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PubMed1997

Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences.

We have performed a comprehensive analysis of the microenvironments surrounding the twenty amino acids. Our analysis includes comparison of amino acid environments with random control environments as well as with each of the other amino acid environments. We describe the amino acid environments with a set of 21 features summarizing atomic, chemical group, residue, and secondary structural features. The environments are divided into radial shells of 1 A thickness to represent the distance of the features from the amino acid C beta atoms. We make the results of our analysis available graphically over the world wide web. To illustrate the validity and utility of our analysis, we used the amino acid comparative profiles to construct a substitution matrix, the WAC matrix, based on a simple summary of the computed environmental differences. We compared our matrix to BLOSUM62 and PAM250 in BLAST searches with query sequences selected from 39 protein families found in the PROSITE database. Although BLOSUM62 was the most sensitive matrix overall, our matrix was more sensitive for some families, and exhibited overall performance similar to PAM250. Our results suggest that the radial distribution of biochemical and biophysical features is useful for comparing amino acid environments, and that similarity matrices based on the geometric distribution of features around amino acids may produce improved search sensitivity.

Amino Acid Sequence↗
PubMed2004

Lead isotopic compositions of environmental certified reference materials for an inter-laboratory comparison of lead isotope analysis.

Lead isotope ratios, viz. 207Pb/206Pb and 208Pb/206Pb, of the commercially available certified reference materials (CRMs) issued in Japan are presented with an objective to provide a data set, which will be useful for the quality assurance of analytical procedures, instrumental performance and method validation of the laboratories involved in environmental lead isotope ratio analysis. The analytical method used in the present study was inductively coupled plasma quadrupole mass spectrometry (ICPQMS) preceded by acid digestion and with/without chemical separation of lead from the matrix. The precision of the measurements in terms of the relative standard deviation (RSD) of triplicated analyses was 0.19% and 0.14%, for 207Pb/20Pb and 208Pb/206Pb, respectively. The trueness of lead isotope ratio measurements of the present study was tested with a few CRMs, which have been analyzed by other analytical methods and reported in various literature. The lead isotopic ratios of 18 environmental matrix CRMs (including 6 CRMs analyzed for our method validation) are presented and the distribution of their ratios is briefly discussed.

Journal Article↗
PubMed2003

The ins and outs of fibronectin matrix assembly.

Cell phenotype is specified by environmental cues embedded in the architecture and composition of the extracellular matrix (ECM). Much has been learned about matrix organization and assembly through analyses of the ECM protein fibronectin (FN). FN matrix assembly is a cell-mediated process in which soluble dimeric FN is converted into a fibrillar network. Binding of cell surface integrin receptors to FN converts it to an active form, which promotes fibril formation through interactions with other cell-associated FN dimers. As FN fibrils form on the outside of the cell, cytoplasmic domains of integrin receptors organize cytoplasmic proteins into functional complexes inside. Intracellular connections to the actin cytoskeletal network and stimulation of certain key intracellular signaling pathways are essential for FN-integrin interactions and propagation of FN fibril formation. Thus, assembly of native functional ECM depends on exquisite coordination between extracellular events and intracellular pathways.

Animals↗
PubMed2005

Disruption of glomerular cell-cell and cell-matrix interactions in hydrocarbon nephropathy.

Environmental chemicals play an etiological role in greater than 50% of idiopathic glomerular diseases. The present studies were conducted to define mechanisms of renal cell-specific hydrocarbon injury. Female rats were given 10 mg/kg benzo(a)pyrene (BaP) once a week for 16 wk. Progressive elevations in total urinary protein, protein/creatinine ratios, and microalbuminuria were observed in rats treated with BaP for up to 16 wk. The nephropathic response involved early reductions in mesangial cell numbers and fibronectin levels by 8 wk, coupled to transient increases in podocyte cellularity. Changes in podocyte numbers subsided by 16 wk and correlated with rebound increases in mesangial cell numbers and fibronectin levels, along with increased alpha-smooth muscle actin and Cu/Zn superoxide dismutase and fusion of podocyte foot processes. In culture, mesangial cells were more sensitive than podocytes to hydrocarbon injury and expressed higher levels of inducible aryl hydrocarbon hydroxylase activity. Naïve mesangial cells exerted a strong inhibitory influence on podocyte proliferation under both direct and indirect coculture conditions, and this response involved a mesangial cell-derived matrix that selectively inhibited podocyte proliferation. These findings indicate that hydrocarbon nephropathy in rats involves disruption of glomerular cell-cell and cell-matrix interactions mediated by deposition of a mesangial cell-derived growth-inhibitory matrix that regulates podocyte proliferation.

