In silico prediction of prolactin molecules as a tool for equine genomics reproduction.

The prolactin hormone is involved in several biological functions, although its main role resides on reproduction. As it interferes on fertility changes, studies focused on human health have established a linkage of this hormone to fertility losses. Regarding animal research, there is still a lack of information about the structure of prolactin. In case of horse breeding, prolactin has a particular influence; once there is an individualization of these animals and equines are known for presenting several reproductive disorders. As there is no molecular structure available for the prolactin hormone and receptor, we performed several bioinformatics analyses through prediction and refinement softwares, as well as manual modifications. Aiming to elucidate the first computational structure of both molecules and analyse structural and functional aspects related to these proteins, here we provide the first known equine model for prolactin and prolactin receptor, which obtained high global quality scores in diverse software's for quality assessment. QMEAN overall score obtained for ePrl was (- 4.09) and QMEANbrane for ePrlr was (- 8.45), which proves the structures' reliability. This study will implement another tool in equine genomics in order to give light to interactions of these molecules, structural and functional alterations and therefore help diagnosing fertility problems, contributing in the selection of a high genetic herd.

Nanoscale density variations induced by high energy heavy ions in amorphous silicon nitride and silicon dioxide.

The cylindrical nanoscale density variations resulting from the interaction of 185 MeV and 2.2 GeV Au ions with 1.0 µm thick amorphous SiN x :H and SiO x :H layers are determined using small angle x-ray scattering measurements. The resulting density profiles resembles an under-dense core surrounded by an over-dense shell with a smooth transition between the two regions, consistent with molecular-dynamics simulations. For amorphous SiN x :H, the density variations show a radius of 4.2 nm with a relative density change three times larger than the value determined for amorphous SiO x :H, with a radius of 5.5 nm. Complementary infrared spectroscopy measurements exhibit a damage cross-section comparable to the core dimensions. The morphology of the density variations results from freezing in the local viscous flow arising from the non-uniform temperature profile in the radial direction of the ion path. The concomitant drop in viscosity mediated by the thermal conductivity appears to be the main driving force rather than the presence of a density anomaly.

Current approaches to avoid the culling of day-old male chicks in the layer industry, with special reference to spectroscopic methods.

The negative correlation between fattening and laying performance prevents breeding improvement in both laying performance and meat yield. Therefore, specialized chicken lines have been bred in order to achieve either an efficient production of high-quality eggs or high growth rates. As a result, day-old male chicks are culled in the layer hatchery, which poses animal welfare and ethical problems. Breeding companies, scientific groups, and hatcheries are attempting to resolve this issue, with a common aim to find feasible alternatives for the routine killing of male layer chicks. Some approaches aim to influence the sex ratio, while others target at the economically feasible use of the male layer offspring, such as the fattening of "laying hen brothers" or crossbreedings of layers and broilers to create "dual-purpose chickens." Another approach is the sex determination prior to hatch. One of the prerequisites of in ovo sex determination is a practicable method that can be used in industry. The analysis needs to be rapid, cost-efficient, and highly precise; in addition, negative impacts on hatching rate, animal health, and/or performance parameters should be limited. Furthermore, sex determination should be performed before the sensory nervous system's response of the chick embryo to certain or potentially harmful stimuli is developed, which according to current knowledge is before the d 7 of incubation.

Decoupling of ionic conductivity from structural dynamics in polymerized ionic liquids.

Charge transport and structural dynamics in low molecular weight and polymerized 1-vinyl-3-pentylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids (ILs) are investigated by a combination of broadband dielectric spectroscopy, dynamic mechanical spectroscopy and differential scanning calorimetry. While the dc conductivity and fluidity exhibit practically identical temperature dependence for the non-polymerized IL, a significant decoupling of ionic conduction from structural dynamics is observed for the polymerized IL. In addition, the dc conductivity of the polymerized IL exceeds that of its molecular counterpart by four orders of magnitude at their respective calorimetric glass transition temperatures. This is attributed to the unusually high mobility of the anions especially at lower temperatures when the structural dynamics is significantly slowed down. A simple physical explanation of the possible origin of the remarkable decoupling of ionic conductivity from structural dynamics is proposed.

FACS-sorted particles reduce the data variance in optical tweezers-assisted dynamic force spectroscopy measurements.

