O uso de fertilizantes minerais nas culturas, inclusive no milho, é uma prática agrícola que provoca danos ambientais e prejuízos econômicos. Uma alternativa promissora, visando melhorar a produtividade e reduzir o uso de fertilizantes, é a utilização de microrganismos benéficos associados às plantas, particularmente as rizobactérias promotoras de crescimento. Essas bactérias vivem na rizosfera e são capazes de colonizar diversos tecidos vegetais, beneficiando o desenvolvimento das plantas através de mecanismos de promoção de crescimento. Na busca por alternativas sustentáveis e mais rentáveis, o presente trabalho teve como objetivo isolar, caracterizar, selecionar e monitorar rizobactérias associadas ao guaranazeiro da Amazônia que possuíssem características promotoras de crescimento vegetal para serem usadas como inoculantes em sementes de milho. Amostras de solo rizosférico de cinco plantas de guaranazeiros foram coletadas e foi realizado o isolamento das rizobactérias. A caracterização molecular foi realizada através do sequenciamento do gene 16S rDNA para análise da diversidade microbiana e identificação das linhagens. Avaliou-se a capacidade das linhagens de produzir ácido indol acético (AIA), fixar nitrogênio atmosférico, solubilizar fosfato inorgânico e de produzir sideróforos. A análise da diversidade microbiana indicou semelhança entre a comunidade bacteriana isolada da rizosfera do guaranazeiro e a do milho encontrada na literatura. Foi observada predominância do filo Proteobacteria, sendo em sua maioria representado pelo gênero Burkholderia. Do total das 101 linhagens obtidas, 89% foram capazes de produzir AIA, 23% fixaram nitrogênio atmosférico, 43% solubilizaram fosfato inorgânico e 24% produziram sideróforos. Cinco linhagens foram selecionadas para o ensaio de promoção de crescimento de milho em casa de vegetação, essas foram identificadas pelo sequenciamento completo do gene 16S rDNA e compuseram os tratamentos como segue: RZ2MS9 - Bacillus sp. (T1), RZ2MS16 - Burkholderia ambifaria (T2) e consórcio (T3) de 5 linhagens (RZ1MS6 - Burkholderia vietnamiensis, RZ1MS11 - Burkholderia sp., RZ2MS9 - Bacillus sp., RZ2MS16 - Burkholderia ambifaria e RZ4MS18 - Delftia acidovorans). As análises estatísticas comprovaram que as linhagens RZ2MS9 (Bacillus sp.) e RZ2MS16 (Burkholderia ambifaria) foram eficientes como promotoras de crescimento em milho, aumentando a altura cerca de 39 e 33%, respectivamente, em relação ao controle, o peso seco da parte aérea cerca de 236 e 114% e do sistema radicular cerca de 248 e 136%, respectivamente, comparado ao controle não inoculado. A linhagem RZ2MS9 (Bacillus sp.) aumentou o conteúdo de Ca nas plantas inoculadas. Para o monitoramento da colonização da bactéria na planta, a linhagem RZ2MS16 (Burkholderia ambifaria) foi transformada com o plasmídio pCM88 e passou a expressar a proteína GFP, sendo possível observar, por microscopia óptica de fluorescência, que, 12 dias após a inoculação na planta, a bactéria encontra-se concentrada no cilindro central da raiz da mesma de onde pode se inserir em algum vaso condutor e colonizar a planta sistematicamente, o que demonstra que a mesma se comporta como endofítica da planta de milho. Assim, fica evidente a importância da exploração de plantas de clima tropical, como o guaranazeiro, como reservatórios de bactérias com enorme potencial biotecnológico. As bactérias estudadas nesse trabalho tem grande potencial para serem utilizadas futuramente como inoculantes. / The use of mineral fertilizers on agricultural crops, including maize, is a practice that causes environmental damage and economical losses. A promising alternative, to improve productivity and reduce fertilizer use is the use of benefical microrganisms associated with plants, particulary the growth-promoting rhizobacteria. These bacteria live in the rhizosphere and are capable of colonizing different plant tissues, benefiting plant growth through mechanisms of growth promotion. In the search for sustainable and more profitable alternative, this study aimed to isolate, characterize, monitor and select rhizobacteria associated with Amazonian guarana that possessed characteristics of plant growth promoters for use as inoculants in maize seeds. Rhizosphere soil samples from five guarana plants were collected and the isolation of rhizobacteria was performed. Molecular characterization was performed by sequencing the 16S rDNA for analysis of microbial diversity and identification of strains. It was evaluated the ability of strains to produce indole acetic acid (IAA), fix atmospheric nitrogen, solubilize inorganic phosphate and produce siderophores. The analysis of microbial diversity indicated similarity between the bacterial community isolated from the rhizosphere of guarana and that found in the literature to maize. It was observed predominance of Proteobacteria phylum, being mostly represented by the genus Burkholderia. Of the total 101 strains obtained, 89% were able to produce IAA, 23% fixed atmospheric nitrogen, 43% solubilized inorganic phosphate and 24% produced siderophores. Five strains were selected for testing growth promotion of maize under greenhouse conditions; these were identified by complete sequencing of the 16S rDNA and compose the treatments as follows: RZ2MS9 - Bacillus sp. (T1), RZ2MS16 - Burkholderia ambifaria (T2) and consortium (T3) of 5 strains (RZ1MS6 - Burkholderia vietnamiensis, RZ1MS11 - Burkholderia sp., RZ2MS9 - Bacillus sp., RZ2MS16 - Burkholderia ambifaria and RZ4MS18 - Delftia acidovorans). Statistical analyzes showed that the strains RZ2MS9 (Bacillus sp.) and RZ2MS16 (Burkholderia ambifaria) were effective as growth promoters in maize, increasing the height about 39 and 33%, respectively, compared to control, shoot dry weight about 236 and 114% and root system about 248 and 136%, respectively, compared to uninoculated control. The strain RZ2MS9 (Bacillus sp.) increased Ca content in inoculated plants. For monitoring of colonization of the bacteria in the plant, the strain RZ2MS16 (Burkholderia ambifaria) was transformed with the plasmid pCM88 and passed to express GFP, being possible to observe by fluorescence microscopy that, 12 days after inoculation on the plant, the bacteria is concentrated in the root central cylinder where the same can be inserted into a vessel conductor and consistently colonize the plant, proving the endophytic life style of this strain during maize interaction. Thus, it is clear the importance of tropical plants, like guarana, as reservoirs of bacteria with great biotechnological potential. The evaluated bacteria accessed in this work have great potential to be used in future as inoculants.

