bluuebunny/crossref_metadata_2025_split huggingface dataset:
cDNA cloning and gene expression of ribosomal S9 protein gene in the mollusk Corbicula fluminea: A new potential biomarker of metal contamination up-regulated by cadmium and repressed by zinc
Authors: Achard-Joris Maud , Gonzalez Patrice , Marie Véronique , Baudrimont Magalie , Bourdineaud Jean-Paul 
Published: January 2006

Abstract
Biological indicators can beused to assess polluted sites, but their success depends on their specificity. The aim of the present study was to identify a specific cadmium biomarker of the freshwater bivalve Corbicula fluminea. Differential display technique was used to identify new molecular indicators for cadmium exposure. Gene expression of C. fluminea transplanted into a cadmium- and zinc-contaminated river was compared to gene expression of bivalves from a reference site. One differentially expressed band was identified, and the entire cDNA sequence coding for the ribosomal protein S9 (rpS9) was cloned. The rpS9 gene expression was studied by real-time reverse transcription–polymerase chain reaction. After controlled cadmium (15 μg/L) and/or zinc (1 mg/L) laboratory contaminations of the bivalves, this gene was shown to be up-regulated by cadmium and down-regulated by zinc. A 48-d transplantation of animals into a polymetallic field contamination in the Lot river basin (Midi-Pyrénées region, France) showed that rpS9 gene regulation was correlated with the fluctuating cadmium and zinc water contents. To our knowledge, the existence of a gene that is up-regulated by cadmium and repressed by zinc is demonstrated here for the first time.
Measurement of temperature dependence for the vapor pressures of twenty-six polychlorinated biphenyl congeners in commercial Kanechlor mixtures by the Knudsen effusion method
Authors: Nakajoh Katsuhiko , Shibata Etsuro , Todoroki Tomohiro , Ohara Atsushi , Nishizawa Katsushi , Nakamura Takashi 
Published: January 2006

Abstract
The vapor pressures of the major congeners in commercial polychlorinated biphenyl (PCB) mixtures (Kanechlors; Kanebuchi Chemical Industry, Tokyo, Japan) have been experimentally determined by Knudsen mass loss effusion. We obtained vapor pressures for the individual PCBs in the crystalline solid, liquid, and subcooled liquid forms as a function of temperature. We derived the thermodynamic parameters, such as the enthalpies of sublimation and vaporization, from the temperature dependence of the vapor pressure by the Clausius–Clapeyron equation. To decide whether the commercial PCB mixtures were ideal solutions, we obtained the activity coefficients by comparing our experimental vapor pressures for pure PCB congeners with those calculated from Kanechlor molar compositional data and vapor pressure values. In many cases, we found that, at 298 K, the values of the activity coefficients of major PCBs in Kanechlor 300 and 500 ranged from 1 to 2. Thus, we suggested that the commercial PCB mixtures show slight positive deviations from ideal solution (Raoult's Law) behavior at ambient temperatures.
Dissolved copper triggers cell death in the peripheral mechanosensory system of larval fish
Authors: Linbo Tiffany L. , Stehr Carla M. , Incardona John P. , Scholz Nathaniel L. 
Published: January 2006

Abstract
Dissolved copper is an increasingly common non–point source contaminant in urban and urbanizing watersheds. In the present study, we investigated the sublethal effects of dissolved copper on the peripheral mechanosensory system, or lateral line, of larval zebrafish (Danio rerio). Zebrafish larvae were exposed to copper (0–65 μg/L), and the cytotoxic responses of individual lateral line receptor neurons were examined using a combination of in vivo fluorescence imaging, confocal microscopy, scanning electron microscopy, and conventional histology. Dissolved copper triggered a dose-dependent loss of neurons in identified lateral line neuromasts at concentrations ≥20 μg/L. The onset of cell death in the larval mechanosensory system was rapid (&lt;1 h). When copper-exposed zebrafish were transferred to clean water, the lateral line regenerated over the course of 2 d. In contrast, the lateral line of larvae exposed continuously to dissolved copper (50 μg/L) for 3 d did not recover. Collectively, these results show that peripheral mechanosensory neurons are vulnerable to the neurotoxic effects of copper. Consequently, dissolved copper in non-point source storm-water runoff has the potential to interfere with rheotaxis, schooling, predator avoidance, and other mechanosensory-mediated behaviors that are important for the migration and survival of fish.
Triazine adsorption by saponite and beidellite clay minerals
Authors: Aggarwal Vaneet , Li Hui , Teppen Brian J. 
Published: January 2006

