bluuebunny/crossref_metadata_2025_split huggingface dataset:
A semi-rational design strategy of directed evolution combined with chemical synthesis of DNA sequences
Authors: Xiong Ai-Sheng , Peng Ri-He , Zhuang Jing , Liu Jin-Ge , Gao Feng , Xu Fang , Cai Bin , Yao Quan-Hong 
Published: November 2007

Abstract
Directed evolution in vitro is a powerful molecular tool for the creation of new biological phenotypes. It is unclear whether it is more efficient to mutate an enzyme randomly or to mutate just the active sites or key sites. In this study, the strategy of a semi-rational design of directed evolution combined with whole sequence and sites was developed. The 1553 bp gene encoding the thermostable β-galactosidase of Pyrococcus woesei was chemically synthesized and optimized for G+C content and mRNA secondary structures. The synthesized gene product was used as a template or as a wild-type control. On the basis of the first round of DNA shuffling, library construction and screening, one mutant of YH6754 was isolated with higher activity. Eight potential key sites were deduced from the sequence of the shuffled gene, and 16 degenerate oligonucleotides were designed according to those eight amino acids. Two variants of YG6765 and YG8252 were screened in the second part of DNA shuffling, library construction and screening. For comparison, one mutant of YH8757 was screened through the same routine rounds of directed evolution with YH6754 as template. The purified β-galactosidase from YH8757 exhibited a lower specific activity at 25°C than those purified from mutated YG6755 and YG8252.
Salivary agglutinin/glycoprotein-340/DMBT1: a single molecule with variable composition and with different functions in infection, inflammation and cancer
Authors: Ligtenberg Antoon J.M. , Veerman Enno C.I. , Nieuw Amerongen Arie V. , Mollenhauer Jan 
Published: November 2007

Abstract
Salivary agglutinin (SAG), lung glycoprotein-340 (gp-340) and Deleted in Malignant Brain Tumours 1 (DMBT1) are three names for identical proteins encoded by the dmbt1 gene. DMBT1/SAG/gp-340 belongs to the scavenger receptor cysteine-rich (SRCR) superfamily of proteins, a superfamily of secreted or membrane-bound proteins with SRCR domains that are highly conserved down to sponges, the most ancient metazoa. On the one hand, DMBT1 may represent an innate defence factor acting as a pattern recognition molecule. It interacts with a broad range of pathogens, including cariogenic streptococci and Helicobacter pylori, influenza viruses and HIV, but also with mucosal defence proteins, such as IgA, surfactant proteins and MUC5B. Stimulation of alveolar macrophage migration, suppression of neutrophil oxidative burst and activation of the complement cascade point further to an important role in the regulation of inflammatory responses. On the other hand, DMBT1 has been demonstrated to play a role in epithelial and stem cell differentiation. Inactivation of the gene coding for this protein may lead to disturbed differentiation, possibly resulting in tumour formation. These data strongly point to a role for DMBT1 as a molecule linking innate immune processes with regenerative processes.
Correlation Between Miniature Cone Tip Resistance and Shear Strength Parameters of Clean and Silty Sand Using a Conventional Triaxial Setup
Authors: Kumar Jyant , Raju K. V. S. B. 
Published: November 2007

Abstract
The ultimate tip resistance of the cone was determined by employing a miniature cone penetrometer of diameter 19.5 mm in conventional triaxial equipment. A number of penetration tests were carried out for clean and silty sands. The variation of the tip resistance was determined with respect to changes in effective vertical stress (σv). It was seen that with this laboratory experimental setup, it is possible to make a reasonable prediction of the ultimate cone tip resistance (qcu). As expected, the tip resistance increases with an increase in (σv). For the same range of the relative density, an increase in proportion of silt was found to generally cause a reduction in the tip resistance. By considering the effect of the overburden stress on internal friction angle of soil mass, it was noted that the magnitude of qcu/σv increases almost linearly with friction angle. The obtained values of qcu compare reasonably well with two different widely used correlations in literature. It is expected that the study will be useful for deriving correlations between shear strength parameters and the cone tip resistance for cohesionless deposits at different values of the effective overburden pressure especially for loose to medium dense states.
Comparison of Harvest Control Policies for Rebuilding Overfished Populations within a Fixed Rebuilding Time Frame
Authors: Babcock Elizabeth A. , McAllister Murdoch K. , Pikitch Ellen K. 
Published: November 2007

