Capítulo 1 A transformação (metaciclogênese) das formas proliferativas epimastigotas do Trypanosoma cruzi em formas não proliferativas e infectivas - tripomastigotas metacíclicos - é um passo crucial que ocorre naturalmente no trato digestivo do inseto vetor reduviídeo. Este processo pode ser reproduzido in vitro em condições químicas definidas quando o meio de diferenciação TAU é suplementado com L-prolina e L-glutamato. Está bem estabelecido que prolina é uma fonte importante de energia e de carbono nos tripanossomatídeos, mas são poucas as evidências de sua participação na diferenciação intracelular do parasita no hospedeiro vertebrado. Este fato nos levou a desenvolver um modelo experimental para verificar se havia uma relação entre concentração de prolina e eclosão de formas tripomastigotas. Culturas mantidas sem L-prolina produziram consistentemente menos formas tripomastigotas quando comparadas a culturas mantidas em L-prolina, 20 - 200 µM. A atividade de transporte de L-prolina foi 15 vezes e 23 vezes maior nos epimastigotas intracelulares em relação a amastigotas e tripomastigotas, respectivamente. A concentração de prolina medida nos epimastígotas intracelulares (0,73 ± 0101 mM) é bem menor que a de amastigotas (6,61 ± 0,01 mM) e tripomastigotas (2,74 ± 0,02 mM). Todos os estágios, no entanto, apresentaram concentração de prolina bem maior do que as células hospedeiras, na ordem de 0,27 ± 0,03 mM. A análise do efeito de prolina sobre os diferentes estágios intracelulares mostrou a importância desse aminoácido na transformação de epimastigotas intracelulares a tripomastigotas. Capítulo 2 A diferenciação das formas infecciosas tripomastigotas do Trypanosoma cruzi a formas amastigotas não-infectivas e replicativas ocorre normalmente no citoplasma de células infectadas. Um estudo sobre o envolvimento de proteínas fosfatase do tipo 1 e 2A na diferenciação extracelular a 37ºC e 33ºC de tripomastigotas a formas amastigotas foi realizado, utilizando-se o clone CL-14 de T cruzi. Demonstrou-se que Caliculina A (um inibidor de proteínas fosfatase 1 e 2A) desencadeia a transformação de tripomastigotas a amastigotas em pH neutro, através da passagem por formas intermediárias flageladas semelhantes aos epimastigotas. O tratamento de tripomastigotas com duas concentrações de Caliculina A (1nM e 5 nM) resultou, após 6 horas de incubação, em mais de 50% de formas epimastigota-símiles. Após 8 horas de tratamento, todos os tripomastigotas estavam diferenciados a formas amastigotas ou epimastigota símiles. Tripomastigotas metacíclicos do clone CL-14 submetidos ao mesmo tratamento com Caliculina A não apresentaram alterações morfológicos dentro do período de incubação de 8 horas. Capítulo 3 Fatores ambientais, como a temperatura, e a presença ou ausência de metabólitos tais como a L-prolina influenciam a diferenciação intracelular do Trypanosoma cruzi do clone CL-14. Estes fatos, juntamente com a ausência de dados na literatura sobre o perfil proteico de epimastigotas intracelulares levou-nos a estudar o perfil de expressão de proteínas durante a transformação de epimastigotas intracelulares a tripomastigotas em culturas celulares mantidas a 37ºC (temperatura restritiva), comparando-as com aquelas cuja manutenção foi feita a 33ºC (temperatura permissiva). Também foram comparados os perfis proteicos quando os parasitas foram obtidos de culturas celulares mantidas na ausência ou presença de diferentes concentrações de L-prolina. Para tanto, foram feitas preparações de frações enriquecidas em membranas e frações citossólicas dos diferentes estágios do parasita para posterior resolução por eletroforese bidimensional. Através desta análise foi possível identificar polipeptídeos comuns entre os diferentes estágios bem como polipeptídeos específicos de cada estágio de desenvolvimento. / Chapter 1 The transformation of the proliferative epimastigotes of Trypanosoma cruzi into the non-proliferative and infective metacyclic trypomastigotes (metacyclogenesis) is a crucial step occuring naturally in the digestive tract of the reduviid insect vector. This process can be reproduced, in vitro, under chemically defined conditions. It is well established that L-proline is an important energy and carbon source for trypanosomatids but no evidence for its participation in the differentiation of vertebrate host stages of the parasite exists in the literature. This fact prompted us to develop an experimental model to study whether a correlation exits between proline concentration and trypomastigote bursting. In fact, cultures maintained in the absence of L-proline consistently produced fewer trypomastigote forms when compared to cultures maintained in 20 - 200 µM L-proline. The transport activity of L-proline was 15-fold and 23-fold higher in intracellular epimastigote-like forms as compared to amastigotes and trypomastigotes, respectively. Interestingly, proline concentration in intracellular epimastigote-like parasites was 0.73 ± 0.01 mM, as compared to 6.61 ± 0.01 mM for amastigotes and 2.74 ± 0.02 mM for trypomastigotes, while host cells showed an intracellular proline concentration of 0.27 ± 0.03 mM. The data suggest the importance of L-proline in the transformation of intracellular epimastigote-like forms to trypomastigotes. Chapter 2 Differentiation of the infective trypomastigote form of Trypanosoma cruzi to the non-infective and replicative amastigotes normally occurs in the cytoplasm of infected cells. A study about the envolvement of protein phosphatases type 1 and 2A in the extracellular differentiation at 37ºC and 33ºC from trypomastigotes to amastigotes was undertaken using the CL-14 clone of T. cruzi. Calyculin A (an inhibitor of protein phosphatases 1and 2A) triggers the transformation of trypomastigotes to amastigotes at neutral pH through epimastigote-like intermediate forms. Treatment of trypomastigotes for 6 hours with two Calyculin A concentrations (1 nM and 5 nM) resulted in more than 50% of epimastigote-like forms. After 8 hours, all trypomastigotes were differentiated to amastigotes or epimastigotes-like forms. Metacyclic trypomastigotes from the CL-14 clone submitted to the same treatment with Calyculin A showed no morphological changes.

