Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (leaves 91-100).

One important objective of prostate cancer (PCa) research is to understand the molecular basis underlying the progression of these cancers from an androgen dependent to an androgen independent state. Hypermethylation of the promoter CpG islands is associated with the transcriptional silencing of specific gene sets in each tumor type and subtype. Transcriptional silencing of antitumor genes via CpG island hypermethylation could be a mechanism mediating PCa progression from an androgen-dependent to an androgen-independent state. Hypermethylation associated gene silencing has been reported for a great number of genes in PCa with the exception of the genes that undergo methylation associated silencing specifically during cancer development to androgen independence. The first aim of this thesis is to identify novel glenes which undergo DNA hypermethylation associated gene silencing during the cancer progression. The androgen-dependent (AD, as defined as the inability of celill to proliferate in the absence of androgen) PCa cell line LNCaP gives rise to the androgen-independent (AI) subline LNCaPcs generated by maintaining LNCaP in medium with charcoal-stripped (CS) serum for over 30 passages. This LNCaP cell model was used to identify differentially methylated sequences between the two genomes using the Methylation-Sensitive Restriction Fingerprinting (MSRF) technique. One sequence identified is located in a 5' CpG island, which encompasses part of the promoter, exon 1, and part of intron 1, of the Peroxisomal Membrane Protein 24 KD (PMP24) gene. PMP24 is silenced in concert with the hypermethylation of its CpG island in AI LNCaPcsand PC-3 cell lines. The silencing is reactivated by the treatment with a DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5AZAdC). PMP24 is specifically silenced in PCa cancer cell lines and shows potential antitumor properties. These results demonstrate the utility of MSRF in the identification of novel, differentially methylated DNA sequences in the genome and suggest that hypermethylation-mediated silencing of PMP24 is an epigenetic event involved in PCa progression to androgen independence. The next study investigated the molecular mechanism for DNA methylation associated gene silencing of PMP24 in AI LNCaPcs and PC-3 cell lines. We demonstrated that PMP24 transcription is repressed by the disruption of transcription factor binding to a critical cis-element by hypermethylation of its promoter CpG island. We found a CpG containing activator protein 2 (AP-2) cis-element in the intron 1 of PMP24 whose first CpG dinucleotidle is essential for the sequence-specific protein binding and the promoter activity of the gene. We presented first in cellulo evidence that the methylation of AP-2 cis-element alone but not the whole CpG island, using a newly developed methylated oligonucleotides treatment, is sufficient for the downregulation of PMP24. Our study is the first to report that the silencing mechanism for PMP24 in AI LNCaPcs and PC-3 is mediated by the complete methylation of a single GpG site of AP-2 cis-element in the intron 1 part of the CpG island, which interferes with transcription factor binding. Most interestingly, the promoter CpG island of PMP24 is hypermethylated in AD LNCaP cells with the incomplete methylation specifically at the AP-2 cis-element. The silencing of PMP24 in AD LNCaP cells was reactivated not by the 5AZAdC treatment but by the treatment with Trichostatin A (TSA), a histone deacetylase inhibitor. An alternative silencing mechanism for PMP24 other than the interference with transcription factor binding by methylation is therefore likely involved at this androgen-dependent stage. During the androgen ablation process, this mechanism is either evolved by the spread of methylation in the promoter CpG island or selected against, leading to the methylation-dominant silencing mechanism in the AI cells as seen in LNCaPcsand PC-3 cells. Taken together, this thesis emphasized the important role of DNA methylation in the progression of PCa into androgen independence. Particular respect should be paid to the specific CpG dinucleotides in cis-elements critical for the promoter activity, whose complete methylation could dominate the silencing mechanism which is independent of androgen. This thesis also pointed to the importance of monitoring the effects of cell culture on the methylation status of genes. Most importantly, this thesis raised the possibility that the silencing mechanisms for PMP24 could be different in AD LNCaP cells as compared to AI LNCaPcs and PC-3 cells. Either the evolution of such mechanism or the selectivity against it during the androgen ablation process would result in a methylation-dominant silencing mechanism of the genes such as PMP24 in AI cells and may contribute to the overall androgen independence of the cells.

