My diploma thesis describes a procedure of creating interactive computer software for company ISH&MSA Čerpadla a.s. in its theoretical part as well as in its practical part. It is a proposal diagram of centrifugal pumps which consists of made and nonmade pumps. After the selection of a certain pump, according to the required parameters of capacity of pump and transit height, the output of the programme is drawing of a flows characteristic, characteristics of coiled paddlewheel and curves of dissipation without any differences in whether the pump is made or not. There is an operating procedure from the initial work with data, short demonstrations from source code, computation of nonmeasured pump to the ascending flows characteristics in practical part of my diploma thesis. In theoretical part, there are explained principles that are needed for comprehension of a pump reform which are used in practical part.

V rámci této práce byla provedena komplexní analýza elektricky vyhřívané bubnové sušičky prádla s cílem identifikovat možnosti optimalizace její konstrukce vedoucí ke zlepšení přestupu tepla. Pro řešení byl zvolen postup využívající výpočtovou dynamiku tekutin (CFD). K dosažení dostatečně detailního popisu zadaného problému byl využit komerční software Fluent společně se speciálně vyvinutým modelem přenosu tepla.

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La polykystose rénale autosomique dominante (PKRAD) est une maladie génétique rénale qui se manifeste par le développement de kystes au rein. Elle résulte de mutations dans le gène PKD1/polycystine-1 (PC-1), contenant un motif coiled-coil et dans le gène PKD2/PC-2 dont les fonctions restent à élucider. À partir d’un chromosome artificiel bactérien, le gène Pkd1 murin (BAC-Pkd1) a été modifié afin de générer 4 lignées de souris transgéniques délété du motif coiled-coil Pkd1Δcoiled-coil et 3 lignées contrôles Pkd1TAG possédant 1-35 copies du transgène. Ces 2 transgènes ont un profil d’expression identique à l’endogène et le niveau dépend du nombre de copies. Alors que les souris Pkd1TAG développent la PKRAD de sévérité proportionnelle au niveau d’expression, les lignées Pkd1Δcoiled-coil en sont épargnées. Ces résultats démontrent l’importance du motif coiled-coil dans la maladie. Les souris Pkd1Δcoiled-coil croisées par Pkd1-/- (létale à la naissance), Pkd1-/- ; Pkd1Δcoiled-coil survivent après la naissance et permettent d’analyser in vivo les interactions, la signalisation et le rôle physiologique du motif coiled-coil. Ces souris Pkd1-/- ; Pkd1Δcoiled-coil avec une copie du transgène présentent des kystes rénaux et meurent ~2 semaines alors que celles à hautes copies n’ont aucun phénotype comme les Pkd1TAG. Les résultats génétiques et biochimiques démontrent que Pc-1Δcoiled-coil est hypomorphe. Bien que Pc-1Δcoiled-coil subit son clivage autoprotéolytique, l’analyse du transport intracellulaire de Pc1Δcoiled-coil montre un délai de maturation. Alors qu’in vitro le trafic Pc-1/Pc-2 dépend du motif coiled-coil pour leur interaction, in vivo une interaction Pc-1Δcoiled-coil/Pc-2 est détectée, suggérant un site d’interaction distinct. Nos études in vivo démontrent que le motif coiled-coil de Pc-1 joue un rôle clé dans sa maturation et l’existence d’un nouveau partenaire de Pc-1 pour son transport intracellulaire. / Autosomal dominant polycystic kidney disease (ADPKD) is the most prevalent genetic disorder that is characterize by the formation of bilateral renal cysts and leads to kidney failure. It results from mutations in the PKD1/polycystin-1(PC-1) gene, containing a coiled-coil motif, and in the PKD2/PC-2 gene, the functions of which remain to be elucidated. From a bacterial artificial chromosome, the murine Pkd1 gene (Pkd1-BAC) was modified in order to obtain 4 transgenic mouse lines deleted from it coiled-coil motif (Pkd1Δcoiled-coil) and 3 Pkd1TAG control lines possessing 1-35 copies of the transgene. These two transgenes have an expression profile identical to the endogenous gene and their expression depends on the number of copies. While Pkd1TAG mice develop ADPKD with a severity proportional to the level of expression, the Pkd1Δcoiled-coil lines are spared. These results demonstrate the importance of the coiled-coil motif in the disease. Pkd1Δcoiled-coil mice crossed by Pkd1-/- (lethal by birth), Pkd1-/-; Pkd1Δcoiled-coil survive after birth and allow the interactions, signaling and physiological role of the coiled-coil motif to be analyzed in vivo. These Pkd1-/-; Pkd1Δcoiled-coil mice with one copy of the transgene