O ψευδάργυρος -Zn ελέγχει τον μεταβολισμό των λιπιδίων και γλυκόζης μέσω Ζn-μεταγραφικών παραγόντων. Δίαιτες υψηλών λιπαρών οδηγούν στην ενδοκυτταρική συσσώρευση ελευθέρων ριζών, μειώνουν την μεταγραφική έκφραση των εκκαθαριστών τους και την ενεργότητα αντιοξειδωτικών ενζύμων και οδηγούν σε μεταβολικό σύνδρομο. Οι πρωτεϊνες του θερμικού shock (Heat shock proteins-HSP) παίζουν σημαντικό ρόλο στην αντίσταση στο κυτταρικό stress ως προσαρμογή ,μετά από έκθεση, σε διάφορα ερεθίσματα. ΣΚΟΠΟΣ : Μελέτη της επίδρασης του διατροφικού Ζn και των Hsp70,στην μεταβονομική των λιπιδίων αίματος και ήπατος ποντικών ΥΛΙΚΟ-ΜΕΘΟΔΟΙ :Ενήλικα αρσενικά ποντίκια: 1. Wild type (Wt) Hybrid (F1/F1) C57Bl/6 x CBA και 2. Transgenic (Tg) human HSP70 overexpressing mice, από ηλικίας ενός μηνός εντάχθηκαν στις παρακάτω διατροφές ,επί 10 εβδομάδες. Διατροφή Αριθμός Wt Αριθμός Tg Chow Diet (30 Zn) 6 10 High Fat Diet (3 Zn) 13 12 High Fat Diet (30 Zn) 9 8 High Fat Diet (300 Zn) 12 12 Σύνθεση των τριών διαιτών υψηλών λιπαρών -HFD: 3mg, 30mg, 300mg Zn /kg τροφής (mucedoola s.r.l Ιtaly-55% Cal από λιπαρά στοιχεία), Chow : δίαιτα ελέγχου Βιοχημικές αναλύσεις: Cholesterol ,Triglycerides ,HDL-cholesterol, Glucose ,Insulin Μετρήσεις μετάλλων και αντιοξειδωτικών παραγόντων: SOD (ερυθρά αιμοσφαίρια ) TAC (ορός αίματος) Zn , Cu (ερυθρά αιμοσφαίρια και ιστός ήπατος) Μεταβονομική ανάλυση και αξιολόγηση λιπιδίων :Εκχύλιση ορού αίματος και ηπατικού ιστού για λήψη Φάσματος 1H-NMR ΣΥΜΠΕΡΑΣΜΑΤΑ 1. Η HF δίαιτα αύξησε σημαντικά ,το τελικό βάρος και τον ρυθμό αύξησης βάρους ,τη χοληστερόλη -CL και την λιποπρωτεϊνη υψηλής πυκνότητας-ΗDL ,την ινσουλίνη –Ins, στα WT & Tg και μείωσε την ολική αντιοξειδωτική ικανότητα-TAC στο πλάσμα και την δραστηριότητα της σουπεροξείδιο-δισμουτάσης-SOD στα ερυθροκύταρα των WΤ και Tg 2. Ο επαρκής διατροφικός Zn (30mg/kgτροφής) φαίνεται να αποτελεί κρίσιμο παράγοντα διαμόρφωσης προστατευτικού ηπατολιπιδαιμικού προφίλ, ποντικών σε υπερλιπιδική δίαιτα. Η αύξηση ή μείωση του Zn σε HFDς φαίνεται να μειώνει την TAC του πλάσματος σε WΤ και Tg ενώ η δραστικότητα της SOD φαίνεται ανάλογη των επιπέδων του Zn Η ανεπάρκεια ή περίσσεια Zn αυξάνει τα αθηρογόνα SFA και μειώνει τα αντι-αθηρογόνα λιπίδια, PC, DU, LA DIAL ,UFA στις HDL, nonHDL και το ήπαρ, στα WΤHFD και στα ΤgHFD 3. Οι HSP70 : Τα διαγονιδιακά ζώα που φέρουν το γονίδιο hHsp70, φαίνεται ότι είτε σε έλλειψη είτε σε περίσσεια Ζn, που συνήθως συνοδεύoνται από μεταβολικό σύνδρομο, κατορθώνουν να διατηρούν καλλίτερους δείκτες λιπιδικού προφίλ σε σχέση με τα WT ζώα. Τα Τg εμφάνισαν σημαντικά χαμηλότερη CL ,TG , HDL σε σύγκριση με τα WT ενώ η HSP70 αύξησε σημαντικά την ενεργότητα της ολικής SOD στα ερυθρά αιμοσφαίρια. Η HSP70 μείωσε τα αθηρογόνα SFA και αύξησε τα αντιαθηρογόνα λιπίδια DIAL, DU, LA, UFA, SM στις HDL, nonHDL , και στο ήπαρ ποντικών που εκτέθηκαν σε HFD και σε όλες τις συγκεντρώσεις Zn. / Zinc –Zn controls lipid and glucose metabolism via Zn-transcription factors. High fat diets –HFDs lead to intracellular free radicals accumulation, decrease the transcriptional expression of their scavengers and anti-oxidative enzymes’ activity leading finally to metabolic syndrome. Heat shock proteins-HSPs play a significant role in cellular resistance response , as an adaptation mechanism, after exposure to various stimuli. SCOPE: To study the effects of nutritional Zn and HSP70s on the metabonomics of serum and liver lipids in mice MATERIALS-METHODS: Male mice: 1. Wild type (Wt) Hybrid (F1/F1) C57Bl/6 x CBA και 2. Transgenic (Tg) human HSP70 overexpressing mice, one month old, were subjected for 10 weeks to the following diets : Diet Number of Wt Number of Tg Chow Diet (30 Zn) 6 10 High Fat Diet (3 Zn) 13 12 High Fat Diet (30 Zn) 9 8 High Fat Diet (300 Zn) 12 12 Composition of the three HF Diets: 3mg, 30mg, 300mg Zn /kg τροφής (mucedoola s.r.l Ιtaly-55% Cal from greasy ingredients),Chow :control diet Biochemical analyses: Cholesterol ,Triglycerides ,HDL-cholesterol, Glucose ,Insulin Metals and antioxidative factors levels: SOD (red blood cells )TAC (blood serum) Zn , Cu (red blood cells and liver tissue) Lipids metabonomics : Blood serum and liver tissue extracts for 1H-NMR spectrum analysis and evaluation CONCLUSIONS 1. HFDiet significantly increased the rate of mice body weight gaining, as well as, cholesterol-CL, high density lipoproteins-HDL, insulin, in WT and Tg mice and decreased plasma total antioxidant capacity-TAC and red blood cell super oxide dismutase –SOD activity , in WT and Tg mice 2.Suficient nutritional Zn (30 mg/kg food) prevails as a crucial modulator of a protective hepato-lipidaemic profil of mice in high fat diet. Zinc deficiency or excessiveness , in HFDiets , decreases plasma TAC in WT and Tg mice, while SOD activity shows proportional to Zn levels. Zinc deficiency or excessiveness increases the atherogenic SFA and decreases the anti –atherogenic lipids : PC, DU, LA DIAL ,UFA, in HDL, nonHDL and liver, in WΤ-HFD and Τg-HFD mice 3. HSP70s : Transgenic mice over-expressing hHsp70 gene and exposed either to Zn deficiency or Zn excessiveness , both driving usually to metabolic syndrome , reveal significantly better lipid profile indicators, comparing to WT mice. Tg mice revealed significantly lower CL , TG , HDL levels compared to WT, while HSP70 in Τg mice significantly increased total SOD activity in red blood cells. HSP70 also decreased the atherogenic SFAs and increased the anti-atherogenic lipids DIAL, DU, LA, UFA, SM in HDL, nonHDL and in the liver of mice exposed to HFDiets and all Zn concentrations

