Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / In the period May 2008 to March 2009 experiment was conducted in an area of the Federal University of Santa Maria, in order to evaluate the characteristics and structural traits of eight native grasses (Andropogon lateralis, Aristida laevis, Axonopus affinis, Erianthus angustifolius, Paspalum notatum, Paspalum plicatulum, Piptochaetium montevidense and Sorghastrum pellitum) under nitrogen levels (zero and 100 kg /ha of nitrogen). The experimental design was of blocks randomized with three replications in factorial arrangement of 8 x 2 (native grasses x nitrogen). Accumulated thermal time of 350 and 700 degree days determined the interval between cuts to the species of prostrate growth habit and caespitose, respectively. The highest rates of elongation were observed in Aristida laevis, Erianthus angustifolius, Paspalum plicatulum and Sorghastrum pellitum when received nitrogen. For leaf appearance rate, phyllochron, leaf senescence rate, duration of elongation, the lifespan of the leaves, number of green leaves and leaf length difference was found between species. / No período de maio de 2008 a março de 2009 foi desenvolvido experimento em área da Universidade Federal de Santa Maria, com o objetivo de avaliar as características morfogênicas e estruturais de oito gramíneas nativas (Andropogon lateralis, Aristida laevis, Axonopus affinis, Erianthus angustifolius, Paspalum notatum, Paspalum plicatulum, Piptochaetium montevidense e Sorghastrum pellitum) sob níveis de adubação nitrogenada (zero e 100 kg/ha de nitrogênio). O delineamento experimental foi o de blocos inteiramente casualizados com três repetições e em arranjo fatorial 8 x 2 (gramíneas nativas x doses de nitrogênio). A soma térmica acumulada de 350 e 700 graus-dia determinou o intervalo entre cortes para as espécies de hábito de crescimento prostrado e cespitoso, respectivamente. As maiores taxas de elongação foliar foram observadas em Aristida laevis, Erianthus angustifolius, Paspalum plicatulum e Sorghastrum pellitum quando receberam adubação nitrogenada. Para taxa de aparecimento foliar, filocrono, taxa de senescência foliar, duração da elongação foliar, duração de vida das folhas, número de folhas verdes e comprimento de lâminas foliares houve diferença entre as espécies avaliadas.

Made available in DSpace on 2015-03-26T13:51:53Z (GMT). No. of bitstreams: 1 texto completo.pdf: 4350402 bytes, checksum: bd6bf9393be337ef287514591c95188f (MD5) Previous issue date: 2011-07-18 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / The ectomycorrhizal association is a mutualistic interaction between plant roots and soil fungi that causes morphophysiological changes in the plant root system. The nutritional benefits result from the capacity of the fungus to increase the uptake of mineral nutrients by the host plant in exchange for photoassimilates. For the ectomycorrhizal association between Scleroderma laeve and Eucalyptus grandis, there is no information on which genes are decisive for the symbiosis and how they relate to the formation of ectomycorrhizas. Transcripts of the genes ras and ef1α were dentified as differentially expressed in many symbiotic associations and are related to signal transduction pathways and protein synthesis, respectively. Thus, the objectives of this work were to establish the ectomycorrhizal association between S. laeve and E. grandis in vitro, to isolate partial sequences of the genes ras and ef1α of S. laeve, and to evaluate the functional expression of these genes during ectomycorrhizal formation. Our works demonstrates the ectomycorrhizal association between S. laeve and E. grandis in vitro for the first time. The typical structures of ectomycorrhizas, such as the mantle and the Hartig net, were observed. At three days of contact between S. laeve and E. grandis roots the beginning of mantle formation could be observed. At 15 days, the mantle was completely formed, the epidermal cells were elongated, and the Hartig net formation was in progress. At 30 days, the ectomycorrhizas presented all the typical morphological structures fully developed. To evaluate gene expression during the association, partial sequences of ras and ef1α were isolated and the transcripts evaluated at the pre-symbiotic phase and at 3, 15 and 30 days after physical contact of the fungus with the plant roots. The transcripts of the gene ef1α were expressed at all evaluated times. Transcripts of ras were only detected in the ectomycorrhizas after three, 15, and 30 days of contact. These results are fundamental for a better understanding of the ectomycorrhizal association between S. laeve and E. grandis and suggest that ras-mediated signal transduction pathways may be functional during the establishment of the symbiosis between the fungus and the host roots. / A associação ectomicorrízica é uma interação mutualista entre raízes de plantas e fungos do solo, resultando em mudanças morfofisiológicas do sistema radicular das plantas. Os benefícios nutricionais advêm da capacidade do fungo em aumentar a absorção de nutrientes minerais pelas plantas, recebendo em troca os fotoassimilados. Na associação entre Scleroderma laeve e Eucalyptus grandis ainda não se tem informações de quais genes são decisivos e estão relacionados a este processo. Transcritos dos genes ras e ef1α foram identificados durante a formação da simbiose e sendo diferencialmente expressos na associação ectomicorrízica, e estão relacionados a vias de transdução de sinal e atuando na síntese protéica, respectivamente. Assim, os objetivos deste trabalho foram estabelecer a associação ectomicorrízica in vitro entre S. laeve e E. grandis, isolar sequências parciais dos genes ras e ef1α do fungo ectomicorrízico S. laeve, e avaliar a expressão funcional destes genes durante as fases de formação das ectomicorrizas. Este trabalho comprova a associação in vitro entre S. laeve e E. grandis, sendo registrada pela primeira vez. As estruturas típicas das ectomicorrizas, como a formação do manto fúngico e da rede de Hartig foram observadas. Nos tempos avaliados, em três dias de contato já havia a formação do manto fúngico. Aos 15 dias, o manto fúngico estava completamente formado, as células da epiderme alongadas e a rede de Hartig, em formação. Aos 30 dias, as ectomicorrizas apresentavam todas as estruturas típicas desenvolvidas. Para avaliar a expressão dos genes durante a associação, sequências parciais dos genes ras e ef1α foram isolados, e os transcritos destes genes foram avaliados na fase pré-simbiótica e aos três, 15 e 30 dias após o contato físico. Os transcritos do gene ef1α foram expressos durante todos os tempos avaliados. Os transcritos do gene ras foram detectados nas ectomicorrizas após três, 15 e 30 dias. Estes resultados são fundamentais para uma melhor compreensão da associação ectomicorrízica entre S. laeve e E. grandis e sugerem que as vias de transdução de sinais mediada por ras podem ser funcionais durante o estabelecimento da simbiose entre os fungos e as raízes de plantas.