show kidney cysts and die ~ 2-weeks while high-copy ones have no phenotype as opposed to Pkd1-/-; Pkd1TAG who eventually develop cyst after 1 year. The genetic and biochemical results demonstrate that Pc-1Δcoiled-coil is hypomorphic. Although Pc-1Δcoiled-coil undergoes its autoproteolytic cleavage, analysis of the intracellular transport of Pc-1Δcoiled-coil shows a delay in maturation. While Pc-1 and Pc-2 appear to interact in vitro through their coiled-coil motif and co-transport, a Pc-1Δcoiled-coil -Pc-2 interaction is conserved in the kidney, suggesting a distinct mechanism of interactions in vivo. Thus, our results show that the coiled-coil motif of Pc-1 in vivo is involved in the maturation independently of Pc-2, highlighting the existence of a critical partner in intracellular transport.

Methods for fast, simple detection of biomarkers to detect and differentiate closely related Bacillus endospores including Bacillus anthracis (BA), Bacillus thuringiensis (BT), Bacillus atrophaeus (BG), and Bacillus cereus (BC) using thermochemolysis and methylation (TCM), coiled wire filament (CWF), solid phase micro extraction (SPME) and gas chromatography-mass spectrometry (GC-MS) were developed. The main biomarkers detected and used for differentiation include dipicolinic acid methyl ester (DPAME), fatty acid methyl esters (FAMEs), 3-methyl-2-butenoic acid methyl ester (3M2BAME), 2-butenoic acid methyl ester (2BAME), and several methylated sugars. TCM of endospores was performed based on hydrolysis and methylation at elevated temperature after the endospores were mixed with sulfuric acid (H2SO4) with or without addition of tetramethylammonium hydroxide (TMAH) in methanol (MeOH). TCM products were then introduced into a heated GC injector port using a coiled wire filament (CWF) or solid phase microextraction (SPME) for detection and differentiation of the endospores by GC-MS.The CWF, which consisted of a tiny platinum helical wire coil attached to a retractable plunger that moved the coil in and out of a syringe needle housing, allowed for sampling to be accomplished by dipping the CWF in an endospore sample suspension, evaporating the suspension liquid, and then introducing the CWF into the injection port to enable on-line TCM. New SPME techniques, including half-half extraction, coated-needle extraction (CNE), and a new home-made polymer coated needle were used to speed up solid phase micro extraction of biomarkers produced from TCM. These simplified the detection of anthrose and other biomarkers. TCM with a CWF and TCM with SPME produced high intensity profiles of DPAME, FAMEs, 2BAME, 3M2BAME and methylated sugars. While the presence of DPAME can be used for the general detection of endospores (Bacillus and Clostridium) and the presence of 3M2BAME for the detection of BA, specific saturated and unsaturated C15, C16, and C17 fatty acid methyl esters and methylated sugars provide additional information for differentiating various Bacillus species grown at different temperatures and in different media. DPAME was detected in samples containing as few as 2,500 and 6,000 endospores using TCM-CWF with and without a concentration step, respectively. GC-MS peak area percent reproducibility for FAMEs using TCM and CWF varied from 3 to 13% (RSD). Better than 97% correct predictability of Bacillus species identity was obtained from a blind experiment consisting of 145 samples using DPAME and specific FAMEs. Conventional SPME and a modified form of "in-needle" extraction allow for detection of the biomarkers in less than 35 min. The detection limits with SPME sample introduction injection were approximately 5 x 103 endospores.Using these approaches, differentiation of Bacillus endospores and other biological agents grown under different conditions were based on the following characteristics: (1) presence of DPAME and specific FAMEs (iso or anteiso C15:0 and iso or anteiso C17:0) in Bacillus endospores, (2) unique presence of 3M2BAME (anthrose by-product) in BA, (3) absence of 2-butenoic acid methyl ester in BG, and (4) presence and absence of specific methylated monosaccharides in various Bacillus species. Clostridium endospores and non-sporulating bacteria, such as Yersinia pestis (YP) and Francisella tularensis (FT) could also be easily distinguished from Bacillus endospores based on the presence and absence of several specific sugar derivatives and fatty acid methyl esters (FAMEs), such as iso or anteiso C15:0 and iso or anteiso C17:0, and > C18 FAMEs which were simultaneously produced during TCM.

