Thesis (Ph. D.) -- University of Texas Southwestern Medical Center at Dallas, 2005. / Vita. Bibliography: 127-154.

Thesis (Ph. D.)--University of Oklahoma. / Bibliography: leaves 95-126.

Thesis (Ph. D.)--Case Western Reserve University, 2006. / [School of Medicine] Department of Pathology. Includes bibliographical references. Available online via OhioLINK's ETD Center.

Thesis (M.S.)--Miami University, Dept. of Zoology, 2006. / Title from first page of PDF document. Includes bibliographical references (p. 56-61).

Thesis (Ph.D.)--University of Florida, 2004. / Typescript. Title from title page of source document. Document formatted into pages; contains 161 pages. Includes Vita. Includes bibliographical references.

Complex multicellular organisms are composed of at least 200 cell types, which contain the same DNA "black box" of genetic information. It is the precise regime according to which they express their genes, exquisitely controlled by gene regulatory circuits, that defines their cellular identity, morphology and function. We have developed an in vivo biotinylation method that uses genetically encoded components in zebrafish, termed biotagging, for genome-wide regulatory analysis of defined embryonic cell populations. By labelling selected proteins in specific cell types, biotagging eliminates background inherent to analyses of complex embryonic environments via highly stringent biochemical procedures and targeting of specific interactions without the need for cell sorting. We utilised biotagging to characterise the in vivo translational landscape on polysomes as well as the transcriptional regulatory landscape in nuclei of migratory neural crest cells, which intermix with environing tissues during their migration. Our migratory neural crest translatome presented both known and novel players of the neural crest gene regulatory network. An in depth look into the active nuclear transcriptome uncovered a complex world of non-coding regulatory RNAs that potentially specify migratory neural crest identity and present evidence of active bidirectional transcription on regions of open chromatin that include putative cis-regulatory elements. Analysis of our transcribed cis-regulatory modules functionally links these elements to known genes that are key to migratory neural crest function and its derivatives. We also identified a novel cohort of circular RNAs enriched at regions of tandem duplicated genes. Last but not least, we recovered developmentally regulated long non-coding RNAs and transcribed transposable elements. To functionally dissect the biological roles of these factors, we have built two Ac/Ds-mediated in vivo toolkits for efficient screening of putative enhancers and for CRISPR/Cas9-based transcriptional modulation. Overall, our methods and findings present a comprehensive view of the active coding and non-coding landscapes of migratory neural crest on a genome-wide scale that refine the current regulatory architecture underlying neural crest identity.

We develop machine learning approaches to predict context specific enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. Occupancy of estrogen receptor alpha (ER-alpha), RNA polymerase (Pol II) and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with estrogen. Two Bayesian classifiers were developed, unsupervised and supervised. The supervised approach uses the correlation of temporal binding patterns at enhancers and promoters and genomic proximity as features and predicts interactions. The method was trained using experimentally determined interactions from the same system and achieves much higher precision than predictions based on the genomic proximity of nearest ER-alpha binding. We use the method to identify a confident set of ER-alpha target genes and their regulatory enhancers genome-wide. Validation with publicly available GRO-Seq data shows our predicted targets are much more likely to show early nascent transcription than predictions based on genomic ER-alpha binding proximity alone. Accuracy of the predictions from the supervised model was compared against the second more complex unsupervised generative approach which uses proximity-based prior and temporal binding patterns at enhancers and promoters to infer protein-mediated regulatory complexes involving individual genes and their networks of multiple distant regulatory enhancers.

