Thesis (Ph. D.)--University of Missouri-Columbia, 2007. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on October 16, 2007) Vita. Includes bibliographical references.

Made available in DSpace on 2014-06-11T19:23:31Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-02-22Bitstream added on 2014-06-13T20:30:19Z : No. of bitstreams: 1 rafacho_bpm_me_botfm.pdf: 770961 bytes, checksum: 6adcd57ea96a701107db6a7e755e749f (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A exposição à fumaça do cigarro resulta em remodelação cardíaca e está relacionada com disfunção ventricular. A atenuação da remodelação cardíaca pode ser importante para melhor prognóstico cardiovascular. A vitamina D (VD) tem se destacado por seu papel na função cardíaca e por atenuar a remodelação cardíaca em modelos de sobrecarga de pressão ou de volume. Objetivo: avaliar a influência da suplementação de VD sobre a remodelação cardíaca induzida pela exposição à fumaça do cigarro (EFC) em ratos, se a VD atua de forma dose dependente e verificar se esta atuação é por mecanismos anti-inflamatórios ou antioxidantes. Métodos: Ratos machos Wistar com 200 a 250g foram alocados em seis grupos: 1) VD0-NEFC, sem suplementação de VD e não EFC; 2) VD1-NEFC, suplementação de 1000 UI VD/kg de ração e não EFC (n=8); 3) VD3-NEFC, suplementação com 3000 UI VD/kg de ração e não EFC; 4) VD0-EFC, sem suplementação de VD e EFC; 5) VD1-EFC, suplementação de 1000 UI VD/kg de ração e EFC; 6) VD3-EFC, suplementação de 3000 UI VD/kg de ração e EFC. Após dois meses, os animais foram submetidos à ecocardiografia e eutanasiados para coleta de material biológico. Foram avaliados porcentagem de colágeno, área seccional do miócito (ASM), estresse oxidativo e marcadores inflamatórios no tecido cardíaco e dosagens sanguíneas de cálcio, fósforo e do metabólito 25-hidroxicolecalciferol. Os dados foram analisados por ANOVA de duas vias e apresentados em media ± erro-padrão. Foi utilizado teste de tendência (correlação de Spearman) para avaliar a resposta de dose dependência. Resultados: a EFC promoveu maior valor de parede posterior do ventrículo esquerdo (EFC = 1,38 ± 0,03; NEFC = 1,26 ± 0,03; p = 0,009), maior diâmetro diastólico do VE corrigido pela tíbia (EFC = 17,7 ± 0,20; NEFC = 17,0 ± 0,002; p = 0,033), maior massa do VE (MVE)... / Exposure to tobacco smoke (ETS) results in cardiac remodeling and it is associated with ventricular dysfunction. Attenuation of cardiac remodeling may be important for better cardiovascular prognosis. Vitamin D (VD) has become known for its role in cardiac function and VD supplementation attenuate cardiac remodeling in models of pressure or volume overload in previous studies. Objective: To evaluate the influence of VD supplementation on cardiac remodeling induced by ETS in rats and whether VD actions are dose-dependent and if these actions involve anti-inflammatory and antioxidant mechanisms. Methods: Male Wistar rats with 200 to 250g were allocated into six groups: 1) VD0- NETS, with no supplementation of VD and no ETS, 2)-VD1-NETS, supplementation with 1000 IU VD/kg of diet and no ETS (n = 8); 3) VD3-NETS, supplemented with 3000 IU VD/kg of diet and no ETS, 4) VD0-ETS, no supplementation of VD and ETS, 5)VD1-ETS, VD supplementation with 1000 IU/kg of diet and ETS, 6) VD3-ETS, VD supplementation of 3000 IU/kg of diet and ETS. After two months, the animals underwent echocardiography and euthanized for tissue collection. The collagen percentage, myocyte cross-sectional area (MCA), oxidative stress and inflammation biomarkers in cardiac tissue were determined. Blood levels of calcium, phosphorus and 25-hydroxycholecalciferol were