No description available.

Exposures to ionising radiation resulting from natural sources or medical diagnostics are generally very low. In contrast, exposures to therapeutic radiation, although, they are often partial exposures, represent much higher doses. Similar levels of exposure may also occur as a consequence of a radiological accident, where it would be necessary to quickly separate individuals requiring urgent medical attention from the “worried-well”. The well-established biodosimetry techniques based on cytogenetics, particularly scoring dicentric chromosomes, are accurate and sensitive, yet, they are unsuitable for mass screening due to limited capacity and the time required for providing dose estimates. Measuring gene expression changes following radiation exposure was suggested over a decade ago to be an alternative method for dose estimation, as it is a quick, sensitive and suitable technique for high throughput application. The qPCR protocol was extensively optimised for increased reproducibility and sensitivity in order to be suitable for biodosimetry purposes. Radiation-responsive transcripts were identified and characterised in terms of temporal- and dose-responses. Finally, candidate transcripts were validated in human blood irradiated ex vivo and in vivo in blood samples obtained from cancer patients undergoing radiotherapy treatment. The data generated here serve as a proof of principle that qPCR-based gene expression assays can be used for radiation biodosimetry purposes to aid classical cytogenetics tools in an event of mass causality.

Master of Science - Science / Normal colonic epithelium bombarded by a range of molecular changes, affecting cell proliferation and apoptosis, result in the initiation of an adenoma and consequently an invasive carcinoma, which is usually lethal. One of the main characteristics of tumour progression is the loss of regulation between the cell cycle and apoptosis. Under normal circumstances, these processes are strictly controlled by a number of regulators and inhibitors. Previous studies have implicated the novel Domain With No Name gene in apoptosis. This study aimed to characterize the expression patterns and levels of the gene in colon cancer and to determine its role in apoptosis. In situ hybridisation, immunocytochemistry and quantitative PCR localised the gene and its products in cancerous and normal colon tissue. Combined with apoptosis detection studies, proliferation assays and Bcl-2 assays, the results suggest that the gene is involved in promoting apoptosis in cancerous cells i.e. the targeting of undesirable cells. Helicobacter pylorus was implicated in the progression of noninvasive colon cancer to the invasive state. From this study DWNN is proposed to be a pro-apoptotic participant in programmed cell death and classification studies such as these allow for potential manipulation of the apoptotic system to serve as a therapeutic corridor.

