BCG é uma das vacinas mais usadas no mundo. Avanços na manipulação genética têm permitido o seu uso como carreador de antígenos heterólogos, porém o aprimoramento dos sistemas de expressão se faz necessário, sendo o promotor um importante elemento, uma vez que regula o nível de produção do antígeno, induzindo uma resposta imunológica adequada. Avaliamos a atividade de diferentes promotores de micobactérias, como o PAg, PAN, PBlaF*, Phsp60 e um promotor ainda não caracterizado do micobacteriófago L5, usando o gene gfp como repórter da expressão, todos clonados no vetor extracromossomal, pLA71. Foi possível avaliar as cepas de M. smegmatis e BCG fluorescentes para quase todas as construções e alguns plasmídeos pLA71-p mostraram características diferentes dependentes da micobactéria transformada. Numa escala de força de expressão, os diferentes promotores se apresentaram como fraco (pLA71-PAN-gfp), médio (pLA71-PBlaf*-gfp) e forte (pLA71-Phsp60-gfp). Os rBCG foram usados para infecção de macrófagos e a atividade dos promotores não foi afetada após a internalização. Para ensaio de localização, camundongos foram inoculados com BCG e foi possível confirmar a presença de colônias (recombinantes ou não) nos pulmões após 1 e 3 dias de inoculação, por plaqueamento em meio sólido e por microscopia confocal. / BCG is one of the most widely used vaccines in the world. Advances in genetic manipulation have allowed their use as a carrier for heterologous antigens, however the improvement of systems of expression is necessary, the promoter being an important element, since it regulates the expression level of the antigen, inducing an adequate immune response. We evaluated the activity of different promoters of mycobacteria, such as PAg, PAN, PBlaF* and Phsp60, and the not yet characterized promoter of the micobacteriophage L5, using GFP as a reporter gene expression activity, all cloned in the extrachromosomal vector, pLA71. It was possible to evaluate promoters in the M. smegmatis and BCG strains, fluorescent for almost all constructions and some pLA71-p plasmids showed different characteristics dependent on the transformed mycobacterium. The different promoters showed expression levels as weak (pLA71-PAN-gfp), medium (pLA71-PBlaf*-gfp) and strong (pLA71-Phsp60-gfp). The rBCG were used for infection of macrophages and the activity of the promoters wasnt affected after internalization. For BCG location test, mice were inoculated and it was possible to confirm the presence of colonies (recombinant or not) in the lungs after 1 and 3 days after inoculation by plating on solid medium and by confocal microscopy.

BCG é uma das vacinas mais usadas no mundo. Avanços na manipulação genética têm permitido o seu uso como carreador de antígenos heterólogos, porém o aprimoramento dos sistemas de expressão se faz necessário, sendo o promotor um importante elemento, uma vez que regula o nível de produção do antígeno, induzindo uma resposta imunológica adequada. Avaliamos a atividade de diferentes promotores de micobactérias, como o PAg, PAN, PBlaF*, Phsp60 e um promotor ainda não caracterizado do micobacteriófago L5, usando o gene gfp como repórter da expressão, todos clonados no vetor extracromossomal, pLA71. Foi possível avaliar as cepas de M. smegmatis e BCG fluorescentes para quase todas as construções e alguns plasmídeos pLA71-p mostraram características diferentes dependentes da micobactéria transformada. Numa escala de força de expressão, os diferentes promotores se apresentaram como fraco (pLA71-PAN-gfp), médio (pLA71-PBlaf*-gfp) e forte (pLA71-Phsp60-gfp). Os rBCG foram usados para infecção de macrófagos e a atividade dos promotores não foi afetada após a internalização. Para ensaio de localização, camundongos foram inoculados com BCG e foi possível confirmar a presença de colônias (recombinantes ou não) nos pulmões após 1 e 3 dias de inoculação, por plaqueamento em meio sólido e por microscopia confocal. / BCG is one of the most widely used vaccines in the world. Advances in genetic manipulation have allowed their use as a carrier for heterologous antigens, however the improvement of systems of expression is necessary, the promoter being an important element, since it regulates the expression level of the antigen, inducing an adequate immune response. We evaluated the activity of different promoters of mycobacteria, such as PAg, PAN, PBlaF* and Phsp60, and the not yet characterized promoter of the micobacteriophage L5, using GFP as a reporter gene expression activity, all cloned in the extrachromosomal vector, pLA71. It was possible to evaluate promoters in the M. smegmatis and BCG strains, fluorescent for almost all constructions and some pLA71-p plasmids showed different characteristics dependent on the transformed mycobacterium. The different promoters showed expression levels as weak (pLA71-PAN-gfp), medium (pLA71-PBlaf*-gfp) and strong (pLA71-Phsp60-gfp). The rBCG were used for infection of macrophages and the activity of the promoters wasnt affected after internalization. For BCG location test, mice were inoculated and it was possible to confirm the presence of colonies (recombinant or not) in the lungs after 1 and 3 days after inoculation by plating on solid medium and by confocal microscopy.

