RETRASO, a code for modeling reactive transport in saturated and unsaturated porous media

The code RETRASO (REactive TRAnsport of SOlutes) simulates reactive transport of dissolved and gaseous species in non-isothermal saturated or unsaturated problems. Possible chemical reactions include aqueous complexation (including redox reactions), sorption, precipitation-dissolution of minerals and gas dissolution. Various models for sorption of solutes on solids are available, from experimental relationships (linear KD, Freundlich and Langmuir isotherms) to cation exchange and surface complexation models (constant capacitance, diffuse layer and triple layer models). Precipitation-dissolution and aqueous complexation can be modelled in equilibrium or according to kinetic laws. For the numerical solution of the reactive transport equations it uses the Direct Substitution Approach. The use of the code is demonstrated by three examples. The first example models various sorption processes in a smectite barrier. The second example models a complex chemical system in a two dimensional cross-section. The last example models pyrite weathering in an unsaturated medium

Remediación agua contaminada por mercurio y portlandita en Flix

Hace unos años se decidió descontaminar el embalse de Flix, afectado por vertidos de residuos por un empresa química durante todo el siglo pasado. •Los residuos formaron 4 lóbulos de sedimentos en el río, con elevadas concentraciones de Mercurio, compuestos orgánicos volátiles (COV´s), residuos de producción de acetileno (Ca(OH)2) y pesticidas organoclorados. •Se ha realizado un modelo 0D de transporte reactivo de la concentración en el agua conforme se excavan los sedimentos transitorio y explícito en excel, calibrado hasta Septiembre 2014 con datos semanales de la empresa extractora FCC. •El modelo concluía dos graves problemas al terminar la excavación: Elevada concentración de Hg y pH (12.4), equilibrado con portlandita •Desde Marzo de 2015 se observó un acusado descenso de pH y Hg. Nuestro objetivo ha sido encontrar la causa de estos descensos, para ello se han realizado simulaciones, muestreos y experimentos de laboratorio. La precipitación CaCO3 debida a la difusión de CO2 atmosférico explica una parte de la disminución de pH, pero resulta insuficiente aun considerando la oxidación de materia orgánica. •El Hg se adsorbido en CaCO3 es alrededor de un 30%, otro 60% parece haberse volatilizado. •La electrolisis en laboratorio reproduce un descenso del Hg de 80% en 3 días. Sólo un 10% de Hg ha sido recuperado en el cátodo. • Se cree que el Hg2+ se reduce a Hg0 y volatiliza. •El pH descendió hasta 3.8, se cree que debido a hidrólisis del agua. •Se esta trabajando en comprobar el Hg0 volatilizado en próximos experimentos.Postprint (published version

Bacillus subtilis RarA Acts as a Positive RecA Accessory Protein

Ubiquitous RarA AAA+ ATPases play crucial roles in the cellular response to blocked replication forks in pro- and eukaryotes. Here, we provide evidence that RarA regulates the activity of the central player in homologous recombination (HR), RecA, in response to DNA damage. During unperturbed growth, absence of RarA reduced the viability of recA, recO and recF15 cells, and during repair of H2O2- or MMS-induced DNA damage, rarA was epistatic to recA, recO and recF. Conversely, the inactivation of rarA partially suppressed the HR defect of mutants lacking end-resection (addAB, recJ, recQ, recS) or branch migration (ruvAB, recG, radA) activity. RarA contributes to RecA thread formation, that are thought to be the active forms of RecA during homology search. The absence of RarA reduced RecA accumulation, and the formation of visible RecA threads in vivo upon DNA damage. When rarA was combined with mutations in genuine RecA accessory genes, RecA accumulation was further reduced in rarA recU and rarA recX double mutant cells, and was blocked in rarA recF15 cells. These results suggest that RarA contributes to the assembly of RecA nucleoprotein filaments onto single-stranded DNA (ssDNA), in concert with RecF, and possibly antagonizes RecA filament disassembly by RecX or RecU.Peer reviewe

An experimental evaluation of the understanding of safety compliance needs with models

