This study has successfully identified transcripts differentially expressed in the salivary gland and midgut and provides candidate genes that are critical to response to parasite invasion. Furthermore, an open-source Glossina resource (G-ESTMAP) was developed that provides interactive features and browsing of functional genomics data for researchers working in the field of Trypanosomiasis on the African continent.

Submitted by MARIA LETICIA GUINDALINI MELLONI null (letmell@yahoo.com.br) on 2016-01-14T15:02:04Z No. of bitstreams: 1 Tese_Maria_Letícia_Guindalini_Melloni.pdf: 683985 bytes, checksum: 53424c1e6da45d38a2d516aeb0a405fd (MD5) / Rejected by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br), reason: Solicitamos que realize uma nova submissão seguindo as orientações abaixo: A versão do trabalho submetida ao Repositório Institucional UNESP deve conter o texto completo. 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Agradecemos a compreensão. on 2016-01-18T11:30:25Z (GMT) / Submitted by MARIA LETICIA GUINDALINI MELLONI null (letmell@yahoo.com.br) on 2016-01-18T11:52:00Z No. of bitstreams: 1 Tese_Maria_Letícia_Guindalini_Melloni.pdf: 1866484 bytes, checksum: 4990d42ce801ec4b8fe8d516cb7568d4 (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-01-18T13:48:32Z (GMT) No. of bitstreams: 1 melloni_mlg_dr_jabo_par.pdf: 733459 bytes, checksum: d8b36f206c9b78d184a6e2627f86b26d (MD5) / Made available in DSpace on 2016-01-18T13:48:32Z (GMT). No. of bitstreams: 1 melloni_mlg_dr_jabo_par.pdf: 733459 bytes, checksum: d8b36f206c9b78d184a6e2627f86b26d (MD5) Previous issue date: 2015-12-15 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Com o intuito de aumentar o conhecimento da rede gênica envolvida no controle do florescimento em cana-de-açúcar, diferentes cultivares de cana-de-açúcar foram submetidos a tratamentos fotoperiódicos de indução e não indução do florescimento em câmara de fotoperíodo. Aos 5, 10 e 20 dias de indução, a folha +1 e a bainha foliar foram coletadas para a identificação de fragmentos diferencialmente expressos (FDEs) por meio da técnica de cDNA-AFLP entre e dentro dos tratamentos fotoperiódicos. Um total de 162 fragmentos foram selecionados e reamplificados. Destes, 63 FDEs tiveram sucesso na reação de reamplificação e foram clonados e sequenciados. As sequências foram confrontadas com seis bancos de sequências: 1. Transcritos do projeto SUCEST ;2. Proteínas do genoma de sorgo; 3. BAC de cana-de-açúcar; 4. Proteínas do genoma de arroz, 5. Proteínas presentes no Phytozome e 6. NCBI. A busca por similaridade se deu pelo uso da ferramenta BLASTn (e-value 1e-5) nos casos do banco SUCEST e dos BACs de cana-de-açúcar e BLASTx (e-value 1e-5) para os demais bancos. Dentre os 63 FDEs, 23 corresponderam a sequências de genes enquanto os outros 40 representam sequências que não estão depositadas nestes bancos (no hits). A maioria das 23 sequencias apresenta similaridade com genes que codificam proteínas hipotéticas ou preditas em diversos organismos. Com base na análise do domínio da proteína realizada pelo Pfam, seis sequências podem estar associadas ao metabolismo da indução do florescimento. Dentre estas as sequencias LM-19, LM-40 e LM-53 se destacaram. A LM-19 possui similaridade com o gene que codifica uma proteína com o domínio DNAJ sendo que proteína com este domínio é considerada mediador da integração dos sinais do florescimento em Arabidopsis thaliana. LM-40 possui similaridade com o gene que codifica proteína de domínio (F-BOX); estudos indicam forte relação deste domínio aos processos de indução ao florescimento. LM-53 tem um domínio de proteína predita semelhante ao domínio da proteína codificada pelo gene CONSTANS que regula a expressão de FLOWERING LOCUS T (FT), que codifica o florígeno em Arabidopsis thaliana e em algumas outras espécies. De maneira geral, a técnica do cDNA-AFLP foi eficiente, na identificação de FDEs ao longo dos tratamentos fotoperiódicos de indução e não indução do florescimento. Os resultados obtidos sugerem que as sequencias LM-19, LM-40 e LM-53 estão vinculadas aos metabolismos de indução do florescimento. É provável que a maioria dos FDEs obtidos possam estar envolvidos nos metabolismos da indução do florescimento, porém ainda não foram identificados na literatura. / In order to increase the knowledge of the gene network involved in sugarcane flowering induction, sugarcane cultivars were submitted to different photoperiod treatments of flowering induction and non-induction in a photoperiod facility. At 5, 10 and 20 days of induction, the +1 leaf and the leaf sheath were collected for the identification of different transcript-derived fragments (TDFs) within and between the photoperiod treatments to apply the cDNA-AFLP technique. A total of 162 TDFs were selected and re-amplified. Of these, 63 TDFs were successful in re-amplification and were cloned and sequenced. The sequences were confronted against 6 sequence databanks (SUCEST transcripts; Sorghum genome proteins; Sugarcane BACs; proteins from rice genome; Phytozome and NCBI). Similarity