Submitted by Claudinei Pracidelli (cpracide@ipen.br) on 2014-12-19T17:14:06Z No. of bitstreams: 0 / Made available in DSpace on 2014-12-19T17:14:06Z (GMT). No. of bitstreams: 0 / Dissertação (Mestrado em Tecnologia Nuclear) / IPEN/D / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Submitted by Claudinei Pracidelli (cpracide@ipen.br) on 2014-12-19T17:14:06Z No. of bitstreams: 0 / Made available in DSpace on 2014-12-19T17:14:06Z (GMT). No. of bitstreams: 0 / A decomposição natural da borracha é muito lenta, devido às suas estruturas vulcanizadas serem extremamente reticuladas formando uma rede tridimensional, tornando o reprocessamento desse material extremamente difícil. O presente trabalho tem como principal objetivo o estudo da aplicação da radiação gama como forma de desvulcanização para a reciclagem/reaproveitamento. Foi avaliada a interação de elastômeros com a radiação ionizante de fonte gama investigando-se as alterações nas propriedades físico-químicas dos materiais. Foram utilizadas formulações de borracha NBR (copolímero de Acrilonitrila-Butadieno) e EPDM (terpolímero etileno-propileno-dieno), provenientes da indústria de borracha, reticuladas por mistura convencional à base de enxofre. Foram preparados master-batch com pó de borracha (refugo industrial) e borracha virgem. O material processado (master-batch) foi irradiado em fonte de 60Co nas doses de 50, 100, 150 kGy e taxa de dose de 5 kGy h-1, à temperatura ambiente. O material irradiado foi incorporado nas formulações clássicas à base de enxofre. As formulações foram caracterizadas por: espectroscopia no infravermelho (FTIR), análise térmica (TG e DTG), tensão na ruptura, alongamento na ruptura, dureza, resistência à abrasão, reometria e inchamento. Os resultados mostraram uma predominância de cisão de cadeia na dose de 50 kGy para a borracha EPDM. Para a borracha nitrílica foi observada a predominância de cisão de cadeia na dose de 100 kGy. Estes resultados mostram a possibilidade do uso da radiação gama para o reaproveitamento/reciclagem das borrachas EPDM e nitrílica. / Dissertação (Mestrado em Tecnologia Nuclear) / IPEN/D / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Muitas respostas moduladas pela luz durante o desenvolvimento das plantas também são reguladas por hormônios vegetais, levando à hipótese da interação entre ambos os fatores. Uma ferramenta valiosa para testar tal interação seria o uso de mutantes fotomorfogenéticos e hormonais, bem como duplos mutantes combinando ambos. Em tomateiro, embora sejam disponíveis mutantes com alterações na biossíntese de fotorreceptores e/ou na transdução do sinal da luz, bem como mutantes no metabolismo e/ou sensibilidade hormonal, esses estão presentes em cultivares diferentes, o que pode limitar seu uso de modo integrado e a construção de duplos mutantes. No presente trabalho, foram introgredidas em uma única cultivar de tomateiro, Micro-Tom (cv. MT), dezenove mutações afetando a biossíntese ou a resposta a fitocromo, bem como aos hormônios auxina (AUX), citocinina (CK), giberelina (GA), ácido abscísico (ABA), etileno (ET) e brassinoesteróides (BR). Tomando-se vantagem de tal coleção, duas respostas notadamente controladas tanto pela luz quanto por hormônios foram estudadas: alongamento e acúmulo de antocianinas em hipocótilos. Para tal, foram utilizadas as seguintes abordagens: i) tratamentos exógenos de diferentes classes hormonais em mutantes fotomorfogenéticos, ii) observação de hipocótilos de mutantes hormonais crescidos na luz e no escuro, iii) observação de duplos mutantes combinando mutações hormonais e fotomorfogenéticas. Assim, o acúmulo de antocianinas foi promovido pela CK e ABA e inibido pela GA, concordando com a redução no mutante deficiente em ABA (notabilis ou not) e no mutante hipersensível à GA (procera ou pro). Apesar do mutante com baixa sensibilidade à AUX (diageotropica ou dgt) acumular exageradamente antocianinas, a aplicação exógena não evidenciou o papel da AUX, sendo, porém, coerente com a sugestão de que esse mutante possui um balanço AUX/CK voltado para CK. Tanto a aplicação exógena quanto a avaliação nos mutantes epinastic (epi), super produção de ET, e Never ripe (Nr), baixa sensibilidade ao ET, sugerem uma função limitada desse hormônio na biossíntese de antocianinas. Na luz e no escuro, AUX, CK, ABA e ET exógenos resultaram