This thesis describes the development and use ofnon-immunoglobulin affinity proteins denoted affibodies asalternatives to antibodies in different immunotechnologyapplications. A 58 aa IgG Fc binding three-helix bundle domainZ, derived from staphylococcal protein A has been used asframework for library constructions, in which the face of themolecule involved in the native binding activity has beenengineered by combinatorial protein engineering. Recruting 13surface-located positions for simultanenous substitutionmutagenesis, using degenerated oligonucleotides for libraryassembly at the genetic level, two libraries differing in thechoice of codons were constructed to serve as general sourcesof novel affinity proteins. The libraries were adapted fordisplay onE. colifilamentous phage particles allowingin vitroselection of desired variants capable ofbinding a given target molecule. In selections using human IgAas target, several new IgA specific affibodies could beidentified. One variant ZIgA1, was further investigated and showed binding toboth IgA1 and IgA2 human subclasses as well as to secretoryIgA. This variant was further demonstrated uesful as ligand inaffinity chromatography purification for recovery of IgA fromdifferent samples including unconditioned human plasma.Affibodies of different specificities were also fused to otherprotein domains to construct fusion proteins of relevance forimmunotechnology applications. Using Fc of human IgG as genefusion partner, "artificial antbodies" could be produced inE. colias homodimeic proteins, where the antigenbinding was confered by N-terminally positioned affibodymoieties of different valencies. One area of application forthis type of constructs was demonstrated through specificdetection of the target protein by Western blotting. Exploitingthe uncomplicated structure of affibody affinity proteins, genefusions between affibodies and the homotetrameric reporterenzyme β-galactosidase were constructed, which could beproduced as soluble proteins intracellularly inE. coli. The potential use of such recombinantimmunoconjugates in immunotechnology was demonstrated in ELISAdot-blot and immunohistochemistry, where in the latter case IgAdepositions in the glomeruli of a human kidney biopsy could bespecfically detected with low background staining ofsurrounding tissues. In a novel format for sandwich ELISA, thepossible advantage of the bacterial origin of the affibodyclass of affinity proteins was investigated. As a means tocircumvent problems associated with the presence of humanheterophilic antibodies in serum, causing bakground signals dueto analyte-independent crosslinking of standard capture anddetection antibody reagents, assay formats based oncombinations of antibody and affibody reagents for capture anddetection were investigated and found to be of potentialuse. <b>Keywords:</b>phage display, combinatorial, affinity, IgAligand, immunohistochemistry, affibody-fusions

ABSTRACT The Swedish Human Proteome Resource (HPR) is a project about mapping of human genes and proteins. It aims to describe the function and distribution of all human genes and corresponding proteins, using in-house produced antibodies and tissue microarrays (TMA) for enzyme based immunohistochemistry. The mono-specific antibodies are used for immunostaining of human tissue. Specific predicted antigens named Protein Epitope Signature Tag (PrEST) are needed to produce mono-specific antibodies. PrEST are produced using recombinant technology from predicted genes and used as immunogens to produce (mono-specific) antibodies in rabbits. In this study, 84 mono-specific antibodies with known specificity to human proteins were used for immunohistochemical analysis of mouse tissues to determine the cross reactivity between mouse and human. For 6 of the 84 antibodies the results differed between mouse and human tissue. A comparison between the PrEST used with the mouse proteome using database search programs showed homologies that were less than 100% in these six cases. Thus, future studies on cross reactivity will focus on how to increase the accuracy in its prediction at the in silico stage of the experiment.

