This diploma thesis deals with study of the rate-dependence of the magnitude of a current through the heart channel that conducts slowly activating component of delayed rectifier outward current (IKs). This property is very important for the IKs channel function. When other repolarizing currents are insufficient, but also when the heart rate accelerates, especially during elevated sympathetic tone, IKs provides so-called repolarization reserve, which prevents excessive lengthening of cardiac action potential repolarization. The IKs channel structure is encoded by the KCNQ1 (pore-forming -subunit) and KCNE1 (modulatory -subunit) genes. Mutations in these genes disrupt the physiological function of the IKs channel and cause inherited arrhythmogenic syndromes, especially long QT syndrome (LQTS). Such mutations include the c.926C>T (p.T309I) mutation in the KCNQ1 gene, which results in LQTS type 1 in heterozygous carriers. The theoretical part of the thesis provides basic information about the IKs channel and the patch clamp technique, this knowledge is necessary for the practical part. The experimental part is focused on cultivation of the CHO cell line and its transient transfection for subsequent electrophysiological measurements by whole-cell patch clamp technique to study the dependence of the IKs magnitude on stimulation frequency, both in the wild type channels (i.e. without mutation) and in those with cotransfected wild type and T309I subunits.

Whole-cell sensors represent an emerging branch in biosensor development since they obviate the need for enzyme/antibody purification and provide the unique opportunity to assess global parameters such as genotoxicity and bioavailability. Yeast species such as Saccharomyces cerevisiae are ideal hosts for whole-cell sensor applications. However, current approaches almost exclusively rely on analyte-induced expression of fluorescent proteins or luciferases that imply issues with light scattering and/or require the supply of additional substrates. In this study, the yeast α-factor mating pheromone, a peptide pheromone involved in cell-cell communication in Saccharomyces cerevisiae, was utilized to create the whole-cell sensor read-out signal, in particular by employing engineered sensor cells that couple the response to a user-defined environmental signal to α-factor secretion. Two novel immunoassays - relying on hydrophobin-based surface engineering - were developed to quantify the α-factor. Hydrophobins are amphiphilic fungal proteins that self-assemble into robust monolayers at hydrophobic surfaces. Two recombinant hydrophobins, either lacking (EAS) or exposing the α-factor pheromone (EAS-α) upon self-assembly, were used to functionalize polystyrene supports. In a first approach (competitive immunoassay), pheromone-specific antibodies initially bound to the functionalized surface (due to the α-factor exposed by the hydrophobin layer) were competitively detached by soluble α-factor. In a second approach, the antibodies were first premixed with pheromone-containing samples and subsequently applied to functionalized surfaces, allowing for the attachment of antibodies that still carried available binding sites (inverse immunoassay). Both immunoassays enabled quantitative assessment of the yeast pheromone in a unique but partially overlapping dynamic range and allowed for facile tuning of the assay sensitivity by adjustment of the EAS-α content of the hydrophobin layer. With a limit of detection of 0.1 nM α-factor, the inverse immunoassay proved to be the most sensitive pheromone quantification assay currently available. Due to the high stability of hydrophobin monolayers, functionalized surfaces could be reused for multiple consecutive measurements. Favorably, both immunoassays proved to be largely robust against the changes in the sample matrix composition, allowing for pheromone quantification in complex sample matrices such as yeast culture supernatants. Hence, these immunoassays could also be applied to study the pheromone secretion of wild-type and engineered Saccharomyces cerevisiae strains. Additionally, a proof-of-concept whole-cell sensor for thiamine was developed by combining the hydrophobin-based immunoassays with engineered sensor cells of Schizosaccharomyces pombe modulating the secretion of the α-factor pheromone in response to thiamine. Since this read-out strategy encompasses intrinsic signal amplification and enables flexible choice of the transducer element, it could contribute to the development of miniaturized, portable whole-cell sensors for on-site application.

