RatDEGdb: a knowledge base of differentially expressed genes in the rat as a model object in biomedical research.

The animal models used in biomedical research cover virtually every human disease. RatDEGdb, a knowledge base of the differentially expressed genes (DEGs) of the rat as a model object in biomedical research is a collection of published data on gene expression in rat strains simulating arterial hypertension, age-related diseases, psychopathological conditions and other human afflictions. The current release contains information on 25,101 DEGs representing 14,320 unique rat genes that change transcription levels in 21 tissues of 10 genetic rat strains used as models of 11 human diseases based on 45 original scientific papers.

Molecular-genetic pathways of hepatitis C virus regulation of the expression of cellular factors PREB and PLA2G4C, which play an important role in virus replication.

The participants of Hepatitis C virus (HCV) replication are both viral and host proteins. Therapeutic approaches based on activity inhibition of viral non-structural proteins NS3, NS5A, and NS5B are undergoing clinical trials. However, rapid mutation processes in the viral genome and acquisition of drug resistance to the existing drugs remain the main obstacles to fighting HCV.

Prioritization of potential pharmacological targets for the development of anti-hepatocarcinoma drugs modulating the extrinsic apoptosis pathway: the reconstruction and analysis of associative gene networks help.

Hepatocellular carcinoma (HCC) is a common severe type of liver cancer characterized by an extremely aggressive course and low survival rates. It is known that disruptions in the regulation of apoptosis activation are some of the key features inherent in most cancer cells, which determines the pharmacological induction of apoptosis as an important strategy for cancer therapy. The computer design of chemical compounds capable of specifically regulating the external signaling pathway of apoptosis induction represents a promising approach for creating new effective ways of therapy for liver cancer and other oncological diseases.

Studying sex differences in responses to fibroblast growth factor 21 administration in obese mice consuming a sweet-fat diet.

In animals, obesity caused by consumption of a sweet-fat diet (SFD) is the most adequate mouse model of human diet-induced obesity. Fibroblast growth factor 21 (FGF21) reduces body weight, beneficially affects taste preferences, and corrects glucose metabolism in obese mice. Sex is known to influence FGF21 effects in different models of diet-induced and hereditary obesity.

Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake Baikal.

DNA repeat composition of low coverage (0.1-0.5) genomic libraries of four amphipods species endemic to Lake Baikal (East Siberia) and four endemic gastropod species of the fam.

Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins.

Hepatitis C virus (HCV) is a risk factor that leads to hepatocellular carcinoma (HCC) development. Epigenetic changes are known to play an important role in the molecular genetic mechanisms of virus-induced oncogenesis. Aberrant DNA methylation is a mediator of epigenetic changes that are closely associated with the HCC pathogenesis and considered a biomarker for its early diagnosis.

A software system for modeling evolution in a population of organisms with vision, interacting with each other in 3D simulator.

Development of computer models imitating the work of the nervous systems of living organisms, taking into account their morphology and electrophysiology, is one of the important and promising branches of computational neurobiology. It is often sought to model not only the nervous system, but also the body, muscles, sensory systems, and a virtual three-dimensional physical environment in which the behavior of an organism can be observed and which provides its sensory systems with adequate data streams that change in response to the movement of the organism. For a system of hundreds or thousands of neurons, one can still hope to determine the necessary parameters and get the functioning of the nervous system more or less similar to that of a living organism - as, for example, in a recent work on the modeling of the Xenopus tadpole.

Small world of the miRNA science drives its publication dynamics.

Many scientific articles became available in the digital form which allows for querying articles data, and specifically the automated metadata gathering, which includes the affiliation data. This in turn can be used in the quantitative characterization of the scientific field, such as organizations identification, and analysis of the co-authorship graph of those organizations to extract the underlying structure of science. In our work, we focus on the miRNA science field, building the organization co-authorship network to provide the higher-level analysis of scientific community evolution rather than analyzing author-level characteristics.

FastContext: A tool for identification of adapters and other sequence patterns in next generation sequencing (NGS) data.

