Characteristics of silica-rich pedofeatures in a buried paleosol

Whitish and whitish-light brown milky-like textural pedofeatures and impregnations were found in the voids and the matrix of buried paleosols older than 2.7 million years in a site in Sardinia, Italy. The pedofeatures were described and analysed using micromorphology, X-ray diffraction and microprobe techniques, and their spatial distribution correlated with field evidence. The suite of analyses showed that the main components of the pedofeatures were more or less ordered silica phases. As well as forming a matrix cement, these pedofeatures also occurred as coatings and infillings in pores. Significant amounts of alumina and, less, Mg, Ca and Fe were also present in the pedofeatures, possibly in the form of silicate coatings and inclusions/impurities, or alumino-silicates of the adjacent soil matrix. A number of hypotheses are drawn on the possible mechanisms of formation of these silica-rich pedofeatures, including the possibility of prolonged weathering of volcanic materials and the resulting formation of colloids and more or less ordered silica phases, with successive dehydration and progressive ordering of phases during the at least 2.5 million years. (C) 2003 Elsevier B.V. All rights reserved.

The release of silicon from amorphous silica and rice straw in Sri Lankan soils

Silicon release from rice straw and amorphous silica when shaken in solution with five Sri Lankan soils was studied indirectly using sorption isotherms and changes in concentration and directly using straw in dialysis bags examined using electron microscopy. The aim was to further our understanding of the processes and factors affecting the release of straw-Si in soils and its availability to rice. The soils (alfisols and ultisols) shaken with 0.1 M NaCl (5 g per 125 mL for 250 days) produced concentrations of 1 - 4 mg L-1 of monosilicic acid-Si. Amorphous silica added to these suspensions (36.5 mg, containing 17 mg Si) raised the concentrations to 20 - 40 mg L-1, and added rice straw (0.5 g, containing 17 mg Si) gave 10 - 25 mg L-1. Sorption isotherms (7 days equilibrations) were used to calculate from the concentrations the amounts of Si released ( 24 - 38% and 8 - 21%, respectively). Both materials gave about 40 mg L-1 of monosilicic acid-Si plus 30 mg L-1 of disilicic acid-Si when shaken in solution alone (5 g per 125 mL). Straw in dialysis bags ( 0.5 g per 25 mL in 0.1 M NaCl) was shaken in soil suspension ( 5 g per 100 mL) for 60 days. Similar concentrations and releases were measured to those obtained above. About one fifth of the mass of straw was lost by decomposition in the first 15 days. A chloroform treatment prevented decomposition, but Si release was unaffected. Disintegration continued throughout the experiments, with phytoliths being exposed and dissolved. Compared to the rate of release from straw into solution without soil, the release of Si into soil suspensions was increased during the first 20 days by adsorption on the soil, but was then reduced probably through the effect of Fe and Al on the phytolith surfaces. The extent of this blocking effect varied between soils and was not simply related to soil pH.

Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis

Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes. Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye and analysed by two-dimensional difference gel electrophoresis. Gel images analysed off-line, using the DeCyder image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Techniques for analysis of proteins by SDS-polyacrylamide gel electrophoresis and Western blotting

The separation of mixtures of proteins by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) is a technique that is widely used—and, indeed, this technique underlies many of the assays and analyses that are described in this book. While SDS-PAGE is routine in many labs, a number of issues require consideration before embarking on it for the first time. We felt, therefore, that in the interest of completeness of this volume, a brief chapter describing the basics of SDS-PAGE would be helpful. Also included in this chapter are protocols for the staining of SDS-PAGE gels to visualize separated proteins, and for the electrotransfer of proteins to a membrane support (Western blotting) to enable immunoblotting, for example. This chapter is intended to complement the chapters in this book that require these techniques to be performed. Therefore, detailed examples of why and when these techniques could be used will not be discussed here.

Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis

Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes, Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.

Colloidal stable silica encapsulated nano-magnetic composite as a novel bio-catalyst carrier

A colloidal stable silica-encapsulated magnetic nano-composite of a controlled dimension is, for the first time, employed to carry beta-lactamase via chemical linkage on the silica overlayer: activity study reflects that this new type of immobilisation allows site (enzyme) isolation, accessibility as good as free enzyme and recovery & reusability upon application of magnetic separation.

