Orientadores: Selma Giorgio, Fernanda Ramos Gadelha / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-25T14:07:59Z (GMT). No. of bitstreams: 1 Codonho_BarbaraSantoni_M.pdf: 2501497 bytes, checksum: d7ceeef1653b2df4a7d52b28ebd16543 (MD5) Previous issue date: 2014 / Resumo: As leishmanioses são um conjunto de doenças causadas pelo protozoário do genêro Leishmania, que atingem milhões de pessoas por ano. O tratamento é realizado primeiramente com antimoniais pentavalentes e, em casos de resistência, são indicadas a pentamidina ou anfotericina B. Todos estes fármacos são tóxicos e induzem efeitos colaterais nos pacientes. Devido a dificuldades no tratamento, o estudo de moléculas presentes no parasita se torna importante. Dentre essas, as heat shock proteins 70 (HSP70) são proteínas essenciais para o ciclo de vida da Leishmania. Durante a passagem do vetor para o hospedeiro vertebrado, o parasita encontra vários tipos de estresses que induzem a uma maior expressão da HSP70. Nesse projeto avaliou-se os efeitos da superexpressão da HSP70 em Leishmania (Leishmania) amazonensis, comparando-se parasitas que superexpressam a proteína HSP70 (pTEX-HSP70) com parasitas contendo somente o vetor (pTEX). Os resultados mostraram que os promastigotas transfectados pTEX e pTEX-HSP70 apresentaram vários aspectos ultraestruturais semelhantes aos não transfectados (WT), porém mostraram ser maiores e com o tamanho da área nuclear maior. A superexpressão da proteína HSP70 conferiu aos parasitas uma fase estacionária de proliferação mais estendida do que a observada em parasitas pTEX. Uma maior resistência e capacidade proliferativa foram observadas nos parasitas pTEX-HSP70 quando submetidos a diferentes condições de estresses (tratamentos com H2O2, choque térmico e ambiente hiperbárico), em relação a parasitas pTEX. Os resultados também mostraram que parasitas pTEX e pTEX-HSP70 infectam culturas de macrófagos peritoneais e macrófagos humanos derivados de sangue periférico, em taxas (% de infecção e número de amastigotas/macrófago) semelhantes a de parasitas WT. O processo de infecção em camundongos BALB/c mostrou que o tamanho da lesão induzida pelos parasitas pTEX e pTEX-HSP70 na pata foi diferente nas primeiras semanas, mas semelhante no curso final da infecção. Adicionalmente, as cargas parasitárias nas lesões dos camundongos BALB/c infectados com os parasitas pTEX e pTEX-HSP70 foram semelhantes, mas maiores que as cargas parasitárias nas lesões induzidas por WT. Além disso, os baços dos camundongos infectados com os parasitas pTEX e pTEX-HSP70 apresentaram visceralização. Ensaios da bioenergética destes promastigotas mostraram que parasitas pTEX-HSP70 apresentam maiores taxas de consumo de O2 do que parasitas pTEX, apesar de apresentarem produção de ATP semelhante. A produção de superóxido nos parasitas pTEX-HSP70 e pTEX foram similares, apesar da liberação de H2O2 ser bem inferior nos de parasitas pTEX-HSP70. Os resultados obtidos indicam que a superexpressão da proteína HSP70 protege a L.(L.) amazonensis de situações de estresse imediato, mas não interfere com a sua capacidade infectiva / Abstract: Leishmaniasis are a group of diseases caused by the protozoan genus Leishmania, which affect millions of people each year. The treatment is performed primarily with pentavalent antimony and resistance cases are indicated pentamidine or amphotericin B. All these drugs are toxic and induce side effects in patients. Due to difficulties in treatment, the study of molecules present in the parasite becomes important. Among these, the heat shock protein 70 (HSP70) proteins are essential for the life cycle of Leishmania. During the transition from vector to vertebrate host, the parasite finds various types of stresses that induce a higher expression of HSP70. In this project was evaluated the effects of overexpression of HSP70 in Leishmania (Leishmania) amazonensis, comparing parasites that overexpressing HSP70 (pTEX-HSP70) protein with parasites containing the empty vector (pTEX). The results showed that transfected promastigotes pTEX and pTEX-HSP70 showed several similar ultrastructural aspects similar to promastigotes of L.(L.) amazonensis untransfected (WT), but proved to be larger and the size of the largest nuclear area. Overexpression of HSP70 protein gave the parasites a stationary phase of proliferation more extended than that observed in parasites pTEX. Higher strength and better proliferative capacity were observed in parasites pTEX-HSP70 when submitted to different stress conditions (hydrogen peroxide, heat shock treatments and hyperbaric environment), in relation to parasites pTEX. The results also showed that pTEX and pTEX-HSP70 parasites infect cultures of peritoneal macrophages and human peripheral blood-derived macrophages in rate (% infection and the number of amastigotes / macrophage) similar to WT parasites. The process of infection in BALB/c mice showed that the size of the induced parasitic pTEX and pTEX-HSP70 foot injury was different in the first few weeks but similar in the final course of infection. Additionally, parasitic loads on the lesions of BALB/c mice infected with pTEX and pTEX-HSP70 parasites were similar, but larger than the parasitic loads in lesions induced by WT. Moreover, spleens from infected with pTEX and pTEX-HSP70 parasites mice showed visceralization. Assays of bioenergetics promastigotes showed that these pTEX-HSP70 parasites consume more O2 than pTEX parasites, despite showing similar ATP production. Superoxide production in parasites pTEX and pTEX-HSP70 were similar, despite the release of hydrogen peroxide is considerably lower than pTEX-HSP70 parasites. The results indicate that overexpression of HSP70 protein protect L.(L.) amazonensis in immediate situations of stress, but does not interfere with its infective capacity / Mestrado / Imunologia / Mestra em Genética e Biologia Molecular

