Au cours des dernières décennies, la méthylation de l'ADN en position 5 de la cytosine est apparue comme une importante modification épigénétique qui joue un rôle essentiel dans le contrôle spécifique de l'expression des gènes. Cependant, les mécanismes impliqués dans la régulation de la méthylation de l'ADN restent incompris. Des études récentes ont montré que des protéines de type oxydases, nommées TET, peuvent catalyser l'oxydation de la 5-méthylcytosine (5mC) et générer des dérivés oxydés de celle-ci ce qui soulève la question du rôle biologique des formes oxydées de la 5mC. L'identification et la caractérisation des protéines interagissant avec ces formes oxydées devraient permettre une meilleure compréhension de la fonction de ces modifications de l'ADN et de la régulation de la méthylation de l'ADN. Dans ce projet, nous avons développé des sondes photoactivables basées sur l'ADN pour capturer, isoler et caractériser les protéines associées à ces modifications épigénétiques de l'ADN. Tout d'abord, nous avons conçu et évalué les propriétés de différentes sondes oligonucléotidiques photoactivables. Nous avons ensuite réalisé une étude méthodologique afin de caractériser au niveau moléculaire les photoadduits obtenus par MALDI-TOF. Enfin, nous avons développé une méthode de pull-down couplé à du photomarquage et associée à une analyse protéomique par spectrométrie de masse afin d’identifier les protéines ayant une affinité spécifique pour ces modifications épigénétiques. / Over the past few decades, DNA methylation at the 5-position of cytosine has emerged as an important epigenetic modification that plays essential roles in the specific control of gene expression. However, the mechanisms involved in the regulation of DNA methylation remain unclear. Recent studies have shown that oxidase proteins, called TETs, can catalyze the oxidation of 5-methylcytosine (5 mC) and generate oxidized derivatives thereof, raising the question of the biological role of the oxidized forms of 5mC. The identification and characterization of proteins interacting with these oxidized forms should allow for a better understanding of the function of these DNA modifications and the regulation of DNA methylation.In this project, we develop DNA-based photoactivatable probes to capture, isolate and characterize the proteins associated with these epigenetic DNA modifications. First, we designed and evaluated the properties of different photoactivatable oligonucleotide probes. We then carried out a methodological study in order to characterize at the molecular level the obtained photoadducts by MALDI-TOF. Finally, we developed a pull-down method coupled to photolabelling and associated with proteomic analysis by mass spectrometry to identify proteins with specific affinity for these epigenetic changes.

Recent bioinformatic analyses identified an operon encoding a potential Type I Secretion System (T1SS) in Treponema pallidum that we hypothesize functions to export key treponemal virulence factors that may contribute to the unique invasiveness and pathogenesis of this spirochete. The membrane fusion protein component (MFP) of T1SSs in other organisms has been shown to play a role in substrate recognition. Hence, the objective of this project is to use the putative MFP, Tp0965, of the potential T. pallidum T1SS to investigate protein-protein interactions with the T. pallidum virulence factor pallilysin (Tp0751) and assess the possibility of the latter being a T1SS substrate. Moreover, protein-protein interactions between Tp0965 and a Treponema phagedenis lysate are investigated with the goal of identifying putative T1SS substrates in this spirochete that could result in the discovery of novel T. pallidum virulence factors via amino acid sequence similarity. Plate-based binding studies and pull-down assays showed a low level of interaction between recombinant Tp0965 and the previously characterized host-component-binding protease, pallilysin, suggesting that the export of this virulence factor could occur via the putative T1SS. Additionally, bioinformatic analyses of the related but cultivable model spirochete T. phagedenis predicted the presence of a potential T1SS homologous to the putative T1SS in T. pallidum. Thus, a more global and unbiased pull-down assay using “bait” Tp0965 and a “prey” T. phagedenis lysate was carried out, followed by mass spectrometric analysis to identify putative novel T1SS substrates with potential homologs in T. pallidum. We successfully identified a T. phagedenis protein, TphBIg, that showed evidence of an interaction with Tp0965. TphBIg seems to possess characteristics of a T1SS substrate suggesting it may be secreted via this system in T. phagedenis. Upon bioinformatic analysis, it was found that TphBIg showed weak amino acid sequence similarity as well as some structural similarity to the T. pallidum protein, Tp0854. Tp0854 is predicted to contain a sialidase and a phosphatase domain with an RTX motif, which is characteristic of some T1SS substrates. Thus, it was hypothesized that if Tp0854 had characteristics of a T1SS, it may interact with Tp0965. Therefore, the phosphatase domain containing the RTX motif was produced recombinantly and plate-based binding studies indeed suggested an interaction with Tp0965, confirming the in