A polymerase chain reaction-based method for isolating clones from a complimentary DNA library in sheep

The sheep (Ovis aries) is favored by many musculoskeletal tissue engineering groups as a large animal model because of its docile temperament and ease of husbandry. The size and weight of sheep are comparable to humans, which allows for the use of implants and fixation devices used in human clinical practice. The construction of a complimentary DNA (cDNA) library can capture the expression of genes in both a tissue- and time-specific manner. cDNA libraries have been a consistent source of gene discovery ever since the technology became commonplace more than three decades ago. Here, we describe the construction of a cDNA library using cells derived from sheep bones based on the pBluescript cDNA kit. Thirty clones were picked at random and sequenced. This led to the identification of a novel gene, C12orf29, which our initial experiments indicate is involved in skeletal biology. We also describe a polymerase chain reaction-based cDNA clone isolation method that allows the isolation of genes of interest from a cDNA library pool. The techniques outlined here can be applied in-house by smaller tissue engineering groups to generate tools for biomolecular research for large preclinical animal studies and highlights the power of standard cDNA library protocols to uncover novel genes.

Fourier spectral methods for fractional-in-space reaction-diffusion equations

Fractional differential equations are becoming increasingly used as a powerful modelling approach for understanding the many aspects of nonlocality and spatial heterogeneity. However, the numerical approximation of these models is demanding and imposes a number of computational constraints. In this paper, we introduce Fourier spectral methods as an attractive and easy-to-code alternative for the integration of fractional-in-space reaction-diffusion equations described by the fractional Laplacian in bounded rectangular domains ofRn. The main advantages of the proposed schemes is that they yield a fully diagonal representation of the fractional operator, with increased accuracy and efficiency when compared to low-order counterparts, and a completely straightforward extension to two and three spatial dimensions. Our approach is illustrated by solving several problems of practical interest, including the fractional Allen–Cahn, FitzHugh–Nagumo and Gray–Scott models, together with an analysis of the properties of these systems in terms of the fractional power of the underlying Laplacian operator.

Double diffusive Marangoni convection flow of electrically conducting fluid in a square cavity with chemical reaction

Double diffusive Marangoni convection flow of viscous incompressible electrically conducting fluid in a square cavity is studied in this paper by taking into consideration of the effect of applied magnetic field in arbitrary direction and the chemical reaction. The governing equations are solved numerically by using alternate direct implicit (ADI) method together with the successive over relaxation (SOR) technique. The flow pattern with the effect of governing parameters, namely the buoyancy ratio W, diffusocapillary ratio w, and the Hartmann number Ha, is investigated. It is revealed from the numerical simulations that the average Nusselt number decreases; whereas the average Sherwood number increases as the orientation of magnetic field is shifted from horizontal to vertical. Moreover, the effect of buoyancy due to species concentration on the flow is stronger than the one due to thermal buoyancy. The increase in diffusocapillary parameter, w caus

TMIO-pyrimid hybrids are profluorescent, site-directed spin labels for nucleic acids

We report the synthesis of a new class of molecules which are hybrids of long-lived tetramethylisoindolinoxyl (TMIO) radicals and the pyrido[1,2-a]benzimidazole (PyrImid) scaffold. These compounds represent a new lead for noncovalently binding nucleic acid probes, as they interact with nucleic acids with previously unreported C (DNA) and C/U (RNA) complementarity, which can be detected by electron paramagnetic resonance (EPR) techniques. They also have promising properties for fluorimetric analysis, as their fluorescent spin-quenched derivatives exhibit a significant Stokes shift

Unimolecular reaction chemistry of a charge-tagged beta-hydroxyperoxyl radical

β-Hydroxyperoxyl radicals are formed during atmospheric oxidation of unsaturated volatile organic compounds such as isoprene. They are intermediates in the combustion of alcohols. In these environments the unimolecular isomerization and decomposition of β-hydroxyperoxyl radicals may be of importance, either through chemical or thermal activation. We have used ion-trap mass spectrometry to generate the distonic charge-tagged β-hydroxyalkyl radical anion, ˙CH2C(OH)(CH3)CH2C(O)O−, and investigated its subsequent reaction with O2 in the gas phase under conditions that are devoid of complicating radical–radical reactions. Quantum chemical calculations and master equation/RRKM theory modeling are used to rationalize the results and discern a reaction mechanism. Reaction is found to proceed via initial hydrogen abstraction from the γ-methylene group and from the β-hydroxyl group, with both reaction channels eventually forming isobaric product ions due to loss of either ˙OH + HCHO or ˙OH + CO2. Isotope labeling studies confirm that a 1,5-hydrogen shift from the β-hydroxyl functionality results in a hydroperoxyalkoxyl radical intermediate that can undergo further unimolecular dissociations. Furthermore, this study confirms that the facile decomposition of β-hydroxyperoxyl radicals can yield ˙OH in the gas phase.

