Proton Environments in Biomimetic Calcium Phosphates Formed from Mesoporous Bioactive CaO-SiO2- P2O5 Glasses in vitro: Insights from Solid-State NMR

When exposed to body fluids, mesoporous bioactive glasses (MBGs) of the CaO{SiO2{P2O5 system develop a bone-bonding surface layer that initially consists of amorphous calcium phosphate(ACP), which transforms into hydroxy-carbonate apatite (HCA) with a very similar composition as bone/dentin mineral. Information from various 1H-based solid-state nuclear magnetic resonance (NMR) experiments were combined to elucidate the evolution of the proton speciations both at the MBG surface and within each ACP/HCA constituent of the biomimetic phosphate layer formed when each of three MBGs with distinct Ca, Si, and P contents was immersed in a simulated body fluid (SBF) for variable periods between 15 min and 30 days. Directly excited magic-angle-spinning (MAS) 1H NMR spectra mainly reflect the MBG component, whose surface is rich in water and silanol (SiOH) moieties. Double-quantum{single-quantum correlation 1H NMR experimentation at fast MAS revealed their interatomic proximities. The comparatively minor H species of each ACP and HCA component were probed selectively by heteronuclear 1H{31P NMR experimentation. The initially prevailing ACP phase comprises H2O and "non-apatitic" HPO2

Nuclear Magnetic Resonance and Metadynamics Simulations Reveal the Atomistic Binding of l -Serine and O-Phospho- l -Serine at Disordered Calcium Phosphate Surfaces of Biocements

Interactions between biomolecules and structurally disordered calcium phosphate (CaP) surfaces are crucial for the regulation of bone mineralization by noncollagenous proteins, the organization of complexes of casein and amorphous calcium phosphate (ACP) in milk, as well as for structure-function relationships of hybrid organic/inorganic interfaces in biomaterials. By a combination of advanced solid-state NMR experiments and metadynamics simulations, we examine the detailed binding of O-phospho-l-serine (Pser) and l-serine (Ser) with ACP in bone-adhesive CaP cements, whose capacity of gluing fractured bone together stems from the close integration of the organic molecules with ACP over a subnanometer scale. The proximity of each carboxy, aliphatic, and amino group of Pser/Ser to the Ca2+ and phosphate species of ACP observed from the metadynamics-derived models agreed well with results from heteronuclear solid-state NMR experiments that are sensitive to the 13C-31P and 15N-31P distances. The inorganic/organic contacts in Pser-doped cements are also contrasted with experimental and modeled data on the Pser binding at nanocrystalline HA particles grown from a Pser-bearing aqueous solution. The molecular adsorption is driven mainly by electrostatic interactions between the negatively charged carboxy/phosphate groups and Ca2+ cations of ACP, along with H bonds to either protonated or nonprotonated inorganic phosphate groups. The Pser and Ser molecules anchor at their phosphate/amino and carboxy/amino moieties, respectively, leading to an extended molecular conformation across the surface, as opposed to an "upright standing"molecule that would result from the binding of one sole functional group

Genomic repeat abundances contain phylogenetic signal

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution

Composition-Structure Correlations of Bioactive Glasses Explored by Multinuclear Solid-state NMR Spectroscopy

