A combination of organic and inorganic cations in the synthesis of transition metal nitrates: preparation and characterization of canted rectangular Ising antiferromagnet (PyH)CsCo2(NO3)6

Pyridinium cesium cobalt nitrate, (PyH)CsCo2(NO3)6, obtained from a nitric acid solution crystallizes in the orthorhombic space group Pnma with unit cell parameters a = 8.6905(14) Å, b = 11.9599(18) Å, c = 18.386(3) Å, V = 1911.0(5) Å3, and Z = 4. It consists of [Co(NO3)3]- layers, in which each Co2+ ion is connected with four monodentate bridging NO3-groups and one bidentate terminal NO3-group, forming a corrugated rectangular net. Magnetization and specific heat measurements show that (PyH)CsCo2(NO3)6 undergoes a long-range canted antiferromagnetic ordering in two steps at TC1 = 5.0 K and TC2 = 2.6 K. The temperature dependence of the magnetic susceptibility and the field dependence of the magnetization measured for (PyH)CsCo2(NO3)6 show that it is an Ising antiferromagnet. In support of these observations, our DFT + U + SOC calculations show that the Co2+ ions of (PyH)CsCo2(NO3)6 have an easy-axis magnetic anisotropy with preferred spin orientation along the b-axis. To a first approximation, the spin lattice of (PyH)CsCo2(NO3)6 is a weakly alternating Ising antiferromagnetic chain (J1/J2 ∼ 0.85), and these chains interact weakly (J3/J2 ∼ 0.07) to form a rectangular Ising antiferromagnetic lattice. In agreement with the prediction for a rectangular Ising antiferromagnet by Onsager, (PyH)CsCo2(NO3)6 undergoes a long-range antiferromagnetic ordering.

Genome constitution and differentiation of subgenomes in Siberian and Far Eastern endemic species of the genus Elymus (Poaceae) according to the sequencing of the nuclear gene waxy

Fifty-three species of perennial grasses in the genus Elymus L. (Poaceae), which are widespread in Russia, are generally assumed to have three haplome combinations: StH, StY and StHY. The StH-genome species, endemic to Russia, remain the least studied. R. Mason-Gamer and co-authors have previously shown in a series of studies that a molecular phylogenetic analysis of the low-copy gene waxy (GBSS1) sequences significantly complements cytogenetic data on the genomic constitution and evolutionary relationships among both North American and Asian species of the genus Elymus. To determine the species’ genomic constitution and to evaluate the level of phylogenetic differentiation, we examined the GBSS1 gene in 18 species of Elymus from Siberia and the Russian Far East, including the fol- lowing 14 endemics: E. charkeviczii, E. jacutensis, E. kamczadalorum, E. komarovii, E. kronokensis, E. lenensis, E. macrourus, E. margaritae, E. subfibrosus, E. sajanensis, E. transbaicalensis, E. peschkovae, E. uralensis, and E. viridiglumis.PCR amplification products of GBSS1 gene fragments (including exons 9–14) were cloned and 6–8 clones per accession were sequenced. It appears that all the species studied have St and H subgenomic gene variations. The most significant differences between the subgenomic variants St and H were found in intron 13. The H subgenome contains a 21-bp-long deletion in intron 13 in all Elymus genotypes, probably derived from a common ancestor of the H and P genomes. Instead of this deletion, all St subgenomes have a relatively conservative sequence similar to that of the genus Pseudoroegneria, whose ancestor is considered to be the donor of the modern St subgenome for all Elymus species. Cluster phylogenetic analysis revealed differentiation in St and H subgenome sequences into two evolutionary variants: St1 vs. St2 and H1 vs. H2, respectively. Variants of the St and H subgenomes were found homologous to various modern species of the ancestral genera Pseudoroegneria and Hordeum: St1 to P. strigosa, St2 to P. spicata, H1 to H. jubatum, and H2 to H. californicum. The details of the relationships between Russian and North American species of the genus, as well as a number of microevolutionary interconnections in the group of boreal endemic species of Siberia and the Russian Far East were revealed. The new results obtained here are essential for the development of a phylogenetically oriented taxonomic system for the genus Elymus.