When plants are exposed to multiple environmental stress factors, one form of stress can affect the response to another stress. This study used seedlings of a new cultivar of wheat(Triticum aestivum L. cv. 1862), grown under factorial combinations of two levels of ultraviolet-B (UV-B)radiation, two salinity regimes and two levels of iron treatment in chelator-buffered nutrient solutions in a growth chamber. A number of morphological and physiological measurements were made. The accumulation of chlorophyll, UVabsorbing compounds and proline in shoots, as well as phytosiderophores (PSs) in root exudates were measured. Feed value measurements included crude protein, water-soluble carbohydrates, acid detergent fibre and Fe in shoots and roots. After 21 days of stress exposure, results showed that Fe deficiency and NaCl stress generally decreased plant growth and function as well as nutritive value, but increased plant biochemical protection traits such as proline accumulation (16.3 fold under salinity stress) and release of PSs (2.4 fold under Fe deficiency). Interestingly, UV-B radiation affected belowground parameters, inducing a 47% reduction in PS release, together with decreasing root DM by 9% and Fe concentration in roots by 7%. When Fe deficiency and NaCl stress were combined, the results showed a decrease in PS release by 3.5 fold compared to unstressed plants. UV-B radiation synergistically increased UV-absorbing compound levels in combination with Fe deficiency, compared to plants grown under optimal Fe levels. This stress combination also resulted in a cumulative effect by decreasing Fe concentration in shoots and roots. However, salt stress did not interact with UV-B radiation for any of the traits measured. In addition, some three-way interactions were noted, with the Fe x NaCl x UV-B stress combination slightly decreasing PS release and resulting in a cumulative effect by decreasing Fe concentration in roots. In conclusion, this study found that aboveground stress factors such as UV-B can affect important aspects of belowground plant function, and that Fe deficiency can interact with UV-B and salinity stress in modifying plant responses to either stress alone.

Mycobacterium tuberculosis, the causative agent of pulmonary tuberculosis, infects one-third of the world’s human population. Despite the multiplicity of antimicrobial mechanisms mounted by its host, M. tuberculosis shows a remarkable ability to survive either by evoking survival strategies or by interference with critical macrophage functions that are required to successfully respond to the infection. It has been postulated that the outcome of exposure to M. tuberculosis (in terms of disease symptoms) largely depends upon the selective gene expression of tuberculosis bacilli along with activation of specific signaling pathways in the infected host cells during different phases of infection. In this perspective, determination of the complete genome sequence of Mycobacterium tuberculosis has provided crucial information with respect to the physiology of this bacterium and the pathogenesis of tuberculosis. However, putative functional annotation to all hypothetical proteins coded by M. tuberculosis genome remains complex. One important outcome of the genome-sequencing project was the discovery of two new multigene families designated PE and PPE. About 10% of the M. tuberculosis coding capacity is devoted to the PE and PPE genes, named for the Pro-Glu (PE) and Pro-Pro-Glu (PPE) motifs near the N terminus of their gene products. In addition to these motifs, proteins of PE family share N-terminal domains of approximately 100 amino acids, whereas the PPE proteins possess an N-terminal domain of about 180 amino acids. Many PE and PPE proteins are composed only of these N-terminal homologous domains. However, other members possess an additional C-terminal segment of variable length, often composed of multiple copies of polymorphic GC rich sequences (PGRS). The uniqueness of the PE genes is further illustrated by the fact that these genes are restricted to mycobacteria. However, despite their abundance in mycobacteria, very little is known regarding the expression or the functions of PE family genes. Although the PE and PPE families of mycobacterial proteins are the focus of intense research, no precise function has so far been unraveled for any member of these families. In perspective of above-mentioned observations, we have chosen Rv0754 as a representative PE family gene. Rv0754 was shown to be upregulated in tubercle bacilli upon infection of bone marrow derived macrophages as well as in M. tuberculosis isolated from alveolar macrophages of infected mice. In the current investigation, we demonstrate that Rv0754 is hypoxia responsive gene based on promoter or transcript expression analysis. Further, extensive bioinformatics analysis predicated that Rv0754 posses possible Phosphoglycerate Mutase domain, an enzyme known for its significant role not only in the glycolytic pathway of the carbohydrate metabolism, but also for the crucial cell fate decision during conditions like oxidative stress as well as infection. Experimental data clearly suggests that hypoxic environment dependent