bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytoplasmic remodeling of erythrocyte raft lipids during infection by the human malaria parasite Plasmodium falciparum
Authors: Murphy Sean C. , Fernandez-Pol Sebastian , Chung Paul H. , Prasanna Murthy S. N. , Milne Stephen B. , Salomao Marcela , Brown H. Alex , Lomasney Jon W. , Mohandas Narla , Haldar Kasturi 
Published: May 2007

AbstractStudies of detergent-resistant membrane (DRM) rafts in mature erythrocytes have facilitated identification of proteins that regulate formation of endovacuolar structures such as the parasitophorous vacuolar membrane (PVM) induced by the malaria parasite Plasmodium falciparum. However, analyses of raft lipids have remained elusive because detergents interfere with lipid detection. Here, we use primaquine to perturb the erythrocyte membrane and induce detergent-free buoyant vesicles, which are enriched in cholesterol and major raft proteins flotillin and stomatin and contain low levels of cytoskeleton, all characteristics of raft microdomains. Lipid mass spectrometry revealed that phosphatidylethanolamine and phosphatidylglycerol are depleted in endovesicles while phosphoinositides are highly enriched, suggesting raft-based endovesiculation can be achieved by simple (non–receptor-mediated) mechanical perturbation of the erythrocyte plasma membrane and results in sorting of inner leaflet phospholipids. Live-cell imaging of lipid-specific protein probes showed that phosphatidylinositol (4,5) bisphosphate (PIP2) is highly concentrated in primaquine-induced vesicles, confirming that it is an erythrocyte raft lipid. However, the malarial PVM lacks PIP2, although another raft lipid, phosphatidylserine, is readily detected. Thus, different remodeling/sorting of cytoplasmic raft phospholipids may occur in distinct endovacuoles. Importantly, erythrocyte raft lipids recruited to the invasion junction by mechanical stimulation may be remodeled by the malaria parasite to establish blood-stage infection.
Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation
Authors: Deibler Richard W , Mann Jennifer K , Sumners De Witt L , Zechiedrich Lynn 
Published: May 2007

Abstract

Background
The genetic code imposes a dilemma for cells. The DNA must be long enough to encode for the complexity of an organism, yet thin and flexible enough to fit within the cell. The combination of these properties greatly favors DNA collisions, which can knot and drive recombination of the DNA. Despite the well-accepted propensity of cellular DNA to collide and react with itself, it has not been established what the physiological consequences are.

Results
Here we analyze the effects of recombined and knotted plasmids in E. coli using the Hin site-specific recombination system. We show that Hin-mediated DNA knotting and recombination (i) promote replicon loss by blocking DNA replication; (ii) block gene transcription; and (iii) cause genetic rearrangements at a rate three to four orders of magnitude higher than the rate for an unknotted, unrecombined plasmid.

Conclusion
These results show that DNA reactivity leading to recombined and knotted DNA is potentially toxic and may help drive genetic evolution.
Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes
Authors: Warnat Patrick , Oberthuer André , Fischer Matthias , Westermann Frank , Eils Roland , Brors Benedikt 
Published: May 2007

Abstract

Background
Neuroblastoma patients show heterogeneous clinical courses ranging from life-threatening progression to spontaneous regression. Recently, gene expression profiles of neuroblastoma tumours were associated with clinically different phenotypes. However, such data is still rare for important patient subgroups, such as patients with MYCN non-amplified advanced stage disease. Prediction of the individual course of disease and optimal therapy selection in this cohort is challenging. Additional research effort is needed to describe the patterns of gene expression in this cohort and to identify reliable prognostic markers for this subset of patients.

Methods
We combined gene expression data from two studies in a meta-analysis in order to investigate differences in gene expression of advanced stage (3 or 4) tumours without MYCN amplification that show contrasting outcomes (alive or dead) at five years after initial diagnosis. In addition, a predictive model for outcome was generated. Gene expression profiles from 66 patients were included from two studies using different microarray platforms.

