Thesis (Ph.D. in Molecular Biology) -- University of Colorado, 2006. / Typescript. Includes bibliographical references (leaves 126-147). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

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The yeast SWI/SNF complex is the prototype of a subfamily of ATP-dependent chromatin remodeling complexes. It consists of eleven stoichiometric subunits including Swi2p/Snf2p, Swi1p, Snf5p, Swi3p, Swp82p, Swp73p, Arp7p, Arp9p, Snf6p, Snf11p, and Swp29p, with a molecular weight of 1.14 mega Daltons. Swi2p/Snf2p, the catalytic subunit of SWI/SNF, is evolutionally conserved from yeast to human cells. Genetic evidence suggests that SWI/SNF is required for the transcriptional regulation of a subset of genes, especially inducible genes. SWI/SNF can be recruited to target promotors by gene specific activators, and in some cases, SWI/SNF facilitates activator binding. Biochemical studies have demonstrated that purified SWI/SNF complex can hydrolyze ATP, and it can use the energy from ATP hydrolysis to generate superhelical torsion, mobilize mononucleosomes, enhance the accessibility of endonucleases to nucleosomal DNA, displace H2A/H2B dimers, induce dinucleosome and altosome formation, or evict nucleosomes. A human homolog of Swi2p/Snf2p, BRG1, is the catalytic subunit of the human SWI/SNF complex. Interestingly, isolated BRG1 alone is able to remodel a mononucleosome substrate. Importantly, mutations in mammalian SWI/SNF core subunits are implicated in tumorigenesis. Therefore, it remains interesting to characterize the role(s) of each subunit for SWI/SNF function. In this thesis project, I dissected SWI/SNF chromatin remodeling function by investigating the role of the SANT domain of the Swi3p subunit. Swi3p is one of the core components of SWI/SNF complex, and it contains an uncharacterized SANT domain that has been found in many chromatin regulatory proteins. Earlier studies suggested that the SANT domain of Ada2p may serve as the histone tail recognition module. For Swi3p, a small deletion of eleven amino acids from the SANT domain caused a growth phenotype similar to that of other swi/snf mutants. In chapter I, I have reviewed recent findings in the function of chromatin remodeling complexes and discuss the molecular mechanism of their action. In chapter II, I characterized the role of the SANT domain of Swi3p. I found that deletion of the SANT domain caused a defect in a genome-wide transcriptional profile, SWI/SNF recruitment, and more interestingly impairment of the SANT domain caused the dissociation of SWI/SNF into several subcomplexes: 1) Swi2p/Arp7p/Arp9p, 2) Swi3p/Swp73p/Snf6p, 3) Snf5p, and 4) Swi1p. Artificial tethering of SWI/SNF onto a LacZ reporter promoter failed to activate the reporter gene in the absence of the SANT domain, although Swi2p can be recruited to the LacZ promoter. We thus demonstrated that the Swi3p SANT domain is critical for Swi3p function and serves as a protein scaffold to integrate these subcomplexes into an intact SWI/SNF complex. In Chapter III, I first characterized the enzymatic activity of the subcomplexes, especially the minimal complex of Swi2p/Arp7p/Arp9p. We found that this minimal subcomplex is fully functional for chromatin remodeling in assays including cruciform formation, restriction enzyme accessibility in mononucleosomal and nucleosomal array substrates, and mononucleosome mobility shift. However, it is defective in ATP-dependent removal of H2A/H2B dimers. Moreover, we found that Swi3p and the N-terminal acidic domain of Swi3p strongly interact with GST-H2A and H2B but not GST-H3 or H4 tails. We purified a SWI/SNF mutant (SWI/SNF-Δ2N) that lacks 200 amino acids within the N-terminal acidic domain of Swi3p. Intriguingly, SWI/SNF-Δ2N failed to catalyze ATP-dependent dimer loss, although this mutant SWI/SNF contains all the subunits and has intact ATP-dependent activity in enhancing restriction enzyme accessibility. These data help to further understand the molecular mechanism of SWI/SNF, and show that H2A/H2B dimer loss is not an obligatory consequence of ATP-dependent DNA translocation, but requires the histone chaperone function of the Swi3p subunit. Based on these findings, we proposed a new model of the structural and functional organization of the SWI/SNF chromatin remodeling machinery: SWI/SNF contains at least four distinct modules that function at distinct stages of the chromatin remodeling process. 