Submitted by Geandra Rodrigues (geandrar@gmail.com) on 2018-01-16T14:44:15Z No. of bitstreams: 1 rodrigojoselupatininogueira.pdf: 2876267 bytes, checksum: bdc1dc017b1978a2518a09845b329662 (MD5) / Rejected by Adriana Oliveira (adriana.oliveira@ufjf.edu.br), reason: Favor corrigir: Silva Filho, Ademar Alves da on 2018-01-22T16:16:44Z (GMT) / Submitted by Geandra Rodrigues (geandrar@gmail.com) on 2018-01-22T16:24:05Z No. of bitstreams: 1 rodrigojoselupatininogueira.pdf: 2876267 bytes, checksum: bdc1dc017b1978a2518a09845b329662 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2018-01-24T12:06:25Z (GMT) No. of bitstreams: 1 rodrigojoselupatininogueira.pdf: 2876267 bytes, checksum: bdc1dc017b1978a2518a09845b329662 (MD5) / Made available in DSpace on 2018-01-24T12:06:25Z (GMT). No. of bitstreams: 1 rodrigojoselupatininogueira.pdf: 2876267 bytes, checksum: bdc1dc017b1978a2518a09845b329662 (MD5) Previous issue date: 2014-08-22 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A administração de medicamentos na pele através da via transcutânea é uma prática que tem sido utilizada pela humanidade ao longo de milênios. Os anti-inflamatórios não esteroidais (AINEs) apresentam-se como uma classe de fármacos de interesse para o desenvolvimento de formulações transcutâneas já que apresentam efeitos gastrointestinais graves ao serem utilizados para o tratamento crônico de doenças, como por exemplo artrite reumatóide. Entre os fármacos desta classe, o ibuprofeno (IBU) representa um bom candidato para a permeação cutânea, já que apresenta baixo peso molecular (206,28), coeficiente de partição (log P) inferior a 4 e curta meia vida plasmática. Uma estratégia efetiva para facilitar a passagem de fármacos pela pele é o emprego de promotores de permeação na pele. Recentemente, alguns trabalhos vem relacionando o uso de terpenos e óleos naturais ricos em terpenos na promoção de permeação cutânea de fármacos. O óleo de copaíba, devido ao seu rico conteúdo em terpenos, apresenta-se como uma ótima escolha de promotor de permeação de fármacos administrados na pele. Neste trabalho foram desenvolvidas duas formulações em creme contendo IBU 5% com duas concentrações diferentes de óleo de copaíba: IBOC5, contendo 5% de óleo de copaíba e IBOC10, com 10% do mesmo óleo. Os ensaios de permeação e penetração in vitro do IBU foram realizados utilizando-se pele de orelha suína como membrana biológica no aparelho de células de difusão vertical do tipo Franz. Já a avaliação da permeação in vivo foi realizada através do teste de atividade anti-inflamatória induzida pelo óleo de cróton em orelhas de camundongos. O fluxo de permeação (J) do IBU nas amostras IBOC5 (35,72 ± 6,35) e IBOC10 (29,78 ±2,41) foram superiores (p < 0,01 e p < 0,05, respectivamente) ao creme controle, sem óleo de copaíba (10,32 ± 1,52) e produto comercial (14,44 ± 2,39). Na análise de penetração, a quantidade de IBU nas amostras IBOC5 e IBOC10 foi maior (p < 0,01 e p < 0,05, respectivamente) na derme quando comparada à epiderme. No ensaio in vivo, as amostras IBOC5 e IBOC10 reduziram (p < 0,05 e p < 0,001, respectivamente) o processo inflamatório quando comparadas ao controle negativo, entretanto, não foram diferentes (p > 0,05) do controle positivo. Face aos resultados, pode-se concluir que a adição do óleo de copaíba apresentou capacidade de promoção de permeação e penetração cutânea do ibuprofeno nas amostras em creme para o teste de células de difusão in vitro. Já o modelo in vivo de edema de orelha em camundongos, sugere-se que este não foi o teste mais adequado para avaliação da permeação do ibuprofeno nas amostras analisadas. / The administration of medications on the skin through transcutaneous routeis a practice that has been used by mankind for millennia. The non-steroidal anti-inflammatory drugs (NSAIDs) have been shown to be a class of drugs of interest for transcutaneous formulation development, since they present severe gastro-intestinal effects when used for treatment of chronic diseases such as rheumatoid arthritis. Among drugs of this class, Ibuprofen (IBU) is considered a good candidate for skin permeation, since it has a low molecular weight (206.28), partition coefficient (log P) lower than 4 and short plasma half-life. Therefore, an effective strategy to facilitate the drug diffusion through the skin is the use of permeation enhancers. Recently, some studies have been reporting the use of terpenes and natural oils rich in terpenes and their roles in promoting cutaneous drug penetration. Copaiba oil, due to its rich content of terpenes, presents itself as a great choice of penetration enhancer for drugs administered on the skin. In this study, two cream formulations containing 5% of IBU were developed: IBOC5 with 5% of Copaiba oil and IBOC10 with 10% of the same oil. In vitro cutaneous penetration/permeation studies of IBU were performed using pig ear skin as biological membrane in the Franz-type diffusion cells. In vivo permeation tests were also performed through anti-inflammatory activity evaluation using Croton oil-induced mouse ear edema test. The permeation flux (J) of IBU samples, IBOC5 (35.72 + 6.35) and IBOC10 (29.78 + 2.41) were significantly higher (p < 0.01 and p < 0.05, respectively) when compared to control cream, without Copaiba oil (10.32 + 1.52) and to commercial product (14.44 + 2.39). In the penetration analysis, the amount of IBU found in the samples IBOC5 and IBOC10 was higher (p < 0.01 and p < 0.05, respectively) in dermis than epidermis. In vivo tests showed that samples IBOC5 and IBOC10 decreased (p < 0.05 e p < 0,001, respectively) inflammatory process when it was compared to the negative control, however they weren’t considered statistically different (p > 0.05) of positive control. Concluding, Copaiba oil showed a significant capability to promote skin penetration and permeation of ibuprofen when it was added into the cream samples, according to the in vitro diffusion cells test results. On the other hand, the results obtained from the in vivo method weren’t enough satisfactory considering the analyzed samples.

