O desenvolvimento de biotecnologia de embriões em animais de produção é prejudicado por perdas no primeiro trimestre da gestação, idade em que o intestino primitivo está sendo estabelecido. O estudo das proteínas contidas no intestino primitivo nesta fase inicial da gestação pode aumentar o conhecimento sobre as vias moleculares envolvidas no desenvolvimento embrionário normal e em perdas de embriões, assim como a sua participação na organogênese e diferenciação celular. Intestino primitivo de embriões de bovinos a partir dos 39 SD ± 4 dias de desenvolvimento (variando de 33 a 45 dias) foram coletados em um matadouro local. As amostras foram processadas e agrupadas para análise proteômica shotgun label-free usando MudPIT (Multidimensional Protein Identification Technology). Análise funcional e de via foram feitas usando FatiGO (www.babelomics.org); Pathway Express (http://vortex.cs.wayne.edu/ ontoexpress) para identificar as ontologias relevantes e vias canônicas ou não-canônicas representada pelas proteínas expressas no Intestino primitivo. Um total de 74 proteínas ou sequências randômicas foram identificadas, correspondentes a 30 proteínas específicas expressas pelo Intestino primitivo bovino. Das 30 proteínas únicas, 21 proteínas foram utilizadas na ontologia e análise de vias. As análises mostraram um enriquecimento de ontologias relacionadas com a ligação (N = 5); atividade catalítica (N = 6); organela intracelular (N = 6). Houve um enriquecimento de ontologias associado às modificações do citoesqueleto; processo de diferenciação celular (N = 3), a migração celular (N = 4) e no metabolismo celular (N = 6). Além disso, a via e a análise de rede mostraram um enriquecimento de vias de comunicação entre células, tais como junções comunicantes e tight e as vias de adesão focal. Além disso, as vias envolvidas no movimento celular (por exemplo, vias de regulação do citoesqueleto de actina e a migração transendotelial de leucócitos) foram extremamente enriquecimento no grupo de proteínas expressas pelo Intestino primitivo bovino. Nossos resultados sugerem que as células do intestino primitivo tem alto perfil migratório e são compostas de células não totalmente diferenciadas, com alto metabolismo celular. A migração e a diferenciação destas células poderiam determinar o destino do embrião em desenvolvimento. Além disso, a compreensão da função e interação de proteínas expressas pelo embrião normal fornecerá informações sobre o impacto das biotecnologias reprodutivas no desenvolvimento do embrião durante a implantação e placentação. / The development of embryo biotechnology in farm animals is hampered by embryo losses in first trimester of gestation, period in which the primitive gut is being established. The study of proteins contained in the primitive gut at this early stage of pregnancy may increase the knowledge about the molecular pathways involved in normal embryonic development and loss of embryos, as well as their involvement in organogenesis and cell differentiation.primitive gut from bovine embryos on day 39 SD± 4 of development (ranging from 33 to 45 days) were collected at a local slaugtherhouse. The samples were processed and pooled for label-free shotgun proteomics analysis using MudPIT (Multidimensional Protein Identification Technology) tandem MSE acquisition. Functional and pathway analysis using FatiGo (www.babelomics.org); Pathway Express (http://vortex.cs.wayne.edu/ ontoexpress) and Ingenuity Pathway Analysis (www.ingenuity.com) were used to identify relevant ontologies and canonical or noncanonical pathways represented by the expressed proteins in the primitive gut. A total of 74 protein sequences were identified corresponding to 30 unique proteins expressed by the bovine primitive gut. out of 30 unique proteins, 21 proteins were used on the ontology and pathway analysis. The ontology analysis showed an enrichment of ontologies related to binding (N=5); catalytic activity (N=6); intracellular organelle (N=6). There was an enrichment of ontologies associated to cytoskeleton modifications; cell differentiation process (N=3); cellular migration (N=4) and cell metabolism (N=6). Furthermore, the pathway and the network analysis showed an enrichment of cell-to-cell communication pathways such as gap and tight junction, and focal adhesion pathways. In addition, pathways involved in cellular movement (regulation of actin cytoskeleton and leukocyte transendothelial migration) were extremely enrichment in the group of proteins expressed by the bovine primitive gut. Our results suggested that the cells from primitive gut have high migratory profile and are composed of not fully differentiated cells with high cellular metabolism. The proper migration and differentiation of these cells would dictate the fate of the developing embryo. Moreover, understanding the function and interaction of proteins expressed by normal embryo will give clues of the impact of the reproductive biotechnologies in embryo development during the window between implantation and placentation.

