Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators.

BACKGROUND: Computational models in systems biology are becoming more important with the advancement of experimental techniques to query the mechanistic details responsible for leading to phenotypes of interest. In particular, Boolean models are well fit to describe the complexity of signaling networks while being simple enough to scale to a very large number of components. With the advance of Boolean model inference techniques, the field is transforming from an artisanal way of building models of moderate size to a more automatized one, leading to very large models. In this context, adapting the simulation software for such increases in complexity is crucial. RESULTS: We present two new developments in the continuous time Boolean simulators: MaBoSS.MPI, a parallel implementation of MaBoSS which can exploit the computational power of very large CPU clusters, and MaBoSS.GPU, which can use GPU accelerators to perform these simulations. CONCLUSION: These implementations enable simulation and exploration of the behavior of very large models, thus becoming a valuable analysis tool for the systems biology community.

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to improve the reusability of these models and their ability to reproduce virtual experiments becomes critical. Correct and effective model annotation in community-supported and standardised formats is necessary for this improvement. Here, we present recent efforts toward a common framework for annotated, accessible, reproducible and interoperable computational models in biology, and discuss key challenges of the field.

Multiscale model of the different modes of cancer cell invasion.

MOTIVATION: Mathematical models of biological processes altered in cancer are built using the knowledge of complex networks of signaling pathways, detailing the molecular regulations inside different cell types, such as tumor cells, immune and other stromal cells. If these models mainly focus on intracellular information, they often omit a description of the spatial organization among cells and their interactions, and with the tumoral microenvironment. RESULTS: We present here a model of tumor cell invasion simulated with PhysiBoSS, a multiscale framework, which combines agent-based modeling and continuous time Markov processes applied on Boolean network models. With this model, we aim to study the different modes of cell migration and to predict means to block it by considering not only spatial information obtained from the agent-based simulation but also intracellular regulation obtained from the Boolean model.Our multiscale model integrates the impact of gene mutations with the perturbation of the environmental conditions and allows the visualization of the results with 2D and 3D representations. The model successfully reproduces single and collective migration processes and is validated on published experiments on cell invasion. In silico experiments are suggested to search for possible targets that can block the more invasive tumoral phenotypes. AVAILABILITY AND IMPLEMENTATION: https://github.com/sysbio-curie/Invasion_model_PhysiBoSS.

Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.

The fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of novel, relevant hypotheses from this enormous quantity of data remains challenging. Logical models have long been used to answer a variety of questions regarding the dynamical behaviours of regulatory networks. As the number of published logical models increases, there is a pressing need for systematic model annotation, referencing and curation in community-supported and standardised formats. This article summarises the key topics and future directions of a meeting entitled 'Annotation and curation of computational models in biology', organised as part of the 2019 [BC]2 conference. The purpose of the meeting was to develop and drive forward a plan towards the standardised annotation of logical models, review and connect various ongoing projects of experts from different communities involved in the modelling and annotation of molecular biological entities, interactions, pathways and models. This article defines a roadmap towards the annotation and curation of logical models, including milestones for best practices and minimum standard requirements.

Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers.

The study of response to cancer treatments has benefited greatly from the contribution of different omics data but their interpretation is sometimes difficult. Some mathematical models based on prior biological knowledge of signaling pathways facilitate this interpretation but often require fitting of their parameters using perturbation data. We propose a more qualitative mechanistic approach, based on logical formalism and on the sole mapping and interpretation of omics data, and able to recover differences in sensitivity to gene inhibition without model training. This approach is showcased by the study of BRAF inhibition in patients with melanomas and colorectal cancers who experience significant differences in sensitivity despite similar omics profiles. We first gather information from literature and build a logical model summarizing the regulatory network of the mitogen-activated protein kinase (MAPK) pathway surrounding BRAF, with factors involved in the BRAF inhibition resistance mechanisms. The relevance of this model is verified by automatically assessing that it qualitatively reproduces response or resistance behaviors identified in the literature. Data from over 100 melanoma and colorectal cancer cell lines are then used to validate the model's ability to explain differences in sensitivity. This generic model is transformed into personalized cell line-specific logical models by integrating the omics information of the cell lines as constraints of the model. The use of mutations alone allows personalized models to correlate significantly with experimental sensitivities to BRAF inhibition, both from drug and CRISPR targeting, and even better with the joint use of mutations and RNA, supporting multi-omics mechanistic models. A comparison of these untrained models with learning approaches highlights similarities in interpretation and complementarity depending on the size of the datasets. This parsimonious pipeline, which can easily be extended to other biological questions, makes it possible to explore the mechanistic causes of the response to treatment, on an individualized basis.

