L1 (LINE-1) retrotransposable elements provide a "fossil" record of the phylogenetic history of murid rodents

The single most difficult problem in phylogenetic analysis is deciding whether a shared taxonomic character is due to common ancestry or one that appeared independently due to convergence, parallelism, or reversion to an ancestral state. Mammalian L1 retrotransposons undergo periodic amplifications in which multiple copies of the elements are interspersed in the genome. Because these elements apparently are transmitted only by inheritance and are retained in the genome, a shared L1 amplification event can only be an inherited ancestral character. We propose that L1 amplification events can be an excellent tool for analyzing mammalian evolution and demonstrate here how we addressed several refractory problems in rodent systematics using L1 DNA as a taxonomic character.      

Structural insight into the molecular basis of polyextremophilicity of short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Thermococcus sibiricus

Biochemical analysis of enantioselective short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Thermococcus sibiricus (TsAdh319) revealed unique polyextremophilic properties of the enzyme – half-life of 1 h at 100 °C, tolerance to high salt (up to 4 M) and organic solvents (50% v/v) concentrations. To elucidate the molecular basis of TsAdh319 polyextremophilicity, we determined the crystal structure of the enzyme in a binary complex with 5-hydroxy-NADP at 1.68 Å resolution. TsAdh319 has a tetrameric structure both in the crystals and in solution with an intersubunit disulfide bond. The substrate-binding pocket is hydrophobic, spacious and open that is consistent with the observed promiscuity in substrate specificity of TsAdh319. The present study revealed an extraordinary number of charged residues on the surface of TsAdh319, 70% of which were involved in ion pair interactions. Further we compared the structure of TsAdh319 with the structures of other homologous short-chain dehydrogenases/reductases (SDRs) from thermophilic and mesophilic organisms. We found that TsAdh319 has the highest arginine and aspartate + glutamate contents compared to the counterparts. The frequency of occurrence of salt bridges on the surface of TsAdh319 is the highest among the SDRs under consideration. No differences in the proline, tryptophan, and phenylalanine contents are observed; the compactness of the protein core of TsAdh319, the monomer and tetramer organization do not differ from that of the counterparts. We suggest that the unique thermostability of TsAdh319 is associated with the rigidity and simultaneous “resilience” of the structure provided by a compact hydrophobic core and a large number of surface ion pairs. An extensive salt bridge network also might maintain the structural integrity of TsAdh319 in high salinity.     

The role of interphase prenucleolar bodies in the recovery of the nucleolar structure after reversible hypotonic treatment

Interphase prenucleolar bodies are globular bodies which accumulate in large numbers in the nucleoplasm of cultivated cells after hypotonic treatment and subsequent return to isotonic conditions; detailed studies of the role of these structures in the recovery of the nucleolus have not yet been performed. The limited mobility of interphase pronucleoli within the nucleus has been demonstrated. Exchange of the major nucleolar protein B23 between prenucleolar bodies and the surrounding nucleoplasm, rather than stable binding of this protein to the prenucleolar bodies, has been demonstrated using fluorescence recovery after photobleaching method. Gradual accumulation of B23 in the recovering nucleolus with concomitant disappearance of prenucleolar bodies has been demonstrated.     

Duration of Voluntary Breath Holding and Blood Parameters

Stange's and Genci's functional tests performed at rest and during exercise and blood tests have shown that the duration of voluntary breath holding depends on appearance in the blood of hypoxia, hypercapnia, and acidosis signs only after the influence of fatigue of respiratory muscles and respiratory center has become insufficient.     

Complex Molecular Diagnostics of Hemophilia A in Russian Patients

Russian Journal of Genetics - Hemophilia A is a frequent X-linked recessive blood clotting disorder. It is caused by mutations in the F8 gene (locus Xq28) and affects 1 in 5000 newborn boys. The...     

