Single nucleotide polymorphism analysis by allele-specific primer extension with real-time bioluminescence detection in a microfluidic device

A microfluidic approach for rapid bioluminescent real-time detection of single nucleotide polymorphism (SNP) is presented. The method is based on single-step primer extension using pyrosequencing chemistry to monitor nucleotide incorporations in real-time. The method takes advantage of the fact that the reaction kinetics differ between matched and mismatched primer-template configurations. We show here that monitoring the initial reaction in real time accurately scores SNPs by comparing the initial reaction kinetics between matched and mismatched configurations. Thus, no additional treatment is required to improve the sequence specificity of the extension, which has been the case for many allele-specific extension assays. The microfluidic approach was evaluated using four SNPs. Three of the SNPs included primer-template configurations that have been previously reported to be difficult to resolve by allele-specific primer extension. All SNPs investigated were successfully scored. Using the microfluidic device, the volume for the bioluminescent assay was reduced dramatically, thus offering a cost-effective and fast SNP analysis method.     

Identification of extracellular nanoparticle subsets by nuclear magnetic resonance

Exosomes are a subset of secreted lipid envelope-encapsulated extracellular vesicles (EVs) of 50–150 nm diameter that can transfer cargo from donor to acceptor cells. In the current purification protocols of exosomes, many smaller and larger nanoparticles such as lipoproteins, exomers and microvesicles are typically co-isolated as well. Particle size distribution is one important characteristics of EV samples, as it reflects the cellular origin of EVs and the purity of the isolation. However, most of the physicochemical analytical methods today cannot illustrate the smallest exosomes and other small particles like the exomers. Here, we demonstrate that diffusion ordered spectroscopy (DOSY) nuclear magnetic resonance (NMR) method enables the determination of a very broad distribution of extracellular nanoparticles, ranging from 1 to 500 nm. The range covers sizes of all particles included in EV samples after isolation. The method is non-invasive, as it does not require any labelling or other chemical modification. We investigated EVs secreted from milk as well as embryonic kidney and renal carcinoma cells. Western blot analysis and immuno-electron microscopy confirmed expression of exosomal markers such as ALIX, TSG101, CD81, CD9, and CD63 in the EV samples. In addition to the larger particles observed by nanoparticle tracking analysis (NTA) in the range of 70–500 nm, the DOSY distributions include a significant number of smaller particles in the range of 10–70 nm, which are visible also in transmission electron microscopy images but invisible in NTA. Furthermore, we demonstrate that hyperpolarized chemical exchange saturation transfer (Hyper-CEST) with ¹²⁹Xe NMR indicates also the existence of smaller and larger nanoparticles in the EV samples, providing also additional support for DOSY results. The method implies also that the Xe exchange is significantly faster in the EV pool than in the lipoprotein/exomer pool.

Diffusion and xenon NMR based methods to determine a very broad range of sizes and sub-sets of extracellular vesicles.     

Domino "[3+3]-cyclization-homo-Michael" reactions of 1,3-bissilyl enol ethers with 1,1-diacylcyclopropanes

The Lewis acid mediated domino "[3+3]-cyclization-homo-Michael" reaction of 1,3-bissilyl enol ethers with 1,1-diacylcyclopropanes allows an efficient one-pot synthesis of functionalized salicylates containing a halogenated side chain. A great variety of substitution patterns could be realized by variation of the starting materials and of the Lewis acid. The mechanism of the domino process was studied.     

Simultaneous determination of perfluoroalkyl phosphonates, carboxylates, and sulfonates in drinking water

A trace analytical method based on high performance liquid chromatography coupled to quadrupole time-of-flight high resolution mass spectrometry was developed for simultaneous determination of perfluoroalkyl phosphonates (PFPAs, carbon chain lengths C6,8,10), perfluoroalkyl carboxylates (PFCAs, C5-12), and perfluoroalkyl sulfonates (PFSAs, C4,6,8,10) in drinking water (tap water). Analytes were enriched on a mixed mode co-polymeric sorbent (C8+quaternary amine) using solid phase extraction. Chromatographic separation was achieved on a Zorbax Extend C18 reversed phase column using a mobile phase gradient consisting of water, methanol, and acetonitrile containing 2mM ammonium acetate and 5 mM 1-methyl piperidine. The mass spectrometer was operated in electrospray negative ion mode. Use of 1-methyl piperidine in the mobile phase resulted in a significant increase in instrument sensitivity for PFPAs through improved chromatographic resolution, background suppression, and increased ionization efficiency. Method detection limits for extraction of 500 mL tap water were in the ranges of 0.095-0.17 ng/L, 0.027-0.17 ng/L, and 0.014-0.052 ng/L for PFPAs, PFCAs, and PFSAs, respectively. Whole method recoveries at a spiking level of 0.5 ng/L to 500 mL HPLC grade water were 40-56%, 56-97%, and 55-77% for PFPAs, PFCAs, and PFSAs, respectively. A matrix effect (signal enhancement) was observed in the detection of PFPAs in tap water extracts, leading to calculated recoveries of 249-297% at a 0.5 ng/L spiking level. This effect resulted in an additional improvement of method sensitivity for PFPAs. To compensate for the matrix effect, PFPAs in tap water were quantified using matrix-matched and extracted calibration standards. The method was successfully applied to the analysis of drinking water collected from six European countries. PFPAs were not detected except for perfluorooctyl phosphonate (PFOPA) at close to the detection limit of 0.095 ng/L in two water samples from Amsterdam, the Netherlands. Highest levels were found for perfluorobutane sulfonate (PFBS, 18.8 ng/L) and perfluorooctanoate (PFOA, 8.6 ng/L) in samples from Amsterdam as well as for perfluorooctane sulfonate (PFOS, 8.8 ng/L) in tap water from Stockholm, Sweden.     