RNA silencing is an evolutionary conserved sequence-specific mechanism of regulation of gene expression. RNA interference (RNAi), a type of RNA silencing in animals, is based on recognition and endonucleolytic cleavage of target mRNA complimentary in sequence to 21-nucleotide (nt) small RNA guides, called small interfering RNAs (siRNAs). Another class of 21-nt small RNAs, called micro RNAs (miRNAs), is endogenously encoded in eukaryotic genomes. Both production of siRNAs from long double-stranded RNA (dsRNA) and biogenesis of miRNAs from hairpin structures are governed by the ribonuclease III enzyme Dicer. Although produced as duplex molecules, siRNAs and miRNAs are assembled into effector complex, called the RNA-induced silencing complex (RISC), as single-strands. A member of the Argonaute family of small RNA-binding proteins lies at the core of all known RNA silencing effector complexes. Plants and animals contain multiple Argonaute paralogs. In addition to endonucleolytic cleavage, Argonaute proteins can direct translational repression/destabilization of mRNA or transcriptional silencing of DNA sequences by the siRNAdirected production of silent heterochromatin. The Schizosaccharomyces pombe genome encodes only one of each of the three major classes of proteins implicated in RNA silencing: Dicer (Dcr1), RNA-dependent RNA polymerase (RdRP; Rdp1), and Argonaute (Ago1). These three proteins are required for silencing at centromeres and for the initiation of transcriptionally silent heterochromatin at the mating-type locus. That only one Dicer, RdRP and Argonaute is expressed in S. pombe might reflect the extreme specialization of RNA silencing pathways regulating targets only at the transcriptional level in this organism. We decided to test if classical RNAi can be induced in S. pombe. We introduced a dsRNA hairpin corresponding to a GFP transgene. GFP silencing triggered by dsRNA reflected a change in the steady-state concentration of GFP mRNA, but not in the rate of GFP transcription. RNAi in S. pombe required dcr1, rdp1, and ago1, but did not require chp1, tas3, or swi6, genes required for transcriptional silencing. We concluded that the RNAi machinery in S. pombecould direct both transcriptional and posttranscriptional silencing using a single Dicer, RdRP, and Argonaute protein. Our findings suggest that, in spite of specialization in distinct siRNA-directed silencing pathways, these three proteins fulfill a common biochemical function. In Drosophila, miRNA and RNAi pathways are both genetically and biochemically distinct. Dicer-2 (Dcr-2) generates siRNAs, whereas the Dicer-1 (Dcr-1)/Loquacious complex produces miRNAs. Argonaute proteins can be divided by sequence similarity into two classes: in flies, the Ago subfamily includes Argonaute1 (Ago1) and Argonaute2 (Ago2), whereas the Piwi subfamily includes Aubergine, Piwi and Argonaute 3. siRNAs and miRNAs direct posttranscriptional gene silencing through effector complexes containing Ago1 or Ago2. The third class of small RNAs, called repeat-associated small interfering RNAs (rasiRNAs), is produced endogenously in the Drosophilagerm line. rasiRNAs mediate silencing of endogenous selfish genetic elements such as retrotransposons and repetitive sequences to ensure genomic stability. We examined the genetic requirements for biogenesis of rasiRNAs in both male and female germ line of Drosophilaand silencing of 8 different selfish elements, including tree LTR retrotransposons, two non-LTR retrotransposons, and three repetitive sequences. We find that biogenesis of rasiRNAs is different from that of miRNAs and siRNAs. rasiRNA production appears not to require Dicer-1 or Dicer-2. rasiRNAs lack the 2´,3´ hydroxy termini characteristic of animal siRNA and miRNA. While siRNAs derive from both the sense and antisense strands of their dsRNA precursors, rasiRNAs accumulate in antisense polarity to their corresponding target mRNAs. Unlike siRNAs and miRNAs, rasiRNAs function through the Piwi, rather than the Ago, Argonaute protein subfamily. We find that rasiRNAs silence their target RNAs posttranscriptionally: mutations that abrogate rasiRNA function dramatically increase the steady-state mRNA level of rasiRNA targets, but do not alter their rate of transcription, measured by nuclear run-on assay. Our data suggest that rasiRNAs protect the fly germ line through a silencing mechanism distinct from both the miRNA and RNAi pathways.

Made available in DSpace on 2016-08-17T18:39:45Z (GMT). No. of bitstreams: 1 4644.pdf: 10384990 bytes, checksum: c8ab8c109d1671b477c700f556bd68bc (MD5) Previous issue date: 2011-08-26 / Universidade Federal de Minas Gerais / The thioredoxin peroxidase (Tpx) is a group of antioxidant proteins that has been widely studied due to its role in the decomposition of different peroxides such as H2O2, peroxynitrite and organic peroxides. The ability of peroxide decomposition by Tpx is related to the presence of a conserved cysteine called peroxidatic cysteine (CysP). Most Tpx has a second cysteine (resolving cysteine - CysR) which forms a disulfide with CysP after peroxide decomposition. In addition to the peroxidase activity, some Tpx have molecular chaperone activity and are also involved in signaling of cell growth induced by hydroperoxides. It has been demonstrated that the Tpx cytosolic isoform of Schizosaccharomyces pombe is able to interact directly with MAPK (Sty1) via mixed disulfide, which is