Background and aim: Persistent stress and life events affect the course of ulcerative colitis (UC) by largely unknown mechanisms. Regulation of epithelial permeability to antigens is crucial for the balance between inflammation and immuno-surveillance, and increased intestinal permeability has been shown in patients with ulcerative colitis. Corticotropin releasing hormone (CRH) has been implicated as an important mediator of stress-induced abnormalities in intestinal mucosal function in animal models. Further cholinergic signalling during stress has been reported to increase bowel ion secretion in humans and uptake of HRP in rodents via activation of mast cells. The overall aim of this thesis was to examine the role of CRH-mediated and cholinergic signalling, and their interaction with mast cells and eosinophils, in the regulation of the mucosal barrier function in the normal human colon and in UC. In vivo studies or the use of surgical specimens for such studies have major shortcomings. Therefore a method with endoscopic biopsies in Ussing chambers was established for studies of protein antigen uptake and electrophysiology in human colonic biopsies, and used in subsequent investigations. Materials and methods: In the four studies a total of 91 healthy volunteers, 3 patients with rectal cancer, and 15 UC patients were included. Biopsies from the sigmoid colon were assessed for macromolecular permeability (Horseradish peroxidase (HRP), and 51Cr-EDTA), and electrophysiology during challenge with sodium caprate (C10), CRH or carbachol. Experiments were repeated with CRH receptor antagonists, carbachol receptor antagonists, mast cell stabilizers and nerve conductance blockers in Ussing chambers. The biopsies were examined by electron and light microscopy for endocytosis of HRP, morphological changes and receptor expression. Moreover, the human mast cell line, HMC-1; was used in studying expression of CRH receptors on mast cells. Results: Endoscopic biopsies of human colon were viable in Ussing chambers, and the technique was shown to be a reliable tool for studies of mucosal permeability to HRP. CRH stimulates transcellular uptake of HRP in human colon via CRH receptor subtypes R1 and R2 on subepithelial mast cells. Further, carbachol acts on muscarinic receptors, located on subepithelial eosinophils. Activated muscarinic M2 and M3 receptors on increased numbers of CRHproducing eosinophils in UC, lead to activation of mast cells and increased macromolecular uptake across the colonic mucosa. This signalling cascade is previously unrecognized, and may be involved in the inflammatory process in UC. Conclusions: In conclusion, we have demonstrated a chain of events leading to increased permeability to the protein antigen HRP in biopsies from healthy volunteers and patients with UC. The important steps begin with a cholinergic signal to muscarinic receptors on the CRH containing eosinophils. The next step includes activation of CRH receptors on mast cells leading to degranulation and increased macromolecular uptake across the epithelium. This explanatory model will have implications for understanding of the pathogenesis of UC and future treatment of the disease.

The sigma-1 receptor (σ-1R) is an endoplasmic reticulum (ER) protein that modulates a number of ion channels. It is hypothesized that σ-1Rs activated with agonist translocate to the plasma membrane. The σ-1R potentiates N-methyl-D-aspartate Receptors (NMDARs), important constituents of synaptic plasticity. NMDARs are anchored in the plasma membrane by Postsynaptic Density Protein-95 (PSD-95). The mechanism behind σ-1R modulation of NMDARs is not known. The results of my investigation confirm that σ-1Rs localize extrasomatically. Following σ-1R activation, σ-1R localization to dendrites and postsynaptic densities (PSDs) is upregulated. Unpublished work from our lab has shown that σ-1Rs associate with PSD-95 and NMDARs. Furthermore, immunocytochemistry (ICC) showed σ-1R colocalization with PSD-95 and NMDAR subunits. After σ-1R activation there was significantly increased colocalization between σ-1R, PSD-95, and GluN2B. Overall, this study may have provided insight into the molecular mechanism behind σ-1R modulation of NMDARs, which could have implications in the understanding of synaptic plasticity.

Neutrophils are implicated in many inflammatory lung disorders. However, the mechanisms regulating neutrophil migration in acute lung inflammation are incompletely understood. Although, integrin β2 mediates neutrophil migration in lungs in response to many stimuli such as E. coli, integrin involved in <i>S. pneumoniae</i> induced neutrophil migration is not known. Therefore, the role of integrin αvβ3 in neutrophil recruitment was tested. First, it was found that the number of neutrophils expressing the integrin subunits αv and β3 is reduced or remains in lung inflammation induced by E. coli or <i>S. pneumoniae</i>, respectively. Next, the role of integrin αvβ3 using β3 knockout mice (β3-/-) and function blocking antibodies was addressed. Neutrophil recruitment did not vary between wild type and β3-/- mice. Although β3 antibodies reduced neutrophil recruitment, similar effect was observed with isotype antibodies. Therefore, one can conclude that integrin αvβ3 is not critical for neutrophil recruitment in <i>S. pneumoniae</i> induced pneumonia. <p>Apart from integrins, TLR4 also regulate neutrophil migration. Because, the pattern of TLR4 expression at various times of lung inflammation is not known, TLR4 expression during different phases of lung inflammation in a rat model of LPS-induced inflammation was studied. TLR4 expression in the septum increased and decreased at 6h and 12-36h of inflammation, respectively. Since these correlate with the time of increase and decline of neutrophil recruitment, the findings support previously observed requirement for TLR4 in neutrophil recruitment. <p>Neutrophils recruited into the lungs regulate the inflammatory process by controlling subsequent monocyte/macrophage recruitment. The mechanisms involved and the pattern of monocyte/macrophage recruitment in lungs are not completely understood. Therefore, the possible involvement of monocyte chemoattractant protein (MCP)-1, which is a premier chemokine in monocyte/macrophage migration and produced by neutrophils and other cells was tested. This was addressed by quantification of monocytes/macrophages at various times and using neutrophil depletion experiments in LPS-induced lung inflammation in rats. It was found that monocytes/macrophages migrate very early and before neutrophils in addition to their migration in the late phase of acute lung inflammation. Neutrophil depletion abrogated both early as well as the late monocyte/macrophage recruitment without altering the expression of MCP-1. Therefore, possibly other chemokines and not MCP-1 are involved in neutrophil dependent monocyte/macrophage recruitment. <p>To conclude, the experiments further the understanding on acute lung inflammation by ruling-out the involvement of integrin αvβ3 and MCP-1 in β2-independent neutrophil migration and neutrophil dependent monocyte/macrophage recruitment, respectively. Further studies are essential to find the integrins and chemokines operating in the above situations. Equally important will be to understand the functional significance of early recruited monocytes/macrophages in the lung.