The main objective of this study was to investigate promoter sequences of putative HSR genes for the presence of unique regulatory elements and modules that might be involved in the regulation of HSR. In order to achieve this objective, an in silico promoter analysis strategy was devised, which focused on the identification of promoter sequences and regulatory elements, and modelling of promoter modules by using Genomatix software tools such as MatInspector and ModelInspector. Results showed that two modules (EGRF_SP1F_01 and SP1F_CEBP_01) were conserved in the promoter sequences of three well-known Hsp-genes (Hsp90, Hsp105β and αβ-crystallin). Screening the 60 target gene promoters for the presence of the two modules revealed that 12 genes (20 %) contained both modules. These included Moesin, Proline-4 hydroxylase, Poly(A) binding protein and Formin-binding protein. None of these genes had been previously associated with heat shock response.

Thesis (Ph.D.). / Written for the Dept. of Plant Science. Title from title page of PDF (viewed 2008/01/12). Includes bibliographical references.

Advances in next-generation sequencing platforms during the past decade have resulted in exponential increases in biological data generation. Besides applications in determining the sequences of genomes and other DNA elements, these platforms have allowed the characterization of cell-wide mRNA pools under different conditions and in different tissues. In 2009, Ingolia and colleagues developed an extension of high-throughput sequencing that provides a snapshot of all cellular mRNA fragments protected by translating ribosomes, dubbed ribosome profiling. This approach allows detection of differential translation activity, annotation of novel protein coding sequences and variants, identification of ribosome pause sites and estimates of de novo protein synthesis. As with other sequencing based methodologies, a major challenge of ribosome profiling has been sorting, filtering and interpreting the gigabytes of data produced during the course of a typical experiment. In this thesis, I developed and applied computational pipelines to interrogate ribosome profiling data in relation to gene expression in several viruses and eukaryotic species, as well as to identify sites of ribosomal pausing and sites of non-canonical translation activity. Specifically, I applied various control analyses for characterizing the quality of profiling data and developed scripts for visualizing genome-based (exon-by-exon) rather than transcript-based ribosome footprint alignments. I also examined the challenge of mapping footprints to repetitive sequences in the genome and propose ways to mitigate the associated problems. I performed differential expression analyses on data from coronavirus-infected murine cells, retrovirus-infected human cells and temperature-stressed Arabidopsis thaliana plants. Dissection of translational responses in Arabidopsis thaliana during heat shock or cold shock revealed several groups of genes that were highly upregulated within 10 minutes of temperature challenge. Analysis of the branches of the unfolded protein and integrated stress responses during coronavirus infection allowed for deconvolution of transcriptional and translational contributions. During the course of these analyses, I identified errors in a recently publicized algorithm for detection of differential translation, and wrote corrections that have now been pulled into the repository for this package. Comparison of the translational kinetics of the dengue virus infection in mosquito and human cell lines revealed host-specific sites of ribosome pausing and RNA accumulation. Analysis of HIV profiling data revealed footprint peaks which were in agreement with previously proposed models of peptide or RNA mediated ribosome stalling. I also developed a simulation to identify transcripts that are prone to generating RPFs with multiple alignments during the read mapping process. Together, the scripts and pipelines developed during the course of this work will serve to expedite future analyses of ribosome profiling data, and the results will inform future studies of several important pathogens and temperature stress in plants.