search was done by using the BLASTn (e-value 1e-5) tool for the SUCEST databank and sugarcane BACs while BLASTx (e-value 1e-5) was use for the other banks. Among the 63 TDFs, 23 corresponded to gene sequences while the remaining 40 represent sequences that are not deposited in these banks (no hits). The majority of the 23 sequences showed similarity with genes coding for hypothetical or predicted proteins of different organisms. Based on the protein domain analysis conducted by Pfam, six sequences may be associated with flowering induction metabolism. Among these: LM-19, LM-40 and LM-53 sequences stood out. LM-19 has similarity to the gene encoding a protein with DnaJ domain. Proteins having this domain are considered as an integrating floral signals mediator in Arabidopsis thaliana. LM-40 has similarity to the gene encoding a protein with (F-BOX) domain. This domain has a strong relationship in flowering induction processes. LM-53 has one of the predicted protein domain similar to the domain of the protein encoded by the CONSTANS gene which governs the expression of FLOWERING LOCUS T (FT), this later one encodes the florigen. Generally the cDNA-AFLP technique was effective in identifying TDFs across the flowering inductive and non-inductive photoperiodic treatments. The results suggest that LM-19, LM-40 and LM-53 sequences are linked to flowering induction metabolisms. Probably, most of the TDF here obtained may be involved in the flowering induction metabolism, although not yet been identified in the literature. / FAPESP: 2013/24020-0

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Made available in DSpace on 2015-03-26T13:32:18Z (GMT). No. of bitstreams: 1 texto completo.pdf: 619084 bytes, checksum: 33699c369d9fd3f595c40375c27f4c43 (MD5) Previous issue date: 2013-01-16 / One of the current objectives of molecular biology is to measure and assess the gene expression profiles in different types of biological tissues, to understand the mechanisms of molecular transformation under certain conditions. Next-generation sequencing (NGS) technologies promote DNA sequencing in platforms capable of generating information about millions of base pairs in a single step. However these technologies still have high cost, making it difficult to obtain large number of repetitions of sample data. Therefore, it becomes necessary the discovery and the improvement of efficient statistical methodologies for optimizing analysis of data generated in genome sequencing platforms. The overall objective of this work was to evaluate the effect of the number of repetitions in the identification of differentially expressed genes, in RNA-Seq experiments, contributing to the clarification of the statistic that researchers will assist in data analysis in RNA-Seq experiments. Specifically, we evaluate empirically the effect of the number of repetitions in the statistical analysis of gene expression in RNA-Seq experiments. To carry out the analyses we used a dataset defined in Li et al. (2008), which compared treated and non-treated cancer cells. That work had four biological replications for the control group (non-treated) and three replications for biological treatment group (cells that have received the treatment). The data was analyzed using the package DESeq from the statistical environment R. A total of 2566 genes were considered differentially expressed (DE) when we evaluate the original and complete dataset. When we analyzed three replications of the control and treatment, we found, on average, 2153 genes DE. From the moment in which only two reps for both treatments were used, were identified, on average, 1241 genes DE. The major change in the number of genes DE was observed when replications were not used. In this case we identified around 44 differentially expressed genes. According to the results generated in the analysis, it was possible to verify that the number of repetitions is an essential factor in order to obtain a significant number of differentially expressed genes. / Um dos objetivos atuais da biologia molecular é medir e avaliar os perfis de expressão gênica em diferentes tipos de tecidos biológicos, para entender os mecanismos de transformação molecular sob determinadas condições. Tecnologias de sequenciamento de Nova Geração (NGS) promovem o sequenciamento de DNA em plataformas capazes de gerar informações sobre milhões de pares de bases em uma única etapa. Porém essas tecnologias ainda apresentam custo elevado, dificultando a obtenção de elevado número de repetições de dados amostrais. Assim, torna-se necessária a descoberta e o aprimoramento de metodologias estatísticas eficientes para a otimização das análises de dados gerados em plataformas de sequenciamento de genomas. O objetivo geral desse trabalho consistiu em avaliar o efeito do número de repetições na identificação de genes diferencialmente expressos, em experimentos de RNA-Seq, contribuindo para o esclarecimento de pesquisadores que venham a auxiliar nas análises de dados em experimentos de RNA-Seq. De forma específica, avaliamos empiricamente