Orientador: Marcelo Brocchi / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-20T14:46:42Z (GMT). No. of bitstreams: 1 Milanez_GuilhermePaier_M.pdf: 1651986 bytes, checksum: 4681c88f937b4fe6f4d915fce0eb3f20 (MD5) Previous issue date: 2012 / Resumo: A Salmonelose e a malária são duas doenças infecciosas negligenciadas de grande prevalência no mundo, mas acometendo particularmente populações humanas que vivem em regiões e países subdesenvolvidos ou em desenvolvimento. Apesar dos esforços ainda não existem formulações vacinais totalmente efetivas no controle destas enfermidades. Desta forma, nosso grupo tem buscado aprimorar a expressão do Domínio M2 do antígeno MAEBL de Plasmodium yoelii, que apresenta similaridade com a proteína de Plasmodium falciparum, em linhagens de Salmonella enterica Typhimurium, atenuadas para virulência. Em estudos prévios constatou-se que a expressão em níveis baixos não seria suficiente para a indução de uma resposta imune protetora. Com isso, ficou clara a necessidade de se aprimorar os níveis de expressão deste antígeno nas linhagens a serem testadas. Para tanto, o vetor de expressão anteriormente utilizado foi modificado, os codons da seqüência a ser expressa foram otimizados para expressão em salmonela e um sinal de secreção periplasmática foi adicionado no início da seqüência a ser expressa. Adicionalmente, modificamos novas linhagens atenuadas de S. enterica desenvolvidas por nosso grupo de tal forma a utiliza-las na expressão de antígenos heterólogos, empregando um sistema letal balanceado (Asd) de estabilização da expressão gênica. Apesar do sucesso na construção dos novos vetores, e da otimização de codons para a expressão, constatamos um possível efeito deletério do domínio M2 quando expresso em grande quantidade, o que impossibilitou a obtenção de algumas construções planejadas. Entretanto, os resultados obtidos na estabilização de plasmídios em novas linhagens vacinais significam um avanço no teste e uso de tais linhagens no desenvolvimento de vacinas multifatoriais / Abstract: Salmonellosis and malaria are two infectious diseases of high prevalence in the world, particularly affecting human populations living in underdeveloped regions and countries or developing countries. Despite several efforts, there is not a vaccinal formulation totally effective to control these diseases. This way, our group has sought to enhance the expression of M2 MAEBL's antigen Domain of Plasmodium yoelii, which is quite similar to same protein of P. falciparum, in attenuated strains of Salmonella enterica Typhimurium. In previous studies we found that the expression at low levels was not sufficient to induce a protective immune response. Thus, there was a clear need to improve M2 expression levels in the new strains to be tested. The expression vector previously used was modified, the m2 sequence was codon-optimized for expression in Salmonella, and a periplasmic secretion signal was added at the beginning of the sequence to be expressed. Additionally, new attenuated S. enterica strains developed by our group were modified in a way to use them in the expression of heterologous antigens, employing a balanced lethal system (ASD) for expression plasmid stabilization. Despite of the new vectors successfully built as well as codon optimization for m2 expression, we found a possible deleterious effect of the M2 domain when expressed in large quantities, making it impossible to obtain some planned constructs. However, the results obtained on stabilization of expression vectors in the new vaccine strains are an important advance for the use of such strains as multifactorial vaccines / Mestrado / Bioquimica / Mestre em Biologia Funcional e Molecular

Microsporidia are obligate intracellular eukaryotic parasites related to fungi, possessing greatly reduced genomic and cellular components. The microsporidian Nosema ceranae threatens honeybee (Apis mellifera) populations. Nosemosis has a complex epidemiology affected by host, pathogen and environmental factors. Although a draft of the N. ceranae genome has been published, the molecular basis underpinning pathogenicity is not known. The lack of established culturing techniques and a tractable genetic system necessitates use of model systems for both host and parasite such as Saccharomyces cerevisiae. I hypothesise effectors essential to disease progression exist amongst N. ceranae secretome genes. In this study I have started characterising these genes using a combination of established and novel techniques for studying microsporidia proteins including bioinformatics, heterologous expression in S. cerevisiae, and the genome-wide analysis platform of Synthetic Genetic Arrays. This effort has yielded new insights into N. ceranae secreted proteins which lack similarity to known sequences. I identified N. ceranae protein NcS77 as a candidate effector implicated in targeting host nuclear pores. NcS50 and NcS85 co-localise with ERG6 a marker for lipid droplets (an organelle known to be targeted by another obligate intracellular pathogen Chlamydia trachomatis) when expressed in S. cerevisiae. N. ceranae polar tube proteins (PTP) induce filament formation when expressed in S. cerevisiae and PTP2 co-localises with the cell wall. Interestingly this phenotype is replicated by another secreted protein which may infer a common function. Together these data contribute to knowledge on N. ceranae pathology bringing us closer to understanding the disease and ultimately lead the way to mitigation.