Our increasing understanding of disease mechanisms coupled with technological advances has facilitated the generation of pharmaceutical proteins, which are able to address yet unmet medical needs. Diseases that were fatal in the past can now be treated with novel biological medications improving and prolonging life for many patients. Pharmaceutical protein production is, however, a complex undertaking, which is by no means problem-free. The demand for more complex proteins and the realization of the importance of post-translational modifications have led to an increasing use of mammalian cells for protein expression. Despite improvements in design and production, the costs required for the development of pharmaceutical proteins still are far greater than those for conventional, small molecule drugs. To render such treatments affordable for healthcare suppliers and assist in the implementation of precision medicine, further progress is needed. In five papers this thesis describes strategies and methods that can help to advance the development and manufacturing of pharmaceutical proteins. Two platforms for antibody engineering have been developed and evaluated, one of which allows for efficient screening of antibody libraries whilst the second enables the straightforward generation of bispecific antibodies. Moreover, a method for epitope mapping has been devised and applied to map the therapeutic antibody eculizumab’s epitope on its target protein. In a second step it was shown how this epitope information can be used to stratify patients and, thus, contribute to the realization of precision medicine. The fourth project focuses on the cell line development process during pharmaceutical protein production. A platform is described combining split-GFP and fluorescence-activated droplet sorting, which allows for the efficient selection of highly secreting cells from a heterogeneous cell pool. In an accompanying study, the split-GFP probe was improved to enable shorter assay times and increased sensitivity, desirable characteristics for high-throughput screening of cell pools. In summary, this thesis provides tools to improve design, development and production of future pharmaceutical proteins and as a result, it makes a contribution to the goal of implementing precision medicine through the generation of more cost-effective biopharmaceuticals for well-characterized patient groups. / <p>QC 20170828</p>