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Les conjugués anticorps-médicament (ADC) représentent une avancée révolutionnaire dans la thérapeutique du cancer en délivrant de manière sélective des médicaments cytotoxiques aux cellules tumorales, minimisant ainsi la toxicité systémique. Les ADC se composent de trois composants principaux : un anticorps monoclonal (mAb) ciblant un antigène spécifique associé à la tumeur, un médicament cytotoxique et un lien qui conjugue le médicament à l’anticorps. Malgré leur potentiel thérapeutique, la fabrication des ADC est confrontée à d’importants défis, nécessitant l’optimisation de plusieurs paramètres, en particulier pour obtenir une technologie de conjugaison optimale et un ratio médicament-anticorps (DAR) optimal. Les méthodes de conjugaison traditionnelles basées sur la chimie donnent souvent lieu à des mélanges hétérogènes avec des DAR variables, ce qui peut affecter négativement l’efficacité thérapeutique et la sécurité du produit final. Pour résoudre ce problème, la conjugaison spécifique au site a émergé comme une méthode plus précise, garantissant que les médicaments cytotoxiques sont attachés à des sites spécifiques sur la molécule d’anticorps. Cette technique vise à produire des ADC homogènes avec des DAR constants, améliorant ainsi leur pharmacocinétique et leur pharmacodynamie. Cependant, les conjugaisons spécifiques au site ne sont pas exemptes de limitations. L’un des principaux défis réside dans la complexité de l’ingénierie des modifications nécessaires. L’introduction de sites de conjugaison spécifiques nécessite un génie génétique précis, ce qui peut être techniquement difficile et chronophage. De plus, les processus de fabrication des ADC spécifiques au site sont plus complexes et nécessitent des techniques sophistiquées et des mesures étendues de contrôle qualité. Ces facteurs peuvent donc affecter la production d’ADC basée sur la conjugaison spécifique au site. Le travail présenté dans cette thèse de doctorat propose l’utilisation d’une paire de peptides hétérologues à haute affinité, à savoir les coiled-coils E/K, pour produire des ADC avec une homogénéité améliorée et un DAR contrôlable. Pour commencer, nous avons conçu, produit et purifié une bibliothèque d’anticorps monoclonaux (trastuzumab) marqués avec divers peptides Ecoil et évalué leur manufacturabilité via une transfection transitoire dans des cellules d’ovaire de hamster chinois (CHO) et avons étudié les caractéristiques des anticorps marqués produits. Nos données montrent que l’ajout de peptides Ecoil aux extrémités C-terminales des chaînes d’anticorps (chaînes légères, chaînes lourdes ou les deux) n’entrave pas la production de constructions chimériques de trastuzumab. De plus, les tests analytiques et cellulaires ont confirmé que les constructions de trastuzumab marquées avec Ecoil ont maintenu leur bioactivité. La position, le nombre et la longueur des peptides Ecoil n’ont eu aucune influence sur l’affinité de liaison et la stabilité des anticorps marqués à leur antigène. Dans le cadre d’une étude supplémentaire et d’une étape supplémentaire pour démontrer la polyvalence des peptides E/K, nous avons également évalué la capture et la libération du trastuzumab marqué avec Ecoil produit à partir d’hydrogels de dextrane macroporeux fonctionnalisés avec le peptide Kcoil (le partenaire de liaison du peptide Ecoil). Ensemble, ces données ont révélé que les peptides Ecoil, quelle que soit leur longueur, leur nombre et leur position sur l’anticorps, n’avaient aucun effet significatif sur la manufacturabilité, la capacité de liaison ou le schéma de libération de l’hydrogel. Sur la base de cette fondation, nous avons exploré l’utilisation de deux peptides d’affinité complémentaires, E-coil (EVSALEK) et K-coil (KVSALKE), pour développer des ADC avec une homogénéité améliorée et un DAR contrôlable. En utilisant une méthode d’analyse par résonance plasmonique de surface (SPR) sur mesure et une chromatographie d’exclusion stérique, nous avons mesuré la dissociation cinétique et la stabilité des complexes formés par le trastuzumab marqué avec Ecoil et la protéine fluorescente rouge monomérique (mRFP) marquée avec Kcoil en tant que substitut