Genes envolvidos com a interação hospedeiro-patógeno são fortemente afetados pela seleção natural positiva. O gene codificante do antígeno sangüíneo Duffy, também conhecido como DARC (Duffy Antigen Receptor for Chemokines), tem um importante papel na invasão dos eritrócitos pelos parasitas causadores da malária, Plasmodium vivax em humanos e Plasmodium knowlesi em outros primatas. A estrutura do gene DARC já é conhecida, estando este presente na região 1q22q23 do cromossomo 1, e sendo composto por dois éxons separados por um grande íntron. Em uma população africana a deleção de um nucleotídeo no domínio GATA-1 da região promotora do gene é responsável pela não expressão de DARC nos eritrócitos e pela resistência à invasão pelo P. Vivax. Além disso, o antígeno DARC age como um receptor promíscuo de quimiocinas, sendo expresso nos eritrócitos, células endoteliais de vênulas e outros tecidos. Devido a esse papel dual, no presente estudo seqüenciou-se regiões homólogas do gene DARC em macacos do Novo e Velho Mundo e utilizando métodos estatísticos procurou-se indícios da seleção natural positiva na sua história evolutiva. Nenhuma nova mutação foi encontrada no promotor ou na região codificante. As árvores filogenéticas pelos métodos de máxima parcimônia, máxima verossimilhança e neighbor-join apresentaram topologias semelhantes com três grande clados monofiléticos reconhecíveis e com a espécie Macaca fascicularis apresentando um perfil polifilético. O teste de seleção positiva pelos métodos de Nei-Gojobori, máxima verossimilhança por ramos e máxima verossimilhança por sítios não demonstraram, estatisticamente, à ação da seleção positiva sobre o gene DARC. Porém, o teste de máxima verossimilhança por sítio em domínios demonstrou que existem regiões do gene DARC sujeitas à diferentes pressões seletivas, mas também falhou em detectar a assinatura da seleção positiva. Os resultados indicam a presença da seleção darwiniana sobre a região de ligação do P. vivax, porém os testes de máxima verossimilhança utilizados, aparentemente, não possuem poder suficiente para detectar a sua assinatura. Além disso, os resultados sugerem que a região de ligação do P. vivax está sob influência de duas pressões seletivas antagônicas (seleção positiva exercida pelo parasita e seleção purificadora exercida pelas quimiocinas) o que pode, também, explicar a não detecção da seleção positiva. / Genes involved in pathogen-host interactions are strongly affected by positive natural selection. The gene of blood Duffy antigen, also known as DARC (Duffy Antigen Receptor for Chemokines), has an important role in the invasion of red blood cells by the parasites that cause malaria, Plasmodium vivax in humans and Plasmodium knowlesi in other primates. The structure of the DARC gene is known, it was mapped in 1q22-q23 region of chromosome 1, and is composed by two exons separated by a large intron. In an African population a nucleic acid deletion in GATA-1 of the gene promoter is responsible for the non-expression of DARC on red blood cells and the resistance to invasion by P. vivax. Moreover, the DARC antigen acts as a promiscuous receptor for chemokines and is expressed in red blood cells, endothelial venules cells and other tissues. Because of this dual role, in this study we sequenced homologous regions of the DARC gene in monkeys of the New and Old World and using statistical methods we tried to detect positive natural selection in their evolutionary history. New mutations were not found at promoter or in coding region. The phylogenetic trees by the methods of maximum parsimony, maximum likelihood and neighbor-join showed similar topologies with three large monophyletic clades recognizable and with the Macaca fascicularis showing a poliphyletic profile. The test of positive selection by the methods of Nei-Gojobori, maximum likelihood by branchs and maximum likelihood by sites not shown, statistically, the action of positive selection on the DARC gene. But the maximum likelihood test using sites divided in domains showed that some regions of the DARC gene are subject to different selective pressures, but also failed to detect the signature of positive selection. The results indicate the presence of darwinian selection on P. vivax binding region, but the maximum likelihood tests used, apparently, do not have enough power to detect its signature. Moreover, the results suggest that P. vivax binding region is under the influence of two opposing selective pressures (positive selection exerted by the parasite and purifying selection exerced by chemokines) that can also explain the non-detection of positive selection.

