bluuebunny/crossref_metadata_2025 huggingface dataset:
Constructing Genetic Linkage Maps Under a Tetrasomic Model
Authors: Luo Z W , Zhang Ze , Leach Lindsey , Zhang R M , Bradshaw John E , Kearsey M J
Published: January 2006

An international consortium has launched the whole-genome sequencing of potato, the fourth most important food crop in the world. Construction of genetic linkage maps is an inevitable step for taking advantage of the genome projects for the development of novel cultivars in the autotetraploid crop species. However, linkage analysis in autopolyploids, the kernel of linkage map construction, is theoretically challenging and methodologically unavailable in the current literature. We present here a theoretical analysis and a statistical method for tetrasomic linkage analysis with dominant and/or codominant molecular markers. The analysis reveals some essential properties of the tetrasomic model. The method accounts properly for double reduction and incomplete information of marker phenotype in regard to the corresponding phenotype in estimating the coefficients of double reduction and recombination frequency and in testing their significance by using the marker phenotype data. Computer simulation was developed to validate the analysis and the method and a case study with 201 AFLP and SSR markers scored on 228 full-sib individuals of autotetraploid potato is used to illustrate the utility of the method in map construction in autotetraploid species.
Gene Expression From Random Libraries of Yeast Promoters
Authors: Ligr Martin , Siddharthan Rahul , Cross Fredrick R , Siggia Eric D
Published: January 2006

Genomewide techniques to assay gene expression and transcription factor binding are in widespread use, but are far from providing predictive rules for the function of regulatory DNA. To investigate more intensively the grammar rules for active regulatory sequence, we made libraries from random ligations of a very restricted set of sequences. Working with the yeast Saccharomyces cerevisiae, we developed a novel screen based on the sensitivity of ascospores lacking dityrosine to treatment with lytic enzymes. We tested two separate libraries built by random ligation of a single type of activator site either for a well-characterized sporulation factor, Ndt80, or for a new sporulation-specific regulatory site that we identified and several neutral spacer elements. This selective system achieved up to 1:104 enrichment of the artificial sequences that were active during sporulation, allowing a high-throughput analysis of large libraries of synthetic promoters. This is not practical with methods involving direct screening for expression, such as those based on fluorescent reporters. There were very few false positives, since active promoters always passed the screen when retested. The survival rate of our libraries containing roughly equal numbers of spacers and activators was a few percent that of libraries made from activators alone. The sequences of ∼100 examples of active and inactive promoters could not be distinguished by simple binary rules; instead, the best model for the data was a linear regression fit of a quantitative measure of gene activity to multiple features of the regulatory sequence.
Detecting Adaptive Trait Introgression BetweenIris fulvaandI. brevicaulisin Highly Selective Field Conditions
Authors: Martin Noland H , Bouck Amy C , Arnold Michael L
Published: January 2006

The idea that natural hybridization has served as an important force in evolutionary and adaptive diversification has gained considerable momentum in recent years. By combining genome analyses with a highly selective field experiment, we provide evidence for adaptive trait introgression between two naturally hybridizing Louisiana Iris species, flood-tolerant Iris fulva and dry-adapted I. brevicaulis. We planted reciprocal backcross (BC1) hybrids along with pure-species plants into natural settings that, due to a flooding event, favored I. fulva. As expected, I. fulva plants survived at much higher rates than I. brevicaulis plants. Backcross hybrids toward I. fulva (BCIF) also survived at significantly higher rates than the reciprocal backcross toward I. brevicaulis (BCIB). Survivorship of BCIB hybrids was strongly influenced by the presence of a number of introgressed I. fulva alleles located throughout the genome, while survivorship in the reciprocal BCIF hybrids was heavily influenced by two epistatically acting QTL of opposite effects. These results demonstrate the potential for adaptive trait introgression between these two species and may help to explain patterns of genetic variation observed in naturally occurring hybrid zones.
Drosophila melanogaster P-glycoprotein: A membrane detoxification system toward polycyclic aromatic hydrocarbon pollutants
Authors: Vaché Christel , Camares Olivier , De Graeve Fabienne , Dastugue Bernard , Meiniel Annie , Vaury Chantal , Pellier Serge , LEoz-Garziandia Eva , Bamdad Mahchid
Published: January 2006

