First principles modelling of the ion binding capacity of finger millet.

Finger millet, a cereal grain widely consumed in India and Africa, has gained more attention in recent years due to its high dietary fibre (arabinoxylan) and trace mineral content, and its climate resilience. The aim of this study was to understand the interactions between potassium (K+), calcium (Ca2+) and zinc (Zn2+) ions and the arabinoxylan structure and determine its ion-binding capacity. Three variations of a proposed model of the arabinoxylan structure were constructed and first principles Density Functional Theory calculations were carried out to determine the cation-binding capacity of the arabinoxylan complexes. Zn2+-arabinoxylan complexes were highly unstable and thermodynamically unfavourable in all three models. Ca2+ and K+ ions, however, form thermodynamically stable complexes, particularly involving two glucuronic acid residues as a binding pocket. Glucuronic acid residues are found to play a key role in stabilising the cation-arabinoxylan complex, and steric effects are more important to the stability than charge density. Our results highlight the most important structural features of the millet fibre regarding ion-storage capacity, and provide valuable preliminary data for confirmatory experimental studies and for the planning of clinical trials where the bioavailability of bound ions following digestion may be tested.

Atomistic modelling and NMR studies reveal that gallium can target the ferric PQS uptake system in P. aeruginosa biofilms.

Intravenous gallium nitrate therapy is a novel therapeutic strategy deployed to combat chronic Pseudomonas aeruginosa biofilm infections in the lungs of cystic fibrosis (CF) patients by interfering with iron (Fe3+) uptake. The therapy is a source of Ga3+, which competes with Fe3+ for siderophore binding, subsequently disrupting iron metabolism and inhibiting biofilm proliferation in vivo. It was recently demonstrated that the Pseudomonas quinolone signal (PQS) can chelate Fe3+ to assist in bacterial iron uptake. However, it is unknown whether exogenous gallium also targets [Fe(PQS)3] uptake, which, in turn, would extend the mechanism of gallium therapy beyond siderophore competition, potentially supporting use of the therapy against P. aeruginosa mutants deficient in siderophore uptake proteins. To that end, the thermodynamic feasibility of iron-for-gallium cation exchange into [Fe(PQS)3] was evaluated using quantum chemical density functional theory (DFT) modelling and verified experimentally using 1H nuclear magnetic resonance (NMR). We demonstrate here that Ga3+ can strongly bind to three PQS molecules and, furthermore, displace and substitute Fe3+ from the native chelate pocket within PQS complexes, through a Trojan horse mechanism, retaining the key structural features present within the native ferric complex. As such, [Fe(PQS)3] complexes, in addition to ferric-siderophore complexes, represent another target for gallium therapy.

A DFT study of the gallium ion-binding capacity of mature Pseudomonas aeruginosa biofilm extracellular polysaccharide.

Intravenous gallium therapy is a non-antibiotic approach to limit Pseudomonas aeruginosa biofilm proliferation, by outcompeting iron for siderophore binding. Gallium therapy represents a viable therapeutic strategy for cystic fibrosis (CF) patients harbouring mucoid P. aeruginosa biofilm lung infections. Siderophore deficient P. aeruginosa isolates still demonstrate a hindered biofilm proliferation when exposed to gallium but it is currently unknown whether exogenous gallium has any disruptive influence on the exopolysaccharide (EPS), the major mucoid P. aeruginosa CF lung biofilm matrix component. To that end, Density-Functional Theory (DFT) was deployed to assess whether gallium (Ga3+) could be substituted into the mature mucoid EPS scaffold in preference of calcium (Ca2+)-the native EPS cross-linking ion. Removal of the stable, bound native calcium ions offers a large enthalpic barrier to the substitution and the mature EPS fails to accommodate exogenous gallium. This suggests that gallium, perhaps, is utilising a novel, possibly unknown, ferric uptake system to gain entry to siderophore deficient cells.

Polyguluronate simulations shed light onto the therapeutic action of OligoG CF-5/20.