In Canada, colorectal cancer is the second leading cause of death from cancer in men and the third leading cause of death from cancer in women. Several factors contribute to the development of cancer. Genetic predisposition, diet, and lifestyle habits are some of the major factors for colorectal cancer development. In the diet related factors, epidemiological studies suggest that consumption of whole grains rich in dietary fiber are associated with low incidence of human colon cancer. Recent studies have also shown that, in addition to dietary fiber, the type of dietary fiber and other compounds such as phenolic acids present in cereal grain bran may also have a role to play in colon cancer prevention. In a recent study, eleven major phenolic acids which differed in anti-oxidant activity were identified in wheat bran from wheat varieties belonging to six different market classes. The main objective of this study was to develop an in vitro cell culture based assay system to study the effect of phenolic acids on colon cancer development. Another objective was to study the effect of phenolic acids on selected molecular markers associated with cell proliferation, apoptosis and inflammation. Two well established colon carcinoma cell lines HT-29 and HCT 116 were treated with varying concentrations of fourteen phenolic acids to study their effect on cell survival and proliferation. In addition, immunohistochemical assays were performed on treated cells for two cell proliferation markers (Cyclin D1 and Ki67), an apoptosis marker (Bax) and three inflammatory markers (Beta-catenin, COX-2 and iNOS). Treatment of phenolic acids inhibited the growth of both the cell lines, however the effects varied with phenolic acid and cell line used in the assay. As determined by IC50, the growth of HCT 116 cells was inhibited the most by caffeic, ellagic, and gallic acids with IC50 of 0.22 mM, 0.17 mM, and 0.15 mM, respectively. On the other hand, caffeic, chlorogenic, and gallic acids are most effective in preventing the growth of HT-29 cells, with IC50 at 0.06 mM, 0.28 mM, and 0.30 mM, respectively. Immunohistochemical and Western Blotting studies revealed that phenolic acids differentially affected markers for cell proliferation, apoptosis and cell inflammation. In most of the cases, phenolic acid treatments up-regulated the pro-apoptosis marker Bax, while it down-regulated cell proliferation marker Cyclin D1. The results clearly show that a cell culture based assay can be used to study the effect of phenolic acids or other chemical constituents isolated from plants to study their effect on colon cancer cell lines. Statistical analysis revealed that only in very limited cases, results of molecular markers correlated to cell growth and proliferation. Therefore, to draw firm conclusions, more detailed and extensive studied need to be completed using different phenolic acids, the two cell lines and more replications. However, this study has developed the necessary protocols and provided some indicative results such as most of the phenolic acids induced pro-apoptosis pathway in both the colon cancer lines. Future studies with extracted phenolic acids from wheat bran using the cell culture system optimized in this study can be used to define the role of different wheat varieties in colon cancer prevention.