RhoB est une petite GTPase rapidement activée par les facteurs de croissance et les stress cellulaires, qui régule des processus biologiques fondamentaux comme la migration, l'angiogenèse, la réparation de l'ADN, l'apoptose ainsi que la réponse à des thérapeutiques anticancéreuses. L'activité des petites GTPases est finement régulée par leur localisation subcellulaire. Cependant, l'activation de RhoB en cellules vivantes n'avait jamais été investiguée. Ce travail a permis d'adapter et de valider une méthode innovante d'analyse des interactions protéine-protéine par complémentation split-GFP tripartite, pour la détection sensible et spécifique de l'activation des petites GTPases en cellules vivantes. Nous avons ensuite développé un modèle cellulaire optimisé par la combinaison de la technologie split-GFP tripartite et d'un intracorps anti-GFP amplificateur de fluorescence, pour détecter la régulation de l'activation de RhoB avec une haute résolution spatiale. Ce biosenseur a mis en évidence la translocation de la forme active de RhoB en réponse au sérum à partir des endosomes pour s'accumuler au niveau de la membrane plasmique, révélant ainsi une nouvelle plateforme de signalisation membranaire de RhoB. Ce biosenseur permettra d'analyser le profil d'activation de RhoB et d'autres petites GTPases, sous d'autres stimulations ou dans différents contextes cellulaires, et d'identifier leurs partenaires et les modulateurs de leur activation. / RhoB is a small GTPase that is rapidly activated in response to growth factors and cellular stress. It regulates fundamental biological processes such as cell migration, angiogenesis, DNA repair, apoptosis and response to anticancer therapies. Small GTPases activity is tightly regulated by their subcellular localization. However, RhoB activation had never been investigated in living cells. In this work, we have adapted and validated an innovative method of protein-protein interactions analysis using tripartite split-GFP complementation, for the sensitive and specific detection of small GTPases activation in living cells. Then, we developed an optimized cellular model by combining the tripartite split-GFP technology with an anti-GFP intrabody fluorescence-enhancer to detect the regulation of RhoB activation with high spatial resolution. This biosensor highlighted the translocation of active RhoB from endosomes to accumulate at the plasma membrane upon serum stimulation, revealing a novel membrane signaling platform of RhoB. Future studies based on this biosensor will enable the analysis of RhoB activation profile and other small GTPases upon various stimuli or in different cellular contexts, as well as the identification of the GTPases partners and activation modulators.

Certaines observations suggèrent que les afférences méchano-sensorielles peuvent moduler l’activité des générateurs centraux du rythme locomoteur (ou Central Pattern Generators, CPGs). Cependant, il est impossible d’explorer les circuits neuronaux sous-jacents chez l’animal en mouvement à l’aide d’enregistrements électrophysiologiques lors d’expériences de locomotion dite « fictive ». Dans cette étude, nous avons enregistré de façon sélective et non-invasive les neurones moteurs et sensoriels dans la moelle épinière pendant la locomotion active en ciblant génétiquement le senseur bioluminescent GFP-Aequorin chez la larve de poisson zèbre. En utilisant l’imagerie calcique à l’échelle des neurones individuels, nous confirmons que les signaux de bioluminescence reflètent bien le recrutement différentiel des groupes de motoneurones spinaux durant la locomotion active. La diminution importante de ces signaux chez des animaux paralysés ou des mutants immobiles démontre que le retour méchano-sensoriel augmente le recrutement des motoneurones spinaux pendant la locomotion active. En accord avec cette observation, nous montrons que les neurones méchano-sensoriels spinaux sont en effet recrutés chez les animaux en mouvement, et que leur inhibition affecte les réflexes d’échappement chez des larves nageant librement. L’ensemble de ces résultats met en lumière la contribution du retour méchano-sensoriel sur la production locomotrice et les différences qui en résultent entre les locomotions active et fictive. / There is converging evidence that mechanosensory feedback modulates the activity of spinal central pattern generators underlying vertebrate locomotion. However, probing the underlying circuits in behaving animals is not possible in “fictive” locomotion electrophysiological recordings. Here, we achieve selective and non-invasive monitoring of spinal motor and sensory neurons during active locomotion by genetically targeting the bioluminescent sensor GFP-Aequorin in larval zebrafish. Using GCaMP imaging of individual neurons, we confirm that bioluminescence signals reflect the differential recruitment of motor pools during motion. Their significant reduction in paralyzed animals and immotile mutants demonstrates that mechanosensory feedback enhances the recruitment of spinal motor neurons during active locomotion. Accordingly, we show that spinal mechanosensory neurons are recruited in moving animals and that their silencing impairs escapes in freely behaving larvae. Altogether, these results shed light on the contribution of mechanosensory feedback to motor output and the resulting differences between active and fictive locomotion.