O desenvolvimento de biotecnologia de embriões em animais de produção é prejudicado por perdas no primeiro trimestre da gestação, idade em que o intestino primitivo está sendo estabelecido. O estudo das proteínas contidas no intestino primitivo nesta fase inicial da gestação pode aumentar o conhecimento sobre as vias moleculares envolvidas no desenvolvimento embrionário normal e em perdas de embriões, assim como a sua participação na organogênese e diferenciação celular. Intestino primitivo de embriões de bovinos a partir dos 39 SD ± 4 dias de desenvolvimento (variando de 33 a 45 dias) foram coletados em um matadouro local. As amostras foram processadas e agrupadas para análise proteômica shotgun label-free usando MudPIT (Multidimensional Protein Identification Technology). Análise funcional e de via foram feitas usando FatiGO (www.babelomics.org); Pathway Express (http://vortex.cs.wayne.edu/ ontoexpress) para identificar as ontologias relevantes e vias canônicas ou não-canônicas representada pelas proteínas expressas no Intestino primitivo. Um total de 74 proteínas ou sequências randômicas foram identificadas, correspondentes a 30 proteínas específicas expressas pelo Intestino primitivo bovino. Das 30 proteínas únicas, 21 proteínas foram utilizadas na ontologia e análise de vias. As análises mostraram um enriquecimento de ontologias relacionadas com a ligação (N = 5); atividade catalítica (N = 6); organela intracelular (N = 6). Houve um enriquecimento de ontologias associado às modificações do citoesqueleto; processo de diferenciação celular (N = 3), a migração celular (N = 4) e no metabolismo celular (N = 6). Além disso, a via e a análise de rede mostraram um enriquecimento de vias de comunicação entre células, tais como junções comunicantes e tight e as vias de adesão focal. Além disso, as vias envolvidas no movimento celular (por exemplo, vias de regulação do citoesqueleto de actina e a migração transendotelial de leucócitos) foram extremamente enriquecimento no grupo de proteínas expressas pelo Intestino primitivo bovino. Nossos resultados sugerem que as células do intestino primitivo tem alto perfil migratório e são compostas de células não totalmente diferenciadas, com alto metabolismo celular. A migração e a diferenciação destas células poderiam determinar o destino do embrião em desenvolvimento. Além disso, a compreensão da função e interação de proteínas expressas pelo embrião normal fornecerá informações sobre o impacto das biotecnologias reprodutivas no desenvolvimento do embrião durante a implantação e placentação. / The development of embryo biotechnology in farm animals is hampered by embryo losses in first trimester of gestation, period in which the primitive gut is being established. The study of proteins contained in the primitive gut at this early stage of pregnancy may increase the knowledge about the molecular pathways involved in normal embryonic development and loss of embryos, as well as their involvement in organogenesis and cell differentiation.primitive gut from bovine embryos on day 39 SD± 4 of development (ranging from 33 to 45 days) were collected at a local slaugtherhouse. The samples were processed and pooled for label-free shotgun proteomics analysis using MudPIT (Multidimensional Protein Identification Technology) tandem MSE acquisition. Functional and pathway analysis using FatiGo (www.babelomics.org); Pathway Express (http://vortex.cs.wayne.edu/ ontoexpress) and Ingenuity Pathway Analysis (www.ingenuity.com) were used to identify relevant ontologies and canonical or noncanonical pathways represented by the expressed proteins in the primitive gut. A total of 74 protein sequences were identified corresponding to 30 unique proteins expressed by the bovine primitive gut. out of 30 unique proteins, 21 proteins were used on the ontology and pathway analysis. The ontology analysis showed an enrichment of ontologies related to binding (N=5); catalytic activity (N=6); intracellular organelle (N=6). There was an enrichment of ontologies associated to cytoskeleton modifications; cell differentiation process (N=3); cellular migration (N=4) and cell metabolism (N=6). Furthermore, the pathway and the network analysis showed an enrichment of cell-to-cell communication pathways such as gap and tight junction, and focal adhesion pathways. In addition, pathways involved in cellular movement (regulation of actin cytoskeleton and leukocyte transendothelial migration) were extremely enrichment in the group of proteins expressed by the bovine primitive gut. Our results suggested that the cells from primitive gut have high migratory profile and are composed of not fully differentiated cells with high cellular metabolism. The proper migration and differentiation of these cells would dictate the fate of the developing embryo. Moreover, understanding the function and interaction of proteins expressed by normal embryo will give clues of the impact of the reproductive biotechnologies in embryo development during the window between implantation and placentation.

