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Post-translational modification (PTM) of proteins by enzymes such as methyltransferases, kinases and deacetylases play a crucial role in the regulation of many metabolic pathways. Determining the substrate scope of these enzymes is essential when studying their biological role. However, the combinatorial nature of possible protein substrate sequences makes experimental screening assays intractable. To predict new substrates for proteins, various computational approaches have been developed. Our method relies on crystallographic data and a novel multistate computational protein design algorithm. We previously used our method to successfully predict four new substrates for SMYD2 (Lanouette S & Davey J.A., 2015), doubling the number of known targets for this PTM enzyme that has been difficult to characterize using other methods. This was possible by first extracting a specificity profile of Smyd2 using our algorithm and subsequently screening a peptide library for matching sequences. However, our method did not yield successful results when attempting to reproduce specificity profiles of other proteins (64% accuracy on average). Different protein environments have demonstrated limitations in the methodology and lead us to further develop the algorithm on a more thorough dataset. Using our new optimized method, specificity profile predictions increase by roughly 20% (84% accuracy on average), independent of the structural template used. The algorithm was then used to blindly predict a specificity profile for the methyltransferase Smyd3, an enzyme for which limited data is currently available. A library of 2550 peptides was screened with the predicted profile, yielding 123 matching sequences. We randomly chose 64 for experimental validation (SPOT peptide array) of methylation by Smyd3 and found 45 methylated and 19 non-methylated peptides (70% success rate). Finally, we released to the community a web version of the algorithm, which can be accessed as http://viper.science.uottawa.ca.

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Android application development has been of interest since the first Android smartphone was released. Applications are constantly getting more complex as well as smartphone hardware is getting better. New ways of developing Android applications are developed with time. There is Model View Presenter architecture that is the most used for android applications now and new View InteractorPresenter Entity Router architecture that is becoming more popular. But there is no empirical data to compare these architectures to understand what architecture will fit better for developing new applications. This thesis aims to compare the MVP and the VIPER android architectures using a few important metrics like maintainability, modifiability, testability, and performance. Results will answer what architecture is better for developing different types of projects. VIPERarchitecture showed better performance results and maintenance metrics comparison shows that both architectures have advantages and disadvantages.

Tropidolaemus wagleri is a species of Asian pitviper with a geographic range including Thailand, Vietnam, Malaysia, Singapore, Bruniei, parts of Indonesia, and the hilippines. Tropidolaemus is a member of the Crotalinae subfamily, within Viperidae. The genus Tropidolaemus includes five species, and was once included within the genus Trimeresurus. While some osteologic characteristics have been noted a comprehensive description of cranial elements has not been produced for T. wagleri. An in-depth description of the cranial skeleton of Tropidolaemus wagleri lays the foundation for future projects to compare and contrast other taxa within Crotalinae and Viperidae. The chosen reference specimen was compared to the presumed younger specimens to note any variation in ontogeny. The study here provides a comprehensive description of isolated cranial elements as well as a description of ontogenetic change within the specimens observed. This study contributes to the knowledge of osteological characters in T. wagleri and provides a foundation for a long term project to identify isolated elements in the fossil record.

Ce travail avait pour objectif de mieux évaluer les critères intrinsèques d’un antivenin et de son utilisation afin d’être le plus efficace possible dans le traitement des envenimations ophidiennes survenant sur le territoire de France métropolitaine. L’immunothérapie est à ce jour le seul traitement étiologique efficace dans la prise en charge des victimes d’envenimation ophidienne. La qualité des antivenins est un élément clé dans l’efficacité et la tolérance de ces traitements. Pour une efficacité optimale, l’immunothérapie doit être administrée le plus rapidement possible. Il ressort enfin que les caractéristiques des envenimations sont en évolution constante sur le territoire métropolitain : émergence de signes neurotoxiques dans les envenimations vipérines ; développement de l’importation de serpents exotiques. Tous ces éléments incitent à une surveillance spécifique par des structures expertes et spécialisées dans le domaine. / This work aimed to assess antivenom criteria in order to be most effective in the treatment of snake bites occurring in metropolitan France. Immunotherapy is the only effective etiological treatment in snake envenomation, considered as a gold standard. Quality of antivenoms is a key element for effectiveness and safety. Immunotherapy should be administered as soon as possible. Finally, it appears that the characteristics of envenomation are constantly changing on the mainland : emergence of neurotoxic signs in viper envenomation; importation of exotic snakes. All these emerging elements need a specific monitoring by expert and specialized structures in France.

