Proteins are the effector molecules of life. They are encoded in DNA that is inherited from generation to generation, but most cellular functions are executed by proteins. Proteins rarely act on their own – most actions are carried out through an interplay of tens of proteins and other biomolecules. Here I describe how synthetic DNA can be used to study proteins and protein complexes. Variants of proximity ligation assays (PLA) are used to generate DNA reporter molecules upon proximal binding by pairs of DNA oligonucleotide-modified affinity reagents. In Paper I, a robust protocol was set up for PLA on paramagnetic microparticles, and we demonstrated that this solid phase PLA had superior performance for detecting nine candidate cancer biomarkers compared to other immunoassays. Based on the protocol described in Paper I I then developed further variants of PLA that allows detection of protein aggregates and protein interactions. I sensitively detected aggregated amyloid protofibrils of prion proteins in paper II, and in paper III I studied binary interactions between several proteins of the NFκB family. For all immunoassays the selection of high quality affinity binders represents a major challenge. I have therefore established a protocol where a large set of protein binders can be simultaneously validated to identify optimal pairs for dual recognition immunoassays (Paper IV).

Pectobacterium carotovorum ssp. carotovorum (Pcc) is implicated in the destruction of ornamental plants in greenhouse recirculating systems. PCR-based detection and quantification of Pcc requires expensive instrumentation and knowledgeable users. This thesis describes the production of polyclonal antibodies and a single-domain antibody fragment (VHH) against Pcc lipopolysaccharide (LPS), and the development of user- friendly diagnostic assays for detection and quantification of the pathogen. Polyclonal ELISAs against heat-killed (HK) Pcc (limit of detection (LOD) = 81 CFU/ml; limit of quantitation (LOQ) = 216 CFU/ml) and Pcc LPS (LOD = 23 ng/ml; LOQ = 76 ng/ml) were developed. A preliminary user-friendly dipstick assay was also developed (≥ 105 CFU/ml). A phage display library was constructed (6.0 x 105 clones/ml), yielding one unique anti-Pcc LPS VHH. Using the Pcc LPS-specific VHH to produce affordable, user- friendly diagnostic assays is feasible since antibody fragments can be produced on a large scale through expression in Escherichia coli or Piccia pastoris. / Flowers Canada, CANADA-ONTARIO RESEARCH AND DEVELOPMENT (CORD) PROGRAM, Canada Research Chairs (CRC) Program, NSERC/NRC

Intermediate filaments are fibrous proteins, appearing in a wide variety of tissue specific forms. The function of these proteins is poorly understood, although they are commonly believed to perform a structural role in the cell. Evidence suggests that the role these proteins play may be more dynamic than was previously believed. To gain more insight into their normal in vivo function, a single-chain monoclonal antibody has been constructed to serve as a specific reagent which can disrupt the intermediate filament network in vivo. The work presented in this thesis represents the first step in an approach which involves the use of single-chain monoclonal antibodies as specific reagents to target and disrupt the function of intracellular proteins. / The polymerase chain reaction was used for the cloning and modification of the heavy and light chain variable regions of the murine monoclonal antibody produced by the TIB 131 hybridoma. The variable regions of the light and heavy IgG chains were initially amplified from cDNA using degenerate 5$ sp prime$ primers and 3$ sp prime$ primers complementary to the constant region of the appropriate chain. The amplification products were cloned individually, sequenced, then modified to include restriction sites suitable for cloning into an expression vector. The two modified variable regions were cloned into an expression vector, and when expressed in either bacteria or in a rabbit reticulocyte lysate system, yielded a protein of the expected molecular weight.

The mucosal antibody repertoire of the cervical mucosa in commercial sex workers from Nairobi, Kenya, who are highly sexually exposed to human immune deficiency virus type-1 (HIV-1) but remain persistently IgG seronegative (HEPS), may represent a novel source of broadly neutralizing monoclonal antibodies (mAbs) against HIV-1. Mucosal IgA specific for HIV-1 envelope (Env) subunit gp41 has been suggested as a correlate of protection in HEPS individuals. The in depth studies at both the gene and function level required to confirm their role in HIV-1 resistance are possible only using recombinant monoclonal IgAs. Human mAbs have traditionally been selected from libraries displayed on the surface of microorganisms (phage, yeast). However, due to inherent limitations, such techniques may not be optimal for isolating such rare mAbs from a pool of cervical B cells. We have developed an antibody selection system based on surface display on mammalian cells and used this technology to isolate four novel monoclonal antibodies, against linear epitopes on gp41, from the IgA repertoire of the cervical mucosa in Kenyan HEPS. Furthermore, three of the four mAbs were shown to bind with surface expressed consensus clade B and clade C Env on mammalian cells. Characterization of the variable region cDNA of the two strongest binding mAbs reveals extensive somatic mutations with a bias of replacement mutations clustering in the complementary determining regions (CDR) indicating antigen-driven affinity maturation had occurred. Affinity matured monoclonal IgAs, such as these, may play a role in the identification of new, vulnerable epitopes on HIV-1, or act as a component in a topical microbicide.

