Use of denaturing gradient gel electrophoresis to detect Actinobacteria associated with the human faecal microbiota

With the exceptions of the bifidobacteria, propionibacteria and coriobacteria, the Actinobacteria associated with the human gastrointestinal tract have received little attention. This has been due to the seeming absence of these bacteria from most clone libraries. In addition, many of these bacteria have fastidious growth and atmospheric requirements. A recent cultivation-based study has shown that the Actinobacteria of the human gut may be more diverse than previously thought. The aim of this study was to develop a denaturing gradient gel electrophoresis (DGGE) approach for characterizing Actinobacteria present in faecal samples. Amount of DNA added to the Actinobacteria-specific PCR used to generate strong PCR products of equal intenstity from faecal samples of five infants, nine adults and eight elderly adults was anti-correlated with counts of bacteria obtained using fluorescence in situ hybridization probe HGC69A. A nested PCR using Actinobacteria-specific and universal PCR-DGGE primers was used to generate profiles for the Actinobacteria. Cloning of sequences from the DGGE bands confirmed the specificity of the Actinobacteria-specific primers. In addition to members of the genus Bifidobacterium, species belonging to the genera Propionibacterium, Microbacterium, Brevibacterium, Actinomyces and Corynebacterium were found to be part of the faecal microbiota of healthy humans.

Temperature-dependent reduction pathways of complexes fac-[Re(CO)3(N-R-imidazole)(1,10-phenanthroline)]+ (R = H, CH3)

Peculiar reduction pathways of the complexes fac-[Re(imH)(CO)3(phen)]+ and fac-[Re(imCH3)(CO)3(phen)]+ (imH = imidazole, imCH3 = N-methylimidazole and phen = 1,10-phenanthroline) have been unravelled by performing combined cyclic voltammetric and in situ IR spectroelectrochemical experiments. In the temperature range of 293–233 K, the initial reduction of the phen ligand in [Re(imH)(CO)3(phen)]+ results in irreversible conversion of the imidazole ligand to 3-imidazolate by a rapid phen•−→ imH intramolecular electron transfer coupled with N H bond cleavage. This process is followed by second phen-localized 1e− reduction producing [ReI(3-im−)(CO)3(phen•−)]−, similar to the analogous 2,2'-bipyridine complex. In contrast to the bpy analogue, the stability of the phen•−-containing complexes is significantly affected by lowering the temperature. At 233 K, a secondary reaction occurs in both [Re(3-im−)(CO)3(phen•−)]− and [Re(imCH3)(CO)3(phen•−)]. The resulting products exhibit v(CO) wavenumbers indistinguishable from those of the parent phen•− complexes; however, their oxidation occurs at a considerably more positive electrode potential. It is proposed that these species are produced by a new C C bond formation between the C(2) site of 3-im− or imCH3 and the C(2) site of the phen•−ligand.

Time-dependent gel to gel transformation of a peptide based supramolecular gelator

A dipeptide with a long fatty acid chain at its N-terminus gives hydrogels in phosphate buffer in the pH range 7.0–8.5. The hydrogel with a gelator concentration of 0.45% (w/v) at pH 7.46 (physiological pH) provides a very good platform to study dynamic changes within a supramolecular framework as it exhibits remarkable change in its appearance with time. Interestingly, the first formed transparent hydrogel gradually transforms into a turbid gel within 2 days. These two forms of the hydrogel have been thoroughly investigated by using small angle X-ray scattering (SAXS), powder X-ray diffraction (PXRD), field emission scanning electron microscopic (FE-SEM) and high-resolution transmission electron microscopic (HR-TEM) imaging, FT-IR and rheometric analyses. The SAXS and low angle PXRD studies substantiate different packing arrangements for the gelator molecules for these two different gel states (the freshly prepared and the aged hydrogel). Moreover, rheological studies of these two gels reveal that the aged gel is stiffer than the freshly prepared gel.

A scanning electron microscopy study of diseased root surfaces conditioned with EDTA gel plus Cetavlon after scaling and root planing

