Modélisation et simulation 3D de la morphogenèse

The embryo of the Drosophila Melanogaster undergoes a series of cell movements during its early development. Gastrulation is the process describing the segregation of the future internal tissues into the interior of the developing embryo. Gastrulation starts with the formation of the ventral furrow, a process commonly known as the ventral furrow invagination. During this process, the most ventrally located blastoderm cells flatten and progressively constrict their apical sides until they are wedge shaped. As a result of these cell-shape changes, the blastoderm epithelium first forms an indentation, the ventral furrow, which is then completely internalized. We focus on the study of the mechanisms that drive the invagination. The main questions that gave birth to this thesis are: “What is the role of the apical constriction of the ventral cells in the invagination?” and “Once the ventral cells are internalized, what is the mechanism that drives the ventral closure?” We attempt to answer to these two questions from a biomechanical point of view. For this purpose, a 3D mesh of the embryo of the Drosophila Melanogaster has been created. Based on this mesh, two “a minima” biomechanical models of the Drosophila embryo have been created, a physically based discrete model and a model based on the Finite Element Method. The results of the simulations in both models show that the geometry of the embryo plays a crucial role in the internalization of the ventral cells. The two models efficiently simulate the internalization of the ventral cells but are incapable of reproducing the ventral closure. We hypothesize that the ventral closure can be explained by the interplay of forces developed in the embryo once the internalized ventral cells undergo cell division. We propose an approach to divide elements in a Finite Element Mesh and we integrate it to the Finite Element Model of the Drosophila Melanogaster.L'embryon de la Drosophila Melanogaster subit une série des mouvements cellulaires pendant son développement. La gastrulation est le processus qui décrit la différentiation des futurs tissus à l'intérieur de l'embryon. La gastrulation commence par la formation du sillon ventral, un processus connu sous le nom de “Ventral Furrow Invagination”. Pendant ce processus, les cellules de la blastoderme positionnées dans la région ventrale de l'embryon, aplatissent et contractent leur surface apicale jusqu'à ce qu'elles deviennent prismatiques. Ce changement de forme cellulaire aboutit à un enfoncement au niveau de la région ventrale, le sillon ventral, qui est ensuite totalement intériorisé. Nous focalisons notre étude sur les mécanismes qui conduisent à l'invagination. Les questions principales auxquelles ce travail de thèse essaie de répondre sont: “Quel est le rôle de la contraction apicale des cellules ventrales dans l'invagination?” et “Quel est le mécanisme qui conduit à la clôture ventrale, une fois les cellules ventrales intériorisées?”. Nous essayons de répondre à ces questions d'un point de vue biomécanique. Dans ce but, un maillage 3D de l'embryon de la Drosophila Melanogaster a été créé. Basés sur ce maillage, deux modèles biomécaniques “a minima” de l'embryon de la Drosophila ont été créés: un modèle physique discret et un modèle basé sur la Méthode des Eléments Finis. Les résultats des simulations des deux modèles montrent que la géométrie joue un rôle décisif dans l'intériorisation des cellules ventrales. Les deux modèles ont permis de simuler l'intériorisation des cellules ventrales mais se trouvent incapables de simuler la clôture ventrale. Notre hypothèse est que la clôture ventrale peut s'expliquer par l'intéraction des forces développées à l'intérieur de l'embryon, une fois que les cellules ventrales commencent à proliférer. Nous proposons une méthode pour diviser des éléments dans un maillage d'éléments finis et ensuite nous expliquons l'intégration de cette méthode dans le modèle des Eléments Finis pour l'embryon de la Drosophila Melanogaster

Design and characterization of enzymatic deglycosylation systems to produce drugs against Alzheimer’s disease