Orientador: Marcelo Menossi Teixeira / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-16T17:06:41Z (GMT). No. of bitstreams: 1 Baldacin_MariaGrazielaZagattoKrug_D.pdf: 4445527 bytes, checksum: 9730d155ac6ebf7d24d427feb43a2acb (MD5) Previous issue date: 2010 / Resumo: A toxidez por alumínio (Al3+) é o principal fator limitante da produção agrícola em grandes áreas do Brasil e do mundo. Sabe-se que a defesa das plantas a este elemento é controlada por múltiplos genes. A caracterização de genes cuja expressão é induzida pelo Al contribui para compreender as defesas ativadas pelas plantas. Neste trabalho identificou-se um cDNA de milho expresso em raízes através da técnica de mRNA differential display. Este cDNA codifica uma seqüência que contem dois domínios LIM, separados por um espaçador de 40-50 resíduos, sendo denominado Zmlim-1. O objetivo deste trabalho é a caracterização deste gene e o seu papel na tolerância ao Al em milho. Em estudos de expressão verificou-se que o gene Zmlim- 1 é induzido por Al e sua expressão é maior na linhagem tolerante, Cat100-6, quando comparado com a linhagem sensível S1587-17. O direcionamento da proteína ZMLIM-1 foi observado em epitélios de cebola bombardeados com a construção fusionada à proteína GFP (green fluorescent protein). A expressão transiente revelou que esta proteína está localizada no citoplasma e no núcleo. A hibridização in situ demonstrou que Zmlim-1 é expresso na maioria das células do ápice de raiz de milho. O sistema de duplo híbrido de levedura permitiu identificar três proteínas que interagem com a proteína ZMLIM-1: duas proteínas da subunidade ribossomal e uma proteína da família OMT envolvida na biossíntese de lignina. Plantas transgênicas silenciando este gene forneceram evidências de que o gene Zmlim-1 pode influenciar a anatomia da raiz e a quantidade de lignina. Este é o primeiro relato de interação OMT com proteínas de domínio LIM, sugerindo um envolvimento desta proteína com a biossíntese de lignina. Plantas transgênicas submetidas ao estresse por Al3+ não apresentaram diferenças com relação às plantas controle não transformadas / Abstract: Aluminum (Al) toxicity is the main factor limiting agricultural production in large areas in Brazil and in the world. It is known that plant defenses against this element are controlled by multiple genes. The characterization of genes whose expression is induced by Al contributes to the understanding of the defenses activated by plants. In this work we identified a cDNA expressed in maize roots using mRNA differential display. This cDNA encodes a sequence that contains two LIM domains separated by a spacer of 40-50 residues, being named Zmlim-1. The purpose of this study was the characterization of this gene and its involvement in Al tolerance in maize. In expression studies it was found that the Zmlim-1 gene was induced by Al and its expression was higher in the tolerant line, Cat100-6 when compared with the sensitive line S1587-17. The subcellular localization of the protein ZMLIM-1 was observed in onion epithelial cells bombarded with a ZMLIM-1::GFP (green fluorescent protein) fusion. The assay of transient expression revealed that this protein is localized in cytoplasm and nucleus. In situ hybridization showed that Zmlim-1 is expressed in most cells of the root apex of maize. The yeast two hybrid system identified three proteins that interact with ZMLIM-1 protein: tworibosomal subunit proteins and a protein from the OMT family involved in lignin biosynthesis. Transgenic plants silenced for this gene have provided evidence that Zmlim-1 gene can influence the anatomy of the root and the amount of lignin in the plants. This is the first report of OMT interaction with LIM domain proteins, suggesting an involvement of this protein with lignin biosynthesis. Transgenic plants subjected to Al3+ stress did not show differences when compared to control, untransformed plants / Doutorado / Genetica Vegetal e Melhoramento / Doutor em Genetica e Biologia Molecular