Burkholderia pseudomallei is the causative agent of Melioidosis, an endemic disease in South East Asia, and is classified as a category B biological agent. Currently, there is no licensed vaccine for this disease; the mortality rate is high due to the incorrect diagnosis and the pathogen insusceptibility to general antibiotics. A mass spectrometry based proteomic approach has been applied in order to identify the proteins that are responsible for pathogenicity.Methods were developed for the proteomic analysis of Burkholderia species using B. vietnamiensis G4, an opportunistic pathogen as the model organism. Both gel-based (LC-MS/MS) and gel-free MudPIT (LC/LC-MS/MS) approaches have been applied for the analysis of the proteins extracted from four different cellular fractions of these bacteria. More than 1200 proteins were identified from these analyses, including many proteins previously identified as virulence factors of these bacteria. Similar methodologies were applied to build a proteome map of non-pathogenic B. thailandensis E264 to use as a reference for the pathogenic studies. Additionally, proteomes of two B. thailandensis strains isolated from two geographical locations were compared to investigate the differences in protein expression of these organisms.Proteins identified from pathogenic B. pseudomallei were compared with the non-pathogenic B. thailandensis and opportunistic pathogen B. vietnamiensis proteins. Many species specific proteins were identified from this proteomic analyses; those proteins can be used as antigen targets to selectively identify these pathogenic bacteria in a complex biological matrix using affinity capture methods.Ticks are vectors that can transmit disease causing pathogens one host to another. Knowing the pathogen reservoir is important in order to control disease spread in the environment. Application of mass spectrometric methods to identify the host blood components from tick vectors was investigated using tick nymphs which feed only once in their life cycle. Using mass spectrometry based proteomics; host specific proteins like hemoglobin and immunoglobulin were identified from a single tick nymph analysis. Additional studies have examined the fatty acid profiles of rabbit and sheep blood fed tick nymphs using SPALDI mass spectrometry. Different fatty acid profiles were obtained for these tick nymphs, but further investigations are required to validate these findings.