Heterosexual intercourse now accounts for the majority of HIV transmission within sub-Saharan Africa. The generation of microbicides and vaccines, therefore, requires a better understanding of the mucosal correlates of protection, including the role of HIV-specific IgA. It is now accepted that not all individuals are equally susceptible to HIV-1 infection, as exemplified by the HIV Exposed Seronegative (HESN) women of the Pumwani Cohort in Nairobi, Kenya. To assess whether mucosal IgA responses contribute to this protection, 3 novel IgA variable genes were cloned from HESN cervical B-cell cDNA. Nine monoclonal IgA Abs were produced, two of which were properly produced from cell culture. The HESN-derived A6/30L and A9/30L variants had a greater specificity for gp120IIIB than their A6/4L and A9/4L counterparts, while the A6 variant recognizes a distinct gp120 epitope compared to the broadly neutralizing antibody IgGb12. Further characterization of these IgA chains may suggest their suitability for use in microbicides or mucosal vaccines.

Monoclonal antibodies (MAbs) have been raised against $ beta$-tubulin of B. pahangi and A. suum. Anti-B. pahangi MAbs were used to investigate the heterogeneity of tubulins from nematodes and mammals. One-dimensional SDS-PAGE showed that MAbs P3D and 1B6 react with $ beta$-tubulin from a number of filarial and intestinal nematodes, but not with tubulin from protozoan and mammalian cells. Two-dimensional SDS-PAGE demonstrated that MAb P3D recognizes two isoforms of $ beta$-tubulin and 1B6 recognizes one. Limited proteolysis showed that MAb 1B6 reacted with the amino-terminal fragments and MAb P3D with the carboxyl-terminal fragments of $ beta$-tubulin. The effect of anti-B. pahangi MAbs on the viability of adult B. pahangi was assessed using MTT assay. It was found that MAbs P3D and 1B6 caused an 80% and 40% reduction respectively, in worm viability, whereas anti-chick MAb 357 or mebendazole drug had no effect. Immunogold labelling of B. pahangi demonstrated the presence of tubulin in the median and basal layers of the cuticle, hypodermal layer and somatic muscle blocks, as well as the uterus of B. pahangi. The reduction in the viability of worms may, therefore, be due to the disruption of microtubules in the body wall muscle of B. pahangi. The total MBZ binding was highest in the intestine followed by the body wall muscle and in the reproductive tract extracts of A. suum. Electron microscopy of A. suum tissues demonstrated that the tubulin content decreased from the intestine through the body wall muscle to the reproductive tract. One dimensional SDS-PAGE revealed the presence of $ alpha,$ $ beta sb1$ and $ beta sb2$ tubulin subunits in all tissues of A. suum. This data confirmed the reduction of tubulin from the intestine through the body wall muscle to the reproductive tract. Two dimensional SDS-PAGE followed by Western blotting demonstrated that $ alpha$ and $ beta$ tubulin isoform patterns are dissimilar in different tissues of A. suum. Body wall muscle, inte

No description available.