expression of Rv0754 imparts resistance to macrophages from oxidative stress. These findings could be attributed to the presence of catalytically active Phosphoglycerate Mutase domain of Rv0754. More often, sophisticated regulation/modulation of key signaling events regulate the critical cell fate decisions during oxidative stress. In this context, TLR2 dependent triggering of PI3K-ERK1/2- NF-κB signaling axis by Rv0754 may be operative in imparting resistance to oxidative stress. Further, Rv0754 triggers COX-2 expression by activating PI3K-ERK1/2-NF-κB cascade in mouse macrophages. These observations are of relevance as Rv0754 is associated with cell wall and is exposed outside the surface of the bacterium suggesting the possible access to intracellular compartments of the infected macrophages. Additionally, Rv0754 elicited humoral antibody reactivities in a panel of human sera or in cerebrospinal fluid samples obtained from different clinical categories of tuberculosis patients. DNA immunizations experiments in mice clearly suggested that Rv0754 is an immunodominant antigen demonstrating significant T cell and humoral reactivity. These observations clearly advocate that Rv0754 protein is expressed in vivo during active infection with M. tuberculosis and that the Rv0754 is immunogenic. Taken together, our findings suggest that Rv0754 is a novel PE_PGRS protein with unique features which could generate conditions that favor survival of the mycobacteria.

One-third of the world’s population is latently infected with Mycobacterium tuberculosis, which causes over 2 million deaths every year. The current live attenuated vaccine, Bacille Calmette-Guerin (BCG), protects against miliary tuberculosis in children, but fails to consistently protect against pulmonary tuberculosis in adults. The global resurgence of tuberculosis, together with the HIV pandemic and emerging multi-drug resistance, has heightened the need for an effective vaccine. Completion of the M. tuberculosis genome sequence paved way for identification of many new candidate antigens for protective vaccine against tuberculosis. This includes the discovery of two multigene families of proteins PE and PPE which constitute 10% of the coding capacity of the M. tuberculosis genome. Members of the PE and PPE protein families are characterized by highly conserved N-terminal domains and the C-terminus, however, exhibit considerable variation in the number of residues as well as in the sequence. Till date, little is known about the functional role of the proteins of PPE or PE family in the biology of M.tuberculosis. Some of the PE_PGRS proteins have been found to be associated with the cell wall and influence interactions with other cells. PE and PPE family of proteins are of potential interest from the point of view of immune response, since they show antigenic variation which may play a role in immune evasion. Very little is known about the immunogenecity of these two classes of proteins and only few proteins have been shown to be potent B or T cell antigens, like Rv3873, Mtb39 and Rv0915c. Two proteins from PE_PGRS subfamily, Rv1759c and Rv3367 are expressed during infection and show antibody response in humans and rabbits, respectively. Rv1196 and Rv0915c from PPE family have been shown to be good T cell antigens. Another study has shown that the PE domain of PE_PGRS protein Rv1818c upon immunization into mice induces good cell mediated immune response in mice, whereas the PGRS domain is responsible for good humoral response. In humans there is increasing evidence to suggest that CD8+ T cells are elicited in response to infection with mycobacteria. CD8+ CTL may play an important role through several mechanisms. They produce potent anti-bacterial cytokines such as IFN-γ and TNF-α in response to antigenic stimulation and IFN-γ is critical for immunity to TB. Thus, identification of antigens and peptides that induce T cell responses could be useful for designing new vaccines to protect against TB. Relatively few epitopes in mycobacterial antigens have so far been identified for human CD8 T cells. In this regard, release of genome sequences of M. tuberculosis has provided an opportunity to identify proteins with vaccine potential that could give immune protection in individuals with different HLA backgrounds. Objectives and scope of the present work 1. Prediction of putative T cell antigens in PE and PPE family of proteins of Mycobacterium tuberculosis through immuno-informatics approach 2. Evaluation of immune response to three of the PE and PPE proteins in mouse model. 3. Evaluation of immune response against chosen PE and PPE proteins of Mycobacterium tuberculosis with Human Peripheral Blood Mononuclear Cells (PBMCs) from PPD positive healthy donors and TB patients. 