Noble gas constraints on the fate of arsenic in groundwater

Groundwater contamination of geogenic arsenic (As) remains a global health threat, particularly in south-east Asia. The prominent correlation often observed between high As concentrations and methane (CH$_{4}$) stimulated the analysis of the gas dynamics in an As contaminated aquifer, whereby noble and reactive gases were analysed. Results show a progressive depletion of atmospheric gases (Ar, Kr and N$_{2}$) alongside highly increasing CH$_{4}$, implying that a free gas phase comprised mainly of CH$_{4}$ is formed within the aquifer. In contrast, Helium (He) concentrations are high within the CH$_{4}$ (gas) producing zone, suggesting longer (groundwater) residence times. We hypothesized that the observed free (CH$_{4}$) gas phase severely detracts local groundwater (flow) and significantly reduces water renewal within the gas producing zone. Results are in-line with this hypothesis, however, a second hypothesis has been developed, which focuses on the potential transport of He from an adjacent aquitard into the (CH$_{4}$) gas producing zone. This second hypothesis was formulated as it resolves the particularly high He concentrations observed, and since external solute input from the overlying heterogeneous aquitard cannot be excluded. The proposed feedback between the gas phase and hydraulics provides a plausible explanation of the anti-intuitive correlation between high As and CH$_{4}$, and the spatially highly patchy distribution of dissolved As concentrations in contaminated aquifers. Furthermore, the increased groundwater residence time would allow for the dissolution of more crystalline As-hosting iron(Fe)-oxide phases in conjunction with the formation of more stable secondary Fe minerals in the hydraulically-slowed (i.e., gas producing) zone; a subject which calls for further investigation

Toward Detecting Polycyclic Aromatic Hydrocarbons on Planetary Objects with ORIGIN

Polycyclic aromatic hydrocarbons (PAHs) are found on various planetary surfaces in the solar system. They are proposed to play a role in the emergence of life, as molecules that are important for biological processes could be derived from them. In this work, four PAHs (pyrene, perylene, anthracene, and coronene) were measured using the ORganics Information Gathering INstrument system (ORIGIN), a lightweight laser desorption ionization-mass spectrometer designed for space exploration missions. In this contribution, we demonstrate the current measurement capabilities of ORIGIN in detecting PAHs at different concentrations and applied laser pulse energies. Furthermore, we show that chemical processing of the PAHs during measurement is limited and that the parent mass can be detected in the majority of cases. The instrument achieves a 3σ detection limit in the order of femtomol mm−2 for all four PAHs, with the possibility of further increasing this sensitivity. This work illustrates the potential of ORIGIN as an instrument for the detection of molecules important for the emergence or presence of life, especially when viewed in combination with previous results by the instrument, such as the identification of amino acids. ORIGIN could be used on a lander or rover platform for future in situ missions to targets in the solar system, such as the icy moons of Jupiter or Saturn

Computational Physics on Graphics Processing Units

The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing on classical molecular dynamics, and on quantum simulations for electronic structure calculations using the density functional theory, wave function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012, Helsinki, Finland, June 10-13, 201

Towards detecting carbon chemistry on planetary objects with the ORIGIN space instrument

Instrumentatio

Dissolved noble gases and stable isotopes as tracers of preferential fluid flow along faults in the Lower Rhine Embayment, Germany

Groundwater in shallow unconsolidated sedimentary aquifers close to the Bornheim fault in the Lower Rhine Embayment (LRE), Germany, has relatively low δ2H and δ18O values in comparison to regional modern groundwater recharge, and 4He concentrations up to 1.7 × 10−4 cm3 (STP) g–1 ± 2.2 % which is approximately four orders of magnitude higher than expected due to solubility equilibrium with the atmosphere. Groundwater age dating based on estimated in situ production and terrigenic flux of helium provides a groundwater residence time of ∼107 years. Although fluid exchange between the deep basal aquifer system and the upper aquifer layers is generally impeded by confining clay layers and lignite, this study’s geochemical data suggest, for the first time, that deep circulating fluids penetrate shallow aquifers in the locality of fault zones, implying  that sub-vertical fluid flow occurs along faults in the LRE. However, large hydraulic-head gradients observed across many faults suggest that they act as barriers to lateral groundwater flow. Therefore, the geochemical data reported here also substantiate a conduit-barrier model of fault-zone hydrogeology in unconsolidated sedimentary deposits, as well as corroborating the concept that faults in unconsolidated aquifer systems can act as loci for hydraulic connectivity between deep and shallow aquifers. The implications of fluid flow along faults in sedimentary basins worldwide are far reaching and of particular concern for carbon capture and storage (CCS) programmes, impacts of deep shale gas recovery for shallow groundwater aquifers, and nuclear waste storage sites where fault zones could act as potential leakage pathways for hazardous fluids

