Revealing the nuclearity of iron citrate complexes at biologically relevant conditions.

Citric acid plays an ubiquitous role in the complexation of essential metals like iron and thus it has a key function making them biologically available. For this, iron(III) citrate complexes are considered among the most significant coordinated forms of ferric iron that take place in biochemical processes of all living organisms. Although these systems hold great biological relevance, their coordination chemistry has not been fully elucidated yet. The current study aimed to investigate the speciation of iron(III) citrate using Mössbauer and electron paramagnetic resonance spectroscopies. Our aim was to gain insights into the structure and nuclearity of the complexes depending on the pH and iron to citrate ratio. By applying the frozen solution technique, the results obtained directly reflect the iron speciation present in the aqueous solution. At 1:1 iron:citrate molar ratio, polynuclear species prevailed forming most probably a trinuclear structure. In the case of citrate excess, the coexistence of several monoiron species with different coordination environments was confirmed. The stability of the polynuclear complexes was checked in the presence of organic solvents.

A simple method for comparing peripheral and central color vision by means of two smartphones.

Information on peripheral color perception is far from sufficient, since it has predominantly been obtained using small stimuli, limited ranges of eccentricities, and sophisticated experimental conditions. Our goal was to consider the possibility of facilitating technical realization of the classical method of asymmetric color matching (ACM) developed by Moreland and Cruz (1959) for assessing appearance of color stimuli in the peripheral visual field (VF). We adopted the ACM method by employing two smartphones to implement matching procedure at various eccentricities. Although smartphones were successfully employed in vision studies, we are aware that some photometric parameters of smartphone displays are not sufficiently precise to ensure accurate color matching in foveal vision; moreover, certain technical characteristics of commercially available devices are variable. In the present study we provided evidence that, despite these shortages, smartphones can be applied for general and wide investigations of the peripheral vision. In our experiments, the smartphones were mounted on a mechanical perimeter to simultaneously present colored stimuli foveally and peripherally. Trying to reduce essential discomfort and fatigue experienced by most observers in peripheral vision studies, we did not apply bite bars, pupil dilatation, and Maxwellian view. The ACM measurements were performed without prior training of observers and in a wide range of eccentricities, varying between 0 and 95°. The results were presented in the HSV (hue, saturation, value) color space coordinates as a function of eccentricity and stimulus luminance. We demonstrated that our easy-to-conduct method provided a convenient means to investigate color appearance in the peripheral vision and to assess inter-individual differences.

Apoplast utilisation of nanohaematite initiates parallel suppression of RIBA1 and FRO1&3 in Cucumis sativus.

Nanoscale Fe containing particles can penetrate the root apoplast. Nevertheless, cell wall size exclusion questions that for Fe mobilisation, a close contact between the membrane integrating FERRIC REDUCTASE OXIDASE (FRO) enzymes and Fe containing particles is required. Haematite nanoparticle suspension, size of 10-20 nm, characterized by 57Fe Mössbauer spectroscopy, TEM, ICP and SAED was subjected to Fe utilisation by the flavin secreting model plant cucumber (Cucumis sativus). Alterations in the structure and distribution of the particles were revealed by 57Fe Mössbauer spectroscopy, HRTEM and EDS element mapping. Biological utilisation of Fe resulted in a suppression of Fe deficiency responses (expression of CsFRO 1, 2 & 3 and RIBOFLAVIN A1; CsRIBA1 genes and root ferric chelate reductase activity). Haematite nanoparticles were stacked in the middle lamella of the apoplast. Fe mobilisation is evidenced by the reduction in the particle size. Fe release from nanoparticles does not require a contact with the plasma membrane. Parallel suppression in the CsFRO 1&3 and CsRIBA1 transcript amounts support that flavin biosynthesis is an inclusive Fe deficiency response involved in the reduction-based Fe utilisation of Cucumis sativus roots. CsFRO2 is suggested to play a role in the intracellular Fe homeostasis.

New aspects of the photodegradation of iron(III) citrate: spectroscopic studies and plant-related factors.