The development of next generation sequencing (NGS) methods has created the need for detailed analysis and control of each protocol step. NGS library preparation protocols may include steps with incorporation of various service sequences, such as sequencing adapters, primers, sample-, cell-, and molecule-specific barcodes. Despite a fairly high level of current knowledge, during the protocol development process researches often have to deal with various kinds of unexpected experiment outcomes, which result either from lack of information, lack of knowledge, or defects in reagent manufacturing.

Human phospholipases A2: a functional and evolutionary analysis.

Phospholipases A2 (PLA2) are capable of hydrolyzing the sn-2 position of glycerophospholipids to release fatty acids and lysophospholipids. The PLA2 superfamily enzymes are widespread and present in most mammalian cells and tissues, regulating metabolism, remodeling the membrane and maintaining its homeostasis, producing lipid mediators and activating inflammatory reactions, so disruption of PLA2-regulated lipid metabolism often leads to various diseases. In this study, 29 PLA2 genes in the human genome were systematically collected and described based on literature and sequence analyses.

Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family.

Many plants and animals have symbiotic relationships with microorganisms, including bacteria. The interactions between bacteria and their hosts result in different outcomes for the host organism. The outcome can be neutral, harmful or have beneficial effects for participants.

Molecular mechanisms of vascular tissue patterning in Arabidopsis thaliana L. roots.

A vascular system in plants is a product of aromorphosis that enabled them to colonize land because it delivers water, mineral and organic compounds to plant organs and provides effective communications between organs and mechanical support. Vascular system development is a common object of fundamental research in plant development biology. In the model plant Arabidopsis thaliana, early stages of vascular tissue formation in the root are a bright example of the self-organization of a bisymmetric (having two planes of symmetry) pattern of hormone distribution, which determines vascular cell fates.

The context signals of mitochondrial miRNAs (mitomiRs) of mammals.

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level in the cytoplasm and play an important role in a wide range of biological processes. Recent studies have found that the miRNA sequences are presented not only in the cytoplasm, but also in the mitochondria. These miRNAs (the so-called mitomiRs) may be the sequences of nuclear or mitochondrial origin; some of them are involved in regulation of the mitochondrial gene functions, while the role of others is still unknown.

Stratifications and foliations in phase portraits of gene network models.

Periodic processes of gene network functioning are described with good precision by periodic trajectories (limit cycles) of multidimensional systems of kinetic-type differential equations. In the literature, such systems are often called dynamical, they are composed according to schemes of positive and negative feedback between components of these networks. The variables in these equations describe concentrations of these components as functions of time.

Earliness and morphotypes of common wheat cultivars of Western and Eastern Siberia.

The global and local climate changes determine the producing of highly-adaptive common (bread) wheat commercial cultivars of a new generation whose optimal earliness matches the climatic features of the territory where the cultivars are farmed. Principal component analysis involving our own and published data has been applied to investigate 98 commercial common wheat cultivars from Western and Eastern Siberia comparing their morphotypes; cultivar zoning time; length of the vegetation period; 1000-grain weight, and inheritance of spring growth habit. It demonstrated that the dominant Vrn gene polymorphism determining the spring growth habit of the Siberian cultivars was minimally polymorphic.

Psycho-emotional stress, folliculogenesis, and reproductive technologies: clinical and experimental data.

Modern life, especially in large cities, exposes people to a high level of noise, high density of population, disrupted sleeping, large amount of excessive and controversial information as well as to other negative factors; all this may cause chronic psycho-emotional stress. The latest publications often use the term "Syndrome of megalopolis", which means disruption of sleeping, high anxiety, and altered reproductive function. Medical treatment of infertility may also be considered as a stress factor, especially when infertility lasts for years and is aggravated with emotional frustration.

Neuronal density in the brain cortex and hippocampus in Clsnt2-KO mouse strain modeling autistic spectrum disorder.

Autistic spectrum disorders (ASD) represent conditions starting in childhood, which are characterized by diff iculties with social interaction and communication, as well as non-typical and stereotyping models of behavior. The mechanisms and the origin of these disorders are not yet understood and thus far there is a lack of prophylactic measures for these disorders. The current study aims to estimate neuronal density in the prefrontal cortex and four hippocampal subf ields, i.