Results
In the combined data set, 72 genes were identified as differentially expressed by meta-analysis at a false discovery rate (FDR) of 8.33%. Meta-analysis detected 34 differentially expressed genes that were not found as significant in either single study. Outcome prediction based on data of both studies resulted in a predictive accuracy of 77%. Moreover, the genes that were differentially expressed in subgroups of advanced stage patients without MYCN amplification accurately separated MYCN amplified tumours from low stage tumours without MYCN amplification.

Conclusion
Our findings support the hypothesis that neuroblastoma consists of two biologically distinct subgroups that differ by characteristic gene expression patterns, which are associated with divergent clinical outcome.
Evaluation of facial composite evidence depends on the presence of other case factors
Authors: McQuiston‐Surrett Dawn , Douglass Amy Bradfield , Burkhardt Samantha G. 
Published: May 2007

Purpose. Previous research on the reliability of eyewitnesses' facial composites suggests that some scepticism is warranted when evaluating their accuracy. The current research examines the degree to which mock jurors evaluate facial composite images as a source of incriminating or exonerating evidence against a defendant, particularly when they are inconsistent with other evidence presented.Method. Mock jurors read a fictitious criminal trial transcript of a person charged with armed robbery. Experiment 1 manipulated the facial composite evidence such that participants viewed a facial composite which was either a good or a poor match to the defendant. Experiment 2 also manipulated the quality of the facial composite evidence, as well as the other case evidence against the defendant. After reading the transcript, participants made several testimony‐relevant judgments about the case.Results. Mock jurors reacted more favourably towards the defendant when the facial composite resembled him than when it did not, but reacted similarly when the composite did not resemble the defendant vs. no composite presented. In addition, assessments of the strength of the composite evidence varied depending on the other case evidence presented.Conclusion. Mock jurors selectively incorporate evidence into their judgments about the credibility of the eyewitness and the culpability of the defendant. They responded to strong vs. weak facial composite evidence as one would expect: A good match composite was viewed as more favourable to the prosecution than a poor match composite. Weak facial composite evidence was largely ignored, however, participants' assessment of the strength of this evidence was adjusted to be consistent with the other evidence presented.
Test of APEX for Nine Forested Watersheds in East Texas
Authors: Wang X. , Saleh A. , McBroom M. W. , Williams J. R. , Yin L. 
Published: May 2007

AbstractHydrologic/water quality models are increasingly used to explore management and policy alternatives for managing water quality and quantity from intensive silvicultural practices with best management practices (BMPs) in forested watersheds due to the limited number of and cost of conducting watershed monitoring. The Agricultural Policy/Environmental eXtender (APEX) model was field‐tested using 6 yr of data for flow, sediment, nutrient, and herbicide losses collected from nine small (2.58 to 2.74 ha) forested watersheds located in southwest Cherokee County in East Texas. Simulated annual average stream flow for each of the nine watersheds was within ± 7% of the corresponding observed values; simulated annual average sediment losses were within ± 8% of measured values for eight out of nine watersheds. Nash‐Sutcliffe efficiency (EF) values ranged from 0.68 to 0.94 based on annual stream flow comparison and from 0.60 to 0.99 based on annual sediment comparison. Similar to what was observed, simulated flow, sediment, organic N, and P were significantly increased on clear‐cut watersheds compared with the control watersheds. APEX reasonably simulated herbicide losses, with an EF of 0.73 andR2of 0.74 for imazapyr, and EF of 0.65 andR2of 0.68 for hexazinone based on annual values. Overall, the results show that APEX was able to predict the effects of silvicultural practices with BMPs on water quantity and quality and that the model is a useful tool for simulating a variety of responses to forest conditions.
Spatial Variation of Soil Phosphorus within a Drainage Ditch Network
Authors: Vaughan Robert E. , Needelman Brian A. , Kleinman Peter J. A. , Allen Arthur L. 
Published: May 2007