Nitrate Controls on the Extent and Type of Metal Retention in Fine-Grained Sediments of a Simulated Aquifer.

Aquifer groundwater quality is largely controlled by sediment composition and physical heterogeneity, which commonly sustains a unique redox gradient pattern. Attenuation of heavy metals within these heterogeneous aquifers is reliant on multiple factors, including redox conditions and redox-active species that can further influence biogeochemical cycling. Here, we simulated an alluvial aquifer system using columns filled with natural coarse-grained sediments and two domains of fine-grained sediment lenses. Our goal was to examine heavy metal (Ni and Zn) attenuation within a complex aquifer network and further explore nitrate-rich groundwater conditions. The fine-grained sediment lenses sustained reducing conditions and served as a sink for Ni sequestration─in the form of Ni-silicates, Ni-organic matter, and a dominant Ni-sulfide phase. The silicate clay and sulfide pools were also important retention mechanisms for Zn; however, Ni was associated more extensively with organic matter compared to Zn, which formed layered double hydroxides. Nitrate-rich conditions promoted denitrification within the lenses that was coupled to the oxidation of Fe(II) and the concomitant precipitation of an Fe(III) phase with higher structural distortion. A decreased metal sulfide pool also resulted, where nitrate-rich conditions generated an average 20% decrease in solid-phase Ni, Zn, and Fe. Ultimately, nitrate plays a significant role in the aquifer's biogeochemical cycling and the capacity to retain heavy metals.

Ligand-Induced U Mobilization from Chemogenic Uraninite and Biogenic Noncrystalline U(IV) under Anoxic Conditions.

Microbial reduction of soluble hexavalent uranium (U(VI)) to sparingly soluble tetravalent uranium (U(IV)) has been explored as an in situ strategy to immobilize U. Organic ligands might pose a potential hindrance to the success of such remediation efforts. In the current study, a set of structurally diverse organic ligands were shown to enhance the dissolution of crystalline uraninite (UO2) for a wide range of ligand concentrations under anoxic conditions at pH 7.0. Comparisons were made to ligand-induced U mobilization from noncrystalline U(IV). For both U phases, aqueous U concentrations remained low in the absence of organic ligands (<25 nM for UO2; 300 nM for noncrystalline U(IV)). The tested organic ligands (2,6-pyridinedicarboxylic acid (DPA), desferrioxamine B (DFOB), N,N'-di(2-hydroxybenzyl)ethylene-diamine-N,N'-diacetic acid (HBED), and citrate) enhanced U mobilization to varying extents. Over 45 days, the ligands mobilized only up to 0.3% of the 370 µM UO2, while a much larger extent of the 300 µM of biomass-bound noncrystalline U(IV) was mobilized (up to 57%) within only 2 days (>500 times more U mobilization). This work shows the potential of numerous organic ligands present in the environment to mobilize both recalcitrant and labile U forms under anoxic conditions to hazardous levels and, in doing so, undermine the stability of immobilized U(IV) sources.

Challenges, Prospects, and Emerging Applications of Inkjet-Printed Electronics: A Chemist's Point of View.

Driven by the development of new functional inks, inkjet-printed electronics has achieved several milestones upon moving from the integration of simple electronic elements (e.g., temperature and pressure sensors, RFID antennas, etc.) to high-tech applications (e.g. in optoelectronics, energy storage and harvesting, medical diagnosis). Currently, inkjet printing techniques are limited by spatial resolution higher than several micrometers, which sets a redhibitorythreshold for miniaturization and for many applications that require the controlled organization of constituents at the nanometer scale. In this Review, we present the physico-chemical concepts and the equipment constraints underpinning the resolution limit of inkjet printing and describe the contributions from molecular, supramolecular, and nanomaterials-based approaches for their circumvention. Based on these considerations, we propose future trajectories for improving inkjet-printing resolution that will be driven and supported by breakthroughs coming from chemistry. Please check all text carefully as extensive language polishing was necessary. Title ok? Yes.

Simulated Aquifer Heterogeneity Leads to Enhanced Attenuation and Multiple Retention Processes of Zinc.