Indiana University-Purdue University Indianapolis (IUPUI) / Hydroxyl radical protein footprinting coupled with mass spectrometry has become an invaluable technique for protein structural characterization. In this method, hydroxyl radicals react with solvent exposed amino acid side chains producing stable, covalently attached labels. Although this technique yields beneficial information, the extensive list of known oxidation products produced increases the complexity of identifying and quantifying oxidation products. The current methods available for quantifying the extent of oxidation either involve manual analysis steps, or limit the number of searchable modifications or the size of sequence database. This creates a bottleneck which can result in a long and arduous analysis process, which is further compounded in a complex sample. In addition to the data complexity, the peptides containing the oxidation products of hydroxyl radical-mediated protein footprinting experiments are typically much less abundant than their unoxidized counterparts. This is inherent to the design of the experiment as excessive oxidation may lead to undesired conformational changes or unfolding of the protein, skewing the results. Thus, as the complexity of the systems studied using this method expands, the detection and identification of these oxidized species can be increasingly difficult with the limitations of data-dependent acquisition (DDA) and one-dimensional chromatography. The recently published in cell FPOP method exemplifies where this field is headed - larger and more complex systems. This dissertation describes two new methodologies and one new technology for hydroxyl radical-mediated protein footprinting, expanding the applicability of the method. First is development of a new footprinting analysis method for both peptide and residue level analysis, allowing for faster quantification of results. This method utilizes a customized multilevel search workflow developed for an on-market search platform in conjunction with a quantitation platform developed using a free Excel add-in, expediting the analysis process. Second is the application of multidimensional protein identification technology (MudPIT) in combination with hydroxyl radical footprinting as a method to increase the identification of quantifiable peptides in these experiments. Last is the design and implementation of a flow system for in cell FPOP, which hydrodynamically focuses the cells, and when used yielded a 13-fold increase in oxidized proteins and 2 orders of magnitude increase in the dynamic range of the method.

Infestações com Rhipicephalus microplus, o carrapato dos bovinos, causam enormes prejuízos econômicos para a pecuária. Os carrapatos estão desenvolvendo resistência aos carrapaticidas que, além dessa desvantagem, deixam resíduos em carne e leite. Vacinas anticarrapato representam uma alternativa sustentável de controle de infestações, mas as atualmente disponíveis têm efeitos parciais e transitórios. Surge, assim, a necessidade de identificar novos antígenos vacinais. Para alcançar esse objetivo este trabalho explora o fato de que bovinos apresentam fenótipos contrastantes e herdáveis de infestações que são específicos de certas raças. Além disso, o nível de imunidade do hospedeiro afeta a transcrição de genes de glândulas salivares do carrapato, órgão que produz proteínas que medeiam o parasitismo. A hipótese de trabalho é a que os diferentes níveis da imunidade anticarrapato do hospedeiro afetam, também, a composição salivar do parasita. Assim, em carrapatos alimentando-se em hospedeiros resistentes as proteínas que são cruciais ao parasitismo poderão estar ausentes ou deficientes na sua saliva e por isso os carrapatos não terminam sua refeição de sangue. A neutralização dessas mesmas proteínas pela imunidade humoral pode ter o mesmo efeito e por isso, essas proteínas constituem bons antígenos vacinais. Assim, o objetivo do trabalho foi identificar novos antígenos vacinais em saliva de fêmeas e glândulas salivares de ninfas, machos e fêmeas de carrapatos alimentados em hospedeiros resistentes e suscetíveis, bem como em larvas não alimentadas oriundas de ovos de fêmeas alimentadas nestes mesmos hospedeiros. Para isso, foram empregadas abordagens de sequenciamento de nova geração \"RNA-Seq\" (454) e abordagens proteômicas, como análise diferencial em gel (DIGE) e Western Blots (imunoproteoma) seguido de sequenciamento de massa, além da tecnologia de identificação de proteínas multidimensionais (ou Multidimensional Protein Identification Technology, MudPIT) para descrever o proteoma das glândulas salivares e da saliva de fêmeas. A análise transcriptômica resultou no sequencimanto de 