Abstract
U.S. law requires that overfished fish populations be rebuilt within 10 years when biologically possible, and otherwise within the time it would take to rebuild in the absence of fishing plus one mean generation time (MGT). Most overfished populations can recover in less than 10 years; the exceptions are populations with very low productivity and some that are severely depleted. A range of harvest control policies, including constant fishing mortalities and variable harvest rate control rules, were compared in terms of their ability to rebuild overfished populations of five species within the required times. The North Atlantic swordfish Xiphias gladius and Gulf of Mexico red snapper Lutjanus campechanus populations were able to rebuild in 10 years, but the white marlin Tetrapturus albidus, sandbar shark Carcharhinus plumbeus, and darkblotched rockfish Sebastes crameri populations were not. The harvest policy that resulted in populations being rebuilt most rapidly was either a control rule that reduced fishing mortality with decreasing biomass or a constant harvest rate designed to meet the current rebuilding time requirement. The control rules we analyzed restricted catches at the beginning of the rebuilding period but allowed catches to increase rapidly as the population was rebuilt. Thus, there was a trade-off between relatively high catches early in the rebuilding period and high catches later in the rebuilding period when the population had been rebuilt and could sustain high catches. Whether the population was rebuilt more rapidly under a fixed rebuilding-time requirement or a control rule depended on the productivity of the population.
Modeling the difference among Cucurbita in uptake and translocation of p,p′-dichlorophenyl-1,1-dichloroethylene
Authors: Gent Martin P. N. , White Jason C. , Eitzer Brian D. , Mattina MaryJane Incorvia 
Published: November 2007

Abstract
Uptake of organic chemicals into plants depends on the properties of the contaminant and the physiology of the plant. A mass balance model based on fugacity was developed to quantify the uptake and transport in plants of a very hydrophobic chemical, p,p′-dichlorophenyl-1,1-dichloroethylene (DDE). The model included processes for sorption or influx of chemical with water from hydroponic solution to root and sorption or exchange of chemical between the shoot and air. Movement among compartments of the plant was governed by the transfer of water in xylem and phloem. The movement of water was entirely determined by transpiration, growth rate, and weight distribution among tissues. This model was used to predict the kinetics of uptake and movement of DDE from hydroponic solution by seedlings of two species of Cucurbitacea, cucumber and zucchini. These predictions were compared to the results of experiments in a companion paper. These experiments showed that the translocation of DDE in zucchini was much greater than in cucumber. The model correctly predicted the negligible uptake into the shoot of cucumber. The model predicted the greater uptake of DDE by zucchini only if the apparent partitioning of DDE in the xylem was 25-fold higher than that expected in pure water. Predictions using similar parameters were made for uptake and distribution of DDE for plants grown into fruit production in field soil contaminated with DDE. To match the observed concentration of DDE in fruit, the model coefficient for partitioning of DDE into water in phloem had to be increased to 200 times that in pure water.
Cholinesterase activity as a biomarker of pesticide exposure inAllolobophora chloroticaearthworms living in apple orchards under different management strategies
Authors: Denoyelle Renaud , Rault Magali , Mazzia Christophe , Mascle Odile , Capowiez Yvan 
Published: November 2007

AbstractThe present study used cholinesterase (ChE) activity in earthworms as a biomarker of pesticide exposure at 17 apple orchards using different pest protection strategies (organic, integrated pest management [IPM], conventional, and abandoned) located within a 300-km2 subregion near Avignon in southeastern France). The most common earthworm species in the 17 orchards was Allolobophora chlorotica. We examined inherent variability in ChE activity that might be attributable to soil characteristics and found that differences in soil structure or type did not significantly influence ChE activity. Furthermore, there was no relation between ChE specific activity and earthworm weight, and thus activity does not require correction for weight. Ten earthworms were collected in two successive months (April and May 2003) from each of the 17 orchards. Compared to the activity in worms from the control abandoned orchards, ChE activity was significantly decreased in earthworms from half the IPM and conventional orchards in April and all these orchards in May. Notably, ChE activity was also lower in earthworms from three organic orchards during May. No relation was observed between ChE decrease and the number of treatments (total or only organophosphorous and carbamate pesticides). Cholinesterase activity in earthworms from abandoned orchards varied between the two collecting periods, illustrating the difficulty in obtaining reference values for the use of ChE as a biomarker in field studies.
Biochemical ripening of dredged sediments. Part 1. Kinetics of biological organic matter mineralization and chemical sulfur oxidation
Authors: Vermeulen Johan , van Gool Martine P. M. , Dorleijn Arne S. , Joziasse Jan , Bruning Harry , Rulkens Wim H. , Grotenhuis J. T. C. (Tim) 
Published: November 2007

