An immunoglobulin (IgG) consists of two antigen-binding fragments (Fab) connected to a crystallisable fragment through hinge regions. This thesis mainly investigates the production methods of Fabs used in structural studies. A cost effective and time saving protocol has been established for the production of recombinant 2F5 Fab, a HIV-1 broadly neutralizing monoclonal antibody fragment, using an Escherichia coli expression system. The integrity of structure and antigen-binding capability of the produced 2F5 Fab was confirmed by determining the crystal structure of the Fab-antigen peptide complex. In parallel, 3H1 Fab, a fragment of an antibody which is involved in detecting misfolded superoxide dismutase, which is related to familial amyotrophic lateral sclerosis, was produced by papain proteolysis of its parent IgG molecule. Both Fab production methods resulted in high yields of pure Fab samples that are crystallisable and ready to be engaged in structural studies using X-ray crystallography.

An immunoglobulin (IgG) consists of two antigen-binding fragments (Fab) connected to a crystallisable fragment through hinge regions. This thesis mainly investigates the production methods of Fabs used in structural studies. A cost effective and time saving protocol has been established for the production of recombinant 2F5 Fab, a HIV-1 broadly neutralizing monoclonal antibody fragment, using an Escherichia coli expression system. The integrity of structure and antigen-binding capability of the produced 2F5 Fab was confirmed by determining the crystal structure of the Fab-antigen peptide complex. In parallel, 3H1 Fab, a fragment of an antibody which is involved in detecting misfolded superoxide dismutase, which is related to familial amyotrophic lateral sclerosis, was produced by papain proteolysis of its parent IgG molecule. Both Fab production methods resulted in high yields of pure Fab samples that are crystallisable and ready to be engaged in structural studies using X-ray crystallography.

In order to optimize productivity of a cell culture it is necessary to understand growth and productivity and couple these features of the culture to extracellular nutrients whose profiles can be manipulated. Also, since growth and productivity are directly affected by cell death mechanisms such as apoptosis, it is imperative to understand these mechanisms. This work describes the development of a differential equation based population balance model of apoptosis in a Chinese Hamster Ovary cell culture producing Anti-RhD monoclonal antibody (mAb). The model was verified in isolation and was then coupled to a metabolic flux model. The model distinguishes between various subpopulations at normal healthy states and at various stages of apoptosis. After finding that glucose and glutamine are not limiting nutrients for this culture, different hypotheses were explored to explain growth arrest. Initially, it was hypothesized that there is some unknown nutrient in either media or serum which is depleted, thus causing growth arrest. Accordingly a first model was developed assuming depletion of this nutrient. Subsequent experiments with different additions of media and serum showed that there is no such nutrient limitation for the media and serum conditions used in most of the experiments. Additional experiments with different culture volumes showed that cell growth was actually controlled by a compound that accumulates and causes pH deviation from its optimal range of operation. Since strong correlations were found between culture volume and growth, it was hypothesized that the compound may be carbon dioxide (CO2), which is inhibitory for growth and may accumulate due to mass transfer limitations. Following this finding, a second model was proposed to take into account the accumulation of this inhibitor, although the specific inhibiting compound could not be exactly identified. This second mathematical model of cell growth was then integrated with a metabolic flux model to provide for a link between intracellular and extracellular species balances, since the latter are the ones to be manipulated for increasing productivity. This final model formulation was then used to describe mAb productivity. The model was also able to reasonably predict all cell subpopulations, nutrients, metabolites and mAb. In an attempt to mitigate the effect of CO2 accumulation and renew the cell growth, culture perfusions were performed. Although this approach resulted in some renewal of growth, the cell concentration progressively decreased after each successive perfusion event. This suggests that irreversible cell damage occurs because of CO2 accumulation. The model was used to describe the perfusion experiments. Agreement between data and model predictions were reasonable. In addition, it was shown that operation with successive perfusions results in a significant increase in productivity and therefore it can be used for further process optimization.