also evaluated. Data were analyzed by two-way ANOVA and presented as mean ± standard error. Spearman correlation test was used to evaluate the dose dependent response. Results: ETS promoted greater value of left ventricular posterior wall (ETS = 1.38 ± 0.03; NETS = 1.26 ± 0.03, p = 0.009), LV diastolic diameter corrected by the tibia (ETS = 17.7 ± 0.20, 17.0 ± NETS = 0.002, p = 0.033), higher LV mass (LVM) (ETS = 603 ± 23; NETS = 509 ± 25, p = 0.007), higher LMV index (ETS = 1.8 ± 0.06; NETS = 1.5 ± 0.07, p = 0.004), increased MCA ... (Complete abstract click electronic access below)

Submitted by Cláudio Spínola Najas (cnajas@gmail.com) on 2018-04-06T20:30:16Z No. of bitstreams: 1 TESE Nova corrigida 2018.pdf: 1836496 bytes, checksum: 5754878942303c31e60421d7ee692e04 (MD5) / Approved for entry into archive by Luciana Pizzani null (luciana@btu.unesp.br) on 2018-04-06T20:47:06Z (GMT) No. of bitstreams: 1 najas_cs_dr_bot.pdf: 1836496 bytes, checksum: 5754878942303c31e60421d7ee692e04 (MD5) / Made available in DSpace on 2018-04-06T20:47:06Z (GMT). No. of bitstreams: 1 najas_cs_dr_bot.pdf: 1836496 bytes, checksum: 5754878942303c31e60421d7ee692e04 (MD5) Previous issue date: 2017-08-28 / O infarto agudo do miocárdio (IAM) é responsável por grande número de hospitalizações e óbitos em todo o mundo. Nos últimos anos, outro fator que vem ganhando destaque na literatura como preditor de má evolução após o IAM é a remodelação ventricular. Na fase aguda do infarto, há desintegração do colágeno interfibrilar. A perda desse tecido de sustentação torna a região mais propensa à distensão e, consequentemente, mais susceptível às deformações, denominada de expansão do infarto. Na fase crônica estudos revelam que a reversão da dilatação, por outro lado, pode ocorrer entre 30 e 60% dos pacientes estando associada à melhora na evolução. Diversos estudos têm demonstrado que medicamentos ou procedimentos que modificam a remodelação ventricular, prevenindo ou retardando a dilatação cardíaca, estão associadas à melhor evolução dos pacientes como a remodelação cardíaca reversa. Outro fator importante é a força de preensão palmar no IAM, diversos estudos mostram que a força do músculo esquelético, se altera em associação com eventos cardíacos, já a composição corporal demonstra que em indivíduos portadores de maior peso magro, tem significativamente maior força que os indivíduos portadores de menor peso magro. No entanto os resultados demonstram a correlação entre peso magro e percentual de gordura pode indicar uma melhor ou pior condição para realizar o esforço isométrico de preensão manual. Objetivo: Avaliar a força da musculatura esquelética e a composição corporal como preditoras de remodelação ventricular, remodelação reversa e disfunção ventricular após o infarto agudo do miocárdio de parede anterior. Metodologia: A análise da força muscular esquelética foi obtida pela técnica de Handgrip, feita por meio de aparelho específico, Hand Dinamometer T-18. Todas as medidas realizadas na mão não dominante, com o paciente sentado, e o cotovelo apoiado na cama. Foi utilizado o método de impedância bioelétrica para a avaliação da composição corporal, principalmente quanto ao volume e percentual de água. Para a remodelação cardíaca, foi realizado o ecocardiograma para avaliar a parede anterior do ventrículo esquerdo. Todas as análises foram realizadas entre o 3º e 5º dia após o infarto. A estatística foi analisada por meio do teste do χ2, o teste t de Student, o teste de Mann-Whitney, considerando nível de significância adotado de 5% para todos os testes. Resultados: Em relação a força muscular e composição corporal, não foram detectadas