Laboratory information systems for research management in biology.

Modern investigations in biology often require the efforts of one or more groups of researchers. Often these are groups of specialists from various scientific fields who generate and share data of different formats and sizes. Without modern approaches to work automation and data versioning (where data from different collaborators are stored at different points in time), teamwork quickly devolves into unmanageable confusion.

Impact of Negative Feedbacks on De Novo Pyrimidines Biosynthesis in .

Earlier studies aimed at investigating the metabolism of endogenous nucleoside triphosphates in synchronous cultures of cells revealed an auto-oscillatory mode of functioning of the pyrimidine and purine nucleotide biosynthesis system, which the authors associated with the dynamics of cell division. Theoretically, this system has an intrinsic oscillatory potential, since the dynamics of its functioning are controlled through feedback mechanisms. The question of whether the nucleotide biosynthesis system has its own oscillatory circuit is still open.

Agent-Based Modeling of Autosomal Recessive Deafness 1A (DFNB1A) Prevalence with Regard to Intensity of Selection Pressure in Isolated Human Population.

An increase in the prevalence of autosomal recessive deafness 1A (DFNB1A) in populations of European descent was shown to be promoted by assortative marriages among deaf people. Assortative marriages became possible with the widespread introduction of sign language, resulting in increased genetic fitness of deaf individuals and, thereby, relaxing selection against deafness. However, the effect of this phenomenon was not previously studied in populations with different genetic structures.

ICBrainDB: An Integrated Database for Finding Associations between Genetic Factors and EEG Markers of Depressive Disorders.

In this study, we collected and systemized diverse information related to depressive and anxiety disorders as the first step on the way to investigate the associations between molecular genetics, electrophysiological, behavioral, and psychological characteristics of people. Keeping that in mind, we developed an internet resource including a database and tools for primary presentation of the collected data of genetic factors, the results of electroencephalography (EEG) tests, and psychological questionnaires. The sample of our study was 1010 people from different regions of Russia.

The finding and researching algorithm for potentially oscillating enzymatic systems.

Many processes in living organisms are subject to periodic oscillations at different hierarchical levels of their organization: from molecular-genetic to population and ecological. Oscillatory processes are responsible for cell cycles in both prokaryotes and eukaryotes, for circadian rhythms, for synchronous coupling of respiration with cardiac contractions, etc. Fluctuations in the numbers of organisms in natural populations can be caused by the populations' own properties, their age structure, and ecological relationships with other species.

Salicylic Acid Affects Root Meristem Patterning via Auxin Distribution in a Concentration-Dependent Manner.

The phytohormone salicylic acid (SA) is well known for its induction of pathogenesis-related proteins and systemic acquired resistance; SA also has specific effects on plant growth and development. Here we analyzed the effect of SA on Arabidopsis () root development. We show that exogenous SA treatment at low (below 50 µM) and high (greater than 50 µM) concentrations affect root meristem development in two different PR1-independent ways.

MIGREW: database on molecular identification of genes for resistance in wheat.

Population structure of fungal infections in wheat differs between wheat varieties and environments. Taking into account evolution of host-pathogen interactions, genetic diversity of both wheat and fungus must be a monitored. In order to catalogue information to support need of wheat pathologists and breeders, who use conventional methods and Molecular Assisted Selection (MAS) techniques, we have developed the Molecular Identification of Genes for Resistance in Wheat (MIGREW) database.

Pluripotency gene network dynamics: System views from parametric analysis.

Multiple experimental data demonstrated that the core gene network orchestrating self-renewal and differentiation of mouse embryonic stem cells involves activity of Oct4, Sox2 and Nanog genes by means of a number of positive feedback loops among them. However, recent studies indicated that the architecture of the core gene network should also incorporate negative Nanog autoregulation and might not include positive feedbacks from Nanog to Oct4 and Sox2. Thorough parametric analysis of the mathematical model based on this revisited core regulatory circuit identified that there are substantial changes in model dynamics occurred depending on the strength of Oct4 and Sox2 activation and molecular complexity of Nanog autorepression.

MAMMOTh: A new database for curated mathematical models of biomolecular systems.

Motivation: Living systems have a complex hierarchical organization that can be viewed as a set of dynamically interacting subsystems. Thus, to simulate the internal nature and dynamics of the entire biological system, we should use the iterative way for a model reconstruction, which is a consistent composition and combination of its elementary subsystems. In accordance with this bottom-up approach, we have developed the MAthematical Models of bioMOlecular sysTems (MAMMOTh) tool that consists of the database containing manually curated MAMMOTh fitted to the experimental data and a software tool that provides their further integration.

Mathematical modeling of auxin transport in protoxylem and protophloem of Arabidopsis thaliana root tips.

Phytohormone auxin is the main regulator of plant growth and development. Nonuniform auxin distribution in plant tissue sets positional information, which determines morphogenesis. Auxin is transported in tissue by means of diffusion and active transport through the cell membrane.

Combined in silico/in vivo analysis of mechanisms providing for root apical meristem self-organization and maintenance.

Background And Aims: The root apical meristem (RAM) is the plant stem cell niche which provides for the formation and continuous development of the root. Auxin is the main regulator of RAM functioning, and auxin maxima coincide with the sites of RAM initiation and maintenance. Auxin gradients are formed due to local auxin biosynthesis and polar auxin transport.

[Hexokinase and lactate dehydrogenase activity, lactic and pyruvic acid content of erythrocytes and acid-base equilibrium in stomach cancer patients after radical operations].

Certain glycolytic enzymes, the level of end metabolites of glycolysis and acid-base equilibrium indices were studied in 106 patients with stomach tumors (stage II-III). It was found that prior to surgery metabolic disturbances in erythrocytes are to be observed, while acid-base indices tend toward metabolic acidosis. After radical surgery, the activity levels of hexokinase and lactate, dehydrogenase as well as concentrations of lactic and pyruvic acids are decreased, acid-base equilibrium being restored much earlier.

[Blood cholinergic activity during ketamine anesthesia].

Blood cholinergic activity in ketamine anesthesia was studied through the acetylcholine level and activity of true and pseudocholinesterase on 30 patients during surgical interventions which were not very traumatic. Ketamine was found to increase acetylcholine blood level and activity of cholinergic enzymes in the blood due to the rise of parasympathetic nervous system tone and to the absence of depressing effect of the anesthetic upon the renal function.