Malaria is a devastating disease which affects almost half of the world’s population. Since the description of the malaria genome sequence, various aspects of the parasite have been studied, including drug resistance mechanisms, epidemiology and surveillance systems. Alarmingly, very little is known about the basic biological processes such as the regulation of the expression of parasite genes. The parasite, Plasmodium falciparum, has developed highly specialized methods of regulating the transcription of genes, starting at the regulation of genes controlling basic cellular processes such as protein synthesis and erythrocyte invasion, followed by the transcriptional regulation of more specialized genes, such as those aiding in immune evasion and pathogenesis. The description of the P. falciparum transcriptome by Bozdech et al. in 2003 revealed a complex, just-in-time and tightly regulated transcription profile of P. falciparum genes. This suggests that the most probable Achilles heel for Plasmodium may be its unique mechanisms of regulating gene expression. Various cis- and trans-regulatory sequences have been identified in P. falciparum, along with possible DNA (and RNA) binding proteins. The first part of this research focussed on transcriptional regulatory mechanisms in which an in silico search identified cis-regulatory sequences in the 5’ untranslated region of the antigenically variant var gene family. Electrophoretic mobility shift assays (EMSA) were used to identify protein binding partners of these sequences, which could ultimately act as transcription factors in regulating the expression of this essential gene family. The second part of the research investigated the involvement of post-transcriptional regulatory mechanisms in the polyamine biosynthetic pathway of P. falciparum. Polyamines have been proven to be crucial for the parasite’s development and therefore, an RNA interference knock-down strategy was used to verify the importance of the polyamine biosynthetic enzymes S-Adenosylmethionine decarboxylase (AdoMetDC), Ornithine decarboxylase (ODC) and Spermidine synthase. It is clear that various mechanisms for gene regulation are used by the parasite and that this is critical for the survival of this organism. The results of this study suggest the potential presence of both double-stranded and single-stranded DNA regulatory proteins within P. falciparum nuclear extract. As controversial as RNA interference remains in P. falciparum, this technique was used as a plausible knock-down strategy of parasite specific genes and certain trends, regarding the visible decreases in gene transcript level after double-stranded RNA treatment, were observed. However, final conclusions as to the feasibility of using RNA interference in P. falciparum remain to be elucidated. This study therefore ultimately lends insight into the transcriptional and post-transcriptional levels of P. falciparum gene regulation. / Dissertation (MSc)--University of Pretoria, 2010. / Biochemistry / unrestricted

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Autophagy is a conserved process that cells use to degrade their own cytoplasmic components by delivery to lysosomes. Autophagy ensures intracellular quality control and is associated with diseases such as cancer and immune disorders. The process of autophagy is controlled by core autophagy (Atg) genes that are conserved from yeast to mammal. Most Atg proteins and their regulators were identified through pioneering studies of the single cell yeast Saccharomyces cerevisiae, and little is known about factors that systematically coordinate autophagy within the tissues of multicellular animals. The goal of this thesis is to identify new autophagy regulators and provide a better understanding of the regulatory mechanisms within multicellular animals. My research determined Macroglobulin complement-related (Mcr), a Drosophila complement orthologue, can activate autophagy during developmental cell death. Unlike most known autophagy regulators, Mcr functions in a cell non-autonomous manner to trigger autophagy in neighboring cells. To my knowledge, this is the first identified autophagy factor that cell non-autonomously activates autophagy. Additionally, I found that Mcr, a secreted protein, instructs the autophagy machinery through the immune receptor Draper, suggesting a relationship between autophagy and the control of inflammation. Lastly, Mcr is dispensable for both nutrient deprivation-induced autophagy in the fat body and developmentally programmed autophagy in the dying midgut of Drosophila. Therefore, this study unveils a mechanism in a multicellular organism by which autophagy is systematically controlled in distinct cell contexts.

No / We organized the first International Symposium on Skin Epigenetics at the Centre for Skin Sciences at the University of Bradford (West Yorkshire, UK) on 2nd and 3rd April 2012. The goal of the Symposium was to bring together two research communities—skin and chromatin biologists—and discuss the most important aspects of epigenetic regulatory mechanisms that control skin development and regeneration. The symposium was attended by more than 80 participants from countries across Europe, Australia, Japan, Singapore, and USA, and representing academic institutions and industry. Epigenetic regulation of gene expression programs in the skin is a novel trend in research in cutaneous biology, and several landmark papers arising in the field were published recently (reviewed in Botchkarev et al., 2012; Botchkareva, 2012; Frye and Benitah, 2012; Yi and Fuchs, 2012; Zhang et al., 2012). The Symposium program included six Keynote lectures, the inaugural John M. Wood Memorial Lecture, and six sessions that covered major levels of epigenetic regulation.

