bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential effects of isomeric incorporation of fluorophenylalanines into PvuII endonuclease
Authors: Dominguez Miguel A. , Thornton Kevin C. , Melendez Maria G. , Dupureur Cynthia M. 
Published: August 2002

AbstractIncorporation of fluorine into proteins has long served as a means of probing structure and function, yet there are few studies that examine the impact of fluorine substitution, particularly at locations distant from the active sites of enzymes. The flexibility of isomeric fluorine incorporation at Phe is used to explore subtle substitution effects on enzyme activity and conformation. The unnatural amino acids o‐, m‐, and p‐fluorophenylalanines were incorporated biosynthetically into the representative PvuII restriction endonuclease. Interestingly, m‐fluoro‐Phe‐PvuII endonuclease exhibits very similar conformational stability to that of the native enzyme, but it exhibits a reproducible, 2‐fold higher average specific activity. Given the level of incorporation and the distribution of species, the species of modified enzyme responsible for this increase in specific activity is most likely even faster. Further, moving the fluorine atom from the meta‐ to the para‐position of Phe results in a 4‐fold decrease in specific activity and a decrease in conformational stability of 1.5 kcal/mol. Since none of the Phe residues in PvuII endonuclease lies near the DNA recognition or catalytic sites, this differential behavior alludes to the impact of subtle changes in enzyme conformation on endonuclease activity and suggests novel ways to influence catalytic behavior. Proteins 2001;45:55–61. © 2001 Wiley‐Liss, Inc.
Filling a cavity dramatically increases pressure stability of the c‐Myb R2 subdomain
Authors: Lassalle Michael W. , Yamada Hiroaki , Morii Hisayuki , Ogata Kazuhiro , Sarai Akinori , Akasaka Kazuyuki 
Published: August 2002

AbstractCavities or packing defects in proteins may generally be related with the dynamics and function of a protein. In the c‐Myb R2 subdomain, its single cavity has been shown to be crucial for its DNA recognition. Cavities are also considered important in determining the pressure stability of a protein. In the present work, high‐pressure proton nuclear magnetic resonance (1H NMR) spectroscopy at 750 MHz is used to study the effect of a cavity‐filling mutation (V103L) on the stability of the c‐Myb R2 subdomain in the pressure range between 1 and 3,700 bar at 5°C. A dramatic increase in the pressure stability of the c‐Myb R2 subdomain is attained, from which we estimate the cavity size to be 35.3 Å3, in good agreement with literature values. We also evaluated the increase in thermodynamic stability ΔGfrom 5.35 kJ/mol to 7.34 kJ/mol by the mutation, giving a clear example of the effect of a cavity on the global stability of a globular protein. Proteins 2001;45:96–101. © 2001 Wiley‐Liss, Inc.
Degradation of herbicides in shallow Danish aquifers: an integrated laboratory and field study
Authors: Albrechtsen Hans‐Jørgen , Mills Margaret S , Aamand Jens , Bjerg Poul L 
Published: August 2002

AbstractDegradation of pesticides in aquifers has been evaluated based on a number of co‐ordinated field and laboratory studies carried out in Danish aquifers. These studies included investigations of vertical and horizontal variability in degradation rates from the vadose zone to an aquifer, the effects of aerobic versus anaerobic conditions, and the importance of concentration on degradation kinetics for a selected range of herbicides. The studies were based on different experimental approaches ranging from simple batch experiments to column studies to field injection experiments and, where appropriate, results were compared. Some herbicides were degraded under aerobic conditions (some phenoxy acids, DNOC and glyphosate) and others under aerobic conditions (other phenoxy acids, DNOC; there was some indication of atrazine transformation). Certain pesticides were not degraded in any investigations (dichlobenil, the dichlobenil metabolite 2,6‐dichlorobenzamide (BAM), bentazone, isoproturon, metamitron and metsulfuron‐methyl). The spatial variability was substantial, since hardly any of the investigated pesticides were degraded in all comparable samples. This means that it is very difficult to claim that a given pesticide is readily degradable in aquifers. However, the experimental approaches used (with incubations lasting more than a year) may not be sensitive enough to verify the low degradation rates that may be significant as a result of the long retention time of groundwaters.© 2001 Society of Chemical Industry
Prediction of pesticide concentrations found in rivers in the UK
Authors: Brown Colin D , Bellamy Pat H , Dubus Igor G 
Published: August 2002