stabilized when the CysR is replaced by a serine residue. Saccharomyces cerevisiae have a nuclear isoform of Tpx (nTPx) and review of the literature shows the importance of this protein in maintaining the telomere silencing and decomposition of organic peroxides in the nucleus. Scale proteomic studies using mass spectrometry and two-hybrid indicate the nTPx association with MAP kinases. However, despite its location and participation in biological processes of relevance, works related to nTPx are scarce. Scale proteomics studies reported the physical interaction between nTPx and Mec3, Gts1, Pc1 and Dog2. These proteins are related to cell signaling or maintenance of telomeric silencing. However, no specific studies were performed to confirm these interactions and if they are established by mixed disulfides. This study aimed to evaluate the interactions previously described in the literature between nTPx and Mec3, Pcl1, Dog2 and Gts1 through the expression and purification of these proteins and in vitro evaluation of interactions as well as in vivo tests using two-hybrid. Several efforts were made with different approaches, nevertheless it was impossible overexpression of Mec3, Pcl1, Dog2, indicating a toxic effect of these proteins on the strains used. Furthermore, we found great success in overexpression of nTPx and nTpxC112S (8 mg and 10 mg per liter of cell culture) in Eschericchia coli strain BL21 (DE3) C43. This is the first time that these proteins were expressed in native form. It was also possible to overexpress the Gts1 protein in the same strain. These results could lead for new approaches in future studies in order to determine these threedimensional structures, by methods such as X-ray crystallography or nuclear magnetic resonance (NMR). Finally, the results obtainedusing the technique of two-hybrid yeast confirmed the interaction in vivo among nTPx and Mec3, Gts1, Dog2. However, opposing the results described in the literature, no interaction was detected between nTPx and PCL1, emphasizing the necessity of specific experiments in addition to the large-scale ones. / As tiorredoxinas peroxidases (TPx), constituem um grupo de proteínas antioxidantes que vêm sendo bastante estudadas pela sua atuação na decomposição de diversos tipos peróxidos, como o H2O2, peroxinitritos e peróxidos orgânicos. A capacidade de decomposição de peróxidos pelas TPx está relacionada a presença de uma cisteína conservada denominada de cisteína peroxidásica (CysP). A maioria das TPx possuem uma segunda cisteína (cisteína de resolução - CysR) a qual forma um dissulfeto com CysP após a decomposição de um peróxido. Adicionalmente, à atividade peroxidásica, algumas TPx possuem atividade de chaperona molecular e também estão envolvidas em processos de sinalização de crescimento celular induzidos por hidroperóxidos. Já foi demonstrado que a isoforma citosólica de TPx de Schizosaccharomyces pombe é capaz de interagir diretamente com uma MAPK (Sty1) através da formação de um dissulfeto misto entre as proteínas, que é estabilizado quando a CysR é substituída por um resíduo de serina. Entretanto, nenhuma interação deste tipo foi descrita para outros organismos. Em Saccharomyces cerevisiae ocorre uma isoforma de TPx no núcleo (nTPx) e a revisão da literatura demonstra a relevância desta proteína na manutenção do silenciamento dos telômeros e decomposição de peróxidos orgânicos no núcleo. Estudos em escala proteômica utilizando espectrometria de massa e duplo híbrido indicam a associação de nTPx com MAP quinases, entretanto, apesar de sua localização e participação em processos biológicos de relevância, trabalhos relacionados com nTPx são escassos. Estudos em escala proteômica relataram a interação física entre nTPx e as proteínas Mec3, Gts1, Pcl1 e Dog2 relacionadas a sinalização celular ou manutenção do silenciamento telomérico. No entanto, não foram efetuados estudos pontuais visando confirmar estas interações como também averiguar a possibilidade das interações entre nTPx e as proteínas supracitadas serem estabelecidas através de dissulfetos mistos. Este trabalho teve por objetivo a avaliação de interações previamente descritas na literatura entre nTPx e Mec3, Pcl1 e Dog2 por meio da expressão e purificação destas proteínas e avaliação in vitro de interações como também in vivo através de ensaios de duplo híbrido. Diversos esforços com diferentes abordagens foram efetuados, entretanto não foi possível a superexpressão de Mec3, Pcl1, Dog2, indicando um efeito tóxico destas proteínas sobre as linhagens utilizadas. Por outro lado, obtivemos grande sucesso na superexpressão de nTPx e nTpxC112S (8 mg e 10 mg por litro de cultura de células) em linhagens de Eschericchia coli BL21 (DE3) C43, o que representa a primeira vez que estas proteínas foram expressas sem trucamentos. Também foi possível expressar na mesma linhagem a proteína Gts1. Estes resultados abrem a possibilidade de estudos posteriores visando a determinação de suas estruturas tridimensionais, por metodologias como cristalografia de raios-X ou ressonância magnética nuclear (RMN). Por fim, os resultados de interação in vivo utilizando a técnica de duplo híbrido em levedura, confirmaram a interação entre nTPx e Mec3, Gts1 e Dog2. Entretanto ao contrario dos resultados descritos na literatura, não foi detectada interação entre nTPx e Pcl1, reforçando que experimentos pontuais são necessários em adição aos experimentos de larga escala.

