High-resolution computer simulations of stacking of weak bases using a transient pH boundary in capillary electrophoresis. 1. Concept and impact of sample ionic strength

The dynamics of focusing weak bases using a transient pH boundary was examined via high-resolution computer simulation software. Emphasis was placed on the mechanism and impact that the presence of salt, namely, NaCl, has on the ability to focus weak bases. A series of weak bases with mobilities ranging from 5 x 10(-9) to 30 x 10(-9) m2/V x s and pKa values between 3.0 and 7.5 were examined using a combination of 65.6 mM formic acid, pH 2.85, for the separation electrolyte, and 65.6 mM formic acid, pH 8.60, for the sample matrix. Simulation data show that it is possible to focus weak bases with a pKa value similar to that of the separation electrolyte, but it is restricted to weak bases having an electrophoretic mobility of 20 x 10(-9) m2/V x s or quicker. This mobility range can be extended by the addition of NaCl, with 50 mM NaCl allowing stacking of weak bases down to a mobility of 15 x 10(-9) m2/V x s and 100 mM extending the range to 10 x 10(-9) m2/V x s. The addition of NaCl does not adversely influence focusing of more mobile bases, but does prolong the existence of the transient pH boundary. This allows analytes to migrate extensively through the capillary as a single focused band around the transient pH boundary until the boundary is dissipated. This reduces the length of capillary that is available for separation and, in extreme cases, causes multiple analytes to be detected as a single highly efficient peak.

Characterization of granite matrix porosity and pore-space geometry by in situ and laboratory methods

Most available studies of interconnected matrix porosity of crystalline rocks are based on laboratory investigations; that is, work on samples that have undergone stress relaxation and were affected by drilling and sample preparation. The extrapolation of the results to in situ conditions is therefore associated with considerable uncertainty, and this was the motivation to conduct the ‘in situ Connected Porosity’ experiment at the Grimsel Test Site (Central Swiss Alps). An acrylic resin doped with fluorescent agents was used to impregnate the microporous granitic matrix in situ around an injection borehole, and samples were obtained by overcoring. The 3-D structure of the porespace, represented by microcracks, was studied by U-stage fluorescence microscopy. Petrophysical methods, including the determination of porosity, permeability and P -wave velocity, were also applied. Investigations were conducted both on samples that were impregnated in situ and on non-impregnated samples, so that natural features could be distinguished from artefacts. The investigated deformed granites display complex microcrack populations representing a polyphase deformation at varying conditions. The crack population is dominated by open cleavage cracks in mica and grain boundary cracks. The porosity of non-impregnated samples lies slightly above 1 per cent, which is 2–2.5 times higher than the in situ porosity obtained for impregnated samples. Measurements of seismic velocities (Vp ) on spherical rock samples as a function of confining pressure, spatial direction and water saturation for both non-impregnated and impregnated samples provide further constraints on the distinction between natural and induced crack types. The main conclusions are that (1) an interconnected network of microcracks exists in the whole granitic matrix, irrespective of the distance to ductile and brittle shear zones, and (2) conventional laboratory methods overestimate the matrix porosity. Calculations of contaminant transport through fractured media often rely on matrix diffusion as a retardation mechanism.

Protein quaternary structure determination using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and chemical crosslinking

