Earthworm occurrence dataset extracted from Russian-language literature.

Background: Earthworms are one of the most important components of temperate ecosystems and groups of soil animals globally, but data on their distribution around the world are still incomplete and uneven. Northern Eurasia is a region for which available data on earthworm distribution is extremely poor. At the same time, generations of Soviet and Russian researchers have performed extensive research and accumulated a large amount of data on the distribution of earthworms in this vast region.

Exploring Compactness and Dynamics of Apomyoglobin.

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) approach has become a valuable analytical complement to traditional methods. HDX-MS allows the identification of dynamic surfaces in proteins. We have shown that the introduction of various mutations into the amino acid sequence of whale apomyoglobin (apoMb) leads to a change in the number of exchangeable hydrogen atoms, which is associated with a change in its compactness in the native-like condition.

Molecular dynamics of three different α-helices in ribosomal protein L25 from .

A true native protein state is realized in a water solution where proteins exhibit their dynamic properties important for the functioning. This is way we have analyzed the dynamics of α-helices inside ribosomal protein L25 from in a water solution. The dynamics of only main chain Cα-atoms have been simulated along the five independent trajectories at a total time 200ns.

Molecular self-assembled helix peptide nanotubes based on some amino acid molecules and their dipeptides: molecular modeling studies.

Context: The paper considers the features of the structure and dipole moments of several amino acids and their dipeptides which play an important role in the formation of the peptide nanotubes based on them. The influence of the features of their chirality (left L and right D) and the alpha-helix conformations of amino acids are taken into account. In particular, amino acids with aromatic rings, such as phenylalanine (Phe/F), and branched-chain amino acids (BCAAs)-leucine (Leu/L) and isoleucine (Ile/I)-as well as corresponding dipeptides (diphenylalanine (FF), dileucine (LL), and diisoleucine (II)) are considered.

The Role of Imitation, Primitives, and Spatial Referent Coordinates in Motor Control: Implications for Writing and Reading.

We review a body of literature related to the drawing and recognition of geometrical two-dimensional linear drawings including letters. Handwritten letters are viewed not as two-dimensional geometrical objects but as one-dimensional trajectories of the tip of the implement. Handwritten letters are viewed as composed of a small set of kinematic primitives.

The permeability of diamond and other microphase-separated morphologies in copolymer films.

A method is proposed for the theoretical assessment of potential membrane properties in materials based on microphase-separated block copolymer films subjected to the etching of one of the components. The concepts of topological permeability and connectivity contrast introduced by the authors are used to compare the percolation characteristics of simple cubic, diamond, and diamond-like morphologies compatible with the slit geometry and specified by a given distribution of the order parameter. The diamond-like morphology, which has the most promising transport characteristics, can be formed in a thin film of diblock copolymer AB placed on a chemically structured substrate.

Influence of Magnesium Source on the Mechanochemical Synthesis of Magnesium-Substituted Hydroxyapatite.

Magnesium, as one of the most abundant cations in the human body, plays an important role in both physiological and pathological processes. In this study, it was shown that a promising biomedical material, Mg-substituted hydroxyapatite (Mg-HA), can be synthesized via a fast mechanochemical method. For this method, the nature of magnesium-containing carriers was shown to be important.

Bifurcation analysis of multistability and hysteresis in a model of HIV infection.

The infectious disease caused by human immunodeficiency virus type 1 (HIV-1) remains a serious threat to hu- man health. The current approach to HIV-1 treatment is based on the use of highly active antiretroviral therapy, which has side effects and is costly. For clinical practice, it is highly important to create functional cures that can enhance immune control of viral growth and infection of target cells with a subsequent reduction in viral load and restoration of the immune status.

The Contribution of the Intestinal Microbiota to the Celiac Disease Pathogenesis along with the Effectiveness of Probiotic Therapy.

The development of many human disorders, including celiac disease (CD), is thought to be influenced by the microbiota of the gastrointestinal tract and its metabolites, according to current research. This study's goal was to provide a concise summary of the information on the contribution of the intestinal microbiota to the CD pathogenesis, which was actively addressed while examining the reported pathogenesis of celiac disease (CD). We assumed that a change in gluten tolerance is formed under the influence of a number of different factors, including genetic predisposition and environmental factors.

Stochastic model for the transfer of gaseous particles in polymer-carbon-nanotube nanocomposites with interfacial regions.

In this work, a stochastic model of gaseous transfer in polymer-carbon-nanotube (CNT) nanocomposites is presented. The model takes into account interfacial areas, i.e.

Structure and Mechanical Response of Polybutylcarbosilane Dendrimers Confined in a Flat Slit: Effect of Molecular Architecture and Generation Number.