Abstract
We investigated the sorption of three triazine herbicides (atrazine, simazine, and metribuzin) by saponite and beidellite clay minerals saturated with K+, Cs+, Na+, and Ca2+. Saponite clay sorbed a larger fraction of each pesticide from aqueous solution than did beidellite clay. The lower cation-exchange capacity in saponite compared to that in beidellite presumably results in a less crowded interlayer, with more siloxane surface being available for adsorption. Generally, Cs-saturated clays sorbed more triazines than did clays saturated by K+, Na+, or Ca2+. We attribute this to the smaller hydrated radius of Cs+, which again increases the siloxane surface that is available for sorption. Furthermore, the relatively weak hydration of Cs+ reduces the swelling of clay interlayers, thus making sorption domains less hydrated and more receptive to hydrophobic molecules. The Cs-saponite manifested a sorption of more than 1% atrazine by weight above equilibrium concentrations of 6 mg/L, which to our knowledge is the largest sorption of neutral atrazine from water yet reported for an inorganic sorbent. Molecular dynamics simulations indicate that atrazine interacts both with clay basal planes and with multiple cations in the clay interlayer.
From organisms to populations: Modeling aquatic toxicity data across two levels of biological organization
Authors: Raimondo Sandy , McKenney Charles L. 
Published: January 2006

AbstractA critical step in estimating the ecological effects of a toxicant is extrapolating organism-level response data across higher levels of biological organization. In the present study, the organism-to-population link is made for the mysid, Americamysis bahia, exposed to a range of concentrations of six toxicants. Organism-level responses observed were categorized as no effect, delayed reproduction, reduced overall reproduction, or both reduced overall reproduction and survival. Population multiplication rates of each toxicant concentration were obtained from matrix models developed from organism-level endpoints and placed into the four categories of organism-level responses. Rates within each category were compared with growth rates modeled for control populations. Population multiplication rates were significantly less than control growth rates only for concentrations at which overall reproduction and both reproduction and survival were significantly less than the control values on the organism level. Decomposition analysis of the significant population-level effects identified reduced reproduction as the primary contributor to a reduced population multiplication rate at all sublethal concentrations and most lethal concentrations. Mortality was the primary contributor to reduced population growth rate only when survival was less than 25% of control survival. These results suggest the importance of altered reproduction in population-level risk assessment and emphasizes the need for complete life-cycle test data to make an explicit link between the organism and population levels.
External heart deformities in passerine birds exposed to environmental mixtures of polychlorinated biphenyls during development
Authors: DeWitt Jamie C. , Millsap Deborah S. , Yeager Ronnie L. , Heise Steve S. , Sparks Daniel W. , Henshel Diane S. 
Published: January 2006

AbstractNecropsy-observable cardiac deformities were evaluated from 283 nestling passerines collected from one reference site and five polychlorinated biphenyl (PCB)–contaminated sites around Bloomington and Bedford, Indiana, USA. Hearts were weighed and assessed on relative scales in three dimensions (height, length, and width) and for externally visible deformities. Heart weights normalized to body weight (heart somatic index) were decreased significantly at the more contaminated sites in both house wren (Troglodytes aedon) and tree swallow (Tachycineta bicolor). Heart somatic indices significantly correlated with log PCB concentrations in Carolina chickadee (Parus carolinesis) and tree swallow and with log 2,3,7,8-tetrachlorodibenzo-p-dioxin toxic equivalent values in tree swallow alone. Ventricular length was increased significantly in eastern bluebirds (Sialia sialis) and decreased significantly in Carolina chickadee and tree swallow from contaminated sites versus the reference site. Heart length regressed significantly against the log PCB concentrations (Carolina chickadee and tree swallow) or the square of the PCB concentrations (red-winged blackbird [Agelaius phoeniceus]) in a sibling bird. The deformities that were observed most at the contaminated sites included abnormal tips (pointed, rounded, or flattened), center rolls, macro- and microsurface roughness, ventricular indentations on the ventral or dorsal surface, lateral ventricular notches, visibly thin ventricular walls, and changes in overall heart shape. A pooled heart deformity index regressed significantly against the logged contaminant concentrations for all species except red-winged blackbird. These results indicate that developmental changes in heart morphometrics and shape abnormalities are quantifiable and may be sensitive and useful indicators of PCB-related developmental impacts across many avian species.
Induction of cytochrome P4501A in African brown house snake (Lamprophis fuliginosus) primary hepatocytes
Authors: Hecker Markus , Murphy Margaret B. , Giesy John P. , Hopkins William A. 
Published: January 2006

