Effect on the mechanical properties of type I collagen of intra-molecular lysine-arginine derived advanced glycation end-product cross-linking.

Non-enzymatic advanced glycation end product (AGE) cross-linking of collagen molecules has been hypothesised to result in significant changes to the mechanical properties of the connective tissues within the body, potentially resulting in a number of age related diseases. We have investigated the effect of two of these cross-links, glucosepane and DOGDIC, on the tensile and lateral moduli of the collagen molecule through the use of a steered molecular dynamics approach, using previously identified preferential formation sites for intra-molecular cross-links. Our results show that the presence of intra-molecular AGE cross-links increases the tensile and lateral Young's moduli in the low strain domain by between 3.0-8.5% and 2.9-60.3% respectively, with little effect exhibited at higher strains.

[Simple is not always easy: genetics in general psychiatry]. / Drie patiënten met langdurig onopgehelderde psychiatrische klachten waarbij genetische diagnostiek uitkomst bracht.

Many of the patients who attend the outpatient mental health clinics already have a long history of psychiatric problems. Their symptoms seem easy to classify, but the misdiagnosis of the patients' underlying problems can lead to a long series of costly referrals as inpatients or to an ineffective treatment outcome. In this article we focus on three patients whose history and background circumstances had been analysed in detail and who had also been subjected to a genetic analysis. The analyses pointed to an etiology-based diagnosis which had important implications for their future treatment and its outcome.

Hybridization of Zinc Oxide Tetrapods for Selective Gas Sensing Applications.

In this work, the exceptionally improved sensing capability of highly porous three-dimensional (3-D) hybrid ceramic networks toward reducing gases is demonstrated for the first time. The 3-D hybrid ceramic networks are based on doped metal oxides (MexOy and ZnxMe1-xOy, Me = Fe, Cu, Al) and alloyed zinc oxide tetrapods (ZnO-T) forming numerous junctions and heterojunctions. A change in morphology of the samples and formation of different complex microstructures is achieved by mixing the metallic (Fe, Cu, Al) microparticles with ZnO-T grown by the flame transport synthesis (FTS) in different weight ratios (ZnO-T:Me, e.g., 20:1) followed by subsequent thermal annealing in air. The gas sensing studies reveal the possibility to control and change/tune the selectivity of the materials, depending on the elemental content ratio and the type of added metal oxide in the 3-D ZnO-T hybrid networks. While pristine ZnO-T networks showed a good response to H2 gas, a change/tune in selectivity to ethanol vapor with a decrease in optimal operating temperature was observed in the networks hybridized with Fe-oxide and Cu-oxide. In the case of hybridization with ZnAl2O4, an improvement of H2 gas response (to ∼7.5) was reached at lower doping concentrations (20:1), whereas the increase in concentration of ZnAl2O4 (ZnO-T:Al, 10:1), the selectivity changes to methane CH4 gas (response is about 28). Selectivity tuning to different gases is attributed to the catalytic properties of the metal oxides after hybridization, while the gas sensitivity improvement is mainly associated with additional modulation of the electrical resistance by the built-in potential barriers between n-n and n-p heterojunctions, during adsorption and desorption of gaseous species. Density functional theory based calculations provided the mechanistic insights into the interactions between different hybrid networks and gas molecules to support the experimentally observed results. The studied networked materials and sensor structures performances would provide particular advantages in the field of fundamental research, applied physics studies, and industrial and ecological applications.

Effect of strontium inclusion on the bioactivity of phosphate-based glasses.

We have conducted first-principles and classical molecular dynamics simulations of various compositions of strontium-containing phosphate glasses, to understand how strontium incorporation will change the glasses' activity when implanted into the body (bioactivity). To perform the classical simulations, we have developed a new interatomic potential, which takes account of the polarizability of the oxygen ions. The Sr-O bond length is âˆ¼2.44-2.49 Å, and the coordination number is 7.5-7.8. The Q n distribution and network connectivity were roughly constant for these compositions. Sr bonds to a similar number of phosphate chains as Ca does; based on our previous work (Christie et al. in J Phys Chem B 117:10652, 2013), this implies that SrO â†” CaO substitution will barely change the dissolution rate of these glasses and that the bioactivity will remain essentially constant. Strontium could therefore be incorporated into phosphate glass for biomedical applications.