Abstract
After dredged sediments have settled in a temporary upland disposal site, ripening starts, which turns waterlogged sediment into aerated soil. Aerobic biological mineralization of organic matter (OM) and chemical oxidation of reduced sulfur compounds are the major biochemical ripening processes. Quantitative data describing these processes are scarce. Therefore, aerobic oxidation and mineralization of five previously anaerobic dredged sediments were studied during a 160-d laboratory incubation experiment at 30°C. A double exponential decay model could adequately describe sulfur oxidation and OM mineralization kinetics. During the first 7 d of incubation, 23 to 80% of the total sulfur was oxidized, after which no further sulfur oxidation was observed. Oxygen used for sulfur oxidation amounted up to 95% of the total oxygen uptake in the first 7 d and up to 45% of the oxygen uptake during the entire incubation period. Mineralization rates of the rapidly mineralizable OM fractions that degraded during the first 14 to 28 d of incubation were 102 to 103 times higher than the mineralization rates of the slowly mineralizable OM during the remaining period. First-order mineralization rates of the slowly mineralizable OM were 0.22 × 10−3 to 0.54 × 10−3 d−1 and can be compared with those of terrestrial soils. Yields of biomass on substrate ranged from 0.08 to 0.45 g Cbiomass/g COM and appeared to be higher for rapidly mineralizing OM than for slowly mineralizing OM. The results of this study can be used to optimize conditions during temporary disposal of sediments, to estimate the potential decrease in OM, and for future studies on the possible link between OM mineralization and degradation of hydrophobic organic contaminants.
Mercury and stable isotopes of carbon and nitrogen in mink
Authors: Lake James L. , Ryba Stephan A. , Serbst Jonathan , Brown IV Charles F. , Gibson Lori 
Published: November 2007

Abstract
Total Hg concentrations and values of stable isotopes (δ15N, δ13C) in tissues of mink (Mustela vison) captured in Rhode Island (USA) during winters of 1999 to 2004 were statistically distinct based on location. Mink captured in salt marsh environments (salt marsh group mink [SMGM]) had significantly lower mean Hg concentrations in liver and muscle tissue, and significantly higher δ15N and δ13C values in muscle, than those in corresponding samples of mink from upland freshwater locations (upland group mink [UPGM]). Stomach content samples obtained from the mink carcasses showed that fish, frogs, and crayfish were the dominant food items in UPGM, but in SMGM, fish predominated. Significant correlations were found for total Hg concentrations and stable isotope values between stomach contents and tissues. Comparisons of increases in Hg concentrations and δ15N values from stomach contents to muscle tissue showed nonsignificant differences between UPGM and SMGM for Hg concentrations (SMGM, factor of 4.2; UPGM, factor of 3.9) and δ15N values (SMGM, difference of 3.9‰; UPGM, difference of 3.1‰). These results suggest that the length of the trophic step and the extent of accumulation of Hg were approximately equal in both mink groups despite the differences in dietary composition and possible differences in accumulation of organic and inorganic Hg. The correspondence of stable isotope values and Hg concentrations between mink tissues and their stomach contents indicates that use of stomach content analysis to identify major prey items, followed by collection and analysis of appropriate field prey, may represent an approach for estimating Hg exposure to mink.
Agricultural pesticides and selected degradation products in five tidal regions and the main stem of Chesapeake Bay, USA
Authors: McConnell Laura L. , Rice Clifford P. , Hapeman Cathleen J. , Drakeford Leticia , Harman-Fetcho Jennifer A. , Bialek Krystyna , Fulton Michael H. , Leight Andrew K. , Allen Gregory 
Published: November 2007