Neutrophils are implicated in many inflammatory lung disorders. However, the mechanisms regulating neutrophil migration in acute lung inflammation are incompletely understood. Although, integrin β2 mediates neutrophil migration in lungs in response to many stimuli such as E. coli, integrin involved in <i>S. pneumoniae</i> induced neutrophil migration is not known. Therefore, the role of integrin αvβ3 in neutrophil recruitment was tested. First, it was found that the number of neutrophils expressing the integrin subunits αv and β3 is reduced or remains in lung inflammation induced by E. coli or <i>S. pneumoniae</i>, respectively. Next, the role of integrin αvβ3 using β3 knockout mice (β3-/-) and function blocking antibodies was addressed. Neutrophil recruitment did not vary between wild type and β3-/- mice. Although β3 antibodies reduced neutrophil recruitment, similar effect was observed with isotype antibodies. Therefore, one can conclude that integrin αvβ3 is not critical for neutrophil recruitment in <i>S. pneumoniae</i> induced pneumonia. <p>Apart from integrins, TLR4 also regulate neutrophil migration. Because, the pattern of TLR4 expression at various times of lung inflammation is not known, TLR4 expression during different phases of lung inflammation in a rat model of LPS-induced inflammation was studied. TLR4 expression in the septum increased and decreased at 6h and 12-36h of inflammation, respectively. Since these correlate with the time of increase and decline of neutrophil recruitment, the findings support previously observed requirement for TLR4 in neutrophil recruitment. <p>Neutrophils recruited into the lungs regulate the inflammatory process by controlling subsequent monocyte/macrophage recruitment. The mechanisms involved and the pattern of monocyte/macrophage recruitment in lungs are not completely understood. Therefore, the possible involvement of monocyte chemoattractant protein (MCP)-1, which is a premier chemokine in monocyte/macrophage migration and produced by neutrophils and other cells was tested. This was addressed by quantification of monocytes/macrophages at various times and using neutrophil depletion experiments in LPS-induced lung inflammation in rats. It was found that monocytes/macrophages migrate very early and before neutrophils in addition to their migration in the late phase of acute lung inflammation. Neutrophil depletion abrogated both early as well as the late monocyte/macrophage recruitment without altering the expression of MCP-1. Therefore, possibly other chemokines and not MCP-1 are involved in neutrophil dependent monocyte/macrophage recruitment. <p>To conclude, the experiments further the understanding on acute lung inflammation by ruling-out the involvement of integrin αvβ3 and MCP-1 in β2-independent neutrophil migration and neutrophil dependent monocyte/macrophage recruitment, respectively. Further studies are essential to find the integrins and chemokines operating in the above situations. Equally important will be to understand the functional significance of early recruited monocytes/macrophages in the lung.

<p>This thesis describes the development and use ofnon-immunoglobulin affinity proteins denoted affibodies asalternatives to antibodies in different immunotechnologyapplications. A 58 aa IgG Fc binding three-helix bundle domainZ, derived from staphylococcal protein A has been used asframework for library constructions, in which the face of themolecule involved in the native binding activity has beenengineered by combinatorial protein engineering. Recruting 13surface-located positions for simultanenous substitutionmutagenesis, using degenerated oligonucleotides for libraryassembly at the genetic level, two libraries differing in thechoice of codons were constructed to serve as general sourcesof novel affinity proteins. The libraries were adapted fordisplay on<i>E. coli</i>filamentous phage particles allowing<i>in vitro</i>selection of desired variants capable ofbinding a given target molecule. In selections using human IgAas target, several new IgA specific affibodies could beidentified. One variant Z_IgA1, was further investigated and showed binding toboth IgA1 and IgA2 human subclasses as well as to secretoryIgA. This variant was further demonstrated uesful as ligand inaffinity chromatography purification for recovery of IgA fromdifferent samples including unconditioned human plasma.Affibodies of different specificities were also fused to otherprotein domains to construct fusion proteins of relevance forimmunotechnology applications. Using Fc of human IgG as genefusion partner, "artificial antbodies" could be produced in<i>E. coli</i>as homodimeic proteins, where the antigenbinding was confered by N-terminally positioned affibodymoieties of different valencies. One area of application forthis type of constructs was demonstrated through specificdetection of the target protein by Western blotting. Exploitingthe uncomplicated structure of affibody affinity proteins, genefusions between affibodies and the homotetrameric reporterenzyme β-galactosidase were constructed, which could beproduced as soluble proteins intracellularly in<i>E. coli</i>. The potential use of such recombinantimmunoconjugates in immunotechnology was demonstrated in ELISAdot-blot and immunohistochemistry, where in the latter case IgAdepositions in the glomeruli of a human kidney biopsy could bespecfically detected with low background staining ofsurrounding tissues. In a novel format for sandwich ELISA, thepossible advantage of the bacterial origin of the affibodyclass of affinity proteins was investigated. As a means tocircumvent problems associated with the presence of humanheterophilic antibodies in serum, causing bakground signals dueto analyte-independent crosslinking of standard capture anddetection antibody reagents, assay formats based oncombinations of antibody and affibody reagents for capture anddetection were investigated and found to be of potentialuse.</p><p><b>Keywords:</b>phage display, combinatorial, affinity, IgAligand, immunohistochemistry, affibody-fusions</p>

No description available.