na inibição do alongamento do hipocótilo, sendo coerente com a promoção em dgt (luz), promoção em sit (luz), inibição em epi (luz e escuro). Por outro lado, GA promoveu o alongamento corroborando a promoção em pro. Contrariando o efeito exógeno da CK, brt reduziu o alongamento na luz e no escuro. No escuro, o único mutante que apresentou alongamento do hipocótilo superior a MT foi o mutante deficiente na biossíntese do phy (aurea ou au). A utilização de duplos mutantes combinando phy- e alterações hormonais mostrou uma interação aditiva (au epi, au Nr, au dgt e au sit), sinergística (au pro) e epinástica (au brt) no acúmulo de antocianinas e alongamento do hipocótilo na luz, porém nessa última resposta, au dgt e au sit indicaram uma interação sinergística. Juntos, esses resultados indicam que, embora phy possui vias distintas da AUX, ET, ABA e GA no controle do acúmulo de antocianinas e alongamento do hipocótilo, parece que esse fotorreceptor partilha vias comuns com CK em ambas as respostas. / Many responses regulated by light during plant development are also regulated by plant hormones, suggesting an interaction between these factors. One important approach to test this hypothesis is the use of photomorphogenic and hormonal mutants and double mutant analysis. Mutants with altered photoreceptor biosynthesis, light signal transduction, hormonal metabolism and hormonal sensitivity are available in tomato. However, since they are in different cultivars, this can be a limitation for their use in a comprehensive study, as well as, for the construction of double mutants. In this work we performed the introgression of nineteen mutations in a single cultivar of tomato, Micro- Tom (cv. MT). These mutations affect biosynthesis or response to phytochrome (phy), auxin (AUX), cytokinin (CK), gibberellin (GA), abscisic acid (ABA), ethylene (ET) and brassinosteroid (BR). Using this collection of hormone mutants, we studied two responses which are controlled by light and hormones: elongation and anthocyanin accumulation in hypocotyls. For this purpose, we used three approaches: i) hormonal treatment in the photomorphogenic mutants, ii) measurement of hypocotyl lengths from hormonal mutants grown under light and dark conditions and iii) double mutant (photomorphogenic-hormonal) analysis. Anthocyanin accumulation was promoted by CK and ABA and inhibited by GA. This is in accordance with the reduction of anthocyanin accumulation in the ABA deficient mutant (not) and in the GA hypersensitive mutant (pro). Although the diageotropica (dgt), auxin-insensitive mutant, showed a high anthocyanin accumulation, the addition of auxin did not supported a role for this hormone in anthocyanin accumulation. On the other hand, this could be due to a low auxin-tocytokinin ratio presented by dgt. Data from mutants with altered metabolism and sensitivity of ethylene, epinastic (epi) and Never ripe (Nr) respectively, and from plants treated with this hormone suggest a limited role of ethylene in the anthocyanin biosynthesis. Exogenous AUX, CK, ABA and ET inhibited the hypocotyl elongation. This is coherent with the promotion of hypocotyl elongation in dgt and sit mutants under light conditions and inhibition of hypocotyl elongation in the epi mutant in the light and dark. On the other hand, GA promoted the hypocotyl elongation corroborating the same effect seen in pro. The brt mutant showed a reduced hypocotyl elongation in light and dark conditions, which contradicts the effect of exogenous cytokinin. The phytochromedeficient aurea (au) mutant was the only one to show an enhanced hypocotyl elongation in the dark compared to the wild type (MT). The combination between photomorphogenic and hormonal mutants (double mutants) showed additive (au epi, au Nr, au dgt e au sit), synergistic (au pro) and epistatic (au brt) interactions considering the anthocyanin accumulation and hypocotyl elongation. Synergistic interaction was observed in the elongation hypocotyl of the au dgt and au sit double mutants. These results indicate that phy and CK may share some signaling/metabolic pathways in the control of anthocyanin accumulation and hypocotyl elongation. On the other hand, our data do not support an interaction between phy and the hormones AUX, ET, ABA and GA in the control of hypocotyls elongation or anthocyanin accumulation.

