A methodology to evaluate different histological preparations of soft tissues: Intervertebral disc tissues study.

A tissue preparation method will inevitably alter the tissue content. This study aims to evaluate how different common sample preparation methods will affect the tissue morphology, biomechanical properties, and chemical composition of samples. The study focuses on intervertebral disc (IVD) tissue; however, it can be applied to other soft tissues. Raman spectroscopy synchronized with nanoindentation instrumentation was employed to investigate the compositional changes of IVD, specifically, nucleus pulposus (NP) and annulus fibrosus (AF), together with their biomechanical properties of IVD. These properties were examined through the following histological specimen types: fresh cryosection (control), fixed cryosection, and paraffin-embedded. The IVD tissue could be located using an optical microscope under three different preparation methods. Paraffin-embedded samples showed the most explicit details where the lamellae structure of AF could be identified. In terms of biomechanical properties, there was no significant difference between the fresh and fixed cryosection (p > 0.05). In contrast, the fresh cryosection and paraffin-embedded samples showed a significant difference (p < 0.05). It was also found that the tissue preparations affected the chemical content of the tissues and structure of the tissue, which are expected to contribute to biomechanical properties changes. Fresh cryosection and fixed cryosection samples are more promising to work with for biomechanical assessment in histological tissues. The findings fill essential gaps in the literature by providing valuable insight into the characteristics of IVD at the microscale. This study can also become a reference for a better approach to assessing the mechanical properties and chemical content of soft tissues at the microscale.

Correlation of the degenerative stage of a disc with magnetic resonance imaging, chemical content, and biomechanical properties of the nucleus pulposus.

Intervertebral disc degeneration (IDD) is closely related to changes in the intervertebral disc (IVD) composition and the resulting viscoelastic properties. IDD is a severe condition because it decreases the disc's ability to resist mechanical loads. Our research aims to understand IDD at the cellular level, specifically the changes in the viscoelastic properties of the nucleus pulposus (NP), which are poorly understood. This study employed a system integrating nanoindentation with Raman spectrometry to correlate biomechanics with subtle changes in the biochemical makeup of the NP. The characterization was, in turn, correlated with the degenerative severity of IVD as assessed using magnetic resonance imaging (MRI) of different patients with spinal stenosis, degenerative spondylolisthesis, and degenerative scoliosis. It is shown that there is an increase in the crosslinking ratio in collagen, a reduction in proteoglycan, and a build-up of minerals upon the rise in the severity level of the disc damage in the NP. Assessment of mechanical characteristics reveals that the increasing disc degeneration makes the NP lose its elasticity, becoming more viscous. This shows that the tissue undergoes abnormalities in weight-bearing ability, which contributes to spinal instability. The correlation of the individual discs shows that grades III and IV have similarities in the changes of Amide I and III toward the storage modulus. In contrast, grades IV and V correlate with mineralization toward the storage modulus. Reduction of proteoglycan has the highest impact on the changes of the storage modulus in all grades of IDD. Connecting compositional alterations to IVD micromechanics at various degrees of degeneration expands our understanding of tissue behavior and provides critical insight into clinical diagnostics, treatment, and tissue engineering.

General Strategy for the Design of DNA Coding Sequences Applied to Nanoparticle Assembly.

The DNA-directed assembly of nano-objects has been the subject of many recent studies as a means to construct advanced nanomaterial architectures. Although much experimental in silico work has been presented and discussed, there has been no in-depth consideration of the proper design of single-strand sticky termination of DNA sequences, noted as ssST, which is important in avoiding self-folding within one DNA strand, unwanted strand-to-strand interaction, and mismatching. In this work, a new comprehensive and computationally efficient optimization algorithm is presented for the construction of all possible DNA sequences that specifically prevents these issues. This optimization procedure is also effective when a spacer section is used, typically repeated sequences of thymine or adenine placed between the ssST and the nano-object, to address the most conventional experimental protocols. We systematically discuss the fundamental statistics of DNA sequences considering complementarities limited to two (or three) adjacent pairs to avoid self-folding and hybridization of identical strands due to unwanted complements and mismatching. The optimized DNA sequences can reach maximum lengths of 9 to 34 bases depending on the level of applied constraints. The thermodynamic properties of the allowed sequences are used to develop a ranking for each design. For instance, we show that the maximum melting temperature saturates with 14 bases under typical solvation and concentration conditions. Thus, DNA ssST with optimized sequences are developed for segments ranging from 4 to 40 bases, providing a very useful guide for all technological protocols. An experimental test is presented and discussed using the aggregation of Al and CuO nanoparticles and is shown to validate and illustrate the importance of the proposed DNA coding sequence optimization.

Elementary surface chemistry during CuO/Al nanolaminate-thermite synthesis: copper and oxygen deposition on aluminum (111) surfaces.

