Topography of Genetic Loci in Tissue Samples: Towards New Diagnostic Tool Using Interphase FISH and High-Resolution Image Analysis Techniques

Using single and dual colour fluorescence in situ hybridisation (FISH) combined with image analysis techniques the topographic characteristics of genes and centromeres in nuclei of human colon tissue cells were investigated. The distributions of distances from the centre‐of‐nucleus to genes (centromeres) and from genes to genes (centromeres to centromeres) were studied in normal colon tissue cells found in the neighbourhood of tumour samples, in tumour cell line HT‐29 and in promyelocytic HL‐60 cell line for comparison. Our results show that the topography of genetic loci determined in 3D‐fixed cell tissue corresponds to that obtained for 2D‐fixed cells separated from the tissue. The distributions of the centre‐of‐nucleus to gene (centromere) distances and gene to gene (centromere to centromere) distances and their average values are different for various genetic loci but similar for normal colon tissue cells, HT‐29 colon tumour cell line and HL‐60 promyelocytic cell line. It suggests that the arrangement of genetic loci in cell nucleus is conserved in different types of human cells. The investigations of trisomic loci in HT‐29 cells revealed that the location of the third genetic element is not different from the location of two homologues in diploid cells. We have shown that the topographic parameters used in our experiments for different genetic elements are not tissue or tumour specific. In order to validate high‐resolution cytometry for oncology, further investigations should include more precise parameters reflecting the state of chromatin in the neighbourhood of critical oncogenes or tumour suppresser genes

Integrative CUT&Tag-RNA-Seq Analysis of Histone Variant MacroH2A1-Dependent Orchestration of Human Induced Pluripotent Stem Cell Reprogramming

Aim: Human induced pluripotent stem cells (iPSCs) are inefficiently derived from somatic cells by overexpression of defined transcription factors. Overexpression of H2A histone variant macroH2A1.1, but not macroH2A1.2, leads to increased iPSC reprogramming by unclear mechanisms. Materials & methods: Cleavage under targets and tagmentation (CUT&Tag) allows robust epigenomic profiling of a low cell number. We performed an integrative CUT&Tag-RNA-Seq analysis of macroH2A1-dependent orchestration of iPSCs reprogramming using human endothelial cells. Results: We demonstrate wider genome occupancy, predicted transcription factors binding, and gene expression regulated by macroH2A1.1 during reprogramming, compared to macroH2A1.2. MacroH2A1.1, previously associated with neurodegenerative pathologies, specifically activated ectoderm/neural processes. Conclusion: CUT&Tag and RNA-Seq data integration is a powerful tool to investigate the epigenetic mechanisms occurring during cell reprogramming

Assessing the impact of low level laser therapy (LLLT) on biological systems: a review

PURPOSE: Low level laser therapy (LLLT) in the visible to near infrared spectral band (390-1100 nm) is absorption of laser light at the electronic level, without generation of heat. It may be applied in a wide range of treatments including wound healing, inflammation and pain reduction. Despite its potential beneficial impacts, the use of lasers for therapeutic purposes still remains controversial in mainstream medicine. Whilst taking into account the physical characteristics of different qualities of lasers, this review aims to provide a comprehensive account of the current literature available in the field pertaining to their potential impact at cellular and molecular levels elucidating mechanistic interactions in different mammalian models. The review also aims to focus on the integral approach of the optimal characteristics of LLLT that suit a biological system target to produce the beneficial effect at the cellular and molecular levels. METHODS: Recent research articles were reviewed that explored the interaction of lasers (coherent sources) and LEDs (incoherent sources) at the molecular and cellular levels. RESULTS: It is envisaged that underlying mechanisms of beneficial impact of lasers to patients involves biological processes at the cellular and molecular levels. The biological impact or effects of LLLT at the cellular and molecular level could include cellular viability, proliferation rate, as well as DNA integrity and the repair of damaged DNA. This review summarizes the available information in the literature pertaining to cellular and molecular effects of lasers. CONCLUSIONS: It is suggested that a change in approach is required to understand how to exploit the potential therapeutic modality of lasers whilst minimizing its possible detrimental effects

Mapping the mechanical properties in nitride coatings at the nanometer scale

We report on a multilayered structure comprising of rock-salt (rs) structured CrN layers of constant thickness and AlN layers of varying thicknesses, which surprisingly enables the growth of metastable zinc-blende (zb) AlN layers for certain layer-thickness combinations. The multilayer exhibits an atomic and electronic structure gradient as revealed using advanced electron microscopy and electron spectroscopy. Gradient structures are also accompanied by a modulation of the chemical compositions. A combined experimental analysis based on valence electrons and inner shell electrons allowed mapping the mechanical properties of the multilayer at the nanometer scale and further unveiled the effect of oxygen impurities on the bulk modulus. We found that the presence of oxygen impurities causes a remarkable reduction of the bulk modulus of rs-CrN while having no significant effect on the bulk modulus of the stable wurtzite structure wz-AlN layers. The findings are unambiguously validated by theoretical calculations using density functional theory. © 2020 Acta Materialia Inc

Synthesis and Characterization of Ta–B–C Coatings Prepared by DCMS and HiPIMS Co-sputtering

