Functions of human papillomavirus E5 oncogene in epithelial cells and in the onset of cervical cancer

Human papillomaviruses (HPVs) are the causal agents of cervical cancer, which is the second most common cancer among women worldwide. Cellular transformation and carcinogenesis depend on the activities of viral E5, E6 and E7 proteins. Alterations in cell-cell contacts and in communication between epithelial cells take place during cervical carcinogenesis, leading to changes in cell morphology, increased cell motility and finally invasion. The aim of this thesis was to study genome-wide effects of the HPV type 16 (HPV-16) E5 protein on the expression of host cell messenger RNAs (mRNAs) and microRNAs by applying microarray technology. The results showed that the HPV-16 E5 protein alters several cellular pathways involved in cellular adhesion, motility and proliferation as well as in the extracellular matrix. The E5 protein was observed to enhance wound healing of epithelial cell monolayers by increasing cell motility in vivo. HPV-16 E5-induced alterations in the expression of cellular microRNAs and their target genes seem to favour increased proliferation and tumorigenesis. E5 was also shown to affect the expression of adherens junction proteins in HaCaT epithelial keratinocytes. In addition, a study of a membrane cytoskeletal cross-linker protein, ezrin, revealed that when activated, it localizes to adherens junctions. The results suggest that ezrin distribution to forming adherens junctions is due to Rac1 activity in epithelial cells. These studies reveal for the first time the holistic effects of HPV-16 E5 protein in promoting precancerous events in epithelial cells. The results contribute to identifyinging novel markers for cervical precancerous stages and to predicting disease behaviour.

Mesoporous silica- and silicon-based materials as carriers for poorly water soluble drugs

New chemical entities with unfavorable water solubility properties are continuously emerging in drug discovery. Without pharmaceutical manipulations inefficient concentrations of these drugs in the systemic circulation are probable. Typically, in order to be absorbed from the gastrointestinal tract, the drug has to be dissolved. Several methods have been developed to improve the dissolution of poorly soluble drugs. In this study, the applicability of different types of mesoporous (pore diameters between 2 and 50 nm) silicon- and silica-based materials as pharmaceutical carriers for poorly water soluble drugs was evaluated. Thermally oxidized and carbonized mesoporous silicon materials, ordered mesoporous silicas MCM-41 and SBA-15, and non-treated mesoporous silicon and silica gel were assessed in the experiments. The characteristic properties of these materials are the narrow pore diameters and the large surface areas up to over 900 m²/g. Loading of poorly water soluble drugs into these pores restricts their crystallization, and thus, improves drug dissolution from the materials as compared to the bulk drug molecules. In addition, the wide surface area provides possibilities for interactions between the loaded substance and the carrier particle, allowing the stabilization of the system. Ibuprofen, indomethacin and furosemide were selected as poorly soluble model drugs in this study. Their solubilities are strongly pH-dependent and the poorest (< 100 µg/ml) at low pH values. The pharmaceutical performance of the studied materials was evaluated by several methods. In this work, drug loading was performed successfully using rotavapor and fluid bed equipment in a larger scale and in a more efficient manner than with the commonly used immersion methods. It was shown that several carrier particle properties, in particular the pore diameter, affect the loading efficiency (typically ~25-40 w-%) and the release rate of the drug from the mesoporous carriers. A wide pore diameter provided easier loading and faster release of the drug. The ordering and length of the pores also affected the efficiency of the drug diffusion. However, these properties can also compensate the effects of each other. The surface treatment of porous silicon was important in stabilizing the system, as the non-treated mesoporous silicon was easily oxidized at room temperature. Different surface chemical treatments changed the hydrophilicity of the porous silicon materials and also the potential interactions between the loaded drug and the particle, which further affected the drug release properties. In all of the studies, it was demonstrated that loading into mesoporous silicon and silica materials improved the dissolution of the poorly soluble drugs as compared to the corresponding bulk compounds (e.g. after 30 min ~2-7 times more drug was dissolved depending on the materials). The release profile of the loaded substances remained similar also after 3 months of storage at 30°C/56% RH. The thermally carbonized mesoporous silicon did not compromise the Caco-2 monolayer integrity in the permeation studies and improved drug permeability was observed. The loaded mesoporous silica materials were also successfully compressed into tablets without compromising their characteristic structural and drug releasing properties. The results of this research indicated that mesoporous silicon/silica-based materials are promising materials to improve the dissolution of poorly water soluble drugs. Their feasibility in pharmaceutical laboratory scale processes was also confirmed in this thesis.