Made available in DSpace on 2015-03-26T13:36:39Z (GMT). No. of bitstreams: 1 texto completo.pdf: 2100606 bytes, checksum: 5e91a2b8b12b7ee39c9e424e7736aa78 (MD5) Previous issue date: 2009-02-18 / Fundação de Amparo a Pesquisa do Estado de Minas Gerais / The main objectives in this work were: i) to find the optimum conditions to disinfect tomato seeds (Solanum lycopersicum Mill.) and eggplant seeds (Solanum melongena L.); ii) to evaluate the influence of the type of sealing in the obtained seedlings and explants; iii) to evaluate the effect of sonication in the morphogenesis in vitro of the tomato explants and in the viability of Agrobacterium tumefaciens cells; iv) to establish the parameters that allow the genetic transformation mediate by A. tumefaciens aiming the genetic silencing mediate by RNAi from myo-inositol-phosphate synthase, using the GmMPIS1 gene. It was checked that the use of deionized water was more efficient to disinfect eggplant seeds than 0.13% v/v chlorine solution. The use of dry disinfection in chlorine cameras is not appropriate to clean the tomato and eggplant seeds due to the gas toxicity and that it also compromises their germination. It was observed that gas exchange helps the seedlings development and leads to a bigger number of explants and with better quality to be used in the genetic transformation via Agrobacterium tumefaciens. Using the SAAT technique (Sonication-assisted Agrobacterium-mediated transformation), the explants and the bacteria suspensions were exposed to ultrasound for 0, 3, 6 and 9 seconds. It was verified that the immersion time from 3 to 6 seconds was appropriate to be used in genetic transformation, since it shown the biggest transient expression areas evaluated by in situ histochemical analysis of the GUS gene, the biggest number of regenerated structures and less mortality in the A. tumefaciens cells. The process was optimized when the immersion of the A. tumefaciens suspension was made 24 hours after the exposition to ultrasound. To make possible to select the transformed plants it was established the dependence of the hygromycin agent lethality and the found concentration of the non-transformed selected cells was 7.5 mg.L-1 in cotyledonary hipocotyledonary and leaf tomato explants. It was found that concentrations above this value were toxic, showing chlorotic and necrotic areas in the explants. A genetic transformation in tomato and eggplant plants was successfully made to check the relation between the MIPS gene and the seeds development by A. tumefaciens containing plasmids with silencing construction by siRNA to the MIPS gene using a conserved sequence of the soy gene GmMIPS. The transgenic nature of the primary regenerators was confirmed by in situ histochemical tests of GUS and by PCR analysis with specific oligonucleotides initiators. The analysis of the genetic expression confirmed the MIPS gene silencing and the morphologic analysis of the fruits confirmed the hypothesis of the relationship between the myo-inositol- phosphate synthase and the seeds development. However, as shown by flow-citometry technique, the process of regeneration in vitro used in the tomato plants transformation protocol changed some transgenic plants to polypoids. This was not observed in eggplant plants. / Este trabalho teve como objetivo: i) a otimização das condições de desinfestação de seentes de tomateiros (Solanum lycopersicum Mill.) e berinjela (Solanum melongena L.); ii) a avaliação da influência do tipo de vedação sobre a qualidade das plântulas e explantes oriundos destas; iii) a avaliação do efeito da sonicação sobre a morfogênese in vitro de explantes de tomateiros e sobre a viabilidade de células de Agrobacterium tumefaciens; iv) o estabelecimento de parâmetros para possibilitar a transformação genética mediada por A. tumefaciens visando ao silenciamento gênico mediado por RNAi da sintase do mio-inositol-fosfato, utilizando-se o gene GmMIPS1. Na desinfestação das sementes de berinjela, comprovou-se que tratamentos utilizando imersão em água deionizada são mais eficientes que imersão em solução de 0,13% v/v de cloro. A utilização de desinfestação a seco, em câmara de gás cloro, não é indicada para a assepsia de sementes de tomate e berinjela, pela toxicidade do gás às sementes, comprometendo sua germinação. Observou-se que as trocas gasosas favorecem o desenvolvimento das plântulas e geram explantes em maior número e de melhor qualidade para utilização de transformação genética via Agrobacterium tumefaciens. Ao se utilizar a técnica de SAAT ( Sonication-assisted Agrobacterium-mediated transformation ), os explantes e a suspensão bacteriana foram expostos a tempos de exposição ao ultra-som (0, 3, 6 e 9 segundos). Verificou-se que o intervalo de 3 a 6 segundos é o indicado para se utilizar em transformação genética, pois resultou nas maiores áreas de expressão transiente avaliada pela análise histoquímica in situ do gene GUS, maior número de estruturas regeneradas e menor mortalidade nas células de A. tumefaciens. O processo foi otimizado quando a imersão em suspensão de A. tumefaciens foi realizado após 24 horas de exposição ao ultra-som. Para ser possível a seleção de transformantes foi estabelecida a curva de letalidade ao agente higromicina e a concentração encontrada para seleção de células não transformadas foi de 7,5 mg.L-1 em explantes cotiledonares, hipocotiledonares e foliares de tomateiro. Dosagens acima de 7,5 mg.L-1 mostratam-se tóxicas, resultando em explantes com áreas cloróticas e necróticas. A fim de verificar a relação do gene MIPS com o desenvolvimento de sementes, a transformação genética foi realizada com sucesso em tomateiro e berinjela, via A. tumefaciens contendo plasmídeo com construção de silenciamento por siRNA para o gene MIPS, utilizando uma seqüência conservada do gene de soja GmMIPS. A natureza transgênica dos regenerantes primários foi confirmada mediante o teste histoquímico in situ de GUS e análise de PCR com oligonucleotídeos iniciadores específicos. A análise de expresão gênica confirmou o silenciamento do gene MIPS, e a análise morfológica dos frutos confirmou a hipótese do relacionamento da mio-inositol-fosfato-sintase com o desenvolvimento de sementes. Porém, conforme detectado pela técnica de citometria de fluxo, o processo de regeneração in vitro adotado no protocolo de transformação de tomateiro, ao contrário de berinjela, induziu poliploidia em algumas plantas transgênicas.