AbstractSWATCATCH is a distributed model combined with databases within a GIS as the POPPIE system to predict pesticide concentrations in rivers at the catchment outlet. The model was evaluated against a dataset of pesticide concentrations in rivers of England and Wales. More than 2000 individual analyses in each of the years 1995 and 1997 covered approximately 150 catchment–pesticide combinations drawn from 29 catchments and 16 pesticides, themselves selected to represent a range of characteristics and properties. SWATCATCH was better able to simulate maximum pesticide concentrations at any time during the year than the proportion of samples containing residues of a particular pesticide above the limit of quantification. The model simulated maximum pesticide concentrations in surface waters which were within a factor of 10 of those observed for 66–74% of catchment–pesticide–year combinations. Simulated and observed frequency of detection could not be differentiated using a χ2 test for 54–67% of simulations. Time series analysis for seven of the 29 catchment–pesticide combinations indicated that measured and detected series of concentrations generally followed similar patterns. The evaluation supports the intended use of the model in assisting the construction of pesticide monitoring programmes.© 2002 Society of Chemical Industry
Antioxidant and hepatoprotective effects of punicalagin and punicalin on acetaminophen‐induced liver damage in rats
Authors: Lin Chun‐Ching , Hsu Yu‐Fang , Lin Ta‐Chen , Hsu Hsue‐Yin 
Published: August 2002

AbstractPunicalagin and punicalin were isolated from the leaves of Terminalia catappa L., a Combretaceous plant distributed throughout tropical and subtropical beaches, which is used for the treatment of dermatitis and hepatitis. Our previous studies showed that both of these compounds exert antioxidative activity. In this study, the antihepatotoxic activity of punicalagin and punicalin on acetaminophen‐induced toxicity in the rat liver was evaluated. After evaluating the changes of several biochemical functions in serum, the levels of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were increased by acetaminophen administration and reduced by punicalagin and punicalin. Histological changes around the hepatic central vein and oxidative damage induced by acetaminophen were also recovered by both compounds. The data show that both punicalagin and punicalin exert antihepatotoxic activity, but treatment with larger doses enhanced liver damage. These results suggest that even if punicalagin and punicalin have antioxidant activity at small doses, treatment with larger doses will possibly induce some cell toxicities. Copyright © 2001 John Wiley & Sons, Ltd.
Heteropteris aphrodisiaca O. Machado : effects of Extract BST 0298 on the oxidative stress of young and old rat brains
Authors: Mattei Rita , Paz Barros Marcelo , Pereira Galvão Suzana Maria , Bechara Etelvino José Henriques , de Araujo Carlini Elisaldo Luiz 
Published: August 2002

AbstractThe plant Heteropteris aphrodisiaca O. Machado is widely employed in Brazilian popular medicine as a stimulant, a tonic and a remedy for nervous debility. Several other plant products with similar therapeutic applications may have such effects based on the antioxidant content of polyphenols (gallates, cathecols, etc.) and flavonoids. The aim of this work was to investigate the effects of Heteropteris aphrodisiaca O. Machado extracts on the antioxidant defences and oxidative stress of young and old rat brains. Tests of lipoperoxidation in vitro, comparing H. aphrodisiaca extracts with butylhydroxytoluene (BHT), a classic antioxidant, showed an efficient inhibition of lipoperoxidation (Q1/2 = 3.3 μg/mL). Chronic treatment of young and old rats with 50 mg plant extract/kg body weight resulted in a significant increase in superoxide dismutase (SOD) activities (40%) in the brain of old rats, but no changes in catalase and glutathione peroxidase (GPX). No significant variations in antioxidant enzyme activities were observed in the brains of young rats. However, significantly lower levels of lipoperoxidation (30%) were detected in the brain of young rats upon plant extract administration, suggesting that H. aphrodisiaca extracts reduced the oxidative stress to brain lipids. Copyright © 2001 John Wiley & Sons, Ltd.
Ab initio calculation of the Young's modulus of α‐polyamides
Authors: Peeters Anik , Van Alsenoy C. , Bartha F. , Bogár F. , Zhang M.‐L. , Van Doren V. E. 
Published: August 2002

