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Density functional theory computations were carried out for 11-vertex nido-p-block-hetero(carba)boranes and -borates containing silicon, germanium, tin, arsenic, antimony, sulfur, selenium and tellurium heteroatoms. A set of quantitative values called "estimated energy penalties" was derived by comparing the energies of two reference structures that differ with respect to one structural feature only. These energy penalties behave additively, i.e., they allow us to reproduce the DFT-computed relative stabilities of 11-vertex nido-heteroboranes in general with good accuracy and to predict the thermodynamic stabilities of unknown structures easily. Energy penalties for neighboring heteroatoms (HetHet and HetHet') decrease down the group and increase along the period (indirectly proportional to covalent radii). Energy penalties for a five- rather than four-coordinate heteroatom, [Het(5k)(1) and Het(5k)(2)], generally, increase down group 14 but decrease down group 16, while there are mixed trends for group 15 heteroatoms. The sum of HetHet' energy penalties results in different but easily predictable open-face heteroatom positions in the thermodynamically most stable mixed heterocarbaboranes and -borates with more than two heteroatoms.
J Mol Model 2006 Jul
PMID:Periodic trends and easy estimation of relative stabilities in 11-vertex nido-p-block-heteroboranes and -borates. 1626 Dec 97

Curcumin has been shown to prevent and inhibit carcinogen-induced tumorigenesis in different organs of rodent carcinogenesis models. Our objective is to study global gene expression profiles elicited by curcumin in mouse liver and small intestine as well as to identify curcumin-regulated nuclear factor E2-related factor 2 (Nrf2)-dependent genes. Wild-type C57BL/6J and Nrf2 knockout C57BL/6J/Nrf2(-/-) mice were given a single oral dose of curcumin at 1,000 mg/kg. Liver and small intestine were collected at 3 and 12 hours after treatments. Total RNA was extracted and analyzed using Affymetrix (Santa Clara, CA) mouse genome 430 array (45K) and GeneSpring 6.1 software (Silicon Genetics, Redwood City, CA). Genes that were induced or suppressed >2-fold by curcumin treatments compared with vehicle in wild-type mice but not in knockout mice were filtered using GeneSpring software and regarded as Nrf2-dependent genes. Among those well-defined genes, 822 (664 induced and 158 suppressed) and 222 (154 induced and 68 suppressed) were curcumin-regulated Nrf2-dependent genes identified in the liver and small intestine, respectively. Based on their biological functions, these genes can be classified into the category of ubiquitination and proteolysis, electron transport, detoxification, transport, apoptosis and cell cycle control, cell adhesion, kinase and phosphatase, and transcription factor. Many phase II detoxification/antioxidant enzyme genes, which are regulated by Nrf2, are among the identified genes. The identification of curcumin-regulated Nrf2-dependent genes not only provides potential novel insights into the biological effects of curcumin on global gene expression and chemoprevention but also points to the potential role of Nrf2 in these processes.
Mol Cancer Ther 2006 Jan
PMID:Modulation of nuclear factor E2-related factor 2-mediated gene expression in mice liver and small intestine by cancer chemopreventive agent curcumin. 1643 61

The lift-off technique is one of the most prevalent methods for fabricating microelectrodes on a flat surface (e.g., a silicon [Si] wafer). It represents an alternative for metal-etching techniques that often utilize hazardous chemicals in order to define a pattern. This chapter presents an example of patterning gold electrodes on an Si wafer.
Methods Mol Biol 2006
PMID:Fabrication of microelectrodes using the lift-off technique. 1650 62

The polymerase chain reaction (PCR) provides an in vitro method for rapid enzymatic amplification of fragments of DNA. Microchip-based PCR devices (with reaction volumes from picoliters to microliters) have been realized using various combinations of silicon, glass, and/or plastic materials. Passivation of exposed surfaces in the microreactor is critical for successful PCR. Silicon and plastic surfaces can be passivated by silanization. With surface passivation, PCR can be performed efficiently and economically in chip-based microreactors. The reduced thermal mass of microchips allows for extremely fast temperature ramping. PCR protocols established for benchtop reactors may need to be adjusted accordingly when transferred to microchips. Here, we provide detailed protocols for microchip PCR including procedures for surface passivation and bonding of glass to silicon with ultraviolet curable glue, because both procedures have a major influence on the success or failure of the PCR.
Methods Mol Biol 2006
PMID:Polymerase chain reaction on microchips. 1650 69

The rearrangements for 2-phospha-4-silabicyclo[1.1.0]butane, analogous to the valence isomerization of the hydrocarbons bicyclobutane, 1,3-butadiene, and cyclobutene, were studied at the (U)QCISD(T)/6-311+G**//(U)QCISD/6-31G* level of theory. The monocyclic 1,2-dihydro-1,2-phosphasiletes are shown to be the thermodynamically preferred product, in contrast to the isomerization of the hydrocarbons, which favors the 1,3-butadiene structure. Furthermore, an unprecedented direct isomerization pathway to the 1,2-dihydro-1,2-phosphasiletes was identified. This pathway is competitive with the isomerization via the open-chain butadienes and becomes favorable when electron-donating substituents are present on silicon. Figure 2-Phospha-4-silabicyclo[1.1.0]butane can isomerize directly into the more stable P,Si-cyclobutene via an unprecedented [sigma2s+sigma2a] process, which becomes favorable over the isomerization via the P,Si-butadiene when electron-donating substituents are present on silicon.
J Mol Model 2006 Jul
PMID:Valence isomerization of 2-phospha-4-silabicyclo[1.1.0]butane: a high-level ab initio study. 1664 34