Iron (Fe) is an essential cofactor for all livings. Although Fe membrane transport mechanisms often utilize FeII, uncoordinated or deliberated ferrous ions can initiate Fenton reactions. FeIII citrate complexes are among the most important complexed forms of FeIII especially in plants that, indeed, can undergo photoreduction. Since leaves as photosynthetic organs of higher plants are generally exposed to illumination in daytime, photoreaction of ferric species may have biological relevance in iron metabolism, the relevance of which is poorly understood. In present work FeIII citrate transformation during the photodegradation in solution and after foliar application on leaves was studied by Mössbauer analysis directly. To obtain irradiation time dependence of the speciation of iron in solutions, four model solutions of different pH values (1.5, 3.3, 5.5, and 7.0) with Fe to citrate molar ratio 1:1.1 were exposed to light. Highly acidic conditions led to a complete reduction of Fe together with the formation of FeII citrate and hexaaqua complexes in equal concentration. At higher pH, the only product of the photodegradation was FeII citrate, which was later reoxidized and polymerized, resulting in the formation of polynuclear stable ferric compound. To test biological relevance, leaves of cabbage were treated with FeIII citrate solution. X-ray fluorescence imaging indicated the accumulation of Fe in the treated leaf parts. Mössbauer analysis revealed the presence of several ferric species incorporated into the biological structure. The Fe speciation observed should be considered in biological systems where FeIII citrate has a ubiquitous role in Fe acquisition and homeostasis.

Brownian dynamics of cylindrical capsule-like particles in a nanopore in an electrically biased solid-state membrane.

We use Brownian dynamics simulations to study the motion of cylindrical capsule-like particles (capsules) as they translocate through nanopores of various radii in an electrically biased silicon membrane. We find that for all pore sizes the electrostatic interaction between the particle and the pore results in the particle localization towards the pore 's center when the membrane and the particle have charges of the same sign (case 1) while in case of the opposite sign charges, the capsule prefers to stay near and along the nanopore wall (case 2). The preferential localization leads to all capsules rotating less while inside the pore compared to the bulk solution, with a larger net charge and/or particle length resulting in a smaller range of rotational movement. It also strongly affects the whole translocation process: in the first case, the translocation is due to the free diffusion along the pore axis and is weakly dependent on the particle charge and the nanopore radius while in the second case, the translocation time dramatically increases with the particle size and charge as the capsule gets "stuck" to the nanopore surface.

Mössbauer, Nuclear Forward Scattering, and Raman Spectroscopic Approaches in the Investigation of Bioinduced Transformations of Mixed-Valence Antimony Oxide.

Mössbauer spectroscopy, nuclear forward scattering, and Raman spectroscopy were applied to study redox transformations of the synthesized mixed-valence (III/V) antimony oxide. The transformations were induced by a culture of a hyperthermophilic archaeon of the genus Pyrobaculum. The applied methods allowed us to reveal the minor decrease of ca. 11.0 ± 1.2% of the antimony(V) content of the mixed-valence oxide with the concomitant increase of antimony(III). The method sensitivities for the quantitative assessment of the Sb(III/V) ratio have been considered.

Siderite-based anaerobic iron cycle driven by autotrophic thermophilic microbial consortium.

Using a sample from a terrestrial hot spring (pH 6.8, 60 °C), we enriched a thermophilic microbial consortium performing anaerobic autotrophic oxidation of hydrothermal siderite (FeCO3), with CO2/bicarbonate as the electron acceptor and the only carbon source, producing green rust and acetate. In order to reproduce Proterozoic environmental conditions during the deposition of banded iron formation (BIF), we incubated the microbial consortium in a bioreactor that contained an unmixed anoxic layer of siderite, perfectly mixed N2/CO2-saturated liquid medium and microoxic (2% O2) headspace. Long-term incubation (56 days) led to the formation of magnetite (Fe3O4) instead of green rust as the main product of Fe(II) oxidation, the precipitation of newly formed metabolically induced siderite in the anoxic zone, and the deposition of hematite (Fe2O3) on bioreactor walls over the oxycline boundary. Acetate was the only metabolic product of CO2/bicarbonate reduction. Thus, we have demonstrated the ability of autotrophic thermophilic microbial consortium to perform a short cycle of iron minerals transformation: siderite-magnetite-siderite, accompanied by magnetite and hematite accumulation. This cycle is believed to have driven the evolution of the early biosphere, leading to primary biomass production and deposition of the main iron mineral association of BIF.

