From the importance of organic carbon in reproduction tests with Eisenia fetida.

The standard Eisenia fetida chronic toxicity reproduction test is normalized and needs up to 8 weeks of experimentation. Many matrixes have shown toxic effects on the earthworms' survey, growth and reproduction. But the food factor may affect the organisms' responses to contaminated media in such tests. We try to evaluate the effect, or not, of the organic carbon content present in the environment, as spreadable organic wastes added in soil, on the reproduction test of Eisenia fetida. We confirm the influence of the organic matter content on earthworm reproduction. This "food" factor must be considered when studying environmental samples rich in organic matter, since that could mask potentially harmful effects. To minimize this potential "food" effect during reproduction tests, we recommend an inverse gradient of organic matter contribution by the "horse dung" food applied in all conditions according to the dose of agricultural amendments tested.

Influence of edaphic conditions and persistent organic pollutants on earthworms in an infiltration basin.

In recent decades, stormwater management has developed to allow stormwater to infiltrate directly into the soils instead of being collected and routed to sewer systems. However, during infiltration, stormwater creates a sediment deposit at the soil surface as the result of high loads of suspended particles (including pollutants), leading to the settlement of sedimentary layers prone to colonization by plants and earthworms. This study aims to investigate the earthworm communities of a peculiar infiltration basin and investigate the influence of edaphic conditions (water content, organic matter content, pH, height of sediment) and of persistent organic pollutants (POPs: PCBs, PCDDs and PCDFs) on these earthworms. Attention was paid to their age (juveniles or adults) and their functional group (epigeic, endogeic, anecic). We found that the earthworm abundance was mostly driven by edaphic conditions, with only a slight impact of POPs, with a significant negative impact of PCBDLno for juveniles and endogeic, and PCDDs for epigeic. On the contrary, the height of the sediment and the water content are beneficial for their presence and reproduction. Furthermore, POPs contents are also linked to physicochemical parameters of the sediment. Bioaccumulation was clearly revealed in the studied site but does not differ between juveniles and adults, except for PCDDs. Conversely, BAF values seemed to vary between functional groups, except for PCBDL non-ortho. It strongly varies with the family types (PCBs versus PCCD/Fs) and between congeners within the same family, with specific strong bioaccumulation for a few congeners.

Bioavailability and bioaccumulation of heavy metals of several soils and sediments (from industrialized urban areas) for Eisenia fetida.

Soils and sediments are susceptible to anthropogenic contamination with Metallic Trace Elements (MTEs) and it can present some risks to ecosystems and human health. The levels of Cd, Cu, Fe, Ni, Pb and Zn were assessed in soils (C, G, K, L) from Estarreja (Portugal) and sediments from a stormwater basin in Lyon (DJG), a harbour (LDB) and a Rhône river site (TRS) (France). An ecotoxicological study was performed with Eisenia fetida (E. fetida) to infer about potential transfer risks to the soil invertebrates. To assess risks associated with MTEs contamination, it is important to know their total concentrations, fractionation and the potential available fractions. CaCl2, DTPA and NaOAc extractions were performed to assess the extractable and available MTEs fractions. The studied sediments were much more contaminated than the soils for all the MTEs analysed. The trace elements fraction linked with DTPA extraction shows higher values when compared with the NaOAc and the CaCl2 pools. Low mortality effects were recorded in the tests with E. fetida. The MTEs levels in soils and sediments and the concentrations bioaccumulated in adult earthworms contributed to a reduction in the number of juveniles produced. E. fetida adults and juveniles accumulated ETMs as follows: Cd > Cu = Zn > Ni > Pb > Fe. Determined BAFs were mostly lower than 1 with some higher values for Cd, Cu and Zn. Calculated SET and ERITME indexes allowed to classify the samples from the most to the less toxic for E. fetida as: LDB > DJG > L > G > C > K > TRS. Despite this order of toxicity, the earthworms exposed to the sediment TRS presented the lowest reproduction rate. The combination of "chemical" measurements with the calculation of BAFs, but especially SET and ERITME indexes can be a useful tool in risk assessment.

Evaluation of phytotoxicity of seaport sediments aged artificially by rotary leaching in the framework of a quarry deposit scenario.