On characterization of deformation microstructure in Boron modified Ti-6Al-4V alloy

Addition of boron in small quantities to various titanium alloys have shown significant improvement in mechanical behavior of materials. In the present study, electron back-scatter diffraction (EBSD) techniques have been applied to investigate the deformation microstructure evolution in boron modified two-phase titanium alloy Ti-6Al-4V. The alloy was hot compressed at 750 degrees C up to 50% height reduction at two different strain rates (10(-3) s(-1) and 1 s(-1)). The EBSD analyses indicated significant differences in deformed microstructure of the base alloy and the alloy containing boron. A strong subgrain formation tendency was observed along with inhomogeneous distribution of dislocations inside large a colonies of Ti64. In contrast, a colonies were relatively strain free for Ti64 + B, with more uniform dislocation density distribution. The observed difference is attributed to microstructural modifications viz, grain size refinement and presence of TiB particles at grain boundary produced due to boron addition. (C) 2010 Elsevier B.V. All rights reserved.

Temperature-Sensitive Src-Transformed Mdck Cells nn 3d Cultures as a Model of Malignant Transformation of Epithelial Cells

The equilibrium between cell proliferation, differentiation, and apoptosis is crucial for maintaining homeostasis in epithelial tissues. In order for the epithelium to function properly, individual cells must gain normal structural and functional polarity. The junctional proteins have an important role both in binding the cells together and in taking part in cell signaling. Cadherins form adherens junctions. Cadherins initiate the polarization process by first recognizing and binding the neighboring cells together, and then guiding the formation of tight junctions. Tight junctions form a barrier in dividing the plasma membranes to apical and basolateral membrane domains. In glandular tissues, single layered and polarized epithelium is folded into tubes or spheres, in which the basal side of the epithelial layer faces the outer basal membrane, and the apical side the lumen. In carcinogenesis, the differentiated architecture of an epithelial layer is disrupted. Filling of the luminal space is a hallmark of early epithelial tumors in tubular and glandular structures. In order for the transformed tumor cells to populate the lumen, enhanced proliferation as well as inhibition of apoptosis is required. Most advances in cancer biology have been achieved by using two-dimensional (2D) cell culture models, in which the cells are cultured on flat surfaces as monolayers. However, the 2D cultures are limited in their capacity to recapitulate the structural and functional features of tubular structures and to represent cell growth and differentiation in vivo. The development of three-dimensional (3D) cell culture methods enables the cells to grow and to be studied in a more natural environment. Despite the wide use of 2D cell culture models and the development of novel 3D culture methods, it is not clear how the change of the dimensionality of culture conditions alters the polarization and transformation process and the molecular mechanisms behind them. Src is a well-known oncogene. It is found in focal and adherens junctions of cultured cells. Active src disrupts cell-cell junctions and interferes with cell-matrix binding. It promotes cell motility and survival. Src transformation in 2D disrupts adherens junctions and the fibroblastic phenotype of the cells. In 3D, the adherens junctions are weakened, and in glandular structures, the lumen is filled with nonpolarized vital cells. Madin-Darby canine kidney (MDCK) cells are an epithelial cell type commonly used as a model for cell polarization. Its-src-transformed variants are useful model systems for analyzing the changes in cell morphology, and they play a role in src-induced malignant transformation. This study investigates src-transformed cells in 3D cell cultures as a model for malignant transformation. The following questions were posed. Firstly: What is the role of the composition and stiffness of the extracellular matrix (ECM) on the polarization and transformation of ts v-src MDCK cells in 3D cell cultures? Secondly: How do the culture conditions affect gene expression? What is the effect of v-src transformation in 2D and in 3D cell models? How does the shift from 2D to 3D affect cell polarity and gene expression? Thirdly: What is the role of survivin and its regulator phosphatase and tensin homolog protein (PTEN) in cell polarization and transformation, and in determining cell fate? How does their expression correlate with impaired mitochondrial function in transformed cells? In order to answer the above questions, novel methods of culturing and monitoring cells had to be created: novel 3D methods of culturing epithelial cells were engineered, enabling real time monitoring of a polarization and transformation process, and functional testing of 3D cell cultures. Novel 3D cell culture models and imaging techniques were created for the study. Attention was focused especially on confocal microscopy and live-cell imaging. Src-transformation disturbed the polarization of the epithelium by disrupting cell adhesion, and sensitized the cells to their environment. With active src, the morphology of the cell cluster depended on the composition and stiffness of the matrix. Gene expression studies revealed a broader impact of src transformation than mere continuous activity of src-kinase. In 2D cultures, src transformation altered the expression of immunological, actin cytoskeleton and extracellular matrix (ECM). In 3D, the genes regulating cell division, inhibition of apoptosis, cell metabolism, mitochondrial function, actin cytoskeleton and mechano-sensing proteins were altered. Surprisingly, changing the culture conditions from 2D to 3D affected also gene expression considerably. The microarray hit survivin, an inhibitor of apoptosis, played a crucial role in the survival and proliferation of src-transformed cells.

