Broadcast Propagation Time in SpaceFibre Networks with Various Types of Spatial Redundancy

Various methods of spatial redundancy can be used in local networks based on the SpaceFibre standard for fault mitigation of network hardware and physical communication channels. Usually, a network developer chooses the method of spatial redundancy according to the number of failures that have to be mitigated, the time required for restoring the normal operation of the network, required overheads and hardware costs. The use of different spatial redundancy mechanisms can cause changes in the structure of the links between network nodes, in case of failure and subsequent mitigation. In turn, this may cause changes in the broadcast transmission paths and the temporal characteristics of their delivery from the source to the receivers. This article focuses on the change in the propagation time of broadcasts in SpaceFibre networks with spatial redundancy. Broadcast propagation rules significantly differ from data-packet propagation rules. Broadcast distribution time is very important for many applications, because broadcasts are generally used to send urgent messages, in particular for time synchronization. Various formal methods have been used to evaluate the propagation characteristics of the broadcast. A method for estimating broadcast propagation time along the shortest routes is proposed. In addition, we provide a formal method to estimate the number of failures, which occurred in the network during the broadcast propagation. This method is based on timed Petri nets; one of its features is the ability to calculate broadcast transmission delays. In addition, as an alternative solution, we propose a method for estimating delays based on time automata theory.

Chromate Resistance Mechanisms in Leucobacter chromiiresistens

Chromate is one of the major anthropogenic contaminants on Earth. Leucobacter chromiiresistens is a highly chromate-resistant strain, tolerating chromate concentrations in LB medium of up to 400 mM. In response to chromate stress, L. chromiiresistens forms biofilms, which are held together via extracellular DNA. Inhibition of biofilm formation leads to drastically decreased chromate tolerance. Moreover, chromate is reduced intracellularly to the less-toxic Cr(III). The oxidation status and localization of chromium in cell aggregates were analyzed by energy-dispersive X-ray spectroscopy coupled to scanning transmission electron microscopy and X-ray absorption spectroscopy measurements. Most of the heavy metal is localized as Cr(III) at the cytoplasmic membrane. As a new cellular response to chromate stress, we observed an increased production of the carotenoid lutein. Carotenoid production could increase membrane stability and reduce the concentration of reactive oxygen species. Bioinformatic analysis of the L. chromiiresistens genome revealed several gene clusters that could enable heavy-metal resistance. The extreme chromate tolerance and the unique set of resistance factors suggest the use of L. chromiiresistens as a new model organism to study microbial chromate resistance.IMPORTANCE Chromate is a highly toxic oxyanion. Extensive industrial use and inadequate waste management has caused the toxic pollution of several field sites. Understanding the chromate resistance mechanisms that enable organisms to thrive under these conditions is fundamental to develop (micro)biological strategies and applications aiming at bioremediation of contaminated soils or waters. Potential detoxifying microorganisms are often not sufficient in their resistance characteristics to effectively perform, e.g., chromate reduction or biosorption. In this study, we describe the manifold strategies of L. chromiiresistens to establish an extremely high level of chromate resistance. The multitude of mechanisms conferring it make this organism suitable for consideration as a new model organism to study chromate resistance.

Arsenic Speciation in Mekong Delta Sediments Depends on Their Depositional Environment

Arsenic contamination in groundwater is pervasive throughout deltaic regions of Southeast Asia and threatens the health of millions. The speciation of As in sediments overlying contaminated aquifers is poorly constrained. Here, we investigate the chemical and mineralogical compositions of sediment cores collected from the Mekong Delta in Vietnam, elucidate the speciation of iron and arsenic, and relate them to the sediment depositional environment. Gradual dissolution of ferric (oxyhydr)oxides with depth is observed down to 7 m, corresponding to the establishment of reducing conditions. Within the reduced sediment, layers originating from marine, coastal or alluvial depositional environments are identified and their age is consistent with a late Holocene transgression in the Mekong Delta. In the organic matter- and sulfur-rich layers, arsenic is present in association with organic matter through thiol-bonding and in the form of arsenian pyrite. The highest arsenic concentration (34-69 ppm) is found in the peat layer at 16 m and suggests the accumulation of arsenic due to the formation of thiol-bound trivalent arsenic (40-55%) and arsenian pyrite (15-30%) in a paleo-mangrove depositional environment (∼8079 yr BP). Where sulfur is limited, siderite is identified, and oxygen- and thiol-bound trivalent arsenic are the predominant forms. It is also worth noting that pentavalent arsenic coordinated to oxygen is ubiquitous in the sediment profile, even in reduced sediment layers. But the identity of the oxygen-bound arsenic species remains unknown. This work shows direct evidence of thiol-bound trivalent arsenic in the Mekong Delta sediments and provides insight to refine the current model of the origin, deposition, and release of arsenic in the alluvial aquifers of the Mekong Delta.

