Vol 63, No 3 (2018)

The problem of storage of the sequences of a number of closely related genomes and analysis of genome variations is considered. A genome graph with the structure of an acyclic directed graph is used to store matching sections of sequences and known variants. An algorithm for rapid mapping of reads to the genome graph is developed to align the individual nucleotide sequence fragments to the genome graph. The algorithm combines rapid searching using hash tables with the algorithm of dynamic programming and solves the problem of exponential growth in the number of paths on the graph. The implementation of the genome graph and the algorithm of the alignment of reads is developed. A comparison with the best-known programs with similar functionality is made.

In this paper, we considered the optimization of the magnetic-resonance imaging properties of nanosystems that are based on ultrasmall nanoparticles of complex iron oxide by modifying their chemical composition with Zn, Mn, Mg, or Co. The relationship between the chemical composition, crystal structure, magnetic phase, and contrast-imaging properties of the nanoparticles was investigated. The comparative cytotoxicity of the nanoparticle solutions on HeLa cells was studied. The prospects for these types of nanosystems for the development of contrast MRI agents with the predominant effect on the T1 or T2 parameters of the body tissues were shown.

Seasonal changes in the levels of phospholipids, diglycerides, cholesterol, and total protein in the blood plasma were investigated during hibernation of the long-tailed ground squirrel Spermophilus undulatus. During the winter period, the levels of phosphatidylcholine, phosphatidylinositol, phosphatidylethanolamine, lysophosphatidylcholine, and sphingomyelin phospholipids (per 1 mg of plasma protein) were increased in both torpid and active ground squirrels by 70–80, 50, 600–700, 70, and 150–200%, respectively; the level of phosphatidylserine did not change in comparison to the summer period. The plasma phospholipid composition differed between hibernating and active summer animals: in winter, the phosphatidylcholine mol % decreased by 20%, phosphatidylinositol and phosphatidylethanolamine increased by 3–4 times, and the phosphatidylserine mol % decreased by 50%, while sphingomyelin and lysophosphatidylcholine did not change in comparison to summer animals. In hibernating ground squirrels, the plasma cholesterol levels increased by two times, the diglyceride content diminished by 60%, and the level of protein (in milligrams per 1 mL plasma) increased by 20%. The simultaneous increase in the levels of cholesterol and total phospholipids, as well as the pronounced specific changes in the levels of individual phospholipids in the blood plasma of hibernating ground squirrels, indicate the involvement of plasma lipoprotein lipids in the molecular mechanisms of adaptation to natural hypobiosis in mammals and a possible role of these mechanisms in systemic reactions to damaging factors.

Exposure of the purple bacteria Rhodobacter sphaeroides MDC6522 isolated from Jermuk mineral springs (Armenia) to extremely high-frequency electromagnetic radiation (51.8 and 53.0 GHz) for 15 min resulted in a pronounced increase in the specific growth rate and H₂ photoemission. However, a significant decrease in the specific growth rate (1.6–2.0 times) was observed when the duration of irradiation was prolonged to 1 h. The maximum effect was at a frequency of 53.0 GHz. During irradiation for 1 h, absorption maxima typical of carotenoids gradually disappeared, and the level of bacteriochlorophyll а complexes decreased. Prolonged irradiation also inhibited the H₂ production during bacterial growth for 72 h, although it was restored after 96 h of growth. The activity of N,N'-dicyclohexylcarbodiimide-sensitive proton F₀F₁- ATPase also decreased in Rh. sphaeroides. These results indicate that the membrane-bound F₀F₁-ATPase may be the main target of action of extremely-high-frequency electromagnetic radiation. The data we obtained can be used in biotechnology for control of growth and hydrogen metabolism of phototrophic bacteria.

Exposure of mouse peritoneal neutrophils to hypomagnetic conditions (magnetic shielding, a residual static magnetic field of 20 nT) for 1.5 h decreased the level of intracellular reactive oxygen species as recorded by changes in the fluorescence intensity of 2,7-dichlorodihydrofluorescein and dihydrorhodamine 123 oxidation products. The effect of a hypomagnetic field was similarly observed after adding a respiratory burst activator (the formylated peptide N-formyl–Met–Leu–Phe or phorbol 12-meristate-13-acetate) to a low concentration.

The probability of determining the effects of amoxicillin, which is one of β-lactam antibiotics, on microbial cells of Escherichia coli by the electroacoustic analysis method was shown for the first time. A piezoelectric resonator with a lateral electric field with a 1-mL liquid container was used as a biological sensor. It has been established that in the presence of amoxicillin the frequency dependence of the real and imaginary parts of the electrical impedance of a resonator loaded with a suspension of sensitive cells differs significantly from those of the resonator with a control of a microbial cell suspension without an antibiotic. When the resonator is loaded with the amoxicillin-resistant cell suspension, these dependencies are virtually the same. These results open prospects for the use of electroacoustic analysis methods to register the effect of β-lactam antibiotics on microbial cells and evaluate their antibacterial activity.

