bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA damage and external lesions in brown bullheads (Ameiurus nebulosus) from contaminated habitats
Authors: Yang Xuan , Meier John , Chang Lina , Rowan Michael , Baumann Paul C. 
Published: October 2006

Abstract
The Comet assay was used to compare levels of DNA damage in brown bullheads (Ameiurus nebulosus) collected from three known contaminated locations, the Cuyahoga River (OH, USA), Ashtabula River (OH, USA; both tributaries to Lake Erie, USA), and Ashumet Pond (Cape Cod, MA, USA), with brown bullheads collected from three paired reference sites, Old Woman Creek (OH, USA), Conneaut River (OH, USA; both tributaries to Lake Erie), and Great Herring Pond (mainland MA, USA), respectively. Blood was sampled from each fish, and the Comet assay was conducted on erythrocytes. The assay results demonstrate that fish from the three contaminated sites each suffered higher DNA damage compared with fish from their respective reference sites. The results also show that the genetic damage was associated with the occurrence of external lesions and deformities in fish. The Comet assay is sufficiently sensitive to detect exposure of natural fish populations to environmental levels of genotoxic contaminants.
Effects of nutrient enrichment, depuration substrate, and body size on the trophic transfer of cadmium associated with microalgae to the benthic amphipod Leptocheirus plumulosus
Authors: Yu Ri-Qing , Fleeger John W. 
Published: October 2006

Abstract
Bioavailability and nutrient effects on the trophic transfer of Cd associated with microalgae to the marine benthic amphipod Leptocheirus plumulosus were investigated. Cadmium assimilation efficiency (AE) of suspension-feeding L. plumulosus significantly varied among three algal species tested (Nitzschia punctata, Thalassiosira weissflogii, and Isochrysis galbana). Depuration substrate greatly influenced Cd AE for L. plumulosus (AE was much higher for nonburrowed amphipods), probably because sediment burrowing allowed L. plumulosus to feed as a surface deposit feeder. The L. plumulosus body size, ranging from 0.5 to 2.0 mm, did not affect Cd AE. Nitrate enrichment from 0 to 180 μM in algal culture significantly increased Cd AE from 9.4 to 18.8% for T. weissflogii, from 10.0 to 27.3% for N. punctata, and from 10.0 to 16.2% for I. galbana; nitrate enrichment from 0 to 60 μM did not influence Cd AE in any algal species tested. Physiological turnover rate constants of Cd in L. plumulosus ranged from 0.016 to 0.025/h for the three species and were independent of nitrate addition. Nitrate enrichment strongly enhanced Cd distribution in algal cytoplasm. Phosphate enrichment (0–7.5 μM) did not significantly affect Cd AEs in L. plumulosus. Overall, a significant linear relationship was observed between the Cd AE of L. plumulosus and the fraction of Cd available in algal cytoplasm. Our work suggests that eutrophication by nitrate enrichment has the potential to enhance the trophic transfer of Cd from microalgae to suspension-feeding benthic invertebrates.
Relating daily solar ultraviolet radiation dose in salt marsh-associated estuarine systems to laboratory assessments of photoactivated polycyclic aromatic hydrocarbon toxicity
Authors: Weinstein John E. , Diamond Stephen A. 
Published: October 2006

Abstract
Estuaries of the southeastern United States not only serve an important nursery function but also are common repositories of polycyclic aromatic hydrocarbons (PAHs) derived from upland activities. Thus, these habitats may be at risk for PAH phototoxicity. To better characterize this risk, a daily survey of ultraviolet-A (UV-A; 320–400 nm) irradiance was performed at Leadenwah Creek (Wadmalaw Island, SC, USA) on June 27 and August 1, 2003. In addition, laboratory assays were completed using two light exposure regimes: One that was typical of historical phototoxicity assessments (continuous light [C-UV]), and a more environmentally realistic regime (ER-UV). On both survey days, irradiance at a depth of 10 cm exhibited a pattern generally similar to that observed at the surface, whereas irradiance at the bottom of the creek was a function of both tidal height and time of day. Total UV-A dose at a 10-cm depth on June 27 and August 1, 2003 was 4.37 and 4.78 J/cm2, respectively. Attenuation coefficients on both days varied as a function of tidal height. In the laboratory, larval grass shrimp (Palaemonetes pugio) exposed to an ER-UV regime for these habitats (photoperiod, 12: 12-h light: dark; total daily UV-A dose, 4.40 J/cm2) exhibited a 2.5-fold decrease in toxicity compared with those exposed to the C-UV regime (photoperiod, 24: 0-h light: dark; total daily UV dose, 1.50 J/cm2), despite a threefold higher UV dose in the ER-UV regime. The lower potency under the ER-UV regime likely is attributable to the presence of a 12-h dark period allowing for recovery. The consequences of these results are discussed in the context of habitat-specific UV-A dose and its relevance to future laboratory assessments of PAH phototoxicity.
Metabolite production in degradation of pyrene alone or in a mixture with another polycyclic aromatic hydrocarbon by Mycobacterium sp.
Authors: Zhong Yin , Luan Tiangang , Zhou Hongwei , Lan Chongyu , Tam Nora Fung Yee 
Published: October 2006