diferenças significativas entre os grupos avaliados para remodelação cardíaca e disfunção com fração de ejeção ˂ 50% (p ˃ 0,05). Resultados semelhantes foram observados na remodelação cardíaca reversa que também não foram encontradas diferenças significativas para os parâmetros de força muscular e composição corporal (p ˃ 0,05). Para as análises de regressão multivariada, o percentual de massa magra mostrou-se como preditora para a remodelação cardíaca reversa quando ajustado por sexo, idade e enzimas CK-MB ( OR= 0,876; p= 0,019 ), assim como o percentual de gordura ajustados para as mesmas variáveis ( OR= 1,145; p= 0,027 ). / Abstract: Acute myocardial infarction (AMI) is responsible for large numbers of hospitalizations and deaths worldwide. In recent years, another factor that has been gaining prominence in the literature as a predictor of poor evolution after AMI is ventricular remodeling. In the acute phase of infarction, there is disintegration of the interfibrillar collagen. The loss of this supporting tissue makes the region more prone to distention and, consequently, more susceptible to deformation, termed infarct expansion. On the other hand, in the chronic phase, studies reveal that the reversal of dilation can occur in between 30 and 60% of patients, being associated with improvement in evolution. Several studies have shown that medications or procedures that modify ventricular remodeling, preventing or delaying cardiac dilatation, such as reverse cardiac remodeling, are associated with better evolution of patients. Another important factor in AMI is the palmar grip strength; several studies show that skeletal muscle strength changes in association with cardiac events, whereas body composition demonstrates that individuals with higher lean weight present significantly greater strength than individuals with lower lean weight. However, results demonstrate that the correlation between lean weight and fat percentage may indicate a better or worse condition to perform the isometric handgrip effort. Objective: To evaluate skeletal muscle strength and body composition as predictors of ventricular remodeling, reverse remodeling, and ventricular dysfunction after acute myocardial infarction of the anterior wall. Methodology: Analysis of skeletal muscle strength was obtained through the Handgrip technique, carried out by means of a specific device, the Hand Dinamometer T-18. All measurements were taken on the non-dominant hand, with the patient seated, and the elbow resting on the bed. The bioelectrical impedance method was used to evaluate body composition, principally regarding the volume and percentage of water. For cardiac remodeling, an echocardiogram was performed to evaluate the left ventricular anterior wall. All analyzes were performed between the 3rd and 5th day after the infarction. The statistics were analyzed using the χ2 test, the Student t test, and the Mann-Whitney test, considering a significance level of 5% for all tests. Results: Regarding muscle strength and body composition, no significant differences were detected between the evaluated groups for cardiac remodeling or dysfunction, with ejection fraction ˂ 50% (p ˃ 0.05). Similar results were observed in the reverse cardiac remodeling, also with no significant differences found for the parameters muscle strength and body composition (p ˃ 0.05). For the multivariate regression analyzes, the percentage of lean mass was shown to be a predictor for reverse cardiac remodeling when adjusted by sex, age, and CK-MB enzymes (OR = 0.876, p = 0.019), as well as the percentage of fat adjusted for the same variables (OR = 1.145, p = 0.027).