Surface and shape modification of mackinawite (FeS) nanocrystals by cysteine adsorption: a first-principles DFT-D2 study.

The control of nanoparticle shape offers promise for improving catalytic activity and selectivity through optimization of the structure of the catalytically active site. Here, we have employed density functional theory calculations with a correction for the long-range interactions (DFT-D2) to investigate the effect of adsorption of the amino acid cysteine on the {001}, {011}, {100}, and {111} surfaces of mackinawite, which are commonly found in FeS nanoparticles. We have calculated the surface energies and adsorption energies for all the surfaces considered, and compared the surface energies of the pure and adsorbed systems. Based on the calculated surface energies, we have simulated the thermodynamic crystal morphology of the pure and cysteine-modified FeS nanoparticles using Wulff's construction. The strength of cysteine adsorption is found to be related to the stability of different surfaces, where it adsorbs most strongly onto the least stable FeS{111} surface via bidentate Fe-S and Fe-N chemical bonds and most weakly onto the most stable FeS{001} surface via hydrogen-bonded interactions; the adsorption energy decreases in the order {111} > {100} > {011} > {001}. We demonstrate that the stronger binding of the cysteine to the {011}, {100}, and {111} surfaces rather than to the {001} facet results in shape modulation of the FeS nanoparticles, with the reactive surfaces more expressed in the thermodynamic crystal morphology compared to the unmodified FeS crystals. Information regarding the structural parameters, electronic structures and vibrational frequency assignments of the cysteine-FeS complexes is also presented.

Catalytic water dissociation by greigite Fe3S4 surfaces: density functional theory study.

The iron sulfide mineral greigite, Fe3S4, has shown promising capability as a hydrogenating catalyst, in particular in the reduction of carbon dioxide to produce small organic molecules under mild conditions. We employed density functional theory calculations to investigate the {001},{011} and {111} surfaces of this iron thiospinel material, as well as the production of hydrogen ad-atoms from the dissociation of water molecules on the surfaces. We systematically analysed the adsorption geometries and the electronic structure of both bare and hydroxylated surfaces. The sulfide surfaces presented a higher flexibility than the isomorphic oxide magnetite, Fe3O4, allowing perpendicular movement of the cations above or below the top atomic sulfur layer. We considered both molecular and dissociative water adsorption processes, and have shown that molecular adsorption is the predominant state on these surfaces from both a thermodynamic and kinetic point of view. We considered a second molecule of water which stabilizes the system mainly by H-bonds, although the dissociation process remains thermodynamically unfavourable. We noted, however, synergistic adsorption effects on the Fe3S4{001} owing to the presence of hydroxyl groups. We concluded that, in contrast to Fe3O4, molecular adsorption of water is clearly preferred on greigite surfaces.

DFT-D2 simulations of water adsorption and dissociation on the low-index surfaces of mackinawite (FeS).

The adsorption and dissociation of water on mackinawite (layered FeS) surfaces were studied using dispersion-corrected density functional theory (DFT-D2) calculations. The catalytically active sites for H2O and its dissociated products on the FeS {001}, {011}, {100}, and {111} surfaces were determined, and the reaction energetics and kinetics of water dissociation were calculated using the climbing image nudged elastic band technique. Water and its dissociation products are shown to adsorb more strongly onto the least stable FeS{111} surface, which presents low-coordinated cations in the surface, and weakest onto the most stable FeS{001} surface. The adsorption energies decrease in the order FeS{111} > FeS{100} > FeS{011} > FeS{001}. Consistent with the superior reactivity of the FeS{111} surface towards water and its dissociation products, our calculated thermochemical energies and activation barriers suggest that the water dissociation reaction will take place preferentially on the FeS nanoparticle surface with the {111} orientation. These findings improve our understanding of how the different FeS surface structures and the relative stabilities dictate their reactivity towards water adsorption and dissociation.