AbstractIn earlier works the supermolecule model has been applied to the calculation of the Young's modulus of crystalline polyethylene and polyamide‐6. In the supermolecule model a crystalline polymer is represented as a single finite chain divided into a head, body, and tail part. The body contains a number of monomer units and is representative for a polymer chain. In this article, this model has been used to study the geometric properties and the elastic moduli of the α form of other polyamides: polyamide‐2 (or polyglycine), polyamide‐3, polyamide‐4, polyamide‐11, and polyamide‐6,6. All calculations have been performed with a linearly constrained body. The results have been compared to other theoretical and experimental results if available. © 2002 Wiley Periodicals, Inc.; DOI 10.1002/qua.2002;10121
Computed molecular surface electrostatic potentials of two groups of reverse transcriptase inhibitors: Relationships to anti‐HIV‐1 activities
Authors: Galvez Gonzalez Oscar , Murray Jane S. , Peralta‐Inga Zenaida , Politzer Peter 
Published: August 2002

AbstractWe have used the GIPF approach (general interaction properties function) to develop analytical representations for the anti‐HIV‐1 potencies of two groups of reverse transcriptase inhibitors. Their activities are expressed in terms of certain statistical properties of their molecular surface electrostatic potentials, computed at the HF/STO‐5G*//HF/STO‐3G* level. The results provide insight into some of the factors that promote inhibition. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 115–121, 2001
Models for protein–zinc ion binding sites. II. The catalytic sites*
Authors: Deerfield David W. , Carter Charles W. , Pedersen Lee G. 
Published: August 2002

AbstractThe first and selected members of the second coordination shells for four model protein–Zn(II) ion catalytic sites have been studied using ab initio computational methodology. The influence of deprotonation on the structure and relative energetics of model complexes was examined. Significant lengthening of the Zn(II)–S, Zn(II)–O, and Zn(II)–N ionic distance is observed as the negative charge about the Zn(II) ion increases. In a model Escheridia coli cytidine deaminase site, we find a substantial lengthening of the Zn–SH2 ionic distance in the active site, which corresponds to the lengthening found for transition state analogs in X‐ray crystal structures. The lowest energy complex of a sulfur‐containing ligand was found to be singly deprotonated, with the complex having an overall charge of +1. The deprotonation of any ligand in a model complex for thermolysin, on the other hand, was found to be endothermic. The influence of other ligands of the metal ion, along with second‐shell ligands, on the energy requirement for deprotonation was also examined for other model systems. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 150–165, 2001
Electrostatic models of inhibitory activity
Authors: Grembecka J. , Kȩdzierski P. , Sokalski W. A. , Leszczyński J. 
Published: August 2002

AbstractVarious models of electrostatic interactions have been applied and tested for several leucine aminopeptidase (LAP) inhibitors interacting with the enzyme active site. Our results indicate that atomic multipoles up to quadrupole moment as well as potential derived Merz–Kollman and RESP charges reproduce reasonably the ab initio electrostatic interaction energies and the expectation values of the molecular electrostatic potential. These electrostatic models together with CHELP atomic point charges, yield the satisfactory correlation of the electrostatic interaction energy with the experimental activities of the inhibitors, in contrast to the results obtained from atomic monopoles (Mulliken charges) and atomic dipoles. Reasonable correlation has been also obtained for the simple electrostatic “key‐lock” model proposed by Náray‐Szabó, in which the LAP active site is represented by set of point charges (“lock”) interacting with the molecular electrostatic potential of each inhibitor (“key”). © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 180–192, 2001
An analysis of the topology of the electron charge density and the reactant–product electronic structure variation along the intrinsic reaction coordinate
Authors: Rincón Luis , Almeida Rafael 
Published: August 2002