Effect of Polarization Reversal in Ferroelectric TiN/Hf0.5Zr0.5O2/TiN Devices on Electronic Conditions at Interfaces Studied in Operando by Hard X-ray Photoemission Spectroscopy

Because of their compatibility with modern Si-based technology, HfO₂-based ferroelectric films have recently attracted attention as strong candidates for applications in memory devices, in particular, ferroelectric field-effect transistors or ferroelectric tunnel junctions. A key property defining the functionality of these devices is the polarization dependent change of the electronic band alignment at the metal/ferroelectric interface. Here, we report on the effect of polarization reversal in functional ferroelectric TiN/Hf_0.5Zr_0.5O₂/TiN capacitors on the potential distribution across the stack and the electronic band line-up at the interfaces studied in operando by hard X-ray photoemission spectroscopy. By tracking changes in the position of Hf_0.5Zr_0.5O₂ core-level lines with respect to those of the TiN electrode in both short- and open-circuit configurations following in situ polarization reversal, we derive the conduction band offset to be 0.7 (1.0) eV at the top and 1.7 (1.0) eV at the bottom interfaces for polarization, pointing up (down), respectively. Energy dispersive X-ray spectroscopy profiling of the sample cross-section in combination with the laboratory X-ray photoelectron spectroscopy reveal the presence of a TiO_x/TiON layer at  both interfaces. The observed asymmetry in the band line-up changes in the TiN/Hf_0.5Zr_0.5O₂/TiN memory stack is explained by different origin of these oxidized layers and effective pinning of polarization at the top interface. The described methodology and first experimental results are useful for the optimization of HfO₂-based ferroelectric memory devices under development.

Ultrathin Hf0.5Zr0.5O2 Ferroelectric Films on Si

Because of their immense scalability and manufacturability potential, the HfO2-based ferroelectric films attract significant attention as strong candidates for application in ferroelectric memories and related electronic devices. Here, we report the ferroelectric behavior of ultrathin Hf0.5Zr0.5O2 films, with the thickness of just 2.5 nm, which makes them suitable for use in ferroelectric tunnel junctions, thereby further expanding the area of their practical application. Transmission electron microscopy and electron diffraction analysis of the films grown on highly doped Si substrates confirms formation of the fully crystalline non-centrosymmetric orthorhombic phase responsible for ferroelectricity in Hf0.5Zr0.5O2. Piezoresponse force microscopy and pulsed switching testing performed on the deposited top TiN electrodes provide further evidence of the ferroelectric behavior of the Hf0.5Zr0.5O2 films. The electronic band lineup at the top TiN/Hf0.5Zr0.5O2 interface and band bending at the adjacent n(+)-Si bottom layer attributed to the polarization charges in Hf0.5Zr0.5O2 have been determined using in situ X-ray photoelectron spectroscopy analysis. The obtained results represent a significant step toward the experimental implementation of Si-based ferroelectric tunnel junctions.