Polycyclic aromatic hydrocarbons (PAHs) are well-known ubiquitous environmental contaminants. Permeability gly-coprotein (P-gp) is a transmembrane detoxification efflux pump transporting various lipophilic xenobiotics, such as PAHs, out of the cells. The existence of a P-gp detoxification system inducible by PAHs was investigated in Drosophila melanogaster. Western blot experiments showed that D. melanogaster expressed a 140-kDa P-gp in Sl2 cells, embryos, and adult flies. Permeability glycoprotein was expressed in adult flies in the head, abdomen, and thorax and sublocalized in the sexual and olfactory organs. Flow cytometry experiments using Drosophila Sl2 cells in the presence of PAHs and target P-gp drug compounds revealed that Drosophila P-gp acted as an efflux detoxification pump. In Drosophila exposed to benzo[a]pyrene or to ambient air polluted by higher or lower PAH concentrations, P-gp expression was clearly showed a dose-dependent increase response. The P-gp induction was detected both in adult flies and in different fly parts, such as the head, thorax, and antennae. Drosophila P-gp acts as a membrane barrier against PAH pollutants.
Tree swallow (Tachycineta bicolor) exposure to polychlorinated biphenyls at the Kalamazoo River superfund site, Michigan, USA
Authors: Neigh Arianne M. , Zwiernik Matthew J. , Bradley Patrick W. , Kay Denise P. , Park Cyrus S. , Jones Paul D. , Newsted John L. , Blankenship Alan L. , Giesy John P.
Published: January 2006

In 1990, a portion of the Kalamazoo River in Michigan, USA, was designated a Superfund site because of the presence of polychlorinated biphenyls (PCBs) in the sediment and floodplain soils. During a four-year period from 2000 to 2003, several avian species were monitored for reproductive effects and concentrations of PCBs in tissues attributed to food chain transfer from contaminated sediments. The tree swallow (Tachycineta bicolor) was chosen as a model receptor for contamination of passerine species. A top-down methodology was used to evaluate the bioaccumulation of PCBs, including non-ortho and mono-ortho congeners, in tree swallow eggs, nestlings, and adults at the Kalamazoo River area of concern (KRAOC) and at an upstream reference site. Generally, a sixfold difference in tissue concentrations of total PCBs was observed between the two sites with concentrations in eggs and nestlings at the KRAOC ranging from 0.95 to 15 μg PCB/g wet weight. Concentrations of 2,3,7,8-tetrachlorodibenzo-p-dioxin equivalents (TEQsWHO-Avian) for PCBs, based on bird-specific World Health Organization toxic equivalence factors, were 10- to 30-fold greater in the KRAOC than at the reference location. Egg and nestling TEQsWHO-Avian ranged from 0.21 to 2.4 ng TEQ/g wet weight at the KRAOC. Hazard quotients calculated from literature-derived toxicity reference values were below 1.0 at both the target and the reference site based on the no-observed-adverse-effect level and the lowest-observed-adverse-effect level.
Speciation of aqueous methylmercury influences uptake by a freshwater alga (Selenastrum capricornutum)
Authors: Gorski Patrick R. , Armstrong David E. , Hurley James P. , Shafer Martin M.
Published: January 2006