Molecular recognition is essential to all biological interactions and processes. Knowledge of the structural basis of recognition offers a powerful mechanism for understanding, predicting and controlling the behaviour of biological systems. In this thesis, we present, firstly a computational and crystallographic analysis of molecular recognition in protein-ligand systems; and secondly, progress towards the synthesis of a fluorescent probe for calcium ion recognition. Class I phosphoinositide 3-kinases (PI3Ks), in particular PI3Kγ, have long been considered promising drug targets for the treatment of inflammatory and autoimmune disorders. As a step towards improved understanding of PI3K binding preferences, we examine the basis on which PI3Kγ distinguishes γ-selective inhibitors AS-605240 and AS-604850, with a ~30-fold preference for the former. Interestingly, despite the chemical similarity of the two ligands, the X-ray structures for their PI3Kγ complexes exhibit the molecules in different conformers, s-cis for AS-604850 and s-trans for AS-605240. Here, we re-examine the PI3Kγ/AS-605240 crystallographic data and find that not only is a s-cis conformation possible but in fact it has a much higher occupancy (87%) than the originally modelled s-trans isomer (13%). Subsequently, to account for the isomeric complexities presented by the ligands, we perform 140 ns MD simulations of the four PI3Kγ complexes in explicit solvent: this reveals similar conformational flexibility at the active site for all systems. Yet, the conformations sampled by the s-cis isomers are more consistent with the conformations reported by the X-ray crystal structures. Subsequent energetic analysis was performed incorporating ensemble-averaging and desolvation effects via the Poisson-Boltzmann continuum solvent model. For both inhibitors the s-cis isomers are predicted to be the most favourable conformations. Additionally, the results indicate a preference for AS-605240, as observed experimentally. The molecular basis for this preference is discussed, together with a comparison of molecular mechanical and quantum chemical treatments of the key ligand-Val882 interaction. This study provides structural, dynamical and energetic insights into the subtle basis of molecular recognition by PI3Kγ.Fluorescent probes have evolved into an extremely useful tool for the detection of calcium in biological systems. Benzothiazole derivatives BTC, and its iminocoumarin analogue BTIC, are two low affinity calcium indicators featuring many desirable properties for cellular calcium measurement. In an effort to produce fluorophores that can be chemically conjugated with a screening protein, such as Green Fluorescent Protein (GFP), we aimed to derivatise BTC and BTIC. Two synthetic approaches towards the synthesis of these potential fluorescent probes are outlined.

Diploma thesis is based on monitoring the succes of transfection of cell linie HEK293. In theoretical part are described principles of transfection methods, cell lines, vectors and reporter genes. HEK293 cells EBNA1 were used for practical part. It was studied the difference between GFP and EGFP plasmids. As well as using various transfection reagents under different culture conditions.