AbstractAgricultural drainage ditches serve as P transport pathways from fields to surface waters. Little is known about the spatial variation of P at the soil‐water interface within ditch networks. We quantified the spatial variation of surficial (0–5 cm) soil P within vegetated agricultural ditches on a farm in Princess Anne, MD with an approximately 30‐yr history of poultry litter application. Ditch soils from 10 ditches were sampled at 10‐m intervals and analyzed for acid ammonium oxalate‐extractable P, Fe, Al (Pox, Feox, Alox), and pH. These variables were spatially autocorrelated. Oxalate‐P (min = 135 mg kg−1, max = 6919 mg kg−1, mean = 700 mg kg−1) exhibited a high standard deviation across the study area (overall 580 mg kg−1) and within individual ditches (maximum 1383 mg kg−1). Several ditches contained distinct areas of high Pox, which were associated with either point‐ or nonpoint‐P sources. Phosphorus was correlated with Aloxor Feoxwithin specific ditches. Across all ditches, Alox(r= 0.80;p <0.001) was better correlated with Poxthan was Feox(r= 0.44;p< 0.001). The high level of spatial variation of soil P observed in this ditch network suggests that spatially distributed sampling may be necessary to target best management practices and to model P transport and fate in ditch networks.
Geostatistical Analysis and Risk Assessment on Soil Total Nitrogen and Total Soil Phosphorus in the Dongting Lake Plain Area, China
Authors: Lu Peng , Su Yirong , Niu Zheng , Wu Jinshui 
Published: May 2007

AbstractNonpoint‐source pollution and water body eutrophication have become increasing concerns for scientists and policymakers. Nitrogen and phosphorus affect environmental pollution, especially lake eutrophication. To assess the environmental risk of soil total nitrogen (TN) and total phosphorus (TP) pollution, a typical ecological unit of Dongting Lake plain was selected as the experimental site. To verify the stationary of the data, a moving windows technique was adopted. Our results showed that Box‐Cox transformation achieved normality in the data set and dampened the effect of outliers. The best theoretical model for semivariogram of TN and TP was a spherical model. The ordinary kriging estimates of TN and TP concentrations were mapped. The integrative comparisons of semivariogram parameters with different trends to the kriging prediction errors of TN and TP indicated that the two‐order trend is preferable. Kriging SDs provided valuable information that will increase the accuracy of TN and TP mapping. The probability kriging method is useful to assess the risk of N and P pollution by providing the conditional probability of N and P concentrations exceeding the threshold concentrations of 3.2 and 1.05 g/kg, respectively. The probability distribution of TN and TP at different levels will be helpful to conduct risk assessment, optimize fertilization, and control the pollution of N and P.
Modeling Riverine Nitrate Export from an East‐Central Illinois Watershed Using SWAT
Authors: Hu X. , McIsaac G. F. , David M. B. , Louwers C. A. L. 
Published: May 2007

AbstractReliable water quality models are needed to forecast the water quality consequences of different agricultural nutrient management scenarios. In this study, the Soil and Water Assessment Tool (SWAT), version 2000, was applied to simulate streamflow, riverine nitrate (NO3) export, crop yield, and watershed nitrogen (N) budgets in the upper Embarras River (UER) watershed in east‐central Illinois, which has extensive maize‐soybean cultivation, large N fertilizer input, and extensive tile drainage. During the calibration (1994–2002) and validation (1985–1993) periods, SWAT simulated monthly and annual stream flows with Nash‐Sutcliffe coefficients (E) ranging from 0.67 to 0.94 and R2 from 0.75 to 0.95. For monthly and annual NO3 loads, E ranged from −0.16 to 0.45 and R2 from 0.36 to 0.74. Annual maize and soybean yields were simulated with relative errors ranging from −10 to 6%. The model was then used to predict the changes in NO3 output with N fertilizer application rates 10 to 50% lower than original application rates in UER. The calibrated SWAT predicted a 10 to 43% decrease in NO3 export from UER and a 6 to 38% reduction in maize yield in response to the reduction in N fertilizer. The SWAT model markedly overestimated NO3 export during major wet periods. Moreover, SWAT estimated soybean N fixation rates considerably greater than literature values, and some simulated changes in the N cycle in response to fertilizer reduction seemed to be unrealistic. Improving these aspects of SWAT could lead to more reliable predictions in the water quality outcomes of nutrient management practices in tile‐drained watersheds.
Occurrence and Bioavailability of Pyrethroids in a Mixed Land Use Watershed
Authors: Budd R. , Bondarenko S. , Haver D. , Kabashima J. , Gan J. 
Published: May 2007