The aims of this study were: (i) to determine the association between p53, bcl-2, pRb, p21, cyclin A and p-glycoprotein immunoexpression and prognosis, and (ii) to determine the frequency of loss of heterozygosity and microsatellite instability at 11 p, 16q and mismatch repair gene loci and their association with prognosis, in nephroblastomas in South African children. There were 138 cases (111 of whom received preoperative chemotherapy) in the immunohistochemical study and, 70 cases (48 with preoperative chemotherapy) in the microsatellite study. The following monoclonal antibodies were used after heat induced epitope retrieval; p53, bcl-2, pRb, p21, cyclin A and p-glycoprotein. Six polymorphic microsatellite markers were selected from the 11p region, 5 from the 16q region and 6 from the loci of known mismatch repair genes. Automated fluorescent DNA technology was used in the analysis. The results of the immunohistochemical and microsatellite studies were correlated with patient age, gender, preoperative chemotherapy, SlOP histological classification, SlOP histological risk group, clinicopathological stage, patient outcome and survival using X2 , Fisher's exact test, Cox regression model and Kaplan-Meier estimates. The majority of patients presented with advanced disease. Anaplastic tumours and high-risk histology were associated with high disease stage. Mortality was directly related to increasing stage and histological risk group. Multivariate analysis showed that clinicopathological stage was the only factor significantly associated with survival (p<0.001) (hr=5.6, 95%CI: 2.1-14.9). High expression of p53 was more frequent in anaplastic tumours suggesting that p53 mutations are common events in this tumour type (p<0.001). Despite the strong association with tumour histology, there was no association with stage. Although p53 expression was found to be a predictor of survival in the univariate analysis this was not retained in the multivariate analysis. Tumours treated with preoperative chemotherapy showed higher bcl-2 immunoreactivity (p=0.027 but lower levels of pRb (p=0.040) and cyclin A expression (p<0.001). All anaplastic tumours showed high expression of pRb compared to the other histological types (p=0.003). Expression of xxii pRb was significantly associated with survival in the univariate analysis but not in the multivariate analysis. High cyclin A expression was associated with high risk histology (p<0.001). Cyclin A expression was found to be a significant predictor of survival in both the univariate (hr=1.7; 95%CI 1.2-2.4; p=0.002) and multivariate analyses (hr=1.7; 95%CI1.1-2.7; p=0.032). Although tumours with high risk histology were more likely to express high levels of p-glycoprotein, this did not reach significance. LOH at 11 p was seen in 64.7% of 68 informative cases. LOH at 11 p13 was more frequent than LOH at 11p15. LOH for both 11p13 and 11p15 was found in 39.7% of all tumours. MSI at 11 p was seen in 22.1 % of informative cases. The majority showed MSI for one marker only. LOH 16q was seen in 66.7% of 66 informative cases. MSI at 16q was seen in 16.7% of cases. LOH for 016S496 and 016S520 appear to be related to tumour histology and risk group. The most frequent locus for LOH was 16q21-22, which is known to harbour important genes, such as, E2F4 and E-cadherin. LOH for MMR markers was seen in 43.5% of 69 informative cases. MSI was seen in 11.6% of tumours. In the multivariate analysis there was no significant correlation between LOH at any of the loci studied and survival. There were no tumours with high frequency MSI. Low frequency MSI was of no clinicopathological significance. The following conclusions are made: (i) p53 mutations determined by high p53 expression is a frequent finding in anaplastic tumours, (ii) Bcl-2 may play a role in the chemoresistance of nephroblastomas, (iii) Rb gene alterations are not important in the development of nephroblastoma and anaplasia, (iv) Cyclin A expression is an independent predictor of survival, (v) p-glycoprotein may be responsible for the chemoresistance in a proportion of nephroblastomas, (vi) MSI is a rare occurrence in nephroblastoma and does not play a role in the development of nephroblastoma, (vii) LOH at 11 p and 16q are frequent findings in nephroblastomas, (viii) LOH for the specific 16q markers (016S496 and 016S520) may have an important prognostic role in nephroblastoma. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2008.