Simulation par le modèle AgriFlux du devenir de l'atrazine et du dééthylatrazine dans un sol du Québec sous mais sucré

Les outils mathématiques sont de plus en plus utilisés pour simuler la contamination d'origine agricole des eaux souterraines. Le modèle AgriFlux permet, à l'aide du module PestiFlux, de simuler les processus responsables du devenir des pesticides dans le sol: ruissellement, volatilisation, adsorption/désorption rapide, adsorption/désorption lente, complexation par la matière organique dissoute, biodégradation en sous-produits, hydrolyse, drainage et lessivage. AgriFlux est utilisé pour simuler le devenir de l'atrazine et du dééthylatrazine sur une parcelle expérimentale de la région de Québec (Québec, Canada) cultivée en maïs sucré (Zea mays, L.) traité à l'atrazine. Des prélèvements d'eau interstitielle ont été réalisés (1986-1990) à l'aide de lysimètres avec succion (0,5 et 1,0 m de profondeur) et analysés pour leur contenu en atrazine et dééthylatrazine. De manière générale, AgriFlux reproduit bien l'évolution des concentrations mesurées, dans le temps et dans le profil de sol (r=0,76). Certains pics de concentrations observés sur le terrain ne sont toutefois pas représentés ou sont décalés dans le temps, ce qui pourrait être attribué à une sous-estimation de la variabilité spatiale des paramètres. Le rapport dééthylatrazine/atrazine est relativement bien simulé en 1988 à 0,5 m, mais est moins représentatif pour les autres données, ce qui pourrait être dû à une certaine imprécision dans la simulation de la biodégradation. Une analyse de sensibilité du modèle aux variations de différents paramètres a montré que le paramètre le plus influent dans les conditions testées est la constante de biodégradation. Les résultats obtenus montrent la pertinence d'AgriFlux (PestiFlux) dans la simulation du devenir des pesticides dans le sol et donc des risques de contamination des eaux souterraines en région agricole.Groundwater and surface water contamination by agricultural practices has become an increasingly preoccupying problem. Mathematical models are valuable tools to help prevent this type of pollution from non-point sources. AgriFlux is a mechanistic, stochastic model simulating the fate of agricultural contaminants in the unsaturated zone at the scale of the agricultural field. AgriFlux, through the PestiFlux module, now simulates pesticide transformations in the soil from their application to the field until their leaching with percolating water. The processes represented include volatilization, complexation by the soluble organic matter, instantaneous adsorption and desorption, slow adsorption and desorption to less available sites, biodegradation to by-products and hydrolysis to non-toxic compounds. The pesticide freely dissolved in solution or complexed with soluble organic matter can be mobilized with runoff, drainage and leaching waterAn application of PestiFlux to an experimental field near Quebec City (Quebec, Canada) is presented. The soil is a well-drained loamy sand cropped from 1986 to 1990 with sweet corn (Zea Mays, L.) receiving atrazine treatments (1.6 to 1.8 kg.ha-1 of active ingredient). Interstitial water was sampled using 12 suction lysimeters located at both the 0.5 and 1.0 m depths in the soil. All stations were sampled monthly in 1986 and 1987 and the collected water was analyzed for atrazine alone. In 1988, the sampling (every two weeks) was limited to the lysimeters which had previously shown the highest pesticide concentrations (two lysimeters at 0.5 m and one lysimeter at 1.0 m). The interstitial water was analyzed for atrazine and deethylatrazine. There was no sampling in 1989. In 1990, all stations were sampled on a weekly basis and a composite water sample obtained for each depth was analyzed for both compounds. Most of the pesticide-related parameters required to run PestiFlux were deduced from the literature, with the exception of the biodegradation rate coefficient which was estimated from field monitoring of atrazine. The parameters required to simulate water fluxes and plant uptake were the same as those used in a previous application of AgriFlux to the same experimental field for the simulation of nitrate fluxes (LAROCQUE and BANTON, 1995).Results show that PestiFlux generally represents well the measured atrazine and deethylatrazine concentrations in the interstitial water at 0.5 and 1.0 m. A linear regression using all measured and simulated concentrations indiscriminately gives a correlation coefficient of 0.76 when using the logarithm of concentrations. The temporal evolution of the pesticide concentrations is relatively well simulated, especially on the long term with an adequate representation of the increase in pesticide concentrations in the soil profile at 1.0 m. This increase is probably due to the fallow existing in 1985 which would have favored leaching of adsorbed pesticide below the soil profile, leaving only low residual pesticide concentrations. Over one growing season, the transport of atrazine and deethylatrazine is well represented by the model, although some peak concentrations are delayed or attenuated. This result could be due to an underestimation of the spatial variability of the different parameters. It is possible that the coefficient of variation of 10% adopted may not represent adequately the spatial variation of some parameters. Nevertheless, most measured concentrations of both compounds are within the mean simulated concentrations and included between two standard deviations. For 1988, most of the measured concentrations are located near the upper limit of the envelope curve which is consistent with the fact that the sampled lysimeters were those yielding the highest concentrations. The simulated concentrations show a generally good representation of the relative atrazine and deethylatrazine concentrations. The ratio of the mean deethylatrazine to atrazine concentrations provides a closer look at the adequacy between the simulated concentrations of both compounds. A comparison between the measured and the simulated ratios shows a good adequacy at 0.5 m in 1988 and both over- and under-estimation of the ratio for the other available data. This is probably due to an imprecision in the simulation of biodegradation rates during some periods. All the parameters used in the simulation have an important uncertainty, due to the significant spatial variation of the parameters in the field and to the imprecise knowledge of some pesticide characteristics. In order to identify the parameters which have the most important influence on the results, an analysis of the sensitivity of the cumulated leaching mass of both compounds at 1.0 m to variations of the different input parameters was performed. The results show that the biodegradation rate has the greatest influence on the results. This is probably due to the importance of this process in the simulated situation. This result confirms the importance of an adequate quantification of this parameter and of its spatial variation. PestiFlux offers a comprehensive representation of pesticide transformations in the soil and is easy to use. As a module of AgriFlux, it has the advantage of being integrated into a well-tested and reliable modeling environment. The presented simulation results show that, apart from some limits due to the quantification of some of the parameters, PestiFlux is a useful and comprehensive tool for estimating potential groundwater pollution by pesticides

