Morphology Analysis of Si Island Arrays on Si(001)

The formation of nanometer-scale islands is an important issue for bottom-up-based schemes in novel electronic, optoelectronic and magnetoelectronic devices technology. In this work, we present a detailed atomic force microscopy analysis of Si island arrays grown by molecular beam epitaxy. Recent reports have shown that self-assembled distributions of fourfold pyramid-like islands develop in 5-nm thick Si layers grown at substrate temperatures of 650 and 750°C on HF-prepared Si(001) substrates. Looking for wielding control and understanding the phenomena involved in this surface nanostructuring, we develop and apply a formalism that allows for processing large area AFM topographic images in a shot, obtaining surface orientation maps with specific information on facets population. The procedure reveals some noticeable features of these Si island arrays, e.g. a clear anisotropy of the in-plane local slope distributions. Total island volume analysis also indicates mass transport from the substrate surface to the 3D islands, a process presumably related to the presence of trenches around some of the pyramids. Results are discussed within the framework of similar island arrays in homoepitaxial and heteroepitaxial semiconductor systems

Large-Scale Evidence for Conservation of NMD Candidature Across Mammals

BACKGROUND: Alternatively-spliced (AS) forms can vary protein function, intracellular localization and post-translational modifications. AS coupled with mRNA nonsense-mediated decay (NMD) can also control the transcript abundance. Here, we have investigated the genome-scale conservation of alternatively-spliced NMD candidates (AS-NMD candidates), in mammals. METHODOLOGY/PRINCIPAL FINDINGS: We mapped>12 million cDNA/EST library transcripts, comprising pooled data from both older and next-generation sequencing techniques, against genomic sequences to annotate AS-NMD candidates generated by in-frame premature termination codons (PTCs), in the human, mouse, rat and cow genomes. In these genomes, we found populations of genes that harbour AS-NMD candidates, varying in number from approximately 149 to 2,051 genes. We discovered that a highly-significant proportion (27%-35%) of AS-NMD candidate genes in mouse, rat and cow, also have human orthologs targeted for NMD. Intron retention was the most abundant type of AS-NMD, ranging from 43% to 67% of genes harbouring an AS-NMD candidate. Groupings of AS-NMD candidate genes either with or without intron retentions also have highly significant AS-NMD conservation, indicating that the trend is not due primarily to conservation of intron retentions. As a subset, the AS-NMD intron retentions are distinguished from non-retained introns by higher GC content, and codon usage similar to the usage in protein-coding sequences. This indicates that most of these alternatively spliced sequences have coded for proteins in the recent evolutionary past. In general, the AS-NMD candidate genes showed a similar pattern of Gene Ontology functional category enrichments in all four species. Genes linked to nucleic-acid interaction and apoptosis, and involved in pathways linked with cancer, were the most common. Finally, we mapped the AS-NMD candidates to mass spectrometry-derived proteomics data, and gathered evidence of truncated polypeptides for at least 10% of all human AS-NMD candidate transcripts. CONCLUSIONS/SIGNIFICANCE: In summary, our analysis provides strong statistical evidence for conservation of functional AS-NMD candidature across Mammalia for a large subset of genes. However, because codon usage of AS-NMD intron retentions is similar to the usage in exons, it is difficult to de-couple conservation of AS-NMD-based regulation from conservation for protein-coding ability, for intron retentions

Disturbed Expression of Splicing Factors in Renal Cancer Affects Alternative Splicing of Apoptosis Regulators, Oncogenes, and Tumor Suppressors

