Raman and surface‐enhanced Raman spectroscopic studies of the 15‐mer DNA thrombin‐binding aptamer

Aptamers are single‐stranded oligonucleotides that selectively bind to their target molecules owing to their ability to form secondary structures and shapes. The 15‐mer (5′‐GGTTGGTGTGGTTGG‐3′) DNA thrombin‐binding aptamer (TBA) binds to thrombin following the formation of a quadruplex structure via the Hoogsten‐type G–G interactions. In the present study, Raman and SERS spectra of TBA and thiolated TBA (used to facilitate covalent bonding to metal nanoparticle) in different conditions are investigated. The spectra of the two analogs exhibit vibrations, such as the C8N7 H2 deformation band at ∼1480 cm⁻¹ of the guanine tetrad, that are characteristic of the quadruplex structure in the presence of K⁺ ions or at low temperature. Interestingly, SERS spectra of the two analogs differ markedly from their respective normal Raman spectra, possibly due to changes in the conformation of the aptamer upon binding, as well as to the specific interaction of individual vibrational modes with the metal surface. In addition, the SERS spectra of the thiolated aptamer show significant changes with different concentrations, which may be due to different orientation of the molecule with respect to the metal surface. This study provides useful information for the development of label‐free aptamer‐based SERS sensors and assays. Copyright © 2009 John Wiley & Sons, Ltd.     

Growing networks with preferential deletion and addition of edges

A preferential attachment model for a growing network incorporating the deletion of edges is studied and the expected asymptotic degree distribution is analyzed. At each time step t=1,2,…, with probability π₁>0 a new vertex with one edge attached to it is added to the network and the edge is connected to an existing vertex chosen proportionally to its degree, with probability π₂ a vertex is chosen proportionally to its degree and an edge is added between this vertex and a randomly chosen other vertex, and with probability π₃=1−π₁−π₂<1/2 a vertex is chosen proportionally to its degree and a random edge of this vertex is deleted. The model is intended to capture a situation where high-degree vertices are more dynamic than low-degree vertices in the sense that their connections tend to be changing. A recursion formula is derived for the expected asymptotic fraction p_k of vertices with degree k, and solving this recursion reveals that, for π₃<1/3, we have p_k∼k^{−(3−7π₃)/(1−3π₃)}, while, for π₃>1/3, the fraction p_k decays exponentially at rate (π₁+π₂)/2π₃. There is hence a non-trivial upper bound for how much deletion the network can incorporate without losing the power-law behavior of the degree distribution. The analytical results are supported by simulations.     

Study on the formation during the production of lead-free piezoceramics at the morphotropic phase boundary

Because of the environmental concerns, the manufacture of ceramics based on lead titanate zirconate [Pb(Zr_1−xTi_x)O₃−PZT] has been condemned because of the lead toxicity. In this context, the electromechanical properties of sodium, potassium and lithium niobate [(Na_0.5−x/2K_0.5−x/2Li_x)NbO₃−NKLN] at the morphotropic phase boundary granted these materials the position of most suitable candidate to replace PZT. However, the production of these ceramics is rather critical mainly because of a natural tendency of forming secondary phases. To help with the studies of the synthesis of this lead-free piezoceramic, this work presents an evaluation of the crystallization of the (Na_0.47K_0.47Li_0.06)NbO₃ phase by solid-state reactions. TG-DTA, XRD, dilatometric and ferroelectric hysteresis analyses indicated that a secondary phase (K₃Li₂Nb₅O₁₅) crystallizes at temperatures above 850 C and also during the sintering of the powders compacts at 1080 C. To prevent the formation of this phase, the addition of Na₂Nb₂O₆.nH₂O microfibers obtained through a microwave hydrothermal synthesis was performed in the sintering process. After to this addition, the suppression of the K₃Li₂Nb₅O₁₅ phase occurred and an increase of the NKLN electrical properties was then obtained.     

In vivo quantitative 1H MRS of cerebellum and evaluation of quantitation reproducibility by simulation of different levels of noise and spectral resolution

A quantitative analysis of cerebellar metabolites in normal subjects has been performed by proton MR spectroscopy (MRS) with relaxation time correction. Quantitation was carried out in seven healthy human subjects with the well-established LCModel program. The prior knowledge utilized for quantitation was obtained from solutions containing the major brain metabolites and MRS investigated under the same experimental conditions. The tissue water signal was used as an internal standard for the in vivo studies. Both in vitro (for the prior knowledge template) and in vivo data were acquired separately at 1.5 T by PRESS sequence (TR, 1500 ms; TE, 30 ms). The absolute concentration of main cerebellar metabolites was corrected for relaxation time effects. Different noise and line broadening conditions were considered and simulated in the spectral processing in order to evaluate the effect of spectral quality on the concentration estimates.     

Investigation of metabolic changes in irradiated rat brain tissue by means of 1H NMR in vitro relaxation study

The effect of irradiation on concentrations and relaxation behaviour of brain metabolites was studied by means of high-resolution 1H NMR in vitro. The studies were performed on rat brains irradiated with the doses of 20 Gy applied in fractions of 2 Gy. Standard procedures were used to obtain HClO4 extracts of rat brains. The 1H NMR studies of the extracts solutions in D2O were performed using a Varian Inova-300 NMR spectrometer. The integral intensities of the metabolite signals were found to change during the irradiation cycle and after it. These changes are accompanied by the variations in the T1 relaxation times. N-acetylaspartate, glycerophosphocholine, phosphocholine, choline, creatine and phosphocreatine, myoinositol and taurine were analysed as potential markers of irradiation injury.     