Abstract
Degradation of pyrene (PYR) alone and in the presence of phenanthrene or fluoranthene by Mycobacterium sp. strain A1-PYR isolated from mangrove sediments was investigated. When PYR was the only polycyclic aromatic hydrocarbon compound and the sole carbon source, only 33% of the added PYR was slowly degraded during 7 d of incubation. Seven metabolites were obtained, including four-ring metabolites (monohydroxypyrene and three different dihydroxypyrenes) and three-ring metabolites (dihydroxyphenanthrene, 4-phenanthrene-carboxylic acid, and 4-phenanthrol), of which more four-ring metabolites accumulated compared with three-ring metabolites. To our knowledge, this is the first report in which PYR was initially attacked by Mycobacterium sp. to form three different dihydroxypyrenes. Pyrene degradation was significantly stimulated when mixed with phenanthrene or fluoranthene. In the presence of fluoranthene, PYR was rapidly degraded (up to 57%), and significant amounts of dihydroxypyrene were formed within 3 d of incubation, followed by a period of minimal PYR degradation from 3 to 7 d with disappearance of fourring metabolites and accumulation of three-ring metabolites. In contrast, PYR was removed completely, and little evidence of metabolites was detected in the presence of phenanthrene. These results showed that PYR was degraded to a larger extent when mixed with another polycyclic aromatic hydrocarbon concomitant with a higher turnover of PYR metabolites. The induction of complex enzyme systems and increase in biomass possibly affected the transformation of PYR metabolites in the mixture with phenanthrene or fluoranthene.
Estimation of polychlorinated biphenyl fugacity ratios
Authors: van Noort Paul C.M. 
Published: October 2006

Abstract
On the quantitative comparison of solubilities or vapor pressures of homologous series, the variation in the effect of crystal structure on solid properties may substantially influence the outcome of the comparison. Usually, the effect of this variation is eliminated by comparing values of the liquid state. The ratio of solid to liquid properties is called the fugacity ratio. Fugacity ratios are usually calculated from fusion thermodynamic data. For 41 polychlorinated biphenyls (PCBs), fusion enthalpy was found to be correlated with fusion entropy. Highly linear correlations were observed for non-ortho-PCBs, mono-ortho-PCBs, and di-ortho-PCBs. Fugacity ratios estimated from the fusion enthalpy-entropy linear regression parameters were equal, within 10% on average, to fugacity ratios calculated from fusion enthalpy for ortho- chlorinated PCBs with melting points below 380 K and for non-ortho-PCBs. For ortho chlorinated PCBs with melting points above 380 K, fugacity ratios were better estimated from a nonlinear regression of fugacity ratios against the melting point and the system temperature. For all 209 PCB congeners, fugacity ratios at 298 K are listed on the basis of experimental fusion data or estimates from the regressions.
Measured partitioning coefficients for parent and alkyl polycyclic aromatic hydrocarbons in 114 historically contaminated sediments: Part 1. KOC values
Authors: Hawthorne Steven B. , Grabanski Carol B. , Miller David J. 
Published: October 2006