4. Immune response to multi-epitope DNA vaccine construct for Mycobacterium tuberculosis. Prediction of MHC class I peptides from PE and PPE proteins. In an effort to identify potential T cell antigens from PE and PPE family of proteins, we have carried out a systematic in silico analysis of the 167 different PE and PPE proteins. Employing immuno-informatics approach, a set of HLA class I binding peptides have been identified from these proteins. Further, their binding abilities have been ascertained using independent methods such as molecular modeling and structural analysis methods. The nonameric sequences from PE and PPE families of proteins were predicted to contain high percentage of binding peptides to human class I HLA, whereas PE_PGRS proteins show relatively low level of binding. This difference is seen in spite of PE and PE_PGRS being Sub-families of the same family, PE. Seventy-one high- as well as low-affinity peptides from both PE and PPE proteins have been analyzed for structural compatibility with crystal structures of HLA in terms of intermolecular energies and were found to correlate well with the corresponding affinities predicted by the BIMAS algorithm. Most of the peptides binding to HLA are specific with very few promiscuous binders. Identification of T cell epitopes from three of the PE/PPE proteins using DNA immunization This work describes the evaluation of immune responses to three of the PE and PPE proteins in mouse model. Three of PE and PPE proteins, coded by Rv1818c, Rv3812 and Rv3018c genes were chosen based on immuno-informatics approach. They were cloned, expressed in prokaryotic and mammalian expression vectors and recombinant protein expressing stable cell lines were made. T lymphocytes from DNA immunized mice recognize synthetic peptides from chosen proteins in vitro, indicating that these peptides are being processed and presented by MHC molecules to T cells. By MHC stabilization assay, 5 of the synthetic peptides were found to stabilize the MHC class I molecules on the cell surface for more than 6 hrs, validating the computational prediction. Recognition of T cell epitopes derived from PE/PPE proteins by human PBMCs This work describes the evaluation of immune response against three of PE and PPE proteins of Mycobacterium tuberculosis with Human Peripheral Blood Mononuclear Cells (PBMCs) from PPD positive Healthy donors and TB patients. Proliferation response of PBMCs from ten PPD positive healthy donors as well as from ten TB patients, indicated that the peptides from PE and PPE proteins of Mtb can sensitize naive T cells and induce peptide specific IFN-γ and also the T cell response to the chosen peptides was both HLA class I restricted and CD8 mediated. After the peptide specific expansion, significant percentage of CD8+ T cells were shown to secrete IFN-γ and stained positive for perforin. Antigen specific CD8+ T cells were found to have cytolytic potential in addition to their cytokine function. Immune response to a multiepitope DNA vaccine in mouse model Minigene poly-epitope vaccine constructs coding for nine peptides derived from identified T cell antigens of PE and PPE proteins and three of the experimentally mapped epitopes from M tuberculosis was designed and constructed. The minigene was used to immunize mice and the immune response was tested. The DNA primed splenocytes recognized the full length poly-epitope protein as well as the individual peptides. T cell response to epitopes was enhanced by mere presence in multi-epitope construct compared to full length antigens. Human PBMCs derived from both PPD+ve and TB patients also recognized the peptides in vitro. It is thus obvious that a large cocktail of proteins are required to achieve reasonable population coverage. Besides, this work suggests the feasibility of designing haplotype specific subunit vaccine, which can be given to individuals with known HLA haplotype. The haplotype specific vaccines can be combined to target a population where the distribution of HLA alleles is known. This work also indicates that use of single or limited number of genes in a DNA vaccine may not be suitable to cover a given population.

Hepatitis delta virus (HDV) is the smallest known mammalian RNA virus, containing a genome of ~ 1700 nt. Replication of HDV is extremely dependent on the host transcription machinery. Previous studies indicated that RNA polymerase II (RNAPII) directly binds to and forms an active preinitiation complex on the right terminal stem-loop fragment (R199G) of HDV genomic RNA, and that the polypyrimidine tract-binding protein-associated splicing factor (PSF) directly binds to the same region. Further studies demonstrated that PSF also binds to the carboxyl-terminal domain (CTD) of RNAP II. In my thesis, co-immunoprecipitation assays were performed to show that PSF stimulates the interaction of RNAPII with R199G. Results of co-immunoprecipitation experiments also suggest that both the RNA recognition motif 2 (RRM2) and N-terminal proline-rich region (PRR) of PSF are required for the interaction between PSF and RNAPII, while the two RNA recognition motifs (RRM1 and RRM2) might be required for the interaction of PSF with R199G. Furthermore, in vitro run-off transcription assays suggest that PSF facilitates the HDV RNA transcription from the R199G template. Together, the above experiments suggest that PSF might act as a transcription factor for the RNAPII transcription of HDV RNA by linking the CTD of RNAPII and the HDV RNA promoter. My experiments provide a better understanding of the mechanism of HDV RNA-dependent transcription by RNAP II.

No description available.