Compression of Weighted Graphs

We propose to compress weighted graphs (networks), motivated by the observation that large networks of social, biological, or other relations can be complex to handle and visualize. In the process also known as graph simplication, nodes and (unweighted) edges are grouped to supernodes and superedges, respectively, to obtain a smaller graph. We propose models and algorithms for weighted graphs. The interpretation (i.e. decompression) of a compressed, weighted graph is that a pair of original nodes is connected by an edge if their supernodes are connected by one, and that the weight of an edge is approximated to be the weight of the superedge. The compression problem now consists of choosing supernodes, superedges, and superedge weights so that the approximation error is minimized while the amount of compression is maximized. In this paper, we formulate this task as the 'simple weighted graph compression problem'. We then propose a much wider class of tasks under the name of 'generalized weighted graph compression problem'. The generalized task extends the optimization to preserve longer-range connectivities between nodes, not just individual edge weights. We study the properties of these problems and propose a range of algorithms to solve them, with dierent balances between complexity and quality of the result. We evaluate the problems and algorithms experimentally on real networks. The results indicate that weighted graphs can be compressed efficiently with relatively little compression error.

Microstructural features of flow instability in α-titanium cylinders under high strain rate compression at 25°C to 400°C

Cylindrical specimens of commercial pure titanium have been compressed at strain rates in the range of 0.1 to 100 s-1 and temperatures in the range of 25-degrees-C to 400-degrees-C. At strain rates of 10 and 100 s-1, the specimens exhibited adiabatic shear bands. At lower strain rates, the material deformed in an inhomogeneous fashion. These material-related instabilities are examined in the light of the ''phenomenological model'' and the ''dynamic materials mode.'' It is found that the regime of adiabatic shear band formation is predicted by the phenomenological model, while the dynamic materials model is able to predict the inhomogeneous deformation zone. The criterion based on power partitioning is competent to predict the variations within the inhomogeneous deformation zone.

X-ray diffraction line profile analysis of deformation microstructure in boron modified Ti-6Al-4V alloy

X-ray diffraction line profile analysis (XRDLPA) techniques have been applied to investigate the deformed microstructure of a recently developed boron modified two-phase titanium alloy Ti-6Al-4V. The alloy was hot compressed at 750 degrees C up to 50% height reduction at two different strain rates (10(-3) S-1 and 1 S-1). Microstructural parameters like average domain size, average microstrain within the domain and dislocation density of the two phases were determined using X-ray diffraction line profile analysis. The results indicate an increase in the microstrain and dislocation density for the alpha-phase and decrease for the beta-phase in the case of boron modified alloys as compared to the normal material. Microstructural modifications viz, the grain refinement and the presence of hard, brittle TiB particles in the case of boron modified alloy are held responsible for the observed difference in the dislocation density. (C) 2010 Elsevier Inc. All rights reserved.

