Asymmetry of Motif Conservation Within Their Homotypic Pairs Distinguishes DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data.

Transcription factors (TFs) are the main regulators of eukaryotic gene expression. The cooperative binding of at least two TFs to genomic DNA is a major mechanism of transcription regulation. Massive analysis of the co-occurrence of overrepresented pairs of motifs for different target TFs studied in ChIP-seq experiments can clarify the mechanisms of TF cooperation.

Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation.

As an important part of lipid metabolism the liver produces large particles called very low density lipoproteins, filled mostly with triglyceride and cholesterol esters mixture. A large percentage of the mixture composition components has a melting point above physiological temperature. Thus solid cluster formation or phase transition could be expected.

[Genetic architecture of anterior abdominal wall hernias].

Objective: To analyze genome-wide studies devoted to polymorphisms of factors of anterior abdominal wall hernias, to study the association of the most common polymorphism In Russian population.

Material And Methods: Searching for literature data was carried out in the RSCI and PubMed databases. We enrolled national and foreign reports.

Developmental and Housekeeping Genes: Two Types of Genetic Organization in the Genome.

We developed a procedure for locating genes on polytene chromosomes and described three types of chromosome structures (gray bands, black bands, and interbands), which differed markedly in morphological and genetic properties. This was reached through the use of our original methods of molecular and genetic analysis, electron microscopy, and bioinformatics data processing. Analysis of the genome-wide distribution of these properties led us to a bioinformatics model of the genome organization, in which the genome was divided into two groups of genes.

Atomistic Mechanism of Friction-Force Independence on the Normal Load and Other Friction Laws for Dynamic Structural Superlubricity.

We explore dynamic structural superlubricity for the case of a relatively large contact area, where the friction force is proportional to the area (exceeding ∼100  nm^{2}) experimentally, numerically, and theoretically. We use a setup composed of two molecular smooth incommensurate surfaces: graphene-covered tip and substrate. The experiments and molecular dynamic simulations demonstrate independence of the friction force on the normal load for a wide range of normal loads and relative surface velocities.

[Onto-phylogenetic prerequisites for development of chronic cystitis in women].

Introduction: Urinary tract infections (UTIs) are among the most common bacterial infections. At the request "cystitis", there are 12,067 publications in the RSCI system (e.library) as of 10/08/2023 and 16,332 articles were screened in the Pubmed.

Detecting Microsatellite Instability in Endometrial, Colon, and Stomach Cancers Using Targeted NGS.

Purpose: To develop a method for testing the MSI based on targeted NGS.

Methods: Based on the results of previous studies, 81 microsatellite loci with high variability in MSI-H tumors were selected, and a method for calculating the MSI score was developed. Using the MSI score, we defined the MSI status in endometral (162), colon (153), and stomach (190) cancers.

[Chronic cystitis: how to prolong the relapse-free period?].

Introduction: Chronic cystitis predominates in the structure of urinary tract infections (UTIs). International guidelines are mainly focused on the treatment of acute uncomplicated cystitis; the approaches for managing patients with chronic cystitis has not been sufficiently developed.

Material And Methods: A total of 91 patients were included in prospective multicenter randomized comparative controlled study.

CisCross: A gene list enrichment analysis to predict upstream regulators in .

Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, made it possible for Arabidopsis. Here we re-processed raw DAP-seq data with MACS2, the most popular peak caller that leads among other ones according to quality metrics.

Motif models proposing independent and interdependent impacts of nucleotides are related to high and low affinity transcription factor binding sites in Arabidopsis.

Position weight matrix (PWM) is the traditional motif model representing the transcription factor (TF) binding sites. It proposes that the positions contribute independently to TFs binding affinity, although this hypothesis does not fit the data perfectly. This explains why PWM hits are missing in a substantial fraction of ChIP-seq peaks.

Microsatellite Instability in Russian Patients with Colorectal Cancer.

The aim of this study was to determine the characteristics of Russian patients with microsatellite instability (MSI) tumors. MSI in the tumor was determined in 514 patients with colon cancer using PCR and subsequent fragment analysis for five markers (NR21, NR24, BAT25, BAT26, and NR27). In the presence of microsatellite instability, the mismatch repair (MMR) system genes were examined using the NGS and MLPA methods to establish the diagnosis of Lynch syndrome.

Structure, Properties, and Phase Transformations of Water Nanoconfined between Brucite-like Layers: The Role of Wall Surface Polarity.