Calcium plays important roles in both eukaryotic and prokaryotic cells. Its actions help to stabilize cell synthesis, growth and development. In this thesis, studies have been completed to determine effects of calcium and pH on bacterial cell growth and protein expression using the bacterial cell strain E.coli BL21(DE3). Our studies demonstrated the addition of calcium addition in the media does not affect growth but increases protein expression, while reducing the pH from 7 to 4 through the addition of 10mM EGTA in LB media inhibits both. Additionally, we report studies on the design, expression, and purification of fluorescent mCherry variants and their differences in their optical properties, including: extinction coefficients , quantum yields and pKa values. Also, we report progress in the crystallization of two GFP calcium sensors: G1 and D1, using 13 and15% PEG 4000 and 3350 respectively in 50mM HEPES buffer (pH 6.8-7.0) in an effort to optimize crystallization.

Introduction It is well known that resident adipose stem/stromal cells (ASCs) are a heterogeneous population of multipotent cells characterized by (a) their ability to adhere to plastic; (b) immunophenotypic expression of certain cell surface markers, while lacking others; and (c) the capacity to differentiate into cells of mesodermal origin including osteocytes, chondrocytes and adipocytes. Adipose derived stromal cells offer great therapeutic potential in multiple medical fields, including, orthopedics, cardiology, oncology and degenerative diseases, to name a few. Combining different disciplines of medicine and engineering, organ and tissue repair can be achieved through tissue engineering and regenerative medicine. Adipose derived stromal cells (ASCs) can be utilized as biological vehicles for vector-based gene delivery systems, since they home to sites of inflammation and infection in vivo. In order to reach the long-term aim of clinical translation of cell-based therapy, preclinical safety and efficacy need to be shown in animal models. This has motivated the development of standardized isolation, characterization and differentiation operating procedures as well as an in vivo tracking system for ASCs and lentiviral vector transduction for a vector-based gene delivery system. Methodology Human ASCs were isolated from lipoaspirate, expanded in culture, immunophenotyped using flow cytometery and induced to differentiate into adipogenic, osteogenic and chondrogenic lineages. Tri-lineage differentiation was confirmed by microscopy. The ASCs were then transduced with green fluorescent protein (GFP)-expressing lentiviral vectors in vitro. The effect of the GFP lentiviral vector on ASCs was investigated by studying ASC immunophenotypic expression of surface markers as well as their capacity to differentiate into osteocytes, chondrocytes and adipocytes. Results The isolated and expanded cell population, from harvested lipoaspirate adhered to recommended ASC identity criteria. The heterogeneity of ASCs was confirmed by the presence of sub-populations. Transduction efficiency in ASC cultures of approximately 80% was observed after introducing a total of 300 μl of concentrated lentiviral vector suspension per 4.8 x 104 cells. No immunophenotypic differences were observed between GFP positive and GFP negative cultures. Flow cytometric analysis revealed a progressive increase in GFP expression following in vitro expansion of transduced ASCs. Both non-transduced and transduced cultures successfully differentiated into osteocytes, chondrocytes and adipocytes. Conclusion The isolated and expanded cell population conformed to the recommended characterization criteria. Heterogeneity was demonstrated with the identification of immunophenotypic sub-populations and semi-quantification of adipogenesis was performed. ASCs were efficiently transduced using the GFP lentiviral vectors produced in our facility. In addition, transduced ASCs maintained adherence to plastic, ASC immunophenotype and were able to differentiate successfully into cells of the three lineages of mesodermal origin. This optimized GFP-ASC transduction technique offers a feasible tracking system as well as a vector-based gene delivery system for future preclinical studies. / Dissertation (MSc)--University of Pretoria, 2015. / tm2015 / Immunology / MSc / Unrestricted