1.999.086 reads que permitiu identificar e classificar 11.676 sequências codificadoras (CDS), muitas das quais (3.600 CDS) contêm peptídeo sinal que é indicativo de secreção, portanto podendo estar presente na saliva e Resumo Gustavo Rocha Garcia apresentar função importante na hematofagia. Por meio de MudPIT, identificamos 321 proteínas salivares diferentes, além de 126 proteínas no DIGE e 266 proteínas nos imunoproteomas. Muitas dessas proteínas podem ser consideradas antígenos potenciais por estarem associadas com a hematofagia/parasitismo, tais como proteases, nucleases, inibidores de proteases, peptídeos antimicrobianos, proteínas de fixação, entre outros, inclusive proteínas ainda não caracterizadas. A maioria dos genes codificantes dessas proteínas está mais expressa em carrapatos alimentados em hospedeiros suscetíveis, principalmente em carrapatos machos. Além disso, muitas dessas proteínas não são reconhecidas por soros bovinos, inclusive soros de bovinos infestados, embora soros de bovinos infestados e resistentes ao carrapato apresente a maioria das reatividades. O conjunto dos resultados sugere que em nível de proteína a composição da saliva também é afetada pelos diferentes níveis de imunidade dos hospedeiros, além de variar com o ciclo de vida do carrapato. Desse modo, concluímos que as estratégias de investigação empregadas foram satisfatórias para identificar um conjunto de antígenos salivares do carrapato R. microplus que representam proteínas alvos para compor vacinas multicomponentes anticarrapato. / Infestation with Rhipicephalus microplus, the cattle tick, causes huge economic losses to livestock. Ticks are developing resistance to acaricides that, besides this disadvantage, leave residues in meat and milk. The anti tick vaccines represent a sustainable alternative of the infestations control, but the currently available has partial and transient effects. Thus arises the need to identify new vaccine antigens. To achieve this goal, this work explores the fact that cattle exhibit contrasting phenotypes and inheritable of infestations that are specific to certain breeds. Furthermore, the level of immunity of the host affects gene transcription tick salivary gland, organ that produces proteins that mediate the parasitism. The working hypothesis is that different levels of anti tick immunity of host affect also the salivary composition of the parasite. So in ticks feeding on resistant hosts the proteins that are crucial to parasitism may be absent or deficient in their saliva, and by this the ticks do not finish your meal blood. The neutralization of these same proteins by humoral immunity can have the same effect and by this, these proteins are good vaccine antigens. So, the aim of the study was to identify new vaccine antigens in saliva from females and salivary glands of nymphs, males and females of ticks fed on resistant and susceptible hosts as well as in unfed larvae originating from eggs of females fed on these same hosts. To this, were employed sequencing approaches of new generation \"RNA-Seq\" (454) and proteomic approaches, such as differential analysis in gel (DIGE) and Western Blots (immunoproteomics) followed by sequencing mass, besides the Multidimensional Protein Identification Technology (MudPIT) to describe the proteome of the salivary glands and saliva of females. The transcriptomics analysis identified 11,676 coding sequences (CDS), many of which (3,600 CDS) contain predicted signal peptide indicative of secretion, therefore may be present in saliva and provide an important function in blood feeding. Through MudPIT, we identify 321 different salivary proteins, besides 126 proteins in DIGE and 266 proteins in immunoproteomics. Many of these proteins may be considered as potential antigens to be associated with the blood meal/ parasitism, such as proteases, nucleases, protease inhibitors, antimicrobial peptides, proteins of attachment, among Abstract Gustavo Rocha Garcia others, including proteins not yet characterized. Most of the genes encoding of these proteins are more expressed in ticks fed on susceptible hosts, especially in male ticks. Moreover, many of these proteins are not recognized by bovine sera, including sera from infested hosts, although sera from infested and resistant host to tick present the most reactivities. The overall results suggest that in protein level, the composition of saliva is also affected by the different levels of immunity of the host, besides vary with the tick life cycle. Thus, we conclude that the research strategies employed were satisfactory to identify a set of tick salivary antigens from R. microplus that represent target proteins for composing anti tick multicomponent vaccines.