Simplification rationnelle des outils hydrologiques de gestion : recommandations méthodologiques pour la construction de modèles semi-empiriques à origine mécaniste

Les modèles de simulation hydrologiques sont reconnus comme des outils mathématiques très performants mais généralement d'application difficile, principalement à cause du nombre élevé des paramètres requis. À l'inverse, les outils actuels de gestion sont généralement développés à l'aide d'approches empiriques limitant leur application. De plus, leurs paramètres ne sont pas des grandeurs mesurables et doivent être ajustés pour chaque situation. Une approche est proposée pour le développement d'outils semi empiriques de gestion. Elle consiste à simuler un grand nombre de scénarios en utilisant un modèle complexe de simulation puis à rationaliser l'information obtenue pour développer un nouveau modèle semi empirique. L'exemple illustrant cette approche concerne l'évaluation des flux d'eau ruisselée à la surface des champs, lessivée vers la nappe souterraine et drainée par les drains agricoles spécifiquement pour le contexte du Québec. À partir des résultats de simulation de 4500 scénarios, une simplification.rationalisation a permis de réduire à 120 le nombre de scénarios de référence à l'aide desquels peuvent être évalués tous les scénarios possibles par de simples interpolations linéaires. Une application de l'algorithme résultant sur un site du Québec a montré la bonne concordance entre les résultats calculés et mesurés. À la fois l'ordre de grandeur du ruissellement et du drainage et leur grandeur relative sont bien évalués.Considering the complexity of the water cycle in soil systems, models are used more than ever in parallel with field investigations to assist in the decision making process (KHAKURAL et ROBERT, 1993). Most available models are either too complicated (many non-measurable parameters) or too simple (empirical or site-specific) to be used as management tools. Such tools should conform to known theory and should be structured to enable efficient analysis of field situations with minimal requirements for parameters (CARSEL et al 1984). However, if the mechanistic models are very performing tools with regards to their representation of the processes and for the accuracy and reliability of their results, they are criticized for their complexity and for the large number of parameters they require. For this reason, their potential application as management tools cannot be recommended especially in preliminary investigations when the methodology has to be straight forward and rapidly implemented. On the other hand, existing management tools are often developed using an empirical approach for a specific context which considerably limits their transferability to different situations. Moreover, their empirical parameters often cannot be measured for the new situations, and must be adjusted for each new application. A new approach conciliating the qualities of both kinds of tools was elaborated for the development of management tools. This approach consists in using mechanistic models for simulating a set of possible situations and in rationalizing the information obtained by simulation through regression analyses or other methods. An example of this methodology is presented in this paper with the development of the hydrological part (runoff, leaching and drainage) of a management tool dedicated to the evaluation of nutrient losses related to manure applications. Developed for the Quebec conditions, 4500 theoretical situations were considered corresponding to ten climates, nine soil textures, 25 crops and two slope values. Independently, agricultural management practices and drainage were taken into account.For the mechanistic simulation of the water budget in the 4500 theoretical situations, the hydrologic module of the mechanistic-stochastic model AgriFlux was used (BANTON et al. 1993b). Because of the important field variability of most parameters, the stochastic AgriFlux model incorporates the variability resulting from field heterogeneity, measurement errors and intrinsic uncertainty related to parameter definition. The soil profile is divided in plot scale homogeneous horizons (or compartments) and a daily time step is used in the calculations. The water budget module in AgriFlux is named HydriFlux and simulates all the water-related processes (precipitations, snowmelt, infiltration, runoff, water uptake by