Chronic mucoid P. aeruginosa cystic fibrosis (CF) lung infections are associated with the development of a biofilm composed of anionic acetylated exopolysaccharide (EPS) alginate, electrostatically stabilised by extracellular Ca2+ ions. OligoG CF-5/20, a low molecular weight guluronate rich oligomer, is emerging as a novel therapeutic capable of disrupting mature P. aeruginosa biofilms. However, its method of therapeutic action on the mucoid biofilm EPS is not definitively known at a molecular level. This work, utilising molecular dynamics (MD) and Density-Functional Theory (DFT), has revealed that OligoG CF-5/20 interaction with the EPS is facilitated solely through bridging Ca2+ ions, which are not liberated from their native EPS binding sites upon OligoG CF-5/20 dispersal, suggesting that OligoG CF-5/20 does not cause disruptions to mature P. aeruginosa biofilms through breaking EPS-Ca2+-EPS ionic cross-links. Rather it is likely that the therapeutic activity arises from sequestering free Ca2+ ions and preventing further Ca2+ induced EPS aggregation.

Atomic-scale interactions between quorum sensing autoinducer molecules and the mucoid P. aeruginosa exopolysaccharide matrix.

Mucoid Pseudomonas aeruginosa is a prevalent cystic fibrosis (CF) lung coloniser whose chronicity is associated with the formation of cation cross-linked exopolysaccharide (EPS) matrices, which form a biofilm that acts as a diffusion barrier, sequestering cationic and neutral antimicrobials, and making it extremely resistant to pharmacological challenge. Biofilm chronicity and virulence of the colony is regulated by quorum sensing autoinducers (QSAIs), small signalling metabolites that pass between bacteria, through the biofilm matrix, regulating genetic responses on a population-wide scale. The nature of how these molecules interact with the EPS is poorly understood, despite the fact that they must pass through EPS matrix to reach neighbouring bacteria. Interactions at the atomic-scale between two QSAI molecules, C4-HSL and PQS-both utilised by mucoid P. aeruginosa in the CF lung-and the EPS, have been studied for the first time using a combined molecular dynamics (MD) and density functional theory (DFT) approach. A large-scale, calcium cross-linked, multi-chain EPS molecular model was developed and MD used to sample modes of interaction between QSAI molecules and the EPS that occur at physiological equilibrium. The thermodynamic stability of the QSAI-EPS adducts were calculated using DFT. These simulations provide a thermodynamic rationale for the apparent free movement of C4-HSL, highlight key molecular functionality responsible for EPS binding and, based on its significantly reduced mobility, suggest PQS as a viable target for quorum quenching.

Dietary and supplemental long-chain omega-3 fatty acids as moderators of cognitive impairment and Alzheimer's disease.

PURPOSE: There is an ever-growing body of literature examining the relationship between dietary omega-3 polyunsaturated fatty acids (ω3 PUFAs) and cerebral structure and function throughout life. In light of this, the use of ω3 PUFAs, namely, long-chain (LC) ω3 PUFAs (i.e., eicosapentaenoic acid and docosahexaenoic acid), as a therapeutic strategy to mitigate cognitive impairment, and progression to Alzheimer's disease is an attractive prospect. This review aims to summarise evidence reported by observational studies and clinical trials that investigated the role of LC ω3 PUFAs against cognition impairment and future risk of Alzheimer's disease. METHODS: Studies were identified in PubMed and Scopus using the search terms "omega-3 fatty acids", "Alzheimer's disease" and "cognition", along with common variants. Inclusion criteria included observational or randomised controlled trials (RCTs) with all participants aged ≥ 50 years that reported on the association between LC ω3 PUFAs and cognitive function or biological markers indicative of cognitive function linked to Alzheimer's disease. RESULTS: Evidence from 33 studies suggests that dietary and supplemental LC ω3 PUFAs have a protective effect against cognitive impairment. Synaptic plasticity, neuronal membrane fluidity, neuroinflammation, and changes in expression of genes linked to cognitive decline have been identified as potential targets of LC ω3 PUFAs. The protective effects LC ω3 PUFAs on cognitive function and reduced risk of Alzheimer's disease were supported by both observational studies and RCTs, with RCTs suggesting a more pronounced effect in individuals with early and mild cognitive impairment. CONCLUSION: The findings of this review suggest that individuals consuming higher amounts of LC ω3 PUFAs are less likely to develop cognitive impairment and that, as a preventative strategy against Alzheimer's disease, it is most effective when dietary LC ω3 PUFAs are consumed prior to or in the early stages of cognitive decline.

Cation complexation by mucoid Pseudomonas aeruginosa extracellular polysaccharide.