In the framework of an ecological risk assessment of seaport sediments for terrestrial ecosystems when deposited in quarries, we simulated the "ageing" of sediments exposed to rain. This experiment highlighted an inflection point at the solid/liquid ratio 1/25, after which the extraction of pollutants increases moderately. The raw sediments studied inhibited the germination of Lolium perenne and Armeria maritima (a halophytic species) seeds. Furthermore, they affected the early development of L.perenne. The same sediments, leached at a ratio of 1/25, presented a reduction of acute (germination) and chronic (growth) phytotoxicity. The bioconcentration factors of the metals studied decreased with the leached sediment, except for Cu which was still clearly identified in root parts. Thus rotary leaching tests and phytotoxicity bioassays can be used to provide an initial assessment of the ability of plants, particularly halophytes, to colonize deposits of dredged seaport sediments.

Selection of a halophytic plant for assessing the phytotoxicity of dredged seaport sediment stored on land.

The filling of dry quarries in coastal areas with sediments dredged in seaports represents a potentially interesting method of recycling of these materials. However, this recycling requires the prior carrying out of an Environmental Risk Assessment of the scenario concerned. For this, the question arose as to the type of plants capable of developing on the surface of such a deposit and the method to implement for assessing the possible phytotoxicity of dredged sediments. To answer this question, we chose to work with halophytic plants to be free from the salt-related effect and to assess only the effect related to the toxic compounds present. Based on the objectives set, these works led to the use of common plants of the French coast, with direct seeding, and with pollution-sensitive plants. Three species of angiosperms, Armeria maritima, Anthemis maritima and Plantago coronopus, were finally tested. As a result of this work, Armeria maritima was retained as the most suitable plant for testing the possible phytotoxic effect of dredged marine sediments stored on land. The results obtained with this plant are as follows: germination of 40 % of the seeds in 31 days, produced biomass of 493 mg FW in 6 months and a capacity to bioaccumulate metal pollutants in roots with 350 and 720 mg/kg DW for Zn and Cu, respectively.

Influences on the establishment and dominance of vegetation in stormwater infiltration basins.

Infiltration basins are widely used in urban environments as a technique for managing and reducing the volume of stormwater. These basins can be spontaneously colonized by wild plants, which can be used as bioindicators of edaphic characteristics. As the basins are anthropogenic environments, the description of plant biodiversity allows the determination of which species colonize such environments and identification of the relationships between plants, basin type and operation. Nineteen infiltration basins were selected according to their catchment types (industrial, urban, agricultural). The dominant species were identified and sampled. Rumex sp., Taraxacum sp. and Artemisia sp. are the three types most represented (88, 61 and 55% respectively of the basins studied). Their families and their respective orders are those most commonly found (Caryophyllales, Asterales and Polygonaceae, Asteraceae). Poaceae is the family grouping with the largest number of different species (11). Although each species occupies only 1 or 2 basins, plants of this family occupy 61% of the basins. Although the catchment characteristics of the 19 basins do not play a direct role in the diversity of plant families, they can influence the presence or absence of certain species. Thus, these plants can be used as bio-indicators of basin soil and operating characteristics, such as sediment depths, inundation frequency and duration.

Assessment of the phytotoxicity of seaport sediments in the framework of a quarry-deposit scenario: germination tests of sediments aged artificially by column leaching.

The aim of the Sustainable Management of Sediments Dredged in Seaports (SEDIGEST) project is to assess the risks of treated port sediments for terrestrial ecosystems when deposited in quarries. We simulated the "ageing" of these sediments up to the "moment" when plants can germinate. Sediments were leached by water percolating through a laboratory column. Sediments 1 and 2, taken from the port of Toulon (France), were dried and aired. Sediment 3, taken from the port of Guilvinec (France), was stabilised with lime. Phytotoxicity was evaluated on the three artificially aged sediments using germination and early development tests (48 h to 7 days) by Phytotoxkit F(TM) bioassays. The three dilutions tested were performed with the reference "ISO substrate" and with Lolium perenne sp. (rye grass), Sinapis alba (white mustard), and Lepidium sativum (watercress). The tests performed with sediments 1 and 2 showed (1) a decrease of their toxicity to the germination of the species selected following leaching and (2) that L. perenne was the most sensitive species. The tests performed with sediment 3 showed that it was improper for colonisation even after leaching simulating 16 months of ageing. These germination tests on aged sediments identified the effects of leaching and made it possible to appreciate the capacity of the sediments to allow colonisation by plants.

Cd, Cu and Zn mobility in contaminated sediments from an infiltration basin colonized by wild plants: the case of Phalaris arundinacea and Typha latifolia.