In the present investigation, a scanning electron microscopy analysis was performed to evaluate the effects of the topical application of ethylenediaminetetraacetic acid (EDTA) gel associated with Cetavlon (EDTAC) in removing the smear layer and exposing collagen fibers following root surface instrumentation. Twenty-eight teeth from adult humans, single rooted and scheduled for extraction due to periodontal reasons, were selected. Each tooth was submitted to manual (scaling and root planing) instrumentation alone or combined with ultrasonic instruments, with or without etching using a 24% EDTAC gel. Following extraction, specimens were processed and examined under a scanning electron microscope. A comparative morphological semi-quantitative analysis was performed; the intensity of the smear layer and the decalcification of cementum and dentinal surfaces were graded in 12 sets using an arbitrary scale ranging from 1 (area covered by a smear layer) to 4 (no smear layer). Root debridement with hand instruments alone or combined with ultrasonic instruments resulted in a similar smear layer covering the root surfaces. The smear layer was successfully removed from the surfaces treated with EDTAC, which exhibited numerous exposed dentinal tubules and collagen fibers. This study supports the hypothesis that manual instrumentation alone or instrumentation combined with ultrasonic instrumentation is unable to remove the smear layer, whereas the subsequent topical application of EDTAC gel effectively removes the smear layer, uncovers dentinal openings and exposes collagen fibers.

Clinical comparison between the bleaching efficacy of 37% peroxide carbamide gel mixed with sodium perborate with established intracoronal bleaching agent

Objective. The aim was to evaluate the bleaching efficacy of sodium perborate/37% carbamide peroxide paste and traditional sodium perborate/distilled water for intracoronal bleaching. Study design. Thirty patients with dark anterior teeth were divided into 2 groups (n = 15): group A: sodium perborate/ distilled water; and group B: sodium perborate/37% carbamide peroxide paste. The bleaching treatment limited each patient to the maximum of 4 changes of the bleaching agent. Initial and final color shades were measured using the Vita Lumin shade guide. Results. Data was analyzed with Wilcoxon test for initial and final comparison according to the bleaching agent, demonstrating efficacy of the bleaching treatment with both agents. Mann-Whitney test was used for comparison of the efficacy of the bleaching agents, showing that there was no significant difference between them. Conclusion. The sodium perborate/37% carbamide peroxide association for intracoronal bleaching has proven to be as effective as sodium perborate/distilled water. (Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2009; 107: e43-e47)

Comparison of agar gel immunodiffusion test, rapid slide agglutination test, microbiological culture and PCR for the diagnosis of canine brucellosis

The performance of the rapid slide agglutination test, with and without 2-mercaptoethanol (RSAT and 2ME-RSAT) and agar gel immunodiffusion test (AGID) was evaluated for the diagnosis of brucellosis in naturally infected dogs. The microbiological culture, PCR and clinical parameters were used as reference. A total of 167 dogs were clinically examined and tested by blood culture, culture of semen/vaginal swab and PCR in blood and semen/vaginal swab. According to the results observed the 167 dogs were divided into three groups: Brucella canis infected dogs (Group 1). B. canis non-infected dogs (Group 2) and dogs with suspected brucellosis (Group 3). The dogs were then tested by RSAT, 2ME-RSAT and AGID. Groups 1 and 2 were used to calculate the diagnostic sensitivity and specificity of the serological tests and the results observed in Group 3 were also discussed. The diagnostic sensitivity of RSAT, 2ME-RSAT and AGID was respectively 70.58%, 31.76%, and 52.94%. The diagnostic specificity of RSAT, 2ME-RSAT and AGID was respectively 83.34%, 100%, and 100%. In dogs with suspected brucellosis 15% were RSAT positive, none was 2ME-RSAT positive and 5% were AGID positive. Although the serological tests are the most commonly used methods for brucellosis diagnosis, a significant proportion of false-negative results were observed highlighting the importance of the direct methods of diagnosis, like blood culture and PCR to improve the diagnosis of canine brucellosis. (c) 2008 Elsevier Ltd. All rights reserved.

Numerical simulation of the liquid phase in SnO(2) thin film deposition by sol-gel-dip-coating

The fluid flow of the liquid phase in the sol-gel-dip-coating process for SnO(2) thin film deposition is numerically simulated. This calculation yields useful information on the velocity distribution close to the substrate, where the film is deposited. The fluid modeling is done by assuming Newtonian behavior, since the linear relation between shear stress and velocity gradient is observed. Besides, very low viscosities are used. The fluid governing equations are the Navier-Stokes in the two dimensional form, discretized by the finite difference technique. Results of optical transmittance and X-ray diffraction on films obtained from colloidal suspensions with regular viscosity, confirm the substrate base as the thickest part of the film, as inferred from the numerical simulation. In addition, as the viscosity increases, the fluid acquires more uniform velocity distribution close to the substrate, leading to more homogenous and uniform films.