plants, evaporation, percolation and drainage) using characteristic water contents and unsaturated hydraulic conductivity.In the example presented, the simulation results obtained by running HydriFlux have shown that the soil water fluxes (runoff and percolation) vary as linear functions of both the annual rain volume (the most important characteristic of the climate) and the logarithm of the saturated hydraulic conductivity (the most important characteristic of the soil type). A reduction of the number of crops could also be achieved by taking into account the water needs and the water uptake curves of the crops. This rationalization-simplification reduced the number of theoretical simulations to be stored in the management tool to 120 (2 climates x 3 textures x 10 crops x 2 slopes). These represent only 2.7% of the initial situations simulated by the mechanistic HydriFlux model. The different water fluxes are stored in the management tool as tables in which direct interpolations are performed to calculate the fluxes corresponding to all the potential intermediary situations. Such developed management tool presents good qualities at the same time for its calculation speed, for its easy parameterization, for the reliability of its evaluation (through the evaluation of the mechanistic model) and for its high transferability and applicability to various situations. The calculations are rapidly done and their programming can be very easily made by using a spreadsheet software.An application of this evaluation method has been done on an experimental site located in Quebec (ENRIGHT et MADRAMOOTOO, 1994), the only one for which both the runoff and the drainage have been measured during many years (1989 to 1991, April to December). The application on two fields (1.84 et 4.63 ha) has shown a good concordance between the calculated and measured results, as well for the magnitude of the fluxes than for the relative importance of these fluxes. Moreover, this application has shown that the variability of the measured values is higher than the calculated ones, attesting of the great influence of the variations in climatic, soil, crop and management conditions on the water budget. However, the good evaluation of the fluxes (for relative and absolute values) confirms the reliability of the proposed approach and of the simplification

Fear of Birth Defects Is a Major Barrier to Soil-Transmitted Helminth Treatment (STH) for Pregnant Women in the Philippines

The World Health Organization recommends anthelminthic treatment for pregnant women after the first trimester in soil-transmitted helminth (STH) endemic regions to prevent adverse maternal-fetal consequences. Although studies have shown the high prevalence of infection in the Philippines, no research has evaluated deworming practices. We hypothesized that pregnant women are not receiving deworming treatment and we aimed to identify barriers to World Health Organization guideline implementation. We conducted key informant interviews with local Department of Health (DOH) administrators, focus group discussions with nurses, midwives, and health care workers, and knowledge, attitudes, and practices surveys with women of reproductive age to elicit perspectives about deworming during pregnancy. Key informant interviews revealed that healthcare workers were not deworming pregnant women due to inadequate drug supply, infrastructure and personnel as well as fear of teratogenicity. Focus group discussions showed that healthcare workers similarly had not implemented guidelines due to infrastructure challenges and concerns for fetal malformations. The majority of local women believed that STH treatment causes side effects (74.8%) as well as maternal harm (67.3%) and fetal harm (77.9%). Women who were willing to take anthelminthics while pregnant had significantly greater knowledge as demonstrated by higher Treatment Scores (mean rank 146.92 versus 103.1, z = −4.40, p<0.001) and higher Birth Defect Scores (mean rank 128.09 versus 108.65, z = −2.43, p = 0.015). This study concludes that World Health Organization guidelines are not being implemented in the Philippines. Infrastructure, specific protocols, and education for providers and patients regarding anthelminthic treatment are necessary for the successful prevention of STH morbidity and mortality among pregnant women

Chironomid-based palaeotemperature estimates for northeast Finland during Oxygen Isotope Stage 3.