AbstractIn this work the topology of the electron charge density and the variations in the reactant and product electronic structures are analyzed along the Fukui intrinsic reaction coordinate (IRC). The systems studied are the ionic and the MenschutkinSN2 reactions. This study is performed at ab initio RHF and MP2 levels, and density functional level, employing the B3LYP functional. The basis set in all cases is of split valence type and includes diffuse and polarization functions in nonhydrogen atoms 6‐31+G*. As a measure of the variations of reactant and product electronic structures, we calculate at the RHF level, the overlap integral between the total wavefunction and the wavefunction based on the reactant (or product) localized fragment orbitals. This integral can be interpreted, in Hilbert space, as the cosine of the angle between the vector representing the electronic structure of the molecule in each point of the IRC and that of reactant (or product) electronic structure. The calculated molecular properties were analyzed in light of the valence bond approach, and qualitative differences were noted depending on the property studied. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
High‐performance liquid chromatography/tandem mass spectrometry for the quantitative analysis of a novel taxane derivative (BAY59‐8862) in biological samples and characterisation of its metabolic profile in rat bile samples
Authors: Sottani Cristina , Colombo Tina , Zucchetti Massimo , Fruscio Robert , D'Incalci Maurizio , Minoia Claudio 
Published: August 2002

AbstractA sensitive, specific, accurate and reproducible high‐performance liquid chromatography (HPLC) analytical method was developed and validated for the quantification of the novel oral taxane analogue BAY59‐8862 in mouse plasma and tissue samples. A fully automated solid‐phase extraction procedure was applied to the plasma after internal standard (IS) addition, with only 0.2 mL volume of the sample loaded on a CN‐Sep‐pak cartridge. In the case of the tissues a very simple acetonitrile extraction was used to recover BAY59‐8862 and its internal standard from liver. The procedure for the quantification of BAY59‐8862 and its IS (IDN5127) is based on high‐performance liquid chromatography/ion spray‐tandem mass spectrometry, operating in selected ion monitoring mode. The retention times of BAY and IS were 7.21 and 10.36 min, respectively. In both plasma and tissue specimens the assay was linear in the range 50–5000 ng/mL (ng/g). The overall precision and accuracy were assessed on three different days. The results for plasma were within 6.1% (precision) and between 99 and 112% (accuracy), and for the liver samples within 7.3% and between 104 and 118%, respectively. The LOD was 5 ng/mL and 20 ng/g in the plasma and liver, respectively. In addition, the biliary excretion of the compound in rats was studied. The study showed that an oxidative chemical reaction was the preferred metabolic pathway for biliary excretion, and two sets of mono‐ and dihydroxylated metabolites were detected by LC/ISP‐MS/MS experiments. With this method, BAY59‐8862 pharmacokinetic was determined in mice. The combined results demonstrate that the methodology can be considered a valid approach to conduct pharmacokinetic and metabolic studies during preclinical and clinical investigations. Copyright © 2001 John7 Wiley & Sons, Ltd.
The Effectiveness of Environmental Dredging: A Study of Three Sites
Authors: Thibodeaux Louis J. , Duckworth Karl T. 
Published: August 2002

AbstractThis manuscript is the result of a research project on the effectiveness of environmental dredging. The
project consisted of technical evaluations of dredging performed at sites in Louisiana, New York, and Michigan.
Models and measurements were used to examine increased water concentrations, post‐dredging sediment
concentrations, effects on biota (primarily fish), contaminant losses, etc., for dredging primarily,
but including the natural‐recovery and capping remediation options. The effectiveness was evaluated by
quantifying 1) enhanced contaminant release during dredging, 2) short‐term on the aquatic
environment and 3) long‐term impacts on the aquatic environment.It was found that existing technologies provide the means to extract large volumes of contaminated
bed‐sediment. Targeted removals of greater than 95 percent are achievable. However, 100 percent removal
was impossible, so that significant contaminants remained. The surficial‐sediment concentrations remained
high, with reduction in the 50 to 75 percent range being typical. The impact on fish in the short term was
nearly always negative. During dredging, significant contaminants enter the water column in both soluble and
particulate form. The long‐term impact of dredging was indeterminate because of the limited observational
database. Complete chemical and biota data sets necessary to quantify the efficiency of the dredge and residual
losses were generally absent at all three sites. 2001 © John Wiley & Sons, Inc.
An Updated Cost Study for Enhanced Sludge Washing of Radioactive Waste
Authors: DeMuth Scott F. , Thayer Gary R. 
Published: August 2002

