Second harmonic generation and broad-band photoluminescence in mesoporous Si/SiO nanoparticles.

Efficient second harmonic generation and broad-band photoluminescence from deeply subwavelength and nontoxic nanoparticles is essential for nanophotonic applications. Here, we explore nonlinear optical response from mesoporous Si/SiO, SiO, and Si nanoparticles, considering various fabrication and treatment procedures. We show that thermal annealing (including femtosecond laser treatment) of mesoporous Si/SiO nanoparticles provides the transformation of Si phase from amorphous to crystalline, enhancing the second harmonic and nonlinear photoluminescent response.

Modulation of GaAs nanowire growth by pre-treatment of Si substrate using a Ga focused ion beam.

We reveal a novel phenomenon observed after self-catalytic growth of GaAs nanowires (NWs) on Si(111) substrates treated with a Ga focused ion beam (FIB). Depending on the ion dose, NW arrays with various geometrical parameters can be obtained. A minor treatment of the substrate enables a slight increase in the surface density of NWs relative to an unmodified substrate area.

Elastic Gallium Phosphide Nanowire Optical Waveguides-Versatile Subwavelength Platform for Integrated Photonics.

Emerging technologies for integrated optical circuits demand novel approaches and materials. This includes a search for nanoscale waveguides that should satisfy criteria of high optical density, small cross-section, technological feasibility and structural perfection. All these criteria are met with self-assembled gallium phosphide (GaP) epitaxial nanowires.

Genetic Adaptation of Siberian Larch ( Ledeb.) to High Altitudes.

Forest trees growing in high altitude conditions offer a convenient model for studying adaptation processes. They are subject to a whole range of adverse factors that are likely to cause local adaptation and related genetic changes. Siberian larch ( Ledeb.

Effect of Si(111) Surface Modification by Ga Focused Ion Beam at 30 kV on GaAs Nanowire Growth.

This paper presents the results of experimental studies of the effect of Si(111) surface modification by Ga-focused ion beam (FIB) at 30 kV accelerating voltage on the features of the epitaxial GaAs nanowire (NW) growth processes. We experimentally established the regularities of the Ga ions' dose effect during surface modification on the structural characteristics of GaAs NW arrays. Depending on the Ga ion dose value, there is one of three modes on the surface for subsequent GaAs NW growth.

Nanoscale Electric Field Probing in a Single Nanowire with Raman Spectroscopy and Elastic Strain.

In this work we investigate the Raman response of extremely strained gallium phosphide nanowires. We analyze new strain-induced spectral phenomena such as 2-fold and 3-fold phonon peak splitting which arise due to nontrivial internal electric field distribution coupled with inhomogeneous strain. We show that high bending strain acts as a probe allowing us to define the electric field distribution with deep subwavelength resolution using the corresponding changes of the Raman spectra.

Annotation of Siberian Larch ( Ledeb.) Nuclear Genome-One of the Most Cold-Resistant Tree Species in the Only Deciduous GENUS in .

The recent release of the nuclear, chloroplast and mitochondrial genome assemblies of Siberian larch ( Ledeb.), one of the most cold-resistant tree species in the only deciduous genus of Pinaceae, with seasonal senescence and a rot-resistant valuable timber widely used in construction, greatly contributed to the development of genomic resources for the larch genus. Here, we present an extensive repeatome analysis and the first annotation of the draft nuclear Siberian larch genome assembly.

SOMSpec as a General Purpose Validated Self-Organising Map Tool for Rapid Protein Secondary Structure Prediction From Infrared Absorbance Data.

A protein's structure is the key to its function. As protein structure can vary with environment, it is important to be able to determine it over a wide range of concentrations, temperatures, formulation vehicles, and states. Robust reproducible validated methods are required for applications including batch-batch comparisons of biopharmaceutical products.

Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: "Dark Repeatome" and Its Abundance in Conifer and Species.

Repetitive elements (RE) and transposons (TE) can comprise up to 80% of some plant genomes and may be essential for regulating their evolution and adaptation. The "repeatome" information is often unavailable in assembled genomes because genomic areas of repeats are challenging to assemble and are often missing from final assembly. However, raw genomic sequencing data contain rich information about RE/TEs.

Flexible Perovskite CsPbBr Light Emitting Devices Integrated with GaP Nanowire Arrays in Highly Transparent and Durable Functionalized Silicones.

The architecture of transparent contacts is of utmost importance for creation of efficient flexible light-emitting devices (LEDs) and other deformable electronic devices. We successfully combined the newly synthesized transparent and durable silicone rubbers and the semiconductor materials with original fabrication methods to design LEDs and demonstrate their significant flexibility. We developed electrodes based on a composite GaP nanowire-phenylethyl-functionalized silicone rubber membrane, improved with single-walled carbon nanotube films for a hybrid poly(ethylene oxide)-metal-halide perovskite (CsPbBr) flexible green LED.

