Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved.

Sample preparation for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) of DNA is critical for obtaining high quality mass spectra. Sample impurity, solvent content, substrate surface and environmental conditions (temperature and humidity) all affect the rate of matrix-analyte co-crystallization. As a result, laser fluence threshold for desorption/ionization varies from spot to spot. When using 3-hydroxypicolinic acid (3-HPA) as the matrix, laser fluence higher than the threshold value reduces mass resolution in time-of-flight (TOF) MS as the excess energy transferred to DNA causes metastable decay. This can be overcome by either searching for 'hot' spots or adjusting the laser fluence. However, both solutions may require a significant amount of operator manipulation and are not ideal for automatic measurements. We have added various sugars for crystallization with the matrix to minimize the transfer of excess laser energy to DNA molecules. Fructose and fucose were found to be the most effective matrix additives. Using these additives, mass resolution for DNA molecules does not show noticeable deterioration as laser energy increases. Improved sample preparation is important for the detection of single nucleotide polymorphisms (SNPs) using primer extension with a single nucleotide. During automatic data acquisition it is difficult to routinely detect heterozygous A/T mutations, which requires resolving a mass difference of 9 Da, unless a sugar is added during crystallization.

Observation and origin of self-organized textures in agates.

One of the most impressive manifestations of spontaneous pattern generation in natural materials is iris agate, which contains submicrometer concentric striations that may cycle several thousand times within an individual specimen. Analysis by secondary ion mass spectroscopy and transmission electron microscopy identified the iris texture as alternating layers of fine-grained, highly defective chalcedony and coarse-grained low-defect quartz. This oscillatory zonation in defect concentration may be ascribed to Ostwald-Liesegang crystallization cycles from silica-rich fluids that are variably polymeric and monomeric. Periodic changes in defect concentration and grain size also are observed with wavelengths of hundreds of micrometers and of centimeters, so that agates reveal textural self-similarity over three length scales.

Mineralogical characteristics of silica polymorphs in relation to their biological activities.

Numerous aspects of silica polymorphs can affect their biological activities, including periodic structures, compositional variations, dissolution characteristics, surface properties, and particle size and shape. For an understanding of mineral-induced pathogenesis from a mechanistic perspective, the links between these properties and biochemical processes must be elucidated. This paper presents some strategies for designing assays to evaluate these properties.

High-resolution and analytical transmission electron microscopy of mineral disorder and reactions.

Crystal defects and chemical reactions occurring at scales beyond the resolution of light microscopes have major effects on the chemical and physical properties of rocks and minerals. High-resolution imaging, diffraction, and chemical analysis in the transmission electron microscope have become important methods for exploring mineral defect structures and reaction mechanisms and for studying the distribution of phases resulting from reactions. These techniques have shown that structural disorder is common in some rock-forming minerals but rare in others. They have also established mechanisms by which many reactions occur at the atomic cluster scale. These data thus provide an atomistic basis for understanding the kinetics of geological reactions. Furthermore, apparent major-element, minor-element, and trace-element chemistry of minerals can be influenced by submicroscopic inclusions or intergrowths, which commonly form as products of solid-state reactions.

The widespread distribution of a novel silica polymorph in microcrystalline quartz varieties.

An x-ray examination of more than 150 specimens of fine-grained quartz varieties from around the world has revealed that more than 10% and as much as 80% of the silica in many samples is actually moganite, a little-known silica polymorph. Rietveld refinements of 50 powder x-ray diffraction patterns produced by fibrous quartz (agate, chalcedony) and nonfibrous quartz (chert, flint) indicate that the concentrations of moganite within each subgroup are widely distributed. The large amount of moganite (>30%) found in cherts from arid, alkaline environments may resurrect length-slow silica as an indicator of evaporitic regimes, and the absence of moganite in weathered and hydrothermally altered silica samples may be a useful measure of fluid-rock interaction.