Les changements de forme des cellules épithéliales sont cruciaux pour la morphogenèse embryonnaire. Chez les embryons de C. elegans, l'activité musculaire sous les cellules épidermiques est l'une des deux forces mécaniques qui dirigent ce processus. Cependant, les mécanismes moléculaires détaillés à travers lesquels l'activité musculaire favorise l'allongement polarisé le long de l'axe antérieur / postérieur (A / P) restent à être totalement compris. Ici, en utilisant l'imagerie rapide-3D, on découvre que les embryons tournent après l'activation musculaire et on décrit le schéma local et global de la rotation de l'embryon induite par activité musculaire. En outre, on a observé que les muscles des côtés opposés de l'embryon se contractent alternativement, expliquant les rotations de l'embryon. Par conséquent, les jonctions adhérentes sont étirées le long de la direction A / P pendant les rotations de l'embryon et sont donc sous une tension plus élevée. Nos résultats préliminaires d'imagerie en molécule unique ont montré que plus de E-cadhérine, matériau de jonction, fusionne avec des jonctions orientées A / P quand il y a une tension élevée sur ces jonctions. / Epithelial cell shape changes is essential for embryonic morphogenesis. In C. elegans embryos, muscle activity from underneath epidermal cells is one of the two mechanical force inputs driving this process. However, the detailed molecular mechanisms through which muscle activity promotes the polarized elongation along the anterior/posterior (A/P) axis remains to be fully understood. Here, using fast-3D imaging, we discover that embryos rotate after muscle activation and we describe the local and global pattern of embryo rotation induced by muscle activity. Furthermore, we observed that muscles located on opposite sides of the embryo mostly contract alternatively, accounting for embryo rotations. As a consequence, adherens junctions get stretched along the A/P direction during embryo rotations and therefore are under higher tension. Our preliminary results from single molecule imaging showed that more junction material E-cadherin fuses with A/P oriented junctions when there is high tension on these junctions.

Les Peptide Nucleic Acids (PNA) sont des oligonucléotides antisens analogues de l’ADN, dont le squelette phosphodiester a été remplacé par un squelette pseudo-peptidique d’unités 2-aminoéthylglycine, sur lequel sont greffées des bases azotées. Des PNA dirigés contre les ARN messagers peuvent inhiber la traduction in vitro et dans les cellules humaines. Lorsqu’ils sont dirigés contre la partie codante du transcrit, des PNA polypyrimidiques peuvent bloquer physiquement l’élongation de la traduction en stoppant la machinerie ribosomale. Le transcrit n’est pas dégradé et une protéine tronquée est générée in vitro. Dans le cas de protéines dont la surexpression conduit à des pathologies, des protéines tronquées inactives peuvent jouer un rôle de dominant négatif dans les cellules. Des protéines tronquées de l’Insulin-like Growth Factor-1 (IGF1R), récepteur cellulaire surexprimé dans de nombreux cancers, inhibent la tumorigénèse et la résistance à l’apoptose de cellules cancéreuses. La pénétration cellulaire des PNA est la principale limite à leur utilisation in vivo et il est nécessaire de développer des transporteurs efficaces pour ces oligonucléotides neutres. Les Cell Penetrating Peptides (CPP) sont des peptides naturels ou synthétiques, qui peuvent être conjugués à différentes molécules pour promouvoir leur internalisation cellulaire. Les objectifs de ce travail de thèse étaient de comprendre les critères requis pour l’arrêt de l’élongation de la traduction par les PNA et d’étudier leur internalisation cellulaire médiée par le CPP (R/W)9. Nous avons montré qu’un couplage covalent entre ce peptide et deux PNA 13-mer permet l’internalisation des conjugués dans un système cellulaire rapporteur, conduisant à leur activité biologique en présence d’un agent lysosomotropique. Les conjugués interagissent avec les glycosaminoglycanes membranaires et sont internalisés par endocytose en moins d’une heure. De plus, les conjugués formés avec un peptide analogue comportant des lysines sont six fois moins internalisés, mettant en évidence l’importance des résidus arginines du peptide (R/W)9 pour l’interaction avec la membrane. Enfin, nous avons montré que le peptide (R/W)9 couplé à un PNA dirigé contre la séquence codante de l’IGF1R permet son internalisation dans les cellules de cancer de la prostate et que le conjugué inhibe spécifiquement l’expression de la chaîne β du récepteur. / Peptide nucleic acids (PNAs) are nucleic acid analogues in which the sugar-phosphate backbone has been replaced by a synthetic peptide backbone, usually comprised of N-(2-aminoethyl)-glycan units. PNAs targeted against mRNA can inhibit translation both in vitro and in human cells. Pyrimidine rich PNAs can physically block translation elongation at targets in the coding region of messenger RNA, giving rise to a truncated protein. Truncated proteins that lack a functional domain and can at the same time inhibit the function of the wild type protein are referred to as dominant negative. Truncated form of Insulin-like Growth Factor-1 receptor (IGF1R), protein overexpressed in numerous cancers, inhibits tumorigenesis and resistance to apoptosis of cancerous cells. One of the biggest limitations to the use of PNAs in vivo is their poor internalization. It is therefore necessary to develop efficient transporters able to enhance the cellular uptake of PNAs. Cell-penetrating peptides (CPPs) are natural or synthetic peptides that can be conjugated to different molecules in order to facilitate their cellular uptake. The objectives of this thesis were to understand the conditions required for the translation elongation arrest by PNAs and to study their cellular internalization mediated by CPP (R/W)9. We have shown that covalent coupling of two 13-mer PNAs to (R/W)9 facilitates their internalization in a reporter cell line, leading to their biological activity in the presence of a lysosomotropic agent such as chloroquine. The conjugates interact with membrane glycosaminoglycans and are internalized by endocytosis in less than one hour. Moreover, conjugates formed with an analogue peptide containing lysines in the place of arginines of (R/W)9 showed to be six time less efficiently internalized, suggesting the importance of arginine residues for the interaction of the conjugate with the membrane. We have also showed that the PNA targeted to the coding region of IGF1R coupled to (R/W)9 is efficiently internalized to prostate cancer cells where it inhibits the expression of the beta chain of the receptor.