A means of analyzing protein quaternary structure using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI MS) and chemical crosslinking was evaluated. Proteins of known oligomeric structure, as well as monomeric proteins, were analyzed to evaluate the method. The quaternary structure of proteins of unknown or uncertain structure was investigated using this technique. The stoichiometry of recombinant E. coli carbamoyl phosphate synthetase and recombinant human farnesyl protein transferase were determined to be heterodimers using glutaraldehyde crosslinking, agreeing with the stoichiometry found for the wild type proteins. The stoichiometry of the gamma subunit of E. coli DNA polymerase III holoenzyme was determined in solution without the presence of other subunits to be a homotetramer using glutaraldehyde crosslinking and MALDI MS analysis. Chi and psi subunits of E. coli DNA polymerase III subunits appeared to form a heterodimer when crosslinked with heterobifunctional photoreactive crosslinkers.^ Comparison of relative % peak areas obtained from MALDI MS analysis of crosslinked proteins and densitometric scanning of silver stained sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) gels showed excellent qualitative agreement for the two techniques, but the quantitative analyses differed, sometimes significantly. This difference in quantitation could be due to SDS-PAGE conditions (differential staining, loss of sample) or to MALDI MS conditions (differences in ionization and/or detection). Investigation of pre-purified crosslinked monomers and dimers recombined in a specific ratio revealed the presence of mass discrimination in the MALDI MS process. The calculation of mass discrimination for two different MALDI time-of-flight instruments showed the loss of a factor of approximately 2.6 in relative peak area as the m/z value doubles over the m/z range from 30,000 to 145,000 daltons.^ Indirect symmetry was determined for tetramers using glutaraldehyde crosslinking with MALDI MS analysis. Mathematical modelling and simple graphing allowed the determination of the symmetry for several tetramers known to possess isologous D2 symmetry. These methods also distinguished tetramers that did not fit D2 symmetry such as apo-avidin. The gamma tetramer of E. coli DNA polymerase III appears to have isologous D2 symmetry. ^

Effects of stimulus with proinflammatory mediators on nitric oxide production and matrix metalloproteinase activity in explants of cranial cruciate ligaments obtained from dogs

OBJECTIVE To evaluate the origin and degree of activity of nitric oxide (NO) and matrix metalloproteinase (MMP) in explants of cranial cruciate ligaments (CCLs) obtained from dogs and cultured with and without inflammatory activators. SAMPLE POPULATION Tissue specimens obtained from 7 healthy adult Beagles that were (mean +/- SD) 4.5 +/- 0.5 years old and weighed 12.5 +/- 0.8 kg. PROCEDURE The CCLs were harvested immediately after dogs were euthanatized, and specimens were submitted for explant culture. Cultures were stimulated by incubation with a combination of interleukin-1, tumor necrosis factor-alpha, and lipopolysaccharide, or they were not stimulated. Culture supernatants were examined for production of NO nitrite-nitrate metabolites (NOts) and activity of MMP Cultured specimens were evaluated by use of immunohistochemical analysis to detect activity of inducible NO synthase (iNOS). RESULTS All ligament explants produced measurable amounts of NOts. Stimulated cultures produced significantly more NOts after incubation for 24 and 48 hours, compared with nonstimulated cultures. Production of MMP in supernatants after incubation for 48 hours was significantly higher in stimulated cultures than in nonstimulated cultures. Cells with positive staining for iNOS were detected on all slides. Positively stained cells were predominantly chondroid metaplastic. There was a significant difference in intensity of cell staining between stimulated and non-stimulated cultures. CONCLUSIONS AND CLINICAL RELEVANCE Explant cultures of intact CCLs obtained from dogs produce iNOS-induced NO. Stimulation of chondroid metaplastic cells in CCL of dogs by use of inflammatory activators can increase production of iNOS, NOts, and MMP.

Dominance of chemokine ligand 2 and matrix metalloproteinase-2 and -9 and suppression of pro-inflammatory cytokines in the epidural compartment after intervertebral disc extrusion in a canine model