Long-term in situ oxidation of biogenic uraninite in an alluvial aquifer: impact of dissolved oxygen and calcium

Oxidative dissolution controls uranium release to (sub)oxic pore waters from biogenic uraninite produced by natural or engineered processes, such as bioremediation. Laboratory studies show that uraninite dissolution is profoundly influenced by dissolved oxygen (DO), carbonate, and solutes such as Ca(2+). In complex and heterogeneous subsurface environments, the concentrations of these solutes vary in time and space. Knowledge of dissolution processes and kinetics occurring over the long-term under such conditions is needed to predict subsurface uranium behavior and optimize the selection and performance of uraninite-based remediation technologies over multiyear periods. We have assessed dissolution of biogenic uraninite deployed in wells at the Rifle, CO, DOE research site over a 22 month period. Uraninite loss rates were highly sensitive to DO, with near-complete loss at >0.6 mg/L over this period but no measurable loss at lower DO. We conclude that uraninite can be stable over decadal time scales in aquifers under low DO conditions. U(VI) solid products were absent over a wide range of DO values, suggesting that dissolution proceeded through complexation and removal of oxidized surface uranium atoms by carbonate. Moreover, under the groundwater conditions present, Ca(2+) binds strongly to uraninite surfaces at structural uranium sites, impacting uranium fate.

Geochemical control on uranium(IV) mobility in a mining-impacted wetland

Wetlands often act as sinks for uranium and other trace elements. Our previous work at a mining-impacted wetland in France showed that a labile noncrystalline U(IV) species consisting of U(IV) bound to Al-P-Fe-Si aggregates was predominant in the soil at locations exhibiting a U-containing clay-rich layer within the top 30 cm. Additionally, in the porewater, the association of U(IV) with Fe(II) and organic matter colloids significantly increased U(IV) mobility in the wetland. In the present study, within the same wetland, we further demonstrate that the speciation of U at a location not impacted by the clay-rich layer is a different noncrystalline U(IV) species, consisting of U(IV) bound to organic matter in soil. We also show that the clay-poor location includes an abundant sulfate supply and active microbial sulfate reduction that induce substantial pyrite (FeS2) precipitation. As a result, Fe(II) concentrations in the porewater are much lower than those at clay-impacted zones. U porewater concentrations (0.02-0.26 μM) are also considerably lower than those at the clay-impacted locations (0.21-3.4 μM) resulting in minimal U mobility. In both cases, soil-associated U represents more than 99% of U in the wetland. We conclude that the low U mobility reported at clay-poor locations is due to the limited association of Fe(II) with organic matter colloids in porewater and/or higher stability of the noncrystalline U(IV) species in soil at those locations.

Characterization of the surfaceome of the metal-reducing bacterium Desulfotomaculum reducens

Desulfotomaculum reducens strain MI-1 is a Gram-positive, sulfate-reducing bacterium also capable of reducing Fe(III). Metal reduction in Gram-positive bacteria is poorly understood. Here, we investigated Fe(III) reduction with lactate, a non-fermentable substrate, as the electron donor. Lactate consumption is concomitant to Fe(III) reduction, but does not support significant growth, suggesting that little energy can be conserved from this process and that it may occur fortuitously. D. reducens can reduce both soluble [Fe(III)-citrate] and insoluble (hydrous ferric oxide, HFO) Fe(III). Because physically inaccessible HFO was not reduced, we concluded that reduction requires direct contact under these experimental conditions. This implies the presence of a surface exposed reductase capable of transferring electrons from the cell to the extracellular electron acceptor. With the goal of characterizing the role of surface proteins in D. reducens and of identifying candidate Fe(III) reductases, we carried out an investigation of the surface proteome (surfaceome) of D. reducens. Cell surface exposed proteins were extracted by trypsin cell shaving or by lysozyme treatment, and analyzed by liquid chromatography-tandem mass spectrometry. This investigation revealed that the surfaceome fulfills many functions, including solute transport, protein export, maturation and hydrolysis, peptidoglycan synthesis and modification, and chemotaxis. Furthermore, a few redox-active proteins were identified. Among these, three are putatively involved in Fe(III) reduction, i.e., a membrane-bound hydrogenase 4Fe-4S cluster subunit (Dred_0462), a heterodisulfide reductase subunit A (Dred_0143) and a protein annotated as alkyl hydroperoxide reductase but likely functioning as a thiol-disulfide oxidoreductase (Dred_1533).