O uso da técnica de RNAi vem sendo avaliada em diversos insetos-pragas pois, é uma estratégia inovadora que pode ser integrada no manejo de importantes pragas agrícolas. Os insetos da Ordem Lepidoptera são reconhecidos por apresentarem recalcitrância à técnica de silenciamento utilizando dsRNA. Assim, ajustes devem ser feitos aos métodos de entrega de dsRNA para que haja estabilidade da molécula até atingir o mRNA alvo de silenciamento no inseto. O silenciamento gênico por RNAi possui potencial de uso para o controle da \"traça-do-tomateiro\" Tuta absoluta (Meyrick, 1917) (Lepidoptera: Gelechiidae), uma das principais pragas do tomateiro no mundo. O objetivo do trabalho foi selecionar e avaliar o silenciamento de genes de T. absoluta, utilizando o método de entrega de dsRNA via bactéria E. coli HT115 (DE3), disponibilizada em dieta artificial. Também, objetivando a aplicabilidade da utilização de bactérias que se desenvolvam no mesmo hábitat de insetos-pragas, estudou-se a colonização das bactérias endofíticas Pantoea agglomerans linhagem 33.1, Burkholderia sp. linhagem SCMS54 e Burkholderia ambifaria linhagem RZ2MS16 em plantas de tomateiro e lagartas de T. absoluta, para posterior transformação e tentativa de utilização como estratégia de entrega de dsRNA para silenciamento de genes alvos de T. absoluta. Foram avaliados, por meio da metodologia de dieta artificial, oito genes de T. absoluta: juvenile hormone inducible protein - JHP; juvenile hormone epoxide hydrolase protein - JHEH; ecdysteroid 25-hydroxylase - PHM; chitin synthase A - CHI; glutathione S-transferase epsilon 2 - GST; carboxylesterase - COE; alkaline phosphatase - AP e; arginine kinase - AK. Por meio de avaliação dos parâmetros biológicos (mortalidade larval; duração da fase larval e peso de pupas) e expressão gênica em cinco períodos de alimentação, comprovou-se a eficiência da metodologia na avaliação do silenciamento gênico por RNAi, sendo possível realizar screening de grande quantidade de genes e avaliar os efeitos do silenciamento gênico no desenvolvimento de T. absoluta. Os genes AK, CHI e JHP apresentaram resultados positivos quanto ao silenciamento gênico e mortalidade larval, sendo promissores para uso de silenciamento por RNAi como estratégia de controle de T. absoluta. Pantoea agglomerans apresentou os melhores resultados de colonização de plantas de tomateiro \"Micro-Tom\" e lagartas de T. absoluta, além de estarem presentes em tecidos preferencialmente utilizados na alimentação das lagartas. Porém, lagartas não apresentaram diferenças na mortalidade larval ao se alimentarem de plantas de tomateiro \"Micro-Tom\" inoculadas com bactérias de P. agglomerans transformadas. / The use of RNAi technique has been evaluated in several insect pests because it is an innovative strategy that can be integrated in the management of important agricultural pests. Insects of the Order Lepidoptera are recognized to present recalcitrance to gene silencing using dsRNA. Thus, adjustments should be done to dsRNA delivery methods to have molecule stability until it reaches the mRNA target for silencing in the insect. Gene silencing by RNAi has potential use to control the tomato leafminer Tuta absoluta (Meyrick, 1917) (Lepidoptera: Gelechiidae), one of the main insect pests of tomato crop worldwide. The objective of this work was to select and evaluate the silencing of T. absoluta genes using dsRNA delivery method via E. coli HT115 (DE3) bacterium, offered in artificial diet. Also, aiming the applicability of the use of bacteria growing in the same habitat of insect pests, we evaluate the colonization of the endophytic bacteria Pantoea agglomerans strain 33.1, Burkholderia sp. strain SCMS54 and Burkholderia ambifaria strain RZ2MS16 in tomato plants and T. absoluta larvae for further transformation and potential use as dsRNA delivery strategy for silencing target genes of T. absoluta. We evaluated eight genes of T. absoluta: juvenile hormone inducible protein - JHP; juvenile hormone epoxide hydrolase protein - JHEH; ecdysteroid 25-hydroxylase - PHM; chitin synthase A - CHI; glutathione S-transferase epsilon 2 - GST; carboxylesterase - COE; alkaline phosphatase - AP and; arginine kinase - AK. Evaluating biological parameters (larval mortality, larval stage duration and pupal weight) and gene expression in five feeding periods, we proved the efficiency of the methodology in the evaluation of gene silencing by RNAi, and evaluated the effects of gene silencing on the development of T. absoluta. The genes AK, CHI and JHP presented positive results regarding gene silencing and larval mortality, being promising to use RNAi silencing as a strategy to control T. absoluta. Pantoea agglomerans showed good results colonizing \"Micro-Tom\" tomato plants and T. absoluta larvae, besides being present in tissues preferentially used by larvae for feeding. However, larvae did not show differences in larval mortality when feeding on tomato plants inoculated with transformed P. agglomerans.