Infiltration basins are shallow reservoirs in which stormwater is temporarily collected in order to reduce water volume in downstream networks. The settling of stormwater particles leads to a contaminated sediment layer. Wild plants can colonize these basins and can also play a role on the fate of heavy metals either directly by their uptake or indirectly by modification of physico-chemical characteristics of the sediment and therefore by modification of the mobility of heavy metals. The aim of this study, carried out in a vegetated infiltration basin, is to assess Cd, Cu and Zn mobility in two zones colonized by different species, Phalaris arundinacea and Typha latifolia. The study was carried out using three single chemical extractions: CaCl2 for the exchangeable phase, acetate buffer for the acido-soluble fraction and diethylenetriamine-pentaacetic acid (DTPA) for the fraction associated to the organic matter. Zn and Cd are mainly associated to carbonated and organic matter phases of the sediment. Moreover, acetate buffer-extractable Zn contents are strongly correlated to carbonates content in the sediment. DTPA-extractable Cu contents are strongly correlated with organic carbon sediment contents. We have also noted that extractable contents were significantly different between both zones whatever the metal.

Benefits and limits of sediment toxicity tests as an aid to decision-making.

With respect to the management of dredged sediments, a crucial issue is whether the removed materials (watered and/or processed) are disposed of or reused in an environmentally sound manner. In this context, the number of studies dealing with hazard or risk assessment has exponentially increased. This emphasis has resulted in the promotion and application of a very large variety of ecotoxicological tests. As a consequence, there is a clear need to highlight the scope and limitations of these tests for their appropriate selection and interpretation. In this paper we discuss the choice, implementation and interpretation of laboratory tests carried out on aquatic organisms at various levels of biological organization. We examine some experimental tools and methods in order to determine how suitable they are in regard to the objectives for which they are employed. To make this discussion more consistent our paper is based on results from research programmes conducted for governmental organizations and industrial partners. The Laboratoire des Sciences de l'Environnement (LSE) was involved with Cemagref de Lyon in a first methodological programme on risk assessment of scenarios of dredged sediment deposition. Another programme for a chemical company was implemented to assess the benefits of a physico-chemical treatment applied to contaminated dredged sediments in a scenario of reuse or deposit in gravel pits. Currently, the LSE is working on a programme of risk assessment for road sediments in valorization scenarios. From these programmes, we expose how single-species tests, as well as more complex bioassays and microcosm tests, can be used in an iterative step of risk assessment. Concerning microcosm tests, we also introduce a more realistic system that has been designed to simulate natural hydraulic conditions of gravel pits to assess the effects of toxicants on gravel pit aquatic biota during the sediment immersion phase and the sediment post-deposition phase (paper in preparation). The benefits of these ecotoxicological approaches are underlined, but limits are discussed with regard to several criteria: ecological relevance, realism, use for decision-making, cost and complexity of methods involved.

MethylScreen: DNA methylation density monitoring using quantitative PCR.

Aberrant gene silencing of genes through cytosine methylation has been demonstrated during the development of many types of cancers including prostate cancer Several genes including GSTP1 have been shown to be methylated in prostate cancer leading to the suggestion and demonstration that methylation status of such genes could be used as cancer diagnosis markers alone or in support of histology. We developed a bisulfite-free alternative, MethylScreen technology, an assay for DNA methylation detection utilizing combined restriction from both methylation-sensitive restriction enzymes (MSRE) and methylation-dependent restriction enzymes (MDRE). MethylScreen was used to analyze the 5' region of GSTP1 in cell lines, in vitro methylated DNA populations, and flash-frozen tissue samples in an effort to characterize the output and analytical performance characteristics of the assay. The output from the quantitative PCR assay suggested that it could not only detect fully methylated molecules in a mixed population below the 1% level, but it could also quantify the abundance of intermediately methylated molecules. Interestingly, the interpreted output from the four quantitative PCRs closely resembled the molecular population as described by clone-based bisulfite genomic sequencing.

Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets.