Der Einsatz von Fasergefügen und insbesondere von Papier geht heute über dessen ursprüngliches Anwendungsgebiet als Informationsträger weit hinaus. Mit alternativen und neuen Aufgabenfeldern des Papiers kommen auch weitere, qualitative Anforderungen hinzu, welche es während der Herstellung, Weiterverarbeitung und Nutzung erfüllen muss. In der Vergangenheit stand verstärkt z.B. die Verbesserung der statischen und dynamischen Festigkeitseigenschaften im Vordergrund. Für viele Anwendungsfälle spielt jedoch auch die Dehnung eine entscheidende Rolle. Beispiele sind Sackpapier oder Elektroisolationspapier. Darum verfolgt diese Arbeit das Ziel, systematisch und anhand eines neuen Dehnungsmodells, qualitativ und quantitativ die Einflüsse der Faser- und Gefügeeigenschaften anhand ausgewählter Prozessbedingungen auf das Kraft-Dehnungsverhalten, aber insbesondere auf dessen Dehnung zu untersuchen. Des Weiteren wurde eine Methode entwickelt, mit der es unter Nutzung eines Röntgen-Computertomographen möglich ist, weitere Gefügeparameter, auch während einer semi-dynamischen Zugprüfung in-situ zu ermitteln. Für die Bewertung der Fasereigenschaften wurden vier Faserstoffe ausgewählt. Zum Einsatz kam ein ungebleichter Nadelholzsulfatzellstoff (UKP), ein gebleichter Eukalyptuszellstoff, Baumwolllinters und Tencel, eine synthetische Cellulosefaser. Diese Faserstoffe sind chemisch und morphologisch analysiert worden, bevor sie sowohl überwiegend fibrillierend als auch überwiegend kürzend in einem Refiner gemahlen wurden. Nach unterschiedlich hohem Eintrag an massenspezifischer Mahlarbeit in den Faserstoff wurden aus der Suspension Papiermuster gebildet, schrumpfungsbehindert getrocknet und charakterisiert. Durch die Mahlung der Faserstoffe erfolgte eine Reduktion deren mittlerer längengewichteter Faserkonturlänge, der Feinstoffanteil konnte gesteigert werden und das Wasserrückhaltevermögen nahm zu. Es konnte ein unterschiedliches Verhalten der Entwicklung des Wasserrückhaltevermögens zwischen dem ungebleichten Nadelholzsulfatzellstoff und dem gebleichten Eukalyptus gegenüber den Baumwolllinters und den Tencelfasern gefunden werden. Das Wasserrückhaltevermögen von Baumwolllinters und den Tencelfasern blieb, unabhängig von der Mahlstrategie, fast bis zum maximalen Eintrag an massenspezifischer Mahlarbeit von ca. 770 kWh/t unbeeinflusst. Mit den erhaltenen Kraft-Dehnungsdiagrammen der Papiermuster, welche durch eine uniaxiale Zugprüfung mit konstanter Dehnungsgeschwindigkeit messtechnisch erfasst wurden, konnte durch eine Kurveneinpassung mit dem entwickelten Dehnungsmodell das jeweilige Kraft-Dehnungsverhalten mathematisch nachgebildet werden. Dieser neue Modellansatz wurde gewählt, nachdem die Auswertung des Ansatzes von Paetow [77;78;79;90] zu große Abweichungen bei bestimmten Papiermustern aufzeigte. Dies ermöglichte die quantitative Auswertung relevanter Parameter der Kraft-Dehnungskurven. Dabei wurden der Elastizitätsmodul, die Reißlänge und die Dehnung bei maximaler Reißlänge bewertet. Eine sehr hohe Reißlänge konnte mit einem fibrillierend gemahlenem, ungebleichtem Nadelholzsulfatzellstoff und eine hohe Dehnung mit einem, ebenfalls fibrillierend gemahlenem Eukalyptuszellstoff erreicht werden. Des Weiteren sind die Reißlänge am Übergang von einem initial linearen in den nicht-linearen Kurventeil, ein Abknickfaktor sowie der weitere Kurvenverlauf nach dem nicht-linearen Bereich, bis zur maximalen Reißlänge des Gefüges bewertet worden. Der letzte Kurvenbereich wurde entweder durch den weiteren, nicht-linearen Verlauf oder durch einen sekundären Linearbereich charakterisiert. Der von Seth und Page [22] dargestellte Einfluss der Faserstoffmahlung auf den Verlauf der Kraft-Dehnungskurve von Papier konnte nicht nachgebildet werden. Dies zeigte auch, dass die in dieser Arbeit gewonnenen Erkenntnisse durch eine Korrektur des Elastizitätsmoduls mit den Kraft-Dehnungskurven nicht mit den Ergebnissen aus [22] übereinstimmen. Die Faserstoffmahlung hat demnach nicht nur einen Einfluss auf die maximal erreichbare Reißlänge und Dehnung, sondern beeinflusst auch den qualitativen Verlauf der Kraft-Dehnungskurve von Papier. Es konnten keine individuellen Einflussgröße der Fasermorphologie und der Prozessparameter auf die Dehnung oder das Kraft-Dehnungsverhalten festgestellt werden, da sich die meisten dieser Eigenschaften direkt mit der eingebrachten, massenspezifischen Mahlarbeit verändern, die Papierdehnung jedoch schon nach Erreichen einer moderaten massenspezifischen Mahlarbeit von ca. 100 – 200 kWh/t nicht weiter steigern ließ. Für eine weitere Bewertung der Einflüsse auf das Kraft-Dehnungsverhalten von Papier wurden Messwerte aus [143] analysiert. Dabei zeigte sich, dass ein Anstieg an Fasern mit einer hohen Faserkräuselung die Reißlänge des Papiers sowie den