Made available in DSpace on 2010-04-20T20:50:59Z (GMT). No. of bitstreams: 3 62818.pdf.jpg: 12937 bytes, checksum: 1e36d7999a24205339f44fc2cb39b008 (MD5) 62818.pdf: 1990676 bytes, checksum: ad7e8efbf8383a6dc1396b30b90b64c7 (MD5) 62818.pdf.txt: 316727 bytes, checksum: d7cdc93a9b5934dbadff748293760a21 (MD5) Previous issue date: 2005-12-02T00:00:00Z / Across the years, study fields such as Political Sciences, Organizations and Economy have dedicated to the subject of the role of regulatory mechanisms on the decision behavior of agents. From different perspectives and approaches, each one of those fields have studied the impact of regulatory instruments on the decision of the players for a given action orientation. From the most frequently quoted instruments on the literature to regulate the action of the agents, we can point out formal and informal regulatory mechanisms. An intense debate over the studies dedicated to the subject has taken place, discussing the efficiency of each of those mechanisms on the player s decision. Given the relevance of such debate, the present study aims to compare the effectiveness of formal and informal regulatory mechanisms on one’s decision of cooperating to social dilemmas. Such dilemmas are situations on which a person, searching for one’s own interests, takes the group to worse results than those that would have been reached if there were cooperation among the group. To reach the goal of this study, we performed an experiment with undergraduate students from EAESP-FGV to test in an experimental environment the behavior of the agents under the pressure of two regulatory mechanisms. The results of this experiment showed that the informal regulatory mechanisms have a greater influence on the player s decision to cooperate and the presence of such mechanisms reduces the necessity of using a formal regulatory mechanism to ensure the cooperation from members of a group. / Ao longo dos anos, campos de estudos como os de ciência política, organizações e economia vêm se debruçando sobre a questão do papel de mecanismos regulativos no comportamento decisório do indivíduo. A partir de óticas e abordagens diferentes, cada um desses campos vem estudando o impacto de instrumentos de regulação na conformação dos atores para determinada orientação de ação. Dos instrumentos mais citados na literatura para regular a ação do ator, podemos apontar os mecanismos formais e informais de regulação. Um intenso debate entre os trabalhos dedicados ao assunto vem sendo travado, discutindo a eficiência de cada um deles na conformação do ator. Dada a relevância desse debate, o presente trabalho teve como objetivo comparar a efetividade de mecanismos formais e informais de regulação na decisão de cooperação do indivíduo em dilemas sociais, que são situações onde cada indivíduo ao buscar seu interesse próprio, leva a coletividade a resultados piores do que aqueles que seriam atingidos, caso houvesse cooperação do grupo. Para alcançarmos o objetivo do trabalho, realizou-se um experimento com alunos da graduação da EAESP-FGV para testar em ambiente laboratorial o comportamento dos agentes sob a pressão dos dois mecanismos de regulação. Os resultados do experimento mostraram que mecanismos informais de regulação têm maior influência na decisão de cooperação do ator, assim como sua presença diminui a necessidade do uso de um mecanismo formal de regulação para assegurar a cooperação dos membros de um grupo.

Bakterielle Wirte wie Escherichia coli dienen der Produktion industrieller rekombinanter Proteine. Dieser Prozess verursacht systemischen Stress und führt zu umfangreichen Veränderungen in mRNA- und Proteinexpression. In meiner Arbeit analysiere ich Regulationsmechanismen der zellulären Reaktion auf diesen Stress. Zudem untersuche ich die zelluläre Ressourcenallokation mittels eines stationären Ganzzellmodells von E. coli, basierend auf der Resource Balance Analysis. Das Modell berücksichtigt Kosten zellulärer Prozesse und Einschränkungen wie Energie, Effizienz und Raum. Es unterstützt die Experimentplanung in der Bioproduktion. Weiterhin habe ich an der Entwicklung von RBApy mitgewirkt, einer Software zur Erstellung und Simulation von RBA-Modellen. Schließlich entwickle ich ein Modell zur Untersuchung der Regulation von Stressreaktionen durch die Tendenz der Zelle, wachstumsoptimale Ressourcenstrategien anzuwenden. Das Modell berücksichtigt zelluläre Beschränkungen und zeigt, dass die erhaltene Stressreaktion der experimentell ermittelten Reaktion ähnelt. Die Integration von Ressourcenzuteilung in Zellmodelle ermöglicht Einsichten in regulatorische Ereignisse und Anpassungen während der Bioproduktion, was zur Optimierung der rekombinanten Proteinexpression in Escherichia coli beiträgt. / Bacterial hosts such as Escherichia coli are used for the production of industrial recombinant proteins. This process causes systemic stress and leads to extensive changes in mRNA and protein expression. In my work, I analyze regulatory mechanisms of the cellular response to this stress. In addition, I investigate cellular resource allocation using a steady-state whole-cell model of E. coli based on resource balance analysis. The model accounts for costs of cellular processes and constraints such as energy, efficiency, and space. It supports experiment design in bioproduction. Furthermore, I contributed to the development of RBApy, a software to create and simulate RBA models. Finally, I developed a model to study the regulation of stress responses by the tendency of the cell to adopt growth-optimal resource strategies. The model accounts for cellular constraints and shows that the obtained stress response resembles the experimentally determined response. Integrating resource allocation into cell models provides insights into regulatory events and adaptations during bioproduction, which contributes to the optimization of recombinant protein expression in Escherichia coli.