Abstract
Polycyclic aromatic hydrocarbon (PAH) partitioning coefficients between sediment organic carbon and water (KOC) values were determined using 114 historically contaminated and background sediments collected from eight different rural and urban waterways in the northeastern United States. More than 2,100 individual KC values were measured in quadruplicate for PAHs ranging from two to six rings, along with the first reported KOC values for alkyl PAHs included in the U.S. Environmental Protection Agency's (U.S. EPA) sediment narcosis model for the prediction of PAH toxicity to benthic organisms. Sediment PAH concentrations ranged from 0.2 to 8,600 μg/g (U.S. EPA 16 parent PAHs), but no observable trends in KOC values with concentration were observed for any of the individual PAHs. Literature KOC values that are commonly used for environmental modeling are similar to the lowest measured values for a particular PAH, with actual measured values typically ranging up to two orders of magnitude higher for both background and contaminated sediments. For example, the median log KOC values we determined for naphthalene, pyrene, and benzo[a]pyrene were 4.3, 5.8, and 6.7, respectively, compared to typical literature KOC values for the same PAHs of 2.9, 4.8, and 5.8, respectively. Our results clearly demonstrate that the common practice of using PAH KOC values derived from spiked sediments and modeled values based on n-octanol–water coefficients can greatly overestimate the actual partitioning of PAHs into water from field sediments.
Quantitative structure-activity relationships for toxicity of nonpolar narcotic chemicals to Pseudokirchneriella subcapitata
Authors: Hsieh Shih-Hung , Hsu Chih-Hsiung , Tsai Din-Yu , Chen Chung-Yuan 
Published: October 2006

Abstract
This study presents data for 27 nonpolar narcotic compounds regarding toxicity to Pseudokirchneriella subcapitata as evaluated using a closed-system algal toxicity test with an exposure time of 48 h. Two test endpoints, dissolved oxygen production and algal growth rate, were used to assess the toxicity of nonpolar narcotic chemicals on algae. Hydrophobicity (1-octanol-water partition coefficient [KOW]) provided satisfactory descriptions for the toxicity of nonpolar narcotic compounds, and quantitative structure–activity relationships based on log KOW were established. The relative sensitivity of various aquatic organisms to nonpolar chemicals was as follows: P. subcapitata &gt; Vibrio fischeri ≥ Nitrosomonas sp. &gt; fathead minnow &gt; Daphnia magna &gt; polytox &gt; activated sludge. In addition, linear relationships were found between the toxicity observed in P. subcapitata and other aquatic organisms, except in the case of Nitrosomonas sp. Therefore, for nonpolar toxicants, the closed-system technique applied in the present study can be an ideal surrogate for other tests, such as fathead minnow and D. magna, that are either time-consuming or labor-intensive. However, because the current toxicity database is based primarily on the conventional batch tests, it cannot provide adequate assessment regarding the effects of various organic toxicants. Therefore, more extensive research is needed to revise the database for the toxicity of organic compounds on phytoplankton using the closed-system technique.
Nd‐Doped TiO2 Nanorods: Preparation and Application in Dye‐Sensitized Solar Cells
Authors: Yao Qiaohong , Liu Junfeng , Peng Qing , Wang Xun , Li Yadong 
Published: October 2006

AbstractMonodispersed Nd‐doped TiO2 nanorods (20 nm×2 nm) were synthesized by solvothermal methods and characterized by TEM, XRD, and EDS. Application of the nanorods for modifying conventional photoanodes in dye‐sensitized solar cells (DSSCs) was investigated. Data show that, after modification, an enhancement of the incident‐photon‐to‐current conversion efficiency (IPCE) in the whole range of visible light was observed and an increase of 33.3 % for overall conversion efficiency was achieved. Our mechanistic proposal is that Nd ions doped on TiO2 nanorods to some extent enhance the injection of excited electrons and decrease the recombination rate of the injected electrons.
Improved catalytic properties of immobilized lipases by the presence of very low concentrations of detergents in the reaction medium
Authors: Fernandez‐Lorente Gloria , Palomo Jose M. , Cabrera Zaida , Fernandez‐Lafuente Roberto , Guisán José M. 
Published: October 2006