Animals↗
PubMed1997

Fate of explosive contaminants in plants.

A great deal of interest has been generated recently in the determination of explosives and explosives by-products in exotic matrices including composts, bioslurries, and plants. The methods traditionally utilized for the analysis of organic and inorganic contaminants in these types of environmental samples are not adequate owing to the unique properties of the material being studied. The methods used to detect the nitramines and their degradation products in a variety of environmental samples requires matrix-specific sample preparation, separation by reversed phase high performance liquid chromatography, and ultra-violet detection. Knowledge of the concentration of the contaminants and the molecular state of their degradation products is helpful in assessing the environmental risks associated with the contaminants as well as the design of remediation technologies. Data that are obtained using analytical methods not designed for the specific matrix encountered may lead to incorrect quantitation. Examples of remediation technologies that necessitate the analysis of other than standard matrices for explosives include composting, aerobic and anaerobic microbial degradation, and plant-assisted degradation. The toxicity and mobility of explosives in the food chain are also of interest, and analytical techniques for studying explosives in plant and animal tissues that provide valid information regarding trace levels in these matrices are also required. The report will address three important points in connection with the problem. The extraction of the contaminants from the matrix requires a different set of extraction techniques than those utilized for standard water and soil extractions. These exotic matrices contain much higher organic content than soil or water and, as a result, are prone to interference from biological molecules.

Biodegradation, Environmental↗
PubMed2004

Organic matrix in produced water from the Osage-Skiatook petroleum environmental research site, Osage county, Oklahoma.

Produced water (water co-produced with oil and gas) constitutes the single largest waste stream for oil and gas industry. Reclaiming this water for beneficial use is thought to be one of the most practical solutions that can solve both environmental and water shortage problems. The feasibility of this practice depends on the ability to remove its chemical content to the levels that meets the appropriate standards. Organic compounds are probably the most difficult fraction to handle. In this paper, the discrete organic compounds and non-volatile, macromolecular organic compounds (i.e., natural organic matter--NOM) of three produced water samples from the Osage-Skiatook Environmental Research site were characterized. Two of the three produced waters had very little contribution from NOM, while one of the samples had about 23% NOM contribution to its organic matrix pool. Fluorescent spectrophotometric scans provided little differentiation among the organic quality of the produced water, while pyrolysis-GC/MS showed that the NOM characteristics of the three produced waters were distinct. Specifically, the overall halogenated content and aromaticity of the NOM were found to be possible qualifiers that distinguish produced water from the coalbed methane well from produced water from the oil well. And the specific chemical fragments that are linked to polysaccharide sources were found to be potential identifiers that distinguish produced water from the newer oil well from produced water from the older oil well. These identifiers were, however, only suggested for this preliminary study. More samples must be included to build a substantial database on produced water NOM to confirm and identify more markers.

Gas Chromatography-Mass Spectrometry↗
PubMed1994

Retinal adhesiveness in surgically enucleated human eyes.

PURPOSE: Retinal adhesion in rabbits and monkeys has been shown to involve the interphotoreceptor matrix and depend on environmental factors, such as temperature, pH, and calcium concentration. This study was designed to see whether these same factors modulate retinal adhesiveness in humans. METHODS: Four surgically enucleated human eyes were studied. Strips of eyecup were placed in experimental baths shortly after enucleation to evaluate environmental conditions. Retinal adhesive strength was quantified by the amount of retinal pigment epithelial pigment adherent to retina peeled from strips of eyecup. Cone and rod sheaths of the interphotoreceptor matrix were studied by microscopic examination of samples stained with the lectins peanut and wheat germ agglutinin. RESULTS: Retinal adhesiveness fell to 0 approximately 40 minutes after enucleation. Adhesive strength was maintained by cold temperature and was weakened by low pH or low calcium in the bath. Cone and rod matrix sheaths became stretched (indicating a bond) as outer segments and retinal pigment epithelium were peeled apart. CONCLUSION: Retinal adhesion in humans appears to involve similar mechanisms as in rabbits and monkeys.