Intra- and Inter-cellular Modeling of Dynamic Interaction between Zika Virus and Its Naturally Occurring Defective Viral Genomes.

Here, we examine the infection dynamics and interactions of two Zika virus (ZIKV) genomes: one is the full-length ZIKV genome (wild type [WT]), and the other is one of the naturally occurring defective viral genomes (DVGs), which can replicate in the presence of the WT genome, appears under high-MOI (multiplicity of infection) passaging conditions, and carries a deletion encompassing part of the structural and NS1 protein-coding region. Ordinary differential equations (ODEs) were used to simulate the infection of cells by virus particles and the intracellular replication of the WT and DVG genomes that produce these particles. For each virus passage in Vero and C6/36 cell cultures, the rates of the simulated processes were fitted to two types of observations: virus titer data and the assembled haplotypes of the replicate passage samples.

Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome.

Background: Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family).

De novo sequencing, assembly and functional annotation of Armillaria borealis genome.

Background: Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm.

Site-specific characterization of SARS-CoV-2 spike glycoprotein receptor-binding domain.

The novel coronavirus SARS-CoV-2, the infective agent causing COVID-19, is having a global impact both in terms of human disease as well as socially and economically. Its heavily glycosylated spike glycoprotein is fundamental for the infection process, via its receptor-binding domains interaction with the glycoprotein angiotensin-converting enzyme 2 on human cell surfaces. We therefore utilized an integrated glycomic and glycoproteomic analytical strategy to characterize both N- and O- glycan site-specific glycosylation within the receptor-binding domain.

Fabrication and electrical study of large area free-standing membrane with embedded GaP NWs for flexible devices.

Flexible optoelectronic structures are required in a wide range of applications. Large scale modified silicone-embedded n-GaP nanowire arrays of a record 6 µm thin membranes were studied. A homogeneous silicone encapsulation was enabled by G-coating using a heavy-load centrifuge.

De novo transcriptome assembly of cold stressed clones of the hexaploid Sequoia sempervirens (D. Don) Endl.

Coast redwood is a very important endemic conifer timber species in Southern Oregon and Northern California in the USA. Due to its good wood properties and fast growth rate it can be considered as a prospective timber species also in other countries with similar or changing toward similar climatic conditions due to global climate warming, such as Germany. In general, it is frost sensitive and suffers from freezing temperatures.

Effect of the Uniaxial Compression on the GaAs Nanowire Solar Cell.

Research regarding ways to increase solar cell efficiency is in high demand. Mechanical deformation of a nanowire (NW) solar cell can improve its efficiency. Here, the effect of uniaxial compression on GaAs nanowire solar cells was studied via conductive atomic force microscopy (C-AFM) supported by numerical simulation.

Control of Conductivity of InGaAs Nanowires by Applied Tension and Surface States.

The electronic properties of semiconductor AIIIBV nanowires (NWs) due to their high surface/volume ratio can be effectively controlled by NW strain and surface electronic states. We study the effect of applied tension on the conductivity of wurtzite InGaAs ( ∼ 0.8) NWs.

Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb).

Background: De novo assembling of large genomes, such as in conifers (~ 12-30 Gbp), which also consist of ~ 80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assembling such genomes lays in computing limitations of nucleotide sequence assembly programs (DNA assemblers). As a rule, modern assemblers are usually designed to assemble genomes with a length not exceeding the length of the human genome (3.

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus.

Background: Gray whale, Eschrichtius robustus (E. robustus), is a single member of the family Eschrichtiidae, which is considered to be the most primitive in the class Cetacea. Gray whale is often described as a "living fossil".

Apoptosis in differentiating C2C12 muscle cells selectively targets Bcl-2-deficient myotubes.

Muscle cell apoptosis accompanies normal muscle development and regeneration, as well as degenerative diseases and aging. C2C12 murine myoblast cells represent a common model to study muscle differentiation. Though it was already shown that myogenic differentiation of C2C12 cells is accompanied by enhanced apoptosis in a fraction of cells, either the cell population sensitive to apoptosis or regulatory mechanisms for the apoptotic response are unclear so far.

Identification of oxidation sites and covalent cross-links in metal catalyzed oxidized interferon Beta-1a: potential implications for protein aggregation and immunogenicity.

Oxidation via Cu(2+)/ascorbate of recombinant human interferon beta-1a (IFNβ1a) leads to highly immunogenic aggregates, however it is unknown which amino acids are modified and how covalent aggregates are formed. In the present work we mapped oxidized and cross-linked amino acid residues in aggregated IFNβ1a, formed via Cu(2+)/ascorbate catalyzed oxidation. Size exclusion chromatography (SEC) was used to confirm extensive aggregation of oxidized IFNβ1a.