Unsteady incompressible flow of magnetized aluminium oxide and titanium oxide nanoparticles with blood base fluid

In this investigation, a mixed convective nanoparticles fluid flow over an inclined plate is deliberated. The effects of slip boundary wall and magnetic field are also considered. The dimensionless governing system for the considered problem is attained by implementing recent definitions of fractional derivatives (FD). The generalized solution is obtained through the Laplace Transformation Scheme (LTS) for the momentum and thermal expressions. To improve the novelty and to demonstrate some more physical perception of the stated research work, some remarkable special cases of velocity distribution through CF and AB-fractional derivative concept are addressed, whose daily life implication is well known in the existing literature. Moreover, to evaluate the physical interest of the stated problem, the outcomes of the obtained system graphical illustrations are made by utilizing MATHEMATICA. As a result, we concluded that the aluminium oxide $A{l}_2{O}_3$ nanoparticles show more decaying behavior as compared to titanium oxide $Ti{O}_2$ nanoparticles for temperature and velocity profile. Furthermore, both fields i.e., momentum and thermal distributions are increased with the help of rising estimations parameter. Current results report novel applications in enhancement of heat transfer, thermal engineering, chemical processes, engineering and electronics devices, solar systems, extrusion processes, fission reactions etc.     

Hall effects and entropy generation applications for peristaltic flow of modified hybrid nanofluid with electroosmosis phenomenon

The electroosmotic peristaltic flow of modified hybrid nanofluid in presence of entropy generation has been presented in this thermal model. The Hall impact and thermal radiation with help of nonlinear relations has also been used to modify the analysis. The assumed flow is considered due to a non-uniform trapped channel. The properties of modified hybrid nanofluid model are focused with interaction of three distinct types of nanoparticles namely copper ($Cu)$, silver ($Ag$) and aluminum oxide ($A{l}_2{O}_3).$ The mathematical modeling and significances of entropy generation and Bejan number are identified. With certain flow assumptions, the governing equations are attained for optimized peristaltic electroosmotic problem. Widely used assumptions of long wave length and low Reynolds number reduced the governing equations in ordinary differential equations. The ND solver is flowed for the solution process. The physical significant of results is observed by assigning the numerical values to parameters.     

Neutron induced radiography in the determination of boron in drinking water

Neutron induced radiography has been applied to the determination of boron concentrations in drinking water, collected from natural springs of Reshian and Muzaffarabad areas of Azad Kashmir, Pakistan, using CR-39 etched track detectors. The technique is based upon the simultaneous irradiation with thermal neutrons of a sample of unknown concentration and a standard of known boron concentration, fixed on a track detector. The subsequent counting of alpha and ⁷Li tracks in the detector resulting from the ¹⁰B(n,)⁷Li nuclear reaction is done after chemical etching. Boron concentration in the sample is determined by comparing ⁷Li and alpha-particle track density with that of a standard of known boron concentration. Boron concentrations in drinking water samples from Muzaffarabad and Reshian area of Azad Kashmir have been found to vary from (0.054±0.001) mg/l to (0.250±0.004) mg/l with an average of (0.16±0.002) mg/l. The observed concentration of boron in drinking water has been found to be less than the provisional Maximum Acceptable Concentration level (0.4 mg//l) of WHO. The drinking water from the reported area has been found to be within safe limits as far as boron related health hazards are concerned.This revised version was published online in November 2005 with corrections to the Cover Date.     

Synthesis, crystal structure, antimicrobial activity and DNA-binding of hydrogen-bonded proton-transfer complex of 2,6-diaminopyridine with picric acid

A proton-transfer (charge transfer) complex formed on the reaction between 2,6-diaminopyridine (donor) and picric acid (acceptor) was synthesized and characterized by FTIR, (1)H NMR, thermal and elemental analysis. The crystal structure determined by single-crystal X-ray diffraction indicates that cation and anion are joined together by strong N(+)-H- -O(-) type hydrogen bonds. The hydrogen-bonded charge transfer (HBCT) complex was screened for its pharmacology such as antimicrobial activity against various fungal and bacterial strains and Calf thymus DNA-binding. The results showed that HBCT complex (100μg/ml) exhibited good antibacterial antifungal activity as that of standard antibiotics Tetracycline and Nystatin. A molecular frame work through H-bonding interactions between neighboring moieties is found to be responsible for high melting point of resulting complex. This has been attributed to the formation of 1:1 HBCT complex.     

Quartic equations and classification of Riemann tensors in general relativity

For space-times in general relativity, the Petrov classification of the Weyl conformai curvature and the Plebaski or Segre classification of the Ricci tensor each depend on the properties of the roots of quartic equations. The coefficients in these quartic equations are in general complicated functions of the space-time coordinates. We review the general theory of quartic equations, and discuss algorithms for determining the existence and values of multiple roots. We consider practical implementation of an algorithm and the consequent Petrov classification. Tests of programs embodying this algorithm, using the computer algebra system CLASSI based on SHEEP, are reported.     

Variational spiked oscillator

A variational analysis of the spiked harmonic oscillator Hamiltonian –d ²/dr² +r ² +/r ^5/2,>0, is reported. A trial function automatically satisfying both the Dirichlet boundary condition at the origin and the boundary condition at infinity is introduced. The results are excellent for a very large range of values of the coupling parameter, suggesting that the present variational function is appropriate for the treatment of the spiked oscillator in all its regimes (strong, moderate, and weak interactions).