La sécurité des biens et des personnes est, de nos jours, une préoccupation première, en particulier lorsqu'elle concerne l'usage des explosifs. Afin de répondre à ces exigences de sécurité, il est nécessaire de pouvoir prédire le comportement des ondes de pression issues d'une explosion, que ce soit à l'intérieur ou à l'extérieur du bâtiment, et leur interaction avec leur environnement. Une importante quantité d'informations sur les ondes de choc se propageant en champ libre est disponible dans la littérature, de sorte que leur comportement est maintenant bien connu. Toutefois, il y a très peu de données disponibles en littérature ouverte sur les explosions en milieu confiné. Les travaux présentés dans ce mémoire de thèse s'inscrivent dans le cadre de l'étude du comportement des ondes de choc en milieu confiné multi-chambres et de l'effet de différents paramètres tels que le volume des cellules ou la largeur du couloir sur les profils de pression à l'intérieur d'un bâtiment. La propagation de l'onde de choc est analysée par l'évolution de certains paramètres du choc (temps d'arrivée, surpression maximale et impulsion positive).Plusieurs essais à échelle réduite ont été réalisés à l'aide d'une maquette modulable, représentative d'un bâtiment pyrotechnique de plein pied, composé de quatre pièces alignées et reliées entre elles par un couloir. / Security is nowadays a real and major concern, especially when explosives are involved. To address this security issue, an accurate prediction of the behavior of shock waves caused by a detonation propagating inside or outside a building and interacting with the surrounding environment is required. Extensive knowledge regarding shock waves in free field can be found in the literature so that their behavior is now well known. However, there is very few information available in the open literature for confined configuration. This study focuses on the behavior of a shock wave within a confined multi-chamber system and on the impact of different parameters such as the size of the rooms and the width of the corridor on the pressure history inside the building. The shock wave propagation is analyzed through the evolution of some of the shock parameters (arrival time, maximum overpressure and positive impulse). Several small-scale experiments have been carried out using an adjustable model of a four-roomed single-story building. The rooms are connected to a single corridor and all on the same side. This model is representative of a pyrotechnic workshop.

Submitted by Sérgio Magalhães (lm_sergio@yahoo.com.br) on 2017-03-16T18:49:31Z No. of bitstreams: 1 Dissertação MPE_Sérgio Lemos de Magalhães_Multiplicadores Fiscais_vf.pdf: 526886 bytes, checksum: 7b7ef2399e09cafeb2990ea538927574 (MD5) / Rejected by Renata de Souza Nascimento (renata.souza@fgv.br), reason: Sérgio, boa noite Por gentileza, rever a formatação do trabalho pois não está de acordo com as normas da ABNT. Verifique o link abaixo, na opção Normas para Apresentação de Monografias, a partir da página 11 onde consta um modelo detalhado de como deve estar o trabalho. Lembramos que os trabalhos devem estar de acordo com as Normas da ABNT ou as Normas da APA: http://sistema.bibliotecas-sp.fgv.br/bkab_normalizacao Grata, on 2017-03-16T22:49:18Z (GMT) / Submitted by Sérgio Magalhães (lm_sergio@yahoo.com.br) on 2017-03-27T11:11:03Z No. of bitstreams: 1 DissertacaoSergioLemos_versão ABNT.pdf: 947842 bytes, checksum: 885e9c52e2428b7002684ff8d6311a5f (MD5) / Approved for entry into archive by Renata de Souza Nascimento (renata.souza@fgv.br) on 2017-03-29T16:51:16Z (GMT) No. of bitstreams: 1 DissertacaoSergioLemos_versão ABNT.pdf: 947842 bytes, checksum: 885e9c52e2428b7002684ff8d6311a5f (MD5) / Made available in DSpace on 2017-03-29T16:58:30Z (GMT). No. of bitstreams: 1 DissertacaoSergioLemos_versão ABNT.pdf: 947842 bytes, checksum: 885e9c52e2428b7002684ff8d6311a5f (MD5) Previous issue date: 2017-02-16 / The work evaluates the behavior of the Brazilian government spending fiscal multiplier between 1996 and 2116. Through a SVAR model, it was analyzed the behavior of the multiplier given a shock in government spending. In addition to the analysis of the standard model, it was also possible to measure, using dummy variables the impact of: the state of the economy, below and above the natural product, and given the present shock, demand or supply. As presented by the national and international literature, the results reflected better performance in the economy in times of product below its potential and in a situation of demand shock. Although it had more favorable results it still lower than 1, demonstrating low efficacy of the multiplier, in which it was pointed out structural situations of the Brazilian economy such as the high indebtedness and public spending as possible vectors of loss of efficiency. Finally, the study evidenced the behavior of the multiplier in a specific situation of negative supply shock in which we had results higher than 1, indicating that the multiplier should be analyzed in certain circumstances. / O trabalho avalia o comportamento do multiplicador fiscal brasileiro de consumo do governo entre os anos de 1996 a 2116. Através de um modelo SVAR analisou-se o comportamento do multiplicador dado um choque no gasto do governo. Além da análise do modelo padrão ainda realizou-se a criação de variáveis dummies mensurando: o estado da economia, abaixo e acima do produto natural, e dado o choque presente, demanda ou oferta. Tal como apresentado pela literatura nacional e internacional os resultados refletiram melhor desempenho na economia em momentos de produto abaixo de seu potencial e em situação de choque de demanda. Apesar de resultados mais favoráveis ainda sim foram inferiores a 1, demonstrando baixa eficácia do multiplicador, no qual foi apontado situações estruturais da economia brasileira tal como o elevado endividamento e gasto publico como possíveis vetores de perda de eficiência. Por fim, o estudo evidenciou o comportamento do multiplicador em situação específica de choque negativo de oferta em que tivemos resultados superiores a 1, indicando que o multiplicador deve ser analisado em determinadas circunstância.