Using a unique microarray platform for cytosine methylation profiling, the DNA methylation landscape of the human genome was monitored at more than 21,000 sites, including 79% of the annotated transcriptional start sites (TSS). Analysis of an oligodendroglioma derived cell line LN-18 revealed more than 4000 methylated TSS. The gene-centric analysis indicated a complex pattern of DNA methylation exists along each autosome, with a trend of increasing density approaching the telomeres. Remarkably, 2% of CpG islands (CGI) were densely methylated, and 17% had significant levels of 5 mC, whether or not they corresponded to a TSS. Substantial independent verification, obtained from 95 loci, suggested that this approach is capable of large scale detection of cytosine methylation with an accuracy approaching 90%. In addition, we detected large genomic domains that are also susceptible to DNA methylation reinforced inactivation, such as the HOX cluster on chromosome 7 (CH7). Extrapolation from the data suggests that more than 2000 genomic loci may be susceptible to methylation and associated inactivation, and most have yet to be identified. Finally, we report six new targets of epigenetic inactivation (IRX3, WNT10A, WNT6, RARalpha, BMP7 and ZGPAT). These targets displayed cell line and tumor specific differential methylation when compared with normal brain samples, suggesting they may have utility as biomarkers. Uniquely, hypermethylation of the CGI within an IRX3 exon was correlated with over-expression of IRX3 in tumor tissues and cell lines relative to normal brain samples.

Enrichment of gene-coding sequences in maize by genome filtration.

Approximately 80% of the maize genome comprises highly repetitive sequences interspersed with single-copy, gene-rich sequences, and standard genome sequencing strategies are not readily adaptable to this type of genome. Methodologies that enrich for genic sequences might more rapidly generate useful results from complex genomes. Equivalent numbers of clones from maize selected by techniques called methylation filtering and High C0t selection were sequenced to generate approximately 200,000 reads (approximately 132 megabases), which were assembled into contigs. Combination of the two techniques resulted in a sixfold reduction in the effective genome size and a fourfold increase in the gene identification rate in comparison to a nonenriched library.

Prevalence of vaginal colonization by drug-resistant Candida species in college-age women with previous exposure to over-the-counter azole antifungals.

We enrolled 382 college-age women in a cross-sectional survey to investigate the relationship between use of over-the-counter (OTC) azole-based antifungal drugs and vaginal colonization by drug-resistant Candida. This study showed no correlation (P=.506) between previous OTC exposure and colonization of drug-resistant Candida in vaginal flora. However, a small number of resistant Candida species isolates were obtained from women with a history of multiple exposures to OTC antifungals; given the widespread use of these products, this may be an emerging concern.

The acid-induced folded state of Sac7d is the native state.

Sac7d unfolds at low pH in the absence of salt, with the greatest extent of unfolding obtained at pH 2. We have previously shown that the acid unfolded protein is induced to refold by decreasing the pH to 0 or by addition of salt (McCrary BS, Bedell J. Edmondson SP, Shriver JW, 1998, J Mol Biol 276:203-224). Both near-ultraviolet circular dichroism spectra and ANS fluorescence enhancements indicate that the acid- and salt-induced folded states have a native fold and are not molten globular. 1H,15N heteronuclear single quantum coherence NMR spectra confirm that the native, acid-, and salt-induced folded states are essentially identical. The most significant differences in amide 1H and 15N chemical shifts are attributed to hydrogen bonding to titrating carboxyl side chains and through-bond inductive effects. The 1H NMR chemical shifts of protons affected by ring currents in the hydrophobic core of the acid- and salt-induced folded states are identical to those observed in the native. The radius of gyration of the acid-induced folded state at pH 0 is shown to be identical to that of the native state at pH 7 by small angle X-ray scattering. We conclude that acid-induced collapse of Sac7d does not lead to a molten globule but proceeds directly to the native state. The folding of Sac7d as a function of pH and anion concentration is summarized with a phase diagram that is similar to those observed for other proteins that undergo acid-induced folding except that the A-state is encompassed by the native state. These results demonstrate that formation of a molten globule is not a general property of proteins that are refolded by acid.

The syntenic relationship of the zebrafish and human genomes.

The zebrafish is an important vertebrate model for the mutational analysis of genes effecting developmental processes. Understanding the relationship between zebrafish genes and mutations with those of humans will require understanding the syntenic correspondence between the zebrafish and human genomes. High throughput gene and EST mapping projects in zebrafish are now facilitating this goal. Map positions for 523 zebrafish genes and ESTs with predicted human orthologs reveal extensive contiguous blocks of synteny between the zebrafish and human genomes. Eighty percent of genes and ESTs analyzed belong to conserved synteny groups (two or more genes linked in both zebrafish and human) and 56% of all genes analyzed fall in 118 homology segments (uninterrupted segments containing two or more contiguous genes or ESTs with conserved map order between the zebrafish and human genomes). This work now provides a syntenic relationship to the human genome for the majority of the zebrafish genome.