The effect of helium on cell survival during cryopreservation was studied using the HeLa and L929 cell lines. Cell suspensions were incubated in an atmosphere of helium, nitrogen, or air and frozen in the presence or absence of glycerol as a cryoprotectant. After thawing, the cell viability was evaluated by the Trypan Blue exclusion test and culture development for 18 h. Helium was found to provide better preservation of cell suspensions compared with nitrogen and air. The positive effect of helium was the greatest in the case of freezing without cryoprotectants (the HeLa cell survival increased by a factor of 1.5–2) and somewhat lower in the case of freezing in the presence of low glycerol concentrations (the L929 cell survival increased by a factor of 1.2–1.5 in the presence of 3% glycerol). Use of helium for cell suspensions may improve cryopreservation methods by making it possible to reduce the concentrations of conventional cryoprotectants, which are generally highly toxic and undesirable to use for cryopreservation of biological material for medical applications.

This review summarizes published data and original findings on the morphology of neurons and glial cells in normal conditions and model conditions that simulate those in the human brain during stroke. Ultrastructural changes that occur in the presence of high concentrations of glutamate (Glu, 0.1–5.0 M) and the NO-generating compound NaNO₂ (0.1–5.0 mM) were studied in the cerebella (frog cerebellum), which is one of the simplest circuitries structurally. Such studies and data analyses are important because hyperstimulation of Glu receptors is a leading pathogenetic factor of neuronal damage during a stroke. High Glu concentrations exert a toxic effect and damage cerebellar neurons and glial cells. Mitochondria are de-energized, ionic homeostasis is distorted, the intracellular Ca²⁺ concentration increases, and constitutive NO synthases are activated in the process. The changes result in an increase in the contents of NO and its transformation products, which are involved in a negative feedback mechanism from postsynaptic neurons to presynaptic cells. Biochemical processes are consequently affected, and morphological changes are induced in neurons and glial cells, leading to their swelling. At the same time, ultrastructural compensatory adaptive mechanisms develop to reduce the damaging effect of high concentrations of Glu and NO-generating compounds.

A static electric charge that foraging bees gain by rubbing their body parts against the substrate surface plays a role in social communication of bees. Vibrations of the charged body of a forager with a frequency of approximately 14 Hz indicate the location of the forager bee in a rich variety of bees within a poorly lit nest. The perception of vibrations of the charged ventral body surface of a forager occurs due to the antennal sensory organs of hive mates. An electric charge produced as the foraging bee moves its wings enhances vibrations of the trichoid sensilla, which act as mechanoreceptors. This provides reliable communication between foraging bees and their hive mates.

This paper reports on a comparison of the extent of length-dependent activation of contraction in the right ventricle myocardium in healthy rats and rats with monocrotaline-induced heart failure on two levels of heart-tissue organization, that is, muscle stripes and isolated cardiomyocytes, within the framework of a single study. It has been shown that a deficiency in the length-dependent increase in the contractile force produced by failing myocardium when expressed in quantitative terms is similar at both levels of organization of myocardial tissue. These findings indicate that the mechanisms of length-dependent regulation of myocardial contractility in the failing heart are suppressed mainly at the cellular level. In muscle strips, the deficiency of the length–tension relationship appears to be more pronounced, most likely because the spatial organization of myocytes affects the integral contractile response of the muscle.

A model of changes in the intracellular conductivity of the myocardium due to its deformation was developed. Macroconductivities were derived using the microstructure-based model proposed by Hand et al. (2009), where the heart tissue was considered as a periodic grid, the cells were rectangular prisms filled with conducting fluid, and the conductivity of gap-junctions was represented through boundary conditions on the sides of these prisms. In deriving the dependence of conductivities on deformation, some generalizations associated with the layered fiber structure for the tissue and nature of deformation were used. Furthermore, it was assumed that the cytoplasm is an isotropic electrolyte with deformation-independent conductivity, conductivities of gap junctions are constant, and cell deformation is the same as the tissue macrodeformation. Using the homogenization method, conductivity values were expressed analytically through the cell size, parameters of the grid periodicity, and electrical properties of the myoplasm and gap junctions. On the basis of these data, the dependence of the conductivity on tissue deformation was shown. First, we considered a simple model where the deformation is a tension–compression along the axes of the material. A model for a general case of deformation was then developed. Finally, this model was generalized in order to take the microstructural anisotropy of the myoplasm into account. Our model was compared with the model proposed by F.V. Sachse. It was shown that both models can be well aligned for elongations in the range from 0.8 to 1.2.

The distribution of the antitumor drug aurumacryl (intraperitoneally injected at a dose of 100 mg/kg) in the bodies of animals with Lewis lung carcinoma was studied. The determination of aurumacryl in the tumors and organs (blood, liver, kidneys, lungs, spleen, and brain) of mice was carried out for 48 h by measuring the gold content in the test tissues using inductively coupled plasma mass spectrometry. We found the preferential accumulation of the drug in the kidneys with an extremely low gold content in the brain and a relatively uniform distribution of aurumacryl between the tumor, liver, lung, and spleen tissues.

The accurate reading of two variants of genetic informatio n is mandatory to perform the ontogenetic program in highly organized multicellular organisms. Physicochemical differences between different portions of the cytoplasm of an egg are insufficient to discriminate these variants. A.A. Ivanov has shown that the formation of differences in the ¹³C isotope content of the DNA copies at early embryological stages is essential for the successful completion of development. Consideration of this fact and the fifth fundamental interaction (the interaction of the spins of macroscopic objects) sheds light on the tremendous delay of the Cambrian explosion.