Uptake of methylmercury (MeHg) by the alga Selenastrum capricornutum was measured in fresh water batch culture bioassays. The concentration of MeHg in the alga increased rapidly (within 15 min), reached a maximum by 6 h, and then declined because of growth dilution. The alga's rapid growth rate (doubling time, ∼10 h) contributed to the importance of growth dilution. Conditional first-order rate constants were calculated for uptake (k1 = 6.95 × 10−9 L/cell/h) and growth (kG = 0.07/h). A competitive synthetic ligand, disodium ethylenediaminetetra-acetate, formed strong complexes with MeHg and reduced MeHg uptake, consistent with the biotic ligand model. A conditional equilibrium formation constant (K) for the MeHg–algae complex was estimated to be approximately 1016 and was used to model the influence of natural ligands on MeHg bioavailability. Model results suggested MeHg would be most bioavailable at concentrations of dissolved organic matter (DOM) less than 10 mg/L and increasingly unavailable at higher DOM concentrations for the specific humic acid modeled. Similarly, at molar concentrations of sulfide (and, possibly, metal–sulfide clusters) equal to approximately half the MeHg concentration, MeHg was predicted to be unavailable to algae because of the formation of strong 2:1 MeHg–sulfide complexes.
Evaluating the risk to aquatic ecosystems posed by leachate from tire shred fill in roads using toxicity tests, toxicity identification evaluations, and groundwater modeling
Authors: Sheehan Patrick J. , Warmerdam John M. , Ogle Scott , Humphrey Dana N. , Patenaude Stacey M.
Published: January 2006

The risk to adjacent aquatic systems posed by leachates from scrap tires used in engineering applications has not been characterized adequately. Toxicity testing, toxicity identification evaluation (TIE), and groundwater modeling were used to determine the circumstances under which tire shreds could be used as roadbed fill with negligible risk to aquatic organisms in adjacent water bodies. Elevated levels of iron, manganese, and several other chemicals were found in tire shred leachates. However, chronic toxicity tests with Ceriodaphnia dubia and fathead minnows (Pimephales promelas) showed no adverse effects caused by leachates collected from tire shreds installed above the water table. Exposure to leachates collected from tire shreds installed below the water table resulted in significant reductions to both survival and reproduction in C. dubia. The TIE results indicated that exposure to soluble metals (likely ferrous iron primarily) and the formation of iron hydroxide precipitates on this invertebrate species likely were the causes of the observed effects. The available chemistry data show that iron concentrations in the affected groundwater decreased substantially within a short distance (0.61 m) downgradient of tire shred fill. Based on geochemical modeling, the use of tire shreds in applications below the water table is appropriate in settings where dissolved oxygen is greater than 2.0 mg/L, pH is greater than 5.8, and a downgradient buffer of approximately 3.0 m exists between the fill and the surface water. For settings with lower dissolved oxygen concentrations or lower pH, results of groundwater modeling indicate that a greater buffer distance (∼11 m) is needed to dilute the leachate to nontoxic levels under various soil and groundwater conditions solely through advection and dispersion processes.
Effect of short-term exposure to methyl-tert-butyl ether andtert-butyl alcohol on the hatch rate and development of the African catfish,Clarias gariepinus
Authors: Moreels David , Lodewijks Pieter , Zegers Hans , Rurangwa Eugène , Vromant Nico , Bastiaens Leen , Diels LUdo , Springael Dirk , Merckx Roel , Ollevier Frans
Published: January 2006

Methyl tert-butyl ether (MTBE), a synthetic chemical used as a fuel additive, has been detected more frequently in the environment than previously. In this study, we examine the effects of MTBE (up to 100 mg/L) and its primary metabolite tert-butyl alcohol (TBA) (up to 1,400 mg/L) on the hatch rate and larval development of the African catfish Clarias gariepinus. Exposure to higher MTBE concentrations resulted in deformed eyes, mouthparts, and spinal cord and in increased larval mortality. Methyl tert-butyl ether exposure had no significant impact on egg viability, whereas TBA induced a decline of hatch rate. The MTBE can be regarded as a pollutant with toxicological effects on catfish larvae at concentrations above 50 mg/L. Although such concentrations greatly surpass present-day concentrations found in surface water (0.088 mg/L), concentrations up to 200 mg/L have been detected in groundwater.
Sorption kinetics of toluene in humic acid: A computational approach
Authors: Shih Yang-Hsin , Wu Shian-Chee , Lin Jyh-Shing , Lee Lien-Feng
Published: January 2006