1) Swi1p and Snf5p modules directly interact with gene specific activators and function as the recruiter; 2) Swi2p/Arp7p/Arp9p generates energy from ATP hydrolysis and disrupts histone/DNA interactions; and 3) Swi3p/Swp73p/Snf6p may play dual roles by integrating each module into a large remodeling complex, as well as functioning as a histone H2A/H2B chaperone to remove dimers from remodeled nucleosomes. Chapter IV is a perspective from current work in this project. I first discuss the interest in further characterizing the essential role of Snf6p, based on its activation of LacZ reporter on its own. Using in vitro translated protein and co-IP studies, I tried to pinpoint the requirement of the SANT domain for SWI/SNF assembly. I found that Swi3p directly interacts with Swp73p, but not with other subunits. When Swi3p is first incubated with Swp73p, Swi3p also interacts with Snf6p, indicating that Swi3p indirectly interacts with Snf6p, therefore forming a subcomplex of Swi3p/Swp73p/Snf6p. This subcomplex can also be reconstituted using in vitro co-translation. Consistent with the TAP preparation of this subcomplex, partial deletion of the SANT domain of Swi3p does not affect the assembly of Swi3p/Swp73p/Snf6p in vitro. However, the assembly of SWI/SNF complex was not detected in the presence of eight essential in vitro translated subunits or from co-translation of all the subunits. I have discussed the interest in further characterizing the histone chaperone role of the Swi3p N-terminal acidic domain and the role of other core subunits of SWI/SNF such as Snf6p for transcriptional regulation.

Nephroblastoma is the most prevalent pediatric kidney tumor, which occurs primarily in younger children with the average age at diagnosis of 42,5 months for girls and 36,5 months for boys. Even though its treatment is currently very succesful and the overall survival rate reaches over 90 %, there are still more things to be discovered and improved. An important role for the right choice of treatment plays not only the histology of tumor, but also the chromosomal changes present at tumor. Some of them (for example 1q gain, simultaneous deletion of 1p and 16q, TP53 deletion) were confirmed as negative prognostic markers because they are associated with an increased risk of relapse or with anaplastic type of nephroblastoma that is included in a high risk group. These changes are therefore used together with the tumor histology for stratification of nephroblastomas. Some of these changes were found in a heterogeneous state (only in a part of the cells) in nephroblastoma, which also complicates the treatment of the patient and which cannot be solved when only one sample is taken from the tumor. In this work we concentrated on the detection of chromosomal changes present in nephroblastomas of 44 patients and their associations with clinical data. We have proved some of the known associations (22q...

PAIVA, Jean Carlos Gomes. Biomonitoring genetic of farmers exposed to pesticides in the municipalities of Tiangua and Ubajara (Ceará, Brazil). 2011. 111 f. : Tese (doutorado) - Universidade Federal do Ceará, Programa de Pós-Graduação em Biotecnologia, Renorbio - Rede Nordeste de Biotecnologia. 2011. / Submitted by demia Maia (demiamlm@gmail.com) on 2016-05-23T17:19:06Z No. of bitstreams: 1 2011_tese_jcgpaiva.pdf: 2591728 bytes, checksum: 4776344bdee5aac282c66c0a37608507 (MD5) / Approved for entry into archive by demia Maia (demiamlm@gmail.com) on 2016-05-23T17:19:52Z (GMT) No. of bitstreams: 1 2011_tese_jcgpaiva.pdf: 2591728 bytes, checksum: 4776344bdee5aac282c66c0a37608507 (MD5) / Made available in DSpace on 2016-05-23T17:19:52Z (GMT). No. of bitstreams: 1 2011_tese_jcgpaiva.pdf: 2591728 bytes, checksum: 4776344bdee5aac282c66c0a37608507 (MD5) Previous issue date: 2011

