Separation performance of single-stranded DNA electrophoresis in photopolymerized cross-linked polyacrylamide gels

Considerable effort has been directed toward optimizing performance and maximizing throughput in ssDNA electrophoresis because it is a critical analytical step in a variety of genomic assays. Ultimately, it would be desirable to quantitatively determine the achievable level of separation resolution directly from measurements of fundamental physical properties associated with the gel matrix rather than by the trial and error process often employed. Unfortunately, this predictive capability is currently lacking, due in large part to the need for a more detailed understanding of the fundamental parameters governing separation performance (mobility, diffusion, and dispersion). We seek to address this issue by systematically characterizing electrophoretic mobility, diffusion, and dispersion behavior of ssDNA fragments in the 70-1,000 base range in a photopolymerized cross-linked polyacrylamide matrix using a slab gel DNA sequencer. Data are collected for gel concentrations of 6, 9, and 12%T at electric fields ranging from 15 to 40 V/cm, and resolution predictions are compared with corresponding experimentally measured values. The data exhibit a transition from behavior consistent with the Ogston model for small fragments to behavior in agreement with the biased reptation model at larger fragment sizes. Mobility data are also used to estimate the mean gel pore size and compare the predictions of several models.     

Effect of photonic crystal structure on the nonlinear optical anisotropy of birefringent porous silicon

Anisotropic photonic crystal structures consisting of birefringent porous silicon layers with alternating porosity were fabricated. The in-plane birefringence formed as a result of anisotropic etching in Si(110) results in unique multilayered structures with two distinct photonic bandgaps for orthogonal light polarizations. Nonlinear optical studies based on the third-harmonic generation from these structures demonstrate variation in the symmetry of the nonlinear optical response.     

Toward Tailor‐Made Biocide Materials Based on Poly(propylene)/Copper Nanoparticles

A set of poly(propylene) composites containing different amounts of copper nanoparticles (CNP) were prepared by the melt mixed method and their antimicrobial behavior was quantitatively studied. The time needed to reduce the bacteria to 50% dropped to half with only 1 v/v % of CNP, compared to the polymer without CNP. After 4 h, this composite killed more than 99.9% of the bacteria. The biocide kinetics can be controlled by the nanofiller content; composites with CNP concentrations higher than 10 v/v % eliminated 99% of the bacteria in less than 2 h. X‐ray photoelectron spectroscopy did not detect CNP at the surface, therefore the biocide behavior was attributed to copper in the bulk of the composite.

     

Air-related mechanisms of noise generation by solid rubber tyres with cavities

There are four main air-related noise generation mechanisms at the tyre/road interface, which were all categorised more than 20 years ago. The first one is the so-called ‘air pumping’ mechanism. Two other air-related phenomena that occur when there are air movements near the contact patch of the tyre are ‘air resonant radiation’ and ‘pipe resonances’ which appear at the footprint of the tyre. In addition to these, there is a forth effect, which is mentioned in the literature, that is occurring due to turbulence effects of the air surrounding the spinning tyre. There has been less focus on the air-related mechanisms than on other types of tyre noise generation mechanisms. This paper attempts to add some detail to current understanding of the air-related noise generation at the tyre road interface and gives some further information on how to identify the differences due to these mechanisms. Specifically in the present paper, a solid rubber tyre running on a vehicle chassis dynamometer is used to study the first two mechanisms. This is done with emphasis on the time history of the recorded signal and not on the frequency spectrum, as is more commonly used. A comparison with existing theoretical models of these mechanisms reveals some of the strength and weaknesses of the current understanding of these phenomena.     

On the constitutive inequalities and acceleration waves in micropolar media

Acceleration waves in nonlinear thermoelastic micropolar media are considered. We establish the kinematic and dynamic compatibility relations for a singular surface of order 2 in the media. An analogy to the Fresnel–Hadamard–Duhem theorem and an expression for the acoustic tensor are derived. The condition for acceleration wave's propagation is formulated as an algebraic spectral problem. It is shown that the condition coincides with the strong ellipticity of equilibrium equations. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Adsorption Reaction Dynamics of Systems Lysozyme and Nanodiamond/Nanosilica at pH=7-13