Adhesiveness↗
PubMedDate not supplied

Synthesis and characterization of injectable poly(N-isopropylacrylamide-co-acrylic acid) hydrogels with proteolytically degradable cross-links.

Hydrogels composed of N-isopropylacrylamide (NIPAAm) and acrylic acid (AAc) were prepared by redox polymerization with peptide cross-linkers to create an artificial extracellular matrix (ECM) amenable for testing hypotheses regarding cell proliferation and migration in three dimensions. Peptide degradable cross-linkers were synthesized by the acrylation of the amine groups of glutamine and lysine residues within peptide sequences potentially cleavable by matrix metalloproteinases synthesized by mammalian cells (e.g., osteoblasts). With the peptide cross-linker, loosely cross-linked poly(N-isopropylacrylamide-co-acrylic acid) [P(NIPAAm-co-AAc)] hydrogels were prepared, and their phase transition behavior, lower critical solution temperature (LCST), water content, and enzymatic degradation properties were investigated. The peptide-cross-linked P(NIPAAm-co-AAc) hydrogels were pliable and fluidlike at room temperature and could be injected through a small-diameter aperture. The LCST of peptide-cross-linked hydrogel was influenced by the monomer ratio of NIPAAm/AAc but not by cross-linking density within the polymer network. A peptide-cross-linked hydrogel with a 97/3 molar ratio of NIPAAm/AAc exhibited a LCST of approximately 34.5 degrees C. Swelling was influenced by NIPAAm/AAc monomer ratio, cross-linking density, and swelling media; however, all hydrogels maintained more than 90% water even at 37 degrees C. In enzymatic degradation studies, breakdown of the peptide-cross-linked P(NIPAAm-co-AAc) hydrogels was dependent on both the concentration of collagenase and the cross-linking density. These results suggest that peptide-cross-linked P(NIPAAm-co-AAc) hydrogels can be tailored to create environmentally-responsive artificial extracellular matrixes that are degraded by proteases.

Acrylamides↗
PubMed1998

Vitronectin decreases microvascular endothelial cell apoptosis.

Angiogenesis after tissue injury occurs in a matrix environment consisting of fibrin, fibronectin, and vitronectin as the major extracellular matrix (ECM) constituents. ECM-integrin interactions is critical for angiogenesis and failure to bind a ligand to certain integrin receptors (alpha[v]beta3 or alpha[v]beta5) inhibits angiogenesis. The ligand that binds to alpha(v)beta3 or alpha(v)beta5 integrin receptors during microvascular angiogenesis has not been identified. Our hypothesis is that provisional matrix molecules provide the environmental context cues to microvascular endothelial cells and promote angiogenesis by decreased programmed cell death. Using cultured human microvascular endothelial cells, we show that vitronectin, in comparison to growth on alternative provisional matrix molecules (fibronectin, fibrinogen plus thrombin), collagen I, and basement membrane molecules (collagen IV), significantly reduces microvascular endothelial cell death in vitro. This reduction was observed using morphologic criteria, TdT-mediated dUTP nick end labeling (TUNEL) assay, histone release into the cytoplasm, and thymidine release into the supernatant. Though our data confirm that vitronectin may bind to more than one integrin receptor to reduce MEC apoptosis, binding to the alpha(v) component appears to be the critical integrin subcomponent for reducing apoptosis.

Apoptosis↗
PubMed1993

Poly(HEMA)-collagen composite as a biomaterial for hard tissue replacement.

This article briefly reviews the possibilities for hard tissue replacement with a new biomaterial. The basic differences found experimentally for polymer (HEMA) and collagen composite at the biological environment are stressed. The influence of the collagen distribution and matrix porosity of composite material on biodegradation is also discussed.

Animals↗
PubMed2002

Static extraction with modified pressurized liquid and on-line fluorescence monitoring. Independent matrix approach for the removal of polycyclic aromatic hydrocarbons from environmental solid samples.