AbstractThe shift in land use patterns within many urban areas has the potential to influence the magnitude and nature of nonpoint‐source pollution. The presence of pyrethroid insecticides in urban surface streams is of particular concern due to the broad spectrum toxicity of pyrethroids to aquatic organisms and the widespread use of pyrethroid products for agricultural and urban pest control. Sediment samples were collected throughout a mixed land use watershed in southern California during two sampling periods and analyzed for a suite of pyrethroids. Bifenthrin and fenpropathrin were found most frequently in the sediment samples, with the highest concentrations associated with sites adjacent to large commercial nurseries. Sediments from residential areas or residential‐commercial mixed areas had fewer detections and significantly lower concentrations than the nursery runoff sediments. No apparent difference was found between wet and dry season concentrations, which may be attributed to the fact that the lack of flow under dry weather conditions rendered pyrethroid residues immobile. Organic carbon‐normalized sediment concentrations were poorly correlated with the freely dissolved pore water concentrations measured by solid phase microextraction (SPME), suggesting factors other than sediment organic carbon content should be considered when relating concentrations to potential toxicities.
Runoff Water Quality from Turfgrass Established Using Volume‐Based Composted Municipal Biosolids Applications
Authors: Hansen N. E. , Vietor D. M. , Munster C. L. , White R. H. , Provin T. L. 
Published: May 2007

AbstractMunicipal programs for turfgrass establishment recommend large volume‐based application rates of composted municipal biosolids (CMB). This study compared runoff water quality among combinations of two common turfgrass establishment practices and two CMB sources. Bryan‐ or Austin‐CMB were incorporated into 5 cm of soil at a rate of 12.5 or 25% by volume (v/v) on an 8.5% slope. Tifway bermudagrass [Cynodon dactylon (L.) Pers. × C. transvaalensis Burtt‐Davy, var. Tifway] sprigs were planted and established; sod, produced at a separate site using either CMB amendment at the 25% v/v rate, was transplanted to the runoff plots on the same day. A mature stand of bermudagrass was used as a control. Runoff water was collected after each of eight natural rain events during the sampling period. Total runoff water loss (mm) was similar for the CMB‐amended sprigged and transplanted sod stands. The concentration of total dissolved P (TDP) in runoff water was greatest from the transplanted sod in the first seven rain events (4.1 to 7.5 mg L−1). The concentration of TDP in runoff water was similar at both the 12.5 and 25% v/v incorporation rates. Regression analysis indicated Mehlich‐3‐extractable soil test P concentrations in soil amended with CMB were positively correlated to concentration and mass loss of dissolved P in runoff. At similar application rates, dissolved P loss in runoff water was reduced by incorporating CMB into the soil on site rather than transplanting sod produced with CMB.
Impact of Ectomycorrhizal Colonization of Hybrid Poplar on the Remediation of Diesel‐Contaminated Soil
Authors: Gunderson J. J. , Knight J. D. , Van Rees K. C. J. 
Published: May 2007

AbstractInfection by ectomycorrhizal (ECM) fungi may benefit hybrid poplar growing in contaminated soils by providing greater access to water and nutrients and possibly protecting the trees from direct contact with toxic contaminants. The objective of this research was to determine the effect of colonization of the ECM fungus Pisolithus tinctorius (Pers.) Coker & Couch on hybrid poplar fine root production, biomass and N and P uptake when grown in diesel‐contaminated soil (5000 mg diesel fuel kg soil−1). Commercially available Mycogrow Tree Tabs were the source of inoculum. A minirhizotron camera was used to provide the data necessary for estimating fine root production. Colonization of hybrid poplar roots (P. deltoides × [P. laurifolia × P. nigra] cv. Walker) by P. tinctorius increased total fine root production in diesel‐contaminated soil to 56.58 g m−2 compared to 22.59 g m−2 in the uncolonized, diesel‐contaminated treatment. Hybrid poplar leaf N and P concentrations were significantly greater in the diesel‐contaminated/ECM‐colonized treatment compared to the diesel‐contaminated/uncolonized treatment after 12 wk, while significantly less diesel fuel was recovered from the soil of the uncolonized treatment compared to the colonized treatment. Both planted treatments removed more contaminants from the soil than an unplanted control. Significantly greater concentrations of total petroleum hydrocarbons (TPH) were found sequestered in hybrid poplar root/fungal‐sheath complexes from the colonized treatment compared to the roots of the uncolonized treatment. The results of this study indicate that over a 12‐wk growth period, ECM colonization of hybrid poplar in diesel‐contaminated soils increased fine root production and whole‐plant biomass, but inhibited removal of TPH from the soil.
Role of Organic Matter in Microbial Transport during Irrigation with Sewage Effluent
Authors: Fine Pinchas , Hass Amir 
Published: May 2007