Mucoid Pseudomonas aeruginosa is a prevalent cystic fibrosis (CF) lung colonizer, producing an extracellular matrix (ECM) composed predominantly of the extracellular polysaccharide (EPS) alginate. The ECM limits antimicrobial penetration and, consequently, CF sufferers are prone to chronic mucoid P. aeruginosa lung infections. Interactions between cations with elevated concentrations in the CF lung and the anionic EPS, enhance the structural rigidity of the biofilm and exacerbates virulence. In this work, two large mucoid P. aeruginosa EPS models, based on ß-D-mannuronate (M) and ß-D-mannuronate-α-L-guluronate systems (M-G), and encompassing thermodynamically stable acetylation configurations-a structural motif unique to mucoid P. aeruginosa-were created. Using highly accurate first principles calculations, stable coordination environments adopted by the cations have been identified and thermodynamic stability quantified. These models show the weak cross-linking capability of Na+ and Mg2+ ions relative to Ca2+ ions and indicate a preference for cation binding within M-G blocks due to the smaller torsional rearrangements needed to reveal stable binding sites. The geometry of the chelation site influences the stability of the resulting complexes more than electrostatic interactions, and the results show nuanced chemical insight into previous experimental observations.

Physiological silicon incorporation into bone mineral requires orthosilicic acid metabolism to SiO44.

Under physiological conditions, the predominant form of bioavailable silicon (Si) is orthosilicic acid (OSA). In this study, given Si's recognized positive effect on bone growth and integrity, we examined the chemical form and position of this natural Si source in the inorganic bone mineral hydroxyapatite (HA). X-ray diffraction (XRD) of rat tibia bone mineral showed that the mineral phase was similar to that of phase-pure HA. However, theoretical XRD patterns revealed that at the levels found in bone, the 'Si effect' would be virtually undetectable. Thus we used first principles density functional theory calculations to explore the energetic and geometric consequences of substituting OSA into a large HA model. Formation energy analysis revealed that OSA is not favourable as a neutral interstitial substitution but can be incorporated as a silicate ion substituting for a phosphate ion, suggesting that incorporation will only occur under specific conditions at the bone-remodelling interface and that dietary forms of Si will be metabolized to simpler chemical forms, specifically [Formula: see text]. Furthermore, we show that this substitution, at the low silicate concentrations found in the biological environment, is likely to be a driver of calcium phosphate crystallization from an amorphous to a fully mineralized state.

Small and dangerous? Potential toxicity mechanisms of common exposure particles and nanoparticles.

We are continuously exposed to large numbers of non-biological, persistent particulates through dermal, oral and inhalation routes. At sizes perfect for cell interactions, such modern particle exposures are derived from human engineering either purposefully (e.g. additives/excipients) or inadvertently (e.g. pollution). Whether oral or dermal exposure to common particles has significantly adverse effects is not yet known. However, relationships between increased morbidity or mortality and airborne particle exposure are well established. Large nanoparticles and microparticles adsorb environmental molecules, including antigens and allergens, and deliver them to cells potentially with an adjuvant effect. Smaller nanoparticles may have enhanced redox activity due to increased surface areas or band gap effects. Under some circumstances, ultrasmall nanoparticles can ligate cellular receptors or interact with other cell machinery and drive distinct cell signalling. These, as well as the potential for inflammasome activation, are discussed as feasible pathways to understanding or de-bunking particle toxicity.

Non-Functionalized Ultrasmall Silica Nanoparticles Directly and Size-Selectively Activate T Cells.

Sub-micron-sized silica nanoparticles, even as small as 10-20 nm in diameter, are well-known for their activation of mononuclear phagocytes. In contrast, the cellular impact of those <10 nm [ i.e., ultrasmall silica nanoparticles (USSN)] is not well-established for any cell type despite anticipated human exposure. Here, we synthesized discrete populations of USSN with volume median diameters between 1.8 to 16 nm and investigated their impact on the mixed cell population of human primary peripheral mononuclear cells. USSN 1.8-7.6 nm in diameter, optimally 3.6-5.1 nm in diameter, induced dose-dependent CD4 and CD8 T-cell activation in terms of cell surface CD25 and CD69 up-regulation at concentrations above 150 µM Sitotal (∼500 nM particles). Induced activation with only ∼2.4 µM particles was (a) equivalent to that observed with typical positive control levels of Staphylococcal enterotoxin B (SEB) and (b) evident in antigen presenting cell-deplete cultures as well as in a pure T-cell line (Jurkat) culture. In the primary mixed-cell population, USSN induced IFN-γ secretion but failed to induce T-cell proliferation or the secretion of IL-2, IL-10, or IL-4. Collectively, these data indicate that USSN initiate activation, with Th1 polarization, of T cells via direct particle-cell interaction. Finally, similarly sized iron hydroxide particles did not induce the expression of T-cell activation markers, indicating some selectivity of the ultrasmall particle type. Given that humans may be exposed to ultrasmall particles and that these materials have emerging bioclinical applications, their off-target immunomodulatory effects via direct T-cell activation should be carefully considered.