Proceedings of: 36th International Conference on Conceptual Modeling, ER 2017, Valencia, Spain, November 6–9, 2017Context: Most safety-critical systems have to fulfil compliance needs specified in safety standards. These needs can be difficult to understand from the text of the standards, and the use of conceptual models has been proposed as a solution. Goal: We aim to evaluate the understanding of safety compliance needs with models. Method: We have conducted an experiment to study the effectiveness, efficiency, and perceived benefits in understanding these needs, with text of safety standards and with UML object diagrams. Results: Sixteen Bachelor students participated in the experiment. Their average effectiveness in understanding compliance needs and their average efficiency were higher with models (17% and 15%, respectively). However, the difference is not statistically significant. The students found benefits in using models, but on average they are undecided about their ease of understanding. Conclusions: Although the results are not conclusive enough, they suggest that the use of models could improve the understanding of safety compliance needs.The research leading to this paper has received funding from the AMASS project (H2020-ECSEL grant agreement no 692474; Spain’s MINECO ref. PCIN-2015-262) and the AMoDDI project (Ref. 11130583). We also thank the subjects that participated in the experiment

Denitrification in a hypersaline lake–aquifer system (Pétrola Basin, Central Spain): The role of recent organic matter and Cretaceous organic rich sediments

Agricultural regions in semi-arid to arid climates with associated saline wetlands are one of the most vulnerable environments to nitrate pollution. The Pétrola Basin was declared vulnerable to NO3 − pollution by the Regional Government in 1998, and the hypersaline lake was classified as a heavily modified body of water. The study assessed groundwater NO3 − through the use of multi-isotopic tracers (δ15N, δ34S, δ13C, δ18O) coupled to hydrochemistry in the aquifer connected to the eutrophic lake. Hydrogeologically, the basin shows two main flow components: regional groundwater flow from recharge areas (Zone 1) to the lake (Zone 2), and a density-driven flow from surface water to the underlying aquifer (Zone 3). In Zones 1 and 2, δ15NNO3 and δ18ONO3 suggest that NO3 − from slightly volatilized ammonium synthetic fertilizers is only partially denitrified. The natural attenuation of NO3 − can occur by heterotrophic reactions. However, autotrophic reactions cannot be ruled out. In Zone 3, the freshwater–saltwater interface (down to 12–16 m below the ground surface) is a reactive zone for NO3 − attenuation. Tritium data suggest that the absence of NO3 − in the deepest zones of the aquifer under the lake can be attributed to a regional groundwater flow with long residence time. In hypersaline lakes the geometry of the density-driven flow can play an important role in the transport of chemical species that can be related to denitrification processes.Depto. de Geodinámica, Estratigrafía y PaleontologíaFac. de Ciencias GeológicasTRUECastilla–La Mancha GovernmentSpanish GovernmentCatalan Governmentpu

The RecU Holliday junction resolvase acts at early stages of homologous recombination

Homologous recombination is essential for DNA repair and generation of genetic diversity in all organisms. It occurs through a series of presynaptic steps where the substrate is presented to the recombinase (RecA in bacteria). Then, the recombinase nucleoprotein filament mediates synapsis by first promoting the formation of a D-loop and later of a Holliday junction (HJ) that is subsequently cleaved by the HJ resolvase. The coordination of the synaptic step with the late resolution step is poorly understood. Bacillus subtilis RecU catalyzes resolution of HJs, and biochemical evidence suggests that it might modulate RecA. We report here the isolation and characterization of two mutants of RecU (recU56 and recU71), which promote resolution of HJs, but do not promote RecA modulation. In vitro, the RecU mutant proteins (RecUK56A or RecUR71A) bind and cleave HJs and interact with RuvB. RecU interacts with RecA and inhibits its single-stranded DNA-dependent dATP hydrolysis, but RecUK56A and RecUR71A do not exert a negative effect on the RecA dATPase and fail to interact with it. Both activities are important in vivo since RecU mutants impaired only in RecA interaction are as sensitive to DNA damaging agents as a deletion mutant

A novel role for RecA under non-stress: promotion of swarming motility in Escherichia coli K-12

