Identification of dichloroacetic acid degrading Cupriavidus bacteria in a drinking water distribution network model

Aims: Bacterial community structure and composition of a drinking water network were assessed to better understand this ecosystem in relation to haloacetic acid (HAA) degradation and to identify new bacterial species having HAA degradation capacities. Methods and Results: Biofilm samples were collected from a model system, simulating the end of the drinking water distribution network and supplied with different concentrations of dichloroacetic and trichloroacetic acids at different periods over the course of a year. The samples were analysed by culturing, denaturing gradient gel electrophoresis (DGGE) and sequencing. Pipe diameter and HAA ratios did not impact the bacterial community profiles, but the season had a clear influence. Based on DGGE profiles, it appeared that a particular biomass has developed during the summer compared with the other seasons. Among the bacteria isolated in this study, those from genus Cupriavidus were able to degrade dichloroacetic acid. Moreover, these bacteria degrade dichloroacetic acid at 18°C but not at 10°C. Conclusions: The microbial diversity evolved throughout the experiment, but the bacterial community was distinct during the summer. Results obtained on the capacity of Cupriavidus to degrade DCAA only at 18°C but not at 10°C indicate that water temperature is a major element affecting DCAA degradation and confirming observations made regarding season influence on HAA degradation in the drinking water distribution network. Significance and Impact of the Study: This is the first demonstration of the HAA biodegradation capacity of the genus Cupriavidu

Identification of Plasmodium vivax Proteins with Potential Role in Invasion Using Sequence Redundancy Reduction and Profile Hidden Markov Models

BACKGROUND: This study describes a bioinformatics approach designed to identify Plasmodium vivax proteins potentially involved in reticulocyte invasion. Specifically, different protein training sets were built and tuned based on different biological parameters, such as experimental evidence of secretion and/or involvement in invasion-related processes. A profile-based sequence method supported by hidden Markov models (HMMs) was then used to build classifiers to search for biologically-related proteins. The transcriptional profile of the P. vivax intra-erythrocyte developmental cycle was then screened using these classifiers. RESULTS: A bioinformatics methodology for identifying potentially secreted P. vivax proteins was designed using sequence redundancy reduction and probabilistic profiles. This methodology led to identifying a set of 45 proteins that are potentially secreted during the P. vivax intra-erythrocyte development cycle and could be involved in cell invasion. Thirteen of the 45 proteins have already been described as vaccine candidates; there is experimental evidence of protein expression for 7 of the 32 remaining ones, while no previous studies of expression, function or immunology have been carried out for the additional 25. CONCLUSIONS: The results support the idea that probabilistic techniques like profile HMMs improve similarity searches. Also, different adjustments such as sequence redundancy reduction using Pisces or Cd-Hit allowed data clustering based on rational reproducible measurements. This kind of approach for selecting proteins with specific functions is highly important for supporting large-scale analyses that could aid in the identification of genes encoding potential new target antigens for vaccine development and drug design. The present study has led to targeting 32 proteins for further testing regarding their ability to induce protective immune responses against P. vivax malaria

Overview of recent TJ-II stellarator results

The main results obtained in the TJ-II stellarator in the last two years are reported. The most important topics investigated have been modelling and validation of impurity transport, validation of gyrokinetic simulations, turbulence characterisation, effect of magnetic configuration on transport, fuelling with pellet injection, fast particles and liquid metal plasma facing components. As regards impurity transport research, a number of working lines exploring several recently discovered effects have been developed: the effect of tangential drifts on stellarator neoclassical transport, the impurity flux driven by electric fields tangent to magnetic surfaces and attempts of experimental validation with Doppler reflectometry of the variation of the radial electric field on the flux surface. Concerning gyrokinetic simulations, two validation activities have been performed, the comparison with measurements of zonal flow relaxation in pellet-induced fast transients and the comparison with experimental poloidal variation of fluctuations amplitude. The impact of radial electric fields on turbulence spreading in the edge and scrape-off layer has been also experimentally characterized using a 2D Langmuir probe array. Another remarkable piece of work has been the investigation of the radial propagation of small temperature perturbations using transfer entropy. Research on the physics and modelling of plasma core fuelling with pellet and tracer-encapsulated solid-pellet injection has produced also relevant results. Neutral beam injection driven Alfvénic activity and its possible control by electron cyclotron current drive has been examined as well in TJ-II. Finally, recent results on alternative plasma facing components based on liquid metals are also presentedThis work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014–2018 under Grant Agreement No. 633053. It has been partially funded by the Ministerio de Ciencia, Inovación y Universidades of Spain under projects ENE2013-48109-P, ENE2015-70142-P and FIS2017-88892-P. It has also received funds from the Spanish Government via mobility grant PRX17/00425. The authors thankfully acknowledge the computer resources at MareNostrum and the technical support provided by the Barcelona S.C. It has been supported as well by The Science and Technology Center in Ukraine (STCU), Project P-507F

Modelling the regional variability of the probability of high trihalomethane occurrence in municipal drinking water