o efeito do número de repetições na análise estatística da expressão gênica em experimentos de RNA-Seq. Para a realização das análises foi utilizado um conjunto de dados definido em Li et al. (2008), o qual comparou células cancerígenas tratadas e não tratadas. Naquele estudo havia quatro repetições biológicas para o grupo controle (células não tratadas) e três repetições biológicas para grupo de tratamento (células que receberam o tratamento). Os dados foram analisados utilizando o pacote DESeq do Programa computacional R. Um total de 2566 genes foram considerados diferencialmente expressos (DE) quando avaliamos o conjunto de dados original completo. Quando analisamos três repetições do controle e do tratamento, nós encontramos, em média, 2153 genes DE. A partir do momento em que apenas duas repetições para ambos os tratamentos foram utilizadas, foram identificadas, em média, 1241 genes DE. A grande alteração no número de genes DE foi observada quando repetições não foram utilizadas. Nesse caso identificamos em torno de 44 genes diferencialmente expressos. De acordo com os resultados gerados nas análises, foi possível verificar que o número de repetições é um fator essencial para se obter um número significativo de genes diferencialmente expressos.

Submitted by Fabiana Gonçalves Pinto (benf@ndc.uff.br) on 2015-12-08T14:16:48Z No. of bitstreams: 1 Paula Isabella Marujo Nunes da Fonseca.pdf: 8021393 bytes, checksum: db9ec4e08561cc9971f856e2cb492cb3 (MD5) / Made available in DSpace on 2015-12-08T14:16:48Z (GMT). No. of bitstreams: 1 Paula Isabella Marujo Nunes da Fonseca.pdf: 8021393 bytes, checksum: db9ec4e08561cc9971f856e2cb492cb3 (MD5) Previous issue date: 2013 / Mestrado Acadêmico em Ciências do Cuidado em Saúde / Estudo trata das emoções vivenciadas pelas equipes multiprofissionais da Central de Transplantes do estado do Rio de Janeiro na entrevista familiar para doação de órgão(s). Após certificação do quadro de morte encefálica, os profissionais da Central de Transplantes buscam comunicação com os familiares sobre o diagnóstico final do potencial doador através da entrevista familiar, momento que envolve grande carga emocional. Diante disso objetivou-se: Caracterizar as emoções vivenciadas pelos profissionais de saúde na entrevista familiar para doação de órgão(s); Analisar o manejo das emoções vivenciadas por estes profissionais na entrevista familiar; e, Discutir medidas para educação emocional dos profissionais entrevistadores. O método utilizado foi da abordagem qualitativa, sendo o estudo do tipo descritivo- interpretativo. Como técnica de pesquisa para coleta dos dados dos 24 sujeitos, acontecida entre jan/maio de 2012, foi aplicado questionário sócio cultural, seguido de entrevista semi estruturada, e posteriormente foram coletados os dados expressivos através da Técnica da Imaginação Ativa proposta por C.G. Jung. O estudo foi submetido ao Comitê de Ética do HUAP/UFF, onde obteve aprovação sob o nº321/11, respeitando a Resolução 466/2012 que trata de pesquisas com seres humanos. Resultados. Dados sócio-culturais: a maioria dos sujeitos são do sexo feminino, possuem média etária de 38,7 anos; 12 coordenadores atuam na instituição entre 2 e 3 anos, e somente 4 desenvolvem esta atividade há mais de 10 anos, sendo estes últimos servidores de vínculo estatutário; 23 destes profissionais possuem outro vínculo empregatício com cargas horárias que variam de 20h à 72,5h/semanais; e, 17 destes profissionais são enfermeiros. Dados da entrevista principal: observou-se grande dificuldade dos sujeitos em caracterizarem suas emoções, as tendo representado de outras maneiras, através de sentimentos, impressões, ações e até sinais físicos. Os sujeitos que rememoraram suas lembranças emocionais relacionadas às situações difíceis vivenciadas na entrevista familiar identificaram: raiva, medo, tristeza e amor. Em relação às características de emoções, surgiram: pavor, nervosismo e angústia (característica do Medo); e, irritação (característica da Raiva); felicidade (característica emocional da Alegria) e satisfação (característica emocional do Prazer). Em relação ao manejo das emoções emergiram: a questão do choro como meio de enfrentamento/alívio; A empatia e suas conseqüências emocionais; e, A projeção do que está por vir, que representam as projeções situacionais que geram benefícios para si ou para os outros. Dados da produção expressiva evidenciaram que através de símbolos culturais como lágrimas, sol e o coração, os sujeitos que não conseguiram assumir ou reconhecer suas emoções ao longo dos depoimentos, conseguiram expor o que lhes afetam na entrevista familiar. Discute-se como meio de educação emocional, um serviço de suporte emocional para que se trabalhe o autoconhecimento dos sujeitos afim de que estes identifiquem através deste processo as melhores medidas para enfrentarem as situações difíceis. Conclui-se que investir no autoconhecimento dos sujeitos pode lhes proporcionar mais qualidade no trabalho e na vida pessoal amortizando os danos a sua saúde mental. / It treats about a study of emotions