silico-predicted interaction. Future experiments to characterize the potential T1SS and substrates in T. pallidum could comprise the functional and structural characterization of the novel putative T1SS substrate, Tp0854. This would include assays to investigate the putative sialidase and phosphatase activities of Tp0854, as well as the identification of Tp0854-Tp0965 interacting sites. Moreover, as a more definite test for T1SS substrate secretion, T. pallidum pallilysin and/or Tp0854 could be expressed heterologously in an E. coli strain harbouring an endogenous T1SS and test for secretion. Similarly, the reconstitution of the T. pallidum putative T1SS in liposomes could be used to further investigate the secretion of pallilysin and/or Tp0854 via this system. Additionally, the optimized unbiased pull-down technique could be further applied to detect more protein-protein interactions within T. pallidum and potentially lead to the identification of more virulence factors that may be secreted via the T1SS. These studies constitute the first investigation of a putative T1SS and substrates within T. pallidum. Thus, insight gained will lead to a better understanding of the mechanisms facilitating T. pallidum host invasion and may reveal new potential vaccine targets to prevent bacterial dissemination and chronic infection. / Graduate

Au niveau mondial, la tuberculose est toujours l’une des dix premières causes de mortalité. L’un des principaux facteurs expliquant ce phénomène est l'émergence de souches du bacille tuberculeux, Mycobacterium tuberculosis, résistantes aux antibiotiques. Ainsi, l’OMS a déclaré prioritaire le développement d'une nouvelle génération d’antituberculeux qui soient efficaces contre les souches résistantes. Des études de criblage phénotypique récentes sur M. tuberculosis ont montré que des voies métaboliques de composés de l’enveloppe, telles que la biosynthèse des acides mycoliques, représentent des cibles thérapeutiques très pertinentes. Les acides mycoliques entrent dans la composition de facteurs de pathogénicité lipidiques du bacille tuberculeux. Ils portent divers types de fonctions chimiques déterminantes pour leurs rôles biologiques. Le système Fatty Acid Synthase de type II (FAS-II) impliqué dans leur biosynthèse constitue une cible thérapeutique validée. En effet, il est essentiel à la survie du bacille, possède des caractéristiques uniques, et a un rôle-clé dans sa virulence et sa persistance chez les organismes infectés. De plus, le système FAS-II est la cible de plusieurs médicaments antituberculeux tels que l’isoniazide et l’éthionamide. FAS-II est constitué d'un ensemble d'enzymes monofonctionnelles acyl carrier protein (ACP)-dépendantes. Une partie de ces protéines a été identifiée par des approches de génomique classique. Malgré cela, 20 ans après le séquençage du génome de M. tuberculosis, la composition complète de ce système ainsi que sa fonction précise restent encore à caractériser. L’objectif des travaux de recherche menés durant ma thèse est de caractériser le système FAS-II mycobactérien selon un nouvel angle d'attaque, à l'échelle du système entier. L'approche adoptée visait à i) développer et valider des méthodes expérimentales pour isoler le système FAS-II sous une forme la plus complète possible, ii) décrypter en profondeur la composition en protéines de FAS-II (collaboration équipe O. Schiltz, IPBS) ; iii) identifier de nouvelles enzymes partenaires potentielles. La 1ère partie de ce travail a consisté à mettre au point l'isolement du système FAS-II de deux mycobactéries, M. smegmatis, une espèce-modèle à croissance rapide, et M. bovis BCG, la souche vaccinale très proche de M. tuberculosis. Deux stratégies complémentaires ont été développées : la co-immunoprécipitation et la Single Step Affinity Purification (SSAP). Plusieurs enzymes du système FAS-II ont été utilisées alternativement comme appâts pour co-purifier des protéines partenaires. De nombreux paramètres ont été optimisés afin d'améliorer le taux d'enrichissement en FAS-II et de conserver le plus possible l’intégrité du système : nature de la protéine-appât, délétion du gène endogène (SSAP), conditions de lyse des bactéries, pontage chimique, étapes de purification... La 2ème partie de ma thèse a porté sur l'analyse par protéomique des fractions de purification obtenues et la 3ème partie a consisté à identifier de nouvelles enzymes partenaires. Le traitement des données a permis 1) de mettre en évidence des interactions physiques entre certaines enzymes du système FAS-II ; 2) de démontrer la présence d’une nouvelle enzyme partenaire du système : cette protéine, nommée HadD, est potentiellement impliquée dans l’une des étapes-clés de la biosynthèse des acides mycoliques nécessaire pour l’introduction des groupements fonctionnels sur ces lipides. / Globally, tuberculosis is still one of the top ten leading causes of death. In 2015, the World Health Organization (WHO) reported nearly 480,000 new cases of multidrug-resistant tuberculosis and called for the development of new antituberculosis agents. Recent phenotypic screening studies on Mycobacterium tuberculosis have shown that envelope metabolic pathways, such as mycolic acid biosynthesis, are highly relevant therapeutic targets. Mycolic acids constitute the lipid moiety of pathogenicity