Membrane tension controls the phase equilibrium in fusogenic liposomes

Fusogenic liposomes have been widely used for molecule delivery to cell membranes and cell interior. However, their physicochemical state is still little understood. We tested mechanical material behavior by micropipette aspiration of giant vesicles from fusogenic lipid mixtures and found that the membranes of these vesicles are fluid and under high mechanical tension even before aspiration. Based on this result, we developed a theoretical framework to determine the area expansion modulus and membrane tension of such pre-tensed vesicles from aspiration experiments. Surprisingly high membrane tension of 2.1 mN m⁻¹ and very low area expansion modulus of 63 mN m⁻¹ were found. We interpret these peculiar material properties as the result of a mechanically driven phase transition between the usual lamellar phase and an, as of now, not finally determined three dimensional phase of the lipid mixture. The free enthalpy of transition between these phases is very low, i.e. on the order of the thermal energy.

The lipid moiety of fusogenic liposomes is in a mixed phase state whose thermodynamic equilibrium depends on membrane tension.     

Highly accurate quantification of allelic gene expression for population and disease genetics

Analysis of allele-specific gene expression (ASE) is a powerful approach for studying gene regulation, particularly when sample sizes are small, such as for rare diseases, or when studying the effects of rare genetic variation. However, detection of ASE events relies on accurate alignment of RNA sequencing reads, where challenges still remain, particularly for reads containing genetic variants or those that align to many different genomic locations. We have developed the Personalised ASE Caller (PAC), a tool that combines multiple steps to improve the quantification of allelic reads, including personalized (i.e., diploid) read alignment with improved allocation of multimapping reads. Using simulated RNA sequencing data, we show that PAC outperforms standard alignment approaches for ASE detection, reducing the number of sites with incorrect biases (>10%) by ∼80% and increasing the number of sites that can be reliably quantified by ∼3%. Applying PAC to real RNA sequencing data from 670 whole-blood samples, we show that genetic regulatory signatures inferred from ASE data more closely match those from population-based methods that are less prone to alignment biases. Finally, we use PAC to characterize cell type–specific ASE events that would be missed by standard alignment approaches, and in doing so identify disease relevant genes that may modulate their effects through the regulation of gene expression. PAC can be applied to the vast quantity of existing RNA sequencing data sets to better understand a wide array of fundamental biological and disease processes.

Allele-specific expression (ASE) is the imbalanced expression of the two alleles of a gene. Whereas many genes are expressed equally from both alleles, gene regulatory differences driven by genetic changes (i.e., regulatory variants) frequently cause the two alleles to be expressed at different levels, resulting in allele-specific expression patterns. With RNA sequencing (RNA-seq) data, the expression from the two alleles can be distinguished and quantified, but this analysis remains susceptible to many technical challenges, despite improved analytical methods (Castel et al. 2015; van de Geijn et al. 2015). To date, ASE analysis has largely been performed in the context of expression quantitative trait loci (eQTL) studies, as an alternative method to identify and characterize effects of regulatory variants on gene expression (Lappalainen et al. 2013; The GTEx Consortium 2020). In these studies, large sample sizes help mitigate the effects of technical biases (Panousis et al. 2014). However, the power of ASE analysis lies in its applicability to individual samples, particularly in the context of rare diseases and other cases where looking at combined haplotypic effects of multiple variants is necessary. Numerous studies have now leveraged the power of ASE in detecting genetic effects on gene regulation (Kumasaka et al. 2016; Findley et al. 2021) and identifying regulatory dysfunction in rare disease samples (Cummings et al. 2017; Mohammadi et al. 2019). In order to draw conclusions about individual samples and loci, the accuracy of ASE calling becomes paramount.One of the main sources of bias in ASE analysis is the alignment of sequencing reads. When short reads are aligned to the reference genome, reads carrying alleles that match to the reference sequence frequently map better than those carrying alternative alleles, leading to false ASE effects (‘reference allele bias’). This effect can be particularly problematic in areas containing a large number of single nucleotide polymorphisms or insertion/deletion events, which can mean that certain regions of the genome are not fully characterized. Similarly, reads that align to multiple locations in the genome can also influence the accuracy of allele counts at heterozygous sites. In the absence of better approaches, such difficult-to-map reads are typically discarded from the analysis (van de Geijn et al. 2015), and consequently sets of genes that contain similar sequences (e.g., within gene families) may suffer from artificially low sequencing coverage and lack of power to detect the effects of genetic regulation. Diploid genome mapping (i.e., use of personalized genome references) has been proposed as a solution to alignment-related artifacts in ASE analysis (Rozowsky et al. 2011; Dobin et al. 2013), but these approaches do not deal with all potential causes of bias, such as differences in the uniquely mappable genome between parental haplotypes (van de Geijn et al. 2015), and they have not been widely adopted, likely due to the lack of a comprehensive pipeline to handle personalized genome coordinates in downstream analysis. Collectively, these problems can inhibit the detection of genes that are under the influence of perturbed or altered regulatory regimes, which may be particularly limiting when trying to understand the underlying etiology of disease.Here, we address some of the remaining challenges in ASE analysis and describe the Personalised ASE Caller (PAC) tool that integrates a series of existing and novel methods to improve the detection of genuine ASE events in short read RNA-seq data. PAC deals with the issues outlined above by implementing parental genome mapping to limit the effects of genetic variation on read alignment and reallocating multimapping reads based on uniquely mapped read coverage to limit the removal of informative sequencing reads. PAC also uses improved read-based phasing approaches to ensure that alleles at heterozygous sites are on the correct genetic background, further improving our ability to accurately align data across these regions, and PAC compares alignment scores between parental genomes for each read, minimizing problems that may arise from aligning data to two different genomes. Finally, these steps are applied within an easy-to-use workflow system that produces allele counts at the single site (converted back to reference genome coordinates) and gene level, which can be easily used in downstream analyses.     