By combining optical tweezers-assisted dynamic force spectroscopy experiments with fluorescence activated cell sorting (FACS), we demonstrate a new approach to reducing the data variance in measuring receptor-ligand interactions on a single molecule level by ensuring similar coating densities. Therefore, the carboxyfluorescein-labelled monophosphorylated peptide tau226-240[pThr231] is anchored on melamine resin beads and these beads are sorted by FACS to achieve a homogeneous surface coverage. To quantify the impact of the fluorescence dye on the bond parameters between the phosphorylated peptide and the corresponding phosphorylation specific anti-human tau monoclonal antibody HPT-104, we perform dynamic force spectroscopy and compare the results to data using unsorted beads covered with the non-fluorescence peptide analogue. Finally, we demonstrate that the data variance of the relative binding frequency is significantly decreased by a factor of 3.4 using pre-sorted colloids with a homogeneous ligand coating compared to using unsorted colloids.

Lift-off protocols for thin films for use in EXAFS experiments.

Lift-off protocols for thin films for improved extended X-ray absorption fine structure (EXAFS) measurements are presented. Using wet chemical etching of the substrate or the interlayer between the thin film and the substrate, stand-alone high-quality micrometer-thin films are obtained. Protocols for the single-crystalline semiconductors GeSi, InGaAs, InGaP, InP and GaAs, the amorphous semiconductors GaAs, GeSi and InP and the dielectric materials SiO2 and Si3N4 are presented. The removal of the substrate and the ability to stack the thin films yield benefits for EXAFS experiments in transmission as well as in fluorescence mode. Several cases are presented where this improved sample preparation procedure results in higher-quality EXAFS data compared with conventional sample preparation methods. This lift-off procedure can also be advantageous for other experimental techniques (e.g. small-angle X-ray scattering) that benefit from removing undesired contributions from the substrate.

Micro-rheology on (polymer-grafted) colloids using optical tweezers.

Optical tweezers are experimental tools with extraordinary resolution in positioning (± 1 nm) a micron-sized colloid and in the measurement of forces (± 50 fN) acting on it-without any mechanical contact. This enables one to carry out a multitude of novel experiments in nano- and microfluidics, of which the following will be presented in this review: (i) forces within single pairs of colloids in media of varying concentration and valency of the surrounding ionic solution, (ii) measurements of the electrophoretic mobility of single colloids in different solvents (concentration, valency of the ionic solution and pH), (iii) similar experiments as in (i) with DNA-grafted colloids, (iv) the nonlinear response of single DNA-grafted colloids in shear flow and (v) the drag force on single colloids pulled through a polymer solution. The experiments will be described in detail and their analysis discussed.

Role of thermodynamics in the shape transformation of embedded metal nanoparticles induced by swift heavy-ion irradiation.

Swift heavy-ion irradiation of elemental metal nanoparticles (NPs) embedded in amorphous SiO(2) induces a spherical to rodlike shape transformation with the direction of NP elongation aligned to that of the incident ion. Large, once-spherical NPs become progressively more rodlike while small NPs below a critical diameter do not elongate but dissolve in the matrix. We examine this shape transformation for ten metals under a common irradiation condition to achieve mechanistic insight into the transformation process. Subtle differences are apparent including the saturation of the elongated NP width at a minimum sustainable, metal-specific value. Elongated NPs of lesser width are unstable and subject to vaporization. Furthermore, we demonstrate the elongation process is governed by the formation of a molten ion-track in amorphous SiO(2) such that upon saturation the elongated NP width never exceeds the molten ion-track diameter.

Charge transport and dipolar relaxations in imidazolium-based ionic liquids.

Charge transport and dipolar relaxations in a series of imidazolium-based ionic liquids are studied by means of broadband dielectric spectroscopy. Despite the shift of more than 5 decades in the dielectric spectra upon systematic variation of the anion, scaling with respect to the dc conductivities and the characteristic rates yields a collapsing plot. The dielectric spectra are described at higher frequencies in terms of dipolar relaxations whereas hopping conduction in a random spatially varying energy landscape is quantitatively shown to dominate the spectra at lower frequencies. The beta-relaxations observed for both the precursor and the ionic liquids are assigned to librational motion of the imidazolium ring. The corresponding dielectric strength exhibits a strong dependence on the anion.

Ionic concentration- and pH-dependent electrophoretic mobility as studied by single colloid electrophoresis.

Optical tweezers are employed to measure separately the complex electrophoretic mobility of a single colloid and the complex electroosmotic response of the surrounding medium in a specially designed microfluidic cell. Using the very same colloid both quantities are determined in dependence on the concentration of the aqueous salt solution (10 (- 5)-10 (- 1) mol l (- 1)), the valence of the ions (K (+) , Ca(2 +) ) and the pH (2.5-8.5). A pronounced effect is observed for all these examined parameters. The dependence on ion concentration agrees qualitatively-for the monovalent case-with the predictions of the standard electrokinetic model.

