Polarization Switching in 2D Nanoscale Ferroelectrics: Computer Simulation and Experimental Data Analysis.

The polarization switching kinetics of nanosized ferroelectric crystals and the transition between homogeneous and domain switching in nanoscale ferroelectric films are considered. Homogeneous switching according to the Ginzburg-Landau-Devonshire (LGD) theory is possible only in two-dimensional (2D) ferroelectrics. The main condition for the applicability of the LGD theory in such systems is its homogeneity along the polarization switching direction.

About electron transfer over long distances with tunable sub/supersonic velocities.

Provided in this paper is a theory of long-range electron transfer with near sound (supersonic or subsonic) velocity along one-dimensional crystal lattices. The theory represents the development of an earlier work by introducing Marcus formulation. To illustrate its application to a realistic case, the theory is used to offer an explanation of two puzzling observations made by Donovan and Wilson in transient photoconduction experiments with non-dopable perfectly crystalline polydiacetylene crystals in the presence of an electric field: transport velocity value close to sound velocity being independent of field for four orders of magnitude of field (10 V/m-10 V/m) and, in the low field values, an ultra-high mobility greater than 20 m/V s.

Amyloidogenic Propensities of Ribosomal S1 Proteins: Bioinformatics Screening and Experimental Checking.

Structural S1 domains belong to the superfamily of oligosaccharide/oligonucleotide-binding fold domains, which are highly conserved from prokaryotes to higher eukaryotes and able to function in RNA binding. An important feature of this family is the presence of several copies of the structural domain, the number of which is determined in a strictly limited range from one to six. Despite the strong tendency for the aggregation of several amyloidogenic regions in the family of the ribosomal S1 proteins, their fibril formation process is still poorly understood.

Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA-protein complexes.

Along with nucleobase pairing, base-base stacking interactions are one of the two main types of strong non-covalent interactions that define the unique secondary and tertiary structure of RNA. In this paper we studied two subfamilies of nucleobase-inserted stacking structures: (i) with any base intercalated between neighboring nucleotide residues (base-intercalated element, BIE, i + 1); (ii) with any base wedged into a hydrophobic cavity formed by heterocyclic bases of two nucleotides which are one nucleotide apart in sequence (base-wedged element, BWE, i + 2). We have exploited the growing database of natively folded RNA structures in Protein Data Bank to analyze the distribution and structural role of these motifs in RNA.

Super Secondary Structures of Proteins with Post-Translational Modifications in Colon Cancer.

New advances in protein post-translational modifications (PTMs) have revealed a complex layer of regulatory mechanisms through which PTMs control cell signaling and metabolic pathways, contributing to the diverse metabolic phenotypes found in cancer. Using conformational templates and the three-dimensional (3D) environment investigation of proteins in patients with colorectal cancer, it was demonstrated that most PTMs (phosphorylation, acetylation, and ubiquitination) are localized in the supersecondary structures (helical pairs). We showed that such helical pairs are represented on the outer surface of protein molecules and characterized by a largely accessible area for the surrounding solvent.

The Arg/N-Degron Pathway-A Potential Running Back in Fine-Tuning the Inflammatory Response?

Recognition of danger signals by a cell initiates a powerful cascade of events generally leading to inflammation. Inflammatory caspases and several other proteases become activated and subsequently cleave their target proinflammatory mediators. The irreversible nature of this process implies that the newly generated proinflammatory fragments need to be sequestered, inhibited, or degraded in order to cancel the proinflammatory program or prevent chronic inflammation.

Brain-related genes are specifically enriched with long phase 1 introns.

Intronic gene regions are mostly considered in the scope of gene expression regulation, such as alternative splicing. However, relations between basic statistical properties of introns are much rarely studied in detail, despite vast available data. Particularly, little is known regarding the relationship between the intron length and the intron phase.

[Relationship between the Interhelical Packing Angles and the Length of α-Helices in Proteins].

Mutual arrangement, or packing, of α-helices in proteins depends on several factors, but, tight packing and the chemical nature of the polypeptide chain are the most important. This study shows, for the first time, that the torsion packing angles between axes of α-helices depend on their length. A database of helical pairs formed by two connected and juxtaposed α-helices has been compiled using the Protein Data Bank.

Novel Apoptotic Mediators Identified by Conservation of Vertebrate Caspase Targets.

Caspases are proteases conserved throughout Metazoans and responsible for initiating and executing the apoptotic program. Currently, there are over 1800 known apoptotic caspase substrates, many of them known regulators of cell proliferation and death, which makes them attractive therapeutic targets. However, most caspase substrates are by-standers, and identifying novel apoptotic mediators amongst all caspase substrates remains an unmet need.

Significance of Beta-Band Oscillations in Autism Spectrum Disorders During Motor Response Inhibition Tasks: A MEG Study.

In Autism Spectrum Disorders (ASD), impaired response inhibition and lack of adaptation are hypothesized to underlie core ASD symptoms, such as social communication and repetitive, stereotyped behavior. Thus, the aim of the present study was to compare neural correlates of inhibition, post-error adaptation, and reaction time variability in ASD and neuro-typical control (NTC) participants by investigating possible differences in error-related changes of oscillatory MEG activity. Twelve male NTC (mean age 20.