This study reports on the deposition and properties of Ta–B–C coatings by the co-sputtering of tantalum, boron carbide, and graphite targets using High Power Impulse Magnetron Sputtering (HiPIMS). It was possible to affect the microstructure of the deposited coatings by altering the deposition temperature or by the application of RF induced self-bias on the substrates without changing their chemical composition. The only identified crystalline phase from the Ta–B–C system present was TaC. The boron content in the coatings shows that the TaC crystallite size can be changed by a factor of 10 by changing the power to the boron carbide target. Mechanical properties of the coatings measured directly after the synthesis yield hardness higher than 40 GPa. After the relaxation of internal stress in the coatings (after one year) and changes in the structure, the hardness of all coatings was close to 36 GPa. According to ab initio calculations, the B incorporation in the fcc lattice of TaC in combination with C vacancies lead to lower (higher) shear-to-bulk modulus ratio (Poisson’s ratio), providing a good basis for improved ductility. All in all, Ta–B–C system shows a good potential as a novel hard protective coating

Erosion and cathodic arc plasma of Nb-Al cathodes: Composite versus intermetallic

Many properties of cathodic arcs from single-element cathodes show a correlation to the cohesive energy of the cathode material. For example, the burning voltage, the erosion rate, or, to a lesser extent, plasma properties like electron temperatures or average ion energy and charge states. For multi-element cathodes, various phases with different cohesive energies can initially be present in the cathode, or form due to arc exposure, complicating the evaluation of such correlations. To test the influence of morphology and phase composition of multi-element cathodes on cathodic arc properties, a Nb-Al cathode model system was used that includes: pure Nb and Al cathodes; intermetallic Nb3Al, Nb2Al and NbAl3 cathodes; and three composite Nb-Al cathodes with atomic ratios corresponding to the stoichiometric ratios of the intermetallic phases. Pulsed cathodic arc plasmas from these cathodes were examined using a mass-per-charge and energy-per-charge analyzer, showing that charge-state-resolved ion energy distributions of plasmas from the intermetallic and corresponding composite cathodes are nearly identical. An examination of converted layers of eroded cathodes using x-ray diffraction and scanning electron microscopy indicates the formation of a surface layer with similar phase composition for intermetallic and their corresponding composite cathode types. The average arc voltages do not follow the trend of cohesive energies of Nb, Al and intermetallic Nb-Al phases, which have been calculated using density functional theory. Possible reasons for this effect are discussed based on the current knowledge of multi-element arc cathodes and their arc plasma available in literature

First principles studies on the impact of point defects on the phase stability of (AlxCr1−x)2O3 solid solutions

Density Functional Theory applying the generalised gradient approximation is used to study the phase stability of (AlxCr1−x)2O3 solid solutions in the context of physical vapour deposition (PVD). Our results show that the energy of formation for the hexagonal α phase is lower than for the metastable cubic γ and B1-like phases–independent of the Al content x. Even though this suggests higher stability of the α phase, its synthesis by physical vapour deposition is difficult for temperatures below 800 °C. Aluminium oxide and Al-rich oxides typically exhibit a multi-phased, cubic-dominated structure. Using a model system of (Al0.69Cr0.31)2O3 which experimentally yields larger fractions of the desired hexagonal α phase, we show that point defects strongly influence the energetic relationships. Since defects and in particular point defects, are unavoidably present in PVD coatings, they are important factors and can strongly influence the stability regions. We explicitly show that defects with low formation energies (e.g. metal Frenkel pairs) are strongly preferred in the cubic phases, hence a reasonable factor contributing to the observed thermodynamically anomalous phase composition

Elasticity of phases in Fe–Al–Ti superalloys: Impact of atomic order and anti-phase boundaries

We combine theoretical and experimental tools to study elastic properties of Fe-Al-Ti superalloys. Focusing on samples with chemical composition Fe71Al22Ti7, we use transmission electron microscopy (TEM) to detect their two-phase superalloy nano-structure (consisting of cuboids embedded into a matrix). The chemical composition of both phases, Fe66.2Al23.3Ti10.5 for cuboids and Fe81Al19 (with about 1 or less of Ti) for the matrix, was determined from an Energy-Dispersive X-ray Spectroscopy (EDS) analysis. The phase of cuboids is found to be a rather strongly off-stoichiometric (Fe-rich and Ti-poor) variant of Heusler Fe2TiAl intermetallic compound with the L21 structure. The phase of the matrix is a solid solution of Al atoms in a ferromagnetic body-centered cubic (bcc) Fe. Quantum-mechanical calculations were employed to obtain an insight into elastic properties of the two phases. Three distributions of chemical species were simulated for the phase of cuboids (A2, B2 and L21) in order to determine a sublattice preference of the excess Fe atoms. The lowest formation energy was obtained when the excess Fe atoms form a solid solution with the Ti atoms at the Ti-sublattice within the Heusler L21 phase (L21 variant). Similarly, three configurations of Al atoms in the phase of the matrix with different level of order (A2, B2 and D03) were simulated. The computed formation energy is the lowest when all the 1st and 2nd nearest-neighbor Al-Al pairs are eliminated (the D03 variant). Next, the elastic tensors of all phases were calculated. The maximum Young’s modulus is found to increase with increasing chemical order. Further we simulated an anti-phase boundary (APB) in the L21 phase of cuboids and observed an elastic softening (as another effect of the APB, we also predict a significant increase of the total magnetic moment by 140 when compared with the APB-free material). Finally, to validate these predicted trends, a nano-scale dynamical mechanical analysis (nanoDMA) was used to probe elasticity of phases. Consistent with the prediction, the cuboids were found stiffer. © 2019 by the authors. Licensee MDPI, Basel, Switzerland