Methanol formation from CO2 catalyzed by Fe3S4{111}: formate versus hydrocarboxyl pathways.

Carbon capture and utilisation is one of the most promising techniques to minimize the impact of the increasing amount of carbon dioxide in the atmosphere. Recently, the mineral greigite was shown to be capable of catalysing CO2 conversion, leading to useful small organic molecules. Here, we have carried out a systematic study of the adsorption and selective reduction of CO2 on the Fe3S4{111} surface. We have considered both formate and hydrocarboxyl key intermediates, leading to different reaction pathways via Eley-Rideal and Langmuir-Hinshelwood mechanisms, and we have built a kinetic model considering the wide range of intermediates in the reaction network. Our results show that the mechanism to produce formic acid takes place via formate intermediate mostly on FeA sites, while methanol is formed via hydrocarboxyl intermediates on FeB sites. From the kinetic model, we have derived a reaction constant comparison and determined the limiting step rates. The overall process takes place under very mild conditions, requiring only a small energy input that might come from a chemiosmotic potential.

Density functional theory study of the effect of helium clusters on tritium-containing palladium lattices.

Density functional theory (DFT) calculations have been employed to calculate the energetics, structures and migration behaviour of helium in palladium tritides. Increasing the tritium concentration in palladium leads to a decrease in the formation energies of helium clusters, indicating that He clusters can form in the lattices. The calculated results show less lattice expansion in Pd defect-containing lattices compared to the perfect lattice owing to smaller lattice distortions. The lowest energy migration path for helium diffusion is along octahedral-tetrahedral-octahedral sites but the energy barrier increases with increasing tritium concentration. Repulsive interactions occur between Pd d and He s orbitals, suggesting that displacement of the metal atoms in the lattice leads to growth of pressure inside the lattices. This process may change the microstructural properties leading to the degradation of the material.

Activation and dissociation of CO2 on the (001), (011), and (111) surfaces of mackinawite (FeS): A dispersion-corrected DFT study.

Iron sulfide minerals, including mackinawite (FeS), are relevant in origin of life theories, due to their potential catalytic activity towards the reduction and conversion of carbon dioxide (CO2) to organic molecules, which may be applicable to the production of liquid fuels and commodity chemicals. However, the fundamental understanding of CO2 adsorption, activation, and dissociation on FeS surfaces remains incomplete. Here, we have used density functional theory calculations, corrected for long-range dispersion interactions (DFT-D2), to explore various adsorption sites and configurations for CO2 on the low-index mackinawite (001), (110), and (111) surfaces. We found that the CO2 molecule physisorbs weakly on the energetically most stable (001) surface but adsorbs relatively strongly on the (011) and (111) FeS surfaces, preferentially at Fe sites. The adsorption of the CO2 on the (011) and (111) surfaces is shown to be characterized by significant charge transfer from surface Fe species to the CO2 molecule, which causes a large structural transformation in the molecule (i.e., forming a negatively charged bent CO2 (-δ) species, with weaker C-O confirmed via vibrational frequency analyses). We have also analyzed the pathways for CO2 reduction to CO and O on the mackinawite (011) and (111) surfaces. CO2 dissociation is calculated to be slightly endothermic relative to the associatively adsorbed states, with relatively large activation energy barriers of 1.25 eV and 0.72 eV on the (011) and (111) surfaces, respectively.

Water in hydroxyapatite nanopores: Possible implications for interstitial bone fluid flow.

The role of bone water in the activity of this organ is essential in structuring apatite crystals, providing pathways for nutrients and waste involved in the metabolism of bone cells and participating in bone remodelling mechanotransduction. It is commonly accepted that bone presents three levels of porosity, namely the vasculature, the lacuno-canalicular system and the voids of the collagen-apatite matrix. Due to the observation of bound state of water at the latter level, the interstitial nanoscopic flow that may exist within these pores is classically neglected. The aim of this paper is to investigate the possibility to obtain a fluid flow at the nanoscale. That is why a molecular dynamics based analysis of a water-hydroxyapatite system is proposed to analyze the effect of water confinement on transport properties. The main result here is that free water can be observed inside hydroxyapatite pores of a few nanometers. This result would have strong implications in the multiscale treatment of the poromechanical behaviour of bone tissue. In particular, the mechanical properties of the bone matrix may be highly controlled by nanoscopic water diffusion and the classical idea that osteocytic activity is only regulated by bone fluid flow within the lacuno-canalicular system may be discussed again.