Abstract
Nutrients, sediment, and toxics from water sources and the surrounding airshed are major problems contributing to poor water quality in many regions of the Chesapeake Bay, an important estuary located in the mid-Atlantic region of the United States. During the early spring of 2000, surface water samples were collected for pesticide analysis from 18 stations spanning the Chesapeake Bay. In a separate effort from July to September of 2004, 61 stations within several tidal regions were characterized with respect to 21 pesticides and 11 of their degradation products. Three regions were located on the agricultural Delmarva Peninsula: The Chester, Nanticoke, and Pocomoke Rivers. Two regions were located on the more urban western shore: The Rhode and South Rivers and the Lower Mobjack Bay, including the Back and Poquoson Rivers. In both studies, herbicides and their degradation products were the most frequently detected chemicals. In 2000, atrazine and metolachlor were found at all 18 stations. In 2004, the highest parent herbicide concentrations were found in the upstream region of Chester River. The highest concentration for any analyte in these studies was for the ethane sulfonic acid of metolachlor (MESA) at 2,900 ng/L in the Nanticoke River. The degradation product MESA also had the greatest concentration of any analyte in the Pocomoke River (2,100 ng/L) and in the Chester River (1,200 ng/L). In the agricultural tributaries, herbicide degradation product concentrations were more strongly correlated with salinity than the parent herbicides. In the two nonagricultural watersheds on the western shore, no gradient in herbicide concentrations was observed, indicating the pesticide source to these areas was water from the Bay main stem.
Speciation, behavior, and bioavailability of copper downstream of a mine-impacted lake
Authors: Martin Alan J. , Goldblatt Robert 
Published: November 2007

AbstractA combination of Cu speciation analysis and toxicity testwork was conducted to assess the behavior, speciation, and bioavailability of Cu in a stream system rich in dissolved organic carbon (DOC) downstream of a mine-impacted lake (East Lake, ON, Canada). Elevated levels (∼50 μg/L) of Cu exist in the lake due to the release of dissolved Cu to the water column from underlying sediments. Most of the Cu present in East Lake and downstream is present as filterable species that represent 74 to 100% of the total. Measurements of labile Cu as measured by diffusive gradients in thin films (DGT) suggest that most of the Cu is unavailable to aquatic biota. The DGT results indicate that 9 to 24% of Cu within the receiving environment is biologically available. Decreases in the labile Cu fraction with distance downstream of East Lake correlate well with increases in the concentration of DOC (r2 = 0.79–0.95), presumably due to the progressive importance of Cu-organic complexes. The relationship between filterable Cu and SO2−4 downstream of East Lake was linear (r2 = 0.99) for all sampling periods, suggesting that decreases in filterable Cu concentration downstream of East Lake could be attributed solely to dilution (i.e., conservative behavior). Variations in the filterable Cu concentration resulting in 50% mortality (LC50 = 96–203 μg/L) and the concentration resulting in an inhibition of reproduction by 25% (IC25 = 75–156 μg/L) with respect to Ceriodaphnia dubia (7-d incubation) in Cu-spiked solutions could be explained by differences in labile-Cu concentrations as determined by DGT. The considerable complexation capacity afforded by lake and stream waters can be attributed to complexation of Cu with abundant DOC (7–17 mg/L). The relevance of the toxicity data to water-effect ratio testwork, and the associated development of site-specific water quality objectives, are discussed.
Measured partition coefficients for parent and alkyl polycyclic aromatic hydrocarbons in 114 historically contaminated sediments: Part 2. Testing the KOCKBC two carbon–type model
Authors: Hawthorne Steven B. , Grabanski Carol B. , Miller David J. 
Published: November 2007

Abstract
Polycyclic aromatic hydrocarbon (PAH) desorption partition coefficients between black carbon and water (KBC) were determined using 114 historically contaminated and background sediments from eight different rural and urban waterways. Black carbon was measured after oxidation at 375°C for 24 h. Organic carbon–water partition coefficients (KOC) required for the calculation of KBC values were determined for two- to six-ring parent and C1- to C4-alkyl PAHs based on the lower range of measured KOC values from the same sediments and comparisons to literature KOC values. Approximately 2,050 log KBC values were determined on sediments having a range of total organic carbon from 0.3 to 42% by weight, black carbon from 0.1 to 40% by weight, and total PAH concentrations (U.S. Environmental Protection Agency 16 parent PAHs) from 0.2 to 8,600 μg/g. Contrary to expectations, PAH partitioning was not better explained using the combined KOC and KBC models rather than the simple KOC model (i.e., KBC values for each individual PAH ranged nearly three orders of magnitude). No effect of PAH concentration on measured KBC values was apparent. Values of KBC also showed no trends with total organic carbon, black carbon, or the presence or absence of a nonaqueous phase liquid. Multiple linear regression analysis with KOC and KBC as fitted values also failed to explain the variance of the experimental data (r2 values typically less than 0.20, and standard errors greater than two orders of magnitude). These results demonstrate that models of PAH partitioning that account for different carbon types, although useful for understanding partitioning mechanisms, cannot yet be used to accurately predict PAH partitioning from historically contaminated sediments.
Polychlorinated dibenzo-p-dioxin, polychlorinated dibenzofuran, and polychlorinated biphenyl accumulation in white-tailed deer (Odocoileus virginianus) near a magnesium smelter in Quebec, Canada
Authors: Tolley Cecilia , Blais Jules M. 
Published: November 2007