AbstractAhough there have been numerous sudies involving fish, birds, and mammals, little is known about the response of the cytochrome P4501A system of snakes to halogenated aromatic hydrocarbons (HAHs). The present study describes the induction of ethoxyresorufin-O-deethylase (EROD) in primary hepatocytes of the African brown house snake (Lamprophis fuliginosus). Hepatocytes were exposed in multiwell plates to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and four different non-ortho-substi-tuted coplanar polychlorinated biphenyls (PCBs 77, 81, 126, and 169). Exposure to TCDD and PCB 126 resulted in a dose-dependent increase in EROD activity, with maximum inducible EROD activities of 177 ± 56 (mean ± SEM) and 101.1 ± 55 pmol/min/mg protein for TCDD and PCB 126, respectively. None of the other PCBs caused a measurable induction of EROD, which suggests reduced inducibility of snake hepatocytes compared to some vertebrate taxa. Median effective concentrations (EC50s) were 0.16 ± 0.03 nM for TCDD and 8.25 ± 4.14 nM for PCB 126. The relative potency (REP20–80) range for PCB 126 was 0.044 to 0.046. Compared to results from in vitro systems using other vertebrate species, both the maximum inducibility and the REPs estimated for L. fuliginosus were within the same range as those reported for mammals and the more sensitive bird species but were greater than the values reported for most fish species. In conclusion, induction of EROD activity in primary hepatocytes appears to be a useful approach for evaluating the dioxin-like potencies of aryl hydrocarbon–receptor agonists in snakes. The test system offers a method for rapid screening of reptilian responsiveness to these compounds using smaller numbers of organisms than with in vivo studies, an important consideration for many declining reptile species.
Joint toxicity of chlorpyrifos and esfenvalerate to fathead minnows and midge larvae
Authors: Belden Jason B. , Lydy Michael J. 
Published: January 2006

Abstract
The joint toxicity of esfenvalerate and chlorpyrifos to the fathead minnow (Pimephales promelas) and the aquatic midge larvae (Chironomus tentans) was determined using comparisons to independent action (IA) and concentration addition (CA) models. Equipotent mixtures of the two insecticides were used for initial testing of both species. A secondary study evaluating the effects of low-level chlorpyrifos on esfenvalerate toxicity also was performed. For fathead minnows, the equipotent mixture and the low-level chlorpyrifos exposure resulted in toxicity greater than that predicted by either model. In both studies, however, the observed concentrations causing 50% effect (EC50) were within a factor of two of the values predicted by the CA model. For midges, the observed EC50s were similar to the values predicted by the CA model, whereas the IA model slightly underpredicted toxicity. The observance of toxicity that was not predicted by either of the conceptual models tested likely results from a toxicokinetic interaction occurring between the toxicants.
Avoidance of polycyclic aromatic hydrocarbon–contaminated sediments by the freshwater invertebratesGammarus pulexandAsellus aquaticus
Authors: De Lange Hendrika J. , Sperber Veerle , Peeters Edwin T. H. M. 
Published: January 2006

AbstractContamination of sediments is a serious problem in most industrialized areas. Sediments are often contaminated with trace metals and organic contaminants like polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs). Bio-assays are often used to determine the effect of contaminants on biota. However, survival or growth may not be the most sensitive endpoints. Behavioral changes often occur at much lower concentrations. Our study aimed to assess the effect of PAHs on habitat choice of two common freshwater invertebrates, the amphipod Gammarus pulex and the isopod Asellus aquaticus. We spiked clean field sediment with a mixture of four PAHs, fluoranthene, pyrene, chrysene, and benzo[k]fluoranthene, to a total concentration of 30 mg PAH/kg dry weight. Both species were offered a choice between PAH-spiked sediments and clean sediments in laboratory experiments. Results show that both species avoid PAH-spiked sediment. Origin of the population, either from a clean reference site or from a polluted site, did not affect habitat choice of either species.
Sequencing Oligonucleotides by Enrichment of Coupling Failures Using Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Spectrometry
Authors: Alazard David , Russell James 
Published: January 2006