BACKGROUND CONTEXT In canine intervertebral disc (IVD) disease, a useful animal model, only little is known about the inflammatory response in the epidural space. PURPOSE To determine messenger RNA (mRNA) expressions of selected cytokines, chemokines, and matrix metalloproteinases (MMPs) qualitatively and semiquantitatively over the course of the disease and to correlate results to neurologic status and outcome. STUDY DESIGN/SETTING Prospective study using extruded IVD material of dogs with thoracolumbar IVD extrusion. PATIENT SAMPLE Seventy affected and 13 control (24 samples) dogs. OUTCOME MEASURES Duration of neurologic signs, pretreatment, neurologic grade, severity of pain, and outcome were recorded. After diagnostic imaging, decompressive surgery was performed. METHODS Messenger RNA expressions of interleukin (IL)-1β, IL-2, IL-4, IL-6, IL-8, IL-10, tumor necrosis factor (TNF), interferon (IFN)γ, MMP-2, MMP-9, chemokine ligand (CCL)2, CCL3, and three housekeeping genes was determined in the collected epidural material by Panomics 2.0 QuantiGene Plex technology. Relative mRNA expression and fold changes were calculated. Relative mRNA expression was correlated statistically to clinical parameters. RESULTS Fold changes of TNF, IL-1β, IL-2, IL-4, IL-6, IL-10, IFNγ, and CCL3 were clearly downregulated in all stages of the disease. MMP-9 was downregulated in the acute stage and upregulated in the subacute and chronic phase. Interleukin-8 was upregulated in acute cases. MMP-2 showed mild and CCL2 strong upregulation over the whole course of the disease. In dogs with severe pain, CCL3 and IFNγ were significantly higher compared with dogs without pain (p=.017/.020). Dogs pretreated with nonsteroidal anti-inflammatory drugs revealed significantly lower mRNA expression of IL-8 (p=.017). CONCLUSIONS The high CCL2 levels and upregulated MMPs combined with downregulated T-cell cytokines and suppressed pro-inflammatory genes in extruded canine disc material indicate that the epidural reaction is dominated by infiltrating monocytes differentiating into macrophages with tissue remodeling functions. These results will help to understand the pathogenic processes representing the basis for novel therapeutic approaches. The canine IVD disease model will be rewarding in this process.

Circulating matrix metalloproteinase 9 levels in relation to sampling methods, femoral and carotid atherosclerosis.

OBJECTIVES To examine whether circulating levels of matrix metalloproteinase 9 (MMP-9) were associated with ultrasound-assessed intima-media thickness (IMT) and echolucent plaques in the carotid and femoral arteries. To examine preanalytical sources of variability in MMP-9 concentrations related to sampling procedures. SUBJECTS AND DESIGN Plasma and serum MMP-9 levels were compared with ultrasound assessed measures of femoral and carotid atherosclerosis, in a cross-sectional study of 61-year-old men (n = 473). Preanalytical sources of variability in MMP-9 levels were examined in 10 healthy subjects. Main outcome measures were circulating levels of MMP-9 in serum and plasma, IMT of the carotid and femoral arteries, and plaque status based on size and echolucency. SETTING Research unit at university hospital. RESULTS Plasma concentrations of total and active MMP-9 were associated with femoral artery IMT independently of traditional cardiovascular risk factors, and were higher in subjects with moderate to large femoral plaques. Plasma MMP-9 concentration was higher in men with echolucent femoral plaques (P = 0.006) compared with subjects without femoral plaques. No similar associations were found for carotid plaques. MMP-9 concentrations were higher in serum than in plasma, and higher when sampling was performed with Vacutainer than with syringe. MMP-9 levels in serum were more strongly associated with peripheral neutrophil count compared with MMP-9 levels in plasma. CONCLUSIONS Plasma MMP-9 levels were associated with atherosclerosis in the femoral artery, and total MMP-9 concentration was higher in men with echolucent femoral plaques. The choice of sample material and sampling method affect the measurements of circulating MMP-9 levels.

(Table 2) Trace element composition of seleceted clast and matrix materials from ODP Site 125-786