Alluvial aquifers serve as one of the main water sources for domestic, agricultural, and industrial purposes globally. Groundwater quality, however, can be threatened by naturally occurring and anthropogenic metal contaminants. Differing hydrologic and biogeochemical conditions between predominantly coarse-grained aquifer sediments and embedded layers or lenses of fine-grained materials lead to variation in metal behavior. Here, we examine processes controlling Zn partitioning within a dual-pore domain-reconstructed alluvial aquifer. Natural coarse aquifer sediments from the Wind River-Little Wind River floodplain near Riverton, WY, were used in columns with or without fine-grained lenses to examine biogeochemical controls on Zn concentrations, retention mechanisms, and transport. Following the introduction of Zn to the groundwater source, Zn preferentially accumulated in the fine-grained lenses, despite their small volumetric contributions. While the clay fraction dominated Zn retention in the sandy aquifer, the lenses supported additional reaction pathways of retention-the reducing conditions within the lenses resulted in ZnS precipitation, overriding the contribution of organic matter. Zinc concentration in the groundwater controlled the formation of Zn-clays and Zn-layered double hydroxides, whereas the extent of sulfide production controlled precipitation of ZnS. Our findings illustrate how both spatial and compositional heterogeneities govern the extent and mechanisms of Zn retention in intricate groundwater systems, with implications for plume behavior and groundwater quality.

Exact solving and sensitivity analysis of stochastic continuous time Boolean models.

BACKGROUND: Solutions to stochastic Boolean models are usually estimated by Monte Carlo simulations, but as the state space of these models can be enormous, there is an inherent uncertainty about the accuracy of Monte Carlo estimates and whether simulations have reached all attractors. Moreover, these models have timescale parameters (transition rates) that the probability values of stationary solutions depend on in complex ways, raising the necessity of parameter sensitivity analysis. We address these two issues by an exact calculation method for this class of models. RESULTS: We show that the stationary probability values of the attractors of stochastic (asynchronous) continuous time Boolean models can be exactly calculated. The calculation does not require Monte Carlo simulations, instead it uses graph theoretical and matrix calculation methods previously applied in the context of chemical kinetics. In this version of the asynchronous updating framework the states of a logical model define a continuous time Markov chain and for a given initial condition the stationary solution is fully defined by the right and left nullspace of the master equation's kinetic matrix. We use topological sorting of the state transition graph and the dependencies between the nullspaces and the kinetic matrix to derive the stationary solution without simulations. We apply this calculation to several published Boolean models to analyze the under-explored question of the effect of transition rates on the stationary solutions and show they can be sensitive to parameter changes. The analysis distinguishes processes robust or, alternatively, sensitive to parameter values, providing both methodological and biological insights. CONCLUSION: Up to an intermediate size (the biggest model analyzed is 23 nodes) stochastic Boolean models can be efficiently solved by an exact matrix method, without using Monte Carlo simulations. Sensitivity analysis with respect to the model's timescale parameters often reveals a small subset of all parameters that primarily determine the stationary probability of attractor states.

Chemical Speciation and Stability of Uranium in Unconventional Shales: Impact of Hydraulic Fracture Fluid.

Uranium and other radionuclides are prominent in many unconventional oil/gas shales and is a potential contaminant in flowback/produced waters due to the large volumes/types of chemicals injected into the subsurface during stimulation. To understand the stability of U before and after stimulation, a geochemical study of U speciation was carried out on three shales (Marcellus, Green River, and Barnett). Two types of samples for each shale were subjected to sequential chemical extractions: unreacted and shale-reacted with a synthetic hydraulic fracture fluid. A significant proportion of the total U (20-57%) was released from these three shales after reaction with fracture fluid, indicating that U is readily leachable. The total U released exceeds labile water-soluble and exchangeable fractions in unreacted samples, indicating that fluids leach more recalcitrant phases in the shale. Radiographic analysis of unreacted Marcellus shale thin sections shows U associated with detrital quartz and the clay matrix in the shale. Detrital zircon and TiO2 identified by an electron microprobe could account for the hot spots. This study shows that significant proportions of U in three shales are mobile upon stimulation. In addition, the extent of mobilization of U depends on the U species in these rocks.

Redox Heterogeneities Promote Thioarsenate Formation and Release into Groundwater from Low Arsenic Sediments.

Groundwater contamination by As from natural and anthropogenic sources is a worldwide concern. Redox heterogeneities over space and time are common and can influence the molecular-level speciation of As, and thus, As release/retention but are largely unexplored. Here, we present results from a dual-domain column experiment, with natural organic-rich, fine-grained, and sulfidic sediments embedded as lenses (referred to as "reducing lenses") within natural aquifer sand. We show that redox interfaces in sulfur-rich, alkaline aquifers may release concerning levels of As, even when sediment As concentration is low (<2 mg/kg), due to the formation of mobile thioarsenates at aqueous sulfide/Fe molar ratios <1. In our experiments, this behavior occurred in the aquifer sand between reducing lenses and was attributed to the spreading of sulfidic conditions and subsequent Fe reductive dissolution. In contrast, inside reducing lenses (and some locations in the aquifer) the aqueous sulfide/Fe molar ratios exceeded 1 and aqueous sulfide/As molar ratios exceeded 100, which partitioned As(III)-S to the solid phase (associated with organics or as realgar (As4S4)). These results highlight the importance of thioarsenates in natural sediments and indicate that redox interfaces and sediment heterogeneities could locally degrade groundwater quality, even in aquifers with unconcerning solid-phase As concentrations.