Forward genetic screening identifies a small molecule that blocks Toxoplasma gondii growth by inhibiting both host- and parasite-encoded kinases

The simultaneous targeting of host and pathogen processes represents an untapped approach for the treatment of intracellular infections. Hypoxia-inducible factor-1 (HIF-1) is a host cell transcription factor that is activated by and required for the growth of the intracellular protozoan parasite Toxoplasma gondii at physiological oxygen levels. Parasite activation of HIF-1 is blocked by inhibiting the family of closely related Activin-Like Kinase (ALK) host cell receptors ALK4, ALK5, and ALK7, which was determined in part by use of an ALK4,5,7 inhibitor named SB505124. Besides inhibiting HIF-1 activation, SB505124 also potently blocks parasite replication under normoxic conditions. To determine whether SB505124 inhibition of parasite growth was exclusively due to inhibition of ALK4,5,7 or because the drug inhibited a second kinase, SB505124-resistant parasites were isolated by chemical mutagenesis. Whole-genome sequencing of these mutants revealed mutations in the Toxoplasma MAP kinase, TgMAPK1. Allelic replacement of mutant TgMAPK1 alleles into wild-type parasites was sufficient to confer SB505124 resistance. SB505124 independently impacts TgMAPK1 and ALK4,5,7 signaling since drug resistant parasites could not activate HIF-1 in the presence of SB505124 or grow in HIF-1 deficient cells. In addition, TgMAPK1 kinase activity is inhibited by SB505124. Finally, mice treated with SB505124 had significantly lower tissue burdens following Toxoplasma infection. These data therefore identify SB505124 as a novel small molecule inhibitor that acts by inhibiting two distinct targets, host HIF-1 and TgMAPK1.

Understanding how a compound blocks growth of an intracellular pathogen is important not only for developing these compounds into drugs that can be prescribed to patients, but also because these data will likely provide novel insight into the biology of these pathogens. Forward genetic screens are one established approach towards defining these mechanisms. But performing these screens with intracellular parasites has been limited not only because of technical limitations but also because the compounds may have off-target effects in either the host or parasite. Here, we report the first compound that kills a pathogen by simultaneously inhibiting distinct host- and parasite-encoded targets. Because developing drug resistance simultaneously to two targets is less likely, this work may highlight a new approach to antimicrobial drug discovery.

Oxidative Dissolution of Biogenic Uraninite in Groundwater at Old Rifle, CO

Reductive bioremediation is currently being explored as a possible strategy for uranium-contaminated aquifers such as the Old Rifle site (Colorado). The stability of U(IV) phases under oxidizing conditions is key to the performance of this procedure. An in situ method was developed to study oxidative dissolution of biogenic uraninite (UO₂), a desirable U(VI) bioreduction product, in the Old Rifle, CO, aquifer under different variable oxygen conditions. Overall uranium loss rates were 50-100 times slower than laboratory rates. After accounting for molecular diffusion through the sample holders, a reactive transport model using laboratory dissolution rates was able to predict overall uranium loss. The presence of biomass further retarded diffusion and oxidation rates. These results confirm the importance of diffusion in controlling in-aquifer U(IV) oxidation rates. Upon retrieval, uraninite was found to be free of U(VI), indicating dissolution occurred via oxidation and removal of surface atoms. Interaction of groundwater solutes such as Ca²⁺ or silicate with uraninite surfaces also may retard in-aquifer U loss rates. These results indicate that the prolonged stability of U(IV) species in aquifers is strongly influenced by permeability, the presence of bacterial cells and cell exudates, and groundwater geochemistry.

Structure of biogenic uraninite produced by Shewanella oneidensis strain MR-1

The stability of biogenic uraninite with respect to oxidation is seminal to the success of in situ bioreduction strategies for remediation of subsurface U(VI) contamination. The properties and hence stability of uraninite are dependent on its size, structure, and composition. In this study, the local-, intermediate-, and long-range molecular-scale structure of nanoscale uraninite produced by Shewanella oneidensis strain MR-1 was investigated using EXAFS, SR-based powder diffraction and TEM. The uraninite products were found to be structurally homologous with stoichiometric U02 under all conditions considered. Significantly, there was no evidence for lattice strain of the biogenic uraninite nanoparticles. The fresh nanoparticles were found to exhibit a well-ordered interior core of diameter ca. 1.3 nm and an outer region of thickness ca approximately 0.6 nm in which the structure is locally distorted. The lack of nanoparticle strain and structural homology with stoichiometric U02 suggests that established thermodynamic parameters for the latter material are an appropriate starting point to model the behavior of nanobiogenic uraninite. The detailed structural analysis in this study provides an essential foundation for subsequent investigations of environmental samples.