TLD measurements and Monte Carlo simulations for glandular dose and scatter fraction assessment in mammography: A comparative study

The main purpose of this study was to validate and compare Mean Glandular Dose (MGD) values obtained using Monte Carlo simulations with experimental values obtained from Entrance Surface Dose (ESD) and depth dose measurements performed in a Hospital mammography unit. ESD and depth dose were measured using ThermoLuminescent Dosimeters (TLDs), and a tissue equivalent mammography phantom recommended by the American College of Radiology (ACR). Measurements and Monte Carlo simulations were also compared with the MGD calculated using the Automatic Exposure Control (AEC) system of the mammographic unit. In the simulations the Doppler energy broadening effect was also taken into account. The simulated ESD are about 5%–10% higher than the measured ESD values. The deviation between the measured and simulated MGD values in the phantom is of about 15%. The MGD evaluated using the AEC system is smaller both with respect to the Monte Carlo simulation and experimental result by a factor of about 15% and 25% respectively. Moreover the BackScatter Factor (BSF) estimated by Monte Carlo simulations was used for the MGD calculation according to the Wu’s method. Finally the inclusion of the energy broadening effect on MGD calculation produces negligible variations on the simulated results.     

Assessment of mitral regurgitation by magnetic resonance imaging

To evaluate the potential of magnetic resonance imaging (MRI) in detection and quantification of mitral regurgitation, 26 pts. with echocardiographically or angiographically documented mitral regurgitation were examined using a 0.5 Tesla superconducting magnet. In each patient a multislice-multiphase study in a sagittal-coronal double angulated projection (four-chamber view equivalent) was performed to assess left and right ventricular volumes, ejection fraction and regurgitant fraction. Additionally a blood flow sensitive cine-study (fast field echo: FFE) was done to visualize direction and area of regurgitant jet. MRI data were compared with quantitative and qualitative assessment of mitral regurgitation by angiography, 2D echocardiography, Doppler sonography and color flow mapping. Using the FFE mode MRI was able to detect the regurgitant jet as a typical signal loss within the left atrium in all patients. The ratio of regurgitant jet area/left atrium area as determined by MRI showed a correlation with a comparable ratio from color Doppler sonography of R = 0.87 (p < 0.001). There was also good agreement in semiquantitative grading of mitral regurgitation between MRI and angiography (R = 0.77, p < 0.001). The determination of left and right ventricular stroke volume allowed the calculation of the regurgitant fraction, which showed a correlation with invasively determined regurgitation fraction of R = 0.84 (p < 0.001). These data provide additional information that MRI may be useful as a noninvasive technique to detect and quantify mitral regurgitation.     

Dynamic processes in the Venice region outlined by environmental isotopes

Research carried out in the last 40 years has shown the scientific importance of groundwater circulation both in the Northern Adriatic sea bed and within the uppermost sedimentary layers of the Venice lagoon and of the Venice plain. Hydrodynamic processes are strictly controlled by a well-cemented sedimentary horizon lying under and around Venice ('caranto'), which plays the role of regional aquitard. This layer was attributed to the subaerial cementation of the Flandrian (8-10 ka Before Present) sedimentary surface. The caranto is generalised as a continuum horizon, being an easy explanation for several environmental, hydrogeological and geotechnical problems, e.g., a base layer for landfills, a confining layer for deep aquifers and the best substratum for locating the oak wooden pile-dwelling needed to support the largest buildings. The preservation of the isotope signal within the deep aquifers and aquiclude system records the changes in surface and groundwater characteristics and suggests the present and past recharge regimes. In this region, the heavily perturbed hydrodynamic conditions do not allow for the use of isotopic signals to derive a correct reconstruction of the present recharge. The perturbations induced by the intensive anthropogenic activity force to follow climate evolution by considering deep groundwater and pore waters. In addition, the presence of carbonatic rocks inside terrigeneous sediments affects the reconstruction of the past. Results indicate that carbonatic rocks are created by seepage, through the sediments, of gaseous carbon compounds from decaying organic layers. The gas interactions with the intra-sedimentary saline and fresh waters produce CO2, inducing the cementation of the sediments.     

EPR spectroscopy of protein microcrystals oriented in a liquid crystalline polymer medium

Correlation of the g-tensor of a paramagnetic active center of a protein with its structure provides a unique experimental information on the electronic structure of the metal site. To address this problem, we made solid films containing metalloprotein (Desulfovibrio gigas cytochrome c(3)) microcrystals. The microcrystals in a liquid crystalline polymer medium (water/hydroxypropylcellulose) were partially aligned by a shear flow. A strong orientation effect of the metalloprotein was observed by EPR spectroscopy and polarizing optical microscopy. The EPR spectra of partially oriented samples were simulated, allowing for molecular orientation distribution function determination. The observed effect results in enhanced sensitivity and resolution of the EPR spectra and provides a new approach towards the correlation of spectroscopic data, obtained by EPR or some other technique, with the three-dimensional structure of a protein or a model compound.