Orientador: Leonardo Antonio Mamede Zornoff / Resumo: O infarto agudo do miocárdio (IAM) é responsável por grande número de hospitalizações e óbitos em todo o mundo. Nos últimos anos, outro fator que vem ganhando destaque na literatura como preditor de má evolução após o IAM é a remodelação ventricular. Na fase aguda do infarto, há desintegração do colágeno interfibrilar. A perda desse tecido de sustentação torna a região mais propensa à distensão e, consequentemente, mais susceptível às deformações, denominada de expansão do infarto. Na fase crônica estudos revelam que a reversão da dilatação, por outro lado, pode ocorrer entre 30 e 60% dos pacientes estando associada à melhora na evolução. Diversos estudos têm demonstrado que medicamentos ou procedimentos que modificam a remodelação ventricular, prevenindo ou retardando a dilatação cardíaca, estão associadas à melhor evolução dos pacientes como a remodelação cardíaca reversa. Outro fator importante é a força de preensão palmar no IAM, diversos estudos mostram que a força do músculo esquelético, se altera em associação com eventos cardíacos, já a composição corporal demonstra que em indivíduos portadores de maior peso magro, tem significativamente maior força que os indivíduos portadores de menor peso magro. No entanto os resultados demonstram a correlação entre peso magro e percentual de gordura pode indicar uma melhor ou pior condição para realizar o esforço isométrico de preensão manual. Objetivo: Avaliar a força da musculatura esquelética e a composição corporal como predit... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Abstract: Acute myocardial infarction (AMI) is responsible for large numbers of hospitalizations and deaths worldwide. In recent years, another factor that has been gaining prominence in the literature as a predictor of poor evolution after AMI is ventricular remodeling. In the acute phase of infarction, there is disintegration of the interfibrillar collagen. The loss of this supporting tissue makes the region more prone to distention and, consequently, more susceptible to deformation, termed infarct expansion. On the other hand, in the chronic phase, studies reveal that the reversal of dilation can occur in between 30 and 60% of patients, being associated with improvement in evolution. Several studies have shown that medications or procedures that modify ventricular remodeling, preventing or delaying cardiac dilatation, such as reverse cardiac remodeling, are associated with better evolution of patients. Another important factor in AMI is the palmar grip strength; several studies show that skeletal muscle strength changes in association with cardiac events, whereas body composition demonstrates that individuals with higher lean weight present significantly greater strength than individuals with lower lean weight. However, results demonstrate that the correlation between lean weight and fat percentage may indicate a better or worse condition to perform the isometric handgrip effort. Objective: To evaluate skeletal muscle strength and body composition as predictors of ventricu... (Complete abstract click electronic access below) / Doutor

Afin de lutter efficacement contre les malversations du dopage, il apparaît essentiel de comprendre les mécanismes conduisant au remodelage musculaire. Dans ce but nous avons analysé les effets d’un β2-agoniste, le clenbutérol, sur le remodelage musculaire et les différentes voies de signalisation qui y sont associées. Nous nous sommes particulièrement intéressés au système des calpaïnes qui a souvent été associé à des phénomènes de remodelage musculaire, principalement dans des modèles d’atrophie. Nous avons montré une sollicitation précoce du système des calpaïnes lors d’un traitement chronique au clenbutérol chez le rat associé à une conversion phénotypique dans les muscles EDL et Soléaire et à une hypertrophie dans le muscle EDL uniquement. Puis, nous avons inhibé l’activité des calpaïnes en parallèle d’un traitement au clenbutérol. Les muscles ayant une activité des calpaïnes diminuée et soumis à un traitement au clenbutérol n’ont pas développé de remodelage musculaire. Ces premiers résultats renforcent l’idée d’une implication des calpaïnes dans le remodelage musculaire induit par un traitement chronique au clenbutérol. / To fight doping in an effective manner, it is essential to understand the mechanisms leading to muscle remodeling. For this purpose we analyzed the effects of clenbuterol, on muscle remodeling and various associated signaling pathways. We were particularly interested with the calpain system which has often been associated with muscle remodeling phenomena, mainly in models of atrophy. We have shown that an early calpain system solicitation during chronic treatment with clenbuterol in rats was associated with a phenotypic conversion in the Soleus and EDL muscles and hypertrophy in the EDL muscle. We then inhibited the activity of calpains with a parallel clenbuterol treatment. The muscles with a reduced activity of calpain and treated with clenbuterol did not develop muscle remodeling. These initial results reinforce the idea of an involvement of calpain in the muscle remodeling induced by chronic treatment with clenbuterol.