AbstractReduction of migration of fecal coliforms (FC) and streptococci (FS) by limiting the leaching in effluent‐irrigated soil was tested in lysimeters packed with quartz sand without or with added biosolids compost or with one of two clayey soils. The 200‐L, 70‐cm‐deep lysimeters were either planted with a Eucalyptus camaldulensis or an Oroblanco citrus tree (in the sand only), or not planted. The Eucalyptus was irrigated with oxidation pond effluent (OPE) and the Oroblanco with mechanical‐biological treatment plant effluent (MBTPE). The leaching fraction (LF) ranged from 0.2 to about 1.0, and the residence time (RT) from under 1 to 40 d. The Eucalyptus was also tested under intermittent leaching (RT 11–20 d) and deficit irrigation (without leaching for about 6 mo) regimes. Under MBTPE irrigation there was little or no leaching of FC and FS. Under OPE irrigation at LF 1 without a Eucalyptus there was little or no bacterial leaching at irrigation rates below 40 L d−1 per lysimeter (RT ≥ 0.8 d). Bacterial counts in the leachate were substantial in the presence of a Eucalyptus tree under LF 0.2 and intermittent leaching regimes, and when sand‐packed unplanted lysimeters received OPE effluent at >45 L d−1 Bacterial recovery peaked at LF 0.2, at up to 45% of the input level. At LF 1 (RT 0.6–2.8 d) and with intermittent leaching the recoveries were minute. Bacterial counts in the washout from the deficit‐irrigated lysimeters were typical of nonpolluted soils. The bacterial concentration and recovery patterns in the leachate mostly matched the organic carbon (OC) load in the irrigation water, and its concentration and bioavailablity in the leachate. We related the leaching patterns of the fecal bacteria to their relative reproduction and die‐off rates, and to the dependence of their regrowth on available carbon sources.
Riparian Plant Material Inputs to the Murray River, Australia
Authors: Esslemont Graeme , Maher William , Ford Phillip , Lawrence Ian 
Published: May 2007

AbstractBy changing riparian plants from Eucalypts to pasture and exotic deciduous trees, modern development has altered the type of carbon assimilated by Australian rivers. To investigate influences of plant litter substrates on biochemical oxygen demand, plant materials entering the Murray River were analyzed for their composition and mineralization potential. Plant materials were distinguished compositionally by two principal components, structural carbon and macronutrients, as: (i) Eucalyptus leaves, (ii) Eucalyptus bark and Casuarina cunninghamiana seed cone, (iii) grasses, (iv) macrophytes, (v) aquatic herbs, (vi) non‐eucalypt leaf (Salix, Casuarina, Acacia). Ratios of C/P (1879–14524) and C/N (65–267) were relatively high in Eucalyptus bark, while mean N/P (7–60) ratios were similar among plant materials. Terrestrial weathering increased C/P and C/N ratios, while N/P ratios remained similar, due to greater loss of N and P relative to C. Aerobic decay experiments showed that nutrient supplementation accelerated decay of all organic substrates, except for grasses that decayed efficiently without supplementation. Aquatic herbs also had substantial carbon availability, macrophytes and non‐eucalypt leaves had intermediate carbon availability, while eucalypt leaf and bark had intermediate to low carbon availabilities. Because biochemical oxygen demand varies with organic substrates sampled from the Murray River, and also with soluble nutrient availability, it is plausible that that modern changes to riverine plant communities and land use have influenced the biogeochemistry of this river toward faster, and more complete, processing of allochthonous carbon.