AbstractThe addition of a very small concentration of a detergent (in many instances under the critical micellar concentration (cmc)) has been found to greatly increase the activity of immobilized lipases, using those from Pseudomonas fluorescens (PFL) and Candida antarctica (isoform B) as model enzymes. However, the detergents may also have a negative effect on enzyme activity; in fact, for all enzyme preparations and substrates the activity/detergent concentration curve reached a maximum value and started to decrease, in many instances even under the initial value. The concentration and nature of the detergent (SDS, CTAB, Triton X‐100, or X‐45) that permitted the maximum hyperactivation was different depending on the substrate. The best hyperactivation values promoted by the presence of detergent were over a 20‐fold factor. The presence of detergents permitted the inhibition of lipases by irreversible covalent inhibitors (e.g., 4‐(2‐aminoethyl)benzenesulfonyl fluoride hydrochloride) (AEBSF) while the enzyme, in the absence of detergent, is not inhibited by these irreversible inhibitors. This suggested that the main effect of the detergents is to shift the conformational equilibrium of lipases toward the open form. Moreover, the presence of detergents also permitted to improve the enantioselectivity exhibited by the immobilized lipases in some cases. For example, the enantioselectivity of PFL‐glyoxyl agarose increased from 40 to more than 100 in the hydrolysis of (±)‐2‐hydroxy‐4‐phenylbutyric acid ethyl ester by using 0.1% CTAB. Biotechnol. Bioeng. 2007;97: 242–250. © 2006 Wiley Periodicals, Inc.
Optimization of enzyme complexes for lignocellulose hydrolysis
Authors: Berlin Alex , Maximenko Vera , Gilkes Neil , Saddler Jack 
Published: October 2006

AbstractThe ability of a commercial Trichoderma reesei cellulase preparation (Celluclast 1.5L), to hydrolyze the cellulose and xylan components of pretreated corn stover (PCS) was significantly improved by supplementation with three types of crude commercial enzyme preparations nominally enriched in xylanase, pectinase, and β‐glucosidase activity. Although the well‐documented relief of product inhibition by β‐glucosidase contributed to the observed improvement in cellulase performance, significant benefits could also be attributed to enzymes components that hydrolyze non‐cellulosic polysaccharides. It is suggested that so‐called “accessory” enzymes such as xylanase and pectinase stimulate cellulose hydrolysis by removing non‐cellulosic polysaccharides that coat cellulose fibers. A high‐throughput microassay, in combination with response surface methodology, enabled production of an optimally supplemented enzyme mixture. This mixture allowed for a ∼twofold reduction in the total protein required to reach glucan to glucose and xylan to xylose hydrolysis targets (99% and 88% conversion, respectively), thereby validating this approach towards enzyme improvement and process cost reduction for lignocellulose hydrolysis. Biotechnol. Bioeng. 2007;97: 287–296. © 2006 Wiley Periodicals, Inc.
Anaerobic digestion of solid material: Multidimensional modeling of continuous‐flow reactor with non‐uniform influent concentration distributions
Authors: Vavilin V.A. , Lokshina L.Y. , Flotats X. , Angelidaki I. 
Published: October 2006

AbstractA new multidimensional (3 and 2D) anaerobic digestion model for cylindrical reactor with non‐uniform influent concentration distributions was developed to study the way in which mixing intensity affects the efficiency of continuous‐flow anaerobic digestion. Batch experiments reported and simulated earlier by Vavilin and Angelidaki (2005) were used to modernize a kinetic scheme and to obtain the corresponding kinetic coefficients. In the new models, hydrolytic microorganisms were included using Contois kinetics for the hydrolysis/acidogenesis degradation of municipal solid waste (MSW). Monod kinetics was applied for description of methanogenesis. Both hydrolytic and methanogenic microorganisms were assumed to be inhibited by high volatile fatty acids (VFA) concentration. According to the new distributed models, the mixing level reduction expressed by increasing dimensionless Peclet number may improve the continuous flow reactor performance at the relatively low influent methanogenic biomass concentration. In the continuously stirred tank reactor (CSTR) there are two steady states with and without methane production at slightly different values of initial methanogenic biomass concentration. In the system, the threshold methanogenic biomass concentration existed because of inhibition by high VFA concentration. High methanogenic biomass concentration is required for efficient anaerobic digestion of MSW in order to avoid possible inhibition due to high VFA build‐up. Thus, CSTR configuration might have unstable dynamics at high organic loading as shown in earlier experiments carried out by Stroot et al. (2001). A gradual increase of organic loading during the start up of a completely mixed digester causing an accumulation of methanogenic biomass is a solution to prevent a probable digester failure. According to the distributed models a plug‐flow reactor with non‐uniform influent concentration distributions where methanogenic and hydrolytic microorganisms are separated has significant methane production and solids removal at the relatively low influent methanogenic biomass concentration. Biotechnol. Bioeng. 2007;97: 354–366. © 2006 Wiley Periodicals, Inc.
Factors Mediating Activity, Selectivity, and Substrate Specificity for the Thiamin Diphosphate‐Dependent Enzymes Benzaldehyde Lyase and Benzoylformate Decarboxylase
Authors: Knoll Michael , Müller Michael , Pleiss Jürgen , Pohl Martina 
Published: October 2006