L’os subit perpétuellement des contraintes mécaniques et physiologiques, ainsi sa qualité et sa résistance à lafracture évoluent constamment au cours du temps à travers le processus de remodelage osseux. Cependant,certaines pathologies osseuses comme l’ostéoporose ou la maladie de Paget altèrent cette dernière et conduisent àune augmentation du risque de fracture osseuse. La qualité osseuse est non seulement définie par la densitéminérale osseuse (DMO) mais également par les propriétés mécaniques ainsi que la microarchitecture. Au total, onévalue en France à environ 3 millions le nombre de femmes et 1 million le nombre d’hommes souffrantd’ostéoporose, pour un coût estimé à 1 milliard d’euros. La prévention par le développement d’outils de diagnosticest nécessaire. Le diagnostic doit permettre d’estimer la qualité osseuse (propriétés mécaniques, activitéscellulaires, architecture). Ces travaux de thèse proposent un modèle innovant permettant de combiner lesdifférents facteurs agissant sur le remodelage osseux, à savoir : (i) le comportement mécanique, (ii) l’activitécellulaire, (iii) le processus de transduction ; visant à traiter les différentes informations d’origines mécanique etbiochimique. Les lois de comportement mécaniques et cellulaires sont issues de modèles validés dans la littératureet la stratégie d’unification voit sa justification à travers différents travaux sur les mécanismes de transduction.Ainsi, l’implémentation de ces trois acteurs du remodelage dans une analyse par éléments finis permet d’obtenirun modèle mécano-biologique du remodelage de l’os trabéculaire. Le modèle est applicable à différentes échelles etpermet d’étudier le niveau de remodelage local modulé par l’activité physique et la concentration de certains agentsbiochimiques. L’application du modèle sur un volume virtuel de fémur selon différents scénarios cliniques donnedes résultats conformes aux observations faites en imagerie médicale. / By continuously undergoing mechanical and physiological stresses, bone quality and bone strength evolve throughremodeling process. However, osteoporosis and Paget’s disease for instance alter bone quality and increase the risk of bone fracture. Bone quality is mainly defined by its Bone Mineral Density (BMD) but mechanical properties and microarchitecture have also to be taken into account for a proper definition. About 3 million of women and 1 million of men suffer from osteoporosis which costs approximately 1 billion Euros per year in France. This highlights the necessity to develop diagnostic tools in order to enable proper bone quality characterization (mechanical properties, cellular activity and architecture).This thesis proposes an original model combining the main bone remodeling constituents which are : (i) the mechanical behavior, (ii) the cellular activity, (iii) the transduction phase ; enabling mechanical and biochemical information processing. Mechanical and cellular behavior models are taken from already published work and the transduction phase model unifying mechanical and biological information is inspired from the literature. Consequently, the implementation of these three main bone remodeling constituents into a finite element analysis gives a plausible mechano-biological model of trabecular bone remodeling. The developed model can be used at different scales in order to study the local amount of bone remodeled, magnified by physical activity and the concentration of some biochemical agents. Its application on virtual volume of femora under different clinical scenarios gives good results in respect to medical images observations.

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2014-04-02T13:33:04Z No. of bitstreams: 1 Delsilene Borges. Avaliação...2013.pdf: 2874154 bytes, checksum: 062e7af1c2af767178820b1b4d1d1bc7 (MD5) / Made available in DSpace on 2014-04-02T13:33:04Z (GMT). No. of bitstreams: 1 Delsilene Borges. Avaliação...2013.pdf: 2874154 bytes, checksum: 062e7af1c2af767178820b1b4d1d1bc7 (MD5) Previous issue date: 2013 / Fundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, Brasil / Na esquistossomose mansônica o fígado é o órgão alvo das agressões patogênicas, onde as lesões hepáticas caracterizam-se principalmente pela presença de granulomas periovulares e formação de fibrose periportal, além de alterações vasculares responsáveis pela hipertensão dentro do sistema venoso portal. A angiogênese precede a maioria dos casos de fibrose, onde se verifica participação direta das células estreladas hepáticas (CEH) e das células endoteliais