Parkinson’s disease, dementia with Lewy bodies and multiple system atrophy are disorders featuring accumulation of Lewy bodies in brain. The main component of these large insoluble intracellular inclusions is the presynaptic protein alpha-synuclein (α-synuclein). It is generally believed that α-synuclein monomers adopt an abnormal conformation that favors the formation of soluble oligomers or protofibrils and, eventually, insoluble fibrils depositing as Lewy bodies. Notably, the intermediately sized oligomers/protofibrils seem to have particular neurotoxic effects. Several factors may influence the formation of α-synuclein oligomers/protofibrils, e.g. the reactive aldehydes 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE) formed during oxidative stress. The overall aims of this thesis were to investigate biophysical and biochemical properties of in vitro generated α-synuclein oligomers, characterize their functional effects on cell and animal disease models as well as to explore whether their formation could be prevented in a cell culture model for oligomerization.  Here, it was found that α-synuclein rapidly formed oligomers after incubation with both ONE and HNE. The resulting oligomers were stable and did not continue to form insoluble fibrils. By comparing HNE- and ONE induced α-synuclein oligomers biochemically they were both found to exhibit extensive β-beta sheet structure and had a molecular size of ~2000 kDa. However, they differed in morphology; the ONE induced α-synuclein oligomers described round amorphous species whereas the HNE induced α-synuclein oligomers appeared as elongated protofibril-like structures. Both these oligomers were cell internalized to varying degrees and induced toxicity in neuroblastoma cells. In addition, the ONE induced α-synuclein oligomers seemed to initiate aggregation of monomeric α-synuclein in vitro, but failed to do so in vivo. Finally, treatment of α-synuclein overexpressing cells with monoclonal antibodies specific for α-synuclein significantly reduced aggregation and lowered levels of the protein, suggesting increased turnover in these cells.  To conclude, this thesis has characterized different oligomeric α-synuclein species, which may have properties similar to soluble species central to the pathogenesis of Parkinson’s disease and other disorders with α-synuclein pathology. For therapeutic strategies it is important to selectively target such harmful protein species and avoid interaction with other forms of α-synuclein, which may have vital physiological cellular functions.

Perlecan is an important basement membrane heparan sulfate (HS) proteoglycan that is essential for various cell signaling events involved in tissue development. Heparanase is a lysosomal enzyme involved in the turnover of HS. This project aimed to assist in researching the structure of HS on perlecan and how this structure changes with tissue development. This will be achieved by generating monoclonal antibodies that have an altered affinity for perlecan after heparanase treatment. Recombinant perlecan domain I was characterized by ELISA and western blotting and used as the antigen for two fusions. The first fusion was focused on the production of IgM the common subtype of anti-glycosaminoglycans antibodies. However, no clones were produced, which may have been due to the lack of feeder layers. In order to address this problem, the fibroblast cell line MRC-5 was used as a feeder layer in the second fusion. From this fusion, we obtained 216 positive cultures, which were screened against full length perlecan from endothelial cells. Of these, 26 cultures were tested against heparanase treated perlecan, and then 2 cultures were chosen for subcloning based on the different immunoreactivity between enzyme treated and nontreated perlecan. From the 2 chosen cultures, 13 sub clones were derived and 10 of them were adapted into a serum free culture environment. The 10 monoclonal antibodies displayed strong immunoreactivity with full length perlecan in ELISA and Western Blotting. When they were used as primary antibodies in Immunocytochemistry, they were able to recognize the native perlecan deposited by human chondrocytes. When the cells were incubated with heparanase, antibody 5D7-2E4 and 13E9-3G5 showed an increase in immunoreactivity while antibody 13E9-3B3 gave a decrease. These three antibodies will be the potential tools used in the future to study perlecan turnover in different cells and tissue. The remaining seven antibodies will also be very useful in the research of perlecan as they have been shown to bind to the protein core. In the future, it will be worth subcloning some of the frozen stored stocks of uncloned hybridomas, where there are potential opportunities to select antibodies, which will react with the carbohydrate chains on perlecan.