Rheumatoid arthritis (RA) is a chronic inflammatory disease with an unknown aetiology characterized by joint destruction. Both genetic and environmental factors contribute to the disease development with HLA-DRB1* alleles and smoking identified as most important. The disease is characterized by the presence of autoantibodies, originally by rheumatoid factor (RF) and more recently by anti citrullinated protein/peptide antibodies (ACPA) and antibodies against carbamylated peptides (CarP). These autoantibodies are present, not only after the onset of disease, but also prior to the onset of symptoms. The development of RA is a gradual process lasting several years before the onset of any joint symptom, but when and if there is a temporal difference in the development both between and within the different antibody systems is currently unknown. B-cells produce the antibodies, and a subset of B-cells, i.e., B-regulatory (Breg) cells, produces interleukin-10, and thus have the ability to down-regulate pro-inflammatory cytokines. Whether the Breg cells are involved in the pathogenesis of RA is, as yet, unknown. The aim of this thesis was to increase knowledge of the pathophysiological processes in the development of RA through identification of factors involved. The analyses involved detection of autoantibodies to post-translationally modified peptides/proteins in addition to RF isotypes, cell surface markers on immune cells in asymptomatic individuals, who have an increased risk of developing RA. In a co-analysis of the registers of patients with RA attending the Department of Rheumatology, with the registers from population based screening programmes within the Biobank of Northern Sweden, blood samples collected from individuals prior to the onset of symptoms were identified, as were those from population control subjects. A cohort of pre-symptomatic individuals also donated samples at the time of receiving a diagnosis of RA. First-degree relatives (FDR) of patients with RA were also identified and included for analyses. The levels of ten different ACPAs, i.e., (fibrinogen (Fib) α563-583(573), Fibα580-600(591), Fibβ62-81a(72), Fibβ62-81b(74), Fibβ36-52, a-enolase (CEP-1), triple helical collagen type II (citC1III), filaggrin (Fil307-324), vimentin (Vim) 2-17, and Vim60-75) were measured using the ImmunoCAP ISAC system (Phadia/ThermoFischer, Uppsala, Sweden) in blood samples from individuals before the onset of symptoms and when diagnosed with RA in comparison with those in population based controls. In a subset of samples, the levels of anti-CarP antibodies were measured using ELISA coated with anti-CarP-FCS, as well as analysis of RF of IgM, IgG and IgA isotype using the EliA assay (Phadia, Uppsala, Sweden). Breg cells were analysed both with and without stimulation ex vivo along with other cell types using flow cytometry in samples from patients with RA, their first degree relatives (FDR) and healthy controls. In paper I it was shown that levels of ACPA were initially restricted to a few antibodies but disseminated over time to involve additional different antibodies. The levels of antibodies to CEP-1, Fibß36-52, and filaggrin were significantly increased. In paper II, anti-CarP antibodies were positive in 5-13% of the individuals negative for the various ACPA studied. The presence of anti-CarP antibodies was significantly related to radiological destruction of joints at baseline, at follow-up after 24 months and to the radiological progress between baseline and 24months. In paper III, the relationships between the frequencies of RF isotypes, the ten different ACPA, anti-CCP2 and anti-CarP antibodies before the onset of any symptoms and the presence of certain combinations of antibodies were associated with a very high risk of developing RA. In paper IV Breg cells from patients with RA are functionally impaired and FDR showed a similar pattern by responding less to stimulation ex vivo than cells from healthy controls. In conclusion, individuals who subsequently develop RA have an increased number and amount of ACPAs, anti-CarP antibodies and RF of IgM, IgG and IgA isotype, several years before symptom onset. Most of the different antibodies analysed remain associated with disease development after adjustments for each separate antibody. In FDRs, Breg cells were functionally altered in that they produce less IL-10 and consequently contribute to a more inflammation-prone status, as in their relatives with RA. These findings contribute to information about the development of RA as well as a given individual’s risk(s) of developing RA and its progression.

Pseudomonas aeruginosa is an opportunistic human pathogen which, like many other Gram negative pathogens, employs quorum sensing - regulated virulence factors to establish an infection in its host. Quorum sensing in P. aeruginosa populations is controlled by low molecular weight (hapten) signalling molecules known as homoserine lactones (HSLs). Blocking bacterial communication using antibodies is an attractive strategy for infection control as QS takes a central role in P. aeruginosa infections, and antibodies can recognise their targets with exquisite specificity. There are two well-studied QS circuits in P. aeruginosa- the Las system and the Rhl system, controlled by two autoinducers compounds, 3-oxo-C12-HSL and C4-HSL respectively. Antibodies raised against HSL compounds can reduce the expression of virulence factors controlled by QS circuit and the immunomodulatory effects of 3- oxo-C12-HSL. In order to generate antibodies with high sensitivities against the autoinducer compounds of P. aeruginosa, a panel of HSL compounds was synthesised, conjugated to the carrier protein and used for sheep immunisation. High specificity anti-HSL antibodies were isolated from an immunised sheep antibody repertoire using phage display technology. These phage antibody hits were converted into single chain antibody (scAb) format, which possessed a HuCκ gene for detection and 6x histidine tag for purification. Soluble scAbs expressed in E. coli were purified and characterised using ELISA. Unique clones showing high sensitivity for free HSL compounds were reformatted into sheep-mouse chimeric IgGs, expressed transiently in COS 7 cells and characterised using biochemical assays. These cross-reactive monoclonal antibodies were shown to recognise HSL compounds in low nanomolar concentrations and have the potential to reduce virulence gene expression in P. aeruginosa.

Pseudomonas Aeruginosa is a common gram-negative bacterium present in the environment. It causes severe infections in immunosuppressed patients. Cystic fibrosis patients are especially at risk of being infected with Pseudomonas Aeruginosa. Ongoing studies are preformed to find alternative therapies to antibiotics, due to increased resistance. One new treatment is intake of specific IgY antibodies against Pseudomonas Aeruginosa as an oral therapy. The problem today is that IgY solutions must be kept frozen until consumed.  In this study we examined the possibility to freeze-dry specific IgY antibodies without losing any activity or specificity of the antibodies. This would be more convenient of patients, as well as it makes transportation and storage easier.  The methods used were ELISA for control of activity, western blot analysis and SDS-PAGE gel for control of specificity. Three different batches of the IgY anti-Pseudomonas Aeruginosa solution were tested. The results showed that no loss in activity occurred that would affect clinical outcome or change of specificity in the antibodies after freeze-drying appears. This indicates that it is possible to replace the liquid antibody to a freeze-dried powder.