AbstractA technique for sequencing oligonucleotides using matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry is described. Coupling failures are extracted from the full‐length 5′‐O‐DMTr‐oligonucleotide in a crude synthesis using C18 purification cartridges. Enhanced signal and resolution of the failure ions are demonstrated during MALDI‐TOF analysis. Sequencing information is confirmed by the mass difference between coupling failures to identify a particular base or structural modification. This procedure eliminates difficulties associated with other mass spectrometric techniques, such as interpretation of data, oligonucleotide length, and backbone, sugar or terminal alterations. An example of sequencing a 16‐mer composed of deoxyribonucleotides, 2′‐O‐methylribonucleotides, and a non‐nucleosidic linker is reported.
Isolation of Glyoxysomes from Pumpkin Cotyledons
Authors: Harrison‐Lowe Nicola , Olsen Laura J. 
Published: January 2006

AbstractPeroxisomes are single‐membrane‐bound organelles found in virtually all eukaryotes. In plants, there are several classes of peroxisomes. Glyoxysomes are found in germinating seedlings and contain enzymes specific for the glyoxylate cycle, including isocitrate lyase and malate synthase. After seedlings become photosynthetic, leaf peroxisomes participate in reactions of the photorespiration pathway and contain characteristic enzymes such as glycolate oxidase and hydroxypyruvate reductase. As leaves begin to senesce, leaf peroxisomes are transformed back into glyoxysomes. Root peroxisomes in the nodules of legumes, for example, sequester enzymes such as allantoinase and uricase, which contribute to nitrogen metabolism in these tissues. Thus, peroxisomes participate in many metabolic pathways and contain specific enzyme complements, depending on the tissue source. All peroxisomes contain catalase to degrade hydrogen peroxide and enzymes to accomplish β‐oxidation of fatty acids. Glyoxysomes can be isolated from pumpkin cotyledons by standard differential centrifugation and density separation, as described in this article.
Searching, Viewing, and Visualizing Data in the Biomolecular Interaction Network Database (BIND)
Authors: Willis Randall C , Hogue Christopher W.V. 
Published: January 2006

AbstractThe Biomolecular Interaction Network Database (BIND) comprises data from peer‐reviewed literature and direct submissions. BIND's data model was the first of its kind to be peer‐reviewed prior to database development, and is now a mature standard data format spanning molecular interactions, small molecule chemical reactions, and interfaces from three‐dimensional structures, pathways, and genetic interaction networks. BIND supports additional file formats to achieve compatibility with other database efforts, including the HUPO PSI Level 2. BIND's latest software spans over 2000 metadata fields and is constructed using the Java Enterprise Systems software platform. Protocols are provided for searching BIND via the Internet, as well as for viewing and exporting search results or individual records. Furthermore, a protocol is provided for visualizing biomolecular interactions within BIND or for transferring this information to the visualization tools Cytoscape and Cn3D.
Using Chado to Store Genome Annotation Data
Authors: Zhou Pinglei , Emmert David , Zhang Peili 
Published: January 2006

AbstractChado is a relational database schema that can be used to manage a wide variety of biological information, including genome annotation, genetic, phenotypic, and expression data. Its flexibility comes from its use of “ontologies,” which are controlled vocabularies that describe data types and the relationships among them. By changing its ontologies, Chado can be customized to suit many different needs. Another aspect that gives Chado its flexibility is its use of a modular design, which means that users can choose to use only those features of Chado that are suitable for their needs. XORT is the main software tool used to move data in and out of Chado databases. XORT uses an XML‐based file format for data import and export; this format is called ChadoXML, The protocols described in this chapter show how to use XORT and related software to import genome annotation data into Chado databases, and how to export data stored in Chado databases into different file formats for report and data mining purposes.
Plasma‐lead concentration: Investigations into its usefulness for biological monitoring of occupational lead exposure
Authors: Bergdahl Ingvar A. , Gerhardsson Lars , Liljelind Ingrid E. , Nilsson Leif , Skerfving Staffan 
Published: January 2006