Assessment of the Phenylketonuria (PKU)-Associated Mutation p.R155H Biochemical Manifestations by Mass Spectrometry-Based Blood Metabolite Profiling

Homozygous siblings with different treatment histories represent an excellent model to study both the phenotypic manifestation of mutations and the efficacy of therapy. We compared phenylketonuria (PKU) manifestations in two different gender siblings who were homozygous carriers of a rare phenylalanine hydroxylase (PAH) mutation, p.R155H, subjected to different treatments. PKU caused by mild mutations may be easily underdiagnosed if the diagnosis is based solely on the phenylalanine (Phe) blood concentration. One of the described patients is an example of this diagnostic error. For reducing diagnostic errors, we suggest the use of more elaborate methods in screening practice, in particular mass spectrometric analysis of blood metabolites, the efficiency of which is demonstrated in the present study.

Interaction of copper with dinitrogen tetroxide in 1-butyl-3-methylimidazolium-based ionic liquids

Ionic liquids that are stable toward oxidation and nitration and are based on the 1-n-butyl-3-methylimidazloium cation (BMIm⁺) can be used as solvents and reaction media for copper dissolution in liquid dinitrogen tetraoxide N₂O₄.

Microbial Community Associated with Thioploca sp. Sheaths in the Area of the Posolski Bank Methane Seep, Southern Baikal

Bacterial mats formed by a colorless sulfur bacterium Thioploca sp. in the area of the Posolski Bank cold methane seep (southern Baikal) were -studied using electron microscopy and phylogenetic analysis. Morphologically the bacteria were identified as Thioploca ingrica.- Confocal microscopy of DAPI-stained samples revealed numerous rod-shaped, filamentous, and spiral microorganisms in the sheaths, as well as in- side and between the trichomes. Transmission electron microscopy revealed nonvacuolated bacteria and small cells-without cell envelopes within the sheath. Bacteria with pronounced intracytoplasmic membranes characteristic; of type I methanotrophs were observed at the outer side of the sheath. Based on analysis of the 16S rRNA gene sequences, the following phyla were idenified in the sheath community: Bacteroidetes, Nitro- spira, Chloroflexi, Planctomycetes, Verrucomicrobia,'y-, and 6-Proteobacteria, Euryarchaeota, Crenarchaeota, and Thaumarchaeota, as well as anammox bacteria. A hypothetical scheme of matter flows in the Lake Baikal bacterial mats was proposed based on the data on metabolism of the cultured homologues.

[Production of gaseous hydrocarbons by microbial communities of Lake Baikal bottom sediments]

Production of gaseous hydrocarbons by the microbial community of the Posolsky Bank methane seep bottom sediments (Southern Baikal) was studied at 4°C. Formation of both methane and a heavier gas- eous hydrocarbon, ethane, was detected in enrichment cultures. The highest methane concentrations (6.15 and 4.51 mmol L(-1)) were revealed in enrichments from the sediments from 55-cm depth incubated with-so- dium acetate and H2/CO2 gas mixture, respectively. A decrease in activity of aceticlastic methanogensand a decrease in methane concentration produced by hydrogenotrophic archaea occurred with depth. The highest concentration of ethane was revealed in enrichments from the microbial community of the layer close to gas hydrates (75 cm) incubated with CO2 as a substrate. According to analysis of the 16S rRNA gene fragments from the clone library, these enrichments were found to contain members of the phylum Crenarchaeota form- ing a separate cluster with members of the class Thermoprotei. The phylum Euryarchaeota was represented by nucleotide sequences of the organisms homologous to members of the orders Methanococcales, Methanosa- rcinales, and Thermoplasmatales.