O objetivo desse experimento foi verificar diferentes planos nutricionais através da utilização de diferentes tipos de levedura na alimentação de frangos de corte no período de 1 a 42 dias. Foram utilizadas leveduras autolizada, hidrolizada e levedura íntegra e sua influência sobre parâmetros de desempenho (ganho de peso, consumo de ração e conversão alimentar) e características de carcaça (rendimento de carcaça, rendimento de peito e rendimento de pernas). Foram utilizados 1.080 pintinhos de corte, machos de um dia de idade, da linhagem Cobb, distribuídos em delineamento experimental inteiramente casualizado, em esquema fatorial 3 x 3: 3 formas de suplementação de levedura no período de 1 a 14 dias (sem levedura, levedura autolisada e levedura hidrolisada) e 3 formas de suplementação no período de 15 a 42 dias (sem suplementação, levedura autolisada e levedura íntegra) mais um tratamento controle positivo, com a adição de um antibiótico promotor de crescimento (APC), totalizando 10 tratamentos, 9 repetições e 12 aves por unidade experimental. As dietas utilizadas foram formuladas a base de milho e farelo de soja, sendo utilizado como APC a bacitracina de zinco na inclusão de 0,5 kg/ton em todas as dietas. No período de 1 a 14 dias foi utilizado o nível de inclusão de 10kg/ton das leveduras autolisada e hidrolisada e no período de 15 a 42 dias, 5kg/ton das leveduras autolisada e íntegra. As análises estatísticas dos dados foram realizadas pelo método da análise de variância com o auxílio do procedimento GLM do SAS (2002) e em caso de significância estatística, as médias foram comparadas pelo teste de Tukey, no nível de 5% de probabilidade. No período de 1 a 14 dias a levedura hidrolisada apresentou melhor viabilidade de uso na dieta. Para a utilização de um programa contínuo, a combinação do uso da levedura hidrolisada no período de 1 a 14 dias e de levedura autolizada no período de 15 a 42 dias, apresenta-se como melhor resposta pelas aves. / The objective of this experiment was to evaluate different nutritional plans using various types of yeasts in broiler chicken feed during a 42-day period. We used autolyzed, hydrolyzed, and whole yeasts and evaluated their influence on performance parameters (weight gain, feed intake, and food conversion) and carcass features (whole chicken yield, breast yield, and leg yield). A total of 1080 1-day-old male Cobb lineage chicks were used and distributed across a completely randomized 3 x 3 factorial experimental design. The treatments were comprised of 3 yeast supplement types during days 1 to 14 (i.e., without yeast, autolyzed yeast, and hydrolyzed yeast), 3 supplement types during days 15 to 42 (as above), and growth-promoting antibiotic (GPA) as positive control for a total of 10 treatments, 9 replications, and 12 birds per experimental unit. The diets were formulated based on corn and soybean meal, and 0.5 Kg/ton of zinc bacitracin was included as the GPA in the control diets. We used 10 Kg/ton of autolyzed and hydrolyzed yeast in days 1 to 14, and 5 Kg/ton of autolyzed and whole yeast during days 15 to 42. Statistical data analyses were conducted using an analysis of variance and the SAS GLM procedure (2002), and statistically significant means were compared using Tukey´s test at the 5% probability level. In days 1 - 14, the hydrolyzed yeast presented the best viability of use in the chicken diet. As an ongoing program, the birds responded best to the combination of hydrolyzed yeast in days 1 to 14 and autolyzed yeast in days 15 to 42.

Previously studies used correlation of DNase I hypersensitivity sites sequencing (DNase-seq) experiments to predict interactions between enhancers and its target promoter gene. We investigate the correlation methods Pearson’s correlation and Mutual Information, using DNase-seq data for 100 cell-types in regions on chromosome one. To assess the performances, we compared our results of correlation scores to Hi-C data from Jin et al. 2013. We showed that the performances are low when comparing it to the Hi-C data, and there is a need of improved correlation metrics. We also demonstrate that the use of Hi-C data as a gold standard is limited, because of its low resolution, and we suggest using another gold standard in further studies.