Interfacial shear rheology of highly confined glassy polymers

We present results on interfacial shear rheology measurements on Langmuir monolayers of two different polymers, poly(vinyl acetate) and poly(methyl methacrylate) as a function of surface concentration and temperature. While for the high glass transition poly(methyl methacrylate) polymer we find a systematic transition from a viscous dominated regime to an elastic dominated regime as surface concentration is increased, monolayers of the low glass transition polymer, poly(vinyl acetate), remain viscous even at very high surface concentrations. We further interpret the results in terms of the soft glassy rheology model of Sollich et al. P. Sollich, F. C. Lequeux, P. Hebraud and M. E. Cates, Phys. Rev. Lett., 1997, 78, 2020-2023] and provide evidence of possible reduction in glass transition temperatures in both poly(methyl methacrylate) and poly(vinyl acetate) monolayers due to finite size effects.

Vesicle and Stable Monolayer Formation from Simple ``Click'' Chemistry Adducts in Water

Click chemistry has been successfully extended into the field of molecular design of novel amphiphatic adducts. After their syntheses and characterizations, we have studied their aggregation properties in aqueous medium. Each of these adducts forms stable suspensions in water. These suspensions have been characterized by dynamic light scattering (DLS) studies and transmission electron microscopy (TEM). The presence of inner aqueous compartments in such aggregates has been demonstrated using dye (methylene blue) entrapment studies. These aggregates have been further characterized using X-ray diffraction (XRD), which indicates the existence of bilayer structures in them. Therefore, the resulting aggregates could be described as vesicles. The temperature-induced order-to-disorder transitions of the vesicular aggregates and the accompanying changes in their packing and hydration have been examined using high-sensitivity differential scanning calorimetry, fluorescence anisotropy, and generalized polarization measurements using appropriate membrane-soluble probe, 1,6-diphenylhexatriene, and Paldan, respectively. The findings of these studies are consistent with each other in terms of the apparent phase transition temperatures. Langmuir monolayer studies confirmed that these click adducts also form stable monolayers on buffered aqueous subphase at the air-water interface.

Autoregressive spectral array for graphical display of EEG data

A graphical display of the frequency content of background,electroencephalogram (EEG) activity is obtained by calculating the spectral estimates using autocorrelation autoregressive method and the classical Fourier transform method, Display of spectral content of consecutive data segments is made using hidden-line suppression technique so as to get a spectral array, The autoregressive spectral array (ASA) is found to be sensitive to baseline drift, Following baseline correction the autoregressive technique is found to be superior to the Fourier method of compressed spectral array (CSA) in detecting the transitions in the frequencies of the signal. The smoothed ASA gives a better picture of transitions and changes in the background activity, The ASA can be made to adapt to specific changes of dominant frequencies while eliminating unnecessary peaks in the spectrum. The utility,of the ASA for background EEG analysis is discussed,

Data compression by linear prediction for storage and transmission of EEG signals

The EEG time series has been subjected to various formalisms of analysis to extract meaningful information regarding the underlying neural events. In this paper the linear prediction (LP) method has been used for analysis and presentation of spectral array data for the better visualisation of background EEG activity. It has also been used for signal generation, efficient data storage and transmission of EEG. The LP method is compared with the standard Fourier method of compressed spectral array (CSA) of the multichannel EEG data. The autocorrelation autoregressive (AR) technique is used for obtaining the LP coefficients with a model order of 15. While the Fourier method reduces the data only by half, the LP method just requires the storage of signal variance and LP coefficients. The signal generated using white Gaussian noise as the input to the LP filter has a high correlation coefficient of 0.97 with that of original signal, thus making LP as a useful tool for storage and transmission of EEG. The biological significance of Fourier method and the LP method in respect to the microstructure of neuronal events in the generation of EEG is discussed.