This thesis has been an attempt to observe the role antibodies play in extending the life span of tumor infected Akr mice.

Orientador: Luciana Gonzaga de Oliveira / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-22T05:28:22Z (GMT). No. of bitstreams: 1 Rampasio_RaquelRodrigues_M.pdf: 2052024 bytes, checksum: 07f4cd2fcba87af264e6efceab06d527 (MD5) Previous issue date: 2012 / Resumo: Epóxidos enantiopuros e dióis vicinais têm sido utilizados na síntese de inúeras moléculas bioativas. Dessa forma, as epóxido-hidrolases microbianas capazes de hidrolisar enantioseletivamente epóxidos racêmicos emergiram como uma alternativa promissora na obtenção destes compostos. Recentemente, a linhagem P. stipitis CCT 2617 foi selecionada por apresentar atividade hidrolítica frente a epóxidos terminais e teve seu genoma completo publicado. Assim, esta levedura foi selecionada para o trabalho de clonagem e expressão de sua epóxido hidrolase. Neste trabalho, a clonagem do gene SEH1, que codifica para a epóxido hidrolase de P. stipitis, foi efetuada com sucesso em P. pastoris, tanto no vetor pPICZa A, quanto no vetor pPICZ B. A clonagem da proteína com a cauda de histidina deve auxiliar na detecção da expressão. A detecção de uma banda, referente a uma proteína de 46 kDa, no gel de eletroforese foi um indício de que a expressão da enzima SEH (contendo o fator a) ocorreu, porém, não conseguimos reproduzir este resultado posteriormente. Além disso, buscamos melhores alternativas para a detecção da atividade enzimática, como o teste de adrenalina e o ensaio baseado em substrato fluorogênico, que devem ser aperfeiçoados para a utilização com células íntegras. A modelagem computacional da estrutura tridimensional da PSEH resultou em um modelo contendo 40% de hélices a e 12% de folhas b. Determinamos que os resíduos que devem fazer parte do sítio ativo são Tyr319, Asp209, Asp352 e His383 e, tendo em vista que a PSEH deve se apresentar na forma de um homodímero com sítio ativo similar ao das EHs de P. aeruginosa, A. radiobacter e A. niger, nossa hipótese é que esta enzima deve hidrolisar epóxidos pouco volumosos e aromáticos com algum nível de enantiosseletividade / Abstract: Enantiopure epoxides and vicinal diols have been used to prepare a number of bioactive molecules. Thus, the microbial epoxide hydrolases able to enantioselectivity hydrolyze racemic epoxides emerged as a promising alternative in the synthesis of these compounds. Recently, the P. stipitis CCT2617 strain was selected due to the presence of hydrolytic activity against terminal epoxides and had its genome completely described. Therefore, this yeast was selected for cloning and expression of the gene SEH1, which was annoted as epoxide hydrolase. In this work, the cloning of SEH1 gene, codifying for the epoxide hydrolase of P. stipitis, was done with success in P. pastoris, both in pPICZa A and pPICZ B vectors. The cloning of the protein with a histidine tag should help in the detection of expression. The detection of a protein with 46 kDa evidenced that the expression of SEH enzyme (containing the a factor) is occurring, however, this result was not reproducible due to the sample degradation. Furthermore, better alternatives for the detection of enzyme activity were performed, as adrenaline test and fluorogenic assay, which must be optimized for application with whole cells. The 3D structure computational modeling of PSEH resulted in a model that contains 40% of a helices and 12% of b sheets. Our hypothesis is that the residues that make part of the active site are Tyr319, Asp209, Asp352 and His 383. And, considering that the PSEH should be in the homodimeric form with an active site similar to that of the EHs of P. aeruginosa, A. radiobacter and A. niger, this enzyme should hydrolyze small and aromatic epoxides probably with some enantioselectivity / Mestrado / Quimica Organica / Mestre em Química