Reversible control of magnetism in FeRh thin films.

The multilayer of approximate structure MgO(100)/[nFe51Rh49(63 Å)/57Fe51Rh49(46 Å)]10 deposited at 200 °C is primarily of paramagnetic A1 phase and is fully converted to the magnetic B2 phase by annealing at 300 °C for 60 min. Subsequent irradiation by 120 keV Ne+ ions turns the thin film completely to the paramagnetic A1 phase. Repeated annealing at 300 °C for 60 min results in 100% magnetic B2 phase, i.e. a process that appears to be reversible at least twice. The A1 → B2 transformation takes place without any plane-perpendicular diffusion while Ne+ irradiation results in significant interlayer mixing.

Atomistic model of a ceria nanoparticle with Ce3 + and Ce4 + atoms.

We develop an atomistic model of a cerium dioxide CeO2 nanoparticle, which we then extend to our model of a ceria nanoparticle with a varied Ce3 + /Ce4 + composition. For a pure CeO2 particle we compute the radial distribution function for all pairs of atoms in the nanoparticle, which we find is in excellent agreement with the reported experimental data. For a particle with a mixed Ce3 + /Ce4 + we adjust the parameters and modify the crystallization procedure to produce a realistic distribution of Ce3 + atoms on the particle. We improve our initial guess of the Lennard-Jones parameters by melting and recrystallizing the nanoparticle, as well as computing the radial distribution function for the nanoparticle at room temperature.

Multiscale simulations of charge and size separation of nanoparticles with a solid-state nanoporous membrane.

Nanoporous membranes provide an attractive approach for rapid filtering of nanoparticles at high-throughput volume, a goal useful to many fields of science and technology. Creating a device to readily separate different particles would require an extensive knowledge of particle-nanopore interactions and particle translocation dynamics. To this end, we use a multiscale model for the separation of nanoparticles by combining microscopic Brownian dynamics simulations to simulate the motion of spherical nanoparticles of various sizes and charges in a system with nanopores in an electrically biased membrane with a macroscopic filtration model accounting for bulk diffusion of nanoparticles and membrane surface pore density. We find that, in general, the separation of differently sized particles is easier to accomplish than of differently charged particles. The separation by charge can be better performed in systems with low pore density and/or smaller filtration chambers when electric nanopore-particle interactions are significant. The results from these simple cases can be used to gain insight in the more complex dynamics of separating, for example, globular proteins.

Syntrophic growth of alkaliphilic anaerobes controlled by ferric and ferrous minerals transformation coupled to acetogenesis.

Redox-active iron minerals can act as energy sources or electron-transferring mediators in microbial syntrophic associations, being important means of interspecies metabolic cooperation in sedimentary environments. Alkaline conditions alter the thermodynamic stability of iron minerals, influencing their availability for interspecies syntrophic interactions. We have modeled anaerobic alkaliphilic microbial associations in ethanol-oxidizing co-culture of an obligate syntroph Candidatus "Contubernalis alkalaceticum" and a facultative lithotroph Geoalkalibacter ferrihydriticus, which is capable of dissimilatory Fe(III) reduction and homoacetogenic oxidation of Fe(II) with CO2. The co-cultures were cultivated with thermodynamically metastable ferric-containing ferrihydrite, or ferrous-containing siderite, or without minerals. Mössbauer spectral analysis revealed the transformation of both minerals to the stable magnetite. In the presence of ferrihydrite, G. ferrihydriticus firstly reduced Fe(III) with ethanol and then switched to syntrophic homoacetogenesis, providing the growth of obligate syntroph on ethanol. The ability of G. ferrihydriticus to accept hydrogen from its syntrophic partner and produce extra acetate from carbonate during ethanol oxidation was confirmed by co-culture growth without minerals. In the presence of siderite, G. ferrihydriticus performed homoacetogenesis using two electron donors simultaneously- siderite and hydrogen. Pieces of evidence for direct and indirect hydrogen-mediated electron exchange between partner organisms were obtained. Relative abundancies of partner organisms and the rate of acetate production by their co-cultures were strongly determined by thermodynamic benefits, which G. ferrihydriticus got from redox transformations of iron minerals. Even the minor growth of G. ferrihydriticus sustained the growth of the syntroph. Accordingly, microbe-to-mineral interactions could represent underestimated drivers of syntrophic interactions in alkaline sedimentary environments.