Antimonite Binding to Natural Organic Matter: Spectroscopic Evidence from a Mine Water Impacted Peatland.

Peatlands and other wetlands are sinks for antimony (Sb), and solid natural organic matter (NOM) may play an important role in controlling Sb binding. However, direct evidence of Sb sequestration in natural peat samples is lacking. Here, we analyzed solid phase Sb, iron (Fe), and sulfur (S) as well as aqueous Sb speciation in three profiles up to a depth of 80 cm in a mine water impacted peatland in northern Finland. Linear combination fittings of extended X-ray absorption fine structure spectra showed that Sb binding to Fe phases was of minor importance and observed only in the uppermost layers of the peatland. Instead, the dominant (to almost exclusive) sequestration mechanism was Sb(III) binding to oxygen-containing functional groups, and at greater depths, increasingly Sb(III) binding to thiol groups of NOM. Aqueous Sb speciation was dominated by antimonate, while antimonite concentrations were low, further supporting our findings of much higher reactivity of Sb(III) than Sb(V) toward peat surfaces. Insufficient residence time for efficient reduction of antimonate to antimonite currently hinders higher Sb removal in the studied peatland. Overall, our findings imply that Sb(III) binding to solid NOM acts as an important sequestration mechanism under reducing conditions in peatlands and other high-organic matter environments.

Isotopic Fingerprint of Uranium Accumulation and Redox Cycling in Floodplains of the Upper Colorado River Basin.

Uranium (U) groundwater contamination is a major concern at numerous former mining and milling sites across the Upper Colorado River Basin (UCRB), USA, where U(IV)-bearing solids have accumulated within naturally reduced zones (NRZs). Understanding the processes governing U reduction and oxidation within NRZs is critical for assessing the persistence of U in groundwater. To evaluate the redox cycling of uranium, we measured the U concentrations and isotopic compositions (δ238U) of sediments and pore waters from four study sites across the UCRB that span a gradient in sediment texture and composition. We observe that U accumulation occurs primarily within fine-grained (low-permeability) NRZs that show active redox variations. Low-permeability NRZs display high accumulation and low export of U, with internal redox cycling of U. In contrast, within high-permeability NRZs, U is remobilized under oxidative conditions, possibly without any fractionation, and transported outside the NRZs. The low δ238U of sediments outside of defined NRZs suggests that these reduced zones act as additional U sources. Collectively, our results indicate that fine-grained NRZs have a greater potential to retain uranium, whereas NRZs with higher permeability may constitute a more-persistent but dilute U source.

Recent Advances in Skin Chemical Sensors.

This review summarizes the latest developments in the field of skin chemical sensors, in particular wearable ones. Five major applications are covered in the present work: (i) sweat analysis, (ii) skin hydration, (iii) skin wounds, (iv) perspiration of volatile organic compounds, and (v) general skin conditions. For each application, the detection of the most relevant analytes is described in terms of transduction principles and sensor performances. Special attention is paid to the biological fluid collection and storage and devices are also analyzed in terms of reusability and lifetime. This review highlights the existing gaps between current performances and those needed to promote effective commercialization of sensors; future developments are also proposed.

Switchable Hydrogel-Gated Organic Field-Effect Transistors.

Stimuli-responsive hydrogels represent a class of materials capable of reversibly switching their morphological and physicochemical characteristics. An ultrathin poly(acrylic acid) film (ca. 6 nm) grafted onto the gate of a p-type EGOFET is studied, and the correlation between the swelling state of the hydrogel and the transistor output characteristics is presented. The hydrogel-related swelling process occurring in basic medium causes an increase in threshold voltage due to the abrupt and intense increase of the negative charge density on the gate electrode. The variation of the drain current during the in situ modification of the pH electrolyte allows a quantitative analysis of the hydrogel switching kinetics. This work shows not only the relevance of EGOFET as an analytical tool in the broad sense, i.e., able to follow in real time phase transition processes of stimuli-responsive materials, but also the relevance of using a hydrogel for field-effect-based (bio)detection according to the ability of such material to overcome the well-known Debye length problematics.

Redox Controls over the Stability of U(IV) in Floodplains of the Upper Colorado River Basin.