Single colloid electrophoresis.

Optical tweezers enable one to trap a single particle without any mechanical contact and to measure its position and the forces acting on it with high resolution (+/-4 nm, +/-160 fN). Taking advantage of a specially designed microfluidic cell the electrophoretic response of the colloid under study and the electroosmotic effect on the surrounding medium are determined using the identical colloid. The former is found to be by more than one order of magnitude larger than the electroosmotic effect. It is shifted in phase with respect to the external field, hence giving rise to a complex electrophoretic mobility which can be theoretically described by a strongly damped driven harmonic oscillator model. By exchanging the medium surrounding the colloid it is possible to deduce the (KCl) concentration dependence of the single colloid electrophoretic response. The results are compared with conventional Zetasizer measurements.

Universal scaling of charge transport in glass-forming ionic liquids.

Charge transport and glassy dynamics of a variety of glass-forming ionic liquids (ILs) are investigated in a wide frequency and temperature range by means of broadband dielectric spectroscopy, differential scanning calorimetry and rheology. While the absolute values of dc conductivity and viscosity vary over more than 11 decades with temperature and upon systematic structural variation of the ILs, quantitative agreement is found between the characteristic frequency of charge transport and the structural alpha-relaxation. This is traced back to dynamic glass transition assisted hopping as the underlying mechanism of charge transport.

First Report of Plasmodiophora brassicae on Rapeseed in the Grand Duchy of Luxembourg.

Rapeseed (Brassica napus L.) is the third most important crop after wheat and barley in the Grand Duchy of Luxembourg. Since 2005, clubroot symptoms in this crop have been reported by farmers in the Gutland Region. In February 2009, plants of the hybrid rapeseed cv. Exocet, with stunted growth, yellow leaves, and club-shaped roots, were sampled from a field in Oberkorn village near Differdange. Microscopic observations of the rapeseed root fragments revealed the presence of the three life stages characteristic of Plasmodiophora brassicae Woronin. Plasmodia and zoosporangia were observed in the root hairs and resting spores were present in root galls. Individual spores were 2 to 3 µm in diameter. Total DNA was extracted from the root galls with a FAST DNA Kit (MP Biomedicals, Irvine, CA). The internal transcribed spacer region (ITS) and 5.8S gene of the rDNA region were amplified with ITS5 and ITS4 primers as described by White et al. (2) and part of this region was sequenced. A BLASTn search in GenBank revealed that the sequence closely resembled (98% identity) sequences of P. brassicae (Genbank Accession No. EF195335) from an isolate of the pathogen from Switzerland. To confirm the presence of the pathogen, seeds of the susceptible ecotype cvi-0 of Arabidopsis thaliana were grown in a soil sample (1 liter) collected near the infected rapeseed plants. After 55 days of growth in a glasshouse at 15 to 20°C, the roots of 11 plants were analyzed. Two showed clear clubroot symptoms and four others exhibited small swellings. The remaining five plants were symptomless, but plasmodia and zoosporangia were found in root hair cells. Clubroot caused by P. brassicae has previously been described on B. napus and other crucifers (1). To our knowledge, this is the first report of clubroot disease caused by P. brassicae in Luxembourg. Because its presence has since been observed in new fields in the Gutland Region and because of the ability of the pathogen to survive for a long period in the soil, this disease could represent a severe threat for cropping of Brassicaceae in Luxembourg and neighboring countries. References: (1) I. R. Crute et al. Plant Breed. Abstr. 50:91, 1980. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic press: San Diego, 1990.

The glass transition of thin polymer films in relation to the interfacial dynamics.

As opposed to measurements on the glass transition of a polymer in the bulk, measurements of thin polymer layers reflect--due to the alterations of the glassy dynamics at the confining interfaces--several contributions acting together to give the net response of a polymer film. This fundamental difference is exemplified in detail for the particular case of broadband dielectric spectroscopy, an experimental tool extensively employed to investigate the glassy dynamics of polymers under condition of geometrical confinement.

Charge transport and glassy dynamics in imidazole-based liquids.