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-07-12T15:56:43Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Dissertação_Anna_Jessica_PPGG.pdf: 2035458 bytes, checksum: 6a4bc578c9eaea104302f33af03c3f21 (MD5) / Made available in DSpace on 2017-07-12T15:56:43Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Dissertação_Anna_Jessica_PPGG.pdf: 2035458 bytes, checksum: 6a4bc578c9eaea104302f33af03c3f21 (MD5) Previous issue date: 2016-03-04 / CNPQ / A infecção pelo Papilomavírus Humano, além de representar uma doença sexualmente transmissível altamente disseminada, é responsável por 5% dos cânceres em humanos, destacando o câncer cervical com altos índices de incidência e mortalidade. Embora comprovadamente eficazes, as vacinas vigentes não combatem infecções já estabelecidas e apresentam um elevado custo de produção. Esse cenário revela a necessidade de estratégias vacinais alternativas. O presente trabalho propõe a expressão de diferentes genes recombinantes em Escherichia coli, uma plataforma biotecnológica econômica, de fácil manipulação e de alto rendimento. Os genes recombinantes utilizados foram: L1 de HPV16 e construções quiméricas basedas na substituição de epítopos da oncoproteína E5 na alça h4 e na região C-terminal de L1, com potencial para geração de antígenos profiláticoterapêuticos e na substituição de epítopos da proteína L2 na região da alça h4 para avaliação de possível neutralização cruzada. Após subclonagem em pGEM-T, esses genes foram clonados em vetor de expressão pAE e linhagens de Escherichia coli BL21 e Rosetta foram transformadas com os vetores de expressão gerados. A confirmação da produção das proteínas se deu por Western blot, a partir de extratos de culturas induzidas com IPTG. Otimizações nos protocolos de indução, lise e preparo das amostras foram realizadas ao longo dos experimentos. Os resultados obtidos demonstraram a produção dos antígenos recombinantes, e deverão ser validados em futuros ensaios imunológicos quanto à capacidade de induzir respostas imunes em animais desafiados. / Human papillomavirus infection, besides to represent a widespread sexually transmitted disease, is responsible for 5% of cancers in humans, highlighting cervical cancer with high rates of incidence and mortality. Although proven effective, the existing vaccines do not eliminate infections already established and have a high cost of production. This scenario shows the need for alternative vaccine strategies. This study proposes the expression of different recombinant genes in Escherichia coli, an economic, easy handling and high performance biotechnology platform. Recombinant genes used were: L1 of HPV16 and chimeric basedas constructions in replacement E5 oncoprotein epitopes on h4 loop and L1 C-terminal region, with the potential to generate prophylactic-therapeutic antigens and replacing L2 protein epitopes in loop region h4 for evaluation of possible cross-neutralization. After subcloning in pGEM-T, these genes were cloned into vector pAE expression and Escherichia coli BL21 and Rosetta were transformed with the expression vectors generated. Confirmation of protein production was performed by Western blot from extracts of cultures induced with IPTG. Optimizations in the induction protocols, lysis and preparation of the samples were carried out throughout the experiments. The results demonstrated the production of recombinant antigens and should be validated in future immunological assays for the ability to induce immune responses in challenged animals.