L'allumage par choc est une approche récente à la fusion par confinement inertiel où les phases de compression et d'allumage par un choc fort sont séparées. Ce schéma est prometteur dans la mesure où il peut générer des gains élevés et être testée sur des installations laser existantes. Par ailleurs, il nécessite des vitesses d'implosions plus faibles permettant ainsi de comprimer une plus grande quantité de combustible et limitant l'impact des instabilités hydrodynamiques. Malgré tout, la physique liée à cette approche reste très largement inconnue surtout du point de vue expérimental. En effet, même si la phase de compression est dans un régime dit collisionnel bien connu (I<1014W=cm2), l'allumage fait intervenir un spike d'une intensité supérieure à 1015W=cm2, régime très fortement non-linéaire où apparaissent des instabilités paramétriques. Ces instabilités peuvent diminuer l'absorption et générer des électrons suprathermiques pouvant préchauffer le coeur de la cible et donc empêcher son allumage. Un deuxième problème est la possibilité de générer un choc fort en présence d'un plasma de couronne qui pourrait, entrer autre, détériorer le couplage laser-cible. Néanmoins, des considérations théoriques tendent à montrer que si on génère des électrons chauds modérément énergétiques (<100keV), non seulement ils ne sont pas dangereux vis-à-vis du préchauffage mais, en plus, ils peuvent améliorer le couplage en déposant leur énergie dans le front de choc et amplifier sa pression. Le travail réalisé dans cette thèse consiste à tester la possibilité de générer un choc fort dans les conditions de l'allumage par choc i.e. en présence d'un plasma de couronne mais aussi d'étudier l'effet des électrons chauds sur le choc en quantifiant leur énergie et leur abondance. / Shock ignition is a novel approach for inertial confinement fusion where the compression and the ignition phases by a strong shock are separated. The scheme is promising to the extent that it can generate very high gains and can be tested on already existing lasers systems. In addition, this concept requires lower implosion velocities that allows for compressing more massive targets which limits the impact of hydrodynamic instabilities. However, the physic issues related to shock ignition are still largely unexplored especially experimentally. Indeed, even if the compression phase takes place in the well-known collisional regime (I<1014W=cm2), ignition requires a spike which intensity exceeds 1015W=cm2.This regime is strongly non-linear with the onset of parametric instabilities. These instabilities may decrease the absorption and can also generate suprathermal electrons that can preheat the central part of the fuel and make the compression less efficient. Another key issue is the capability of launching a strong shock in presence of a plasma corona which can deteriorate the laser-target coupling and produce lamentation. Nevertheless, theoretical considerations tend to show that if the energy of fast electrons is moderate (<100keV), they could improve the coupling, deposit their energy in the shock front and hence amplify it. The work presented in this thesis consists in testing these two issues : launching a strong shock in the conditions corresponding to shock ignition i.e. in presence of a plasma corona and study the effect of hot electrons on the shock strength by measuring their energy and their quantity.

Masters of Science / The main objective of this study was to investigate promoter sequences of putative HSR genes for the presence of unique regulatory elements and modules that might be involved in the regulation of HSR. In order to achieve this objective, an in silico promoter analysis strategy was devised, which focused on the identification of promoter sequences and regulatory elements, and modelling of promoter modules by using Genomatix software tools such as MatInspector and ModelInspector. Results showed that two modules (EGRF_SP1F_01 and SP1F_CEBP_01) were conserved in the promoter sequences of three well-known Hsp-genes (Hsp90, Hsp105β and αβ-crystallin). Screening the 60 target gene promoters for the presence of the two modules revealed that 12 genes (20 %) contained both modules. These included Moesin, Proline-4 hydroxylase, Poly(A) binding protein and Formin-binding protein. None of these genes had been previously associated with heat shock response. / South Africa

Molecular chaperones are a group of proteins which maintain cellular homeostasis by assisting de novo protein folding and their refolding to native state after destabilization due to external stress. They are also known as heat shock proteins as they were first discovered as a response to heat stress. It is now well established that the function of this group of proteins is not only restricted to protein homeostasis but also extends to diverse cellular processes such signal transduction, development and differentiation. Heat shock protein 90 (Hsp90) is one of the most abundant molecular chaperones that is highly conserved from prokaryotes to eukaryotes. Hsp90 is an essential chaperone and is required for the viability of all eukaryotes examined so far including yeast, Drosophila and Caenorhabditis elegans. Hsp90 has emerged as an important regulator of cellular activities by virtue of its ability to interact with a diverse set of client proteins many of which include transcription factors, protein kinases and signaling molecules. Through interaction with these proteins it is involved in regulating cellular processes including growth, cell cycle, endocrine functions, apoptosis, differentiation and development. Further in Drosophila and plants, Hsp90 is thought to function as a capacitor for morphological evolution and phenotypic variation. Recently, it has also been implicated in the emergence of drug resistance in Candida albicans. Furthermore, the importance of Hsp90 in disease states, particularly in cancer, is strongly evident, where chaperoning of mutated and oncogenic proteins is critical for continuous proliferation of cells. This has led to the development of Hsp90 inhibitors as an anti-cancer drug. Geldanamycin (GA), a benzoquinone ansamycin was the first molecule shown to inhibit Hsp90 activity by binding to its ATP binding domain. A derivative of GA, 17-allylamino-17-demethoxygeldanamycin (17AAG), has shown promise in clinical studies and has entered Phase III clinical trials. Hsp90 has been shown to be important for growth and development of many protozoan parasites. Inhibition of Hsp90 function in Leishmania, Emiera, Toxoplasma, Trypanosoma as well as Plasmodium causes a block in their developmental cycle. Previous studies from our laboratory have shown that inhibition of Hsp90 function prevents growth of malaria parasite in human erythrocytes in vitro. P. falciparum Hsp90 (PfHsp90) has also been shown to regulate parasite growth during the febrile episodes that are characteristic of malaria. While most of the studies highlighting the importance of PfHsp90 have relied on its pharmacological inhibition, its biochemical characterization and quantitative measurement of its interaction with GA in isolated system has not been explored. It was also not understood whether the in vitro model of Hsp90 inhibition could translate into inhibition of the parasite growth in an animal model of malaria. Since Hsp90 is a split ATPase requiring proper co-ordination between the residues on its N-terminal and middle domains, it would be desirable to biochemically characterize full length PfHsp90 to gain insights into its potential as an anti-malarial target. The present study was initiated with an objective of understanding the biochemical properties of Hsp90 from P. falciparum in terms of ATP binding, ATP hydrolysis and its GA binding ability. We have also examined the potential of PfHsp90 to serve as a chemotherapeutic target using its clinically well-established inhibitor, 17AAG, in a preclinical mice model. Apart from using in vitro and in vivo models of malaria, we have also explored the efficacy of 