Brownian dynamics of a neutral protein moving through a nanopore in an electrically biased membrane.

The ability to separate proteins is desirable for many fields of study, and nanoporous membranes may offer a method for rapid protein filtration at high throughput volume, provided there is an understanding of the protein dynamics involved. In this work, we use Brownian dynamics simulations to study the motion of coarse-grained proteins insulin and ubiquitin in an electrically biased membrane. In our model, the protein is subjected to various biases applied to the silicon membrane equipped with a nanopore of different radii. The time each protein takes to find a cylindrical nanopore embedded in a thin silicon membrane, attempt to translocate it (waiting time), and successfully translocate it in a single attempt (translocation time) is calculated. We observe insulin finding the nanopore and translocating it faster than the electrically neutral ubiquitin due to insulin's slightly smaller size and net negative charge. While ubiquitin's dynamics is also affected by the size of the pore, surprisingly, its translocation process is also noticeably changed by the membrane bias. By investigating the protein's multipole moments, we demonstrate that this behavior is largely due to the protein's dipole and quadrupole interactions with the membrane potential.

Brownian dynamics simulations of the ionic current traces for a neutral nanoparticle translocating through a nanopore.

In this work, the ionic current blockades due to the translocation of a neutral spherical nanoparticle through a nanopore in a solid state membrane are computed. We use a Brownian dynamics approach, in conjunction with a full three-dimensional self-consistent solution of the Poisson-Nernst-Planck and Navier-Stockes system of equations to describe realistic ionic current response arising due to the random motion of a nanoparticle through a nanopore. We find that in addition to the usual geometric blockade, the variations of the current along the axis of the pore are largely caused by a concentration polarization induced by the presence of the translocating nanoparticle in the nanopore while the current changes in the radial (perpendicular to the axis) direction occur because of the local build up of the ionic charge between the particle and the nanopore surface. By performing statistical analysis of the current traces, we also observe that, in general, smaller current blockade values correspond to faster translocation times, while increased dwell times result in a larger current decrease.

Finite element modeling to analyze TEER values across silicon nanomembranes.

Silicon nanomembranes are ultrathin, highly permeable, optically transparent and biocompatible substrates for the construction of barrier tissue models. Trans-epithelial/endothelial electrical resistance (TEER) is often used as a non-invasive, sensitive and quantitative technique to assess barrier function. The current study characterizes the electrical behavior of devices featuring silicon nanomembranes to facilitate their application in TEER studies. In conventional practice with commercial systems, raw resistance values are multiplied by the area of the membrane supporting cell growth to normalize TEER measurements. We demonstrate that under most circumstances, this multiplication does not 'normalize' TEER values as is assumed, and that the assumption is worse if applied to nanomembrane chips with a limited active area. To compare the TEER values from nanomembrane devices to those obtained from conventional polymer track-etched (TE) membranes, we develop finite element models (FEM) of the electrical behavior of the two membrane systems. Using FEM and parallel cell-culture experiments on both types of membranes, we successfully model the evolution of resistance values during the growth of endothelial monolayers. Further, by exploring the relationship between the models we develop a 'correction' function, which when applied to nanomembrane TEER, maps to experiments on conventional TE membranes. In summary, our work advances the the utility of silicon nanomembranes as substrates for barrier tissue models by developing an interpretation of TEER values compatible with conventional systems.

Brownian dynamics of a protein-polymer chain complex in a solid-state nanopore.