experienced by multidisciplinary teams of Transplant Center of the State of Rio de Janeiro in the family interview for organ donation (s). After certification of brain death, the professionals at the Transplant Center seek communication with family members about the final diagnosis of the potential donor through family interview, moment that involving a big emotionally charged. Therefore this study aimed to: characterize the emotions experienced by health professionals in family interview for Organ Donation(s); Analyze the management of emotions experienced by these professionals in the family interview; and Discuss measures for emotional education for the interviewers. The method used was the qualitative approach, and the study is descriptive-interpretative type . As a research technique to collect data from 24 subjects, between Jan / May 2012, was used a sociocultural survey, followed by semi -structured interview. Subsequently was applied the Active Imagination Technique proposed by CG Jung. The study was submitted to the Ethics Committee of the HUAP / UFF , which was approved under No. 321/11 , subject to Resolution 466/2012 which deals with human research . Results. Socio- cultural data: most subjects are female , have an average age of 38.7 years, 12 coordinators working in the institution between 2 and 3 years, and only 4 developed this activity for more than 10 years, the latter being servers statutory bond; 23 of these professionals have other employment with workloads ranging from 20h to 72.5h/week , and 17 of these professionals are nurses. Data from the main interview: there was great difficulty in characterizing subjects of their emotions, and represented in other ways, through feelings, impressions, actions and even physical signs. Subjects who recalled their emotional memories related to difficult situations experienced in family interview identified: anger, fear , sadness and love . Regarding the characteristics of emotions emerged: fear , nervousness and anxiety (characteristic of Fear ), and irritation ( characteristic of Anger), happiness (emotional characteristic of Joy) and satisfaction (emotional characteristic of Pleasure). Regarding the management of emotions emerged: the issue of crying as a means of coping/relief; Empathy and its emotional consequences, and the projection of what is to come , representing the situational projections that generate benefits for hemselves or others. Data showed that the impressive output through cultural symbols such as tears, sun and heart, the subjects who failed to assume or acknowledge their emotions over the testimony, managed to expose that affect them in the family interview . It is discussed as a means of emotional education , a service of emotional support in order to work the self-knowledge of the subject in order that through this process they identify the best measures to cope with difficult situations. Conclusion: Invest in self-knowledge for the subjects can provide them with better quality in work and personal life amortizing damage in your mental health.

Philosophiae Doctor - PhD / This study has successfully identified transcripts differentially expressed in the salivary gland and midgut and provides candidate genes that are critical to response to parasite invasion. Furthermore, an open-source Glossina resource (G-ESTMAP) was developed that provides interactive features and browsing of functional genomics data for researchers working in the field of Trypanosomiasis on the African continent. / South Africa

Les éléments transposables sont des composants majeurs de la plupart des génomes, et leur impact sur l’évolution des génomes est maintenant bien documenté. Cependant, la manière par laquelle ils participent au transcriptome n’est pas encore clairement établie. En utilisant le génome séquencé de Drosophila melanogaster et les bibliothèques d’EST, nous avons déterminé les insertions d’éléments transposables qui sont transcrites sans équivoque, ainsi que leur localisation dans le génome séquencé de D.melanogaster. Nous montrons que la plupart des familles d’éléments transposables sont transcrites, et nous identifions spécifiquement 69 insertions d’éléments transposables exprimés, dont la moitié réside dans des gènes, la plupart dans des introns et des régions régulatrices 5’UTR. / Transposable elements (TEs) are major components of most genomes, and their impact on genome evolution is now well documented. However, the way they affect the transcriptome is still not clearly established. Using the sequenced genome of Drosophila melanogaster and EST libraries (“Expressed Sequence Tag”, large tags (~500bp) corresponding to subsequences of a transcribed cDNA sequences), we describe here the TE insertions that are unequivocally transcribed, and we have determined their location in the sequenced genome of Drosophila melanogaster. We show that most TE families are transcribed, and we have specifically identified 69 expressed TE insertions, half of which are located inside genes, mostly within introns and 5′UTRs regulatory regions.

