The transcription initiation is the first step in gene expression and an important regulation step in all living organisms. In bacteria, it has been proposed that DNA bending and its wrapping on the surface of E. coli RNAP might facilitate the opening of the transcription bubble, which is necessary for the initiation of gene transcription. In this work, it is shown the first structural study to evaluate a DNA wrapping model, including its length and the relative position in the bacterial transcription initiation complex (RP complex), assembled between RNA polymerase-σ70 holoenzyme (RNAP) and a λPR promoter (-100 to +30 wild type). RP complex was prepared and negatively stained with 2% uranyl acetate on a thin-carbon coated grid and the data acquisition of 500 images was performed in a JEM-2100 (JEOL, Japan) microscope equipped with an F-416 CMOS camera (TVIPS, Germany). Single particle analysis of 16,015 particles, grouped in 666 class-averages, was conducted using IMAGIC 4D software (Image Science, Germany) to obtain a three-dimensional model of the RP complex at 20Å resolution. After the rigid-body fitting of the RNAP crystallographic structure (PDB 4YG2) and the modeled DNA promoter, it was observed that the regions 1.2 and 4.2 of the σ70 subunit interacts with the consensus zones, -10 and -35 hexamers of the promoter. Furthermore, it was possible to observe that αCTDs (C-terminal domain) in both alpha subunits would be oriented to facilitate the interaction with the first and second UP-elements regions, respectively (centered around –50 and -75 positions in the promoter). These was enabled by the presence of the characteristics motifs helix-hairpin-helix in these domains. In addition, the downstream DNA, from the transcription bubble, appears to be inside the protein main channel, oriented in a way to enable interactions with the RNAP clamp and jaws. Finally, it was observed that the DNA wrapping has ~32 nm of total length and involves a promoter bent of ~255° around the RNAP surface. The 3D-model obtained in this study is the very first direct structural confirmation of the DNA promoter wrapping in a bacterial transcription initiation complex. / A iniciação da transcrição é o primeiro passo na expressão gênica e importante ponto de regulação em todos os organismos vivos. Em bactérias, foi proposto que o enovelamento do DNA na superfície da RNAP de E. coli pode facilitar a abertura da bolha de transcrição, necessária para o início da transcrição gênica. Neste trabalho, é apresentado o primeiro estudo estrutural direto para avaliar o comprimento do enovelamento do DNA e sua posição no complexo de iniciação da transcrição bacteriana (complexo RP), montado entre a holoenzima RNA polimerase-σ70 (RNAP) e um promotor λPR (-100 para +30, tipo selvagem). Amostras do complexo RP foram preparadas e contrastadas negativamente com 2% de acetato de uranila em uma grade com filme fino de carbono e a aquisição de 500 imagens foi realizada em um microscópio JEM-2100 (Jeol, Japão) equipado com uma câmera CMOS F-416 (TVIPS, Alemanha). A análise de partículas isoladas de 16.015 partículas, agrupadas em 666 médias de classe, foi conduzida usando o software IMAGIC 4D (Image Science, Alemanha) para obter um modelo tridimensional do complexo RP, a 20Å de resolução, estimado pelo critério de ½ bit. Após o ajuste de corpo rígido da estrutura cristalográfica da RNAP (PDB 4YG2) e do promotor de DNA modelado, observou-se que as regiões 1.2 e 4.2 da subunidade σ70 interagem com as zonas de consenso, hexâmeros -10 e -35, do promotor. Além disso, foi possível observar que os αCTDs (domínio C-terminal) em ambas as subunidades alfa estariam orientados para facilitar uma possível interação com a primeira e segundas regiões dos elementos UP, respectivamente (centradas em torno das posições –50 e -75 do promotor). Estas seriam possíveis devido à presença de alguns motivos de características hélice-grampo-hélice nesses domínios. Além disso, a região do promotor, downstream da bolha de transcrição, parece estar dentro do canal principal da proteína, orientado de forma a possibilitar interações com o clamp e jaw da RNAP. Finalmente, foi observado que o comprimento total do enovelamento de DNA envolve cerca de 32 nm e 255° de rotação do DNA ao redor da superfície da RNAP. Portanto, este modelo 3D é a primeira confirmação estrutural direta do enovelamento de DNA em um complexo bacteriano de iniciação da transcrição.