Les cyanobactéries ont développé des mécanismes de photo-protection pour se prémunir des dommages causés par un excès de lumière. L’un d’eux repose sur l’activité de l’Orange Caroténoïde Protéine (OCP), protéine soluble qui attache un kéto-caroténoïde, l’hydroxy-echinenone. Sous illumination, l’OCP se photo-convertit en forme active et interagit avec les phycobilisomes pour dissiper l’énergie collectée sous forme de chaleur. En conséquence, l’énergie d’excitation reçue par les centres réactionnels et la fluorescence du complexe photosynthétique diminuent. L’OCP a aussi la faculté de neutraliser l’oxygène singulet pour lutter contre la photo-oxydation. J’ai développé un système d’expression hétérologue pour reconstituer la voie de biosynthèse de cette protéine dans E.coli. Ce système permet l’obtention d’une grande quantité d’OCP liant son caroténoïde in vivo. Grâce à ce système robuste et rapide, les OCPs de trois cyanobactéries : Synechocystis, Arthrospira et Anabaena ont été produites, liant différents caroténoïdes. Toutes les OCPs recombinantes sont photo-actives et capables de quencher la fluorescence des phycobilisomes in vitro. Elles possèdent toutes la faculté de neutraliser l'oxygène singulet quel que soit le caroténoïde lié. Ce système d'expression hétérologue nous a permis d’élucider les déterminants structurels impliqués dans la photo-activation et la structure de la forme active de l’OCP. Il constitue une avancée fondamentale dans l'étude des protéines à caroténoïde et dans la production d'antioxydants solubles qui présentent un grand intérêt pour l’industrie de la santé. / Cyanobacteria have developed some photo-protective mechanisms to protect themselves from stress caused by excess light. One of them relies on the activity of the soluble Orange Carotenoid Protein (OCP) that binds a keto-carotenoid, the hydroxyechinenone. Under illumination, the OCP gets photo-converted to an active form and can interact with phycobilisomes to dissipate the collected energy as heat. Consequently, the excitation energy arriving at the photosynthetic reaction centers and the phycobilisome fluorescence emission decrease. The OCP can also quench the singlet oxygen to fight against photo-oxidation. I developed a heterologous expression system in which the biosynthetic pathway of the OCP is built in E.coli. The expression system allows the production of a large amount of OCP binding its carotenoid in vivo. Thanks to this robust and fast expression system, OCPs from three different cyanobacteria: Synechocystis, Anabaena and Arthrospira were produced, binding different carotenoids. All recombinant OCPs are photoactive and able to induce a large phycobilisome fluorescence quenching. Moreover, they all have the ability to quench the singlet oxygen, whatever the bound carotenoid. This heterologous expression system allowed us to elucidate the structural determinants involved in the photo-activation and structure of the active form of the OCP. This work represents a fundamental advance in the study of caroteno-proteins and in the production of others soluble antioxidants that are of great interest to the health industry.