The Australian paralysis tick, Ixodes holocyclus causes a potentially fatal paralysis in domestic animals, livestock and humans with companion animals (mainly dogs) most commonly affected. Current treatment regimes include administration of a commercial tick anti-serum (TAS), prepared as hyperimmune serum in dogs, to neutralise the effects of the toxin. However, each new batch must be standardised using an expensive and highly subjective bioassay performed in neonatal mice. There is currently an urgent need for a more cost effective and rapid in vitro assay that can be more objectively and accurately quantified. Further understanding of the composition of the toxin molecule is also required to develop toxin-specific reagents necessary for these assays. One of the main objectives of this study was to develop a suitable immunoassay to replace the existing mouse bioassay for assessing batches of tick anti-sera for use in tick paralysis therapy in dogs. Initially an enzyme-linked immunosorbent assay (ELISA) was established to detect and quantify antibody specific for I. holocyclus toxin in dog sera. Using a partially purified antigen extracted from I. holocyclus salivary glands, good discrimination was achieved between reactive (hyperimmune) and non-reactive (naïve) sera. The hyperimmune dog sera reacted very strongly with the antigen compared to negligible reactions of serum from dogs not exposed to I. holocyclus. The reactions of hyperimmune sera were also significantly weaker to a non-toxin antigen control extracted from the salivary glands of the non-toxic tick Rhipicephalus microplus, indicating the assay was detecting toxin-specific responses. Furthermore, each of the hyperimmune sera that reacted strongly and specifically with the I. holocyclus antigen in the ELISA also strongly neutralised toxin in the mouse bioassay. Together these findings support the suitability of this ELISA for assessing the potency of batches of commercial dog hyperimmune sera for use as therapy for tick paralysis in dogs. Sera from dogs that were experimentally infested with ticks and sera from patient dogs, presenting at veterinary clinics with signs of tick paralysis, were also screened for antibodies to I. holocyclus antigen using the ELISA. Twenty-eight out of 29 sera from animals with single or multiple exposures to ticks failed to recognise the I. holocyclus antigen indicating the ELISA is not suitable as a diagnostic test to detect toxin-specific antibodies in animals with limited exposure to I. holocyclus infestation. A panel of toxin-specific monoclonal antibodies (mAbs) was produced as research tools to analyse and purify tick toxin components. Rats were successfully immunised against tick toxin using a combination of inoculation of partially purified salivary gland antigen and exposure to tick infestation. The latter approach preserved the native confirmation of the toxin using a natural route of immunisation and rats were chosen due to their high tolerance of multiple tick infestations over several days. While fusion of rat spleen cells with mouse myeloma cells has been reported several times in the literature, the resulting hybridomas are unstable with fastidious culture requirements. Optimisation of the culture conditions revealed that most rat-mouse hybridoma lines grew best in serum-free medium supplemented with 5% foetal bovine serum. Of 600 hybridomas produced, only 12 were shown to be specific for the Ixodes antigen, as determined by ELISA. A selection of these hybridomas representing various patterns of affinity and/or antigen specificity were further analysed for toxin-neutralising ability in a mouse bioassay. Notably, the most potent toxin-neutralising mAb in mice, showed a specific but relatively moderate reaction to Ixodes antigen in the ELISA. The most potent toxin-neutralising mAbs inactivated toxin as strongly as the commercial TAS used for immunotherapy in dogs with tick paralysis. This suggests that mAbs may present an alternative source of immunotherapy, providing a potentially endless supply of a highly consistent reagent and negating the need to use live animals for both the production of tick antiserum and the continual testing of reagent batches. The toxin-neutralising mAbs were also used to analyse I. holocyclus toxin in polyacrylamide gel electrophoresis (PAGE) and Western blot to identify specific toxin proteins. The most potent neutralising mAbs consistently recognised high MW proteins (100-200 kDa) in a smeared pattern. Although this was contrary to previous reports of low molecular weight components (3-5 kDa) in holocyclotoxin, this study was the first to use mAbs prepared to native toxin. The large molecular weight structures likely represent presucursors to, or complexes of the smaller peptides, previously identified. When the Toxin-neutralising mAbs were assessed as ligands to affinity purify toxin components from crude Ixodes SG extracts, toxin components of 110 and 32 kDa were consistently identified. These purified proteins represent good candidates for N-terminal sequencing to further identify the toxin components in I.holocyclus salivary glands.

Soluble amyloid-beta (Aβ) aggregates, including Aβ protofibrils, play a central role in Alzheimer’s disease (AD) and constitute a potential diagnostic biomarker and a therapeutic target. Aβ protofibrils promote synapse dysfunction and neurodegeneration, but the mechanisms behind these effects remain unclear. The aim of this thesis was to increase the knowledge of Aβ protofibrils in AD pathology. When measuring low abundant antigens, such as soluble Aβ aggregates, in plasma and CSF by immunoassays, there is a possibility of interference by heterophilic antibodies (HA). In paper I, we show that HA generate false positive signals, by cross-binding the assay antibodies, when plasma and CSF from AD patients and healthy controls were analyzed for soluble Aβ aggregates, using sandwich ELISAs. Natural anti-Aβ antibodies exist in AD patients and healthy individuals. Circulating Aβ and anti-Aβ antibodies may form immune complexes, masking epitopes on the anti-Aβ antibody, which makes the anti-Aβ antibody concentration difficult to measure. In paper II, the ELISpot technique enabled us to successfully measure B cell production of anti-Aβ antibodies. Our results show that anti-Aβ protofibril antibody production is present in both AD patients and healthy individuals, but is significantly higher in AD patients, indicating that the immune system attempt to eliminate the toxic Aβ species. Insufficient lysosomal degradation is proposed to cause sporadic AD. In paper III, we used a co-culture system of astrocytes, neurons and oligodendrocytes, to clarify the role of astrocytes in Aβ protofibril clearance. Astrocytes are the most prominent glial cell type in the brain, but their role in AD remains elusive. We found that astrocytes effectively engulf, but inefficiently degrade Aβprotofibrils. This result in a high intracellular load of toxic, partly N-terminally truncated Aβ and lysosomal dysfunction. Moreover, we found that secretion of microvesicles, containing N-terminally truncated Aβ, induce neuronal apoptosis. In paper IV, we show that treatment with the protofibril selective antibody mAb158 lead to enhanced Aβ clearance and thereby prevent Aβ neurotoxicity. Taken together, this thesis contributes with important knowledge on the role of Aβ protofibrils in AD pathogenesis and technical aspects that should be considered when measuring Aβ in human tissues.