Shipboard examination of volcanic and sedimentary strata at Site 786 suggested that at least four types of breccias are present: flow-top breccias, associated with cooling and breakup on the upper surface of lava flows; autobreccias, formed by in-situ alteration at the base of flows; fault-gouge breccias; and true sedimentary breccias derived from weathering and erosion of underlying flows. It is virtually impossible to assess the origin of breccia matrix by textural and mineralogical analyses alone. However, it is fundamental for our understanding of breccia provenance to determine the source component of the matrix material. Whether the matrix is uniquely clastderived can be determined by geochemical fingerprinting. Trace elements that are immobile during weathering and alteration do not change their relative abundances. A contribution to the matrix from any source with an immobile trace element signature different from that of the clasts would appear as a perturbation of the trace element signature of the matrix. Trace element analysis of bulk samples from clasts and matrix material in individual breccia units was undertaken in a fashion similar to that used by Brimhall and Dietrich (1987, doi:10.1016/0016-7037(87)90070-6) in analyzing soil provenance: (1) to help distinguish between sedimentary and volcanic breccias, (2) to determine the degree of mixing and depth of erosion in sedimentary breccias, and (3) to analyze the local provenance of the individual breccia components (matrix and clasts). The following elements were analyzed by X-ray fluorescence (XRF): Rb, Sr, Ba, U, Zr, Cu, Zn, Ti, Cr, and V. Of these elements, Zr and Ti probably exhibit truly immobile behavior (Humphris and Thompson, 1978, doi:10.1016/0016-7037(78)90222-3 ). The remaining elements are useful as a reference for the extent of compositional change during the formation of matrix material (Brimhall and Dietrich, 1987, doi:10.1016/0016-7037(87)90070-6).

Composition of matrix glasses and melt inclusions of fallout tephra from ODP Hole 125-782A

We studied the systematics of Cl, F and H2O in Izu arc front volcanic rocks using basaltic through rhyolitic glass shards and melt inclusions (Izu glasses) from Oligocene to Quaternary distal fallout tephra. These glasses are low-K basalts to rhyolites that are equivalent to the Quaternary lavas of the Izu arc front (Izu VF). Most of the Izu glasses have Cl ~400-4000 ppm and F ~70-400 ppm (normal-group glasses). Rare andesitic melt inclusions (halogen-rich andesites; HRA) have very high abundances of Cl (~6600-8600 ppm) and F (~780-910 ppm), but their contents of incompatible large ion lithophile elements (LILE) are similar to the normal-group glasses. The preeruptive H2O of basalt to andesite melt inclusions in plagioclase is estimated to range from ~2 to ~10 wt% H2O. The Izu magmas should be undersaturated in H2O and the halogens at their preferred levels of crystallization in the middle to lower crust (~3 to ~11 kbar, ~820° to ~1200°C). A substantial portion of the original H2O is lost due to degassing during the final ascent to surface. By contrast, halogen loss is minor, except for loss of Cl from siliceous dacitic and rhyolitic compositions. The behavior of Cl, F and H2O in undegassed melts resembles the fluid mobile LILE (e.g.; K, Rb, Cs, Ba, U, Pb, Li). Most of the Cl (>99%), H2O (>95%) and F (>53%) in the Izu VF melts appear to originate from the subducting slab. At arc front depths, the slab fluid contains Cl = 0.94+/-0.25 wt%, F = 990+/-270 ppm and H2O = 25+/-7 wt%. If the subducting sediment and the altered basaltic crust were the only slab sources, then the subducted Cl appears to be almost entirely recycled at the Izu arc (~77-129%). Conversely, H2O (~13-22% recycled at arc) and F (~4-6% recycled) must be either lost during shallow subduction or retained in the slab to greater depths. If a seawater-impregnated serpentinite layer below the basaltic crust were an additional source of Cl and H2O, the calculated percentage of Cl and H2O recycled at arc would be lower. Extrapolating the Izu data to the total length of global arcs (~37000 km), the global arc outflux of fluid-recycled Cl and H2O at subduction zones amounts to Cl ~2.9-3.8 mln ton/yr and H2O ~70-100 mln ton/yr, respectively - comparable to previous estimates. Further, we obtain a first estimate of global arc outflux of fluid-recycled F of ~0.3-0.4 mln ton/yr. Despite the inherent uncertainties, our results support models suggesting that the slab becomes strongly depleted in Cl and H2O in subduction zones. In contrast, much of the subducted F appears to be returned to the deep mantle, implying efficient fractionation of Cl and H2O from F during the subduction process. However, if slab devolatilization produces slab fluids with high Cl/F (~9.5), slab melting will still produce components with low Cl/F ratios (~0.9), similar to those characteristic of the upper continental crust (Cl/F ~0.3-0.9).