Thesis (MSc (Biomedical Sciences))--Cape Peninsula University of Technology, 2019 / Background: Baculoviruses have great potential as alternatives to conventional chemical insecticides. The large scale adoption of such agents has however been hampered by the slow killing times exhibited by these bio-insecticides, limitation to single target insect and difficulty of large scale production of these preparations. Trichoplusia ni single nucleopolyhedrovirus (TnSNPV), initially identified in the Eastern Cape region of South Africa, has potential as a biocontrol agent as it possesses a higher speed of kill compared to other baculoviruses. Aims and methods: The main objective of this study was the identification, molecular characterisation and cloning of a structural core gene (polyhedrin) and three auxiliary genes, the inhibitor of apoptosis (iap2 and iap3) and the ecdysteroid UDP-glucosyltransferase (egt) genes, from TnSNPV in order to delineate its phylogenetic relationship to a Canadian isolate of the same virus and to other baculoviruses. In addition, the genes were expressed in an Escherichia coli (E. coli) based system as a prelude to genetic modification to increase the pesticidal property of the virus. Results: The genome size of the South African strain of TnSNPV was estimated at 160 kb and is significantly larger than the Canadian isolate of TnSNPV and may reflect genetic variation as the two strains have adapted to varying environmental conditions. Occlusion bodies of the South African strain of TnSNPV were visualised by Transmission Electron Microscopy and consisted of rod shaped single virions composed of a single enveloped nucleocapsid. Insect bioassays showed that the median lethal time (LT50) of the virus strain averaged 1.8 days which is significantly faster than other baculoviruses. The South African and Canadian strains of TnSNPV share nucleotide similarities greater than 95% for the genes analysed in this study, which indicates that they are closely related. From this analysis, the South African strain of TnSNPV identifies as a Group II NPV with the closest relatives being the Canadian strain of TnSNPV and ChchNPV. The topology of the tree for the polyhedrin protein was better resolved than that of the IAP2, IAP3 and EGT proteins and was comparable to the tree inferred from a concatenated data set consisting of complete polyhedrin/granulin, LEF8, and LEF9 proteins of 48 completely sequenced genomes. For the IAP2, IAP3 and EGT proteins, the separation of the lepidopteran and hymenopteran specific baculoviruses was not evident while the separation of Group I and II Alphabaculoviruses diverged from that observed from the baculovirus core gene polyhedrin as well as the tree inferred from complete polyhedrin/granulin, LEF8, and LEF9 proteins. Five distinct groups relating to IAP-1, 2, 3, 4 and 5 could be distinguished from the tree inferred from all IAP proteins from 48 fully sequenced baculoviruses. From this analysis, the IAP protein from the South African isolate of TnSNPV can be designated as an IAP3 due to sequence homology to other IAP3 proteins. Similarly, the IAP2 can be confirmed as an IAP2 protein as it clusters with other IAP2 proteins. RNA transcripts of the four genes were detected by RT-PCR at one hr after induction with Larabinose in BL21-A1 E. coli and persisted until four hrs post induction. Antisera directed against the C-terminal 6X His tag was able to detect the recombinant proteins at two hours after induction confirming the rapid rise in expression of the proteins which persisted at high levels until four hrs after induction. The discrepancy observed with the predicted molecular mass of the EGT protein and the migration on SDS-PAGE may be due to the absence of posttranslational modification in the E. coli expression system and the hydrophobic residues present in the N-terminal signal sequence. Conclusion: Sequence and phylogenetic analysis suggest that the two isolates of TnSNPV have been exposed to similar evolutionary pressures and evolved at similar rates and represent closely related but distinct variants of the same virus. The difference in genome size between the two strains is likely to reflect actual genetic differences as the strains have adapted to their local environments and hosts and the extent of the differences will only be apparent as more sequencing results become available. Phylogenetic analysis of the IAP and EGT proteins yields a tree that varies from the phylogenetic reconstruction observed for the polyhedrin gene as well as the concatenated data set consisting of complete polh/gran, LEF8, and LEF9 proteins and highlights the risks inherent in inferring phylogenetic relationships based on single gene sequences. The tree inferred from the concatenated data set of polh/gran, LEF8, and LEF9 proteins was a quick and reliable method of identification particularly, when whole genome data is unavailable and mirrors the accepted lineage of baculoviruses. Expression of the recombinant IAP2, IAP3, EGT and polyhedrin was confirmed by RT-PCR and immunoblot analysis and rose rapidly after induction and persisted at high levels. It is as yet unclear if the expressed proteins are functional particularly as post translation modifications are lacking in this system.