A linhagem de ratos espontaneamente hipertensos (SHR) tem sido utilizada para como modelo animal para hipertensão humana, uma vez que estes animais desenvolvem pressóricos aumentados, hipertrofia ventricular esquerda, aumento de colágeno intersticial e disfunção diastólica. Embora o excesso de colágeno fibrilar tenha sido bem estudado neste modelo e esteja envolvido na insuficiência cardíaca observada, não há estudos quantitativos acurados (baseados na estereologia) para avaliar precisamente o volume tecidual ocupado pelo colágeno fibrilar e o remodelamento das fibrilas de colágeno segundo seu diâmetro uma vez que variações no diâmetro das fibrilas têm grande impacto funcional Mais ainda, nunca foi estudado neste modelo o remodelamento das fibras do sistema elástico (oxitalânicas, elaunínicas e elásticas propriamente ditas), que juntamente com o componente colagênico são responsáveis pelas características biomecânicas do tecido. Assim sendo, os corações de ratos Wistar (WIS), Wistar Kyoto (WKY) e SHR foram submetidos a análise hemodinâmicas e foram processados para microscopia de luz e eletrônica, segundo amostragem estereológica. Cortes corados com HE foram utilizados para avaliação do diâmetro dos cardiomiócitos e do volume absoluto do coração e do ventrículo esquerdo; cortes corados com Picrossirius-hematoxilina foram utilizados para a avaliação da fração de volume ocupada por colágeno no ventrículo esquerdo e volume absoluto de colágeno; cortes ultra-finos foram utilizados para avaliação do diâmetro das fibrilas de colágeno cortadas transversalmente e para avaliação da distribuição das fibras oxitalânicas, elaunínicas e elásticas. Os resultados mostram que a hipertrofia ventricular dos animais SHR deveu-se à hipertrofia dos cardiomiócitos associada à maior quantidade de colágeno fibrilar (3,8 x maior no SHR que no WIS). A análise ultraestrutural mostrou que as fibrilas de colágeno no endomísio variam, em nanômetros, de 31 a 53 nos animais WIS, de 36 a 67 nos WKY e de 31 a 85 nos SHR, com medianas respectivamente de 39,58, 48,38 e 54,39, sendo que do ponto de vista estatístico a distribuição dos diâmetros das fibrilas colágenas dos animais SRH é diferente das outras duas linhagens.A análise uttra-estrutural das fibras do sistema elástico mostrou que as fibras oxitalânicas, elaunínicas e elásticas apresentam uma distribuição diferencial nos diversos compartimentos da parede cardíaca dos animais, sendo que nas três linhagens há fibras elásticas propriamente ditas no endocárdio e epicárdio; no entanto, no perimísio as fibras elásticas e elaunínicas aparecem raramente nos ratos SRH e com maior freqüência nos WIS e WKY; no endomísio dos ratos SRH não foi possível observar a mesma riqueza de fibras elásticas e elaunínicas presentes nas outras linhagens, havendo assim um predomínio de fibras oxitalânicas no vi endomísio dos animais SHR. Os resultados mostram que, além das modificações quantitativas no conteúdo de colágeno no miocárdio do ventrículo esquerdo dos animais SHR, há também uma alteração qualitativa na população de fibrilas colagênicas que passa a ser constituída por fibrilas mais grossas. Mais ainda, os resultados mostram que, em relação às fibras do sistema elástico, a predominância de fibras oxitalânicas no endomísio dos animais SHR sugere que as forças de tensão maiores no coração destes animais modulem não somente o sistema colagênico mas também o sistema elástico no sentido de acumular fibras que suportam melhor as cargas, contribuindo para a perda da complacência