Orientador: Lea Rodrigues Simioni / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-25T13:45:35Z (GMT). No. of bitstreams: 1 Floriano_RafaelStuani_D.pdf: 3786286 bytes, checksum: a2855e3dd5b20280b1bf65e08007ab09 (MD5) Previous issue date: 2014 / Resumo: Neste trabalho, nós examinamos a atividade neuromuscular do veneno de Bothriopsis bilineata smaragdina (serpente de floresta) e de sua toxina Bbil-TX (fosfolipase A2 Asp49) em preparações nervo-músculo isoladas de vertebrados. Em preparações BC, o veneno causou bloqueio neuromuscular concentração-dependente (0,1-30 ?g/mL) que não foi reversível por lavagem, com 50% de bloqueio ocorrendo em 90-15 min. Contratura muscular em resposta à ACh exógena e ao KCl não foram afetadas pelo veneno, mas houve um discreto aumento na liberação de CK após 60 min [UI/mL: de 80 ± 15 (basal) para 113 ± 22; n = 6; p > 0,05]. Em preparações NFD, o veneno (1, 10 e 30 ?g/mL) produziu marcante facilitação da neurotransmissão (~120% de aumento acima do basal) com a maior concentração seguida por bloqueio neuromuscular completo após 120 min; os efeitos com as menores concentrações foram considerados menos marcantes. O veneno aumentou o conteúdo quântico após 15 e 30 min de incubação seguido por significativa inibição ?90 min. No entanto, o veneno não alterou o potencial de membrana muscular ou a resposta despolarizante ao carbacol. Em ambas as preparações, incubação a 22-24 °C ao invés de 37 °C atrasou o início do bloqueio, como fez também a inibição da atividade PLA2 do veneno. Em preparações NFD curarizadas, o veneno produziu apenas uma discreta facilitação muscular. Estes resultados indicam que o veneno de B. b. smaragdina causa bloqueio neuromuscular in vitro por um mecanismo pré-sináptico envolvendo PLA2. Também foi investigada a atividade neuromuscular de Bbil-TX, uma PLA2 com atividade catalítica isolada do veneno de B. b. smaragdina, em preparações BC e NFD. Em preparações BC, Bbil-TX (35-702 nM) causou bloqueio tempo- e concentração-dependente que não foi reversível por lavagem; os tempos para causar 50% de bloqueio foram 87 ± 7, 41 ± 7 e 19 ± 2 min (média ± EPM; n = 4-6) para 70, 351 and 702 nM, respectivamente. Contraturas musculares à ACh exógena e KCl não foram alteradas. A toxina (702 nM) também não alterou as respostas contráteis de preparações BC curarizadas (d-Tc; 14,8 ?M) e diretamente estimuladas. No entanto, Bbil-TX (702 nM) produziu moderada alteração morfológica (fibras edemaciadas e/ou hipercrômicas) em BC; houve também uma progressiva liberação de CK [UI/mL: de 116 ± 17 (basal) para 961 ± 48 após 60 min; n = 6; p < 0,05]. O bloqueio neuromuscular induzido por Bbil-TX (351 nM) foi significativamente inibido a 22-24 °C e o pré-tratamento com p-BPB aboliu seu bloqueio. Bbil-TX (210 nM, 702 nM e 2 ?M; n = 4-6) causou bloqueio parcial tempo- e concentração-dependente em preparações NFD (52 ± 2% com a maior concentração). Bbil-TX (2 ?M) também reduziu significativamente a frequência de PsPTM/min [de 26 ± 2,5 (basal) para 10 ± 1 após 60 min; n = 5; p < 0,05] e o conteúdo quântico [de 94 ± 14 (basal) para 24 ± 3 após 60 min; n = 5; p < 0,05] de preparações NFD, mas causou apenas uma discreta alteração do potencial de membrana em repouso [de -80 ± 1 mV (basal) para -66 ± 2 mV após 120 min; n = 5; p < 0,05], com nenhuma alteração significativa na resposta despolarizante ao carbacol. Estes resultados mostram que Bbil-TX é uma PLA2 pré-sináptica que contribui para o bloqueio neuromuscular causado pelo veneno de B. b. smaragdina. A atividade neuromuscular do veneno de B. b. smaragdina e o mecanismo de ação de Bbil-TX no sistema nervoso periférico foi examinado também em outras preparações neuromusculares isoladas de camundongo. Em preparações NFD mantidas em solução fisiológica com baixo Ca2+, o veneno de B. b. smaragdina (3 ?g/mL) produziu uma alteração trifásica nas respostas contráteis enquanto que a maior concentração (10 ?g/mL) produziu uma abrupta e marcante contratura inicial a qual foi seguida por facilitação neuromuscular, oscilações rítmicas das contrações evocadas, alterações na linha de base e progressivo bloqueio neuromuscular. O veneno também atrasou a fase de relaxamento da resposta contrátil aumentando o tempo de decaimento constante. Em condições de baixo