Control of Dielectric and Mechanical Properties of Styrenic Block Copolymer by Graphite Incorporation

The structure–property relationship of dielectric elastomers, as well as the methods of improving the control of this relationship, has been widely studied over the last few years, including in some of our previous works. In this paper, we study the control, improvement, and correlation, for a significant range of temperatures, of the mechanical and dielectric properties of polystyrene-b-(ethylene-co-butylene)-b-styrene (SEBS) and maleic-anhydride-grafted SEBS (SEBS-MA) by using graphite (G) as filler in various concentrations. The aim is to analyze the suitability of these composites for converting electrical energy into mechanical energy or vice versa. The dielectric spectroscopy analysis performed in the frequency range of 10 to 1 MHz and at temperatures between 27 and 77 °C emphasized an exponential increase in real permittivity with G concentration, a low level of dielectric losses (≈10⁻³), as well as the stability of dielectric losses with temperature for high G content. These results correlate well with the increase in mechanical stiffness with an increase in G content for both SEBS/G and SEBS-MA/G composites. The activation energies for the dielectric relaxation processes detected in SEBS/G and SEBS-MA/G composites were also determined and discussed in connection with the mechanical, thermal, and structural properties resulting from thermogravimetric analysis, differential scanning calorimetry, Fourier-transform infrared spectroscopy and X-ray photoelectron spectroscopy analyses.     

Growth of Nitrogen Incorporated Ultrananocrystalline Diamond Coating on Graphite by Hot Filament Chemical Vapor Deposition

This article shows the results of experiments to grow Nitrogen incorporated ultrananocrystalline diamond (N-UNCD) films on commercial natural graphite (NG)/Cu anodes by hot chemical vapor deposition (HFCVD) using a gas mixture of Ar/CH₄/N₂/H₂. The experiments focused on studying the effect of the pressure in the HFCVD chamber, filament-substrate distance, and temperature of the substrate. It was found that a substrate distance of 3.0 cm and a substrate temperature of 575 C were optimal to grow N-UNCD film on the graphite surface as determined by Raman spectroscopy, SEM, and TEM imaging. XPS analysis shows N incorporation through the film. Subsequently, the substrate surface temperature was increased using a heater, while keeping the substrate-filament distance constant at 3.0 cm. In this case, Raman spectra and SEM images of the substrate surface showed a major composition of graphite in the film as the substrate-surface temperature increased. Finally, the process pressure was increased to 10 Torr where it was seen that the growth of N-UNCD film occurred at 2.0 cm at a substrate temperature of 675 C. These results suggest that as the process pressure increases a smaller substrate-filament distance and consequently a higher substrate surface temperature can still enable the N-UNCD film growth by HFCVD. This effect is explained by a mean free path analysis of the main precursors H₂ and CH₃ molecules traveling from the filament to the surface of the substrate The potential impact of the process developed to grow electrically conductive N-UNCD films using the relatively low-cost HFCVD process is that this process can be used to grow N-UNCD films on commercial NG/Cu anodes for Li-ion batteries (LIBs), to enable longer stable capacity energy vs. charge/discharge cycles.     

Deformation-Induced Martensitic Transformation in Laser Cladded 304 Stainless Steel Coatings

There are only a few cost-effective solutions for coating applications in combined mechanical loading and corrosive environments. Stainless steel AISI 304 has the potential to fill this niche, showing excellent corrosion resistance while utilizing the deformation-induced phase transformation from γ-austenite to α’-martensite, which results in an increase in strength. However, it is not known whether this can occur in laser cladded material. Therefore, laser cladded AISI 304 coatings in as-cladded condition and after heat treatment at 1100 °C for 60 min were investigated before and after bending deformation, by means of light microscopy, energy-dispersive X-ray spectroscopy and electron backscatter diffraction. It was shown that due to the dendritic microstructure accompanied by an inhomogeneous distribution of the main alloying elements (Cr and Ni), no deformation-induced phase transformation occurred in the as-cladded coating. The applied approach with subsequent solution heat treatment at 1100 °C for 60 min resulted in a homogeneous γ-austenite microstructure, so that a deformation-induced martensitic transformation (DIMT) could occur in the coatings. However, the volume fraction of martensite that had been formed locally at individual shear bands was rather low, which can be possibly attributed to the high Ni content of the feedstock, stabilizing the γ-austenite microstructure. This study shows the possibility of exploiting the DIMT mechanism in heat-treated laser-cladded AISI 304 coatings.     