This PhD thesis presents a study of structure-composition correlations of bioactive glasses (BGs) by employing solid-state Nuclear Magnetic Resonance (NMR) spectroscopy. Silicate-based Na2O−CaO−SiO2−P2O5 BGs are utilized clinically and are extensively investigated for bone regeneration purposes. Once implanted in the human body, they facilitate bone regeneration by partially dissolving in the body fluids, followed by the formation of a biomimetic surface-layer of calcium hydroxy-carbonate apatite (HCA). Eventually, the implanted BG totally integrates with the bone. The bioactivity of melt-prepared BGs depends on their composition and structure, primarily on the phosphorus content and the average silicate-network connectivity (NC). We explored these composition-structure relationships for a set of BGs for which the NC and phosphorus contents were varied independently. The short-range structural features of the glasses were explored using 29Si and 31P magic-angle-spinning (MAS) NMR spectroscopy. 31P MAS NMR revealed that the orthophosphate content is directly proportional to the total P content of the glass, with a linear correlation observed between the orthophosphate content and the silicate network connectivity. The bearings of the results for future BG design are discussed. By using multiple-quantum coherence-based 31P NMR experiments, the spatial distribution of orthophosphate groups was probed in the melt prepared BGs, as well as in two mesoporous bioactive glasses prepared by an evaporation-induced self-assembly technique. The results evidence randomly distributed orthophosphate groups in the melt-prepared BGs, whereas the pore-walls of the mesoporous bioactive glasses constitute nanometer-sized clusters of calcium phosphate. The distribution of Na+ ions among the phosphate/silicate groups were studied by heteronuclear dipolar-based 23Na−31P NMR experiments, verifying that sodium is dispersed nearly randomly in the glasses. The phosphorus and proton environments in biomimetically grown HCA were investigated by using 1H and 31P MAS NMR experiments. Our studies revealed that the biomimetic HCA shared many local structural features with synthetic and well-ordered hydroxy-apatite.At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Accepted.</p

Na/Ca Intermixing around Silicate and Phosphate Groups in Bioactive Phosphosilicate Glasses Revealed by Heteronuclear Solid-State NMR and Molecular Dynamics Simulations

We characterize the intermixing of network-modifying Na⁺/Ca²⁺ ions around the silicate (<i>Q</i>_Si^<i>n</i>) and phosphate (<i>Q</i>_P^<i>n</i>) tetrahedra in a series of 16 Na₂O–CaO–SiO₂–P₂O₅ glasses, whose P content and silicate network connectivity were varied independently. The set includes both bioactive and bio<i>in</i>active compositions and also encompasses two soda-lime-silicate members devoid of P, as well as two CaO–SiO₂ glasses and one Na₂O–SiO₂–P₂O₅ glass. The various Si/P↔Na/Ca contacts were probed by molecular dynamics (MD) simulations together with heteronuclear magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) experimentation utilizing ²³Na­{³¹P} and ²³Na­{²⁹Si} REDOR, as well as ³¹P­{ ²³Na} and ²⁹Si­{²³Na} REAPDOR. We introduce an approach for quantifying the extent of Na⁺/Ca²⁺ ordering around a given <i>Q</i>_P^<i>n</i> or <i>Q</i>_Si^<i>n</i> group, encoded by the preference factor 0⩽ <i>P</i>_<i>M</i> ⩽ 1 conveying the relative weights of a random cation intermixing (<i>P</i>_<i>M</i> = 0) and complete preference/ordering (<i>P</i>_<i>M</i> = 1) for one of the species <i>M</i>, which represents either Na⁺ or Ca²⁺. The MD-derived preference factors reveal phosphate and silicate species surrounded by Na⁺/Ca²⁺ ions intermixed nearly randomly (<i>P</i>_<i>M</i> ≲ 0.15), except for the <i>Q</i>_Si⁴ and <i>Q</i>_Si¹ groups, which manifest more significant cation ordering with preference for Na⁺ and Ca²⁺, respectively. The overall weak preferences are essentially independent of the Si and P contents of the glass, whereas <i>P</i>_<i>M</i> primarily correlates with the total amount of network modifiers: as the latter is increased, the Na/Ca distribution around the {<i>Q</i>_P⁰, <i>Q</i>_Si¹, <i>Q</i>_Si²} groups with preference for Ca²⁺ tend to randomize (i.e., <i>P</i>_Ca decreases), while the <i>P</i>_Na-values grow slightly for the {<i>Q</i>_P¹, <i>Q</i>_Si³, <i>Q</i>_Si⁴} species already preferring coordination of Na. The set of experimental preference factors {<i>P</i>_Ca} for the orthophosphate (<i>Q</i>_P⁰) groups extracted from ³¹P­{²³Na} REAPDOR NMR-derived <i>M</i>₂(P–Na) dipolar second moments agrees well with the MD-generated counterparts. Our results on the Na/Ca intermixing in soda-lime-silicate glasses are discussed in relation to previous reports, highlighting the dependence of the conclusion on the approach to data evaluation