BACKGROUND: Bacterial motility is a crucial factor in the colonization of natural environments. Escherichia coli has two flagella-driven motility types: swimming and swarming. Swimming motility consists of individual cell movement in liquid medium or soft semisolid agar, whereas swarming is a coordinated cellular behaviour leading to a collective movement on semisolid surfaces. It is known that swimming motility can be influenced by several types of environmental stress. In nature, environmentally induced DNA damage (e.g. UV irradiation) is one of the most common types of stress. One of the key proteins involved in the response to DNA damage is RecA, a multifunctional protein required for maintaining genome integrity and the generation of genetic variation. RESULTS: The ability of E. coli cells to develop swarming migration on semisolid surfaces was suppressed in the absence of RecA. However, swimming motility was not affected. The swarming defect of a ΔrecA strain was fully complemented by a plasmid-borne recA gene. Although the ΔrecA cells grown on semisolidsurfaces exhibited flagellar production, they also presented impaired individual movement as well as a fully inactive collective swarming migration. Both the comparative analysis of gene expression profiles in wild-type and ΔrecA cells grown on a semisolid surface and the motility of lexA1 [Ind-] mutant cells demonstrated that the RecA effect on swarming does not require induction of the SOS response. By using a RecA-GFP fusion protein we were able to segregate the effect of RecA on swarming from its other functions. This protein fusion failed to regulate the induction of the SOS response, the recombinational DNA repair of UV-treated cells and the genetic recombination, however, it was efficient in rescuing the swarming motility defect of the ΔrecA mutant. The RecA-GFP protein retains a residual ssDNA-dependent ATPase activity but does not perform DNA strand exchange. CONCLUSION: The experimental evidence presented in this work supports a novel role for RecA: the promotion of swarming motility. The defective swarming migration of ΔrecA cells does not appear to be associated with defective flagellar production; rather, it seems to be associated with an abnormal flagellar propulsion function. Our results strongly suggest that the RecA effect on swarming motility does not require an extensive canonical RecA nucleofilament formation. RecA is the first reported cellular factor specifically affecting swarming but not swimming motility in E. coli. The integration of two apparently disconnected biologically important processes, such as the maintenance of genome integrity and motility in a unique protein, may have important evolutive consequences

Supporting Data Collection in Complex Scenarios with Dynamic Data Collection Processes

Nowadays, companies have to report a large number of data sets (e.g., sustainability data) regarding their products to different legal authorities. However, in today's complex supply chains products are the outcome of the collaboration of many companies. To gather the needed data sets, companies have to employ cross-organizational and long-running data collection processes that imply great variability. To support such scenarios, we have designed a lightweight, automated approach for contextual process configuration. That approach can capture the contextual properties of the respective situations and, based on them, automatically configure a process instance accordingly, even without human involvement. Finally, we implemented our approach and started an industrial evaluation

Towards the Composition of Services by End-Users: A Mobile-Based Solution

[EN] Nowadays, we live surrounded by heterogeneous and distributed services that are available to people anytime and anywhere. Even though these services can be used individually, it is through their synchronized and combined usage that end-users are provided with added value. However, existing solutions to service composition are not targeted at ordinary end-users. In fact, these solutions require technical knowledge to deal with the technological heterogeneity in which they are offered to the market. To this end, the paper presents a tool-supported platform that is aided by: (1) EUCalipTool, an end-user mobile tool that implements a Domain Specific Visual Language, which has been specifically designed to compose services on mobile devices; (2) a Faceted Service Registry, which plays the role of gateway between service implementations and end-users, hiding technological issues from the latter when including services in a composition; and (3) a Generation Module, which transforms end-user descriptions into BPMN specification that are interpreted by an execution infrastructure developed for that purpose.This work has been developed with the financial support of the Spanish State Research Agency under the project TIN2017-84094-R and co-financed with ERDF.Valderas, P.; Torres Bosch, MV.; Pelechano Ferragud, V. (2020). Towards the Composition of Services by End-Users: A Mobile-Based Solution. 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