Tese de doutoramento, Farmácia (Química Farmacêutica e Terapêutica), Universidade de Lisboa, Faculdade de Farmácia, 2011This study focused on the research of new bioactive constituents from four species of the Plectranthus plants. Previous works on plants of the genus Plectranthus (Lamiaceæ) evidenced that some of their constituents possess interesting biological activities. The antimicrobial activity of the plant extracts and of the isolated metabolites was thoroughly searched. Antioxidant, anticholinesterase and anti-inflammatory properties of some compounds were also screened. The phytochemical study of the acetone extracts of Plectranthus ornatus Codd., P. ecklonii Benth., P. porcatus Winter & Van Jaarsv and P. saccatus Benth. rendered several terpenoid constituents mostly diterpenes. From P. ornatus three new forskolin-like labdane diterpenes (6-O-acetylforskolin, 1,6-di-O-acetylforskolin and 1,6-di-O-acetyl-9-deoxyforskolin), a new diterpene with the rare halimane skeleton (11R*-acetoxyhalima-5,13E-dien-15-oic acid), and two known labdane diterpenes were isolated; the rhinocerotinoic acid which was found in Plectranthus species for the first time, and plectrornatin C. Six known triterpenoids were also identified as mixtures. The study of P. ecklonii led to the isolation of two known abietanes, sugiol and parvifloron D. Sugiol was obtained from Plectranthus species for the first time. Four known triterpenoids were also identified as mixtures. P. porcatus, a plant not hitherto studied, yield a new spiro-abietane diterpene [(13S,15S)-6β,7α,12α,19-tetrahydroxy-13β,16-cyclo-8-abietene-11,14-dione]. A new beyerane diterpene (ent-7α-acetoxy-15-beyeren-18-oic acid) was isolated from P. saccatus. Attempting to find novel bioactive prototypes from the more potent antibacterial diterpenes, isolated in higher yields, some diterpene derivatives were prepared. Nine new derivatives were obtained from (11R*,13E)-11-acetoxyhalima-5,13-dien-15-oic acid (P. ornatus). A new 2β-(4-hydroxy)benzoyloxy derivative of microstegiol was prepared from parvifloron D (P. ecklonii). From the 7α-acetoxy-6β-hydroxyroyleanone (isolated in the past from P. grandidentatus) thirteen ester derivatives were synthesized, whereof ten were new compounds. The unequivocal chemical structures of pure compounds (natural and derivatives) were deduced from their spectroscopic (IR, MS, 1D and 2D NMR experiments) and physico-chemical data, as well as from literature information. The preliminary antimicrobial activity screenings of all the isolated metabolites showed that several diterpenes inhibited the growth of the Gram positive bacteria tested. In addition, the minimum inhibitory concentration against standard and clinical isolates of sensitive and resistant Staphylococcus and Enterococcus strains was determined for the antibacterial metabolites and their synthesized derivatives. The (11R*,13E)-11-acetoxyhalima-5,13-dien-15-oic acid and its (11R*,13E)-halima-5,13-diene-11,15-diol derivative were the more active halimanes. Parvifloron D was less active than its microstegiol 2β-(4-hydroxy)benzoate derivative, but both showed more potent antibacterial activities than the halimane diterpenoids. The three 12-O-benzoyl esters derivatives of the 7α-acetoxy-6β-hydroxyroyleanone prototype revealed to be more potent growth inhibitors against Staphylococcus and Enterococcus strains than the prototype. The 6β-propionyloxy-12-O-propionyl derivative also showed to be more active against Enterococcus than the prototype. Generally, the 12-esters and the 6,12-diesters were more active against Enterococcus than Staphylococcus strains. The hydrophobic extra-interactions with the bacterial targets seem to play an important role on the activity of royleanones derivatives prepared. Taking into account the IC50 values which expressed the scavenging DPPH radical ability, the isolated metabolite parvifloron D as well as 7α-acetoxy-6β-hydroxyroyleanone showed in vitro antioxidant activity. The in vitro acetylcholinesterase assay did not detect any activity for all the newly isolated diterpenes and 7α-acetoxy-6β-hydroxyroyleanone. The COX inhibitor screening assay was tested on 6-O-acetylforskolin, rhinocerotinoic acid, plectrornatin C, (11R*,13E)-halima-5,13-diene-11,15- diol, 11R*-acetoxyhalima-5,13E-dien-15-oic acid and on its methyl ester, for their ability to inhibit COX-2. The preliminary results encourage further studies aiming to confirm and to examine its potential anti-inflammatory activity in a more robust approach.Este estudo teve como objectivo a pesquisa de novos constituintes bioactivos