factors of the tubercle bacillus. They are essential mycobacterial fatty acids holding various chemical functions decisive for their biological roles. The Fatty Acid Synthase type II (FAS-II) system involved in their biosynthesis is a relevant and validated therapeutic target. Indeed, it is essential to the survival of the bacillus, has unique features, and plays a key role in its virulence and persistence in infected organisms. In addition, the FAS-II system is the target of several antituberculosis drugs such as isoniazid and ethionamide. FAS-II is made of discrete monofunctional acyl carrier protein (ACP)-dependent proteins. Some of these proteins have been identified by conventional genomic approaches. However, 20 years after the M. tuberculosis genome sequencing, the complete composition of this system and its precise function remain poorly known. The objective of my PhD project is to characterize the mycobacterial FAS-II multienzyme system with a completely new line of attack, at the scale of the entire system. The adopted approach was aimed at i) developing and validating experimental methods to isolate the FAS-II system in the most complete form, ii) deciphering the FAS-II protein composition (collaboration with O. Schiltz's team, IPBS); iii) identifying potential new partner enzymes. The first part of this work consisted of developing the isolation of the FAS-II system from two mycobacteria, M. smegmatis, a fast-growing model species, and M. bovis BCG, the vaccine strain very close to M. tuberculosis. Two complementary strategies were developed: co-immunoprecipitation and Single Step Affinity Purification (SSAP). Several enzymes of the FAS-II system were used alternatively as a bait in an attempt to co-purify partner proteins. To improve the level of FAS-II enrichment and to preserve as much as possible the integrity of the system, many parameters were optimized: nature of the bait protein, endogenous gene deletion (SSAP), bacteria lysis conditions, chemical cross-link, purification steps… The second part of my thesis focused on the proteomics analysis of the purification fractions obtained and the third part consisted in identifying new partner enzymes. The data processing allowed: 1) to demonstrate the presence of physical interactions between some FAS-II system enzymes; 2) to demonstrate the presence of a new partner enzyme of the system: this protein, called HadD, is potentially involved in one of the key steps of the mycolic acid biosynthesis pathway necessary for the introduction of functional groups on these lipids. The results obtained thanks to the optimized co-immunoprecipitation and SSAP protocols have contributed to the knowledge of the mycobacterial FAS-II system and bring promising leads for the discovery of new partner enzymes.

This bachelor thesis examines how a user can experience different color combinations and how those effect a navigation menu on a website. This with regards on the users first impression. Furthermore, were also different contrasts examined. This thesis also investigates how a navigation menu is being perceived on the basis that it is more appealing in its design, but lacks contrast, comparatively to a design that has strong contrast but do not satisfy the user. Moreover, if color combinations and its placement together with the contrast can increase the efficiency in a navigation process. The colors that were tested were blue and red. Three prototypes were designed which had different color and contrast combinations, but the main colors were blue and red. A qualitative method was being used to examine the impact colors and contrasts can have. An unstructured observation was applied to study the user’s behavior and which prototype was most effective. Moreover, was a think-aloud test where the users had to think-aloud. This method generated an understanding about users first impression and how effective the navigation menu was. Lastly, a semi-structured interview was applied to create a greater understanding about colors impact on the users. The results showed that color and contrast have a big influence on a user’s first impression, but also on a navigation menus’ effectiveness. A more appealing menu with low contrast was being preferred over a menu with high contrast but a less appealing design.

Syftet med projektet var att utveckla en multiplexanalys för att detektera antigen från SARS-CoV-2, influensa och respiratoriskt syncytial virus genom att använda en masspektrometrisk metod som involverar antigenspecifika bindare. Bindarna klonades, renades och biotinylerades innan de användes i en analys utvecklad genom en målinriktad metod som involverade antigenerna. En slutsats som drog var att det var möjligt för Avi-märkta bindare att specifikt binda antigen-härledda peptidmål i multiplexanalysen. / The purpose of project was to develop a multiplex assay capable of detecting antigens from SARSCoV-2, influenza and respiratory syncytial virus by utilizing a mass spectrometric approach involving antigen-specific binders. Binders were cloned, purified and biotinylated before being employed in an assay developed by though a targeted method involving the antigens. It was concluded to be possible for Avi-tagged binders to specifically bind antigen-derived peptide targets in the multiplex assay.