The coupling of a static pressurized liquid extractor to a flow injection manifold has allowed real-time on-line fluorescence monitoring of the polycyclic aromatic hydrocarbons (PAHs) extracted from environmental solid samples, which can be used for either screening or semiquantitative purposes. Sodium dodecyl sulfate (SDS) was added to the water for favoring the extraction of the low-polar analytes. Different solid samples such as sandy soil, river sediments, trout and sardine spiked with the target PAHs were subjected to several 15-min static extraction cycles with SDS-water, at 200 degrees C. The results obtained demonstrated that fluorometric monitoring of static pressurized liquid extraction constitutes an approach as efficient as conventional Soxhlet for the extraction of PAHs from solid samples but with the following positive features: (a) drastic reduction of the extraction time as the extraction kinetics can be monitored and thus the end of the leaching step determined independently of the sample matrix; (b) use of water as extractant thus given place to an environmentally friendly method; and (c) coupling of static extraction to subsequent dynamic steps. The method has been applied to a certified reference material (CRM 524, BCR, industrial soil/organics) for quality assurance/validation. The total content of each analyte was determined by HPLC-fluorimetric detection.

Chromatography, High Pressure Liquid↗
PubMed2001

Microbial inhibitors for U.S. EPA drinking water methods for the determination of organic compounds.

Preservation of chemical analytes in drinking water samples is necessary to obtain accurate information concerning contaminant occurrence. Sample preservation to prevent biodegradation is important for most samples and analytes. With the unique demands of environmental methods, it is not always possible to kill all microorganisms without having undesirable effects. To find a suitable preservative, the sample, analysis, and preservation needs should be considered. During method development of U.S. Environmental Protection Agency (EPA) Methods 526 (for unstable semivolatile compounds) and 532 (for phenylurea pesticides), a number of studies were conducted to identify compatible microbial inhibitors. Copper sulfate was successfully used in Method 532 and is an excellent first-choice antimicrobial agent for many applications. Copper sulfate can catalyze hydrolysis reactions for some pesticides such as those analyzed in Method 526. Under these conditions, a nonmetal compound of antimicrobial activity must be considered. During the development of Method 526, a survey of alternate organic based antimicrobial compounds found that diazolidinyl urea worked well in the method. Several other candidate microbial inhibitors were identified that could have application to other environmental methods. A general approach to selecting antimicrobial compounds in future environmental methods in water matrixes is discussed.

Anti-Infective Agents, Local↗
PubMed1994

Restricted maximum likelihood procedures for the estimation of additive and nonadditive genetic variances and covariances in multibreed populations.

Restricted maximum-likelihood procedures were developed to estimate additive and nonadditive genetic and environmental covariances for multiple traits in multibreed populations. The computational procedure follows the expectation-maximization (EM) algorithm, where the set of equations in the maximization step is solved by successive approximations. This computational procedure does not guarantee convergence to a symmetric positive-definite covariance matrix. Thus, computer programs will need to incorporate restrictions in the maximization step to ensure positive definiteness of each covariance matrix. Additive genetic and environmental covariances were modeled in subclass form (zeros and ones in the design matrices). Nonadditive genetic covariances were modeled in regression form (any value between and including zero and one in the design matrices). Computational requirements will be larger than for intrabreed analyses. Appropriate simplifying assumptions and numerical techniques (e.g., sparse and iterative numerical techniques) will be required for the implementation of these multibreed covariance estimation procedures. Number of iterations (5 to 12) and computing times (57 to 113 min) to achieve convergence when estimating 21 genetic and environmental covariances in five small simulated multibreed data sets (two breeds, 25,200 to 50,400 calves, 120 to 135 unrelated bulls) suggest that these procedures are computationally feasible.

Algorithms↗
PubMed2002

Laser-induced multidimensional fluorescence spectroscopy in Shpol'skii matrixes for the analysis of polycyclic aromatic hydrocarbons in HPLC fractions and complex environmental extracts.

Fluorescence measurements are easily made with the aid of a cryogenic fiber optic probe. Emission wavelength time matrixes, excitation emission matrixes, and time-resolved excitation emission matrixes are rapidly collected with a pulsed tunable dye laser, a spectrograph, and an intensified charged-coupled device. Compound identification is based on spectral and lifetime information. The potential of this approach for supporting high-performance liquid chromatography analysis and for the direct determination of benzo[a]pyrene without previous separation is demonstrated.

Chromatography, High Pressure Liquid↗
PubMed2001

High resolution ID-ICP-MS certification of an estuary water reference material (LGC 6016) and analysis of matrix induced polyatomic interferences.