Increases in basolateral amygdala (BLA) activity drive avoidance-seeking behavior that may be associated with stress induced drug seeking. Activity of BLA pyramidal neurons is regulated by local and paracapsular gamma aminobutyric acid (GABA) interneurons. The lateral paracapsular interneurons (LPCs) border the external capsule, receive dense cortical/thalamic input and provide feed-forward inhibition onto BLA principle neurons. The GABAergic LPCs also express high concentrations of g-protein coupled µ-opioid receptors (MORs). Therefore, the effects of opiates on LPC activity and local GABA release were examined. Fluorescently double labeled LPCs were observed in glutamate decarboxylase (GAD) 65-mcherry/GAD67-green fluorescent protein (GFP) transgenic mice. Whole-cell electrophysiology experiments demonstrated that acute exposure to [D-Ala2, N-Me-Phe4, Gly5-ol]-enkephalin (DAMGO; a synthetic selective MOR agonist), reduced LPC firing and spontaneous inhibitory postsynaptic current (sIPSC) frequency in LPCs, with no apparent effect on spontaneous excitatory currents (sEPSCs). Current injection induced firing in LPC neurons, but less effectively than in saline controls. Morphine-exposed mice (10mg/kg/day, across 5 days, 1-2 days off) had increased sIPSCs compared to saline-injected controls, as well as enhanced adenylyl cyclase (AC) activity. Together these data show that LPC neurons are a highly sensitive targets for opiate-induced inhibition, and that long-term opiate exposure results in impaired LPC excitability, possibly contributing to anxiety observed during opiate withdrawal.

Die Durchführung von Experimenten und das mathematische Modellieren von zellulären Prozessen gehören in der Systembiologie untrennbar zusammen. Das gemeinsame Ziel ist die Aufklärung des Zusammenspiels intrazellulärer Prozesse wie Metabolismus, Genexpression oder Signaltransduktion. Während sich molekularbiologische Untersuchungen mit den molekularen Mechanismen einzelner isolierter Systeme beschäftigen, zielt die Systembiologie auf die Aufklärung der Zusammenhänge ganzer Prozesse und schließlich auch ganzer Zellen ab. Die Verfügbarkeit von umfangreichen Datensätzen und die steigenden Möglichkeiten im Bereich der Computersimulation haben in den letzten Jahren den Weg geebnet, um auch Ganzzellsimulationen nicht mehr unmöglich erscheinen zu lassen. Diese Arbeit stellt das erste eukaryotische Ganzzellmodell der Bäckerhefe Saccharomyces cerevisiae vor. Hefe als eukaryotischer Modellorganismus ist hierbei der perfekte Kandidat für die Erstellung eines solchen Modells. Er bietet, als wohl meist erforschter eukaryotischer Einzeller in Verbindung mit der Verfügbarkeit einer großen Menge experimenteller Daten, beste Voraussetzungen zur Erstellung eines solchen Modells. Das Projekt ist hierbei in drei Teile gegliedert: i) Die Erstellung eines modularen Ganzzellmodells das alle zellulären Funktionen wie Zellzyklus, Genexpression, Metabolismus, Transport und Wachstum abbildet. ii) Die Implementation einer spezialisierten Simulationsumgebung in Verbindung mit einer Datenbank, um die Erstellung, Simulation und Parametrisierung von Modulen zu ermöglichen. iii) Die Durchführung von Experimenten, um einen ganzheitlichen Datensatz zu erlangen, der Wachstum, Genexpression und Metabolismus abbildet. Die hier vorgestellte Arbeit liefert nicht nur ein mathematisches Modell, sondern benennt auch die Herausforderungen, die während der Arbeit an einem Ganzzellmodell auftreten und stellt mögliche Lösungsansätze vor. / In systems biology experiments and mathematical modeling are going hand in hand to gain and increase understanding of cellular processes like metabolism, gene expression, or signaling pathways. While molecular biology investigates single isolated parts and molecular mechanisms of cellular processes, systems biology aims at unraveling the whole process and ultimately whole organisms. Today the availability of comprehensive high-throughput data and computational power paved the way to increase the size of analyzed systems to reach the cellular level. This thesis presents the first whole-cell model (WCM) of a eukaryotic cell, the yeast Saccharomyces cerevisiae. This established model organism is the perfect candidate for the implementation of a holistic model based on the available experimental data and the accumulated biological knowledge. The project is split into three parts: i) The creation of a modular functional-complete whole-cell model, combining the processes cell cycle, gene expression, metabolism, transport, and growth. ii) The implementation of a specialized simulation environment and a database to support module creation, simulation, and parameterization. iii) The elicitation of experimental data by conducting an experiment to achieve a comprehensive data set for parameterization, combining growth, metabolic, proteomic, and transcriptomic data. The presented work provides not only a simple mathematical model but also addresses challenges occurring during the development of whole-cell models and names possible solutions and new methodologies required for the creation of WCMs.