Low-temperature sol-gel preparation of ordered nanoparticles of tungsten carbide/oxide

Tungsten carbide/oxide particles have been prepared by the gel precipitation of tungstic acid in the presence of an organic gelling agent [10% ammonium poly(acrylic acid) in water, supplied by Ciba Specialty Chemicals]. The feed solution; a homogeneous mixture of sodium tungstate and ammonium poly(acrylic acid) in water, was dropped from a 1-mm jet into hydrochloric acid saturated hexanol/concentrated hydrochloric acid to give particles of a mixture of tungstic acid and poly(acrylic acid), which, after drying in air at 100 degrees C and heating to 900 degrees C in argon for 2 h, followed by heating in carbon dioxide for a further 2 h and cooling, gives a mixture of WO, WC, and a trace of NaxWO3, with the carbon for the formation of WC being provided by the thermal carbonization of poly(acrylic acid). The pyrolyzed product is friable and easily broken down in a pestle and mortar to a fine powder or by ultrasonics, in water, to form a stable colloid. The temperature of carbide formation by this process is significantly lower (900 degrees C) than that reported for the commercial preparation of tungsten carbide, typically > 1400 degrees C. In addition, the need for prolonged grinding of the constituents is obviated because the reacting moieties are already in intimate contact on a molecular basis. X-ray diffraction, particle sizing, transmission electron microscopy, surface area, and pore size distribution studies have been carried out, and possible uses are suggested. A flow diagram for the process is described.

Thermoselective phase property of silica tethered with fluorinated chains for controlled 'release' and 'capture' of catalytic fluorous tin species

The temperature dependent mixing of organic and fluorous phases is one of the key principals of fluorous biphasic systems (FBS). Given the high cost of the perfluorous solvents and their impacts to the environment, it is apparent that elimination of these solvents in bulk quantity in the FBS is advantageous. We report for the first time, the surface coverage of silica with a fluorous solvent like material that traps (at ambient temperatures) and releases (at elevated temperatures) a fluorous tin bromide in organic solvent. Here, we demonstrate the catalytic utilisation of this species for the hydrocyclisation of 6-bromo-1-hexene with NaBH4. (C) 2002 Elsevier Science B.V. All rights reserved.

Silica coated noble metal nanoparticle hydrosols as supported catalyst precursors

Synthesis of well-defined nanoparticles has been intensively pursued not only for their fundamental scientific interest, but also for many technological applications. One important development of the nanomaterial is in the area of chemical catalysis. We have now developed a new aqueous-based method for the synthesis of silica encapsulated noble metal nanoparticles in controlled dimensions. Thus, colloid stable silica encapsulated similar to 5 nm platinum nanoparticle is synthesized by a multi-step method. The thickness of the silica coating could be controlled using a different amount of silica precursor. These particles supported on a high surface area alumina are also demonstrated to display a superior hydrogenation activity and stability against metal sintering after thermal activation.

Novel lanthanide luminescent materials based on complexes of 3-hydroxypicolinic acid and silica nanoparticles

New lanthanide complexes of 3-hydroxypicolinic acid (HpicOH) were prepared: [Ln(H2O)(picOH)(2)(mu-HpicO)].3H(2)O (Ln = Eu, Tb, Er). The complexes were characterized using photoluminescence, infrared, Raman, and H-1 NMR spectroscopy, and elemental analysis. The crystal structure of [Eu(H2O)(picOH)(2)(mu-HpicO)] . 3H(2)O 1 was determined by X-ray diffraction. Compound 1 crystallizes in a monoclinic system with space group P2(1)/c and cell parameters a = 9.105(13) Angstrom, b = 18.796(25) Angstrom, and c = 13.531(17) Angstrom, and beta = 104.86(1) deg. The 3-hydroxypicolinate ligands coordinate through both N,O- or O,O- chelation to the lanthanide ions, as shown by X-ray and spectroscopic results. Photoluminescence measurements were performed for the Eu(III) and Tb(III) complexes; the Eu(III) complex was investigated in more detail. The Eu(III) compound is highly luminescent and acts as a photoactive center in nanocomposite materials whose host matrixes are silica nanoparticles.

Difference gel electrophoresis

DIGE is a protein labelling and separation technique allowing quantitative proteomics of two or more samples by optical fluorescence detection of differentially labelled proteins that are electrophoretically separated on the same gel. DIGE is an alternative to quantitation by MS-based methodologies and can circumvent their analytical limitations in areas such as intact protein analysis, (linear) detection over a wide range of protein abundances and, theoretically, applications where extreme sensitivity is needed. Thus, in quantitative proteomics DIGE is usually complementary to MS-based quantitation and has some distinct advantages. This review describes the basics of DIGE and its unique properties and compares it to MS-based methods in quantitative protein expression analysis.