da parede ventricular / The strain of spontaneously hypertensive rats (SHR) has been used as an animal model for human hypertension, since these animals develop increased blood pressure, left ventricular hypertrophy, increased interstitial collagen and diastolic dysfunction. Although excess fibrillar collagen has been well studied in this model and is involved in observed heart failure, there are no accurate quantitative studies (i.e., based on stereology) to precisely assess the volume of tissue occupied by fibrillar collagen neither the remodeling of collagen fibrils with respect to their diameters, and such studies are very important because variations in the diameter of the fibrils have a major functional impact. Moreover, the remodeling of elastic system fibers (oxytalan, elauninic and elastic proper), which together with the collagenous component are responsible for biomechanical features of the tissue, has never been studied in this model. Thus, the hearts of Wistar (WIS), Wistar Kyoto (WKY) and SHR rats went through hemodynamic analysis and were processed for light and electron microscopy, according to stereological sampling criteria. HE-stained sections were used to evaluate the diameter of the cardiomyocytes and the absolute volume of the heart while left ventricular sections stained by Picrosirius-hematoxylin were used to evaluate the volume fraction occupied by collagen in the left ventricle as well as its absolute volume of collagen; ultra-thin sections were used for evaluation of the diameter of transversally sectioned collagen fibrils and for evaluation of the distribution of oxytalan, elauninic and elastic proper fibers. The results show that the ventricular hypertrophy of SHR rats was due to cardiomyocyte hypertrophy associated with a higher amount of fibrillar collagen (3.8 times as high as in the WIS rats). The ultrastructural analysis showed that the collagen fibrils in the endomysium range in nanometers, from 31 to 53 in WIS animals, 36 to 67 in the WKY and 31 to 85 in SHR, with medians 39.58, 48.38 and 54.39, respectively. The distribution of diameters of collagen fibrils is statistically different in SRH animals when compared to the other two strains. The ultrastructural analysis of the fibers of the elastic system showed that oxytalan, elauninic and elastic fibers present a differential distribution across the various compartments of the heart wall of the animals. In the three strains there are elastic fibers proper in the endocardium and epicardium, while in the perimysium, the elastic fibers proper and the elauninic fibers rarely appear in SRH rats, being more frequent in WIS and WKY rats; the endomysium of SRH rats did not exhibit the same richness of elastic fibers proper and elauninic fibers present in other strains, occurring thus a predominance of oxytalan fibers in the endomysium of SHR rats. viii The results also show that, in addition to the quantitative changes in collagen content of left ventricular myocardium of SHR rats, there is a qualitative alteration in the population of collagen fibrils that is richer in thicker fibrils. Moreover, the results show that, with respect to the fibers of the elastic system, the predominance of the oxytalan fibers in the endomysium of SHR rats suggests that the higher tensile forces in the hearts of these animals modulate not only the collagenous system but also the elastic system, entailing accumulation of fibers suited to better support the loads, contributing to the loss of ventricular wall compliance