Capítulo 1 A transformação (metaciclogênese) das formas proliferativas epimastigotas do Trypanosoma cruzi em formas não proliferativas e infectivas - tripomastigotas metacíclicos - é um passo crucial que ocorre naturalmente no trato digestivo do inseto vetor reduviídeo. Este processo pode ser reproduzido in vitro em condições químicas definidas quando o meio de diferenciação TAU é suplementado com L-prolina e L-glutamato. Está bem estabelecido que prolina é uma fonte importante de energia e de carbono nos tripanossomatídeos, mas são poucas as evidências de sua participação na diferenciação intracelular do parasita no hospedeiro vertebrado. Este fato nos levou a desenvolver um modelo experimental para verificar se havia uma relação entre concentração de prolina e eclosão de formas tripomastigotas. Culturas mantidas sem L-prolina produziram consistentemente menos formas tripomastigotas quando comparadas a culturas mantidas em L-prolina, 20 - 200 µM. A atividade de transporte de L-prolina foi 15 vezes e 23 vezes maior nos epimastigotas intracelulares em relação a amastigotas e tripomastigotas, respectivamente. A concentração de prolina medida nos epimastígotas intracelulares (0,73 ± 0101 mM) é bem menor que a de amastigotas (6,61 ± 0,01 mM) e tripomastigotas (2,74 ± 0,02 mM). Todos os estágios, no entanto, apresentaram concentração de prolina bem maior do que as células hospedeiras, na ordem de 0,27 ± 0,03 mM. A análise do efeito de prolina sobre os diferentes estágios intracelulares mostrou a importância desse aminoácido na transformação de epimastigotas intracelulares a tripomastigotas. Capítulo 2 A diferenciação das formas infecciosas tripomastigotas do Trypanosoma cruzi a formas amastigotas não-infectivas e replicativas ocorre normalmente no citoplasma de células infectadas. Um estudo sobre o envolvimento de proteínas fosfatase do tipo 1 e 2A na diferenciação extracelular a 37ºC e 33ºC de tripomastigotas a formas amastigotas foi realizado, utilizando-se o clone CL-14 de T cruzi. Demonstrou-se que Caliculina A (um inibidor de proteínas fosfatase 1 e 2A) desencadeia a transformação de tripomastigotas a amastigotas em pH neutro, através da passagem por formas intermediárias flageladas semelhantes aos epimastigotas. O tratamento de tripomastigotas com duas concentrações de Caliculina A (1nM e 5 nM) resultou, após 6 horas de incubação, em mais de 50% de formas epimastigota-símiles. Após 8 horas de tratamento, todos os tripomastigotas estavam diferenciados a formas amastigotas ou epimastigota símiles. Tripomastigotas metacíclicos do clone CL-14 submetidos ao mesmo tratamento com Caliculina A não apresentaram alterações morfológicos dentro do período de incubação de 8 horas. Capítulo 3 Fatores ambientais, como a temperatura, e a presença ou ausência de metabólitos tais como a L-prolina influenciam a diferenciação intracelular do Trypanosoma cruzi do clone CL-14. Estes fatos, juntamente com a ausência de dados na literatura sobre o perfil proteico de epimastigotas intracelulares levou-nos a estudar o perfil de expressão de proteínas durante a transformação de epimastigotas intracelulares a tripomastigotas em culturas celulares mantidas a 37ºC (temperatura restritiva), comparando-as com aquelas cuja manutenção foi feita a 33ºC (temperatura permissiva). Também foram comparados os perfis proteicos quando os parasitas foram obtidos de culturas celulares mantidas na ausência ou presença de diferentes concentrações de L-prolina. Para tanto, foram feitas preparações de frações enriquecidas em membranas e frações citossólicas dos diferentes estágios do parasita para posterior resolução por eletroforese bidimensional. Através desta análise foi possível identificar polipeptídeos comuns entre os diferentes estágios bem como polipeptídeos específicos de cada estágio de desenvolvimento. / Chapter 1 The transformation of the proliferative epimastigotes of Trypanosoma cruzi into the non-proliferative and infective metacyclic trypomastigotes (metacyclogenesis) is a crucial step occuring naturally in the digestive tract of the reduviid insect vector. This process can be reproduced, in vitro, under chemically defined conditions. It is well established that L-proline is an important energy and carbon source for trypanosomatids but no evidence for its participation in the differentiation of vertebrate host stages of the parasite exists in the literature. This fact prompted us to develop an experimental model to study whether a correlation exits between proline concentration and trypomastigote bursting. In fact, cultures maintained in the absence of L-proline consistently produced fewer trypomastigote forms when compared to cultures maintained in 20 - 200 µM L-proline. The transport activity of L-proline was 15-fold and 23-fold higher in intracellular epimastigote-like forms as compared to amastigotes and trypomastigotes, respectively. Interestingly, proline concentration in intracellular epimastigote-like parasites was 0.73 ± 0.01 mM, as compared to 6.61 ± 0.01 mM for amastigotes and 2.74 ± 0.02 mM for trypomastigotes, while host cells showed an intracellular proline concentration of 0.27 ± 0.03 mM. The data suggest the importance of L-proline in the transformation of intracellular epimastigote-like forms to trypomastigotes. Chapter 2 Differentiation of the infective trypomastigote form of Trypanosoma cruzi to the non-infective and replicative amastigotes normally occurs in the cytoplasm of infected cells. A study about the envolvement of protein phosphatases type 1 and 2A in the extracellular differentiation at 37ºC and 33ºC from trypomastigotes to amastigotes was undertaken using the CL-14 clone of T. cruzi. Calyculin A (an inhibitor of protein phosphatases 1and 2A) triggers the transformation of trypomastigotes to amastigotes at neutral pH through epimastigote-like intermediate forms. Treatment of trypomastigotes for 6 hours with two Calyculin A concentrations (1 nM and 5 nM) resulted in more than 50% of epimastigote-like forms. After 8 hours, all trypomastigotes were differentiated to amastigotes or epimastigotes-like forms. Metacyclic trypomastigotes from the CL-14 clone submitted to the same treatment with Calyculin A showed no morphological changes.