17AAG in the P. falciparum samples collected from malaria patients. Additionally, we have examined the relevance of chaperones, in particular PfHsp90 in the samples collected from malaria patients. Finally, we have attempted to understand the unexplored biology of another malaria parasite P. vivax by a high throughput proteomics approach. Biochemical characterization of PfHsp90 and its comparison with host Hsp90 Hsp90 belongs to GHKL (gyrase, Hsp90, histidine kinase, MutL) protein family having a characteristic novel ATP-binding Bergerat fold. The ATP binding pocket of GHKL family differs from the conventional nucleotide binding fold in the formation of a cone shaped pocket made up of four anti-parallel β-sheets and three α helices as opposed to parallel βsheets surrounded by α-helices in the latter. The most distinctive feature of Bergerat fold is the presence of ATP lid. Further, even within the GHKL family members the composition and the conformation of this ATP-lid differs, leading to different solvent exposure of the bound ATP. All Hsp90s from different organisms, characterized so far, have been shown to posses ATP binding and hydrolysis activity but so far PfHsp90 ATPase activity has not been characterized. Using intrinsic tryptophan fluorescence measurements, we found PfHsp90 to bind ATP with about 30% higher affinity than human Hsp90 (hHsp90). We further, 32 determined the ATPase activity of PfHsp90 by monitoring the direct conversion of (γ-P) 32-2 ATP to Pi. PfHsp90 bound and hydrolyzed ATP with a Km of 611 µM and kcat of 9.9 x 10 -1m . Interestingly, PfHsp90 showed six times higher ATPase activity as compared to its human homologue and more intriguingly the ATPase activity exhibited by PfHsp90 was highest among all the Hsp90s studied so far. Previous studies from our laboratory have provided sufficient evidence for inhibitory action of GA on Plasmodium growth inside the infected erythrocytes. GA is known to exert its inhibitory effect by binding to the ATP binding domain of Hsp90 thus inhibiting its chaperone activity. Earlier reports have shown that despite a high similarity between the ATP/GA binding region in Hsp90 from different organisms, there is a difference in their ability to bind GA. For example, in spite of all the hallmarks of ATP-binding pocket of Hsp90 family C. elegans Hsp90 does not bind GA. We have employed fluorescence spectroscopy to examine whether PfHsp90 can bind to GA. In parallel, we have also determined the binding affinity of human Hsp90 (hHsp90) to GA. We observed small but reproducible differences in the binding affinity of GA to Hsp90s from human host and P. falciparum with latter having fourfold higher affinity. A sequence analysis of the GA binding domain of Hsp90s from P. falciparum and human host showed a homologous substitution of K112 of hHsp90 to R98 in PfHsp90. In order to examine the effect of this substitution, if any, on the observed difference in GA binding abilities, we mutated R98 to K in PfHsp90. However, we did not find any difference in the binding ability of R98K PfHsp90 to GA, suggesting that this homologous substitution has minimal or no effect on drug protein interaction in vitro. However, in view of this phylogenetically conserved substitution, we cannot rule out its role in vivo. The chaperone function of Hsp90 is dependent on its ATPase activity which is susceptible to GA mediated inhibition. We next examined the extent of inhibition of GA on the ATPase activity of Hsp90s from P. falciparum and human host. Interestingly, we found the PfHsp90-ATPase activity to be three times more sensitive than hHsp90-ATPase activity to GA mediated inhibition suggesting that the malaria parasite, P. falciparum is likely to be more sensitive to GA when compared to human host. This result is in accordance with a recent study, which has shown that yeast expressing PfHsp90 in lieu of native yeast Hsp90 was more sensitive to GA than yeast expressing either yeast Hsp90 or human Hsp90. Acetylation of Plasmodium falciparum Hsp90 Post-translational modification of Hsp90 such as acetylation has been shown to affect its binding with GA. We first examined whether, PfHsp90 can be acetylated. With the use of various purified Histone acetyl transferases (HATs) of human origin, we have shown PfHsp90 to undergo acetylation in vitro. We found that among different HATs (pCAF, Gcn5 and p300) used, only p300 was able to acetylate PfHsp90 suggesting a role for it in PfHsp90 in vivo acetylation as well. We next examined the in vivo acetylation status of PfHsp90 from parasite lysate. To enrich the acetylated fraction of PfHsp90, we have used Histone deacetylase (HDAC) inhibitor, trichostatin A (TSA). Immunoprecipitation of PfHsp90 followed by immunoblotting with an acetyl-lysine antibody confirmed that PfHsp90 undergoes acetylation in vivo. In order to identify the lysine residues which underwent acetylation we subjected the acetylation enriched fraction of PfHsp90 to in-gel trypsin digestion followed by mass spectrometry. Analysis of trypsin digested PfHsp90 from the parasites identified three sites of acetylation, one of which overlapped with PfHsp90 cochaperone (Aha1 and p23) binding residue, suggesting that acetylation could play a potential role in modulating PfHsp90 multi-chaperone complex assembly. Indeed, treatment of P. falciparum cultures with a HDAC-inhibitor resulted in partial dissociation of PfHsp90 complex as observed from size-exclusion chromatography. Adding to this observation, we also found that co-treatment of TSA and GA showed a synergistic and additive effect in inhibiting parasite growth in vitro. The above results suggest the possibility of using Hsp90 inhibitor in combination with HDAC inhibitor to arrest Plasmodium growth and development. Clinically tested GA-analogue 17AAG inhibits Plasmodium growth in vitro and in vivo The specificity of GA inside the cell has been a matter of debate since the discovery of its medicinal importance. In the past, Hsp90 has been implicated as a target of GA by carrying out immunoblotting of GA pull-down fraction with an anti-Hsp90 antibody. Crystal structure of GA with yeast Hsp90 has shown it to bind within the well conserved ATP-binding pocket of Hsp90. However, the specificity of GA inside the cell is still a conjecture. We have performed GA pull down assays from the parasite lysate followed by Coomassie Blue staining, which gave a single band corresponding to 86 kDa PfHsp90. The identity of PfHsp90 was further confirmed by immunoblotting with antibody specific to PfHsp90. This result indicates that inside the cells, inhibitory effect of GA is mediated by and large through its interaction with Hsp90. However, we cannot rule out the presence of other minor, less significant, interactors of GA. Earlier work from our laboratory has shown that GA inhibits Plasmodium growth inside the infected erythrocytes. However, issues related to GA toxicity have excluded its development as a therapeutic. Nevertheless, interest in this class of molecule has led to the generation of a large number of less toxic derivatives of GA. One classical example is 17AAG which has gained clinical importance over the years and has entered in phase III trial. Intrigued by the clinical success of 17AAG, we were interested in determining its ability to modulate parasite growth. Indeed, 17AAG was able to inhibit parasite growth in a manner similar to that of GA. We further extended our study to parasites isolated from patient samples. Here too, we found 17AAG to be effective in inhibiting growth of the parasite. Finally, we examined the efficacy of 17AAG at a pre-clinical level using a mouse model of malaria. Using Peters’ four-day test we found 17AAG, to be effective in attenuating parasite growth and prolonging the survival of parasite infected mice (n=4, p=0.00692; n=10, p=0.001). Clinical relevance of heat shock proteins of Plasmodium falciparum A recent study using in vivo expression profiles of parasites derived from blood samples of infected patients has revealed previously unknown