The in vitro cell culture models of human pluripotent stem cells (hPSC)-derived cardiomyocytes (CMs) have gained a predominant value in the field of drug discovery and is considered an attractive tool for cardiovascular disease modellings. However, despite several reports of different protocols for the hPSC-differentiation into CMs, the development of an efficient, controlled and reproducible 3D differentiation remains challenging. The main aim of this research study was to understand the changes in the gene expression as an impact of spatial orientation ofhPSC-derived CMs in 2D(two-dimensional) and 3D(three-dimensional) culture conditions and to identify the topologically important Hub and Hub-Bottleneck proteins using centrality measures to gain new knowledge for standardizing the pre-clinical models for the regeneration of CMs. The above-mentioned aim was achieved through an extensive bioinformatic analysis on the list of differentially expressed genes (DEGs) identified from RNA-sequencing (RNA-Seq). Functional annotation analysis of the DEGs from both 2D and 3D was performed using Cytoscape plug-in ClueGO. Followed by the topological analysis of the protein-protein interaction network (PPIN) using two centrality parameters; Degree and Betweeness in Cytoscape plug-in CenTiScaPe. The results obtained revealed that compared to 2D, DEGs in 3D are primarily associated with cell signalling suggesting the interaction between cells as an impact of the 3D microenvironment and topological analysis revealed 32 and 39 proteins as Hub and Hub-Bottleneck proteins, respectively in 3D indicating the possibility of utilizing those identified genes and their corresponding proteins as cardiac disease biomarkers in future by further research.

Expressed emotion (EE), the affective attitudes and behaviors of one toward another, can affect caregivers’ behaviors toward their child. Research examining associations between EE and child/family outcomes is mixed; these associations may be affected by other influences such as the presence of a chronic disease or parent mental health. In this study of families living in an urban area, we examined associations between EE and child outcomes (anxiety/depressive symptoms) and family functioning, with parent anxiety as a covariate. We evaluated child asthma status as a moderator as the presence of a chronic illness may strengthen the association between EE and child/family outcomes. Ninety-four children (mean±SD age=8.83±2.03 years, 48.9% female, 92.6% African American; 47 with asthma) and their parents (81.3% annual household income less than $25,000) completed an observational study including interviews and questionnaires. Measures included the Multidimensional Anxiety Scale for Children (MASC), Children’s Depressive Symptoms Inventory (CDI), Self-Report Family Inventory (SFI), Generalized Anxiety Disorder scale (GAD-7), and Five-Minute Speech Sample (FMSS) coded for EE. To examine study aims, regression analyses were conducted using PROCESS macro version 3.4. Asthma status (yes/no) was examined as a moderator. EE was associated with child anxiety symptoms, controlling for parent anxiety symptoms (F(1,70) =7.67, p=0.007). Criticism was also positively associated with asthma control (F(1,39)=4.33, p=.04, R2=.08). Asthma status did not moderate any of the associations. Results suggested that high levels of caregiver EE were associated with child anxiety symptoms, but asthma status did not moderate associations. It is possible that regardless of additional family demands related to asthma, EE is associated with child anxiety. Further examination into other systemic stressors (e.g., poverty, access to care) that may moderate these associations is warranted, as well as the impact that minimizing parent anxiety might have on overall EE.

The thesis deals with the theme of empathy of teacher in educational theory and teaching practice. Its objective is to bring on an analysis of major Czech and foreign educational theories an overview of empathy as specific skills of teacher, its development and position within the given educational concept. The theoretical part first deals with the development of the concept of empathy in the context of psychology, differences between the concepts of sympathy and empathy, its relationship to sex, emotional intelligence, sociability, then focuses on empathy in the context of educational communication at school. The main part consists of analysis of important domestic pedagogical concepts of domestic authors, such as Comenius, Lindner, Úlehla, Chlup, Uher and Příhoda. Among foreign authors are, for example, Rousseau, Pestalozzi, Herbart, Dewey, Steiner and Rogers. The aim of the empirical part is to implement and with the use of relevant research tools to verify the effectiveness of the learning program developing empathy of future teachers. The thesis should contribute to a deeper understanding of empathy in the educational process, both within the theoretical, based on reflection of this phenomenon in educational theories, and especially in practice in connection with the preparation of future...