Made available in DSpace on 2014-06-11T19:26:05Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-02-17Bitstream added on 2014-06-13T20:54:04Z : No. of bitstreams: 1 freitas_pc_me_sjrp.pdf: 528091 bytes, checksum: d630cd8e1a7a4fdc34c7e9200a36b8b5 (MD5) / Síndromes Mielodisplásicas (SMD) compreendem um conjunto heterogêneo de doenças hematopoéticas caracterizadas por hematopoese ineficaz, que geralmente apresentam citopenias no sangue periférico, medula óssea hipercelular, diferenciação celular displásica e propensão ao desenvolvimento de leucemia mielóide aguda. São classificadas em oito tipos e a incidência anual é estimada entre dois e 12 casos por 100.000 pessoas da população em geral e em até 50 casos por 100.000 indivíduos com idades superiores a 60 anos. A análise cromossômica das células da medula óssea dos doentes ao diagnóstico detecta alterações diretamente relacionadas com o prognóstico em aproximadamente 50% dos casos. Alguns genes também foram relacionados à etiologia e prognóstico das mielodisplasias. O gene FOXO3, um supressor de tumor, embora não estudado anteriormente em SMD, é um dos genes que mais se expressam no tecido hematopoético normal. Alterações neste gene poderiam resultar em hematopoese anormal, pois já foram relacionadas a outros tipos de câncer, com mutações descritas no éxon 1. O objetivo deste trabalho foi estudar células da medula óssea de doentes com SMD de qualquer tipo, ao diagnóstico, para investigar a presença de alterações cromossômicas e de mutações no éxon 1 do FOXO3. A análise citogenética foi realizada em metáfases submetidas ao bandamento GTG, obtidas de culturas de curta duração de células da medula, sem estimulação mitogênica. Para a análise molecular foi extraído o DNA, realizada a amplificação gênica pela Reação em Cadeia da Polimerase e realizado o sequenciamento direto do éxon 1. Entre os 25 casos analisados, três (12%) apresentaram alterações cromossômicas clonais isoladas: deleção intersticial do braço longo do cromossomo 5; monossomia do cromossomo 21 e monossomia do cromossomo 22. Todas puderam ser relacionadas... / Myelodysplastic syndrome (MDS) constitute a heterogeneous group of hematopoietic diseases characterized by ineffective hematopoiesis usually with peripheral blood cytopenia, hypercellular bone marrow, dysplastic differentiation and a tendency to evolve to acute myeloid leukemia. They are classified in eight categories by the World Health Organization. The annual incidence is estimated at between two and 12 cases per 100,000 individuals in the general population and up to 50 cases per 100,000 of over 60-year olds. A chromosomal analysis of bone marrow cells at diagnosis identifies changes directly related to prognosis in approximately 50% of cases. Additionally, some genes are also associated to the etiology and prognosis of myelodysplasia. Although not previously studied in respect to MDS, a tumor suppressor, FOXO3, is one of the most commonly expressed genes in normal hematopoietic tissue. Changes in this gene could therefore result in abnormal hematopoiesis, as mutations described in exon 1 have already been associated with other types of cancer. The aim of this study was to investigate chromosomal alterations and mutations in exon 1 of FOXO3 in bone marrow cells from patients diagnosed with any type of MDS. Cytogenetic analysis was performed on metaphases submitted to GTG banding, obtained from short-term cultures of bone marrow cells without mitogenic stimulation. To evaluate mutations in the FOXO3 gene, DNA was extracted from the bone marrow, gene amplification was achieved by polymerase chain reaction and direct sequencing was performed. Of the 25 cases analyzed, three (12%) showed clonal chromosomal abnormalities in isolation characterized as the interstitial deletion of the long arm of chromosome 5, monosomy 21 and monosomy 22. All were correlated to the diagnosis and/or prognosis of patients. No mutations were detected in exon 1, but the 159C>T polymorphism was detected... (Complete abstract click electronic access below)