Since the publication of the complete sequence of the human genome in 2003 there has been great interest in exploring the functions of the proteins encoded by the genes. To reveal the function of each and every protein, investigation of protein localization at the subcellular level has become a central focus in this research area, since the localization and function of a protein is closely related. The objective of the studies presented in this doctoral thesis was to systematically explore the human proteome at the subcellular level using bioimaging and to develop techniques for validation of the results obtained. A common imaging technique for protein detection is immunofluorescence (IF), where antibodies are used to target proteins in fixated cells. A fixation protocol suitable for large-scale IF studies was developed and optimized to work for a broad set of proteins. As the technique relies on antibodies, validation of their specificity to the target protein is crucial. A platform based on siRNA gene silencing in combination with IF was set-up to evaluate antibody specificity by quantitative image analysis before and after suppression of its target protein. As a proof of concept, the platform was then used for validation of 75 antibodies, proving it to be applicable for validation of antibodies in a systematic manner. Because of the fixation, there is a common concern about how well IF data reflects the in vivo subcellular distribution of proteins. To address this, 500 proteins were tagged with green fluorescent protein (GFP) and used to compare protein localization results between IF to those achieved using GFP tagged proteins in live cells. It was concluded that protein localization data from fixated cells satisfactory represented the situation in vivo and together exhibit a powerful approach for confirming localizations of yet uncharacterized proteins. Finally, a global analysis based on IF data of approximately 20 % of the human proteome was performed, providing a first overview of the subcellular landscape in three different cell lines. It was found that the intracellular distribution of proteins is complex, with many proteins occurring in several organelles. The results also confirmed the close relationship between protein function and localization, which in a way further strengthens the accuracy of the IF approach for detection of proteins at the subcellular level. / <p>QC 20121017</p> / The Human Protein Atlas

Millions of years of evolution have resulted in an immense number of different proteins, which participate in virtually every process within cells and thus are of utmost importance for allknown forms of life. In addition, there are several examples of natural proteins which have found use in applications outside their natural environment, such as the use of enzymes infood industry and washing powders or the use of antibodies in diagnostic, bioseparation or therapeutic applications. To improve the performance of proteins in such applications, anumber of techniques, all collectively referred to as ‘protein engineering’, are performed in thelaboratory.Traditionally, methods involving ‘rational design’, where a few alterations are introduced atspecific protein locations to hopefully result in expected improvements have been applied.However, the use of more recent techniques involving a simultaneous construction of a large number of candidate variants (protein libraries) by various diversification principles, fromwhich rare clones showing enhanced properties can be isolated have contributed greatly to thefield of protein engineering.In the present thesis, different protein traits of biotechnological importance have beenaddressed for improvements by the use of such methods, in which there is a crucial need tomaintain a clonal link between the genotype and the phenotype to allow an identification of protein library members isolated by virtue of their functional properties. In all protein library investigations included in this thesis this coupling has been obtained by Escherichia coli bacterialcell-membrane compartmental confinement.In a first study, a combination of error prone PCR and gene-shuffling was applied to the Tobacco Etch Virus (TEV)-protease gene in order to produce collections from which genesencoding variants showing an enhanced soluble expression of the enzyme frequently used inbiotechnology to cleave fusion proteins were identified. Using Green Fluorescence Protein(GFP)-based cell fluorescence analysis, a clone with a five-fold increase in the yield of solubly produced protein was successfully isolated. In a second study, a novel and different GFPbased selection system, in addition also involving targeted in vivo protein degradation principles,was employed for investigations of the substrate sequence space of the same protease. In two additional studies, a selection system denoted Protein Fragment Complementation Assay(PCA), based on the affinity driven structural complementation of a genetically split β-lactamase enzyme was used to identify variants having desired target protein binding abilities,including both specificity and affinity. Using Darwinian principles concerning clonal growth advantages, affibody binding proteins showing sub-nanomolar dissociation constants to thehuman cytokine TNF-α were isolated. Taken together, these studies have shown that the bacterial format is very well suited for use in various aspects of protein library selection. / QC 20100729

L'action de la dopamine dans les cellules est transmise par sa fixation sur des récepteurs qui appartiennent à deux classes, D1 et D2. Quatre sous-types du récepteur D1 (D1A, D1B/D5, D1C et D1D) ont été clonés jusqu'à présent chez les vertébrés. L'analyse évolutive montre que les sous-types D1A et D1B sont les plus conservés alors que les sous-types D1C et D1D sont absents chez les mammifères. Malgré cette diversité, les fonctions de la dopamine dans l'organisme ne peuvent pas être rapportées à l'action d'un sous-type précis. C'est pourquoi au cours de ce travail nous avons identifié des caractères fonctionnels capables de distinguer chacun des sous-types et de comprendre pour quelle raison ils ont été conservés chez les vertébrés. La désensibilisation est un des paramètres fonctionnels les plus important. Le récepteur D1A se caractérise par une baisse d'activité forte et biphasique, le récepteur D1B par un profil proche avec une amplitude plus faible conséquence de son activité constitutive. Enfin, le récepteur D1C ne semble pas être capable de se désensibiliser. La construction de chimères entre chacun des sous-types du récepteur D1 et la protéine GFP ont permis la visualisation des récepteurs au cours de la désensibilisation. Elles montrent que l'internalisation ne semble pas, pour les récepteurs D1 de la dopamine, intervenir dans le processus de désensibilisation fonctionnelle. L'activation simultanée des récepteurs A1 de l'adénosine bloque l'activité des récepteurs D1. L'analyse des voies de signalisation MAPK a montré que l'activation de la voie ERK était rapide et forte, et différente selon les sous-types. La voie p38 n'est que faiblement activée et la voie JNK semble ne pas l'être du tout. Il semble donc que les mécanismes d'activation et de régulation des voies de signalisation différencient les sous-types du récepteur D1 chez les vertébrés. Ces paramètres participent de façon majeure à la transmission régulée des fonctions de la dopamine dans l'organisme.