[Microbial communities of the discharge zone of oil- and gas-bearing fluids in low-mineral Lake Baikal]

At the site of natural ingress of oil microbial diversity in the Central Baikal bottom sediments differing in the chemical composition of pore waters was studied by molecular biological techniques. The sediments saturated with oil and methane were found to contain members of 10 bacterial and 2 archaeal phyla. The oxidized sediment layer contained methanotrophic bacteria belonging to the Alphaproteobacteria, which had a specific structure of the pmoA gene and clustered together with uncultured methanotrophs from cold ecosystems. The upper sediment layer contained also oil-oxidizing bacteria and the alkB genes most colsely related to those of Rhodococcus. The microbial community of reduced sediments exhibited lower diversity and was represented mostly by the organisms involved in hydrocarbon biodegradation.

[Phenotypic variation of spermatogenesis and a search for associations with genetic polymorphism in 13 inbred mouse strains]

Adult mice of the BALB/cLac, PT, CBA/Lac, DD/He, A/He, SWR, NZB, GR, DBA/2J, CC57Br, C57 B1/6J, A/Sn, and YT inbred strains were tested for the count, motility, and morphology of sperms from the caudal region of the epididymis. The protein-coding regions of the cytochrome P450 aromatase (CYP19a1), estrogen receptor 2 (ESR2), steroidogenic factor 1 (Nr5a1), and sex-determining (Sry) gene were sequenced. A substantial genetic heterogeneity for the genes was observed, as well as a phenotypic variation in spermatogenetic parameters, but the variation was rather discordant. The specifics of the interstrain variation in spermatogenetic parameters indicated that a physiological compensatory mechanism increases certain spermatogenetic parameters when other ones are low to maintain male fertility at a level sufficient for successful reproduction. For instance, a high sperm production compensated for a low sperm motility in DD/He males. In the issue of the protein-coding regions sequencing of the analyzed genes, 16 various mutations were observed. The decreases in proportion of motile sperms and in their velocity were attributed to mutations (I63T and W133L) of the Sry gene in the DD/He strain.

[Mutation analysis of the phenylalanine hydroxylase gene of phenylketonuria patients of Kemerovskaya Oblast' and Saha Republic]

Phenylketonuria (PKU) associated mutations in phenylalanine hydroxylase (PAH) gene were identified by direct DNA sequencing in 46 PKU patients and members of their families from Kemerovskaya Region and Saha Republic. Mutations found included both widespread known mutations (R158Q, R252W, R261Q, P281L, IVS10-11G>A, R408W, IVS12+1G>A) and several rare mutations (IVS2+5G>A, R155H, Y168H, W187R, E221_D222>Efs, A342T, Y386C, IVS11+1G>C). We observed the increase in diversity of PKU-associated alleles in the populations studied, probably due to their complex mixed ethnic structure.

Superconductivity without nesting in LiFeAs

We have studied the electronic structure of the nonmagnetic LiFeAs (T(c)∼18  K) superconductor using angle-resolved photoemission spectroscopy. We find a notable absence of the Fermi surface nesting, strong renormalization of the conduction bands by a factor of 3, high density of states at the Fermi level caused by a van Hove singularity, and no evidence for either a static or a fluctuating order except superconductivity with in-plane isotropic energy gaps. Our observations suggest that these electronic properties capture the majority of ingredients necessary for the superconductivity in iron pnictides.

Weak superconducting pairing and a single isotropic energy gap in stoichiometric LiFeAs

We report superconducting (SC) properties of stoichiometric LiFeAs (T(c)=17 K) studied by small-angle neutron scattering (SANS) and angle-resolved photoemission (ARPES). Although the vortex lattice exhibits no long-range order, well-defined SANS rocking curves indicate better ordering than in chemically doped 122 compounds. The London penetration depth lambda(ab)(0)=210+/-20 nm, determined from the magnetic field dependence of the form factor, is compared to that calculated from the ARPES band structure with no adjustable parameters. The temperature dependence of lambda(ab) is best described by a single isotropic SC gap Delta(0)=3.0+/-0.2 meV, which agrees with the ARPES value of Delta(0)(ARPES)=3.1+/-0.3 meV and corresponds to the ratio 2Delta/k(B)T(c)=4.1+/-0.3, approaching the weak-coupling limit predicted by the BCS theory. This classifies LiFeAs as a weakly coupled single-gap superconductor.