Tetragonal-cubic phase boundary in nanocrystalline ZrO(2)-Y(2)O(3) solid solutions synthesized by gel-combustion

By means of synchrotron X-ray powder diffraction (SXPD) and Raman spectroscopy, we have detected, in a series of nanocrystalline and compositionally homogeneous ZrO(2)-Y(2)O(3) solid solutions, the presence at room temperature of three different phases depending on Y(2)O(3) content, namely two tetragonal forms and the cubic phase. The studied materials, with average crystallite sizes within the range 7-10 nm, were synthesized by a nitrate-citrate gel-combustion process. The crystal structure of these phases was also investigated by SXPD. The results presented here indicate that the studied nanocrystalline ZrO(2)-Y(2)O(3) solid solutions exhibit the same phases reported in the literature for compositionally homogeneous materials containing larger (micro)crystals. The compositional boundaries between both tetragonal forms and between tetragonal and cubic phases were also determined. (C) 2011 Elsevier B.V. All rights reserved.

Ionization and Structural Changes of the DMPG Vesicle along Its Anomalous Gel-Fluid Phase Transition: A Study with Different Lipid Concentrations

Dispersions of saturated anionic phospholipid dimyristoyl phosphatidylglycerol (DMPG) have been extensively studied regarding their peculiar thermostructural behavior. At low ionic strength, the gel-fluid transition is spread along nearly 17 degrees C, displaying several thermal events in the calorimetric profile that is quite different from the single sharp peak around 23 degrees C found for higher ionic strength DMPG dispersions. To investigate the role of charge in the bilayer transition, we carefully examine the temperature dependence of the electrical conductivity of DMPG dispersions at different concentrations, correlating the data with the corresponding differential scanning calorimetry (DSC) traces. Electrical conductivity together with electrophoretic mobility measurements allowed the calculation of the dependence of the degree of ionization of DMPG vesicles on lipid concentration and temperature. It was shown that there is a decrease in vesicle charge as the lipid concentration increases, which is probably correlated with the increase in the concentration of bulk Na(+). Apart from the known increase in the electrical conductivity along the DMPG temperature transition region, a sharp rise was observed at the bilayer pretransition for all lipid concentrations studied, possibly indicating that the beginning of the chain melting process is associated with an increase in bilayer ionization. It is confirmed here that the gel-fluid transition of DMPG at low ionic strength is accompanied by a huge increase in the dispersion viscosity. However, it is shown that this measured macroviscosity is distinct from the local viscosity felt by either charged ions or DMPG charged aggregates in measurements of electrical conductivity or electrophoretic mobility, Data presented here give support to the idea that DMPG vesicles, at low ionic strength, get more ionized along the temperature transition region and could be perforated and/or deformed vesicle structures.

MRI study of radiation effect on Fricke gel solutions

The quality control optimization of medical processes that use ionizing radiation in the treatment of diseases like cancer is a key element for patient safety and success of treatment. The major medical application of radiation is radiotherapy, i.e. the delivery of dose levels to well-defined target tissues of a patient with the purpose of eliminating a disease. The need of an accurate tumour-edge definition with the purpose of preserving healthy surrounding tissue demands rigorous radiation treatment planning. Dosimetric methods are used for dose distribution mapping region of interest to assure that the prescribed dose and the irradiated region are correct. The Fricke gel (FXG) is the main dosimeter that supplies visualization of the three-dimensional (3D) dose distribution. In this work the dosimetric characteristics of the modified Fricke dosimeter produced at the Radiation Metrology Centre of the Institute of Energetic and Nuclear Research (IPEN) such as gel concentration dose response dependence, xylenol orange addition influence, dose response between 5 and 50Gy and signal stability were evaluated by magnetic resonance imaging (MRI). Using the same gel solution, breast simulators (phantoms) were shaped and absorbed dose distributions were imaged by MRI at the Nuclear Resonance Laboratory of the Physics Institute of Sao Paulo University. (C) 2007 Elsevier Ltd. All rights reserved.

2-(4,5,6,7-tetrafluorobenzimidazol-2-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyl, a hydrogen-bonded organic quasi-1D ferromagnet

The title radical (F4BlmNN) is a stable nitronylnitroxide that forms hydrogen-bonded NH center dot center dot center dot ON chains in the solid state. The chains assemble the F4BlmNN molecules to form stacked contacts between the radical groups, in a geometry that is expected to exhibit ferromagnetic (FM) exchange based on spin polarization (SP) models. The experimental magnetic susceptibility of F4BlmNN confirms the expectation, showing 1-D Heisenberg chain FM exchange behavior over 1.8-300 K with an intrachain exchange constant Of J(chain)/k = +22 K. At lower temperatures, ac magnetic susceptibility and variable field heat capacity measurements show that F4BlmNN acts as a quasi-1-D ferromagnet. The dominant ferromagnetic exchange interaction is attributable to overlap between spin orbitals of molecules within the hydrogen-bonded chains, consistent with the SP model expectations. The chains appear to be antiferromagnetically exchange coupled, giving cusps in the ac susceptibility and zero field heat capacity at lower temperatures. The results indicate that the sample orders magnetically at about 0.7 K. The magnetic heat capacity ordering cusp shifts to lower temperatures as external magnetic field increases, consistent with forming a bulk antiferromagnetic phase below a Neel temperature of T-N(0) = 0.72 K, with a critical field of H-c approximate to 1800 Oe. The interchain exchange is estimated to be zJ/k congruent to (-)0.1 K.