Abstract not available

<p>Metastable (Ti,Si)N alloy and TiN/SiNx multilayer thin solid films as well as SiNx/TiN surfaces have been explored. Cubic Ti1-xSixN (0≤x≤0.14) films deposited onto cemented carbide (WC-Co) substrates by arc evaporation exhibited a competitive columnar growth mode where the structure transforms to a feather-like nanostructure with increasing Si content as revealed by x-ray diffraction and transmission electron microscopy. X-ray photoelectron spectroscopy revealed the presence of Ti-N and Si-N bonding, but no amorphous Si3N4. Band structure calculations showed that phase separation of NaClstructure Ti1-xSixN solid solution into cubic SiN and TiN phases is energetically favorable. The metastable microstructure, however, was maintained for the Ti0.86Si0.14N film annealed at 900°C, while recrystallization in the cubic state took place at 1100°C annealing during 2h. The Si content influenced the film hardness close to linearly, by combination of solid-solution hardening in the cubic state and defect hardening. For x=0 and x=0.14, nanoindentation gave a hardness of 29.9±3.4 GPa and 44.7±1.9 GPa, respectively. The hardness was retained during annealing at 900°C.</p><p>Nanostructured materials, e.g., nanocomposites and nanolaminates, are defined by internal interfaces, of which the nature is still under debate. In this work two-phase model systems were explored by depositing SiNx/TiN nanolaminate films, including superlattices containing cubic SiNx, by dual target reactive magnetron sputtering. It is demonstrated that the interfacial phase of SiNx onto TiN(001) and TiN(111) can be crystalline, and even epitaxial with complex surface reconstructions. Using in situ structural analyses combined with ab initio calculations, it is found that SiNx layers grow epitaxially, giving rise to strong interfacial bonding, on both TiN(001) and TiN(111) surfaces. In addition, TiN overlayers grow epitaxially on SiNx/TiN(001) bilayers in nanolaminate structures. These results provide insight into the development of design rules for novel nanostructured materials.</p> / Report code: LiU-TEK-LIC-2006:51.

<p>Ultrastructural studies of airway epithelium in airway disease are important for diagnosis and understanding the underlying pathology which helps clinicians to improve the patients' treatment.</p><p>Airway biopsies from a 5-month old boy with respiratory problems and gastro-oesophageal reflux were studied by transmission electron microscopy (TEM). The tracheal columnar cells showed accumulation of lamellar bodies, indicative of lysosomal storage disease. The patient was diagnosed with Gaucher disease type 2.</p><p>Shedding of airway epithelial cells is commonly found in asthma. The attachment of these cells to the basal lamina was investigated by TEM of biopsies from patients with asthma and healthy controls. The contact area between columnar cells and basal lamina in asthmatics was significantly less than in controls. Attachment of columnar cells to the basal lamina occurs mainly indirectly, via desmosomal attachment to basal cells. </p><p>Primary ciliary dyskinesia (PCD) is a congenital disease. It is important to differentiate PCD from acquired (secondary) ciliary dyskinesia (SCD). The number of dynein arms determined by TEM was 1.5 and 1.4 for outer and inner dynein arms, respectively in PCD, versus 7.9 and 5.2 for controls and 8.1 and 5.9 in SCD. Compared to PCD patients, SCD patients have more structurally abnormal cilia. A significant difference was found in orientation of the central microtubule pair between PCD and SCD, but also overlap. </p><p>Leukotriene receptor antagonists are a new treatment for asthma. Both corticosteroids and montelukast caused apoptosis and necrosis of airway epithelial cells, and reduced the expression of intercellular adhesion molecule-1. Treatment of cells with tumor necrosis factor-α or interferon-γ reduced the fraction of the lateral cell membrane occupied by desmosomes and this effect was counteracted by corticosteroids. </p>

<p>The spectroscopic, SEM and Raman measurements on carbon nanotubes under the exact conditions of which OES analysis were made showed that at<br /> a pressure of 400 Torr and a flow rate of 200 sccm, the quality and quantity of single-walled carbon nanotubes was the highest.</p>