AbstractThis article updates previous cost savings studies conducted to evaluate the use of enhanced sludge washing
(ESW) of high‐level radioactive waste at the United States Department of Energy Hanford Site.
The cost savings estimate was updated using stochastic analysis based on new information from the
Independent Review of Hanford High Level Waste Volume and the more recent Tank Waste
Remediation System Operation and Utilization Plan. It is estimated that implementation of ESW in the
tank waste remediation system (TWRS) at the Hanford Site can save approximately $4.8 billion
compared to the use of an alternative, simpler water wash. The simpler water wash dissolution was found to be
85 percent as effective as the ESW dissolution. Further, the updated remediation cost estimate of $4.8
billion savings is uncertain only within ±$1.6 billion at the 95 percent confidence interval.
© 2002 Wiley Periodicals, Inc.
Silencing of gene expression: implications for design of retrovirus vectors
Authors: Pannell Dylan , Ellis James 
Published: August 2002

AbstractTranscriptional silencing of retroviruses poses a major obstacle to their use as gene therapy vectors. Silencing is most pronounced in stem cells which are desirable targets for therapeutic gene delivery. Many vector designs combat silencing through cis‐modifications of retroviral vector sequences. These designs include mutations of known retroviral silencer elements, addition of positive regulatory elements and insulator elements to protect the transgene from negative position effects. Similar strategies are being applied to lentiviral vectors that readily infect non‐dividing quiescent stem cells. Collectively these cis‐modifications have significantly improved vector design but optimal expression may require additional intervention to escape completely the trans‐factors that scan for foreign DNA, establish silencing in stem cells and maintain silencing in their progeny. Cytosine methylation of CpG sites was proposed to cause retroviral silencing over 20 years ago. However, several studies provide evidence that retrovirus silencing acts through methylase‐independent mechanisms. We propose an alternative silencing mechanism initiated by a speculative stem cell‐specific ‘somno‐complex’. Further understanding of retroviral silencing mechanisms will facilitate better gene therapy vector design and raise new strategies to block transcriptional silencing in transduced stem cells. Copyright © 2001 John Wiley & Sons, Ltd.
Historical patterns of river stage and fish communities as criteria for operations of dams on the Illinois river
Authors: Koel Todd M. , Sparks Richard E. 
Published: August 2002

AbstractThe hydrologic regime of the Illinois River has been altered over the past 100 years. Locks and dams regulate water surface elevations and flow, enabling commercial navigation to continue year round. This study relates changes in water surface elevation to fish abundance in the river, and establishes target criteria for operating locks and dams. Using long‐term records of daily river stage, we identified ecologically meaningful hydrological parameters for eight gage locations along the Illinois River. Inter‐annual variability of a long‐term fisheries dataset beginning in 1957 was related to variability in stage, flood and recession duration, frequency, timing, and rate of change of water levels. Reversals in water surface elevation, maximum stage levels, and length of the spring flood were the most important parameters influencing abundance of age‐zero fishes in annual collections. Smallmouth buffalo (Ictiobus bubalus), black crappie (Pomoxis nigromaculatus), freshwater drum (Aplodinotus grunneins), and white bass (Morone chrysops) were most abundant in samples during years that approximated the natural water level regime. Of the 33 hydrologic parameters evaluated for the entire water year from an Illinois River gage site on La Grange Reach, all except average stage in January and Julian date (JD) of maximum stage had moderate or high hydrologic alteration based on the historical range of variation (RVA). The highest degree of hydrologic alteration was for minimum stage levels (1‐day, 3‐day, and 7‐day), rate‐of‐rise, and rate‐of‐fall. Other parameters that have been severely altered were 30‐day minimum stage, 90‐day maximum stage, and the annual number of water level reversals. Operations of the La Grange and Peoria locks and dams could be modified so water level variability would approximate that of the late 1800s, when fish and wildlife resources were abundant. The water regime could be regulated to maintain navigation and improve conditions for native plants and animals without increasing flood damages. Copyright © 2002 John Wiley & Sons, Ltd.