Drosophila meridionalis é uma espécie endêmica da América do Sul, sendo amplamente distribuída na Costa Atlântica do Brasil. Com o objetivo de elaborar uma hipótese filogeográfica para esta espécie foram obtidas sequências do gene nuclear period e do gene mitocondrial COI. Foram calculados os índices de diversidade nucleotídica e realizados os testes: AMOVA, testes de neutralidade, a Mismatch Distribution, Bayesian Skyline Plot, NCPA. Foram obtidas três redes pelo gene COI, denominadas A (populações do interior), B (populações do litoral sul) e C (populações do litoral sudeste e oriental) e uma única rede obtida para o gene period, esta rede divide as populações em dois grupos sendo o primeiro congruente com a rede A e o segundo compreendendo as redes B e C, do gene COI. A AMOVA mostrou uma estruturação alta e significativa entre as populações do interior e o litoral para os dois genes (ct=0,72 gene COI; ct=0,70 gene period), que pode ser explicada pela presença de barreiras geográficas, como a Serra do Mar. Eventos de expansão populacional e de fluxo gênico restrito com isolamento por distância foram detectados nas populações do litoral e o interior respectivamente. A expansão da área de ocorrência de D. meridionalis provavelmente teve inicio com as populações do litoral do Rio Grande de Sul, em direção ao litoral de Santa Catarina com posterior colonização a longa distância dos estados de São Paulo, Rio de Janeiro e Bahia. Migrações assincrônicas de indivíduos de populações litorâneas de São Paulo e Santa Catarina provavelmente colonizaram o interior de São Paulo, e a partir destas populações, se iniciara uma expansão populacional em direção ao sul pelo interior, colonizando o Paraná e Rio Grande do Sul. A análise bayesiana (MCCT) indicou que o tempo do ancestral comum mais recente (TMRCA) para todos os haplótipos de D. meridionalis é de 81.700 anos atrás, data que marca a separação das populações do interior e do litoral aproximadamente no final do Pleistoceno. Eventos similares têm sido sugeridos para explicar a distribuição geográfica de espécies do cluster D. buzzatii, que ocorrem em simpatria em grande parte com populações de D. meridionalis. Esta espécie, como as espécies do cluster D. buzzatii, apresentou indicativos de flutuações demográficas, podendo estar associadas à expansão e contração da distribuição da vegetação xerofítica, durante as oscilações paleoclimáticas do Pleistoceno. / Drosophila meridionalis is an endemic species of South America, being widely distributed in the Atlantic Coast of Brazil. Aiming to develop a phylogeographic hypothesis for this species, sequences of mitochondrial COI and nuclear period genes were obtained. The diversity indexes, AMOVA, neutrality tests, Mismatch Distribution, Bayesan Skyline Plot and NCPA were calculated. We obtained three networks for the COI gene, denominated A (inland populations), B (south coast populations) and C (eastern and southeastern coast populations) and a single network obtained for the period gene, this network divides the population into two groups, being the first congruent with the network A of the COI gene and the second comprising the networks B and C of the COI gene. The AMOVA results, showed a high and significant structuring among inland and coastal populations, for both genes (ct=0,72 COI gene; ct=0,70 period gene), that can be explained by the presence of geographical barriers, such as Serra do Mar. Population expansion events and restricted gene flow with isolation by distance events were detected in coastal and inland populations respectively. The expansion of the area of occurrence of D. meridionalis probably was initiated with the populations of the coast of Rio Grande do Sul, towards the coast of Santa Catarina with subsequent long-distance colonization of the states of São Paulo, Rio de Janeiro and Bahia. Asynchronic migrations of individuals from coastal populations of São Paulo and Santa Catarina probably colonized the inland of São Paulo, and from these populations, a population expansion towards the south through the inland was initiated, colonizing the states of Paraná and Rio Grande do Sul. The bayesian analysis (MCCT) indicated that the time of the most recent common ancestor (TMRCA) for all haplotypes of D. meridionalis is from 81,700 years ago, a date that marks the separation of inland and coastal populations approximately at the end of the Pleistocene. Similar events have been suggested to explain the geographic distribution of species of the cluster D. buzzatii, occurring in sympatry largely with populations of D. meridionalis. This species, as the cluster D. buzzatii species, presented indicatives of demographic fluctuations, which can be associated with the expansion and contraction of the distribution of xerophytic vegetation, during the paleoclimatic fluctuations of the Pleistocene.

Thesis (M. Phil.)--Chinese University of Hong Kong. / Bibliography: leaves 158-185.

No description available.