de quatro espécies de plantas do género Plectranthus. A actividade antimicrobiana dos extractos obtidos e dos metabolitos isolados foi realizada e foram testadas as propriedades anti-oxidante, anti-colinesterase e anti-inflamatória de alguns compostos. O estudo fitoquímico dos extractos de acetona de Plectranthus ornatus Codd., P. ecklonii Benth., P. porcatus Winter & Van Jaarsv. e P. saccatus Benth. originou diversos constituintes terpénicos, principalmente diterpenos. Três novos diterpenos do tipo forskolina (6-O-acetilforskolina; 1,6-di-O-acetilforskolina e 1,6-di-O-acetil-9-deoxiforskolina) foram isolados de P. ornatus. Foram também identificados um novo diterpeno com o raro esqueleto de halimano (ácido 11R*-acetoxihalima-5,13E-dien-15-óico), dois diterpenos labdânicos conhecidos; o ácido rinocerotinóico encontrado pela primeira vez em espécies do género Plectranthus, e a plectrornatina C. Seis triterpenos já conhecidos foram igualmente identificados na forma de misturas. O estudo de P. ecklonii originou o isolamento de dois abietanos conhecidos: o sugiol e a parviflorona D. O sugiol foi isolado pela primeira vez de espécies Plectranthus. Outros quatro triterpenos conhecidos foram identificados também como misturas. A planta P. porcatus, até à data não estudada, originou um novo diterpeno spiro-abietânico [(13S,15S)-6β,7α,12α,19-tetrahidroxi-13β,16-ciclo-8-abietene-11,14-diona]. Um novo diterpeno com esqueleto de beierano (ácido ent-7α-acetoxi-15-beieren-18-óico) foi isolado de P. saccatus. Na tentativa de obter novos protótipos bioactivos, vários derivados foram preparados, a partir dos diterpenos antibacterianos mais potentes e isolados em maior quantidade. Nove novos derivados foram obtidos do ácido (11R*,13E)-11-acetoxihalima-5,13-dien-15-óico (P. ornatus). Um novo derivado 2β-(4-hidroxi)benzoilado do microstegiol, foi preparado a partir da parviflorona D (P. ecklonii). Treze ésteres derivados da 7α-acetoxi-6β-hidroxiroyleanona (isolada anteriormente de P. grandidentatus) foram sintetizados, sendo de assinalar que dez dos derivados são compostos novos. A determinação estrutural dos compostos puros (naturais e derivados) foi deduzida por espectroscopia (IV, EM, RMN 1D e 2D), propriedades físico-químicas e com base na informação obtida da literatura. O estudo preliminar da actividade antimicrobiana de todos os metabolitos isolados, mostrou que diversos diterpenos inibem o crescimento de bactérias de Gram positivo. A concentração mínima inibitória (CMI) dos metabolitos e seus derivados foi determinada em estirpes de Staphylococcus e Enterococcus, tanto em bactérias padrão como em isolados clínicos resistentes e sensíveis a antibióticos. O ácido (11R*,13E)-11-acetoxihalima-5,13-dien-15-óico e o seu derivado (11R*,13E)-halima-5,13-diene-11,15-diol foram os halimanos mais activos. A parviflorona D foi menos activa do que o seu correspondente derivado 2β-(4-hidroxi)benzoilado, mas ambos apresentaram uma actividade antibacteriana mais potente do que os diterpenos com esqueleto de halimano. x Os três 12-O-benzoil-ésteres derivados do protótipo 7α-acetoxi-6β-hidroxiroyleanona revelaram ser inibidores mais potentes do que a royleanona-protótipo, contra as estirpes testadas de Staphylococcus e Enterococcus. O derivado 6β-propioniloxi-12-O-propionilo mostrou ser o mais activo contra as estirpes testadas de Enterococcus do que o protótipo. De um modo geral, os derivados 12-ésteres e os 6,12-diésteres foram mais activos contra as estirpes de Enterococcus do que as estirpes de Staphylococcus testadas. As interacções hidrofóbicas com os alvos bacterianos parecem ter um papel importante na actividade antibacteriana dos derivados de royleanona preparados. Os metabolitos parviflorona D e a 7α-acetoxi-6β-hidroxiroyleanona demostraram possuir actividade antioxidante in vitro, tendo em conta os valores de IC50 que expressam a actividade anti-oxidante com base na captura do radical DPPH. Todos os novos diterpenos isolados e derivados obtidos neste trabalho foram testados e não revelaram possuir actividade inibitória da acetilcolinesterase in vitro. A actividade anti-inflamatória foi testada nos compostos 6-O-acetilforskolina, ácido rinocerotinóico, plectrornatina C, (11R*,13E)-halima-5,13-diene-11,15-diol, ácido 11R*-acetoxihalima-5,13E-dien-15-óico e no seu éster metílico, através da sua capacidade de inibir a COX-2. Os resultados preliminares obtidos apoiam a necessidade de estudos futuros de forma a confirmar, explorar e discutir uma potencial actividade anti-inflamatória.Fundação para a Ciência e a Tecnologia (SFRH / BD / 30716 / 2006