O glioblastoma (GBM) é o tumor cerebral maligno mais comum e agressivo em adultos. Uma combinação de terapia padrão com outras terapias baseadas no conhecimento de sua biologia é necessária para melhorar a sobrevida de pacientes com GBM. Muitos estudos foram desenvolvidos em busca de proteínas de membrana expressas em GBM, pois são potenciais alvos para imunoterapia. A proteína transmembrânica CD99 foi descrita como altamente expressa em astrocitomas de diferentes graus de malignidade. Embora seu mecanismo de ação ainda não seja totalmente compreendido, CD99 está envolvido na adesão e migração celular em diferentes tipos de tumores. O gene CD99 codifica duas proteínas distintas, denominadas isoforma 1, maior, de 32 kDa, e isoforma 2, gerada por splicing alternativo e menor, de 28 kDa. No presente estudo, foi demonstrada a expressão predominante da isoforma 1 em astrocitomas de diferentes graus de malignidade em comparação com o cérebro normal, bem como na linhagem celular de GBM humano U87MG. O transcriptoma das células U87MG transfectadas com siRNA para CD99 foi analisado em relação ao controle. Um total de 2.670 genes diferencialmente expressos foi identificado. Uma análise de enriquecimento no banco de dados DAVID revelou os seguintes processos como os mais significativos: junções aderentes célula-célula; adesão célula-célula envolvendo ligação de caderina e adesão celular. Ensaios funcionais baseados nestes achados (migração, invasão e adesão) foram realizados com células U87MG após o silenciamento de CD99 com dois shRNAs diferentes. A eficiência de silenciamento foi de 80 e 97%, para o shCD991 e 2, respectivamente, confirmada a nível de expressão do gene e da proteína. O silenciamento de CD99 reduziu a migração e invasão para ambos os shRNAs, com diminuição mais acentuada da migração para o shCD99 2, com maior nível de silenciamento de CD99. No ensaio de adesão, a linhagem U87MG shCD99 1 apresentou propriedades adesivas mais baixas que o controle, enquanto o shCD99 2 apresentou resultado oposto, com maior adesão celular do que seu controle. Provavelmente o silenciamento de CD99 afetou a redução da adesão celular em um padrão distinto, sugerindo que o resultado pode ser dependente do nível de expressão remanescente de CD99. Além disso, o CD99 e a faloidina colocalizaram nos lamelipódios e filopódios, sugerindo um papel importante no rearranjo do citoesqueleto. Foi demostrado, ainda, que o silenciamento de CD99 levou à redução da proliferação celular in vitro e diminuição do tumor in vivo. Camundongos imunodeficientes nos quais foram implantadas células silenciadas no cérebro apresentaram uma maior sobrevida que os animais que receberam células controle. A via de sinalização pela qual CD99 modula a proliferação no GBM ainda precisa ser elucidada. Migração, invasão e proliferação são as principais características do GBM que limitam uma ressecção cirúrgica completa e, consequentemente, levam frequentemente à recorrência. Portanto, análises posteriores das vias ativadoras do CD99 no contexto da migração, invasão, proliferação celular e apoptose são válidas para revelar novas estratégias terapêuticas para limitar a progressão do GBM / Glioblastoma (GBM) is the most common and aggressive malignant brain tumor in adults. A combination of standard therapy with other biologically based therapies is necessary to improve the survival of patients with GBM. Many studies have been developed in pursuit of expressed membrane proteins in GBM, which are potential targets for immunotherapy. The transmembrane protein CD99 is highly expressed in different malignant grades of astrocytomas. Although its mechanism of action is not still fully understood, CD99 is involved in cell adhesion and migration in different type of tumors. The CD99 gene encodes two distinct transmembrane proteins, named isoform 1, longer with 32 kDa, and isoform 2, generated by alternative splicing, shorter with 28 kDa. In the present study, we demonstrated predominant expression of isoform 1 in astrocytomas of different malignant grades compared to normal brain, and in the human GBM cell line U87MG. The transcriptome of U87MG cell line transfected with siRNA for CD99 was analyzed in relation to control. A total of 2.670 differentially expressed genes were identified. An enrichment analysis by DAVID Bioinformatics Database revealed the following processes as the most significant: cell-cell adherens junction; cadherin binding involved in cell-cell adhesion and cell-cell adhesion. Functional assays based on these findings (migration, invasion and adhesion) were performed with U87MG cells after knocking down CD99 with two different shRNAs. The CD99 silencing efficiency was 80 and 97%, for shCD99 1 and 2, respectively, confirmed at gene and protein level. The CD99 knockdown reduced migration and invasion for both shRNA, with the highest decrease of migration observed in the higher CD99 knocked down cells. In adhesion assay, shCD99 1 U87MG showed lower adhesive properties than the control, whereas shCD99 2 cells presented opposite results, with higher cell adhesion than control. Probably CD99 knockdown affected in the reduction of cell adhesion in a distinct pattern, suggesting that the result is dependent on CD99 remaining expression level. Additionally, CD99 and phalloidin colocalized at lamellipodia and filopodia, sugesting that CD99 plays an important role to cytoskeleton rearrangement. It has also been demonstrated that CD99 silencing caused reduction of cell proliferation in vitro and decreased tumor in vivo. Immunodeficient mice in which knocked down cells were implanted in the brain had a longer survival than animals that received control cells. The signaling pathway by which CD99 modulates proliferation in GBM still needs to be elucidated. Migration, invasion and proliferation are major characteristics of GBM, which limits the complete surgical tumor resection, and consequently leads to tumor recurrence. Therefore, further analysis of CD99 activating pathways in the context of cell migration, invasion, proliferation and apoptosis is worthwhile to unveil new therapeutic strategies to halt GBM progression