Broadband dielectric spectroscopy, differential scanning calorimetry, rheology, and pulsed field gradient-nuclear magnetic resonance (PFG NMR) are combined to study glassy dynamics and charge transport in a homologous series of imidazole-based liquids with systematic variation of the alkyl chain length. The dielectric spectra are interpreted in terms of dipolar relaxation and a conductivity contribution. By applying the Einstein, Einstein-Smoluchowski, and Stokes-Einstein relations, translational diffusion coefficients--in quantitative agreement with PFG NMR measurements--are obtained. With increasing alkyl chain length, it is observed that the viscosity increases, whereas the structural alpha-relaxation rate decreases, in accordance with Maxwell's relation. Between the rate omega(e) of electrical relaxation and the rate omega(alpha) of the structural alpha-relaxation, scaling is observed over more than six decades with a decoupling index of about 2.

Charge transport and mass transport in imidazolium-based ionic liquids.

The mechanism of charge transport in the imidazolium-based ionic liquid 1,3-dimethylimidazolium dimethylphosphate is analyzed by combining broadband dielectric spectroscopy (BDS) and pulsed field gradient nuclear magnetic resonance (PFG NMR). The dielectric spectra are dominated-on the low-frequency side-by electrode polarization effects while, for higher frequencies, charge transport in a disordered matrix is the underlying physical mechanism. Using the Einstein and Einstein-Smoluchowski equations enables one to determine-in excellent agreement with direct measurements by PFG NMR-the diffusion coefficient of the charge carriers. By that, it becomes possible to extract from the dielectric spectra separately the number density and the mobilities of the charge carriers and the type of their thermal activation. It is shown that the observed Vogel-Fulcher-Tammann (VFT) dependence of the dc conductivity can be traced back to a similar temperature dependence of the mobility while for the number density an Arrhenius-type thermal activation is found. Extrapolating the latter to room temperature indicates that nearly all charge carriers are participating in the conduction process.

Electrical conductivity and translational diffusion in the 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid.

Broadband dielectric and terahertz spectroscopy (10(-2)-10(+12) Hz) are combined with pulsed field gradient nuclear magnetic resonance (PFG-NMR) to explore charge transport and translational diffusion in the 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid. The dielectric spectra are interpreted as superposition of high-frequency relaxation processes associated with dipolar librations and a conductivity contribution. The latter originates from hopping of charge carriers on a random spatially varying potential landscape and quantitatively fits the observed frequency and temperature dependence of the spectra. A further analysis delivers the hopping rate and enables one to deduce--using the Einstein-Smoluchowski equation--the translational diffusion coefficient of the charge carriers in quantitative agreement with PFG-NMR measurements. By that, the mobility is determined and separated from the charge carrier density; for the former, a Vogel-Fulcher-Tammann and for the latter, an Arrhenius temperature dependence is obtained. There is no indication of a mode arising from the reorientation of stable ion pairs.

Broadband dielectric studies on the interfacial dynamics enabled by use of nanostructured electrodes.

By employing silica nanostructures as spacers, an experimental approach is developed to enable one broadband dielectric measurements on the molecular dynamics taking place in the immediate (nanometric) vicinity of solid interfaces. This development renders to broadband dielectric spectroscopy--traditionally a bulk technique--the character of an interfacial method.

Structure-property relationships in major ampullate spider silk as deduced from polarized FTIR spectroscopy.

Polarized Fourier Transform Infrared (FTIR) spectroscopy is employed to study structure-property relationships in major ampullate spider silk being exposed to an external mechanical strain. From the measured infrared dichroism of aminoacid-residue - specific bands the molecular order parameter, the frequency width at half-maximum (FWHM) and the spectral position of the absorption maximum are determined in dependence on the external strain. For the highly ordered alanine-rich beta sheets a change in the vibrational potential is found for macroscopic strains as low as a few percent. It can be quantitatively described by a quantum-mechanical approach in which the mechanical strain is treated as a weak external perturbation. The immediate microscopic response to the external field proves that beta -sheeted crystals are tightly interconnected by pre-stretched chains as suggested recently (Y. Liu et al., Nat. Mater. 4, 901 (2005)).

Forces between single pairs of charged colloids in aqueous salt solutions.

Forces between single pairs of negatively charged micrometer-sized colloids in aqueous solutions of monovalent, divalent, or trivalent counter-ions at varying concentrations have been measured by employing optical tweezers. The experimental data have been analyzed by using the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory and a numerical solution of the Poisson-Boltzmann (PB) equation. With monovalent counterions, the data are well described by the DLVO and PB theories, suggesting that the DLVO theory is adequate to describe the colloidal forces at these conditions. At higher counter-ion valence, the approximations within the two theories become evident.