A causa mais frequente de surdez de herança autossômica recessiva são as mutações no lócus DFNB1, onde estão os genes GJB2 e GJB6. Dentre os indivíduos com deficiência auditiva associada a esse lócus, 10% a 50% apresentam uma única mutação recessiva no gene GJB2, frequência muito superior à esperada em função da frequência de heterozigotos na população geral. Apesar de alguns desses casos terem sido elucidados após a identificação de grandes deleções no gene GJB6 ou nas suas proximidades, a existência de muitos indivíduos com uma única mutação patogênica no gene GJB2 sugere que a haplo-insuficiência nesse gene possa interagir com outras mutações no mesmo gene, no gene GJB6 vizinho, ou até em outros genes. O objetivo desse estudo foi identificar novos alelos patogênicos, novas proteínas e novos genes que interagem com o lócus DFNB1, do ponto de vista molecular e celular, e que possam ser responsáveis por surdez de herança autossômica recessiva. Desse modo, pretendemos contribuir para o esclarecimento da patogênese da surdez de herança autossômica recessiva. Nesse trabalho, três tipos de estudos foram realizados, com metodologias próprias. Na primeira parte, buscamos identificar novos alelos patogênicos no lócus DFNB1 que poderiam ser responsáveis por surdez quando presentes em heterozigose composta com outros alelos patogênicos nos genes GJB2 e GJB6. Foi realizada a análise do DNA de 16 pacientes surdos portadores de uma única mutação patogênica em um desses dois genes por meio: (i) do sequenciamento das regiões codificadora, promotora e doadora de splicing (intron 1) do gene GJB2, (ii) da triagem de uma deleção de 200 kb localizada a 130 kb da proximidade distal da região 5\' do gene GJB6 e (iii) da pesquisa de variações no número de cópias de um ou mais exons dos genes GJB2, GJB6, GJB3 e WFS1 por MLPA (Multiplex Ligation-dependent Probe Amplification). Detectamos uma segunda mutação provavelmente patogênica em dois dos 16 pacientes heterozigotos: em um deles, a mutação p.L76P (c.C227T) foi identificada na região de código do gene GJB2 e foi por nós descrita pela primeira vez; no segundo caso, uma duplicação (0,4-1,2Kb) que inclui a região de código do gene GJB2 foi detectada, também inédita na literatura. Na segunda parte, tivemos como objetivo obter um modelo experimental para estudos funcionais in vitro da proteína codificada pelo gene GJB2, a conexina 26, em seu local de expressão que são as células de suporte do órgão de Corti. Padronizamos o cultivo in vitro de células progenitoras do órgão de Corti de camundongos e de cobaias e conseguimos obter a diferenciação in vitro das otoesferas dos camundongos em células que expressam marcadores de células ciliadas (Miosina VIIa e Jagged2) e de células de suporte (p27kip e Jagged1). Por fim, na terceira parte, buscamos por proteínas que interagem com a conexina 26 por meio de ensaios de precipitação por afinidade. Para isso, produzimos clones recombinantes de uma proteína de fusão GST-Cx26 e de uma proteína controle (GST), e realizamos sua expressão in vitro em bactérias E.coli B21. Ensaios de precipitação por afinidade entre a proteína de fusão GST-Cx26 ou GST sozinha e proteínas extraídas de cérebro ou fígado de camundongos foram realizados em diferentes condições. A identificação e a análise das proteínas presentes em bandas de SDS-PAGE, obtidas no ensaio de precipitação com a proteína de fusão GST-Cx26 e ausentes no ensaio com a GST, foram realizadas por espectrometria de massas. Identificamos um total de 49 proteínas candidatas a interagirem com a região C-terminal da Cx26. Realizamos diversas análises in silico e em literatura específica e após exclusão de candidatas por: (i) redundância de representação no ensaio GST-Cx26, (ii) diferença entre a massa molecular esperada e a obtida, (iii) precipitação inespecífica e (iv) localização subcelular incompatível com a conexina 26, selecionamos um total de 22 proteínas candidatas a interagirem com a região C-terminal da conexina 26, para estudos futuros. A confimação da interação entre essas 22 proteínas e a conexina 26 é desejável por meio de estudos de co-localização e imuno-coprecipitação / The most frequent causes of nonsyndromic recessive hearing loss are mutations in locus DFNB1, in the GJB2 and GJB6 genes. Among the individuals with hearing loss with mutations in this locus, 10% to 50% present a single recessive mutation in the GJB2 gene, frequency much higher than expected taking into account the frequency of heterozygotes in the general population. Although some of these cases have been elucidated after the identification of large deletions in GJB6 or its surrounding regions, the