NADPH:cytochrome P450 reductase (CPR) is a 78 kDa flavoprotein, which is together with cytochrome P450 component of monooxygenase system bound in the membrane of the endoplasmic reticulum. Monooxygenase system is involved in the metabolism of a wide range of organic substances, including drugs or various pollutants present in the environment (polycyclic aromatic hydrocarbons, aromatic amines, etc.). CPR works as a transporter of reducing equivalents from NADPH to the cytochromes P450. For proper interaction with cytochromes P450, intact N-terminal hydrophobic domain anchoring protein in the membrane is needed. Removing this domain, e.g. during trypsin proteolysis, gives rise a soluble CPR (72 kDa) and cause loss of catalytic activity towards cytochrome P450. During heterologous expression in E. coli proteolytically sensitive site of CPR (Lys56 - Ile57) is cleaved by intracellular trypsin-like proteases, that may negatively affect the yields of native 78 kDa protein. This thesis describes the heterologous expression, purification and characterization of two forms of rat CPR. WtCPR is a protein naturally occurring in rats (Wistar strain), while mCPR contains one amino acid substitution (K56Q) in the site of proteolytic degradation. The result of that substitution is proteolytically stable CPR,...

Philosophiae Doctor - PhD / The World Health Organisation predicts that by the year 2050, 10 million people could die annually as a result of infections caused by multidrug resistant bacteria. Individuals with compromised immune systems, caused by underlying disease such as HIV, MTB and COVID-19, are at a greater risk. Antibacterial resistance is a global concern that demands the discovery of novel drugs. Natural products, used since ancient times to treat diseases, are the most successful source of new drug candidates with bioactivities including antibiotic, antifungal, anticancer, antiviral, immunosuppressive, anti-inflammatory and biofilm inhibition. Marine bioprospecting has contributed significantly to the discovery of novel bioactive NPs with unique structures and biological activities, superior to that of compounds from terrestrial origin. Marine invertebrate symbionts are particularly promising sources of marine NPs as the competition between microorganisms associated with invertebrates for space and nutrients is the driving force behind the production of antibiotics, which also constitute pharmaceutically relevant natural products.

Philosophiae Doctor - PhD / bioassay guided isolation approach was then used to isolate the high molecular weight antibacterial compound (50kDa-100kDa) from T. actiniarum fermentations. With common protein isolation, purification and detection methods failing to provide insight into the nature of the antibacterial compound, we hypothesized that the active agent is not proteinaceous in nature and may be a high molecular weight exopolysaccharide. Extraction and antibacterial screening of the exopolysaccharide fraction from T. actiniarum showed antibacterial activity as well as lytic activity when subjected to a zymography assay using Pseudomonas putida whole cells as a substrate. Additionally, the biosynthetic pathways for the production of poly-β-1, 6-N-acetyl-glucosamine (PNAG), an exopolysaccharide involved in biofilm formation and chondroitin sulfate, a known and industrially important glycosaminoglycan with antibacterial and anti-inflammatory activity was identified and the mechanism may be novel. Genome mining identified a variety of novel secondary metabolite gene clusters which could potentially encode other novel bioactivities. Therefore a bioassay guided isolation, focused on the small (<3kDa) molecules, was pursued. Secondary metabolites were extracted, fractionated and screened for biofilm inhibition, antibacterial and anticancer activity and activity was observed in all assays. Active fractions were dereplicated by UHPLC-QToF-MS and compounds of interest were isolated using mass guided preparative HPLC. The purity of the isolated compounds was assessed using UHPLC-QToF-MS and NMR and the structure of the target compounds elucidated. Structures that could be determined were the bile acids cholic acid and 3-oxo cholic acid and although not responsible for the observed activities, this is the first report of bile acid production for this genus. This is the first study investigating the bioactive potential of the strain and the first demonstrating that T. actiniarum is a promising source of potentially novel pharmaceutically relevant natural products depicted through both culture-dependent and culture-independent approaches.