Objetivos: avaliar a contribuição do fluxo anormal no ducto venoso de 11 a 13 6/7 semanas no rastreamento de anomalias cromossômicas, defeitos estruturais e prognóstico gestacional. Método: 1221 gestações únicas foram submetidas a Dopplervelocimetria do ducto venoso após o rastreamento pela translucência nucal (TN). Resultados: os defeitos cromossômicos foram diagnosticados em 22 fetos. O fluxo no ducto venoso estava anormal em 84 fetos, a TN estava acima do 95o percentil em 160 casos e ambos marcadores estiveram anormais em 41 fetos. A sensibilidade, especificidade, valores preditivos positivo e negativo para defeitos cariotípicos corresponderam respectivamente a 86,4%, 86,9%, 11,9% e 99,7% considerando a TN aumentada, 68,2%, 96,9%, 31,3%, 99,3% para anomalias do fluxo do ducto venoso e 68,2%, 97,6%, 36,6%, 99,3% analisando ambos os marcadores. Investigando malformações estruturais, esses valores foram de 43,8%, 92,9%, 8,3%, 99,1% para uma TN aumentada, 25%, 92,6%, 4,8%, 98,8% para anomalias do fluxo do ducto venoso e 25%, 97,9%, 15,4%, 98,9% para ambos os marcadores. Nos casos com TN aumentada, a proporção de nascidos vivos morfológica e cariotipicamente normais diminui de 93,8% nos fetos com fluxo no ducto venoso normal para 77,3%, quando anormal. Conclusão: a avaliação do ducto venoso de 11 a 13 6/7 semanas de gestação pode ser utilizada no rastreamento de anomalias cromossômicas fetais e pode ajudar a reduzir a taxa de falso-positivo quando combinado com a medida da TN. Em fetos com TN aumentada o fluxo anormal no ducto venoso aumenta a probabilidade de resultados gestacionais adversos / Objective: To evaluate the association between abnormal ductus venosus at 11 - 13 6/7 weeks\' gestation and chromosomal abnormalities, structural defects and fetal outcome. Methods: Ductus venosus waveform (DVFVW) and nuchal translucency (NT) thickness were prospectively evaluated in 1221 singleton pregnancies. Results: The DVFVW was abnormal in 84 cases, NT was above the 95th centile in 160 cases and both markers were observed in 41 fetuses. Chromosomal defects were diagnosed in 22 fetuses. The sensitivity, specificity and positive predictive values for an abnormal karyotype were respectively 86.4%, 86.9%, 11.9% for an increased NT; 68.2%, 96.9%, 31.3% for DVFVW abnormalities and 68.2%, 97.6%, 36.6% for both markers. Regarding structural defects, this values were 43.8%, 92.9%, 8.3% for an abnormal NT, 25%, 92.6%, 4.8% for DVFVW abnormalities and 25%, 97.9%, 15.4% for both. Considering those cases of unexplained fetal demise, the percentages were 44.4%, 85.9%, 5% for NT abnormalities, 22.2%, 92.6%, 4.8% for an abnormal DVFVW and 22.2%, 98%, 15.4% for both. In cases with increased NT measurement, the percentage of livebirths with normal karyotype and no major fetal structural defects decreased from 93.8% in normal DVFVW fetuses to 77.3%, when abnormal. Conclusion: Ductus venosus assessment at 11 - 13 6/7 weeks\' gestation is useful in screening for fetal chromosomal abnormalities and may help to reduce the false-positive rate when combining with NT thickness measurement. Abnormal DVFVW is also associated with an increase of adverse perinatal outcome in fetuses with enlarged NT. However, the value of DVFVW assessment in cases with normal NT measurement is unclear

Made available in DSpace on 2014-10-09T12:45:37Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:08:41Z (GMT). No. of bitstreams: 0 / Tese (Doutoramento) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN/CNEN-SP

Submitted by Claudinei Pracidelli (cpracide@ipen.br) on 2015-07-23T11:16:06Z No. of bitstreams: 0 / Made available in DSpace on 2015-07-23T11:16:06Z (GMT). No. of bitstreams: 0 / Dissertação (Mestrado em Tecnologia Nuclear) / IPEN/D / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Made available in DSpace on 2015-03-26T13:42:17Z (GMT). No. of bitstreams: 1 texto completo.pdf: 4676037 bytes, checksum: 95dde20b76c33bfd09f530eb8a65e6e5 (MD5) Previous issue date: 2010-07-19 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / The tribe Attini consists of a monophyletic group that includes about 230 species in 14 genera. Different biological substrate are utilized by these ants for cultivation of the symbiotic fungus on which they feed and are necessarily dependent. This tribe includes