de médicament. La stabilité in vitro a également été évaluée dans le sérum sanguin à l’aide d’un test ELISA en interne avant les études in vivo. Ensuite, pour évaluer les performances in vivo, nous avons mené des études de biodistribution et de localisation tumorale dans des modèles de souris xénogreffées HER2. Ces expériences ont démontré la stabilité de nos ADC dans la circulation sanguine et leur accumulation efficace sur le site de la tumeur. En général, ce projet vise à démontrer la faisabilité et la polyvalence du système d’affinité E/K pour la conjugaison spécifique au site de molécules thérapeutiques sur le squelette d’anticorps sans modifications chimiques complexes/préjudiciables. La fabrication simplifiée des ADC en utilisant cette méthode de “conjugaison en une seule étape” présentée ici ouvre la voie au développement de nouvelles méthodes dans la production d’ADC avec potentiellement une pharmacocinétique, une bioactivité et une stabilité améliorée. / Antibody-drug conjugate (ADC) represents a transformative breakthrough in cancer therapeutics by selectively delivering cytotoxic drugs to tumor cells, thereby minimizing systemic toxicity. ADC consists of three main components: a monoclonal antibody (mAb) targeting a specific tumor-associated antigen, a cytotoxic drug, and a linker that conjugates the drug to the antibody. Despite their therapeutic potential, the manufacturing of ADCs faces significant challenges, requires the optimization of several parameters particularly in achieving optimal conjugation technology and drug-to-antibody ratio (DAR). Traditional chemical-based conjugation methods often result in heterogeneous mixtures with variable DARs, which can adversely affect the therapeutic efficacy and safety of the final product. To address this issue, site-specific conjugation has emerged as a more precise method, ensuring that cytotoxic drugs are attached to specific sites on the antibody molecule. This technique aims to produce homogeneous ADCs with consistent DARs, thereby enhancing their pharmacokinetics and pharmacodynamics. However, site-specific conjugations are not exempt from limitations. One of the main challenges is the complexity involved in engineering the necessary modifications. Introducing specific conjugation sites requires precise genetic engineering, which can be technically challenging and time-consuming. Moreover, site-specific ADC manufacturing processes are more complex and require sophisticated techniques and extensive quality control measures. These factors can therefore affect ADC production based on site-specific conjugation. The work presented in this doctoral thesis proposed use of a high-affinity peptide pair, namely the E/K coiled-coils, to produce ADCs with improved homogeneity and controllable DAR. To begin with, we designed, produced, and purified a library of monoclonal antibodies (trastuzumab) tagged with various Ecoil peptides and evaluated their manufacturability via transient transfection in Chinese hamster ovary (CHO) cells and investigated the characteristics of the produced tagged antibodies. Our data show that the addition of Ecoil tags at the C-termini of antibody chains (light chains, heavy chains, or both) does not hinder the production of chimeric trastuzumab constructs. Further, analytical and cell-based assays confirmed that the Ecoil-tagged trastuzumab constructs maintained their bioactivity. The position, number, and length of the Ecoil tags had no influence on the binding affinity and stability of tagged antibodies to HER2 antigen. As an additional study and an extra step towards demonstrating the versatility of the E/K affinity peptides, we also evaluated the capture and release of produced Ecoil-tagged trastuzumab from macroporous dextran hydrogels functionalized with Kcoil peptide (the Ecoil peptide binding partner). Together, these data revealed that the Ecoil tags, regardless of their length, number, and position on the antibody, had no significant effect on manufacturability, binding capacity, or release pattern from the hydrogel. Building on this foundation, we explored the use of two complementary affinity peptides, E-coil (EVSALEK) and K-coil (KVSALKE), to develop ADCs with