The surface chemistry associated with the synthesis of energetic nanolaminates controls the formation of the critical interfacial layers that dominate the performances of nanothermites. For instance, the interaction of Al with CuO films or CuO with Al films needs to be understood to optimize Al/CuO nanolaminates. To that end, the chemical mechanisms occurring during early stages of molecular CuO adsorption onto crystalline Al(111) surfaces are investigated using density functional theory (DFT) calculations, leading to the systematic determination of their reaction enthalpies and associated activation energies. We show that CuO undergoes dissociative chemisorption on Al(111) surfaces, whereby the Cu and O atoms tend to separate from each other. Both Cu and O atoms form islands with different properties. Copper islanding fosters Cu insertion (via surface site exchange mechanism) into the subsurface, while oxygen islands remain stable at the surface. Above a critical local oxygen coverage, aluminum atoms are extracted from the Al surface, leading to oxygen-aluminum intermixing and the formation of aluminum oxide (γ-alumina). For Cu and O co-deposition, copper promotes oxygen-aluminum interaction by oxygen segregation and separates the resulting oxide from the Al substrate by insertion into Al and stabilization below the oxide front, preventing full mixing of Al, Cu, and O species.

Toward in silico biomolecular manipulation through static modes: atomic scale characterization of HIV-1 protease flexibility.

Probing biomolecular flexibility with atomic-scale resolution is a challenging task in current computational biology for fundamental understanding and prediction of biomolecular interactions and associated functions. This paper makes use of the static mode method to study HIV-1 protease considered as a model system to investigate the full biomolecular flexibility at the atomic scale, the screening of active site biomechanical properties, the blind prediction of allosteric sites, and the design of multisite strategies to target deformations of interest. Relying on this single calculation run of static modes, we demonstrate that in silico predictive design of an infinite set of complex excitation fields is reachable, thanks to the storage of the static modes in a data bank that can be used to mimic single or multiatom contact and efficiently anticipate conformational changes arising from external stimuli. All along this article, we compare our results to data previously published and propose a guideline for efficient, predictive, and custom in silico experiments.

A computational chemist approach to gas sensors: modeling the response of SnO2 to CO, O2, and H2O gases.

A general bottom-up modeling strategy for gas sensor response to CO, O(2), H(2)O, and related mixtures exposure is demonstrated. In a first stage, we present first principles calculations that aimed at giving an unprecedented review of basic chemical mechanisms taking place at the sensor surface. Then, simulations of an operating gas sensor are performed via a mesoscopic model derived from calculated density functional theory data into a set of differential equations. Significant presence of catalytic oxidation reaction is highlighted.

The electrostatic probe: a tool for the investigation of the Aß(1-16) peptide deformations using the static modes.

We investigate the conformational changes of the Amyloid ß(1-16) peptide induced by moving Zn(2+) ions in the solvent, which we call the electrostatic probe. We use our recently developed approach of static modes which allows treating the flexibility of biological molecules at the atomic scale. Starting from an experimental apostructure, we find that several ion impacts allow the transition of the peptide toward its folded conformation, observed experimentally in the presence of Zn(2+) ions. This result shows the ability of our model and its associated software tool to describe properly the conformational changes and opens a new path toward the molecule/molecule docking problem.

Atomic scale determination of enzyme flexibility and active site stability through static modes: case of dihydrofolate reductase.

A Static Mode approach is used to screen the biomechanical properties of DHFR. In this approach, a specific external stimulus may be designed at the atomic scale granularity to arrive at a proper molecular mechanism. In this frame, we address the issues related to the overall molecular flexibility versus loop motions and versus enzymatic activity. We show that backbone motions are particularly important to ensure DHFR domain communication and notably highlight the role of a α-helix in Met20 loop motion. We also investigate the active site flexibility in different bound states. Whereas in the occluded conformation the Met20 loop is highly flexible, in the closed conformation backbone motions are no longer significant, the Met20 loop is rigidified by new intra- and intermolecular weak bonds, which stabilizes the complex and promotes the hydride transfer. Finally, while various simulations, including I14 V and I14A mutations, confirm that Ile14 is a key residue in catalytic activity, we isolate and characterize at the atomic scale how a specific intraresidue chemical group makes it possible to assist ligand positioning, to direct the nicotinamide ring toward the folate ring.

Delayed onset of photochromism in molybdenum oxide films caused by photoinduced defect formation.

We report the photochromic properties of amorphous MoO3 films deposited by dc sputtering with different O2 flow rates. The kinetics of film coloration under UV light irradiation is determined using optical transmission spectroscopy. Changes in the absorbance and refractive index were derived from the analysis of transmittance spectra. The absorbance spectra exhibited a growing broad peak centered around 830 nm, which was induced by the UV irradiation. In the early stages of irradiation, the absorbance of the films did not change but their refractive indices did change. This induction time was correlated with the O2 partial pressure during the film deposition, which was controlled by the O2 flow rate. The origins of this observation are discussed.

Nanoscale actuation of electrokinetic flows on thermoreversible surfaces.

We report on a novel approach for controlling nanohydrodynamic properties at the solid-liquid interfaces through the use of stimuli-responding polymer coatings. The end-tethered polymers undergo a phase separation upon external activation. The reversible change in the thickness and polarity of the grafted polymers yields in a dynamic control of the surface-generated, electrokinetic phenomena. Nonactivated, swollen polymers are thicker than the electrical double layer (EDL) and prohibit the development of an EOF even on charged surfaces. On the other hand, activated polymer chains shrink and become thinner than the EDL and allow for the EOF to build up unimpeded. We show here that, for given experimental conditions, the EOF velocity on the shrunken surface is 35 times greater than the one on the nonactivated surface. Furthermore, we reveal that coupling of such surfaces with dense arrays of thermal actuators developed in our laboratory can lead to novel micro- and nanofluidic devices.