Transthyretin gene V30M,H90N,and (del9) mutations in cardiomyopathy patients from St. Petersburg

A search of transthyretin (TTR) gene mutations was performed in patients with cardiomyopathies from St. Petersburg. Mutations H90N, V30M and deletion (del9) of nucleotides GACTTCTCC in position 6776 from the start codon of the TTR gene (in position 98782 according to reference sequence AC079096 (NCBI) was found. The H90N mutation in the third exon of TTR gene was detected in a son of a cardiomyopathy patient and in his mother, which lacked any clinical manifestations. Mutation V30M in exon 2 of TTR gene was found in heterozygous in one of the probands. Deletion (del9) was revealed in a patient with cardiomyopathy and in his two daughters from different marriages, who had no clinical manifestations of the disease. All the mutations revealed in this study were previously identified in other populations.     

Self-organization of endoplasmic reticulum aggregates in cells with overexpression of nucleoporin POM121

The nuclear pore complexes are complex protein structures located in the nuclear envelope, where they control the nuclear-cytoplasmic transport, and inside the stacks of endoplasmic reticulum cisternae, annulate lamellae. After overexpression of some nucleoporins, numerous granules are visible in the cytoplasm. According to the published data, these granules are the annulate lamellae. In the current paper, the structural organization of POM121-containing granules was analyzed using correlative light and electron microscopy. The ultrastructural study demonstrates that POM121-containing granules are not annulate lamellae but aggregates of endoplasmic reticulum membranes. Thus, overexpressed POM121 is not able to induce the annulate lamella formation. The mechanisms of self-organization of non-functional structures (such as the aggregates of endoplasmic reticulum membranes described here) and possible involvement of these mechanisms in the formation of cellular structures are discussed.     

Perichromosomal layer proteins associate with chromosome scaffold and nuclear matrix throughout the cell cycle

According to the radial loop model of chromosome organization, a major role in the formation and maintenance of chromosomes is played by the residual structures (the nuclear matrix in interphase nuclei and the chromosome scaffold in metaphase chromosomes). However, in vivo microscopy has recently revealed that the components of these “static” structures are highly mobile and continuously exchanged between specific target sites and the nucleoplasm or cytoplasm. This contradiction between predicted stability and observed dynamics led us to reexamine the principles underlying the association of proteins with residual structures. In the present paper, we have analyzed the association of two perichromosomal layer proteins, pKi-67 and B23, with the residual structures. The results show that these two proteins are associated with residual structures throughout the cell cycle; only those structures change that contain proteins precipitated by 2 M NaCl (nucleoli, perichromosomal layer, prenucleolar bodies, cytoplasm of mitotic cells). Both pKi-67 and B23 remain associated with the nuclear matrix even when they are translocated to nucleoplasmic foci due to inhibitor action or hypotonic treatment. However, in most cases it remains possible to extract a structurally visible protein fraction with 2 M NaCl (protein distributed in nucleoplasm). One may suppose that the protein fraction associated with residual structures includes molecules interacting with their binding sites at the moment of permeabilization, while the free proteins are extracted (i.e., during the interaction with binding sites, these proteins form salt-resistant complexes; however, on diffusion the same proteins are extractable by the high-salt solution). The residual structures may be considered as a “snapshot” of all proteins transiently (or statically) bound to their target sites at the moment of permeabilization. The article is published in the original.     

Proteomic analysis of mitochondria from the Bos taurus heart. II. Identification of mitochondrial soluble proteins

A fraction of the so-called mitochondrial soluble proteins was obtained after the destruction of purified mitochondria by sonication according to the previously found approach to the identification of protein subsets of the Bos taurus heart proteome. A tryptic destruction of these proteins was achieved. Approximately half of the tryptic hydrolysate was separated into two fractions of cysteine-containing and cysteine-free peptides by covalent chromatography on Thiopropyl Sepharose 4B. The cysteine-containing peptides were modified by iodoacetamide. The peptides were mass-spectrometrically identified in all the three fractions of tryptic hydrolysate, and the proteins were searched for in the amino acid sequence databases. There were 213 unique proteins reliably identified.