Abstract
Polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) as well as polychlorinated biphenyls (PCBs) were measured in white-tailed deer (Odocoileus virginianus) near a magnesium-refining facility in Quebec (Canada) known to be a source of chlorinated organic compounds to the area. We compared contaminant concentrations in deer caught one year before the start of magnesium production with those measured three years later. Total PCB concentrations were spatially uniform in deer before magnesium production, but after magnesium production began, concentrations were higher near the smelter and decreased with distance. Many of the midrange PCB homologues that bioconcentrate most in deer showed similar relationships. Concentrations of coplanar PCB congeners and cytochrome P4501A expression in deer liver were examined in a subset of the samples, and these also showed a significant inverse relationship with distance after magnesium production began. This pattern was not observed for PCDD/F concentrations in deer. The risk involved for the human population in consuming local deer meat was assessed by applying contaminant concentrations measured in the present study to Health Canada consumption guidelines. Contaminants in deer were not shown to pose a serious risk to the population, but the number of portions of deer from beyond 20 km that could be safely consumed was less restrictive than the number for deer from within a 5-km radius of the magnesium smelter.
Microcystin kinetics (bioaccumulation and elimination) and biochemical responses in common carp (Cyprinus carpio) and silver carp (Hypophthalmichthys molitrix) exposed to toxic cyanobacterial blooms
Authors: Adamovský Ondřej , Kopp Radovan , Hilscherová Klára , Babica Pavel , Palíková Miroslava , Pašková Veronika , Navrátil Stanislav , Maršálek Blahoslav , Bláha Luděk 
Published: November 2007

Abstract
Two species of common edible fish, common carp (Cyprinus carpio) and silver carp (Hypophthalmichthys molitrix), were exposed to a Microcystis spp.–dominated natural cyanobacterial water bloom for two months (concentrations of cyanobacterial toxin microcystin, 182–539 μg/g biomass dry wt). Toxins accumulated up to 1.4 to 29 ng/g fresh weight and 3.3 to 19 ng/g in the muscle of silver carp and common carp, respectively, as determined by enzyme-linked immunosorbent immunoassay. Concentrations an order of magnitude higher were detected in hepatopancreas (up to 226 ng/g in silver carp), with a peak after the initial four weeks. Calculated bioconcentration factors ranged from 0.6 to 1.7 for muscle and from 7.3 to 13.3 for hepatopancreas. Microcystins were completely eliminated within one to two weeks from both muscle and hepatopancreas after the transfer of fish with accumulated toxins to clean water. Mean estimated elimination half-lives ranged from 0.7 d in silver carp muscle to 8.4 d in common carp liver. The present study also showed significant modulations of several biochemical markers in hepatopancreas of fish exposed to cyanobacteria. Levels of glutathione and catalytic activities of glutathione S-transferase and glutathione reductase were induced in both species, indicating oxidative stress and enhanced detoxification processes. Calculation of hazard indexes using conservative U.S. Environmental Protection Agency methodology indicated rather low risks of microcystins accumulated in edible fish, but several uncertainties should be explored.
Practice alert: CPR revises its arbitration rules, both domestic and international
Authors: Bleemer Russ 
Published: November 2007

AbstractPhiladelphia's Stradley Ronon wins the first CPR Law Firm Award for Excellence in ADR. Also: CPR's arbitration rules are revised; Web site podcasts are launched; the January 2007 CPR Annual Meeting agenda is announced, and CPR releases its full Corporate Leadership Award Dinner sponsor list