sinusoidais (CES) que são estimuladas, principalmente por macrófagos do tipo II (M2) – ativados alternativamente. O tratamento para esquistossomose é feito pelo uso do praziquantel (PZQ), o qual é capaz de promover cura parasitológica e reparo das lesões hepáticas, todavia pouco se sabe sobre os componentes celulares envolvidos na angiogênese durante o reparo do fígado. Este trabalho teve como objetivo estudar o remodelamento das lesões hepáticas pós-tratamento e investigar a participação das CEH, CES e macrófagos M2 no processo de reparo das lesões. Após aprovação pela Comissão de Ética no Uso de Animais (CEUA-CPqGM), protocolo nº 006/2011, 80 camundongos Swiss Webstar foram utilizados, destes 70 foram infectados com 50 cercárias do Schistossoma mansoni e dez permaneceram intactos. Quatro meses após infecção foi realizado tratamento com PZQ (400mg/Kg) em parte dos animais infectados, formando assim três grupos: um controle, um infectado não tratado e outro infectado e tratado. Em diferentes intervalos de tempo foram realizadas três hepatectomias parciais: a primeira com quatro meses de infecção (antes do tratamento); a segunda com seis meses de infecção e dois meses de tratamento; a terceira com oito meses de infecção e quatro de tratamento. Os fragmentos hepáticos coletados foram submetidos a avaliações morfológicas e estudos imuno-histoquímicos para visualização de componentes celulares – macrófagos M2 (Ym1), CEH (α-SMA) e CES (CD31). Análises morfométricas foram realizadas para quantificação do percentual de tecido fibroso e das células imunomarcadas. Nossos resultados demonstraram que após dois meses de tratamento com PZQ foi possível observar reabsorção do tecido fibroso hepático com redução da expressão de macrófagos M2 e CEH. Quatro meses após a quimioterapia verifica-se aumento no número de células endoteliais. Esses resultados sugerem que macrófagos M2 e CEH têm participação ativa na formação do tecido fibroso, exercendo pouca influência na fase involutiva do granuloma. Todavia, a intensa proliferação de CES nos granulomas involutivos, confirma o importante papel da angiogênese no remodelamento das lesões hepáticas. / The liver is a target for pathogenic attacks during schistosomiasis, showing periovular granulomas and the formation of periportal fibrosis, besides vascular changes responsible for hypertension within portal venous system. Angiogenesis precedes most cases of fibrosis, which can be verified the presence of hepatic stellate cells (HSC) and liver sinusoidal endothelial cells (LSEC) stimulated mostly by macrophages type II (M2) – alternatively activated. Schistosomiasis treatment is based on praziquantel (PZQ), which enables parasitological cure and resolution of liver cells. However, knowledge regarding active cell components on angiogenesis during liver regeneration is scarce. Our goal was to study the remodeling of liver injuries during post-treatment phase and investigate the role of HSC, LSEC and macrophages (M2) on the process of resolution of injuries. After the approval of ethical committee for animal research of the CPQGM-FIOCRUZ, record number 006/2011, 80 mice Swiss Webstar were used, which 70 were infected by 50 cercariae of Schistossoma mansoni and ten remained intact. Four months after infection a treatment with PZQ (400mg/Kg) was started in part of infected animals, constituting three different groups: normal, non-treated infected and treated and infected. In different times three partial hepatectomias were made: the first on four months of infection (before treatment); the second with six months of infection and two months of treatment; and the third with eight months of infection and four months of treatment. In all liver fragments collected for morphological evaluations were performed and immunohistochemistry studies were made to visualize macrophages M2 (Yml), HSC (α-SMA) and LSEC (CD31). Morphometric analysis was performed to quantify percentage of fibrosis and the immunostainig cells. Our results show that after two months of PQZ treatment it is possible to observe fibrosis resorption in the liver, with reduction of macrophages M2 expression and HSC. Four months after chemotherapy an increase on the number of LSEC was verified. These results suggest that macrophages M2 and HSC are active on the formation of fibrosis tissue, playing little influence on the evolving phase of the granuloma. Nevertheless, intense proliferation of LSEC observed on involute granulomas confirm the important role for angiogenesis on remodeling of liver injuries.