Orientadores: Fernando Ferreira Costa, Anderson Ferreira da Cunha / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-22T17:06:48Z (GMT). No. of bitstreams: 1 Branco_DianaSantos_D.pdf: 12860329 bytes, checksum: 5c5da209d2a41c9596907283c3c9e5e8 (MD5) Previous issue date: 2013 / Resumo: Os mecanismos moleculares envolvidos no perfil de expressão durante a eritropoese tem sido objeto de numerosas investigações como, por exemplo, o estudo da regulação gênica em células de linhagem eritroide. Esses estudos permitem a identificação de novos genes com potencial participação nesse processo e, adicionalmente, possibilitam um melhor entendimento dos genes já identificados na maturação das células eritroides e que possam estar envolvidos na produção de hemoglobinas. Nosso grupo de pesquisa identificou os diversos genes diferencialmente expressos durante a eritropoese. Dentre eles, os fatores de transcrição, EYA3 e HES6 e a latexina, LX, apresentaram maior expressão na fase final da eritropoese in vitro. Nossos dados sugerem participação dos genes EYA3 e LX, nas fases intermediaria e final da diferenciação eritroide, na expressão dos genes das globinas alfa e gama e na produção de HbF in vitro. Adicionalmente, no modelo in vivo zebrafish, os genes eya1, eya2, eya3, eya4, hes6 e hes13 apresentaram padrão de expressão ubíquo, enquanto que o gene lxn apresentou expressão especifica na ICM, tornando-o o candidato mais promissor para ser silenciado. O silenciamento desse gene em zebrafish apresentou fenótipo anêmico em embriões 72hpf, mas não em 48hpf, sugerindo que a anemia e decorrente de um processo no final da diferenciação eritroide, corroborando os dados encontrados em cultura in vitro. Estudos adicionais são necessários para compreensão dos mecanismos e vias envolvidos na participação do gene LX, durante o processo de diferenciação eritroide. Outros genes com potencial participação no processo de eritropoese são CLPX, TRAK2 E GFI. O gene CLPX codifica a caseinolytic peptidase X, uma proteína xvii altamente conservada durante a evolução e que apresenta função de chaperona dependente de ATP. Os dados deste trabalho mostram que o silenciamento do gene clpx1 reduziu significativamente os níveis de hemoglobinizacao e produção de eritrócitos em zebrafish. Contudo, estudos adicionais para o gene clpx2 precisam ser realizados para melhor compreender a possível função desses genes na produção de Heme. O gene TRAK2, por sua vez, e uma Trafficking Protein, Kinesin-Binding 2, envolvida no movimento da mitocôndria ao longo dos microtubulos. Os resultados obtidos em colaboração com o pesquisador Jeffrey Miller, M.D. (NIH/NIDDK) mostraram envolvimento desse gene na eritropoese em modelo in vitro de cultura primaria. No presente estudo, dentre os ortologos para o gene TRAK2 humano avaliados, apenas o trak1.1 parece ter sua função conservada nos teleósteos. O silenciamento desse gene gerou fenótipo anêmico nos embriões avaliados, corroborando os dados obtidos originalmente em cultura de células primaria. Finalmente, os fatores de transcrição de zebrafish gfi1aa, gfi1ab e gfi1b, ortologos aos fatores de transcrição da família Grow Factor Independence (GFI) em humanos também tiveram seu papel avaliado na hematopoese. Nossos dados mostram participação de gf1aa fase inicial de hematopoese e de gf1b na hematopoese definitiva. Também foi determinada a relação epistática entre os fatores gfi e os fatores de transcrição chave hematopoiéticos, mostrando que gfi1aa e gfi1b, juntamente com lmo2, scl, runx-1 e c-myb atuam como reguladores de HSPC em teleósteos / Abstract: Molecular mechanisms involved in expression profile during erythropoiesis have been the subject of numerous investigations such study of gene regulation in erythroid cell culture. These studies allow us to identify new genes potentially involved in erythroid differentiation and additionally to investigate genes already known as regulators of red blood cells and hemoglobin production. Our research group identified several genes differentially expressed during erythropoiesis. Among them, the transcription factors, EYA3 and HES6 and the latexin, LX, were found to have higher expression in the final phase of the in vitro erythropoiesis. Our data suggest that EYA3 and LX, are involved in the intermediate and final stages of erythropoiesis, expression pattern of alfa and gama globin and HbF production in vitro. Additionally in zebrafish model, eya1, eya2, eya3, eya4, hes6 and hes13 showed a ubiquitous expression pattern, while lxn showed specific expression in the ICM, making it the most promising candidate to be knockdowned. lxn knockdown in zebrafish showed anemic phenotype at 72hpf embryos, but not at 48hpf, suggesting that the anemia results is due to a process in the end of the erythroid differentiation, corroborating the results found for in vitro cultures. Additional studies are necessary to understand the mechanisms and pathways involved in the participation of the LX, gene during the process of erythroid differentiation. CLPX, TRAK2 and GFI transcription factors are also potentially candidates to be involved in erythropoiesis. CLPX gene codes for caseinolytic peptidase X, a protein highly conserved during evolution, which presents an ATP-dependent chaperone function. Data from this study showed that clpx1 knockdown reduced significantly hemoglobinization levels and erythroid production in zebrafish. However, future studies xv for the clpx2 gene is needed to better understand the function of these genes in the heme production. TRAK2 gene, in turn, is a Trafficking Protein, Kinesin-Binding 2, involved in mitochondrial movement along microtubules. Results obtained in collaboration with the researcher Jeffrey Miller, M.D. (NIH/NIDDK), showed the involvement of this gene in erythropoiesis in primary culture in vitro models. In this study, from the orthologs for the human TRAK2 gene analyzed, only trak1.1 appears to have its function conserved in teleosts. The silencing of this gene generated anemic phenotype in the embryos tested, corroborating the original results obtained in primary cell culture. Finally, gfi1aa, gfi1ab and gfi1b zebrafish transcription factors, orthologous to the Grow Factor Independence (GFI) family transcription factors in humans, also had their function evaluated in hematopoiesis. Our data suggest is involved in the initial phase of hematopoiesis while gf1b has a role in the definite hematopoiesis. The epistatic relation between the gfi and the hematopoietic key transcription factors was also determined, showing that gfi1aa and gfi1b, together with lmo2, scl, runx-1 and c-myb also act as regulators of HSPC in teleosts / Doutorado / Genetica Vegetal e Melhoramento / Doutora em Genética e Biologia Molecular