AbstractBenzaldehyde lyase from Pseudomonas fluorescens and benzoylformate decarboxylase from Pseudomonas putida are homologous thiamin diphosphate‐dependent enzymes that catalyze carboligase and carbolyase reactions. Both enzymes catalyze the formation of chiral 2‐hydroxy ketones from aldehydes. However, the reverse reaction has only been observed with benzaldehyde lyase. Whereas benzaldehyde lyase is strictly R specific, the stereoselectivity of benzoylformate decarboxylase from P. putida is dependent on the structure and orientation of the substrate aldehydes. In this study, the binding sites of both enzymes were investigated by using molecular modelling studies to explain the experimentally observed differences in the activity, stereo‐ and enantioselectivity and substrate specificity of both enzymes. We designed a detailed illustration that describes the shape of the binding site of both enzymes and sufficiently explains the experimental effects observed with the wild‐type enzymes and different variants. These findings demonstrate that steric reasons are predominantly responsible for the differences observed in the (R)‐benzoin cleavage and in the formation of chiral 2‐hydroxy ketones.
SECM Visualization of Spatial Variability of Enzyme‐Polymer Spots. Part 2: Complex Interference Elimination by Means of Selection of Highest Sensitivity Sensor Substructures and Artificial Neural Networks
Authors: Maciejewska Monika , Schäfer Dominik , Schuhmann Wolfgang 
Published: October 2006

AbstractPolymer spots with entrapped glucose oxidase were fabricated on glass surfaces and the localized enzymatic response was subsequently visualized using scanning electrochemical microscopy (SECM) in the generator–collector mode. SECM images were obtained under simultaneous variation of the concentration of glucose (0–6 mM) and ascorbic acid (0–200 μM), or, in a second set of experiments, of glucose (0–2 mM) and 2‐deoxy‐D(+)‐glucose (0–4 mM). Aiming at the quantification of the mixture components discretization of the response surfaces of the overall enzyme/polymer spot into numerous spatially defined microsensor substructures was performed. Sensitivity of sensor substructures to measured analytes was calculated and patterns of variability in the data were analyzed before and after elimination of interferences using principal component analysis. Using artificial neural networks which were fed with the data provided by the sensor substructures showing highest sensitivity for glucose, glucose concentration could be calculated in solutions containing unknown amounts of ascorbic acid with a good accuracy (RMSE 0.17 mM). Using, as an input data set, measurements provided by sensing substructures showing highest sensitivity for ascorbic acid in combination with the response of the sensors showing highest dependence on the glucose concentration, the error of the ascorbic acid concentration calculation in solution containing the unknown amount of glucose was 10 μM. Similarly, prediction of the glucose concentration in the presence of 2‐deoxy‐D(+)‐glucose was possible with a RMSE of 0.1 mM while the error of the calculation of 2‐deoxy‐D(+)‐glucose concentrations in the presence of unknown concentrations of glucose was 0.36 mM.
QCM Immunosensor Based on Polyamidoamine Dendrimers
Authors: Svobodová Lenka , Šnejdárková Maja , Polohová Vladimíra , Grman Igor , Rybár Peter , Hianik Tibor 
Published: October 2006

AbstractThe poly(amidoamine)(PAMAM) dendrimers of fourth generation (G4) and 1‐hexadecanethiol (HDT) has been used for formation of self assembled monolayers on a gold surface for preparation of quartz crystal microbalance (QCM) immunosensor for detection of human IgG. The anti‐IgG antibodies were immobilized on a surface of G4‐HDT layers or those covered by Protein A. In later case the oriented immobilization of anti‐IgG takes place due to preferred interaction of Fc portion of antibodies with the Protein A. The detection limit in a flow mode was 7 nM both for biosensor with and without Protein A. However, in the case of Protein A the number of bounded Ab was 1.4 times lower in comparison with those without Protein A. Thus, the sensitivity of the Protein A based sensor was higher due to orientation effect in comparison with randomly oriented Ab at a dendrimer surface without Protein A. Increased concentration of IgG and formation of Ab‐Ag complexes resulted in increase of motional resistance, that suggest increased contribution of viscoelasticity, as revealed from impedance analysis. The most important property of the immunosensor was its ability for regeneration using 0.1 M glycine‐HCl.