AbstractBackgroundThe lead concentration in plasma is correlated to that in whole blood with a two to fourfold variation. It has never been investigated if this variation is inter‐individual.MethodsLead and hemoglobin were determined in blood and plasma from 13 lead workers with a history of relatively high blood‐lead concentrations, sampled three times during 1 day. The variation in the distribution of lead between cells and plasma was studied, but not the variation in the lead concentrations as such.ResultsBlood hemoglobin decreased with rising plasma lead (0.9–3.0 µg/L). Regarding the distribution of lead, no effect of current exposure during the day or of recent meals appeared. As much as 84% of the overall variance of the distribution of lead between cells and plasma could be attributed to individual factors. After adjustment for erythrocyte volume fraction this decreased to 67%. Plasma samples with elevated hemoglobin concentrations (due to in vitro hemolysis) had somewhat elevated lead concentrations.ConclusionsPlasma lead is not significantly altered by variation in a single day's exposure and, therefore, the choice of time of the day is not critical for sampling. However, plasma lead is negatively correlated to blood hemoglobin and mild hemolysis (not visible by the eye) in a sample may increase plasma lead with up to 30%. Finally, plasma provides lead exposure information that differs from whole blood, but it is not clear which one of these is the biomarker with the closest relation to exposure and/or effects. Am. J. Ind. Med. 49:93–101, 2006. © 2006 Wiley‐Liss, Inc.
Cathodic electrochemiluminescence of acetonitrile, acetonitrile–1,10‐phenanthroline and acetonitrile–ternary Eu(III) complexes at a gold electrode
Authors: Yu Hong‐Xiao , Cui Hua , Guan Jun‐Bo 
Published: January 2006

AbstractCathodic electrochemiluminescence (ECL) behaviours of the acetonitrile, acetonitrile–1,10‐phenanthroline (phen) and acetonitrile–ternary Eu(III) complex systems at a gold electrode were studied. One very weak cathodic ECL‐2 at −3.5 V was observed in 0.1 mol/L tetrabutylammonium tetrafluoroborate (TBABF4) acetonitrile solution. When 10 mmol/L tetrabutylammonium peroxydisulphate [(TBA)2S2O8] was added to 0.1 mol/L TBABF4 acetonitrile solution, another cathodic ECL‐1 at −2.7 V appeared and the potential for ECL‐2 was shifted from −3.5 to −3.1 V. Furthermore, ECL‐2 intensity was enhanced about 20‐fold. When 1 × 10−4 mol/L phen was added to 0.1 mol/L TBABF4 + 10 mmol/L (TBA)2S2O8 acetonitrile solution, the ECL intensities of ECL‐1 and ECL‐2 were enhanced about 20‐fold compared with those of 0.1 mol/L TBABF4 + 10 mmol/L (TBA)2S2O8 acetonitrile solution. The maximum emission peaks of ECL‐1 and ECL‐2 in the three systems mentioned above appeared at about 530 nm. The products obtained by electrolysing 0.1 mol/L TBABF4 acetonitrile solution at −3.5 V for 20 min were analysed by Fourier Transform Infrared (FTIR) spectra and gas chromatography–mass spectrometry (GC–MS) and the emitter of ECL‐1 and ECL‐2 was identified as excited state polyacetonitrile. When ternary Eu(III) complexes were presented in 0.1 mol/L TBABF4 + 10 mmol/L (TBA)2S2O8 acetonitrile solution, another maximum emission peak with a narrow band centred at about 610 nm appeared in ECL‐1 in addition to the maximum emission peaks at about 530 nm for ECL‐1 and ECL‐2. The emitter of ECL emission at 610 nm was identified as the excited states Eu(III)*. The mechanisms for cathodic ECL behaviours of the acetonitrile, acetonitrile–phen and acetonitrile–ternary Eu(III) complex systems at a gold electrode have been proposed. The extremely sharp emission bands for ternary Eu(III) complexes may have analytical potential. Copyright © 2006 John Wiley & Sons, Ltd.