Growth Response of Drought-Stressed Pinus sylvestris Seedlings to Single- and Multi-Species Inoculation with Ectomycorrhizal Fungi

Many trees species form symbiotic associations with ectomycorrhizal (ECM) fungi, which improve nutrient and water acquisition of their host. Until now it is unclear whether the species richness of ECM fungi is beneficial for tree seedling performance, be it during moist conditions or drought. We performed a pot experiment using Pinus sylvestris seedlings inoculated with four selected ECM fungi (Cenococcum geophilum, Paxillus involutus, Rhizopogon roseolus and Suillus granulatus) to investigate (i) whether these four ECM fungi, in monoculture or in species mixtures, affect growth of P. sylvestris seedlings, and (ii) whether this effect can be attributed to species number per se or to species identity. Two different watering regimes (moist vs. dry) were applied to examine the context-dependency of the results. Additionally, we assessed the activity of eight extracellular enzymes in the root tips. Shoot growth was enhanced in the presence of S. granulatus, but not by any other ECM fungal species. The positive effect of S. granulatus on shoot growth was more pronounced under moist (threefold increase) than under dry conditions (twofold increase), indicating that the investigated ECM fungi did not provide additional support during drought stress. The activity of secreted extracellular enzymes was higher in S. granulatus than in any other species. In conclusion, our findings suggest that ECM fungal species composition may affect seedling performance in terms of aboveground biomass

Benchmarking Ontologies: Bigger or Better?

A scientific ontology is a formal representation of knowledge within a domain, typically including central concepts, their properties, and relations. With the rise of computers and high-throughput data collection, ontologies have become essential to data mining and sharing across communities in the biomedical sciences. Powerful approaches exist for testing the internal consistency of an ontology, but not for assessing the fidelity of its domain representation. We introduce a family of metrics that describe the breadth and depth with which an ontology represents its knowledge domain. We then test these metrics using (1) four of the most common medical ontologies with respect to a corpus of medical documents and (2) seven of the most popular English thesauri with respect to three corpora that sample language from medicine, news, and novels. Here we show that our approach captures the quality of ontological representation and guides efforts to narrow the breach between ontology and collective discourse within a domain. Our results also demonstrate key features of medical ontologies, English thesauri, and discourse from different domains. Medical ontologies have a small intersection, as do English thesauri. Moreover, dialects characteristic of distinct domains vary strikingly as many of the same words are used quite differently in medicine, news, and novels. As ontologies are intended to mirror the state of knowledge, our methods to tighten the fit between ontology and domain will increase their relevance for new areas of biomedical science and improve the accuracy and power of inferences computed across them

Prospective Monitoring Reveals Dynamic Levels of T Cell Immunity to Mycobacterium Tuberculosis in HIV Infected Individuals

Monitoring of latent Mycobacterium tuberculosis infection may prevent disease. We tested an ESAT-6 and CFP-10-specific IFN-γ Elispot assay (RD1-Elispot) on 163 HIV-infected individuals living in a TB-endemic setting. An RD1-Elispot was performed every 3 months for a period of 3–21 months. 62% of RD1-Elispot negative individuals were positive by cultured Elispot. Fluctuations in T cell response were observed with rates of change ranging from −150 to +153 spot-forming cells (SFC)/200,000 PBMC in a 3-month period. To validate these responses we used an RD1-specific real time quantitative PCR assay for monokine-induced by IFN-γ (MIG) and IFN-γ inducible protein-10 (IP10) (MIG: r = 0.6527, p = 0.0114; IP-10: r = 0.6967, p = 0.0056; IP-10+MIG: r = 0.7055, p = 0.0048). During follow-up 30 individuals were placed on ARVs and 4 progressed to active TB. Fluctuations in SFC did not correlate with CD4 count, viral load, treatment initiation, or progression to active TB. The RD1-Elispot appears to have limited value in this setting