improved homogeneity and controllable DAR. Using a tailored surface plasmon resonance (SPR) assay and size exclusion chromatography(SEC), we measured the kinetics of dissociation and stability of the complexes formed by Ecoil-tagged trastuzumab and Kcoil-tagged monomeric red fluorescent protein (mRFP) as a drug surrogate. The in vitro stability was also assessed in blood serum using an in-house enzyme-linked immunosorbent assay (ELISA) prior to the in vivo studies. Next, to evaluate the in vivo performance, we conducted biodistribution and tumor localization studies in HER2 xenograft mouse models, specifically using SKOV-3 cells, which exhibit deregulated HER2 expression. These experiments demonstrated the stability of our ADCs in blood circulation and their effective accumulation at the tumor site. Overall, this project aims to demonstrate the feasibility and versatility of the E/K coiled coil affinity system for site-specific conjugation of the payload to the antibody backbone without complex/detrimental chemical modifications. The simplified manufacturing of ADCs using this “single-step conjugation” method shown here paves the way for developing new methods in production of ADCs with potentially enhanced pharmacokinetics, bioactivity, and stability.

<p> We developed some universal platforms to overexpress the minimal functional entities of ion channels. The modular property of ion channels have been demonstrated from many aspects, such as crystal structures, chimeric channel experiments and discovery of similar modules in distantly related protein families. Thus it should be feasible to express each module independent of other channel modules. The pore-forming module of ion channels has multiple important properties as selectivity, conductivity and drug-binding. If it can be overexpressed, it will provide valuable information about channel selectivity to different ions and structural bases for drug binding as well as important application in drug screening and rational drug design. </p> <p> To test this, we first used the model channel KcsA to identify the minimal requirements for a pore-forming domain to functionally exist independently. Chapter 2 of this thesis explains in detail how the wild type C-terminal cytoplasmic domain of KcsA functions. We found that this domain has dual function as pH-sensor and tetramerization domain, and it is essential for the expression of the pore-forming domain of KcsA. Once we knew the physiological role of the cytoplasmic domain, the scenario was set to answer the question of how to make it better for the application of structural and functional studies. </p> <p> In chapter 3 and chapter 4, we replaced the wild type C-terminal domain with non-native tetramerization domains. We identified the direct correlation between protein expression level and overall thermostability of pore-forming domains. The C-terminal tetramerization domains stabilize channels in a cooperative way and play a critical way in in vivo channel assembly. The selection of the linker between pore-forming domain and tetramerization domain, the splicing motif, and the handedness of C-terminal tetrameric coiled coils all affect channel expression level and stability. </p> <p> We applied our finding in KcsA to a wide range of ion channels in chapter 5, including voltage-gated potassium channels, Ca2+-gated potassium channels, inwardrectifying potassium channels, cyclic nucleotide-gated potassium channels and voltagegated sodium channels. We managed to express similar minimal structural modules from these more structurally complicated channels with the assistance of different cytoplasmic tetramerization domains. Several minimal channels expressed well and showed similar biophysical and functional property as the wild type channels. </p> <p> These studies demonstrate that the pore-forming modules of ion channels can be expressed independently while retaining the proper structure and drug-binding properties as their wild type predecessors when using our universal expression platform. The potential application in structural studies and drug-screening is promising. </p> / Thesis / Doctor of Philosophy (PhD)

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