Ca2+, Bbil-TX (210 nM) causou um progressivo aumento na amplitude das respostas contráteis (83 ± 19 % acima dos valores basais após 120 min) em preparações NFD; não houve alteração no tempo de decaimento constante após tratamento com a toxina. O veneno de B. b. smaragdina (10 ?g/mL) e Bbil-TX (210 nM) causaram discreta alteração na amplitude do potencial de ação composto registrado em preparações NC de camundongo (veneno: 20 ± 2,1% e toxina: 17 ± 2,4% de redução abaixo dos valores basais; n = 3; p < 0,05) e nenhum efeito significativo sobre o tempo de subida e a latência; Tetrodotoxina (3,1 nM) bloqueou os potenciais no final dos experimentos. Em preparações TSn-m, veneno (10 ?g/mL) e Bbil-TX (210 nM) causaram significativa redução na forma de onda perineural associada à corrente K+ (veneno: 35 ± 7,2% e toxina: 26 ± 1,4% de redução abaixo dos valores basais; p < 0,05; n = 3-5) enquanto que a amplitude da corrente de Na+ não foi significativamente afetada (veneno: 18 ± 3,3% e toxina: 15 ± 2,4% de redução abaixo dos valores basais; p > 0,05; n = 3-5). Bbil-TX (210 nM) causou aumento nos valores de conteúdo quântico de preparações TSn-m mantidas em baixo Ca2+ [de 9,6 ± 1,1 (t0) para 31,4 ± 7,7 (t60), p < 0,05; n = 4]. O veneno (3 ?g/mL) e toxina (210 nM) induziram aumento na fluorescência ao cálcio em células SK-N-SH marcadas com indicador sensível ao Ca2+ Fluo3 AM (4 ?M) e mantidas em solução fisiológica com normais condições de Ca2+ ou com baixo Ca2+. Em células mantidas em Ca2+ normal, o aumento na amplitude de fluorescência foi acompanhado por irregular e frequente movimento de Ca2+. Em preparações TSn-m marcadas com Fluo4 AM (4 ?M), o veneno de B. b. smaragdina causou imediato aumento na concentração de Ca2+ intracelular de fibras musculares seguido por frequente oscilação na fluorescência e contratura muscular; Bbil-TX não induziu nenhuma alteração na fluorescência ao cálcio em fibras musculares de preparações TSn-m. Secções de preparações NFD pré-tratadas com Bbil-TX (210 nM) destinadas à imunohistoquímica foram marcadas positivamente para receptores juncionais de ACh mas houve perda de marcação para as proteínas pré-sináptica sinaptofisina e SNAP25. Juntos, estes dados indicam que Bbil-TX tem alta seletividade de ação sobre a região pré-sináptica semelhantemente a outras neurotoxinas PLA2 modulando a atividade neuromuscular do veneno de B. b. smaragdina / Abstract: In this work, we examined the neuromuscular activity of Bothriopsis bilineata smaragdina (forest viper) venom and its toxin Bbil-TX (Asp49 phospholipase A2) in vertebrate isolated nerve-muscle preparations. In chick biventer cervicis preparations (BC) the venom caused concentration-dependent (0.1-30 ?g/ml) neuromuscular blockade that was not reversed by washing, with 50% blockade occurring in 15-90 min. Muscle contractures to exogenous acetylcholine and KCl were unaffected by the venom, but there was a slight increase in creatine kinase release after 60 min [IU/ml: from 80 ± 15 (basal) to 113 ± 22; n = 6; p > 0.05]. In mouse phrenic nerve-diaphragm preparations (PND), the venom (1, 10 and 30 ?g/ml) produced marked facilitation (~120% increase above basal) at the highest concentration followed by neuromuscular blockade; the effects at lower concentrations were considerably less marked. The venom increased quantal content values after 15 and 30 min followed by significant inhibition at ?90 min. However, the venom did not alter the muscle membrane resting potential or the response to exogenous carbachol. In both preparations, incubation at 22 °C instead of 37 °C delayed the onset of blockade, as did inhibition of venom PLA2 activity. In curarized mouse preparations, the venom produced only muscle facilitation. These results indicate that B. b. smaragdina venom causes neuromuscular blockade in vitro by a presynaptic mechanism involving PLA2. It was also investigated the neuromuscular activity of Bbil-TX, a PLA2 with catalytic activity isolated from B. b. smaragdina venom, in BC and PND preparations. In BC preparations, Bbil-TX (35-702 nM) caused time- and concentration-dependent blockade that was not reversed by washing; the times for 50% blockade were 87 ± 7, 41 ± 7 and 19 ± 2 min (mean ± SEM; n = 4-6) for 70, 351 and 702 nM, respectively. Muscle contractures to