Bio-inspired CO2 conversion by iron sulfide catalysts under sustainable conditions.

The mineral greigite presents similar surface structures to the active sites found in many modern-day enzymes. We show that particles of greigite can reduce CO2 under ambient conditions into chemicals such as methanol, formic, acetic and pyruvic acid. Our results also lend support to the Origin of Life theory on alkaline hydrothermal vents.

The surface chemistry of NO(x) on mackinawite (FeS) surfaces: a DFT-D2 study.

We present density functional theory calculations with a correction for the long-range interactions (DFT-D2) of the bulk and surfaces of mackinawite (FeS), and subsequent adsorption and dissociation of NO(x) gases (nitrogen monoxide (NO) and nitrogen dioxide (NO2)). Our results show that these environmentally important molecules interact very weakly with the energetically most stable (001) surface, but adsorb relatively strongly onto the FeS(011), (100) and (111) surfaces, preferentially at Fe sites via charge donation from these surface species. The NOx species exhibit a variety of adsorption geometries, with the most favourable for NO being the monodentate Fe-NO configuration, whereas NO2 is calculated to form a bidentate Fe-NOO-Fe configuration. From our calculated thermochemical energy and activation energy barriers for the direct dissociation of NO and NO2 on the FeS surfaces, we show that NO prefers molecular adsorption, while dissociative adsorption, i.e. NO2 (ads) → [NO(ads) + O(ads)] is preferred over molecular adsorption for NO2 onto the mackinawite surfaces. However, the calculated high activation barriers for the further dissociation of the second N-O bond to produce either [N(ads) and 2O(ads)] or [N(ads) and O2(ads)] suggest that complete dissociation of NO2 is unlikely to occur on the mackinawite surfaces.

X-linked congenital ptosis and associated intellectual disability, short stature, microcephaly, cleft palate, digital and genital abnormalities define novel Xq25q26 duplication syndrome.

Submicroscopic duplications along the long arm of the X-chromosome with known phenotypic consequences are relatively rare events. The clinical features resulting from such duplications are various, though they often include intellectual disability, microcephaly, short stature, hypotonia, hypogonadism and feeding difficulties. Female carriers are often phenotypically normal or show a similar but milder phenotype, as in most cases the X-chromosome harbouring the duplication is subject to inactivation. Xq28, which includes MECP2 is the major locus for submicroscopic X-chromosome duplications, whereas duplications in Xq25 and Xq26 have been reported in only a few cases. Using genome-wide array platforms we identified overlapping interstitial Xq25q26 duplications ranging from 0.2 to 4.76 Mb in eight unrelated families with in total five affected males and seven affected females. All affected males shared a common phenotype with intrauterine- and postnatal growth retardation and feeding difficulties in childhood. Three had microcephaly and two out of five suffered from epilepsy. In addition, three males had a distinct facial appearance with congenital bilateral ptosis and large protruding ears and two of them showed a cleft palate. The affected females had various clinical symptoms similar to that of the males with congenital bilateral ptosis in three families as most remarkable feature. Comparison of the gene content of the individual duplications with the respective phenotypes suggested three critical regions with candidate genes (AIFM1, RAB33A, GPC3 and IGSF1) for the common phenotypes, including candidate loci for congenital bilateral ptosis, small head circumference, short stature, genital and digital defects.

Adsorption of methylamine on mackinawite (FES) surfaces: a density functional theory study.