Infestações com Rhipicephalus microplus, o carrapato dos bovinos, causam enormes prejuízos econômicos para a pecuária. Os carrapatos estão desenvolvendo resistência aos carrapaticidas que, além dessa desvantagem, deixam resíduos em carne e leite. Vacinas anticarrapato representam uma alternativa sustentável de controle de infestações, mas as atualmente disponíveis têm efeitos parciais e transitórios. Surge, assim, a necessidade de identificar novos antígenos vacinais. Para alcançar esse objetivo este trabalho explora o fato de que bovinos apresentam fenótipos contrastantes e herdáveis de infestações que são específicos de certas raças. Além disso, o nível de imunidade do hospedeiro afeta a transcrição de genes de glândulas salivares do carrapato, órgão que produz proteínas que medeiam o parasitismo. A hipótese de trabalho é a que os diferentes níveis da imunidade anticarrapato do hospedeiro afetam, também, a composição salivar do parasita. Assim, em carrapatos alimentando-se em hospedeiros resistentes as proteínas que são cruciais ao parasitismo poderão estar ausentes ou deficientes na sua saliva e por isso os carrapatos não terminam sua refeição de sangue. A neutralização dessas mesmas proteínas pela imunidade humoral pode ter o mesmo efeito e por isso, essas proteínas constituem bons antígenos vacinais. Assim, o objetivo do trabalho foi identificar novos antígenos vacinais em saliva de fêmeas e glândulas salivares de ninfas, machos e fêmeas de carrapatos alimentados em hospedeiros resistentes e suscetíveis, bem como em larvas não alimentadas oriundas de ovos de fêmeas alimentadas nestes mesmos hospedeiros. Para isso, foram empregadas abordagens de sequenciamento de nova geração \"RNA-Seq\" (454) e abordagens proteômicas, como análise diferencial em gel (DIGE) e Western Blots (imunoproteoma) seguido de sequenciamento de massa, além da tecnologia de identificação de proteínas multidimensionais (ou Multidimensional Protein Identification Technology, MudPIT) para descrever o proteoma das glândulas salivares e da saliva de fêmeas. A análise transcriptômica resultou no sequencimanto de 1.999.086 reads que permitiu identificar e classificar 11.676 sequências codificadoras (CDS), muitas das quais (3.600 CDS) contêm peptídeo sinal que é indicativo de secreção, portanto podendo estar presente na saliva e Resumo Gustavo Rocha Garcia apresentar função importante na hematofagia. Por meio de MudPIT, identificamos 321 proteínas salivares diferentes, além de 126 proteínas no DIGE e 266 proteínas nos imunoproteomas. Muitas dessas proteínas podem ser consideradas antígenos potenciais por estarem associadas com a hematofagia/parasitismo, tais como proteases, nucleases, inibidores de proteases, peptídeos antimicrobianos, proteínas de fixação, entre outros, inclusive proteínas ainda não caracterizadas. A maioria dos genes codificantes dessas proteínas está mais expressa em carrapatos alimentados em hospedeiros suscetíveis, principalmente em carrapatos machos. Além disso, muitas dessas proteínas não são reconhecidas por soros bovinos, inclusive soros de bovinos infestados, embora soros de bovinos infestados e resistentes ao carrapato apresente a maioria das reatividades. O conjunto dos resultados sugere que em nível de proteína a composição da saliva também é afetada pelos diferentes níveis de imunidade dos hospedeiros, além de variar com o ciclo de vida do carrapato. Desse modo, concluímos que as estratégias de investigação empregadas foram satisfatórias para identificar um conjunto de antígenos salivares do carrapato R. microplus que representam proteínas alvos para compor vacinas multicomponentes anticarrapato. / Infestation with Rhipicephalus microplus, the cattle tick, causes huge economic losses to livestock. Ticks are developing resistance to acaricides that, besides this disadvantage, leave residues in meat and milk. The anti tick vaccines represent a sustainable alternative of the infestations control, but the currently available has partial and transient effects. Thus arises the need to identify new vaccine antigens. To achieve this goal, this work explores the fact that cattle exhibit contrasting phenotypes and inheritable of infestations that are specific to certain breeds. Furthermore, the level of immunity of the host affects gene transcription tick salivary gland, organ that produces proteins that mediate the parasitism. The working hypothesis is that different levels of anti tick immunity of host affect also the salivary composition of the parasite. So in ticks feeding on resistant hosts the proteins that are crucial to parasitism may be absent