Plant diseases remain a major obstruction to meeting the world’s increased demand for soybean oil and protein. Reducing the losses caused by diseases in order to improve crop production is a high priority for agricultural research. The need for novel strategies for plant disease control cannot be overstated. In the present study, selected defense-related genes were silenced and/or overexpressed in soybean using a virus-based vector and the resultant plants were tested for their responses to pathogens. The first part of the study focused on Rps1k (Resistance to Phytophthora sojae) gene. The two conserved domains encoding ‘P-Loop NTPase’ and ‘PLN03210’ of Rps1k were independently overexpressed. Stem inoculation assays for the overexpressing plants showed significant resistance to virulent races; 90% standing plants compared to 10% in controls. Lesion length was greatly restricted only in case of plants overexpressing ‘PLN03210’. Simultaneous silencing of Rps1k-1 and Rps1k-2 resulted in remarkable susceptibility to avirulent races when tested by a detached-leaf assay. The second part of the study entailed silencing/overexpression of the chlorophyllase genes GmCLH1 and GmCLH2 and testing the responses of the silenced/overexpressing plants to the sudden death pathogen Fusarium virguliforme. Four weeks post root inoculation, GmCLH2-silenced plants showed enhanced resistance while the GmCLH2-overexpressing plants exhibited markedly increased susceptibility when compared to empty vector control. RT-PCR assay of PR genes revealed elevated expression of PR2 and PR4 in GmCLH2-silenced plants. In the third part of the study, soybean plants silenced for a leucine-rich repeat receptor-like kinase (GmRLK3) gene were examined for their responses to different pathogens. Silencing of GmRLK3 enhanced susceptibility to infection with Alternaria tenuissima or Sclerotinia sclerotiorum as revealed by rapid disease progress on treated leaves. Surprisingly, silencing of GmRLK3 in known susceptible soybean cultivars rendered the silenced plants resistant to P. sojae. The ensuing partial resistance to P. sojae was consistent with results of RT-PCR assays that showed a significant increase in the transcript level of the osmotin-encoding gene (PR5a) in the GmRLK3-silenced plants. PR5a is considered a marker for systemic acquired resistance.

Reducing the production cost of industrial biofuels will greatly facilitate their proliferation and co-integration with fossil fuels. The cost of feedstock is the largest cost in most fermentation bioprocesses and therefore represents an important target for cost reduction. Meanwhile, the biorefinery concept advocates revenue growth through complete utilization of by-products generated during biofuel production. Taken together, the production of biofuels from low-cost crude glycerol, available in oversupply as a by-product of bioethanol production, in the form of thin stillage, and biodiesel production, embodies a remarkable opportunity to advance affordable biofuel development. However, few bacterial species possess the natural capacity to convert glycerol as a sole source of carbon and energy into value-added bioproducts. Of particular interest is the anaerobe Clostridium pasteurianum, the only microorganism known to convert glycerol alone directly into butanol, which currently holds immense promise as a high-energy biofuel and bulk chemical. Unfortunately, genetic and metabolic engineering of C. pasteurianum has been fundamentally impeded due to a complete lack of genetic tools and techniques available for the manipulation of this promising bacterium. This thesis encompasses the development of fundamental genetic tools and techniques that will permit extensive genetic and metabolic engineering of C. pasteurianum. We initiated our genetic work with the development of an electrotransformation protocol permitting high-level DNA transfer to C. pasteurianum together with accompanying selection markers and vector components. The CpaAI restriction-modification system was found to be a major barrier to DNA delivery into C. pasteurianum which we overcame by in vivo methylation of the recognition site (5’-CGCG-3’) using the M.FnuDII methyltransferase. Systematic investigation of various parameters involved in the cell growth, washing and pulse delivery, and outgrowth phases of the electrotransformation procedure significantly elevated the electrotransformation efficiency up to 7.5 × 104 transformants µg-1 DNA, an increase of approximately three orders of magnitude. Key factors affecting the electrotransformation efficiency include cell-wall-weakening using glycine, ethanol-mediated membrane solubilization, field strength of the electric pulse, and sucrose osmoprotection. Following development of a gene transfer methodology, we next aimed to sequence the entire genome of C. pasteurianum. Using a hybrid approach involving 454 pyrosequencing, Illumina dye sequencing, and single molecule real-time sequencing platforms, we obtained a near-complete genome sequence comprised of 12 contigs, 4,420,100 bp, and 4,056 candidate protein-coding genes with a GC content of 30.0%. No extrachromosomal elements were detected. We provide an overview of the genes and pathways involved in the organism’s central fermentative metabolism. We used our developed electrotransformation procedure to investigate the use of established clostridial group II intron biology for constructing chromosomal gene knockout mutants of C. pasteurianum. Through methylome analysis of C. pasteurianum genome sequencing data and transformation assays of various vector deletion constructs, we identified a new Type I restriction-modification system that inhibits transfer of vectors harboring group II intron gene knockout machinery. We designated the new restriction system CpaAII and proposed a recognition sequence of 5’-AAGNNNNNCTCC-3’. Overcoming restriction by CpaAII, in addition to low intron retrohoming efficiency, allowed the isolation of a gene knockout mutant of