Made available in DSpace on 2014-07-29T15:16:35Z (GMT). No. of bitstreams: 1 Kelly Pacheco de Castro.pdf: 746240 bytes, checksum: b56c21e04b1a4191824bfab81746d0d2 (MD5) Previous issue date: 2008-01-31 / The dimorphic fungus Paracoccidioides brasiliensis is the causative agent of the most frequent systemic mycosis in Latin America. In humans, infection starts by inhalation of fungal propagules, which reach the pulmonary epithelium and differentiate into the yeast parasitic phase. Here we describe the characterization of a proline-rich protein (PRA/Ag2) homologue of P. brasiliensis, a predictable cell wall protein, first identified in Coccidioides immitis. The protein, the cDNA and genomic sequences were analyzed. Southern blot analysis suggested that there is one copy of the gene in P. brasiliensis. The cloned cDNA was expressed in Escherichia coli and the purified rPbPRA/Ag2 was used to obtain polyclonal antibody. The purified recombinant protein was recognized by sera of patients with proven paracoccidioidomycosis and not by sera of healthy individuals. Immunoelectron microscopy and biochemical studies demonstrated the presence of PbPRA/Ag2 in the fungal cell wall, linked through a GPIanchor. The expression of the Pbpra/ag2 gene was analyzed by real time PCR and results demonstrated developmental regulation in phases of P. brasiliensis, with a higher expression in the mycelium saprobic phase. The protein expression analyses corroborate the transcript levels. / O fungo dimórfico Paracoccidioides brasiliensis é o agente causador da micose sistêmica mais prevalente na América Latina. Em humanos, a infecção se dá pela inalação de propágulos do fungo, que ao alcançarem o epitélio pulmonar transformam se na fase leveduriforme, parasitária, do fungo P. brasiliensis. Neste trabalho,descrevemos a caracterização de um homólogo de PRA/Ag2 (Antígeno rico em prolina), uma proteína predita de parede celular, primeiramente identificada em Coccidioides immitis. A proteína, o cDNA e a seqüência genômica foram analisados. Análises através de Southern blot sugerem que há somente uma cópia do gene em P.brasiliensis. O cDNA clonado foi expresso em Escherichia coli e a rPbPRA/Ag2 purificada foi utilizada para obtenção do anticorpo policlonal. A proteína recombinante purificada foi reconhecida pelo soro de pacientes com paracoccidioidomicose comprovada e não foi reconhecida pelo soro de pacientes saudáveis. Microscopia eletrônica e estudos bioquímicos demonstraram a presença do PbPRA/Ag2 na parede celular de P. brasiliensis, ligada através de uma âncora de GPI. A expressão do gene que codifica Pbpra/ag2 foi analisada através de PCR em Tempo Real e os resultados demonstraram regulação da expressão nas fases de P. brasiliensis, com maior nível de expressão na fase miceliana. Análises da expressão protéica corroboram os resultados da RT-PCR em Tempo Real.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-07-20T19:32:21Z No. of bitstreams: 1 virginiafernandesbraga.pdf: 2075207 bytes, checksum: 720e5dba0516d172aec1843372dcecc2 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2016-07-22T15:25:58Z (GMT) No. of bitstreams: 1 virginiafernandesbraga.pdf: 2075207 bytes, checksum: 720e5dba0516d172aec1843372dcecc2 (MD5) / Made available in DSpace on 2016-07-22T15:25:58Z (GMT). No. of bitstreams: 1 virginiafernandesbraga.pdf: 2075207 bytes, checksum: 720e5dba0516d172aec1843372dcecc2 (MD5) Previous issue date: 2011-04-20 / Pitcairnia albiflos Herb. (Bromeliaceae) atualmente se encontra na lista de espécies ameaçadas de extinção. Essa espécie é endêmica dos afloramentos rochosos do município do Rio de Janeiro, RJ, e vem sofrendo com o pisoteio de alpinistas, queimadas, invasão de gramíneas exóticas e extrativismo vegetal. A micropropagação pode ser utilizada como alternativa às condições de risco em que as populações dessa espécie se encontram submetidas, visando à recomposição de populações ameaçadas em ambiente natural, assim como o abastecimento do mercado consumidor. A etapa final da micropropagação é a aclimatização, período em que as plantas ficam mais susceptíveis e sofrem com o estresse oxidativo devido às mudanças nas condições ambientais. No presente trabalho foram avaliadas as atividades enzimáticas antioxidativas da CAT, SOD, POD, PPO e o conteúdo de prolina, além dos teores de pigmentos fotossintéticos em plantas de Pitcairnia albiflos cultivados in vitro, em meios de cultura contendo duas concentrações de sacarose (15 ou 30 g L-1), tampas não vedadas que permitiam trocas gasosas e frascos vedados com tampas e filme plástico de PVC, que impediam a ventilação. Sob essas condições, as plantas foram cultivadas em meios contendo GA3 ou ANA. Após o período de crescimento in vitro, as plantas foram transferidas para condições ex vitro em casa de vegetação. As análises supra-citadas e a determinação dos teores de carboidratos solúveis totais, sacarose, amido, açúcares redutores, conteúdo relativo de água e suculência também foram realizadas nas plantas previamente cultivadas in vitro com 15 ou 30 g L-1 de sacarose