or deficient in their saliva, and by this the ticks do not finish your meal blood. The neutralization of these same proteins by humoral immunity can have the same effect and by this, these proteins are good vaccine antigens. So, the aim of the study was to identify new vaccine antigens in saliva from females and salivary glands of nymphs, males and females of ticks fed on resistant and susceptible hosts as well as in unfed larvae originating from eggs of females fed on these same hosts. To this, were employed sequencing approaches of new generation \"RNA-Seq\" (454) and proteomic approaches, such as differential analysis in gel (DIGE) and Western Blots (immunoproteomics) followed by sequencing mass, besides the Multidimensional Protein Identification Technology (MudPIT) to describe the proteome of the salivary glands and saliva of females. The transcriptomics analysis identified 11,676 coding sequences (CDS), many of which (3,600 CDS) contain predicted signal peptide indicative of secretion, therefore may be present in saliva and provide an important function in blood feeding. Through MudPIT, we identify 321 different salivary proteins, besides 126 proteins in DIGE and 266 proteins in immunoproteomics. Many of these proteins may be considered as potential antigens to be associated with the blood meal/ parasitism, such as proteases, nucleases, protease inhibitors, antimicrobial peptides, proteins of attachment, among Abstract Gustavo Rocha Garcia others, including proteins not yet characterized. Most of the genes encoding of these proteins are more expressed in ticks fed on susceptible hosts, especially in male ticks. Moreover, many of these proteins are not recognized by bovine sera, including sera from infested hosts, although sera from infested and resistant host to tick present the most reactivities. The overall results suggest that in protein level, the composition of saliva is also affected by the different levels of immunity of the host, besides vary with the tick life cycle. Thus, we conclude that the research strategies employed were satisfactory to identify a set of tick salivary antigens from R. microplus that represent target proteins for composing anti tick multicomponent vaccines.

Submitted by DHARA CARLESSO ZAMPIVA (dhara.zampiva@univates.br) on 2018-08-20T17:17:13Z No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) / Rejected by Ana Paula Lisboa Monteiro (monteiro@univates.br), reason: Inserir o Lattes do autor. on 2018-09-11T18:28:07Z (GMT) / Submitted by DHARA CARLESSO ZAMPIVA (dhara.zampiva@univates.br) on 2018-09-17T17:18:08Z No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) / Approved for entry into archive by Ana Paula Lisboa Monteiro (monteiro@univates.br) on 2018-10-03T16:31:01Z (GMT) No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) / Made available in DSpace on 2018-10-03T16:31:01Z (GMT). No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) Previous issue date: 2018-08-20 / High levels of Schizotetranychus oryzae phytophagous mite infestation on rice leaves can severely affect pro- ductivity. Physiological characterization showed that S. oryzae promotes a decrease in chlorophyll concentration and the establishment of a senescence process in rice leaves. Late-infested leaves also present high levels of superoxide radical and hydrogen peroxide accumulation, along with high levels of membrane integrity loss, which is indicative of cell death. To better understand the rice molecular responses to high levels of mite in-festation, we employed the Multidimensional Protein Identification Technology (MudPIT) approach to identify differentially expressed proteins. We identified 83 and 88 proteins uniquely present in control and late-infested leaves, respectively, along with 11 and one proteins more abundant in control and late-infested leaves, re-spectively. S. oryzae infestation induces a decreased abundance of proteins related to translation, protease in-hibition, and photosynthesis. On the other hand, infestation caused increased abundance of proteins involved in protein modification and degradation. Our results also suggest that S. oryzae infestation interferes with in-tracellular transport, DNA structure maintenance, and amino acid and lipid metabolism in rice leaves. Proteomic data were positively correlated with enzymatic assays and RT-qPCR analysis. Our findings describe the protein expression patterns of late-infested rice leaves and suggest several targets which could be tested in future bio-technological approaches aiming to avoid the population increase of phytophagous mite in rice plants.