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cancer. One of the processes disturbed in this cancer type is alternative splicing, although phenomena underlying these disturbances remain unknown. Alternative splicing consists of selective removal of introns and joining of residual exons of the primary transcript, to produce mRNA molecules of different sequence. Splicing aberrations may lead to tumoral transformation due to synthesis of impaired splice variants with oncogenic potential. In this paper we hypothesized that disturbed alternative splicing in ccRCC may result from improper expression of splicing factors, mediators of splicing reactions. METHODOLOGY/PRINCIPAL FINDINGS: Using real-time PCR and Western-blot analysis we analyzed expression of seven splicing factors belonging to SR proteins family (SF2/ASF, SC35, SRp20, SRp75, SRp40, SRp55 and 9G8), and one non-SR factor, hnRNP A1 (heterogeneous nuclear ribonucleoprotein A1) in 38 pairs of tumor-control ccRCC samples. Moreover, we analyzed splicing patterns of five genes involved in carcinogenesis and partially regulated by analyzed splicing factors: RON, CEACAM1, Rac1, Caspase-9, and GLI1. CONCLUSIONS/SIGNIFICANCE: We found that the mRNA expression of splicing factors was disturbed in tumors when compared to paired controls, similarly as levels of SF2/ASF and hnRNP A1 proteins. The correlation coefficients between expression levels of specific splicing factors were increased in tumor samples. Moreover, alternative splicing of five analyzed genes was also disturbed in ccRCC samples and splicing pattern of two of them, Caspase-9 and CEACAM1 correlated with expression of SF2/ASF in tumors. We conclude that disturbed expression of splicing factors in ccRCC may possibly lead to impaired alternative splicing of genes regulating tumor growth and this way contribute to the process of carcinogenesis

Band tail states in microcrystalline silicon solar cells probed by photoluminescence and open circuit voltage

Thin film p-i-n microcrystalline silicon (mu c-Si:H) solar cells were studied by photoluminescence (PL) spectroscopy and open circuit voltage, V-oc. By this means, the cause of the commonly observed increase of V-oc when the silane concentration in the gas phase for the preparation of the intrinsic absorber layers is raised is addressed. The hot wire chemical vapour deposition (HW-CVD) technique was used for the preparation of films and intrinsic absorber layers of solar cells with efficiencies higher than 9%. By monitoring V-oc and the PL energy, E-PL, as a function of temperature, information on the photogenerated carrier distributions and the splitting of the quasi-Fermi energies was gained and the effect of states in the gap was studied by comparison with results from a crystalline p-i-n diode. An increase of E-PL and V-oc for increasing SC and decreasing temperature is attributed to the shift of the excess carrier distributions to higher energies. It is proposed that this shift is limited by band tail states. It is proposed that increasing SC leads to a reduction of the density of band tail states, due to structural relaxation of the mu c-Si:H network by the presence of hydrogen or hydrogenated amorphous silicon

A comparison of model calculations and experimental results on photoluminescence energy and open circuit voltage of µc-Si:H solar cells

A simple model is proposed to calculate photoluminescence (PL) spectra and open circuit voltages (V-oc) in thin film p-i-n microcrystalline silicon (mu c-Si:H) solar cells with different structural compositions, as a function of temperature. By using a new technique, namely voltage-modulated PL on solar cells, experimental data are obtained that can be directly compared with the model. The model is based on the distributions of electrons and holes in quasi-equilibrium conditions. Recombination between the two distributions determines the PL band (energy and width of the spectrum). A symmetrical density of states distribution (DOS) described by a superposition of a DOS like that in c-Si and band tail states for the conduction and valence bands is assumed, The best agreement between the model calculations and experimental results for two solar cells with different structural properties is obtained by using an E-o approximate to 0.031 eV for the slope of both exponential band tail states

Modeling of photoluminescence spectra and quasi-Fermi level splitting in μc-Si:H solar cells

We developed a model describing the photoluminescence spectra from hydrogenated microcrystalline silicon (μc-Si:H). From the model we derived analytical relations between the separation of the quasi-Fermi levels and PL-peak energy and intensity. These relations may be useful when photoluminescence or electroluminescence based methods are applied for characterization of μc-Si:H solar cells and modules. We compared the model with experimental PL spectra from a μc-Si:H solar cell. Our model can consistently explain the relation between the measured PL-peak intensity, energy and the measured open circuit voltage of the μc-Si:H solar cell