisteem (TKS) bestaan uit ‘n histidine kinase naamlik (DevS) en ‘n reaksie reguleerder DevR. DevS en DevR is betrokke by die regulering van die dormante stadium van Mycobacterium tuberculosis. Hierdie meganisme kan ‘n deurbraak dwelm teiken vir die behandeling van sluimerende tuberkulose wees. Die meganisme van hierdie bindings interaksies is van kritieke belang, tesame met die ontwikkeling van 'n erkende inhibeerder toets. ‘n Gedetaileerde in silico analise van die aminosuur volgordes wat 'n rol speel in die binding van die reseptor DevR aan beide DevS sowel as die teiken DNS is voltooi. ‘n Model van die DevS struktuur is saamgstel met behulp van homoloë proteïen strukture. In silico mering van DevS aan DevR het `n stel van die waarskynlike kandidaat strukture verskaf, aangesien meer as een konformasie met soortgelyke merings energieë waargeneem is. Die mees waarskynlike vorm kan alleenlik geïndentifiseer word na kristallisasie van hierdie kompleks. Die funksionele uitdrukking en suiwering van die Dev TKS proteine is gevolglik uitgevoer. Funksionele Dev TKS proteïene is verkry deur denaturerende HIS-select nikkel affiniteit jel suiwering, in die vorm van matriks-geassisteerde hervouing te gebruik. Ten einde die binding te verstaan tussen DevR en DNS konsensus volgordes, sowel as die aard van hierdie interaksies, is 'n model gebou van die volle lengte DevR dimeer binding aan DNS konsensus volgordes. Hierdie model is gevalideer deur punt mutasies in DevR te skep en die gevolge daarvan te beoordeel met elektroforetiese mobiliteits verskuiwing reaksie analises. Dit is bevind dat K179I en N183L mutante, verhoed die binding van DevR aan die DNS konsensus volgordes. Die gebruik van DevR en DevS bindings in ‘n dwelm ontwikkelingsprogram, benodig die fundamentele begrip van hoe die interaksies plaasvind, sowel as akkurate protokolle om die interaksies te meet. Die BIAcore instrument, ’n SPR-gebaseerde biosensor, is ingespan om die bindings affiniteit van DevR aan beide DevS en die fragment van DevS (DevS201) te ondersoek. Om voldoende sterk binding tussen DevS en die DevR te verseker, moet die KD in die nM omgewing wees. Die KD is bepaal as 255 nM en 184 nM vir DevS201 en DevS, onderskeidelik. Die afleiding kan dus gemaak word dat DevS201 sterk genoeg aan DevR bind om in verdere studies gebruik te kan word, en dat die BIAcore gebruik kan word om klein-molekule inhibeerders van DevR-DevS interaksies te toets.

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Apart from its primary function in the synaptic hydrolysis of acetylcholine, acetylcholinesterase (AChE) has been shown through in vitro demonstrations to be able to promote various non-cholinergic functions, including cell adhesion and neurite outgrowth, differentiation, and amyloidosis. AChE was also shown to bind to mouse laminin-111 in vitro by an electrostatic mechanism. Previous results suggest that the site on AChE recognised by certain monoclonal antibodies (MAbs) might be critical for differentiation. These MAbs were found to inhibit both laminin binding and cell adhesion in neuroblastoma cells. In this study, the structure and characteristics of this site were investigated, using the AChE-laminin interaction as a template as well as a detailed epitope analysis of the MAbs. The interaction sites of AChE and laminin were investigated using phage display, modelling and docking, synthetic peptides, enzyme linked immunosorbent assays (ELISAs) and conformational interaction site mapping. Docking of AChE with the single-chain variable fragments (scFvs) produced from the phage display showed the major recognition motifs to be the 90Arg-Glu-Leu-Ser-Glu-Asp motif, the 40Pro-Pro-Met-Gly sequence, and the 59Val-Val-Asp-Ala-Thr-Thr (human) motif. Mouse AChE was found to interact with the basic structures Val2718-Arg-Lys-Arg- Leu2722; Tyr2738-Tyr2739, Tyr2789-Ile-Lys-Arg-Lys2793; and Val2817-Glu-Arg-Lys2820, on the 1 G4 domain of laminin. ELISAs using synthetic peptides confirmed the involvement of the AG-73 site (2719-2729). This site overlaps with laminin’s heparin-binding site. Docking showed the