exogenous ACh and KCl were unaffected. The toxin (702 nM) also did not affect the twitch-tension of directly stimulated, curarized (d-Tc, 14.8 ?M) BC preparations. However, Bbil-TX (702 nM) produced mild morphological alterations (edematous and/or hyperchromic fibers) in BC; there was also a progressive release of CK [IU/ml: from 116 ± 17 (basal) to 961 ± 48 after 60 min; n = 6; p < 0.05]. Bbil-TX (351 nM)-induced blockade was markedly inhibited at 22-24 °C and pretreatment with p-BPB abolished the neuromuscular blockade. Bbil-TX (210 nM, 702 nM and 2 ?M; n = 4-6) caused partial time- and concentration-dependent blockade in PND preparations (52 ± 2% at the highest concentration). Bbil-TX (2 ?M) markedly reduced the MEPPs frequency/min [from 26 ± 2.5 (basal) to 10 ± 1 after 60 min; n = 5; p < 0.05] and the quantal content [from 94 ± 14 (basal) to 24 ± 3 after 60 min; n = 5; p < 0.05] of PND preparations, but caused only minor depolarization of the membrane resting potential [from -80 ± 1 mV (basal) to -66 ± 2 mV after 120 min; n = 5; p < 0.05], with no significant change in the depolarizing response to exogenous carbachol. These results show that Bbil-TX is a presynaptic PLA2 that contributes to the neuromuscular blockade caused by B. b. smaragdina venom. The neuromuscular activity of B. b. smaragdina venom and the mechanism of action of Bbil-TX on peripheral nervous system have been further examined in mouse nerve-muscle preparations in vitro. In PND preparations maintained in low Ca2+ physiological salt solution (PSS), B. b. smaragdina venom (3 ?g/ml) caused a triphasic change in twitch height while the xv highest concentration (10 ?g/ml) produced an abrupt and marked initial contracture which was followed by neuromuscular facilitation, rhythmic oscillation of nerve evoked twitch, alteration in base line and progressive blockade. The venom also slowed the relaxation phase of the muscle twitch increasing the constant decay time. Under low Ca2+ conditions, Bbil-TX caused a progressive increase in twitch amplitude (83 ± 19 % above basal values after 120 min) in PND preparations; there was no change in the constant decay time after treatment with toxin. B. b. smaragdina venom (10 ?g/ml) and Bbil-TX (210 nM) caused minor changes in the amplitude of the compound action potential (CAP) recorded from SN preparations (venom: 20 ± 2.1 % and toxin: 17 ± 2.4 % of reduction below basal values; n = 3; p < 0.05) and no significant effect on rise time and latency; tetrodotoxin (3.1 M) blocked the CAP at the end of the experiments. In TSn-m preparations, both venom (10 ?g/ml) and Bbil-TX (210 nM) caused significant reduction in the perineural waveform associated with the outward K+ current (venom: 35 ± 7.2 % and toxin: 26 ± 1.4 % of reduction below basal values; p < 0.05; n = 3-5) while the amplitude of the inward Na+ current was not significantly affected (venom: 18 ± 3.3 % and toxin: 15 ± 2.4 % of reduction below basal values; p > 0.05; n = 3-5). Bbil-TX (210 nM) caused progressive increase in quantal content in TSn-m preparations maintained in low Ca2+ PSS [from 9.6 ± 1.1 (t0) to 31.4 ± 7.7 (t60), p < 0.05; n = 4]. Venom (3 ?g/ml) and toxin (210 nM) induced increase in calcium fluorescence in neuroblastoma cell line SK-N-SH loaded with calcium sensitive indicator Fluo3 AM (4 ?M) and maintained in low Ca2+ or normal Ca2+ PSS. In those cells maintained in normal Ca2+ PSS, the increase in fluorescence amplitude was accompanied by irregular and frequent calcium transients. In TSn-m preparations loaded with Fluo4 AM (4 ?M), B. b. smaragdina venom (10 ?g/ml) caused immediate increase in Ca2+ intracellular of muscle fibres followed by frequent oscillation in fluorescence and muscle contracture; Bbil-TX did not induce any change in calcium fluorescence in TSn-m preparations. Immunohistochemical sections of PND preparations pretreated with Bbil-TX (210 nM) were labeled positively for junctional ACh receptors but there was loss of labeling for presynaptic proteins synaptophysin and SNAP25. Together, these data indicate that Bbil-TX has high selectivity of action under the presynaptic region similarly as other PLA2 neurotoxins modulating the neuromuscular activity of B. b. smaragdina venom / Doutorado / Farmacologia / Doutor em Farmacologia