C. pasteurianum with a disrupted CpaAI Type II restriction system. The resulting mutant strain should be efficienty transformed with plasmid DNA lacking M.FnuDII methylation. Lastly, we investigated the use of plasmid-based gene overexpression and chromosomal gene downregulation to alter gene expression in C. pasteurianum. Using a β-galactosidase reporter gene, we characterized promoters corresponding to the ferredoxin and thiolase genes of C. pasteurianum and show that both promoters permitted high-level, constitutive gene expression. The thiolase promoter was then utilized to drive transcription of an antisense RNA molecule possessing complementarity to mRNA of our β-galactosidase reporter gene. Our antisense RNA system demonstrated 52-58% downregulation of plasmid encoded β-galactosidase activity throughout the duration of growth. In an attempt to perturb the central fermentative metabolism of C. pasteurianum and enhance butanol titers, we prepared several antisense RNA constructs for downregulation of 1,3-propanediol, butyrate, and hydrogen production pathways. The resulting downregulation strains are expected to exhibit drastically altered central fermentative metabolism and product distribution. Taken together, we have demonstrated that C. pasteurianum is amendable to genetic manipulation through the development of methods for plasmid DNA transfer and gene overexpression, knockdown, and knockout. Further, our genome sequence should provide valuable nucleotide sequence information for the application of our genetic tools. Thus, the genome sequence, electrotransformation method, and associated genetic tools and techniques reported here should promote extensive genetic manipulation and metabolic engineering of this biotechnologically important bacterium.

Les cellules souches somatiques présentent habituellement un comportement très différent des cellules souches pluripotentes. Les bases moléculaires de l’auto-renouvellement des cellules souches embryonnaires ont été récemment déchiffrées grâce à la facilité avec laquelle nous pouvons maintenant les purifier et les maintenir en culture durant de longues périodes de temps. Par contre, il en va tout autrement pour les cellules souches hématopoïétiques. Dans le but d’en apprendre davantage sur le fonctionnement moléculaire de l’auto-renouvellement des cellules souches hématopoïétiques, j’ai d’abord conçu une nouvelle méthode de criblage gain-de-fonction qui répond aux caprices particuliers de ces cellules. Partant d’une liste de plus de 700 facteurs nucléaires et facteurs de division asymétrique candidats, j’ai identifié 24 nouveaux facteurs qui augmentent l’activité des cellules souches hématopoïétiques lorsqu’ils sont surexprimés. J’ai par la suite démontré que neuf de ces facteurs agissent de manière extrinsèque aux cellules souches hématopoïétiques, c’est-à-dire que l’effet provient des cellules nourricières modifiées en co-culture. J’ai également mis à jour un nouveau réseau de régulation de transcription qui implique cinq des facteurs identifiés, c’est-à-dire PRDM16, SPI1, KLF10, FOS et TFEC. Ce réseau ressemble étrangement à celui soutenant l’ostéoclastogénèse. Ces résultats soulèvent l’hypothèse selon laquelle les ostéoclastes pourraient aussi faire partie de la niche fonctionnelle des cellules souches hématopoïétiques dans la moelle osseuse. De plus, j’ai identifié un second réseau de régulation impliquant SOX4, SMARCC1 et plusieurs facteurs identifiés précédemment dans le laboratoire, c’est-à-dire BMI1, MSI2 et KDM5B. D’autre part, plusieurs indices accumulés tendent à démontrer qu’il existe des différences fondamentales entre le fonctionnement des cellules souches hématopoïétiques murines et humaines. / Somatic stem cells usually exhibit a very different behavior compared to pluripotent stem cells. The molecular basis of embryonic stem cell self-renewal was recently decrypted by the relative straightforwardness with which we can now purify and maintain these cells in culture for long periods of time. However, this is not the case with hematopoietic stem cells. In order to elucidate the molecular mechanisms of hematopoietic stem cell self-renewal, I developed a novel gain-of-function screening strategy, which bypasses some constraints found with these cells. Starting from a list of more than 700 candidate nuclear factors and asymmetric division factors, I have identified 24 new factors that increase hematopoietic stem cell activity when overexpressed. I have also found that nine of these factors act extrinsically to hematopoietic stem cells, i.e., the effect comes from the engineered feeder cells in co-culture. Moreover, I have revealed a new transcriptional regulatory network including five of the factors identified, i.e., PRDM16, SPI1, KLF10, FOS and TFEC. This network is particularly similar to that involved in osteoclastogenesis. These results raise the hypothesis that osteoclasts might also be part of the functional hematopoietic stem cell niche in the bone marrow. Furthermore, I have identified a second regulatory network involving SOX4, SMARCC1 and several factors previously identified in the laboratory, i.e., BMI1, MSI2 and KDM5B. Besides, several lines of evidence tend to show that there are fundamental differences between mouse and human hematopoietic stem cells.