Molecular dynamics, a computational technique aiming to describe the time-dependent movement of molecules, has been applied to study the sorption kinetics of volatile organic contaminants in soil organic matter. The molecular dynamics simulation results obtain reasonably accurate estimates of diffusion rates and activation energy of the penetration of a volatile organic compound molecule into a model humic substance. The sorption rate of toluene to humic acid decreases with the density of the humic acid matrix and increases with temperature. All the present results indicate that the sorption of toluene into humic acid is mainly diffusion controlled. Finally, the present studies have shown that molecular dynamics of volatile organic compounds in humic substances yields meaningful results, which help in the understanding of diffusion at the molecular level and which facilitate the problem-solving capability for removing the contaminants from the soils.
Chlorfenapyr and mallard ducks: Overview, study design, macroscopic effects, and analytical chemistry
Authors: Albers Peter H. , Klein Patrice N. , Green David E. , Melancon Mark J. , Bradley Brian P. , Noguchi GEORGE
Published: January 2006

The first commercial pesticide derived from a class of compounds known as halogenated pyrroles was registered for use in the United States in 2001. Chlorfenapyr degrades slowly in soil, sediment, and water and is highly toxic to birds. Information on biochemical or histological endpoints in birds is lacking; therefore, a two-year study was conducted to provide information needed to develop diagnostic criteria for chlorfenapyr toxicosis. In the first year, male mallard ducks were fed concentrations of 0, 2, 5, or 10 ppm technical chlorfenapyr or 5 ppm of a formulated product in their diet during a 10-week chronic exposure study. Survival, body weight, feed consumption (removal), behavior, and molt progression were monitored. Feed and liver were analyzed for chlorfenapyr and two metabolites. Five of 10 ducks in the 10-ppm group died, and neurotoxic effects were observed in the 5-and 10-ppm groups. Feed removal increased for ducks receiving chlorfenapyr and body weights of 5- and 10-ppm ducks were reduced. Loss of body fat, muscle atrophy, and bile retention were suggestive of metabolic disruption or a decreased ability to digest and absorb nutrients. Liver and kidney weights and liver and kidney weight/body weight ratios exhibited a positive response to concentrations of chlorfenapyr in the diet. Emaciation and elevated organ weight/body weight ratios are candidates for a suite of indicators of chronic chlorfenapyr exposure. Liver is the preferred tissue for chemical confirmation of exposure.
Effects of copper on enchytraeids in the field under differing soil moisture regimes
Authors: Maraldo Kristine , Christensen Bent , Strandberg Beate , Holmstrup Martin
Published: January 2006

The aims of this study were to investigate the combined effects of drought stress and copper pollution on enchytraeids under natural conditions in the field and to compare the results of laboratory toxicity tests with results of the field study. Such studies were conducted to increase the understanding of interactions between chemicals and natural stressors and assess the predictive value of standardized laboratory tests with enchytraeids. The combined effect of copper and summer drought on enchytraeids was investigated in an old copper-contaminated field site at Hygum, Denmark, in three areas with different copper burdens. Each area consisted of five plots, which were divided into two subplots: one control and one drought subplot in which precipitation was excluded for a 45-d period during summer. Enchytraeids were sampled in spring (before the enforced drought began) and in autumn (after recovery from drought). Clear effects of copper were evident in both the field and the laboratory experiment. The field population density and species composition was highly affected by copper at concentrations in the range 300 to 500 mg Cu/kg dry soil and higher. In particular, a greatly impoverished species diversity was found in the copper-polluted areas. The effects of copper in the field compared reasonably well with the results of the laboratory tests. Surprisingly, possible effects of summer drought in the field were not detected in the autumn sampling, perhaps because of rapid recovery of the enchytraeid populations in both unpolluted and copper-polluted areas.
Triclosan in a North Texas wastewater treatment plant and the influent and effluent of an experimental constructed wetland
Authors: Waltman Elise Lyn , Venables Barney J. , Waller William T.
Published: January 2006