Aquifers in the Upper Colorado River Basin (UCRB) exhibit persistent uranium (U) groundwater contamination plumes originating from former ore processing operations. Previous observations at Rifle, Colorado, have shown that fine grained, sulfidic, organic-enriched sediments accumulate U in its reduced form, U(IV), which is less mobile than oxidized U(VI). These reduced sediment bodies can subsequently act as secondary sources, releasing U back to the aquifer. There is a need to understand if U(IV) accumulation in reduced sediments is a common process at contaminated sites basin-wide, to constrain accumulated U(IV) speciation, and to define the biogeochemical factors controlling its reactivity. We have investigated U(IV) accumulation in organic-enriched reduced sediments at three UCRB floodplains. Noncrystalline U(IV) is the dominant form of accumulated U, but crystalline U(IV) comprises up to ca. 30% of total U at some locations. Differing susceptibilities of these species to oxidative remobilization can explain this variability. Particle size, organic carbon content, and pore saturation, control the exposure of U(IV) to oxidants, moderating its oxidative release. Further, our data suggest that U(IV) can be mobilized under deeply reducing conditions, which may contribute to maintenance and seasonal variability of U in groundwater plumes in the UCRB.

Multianalytical Study of the Binding between a Small Chiral Molecule and a DNA Aptamer: Evidence for Asymmetric Steric Effect upon 3'- versus 5'-End Sequence Modification.

Nucleic acid aptamers are involved in a broad field of applications ranging from therapeutics to analytics. Deciphering the binding mechanisms between aptamers and small ligands is therefore crucial to improve and optimize existing applications and to develop new ones. Particularly interesting is the enantiospecific binding mechanism involving small molecules with nonprestructured aptamers. One archetypal example is the chiral binding between l-tyrosinamide and its 49-mer aptamer for which neither structural nor mechanistic information is available. In the present work, we have taken advantage of a multiple analytical characterization strategy (i.e., using electroanalytical techniques such as kinetic rotating droplet electrochemistry, fluorescence polarization, isothermal titration calorimetry, and quartz crystal microbalance) for interpreting the nature of binding process. Screening of the binding thermodynamics and kinetics with a wide range of aptamer sequences revealed the lack of symmetry between the two ends of the 23-mer minimal binding sequence, showing an unprecedented influence of the 5' aptamer modification on the bimolecular binding rate constant kon and no significant effect on the dissociation rate constant koff. The results we have obtained lead us to conclude that the enantiospecific binding reaction occurs through an induced-fit mechanism, wherein the ligand promotes a primary nucleation binding step near the 5'-end of the aptamer followed by a directional folding of the aptamer around its target from 5'-end to 3'-end. Functionalization of the 5'-end position by a chemical label, a polydA tail, a protein, or a surface influences the kinetic/thermodynamic constants up to 2 orders of magnitude in the extreme case of a surface immobilized aptamer, while significantly weaker effect is observed for a 3'-end modification. The reason is that steric hindrance must be overcome to nucleate the binding complex in the presence of a modification near the nucleation site.

Physico-Chemical Heterogeneity of Organic-Rich Sediments in the Rifle Aquifer, CO: Impact on Uranium Biogeochemistry.

The Rifle alluvial aquifer along the Colorado River in west central Colorado contains fine-grained, diffusion-limited sediment lenses that are substantially enriched in organic carbon and sulfides, as well as uranium, from previous milling operations. These naturally reduced zones (NRZs) coincide spatially with a persistent uranium groundwater plume. There is concern that uranium release from NRZs is contributing to plume persistence or will do so in the future. To better define the physical extent, heterogeneity and biogeochemistry of these NRZs, we investigated sediment cores from five neighboring wells. The main NRZ body exhibited uranium concentrations up to 100 mg/kg U as U(IV) and contains ca. 286 g of U in total. Uranium accumulated only in areas where organic carbon and reduced sulfur (as iron sulfides) were present, emphasizing the importance of sulfate-reducing conditions to uranium retention and the essential role of organic matter. NRZs further exhibited centimeter-scale variations in both redox status and particle size. Mackinawite, greigite, pyrite and sulfate coexist in the sediments, indicating that dynamic redox cycling occurs within NRZs and that their internal portions can be seasonally oxidized. We show that oxidative U(VI) release to the aquifer has the potential to sustain a groundwater contaminant plume for centuries. NRZs, known to exist in other uranium-contaminated aquifers, may be regionally important to uranium persistence.

Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H†NMR Spectroscopy and Molecular Modeling.

Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand-binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design-of-experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L-tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg(2+) -ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand-observed NMR spectroscopic techniques and molecular mechanics.