A stochastic exponential Euler scheme for simulation of stiff biochemical reaction systems

In order to simulate stiff biochemical reaction systems, an explicit exponential Euler scheme is derived for multidimensional, non-commutative stochastic differential equations with a semilinear drift term. The scheme is of strong order one half and A-stable in mean square. The combination with this and the projection method shows good performance in numerical experiments dealing with an alternative formulation of the chemical Langevin equation for a human ether a-go-go related gene ion channel mode

Revisiting the CO oxidation reaction on various Au/TiO2catalysts: Roles of the surface OH groups and the reaction mechanism

This work aims to understand the influence of TiO2 surface structure in Au/TiO2 catalysts on CO oxidation. Au nanoparticles (3 wt%) in the range of 4 to 8 nm were loaded onto four kinds of TiO2 surfaces, which had different surface structures and were synthesized by calcining hydrogen titanate nanotubes at various temperatures and in different atmospheres. The Au catalyst supported on anatase nanorods exhibited the highest activity in CO oxidation at 30 °C among all the five Au/TiO2 catalysts including the reference catalyst of Au/TiO2-P25. X-ray photoelectron spectroscopy (XPS) and infrared emission spectra (IES) results indicate that the anatase nanorods have the most active surface on which water molecules can be strongly adsorbed and OH groups can be formed readily. Theoretical calculation indicates that the surface OH can facilitate the O2 adsorption on the anatase surface. Such active surface features are conducive to the O2 activation and CO oxidation

Combining the diaza-Diels-Alder reaction and palladium-catalyzed aminations to prepare amino-substituted porphyrins

A strategy to tackle the synthesis of azoporphyrins with unsubstituted terminal meso positions was investigated. It comprised the combination of diaza-Diels–Alder (DADA) reaction of 1,3-dienes with dialkyl azodicarboxylates, decarboxylative hydrolysis of the bis(carbamates), palladium-catalyzed amination of bromoporphyrin precursors, and retro-DADA reactions to release the ultimate targets. The somewhat confused historical results on the DADA reactions of 1,3-cyclohexadiene were clarified, but the hydrolyses yielded extremely air-sensitive amines which decomposed completely in minutes via autooxidation and retro-DADA reaction. With anthracene or 2,3-dimethyl-1,3-butadiene as the diene, the synthesis of azoporphyrin was not achieved but three amino-substituted porphyrins were obtained in moderate yields under mild conditions. The X-ray crystal structures of several of the intermediates and the final aminoanthracene-porphyrin nickel(II) complex were determined.

Probabilistic assessment of herbicide runoff from Japanese rice paddies: The effects of local meteorological conditions and site-specific water management

Uncertainty assessments of herbicide losses from rice paddies in Japan associated with local meteorological conditions and water management practices were performed using a pesticide fate and transport model, PCPF-1, under the Monte Carlo (MC) simulation scheme. First, MC simulations were conducted for five different cities with a prescribed water management scenario and a 10-year meteorological dataset of each city. The effectiveness of water management was observed regarding the reduction of pesticide runoff. However, a greater potential of pesticide runoff remained in Western Japan. Secondly, an extended analysis was attempted to evaluate the effects of local water management and meteorological conditions between the Chikugo River basin and the Sakura River basin using uncertainty inputs processed from observed water management data. The results showed that because of more severe rainfall events, significant pesticide runoff occurred in the Chikugo River basin even when appropriate irrigation practices were implemented. © Pesticide Science Society of Japan.

Site and gender specificity of inheritance of bone mineral density

Differences in genetic control of BMD by skeletal sites and genders were examined by complex segregation analysis in 816 members of 147 families with probands with extreme low BMD. Spine BMD correlated more strongly in male-male comparisons and hip BMD in female-female comparisons, consistent with gender- and site-specificity of BMD heritability. Introduction: Evidence from studies in animals and humans suggests that the genetic control of bone mineral density (BMD) may differ at different skeletal sites and between genders. This question has important implications for the design and interpretation of genetic studies of osteoporosis. Methods: We examined the genetic profile of 147 families with 816 individuals recruited through probands with extreme low BMD (T-score < −2.5, Z-score < −2.0). Complex segregation analysis was performed using the Pedigree Analysis Package. BMD was measured by DXA at both lumbar spine (L1-L4) and femoral neck. Results: Complex segregation analysis excluded purely monogenic and environmental models of segregation of lumbar spine and femoral neck BMD in these families. Pure polygenic models were excluded at the lumbar spine when menopausal status was considered as a covariate, but not at the femoral neck. Mendelian models with a residual polygenic component were not excluded. These models were consistent with the presence of a rare Mendelian genotype of prevalence 3–19 %, causing high BMD at the hip and spine in these families, with additional polygenic effects. Total heritability range at the lumbar spine was 61–67 % and at the femoral neck was 44–67 %. Significant differences in correlation of femoral neck and lumbar spine BMD were observed between male and female relative pairs, with male-male comparisons exhibiting stronger lumbar spine BMD correlation than femoral neck, and female-female comparisons having greater femoral neck BMD correlation than lumbar spine. These findings remained true for parent-offspring correlations when menopausal status was taken into account. The recurrence risk ratio for siblings of probands of a Z-score < −2.0 was 5.4 at the lumbar spine and 5.9 at the femoral neck. Conclusions: These findings support gender- and site-specificity of the inheritance of BMD. These results should be considered in the design and interpretation of genetic studies of osteoporosis.