The dynamic nature of eukaryotic chromatin enables the packaging of large amounts of genetic material in a small space. At the same time, it provides controlled access to genomic DNA for a variety of nuclear processes for example, transcription and DNA repair. The transition between open and closed chromatin states is largely governed by ATP-dependent chromatin remodeling complexes, which operate on nucleosomes in concert, to modulate chromatin structure and composition. Exchange of the canonical and variant forms of histones in nucleosomes, and altering the spacing between consecutive nucleosomes, are two major ways which regulate chromatin-based processes and chromatin higher-order organization. The evolutionarily conserved INO80 and ISW1a complexes mediate these two aspects of nucleosome remodeling, respectively. Despite sharing conserved domain architecture of the core remodeling machinery, chromatin remodelers differ significantly in their modes of interaction with nucleosomes, and how they alter histone-DNA contacts. In this study, we have used a site-specific photocrosslinking approach coupled with peptide mapping to determine the interactions of subunits and domains of the S. cerevisiae INO80 and ISW1a complexes with nucleosomes. We find that specific interactions of remodelers with different regions of the nucleosome largely dictate their specialized functions and mechanisms. The ATP-dependent helicase-like (ATPase) domains of remodelers belonging to the ISWI and SWI/SNF families translocate along DNA close to the center of nucleosomes in order to mobilize, space or disassemble nucleosomes. In contrast, we observed that INO80 has a strikingly distinct mechanism, which is different even from its paralog SWR1. INO80 mobilizes nucleosomes as well as catalyzes the exchange of histone variant H2A.Z for the canonical histone H2A, while SWR1 mediates the reverse exchange of H2A for H2A.Z, without being able to mobilize nucleosomes. We have found that INO80, in order to promote H2A-H2B dimer exchange, translocates along DNA at the H2A-H2B interface close to the edge of nucleosomes and persistently displace DNA from H2A-H2B. Blocking either DNA translocation or the accumulation of DNA torsions close to the edge of the nucleosome interferes with this dimer exchange by INO80. SWR1 and other SWI/SNF and ISWI remodeling complexes translocate along DNA at the H3-H4 interface and do not persistently displace DNA from the histone octamer as does INO80. This study shows for the first time an ATP-dependent chromatin remodeler that invades nucleosomes at the DNA entry site instead of the center − a more logical approach for the displacement of H2A-H2B. We also investigated nucleosomal DNA interactions of other INO80 subunits and domains to understand the architecture of INO80 bound to nucleosomes. We found that the HSA (helicase-SANT-associated) domain of Ino80 along with actin-related protein (Arp) subunits Arp8 and Arp4 bind to the extranucleosomal DNA and is potentially involved in a coupling mechanism with the ATPase domain to regulate its activity. We also mapped the DNA binding regions of Arp8 and Arp4, which might be involved in recruiting INO80 to genomic sites. The ISWI remodeler ISW1a regulates the distance (spacing) between nucleosomes in an array by simultaneously interacting with two nucleosomes and directionally remodels one of them. We mapped DNA interactions of ISW1a subunits in mono- and di-nucleosomes. Our results show that the catalytic Isw1 subunit specifically interacts with the region of DNA translocation and DNA entry site of the asymmetrically positioned nucleosome in a di-nucleosome, which is preferentially mobilized. In contrast, the Ioc3 subunit interacts extensively with the linker DNA as well as the extranucleosomal DNA of the un-remodeled nucleosome. This bias in nucleosomal DNA interactions of ISW1a enables directional remodeling, which reveals the molecular basis of nucleosome spacing. We have identified a novel domain within the non-catalytic Ioc3 subunit of ISW1a that regulates nucleosome spacing. We found that when this domain is deleted, the catalytic Isw1 subunit loses its specificity and interacts with both the nucleosomes of a di-nucleosome substrate. This is consistent with the domain-deleted ISW1a mobilizing both nucleosomes efficiently, leading to the loss of its nucleosome spacing activity. In summary, this dissertation explores how different remodeling complexes have customized and regulated modes of nucleosome interaction in order to accomplish specialized remodeling outcomes. INO80 places its ATPase domain for translocation at the H2A-H2B dimer interface and persistently displaces DNA from its surface to promote H2A.Z exchange. Nucleosome spacing by ISW1a requires the catalytic Isw1 subunit to engage with and reposition one out of two consecutive nucleosomes in an array, while the Ioc3 subunit likely monitors the distance between them.

