Analysis of mitochondrial DNA: Taxonomic and phylogenetic relationships in two fish taxa (Pisces: Mugilidae and Cyprinidae)

To solve some systematic questions as well as to study genetic variability and evolutionary relationships in two groups of fish belonging to the Mugilid (Mugilidae) and Cyprinid (Cyprinidae) families, we have used restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) fragments amplified in polymerase chain reaction. The analysis of three mtDNA fragments of 7220 bp total length of six Mugilid species has shown that Mediterranean Liza aurata, L. ramada, L. saliens, and Chelon labrosus form a common cluster, L. aurata and C. labrosus being the closest relatives, whereas L. haematocheilus (syn. C. haematocheilus) of the Sea of Japan forms a sister group to the Mediterranean cluster. It was found that Chelon and Liza genera are paraphyletic, and therefore their division into two genera is unnatural and they should be synonymized. According to priority, Liza species should be ascribed to Chelon genus. Mugil cephalus is the most distant compared to the rest of the species studied. The level of genetic divergence between allopatric samples of M. cephalus from the Sea of Japan and the Mediterranean Sea has proved to be very high—4.5% of nucleotide substitutions. The analysis of four mtDNA fragments of 9340 bp total length of six Cyprinid species has shown that L. waleckii is the most genetically distant. Pseudaspius leptocephalus is a sister group to Tribolodon species. All Tribolodon species form a common cluster with T. sachalinensis as a root. The remaining species form two branches, one of which includes T. nakamurai and T. brandtii, another one combines T. hakonensis and a new form of Tribolodon revealed that is close to T. hakonensis by its mtDNA (2.4% of nucleotide substitutions). This new form might be an independent species. Published in Russian in Biokhimiya, 2007, Vol. 72, No. 12, pp. 1651–1658.     

Comparative analysis of mitochondrial DNA variation in four species of Far Eastern redfins of the genus Tribolodon (Pisces, Cyprinidae)

The variability of mtDNA in four Far Eastern endemic species of the genus Tribolodon was studied in the significant part of their areas. There was no close relationship between the lifetime and the level of mtDNA variability. The relation between the population genetic structure and the level of amphidromic species was revealed. The presence of mtDNA phylogroup differed in three of the four species shows that there was a long period of independent intraspecific divergent evolution in the history of these species. This period falls on aproximately the same historical age, and, apparently, is caused by one and the same factors. The period was not enough long and ended in the integration of genetically independent units into a single species.     

Interrelations of the Autogenic Somatomotor Excitation of the Cardiac Activity in Developing Rats

In developing rats aged from newborns to 1.5 months, regularities were studied of the heart rate fluctuations associated with periodic bursts of the endogenous somatomotor excitation characteristic of early stages of postnatal ontogenesis of immature born animals. It has been established that decelerations predominate on the background of the motor bursts for the first week of life, whereas accelerations, since the beginning of the 3rd week. The heart rhythm changes can precede or lag behind the beginning of the motor excitation, which allows judging about the existence of two mechanisms of the interaction: about the heart reaction to motor activity and about the central drivers acting simultaneously on the both systems. Experiments with chronic desympathization and block of -adrenoreceptors indicate a participation of the sympathetic nervous system in formation of the motor-cardiac interaction.     

Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins

Here we present a systematic analysis of accessible surface areas and hydrogen bonds of 2554 globular proteins from four structural classes (all-α, all-β, α/β and α+β proteins) that is aimed to learn in which structural class the accessible surface area increases with increasing protein molecular mass more rapidly than in other classes, and what structural peculiarities are responsible for this effect. The beta structural class of proteins was found to be the leader, with the following possible explanations of this fact. First, in beta structural proteins, the fraction of residues not included in the regular secondary structure is the largest, and second, the accessible surface area of packaged elements of the beta-structure increases more rapidly with increasing molecular mass in comparison with the alpha-structure. Moreover, in the beta structure, the probability of formation of backbone hydrogen bonds is higher than that in the alpha helix for all residues of α+β proteins (the average probability is 0.73±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without proline) and α/β proteins, except for asparagine, aspartic acid, glycine, threonine, and serine (0.70±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without the proline residue). There is a linear relationship between the number of hydrogen bonds and the number of amino acid residues in the protein (Number of hydrogen bonds=0.678·number of residues-3.350).     

Molecular Analysis of Structural Abnormalities in Papillary Thyroid Carcinoma Genome

Rearrangements of the protooncogene RET (RET/PTC) and somatic mutations of the gene BRAF are the most common events in the etiopathogenesis of papillary thyroid carcinoma (PTC). The rates of RET/PTC rearrangements and BRAF mutations in different nodular formations of the thyroid gland (TG) have been estimated. Comparative expression analysis of the extracellular (EC) and tyrosine kinase (TK) domains of RET has shown that 14% (12 out of 85) of PTC cases are RET/PTC-positive, including one RFP/RET-, two RET/PTC3-, and seven RET/PTC1-positive tumors, as well as two unidentified chimeric RET/PTC oncogenes. The standard T1796A transversion in the gene BRAF has been found in 60% (55 out of 91) PTC cases with the use of amplification refractory mutation system–polymerase chain reaction (ARMS–PCR). Somatic mutation G1753A and deletion del1800_1811 have been identified in PTC for the first time. The absence of the BRAF mutations in RET/PTC-positive tumors allows these two genetic defects to be regarded as alternative mechanisms of the RAS–RAF–MEK–ERK mitogen-activated protein (MAP) kinase cascade activation in PTCs. In none of the three follicular thyroid carcinomas (FTCs), 11 follicular thyroid adenomas (FTAs), and 13 nodular goiters have either BRAF mutations or RET/PTC rearrangements been found. Thus, the RET/PTC chimeric oncogenes and BRAF somatic mutations are specific markers of PTC and can be used for the preoperative diagnosis of these tumors.     

Haloarcula marismortui archaellin genes as ecoparalogs

The genome of haloarchaeon Haloarcula marismortui contains two archaellin genes—flaA2 and flaB. Earlier we isolated and characterized two H. marismortui strains in that archaella consisting of FlaA2 archaellin (with a minor FlaB fraction) or of FlaB only. Both the FlaA2 and FlaB strains were motile and produced functional helical archaella. Thus, it may seem that the FlaA2 archaellin is redundant. In this study we investigated the biological roles of archaellin redundancy and demonstrated that FlaA2 archaellin is better adapted to more severe conditions of high temperature/low salinity, while FlaB has an advantage with increasing salinity. We used the thermodynamic data and bioinformatics sequence analysis to demonstrate that archaella formed by FlaA2 are more stable than those formed by FlaB. Our combined data indicate that the monomer FlaA2 archaellin is more flexible and leads to more compact and stable formation of filamentous structures. The difference in response to environmental stress indicates that FlaA2 and FlaB replace each other under different environmental conditions and can be considered as ecoparalogs.