existence of many individuals with a single pathogenic mutation in the GJB2 gene suggests that haplo-insufficiency of this gene may interact with other types of mutations in the same gene, in the neighbor gene GJB6, or even in other genes. The aim of this study was to identify new pathogenic alleles, proteins and genes that interact with the locus DFNB1, from the molecular and cellular perspective, and that may be responsible for autosomal recessive deafness. Thus, we aimed to contribute to the understanding of the pathogenesis of autosomal recessive deafness. In this work, three different types of studies were performed, each one with a particular methodology. In the first part, we searched for new pathogenic alleles in the locus DFNB1 that could be responsible for deafness, when present in compound heterozygosis with other pathogenic alleles in GJB2 and GJB6 genes. We performed DNA analysis in samples from 16 deaf patients, carriers of a single pathogenic mutation in one of these two genes by: (i) sequencing the coding, promoter and splice donor (intron 1) regions of the GJB2 gene, (ii) screening for a deletion of 200 kb located 130 kb upstream from GJB6 gene and (iii) investigating copy number variations in of one or more exons of the genes GJB2, GJB6, GJB3 and WFS1 by MLPA (Multiplex Ligation-dependent Probe Amplification). We detected a second mutation, probably pathogenic, in two of the 16 heterozygous patients: in one case, the p.L76P (c.C227T) mutation was identified in the coding region of the GJB2 gene and was firstly described by us; in the second case, a novel duplication (0.4 - 1.2 Mb) that includes the coding region of the GJB2 gene was detected. In the second part, our objective was to obtain an experimental model for in vitro functional studies of the protein encoded by the GJB2 gene, connexin 26, in its site of expression, that is, in the supporting cells of the organ of Corti. We standardized the culturing of guinea pigs and mice progenitor cells of organ of Corti. We were also able to induce differentiation of mice\'s otospheres into cells that express markers of hair (myosin VIIa and Jagged2) and supporting cells (p27kip and Jagged1). Finally, we searched for connexin 26 interacting proteins by pull-down assays. Recombinant clones expressing a fusion protein GST-Cx26 and a control protein (GST) were produced, so that in vitro expression in E. coli B21 could be performed. Pull-down experiments, perfomed with fusion protein GST-Cx26 or GST alone, and with proteins from mice brain or liver extracts were done under several different conditions. The identification and analysis of proteins present in SDS-PAGE bands in experiments performed with the fusion protein GST-Cx26, and absent in the GST assay, were performed by mass spectrometry. We identified a total of 49 candidate proteins for interaction with the C-terminal region of Cx26. In silico analyses performed in several databases and search in the literature allowed exclusion of candidates by: (i) redundancy of representation in the GST-Cx26 experiments; (ii) discrepancy between the expected and the obtained molecular weight; (iii) nonspecific precipitation and (iv) subcellular localization incompatible with connexin 26 localization. Summing up, we selected a total of 22 candidate proteins to interact with the C-terminal region of connexin 26. Confirmation of the interaction between these proteins and connexin 26 is planned to be performed by co-localization studies and by immuno-coprecipitation

Submitted by IGOR HENRIQUE SENA DA SILVA null (igor.sena@outlook.com.br) on 2017-09-05T13:59:07Z No. of bitstreams: 1 DISSERTAÇÃO_Igor_Henrique_Sena_Silva.pdf: 1536012 bytes, checksum: da24e2e008037696caee4c8842fc8f05 (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-09-06T13:13:51Z (GMT) No. of bitstreams: 1 silva_ihs_me_jabo.pdf: 1536012 bytes, checksum: da24e2e008037696caee4c8842fc8f05 (MD5) / Made available in DSpace on 2017-09-06T13:13:51Z (GMT). No. of bitstreams: 1 silva_ihs_me_jabo.pdf: 1536012 bytes, checksum: da24e2e008037696caee4c8842fc8f05 (MD5) Previous issue date: 2017-07-26 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Helicoverpa armigera é uma praga altamente polífaga e ataca culturas de grande importância agrícola em diversos países do mundo. O controle desta praga é realizado primariamente por inseticidas químicos. Porém, o uso indiscriminado do controle químico levou a resistência de populações desta praga a maioria dos inseticidas químicos usados para seu controle, dificultando o seu manejo no campo. Além do controle químico, o controle de H. armigera tem sido realizado com uso de plantas transgênicas