Les bioréacteurs de grandes dimensions, en raison de phénomènes de transfert limitant, sont le siège d’hétérogénéités se traduisant par des gradients locaux de concentration et température. Les microorganismes circulant au sein de ces bioréacteurs subissent donc des fluctuations environnementales qui peuvent affecter leur comportement aux niveaux métaboliques et/ou moléculaires. La réponse microbienne est fonction de la nature, de l’intensité, de la fréquence et de la durée de la perturbation. L’objectif de ce travail est l’étude quantitative de l’impact de l’intensité, la fréquence et l’amplitude d’un stress nutritionnel sur le comportement dynamique d’Escherichia coli, à savoir des ajouts pulsés de glucose lors de cultures continues en régime permanent. Un effort particulier est consacré au développement et à la validation des outils expérimentaux indispensables pour une caractérisation rigoureuse des dynamiques de réponses transitoires sur des échelles de temps allant de secondes à quelques minutes. Pour permettre le suivi in situ et en temps réel des changements métaboliques et moléculaires, une souche bioluminescente est mise en œuvre. Les réponses transitoires sont caractérisées par les vitesses spécifiques, les rendements, les profils d’induction transcriptionnelle, les temps caractéristiques. Selon les différents scenarii réalisés, l’ajustement du métabolisme face aux hétérogénéités de substrat est quantifié selon des échelles de temps aux niveaux macroscopiques et/ou moléculaires ; ces résultats originaux contribuent ainsi à l’implémentation des connaissances sur les interactions dynamiques entre les phénomènes biologiques et les phénomènes physiques ; l’enjeu réside à terme en l’amélioration des processus d’optimisation et d’extrapolation des bioprocédés par l’identification et la quantification des dynamiques des phénomènes limitants / Ineffective mixing entailing heterogeneity issues within industrial bioreactors have been reported to affect microbial metabolisms at cellular and/or molecular levels. Substrate gradients inside large-scale bioreactors are common environmental fluctuations that microorganisms would have to encouter along with the bioprocess. Depending on intensity, frequency and duration of those fluctuations, microorganisms may respond in a different manner. The objective of this work is to study the impact of intensity, frequency and amplitude of glucose perturbations on the dynamics of Escherichia coli responses. An E. coli bioluminescent strain is used for in situ and real-time monitoring of both metabolic and transcriptional changes. For this purpose, short-term glucose excess was simulated, using pulse-based experiments into glucose-limited chemostat cultures. In addition, an important effort is devoted to the development and validation of technical and mathematical tools in order to acquire quantitative and kinetic data on time scales from seconds to minutes. The transient responses are characterized, using specific rates, yields, transcriptional induction profiles and characteristic response times, and are compared in the different defined perturbation scenarios. The results reflected the fact that short-term heterogeneities of substrate affect both cell metabolism and regulation at macroscopic and/or molecular levels. Quantitative understandings of the dynamics during transient responses to environmental perturbations can thus shed light on the bioprocess optimization

S. pneumoniae é um patógeno de grande impacto em saúde pública e vacinas comerciais têm cobertura limitada e alto custo. Como alternativa, desenvolveu-se uma vacina celular de baixo custo, cuja produção envolve apenas a separação das bactérias do caldo e sua inativação. Neste trabalho, foram avaliados processos descontínuo, descontínuo alimentado e contínuo com reciclo de células, cuja produção de biomassa foi 3 vezes maior que a do descontínuo. Vacinas obtidas nos 3 processos foram utilizadas em ensaios de imunização de camundongos e induziram níveis similares de IgG e IL-17A. Anticorpos ligaram-se e induziram a deposição de moléculas do sistema complemento sobre a superfície do pneumococo. Ademais, induziram fagocitose de diferentes cepas encapsuladas da bactéria. Camundongos imunizados foram protegidos contra sepse após aspiração da cepa virulenta WU2. Portanto, o processo contínuo com reciclo permitiu a obtenção de maior número de doses sem alterar a qualidade da vacina e o ensaio opsonofagocítico poderia ser utilizado como potencial correlato de proteção. / S. pneumoniae is a pathogen of great impact on public health and commercially available vaccines have limited coverage and high cost. As alternative, a low-cost whole cell vaccine was developed, whose production involves only the cell separation and inactivation. In this work, we evaluated batch, fed-batch and continuous cultivation with cell recycle. The biomass production was 3-fold higher in continuous process than batch. Vaccines obtained from these 3 processes were used to immunize mice and all vaccines induced comparable levels of IgG and IL-17A. Antibodies were able to bind and induce deposition of complement onto pneumococcal surface, besides to induce phagocytosis of several encapsulated pneumococcal strains in opsonophagocytic assays. Immunized mice were protected from fatal aspiration-sepsis using the virulent pneumococcal strain WU2. Therefore, the continuous process with cell recycle yielded a higher number of doses without altering the quality of the vaccine and opsonophagocytic assay could be used as a potential correlate of protection.