Site-controlled growth of Ge nanostructures on Si(100) via pulsed laser deposition nanostenciling

The authors combine nanostenciling and pulsed laser deposition to patterngermanium(Ge)nanostructures into desired architectures. They have analyzed the evolution of the Ge morphology with coverage. Following the formation of a wetting layer within each area defined by the stencil’s apertures, Gegrowth becomes three dimensional and the size and number of Ge nanocrystals evolve with coverage. Micro-Raman spectroscopy shows that the deposits are crystalline and epitaxial. This approach is promising for the parallel patterning of semiconductor nanostructures for optoelectronic applications.

In situ reaction furnace for real-time XRD studies

The new furnace at the Materials Characterization by X-ray Diffraction beamline at Elettra has been designed for powder diffraction measurements at high temperature (up to 1373 K at the present state). Around the measurement region the geometry of the radiative heating element assures a negligible temperature gradient along the capillary and can accommodate either powder samples in capillary or small flat samples. A double capillary holder allows flow-through of gas in the inner sample capillary while the outer one serves as the reaction chamber. The furnace is coupled to a translating curved imaging-plate detector, allowing the collection of diffraction patterns up to 2[theta] [asymptotically equal to] 130°.

Artificial Neural Network Based Automatic Emergency Landing Site Selection for UAVs and Highly Automated Aircraft

In this report an artificial neural network (ANN) based automated emergency landing site selection system for unmanned aerial vehicle (UAV) and general aviation (GA) is described. The system aims increase safety of UAV operation by emulating pilot decision making in emergency landing scenarios using an ANN to select a safe landing site from available candidates. The strength of an ANN to model complex input relationships makes it a perfect system to handle the multicriteria decision making (MCDM) process of emergency landing site selection. The ANN operates by identifying the more favorable of two landing sites when provided with an input vector derived from both landing site's parameters, the aircraft's current state and wind measurements. The system consists of a feed forward ANN, a pre-processor class which produces ANN input vectors and a class in charge of creating a ranking of landing site candidates using the ANN. The system was successfully implemented in C++ using the FANN C++ library and ROS. Results obtained from ANN training and simulations using randomly generated landing sites by a site detection simulator data verify the feasibility of an ANN based automated emergency landing site selection system.

Metal-free graphitic carbon nitride as mechano-catalyst for hydrogen evolution reaction

Graphitic carbon nitride (g-C3N4), as a promising metal-free catalyst for photo-catalytic and electrochemical water splitting, has recently attracted tremendous research interest. However, the underlying catalytic mechanism for the hydrogen evolution reaction (HER) is not fully understood. By using density functional theory calculations, here we have established that the binding free energy of hydrogen atom (ΔGH∗0) on g-C3N4 is very sensitive to mechanical strain, leading to substantial tuning of the HER performance of g-C3N4 at different coverages. The experimentally-observed high HER activity in N-doped graphene supported g-C3N4 (Zheng et al., 2014) is actually attributed to electron-transfer induced strain. A more practical strategy to induce mechanical strain in g-C3N4 is also proposed by doping a bridge carbon atom in g-C3N4 with an isoelectronic silicon atom. The calculated ΔGH∗0 on the Si-doped g-C3N4 is ideal for HER. Our results indicate that g-C3N4 would be an excellent metal-free mechano-catalyst for HER and this finding is expected to guide future experiments to efficiently split water into hydrogen based on the g-C3N4 materials.

Ultrafast and reversible multiblock formation by the SET-Nitroxide radical coupling reaction

The single electron transfer-nitroxide radical coupling (SET-NRC) reaction has been used to produce multiblock polymers with high molecular weights in under 3 min at 50◦C by coupling a difunctional telechelic polystyrene (Br-PSTY-Br)with a dinitroxide. The well known combination of dimethyl sulfoxide as solvent and Me6TREN as ligand facilitated the in situ disproportionation of CuIBr to the highly active nascent Cu0 species. This SET reaction allowed polymeric radicals to be rapidly formed from their corresponding halide end-groups. Trapping of these carbon-centred radicals at close to diffusion controlled rates by dinitroxides resulted in high-molecular-weight multiblock polymers. Our results showed that the disproportionation of CuI was critical in obtaining these ultrafast reactions, and confirmed that activation was primarily through Cu0. We took advantage of the reversibility of the NRC reaction at elevated temperatures to decouple the multiblock back to the original PSTY building block through capping the chain-ends with mono-functional nitroxides. These alkoxyamine end-groups were further exchanged with an alkyne mono-functional nitroxide (TEMPO–≡) and ‘clicked’ by a CuI-catalyzed azide/alkyne cycloaddition (CuAAC) reaction with N3–PSTY–N3 to reform the multiblocks. This final ‘click’ reaction, even after the consecutive decoupling and nitroxide-exchange reactions, still produced high molecular-weight multiblocks efficiently. These SET-NRC reactions would have ideal applications in re-usable plastics and possibly as self-healing materials.