Creation of transgenic mice susceptible to coronaviruses: a platform for studying viral pathogenesis and testing vaccines.

Over the past 20 years, coronaviruses have caused three epidemics: SARS-CoV, MERS-CoV, and SARS-CoV2, with the f irst two having a very high lethality of about 10 and 26 %, respectively. The last outbreak of coronavirus infection caused by SARS-CoV2 in 2019 in China has swept the entire planet and is still spreading. The source of these viruses in humans are animals: bats, Himalayan civets, and camels.

The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep.

In recent years, the number of genome-wide association studies (GWAS) carried out for various economically important animal traits has been increasing. GWAS discoveries provide summary statistics that can be used both for targeted marker-oriented selection and for studying the genetic control of economically important traits of farm animals. In contrast to research in human genetics, GWAS on farm animals often does not meet generally accepted standards (availability of information about effect and reference alleles, the size and direction of the effect, etc.

Characterization of demethylating DNA glycosylase ROS1 from Nicotiana tabacum L.

One of the main mechanisms of epigenetic regulation in higher eukaryotes is based on the methylation of cytosine at the C5 position with the formation of 5-methylcytosine (mC), which is further recognized by regulatory proteins. In mammals, methylation mainly occurs in CG dinucleotides, while in plants it targets CG, CHG, and CHH sequences (H is any base but G). Correct maintenance of the DNA methylation status is based on the balance of methylation, passive demethylation, and active demethylation.

Biochemical and technological properties of moose (Alces alces) recombinant chymosin.

Recombinant chymosins (rСhns) of the cow and the camel are currently considered as standard milk coagulants for cheese-making. The search for a new type of milk-clotting enzymes that may exist in nature and can surpass the existing "cheese-making" standards is an urgent biotechnological task. Within this study, we for the first time constructed an expression vector allowing production of a recombinant analog of moose chymosin in the expression system of Escherichia coli (strain SHuffle express).

Social behavior and spatial orientation in rat strains with genetic predisposition to catatonia (GC) and stereotypes (PM).

Various psychopathologies, including schizophrenia, bipolar disorder and major depression, are associated with abnormalities in social behavior and learning. One of the syndromes that may also take place in these disorders is catatonia. Catatonia is a psychomotor syndrome in which motor excitement, stereotypy, stuporous state, including the phenomenon of "waxy flexibility" (catalepsy), can be observed.

Estradiol-dependent and independent effects of FGF21 in obese female mice.

The f ibroblast growth factor 21 (FGF21) synthesized in the liver, acting as a hormone, increases insulin sensitivity and energy expenditure. FGF21 administration has potent benef icial effects on obesity and diabetes in humans, cynomolgus monkey, and rodents. The therapeutic effects of FGF21 have been studied mainly in males.

Developmental and hormonal regulation of Arabidopsis thaliana ornithine-delta-aminotransferase.

Ornithine aminotransferase (OAT) catalyzes transfer of the delta-amino group from L-ornithine to oxo-glutarate. In plants, this reaction biochemically connects urea cycle, proline cycle, and polyamine biosynthesis pathway. OAT activity is shown to be associated with biotic and abiotic stress responses and nitrogen metabolism, but its physiological role is still unclear.

TCF7L2 gene polymorphism in populations of f ive Siberian ethnic groups.

Investigation of the frequencies of functionally signif icant gene variants in the context of medical biology and gene geography is a relevant issue for studying the genetic structure of human populations. The transition from a traditional to an urbanized lifestyle leads to a higher incidence of civilizational diseases associated with metabolic disorders, including type 2 diabetes mellitus. The goal of the present paper is to analyze the frequencies of functionally signif icant gene alleles in the metabolic prof iles of indigenous Siberian peoples to identify the gene pool resilience, evaluate the susceptibility of various ethnic groups to metabolic disorders under changing environmental conditions, and predict the epidemiological situation that may occur in the near future.