Resumo: A cisticercose é uma das principais causas de perdas econômicas na pecuária de corte brasileira devido às condenações da carne para o controle do complexo teníase-cisticercose. O tratamento quimioterápico pode ser utilizado para o controle da infecção nos animais, mas sua eficácia deve ser monitorada por testes de diagnóstico que detectem parasitas vivos ou seus produtos. Na presente pesquisa, anticorpos monoclonais contra antígenos totais (TAEB) e de fluido vesicular (TAEF) de metacestóides de Taenia saginata foram produzidos através de fusão celular, utilizando-se células de baço de camundongos BALB/c imunizados. Cinco fusões TAEB e quatro TAEF foram realizadas e os sobrenadantes de cultura foram triados por teste ELISA indireto. Dez e nove híbridos pertencentes aos protocolos TAEB e TAEF, respectivamente, foram selecionados e clonados. As linhagens celulares clonadas foram mantidas em meio de cultura para a obtenção dos anticorpos monoclonais, resultando em 18 clones IgG1 e 32 IgM reativos para TAEB e 9 IgG1 e 9 IgM para TAEF. Dentre esses clones, 5 do protocolo TAEB e 5 TAEF foram selecionados para produção de líquido ascítico, através da injeção dos clones em camundongos BALB/c. A avaliação da identificação antigênica dos anticorpos produzidos aos antígenos homólogos foi realizada por meio de western blotting, resultando em reatividade com frações protéicas de baixo peso molecular (< 18kDa), 43, 55, 66 e 100kDa. A imunofluorescência indireta demonstrou que os anticorpos monoclonais avaliados reconhecem antígenos presentes tanto do escólex quanto da membrana vesicular de metacestóides de bovinos naturalmente infectados. Os anticorpos monoclonais produzidos poderão ser utilizados para detecção de antígenos circulantes na avaliação da eficácia do tratamento de bovinos infectados, evitando assim perdas econômicas e danos à saúde pública. / Abstract: Cysticercosis is a major cause of economic losses in the Brazilian bovine chain production due to meat condemnation for the taeniasis-cysticercosis complex control. Chemotherapy can be used to control infection in cattle but treatment efficacy should be monitored by diagnostic tests that can detect live parasites or their products. Monoclonal antibodies against Taenia saginata metacestode crude (TAEB) and cyst fluid (TAEF) antigens were produced by cell fusion procedures using spleen cells from immunized BALB / c mice. Five TAEB and four TAEF fusions were performed and the culture supernatants from these cell cultures were screened by indirect ELISA assay. Ten TAEB and nine TAEF hybrids were selected and cloned. Cloned cell lines were grown in culture medium to collect the monoclonal antibodies, resulting in 18 IgG1 and 32 IgM clones reactive to TAEB and 9 IgG1 and 9 IgM clones reactive to TAEF. Five TAEB and five TAEB clones were selected for ascitic fluid production by injection in BALB/c mice and further harvesting. Western blotting was performed to test the antigenic identification by the antibodies produced resulting in reactivity to protein fractions of low molecular weight (<18kDa) and to 43, 55, 66 and 100kDa. The indirect immunofluorescence test showed that monoclonal antibodies recognize antigens from both the scolex and the bladder wall of metadestodes from naturally infected bovine. The monoclonal antibodies obtained can be useful for detection of circulant antigens in treatment efficacy evaluation preventing economic losses and public health injury. / Orientador: Cáris Maroni Nunes / Coorientador: Elenice Deffune / Banca: Valéria Marçal Félix de Lima / Banca: Rosana Rossi Ferreira / Mestre