Quantitative palaeotemperature estimates for the earlier part of Oxygen Isotope Stage (OIS-) 3 are inferred from subfossil chironomid remains. The high-latitudinal study site of Sokli, northeast Finland, provides for a unique lacustrine deposit covering the earlier part of OIS-3, and the chironomid remains found in the sediments show that a shallow lake with a diverse fauna was present at the study site throughout the record. Using a Norwegian calibration data set as a modern analogue, mean July air temperatures are reconstructed. The chironomid-inferred July air temperatures are surprisingly high, reaching values similar to the current temperature at the study site. Other proxies that were applied to the sediments included the analysis of botanical and zoological macro-remains, and our results concur with temperature estimates derived from climate indicator taxa. Summer temperatures for interstadial conditions, reconstructed with climate models, are as high as our proxy-based palaeotemperatures

Intraregional variability in chironomid-inferred temperature estimates and the influence of river inundations on lacustrine chironomid assemblages.

Floodplain lakes are rarely analysed for fossil chironomids and usually not incorporated in modern chironomid-climate calibration datasets because of the potential complex hydrological processes that could result from flooding of the lakes. In order to investigate this potential influence of river inundations on fossil chironomid assemblages, 13 regularly inundated lakes and 20 lakes isolated from riverine influence were sampled and their surface sediments analysed for subfossil chironomid assemblages. The physical and chemical settings of all lakes were similar, although the variation in the environmental variables was higher in the lakes isolated from riverine influence. Chironomid concentration and taxon richness show significant differences between the two classes of lakes, and the variation in these variables is best explained by loss-on-ignition of the sediments (LOI). Relative chironomid abundances show some differences between the two groups of lakes, with several chironomid taxa occurring preferentially in one of the two lake-types. The variability in chironomid assemblages is also best explained by LOI. Application of a chironomid-temperature inference model shows that both types of lakes reconstruct July air temperatures that are equal to, or slightly underestimating, the measured temperature of the region. We conclude that, although there are some differences between the chironomid assemblages of floodplain lakes and of isolated lakes, these differences do not have a major effect on chironomid-based temperature reconstruction. © 2007 Springer Science+Business Media B.V

Comparative Proteomic Analysis of the PhoP Regulon in Salmonella enterica Serovar Typhi Versus Typhimurium

Background: S. Typhi, a human-restricted Salmonella enterica serovar, causes a systemic intracellular infection in humans (typhoid fever). In comparison, S. Typhimurium causes gastroenteritis in humans, but causes a systemic typhoidal illness in mice. The PhoP regulon is a well studied two component (PhoP/Q) coordinately regulated network of genes whose expression is required for intracellular survival of S. enterica. Methodology/Principal Findings: Using high performance liquid chromatography mass spectrometry (HPLC-MS/MS), we examined the protein expression profiles of three sequenced S. enterica strains: S. Typhimurium LT2, S. Typhi CT18, and S. Typhi Ty2 in PhoP-inducing and non-inducing conditions in vitro and compared these results to profiles of $phoP^−/Q^−$ mutants derived from S. Typhimurium LT2 and S. Typhi Ty2. Our analysis identified 53 proteins in S. Typhimurium LT2 and 56 proteins in S. Typhi that were regulated in a PhoP-dependent manner. As expected, many proteins identified in S. Typhi demonstrated concordant differential expression with a homologous protein in S. Typhimurium. However, three proteins (HlyE, STY1499, and CdtB) had no homolog in S. Typhimurium. HlyE is a pore-forming toxin. STY1499 encodes a stably expressed protein of unknown function transcribed in the same operon as HlyE. CdtB is a cytolethal distending toxin associated with DNA damage, cell cycle arrest, and cellular distension. Gene expression studies confirmed up-regulation of mRNA of HlyE, STY1499, and CdtB in S. Typhi in PhoP-inducing conditions. Conclusions/Significance: This study is the first protein expression study of the PhoP virulence associated regulon using strains of Salmonella mutant in PhoP, has identified three Typhi-unique proteins (CdtB, HlyE and STY1499) that are not present in the genome of the wide host-range Typhimurium, and includes the first protein expression profiling of a live attenuated bacterial vaccine studied in humans (Ty800)

The p53 Tumor Suppressor Is Stabilized by Inhibitor of Growth 1 (ING1) by Blocking Polyubiquitination