e GA3 em tubos com tampas vedadas, após submissão das mesmas a estresse hídrico durante 24, 38 ou 52 dias. Após o período de estresse hídrico, as plantas foram reidratadas durante 34 dias sob irrigação periódica em casa de vegetação. Nos tecidos cultivados in vitro percebeu-se o surgimento de características de hiperidricidade nas plantas cultivadas com 15 g L-1 de sacarose, GA3 e tubos com tampas vedadas, o que foi evidenciado pelo menor acúmulo de prolina, aumento das atividades das enzimas antioxidantes e menor acúmulo de pigmentos fotossintetizantes. Na condição ex vitro, as plantas cultivadas anteriormente em meio de cultura contendo 15 g L-1 de sacarose apresentaram maior atividade das enzimas antioxidantes não havendo, em alguns casos, diferenças significativas em comparação com a concentração mais elevada de sacarose. Nessa condição o acúmulo de prolina foi menor, o que é indicativo de maior estresse oxidativo nessas plantas durante a aclimatização. Durante o estresse hídrico houve queda na atividade de todas as enzimas estudadas, embora essa queda tenha sido mais acentuada para as plantas que inicialmente foram cultivadas com 15 g L-1 de vi sacarose. O acúmulo de prolina aumentou com o prolongamento do estresse hídrico, sendo maior nas plantas que foram cultivadas in vitro com 30 g L-1 de sacarose. Não houve diferenças significativas no conteúdo de pigmentos fotossintetizantes e nas suas relações para nenhuma das concentrações de sacarose, exceto para os carotenóides totais, que apresentaram aumento significativo ao longo do período de estresse hídrico para as plantas previamente cultivadas com a menor concentração de sacarose. Os conteúdos de carboidratos solúveis totais e sacarose aumentaram com o prolongamento do estresse, sendo mais acentuados na concentração de 30 g L-1 de sacarose. Os conteúdos de amido, o conteúdo relativo de água e a suculência apresentaram redução com o aumento do estresse hídrico. Após a reidratação, todas as plantas mostraram capacidade de recuperação, apresentando valores próximos aos dos controles para todas as variáveis analisadas. Ressalta-se, todavia, que as plantas tratadas com 30 g L-1 de sacarose tiveram melhor recuperação quando comparadas com aquelas que foram tratadas com 15 g L-1 de sacarose. Em função dos resultados obtidos, é possível concluir que a concentração de sacarose utilizada in vitro apresenta influência no processo de aclimatização ex vitro e também, posteriormente, no campo, na capacidade de recuperação das plantas à seca quando elas são submetidas a estresse hídrico. As plantas cultivadas in vitro com 15 g L-1 de sacarose se mostraram mais sensíveis à seca e, possivelmente, não sobreviveriam caso fossem transferidas dos tubos de ensaio diretamente para o campo. As plantas cultivadas in vitro com 30 g L-1 de sacarose aparentemente eram mais resistentes ao processo de aclimatização ex vitro, apresentando maiores chances de sobrevivência em campo, maior tolerância à seca e maior capacidade de recuperação após períodos prolongados de estresse hídrico. / Pitcairnia albiflos Herb. (Bromeliaceae) is currently in the list of endangered species. This species is endemic of the inselbergs of the city of Rio de Janeiro, RJ, and has been suffering with the mountaineer’s trampling, wildfires, invasion of exotic grasses and plant extraction. The micropropagation can be used as an alternative to the risk conditions under which populations of this species are submitted, aiming at the recomposition of endangered populations in the natural environment, as well as the supply of the consumer market. The final stage of the micropropagation is the acclimatization, period in which the plants become more susceptible and suffer from oxidative stress due to the changes in the environmental conditions. In the present study it were evaluated the antioxidative enzymatic activities of CAT, SOD, POD, PPO and proline content, besides the levels of photosynthetic pigments in plants of Pitcairnia albiflos grown in vitro in culture mediums containing two sucrose concentrations (15 or 30 g L-1). Part was covered with unsealed lids that allowed gas exchanges and part was kept in sealed flasks with lids and PVC plastic film, that didn’t allow the ventilation. Under these conditions, the plants were cultivated in culture mediums containing GA3 or NAA. After the in vitro growth period, the plants were transferred to ex vitro conditions at a greenhouse. The above mentioned analyses and the determination of total soluble carbohydrate levels, sucrose, starch, reducer sugars, relative water content and succulence were also performed on the plants previously grown in vitro with 15 or 30 g L-1 of sucrose and GA3 in tubes with sealed lids, after the submission of these to water stress during 24, 38 or 52 days. After the water stress period, the plants were rehydrated for 34 days under regular irrigation at the greenhouse. In the in vitro cultivated tissues it was noted the emergence of hyperhydricity characteristics in the plants grown with 15 g L-1 of sucrose, GA3 and