The interaction of water with confining surfaces is primarily governed by the wetting properties of the wall material-in particular, whether it is hydrophobic or hydrophilic. The hydrophobicity or hydrophilicity itself is determined primarily by the atomic structure and polarity of the surface groups. In the present work, we used molecular dynamics to study the structure and properties of nanoscale water layers confined between layered metal hydroxide surfaces with a brucite-like structure.

Computational Indicator Approach for Assessment of Nanotoxicity of Two-Dimensional Nanomaterials.

The increasing growth in the development of various novel nanomaterials and their biomedical applications has drawn increasing attention to their biological safety and potential health impact. The most commonly used methods for nanomaterial toxicity assessment are based on laboratory experiments. In recent years, with the aid of computer modeling and data science, several in silico methods for the cytotoxicity prediction of nanomaterials have been developed.

Collision of nanoparticles of covalently bound atoms: Impact of stress-dependent adhesion.

The impact of nanoparticles (NPs) composed of atoms with covalent bonding is investigated numerically and theoretically. We use recent models of covalent bonding of carbon atoms and elaborate a numerical model of amorphous carbon (a-C) NPs, which may be applied for modeling soot particles. We compute the elastic moduli of the a-C material which agree well with the available data.

[The use of complex herbal supplements for the prevention and treatment of urinary tract infections. The analysis of active components].

Urinary tract infections, especially recurrent cases, are caused by uropathogens, which, after repeated courses of antibiotic therapy, can develop antibiotic resistance, which requires a search for an alternative treatment strategy. In this regard, the restoration of nonspecific protective factors that normally prevent the adhesion and colonization of pathogens is of interest for clinicians. To date, scientific data has been accumulated about the anti-uropathogenic and antiadhesive activity of many plant extracts.

Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.

The most popular model for the search of ChIP-seq data for transcription factor binding sites (TFBS) is the positional weight matrix (PWM). However, this model does not take into account dependencies between nucleotide occurrences in different site positions. Currently, two recently proposed models, BaMM and InMoDe, can do as much.

[Protection of the prostate in conditions of chronic pelvis varicose].

Introduction: Chronic prostatitis is the most common urological disease. The morphological outcome of chronic inflammation is sclerosis, leading to the loss of functional active tissue. Venous congestion of the small pelvis can act as a trigger factor in the development of prostate sclerosis.

How risky is it to visit a supermarket during the pandemic?

We performed large-scale numerical simulations using a composite model to investigate the infection spread in a supermarket during a pandemic. The model is composed of the social force, purchasing strategy and infection transmission models. Specifically, we quantified the infection risk for customers while in a supermarket that depended on the number of customers, the purchase strategies and the physical layout of the supermarket.

Genetic and phenotypic characteristics of Russian patients with BRAF-mutated colorectal cancer.

Colorectal cancer (CRC) is one of the most common malignancies in the world. It's estimated about 1.8 M new CRC cases worldwide per year.

Unique Combination of Diamond-Blackfan Anemia and Lynch Syndrome in Adult Female: A Case Report.

We present an extremely rare clinical case of a 38-year-old Russian patient with multiple malignant neoplasms of the uterus and colon caused by genetically confirmed two hereditary diseases: Diamond-Blackfan anemia and Lynch syndrome. Molecular genetic research carried out by various methods (NGS, Sanger sequencing, aCGH, and MLPA) revealed a pathogenic nonsense variant in the gene: NM_000179.2: c.

SeqURE - a new copy-capture based method for sequencing of unknown Retroposition events.

Background: Retroelements (REs) occupy a significant part of all eukaryotic genomes including humans. The majority of retroelements in the human genome are inactive and unable to retrotranspose. Dozens of active copies are repressed in most normal tissues by various cellular mechanisms.

Computer-Aided Design of Boron Nitride-Based Membranes with Armchair and Zigzag Nanopores for Efficient Water Desalination.

Recent studies have shown that the use of membranes based on artificial nanoporous materials can be effective for desalination and decontamination of water, separation of ions and gases as well as for solutions to other related problems. Before the expensive stages of synthesis and experimental testing, the search of the optimal dimensions and geometry of nanopores for the water desalination membranes can be done using computer-aided design. In the present study, we propose and examine the assumption that rectangular nanopores with a high aspect ratio would demonstrate excellent properties in terms of water permeation rate and ion rejection.