Sucrose is the major transported photoassimilate in plants and is degraded concurrently by two enzymes: invertases and sucrose synthase. Sucrose synthase catalyzes the reversible conversion of UDP and sucrose to form fructose and UDP-glucose, the latter being the activated substrate for many metabolic processes including cellulose biosynthesis. There is evidence that sucrose synthase is phosphorylated as a regulatory mechanism of carbon allocation at a conserved N-terminal serine residue. The phosphorylation or dephosphorylation at this specific site has also been found to shift the protein localization in a tissue and species specific manner. A literature study of the functional regulation of sucrose synthase in plants has highlighted several scientific questions: Is sucrose synthase cellular localization regulated by phosphorylation of an N-terminal conserved serine residue? What are the regulatory mechanisms underlying within and between species variation in sucrose synthase localization? Does sucrose synthase associate with the cellulose synthase enzyme complex? Can cellulose biosynthesis be increased by over-expression of the membrane-associated form of sucrose synthase? The aim of this M.Sc study was to determine the subcellular localization of Eucalyptus grandis sucrose synthase 1 (EgSUSY1) fusion proteins expressed in Arabidopsis thaliana plants. This was investigated through modifying the 11th serine residue of EgSUSY1 into either a non-polar alanine residue that cannot be phosphorylated (S11A), or into a negatively charged glutamic acid residue which may mimic phosphorylation at this site (S11E). The modified proteins were translationally fused to green fluorescent protein (GFP) and expressed in transgenic Arabidopsis thaliana. The proteins’ subcellular localization were analysed in planta using laser scanning confocal microscopy (LSCM). Findings in this study point to the peripheral localization of modified and unmodified GFPEgSUSY1 proteins with a prominent cytoplasmic component. No evidence was found for the localization of modified or unmodified GFP-EgSUSY1 proteins within the extracellular matrix. The current study did not establish nor negate plasma membrane association of any of the GFP-EgSUSY1 fusion proteins. It was concluded that alternative methodologies need to be explored to further address issues surrounding subcellular localization of sucrose synthase. These studies will not only aid in defining the role of this enzyme in carbon allocation, but also add to our expanding knowledge of cellulose biosynthesis and cell wall formation. Copyright 2011, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. Please cite as follows: Sauer, J 2011, The subcellular localization of eucalyptus grandis sucrose synthase 1 (EgSUSY1) fusion proteins expressed in Arabidopsis thaliana, MSc dissertation, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-02102012-102209 / > C12/4/111/gm / Dissertation (MSc)--University of Pretoria, 2011. / Genetics / unrestricted

Skeletal muscle satellite cells (myoblasts) are the primary stem cells of skeletal muscle which contribute to growth, maintenance, and repair of the muscles. Satellite cells are the first stem cells used for cellular cardiomyoplasty more than 20 years ago. The isolation, culture, labeling, and identification of satellite cells are described in detail here. The implantation and outcomes of cellular cardiomyoplasty using satellite cells have been summarized in the previous chapter (Chapter 1).

Skeletal muscle satellite cells (myoblasts) are the primary stem cells of skeletal muscle which contribute to growth, maintenance, and repair of the muscles. Satellite cells are the first stem cells used for cellular cardiomyoplasty more than 20 years ago. The isolation, culture, labeling, and identification of satellite cells are described in detail here. The implantation and outcomes of cellular cardiomyoplasty using satellite cells have been summarized in the previous chapter (Chapter 1).

Die Regulation des Kohlenstoffkatabolismus erfolgt in Escherichia coli wesentlich über den Einfluss der intrazellulären cAMP-Konzentration auf die Expression der Gene des crpA-Modulon. cAMP wird durch die Adenylatzyklase CyaA synthetisiert, die wiederum durch phosphoryliertes IIACrr aktiviert wird. Im Rahmen eines Stoffwechselmodellierungsprojektes sollten durch die Entwicklung von Systemen zur quantitativen Messung der intrazellulären cAMP-Konzentration und des Phosphorylierungszustands von IIACrr zwei entscheidende Parameter dieses Regulationsnetzwerkes untersucht werden. Zu diesem Zweck wurde ein System zur reproduzierbaren, direkten Messung der intrazellulären cAMP-Konzentration in E. coli etabliert. Zur in vivo Bestimmung der intrazellulären cAMP-Konzentration wurden zwei verschiedene durch cAMP·CrpA regulierte Promotoren mit den Reportergenen für ß-Galaktosidase oder Aequorin (grün fluoreszierendes Protein) fusioniert und in drei verschiedenen Messkonstrukten untersucht. Die Zugabe von Pyruvat zu gehungerten Zellen führte zu einer Desphosphorylierung von IIACrr. Der so direkt gezeigte Einfluss des PEP/Pyruvat Verhältnisses auf das Phosphorylierungsgleichgewicht von IIACrr zeigt einen Mechanismus, über den PTS-unabhängige Substrate den Phosphorylierungszustand von IIACrr verändern und somit die Aktivität der Adenylatzyklase beeinflussen können. Bei der Untersuchung zur zellulären Lokalisation der Adenylatzyklase in E. coli mit Hilfe einer CyaA-Aequorin-Fusion wurde nach Überexpression des Fusionsproteins eine lokale Anhäufung der Fluoreszenz an den Zellpolen beobachtet. Da bei geringerer Expression der Fusion kein Fluoreszenzsignal mehr erfasst werden konnte, war eine endgültige Lokalisierung der Adenylatzklase mit dieser Methode nicht möglich.