tubes with sealed lids, which was evidenced by the lowest proline accumulation, the increased in the antioxidative enzymatic activities and the lowest accumulation of photosynthetic pigments. In the ex vitro condition, the plants previously grown in culture mediums containing 15 g L-1 of sucrose presented larger antioxidative enzymatic activities, which did not show, in some cases, significant differences compared with the largest concentration of sucrose. In this condition, the proline accumulation was lower, which is an indicative of larger oxidative stress in these plants during acclimatization. During the water stress, there was a fall in the activity of all studied enzymes, although that fall had been more evident in the plants that were initially cultivated with 15 g L-1 of sucrose. The proline accumulation increased with the extension of the water stress, being larger in the plants grown in vitro with 30 g L-1 of sucrose. There were no viii significant differences in the content of photosynthetic pigments and in their relation with any sucrose concentrations, except for total carotenoids, which significantly increased over the period of water stress for the plants previously grown with the lowest concentration of sucrose. The contents of total soluble carbohydrates and sucrose increased with the extension of the stress, being more accentuated in the 30 g L-1 of sucrose concentration. The contents of starch, the relative content of water and succulence presented a reduction with the increase of water stress. After the rehydration, all plants showed recovery capacity, presenting values close to those from the control groups for all the analyzed variables. It should be noted, however, that the plants treated with 30 g L-1 of sucrose had better recovery compared with those that were treated with 15 g L-1 of sucrose. According to the obtained results, it is possible to conclude that the concentration of sucrose used in vitro presents influence on the process of ex vitro acclimatization and also, later in the field, in the recovery capacity of the plants to drought when they are submitted to water stress. The plants grown in vitro with 15 g L-1 of sucrose were more sensitive to drought and, possibly, would not survive if they were transferred from the test tubes directly to the field. The plants grown in vitro with 30 g L-1 of sucrose were apparently more resistant to the ex vitro acclimatization process, presenting greater survival chances in the field, larger drought tolerance and larger recovery capacity after extended periods of water stress.

Abstract Spontaneous changes in protein systems, such as the binding of a ligand to an enzyme or receptor, are characterized by a decrease of free energy. Despite the recent developments in computing power and methodology, it remains challenging to accurately estimate free energy changes. Major issues are still concerned with the accuracy of the underlying model to describe the protein system and how well the calculation in fact emulates the behaviour of the system. This thesis is largely concerned with the quality of current free energy calculation methods as applied to protein-ligand systems. Several methodologies were employed to calculate Gibbs standard free energies of binding for a collection of protein-ligand complexes, for which experimental affinities were available. Calculations were performed using system description with different levels of accuracy and included a continuum approach, which considers the protein and the ligand at the atomic level but includes solvent as a polarizable continuum, and an all-atom approach that relies on molecular dynamics simulations. In most such applications, the effects of ionic strength are neglected. However, the severity of this approximation, in particular when calculating free energies of charged ligands, is not very clear. The issue of incorporating ionic strength in free energy calculations by means of explicit ions was investigated in greater detail and considerable attention was given to the affinities of charged peptides in the presence of explicit counter-ions. A second common approximation is concerned with the description of ligands that exhibit multiple protonation states. Because most of current methods do not model changes in the acid dissociation constants of titrating groups upon binding, protonation equilibria of such ligands are not taken into account in free energy calculations. The implications of this approximation when predicting affinities were analysed. Finally, when calculating free energies of binding, a correct description of the interactions between the protein and the ligand is of fundamental importance. However, active sites of enzymes, where strained conformations may hold a functional role, are not always accurately modelled by molecular mechanics force fields. The case of a strained planar proline in the active site of triosephosphate isomerase was investigated using an hybrid quantum mechanics/molecular mechanics method, which implies a higher level of accuracy.