Proteomics refers to global characterization of the full set of proteins present in a biological sample. Various analytical disciplines contribute to proteomics but mass spectrometry became method of choice for analysis of complex protein samples. Mass spectrometry allows for high throughput analysis of the proteome but, moreover, it has the ability to acquire higher-order information such as post-translational modifications (PTM). Glycosylation is the most abundant PTM on eukaryotic proteins. This dissertation will focus on method development for structural proteomics that will be utilized to explain the glycoproteome of obligate intracellular protozoan parasite Toxoplasma gondii as a model system. Optimization of sample preparation is addressed in the first part of this dissertation. Sample preparation for mass spectrometry analysis is a critical step in the proteomics workflow because the quality and reproducibility of sample extraction and preparation significantly impacts the separation and identification capabilities of mass spectrometers. Also, there are problems unique to intracellular parasites as limited amount, host cell impurity and choice of the host. The additional obstacle is to extract only glycosylated proteins for which there is no one standard method. Here we report the optimal sample preparation method utilizing agarose bound Concanavalin A (Con A) beads to efficiently pull down glycoproteins, dialyze and analyze them using MuDPIT. This method was further enhanced by passing the non-retained protein fraction (first flow-through) through a second Con A column and then passing the second non-retained protein fraction (second flow-through) through the third Con A column (3 sequential pull-downs) yielding 394 benchmark proteins. Glycoproteome of Toxoplasma gondii is not yet fully understood. However, evidence suggests that glycosylation could be essential for cyst formation and maintenance which is characteristic of chronic stage of disease. The focus of the second part of dissertation is to better understand the differences in glycoproteomes of tachizoites and tissue cysts. Cyst proteins pulled down using optimized sample preparation method that do not appear in the tachyzoites pulldowns could be critical elements in the structural stability of the tissue cyst.

Indiana University-Purdue University Indianapolis (IUPUI) / Histones are highly basic proteins which when digested by trypsin are hard to analyze using mass spectrometry. Because histones are basic nuclear proteins, a nuclei prep followed by acid extraction is the best purification strategy to increase overall abundance of purified histones. Blocking the lysine residues and cleaving with trypsin is a useful technique to increase detection of histone peptides using MudPIT. In particular, carbamylation and propionylation are the best two methods to block lysine residues. Using both propionylation and carbamylation along with no treatment has been shown to increase the identification of unmodified and modified histone peptides when coupled with MudPIT analysis.

Indiana University-Purdue University Indianapolis (IUPUI) / The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) subunit Rpb1 must exist in a hypophosphorylated state prior to forming a competent transcription initiation complex. However, during transcription, specific kinases and phosphatases act on the RNAPII CTD to regulate its phosphorylation state, which serves to recruit sequence-specific and general transcription factors at the appropriate stage of transcription. A key phosphatase involved in this process, Rtr1 (Regulator of Transcription 1), was shown to regulate a key step important for transcription elongation and termination. Although the role that Rtr1 plays in regulating RNAPII transcription has been described, the mechanism involved in the recruitment of Rtr1 to RNAPII during transcription has not been elucidated in yeast. Consequently, the present work utilized both affinity purification schemes in Saccharomyces cerevisiae and mass spectrometry to identify key Rtr1-interacting proteins and post-translational modifications that potentially play a role in recruiting Rtr1 to RNAPII. In addition to RNAPII subunits, which were the most consistently enriched Rtr1-interacting proteins, seven proteins were identified that are potentially involved in Rtr1 recruitment. These included PAF complex subunits (Cdc73, Ctr9, Leo1), the heat shock protein Hsc82, the GTPase Npa3, the ATPase Rpt6, and Spn1. Indirect evidence was also uncovered that implicates that the CTDK-I complex, a kinase involved in RNAPII CTD phosphorylation, is important in facilitating interactions between Rtr1, RNAPII, and select transcription factors. Additionally, a putative phosphorylation site was identified on Ser217 of Rtr1 that may also play a role in its recruitment to RNAPII during transcription.