que expressam a proteína Cry1Ac de Bacillus thuringiensis (Bt) ou por bioinseticidas que contem esta e outras proteínas. No entanto, estudos têm demonstrado uma diminuição significativa na susceptibilidade de H. armigera às proteínas Cry com o aumento de seu desenvolvimento larval. O mecanismo de resistência mais comum dos insetos às proteínas Cry é a redução de ligação da proteína aos receptores presentes na membrana, levando a uma menor afinidade de ligação da proteína aos receptores intestinais. Desta forma, o objetivo deste trabalho foi avaliar a susceptibilidade de lagartas de diferentes ínstares de H. armigera à Cry1Ac e correlacionar com a capacidade de ligação da proteína Cry1Ac às microvilosidades apicais das células colunares do intestino médio (BBMVs) isoladas de todos ínstares larvais. Além disso, por meio de ensaios de imunoprecipitação e análise por cromatografia líquida acoplada a espectrofotometria de massa, identificar as proteínas envolvidas na interação com a proteína Cry1Ac no segundo e quinto ínstares de H. armigera. Foi observada uma redução significativa na susceptibilidade dos últimos ínstares larvais de H. armigera à proteína Cry1Ac comparado aos ínstares iniciais. Os valores estimados de CL50 variaram de 31,1 a 2525,7 ng de proteína/cm² de dieta, em lagartas de primeiro e sexto ínstar, respectivamente. Estes resultados evidenciam uma diferença de 80 vezes na susceptibilidade à proteína Cry1Ac do último para o primeiro ínstar. Nos testes de ligação de ELISA da proteína Cry1Ac às BBMVs dos diferentes ínstares, foi constatada uma diminuição total na capacidade de ligação da proteína Cry1Ac as BBMVs dos estádios mais tardios comparados aos iniciais, com afinidade de ligação aparente de 3,88 vezes menor no último ínstar comparado ao primeiro. Assim, uma clara correlação direta entre toxicidade de Cry1Ac e a afinidade de ligação da proteína às BBMVs de H. armigera foi demonstrada. Os resultados dos ensaios de imunoprecipitação demonstraram um padrão diferenciado de interação com a proteína Cry1Ac no segundo e quinto ínstar. A proteína fosfatase alcalina (ALP) foi identificada apenas no segundo ínstar, bem como, outras proteínas de membrana, como proibitina e uma proteína de canal iônico, que podem estar envolvidas para a alta toxicidade de Cry1Ac em ínstares iniciais de H. armigera. A identificação e o papel funcional das proteínas de ligação nos diferentes estádios de desenvolvimento de H. armigera, facilitará a elucidação do mecanismo de ação da proteína Cry1Ac e poderá ajudar a propor estratégias que retardem a evolução da resistência dos insetos às cultivares transgênicas que expressam esta proteína. / Helicoverpa armigera is a highly polyphagous pest and attacks important crops worldwide. The control of this pest is carried out primarily by chemical insecticides. However, the indiscriminate use of chemical control, led to pest populations to develop resistance to most of the chemical insecticides used for their control, making it difficult to management in the field. In addition to chemical control, H. armigera has been done by transgenic crops expressing Cry1Ac toxin from Bacillus thuringiensis (Bt) or by biopesticides that contains Cry1Ac or other toxins. However, studies have demonstrated a susceptibility decrease of H. armigera to Cry toxins with their larval development increase. The most common mechanism of resistance used by insects against Cry toxins is the reduced toxin binding to receptors present on the membrane, leading to a lower binding affinity of the toxin to intestinal receptors. Thus, the objective of this work was to evaluate the susceptibility of different instar larvae of H. armigera to Cry1Ac toxin and to correlate with the Cry1Ac toxin binding capacity to BBMV isolated from all larval instar. Furthermore, by pull-down techniques and liquid chromatography coupled to mass spectrometry analysis, to identify the proteins involved in the Cry1Ac toxin interaction in the second and fifth instars of H. armigera. A significant reduction in the susceptibility of the late instars of H. armigera to Cry1Ac toxin was observed compared to early instars. LC50 estimated values ranged from 31.1 to 2525.7 ng of toxin/cm2 of diet in first and sixth instar larvae, respectively. These results point a difference of 80-fold in the susceptibility to Cry1Ac toxin from late to first larval instar. In the ELISA binding assays results to BBMV of the different instars was found a total decrease in the binding capacity of Cry1Ac toxin to BBMVs from late instars compared to BBMV from early instars, presenting an apparent binding affinity of 3.88 times lower in the last