Intravenous Irons: From Basic Science to Clinical Practice.

Iron is an essential trace mineral necessary for life, and iron deficiency anaemia (IDA) is one of the most common haematological problems worldwide, affecting a sixth of the global population. Principally linked to poverty, malnutrition and infection in developing countries, in Western countries the pathophysiology of IDA is primarily linked to blood loss, malabsorption and chronic disease. Oral iron replacement therapy is a simple, inexpensive treatment, but is limited by gastrointestinal side effects that are not inconsequential to some patients and are of minimal efficacy in others. Third generation intravenous (IV) iron therapies allow rapid and complete replacement dosing without the toxicity issues inherent with older iron preparations. Their characteristic, strongly-bound iron-carbohydrate complexes exist as colloidal suspensions of iron oxide nanoparticles with a polynuclear Fe(III)-oxyhydroxide/oxide core surrounded by a carbohydrate ligand. The physicochemical differences between the IV irons include mineral composition, crystalline structure, conformation, size and molecular weight, but the most important difference is the carbohydrate ligand, which influences complex stability, iron release and immunogenicity, and which is a unique feature of each drug. Recent studies have highlighted different adverse event profiles associated with third-generation IV irons that reflect their different structures. The increasing clinical evidence base has allayed safety concerns linked to older IV irons and widened their clinical use. This review considers the properties of the different IV irons, and how differences might impact current and future clinical practice.

Synthetic mimetics of the endogenous gastrointestinal nanomineral: Silent constructs that trap macromolecules for intracellular delivery.

Amorphous magnesium-substituted calcium phosphate (AMCP) nanoparticles (75-150nm) form constitutively in large numbers in the mammalian gut. Collective evidence indicates that they trap and deliver luminal macromolecules to mucosal antigen presenting cells (APCs) and facilitate gut immune homeostasis. Here, we report on a synthetic mimetic of the endogenous AMCP and show that it has marked capacity to trap macromolecules during formation. Macromolecular capture into AMCP involved incorporation as shown by STEM tomography of the synthetic AMCP particle with 5nm ultra-fine iron (III) oxohydroxide. In vitro, organic cargo-loaded synthetic AMCP was taken up by APCs and tracked to lysosomal compartments. The AMCP itself did not regulate any gene, or modify any gene regulation by its cargo, based upon whole genome transcriptomic analyses. We conclude that synthetic AMCP can efficiently trap macromolecules and deliver them to APCs in a silent fashion, and may thus represent a new platform for antigen delivery.

A model for the effects of germanium on silica biomineralization in choanoflagellates.

Silica biomineralization is a widespread phenomenon of major biotechnological interest. Modifying biosilica with substances like germanium (Ge) can confer useful new properties, although exposure to high levels of Ge disrupts normal biosilicification. No clear mechanism explains why this disruption occurs. Here, we study the effect of Ge on loricate choanoflagellates, a group of protists that construct a species-specific extracellular lorica from multiple siliceous costal strips. High Ge exposures were toxic, whereas lower Ge exposures produced cells with incomplete or absent loricae. These effects can be ameliorated by restoring the germanium : silicon ratio, as observed in other biosilicifying organisms. We developed simulations of how Ge interacts with polymerizing silica. In our models, Ge is readily incorporated at the ends of silica forming from silicic acid condensation, but this prevents further silica polymerization. Our 'Ge-capping' model is supported by observations from loricate choanoflagellates. Ge exposure terminates costal strip synthesis and lorica formation, resulting in disruption to cytokinesis and fatal build-up of silicic acid. Applying the Ge-capping model to other siliceous organisms explains the general toxicity of Ge and identifies potential protective responses in metalloid uptake and sensing. This can improve the design of new silica biomaterials, and further our understanding of silicon metabolism.