We have used density functional theory calculations to investigate the interaction between methylamine (CH3NH2) and the dominant surfaces of mackinawite (FeS), where the surface and adsorption properties of mackinawite have been characterized using the DFT-D2 method of Grimme. Our calculations show that while the CH3NH2 molecule only interacts weakly with the most stable FeS(001), it adsorbs relatively strongly on the FeS(011) and FeS(100) surfaces releasing energies of 1.26 eV and 1.51 eV, respectively. Analysis of the nature of the bonding reveals that the CH3NH2 molecule interacts with the mackinawite surfaces through the lone-pair of electrons located on the N atom. The electron density built up in the bonding region between N and Fe is very much what one would expect of covalent type of bonding. We observe no significant adsorption-induced changes of the FeS surface structures, suggesting that amine capping agents would not distort the FeS nanoparticle surfaces required for active heterogeneous catalytic reactions. The vibrational frequencies and the infrared spectra of adsorbed methylamine have been calculated and assignments for vibrational modes are used to propose a kinetic model for the desorption process, yielding a simulated temperature programmed desorption with a relative desorption temperature of <140 K at the FeS(011) surface and <170 K at FeS(100) surface.

Pathogenic or not? Assessing the clinical relevance of copy number variants.

The availability of commercially produced genomic microarrays has resulted in the wide spread implementation of genomic microarrays, often as a first-tier diagnostic test for copy number variant (CNV) screening of patients who are suspected for chromosomal aberrations. Patients with intellectual disability (ID) and/or multiple congenital anomalies (MCA) were traditionally the main focus for this microarray-based CNV screening, but the application of microarrays to other (neurodevelopmental) disorders and tumor diagnostics has also been explored and implemented. The diagnostic workflow for patients with ID is now well established, relying on the identification of rare CNVs and determining their inheritance patterns. However, experience gained through screening large numbers of samples has revealed many subtleties and complexities of CNV interpretation. This has resulted in a better understanding of the contribution of CNVs to genomic disorders not only via de novo occurrence, but also via X-linked and recessive inheritance models as well as through models taking into account mosaicisms, imprinting, and digenic inheritance. In this review, we discuss CNV interpretation within the context of these different genetic disease models and common pitfalls that can occur when searching for supportive evidence that a CNV is clinically relevant.

A comparative DFT study of the mechanical and electronic properties of greigite Fe3S4 and magnetite Fe3O4.

Greigite (Fe3S4) and its analogue oxide, magnetite (Fe3O4), are natural minerals with an inverse spinel structure whose atomic-level properties may be difficult to investigate experimentally. Here, [D. Rickard and G. W. Luther, Chem. Rev. 107, 514 (2007)] we have calculated the elastic constants and other macroscopic mechanical properties by applying elastic strains on the unit cells. We also have carried out a systematic study of the electronic properties of Fe3S4 and Fe3O4, where we have used an ab initio method based on spin-polarized density functional theory with the on-site Coulomb repulsion approximation (Ueff is 1.0 and 3.8 eV for Fe3S4 and Fe3O4, respectively). Comparison of the properties of Fe3S4 and Fe3O4 shows that the sulfide is more covalent than the oxide, which explains the low magnetization of saturation of greigite cited in several experimental reports.

The interaction of hydrogen with the {010} surfaces of Mg and Fe olivine as models for interstellar dust grains: a density functional theory study.

There is no consensus as yet to account for the significant presence of water on the terrestrial planets, but suggested sources include direct hydrogen adsorption from the parent molecular cloud after the planets' formation, and delivery of hydrous material via comets or asteroids external to the zone of the terrestrial planets. Alternatively, a more recent idea is that water may have directly adsorbed onto the interstellar dust grains involved in planetary formation. In this work, we use electronic structure calculations based on the density functional theory to investigate and compare the bulk and {010} surface structures of the magnesium and iron end-members of the silicate mineral olivine, namely forsterite and fayalite, respectively. We also report our results on the adsorption of atomic hydrogen at the mineral surfaces, where our calculations show that there is no activation barrier to the adsorption of atomic hydrogen at these surfaces. Furthermore, different surface sites activate the atom to form either adsorbed hydride or proton species in the form of hydroxy groups on the same surface, which indicates that these mineral surfaces may have acted as catalytic sites in the immobilization and reaction of hydrogen atoms to form dihydrogen gas or water molecules.