v anglickom jazyku Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Biophysics and Physical Chemistry Student: Juliána Klimová Supervisor: Mgr. Pavel Bárta, Ph.D. Name of the work: In vitro saturation study of 99m Tc-HYNIC-ramucirumab on SKOV3 cell line. The passive immunotherapy is based on the use of already active immune system components (monoclonal antibodies), which play an important role in cancer cells elimination in the organism. The active immunotherapy tries to stimulate an active anticancer response via an appropriate form of an immunization. When monoclonal antibodies bind to cancer cells, those cells become a selected target for the following removal. The enhancement of the anti- cancer affect of monoclonal antibodies is possible due to the attachment of therapeutic agents like cytostatics, toxins and radionuclides. This presented master thesis is focused on the radiolabeling of the monoclonal antibody ramucirumab, which is directed against the vascular endothelial growth factor type 2 (VEGFR 2), which is often present in cells of some types of cancerous diseases. Within the experimental work, at first, there was a conjugation of chelating agent succinimidyl-6-hydrazino-nicotinamide (HYNIC) on the monoclonal antibody. After this step, radionuclide 99m...

Toxoplasma gondii is an obligate intracellular protozoan that belongs to the Apicomplexa phylum and causes toxoplasmosis which is especially severe in immunocompromised individuals and who acquired the infection by congenital transmission. Dense granules are organelles involved in this parasite invasion and replication of the parasite inside the cell. Among the proteins secreted by dense granules, jointly called GRAs, the GRA 2 is particularly immunogenic. In the present work, we aim to study the role of this protein in inducing adaptive immune response by produced and characterized a monoclonal antibody against GRA2. The parasite treated with this antibody showed the lowest rate of replication in intracellular proliferation assay compared to treatment with irrelevant antibody. The epitopes of this protein that binds to the monoclonal antibody have been mapped by phage display. Through bioinformatics analysis, epitopes for B cells and T GRA2 were predicted and based on that and on the results of phage display amino acid sequences were chosen to synthesize two peptides that were tested as potential vaccine. Immunization tests were carried out in C57BL/6 mice with synthetic peptides and these animals were subsequently infected with T. gondii. There was a significant reduction in mortality in the group immunized with the mixture of both peptides. The negative control group, immunized only with BSA, showed the highest mortality and analysis of cytokine present in the sera of these animals there was a predominance of proinflammatory cytokines while antiinflammatory cytokines were shown to be almost nonexistent in the serum of these animals. Given these results, it was found that the group with higher survival showed better Th1/Th2 balance. This demonstrates that immunization with epitopes recognized by both B cells and T cells appear to be more effective. Thus, peptide mimetics GRA2 regions of the protein may be likely candidates for the development of vaccines against toxoplasmosis. / Toxoplasma gondii é um protozoário do filo Apicomplexa intracelular obrigatório causador da toxoplasmose, que é especialmente grave em indivíduos imunocomprometidos e em indivíduos que adquiriram a infecção por transmissão congênita. Grânulos densos são organelas deste parasito envolvidas no processo de invasão e replicação do parasito no interior da célula. Dentre as proteínas secretadas pelos grânulos densos, chamadas conjuntamente de GRAs, a GRA 2 é particularmente imunogênica. No presente trabalho, no sentido de estudar a participação dessa proteína na indução da resposta imune adaptativa, foi produzido e caracterizado um anticorpo monoclonal contra GRA2. O parasito tratado com esse anticorpo apresentou menor taxa de replicação em ensaio de proliferação intracelular comparado ao tratamento com anticorpo irrelevante. Os epítopos de ligação da proteína GRA2 ao anticorpo monoclonal foram mapeados por phage display. Por meio de análises de bioinformática, epítopos para células B e T da GRA2 foram preditos e com base nisso e nos resultados do phage display foram escolhidas seqüências de aminoácidos para sintetizar dois peptídeos que foram testados quanto ao potencial vacinal. Foram feitos ensaios de imunização em camundongos C57BL/6 com estes peptídeos sintéticos e os animais foram posteriormente infectados com T. gondii. Foi observada redução significativa na mortalidade no grupo imunizado com a mistura de ambos os peptídeos. O grupo controle negativo, imunizado somente com BSA, apresentou a maior mortalidade e nas análises de produção de citocinas presentes nos soros destes animais observou-se uma predominância de citocinas pró-inflamatórias enquanto as citocinas anti-inflamatórias mostraram-se quase inexistentes no soro destes animais. Tendo em vista esses resultados, percebeu-se que o grupo com maior sobrevivência apresentou melhor balanço Th1/Th2. Isso demonstra que a imunização com epítopos reconhecidos tanto por células B quanto por células T parece ser mais efetiva. Assim, peptídeos miméticos de regiões da proteína GRA2 podem ser prováveis candidatos no desenvolvimento de vacinas anti Toxoplasmose. / Doutor em Imunologia e Parasitologia Aplicadas