Synthesis, characterization and modelling of zinc and silicate co-substituted hydroxyapatite.

Experimental chemistry and atomic modelling studies were performed here to investigate a novel ionic co-substitution in hydroxyapatite (HA). Zinc, silicate co-substituted HA (ZnSiHA) remained phase pure after heating to 1100 °C with Zn and Si amounts of 0.6 wt% and 1.2 wt%, respectively. Unique lattice expansions in ZnSiHA, silicate Fourier transform infrared peaks and changes to the hydroxyl IR stretching region suggested Zn and silicate co-substitution in ZnSiHA. Zn and silicate insertion into HA was modelled using density functional theory (DFT). Different scenarios were considered where Zn substituted for different calcium sites or at a 2b site along the c-axis, which was suspected in singly substituted ZnHA. The most energetically favourable site in ZnSiHA was Zn positioned at a previously unreported interstitial site just off the c-axis near a silicate tetrahedron sitting on a phosphate site. A combination of experimental chemistry and DFT modelling provided insight into these complex co-substituted calcium phosphates that could find biomedical application as a synthetic bone mineral substitute.

Structural changes in zirconolite under α-decay.

We report the simulation of alpha recoil cascades in zirconolite (CaZrTi(2)O(7)) using the molecular dynamics method under a variety of simulation conditions. Interatomic potentials have been developed through fitting to crystalline and melted structures and their energy surfaces obtained from ab initio calculations. Single and double cascades have been modelled, showing that damage recovery in damaged crystalline material is greatly impaired when there are multiple events. The calcium ions are significantly easier to displace than other ions, which is consistent with a recent ab initio study of defect energies.

Emission Quenching in PbSe Quantum Dot Arrays by Short-Term Air Exposure.

Clear evidence for two emitting states in PbSe nanocrystals (NCs) has been observed. The flow of population between these two states as temperature increases is interrupted by the presence of nonradiative trap states correlated with the exposure of the NC film to air. Quenching of the higher-energy emission begins after only seconds of exposure, with the effect saturating after several days. Unlike short-term oxygen-related effects in solution, the emission quenching appears to be irreversible, signaling a distinction between surface reactivity in NCs in films and that in solution. The origin of the two emissive centers and the impact of trapping on other NC film properties (e.g., electron/hole mobilities) remain important issues to be resolved.

Zinc incorporation into hydroxylapatite.

By theoretical modeling and X-ray absorption spectroscopy, the local coordination structure of Zn incorporated into hydroxylapatite was examined. Density function theory (DFT) calculations show that Zn favors the Ca2 site over the Ca1 site, and favors tetrahedral coordination. X-ray absorption near edge structure (XANES) spectroscopy results suggest one dominant coordination environment for the incorporated Zn, and no evidence was observed for other Zn-containing phases. Extended X-ray absorption fine structure (EXAFS) fitting of the synthetic samples confirms that Zn occurs in tetrahedral coordination, with two P shells at approximately 2.85-3.07A, and two higher Ca shells at approximately 3.71-4.02A. These fit results are consistent with the most favored DFT model for Zn substitution in the Ca2 site.

Probing the surface structure of hydroxyapatite using NMR spectroscopy and first principles calculations.

The surface characteristics of hydroxyapatite (HA) are probed using a combination of NMR spectroscopy and first principles calculations. The NMR spectrum is taken from a bone sample and the first principles calculations are performed using a plane-wave density functional approach within the pseudopotential approximation. The computational work focuses on the (100) and (200) surfaces, which exhibit a representative range of phosphate, hydroxyl and cation bonding geometries. The shielding tensors for the 31P, 1H and 17O nuclei are calculated from the relaxed surface structures using an extension of the projector augmented-wave method. The calculated 31P chemical shifts for the surface slab are found to be significantly different from the bulk crystal and are consistent with the NMR data from bone and also synthetically prepared nanocrystalline samples of HA. Rotational relaxations of the surface phosphate ions and the sub-surface displacement of other nearby ions are identified as causing the main differences. The investigation points to further calculations of other crystallographic surfaces and highlights the potential of using NMR with ab initio modelling to fully describe the surface structure and chemistry of HA, which is essential for understanding its reactivity with the surrounding organic matrix.