instars than the first. Thus, a clearly correlation between Cry1Ac toxicity and binding toxin affinity to H. armigera BBMV has been demonstrated. The pull-down assays demonstrated a different pattern of the interaction between Cry1Ac toxin with the second and fifth instars. The protein phosphatase alkaline (ALP) was identified only in the second instar, as well as, other membrane proteins, as prohibitin and an ion channel protein, which may be involved for higher toxicity of Cry1Ac in early instars of H. armigera. The identification and functional role of binding proteins in the different stages of development of H. armigera will facilitate the elucidation of the Cry1Ac toxin mechanism of action and will may help to propose strategies that delay the insect resistance evolution to transgenic crops that express this protein. / FAPESP: 2015/24330-5

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O Vírus da Imunodeficiência Humana (HIV) é o agente etiológico da Síndrome da Imunodeficiência Adquirida (AIDS). A AIDS é uma doença de distribuição mundial, e estima-se que existam atualmente pelo menos 36,9 milhões de pessoas infectadas com o vírus. Durante o seu ciclo replicativo, o HIV promove diversas alterações na fisiologia da célula hospedeira a fim de promover sua sobrevivência e potencializar a replicação. A rápida progressão da infecção pelo HIV-1 em humanos e em modelos animais está intimamente ligada à função da proteína acessória Nef. Dentre as diversas ações de Nef está a regulação negativa de proteínas importantes na resposta imunológica, como o receptor CD4. Sabe-se que esta ação resulta da indução da degradação de CD4 em lisossomos, mas os mecanismos moleculares envolvidos ainda são totalmente elucidados. Nef forma um complexo tripartite com a cauda citosólica de CD4 e a proteína adaptadora 2 (AP-2), em vesículas revestidas por clatrina nascentes, induzindo a internalização e degradação lisossomal de CD4. Pesquisas anteriores demonstraram que o direcionamento de CD4 aos lisossomos por Nef envolve a entrada do receptor na via dos corpos multivesiculares (MVBs), por um mecanismo atípico, pois, embora não necessite da ubiquitinação de carga, depende da ação de proteínas que compõem os ESCRTs (Endosomal Sorting Complexes Required for Transport) e da ação de Alix, uma proteína acessória da maquinaria ESCRT. Já foi reportado que Nef interage com subunidades dos complexos AP-1, AP-2, AP-3 e Nef não parece interagir com subunidades de AP-4 e AP-5. Entretanto, o papel da interação de Nef com AP-1 e AP-3 na regulação negativa de CD4 ainda não está totalmente elucidado. Ademais, AP-1, AP-2 e AP-3 são potencialmente heterogêneos devido à existência de isoformas múltiplas das subunidades codificadas por diferentes genes. Todavia, existem poucos estudos para demonstrar se as diferentes combinações de isoformas dos APs são formadas e se possuem propriedades funcionais distintas. O presente trabalho procurou identificar e caracterizar fatores celulares envolvidos na regulação do tráfego intracelular de proteínas no processo de regulação negativa de CD4 induzido por Nef. Mais especificamente, este estudo buscou caracterizar a participação do complexo AP-1 na modulação negativa de CD4 por Nef de HIV-1, através do estudo funcional das duas isoformas de ?-adaptina, subunidades de AP-1. Utilizando a técnica de Pull-down demonstramos que Nef é capaz de interagir com ?2. Além disso, nossos dados de Imunoblot indicaram que a proteína ?2-adaptina, e não ?1-adaptina, é necessária no processo de degradação lisossomal de CD4 por Nef e que esta participação é conservada para degradação de CD4 por Nef de diferentes cepas virais. Ademais, por citometria de fluxo, o silenciamento de ?2, e não de ?1, compromete a diminuição dos níveis de CD4 por Nef da membrana plasmática. A análise por imunofluorêsncia indireta também revelou que a diminuição dos níveis de ?2 impede a redistribuição de CD4 por Nef para regiões perinucleares, acarretando no acúmulo de CD4, retirados por Nef da membrana plasmática, em endossomos primários. A depleção de ?1A, outra subunidade de AP-1, acarretou na diminuição dos níveis celulares de ?2 e ?1, bem como, no comprometimento da eficiente degradação de CD4 por Nef. Além disso, foi possível observar que, ao perturbar a maquinaria ESCRT via super-expressão de HRS (uma subunidade do complexo ESCRT-0), ocorreu um acumulo de ?2 em endossomos dilatados contendo HRS-GFP, nos quais também detectou-se CD4 que foi internalizado por Nef. Em conjunto, os resultados indicam que ?2-adaptina é uma importante molécula para o direcionamento de CD4 por Nef para a via ESCRT/MVB, mostrando ser uma proteína relevante no sistema endo-lisossomal. Ademais, os resultados indicaram que as isoformas ?