Solid-density plasma nanochannel generated by a fast single ion in condensed matter

A plasma model of relaxation of a medium in heavy-ion tracks in condensed matter is proposed. The model is based on three assumptions: the Maxwell distribution of plasma electrons, localization of plasma inside the track nanochannel, and constant values of the plasma electron density and temperature during the x-ray irradiation. The model of multiple ionization of target atoms by a fast projectile ion is used to determine the initial conditions. An analysis of the results of the calculations performed makes it possible to define when the atomic relaxation model is a very rough approximation and the plasma relaxation model must be used. It is demonstrated that the plasma relaxation model adequately describes the x-ray spectra observed upon interaction of a fast ion with condensed target. The comparison with the experimental data justifies the reliability of the plasma relaxation model. Preassumptions of plasma relaxation model are validated by the molecular-dynamics simulation. An x-ray spectral method based on the plasma relaxation model is proposed for diagnostics of the plasma in fast ion tracks. The results obtained can be useful in examining the initial stage of defect formation in solids under irradiation with single fast heavy ions.

[Independent origin of rare Y168H mutation of human phenylalanine hydroxylase gene in Russia]

Mutation Y168H of the human phenylalanine hydroxylase (PAH) gene determining phenylketonuria was described only twice: in a patient from Catalonia (Spain) and by us in a patient from Western Siberia (Russia). The association of Y168H in these families with allelic variants of STR and VNTR repeats and a number of neutral point polymorphisms of the PHA gene (IVS3nt-22C > T, Q232Q, V245V, L385L) was studied in this work. The Y186H mutation in these families was found to be associated with different haplotypes. Strong linkage of the selected markers and the mutation region excludes recombination as a possible cause of association of Y168H with different haplotypes. It was concluded that Y168H occurred independently in different populations.

[Universal method for single nucleotide substitution identification]

A new approach to the identification of point mutations by allele-specific PCR was proposed. The mutation R408W of the human phenylalanine hydroxylase gene was used as a model. A high specificity of the approach was achieved by the use of primers partially complementary to the genomic DNA. Polyethylene glycol covalently attached to one of the allele-specific primers provides for the differential identification of the PCR products due to a change in electrophoretic mobility.

[Detection of the Bartonella DNA by the method of nested PCR in patients after tick bites in Novosibirsk region]

Arthropod-borne bacterial pathogen Bartonella DNA was detected in human blood cells after tick bites in summer 2003 and 2004 in Novosibirsk region by nested PCR with primers specific to groEL gene of HSP60 protein. Comparative assay of 190 p.b. of long PCR fragment revealed that the nucleotide sequences might belong to Bartonella henselae and Bartonella quintana.

[Identification of mutation of the phenylalanine hydroxylase gene using an automated DNA sequencer]

Mutations were studied in phenylalanine hydroxylase gene of phenylketonuria patients from Kemerovo oblast and Altaiskii krai (15 and 2 families, respectively). The following mutations were identified in exons of this gene: R408W, R261Q, R243Q, Y414C, Y386C, P281L, Y168H, R68S (lead to amino acid substitutions), R243X (leads to stop codon formation), and three splice site mutations (IVS12nt 1g-->a, IVS2nt-13t-->g, IVS7nt 1g-->a).

[False aneurysms of anastomoses after aorto-femoral reconstruction]

The results of clinical, microbiological and histological studies in 141 patients with complications of the aorto-femoral graft revascularization were analyzed. The main group consisted of 44 patients with false aneurysms of vascular anastomoses. The findings obtained show that in 91.3% of cases the alterations in the wall of the artery adjacent to the anastomosis with false aneurysms resulted from chronic inflammatory reaction, the most common pathogens being St. Aureus and St. epidermidis. The optimal variants of revascularization of the extremity after resection are proposed. In case of distal anastomotic pseudoaneurysm the surgical strategy depends on the primary localization of the false aneurysm.