We study the movement of a polymer attached to a large protein inside a nanopore in a thin silicon dioxide membrane submerged in an electrolyte solution. We use Brownian dynamics to describe the motion of a negatively charged polymer chain of varying lengths attached to a neutral protein modeled as a spherical bead with a radius larger than that of the nanopore, allowing the chain to thread the nanopore but preventing it from translocating. The motion of the protein-polymer complex within the pore is also compared to that of a freely translocating polymer. Our results show that the free polymer's standard deviations in the direction normal to the pore axis is greater than that of the protein-polymer complex. We find that restrictions imposed by the protein, bias, and neighboring chain segments aid in controlling the position of the chain in the pore. Understanding the behavior of the protein-polymer chain complex may lead to methods that improve molecule identification by increasing the resolution of ionic current measurements.

Electro-osmotic flow through nanopores in thin and ultrathin membranes.

We theoretically study how the electro-osmotic fluid velocity in a charged cylindrical nanopore in a thin solid state membrane depends on the pore's geometry, membrane charge, and electrolyte concentration. We find that when the pore's length is comparable to its diameter, the velocity profile develops a concave shape with a minimum along the pore axis unlike the situation in very long nanopores with a maximum velocity along the central pore axis. This effect is attributed to the induced pressure along the nanopore axis due to the fluid flow expansion and contraction near the exit or entrance to the pore and to the reduction of electric field inside the nanopore. The induced pressure is maximal when the pore's length is about equal to its diameter while decreasing for both longer and shorter nanopores. A model for the fluid velocity incorporating these effects is developed and shown to be in a good agreement with numerically computed results.

Protein permeation through an electrically tunable membrane.

Protein filtration is important in many fields of science and technology such as medicine, biology, chemistry, and engineering. Recently, protein separation and filtering with nanoporous membranes has attracted interest due to the possibility of fast separation and high throughput volume. This, however, requires understanding of the protein's dynamics inside and in the vicinity of the nanopore. In this work, we utilize a Brownian dynamics approach to study the motion of the model protein insulin in the membrane-electrolyte electrostatic potential. We compare the results of the atomic model of the protein with the results of a coarse-grained and a single-bead model, and find that the coarse-grained representation of protein strikes the best balance between the accuracy of the results and the computational effort required. Contrary to common belief, we find that to adequately describe the protein, a single-bead model cannot be utilized without a significant effort to tabulate the simulation parameters. Similar to results for nanoparticle dynamics, our findings also indicate that the electric field and the electro-osmotic flow due to the applied membrane and electrolyte biases affect the capture and translocation of the biomolecule by either attracting or repelling it to or from the nanopore. Our computational model can also be applied to other types of proteins and separation conditions.

Nanopore gating with an anchored polymer in a switching electrolyte bias.

In this work, we theoretically study the interaction between a solid state membrane equipped with a nanopore and a tethered, negatively charged polymer chain subjected to a time-dependent applied electrolyte bias. In order to describe the movement of the chain in the biomolecule-membrane system immersed in an electrolyte solution, Brownian dynamics is used. We show that we can control the polymer's equilibrium position with various applied electrolyte biases: for a sufficiently positive bias, the chain extends inside the pore, and the removal of the bias causes the polymer to leave the pore. Corresponding to a driven process, we find that the time it takes for a biomolecular chain to enter and extend into a nanopore in a positive bias almost increases linearly with chain length while the amount of time it takes for a polymer chain to escape the nanopore is mainly governed by diffusion.

The Influence of Monocular Spatial Cues on Vergence Eye Movements in Monocular and Binocular Viewing of 3-D and 2-D Stimuli.

The influence of monocular spatial cues on the vergence eye movements was studied in two series of experiments: (I) the subjects were viewing a 3-D video and also its 2-D version-binocularly and monocularly; and (II) in binocular and monocular viewing conditions, the subjects were presented with stationary 2-D stimuli containing or not containing some monocular indications of spatial arrangement. The results of the series (I) showed that, in binocular viewing conditions, the vergence eye movements were only present in the case of 3-D but not 2-D video, while in the course of monocular viewing of 2-D video, some regular vergence eye movements could be revealed, suggesting that the occluded eye position could be influenced by the spatial organization of the scene reconstructed on the basis of the monocular depth information provided by the viewing eye. The data obtained in series (II), in general, seem to support this hypothesis.