Impact of Host Genes and Strand Selection on miRNA and miRNA* Expression

Dysregulation of miRNAs expression plays a critical role in the pathogenesis of genetic, multifactorial disorders and in human cancers. We exploited sequence, genomic and expression information to investigate two main aspects of post-transcriptional regulation in miRNA biogenesis, namely strand selection regulation and expression relationships between intragenic miRNAs and host genes. We considered miRNAs expression profiles, measured in five sizeable microarray datasets, including samples from different normal cell types and tissues, as well as different tumours and disease states. First, the study of expression profiles of “sister” miRNA pairs (miRNA/miRNA*, 5′ and 3′ strands of the same hairpin precursor) showed that the strand selection is highly regulated since it shows tissue-/cell-/condition-specific modulation. We used information about the direction and the strength of the strand selection bias to perform an unsupervised cluster analysis for the sample classification evidencing that is able to distinguish among different tissues, and sometimes between normal and malignant cells. Then, considering a minimum expression threshold, in few miRNA pairs only one mature miRNA is always present in all considered cell types, whereas the majority of pairs were concurrently expressed in some cell types and alternatively in others. In a significant fraction of concurrently expressed pairs, the major and the minor forms found at comparable levels may contribute to post-transcriptional gene silencing, possibly in a coordinate way. In the second part of the study, the behaved tendency to co-expression of intragenic miRNAs and their “host” mRNA genes was confuted by expression profiles examination, suggesting that the expression profile of a given host gene can hardly be a good estimator of co-transcribed miRNA(s) for post-transcriptional regulatory networks inference. Our results point out the regulatory importance of post-transcriptional phases of miRNAs biogenesis, reinforcing the role of such layer of miRNA biogenesis in miRNA-based regulation of cell activities

Structural characterization of light elements in semiconductor materials by means of selected nuclear reactions

Materials and structures for microelectronics are characterized by a continuous decrease of their dimensions. Nanostructured materials are currently required to design and produce novel devices. We will show that, in spite of their relatively poor lateral resolution, selected nuclear reactions or ad-hoc studied resonances in the elastic cross section of alpha particles, in random and channelling configuration, can accurately quantify and provide the lattice location of different light elements in various semiconductor matrices. Different systems of current interest will be described. Moreover physical results obtained by combining nuclear reactions with Rutherford BackScattering (RBS), High Resolution X-Ray Diffraction (HRXRD) and Secondary Ion Mass Spectrometry (SIMS) analysis will be discussed. In particular the relation between the lattice parameter and the light impurity concentration in the case of Si-C ,Si-Ge-C ,Ga-As-N-(In) dilute alloys and of B-doped silicon will be described. We will also show some results on hydrogenated (deuterated) dilute nitrides

New Opportunities to Study Defects by Soft X-Ray Absorption Fine Structure

X-ray absorption fine structure can determine the local structure of most atoms in the periodic table. The great recent improvements in the performance of synchrotron radiation sources and techniques and advances in the simulations of the spectra have opened new opportunities, especially in the study of dilute systems in the soft X-ray range. In this contribution we will show some recent results that demonstrate how semiconductor physics may greatly benefit from such progress. In fact, doping or alloying of semiconductors with light elements, that have K absorption edges in the soft X-ray range, is widely employed to tune semiconductor properties. X-ray absorption fine structure investigations on such systems can give an important contribution towards the understanding and optimization of technological processes

Ion beam characterization of Fe implanted GaN

Fe ion implantation in GaN has been investigated by means of ion beam analysis techniques. Implantations at an energy of 150 keV and fluences ranging from 2 x 10^15 to 1 x 10^16 cm^-2 were done, both at room temperature and at 623 K. Secondary Ions Mass Spectrometry was used to determine the Fe implantation profiles, whereas Rutherford Backscattering in channeling conditions with a 2.2 MeV 4He^+ beam allowed us to follow the damage evolution. Particle Induced X-ray Emission in channeling conditions with a 2 MeV H+ beam was employed to study the lattice location of Fe atoms after implantation. The results show that a high fraction of Fe-implanted atoms are located in high symmetry sites in low fluence implanted samples, where the damage level is lower, whereas the fraction of randomly located Fe atoms increases by increasing the fluence and the resulting damage. Moreover, dynamical annealing present in high temperature implantation has been shown to favor the incorporation of Fe atoms in high symmetry sites

MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update).