Doctor of Philosophy(PhD) / Two recently identified transient receptor potential (TRP) channels, TRPM8 and TRPA1, have been proposed to play an important role in mammalian cool and cold peripheral sensory transduction. When expressed in cell-lines the cloned TRPM8 and TRPA1 receptors have distinct pharmacological and temperature response characteristics. Although these receptors are also transported to the central terminals of primary afferents, little is known about their centrally mediated actions. In this thesis, I use an in vitro electrophysiological approach to investigate the dorsal horn processing of cool afferent modalities and the role of TRP ion channels. The results of this thesis provide further information on thermal processing, indicate direction for further research and suggest possible therapeutic targets for the management of abnormal cold sensory processing. Initial experiments demonstrate that the cooling agents and known TRPM8 and TRPA1 agonists, menthol and icilin, inhibit primary afferent evoked excitatory postsynaptic currents (EPSCs) in rat spinal cord dorsal horn neurons. In addition, temperature reduction, menthol and icilin increase the frequency of miniature EPSCs without affecting amplitude distribution or kinetics. Little or no direct postsynaptic effect on dorsal horn neurons, GABAergic or glycinergic transmission was found. In combination, these observations demonstrate that temperature reduction, menthol and icilin act presynaptically to increase the probability of glutamate release from primary afferent fibres. Further examination of the changes in glutamatergic synaptic transmission induced by temperature reduction, menthol and icilin reveals a subset of neurons sensitive to innocuous cool (< 29 oC) and low concentrations of icilin (3-10 µM) which closely match the temperature activation and pharmacological profile of TRPM8. In addition, the majority of lamina I and II neurons displayed characteristics partly consistent with TRPA1-activation, including a concentration-dependent response to icilin and blockade by ruthenium red. The present experiments did not allow thermal characterisation of these TRPA1-like responses. Together these observations indicate that the effects of menthol and icilin on glutamatergic synaptic transmission in the superficial dorsal horn are mediated by TRPM8 and possibly by TRPA1. Examination of the anatomical location of neurons activated by temperature reduction, menthol, icilin and capsaicin allowed the central termination pattern of thermoreceptive primary afferent fibres with specific TRP-like response characteristics to be determined. TRPM8-like presynaptic activation was confined to a subpopulation of neurons located in lamina I and outer lamina II, while the majority of neurons throughout laminae I and II received inputs sensitive to menthol, high concentrations of icilin and capsaicin. These findings suggest that innocuous cool sensation projects to a specific subpopulation of superficial dorsal horn neurons unlike other modalities (mediated by TRPV1, possibly TRPA1 and other receptors), which non-selectively engage circuits within the entire superficial dorsal horn. No morphological specificity was identified for recovered neurons after electrophysiological characterisation. Finally, mu-opioids were shown to inhibit basal glutamatergic synaptic transmission as well as menthol- and icilin-induced transmission in the superficial dorsal horn. Of particular interest, delta-opioids selectively inhibited icilin-induced synaptic transmission within the same location. The selective effect of delta-opioids suggests a possible role in modulating receptors activated by icilin (TRPM8 and TRPA1). Overall, this thesis provides further evidence that TRPM8 is responsible for the transduction of innocuous cold sensation in mammals and is a potential therapeutic target in humans with cold hyperaesthesia secondary to abnormal thermal processing. The use of delta-opioid agonists warrants further investigation in cold hypersensitivity states and potentially other forms of pain.