The regional variability of the probability of occurrence of high total trihalomethane (TTHM) levels was assessed using multilevel logistic regression models that incorporate environmental and infrastructure characteristics. The models were structured in a three-level hierarchical configuration: samples (first level), drinking water utilities (DWUs, second level) and natural regions, an ecological hierarchical division from the Quebec ecological framework of reference (third level). They considered six independent variables: precipitation, temperature, source type, seasons, treatment type and pH. The average probability of TTHM concentrations exceeding the targeted threshold was 18.1 %. The probability was influenced by seasons, treatment type, precipitations and temperature. The variance at all levels was significant, showing that the probability of TTHM concentrations exceeding the threshold is most likely to be similar if located within the same DWU and within the same natural region. However, most of the variance initially attributed to natural regions was explained by treatment types and clarified by spatial aggregation on treatment types. Nevertheless, even after controlling for treatment type, there was still significant regional variability of the probability of TTHM concentrations exceeding the threshold. Regional variability was particularly important for DWUs using chlorination alone since they lack the appropriate treatment required to reduce the amount of natural organic matter (NOM) in source water prior to disinfection. Results presented herein could be of interest to authorities in identifying regions with specific needs regarding drinking water quality and for epidemiological studies identifying geographical variations in population exposure to disinfection by-products (DBPs)

Impact of catchment geophysical characteristics and climate on the regional variability of dissolved organic carbon (DOC) in surface water

Dissolved organic carbon (DOC) is a recognized indicator of natural organic matter (NOM) in surface waters. The aim of this paper is twofold: to evaluate the impact of geophysical characteristics, climate and ecological zones on DOC concentrations in surface waters and, to develop a statistical model to estimate the regional variability of these concentrations. In this study, multilevel statistical analysis was used to achieve three specific objectives: (1) evaluate the influence of climate and geophysical characteristics on DOC concentrations in surface waters; (2) compare the influence of geophysical characteristics and ecological zones on DOC concentrations in surface waters; and (3) develop a model to estimate the most accurate DOC concentrations in surface waters. The case study involved 115 catchments from surface waters in the Province of Quebec, Canada. Results showed that mean temperatures recorded 60 days prior to sampling, total precipitation 10 days prior to sampling and percentages of wetlands, coniferous forests and mixed forests have a significant positive influence on DOC concentrations in surface waters. The catchment mean slope had a significant negative influence on DOC concentrations in surface waters. Water type (lake or river) and deciduous forest variables were not significant. The ecological zones had a significant influence on DOC concentrations. However, geophysical characteristics (wetlands, forests and slope) estimated DOC concentrations more accurately. A model describing the variability of DOC concentrations was developed and can be used, in future research, for estimating DBPs in drinking water as well evaluating the impact of climate change on the quality of surface waters and drinking water

Investigating social inequalities in exposure to drinking water contaminants in rural areas

Few studies have assessed social inequalities in exposure to drinking water contaminants. This study explores this issue in 593 rural municipalities of Québec, Canada. Quartiles of an ecological composite deprivation index were used as a proxy of socioeconomic status. Total trihalomethanes (TTHMs) and lead were chosen as proxies of chemical drinking water quality. The results show that the majority of deprived rural municipalities apply no treatment to their water (26%) or use a basic treatment (51%), whereas a relative majority of the wealthiest municipalities (40%) use advanced treatment. The proportion of municipalities having important lead (>5 µg/L) levels is highest in most deprived municipalities. Moreover, most deprived municipalities have a higher risk of high tap lead levels (RR = 1.33; 95%CI: 1.30, 1.36). Conversely, most deprived municipalities have a lower risk of high TTHMs levels (RR = 0.78; 95%CI: 0.69, 0.86). These findings suggest an environmental inequality in drinking water contaminants distribution in rural municipalities

Open the SterivexTM casing : an easy and effective way to improve DNA extraction yields

We describe an inexpensive, reliable, and easily executed improvement for the extraction of DNA from SterivexTM filter units, that involves the separation of the SterivexTM filter from its casing. Our study demonstrates that our modification of the original extraction protocol significantly increased DNA yields, with an average increase of 4.1‐fold more DNA than with the standard approach. A comparison of the diversity after Illumina MiSeq sequencing of bacterial communities extracted with both the standard approach and the proposed one indicated that our modified protocol has no or little impact on the results. This protocol provides a relatively straight forward means to achieve higher yields of DNA from the extraction of SterivexTM cartridges without altering the community composition and will likely be of interest to a wide range of scientists that use techniques based on the recovery of DNA from filters

Haloacetic acid degradation by a biofilm in a simulated drinking water distribution system

Haloacetic acids (HAAs) are disinfection by-products formed as a result of the reaction between chlorine and natural organic matter found in water. HAA concentrations have been observed to decrease at distribution system extremities. This decrease is associated with microbiological degradation by pipe wall biofilm. The objective of this study was to evaluate HAA degradation in a drinking water system in the presence of a biofilm and to identify the factors that influence this degradation. Degradation of dichloracetic acid (DCAA) and trichloroacetic acid (TCAA) was observed in a simulated distribution system. The results obtained showed that different parameters came into play simultaneously in the degradation of HAAs, including retention time, water temperature, biomass, composition of organic matter, and pipe diameter. Seasonal variations had a major effect on HAA degradation and biomass quantity was lower by 1 to 2 logs in the winter and spring compared with the fall. HAA removal decreased with increasingly large pipe diameters. The specific effects of each of these factors were difficult to isolate from each other owing to interactions