physiological diversity in the biology of malaria parasites. According to gene expression profiles, parasites were clustered into three different physiological states – starvation, glycolysis dependent active growth and environmental stress response. In order to examine the clinical relevance of molecular chaperones in malaria, we reanalyzed the previously published gene expression data of clinical parasites from 46 patients. Our analysis of this data showed that organellar chaperones were up-regulated upon starvation (cluster1) while cytosolic chaperones such as Hsp90 were up-regulated in active growth conditions (cluster2) indicating up-regulation of distinct group of Hsps in response to different environmental cues. Interestingly, Hsp90 and its co-chaperones, previously implicated as drug targets in malaria, clustered in the same group. Further, some patients of cluster 3 (environmental stress response) showed higher expression of Hsp90 while others showed lower expression. In general, cluster 3 group of patients were heterogeneous in terms of expression of chaperones. Using non-negative matrix factorization (NMF), cluster 3 was sub-clustered into two groups 3a and 3b. Cluster 3b showed up-regulation of cytosolic chaperones similar to cluster 2 indicating these two clusters are inter-related. Most of the Hsp90 dependent pathways such as trafficking, signaling, anti apoptotic and pro-survival found to be most active in cluster 2 indicating the dependence of this group of parasites on Hsp90. The two main outcomes of our chaperone analysis are (1) the up-regulation of molecular chaperones in parasites are not a general response to hostile conditions as perceived previously, but is largely determined by the host factors and may differ from one host to another (2) the disease specific pathways may exist in natural condition by the up-regulation of specific chaperone and its interactors as a response to different host environment. Clinical proteomics of human malarial parasites Much of our understanding about the life cycle of parasites and importance of parasite proteins have been gleaned from the studies in laboratory strain or with the laboratory adapted clinical parasites. Although, these studies provide us first hand information about the functionality and the importance of these proteins, but they often fail to mimic the actual disease environment. In the patient, parasites are exposed to host factors such as hormones, metabolites, inflammatory mediators which can influence the expression of proteins and thus parasite biology. Further, instead of parasite exposure to 37°C temperature throughout the erythrocytic cycle in vitro, it is exposed to several rounds of febrile episodes inside human, which can also influence the parasite life cycle. Furthermore, clinical analysis is important to validate the presence and expression of drug targets in actual disease environment. Therefore, analysis of malaria parasite from clinical settings has become an important component in our laboratory and this thesis. Proteomic analysis of clinical samples has emerged as an important tool to understand the proteins dynamicity as response to disease environment. We have initiated clinical proteomic study of P. falciparum, the cause of most common and fatal malaria in humans and extended it further to the neglected malaria parasite P. vivax. The study of P. vivax has largely been over-shadowed by the enormous attention devoted to P. falciparum. Notably, the drugs which have been discovered against P. falciparum are not as effective against P. vivax. Further several unique features of P. vivax such as dormant hyponozoites, reticulocyte host preference and formation of specialized caveolae vesicle complex structure distinguish its biology from P. falciparum and warrant concerted effort directed at this parasite. A major limitation in studying this parasite is the absence of a long-term culturing system. Therefore, research on this parasite requires samples obtained directly from patients. In spite of the inherent difficulty in obtaining such samples, this method provides us an opportunity to study this parasite in its real environment which has a huge effect on the expression as well as function of parasites and host proteins. Our current knowledge about the life cycle of this parasite has been gained from the recently published transcriptome study. Even though transcriptome analyses provide useful understanding at the level of gene expression, they do not reflect the active protein component of a cell. In other words, most of disease outcome is a result of interaction of the protein component with the environment. We therefore attempted to understand the protein component of this parasite in the disease environment to shed light on its pathogenicity. Despite facing several challenges in the way of proteomic analysis of this parasite such as availability of samples, low parasitemia, contamination of parasite proteins with abundant host proteins etc, we were able to identify 154 P. vivax proteins abundantly expressed in clinical environment using mass-spectrometry based approach. We found many proteins unique to this parasite along with known drug targets. This study is the first of its kind and could prove to be a very important step towards gaining insights into the physiology of this parasite.This study serves as a proof-of-principle method which in future is likely to help in identifying many more potential drug targets, vaccine candidates and diagnostic markers from clinically relevant samples as opposed to cultured samples. Summary Despite the importance of PfHsp90 in malaria biology, it has not been characterized in terms of its biochemical properties and its interaction with the inhibitor. In this study, we have successfully cloned, expressed, purified and characterized full length PfHsp90. We found that PfHsp90 exhibits a hyper-ATPase activity and is more sensitive to GA mediated inhibition as compared to human Hsp90. We have also shown that its sensitivity towards GA is dependent on its acetylation status as treatment of infected erythrocytes with HDAC inhibitors increases its sensitivity to GA. Using a pull-down assay, we have determined, unequivocally, that GA specifically binds to Hsp90. Most importantly, we have demonstrated that 17AAG, a clinically well-established inhibitor of Hsp90, inhibits parasite growth in a laboratory strain, field isolates and an in vivo mouse model of malaria. Overall, our biochemical characterization and drug interaction studies underscore the importance of PfHsp90 as a potent drug target and its inhibitors as a candidate drugs for the treatment of malaria, one of the deadly human infectious diseases. Our efforts to understand the importance of molecular chaperones in parasites isolated directly from patient samples (clinical setting) has revealed conspicuous association of Hsps with previously defined parasite physiological states. In particular, parasites obtained from a specific group of patients exhibited heightened dependence on Hsp90-dependent pro-survival pathways, indicating an increased response to host stressors in this group of parasites. Thus, parasite encoded chaperones, in particular PfHsp90, play a major role in defining the pathogenesis of malaria. A disease is an outcome of interaction between pathogens and its host, therefore it is important to study parasite in its real environment to understand disease pathogenesis. Our lab has previously reported the first ever proteomic analysis of P. falciparum from malaria patients. In this study, we have made an attempt to understand the unexplored biology of another important malaria parasite P. vivax. We have used a mass-spectrometry based approach to identify the protein content of this parasite. This technically challenging attempt has enabled us to identify many proteins. This study is an important step towards understanding the biology of this parasite in dearth of any information available on the proteins involved in this parasite’s pathogenicity.

