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.

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.

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.

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.

Direct calculation of cryo-EM and crystallographic model maps for real-space refinement.

This work addresses the problem of the calculation of limited-resolution maps from an atomic model in cryo-electron microscopy and in X-ray and neutron crystallography, including cases where the resolution varies from one molecular region to another. Such maps are necessary in real-space refinement for comparison with the experimental maps. For an appropriate numeric comparison, the calculated maps should reproduce not only the structural features contained in the experimental maps but also the principal map distortions.

Analytic modeling of inhomogeneous-resolution maps in cryo-electron microscopy and crystallography.

Refinement of macromolecular atomic models versus experimental maps in crystallography and cryo-electron microscopy is a critical step in structure solution. For an appropriate comparison, model maps should mimic the imperfections in the experimental maps, mainly atomic disorder and limited resolution, which are often inhomogeneous over the molecular region. In the suggested method, these model maps are calculated as the sum of atomic contributions expressed through a specifically designed function describing a solitary spherical wave.

Toward Real Real-Space Refinement of Atomic Models.

High-quality atomic models providing structural information are the results of their refinement versus diffraction data (reciprocal-space refinement), or versus experimental or experimentally based maps (real-space refinement). A proper real-space refinement can be achieved by comparing such a map with a map calculated from the atomic model. Similar to density distributions, the maps of a limited and even inhomogeneous resolution can also be calculated as sums of terms, known as atomic images, which are three-dimensional peaky functions surrounded by Fourier ripples.

Disulfiram Oxy-Derivatives Suppress Protein Retrotranslocation across the ER Membrane to the Cytosol and Initiate Paraptosis-like Cell Death.

Disulfiram (DSF) and its derivatives were here investigated as antineoplastic agents, and their important feature is the ability to influence the UPS. We have recently shown that hydroxocobalamin catalyzes the aerobic oxidation of diethyldithiocarbamate to form disulfiram and its oxy-derivatives (DSFoxy; i.e.

Shifts in the eye-centered frame of reference may underlie saccades, visual perception, and eye-hand coordination.

Conventional, computational theories limit the understanding of how action and perception are controlled. In an alternative scheme, the nervous system controls the values of physical and neurophysiological parameters that predetermine the choice of the spatial frames of reference (FRs) for action and perception. For example, all possible eye positions, Q, can be considered as comprising a spatial FR in which extraocular muscles (EOMs) stabilize gaze directions.

ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs.

We present ANANASTRA, https://ananastra.autosome.org, a web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events.

Molecular modelling and computational studies of peptide diphenylalanine nanotubes, containing waters: structural and interactions analysis.

The work is devoted to computer studies of the structural and physical properties of such self-organizing structures as peptide nanotubes (PNT) based on diphenylalanine (FF) dipeptide with different initial isomers of the left (L-FF) and right (D-FF) chiralities of these dipeptides. The structures under study are considered both with empty anhydrous and with internal cavities filled with water molecules. Molecular models of both chiralities are investigated using quantum-chemical DFT and semi-empirical methods, which are in consistent with the known experimental data.

Determination of the Most Stable Packing of Peptides from Ribosomal S1 Protein, Protein Bgl2p, and Aβ peptide in β-layers During Molecular Dynamics Simulations.

Our task was to determine the most stable packing of peptides in β-layers to construct an oligomer structure for fibril growth. The β-layers consisting of eight short peptides with the amino acid sequences IVRGVVVAID, VDSWNVLVAG (VESWNVLVAG), KLVFFAEDVG, and IIGLMVGGVV were built. These sequences correspond to the amyloidogenic regions of ribosomal S1 protein from E.

Ground beetles (Carabidae) in urban habitats of Kaluga City (Russia).

Background: Ground beetles (Carabidae, Coleoptera) are one of the most species-rich and well-studied insect families. However, the number of published datasets is disproportionately low against the biodiversity of this group. According to GBIF, only a fifth of the percentage of all published data covers ground beetles.

The extremely high diversity of Collembola in relict forests of Primorskii Krai of Russia.

Background: The diversity of soil animals of relict forest ecosystems in East Asia continues to be insufficiently studied and almost not represented in international databases, including GBIF. This article is based on 7550 records of 175 species which were collected in Ussuriiskii, Sikhote-Alinskii and Kedrovaya Pad' natural reserves of Russian Far East in 2016-2017. A multi-scale sampling design allowed us to estimate population densities and local species richness of Collembola at areas of different sizes.

Current Approaches in Supersecondary Structures Investigation.

Proteins expressed during the cell cycle determine cell function, topology, and responses to environmental influences. The development and improvement of experimental methods in the field of structural biology provide valuable information about the structure and functions of individual proteins. This work is devoted to the study of supersecondary structures of proteins and determination of their structural motifs, description of experimental methods for their detection, databases, and repositories for storage, as well as methods of molecular dynamics research.

Changes in Protein Structural Motifs upon Post-Translational Modification in Kidney Cancer.

Post-translational modification (PTM) leads to conformational changes in protein structure, modulates the biological function of proteins, and, consequently, changes the signature of metabolic transformations and the immune response in the body. Common PTMs are reversible and serve as a mechanism for modulating metabolic trans-formations in cells. It is likely that dysregulation of post-translational cellular signaling leads to abnormal proliferation and oncogenesis.

Proteomic and molecular dynamic investigations of PTM-induced structural fluctuations in breast and ovarian cancer.

Post-translational processing leads to conformational changes in protein structure that modulate molecular functions and change the signature of metabolic transformations and immune responses. Some post-translational modifications (PTMs), such as phosphorylation and acetylation, are strongly related to oncogenic processes and malignancy. This study investigated a PTM pattern in patients with gender-specific ovarian or breast cancer.

Pseudogap Isotope Effect as a Probe of Bipolaron Mechanism in High Temperature Superconductors.

A theory of a pseudogap phase of high-temperature superconductors where current carriers are translation invariant bipolarons is developed. A temperature T* of a transition from a pseudogap phase to a normal one is calculated. For the temperature of a transition to the pseudogap phase, the isotope coefficient is found.