Ab initio study of the EFG at the N sites in imidazole

We study the nuclear quadrupole interaction at the nitrogen sites in the molecular and crystalline phases of the imidazole compound. We use PAW which is a state-of-the-art method to calculate the electronic structure and electric field gradient at the nucleus in the framework of the density functional theory. The quadrupole frequencies at both imino and amino N sites are in excellent agreement with measurements. This is the first time that the electric field gradient at crystalline imidazole is correctly treated by an ab initio theoretical approach.

Elaboration and optimization of (Y,Er)Al(3)(BO(3))(4) glassy planar waveguides through the sol-gel process

In this work, a sol-gel route was used to prepare Y(0.9)Er(0.1)Al(3)(BO(3))(4) glassy thin films by spin-coating technique looking for the preparation and optimization of planar waveguides for integrated optics. The films were deposited on silica and silicon substrates using stable sols synthesized by the sol-gel process. Deposits with thicknesses ranging between 520 and 720 nm were prepared by a multi-layer process involving heat treatments at different temperatures from glass transition to the film crystallization and using heating rates of 2 degrees C/min. The structural characterization of the layers was performed by using grazing incidence X-ray diffraction and Raman spectroscopy as a function of the heat treatment. Microstructural evolution in terms of annealing temperatures was followed by high resolution scanning electron microscopy and atomic force microscopy. Optical transmission spectra were used to determine the refractive index and the film thicknesses through the envelope method. The optical and guiding properties of the films were studied by m-line spectroscopy. The best films were monomode with 620 nm thickness and a refractive index around 1.664 at 980 nm wavelength. They showed good waveguiding properties with high light-coupling efficiency and low propagation loss at 632.8 and 1550 nm of about 0.88 dB/cm. (C) 2009 Elsevier B.V. All rights reserved.

Er:YAl(3)(BO(3))(4) glassy thin films from polymeric precursor and sol-gel methods: Waveguides for integrated optics

This paper presents the characterization of single-mode waveguides for 980 and 1550 nm wavelengths. High quality planar waveguide structure was fabricated from Y(1-x)Er(x)Al(3)(BO(3))(4) multilayer thin films with x = 0.02, 0.05, 0.1, 0.3, and 0.5, prepared through the polymeric precursor and sol-gel methods using spin-coating. The propagation losses of the planar waveguides varying from 0.63 to 0.88 dB/cm were measured at 632.8 and 1550 nm. The photoluminescence spectra and radiative lifetimes of the Er(3+) (4)I(13/2) energy level were measured in waveguiding geometry. For most samples the photoluminescence decay was single exponential with lifetimes in between 640 mu s and 200 mu s, depending on the erbium concentration and synthesis method. These results indicate that Er doped YAl(3)(BO(3))(4) compounds are promising for low loss waveguides. (C) 2009 Elsevier B.V. All fights reserved.

Effect of Lithium Nitrate on the Alkali-Silica Reaction Gel

Lithium nitrate has been used to prevent and to mediate the expansion caused by alkali-silica reaction (ASR). However, there is limited information on how it affects the existing reaction products caused by ASR. The aim of the present work is to determine the modifications caused by the LiNO3 treatment on the structure of the gel produced by ASR. ASR gel samples obtained from a concrete dam were exposed to an aqueous solution of lithium nitrate and sodium hydroxide with molar LiNO3/NaOH = 0.74, and the resulting products were analyzed by X-ray diffraction, infrared spectroscopy, and solid-state nuclear magnetic resonance of Si-29, Na-23, and Li-7. The treatment of the gel samples produces significant structural modifications in ASR products. A new amorphous silicate compound incorporating Li+ ions is formed, with an average silicate network that can be described as linear in contrast with the layered structure of the original gel. This elimination of the layered structure after the Li-based treatments may be related to the reduction of the tendency of the gel to expand. Also, several crystalline compounds containing potassium indicate the release of this species from the original ASR gel.