The antimicrobial triclosan was analyzed in unfiltered samples from influent, effluent, and receiving stream and before and after a pilot-scale constructed wetland at a North Texas municipal wastewater treatment plant. Triclosan concentrations were reduced by 97 to 99% by the activated sludge treatment plant. Effluent concentrations were further reduced by passage through the constructed wetland, but receiving stream concentrations were not statistically significantly different from effluent concentrations. Effluent concentrations of triclosan were seasonal with highest concentrations occurring during the summer months. The effluent-dominated receiving stream maximum concentrations during summer months were below reported algal no-observed-effect concentrations based on biomass and growth rate but exceeded concentrations reported to cause shifts in algal community structure.
Metallothionein gene expression and protein levels in triploid and diploid oysters Crassostrea gigas after exposure to cadmium and zinc
Authors: Marie Véronique , Gonzalez Patrice , Baudrimont Magalie , Boutet Isabelle , Moraga Dario , Bourdineaud Jean-Paul , Boudou Alain
Published: January 2006

Quantitative real-time polymerase chain reaction (PCR) was used to compare for the first time the differential expression of metallothionein (MT) isoform genes, together with biosynthesis of the total MT proteins, in the gills of triploid and diploid juvenile Pacific oyster Crassostrea gigas in response to cadmium (Cd) and zinc (Zn) exposure. Oysters were exposed to Cd (0.133 μM), Zn (15.3 μM), and Cd+Zn for 14 d. Results showed similar response capacities to metal exposures in the two populations. No significant difference was revealed in terms of MT gene expression, MT protein synthesis, and Cd accumulation. However, triploid oysters bioaccumulated Zn 30% less efficiently than diploid oysters. Among the three MT isoform genes, CgMT2 appeared to be more expressed than CgMT1, whereas CgMT3 appeared to be anecdotal (106 times lower than CgMT2). CgMT2 and CgMT1 gene expression levels were increased sevenfold in the presence of Cd, whereas Zn appeared to have no effect. A twofold increase in MT protein levels occurred in response to Cd exposure. Discrepancies between mRNA and protein levels suggest that in C. gigas MT are regulated at the transcriptional level, as well as at the translational level.
Metabolism of uniconazole-P in water-sediment systems under illumination
Authors: Kodaka Rika , Sugano Terumi , Katagi Toshiyuki
Published: January 2006

Aerobic soil metabolism of uniconazole-P ([S]-E-1-[4-chlorophenyl]-4,4-dimethyl-2-[1,2,4-triazole-1-yl]-penten-3-ol) and the effect of illumination on metabolic profiles were studied in the water–sediment system when spiked to water. Uniconazole-P was gradually partitioned to the sediment with an aquatic half-life of 6.9 d in darkness with formation of bound residues. Illumination of the system from a xenon lamp (>290 nm) greatly accelerated the degradation of uniconazole-P via photoinduced isomerization between E- and Z-isomers with a subsequent intramolecular cyclization, and its aquatic half-life was greatly reduced to 0.6 d. Kinetic analysis based on compartment models suggested the possible contribution of photodegradation at the water-sediment interface, leading to more formation of the cyclized derivative in the sediment.
Application of toxicity identification evaluation to sediment in a highly contaminated water reservoir in southeastern Brazil
Authors: Araújo Rosalina P. A. , Botta-Paschoal Clarice M. R. , Silvério Patrícia F. , Almeida Fernanda V. , Rodrigues Paulo F. , Umbuzeiro Gisela A. , Jardim Wilson F. , Mozeto Antonio A.
Published: January 2006

Rasgão Reservoir, located close to the Metropolitan region of São Paulo, Brazil, has been analyzed previously, and its sediment was found to be highly toxic, with high levels of metals and polycyclic aromatic hydrocarbons and a complete absence of benthic life. Polychlorinated biphenyls also were present, as was mutagenic activity, detected with the Salmonella/microsome assay. Because of the extremely complex mixture of contaminants in these sediments, a toxicity identification evaluation was performed on the pore water and elutriate using Ceriodaphnia dubia and Vibrio fischeri. Toxicity characterization, identification, and confirmation procedures were performed in one representative sample of the reservoir, and the results indicated that ammonia was the main cause of the toxicity detected with C. dubia in both sediment pore water and elutriate. Chemical analysis corroborated this observation by revealing un-ionized ammonia concentrations as high as 5.14 mg/L in pore water and 2.06 mg/L in elutriate. These high ammonia levels masked possible toxicity caused by other classes of compounds. The toxicity detected with V. fischeri decreased with the time of sample storage and was related to the organic fraction of the pore water and the elutriate, in which compounds such as benzothiazole and nonylphenol were detected.
Characterization of putative ligands for a fish gonadal androgen receptor in a pulp mill effluent
Authors: Larsson D. G. Joakim , Adolfsson-Erici Margaretha , Thomas Peter
Published: January 2006