Adsorption reactions between surfaces of nanodiamond and nanosilica with diameter of 100 nm prepared as suspension solutions of 0.25 μg/μL and lysozyme molecule with different concentrations of 7 mmol/L PPBS at pH=7, 9, 11, and 13 have been investigated by fluores-cence spectroscopy. Adsorption reaction constants and coverages of lysozyme with different concentrations of 0-1000 nmol/L under the influences of different pH values have been ob-tained. Helicities and conformations of the adsorbed lysozyme molecules, free spaces of every adsorbed lysozyme molecule on the surfaces of nanoparticles at different concentrations and pH values have been deduced and discussed. The highest adsorption capabilities for both sys-tems and conformational efficiency of the adsorbed lysozyme molecule at pH=13 have been obtained. Lysozyme molecules can be prepared, adsorbed and carried with optimal activity and helicity, with 2 and 10 mg/m2 on unit nanosurface, 130 and 150 mg/g with respect to the weight of nanoparticle, within the linear regions of the coverages at around 150-250 nmol/L and four pH values for nanodiamond and nanosilica, respectively. They can be prepared inthe tightest packed form, with 20 and 55 mg/m2, 810-1680 and 580-1100 mg/g at threshold concentrations and four pH values for nanodiamond and nanosilica, respectively.     

Simplified box orbitals for molecules containing atoms beyond Ar

Simplified Box Orbitals (SBOs) are a kind of spatially restricted basis functions with a similar use to Slater functions, but fulfilling an exact version of the zero-differential overlap approximation. These functions also allow for a drastic reduction in the number of bielectronic integrals when dealing with huge systems, and can be adapted to study confined systems such as molecules in solution. In previous studies, the necessary SBOs parameters to be used for different elements were defined. However, the accuracy of those basis functions decreases with the atomic number of the atoms under study, and therefore their use was discouraged beyond the Ar atom. In the present study, we verify that slightly increasing the terms of SBOs for a better definition, is enough to correctly handling atoms beyond Ar. This, together with other improvements exposed in this work, allowed obtaining accurate SBOs for K–Kr atoms. To make possible the use of SBOs in standard quantum chemistry calculation software, Gaussian expansions to the proposed basis functions–were achieved. Then, simple formulas for directly obtaining those expansions were deduced. Finally, the results of an SZ basis set of the proposed SBOs are analysed and compared with a similar STO basis set.     

Synthesis and Cytotoxicity of 1,4‐Dihydropyridines and an Unexpected 1,3‐Oxazin‐6‐one

Eight heterocycles have been prepared in a one‐pot reaction manner based on the Hantzsch dihydropyridine synthesis. The synthesis afforded seven dihydropyridines (DHP) and one unexpected 1,3‐oxazin‐6‐one. Their structures were confirmed based on NMR spectroscopy and mass spectrometry. The obtained products have been evaluated for their cytotoxicity against eight cancer cell lines and one normal cell line. Two halogenated DHPs ( 7 and 8 ) displayed cytotoxicity toward all the nine tested cancer cell lines with IC₅₀ values from 4.10 to 58.90 μm, while others showed selective activities. DHPs ( 7 and 8 ) bearing a Me group at C(2) and C(6) as well as a halogenated substituent at C(4′) were more antiproliferative than the others.     

Overlap of Doxycycline Fluorescence with that of the Redox-Sensitive Intracellular Reporter roGFP

Tetracycline-inducible systems allow for either suppression or induction of transgene expression to facilitate studies of cell physiology. Doxycycline is a preferred inducer for these gene expression systems due to its membrane permeability; however, the heterocyclic structure of doxycycline exhibits fluorogenic properties that can potentially bias measurement of other fluorochromes. Thus the simultaneous use of tetracycline-inducible systems and fluorescent proteins as reporter genes or as intracellular biosensors may lead to potentially confounding results. Herein, using cells which co-express the ratiometric redox sensitive intracellular reporter, roGFP, and a tetracycline-inducible reporter plasmid encoding the reporter gene, mCherry, as a model system, we describe the overlapping intracellular fluorescent signals between doxycycline and commonly used intracellular fluorescent probes. In our cells, the addition of doxycycline to cells caused a dose- and time-dependent increase in cell fluorescence with 405 nm excitation which overlapped with that of the oxidized configuration of roGFP. Incubating cells in concentrations of doxycycline less than 1 μg/mL and removing doxycycline from the media 60 min before performing experiments eliminated fluorescence interference while still maintaining maximal reporter transgene activation.