major component of the interaction site on AChE to be the acidic Arg90-Glu-Leu-Ser-Glu-Asp95 (omega loop), and also involving the Pro40-Pro-Val42, Arg46 (linked to Glu94 by a salt bridge) and the hexapeptide Asp61 Ala-Thr-Thr-Phe-Gln66. Epitope analysis showed the MAb’s major recognition site to be the sequence Pro40-Pro- Met-Gly-Pro-Arg-Arg-Phe48 (human AChE). The MAbs also reacted with the prolinerich sequences Pro78-Gly-Phe-Glu-Gly-Thr-Glu84 and Pro88-Asn-Arg-Glu-Leu-Ser-Glu- Asp95. These results define the interaction sites involved in the AChE-laminin interaction and suggest that the interaction plays a role in cell adhesion. Despite the in vitro demonstrations of the importance of AChE’s non-classical functions, the AChE knockout survives. Results from this study suggest the possibility of functional redundancy between AChE and other molecules in early development. Using these in vitro findings that AChE is able to bind laminin-111, information on the interaction sites, as well as results from the monoclonal antibody (MAb) epitope analysis, the idea of redundancy was investigated. Docking and bioinformatics techniques were used to investigate structurally similar molecules that have comparable spatiotemporal expression patterns in the embryonic nervous system. AChE has been shown to be involved in the pathogenesis of Alzheimer’s disease, thus molecules associated with brain function and neurodegeneration were also investigated. Molecules with which AChE could be possibly redundant are syndecans, glypicans, perlecan, neuroligins and the low-density lipoprotein receptors and their variants. AChE was observed to dock with growth arrest-specific protein 6 (Gas6) as well as apolipoprotein E3 (ApoE-3) at the same site as the laminin interaction. The AChE interaction site was shown to resemble the apolipoprotein-binding site on the low density lipoprotein receptor, and related molecules, including the low density lipoprotein receptor-related molecule (LRP) and the sortilin-related receptor (SORL1). These molecules, along with apoE, are associated with Alzheimer’s disease. Resemblances to the triggering receptor on myeloid cells (TREM1) were also suggested; this is interesting as AChE has been implicated in both haematopoiesis and haematopoietic cancers. Coimmunoprecipitation results, applied to investigate alternative ligands for AChE, confirmed the AChE-laminin interaction in neuroblastoma cells, and also suggested the existence of other binding partners. In conclusion, characterisation of the AChE-laminin interaction sites and investigation of structurally similar sites in other molecules suggests a role for AChE in the stabilization of the basement membrane of developing neural cells and provides a feasible explanation for the survival of the knockout mouse. Furthermore, the demonstrated similarity of the AChE interaction site to sites on molecules, notably the low density lipoprotein receptor family and SORL1 and their apolipoprotein ligands that are implicated in the pathology of Alzheimer’s disease, as well as the possible link to haematopoietic differentiation and cancers, warrants further investigation. / AFRIKAANSE OPSOMMING: Talle in vitro studies wys dat die ensiem asetielcholienesterase (AChE), behalwe vir sy klassieke rol in die hidrolise van asetielcholien (ACh), ‘n aantal nie-cholinerge rolle vertolk insluitend in sel adhesie, in die uitgroei van neurieten, in differensiering, asook in amyloidosis. Dit is vooraf gewys dat AChE, met behulp van elektrostatiese meganismes, in vitro met muis laminin-111 kan bind. Dit word verneem dat die area op AChE wat herken word deur monoklonale teenliggaampies (MAbs), moontlik ‘n kritiese area is met betrekking tot differensiasie. Dieselfde MAbs is gevind om beide die laminin-interaksie, sowel as sel adhesie van neuroblastoma selle, te inhibeer. In hierdie projek word die struktuur en eienskappe van die betrokke kritiese areas ondersoek deur die AChE-laminin interaksie te gebruik as sjabloon. ‘n Gedetailleerde analise van die teenliggaam epitoop het ook geskied. Met behulp van faag vertoon, modellering