Elastizitätsmodul signifikant reduziert. Die Reißlänge am Kurvenübergang vom initial linearen in den nicht-linearen Teil bleibt dabei jedoch konstant. Ein anderes Verhalten, welches mit den Ergebnissen von Seth und Page [22] sowie Lowe [12] übereinstimmt, ist die Auswirkung eines kationischen Additivs wie z.B. Stärke auf die Entwicklung des Kraft-Dehnungsverhaltens. Es konnte nachgewiesen werden, dass das Additiv keinerlei Einfluss auf den initial linearen sowie den nicht-linearen Teil der Kraft-Dehnungskurve hat, sondern nur den sekundären, linearen Kurvenbereich in Abhängigkeit der Dosiermenge beeinflusst. Dabei wurde die Steigung im sekundären Linearbereich bestimmt. Dieses Verhalten führte zu einer Erweiterung der Theorie von Kallmes [82], welcher nach einem Anstieg der Festigkeit und der Dehnung, ab einer kritischen, relativen Bindungsfläche nur noch einen Anstieg der Festigkeit vorhersagte, jedoch nicht mehr der Dehnung. Auf Grund der in dieser Arbeit gewonnenen Erkenntnisse müssen drei Fälle der Entwicklung des Kraft-Dehnungsverhaltens von Fasergefügen unterschieden werden, welche primär von der Homogenität der Spannungsverteilung im Fasergefüge abhängig sind und z.B. durch die Faserkräuselung oder Blattformation beeinflusst werden kann. Diese neue Ansicht basiert auf dem Verhältnis zwischen der Bindungsenergie der Faser-Faserbindung und dem formbasierten sowie dem längenbasierten Arbeitsaufnahmevermögen der Fasern. Der erste Fall der Gefügedehnung beschreibt das Verhalten, wenn die Bindungsenergie geringer ist als das formbasierte Arbeitsaufnahmevermögen. Dies führt zu einem Auseinandergleiten des Fasergefüges. Dieses Verhalten konnte mit der Analyse von Papierproben aus Linters im Röntgen-Computertomograph qualitativ nachgewiesen werden. Steigt die Bindungsenergie an, wie es der zweite Fall voraussetzt, kann das formbasierte Arbeitsvermögen der Fasern überwunden werden und steht als Dehnvermögen zur Verfügung. Um auch, wie es der dritte Fall beschreibt, das längenbasierte Dehnvermögen der Fasern nutzen zu können, muss die Bindungsenergie zusätzlich durch z.B. ein Additiv oder hohe Drücke in einer Nasspresse weiter steigen. Die erweiterte Theorie bildet nun das gesamte Kraft-Dehnungsverhalten von Fasergefügen ab und muss in weiteren Arbeiten zur Papieranalyse verifiziert werden. Eine wertvolle Ergänzung der zu ermittelnden Gefügeparameter kann durch die entwickelte Methode mit der Röntgen-Computertomographie geleistet werden.

This thesis presents the results of computer simulation studies of the structure, dynamics, and deformation of cross-linked polymer gels. Obtaining a fundamental understanding of the interrelation between the detailed structure and the properties of polymer gels is a challenge and a key issue towards designing materials for specific purposes. A new off-lattice method for constructing a closed network is presented that is free from defects, such as looping chains and dangling ends. Using these model networks in Brownian dynamics simulations, I show results for the structure and dynamics of bulk gels and describe a novel approach using spherical boundary conditions as an alternative to the periodic boundary conditions commonly used in simulations. This algorithm was also applied for simulating the diffusion of tracer particles within a static and dynamic network, to illustrate the quantitative difference and importance of including network mobility for large particles, as dynamic chains facilitate the escape of particles that become entrapped. I further investigate two technologically relevant properties of polymer gels: their stimuli-responsive behaviour and their mechanical properties. The collapse of core-shell nanogels was studied for a range of parameters, including the cross-linking degree and shell thickness. Two distinct regimes of gel collapse could be observed, with a rapid formation of small clusters followed by a coarsening stage. It is shown that in some cases, a collapsing shell may lead to an inversion of the core-shell particle which exposes the core polymer chains to the environment. This thesis also explores the deformation of bimodal gels consisting of both short and long chains, subject to uniaxial elongation, with the aim to understand the role of both network composition as well as structural heterogeneity on the mechanical response and the reinforcement mechanism of these materials. It is shown that a bimodal molecular weight distribution alone is sufficient to strongly alter the mechanical properties of networks compared to the corresponding unimodal networks with the same number-average chain length. Furthermore, it is shown that heterogeneities in the form of high-density short-chain clusters affect the mechanical properties relative to a homogeneous network, primarily by providing extensibility.