Case management: the current best practices and the next generation of innovation.

Eight published literature reviews of case management were evaluated to determine areas of consensus regarding outcomes associated with full service, broker, and hybrid models. Full service was recommended for "best practice" status and the effectiveness of the broker model was seriously questioned. Research evaluating para-professional and peer assisted models of case management, a potential method for improving outcomes, was also reviewed. One promising peer-assisted model was identified and described. Although the use of paraprofessionals and peers in case management holds promise, much more research is needed before the effectiveness of this approach can be confidently determined.

MaskerAid: a performance enhancement to RepeatMasker.

UNLABELLED: Identifying and masking repetitive elements is usually the first step when analyzing vertebrate genomic sequence. Current repeat identification software is sensitive but slow, creating a costly bottleneck in large-scale analyses. We have developed MaskerAid, a software enhancement to RepeatMasker that increased the speed of masking more than 30-fold at the most sensitive setting. AVAILABILITY: On request from the authors (see http://sapiens.wustl.edu/MaskerAid). CONTACT: maskeraid@watson.wustl.edu

Molecular refinement of the 1p36 deletion syndrome reveals size diversity and a preponderance of maternally derived deletions.

The deletion of chromosome 1p36 is a newly recognized, relatively common contiguous gene deletion syndrome with a variable phenotype. The clinical features have recently been delineated and molecular analysis indicates that the prevalence of certain phenotypic features appears to correlate with deletion size. Phenotype/genotype comparisons have allowed the assignment of certain clinical features to specific deletion intervals, significantly narrowing the regions within which to search for candidate genes. We have extensively characterized the deletion regions in 30 cases using microsatellite markers and fluorescence in situ hybridization analyses. The map order of 28 microsatellite markers spanning the deletion region was obtained by a combination of genotypic analysis and physical mapping. The deletion region was divided into six intervals and breakpoints were found to cluster in mainly two regions. Molecular analysis of the deletions showed that two patients had complex re-arrangements; these cases shared their distal and proximal breakpoints in the two common breakpoint regions. Of the de novo deletions ( n = 28) in whichparental samples were available and the analysis was informative ( n = 27), there were significantly morematernally derived deletions ( n = 21) than paternally derived deletions ( n = 6) (chi1(2) = 8.35, P < 0.0001). Phenotype/genotype correlations and refinements of critical regions in our naturally occurring deletion panel have delineated specific areas in which to focus the search for the causative genes for the features of this syndrome.

Effects of nitrogen source on growth and activity of nitrogen-assimilating enzymes in Douglas-fir seedlings.

Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) seedlings were grown for 68 days in a growth chamber in nutrient solutions with ammonium, nitrate or ammonium nitrate as the nitrogen source. Among the nitrogen sources tested, whole-seedling biomass, relative growth rate (RGR), root and shoot elongation, and number of lateral roots, were greatest in seedlings grown with ammonium. In the absence of nitrogen, plant growth and formation of lateral roots were poor. Initially, glutamine synthetase, NAD-glutamate dehydrogenase and aspartate aminotransferase activities were high in young roots and shoots, but all three enzymatic activities decreased after one month of culture. In root apices, glutamine synthetase and aspartate aminotransferase activities were higher than NAD-glutamate dehydrogenase activity. Enzymatic activities were often higher in ammonium-fed seedlings than in seedings supplied with the other forms of nitrogen. Activities of all three enzymes were significantly reduced in seedlings grown in the absence of nitrogen. The beneficial effect of ammonium is discussed on the basis of its involvement in the assimilation pathways of Douglas-fir.

Evaluation of problem solving and communication skills of persons with schizophrenia.

Although much research has shown positive outcomes of teaching problem solving and communication skills to persons with schizophrenia, the amount of research on the assessment of these two sets of skills has been modest. The current study demonstrates an effective model for their assessment and includes a previously neglected procedure to determine if subjects attended to the skill prompts. It replicates and expands prior findings on problem solving and communication skills. Results indicated that persons with schizophrenia were generally deficit in problem solving skills. Persons without schizophrenia seemed to use more behavioral information when deciding if a problem existed and they were better able to differentiate between appropriate and inappropriate solutions to problems. Persons with schizophrenia were found to be deficit in communication skills that facilitate interaction and showed a style that subordinated their wants to those of others.