A espécie humana sempre foi fascinada pela variação de cor exibida pelos animais. Atualmente, investigações genéticas têm permitido que os pesquisadores caracterizem os mecanismos moleculares envolvidos na produção de pigmentos que afetam fenótipos de cor bem como na percepção de tal variação de cor entre diferentes espécies. Essa tese apresenta três investigações sobre esses assuntos. Na primeira, foi estudada a base molecular para a evolução da cor de plumagem em Ramphastidae. Essa família de aves inclui tucanos, araçaris e saripocas, possuindo uma ampla variação em plumagem. Foi encontrada seleção positiva no gene do receptor da melanocortina-1 (MC1R) no ramo que leva ao gênero Ramphastos, sugerindo que a plumagem mais escura nessas espécies foi favorecida pela seleção natural. Interessantemente, três de cinco substituições de aminoácido encontradas nesse gênero foram associadas ao melanismo em outras espécies de aves. No segundo estudo, uma análise do gene MC1R foi geia em perus domésticos (Meleagris gallopavo) brancos e pigmentados. Esse gene é um dos pelo menos cinco locos genéticos conhecidos que determinam a cor da plumagem nessa espécie, e três alelos funcionais já foram caracterizados (B, b+, b1). Os resultados mostraram que as aves brancas têm alguma diversidade genética em nível de DNA, mas quase todos os alelos foram b+, com um único alelo b1 encontrado, sugerindo que essas aves têm um valor limitado para o cruzamento e desenvolvimento de novas variedades coloridas. Entre as aves coloridas, os resultados mostraram que a classificação fenotípica da plumagem feita pelos criadores brasileiros não é preditiva para os alelos que podem ser encontrados no gene MC1R. Finalmente, no terceiro estudo a base molecular da visão colorida em uacari (Cacajao calvus) foi explorada. Essa é uma espécie de primata do Novo Mundo que exibe uma distintiva face avermelhada intensa, um sistema social complexo, e uma dieta especializada. O loco da opsina ligado ao cromossomo X foi caracterizado, e os resultados revelaram a ocorrência de extensivo polimorfismo molecular e o maior número de alelos funcionais (seis) já encontrados em uma espécie de primata. Esse achado provavelmente deriva de seleção para visão tricromática, talvez mediada por seleção sexual. Em conjunto, esses resultados mostram a importância de estudos moleculares que permitam uma melhor compreensão da evolução e manutenção da variação biológica associada à produção e percepção de cores em diferentes grupos de vertebrados. / Humans have been always fascinated by body color variation in animals. Current genetic investigations have allowed researchers to characterize the molecular mechanisms involved in the production of pigments affecting color phenotypes, as well as in the perception of such color variation among different species. This thesis presents three investigations concerning these subjects. In the first, the molecular basis for the evolution of plumage coloration in Ramphastidae was studied. This bird family includes toucans and toucanets, showing wide plumage variation. Positive selection in the melanocortin-1 receptor (MC1R) gene was found in the branch leading to the genus Ramphastos, suggesting that the darker plumage in these species was favored by natural selection. Interestingly, three out of five aminoacid substitutions found in this genus have been associated to melanism in other bird species. In the second study, an analysis of the MC1R gene was performed in white and pigmented domestic turkeys (Meleagris gallopavo). This gene is one of the at least five genetic loci known to determine plumage color in this species, and three functional alleles have been identified (B, b+, b1). The results showed that white birds have some genetic diversity at the DNA level, but almost all alleles were b+, with a single b1 allele found, suggesting that these birds have a limited value for breeding new color varieties. Among colored birds, the results showed that the plumage phenotypic classification used by Brazilian breeders is not predictive of the alleles that can be found in the MC1R gene. Finally, in the third study, the basis of color vision in uakari (Cacajao calvus) was explored. This is a species of New World primate exhibiting a distinctive intense red face, a complex social system, and a specialized diet. The X-lined Opsin locus was characterized, and the results revealed the occurrence of extensive molecular polymorphism and the largest number of functional alleles (six) ever found for a primate. This finding possibly derives from selection for trichromatic vision, perhaps mediated by sexual selection. Taken together, these results show the importance of molecular studies allowing a better understanding of the evolution and maintenance of biological variation associated to color production and perception in different vertebrate groups.

Thesis (Ph.D.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / DNA sequencing techniques have evolved to the point where one can sequence millions of bases per minute, while our capacity to use this information has been left behind. One particularly notorious example is in the area of gene regulatory networks. A molecular study of gene regulation proceeds one protein at a time, requiring bench scientists months of work purifying transcription factors and performing DNA footprinting studies. Massive scale options like ChIP-Seq and microarrays are a step up, but still require considerable resources in terms of manpower and materials. While computational biologists have developed methods to predict protein function from sequence, gene locations from sequence, and even metabolic networks from sequence, the space of regulatory network reconstruction from sequence remains virtually untouched. Part of the reason comes from the fact that the components of a regulatory interaction, such as transcription factors and binding sites, are difficult to detect. The other, more prominent reason, is that there exists no "recognition code" to determine which transcription factors will bind which sites. I've created a pipeline to reconstruct regulatory networks starting from an unannotated complete genomic sequence for a prokaryotic organism. The pipeline predicts necessary information, such as gene locations and transcription factor sequences, using custom tools and third party software. The core step is to determine the likelihood of interaction between a TF and a binding site using a black box style recognition code developed by applying machine learning methods to databases of prokaryotic regulatory interactions. I show how one can use this pipeline to reconstruct the virtually unknown regulatory network of Bacillus anthracis. / 2031-01-01

No description available.