Introduction Nucleotide excision repair (NER) is a highly conserved pathway involved in repair of a wide variety of structurally unrelated DNA lesions. One of the well characterized NER systems is from E. coli which involves UvrABC nucleases. NER consists of two related sub-pathways: global genomic repair (GGR), which removes lesions from the overall genome, and transcription coupled repair (TCR), which removes lesions from the transcribed strand of active genes. Bulky DNA lesions such as cyclobutane pyrimidine photodimers (CPD) induced by UV irradiation block RNA polymerase (RNAP) during transcription. In bacteria, a gene product of mfd called transcription repair coupling factor (TRCF) or Mfd is required for TCR. Bacterial Mfd interacts with the stalled RNAP, displaces it from the DNA and recruits NER proteins at the site of damage. Mfd, thus contributes to the faster repair of the transcribed strand compared to the non-transcribed strand for similar kind of lesions. Intracellular pathogens like M. tuberculosis are constantly exposed to a variety of stress conditions inside the host, mainly due to host defense systems and antibiotic treatments. It is therefore, extremely important for bacteria to have DNA damage repair and reversal mechanisms that can efficiently counteract these effects. However, very little is known about DNA repair systems in M. tuberculosis compared to other bacteria. Sequencing of M. tuberculosis genome revealed the presence of NER associated genes including a putative mfd. Additionally, due to the high GC content of genome as well as the DNA damage prone host environment, the transcription in M. tuberculosis may encounter the problems, which are not apparent in other bacteria. Therefore, the gene like mfd may play very important role in physiology of M. tuberculosis. In the present study, we describe the biochemical and functional characterization of Mfd from M. tuberculosis (MtbMfd) and discuss its unusual properties. Biochemical characterization of MtbMfd Genome analysis of M. tuberculosis as well as the sequence alignment studies revealed that MtbMfd is 1234 amino acids long multifunctional protein having various domains specialized for different functions. Cloning of Mtbmfd was carried out by reconstructing the full length gene from three PCR amplified fragments using genomic DNA as a template. Complementation study using Mtbmfd suggested that the gene of interest complements E. coli counterpart and increases survival of UV irradiated cells. To further characterize the function of Mtbmfd, a road block reporter assay was performed, which indicates that the MtbMfd interacts with stalled E. coli RNAP and displaces it from the site of transcription resulting in low reporter gene activity. The MtbMfd protein was expressed and purified by using various chromatographic techniques, and confirmed by mass spectrometry. In addition to full length protein, a number of truncated MtbMfd constructs were generated and purified to homogeneity. Mfd is a motor protein and requires ATP hydrolysis in order to translocate along DNA. The signature motifs of superfamily 2 helicases / ATPases are present at the C-terminal of Mfd along with translocase motif which is highly homologous to motif present in RecG helicase. To analyze the kinetics of ATP hydrolysis of MtbMfd and its truncated proteins, ATPase reactions were carried out using γ32P-ATP as a tracer. Wild-type MtbMfd exhibited ATPase activity, which was stimulated ~1.5 fold in presence of dsDNA. The mutant MtbMfd (D778A), which harbors mutation in one of the key residues of Walker B motif of the ATPase domain showed negligible ATPase activity indicating the importance of residue D778 for ATP hydrolysis. While the C-terminal domain (CTD) comprising amino acids 600 to 1234 showed elevated ATPase activity, the N-terminal domain (NTD) containing the first 500 amino acid residues was able to bind ATP but deficient in hydrolysis. Deletion of 184 amino acids from the C-terminal end of MtbMfd (MfdΔC) increased the ATPase activity by ~10-fold compared to full-length MtbMfd. The translocase activity of MtbMfd was measured by an oligonucleotide displacement assay and it was found that full length MtbMfd and CTD have a very weak translocase activity whereas, MfdΔC exhibited efficient translocation along DNA in ATP dependent manner. These results provide a direct correlation between translocase and ATPase activity of MtbMfd, and suggest possibly an auto-regulatory function for the extreme C-terminus of MtbMfd. Oligomeric status of MtbMfd was determined using various techniques including gel filtration chromatography and it was found that MtbMfd exists as monomer and hexamer in solution. The monomer showed increased ATPase activity and susceptibility to proteases compared to the hexameric form. MfdΔC, on the other hand, was predominantly monomer in solution implicating importance of the extreme C-terminal region in oligomerization of protein. Taken together, the biochemical evidence suggests that monomeric MtbMfd is an active form and oligomerization provides stability to the protein. One important finding of the present study is the binding of ATP to NTD of MtbMfd. All Mfd NTDs resemble UvrB and possesses the degenerate ATPase motifs. Indeed, on the basis of sequence and structural similarities, it has been suggested that Mfds have evolved from UvrB incorporating an additional translocase activity. UvrB has a cryptic ATPase activity while the NTD of Mfd may have lost the activity as it possesses degenerate Walker motifs. In contrast, NTD of MtbMfd binds ATP but is hydrolysis deficient. A closer comparison of the amino acid sequences in the Walker A motif reveal that conserved K 45 of UvrB has been replaced by R in case of NTD of MtbMfd. It has been shown previously that mutation of K 45 to A, D and R led to a loss of ATPase activity of UvrB. Thus, MtbMfd seems to be a natural mutant of UvrB. Since NTD harbors an intact UvrA interacting domain, when it is expressed it may sequester the cellular pool of UvrA leading to dominant negative phenotype. When UV survival assays were carried out, cells expressing NTD showed hyper-sensitivity to UV light – a typical characteristic of NER deficiency. In addition, in vitro NER assay clearly suggested that NTD sequesters pool of UvrA inside the cell and blocks both GGR and TCR which further affects the mutation frequency of bacterial cells. Influence of MtbMfd on elongation state of RNAP The movement of RNAP along the template during transcription elongation is not uniform and is interrupted due to various factors. To overcome transcription elongation interruptions, a number of proteins viz. Mfd, Gre and Nus act on RNAP and modify its activity. RNAP displacement and transcript release experiments showed that MtbMfd influenced the elongating RNAP by more than one way. MtbMfd displaced stalled RNAP, which was blocked by NTP starvation on T7A1 promoter based template in a concentration and time-dependent manner. RNAP displacement activity of MtbMfd was shown to depend on ATP or dATP hydrolysis. On the other hand nucleotides like ADP, GTP, CTP and ATPγS did not support the RNAP displacement activity. However, in presence of ATPγS, MtbMfd was able to bind stalled complex but unable to displace RNAP suggesting that ATP or dATP hydrolysis is important for MtbMfd function. On the other hand, MtbMfd did not affect initiating RNAP when σ factor was still bound suggesting that upstream DNA is necessary for Mfd function. To assay RNA or transcript release activity of MtbMfd after transcription complex disruption, immobilized transcription complex assay was carried out. Immobilized stalled complex was generated by UTP and CTP starvation on biotinylated T7A1 promoter based template which can be affixed to temporary pellet in presence of streptavidin beads. It was found that MtbMfd released RNA into a supernatant fraction in a concentration-dependent manner suggesting that MtbMfd releases transcript after ternary complex disruption. MtbMfd released transcript in an energy-dependent manner and both ATP and dATP supported the activity, which allows the complete separation of RNA release from RNA synthesis inside the cell. An ATPase mutant of MtbMfd (MfdD778A) failed to release transcript, which further supported that ATP hydrolysis is important for MtbMfd function. Since both Mfds and RNAPs are evolutionary conserved proteins, to analyze the effect of MtbMfd on other bacterial RNAPs, displacement and release assays were carried out. Stalled complexes were generated using EcoRNAP (E. coli), MsRNAP (M. smegmatis) and MtbRNAP (M. tuberculosis) on T7A1 promoter based template. It was observed that MtbMfd was able to displace all the three RNAPs from stalled elongation complex as well as released transcript with varying efficiency. MtbMfd showed optimal displacement and release activity in presence of mycobacterial RNAPs. Transcription elongation complexes adopt various conformations and exist as different isomerized states during elongation. In an active elongation complex the 3'-OH polymerizing end of transcript aligns with an active centre of the RNAP. However, one of the most common and intrinsic properties of RNAP is backtracking or reverse translocation, which leads to misalignment of 3'-OH polymerizing end from an active centre of the polymerase. It is of interest to know if backtracking affects MtbMfd function. It is likely that complexes blocked by lesions inside the cell might tend to backtrack, and different translocational isomers possibly have different sensitivities to MtbMfd action which may illuminate the overall mechanism of MtbMfd. Backtracking of RNAP was induced on +20 and +39 stalled complexes and the effect of MtbMfd was analyzed in presence of NTPs in the reaction. It was found that arrested or backtracked complexes were restored to the forward position by the activity of MtbMfd in presence of NTP resulting into productive elongation. These results suggest that arrested RNAP again resumes transcription if conditions are favorable; otherwise, MtbMfd further assists RNAP to dissociate which leads to release of transcript. Anti-backtracking activity of MtbMfd might have important function in cellular metabolism and it has been speculated that Mfd could play more general role during transcription apart from repair. To explore the role of MtbMfd as a transcription factor and effect of MtbMtb on transcription processes in the mycobacteria, a variety of T7A1 promoter based templates were generated. These templates were derived from genes of M. tuberculosis and E. coli having varying GC content (39-81 %). The rationale behind this experiment is that the high GC content of mycobacteria and the template derived from mycobacterial genes may pose as sequence dependent structural constraints and hence block the RNAP during transcription. By anti-backtracking activity of MtbMfd these paused complexes may get relieved, leading to efficient transcription by RNAP which may lead to the formation of more full length transcript. To analyze the effect of MtbMfd, purified templates of different GC content were incubated with RNAP and MtbMfd to carry out in vitro transcription. Although, in case of multiple rounds of transcription, multiple pauses were observed even in presence of MtbMfd. However, in presence MtbMfd around 1.5 - 2 fold increased full-length transcripts were observed suggesting that MtbMfd assisted RNAP during elongation to overcome sequence dependent pause. To avoid multiple pauses that are likely to occur due to the initiation of multiple round of transcription, and trailing effect of RNAP itself, single round of transcriptions were carried out in presence of heparin. Sequence specific pauses were observed with increasing GC percentage in template suggesting that indeed high GC content contributes to transcription pause. At the same time, MtbMfd in the reaction increased the amount of full length transcript by 1.5 - 2.0 fold probably by pushing paused RNAP forward to resume elongation. Taken together, this study investigates the biochemical properties of MtbMfd and its mechanism of action. In addition, it explores the importance of the coupling of transcription to repair in M. tuberculosis as well as the overall proof reading mechanism of transcription elongation in the GC rich genome of mycobacteria.