-adaptinas não só possuem funções distintas, mas também parecem compor complexos AP-1 com diferentes funções celulares, já que apenas a variante AP-1 contendo ?2, mas não ?1, participa da regulação negativa de CD4 por Nef. Estes estudos contribuem para o melhor entendimento dos mecanismos moleculares envolvidos na atividade de Nef, que poderão também ajudar na melhor compreensão da patogênese do HIV e da síndrome relacionada. Em adição, este trabalho contribui para o entendimento de processos fundamentais da regulação do tráfego de proteínas transmembrana no sistema endo-lisossomal. / The Human Immunodeficiency Virus (HIV) is the etiologic agent of Acquired Immunodeficiency Syndrome (AIDS). AIDS is a disease which has a global distribution, and it is estimated that there are currently at least 36.9 million people infected with the virus. During the replication cycle, HIV promotes several changes in the physiology of the host cell to promote their survival and enhance replication. The fast progression of HIV-1 in humans and animal models is closely linked to the function of an accessory protein Nef. Among several actions of Nef, one is the most important is the down-regulation of proteins from the immune response, such as the CD4 receptor. It is known that this action causes CD4 degradation in lysosome, but the molecular mechanisms are still incompletely understood. Nef forms a tripartite complex with the cytosolic tail of the CD4 and adapter protein 2 (AP-2) in clathrin-coated vesicles, inducing CD4 internalization and lysosome degradation. Previous research has demonstrated that CD4 target to lysosomes by Nef involves targeting of this receptor to multivesicular bodies (MVBs) pathway by an atypical mechanism because, although not need charging ubiquitination, depends on the proteins from ESCRTs (Endosomal Sorting Complexes Required for Transport) machinery and the action of Alix, an accessory protein ESCRT machinery. It has been reported that Nef interacts with subunits of AP- 1, AP-2, AP-3 complexes and Nef does not appear to interact with AP-4 and AP-5 subunits. However, the role of Nef interaction with AP-1 or AP-3 in CD4 down-regulation is poorly understood. Furthermore, AP-1, AP-2 and AP-3 are potentially heterogeneous due to the existence of multiple subunits isoforms encoded by different genes. However, there are few studies to demonstrate if the different combinations of APs isoforms are form and if they have distinct functional properties. This study aim to identify and characterize cellular factors involved on CD4 down-modulation induced by Nef from HIV-1. More specifically, this study aimed to characterize the involvement of AP-1 complex in the down-regulation of CD4 by Nef HIV-1 through the functional study of the two isoforms of ?-adaptins, AP-1 subunits. By pull-down technique, we showed that Nef is able to interact with ?2. In addition, our data from immunoblots indicated that ?2- adaptin, not ?1-adaptin, is required in Nef-mediated targeting of CD4 to lysosomes and the ?2 participation in this process is conserved by Nef from different viral strains. Furthermore, by flow cytometry assay, ?2 depletion, but not ?1 depletion, compromises the reduction of surface CD4 levels induced by Nef. Immunofluorescence microscopy analysis also revealed that ?2 depletion impairs the redistribution of CD4 by Nef to juxtanuclear region, resulting in CD4 accumulation in primary endosomes. Knockdown of ?1A, another subunit of AP-1, resulted in decreased cellular levels of ?1 and ?2 and, compromising the efficient CD4 degradation by Nef. Moreover, upon artificially stabilizing ESCRT-I in early endosomes, via overexpression of HRS, internalized CD4 accumulates in enlarged HRS-GFP positive endosomes, where co-localize with ?2. Together, the results indicate that ?2-adaptin is a molecule that is essential for CD4 targeting by Nef to ESCRT/MVB pathway, being an important protein in the endo-lysosomal system. Furthermore, the results indicate that ?-adaptins isoforms not only have different functions, but also seem to compose AP-1 complex with distinct cell functions, and only the AP-1 variant comprising ?2, but not ?1, acts in the CD4 down-regulation induced by Nef. These studies contribute to a better understanding on the molecular mechanisms involved in Nef activities, which may also help to improve the understanding of the HIV pathogenesis and the related syndrome. In addition, this work contributes with the understanding of primordial process regulation on intracellular trafficking of transmembrane proteins.