Due to the absence of specific interactions, carbosilane dendrimers are ideal models to study the effect of a hyperbranched regular structure on the molecular response to external influences. In this work, we have studied the conformational behavior of single polybutylcarbosilane dendrimers under confinement between impermeable flat surfaces using atomistic molecular dynamics simulations. Dendrimers of different generations belonging to two homologous series with a tetra-functional core and three- and four-functional branches were simulated.

Biodistribution of Mesenchymal Stromal Cells Labeled with [Zr]Zr-Oxine in Local Radiation Injuries in Laboratory Animals.

Background: Tracking the migration pathways of living cells after their introduction into a patient's body is a topical issue in the field of cell therapy. Questions related to studying the possibility of long-term intravital biodistribution of mesenchymal stromal cells in the body currently remain open.

Methods: Forty-nine laboratory animals were used in the study.

Multiple Non-Canonical Base-Stacking Interactions as One of the Major Determinants of RNA Tertiary Structure Organization.

Stacking interactions of heterocyclic bases of ribonucleotides are one of the most important factors in the organization of RNA secondary and tertiary structure. Most of these (canonical) interactions are formed between adjacent residues in RNA polynucleotide chains. However, with the accumulation of data on the atomic tertiary structures of various RNAs and their complexes with proteins, it has become clear that nucleotide residues that are not adjacent in the polynucleotide chains and are sometimes separated in the RNA primary structure by tens or hundreds of nucleotides can interact via (non-canonical) base stacking.

Effect of Magnesium Substitution on Structural Features and Properties of Hydroxyapatite.

Hydroxyapatite (HAP) is the main mineral component of bones and teeth. It is widely used in medicine as a bone filler and coating for implants to promote new bone growth. Ion substitutions into the HAP structure highly affect its properties.

The Fate and Functionality of Alien tRNA Fragments in Culturing Medium and Cells of .

Numerous observations have supported the idea that various types of noncoding RNAs, including tRNA fragments (tRFs), are involved in communications between the host and its microbial community. The possibility of using their signaling function has stimulated the study of secreted RNAs, potentially involved in the interspecies interaction of bacteria. This work aimed at identifying such RNAs and characterizing their maturation during transport.

Molecular Dynamics Simulation of Self-Assembly Processes of Diphenylalanine Peptide Nanotubes and Determination of Their Chirality.

In this work, we further developed a new approach for modeling the processes of the self-assembly of complex molecular nanostructures using molecular dynamics methods; in particular, using a molecular dynamics manipulator. Previously, this approach was considered using the example of the self-assembly of a phenylalanine helical nanotube. Now, a new application of the algorithm has been developed for implementing a similar molecular dynamic self-assembly into helical structures of peptide nanotubes (PNTs) based on other peptide molecules-namely diphenylalanine (FF) molecules of different chirality L-FF and D-FF.

Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation.

In X-ray crystallography and cryo-EM, experimental maps can be heterogeneous, showing different level of details in different regions. In this work we interpret heterogeneity in terms of two parameters, assigned individually for each atom, combining the conventional atomic displacement parameter with the resolution of the atomic image in the map. We propose a local real-space procedure to estimate the values of these heterogeneity parameters, assuming that a fragment of the density map and atomic positions are given.

Comparison of deep learning models with simple method to assess the problem of antimicrobial peptides prediction.

Antibiotic-resistant strains are an emerging threat to public health. The usage of antimicrobial peptides (AMPs) is one of the promising approaches to solve this problem. For the development of new AMPs, it is necessary to have reliable prediction methods.

Molecular dynamics of α-helical structure: poly-l-glutamic acid.

Communicated by Ramaswamy H. Sarma.

The Strategies of Development of New Non-Toxic Inhibitors of Amyloid Formation.

In recent years, due to the aging of the population and the development of diagnostic medicine, the number of identified diseases associated with the accumulation of amyloid proteins has increased. Some of these proteins are known to cause a number of degenerative diseases in humans, such as amyloid-beta (Aβ) in Alzheimer's disease (AD), α-synuclein in Parkinson's disease (PD), and insulin and its analogues in insulin-derived amyloidosis. In this regard, it is important to develop strategies for the search and development of effective inhibitors of amyloid formation.

Structural and functional analysis of actin point mutations leading to nemaline myopathy to elucidate their role in actin function.

In this work, we analyzed 78 mutations in the actin protein that cause the disease nemaline myopathy. We analyzed how these mutations are distributed in important regions of the actin molecule (folding nucleus, core of the filament, amyloidogenic regions, disordered regions, regions involved in interaction with other proteins). It was found that 54 mutations (43 residues) fall into the folding nucleus ( ≥ 0.

Molecular Dynamics Simulation of the Thermal Behavior of Hydroxyapatite.

Hydroxyapatite (HAP) is the main mineral component of bones and teeth. Due to its biocompatibility, HAP is widely used in medicine as a filler that replaces parts of lost bone and as an implant coating that promotes new bone growth. The modeling and calculations of the structure and properties of HAP showed that various structural defects have a significant effect on the properties of the material.