Use of running fractal dimension for the analysis of changing patterns in electroencephalograms

Running fractal dimensions were measured on four channels of an electroencephalogram (EEG) recorded from a normal volunteer. The changes in the background activity due to eye closure were clearly differentiated by the fractal method. The compressed spectral array (CSA) and the running fractal dimensions of the EEG showed corresponding changes with respect to change in the background activity. The fractal method was also successful in detecting low amplitude spikes and the changes in the patterns in the EEG. The effects of different window lengths and shifts on the running fractal dimension have also been studied. The utility of fractal method for EEG data compression is highlighted.

Influence of initial texture on the microstructural instabilities during compression of commercial ?-Titanium at 25 °C to 400 °C

Cylindrical specimens of textured commercial pure alpha-titanium plate, cut with the cylinder axis along the rolling direction for one set of experiments and in the long transverse direction for the other set, were compressed at strain rates in the range of 0.001 to 100 s-1 and temperatures in the range of 25-degrees-C to 400-degrees-C. At strain rates greater-than-or-equal-to 1 s-1, both sets of specimens exhibited adiabatic shear bands, but the intensity of shear bands was found to be higher in the rolling direction specimens than in the long transverse direction specimens. At strain rates -0.1 s-1, the material deformed in a microstructurally inhomogeneous fashion. For the rolling direction specimens, cracking was observed at 100-degrees-C and at strain rates -0.1 s-1. This is attributed to dynamic strain aging. Such cracking was not observed in the long transverse specimens. The differences in the intensity of adiabatic shear bands and that of dynamic strain aging between the two sets of test specimens are attributed to the strong crystallographic texture present in these plates.

Lossless and lossy image compression using Boolean function minimization

A novel approach for lossless as well as lossy compression of monochrome images using Boolean minimization is proposed. The image is split into bit planes. Each bit plane is divided into windows or blocks of variable size. Each block is transformed into a Boolean switching function in cubical form, treating the pixel values as output of the function. Compression is performed by minimizing these switching functions using ESPRESSO, a cube based two level function minimizer. The minimized cubes are encoded using a code set which satisfies the prefix property. Our technique of lossless compression involves linear prediction as a preprocessing step and has compression ratio comparable to that of JPEG lossless compression technique. Our lossy compression technique involves reducing the number of bit planes as a preprocessing step which incurs minimal loss in the information of the image. The bit planes that remain after preprocessing are compressed using our lossless compression technique based on Boolean minimization. Qualitatively one cannot visually distinguish between the original image and the lossy image and the value of mean square error is kept low. For mean square error value close to that of JPEG lossy compression technique, our method gives better compression ratio. The compression scheme is relatively slower while the decompression time is comparable to that of JPEG.

Enhancement of uniaxial magnetic anisotropy in Fe thin films grown on GaAs(001) with an MgO underlayer

The understanding and control of anisotropy in Fe films grown on cubic systems such as GaAs and MgO has been of interest from the point of view of applications in devices. We report magnetic anisotropy studies on Fe/GaAs(001) and Fe/MgO/GaAs(001) prepared by pulsed laser deposition. In Fe/GaAs(001), magneto optical Kerr effect (MOKE) measurements revealed a dominant uniaxial anisotropy for Fe thickness less than 20 monolayers (ML) and this was confirmed by ferromagnetic resonance (FMR) studies. Multiple steps in the hysteresis loops were observed for Fe films of thickness 20 and 25 ML. Whereas, in Fe/MgO/GaAs(001), even at 25 ML of Fe, the uniaxial anisotropy remained dominant. The anisotropy constants obtained from FMR spectra have shown that the relative strength of uniaxial anisotropy is higher as compared to the cubic anisotropy constant in the case of Fe/MgO/GaAs(001). (C) 2011 American Institute of Physics. doi:10.1063/1.3556941]