Heat shock proteins (Hsps) are a class of molecular chaperones which were first discovered as proteins up-regulated in response to heat stress in Drosophila. Later, it was found that these set of proteins get up-regulated as a general stress response associated with destabilization of native protein structures. Over a period of time, intricate involvement of Hsps in various biological processes has been well established. Heat shock protein 90 (Hsp90) is one of the important representative of this class of proteins. Hsp90 is an essential molecular chaperone which is evolutionarily conserved. It has a selective set of proteins to chaperone called as clients, which majorly include transcription factors and protein kinases. Through its interaction with its clients it modulates cell cycle, signal transduction, differentiation, development and evolution. Previous studies from Candida, Leishmania and Plasmodium have implicated Hsp90 to be involved in stage transition and growth. It is also critically involved in regulating growth of other protozoans such as Dictyostelium, Entamoeba and Trypanosoma. Thus, selective inhibition of Hsp90 has been explored as an intervention strategy against important human diseases such as cancer, malaria and other protozoan diseases. In Plasmodium falciparum, Hsp90 plays a critical role in stage transition. The parasite inside the human RBC develops from ring to trophozoite to schizont stage and inhibition of Hsp90 using specific pharmacological inhibitor arrests the growth of parasite at ring stage. In Dictyostelium, it has been observed that Hsp90 function is required for development. Inhibition of Hsp90 causes mound arrest and stops the cells from entering to its next developmental stage, fruiting bodies. In parallel, Hsp90 in Candida has been shown to be involved in morphogenesis. In nature Candida exists as a single cell yeast form and upon entry into the human host these yeast forms undergo morphogenesis to form virulent filamentous fungi. Inhibition of Hsp90 mimics temperature mediated morphogenesis. All together, these studies suggest that Hsp90 functions in a context dependent manner and each biological system explored has given new insights into the Hsp90 biology. Giardia lamblia, a protozoan parasite of humans and animals, is an important cause of diarrheal disease causing significant morbidity and also mortality in tropical countries. In the present study we focus on the biology of Hsp90 from Giardia lamblia. Giardia has a biphasic life cycle with infective cyst stage and pathogenic trophozoite stage. These cysts are present in the environment and enter mammalian host through oral route. They undergo a process called as excystation in the intestine giving rise to trophozoites. The trophozoites so formed colonize the upper part of the small intestine which causes the symptoms of giardiasis. Some of the trophozoites escape from the nutrition rich milieu of the upper part of small intestine to the lower part. In this region, trophozoites undergo a process called as encystation, wherein each trophozoite forms a cyst which escapes through faeces back into the environment. As seen in the life cycle of Giardia there are two major biological transitions, excystation and encystation; and till date no definitive player or pathway is known to regulate these processes. With the knowledge of Hsp90 playing an important role in similar biological transitions in other organisms we were encouraged to study role of Hsp90 in Giardia lamblia. Trans-splicing based generation of a full length Hsp90 in Giardia lamblia To understand the role of Hsp90, we first carried out sequence alignment of Hsp90 predicted ORFs in Giardia genome with yeast Hsp90. On alignment we observed that Hsp90 in Giardia is discontinuous and is annotated to be encoded by two different ORFs. Hsp90 in most organisms is coded by a single ORF with none to many cis-spliced introns. In a relatively intron poor organism G. lamblia, cytosolic Hsp90 is coded by two different ORFs separated by 777 kb in the genome. On multiple sequence alignment, we noticed that these two ORFs correspond to two independent regions of the Hsp90 protein. The ORFs are designated as hspN and hspC, containing the N-terminal and the C-terminal region of the protein respectively. We began our study by sequencing whole genome of Giardia lamblia clinical strain. Our genome sequencing confirmed the split nature of hsp90 and showed high ‘synteny’ between the other sequenced isolates. Using PCR based approach we have ruled out the possibility of having a full length gene in the genome. In contradiction to the genome result, we have observed a higher molecular weight protein in the lysate on proteomic analysis which was further confirmed by western blotting. The protein was observed to have a molecular weight of 80 kDa which could be a resultant of combination of two ORFs, suggesting the presence of a full length mRNA for Hsp90. PCR amplification using primers against both the fragments resulted in amplification of 2.1 kb product from the RNA pool of Giardia. Sequencing of this product showed that hspN and hspC were stitched together to form a mature messenger for full length Hsp90. In total our results suggest a post transcriptional process, trans-splicing, to be involved in the construction of Hsp90. The transition marked by this fusion coincides with the canonical GU¬AG splice site transitions as observed in other eukaryotes. Interestingly, a 26 nt near-complementary region was observed inside and upstream of hspN and hspC ORFs respectively. Put together these results suggest that the 26 nt complementary region acts as the positioning element to bring these two precursors in spatial proximity. With efficient spliceosomal activity these two precursor forms are trans-spliced to generate a full length cytosolic Hsp90 in Giardia. There are only four genes which have cis-spliced introns in the Giardia genome and the core components of the spliceosomal machinery are also present. The presence of canonical splice site in both the transcripts suggests that these transcripts are fused together by the spliceosomal machinery by the phenomenon of trans-splicing. The formation of full length Hsp90 RNA by its fragmented gene is the first example of trans-splicing in Giardia. To understand, are there any other genes which are also similarly trans-spliced we have carried out shotgun proteomic analysis of the total cell