Fish exposed to pulp and paper mill effluents often become masculinized. A plausible hypothesisis that this is caused by activation of androgen receptors. The present study aimed to investigate if ligands for the fish gonadal androgen receptor (AR2) are present in pulp mill effluent and to characterize/identify these compounds. Extracts of both primary and biologically treated effluents from a Swedish kraft pulp mill were fractionated chemically. Fractions were tested in competitive binding assays for AR2 from ovaries of the Atlantic croaker (Micropogonias undulatus). Primary effluent contained 96 ng dihydrotestosterone equivalents/L, whereas biologically treated effluent was 16 times less potent. Further fractionations and assays of binding activities were performed on the primary effluent. Eight final fractions displaced androgen in the binding assay, and gas chromatography/mass spectrometry (GC/MS) analyses revealed that these contained 37 detectable compounds that were not present in inactive fractions. The majority were moderately polar compounds between 200 and 400 g/mol with hydroxyl/carbonyl groups. Two compounds were ruled out because of their lack of binding to AR2. The mass spectra of a third compound matched that of 4-hydroxy-3 (2-(4-hydroxy-3methoxophenyl)ethyl)-5-metoxyacetophenon, but the remaining candidates could not be fully identified. A search for 21 known steroidal AR2 ligands showed that progesterone, a relatively strong AR2 ligand, was present in the primary effluent (1.6 μg/L) but was removed during the biological treatment step. The detection of multiple fractions with significant binding activity indicates that a variety of compounds in effluents have the potential to masculinize fish near pulp mills via an androgen receptor-mediated mechanism.
Organochlorine compounds (polychlorinated biphenyls and pesticides) and polycyclic aromatic hydrocarbons in populations of Hexaplex trunculus affected by imposex in the Lagoon of Venice, Italy
Authors: Maran Chiara , Centanni Elena , Pellizzato Francesca , Pavoni Bruno
Published: January 2006

Concentrations of polychlorinated biphenyls (PCBs), organochlorine pesticides, and polycyclic aromatic hydrocarbons (PAHs) were measured in gastropods from the Lagoon of Venice, Italy. The visceral coil and the rest of the soft body of organisms (Hexaplex trunculus) sampled at two stations inside the lagoon and three stations on the seaward side were analyzed to evaluate their contamination levels. Preferential accumulation of PCBs and pesticides in the visceral coil (>80%) compared with the rest of the soft body was observed, whereas on average, PAHs showed no preferential partitioning. Differences between levels of organochlorine contaminants in the gastropods highlighted a gradient of pollution from the stations inside the lagoon (PCBs, 45–363 ng/g; pesticides, 4–51 ng/g) to the sea (PCBs, 13–131 ng/g; pesticides, 2–29 ng/g). The possible role of the three classes of contaminants, in addition to that of organotin compounds (OTCs), previously analyzed in the same samples, in causing one of the anatomic modifications because of imposex in this gastropod also was studied. A modeling approach by partial least squares (PLS) in latent variables was applied to explain the penis length of imposex-affected females with concentrations of organic pollutants. The synergistic role of PCBs, pesticides, and OTCs was evidenced, whereas the contribution of PAHs appeared to be very low.
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

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

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

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 (<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

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

A 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

Necropsy-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

Ahough 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

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

Contamination 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

A 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

Peroxisomes 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

The 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

Chado 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

Background

The 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.

Methods

Lead 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.

Results

Blood 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.

Conclusions

Plasma 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.