AN ABSTRACT OF THE DISSERTATION OF SOLOMON G. HAILU, for the Doctor of Philosophy degree in Molecular Biology, Microbiology and Biochemistry, presented on August 22, 2017, at Southern Illinois University, School of Medicine. TITLE: DISTINCT GENOME WIDE FUNCTIONS OF CHROMATIN REMODELERS IN NUCLEOSOME ORGANIZATION AND TRANSCRIPTION REGULATION MAJOR PROFESSOR: Dr. Blaine Bartholomew Chromatin remodelers are conserved from yeast to humans and are the gatekeepers of chromatin. They regulate transcription by occluding or exposing DNA regulatory elements globally. They are crucial for DNA processes such as DNA replication, repair and recombination. In addition, they are critical in developmental processes and differentiation. Chromatin remodelers are categorized into several families based on their conserved ATPase domain, an essential component required for their DNA translocation ability. In this study, we investigated the role yeast ISWI and SWI/SNF family of chromatin remodelers play on nucleosome rearrangement and transcription regulation by targeted mutagenesis of domains in accessory subunits and at the C-terminus of the catalytic subunit. All members of the ISWI family (ISW1a, ISW1b, ISW2) share a conserved C-terminal HAND, SANT and SLIDE domains, which are important for sensing linker DNA. We find an auto-regulation of ISWI complexes by the SLIDE domain, independent of the histone H4 Nterminal tail. Our protein-protein chemical crosslinking and mass spectrometry (CX-MS) analysis indicate that the SLIDE domain regulates the ATPase core through N terminal domains of the accessory subunit Itc1. Moreover, we show that the accessory subunits of ISWI modulate the ATPase activity and specificity of ISWI complexes. The DNA sensing ability of the SLIDE domain is required for the in vivo nucleosome spacing and transcription regulation by ISWI. We find that while ISW2 primarily regulates transcription at the 5’ end of genes, ISW1a is important in transcription elongation by rearranging nucleosomes starting at the +2 nucleosome and through the rest of the body of genes towards the 3’ end. ISW1b on the other hand rearrange nucleosomes in the gene body to facilitate suppression of cryptic transcription. For the first time, we show the potential division of labor between ISW1a and ISW1b during transcription elongation. On the other hand, SWI/SNF chromatin remodelers are essential epigenetic factors that are frequently mutated in cancer and neurological disorders. They harbor a C-terminal SnAC and AT hook domains that positively regulate their DNA dependent ATPase activity and nucleosome mobilizing capabilities. By deleting the AT hook motifs, we have identified the role of SWI/SNF in organizing the -1 and +1 nucleosomes at transcription start sites flanking the nucleosome free region (NFR). Our RNA-seq analysis shows SWI/SNF positively regulates the bi-directional transcription of non-coding RNA (ncRNA) which are activated when the AT hook motifs are deleted. Moreover, AT hooks regulate such activities of SWI/SNF through direct protein-protein interactions with the ATPase core as evidenced by our chemical crosslinking and mass spectrometry (CX-MS) analysis.

xvii, 146 p. : ill. A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / This thesis examines the role of cultural heritage in adaptively reused historic industrial buildings in Portland, Oregon. While it has been argued that adaptive reuse contributes to the ecological and economic initiatives of sustainability, this research explores how adapting historic industrial buildings for modern reuse can also be socially and culturally sustainable for communities. Industrial buildings provide physical evidence of a rich cultural and industrial past and there are opportunities to share this heritage with a building's new users and/or the surrounding community. Case studies include selectively chosen National Register nominated buildings that meet specific criteria, share a common regulatory framework, and provide insightful information regarding the relationship between history and new use. Strengths and challenges of conveying industrial heritage in modern use as well as opportunities for developers of historic properties to highlight and improve upon this process are identified. / Committee in Charge: Robert Z. Melnick, FASLA, Chair; Doug Blandy, Ph.D