Les cellules souches somatiques présentent habituellement un comportement très différent des cellules souches pluripotentes. Les bases moléculaires de l’auto-renouvellement des cellules souches embryonnaires ont été récemment déchiffrées grâce à la facilité avec laquelle nous pouvons maintenant les purifier et les maintenir en culture durant de longues périodes de temps. Par contre, il en va tout autrement pour les cellules souches hématopoïétiques. Dans le but d’en apprendre davantage sur le fonctionnement moléculaire de l’auto-renouvellement des cellules souches hématopoïétiques, j’ai d’abord conçu une nouvelle méthode de criblage gain-de-fonction qui répond aux caprices particuliers de ces cellules. Partant d’une liste de plus de 700 facteurs nucléaires et facteurs de division asymétrique candidats, j’ai identifié 24 nouveaux facteurs qui augmentent l’activité des cellules souches hématopoïétiques lorsqu’ils sont surexprimés. J’ai par la suite démontré que neuf de ces facteurs agissent de manière extrinsèque aux cellules souches hématopoïétiques, c’est-à-dire que l’effet provient des cellules nourricières modifiées en co-culture. J’ai également mis à jour un nouveau réseau de régulation de transcription qui implique cinq des facteurs identifiés, c’est-à-dire PRDM16, SPI1, KLF10, FOS et TFEC. Ce réseau ressemble étrangement à celui soutenant l’ostéoclastogénèse. Ces résultats soulèvent l’hypothèse selon laquelle les ostéoclastes pourraient aussi faire partie de la niche fonctionnelle des cellules souches hématopoïétiques dans la moelle osseuse. De plus, j’ai identifié un second réseau de régulation impliquant SOX4, SMARCC1 et plusieurs facteurs identifiés précédemment dans le laboratoire, c’est-à-dire BMI1, MSI2 et KDM5B. D’autre part, plusieurs indices accumulés tendent à démontrer qu’il existe des différences fondamentales entre le fonctionnement des cellules souches hématopoïétiques murines et humaines. / Somatic stem cells usually exhibit a very different behavior compared to pluripotent stem cells. The molecular basis of embryonic stem cell self-renewal was recently decrypted by the relative straightforwardness with which we can now purify and maintain these cells in culture for long periods of time. However, this is not the case with hematopoietic stem cells. In order to elucidate the molecular mechanisms of hematopoietic stem cell self-renewal, I developed a novel gain-of-function screening strategy, which bypasses some constraints found with these cells. Starting from a list of more than 700 candidate nuclear factors and asymmetric division factors, I have identified 24 new factors that increase hematopoietic stem cell activity when overexpressed. I have also found that nine of these factors act extrinsically to hematopoietic stem cells, i.e., the effect comes from the engineered feeder cells in co-culture. Moreover, I have revealed a new transcriptional regulatory network including five of the factors identified, i.e., PRDM16, SPI1, KLF10, FOS and TFEC. This network is particularly similar to that involved in osteoclastogenesis. These results raise the hypothesis that osteoclasts might also be part of the functional hematopoietic stem cell niche in the bone marrow. Furthermore, I have identified a second regulatory network involving SOX4, SMARCC1 and several factors previously identified in the laboratory, i.e., BMI1, MSI2 and KDM5B. Besides, several lines of evidence tend to show that there are fundamental differences between mouse and human hematopoietic stem cells.

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