Author Correction: Chronicles of nature calendar, a long-term and large-scale multitaxon database on phenology.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Effects of generation number, spacer length and temperature on the structure and intramolecular dynamics of siloxane dendrimer melts: molecular dynamics simulations.

The structure and properties of polysiloxane dendrimer melts are studied by extensive atomistic molecular dynamics simulations. Two homologous series differing in the spacer length are considered. In the first series the dendrimer spacers are the shortest ones, comprising only one oxygen atom, while in the second series the spacers consist of two oxygen atoms with the silicon atom in between.

Disordered Residues and Patterns in the Protein Data Bank.

We created a new library of disordered patterns and disordered residues in the Protein Data Bank (PDB). To obtain such datasets, we clustered the PDB and obtained the groups of chains with different identities and marked disordered residues. We elaborated a new procedure for finding disordered patterns and created a new version of the library.

A Population Model of Deep Brain Stimulation in Movement Disorders From Circuits to Cells.

For more than 30 years, deep brain stimulation (DBS) has been used to target the symptoms of a number of neurological disorders and in particular movement disorders such as Parkinson's disease (PD) and essential tremor (ET). It is known that the loss of dopaminergic neurons in the substantia nigra leads to PD, while the exact impact of this on the brain dynamics is not fully understood, the presence of beta-band oscillatory activity is thought to be pathological. The cause of ET, however, remains uncertain, however pathological oscillations in the thalamocortical-cerebellar network have been linked to tremor.

Chronicles of nature calendar, a long-term and large-scale multitaxon database on phenology.

We present an extensive, large-scale, long-term and multitaxon database on phenological and climatic variation, involving 506,186 observation dates acquired in 471 localities in Russian Federation, Ukraine, Uzbekistan, Belarus and Kyrgyzstan. The data cover the period 1890-2018, with 96% of the data being from 1960 onwards. The database is rich in plants, birds and climatic events, but also includes insects, amphibians, reptiles and fungi.

Unique -mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling.

The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker -mers turned out to be capable of identifying not only species, but also strains of microorganisms with known genomes. Here, we evaluated the ability of genus-specific -mers to distinguish eight phylogroups of (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn's disease.

How Quickly Do Proteins Fold and Unfold, and What Structural Parameters Correlate with These Values?

The correlations between the logarithm of the unfolding rate of 108 proteins and their structural parameters were calculated. We showed that there is a good correlation between the logarithm of folding and unfolding rates (0.79) and protein stability and unfolding rate (0.

YB-3 substitutes YB-1 in global mRNA binding.

Y-box binding proteins are DNA- and RNA-binding proteins with an evolutionarily ancient and conserved cold shock domain. The Y-box binding protein 1 (YB-1) is the most studied due to its abundance in somatic cells. YB-1 is involved in a variety of cellular processes, including proliferation, differentiation and stress response.

Discrete-breather-assisted charge transport along DNA-like molecular wires.

Mobile discrete breathers (MDBs) are here suggested as localized excitations underlying the trapping and transport of charged particles (electron or hole) along a DNA-like molecular wire with anchored ends such as attached to two electrodes. For illustration the Peyrard-Bishop-Dauxois-Holstein (PBDH) model is used. MDBs are excited by imposing appropriate disturbances to velocities or space positions of adjacent nucleotide pairs or lattice units of the wire.

Stochastic models for description of structural-statistical properties in DNA sequences.

New stochastic models based on a notion of stochastic codon are proposed. These models, presented by special random strings, describe practical structural-statistical properties which are peculiar to coding DNA both from prokaryotic and eukaryotic genomes. In such the case coding regions are considered as the realizations of random strings.

Minor C allele of the SNP rs7873784 associated with rheumatoid arthritis and type-2 diabetes mellitus binds PU.1 and enhances TLR4 expression.

Toll-like receptor 4 (TLR4) is an innate immunity receptor predominantly expressed on myeloid cells and involved in the development of various diseases, many of them with complex genetics. Here we present data on functionality of single nucleotide polymorphism rs7873784 located in the 3'-untranslated region (3'-UTR) of TLR4 gene and associated with various pathologies involving chronic inflammation. We demonstrate that TLR4 3'-UTR strongly enhanced the activity of TLR4 promoter in U937 human monocytic cell line while minor rs7873784(C) allele created a binding site for transcription factor PU.

What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants.

Many problems of modern genetics and functional genomics require the assessment of functional effects of sequence variants, including gene expression changes. Machine learning is considered to be a promising approach for solving this task, but its practical applications remain a challenge due to the insufficient volume and diversity of training data. A promising source of valuable data is a saturation mutagenesis massively parallel reporter assay, which quantitatively measures changes in transcription activity caused by sequence variants.

Global distribution of earthworm diversity.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass.

After-effects of 10 Hz tACS over the prefrontal cortex on phonological word decisions.

Introduction: Previous work in the language domain has shown that 10 Hz rTMS of the left or right posterior inferior frontal gyrus (pIFG) in the prefrontal cortex impaired phonological decision-making, arguing for a causal contribution of the bilateral pIFG to phonological processing. However, the neurophysiological correlates of these effects are unclear. The present study addressed the question whether neural activity in the prefrontal cortex could be modulated by 10 Hz tACS and how this would affect phonological decisions.