lysate obtained from Giardia trophozoites. Using Hsp90 as template, in our proteomic datasets, we have designed an algorithm for identification of additional trans-spliced gene products at the protein level. We have identified a total of 476 proteins of which hypothetical proteins constitute the major class followed by metabolic enzymes. We have compared the theoretical molecular weights for the identified proteins with the experimentally determined mass. Any discrepancy in the molecular mass was further analyzed and we assigned a gene to be potentially trans-spliced based on three criteria: if they were encoded by two or more different ORFs (loci), absence of a single full length counterpart and presence of splice sites with branch point and positional elements. Using this algorithm we were able to identify dynein as a potential candidate of trans-splicing reaction which was confirmed by the nucleotide sequence analysis of the predicted ORFs. Interestingly, dynein gene fragments were observed to be scattered on different chromosomes with minor splice sites unlike hsp90 genes. In vivo Expression of Hsp90 sub-fragments, HspN and HspC In the mature Hsp90 mRNA formed upon trans-splicing, 33 additional codons are present right between hspN and hspC sequences and they were acquired from the upstream region of hspC ORF. The 33 codons encode for an important region of Hsp90 which harbours the conserved catalytic “Arg” residue; suggesting that the full length Giardia Hsp90 (GlHsp90) formed could be an active ATPase. To confirm the same we have carried out in vitro characterization of trans-spliced Hsp90. Towards this, we have cloned, expressed and purified His tag-GlHsp90. As a first step, highly purified protein was used to assess its efficiency in binding to it cognate ligand, ATP, and the known inhibitors. Our binding studies show that GlHsp90 binds to ATP with a dissociation constant of 628 M and to its inhibitors, GA and 17AAG with 1.5 μM and 17.5 μM respectively. The bound ATP will be subsequently cleaved by Hsp90 which is an essential step in the chaperone cycle. As determined in our ATPase assay we observed that GlHsp90 hydrolyzes bound ATP with the catalytic efficiency of 4.4 × 10-5μM-1.min-1which confirms that Hsp90 generated upon trans-splicing is an active ATPase. The uniqueness of the hsp90 gene arrangement in Giardia posed a new question. Do these gene fragments also get translated? Our results suggest that HspN and HspC are poly¬adenylated. In order to determine the levels of these transcripts we performed qRT-PCR using primers specific to HspN, HspC and GlHsp90. We have observed that, in comparison with HspN transcript level, HspC and GlHsp90 transcripts are 15 and 75 folds higher respectively. To check for the presence of translation products of these transcripts, we have re-analyzed our proteomic datasets wherein we could identify peptides corresponding to HspN and HspC in their respective molecular weight region, 45 to 35 kDa. To confirm the proteomic data, western blot analysis was performed for trophozoite lysate on both 1D and 2D gels using anti-HspN antibody. Two specific bands (1D) / spots (2D) corresponding to the full length Hsp90 and HspN were identified. Gel filtration analysis revealed that HspN co¬eluted with full length Hsp90 thereby suggesting that both the proteins are in a same complex. With the background that HspN and HspC are present at the protein level, we asked if these fragments in combination can hydrolyse ATP. We reconstituted recombinant HspN and HspC in equimolar amounts and scored for the hydrolysis of ATP. However, no Pi release was observed. To determine whether HspN and HspC could modulate Hsp90 function, ATPase activity was monitored in the presence of HspN or HspC, in vitro. It was observed that ATPase activity was inhibited by both the fragments thus suggesting that HspN and HspC negatively regulate Hsp90 ATPase activity. Role of Hsp90 in Giardia encystation Giardia has a biphasic life cycle with proliferative trophozoites and latent cyst stage. In Giardia, in vitro encystation was established nearly two decades back by modulating the medium conditions. However, the mechanism and triggers underlying this transition are not well characterized. To understand whether Hsp90 has any role in this transition, in vitro conversion of trophozoites to cysts was achieved. The cysts obtained showed all the characteristic features of mature Giardia cyst with cyst wall protein 1 (CWP1) on the cyst wall and four nuclei as determined by immunofluorescence analysis. Further, the levels of Hsp90 in trophozoites were compared with mature cysts at both transcript and protein levels and it was found that cysts show more than 50% reduction in the level of Hsp90 in comparison with normal trophozoites. In accordance, exogenous inhibition of Hsp90 using 17AAG promoted the formation of cysts in vitro by 60 folds in a dose dependent manner; however, the window period of Hsp90 function compromise plays an important role in this process. Higher numbers of cysts were obtained from the cells treated with inhibitors during pre-encystation condition but inhibition of Hsp90 during encystation did not affect the formation of cysts, suggesting that Hsp90 down-regulation plays an important role during commitment towards encystation. To further show that cyst formation is a specific response to Hsp90 inhibition we have carried out encystation in the presence of metranidazole and from heat shocked cells; however, in both the conditions we did not observe any significant change in cyst formation, thus confirming that Hsp90 plays an important role during encystation in Giardia lamblia. Summary In Conclusion, Our study throws light on a unique aspect of Hsp90 biology in Giardia Lamblia, wherein the formation of the full length protein is dependent on a unique trans splicing reaction of its gene components representing different domains. We have also shown that HsP90 fragments, HspN and HspC, are also expressed in Trophozoites. Our in vitro data suggests that these fragments possibly regulate the function of Hsp90. Furthermore, the full length of Hsp90 plays an important role in stage transition in Giardia wherein inhibition of Hsp90 induces encystations. The study has opened many new avenues for research. Understanding the exact role of HspN and HspC in vivo will provide better appreciation for the evolution of such a complex biogenesis of an essential protein.