Interaction of the conserved oligomeric Golgi complex with t-SNARE Syntaxin5a/Sed5 enhances intra-Golgi SNARE complex stability

Tethering factors mediate initial interaction of transport vesicles with target membranes. Soluble N-ethylmaleimide–sensitive fusion protein attachment protein receptors (SNAREs) enable consequent docking and membrane fusion. We demonstrate that the vesicle tether conserved oligomeric Golgi (COG) complex colocalizes and coimmunoprecipitates with intra-Golgi SNARE molecules. In yeast cells, the COG complex preferentially interacts with the SNARE complexes containing yeast Golgi target (t)-SNARE Sed5p. In mammalian cells, hCog4p and hCog6p interact with Syntaxin5a, the mammalian homologue of Sed5p. Moreover, fluorescence resonance energy transfer reveals an in vivo interaction between Syntaxin5a and the COG complex. Knockdown of the mammalian COG complex decreases Golgi SNARE mobility, produces an accumulation of free Syntaxin5, and decreases the steady-state levels of the intra-Golgi SNARE complex. Finally, overexpression of the hCog4p N-terminal Syntaxin5a-binding domain destabilizes intra-Golgi SNARE complexes, disrupting the Golgi. These data suggest that the COG complex orchestrates vesicular trafficking similarly in yeast and mammalian cells by binding to the t-SNARE Syntaxin5a/Sed5p and enhancing the stability of intra-Golgi SNARE complexes.

Synthesis, testing, and characterization of a novel Nafion membrane with superior performance in photoassisted immobilized Fenton catalysis

A new type of Nafion/Fe structured membrane ensuring faster kinetics, higher efficiency, and mechanical properties has been prepared and will be compared in its performance with the Fe-exchanged commercial Dupont 117 Nafion/Fe membrane during the abatement of model organic compounds. During the casting of the laboratory Nafion sample, the iron ions were introduced directly into the Nafion oligomer solution. This novel laboratory Nafion/Fe was tested as an immobilized catalyst in the degradation of several toxic pollutants showing a faster photoassisted degradation kinetics and a wider effective photocatalytic pH range compared to the Fe-exchanged commercial Dupont 117 Nafion/Fe membrane. When carrying out Ar ion sputtering of the 50 topmost catalyst layers, evidence is presented by X-ray photoelectron spectroscopy that Fe ions are found in the inner Nafion layers and seem to be responsible for the immobilized photoassisted Fenton processes leading to the degradation of 4-chorophenol (4-CP) taken as a model organic pollutant for the degradation process reported in this study. In the laboratory sample, the iron oxy/hydroxy Nafion moiety undergoes a transition to a more stable Nafion/Fe species during 4-CP degradation as determined by X-ray diffraction. This more stable form shows a higher iron dispersion and crystallinity compared to the fresh sample and is stabilized by the Nafion matrix avoiding the formation of separate iron phases. By infrared absorption (Fourier transform infrared), evidence is presented for the band of akaganeite-like species at 870 cm(-1) on the laboratory Nafion/Fe sample. This band disappears after 4-CP degradation because of the formation of the more highly dispersed iron species. Sputtering experiments show a decrease of F-containing groups in the laboratory Nafion/Fe samples closer to the catalyst upper layer while the amounts of Fe, C, and in particular O species increase in the topmost layer(s). In particular, the oxygenated species develop in the Nafion/Fe up to approximately 50 A below the catalyst surface. These species remain stable during the long-term Nafion/Fe degradation of 4-CP. Dynamo-mechanical analysis performed on laboratory Nafion/ Fe membrane samples revealed that these membranes possessed a greater mechanical modulus and resistance than the commercial Dupont 117 Nafion membrane.