The INhibitor of Growth tumor suppressors (ING1-ING5) affect aging, apoptosis, DNA repair and tumorigenesis. Plant homeodomains (PHD) of ING proteins bind histones in a methylation-sensitive manner to regulate chromatin structure. ING1 and ING2 contain a polybasic region (PBR) adjacent to their PHDs that binds stress-inducible phosphatidylinositol monophosphate (PtIn-MP) signaling lipids to activate these INGs. ING1 induces apoptosis independently of p53 but other studies suggest proapoptotic interdependence of ING1 and p53 leaving their functional relationship unclear. Here we identify a novel ubiquitin-binding domain (UBD) that overlaps with the PBR of ING1 and shows similarity to previously described UBDs involved in DNA damage responses. The ING1 UBD binds ubiquitin with high affinity (Kd∼100 nM) and ubiquitin competes with PtIn-MPs for ING1 binding. ING1 expression stabilized wild-type, but not mutant p53 in an MDM2-independent manner and knockdown of endogenous ING1 depressed p53 levels in a transcription-independent manner. ING1 stabilized unmodified and six multimonoubiquitinated forms of wild-type p53 that were also seen upon DNA damage, but not p53 mutants lacking the six known sites of ubiquitination. We also find that ING1 physically interacts with herpesvirus-associated ubiquitin-specific protease (HAUSP), a p53 and MDM2 deubiquitinase (DUB), and knockdown of HAUSP blocks the ability of ING1 to stabilize p53. These data link lipid stress signaling to ubiquitin-mediated proteasomal degradation through the PBR/UBD of ING1 and further indicate that ING1 stabilizes p53 by inhibiting polyubiquitination of multimonoubiquitinated forms via interaction with and colocalization of the HAUSP-deubiquitinase with p53

Competitive Repair by Naturally Dispersed Repetitive DNA during Non-Allelic Homologous Recombination

Genome rearrangements often result from non-allelic homologous recombination (NAHR) between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs) induce NAHR–dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR) occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR–dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer

Application of In Vivo Induced Antigen Technology (IVIAT) to Bacillus anthracis

In vivo induced antigen technology (IVIAT) is an immuno-screening technique that identifies bacterial antigens expressed during infection and not during standard in vitro culturing conditions. We applied IVIAT to Bacillus anthracis and identified PagA, seven members of a N-acetylmuramoyl-L-alanine amidase autolysin family, three P60 family lipoproteins, two transporters, spore cortex lytic protein SleB, a penicillin binding protein, a putative prophage holin, respiratory nitrate reductase NarG, and three proteins of unknown function. Using quantitative real-time PCR comparing RNA isolated from in vitro cultured B. anthracis to RNA isolated from BALB/c mice infected with virulent Ames strain B. anthracis, we confirmed induced expression in vivo for a subset of B. anthracis genes identified by IVIAT, including L-alanine amidases BA3767, BA4073, and amiA (pXO2-42); the bacteriophage holin gene BA4074; and pagA (pXO1-110). The exogenous addition of two purified putative autolysins identified by IVIAT, N-acetylmuramoyl-L-alanine amidases BA0485 and BA2446, to vegetative B. anthracis cell suspensions induced a species-specific change in bacterial morphology and reduction in viable bacterial cells. Many of the proteins identified in our screen are predicted to affect peptidoglycan re-modeling, and our results support significant cell wall structural remodeling activity during B. anthracis infection. Identification of L-alanine amidases with B. anthracis specificity may suggest new potential therapeutic targets

Looking forward through the past: identification of 50 priority research questions in palaeoecology

1. Priority question exercises are becoming an increasingly common tool to frame future agendas in conservation and ecological science. They are an effective way to identify research foci that advance the field and that also have high policy and conservation relevance. 2. To date, there has been no coherent synthesis of key questions and priority research areas for palaeoecology, which combines biological, geochemical and molecular techniques in order to reconstruct past ecological and environmental systems on time-scales from decades to millions of years. 3. We adapted a well-established methodology to identify 50 priority research questions in palaeoecology. Using a set of criteria designed to identify realistic and achievable research goals, we selected questions from a pool submitted by the international palaeoecology research community and relevant policy practitioners. 4. The integration of online participation, both before and during the workshop, increased international engagement in question selection. 5. The questions selected are structured around six themes: human–environment interactions in the Anthropocene; biodiversity, conservation and novel ecosystems; biodiversity over long time-scales; ecosystem processes and biogeochemical cycling; comparing, combining and synthesizing information from multiple records; and new developments in palaeoecology. 6. Future opportunities in palaeoecology are related to improved incorporation of uncertainty into reconstructions, an enhanced understanding of ecological and evolutionary dynamics and processes and the continued application of long-term data for better-informed landscape management