Au cours de ce travail expérimental, nous nous sommes intéressés aux propriétés photo-physiques d'un mutant de la protéine Fuorescente verte (Green Fluorescent Protein, GFP). Plus particulièrement, nous avons caractérisé par spectroscopie femtoseconde résolue spectralement la dynamique des états excités de ce mutant. Nous avons tout d'abord comparé les résultats obtenus avec ceux de la protéine naturelle. Cela nous a permis de montrer que la dynamique des états excités s'avère très sensible aux modifcations de l'environnement proche de la partie optiquement active de la protéine. Dans une deuxième partie qui concerne l'étude de fusion génétique fragment d'anticorps-GFP, nous avons utilisé la sensibilité offerte par la dynamique des états excités de la protéine pour caractériser l'état de repliement de l'anticorps fusionné. Une autre partie de ce travail a été consacrée à l'étude des propriétés dynamiques de certains dérivés de la coumarine dont la nature de rotors moléculaires a été évoquée dans la littérature. Nous avons montré que la dynamique des états excités ne présente pas de signatures d'un tel comportement. Parallèlement aux études dynamiques, nous avons étudié le vieillissement ou diminution du nombre de molécules fluorescentes d'un ensemble bien déterminé de GFP sous illumination continue. Cette étude a mis en évidence le fait que l'évolution temporelle du système est gouvernée par une statistique de Lévy. L'une des conséquences principales étant l'existence d'un état instable à durée de vie moyenne infnie.

Mathematical models of signal transduction pathways are characterized by a large number of proteins and uncertain parameters, yet only a limited amount of quantitative data is available. The dissertation addresses this problem using two different approaches: the first approach deals with a model simplification procedure for signaling pathways that reduces the model size but retains the physical interpretation of the remaining states, while the second approach deals with creating rich data sets by computing transcription factor profiles from fluorescent images of green-fluorescent-protein (GFP) reporter cells. For the first approach a model simplification procedure for signaling pathway models is presented. The technique makes use of sensitivity and observability analysis to select the retained proteins for the simplified model. The presented technique is applied to an IL-6 signaling pathway model. It is found that the model size can be significantly reduced and the simplified model is able to adequately predict the dynamics of key proteins of the signaling pathway. An approach for quantitatively determining transcription factor profiles from GFP reporter data is developed as the second major contribution of this work. The procedure analyzes fluorescent images to determine fluorescence intensity profiles using principal component analysis and K-means clustering, and then computes the transcription factor concentration from the fluorescence intensity profiles by solving an inverse problem involving a model describing transcription, translation, and activation of green fluorescent proteins. Activation profiles of the transcription factors NF-κB, nuclear STAT3, and C/EBPβ are obtained using the presented approach. The data for NF-κB is used to develop a model for TNF-α signal transduction while the data for nuclear STAT3 and C/EBPβ is used to verify the simplified IL-6 model. Finally, an approach is developed to compute the distribution of transcription factor profiles among a population of cells. This approach consists of an algorithm for identifying individual fluorescent cells from fluorescent images, and an algorithm to compute the distribution of transcription factor profiles from the fluorescence intensity distribution by solving an inverse problem. The technique is applied to experimental data to derive the distribution of NF-κB concentrations from fluorescent images of a NF-κB GFP reporter system.

Understanding the functional impact of physical interactions between proteins and DNA on gene expression is important for developing approaches to correct disease-associated gene dysregulation. I conducted a systematic, functional genetic analysis of protein-DNA interactions in the promoter region of the yeast ribonucleotide reductase subunit gene RNR3. I measured the transcriptional impact of systematically perturbing the major transcriptional regulator, Crt1, and three X-box sites on the DNA known to physically bind Crt1. This analysis revealed interactions between two of the three X-boxes in the presence of Crt1, and unexpectedly, a significant functional role of the X-boxes in the absence of Crt1. Further analysis revealed Crt1- independent regulators of RNR3 that were impacted by X-box perturbation. Taken together, these results support the notion that higher-order X-box-mediated interactions are important for RNR3 transcription, and that the X-boxes have unexpected roles in the regulation of RNR3 transcription that extend beyond their interaction with Crt1.