Structural and vibrational features of silanol group are investigated in detail by quantum calculations and normal mode analysis. The structural parameters, charge distributions, force fields, vibrational wavenumbers, potential energy distributions of normal modes and derivatives of the electric dipole moment are analyzed in relation to the nature of the substituents adjacent to the silanol group. The calculations results are discussed in light of available experimental data. Although the OH stretching mode has already been well localized in various silanols, both the Si-(OH) stretching and SiOH bending vibrations have not been yet finely analyzed leading to some discrepancies reported in literature. Clarified assignments of these vibrations are proposed on the basis of normal mode analysis and of SiOH-->SiOD isotopic exchange. The following spectral ranges are determined: 790-1030 cm-1 for nuSi-(OH), 790-1010 cm-1 for nuSi-(OD), 790-900 cm-1 for deltaOH and 580-640 cm-1 for deltaOD. The nuSi-(OH)/nuSi-(OD) wavenumbers are highly dependent on silicon substituents: electron-withdrawing groups induce shifts to higher wavenumbers while electron-releasing groups induce shifts to lower wavenumbers. In alkylsilanols, the SiOH bending is observed at higher wavenumber than the stretching vibration. Analysis of infrared intensities and dipole derivatives in internal coordinates gives explanations to spectral "anomalies" observed in experimental measurements such as well defined and intense nuSi-(OD) absorption in contrast with very low intensity for nuSi-(OH). Numerous empirical correlations are established allowing reconstruction of both SiOH force field and SiOH structural parameters with knowledge of few experimental data.
Spectrochim Acta A Mol Biomol Spectrosc 2006 Jun
PMID:Vibrational properties of silanol group: from alkylsilanol to small silica cluster. Effects of silicon substituents. 1667 54

In the present chapter, some basic definitions about the photolithography process are explained and then the standard preparation of the silicon wafer, the fabrication of the mold, and the preparation and assembly of poly(dimethylsiloxane) (PDMS)-based microchips are discussed. The purpose of this chapter is to describe the most used techniques for preparation of PDMS microchips. A list of tips is included in order to provide a troubleshooting guide for the most common difficulties found during the fabrication process. Some recent alternative approaches to microfabrication are also discussed.
Methods Mol Biol 2006
PMID:Micro-molding for poly(dimethylsiloxane) microchips. 1679 Aug 64

Fabrication of microfluidic channels in common commercially available thermoplastic materials can be easily accomplished using hot embossing or ultraviolet (UV) laser ablation. Hot embossing involves replication of a microfluidic network in a polymer substrate from a stamp (or template) fabricated in silicon or metal. UV laser ablation is performed by either exposing the polymer substrate through a mask or by using a laser direct-write process. The resulting polymer microfluidic channels are most often sealed with another polymer piece using thermal bonding or solvent bonding to complete the fabrication procedure. Unlike their silicon and glass counterparts, polymer microfluidic systems can be fabricated by these methods in less than 1 h, making the materials attractive for both research prototyping and commercialization.
Methods Mol Biol 2006
PMID:Fabrication of polymer microfluidic systems by hot embossing and laser ablation. 1679 Aug 65

Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy was applied for the first time to detect the structural changes upon photoreactions of redox cofactors in photosystem II (PSII). The PSII-enriched membranes from spinach were adsorbed on the surface of a silicon prism, and FTIR measurements of various redox cofactors were performed for the same sample but under different conditions by exchanging buffers in a flow cell. Light-induced FTIR difference spectra upon redox reactions of the oxygen-evolving Mn cluster, the primary quinone electron acceptor QA, the redox-active tyrosine YD, the primary electron acceptor pheophytin, and the primary electron donor chlorophyll P680 were successively recorded in buffers including different redox reagents and inhibitors. All of these cofactors remained active in the PSII membranes on the silicon surface, and the resultant spectra were basically identical to those previously recorded by the conventional transmission method. These ATR-FTIR measurements enable accurate comparison between reactions of different active sites in a single PSII sample. The present results demonstrated that the ATR-FTIR spectroscopy is a useful technique for investigation of the reaction mechanism of PSII.
Spectrochim Acta A Mol Biomol Spectrosc 2007 Apr
PMID:Selective detection of the structural changes upon photoreactions of several redox cofactors in photosystem II by means of light-induced ATR-FTIR difference spectroscopy. 1687 88

We have designed, fabricated and tested a real-time micro polymerase chain reaction (microPCR) system. It consists of a microscope glass cover slip placed on top of a micromachined silicon chip integrated with a heater and a temperature sensor. A single microL of a sample containing DNA was placed on the glass and encapsulated with mineral oil to prevent the evaporation of water, thus forming a virtual reaction chamber (VRC). The PCR chip required half a second to heat up from 72 to 94 degrees C and two seconds to cool from 94 to 55 degrees C, corresponding to a cooling rate of -20 K s(-1). The real-time PCR yield was determined by a fluorescence method. The melting curve analysis method as well as capillary electrophoresis was performed to determine the purity of the PCR product. As the glass slip is disposable, cross-contamination from sample to sample is eliminated. The total cost of running the PCR is given by the value of the cover slip and its treatment.
Mol Biosyst 2006 Jun
PMID:Disposable real-time microPCR device: lab-on-a-chip at a low cost. 1688 Sep 47


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