Reliable trace metal analysis of environmental samples is dependent upon the availability of high accuracy, matrix reference standards. Here, we present Cd, Cu, Ni, Pb and Zn isotope dilution determination for an estuary water certified reference material (LGC 6016). This work highlights the need for high-accuracy techniques in the development of trace element CRMs rather than conventional inter-laboratory trials. Certification of the estuary water LGC6016 was initially determined from a consensus mean from 14 laboratories but this was found to be unsatisfactory due to the large discrepancies in the reported concentrations. The material was re-analysed using isotope dilution ICP-MS techniques. Pb and Cd were determined using a conventional quadrupole ICP-MS (Elan 5000). Cu, Zn and Ni were determined using a magnetic sector ICP-MS (Finnigan Element), which allowed significant polyatomic interferences to be overcome. Using the magnetic sector instrument, precise mass calibration to within 0.02 amu permitted identification of the interferences. Most interferences derived from the sample matrix. For example, the high Na content causes interferences on 63Cu, due to the formation of 40Ar23Na and 23Na2 16O1H, which in a conventional quadrupole instrument would relate to an erroneous increase in signal intensity by up to 20%. For each analyte a combined uncertainty calculation was performed following the Eurachem/GTAC and ISO guideline. For each element a combined uncertainty of 2-3% was found, which represents a 10-fold improvement compared to certification by inter-laboratory comparison. Analysis of the combined uncertainty budget indicates that the majority of systematic uncertainty derives from the instrumental isotope ratio measurements.

Calibration↗
PubMed2000

Evaluation and validation of a commercial ELISA for diazinon in surface waters.

The performance of a commercially available microtiter plate ELISA kit for the determination of diazinon was evaluated for sensitivity, selectivity, intra-assay repeatability, accuracy, and matrix effects in fortified distilled water and filtered and unfiltered environmental surface water samples. Repeatability and reproducibility studies show that the kit satisfies current EPA criteria for the assessment of analytical methods. Mean recoveries from spiked samples averaged 80.3, 95.5, and 103.5% from distilled, unfiltered surface, and filtered surface waters, respectively. The experimentally determined method detection limit (MDL) for the commercial diazinon microtiter plate format (0.0159 microg L(-)(1)) was comparable to the least detectable dose (LDD) established by the manufacturer (0.022 microg L(-)(1)). Specificity studies indicate that the diazinon polyclonal antibody can readily distinguish the target compound from other structurally similar organophosphorus analogues, with the exception of diazoxon. Cross-reactivity with the oxon was approximately 29%, while reactivity with pirimiphos-methyl, pirimiphos-ethyl, and chlorpyrifos-ethyl was negligible. A slight matrix effect was discovered to be present in both filtered and unfiltered environmental water matrixes, but its effect on the immunoassays is insignificant within experimental error. For validation of the microtiter plate ELISA format, environmental surface and storm runoff water samples were collected, split, and analyzed directly by ELISA and by liquid-liquid extraction followed by GC (California State Department of Food and Agriculture method EM 46.0). Results of the two analytical methods were then compared statistically. A close correlation was found between methods for unspiked and untreated river water samples (r = 0.969) while a much less robust correlation was obtained for runoff waters (r = 0.728). Results from runoff waters exhibit a particularly high positive bias for the ELISA method relative to the GC method. Cross-reactivity of diazoxon and probably other unidentified cross-reacting components may be responsible for the exaggerated account of the target analyte in surface and runoff waters. While excellent for screening purposes, further study is required to elucidate and quantify the factors responsible for the consistent overestimation of ELISA results before the kit can be employed routinely for regulatory compliance monitoring.

Diazinon↗
PubMed1988

Spiked natural matrix materials as quality assessment samples.

The Environmental Measurements Laboratory has conducted the Quality Assessment Program (QAP) since 1976 to evaluate the quality of the environmental radioactivity data, which is reported to the Department of Energy by as many as 42 commercial contractors involved in nuclear work. In this program, matrix materials of known radionuclide concentrations are distributed routinely to the contractors and the reported results are compared. The five matrices used are: soil, vegetation, animal tissue, water and filter paper. Environmental soil, vegetation and animal tissue are used, but the water and filter paper samples are prepared by spiking with known amounts of standard solutions traceable to the National Bureau of Standards. A summary of results is given to illstrate the successful operation of the program. Because of the difficulty and high cost of collecting large samples of natural matrix material and to increase the versatility of QAP, an attempt was recently made to prepare the soil, vegetation and animal tissue samples with spiked solutions. A description of the preparation of these reference samples and the results of analyses are presented along with a discussion of the pitfalls and advantages of this approach.

Animals↗