The Influence of Nanosilica on Properties of Cement Based on Tetracalcium Phosphate/Monetite Mixture with Addition of Magnesium Pyrophoshate

The effect of nanosilica on the microstructure setting process of tetracalcium phosphate/nanomonetite calcium phosphate cement mixture (CPC) with the addition of 5 wt% of magnesium pyrophosphate (assigned as CT5MP) and osteogenic differentiation of mesenchymal stem cells cultured in cement extracts were studied. A more compact microstructure was observed in CT5MP cement with 0.5 wt% addition of nanosilica (CT5MP1Si) due to the synergistic effect of Mg₂P₂O₇ particles, which strengthened the cement matrix and nanosilica, which supported gradual growth and recrystallization of HAP particles to form compact agglomerates. The addition of 0.5 wt% of nanosilica to CT5MP cement caused an increase in CS from 18 to 24 MPa while the setting time increased almost twofold. It was verified that adding nanosilica to CPC cement, even in a low amount (0.5 and 1 wt% of nanosilica), positively affected the injectability of cement pastes and differentiation of cells with upregulation of osteogenic markers in cells cultured in cement extracts. Results revealed appropriate properties of these types of cement for filling bone defects.     

Effect of TiO2 Additives on the Stabilization of h-YbFeO3 and Promotion of Photo-Fenton Activity of o-YbFeO3/h-YbFeO3/r-TiO2 Nanocomposites

Nanostructured hexagonal rare-earth orthoferrites (h-RfeO₃, R = Sc, Y, Tb-Lu) are well known as a highly effective base for visible-light-driven heterojunction photocatalysts. However, their application is limited by metastability, leading to difficulties in synthesis due to the irreversible transformation to a stable orthorhombic structure. In this work, we report on a simple route to the stabilization of h-YbFeO₃ nanocrystals by the synthesis of multiphase nanocomposites with titania additives. The new I-type heterojunction nanocomposites of o-YbFeO₃/h-YbFeO₃/r-TiO₂ were obtained by the glycine–nitrate solution combustion method with subsequent heat treatment of the products. An increase in the mole fraction of the h-YbFeO₃ phase in nanocomposites was found with the titanium addition, indicating its stabilizing effect via limiting mass transfer over heat treatment. The complex physicochemical analysis shows multiple contacts of individual nanocrystals of o-YbFeO₃ (44.4–50.6 nm), h-YbFeO₃ (7.5–17.6 nm), and rutile r-TiO₂ (~5 nm), confirming the presence of the heterojunction structure in the obtained nanocomposite. The photocatalytic activity of h-YbFeO₃/o-YbFeO₃/r-TiO₂ nanocomposites was evaluated by the photo-Fenton degradation of the methyl violet under visible light (λ ≥ 400 nm). It was demonstrated that the addition of 5 mol.% of TiO₂ stabilizes h-YbFeO₃, which allowed us to achieve a 41.5 mol% fraction, followed by a three-time increase in the photodecomposition rate constant up to 0.0160 min⁻¹.     

Interlayer and Intralayer Excitons in AlN/WS2 Heterostructure

The study of intra and interlayer excitons in 2D semiconducting vdW heterostructures is a very hot topic not only from a fundamental but also an applicative point of view. Due to their strong light–matter interaction, Transition Metal Dichalcogenides (TMD) and group-III nitrides are particularly attractive in the field of opto-electronic applications such as photo-catalytic and photo-voltaic ultra-thin and flexible devices. Using first-principles ground and excited-state simulations, we investigate here the electronic and excitonic properties of a representative nitride/TMD heterobilayer, the AlN/WS2. We demonstrate that the band alignment is of type I, and low energy intralayer excitons are similar to those of a pristine WS2 monolayer. Further, we disentangle the role of strain and AlN dielectric screening on the electronic and optical gaps. These results, although they do not favor the possible use of AlN/WS2 in photo-catalysis, as envisaged in the previous literature, can boost the recently started experimental studies of 2D hexagonal aluminum nitride as a good low screening substrate for TMD-based electronic and opto-electronic devices. Importantly, our work shows how the inclusion of both spin-orbit and many-body interactions is compulsory for the correct prediction of the electronic and optical properties of TMD/nitride heterobilayers.