Ultrastructural studies of airway epithelium in airway disease are important for diagnosis and understanding the underlying pathology which helps clinicians to improve the patients' treatment. Airway biopsies from a 5-month old boy with respiratory problems and gastro-oesophageal reflux were studied by transmission electron microscopy (TEM). The tracheal columnar cells showed accumulation of lamellar bodies, indicative of lysosomal storage disease. The patient was diagnosed with Gaucher disease type 2. Shedding of airway epithelial cells is commonly found in asthma. The attachment of these cells to the basal lamina was investigated by TEM of biopsies from patients with asthma and healthy controls. The contact area between columnar cells and basal lamina in asthmatics was significantly less than in controls. Attachment of columnar cells to the basal lamina occurs mainly indirectly, via desmosomal attachment to basal cells. Primary ciliary dyskinesia (PCD) is a congenital disease. It is important to differentiate PCD from acquired (secondary) ciliary dyskinesia (SCD). The number of dynein arms determined by TEM was 1.5 and 1.4 for outer and inner dynein arms, respectively in PCD, versus 7.9 and 5.2 for controls and 8.1 and 5.9 in SCD. Compared to PCD patients, SCD patients have more structurally abnormal cilia. A significant difference was found in orientation of the central microtubule pair between PCD and SCD, but also overlap. Leukotriene receptor antagonists are a new treatment for asthma. Both corticosteroids and montelukast caused apoptosis and necrosis of airway epithelial cells, and reduced the expression of intercellular adhesion molecule-1. Treatment of cells with tumor necrosis factor-α or interferon-γ reduced the fraction of the lateral cell membrane occupied by desmosomes and this effect was counteracted by corticosteroids.

In this thesis, firstly, carbon-supported platinum nanoparticle catalysts have been prepared by using PtCl4 and H2PtCl6 as starting materials and 1-hexanethiol, and tert-octanethiol, as surfactants for the first time. Secondly, these prepared catalysts were heated to 200 &deg / C, 300 &deg / C, and 400 &deg / C for 4 h under argon gas. Lastly, PtRu/C catalysts, which have different atomic percent ratios of Pt and Ru (Pt/Ru: 0.8, 2.1 and 3.5), were prepared using PtCl4 and RuCl3 as starting materials and tert-octanethiol as a surfactant. Each was characterized by X-ray diffraction, transmission electron microscopy, energy dispersive analysis, X-ray photoelectron spectroscopy, cyclic voltammetry, and elemental analysis, and their activities were determined toward the methanol oxidation reaction. It has been found that all prepared catalysts are more active toward methanol oxidation reaction compared to the commercial catalysts. It was also found that increasing the temperature during the heat treatment process results in an enlargement of platinum particle size and a decrease in catalytic activity in the methanol oxidation reaction. Transmission electron microscopy shows that platinum nanoparticles are homogeneously dispersed on the carbon support and exhibited a narrow size distribution with an average particle size of about 2-3 nm in diameter. X-ray photoelectron spectra of all catalysts indicated that most of the platinum nanoparticles (&gt / 70 %) have an oxidation state of zero and rest (&lt / 30 %) have a +4 oxidation state with (Pt 4f7/2) binding energies of 71.2-72.2 and 74.3-75.5 eV, respectively.

Properties of magnetic thin film devices cannot be understood without detailed knowledge of their structure. For this purpose, a variety of thin film and multilayer systems have been studied. Both reciprocal space (low energy electron diffraction, reflection high energy electron diffraction, X-ray diffraction and reflectometry) and direct space (transmission electron microscopy) as well as Rutherford backscattering spectrometry have been applied. To gain understanding of an oxidation procedure for the growth of magnetite layers, thermal stability of iron layers on molybdenum seed layers has been investigated. Following the mosaicity and the out-of-plane coherence length over different ratios between the constituting layers allowed a deeper understanding of the limits of metallic superlattices. This, together with an approach to use hydrogen in the process gas during magnetron sputter epitaxy, opens routes for the growth of metallic superlattices of superior quality. A non-isostructural multilayer/superlattice system, Fe/MgO, has been investigated. In turn, this gave more understanding how superlattice diffraction patterns are suppressed by strain fields. As an alternative route to single-crystalline superlattices, amorphous multilayers present interesting opportunities. In this context, crystallization effects of iron/zirconium layers on alumiunium oxide were studied. Understanding these effects enables significant improvement in the quality of amorphous multilayers, and allows avoiding these, growing truly amorphous layers. Both the substantial improvement in quality of metallic superlattices, approaching true single-crystallinity, as well as the improvements in the growth of amorphous multilayers give rise to opportunities in the field of magnetic coupling and superconducting spin valves.

No description available.