CHARACTERIZING THE ROLE OF C. ALBICANS SOD4: AN FE REGULATED CU-ONLY SOD ENZYME

Candida albicans is one of the most prevalent human fungal pathogens. Interestingly, it encodes three Cu-only superoxide dismutase (SOD) enzymes (SOD4, SOD5, SOD6). These Cu-only SODs represent a new class of extracellular SODs that are found throughout the fungal kingdom. C. albicans SOD5 was the first member in this class to be characterized structurally via X-ray crystallography and remains the only member of this class for which a structure exists. Biochemical studies on SOD5 revealed it to be a highly active SOD enzyme. SOD5 is important for both fungal defense against reactive oxygen species and morphogenesis signaling in C. albicans. In addition, SOD5 has been shown to be a virulence factor in rodent models of Candida infection. SOD4 shares a 72% sequence identity with SOD5, but little is known about its unique role in C. albicans biology. In this thesis, I characterized the SOD4 protein and studied its role in C. albicans and related Candida spp. First, I found SOD4 has different surface charges compared to SOD5, but that they are otherwise very similar at the biochemical level (Chapter 2). I found that SOD4, like SOD5 is a highly efficient monomeric SOD enzyme requiring only Cu as a cofactor and has similar Cu binding properties (Chapter 2). C. albicans transcriptionally upregulates SOD4 during iron deprivation, a response that is also demonstrated by other Candida species and may be conserved in the CTG fungal clade (Chapter 2). C. tropicalis, like C. albicans, also produces a burst of ROS during hyphal morphogenesis that coincides with induction of a Cu-only SOD enzyme (Chapter 2). I also determined that in the emerging fungal pathogen C. auris, SOD4 is an active SOD enzyme despite its divergence from the SOD4 and SOD5 sequences of C. albicans (Chapter 2). Currently, there are no published structures of SOD4 proteins. In Chapter 3 of this thesis, I studied SOD4 and SOD5 by NMR to gain insight into their structures in solution and determine the feasibility of future NMR-based assays. Previous in vivo studies indicated that sod5∆/∆ mutants of C. albicans had decreased virulence in the lateral tail vein model of disseminated candidiasis in mice and were incapable of forming biofilms in a central venous rat catheter model. Surprisingly, we found that sod4∆/∆ yeast did not have decreased ability to cause invasive infection in mice and were still capable of producing robust biofilms on rat venous catheters in vivo (Chapter 4). We found there may be some increased immune cell infiltration in these models, and perhaps the loss of SOD4 alters immune cell signaling. This thesis research adds structural and biochemical information to the knowledge of this unique class of enzymes and their role in fungal pathogenesis

Inhibition of tumourigenicity of small cell lung cancer cells by suppressing Id3 expression.

Id3 is over-expressed in small cell lung cancer (SCLC). To test whether the tumourigenicity of SCLC cells can be inhibited by suppressing Id3 expression, we transfected siRNA into SCLC cell line GLC-19 and established two sublines (G-Id3-1 and G-Id3-7) which expressed only 30% of the level of Id3 measured in control transfectants. Suppression of Id3 expression in both G-Id3-1 and G-Id3-7 cells produced significant reductions in proliferation rates and in numbers of colonies formed in soft agar assay. When G-Id3-1, G-Id3-7 and the control transfectants were inoculated subcutaneously into 3 groups (8 each) of nude mice, respectively, all (100%) inoculated animals produced tumours. Although there was no difference in tumour incidents amongst the 3 groups, significant reductions were observed in both size and weight of tumours produced by either G-Id3-1 or G-Id3-7 cells. While the final average volume of tumours produced in control group was 1012.1+/-394 mm(3), it was significantly reduced (p2.4-fold higher than that in control. The results in this study suggest that highly expressed Id3 in SCLC cells may be an important therapeutic target for tumour suppression