the leaf-cutting ants (Atta Fabricius and Acromyrmex Mayr) that are known as important agricultural pests. The usage of cytogenetics in the family Formicidae has made significant contributions in the study of more than 750 ant species. Only 10% of Attini’s species have some sort of cytogenetic data available. This work aimed at cytogenetically studying six Acromyrmex species and seven species of the tribe Attini divided into four genera: Apterostigma Mayr, Mycocepurus Forel, Sericomyrmex Mayr and Trachymyrmex Forel. Some of the species were also submitted to banding techniques. The karyotypes observed were: Apterostigma madidiense Weber (n=23, 7m + 10sm + 5st + 1a), Apterostigma steigeri Santschi (2n=22, 20m + 2sm), Mycocepurus goeldii (2n=8, 4m + 4sm), Sericomyrmex sp. (2n=50, 44m + 6 sm; n=25, 22m + 3 sm), Trachymyrmex fuscus Emery (2n=18, 16m + 2sm; n=9, 8m + 1sm), Trachymyrmex relictus Borgmeier (2n=20m, n=10m) and Trachymyrmex sp. (2n=22, 18m + 4sm). A size polymorphism on a short arm of a submetacentric pair from Trachymyrmex fuscus was also pointed out. The possible causes of chromosomal segment duplication were discussed. All studied species of the genus Acromyrmex presented 2n=38. Each species showed a different karyotype in relation to morphology (A. balzani: 12m + 10sm + 14st + 2a; A. coronatus: 12m + 12sm + 12st + 2a; A. disciger: 10m + 12sm + 14st + 2a; A. niger: 12m + 18sm + 6st + 2a; A. rugosus: 16m + 12sm + 8st + 2a; A. echinatior: 8m + 6sm + 14st + 10a), in the distribution of heterocromatin (C banding) and GC rich regions (CMA3). For three species (A. coronatus, A. disciger, A. niger) the first subtelocentric pair was the bearer of ribosomal genes. Acromyrmex species presented stability in the number of chromosome with differences in the karyotype. The results suggest that many chromosomal rearrangements such as translocations, growth of heterochromatin and inversion may have occurred during their differentiation, contributing to the karyotype variability found. / A tribo Attini é um grupo monofilético que inclui mais de 230 espécies agrupadas em 14 gêneros. Nesta tribo estão incluídas as formigas cortadeiras (Atta e Acromyrmex), consideradas importantes pragas agrícolas. A utilização da citogenética na família Formicidae tem mostrado importante contribuição nas mais de 750 espécies de formigas estudadas. Os dados citogenéticos são reportados para 10% das espécies da tribo Attini. O presente trabalho teve como objetivo o estudo citogenético de seis espécies do gênero Acromyrmex e de sete espécies de Attini distribuídas em quatro gêneros: Apterostigma, Mycocepurus, Sericomyrmex e Trachymyrmex. Parte das espécies foi submetida a técnicas de bandamentos cromossômicos. Os cariótipos observados foram: Apterostigma madidiense Weber (n=23, 7m + 10sm + 5st + 1a), A. steigeri Santschi (2n=22, 20m + 2sm), Mycocepurus goeldii (Forel) (2n=8, 4m + 4sm), Sericomyrmex sp. (2n=50, 44m + 6sm; n=25, 22m + 3sm), Trachymyrmex fuscus Emery (2n=18, 16m + 2sm; n=9, 8m + 1sm), T. relictus Borgmeier (2n=20m, n=10m) e Trachymyrmex sp. (2n=22, 18m + 4sm). Trachymyrmex fuscus apresentou polimorfismo de tamanho no braço curto do par submetacêntrico. As possíveis causas da duplicação do segmento cromossômico são discutidas. As seis espécies do gênero Acromyrmex apresentaram 2n=38 cromossomos. Cada espécie mostrou um cariótipo diferente em relação à morfologia (A. balzani: 12m + 10sm + 14st + 2a; A. coronatus: 12m + 12sm + 12st + 2a; A. disciger: 10m + 12sm + 14st + 2a; A. niger: 12m + 18sm + 6st + 2a; A. rugosus: 16m + 12sm + 8st + 2a; A. echinatior: 8m + 6sm + 14st + 10a) e variações na distribuição de heterocromatina (banda C) e regiões ricas em GC (CMA3). Em três espécies (A. coronatus, A. disciger, A. niger) o par subtelocêntrico de maior tamanho foi o portador de genes ribossomais. As espécies do gênero Acromyrmex apresentaram estabilidade no número cromossômico com diferenças no cariótipo. Isto sugere que rearranjos do tipo translocações, crescimento de heterocromatina e inversão devem ter ocorrido durante a evolução das espécies deste gênero, levando a modificações nos cariótipos das diferentes espécies.