Doctor of Philosophy(PhD) / Two recently identified transient receptor potential (TRP) channels, TRPM8 and TRPA1, have been proposed to play an important role in mammalian cool and cold peripheral sensory transduction. When expressed in cell-lines the cloned TRPM8 and TRPA1 receptors have distinct pharmacological and temperature response characteristics. Although these receptors are also transported to the central terminals of primary afferents, little is known about their centrally mediated actions. In this thesis, I use an in vitro electrophysiological approach to investigate the dorsal horn processing of cool afferent modalities and the role of TRP ion channels. The results of this thesis provide further information on thermal processing, indicate direction for further research and suggest possible therapeutic targets for the management of abnormal cold sensory processing. Initial experiments demonstrate that the cooling agents and known TRPM8 and TRPA1 agonists, menthol and icilin, inhibit primary afferent evoked excitatory postsynaptic currents (EPSCs) in rat spinal cord dorsal horn neurons. In addition, temperature reduction, menthol and icilin increase the frequency of miniature EPSCs without affecting amplitude distribution or kinetics. Little or no direct postsynaptic effect on dorsal horn neurons, GABAergic or glycinergic transmission was found. In combination, these observations demonstrate that temperature reduction, menthol and icilin act presynaptically to increase the probability of glutamate release from primary afferent fibres. Further examination of the changes in glutamatergic synaptic transmission induced by temperature reduction, menthol and icilin reveals a subset of neurons sensitive to innocuous cool (< 29 oC) and low concentrations of icilin (3-10 µM) which closely match the temperature activation and pharmacological profile of TRPM8. In addition, the majority of lamina I and II neurons displayed characteristics partly consistent with TRPA1-activation, including a concentration-dependent response to icilin and blockade by ruthenium red. The present experiments did not allow thermal characterisation of these TRPA1-like responses. Together these observations indicate that the effects of menthol and icilin on glutamatergic synaptic transmission in the superficial dorsal horn are mediated by TRPM8 and possibly by TRPA1. Examination of the anatomical location of neurons activated by temperature reduction, menthol, icilin and capsaicin allowed the central termination pattern of thermoreceptive primary afferent fibres with specific TRP-like response characteristics to be determined. TRPM8-like presynaptic activation was confined to a subpopulation of neurons located in lamina I and outer lamina II, while the majority of neurons throughout laminae I and II received inputs sensitive to menthol, high concentrations of icilin and capsaicin. These findings suggest that innocuous cool sensation projects to a specific subpopulation of superficial dorsal horn neurons unlike other modalities (mediated by TRPV1, possibly TRPA1 and other receptors), which non-selectively engage circuits within the entire superficial dorsal horn. No morphological specificity was identified for recovered neurons after electrophysiological characterisation. Finally, mu-opioids were shown to inhibit basal glutamatergic synaptic transmission as well as menthol- and icilin-induced transmission in the superficial dorsal horn. Of particular interest, delta-opioids selectively inhibited icilin-induced synaptic transmission within the same location. The selective effect of delta-opioids suggests a possible role in modulating receptors activated by icilin (TRPM8 and TRPA1). Overall, this thesis provides further evidence that TRPM8 is responsible for the transduction of innocuous cold sensation in mammals and is a potential therapeutic target in humans with cold hyperaesthesia secondary to abnormal thermal processing. The use of delta-opioid agonists warrants further investigation in cold hypersensitivity states and potentially other forms of pain.