Submitted by Fabiano Vassallo (fabianovassallo2127@gmail.com) on 2017-04-18T18:48:21Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Área de Proteção à expressão - um estudo de relações discursivoas em área de proteção ambiental.pdf: 3806111 bytes, checksum: aa04faffcceabc7390692aca338f8e7c (MD5) / Approved for entry into archive by Josimara Dias Brumatti (bcgdigital@ndc.uff.br) on 2017-04-25T14:29:41Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Área de Proteção à expressão - um estudo de relações discursivoas em área de proteção ambiental.pdf: 3806111 bytes, checksum: aa04faffcceabc7390692aca338f8e7c (MD5) / Made available in DSpace on 2017-04-25T14:29:41Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Área de Proteção à expressão - um estudo de relações discursivoas em área de proteção ambiental.pdf: 3806111 bytes, checksum: aa04faffcceabc7390692aca338f8e7c (MD5) / O presente estudo tem como objetivo principal investigar as estratégias discursivas de silenciamento e de resistência construídas por agricultores e especialistas ambientais nas situações de comunicação que envolvem o processo de implantação e gestão da Área de Proteção Ambiental (APA) Macaé de Cima, localizada na região serrana do estado do Rio de Janeiro. Como corpus de análise utilizam-se textos que documentam discussões acerca desse processo, cujos sujeitos falantes constroem estratégias de silenciamento e de resistência. A investigação dessas construções discursivas se fundamenta na Teoria Semiolinguística de Análise do Discurso, de acordo com as pesquisas de Patrick Charaudeau (2009, 2010, 2011,2013) a respeito dos modos de organização do discurso, dos conceitos de língua, discurso, sujeito e identidade. Utiliza-se, ainda, o instrumental teórico a respeito dos processos de referenciação e de designação, filiado à Linguística Textual. As construções discursivas de silenciamento e resistência são examinadas de acordo com os pressupostos de Eni Orlandi (2007). O estudo evidenciou que ambas as estratégias são continuamente utilizadas pelos dois grupos envolvidos no contexto de discussão da APA, no entanto, os discursos de resistência são construídos em maior número pelo sujeito-agricultor ao objetivar defender suas tradicionais técnicas de uso da terra / This paper aims to investigate some discursive strategies of silencing and resistance produced by farmers and environmental specialists on situations of communication which involve the process of implementation and management of the environment protection area Macaé de Clima (Área de Proteção Ambiental Macaé de Clima – APA), located in the mountainous region of Rio de Janeiro. Some texts which document the discussions concerning this process will constitute the corpus of this exposition. The investigation of these discursive productions is based on Semiolinguistic Theory of Discourse Analysis, according to researchers developed by Patrick Charaudeau (2009, 2010, 2011, 2013) related to the modes of organization of the discourse, concepts of language, discourse, subject and identity. Studies of reference and designation are also used on this analysis. Furthermore, the discursive productions of silencing and resistance are examined by the assumptions postulated by Eni Orlandi (2007). The study has shown that both strategies are continuously used by both groups involved in the context of the discussion of the APA, however, the discourse of resistance are built in greater number by subject-farmer , in order to defend their traditional techniques for the use of the land

Chapter I introduces the Vancouver Island or ‘Douglas’ Treaties of 1850-54, entered into between several Vancouver Island First Nations and Hudson’s Bay Company Chief Factor, James Douglas, acting as agent of the Crown. The written versions purported to extinguish the aboriginal title of the First Nations to their land. Recent research has indicated that these documents do not accurately reflect what was agreed between the parties at the treaty meetings. The goal of the dissertation is to ascertain the likely terms of the treaties. This task also posed my major research challenge, as very little contemporaneous documentation exists of the formation of the treaties. There are a number of first- and second-hand accounts reduced to writing long after the events described, but they have received little attention from scholars until now. Chapter II is devoted to a critical analysis and comparison of the extant First Nation and colonial accounts, from which I conclude that the treaties were likely agreements by the First Nations to share not cede their land. Chapter III makes a comparison with first person accounts of the Washington or ‘Stevens’ Treaties of 1854-55, entered into between vii viii Native American tribes and the United States government. I conclude that these accounts bolster the likelihood that the Vancouver Island agreements were sharing treaties. Chapter IV follows up on a fascinating connection between the written versions of the Vancouver Island Treaties and an agreement concerning land between the Ngai Tahu Moari of New Zealand’s south island and Henry Kemp, acting as agent of the Crown. The comparison provides a number of useful contrasts and parallels with the Vancouver Island Treaties. Chapter V describes the silencing of the Vancouver Island Treaties by the policies of successive governments, the inattention of scholars and the decisions of Canadian courts. Finally, Chapter VI reviews existing and potential categories of historical treaties between First Nations and the Crown. By analogy with treaty categories in international law and the work of political and legal theorists, I make the case for the Vancouver Island Treaties as examples of modus vivendi (interim or framework agreements). / Graduate / 2017-02-24