MAGIA(2) (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. miRNAs are fundamental post-transcriptional regulators of several key biological and pathological processes. As miRNAs act prevalently through target degradation, their expression profiles are expected to be inversely correlated to those of the target genes. Low specificity of target prediction algorithms makes integration approaches an interesting solution for target prediction refinement. MAGIA(2) performs this integrative approach supporting different association measures, multiple organisms and almost all target predictions algorithms. Nevertheless, miRNAs activity should be viewed as part of a more complex scenario where regulatory elements and their interactors generate a highly connected network and where gene expression profiles are the result of different levels of regulation. The updated MAGIA(2) tries to dissect this complexity by reconstructing mixed regulatory circuits involving either miRNA or transcription factor (TF) as regulators. Two types of circuits are identified: (i) a TF that regulates both a miRNA and its target and (ii) a miRNA that regulates both a TF and its target

Substitutional and clustered B in ion implanted Ge: Strain determination

The lattice strain induced both by substitutional and clustered B in B-implanted Ge samples has been investigated by means of high resolution x-ray diffraction HRXRD. The main results can be summarized as follows: while substitutional i.e., electrically active B exhibits a negative strain, clustered i.e., electrically inactive B reverses the lattice strain from negative to positive values, the latter being much higher with respect to those found for clustered B in Si. In particular, the lattice volume modification for each B atom V induced by substitutional VSub and clustered VCl B is VSub= 1212.4 \uc53 and VCl=+14.8 \uc53, respectively. These unexpected results demonstrate the ability of HRXRD to quantitatively detect the amount of electrically inactive and active B

Strain relaxation of SiGe in a Si/SiGe/Si heterostructure under proton irradiation

We have studied the mechanisms underlying strained layer relaxation by means of point defect interaction. During high temperature 300 \ub0C proton irradiation, vacancies generated in the vicinity of SiGe layer migrate and accumulate within the compressively strained SiGe layer. The accumulating vacancies are stabilized by hydrogen, which diffuses from the implanted region, thus allowing the nucleation and growth of hydrogen-vacancy V-H complexes. The formation of V-H complexes is accompanied by gradual strain relief in SiGe layer. Since the diffusion of both vacancies and hydrogen is limited by the irradiation temperature, strain relaxation of the SiGe layer is not realized during room temperature 20 \ub0C proton irradiation. The study supports the idea that the compressive stress in the SiGe layer induces the indiffusion of vacancies and H, and reveals the important role of point defects in the strain relaxation of the strained SiGe layer

On the Strain Induced by Arsenic into Silicon

The strain induced by substitutional arsenic into the silicon lattice was investigated experimentally. First, a combination of multiple implantations was used to obtain a flat arsenic profile in the first 150 nm of the substrate. Although a full activation of the dopants could be achieved, the EOR defects resulting from the implants were not dissolved and prevented reliable strain measurements. A single implantation was then used. Annealing conditions were carefully chosen to obtain a nearly flat arsenic profile in the first 400 nm of the substrate and to dissolve the EOR defects. Sheet resistance, TEM and RBS measurements confirmed the full activation of the samples and the dissolution of the EOR defects. HRXRD was then used to characterize the strain. The interpretation of the measurements via strain simulation indicated a lattice strain of (-1.5 +/- 0.7)x10(-5) associated with a lattice contraction at a concentration of 2x10(20) cm(-3). This value is significantly lower than the values reported in literature

High-level incorporation of antimony in germanium by laser annealing

In this work we investigate pulse laser annealing as an alternative approach to reach high-level incorporation of Sb in substitutional location in crystalline germanium. Laser irradiation is demonstrated to recover also those structural defects, like honeycomb structures, that form during high-fluence heavy-ion implantations in Ge and that cannot be eliminated by conventional thermal treatments. Indeed, concentrations of substitutional Sb higher than 1 71021\u2002at./cm3 have been obtained, well above the solid solubility of Sb in Ge. The strain induced on the Ge host lattice is also investigated, evidencing that the obtained Sb doped Ge layer is pseudomorphic to the Ge substrate while positively strained by the substitutional Sb atoms present within the Ge matrix. The kinetics of this Sb-rich Ge alloy phase is finally investigated, showing that most of Sb goes out of lattice with increasing the annealing temperature up to 488\u2009\ub0C, leading to a decrease in the related lattice deformation. These results are very relevant for the future high-mobility channel technology