Im Bereich der Umwelttechnik bieten sich vielversprechende Einsatzmöglichkeiten für Sol-Gel-immobilisierte Mikroorganismen sowohl für die Entfernung als auch für die Detektion von Schadstoffen an. Für einen effizienten Einsatz sind zum einen eine hohe Langzeitaktivität und -vitalität der eingebetteten Zellen als auch eine gute Lagerbeständigkeit wichtig. Neben einer hohen Makroporosität, die sowohl für einen guten Stoffaustausch mit der Umgebung sorgt sowie den Zellen Raum für Zellteilung bietet, ist vor allem auch die Aufrechterhaltung der Feuchtigkeit in der Immobilisierungsmatrix während der Immobilisierung, der Lagerung und des Einsatzes wichtig. Besonders vorteilhaft hat sich hier eine Immobilisierung in dünnen SiO2-Schichten auf Blähtonbruchstücken erwiesen, da dieses Trägermaterial neben einer hohen Makroporosität auch ein hohes Wasserspeichervermögen besitzt. Immobilisiert in dünnen SiO2-Schichten auf Blähton konnten diverse Schadstoff-abbauende Mikroorganismen mehrere Monate auch außerhalb eines flüssigen Mediums unter feuchten Bedingungen gelagert werden, ohne dass ihre Abbauleistung erheblich sank. Ein weiteres Verfahren um Immobilisierungsmaterialien mit überdurchschnittlich hoher Makroporosität bei gleichzeitig hoher Stabilität zu erzeugen, stellt das Freeze-Gelation Verfahren dar. Über einen Gefriertrocknungsschritt können hier zudem die zu immobilisierenden Zellen in eine trocken lagerfähige Form überführt werden, wodurch Handhabung sowie Lagerung und Transport vereinfacht werden. Außerdem kann durch Wahl der Einfrierbedingungen und Zugabe von Füllstoffen zu dem SiO2-Sol entscheidend die Porenstruktur der Immobilisierungsmatrix beeinflusst und den Anforderungen entsprechend eingestellt werden. Allerdings zeigte sich, dass diese Methode nicht für alle Mikroorganismen gleichermaßen geeignet ist. Trotz diverser kryoprotektiver Maßnahmen konnte keine ausreichende Überlebensrate für sensible Stämme wie Aquincola tertiaricarbonis L108 erzielt werden. Neben der Erhöhung der Makroporosität der SiO2-Matrix wurde versucht das Sol-Gel-Verfahren mit einem flexiblen organischen Polymer (Na-Alginat) zu kombinieren, um eine Immobilisierungsmatrix mit einem weichen Kern zu erzeugen, der Zellteilung zulässt. Als zusätzlicher Vorteil des entwickelten Alginat/SiO2-Hybridmaterials erwies sich, dass dieses auch auf einfache Weise mittels Drucktechniken in definierten Spots abgelegt werden kann und so die Zellen in Arrays abgelegt werden können. Das Potential dieser Methodik für die Entwicklung von Ganzzellsensoren wurde am Beispiel der Grünalge Chlorella vulgaris als Modell-Sensorzelle demonstriert und für die Detektion von Atrazin als Modellsubstanz eingesetzt.

S. pneumoniae é um patógeno de grande impacto em saúde pública e vacinas comerciais têm cobertura limitada e alto custo. Como alternativa, desenvolveu-se uma vacina celular de baixo custo, cuja produção envolve apenas a separação das bactérias do caldo e sua inativação. Neste trabalho, foram avaliados processos descontínuo, descontínuo alimentado e contínuo com reciclo de células, cuja produção de biomassa foi 3 vezes maior que a do descontínuo. Vacinas obtidas nos 3 processos foram utilizadas em ensaios de imunização de camundongos e induziram níveis similares de IgG e IL-17A. Anticorpos ligaram-se e induziram a deposição de moléculas do sistema complemento sobre a superfície do pneumococo. Ademais, induziram fagocitose de diferentes cepas encapsuladas da bactéria. Camundongos imunizados foram protegidos contra sepse após aspiração da cepa virulenta WU2. Portanto, o processo contínuo com reciclo permitiu a obtenção de maior número de doses sem alterar a qualidade da vacina e o ensaio opsonofagocítico poderia ser utilizado como potencial correlato de proteção. / S. pneumoniae is a pathogen of great impact on public health and commercially available vaccines have limited coverage and high cost. As alternative, a low-cost whole cell vaccine was developed, whose production involves only the cell separation and inactivation. In this work, we evaluated batch, fed-batch and continuous cultivation with cell recycle. The biomass production was 3-fold higher in continuous process than batch. Vaccines obtained from these 3 processes were used to immunize mice and all vaccines induced comparable levels of IgG and IL-17A. Antibodies were able to bind and induce deposition of complement onto pneumococcal surface, besides to induce phagocytosis of several encapsulated pneumococcal strains in opsonophagocytic assays. Immunized mice were protected from fatal aspiration-sepsis using the virulent pneumococcal strain WU2. Therefore, the continuous process with cell recycle yielded a higher number of doses without altering the quality of the vaccine and opsonophagocytic assay could be used as a potential correlate of protection.