en hegting, sintetiese peptiede, ensiem-gekoppelde immunosorbent toetse (ELISAs) en konformasie interaksie area kartering, is die betrokke interaksie areas bestudeer. Hegting van enkel-ketting varierende fragment (scFv) volgordes, verkry vanaf die vaag vertoon, aan AChE dui dat die hoof herkennings motiewe die 90Arg-Glu-Leu-Ser-Glu-Asp motief, die 40Pro-Pro- Met-Gly volgorde, en die 59Val-Val-Asp-Ala-Thr-Thr (mens) motief is. ‘n Interaksie tussen muis AChE en die 1 G4 domein van laminin is gevind. Die interaksie betrek die basiese structure: Val2718-Arg-Lys-Arg-Leu2722; Tyr2738-Tyr2739, Tyr2789-Ile-Lys-Arg- Lys2793; en Val2817-Glu-Arg-Lys2820. Die betrokkenheid van die AG-73 (2719-2729) area by hierdie interaksie is bevestig met ELISA eksperimente wat sintetiese peptiede inkorporeer. Die AG-73 area oorvleuel die heparin interaksie area op laminin. Hegtings eksperimente wys dat die hoof komponent van die interaksie area op AChE die suur volgorde Arg90-Glu-Leu-Ser-Glu-Asp95 op die omega-lus is. Die interaksie betrek ook die Pro40-Pro-Val42, Arg46 (gekoppel aan Glu94 deur ‘n sout-brug) en die heksapeptied Asp61 Ala-Thr-Thr-Phe-Gln66 motiewe. Analise van die MAb epitoop wys die hoof erkennings area as volgorde Pro40-Pro-Met-Gly-Pro-Arg-Arg-Phe48 (mens AChE). Die MAbs blyk ook gunstig te wees teenoor prolien-ryke volgordes soos Pro78-Gly-Phe-Glu-Gly-Thr-Glu84 en Pro88-Asn-Arg-Glu-Leu-Ser-Glu-Asp95. Die areas betrokke by die AChElaminin interaksie is dus gedefinieer en ‘n moontlike rol vir hierdie interaksie in sel adhesie word voorgestel. Die noodsaaklikheid van AChE se nie-klassieke funksies word bevraagteken na die oorlewing van die AChE uitklop-muis. Resultate hier dui op die moontlikheid van funksionele oortolligheid as verduideliking hiervan, spesifiek met betrekking tot molekules betrokke in vroëe ontwikkeling asook in die proses van neurale agteruitgang. Deur gebruik te maak van die in vitro demonstrasies van die AChE-laminin interaksie, informasie verkry ten opsigte van die betrokke interaksie areas, asook resultate verkry vanaf die monoklonale teenliggaam (MAb) epitoop analise, word die idee van funksionele oortolligheid ondersoek. Hegtings en bioinformatika tegnieke is gebruik om molekules met soortgelyke strukture en uitdrukkings patrone in die embrioniese senuweestelses te ondersoek. Ko-immuno presipitasie tegnieke is gebruik om so moontlike alternatiewe ligande vir AChE te ondersoek. Moontlike funksionele oortolligheid van AChE met die volgende molekules is gevind: syndecan; glypican; perlecan; neuroligin; asook die lae-digtheid lipoproteien (LDL) reseptore en hul variante. Hegting van AChE met ’growth arrest-specific’ proteien 6 (Gas6) en die apolipoproteien E3 (apoE3) is gedemonstreer en gevind om dieselfde area as die laminin interaksie te betrek. Die betrokke interaksie area op AChE het ooreenstemminge met die apolipoproteien interaksie area op die LDL reseptor asook met verwante molekules soos die lae-digtheids lipoproteien reseptor-geassosieerde molekuul (LRP) en die sortilingeassosieerde reseptor (SORL1). Hierdie molekules, insluitend apoE, speel beduidende rolle in die patologie van Alzheimer se siekte. Ooreenkomste tussen AChE en die verwekkings reseptor op myeloïde selle (TREM1) is ook voorgestel, die interaksie is van belang siende dat AChE voorheen geassosieer is met beide haematopoiesis en haematopoietiese kankers. Ko-immuno presipitasie resultate bevestig die AChE-laminin interaksie en dui op die moontlike teenwoordigheid van alternatiewe ligande vir AChE in vivo. In konklusie, karakterisering van die AChE-laminin interaksie areas, gepaard met identifisering van struktureel ooreenstemmende areas in ander molekules, dui op ‘n rol vir AChE in die stabilisering van die basale membraan en verskaf dus ‘n geldige verduideliking vir die oorlewing van die AChE uitklop-muis. Die ooreenstemming van die AChE interaksie area met areas op ander molekules (spesifiek geassosieer met Alzheimer se siekte), asook die moontlike assosiasie van AChE met haematopoietiese differensiering en kanker, lê die grondslag vir verdere ondersoeke.