The Structural Arrangement and Relative Abundance of Aliphatic Units May Effect Long-Wave Absorbance of Natural Organic Matter as Revealed by 1H NMR Spectroscopy.

The objective of this study was to shed light on structural features which underlay intensity of long wave absorbance of natural organic matter (NOM) using 1H NMR spectroscopy. For this purpose, a set of the NOM samples was assembled from arctic and nonarctic sampling sites (the Kolyma river basin and Moscow region, respectively). It was to ensure a substantial difference in the humification degree of the isolated organic matter-the biogeochemical proxy of the long-wave absorbance of NOM. The assembled NOM set was analyzed using solution-state 1H NMR spectroscopy. The distribution of both backbone and exchangeable protons was determined using acquisition of spectra in three different solvents. The substantially higher contribution of nonfunctionalized aliphatic moieties CHn (e.g., materials derived from linear terpenoids, MDLT) in the arctic NOM samples was revealed as compared to the nonarctic ones. The latter were characterized with the higher content of CHα protons adjacent to electron-withdrawing groups which belong to carboxyl rich alicyclic moieties (CRAMs) or to aromatic constituents of NOM. We have calculated a ratio of CHn to CHα protons as a structural descriptor which showed significant inverse correlation to intensity of long wave absorbance assessed with a use of E4/ E6 ratio and the slope of absorption spectrum. The steric hindrance of aromatic chromophoric groups of the NOM ensemble by bulky nonfunctionalized aliphatic moieties (e.g., MDLT) was set as a hypothesis for explanation of this phenomenon. The bulky aliphatics might increase a distance between the interacting groups resulting in inhibition of electronic (e.g., charge-transfer) interactions in the NOM ensemble. The obtained relationships were further explored using Fourier transform mass spectrometry as complementary technique to 1H NMR spectroscopy. The data obtained on correlation of molecular composition of NOM with 1H NMR data and optical properties were very supportive of our hypothesis that capabilities of NOM ensemble of charge transfer interactions can be dependent on structural arrangement and relative abundance of nonabsorbing aliphatic moieties.

[Gene mutations in patients with hereditary cavernous malformations]. / Analiz mutatsii genov u bol'nykh s nasledstvennymi kavernoznymi mal'formatsiiami TsNS.

AIM: To identify mutations in cerebral cavernous malformation (CCM) genes in patients with hereditary and sporadic CCMs in the Russian population. MATERIAL AND METHODS: Blood samples from 73 randomly selected patients, including 29 MRI-confirmed familial cases, 8 clinically confirmed familial cases and 38 so-called sporadic cases, were examined. A search for large deletions/duplications was performed using multiplex ligation-dependent probe amplification (MPLA). For MLPA-negative samples, the whole genome sequencing was performed to search for single nucleotide polymorphisms (SNP). RESULTS: Deletions in three genes (ССМ1, ССМ2, ССМ3) were identified in 14 patients, including 5 without definitely established familial type, in whom the familial character of disease was not confirmed by clinical and neuroimaging results. SNP mutations were found in 13 patients, CCM gene mutations in 27. Mutations were detected in 91.7% of familial cases. In two patients, new CCM3 deletions were identified. Gene distribution was as follows: 60.7 for CCM1, 32.2 for CCM2 and 7.1% for CCM3. In two members of a family with hereditary CCMs, no high effect mutations in the known CCM genes were found. Patients with mutations had greater severity of disease. Two patients with CCM3 mutations demonstrated the most aggressive clinical course. De novo formation and growth of CCM were observed only in patients with mutations. CONCLUSION: The distribution of pathogenic mutations in known CCM genes is consistent with other large-scale studies. Familial CCMs are associated with more severe disease course and may be caused by mutations beyond the known CCM genes.

Biological activity of novel synthetic derivatives of carnosine.

Two novel derivatives of carnosine--(S)-trolox-L-carnosine (STC) and (R)-trolox-L-carnosine (RTC) are characterized in terms of their antioxidant and membrane-stabilizing activities as well as their resistance to serum carnosinase. STC and RTC were synthesized by N-acylation of L-carnosine with (S)- and (R)-trolox, respectively. STC and RTC were found to react more efficiently with 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) and protect serum lipoproteins from Fe(2+)-induced oxidation more successfully than carnosine and trolox. At the same time, STC, RTC and trolox suppressed oxidative hemolysis of red blood cells (RBC) less efficiently than carnosine taken in the same concentration. When oxidative stress was induced in suspension of cerebellum granule cells by their incubation with N-methyl-D-aspartate (NMDA), or hydrogen peroxide (H(2)O(2)), both STC and RTC more efficiently decreased accumulation of reactive oxygen species (ROS) than carnosine and trolox. Both STC and RTC were resistant toward hydrolytic degradation by human serum carnosinase. STC and RTC were concluded to demonstrate higher antioxidant capacity and better ability to prevent cerebellar neurons from ROS accumulation than their precursors, carnosine and trolox.

[Evaluation of the effect of late blight-resistant potato plants on the structure of bacterial associations in soil].

We studied the compositions of microbial associations isolated from soils where nontransgenic and transgenic late blight-resistant lines of potato varieties Lugovskoi, Charodei, and Golubizna had been grown. The analysis was based on denaturing gradient gel electrophoresis of total amplificates of 16S rRNA gene fragments and analysis of libraries of nifH gene fragments. Neither method revealed significant differences in the structure of the microbial associations isolated from soils with control or transgenic plants. The minor differences detected in the microflora ranges were no greater than those in the rhizospheres of different nontransgenic potato varieties.

[Use of DIR-PCR for elaboration of molecular markers of intraspecies bacterial groups as exemplified by Bacillus thuringiensis].

A recently developed PCR-fingerprinting method, the so-called DIR (diverged inverted repeats)-PCR, was used for quick search for molecular markers of Bacillus thuringiensis subspecies carrying the cry1 genes. The analysis of the fingerprints obtained by this method made it possible to reveal PCR fragments characteristic of the subspecies that produce proteins toxic for insects of the order Lepidoptera. Cloning and sequencing of these fragments allowed systems of SCAR (sequence characterized amplified region) primers to be designed, which are specific to the above group of B. thuringiensis strains. Comparison of the specific fragments with sequences available in the GenBank database revealed their homology with the rpoC gene family and the adjacent spacer region, suggesting chromosomal localization of these markers. This increases the reliability of the designed system of SCAR primers, because plasmids may be lost or transferred by transformation between closely related strains. It was demonstrated that the DIR-PCR method allows markers to be developed that are linked to diagnostic genotypic and phenotypic characteristics of bacteria.

[Chlorobaculum macestae sp. nov., a new green sulfur bacterium].

The investigated green sulfur bacterium, strain M, was isolated from a sulfidic spring on the Black Sea Coast of the Caucasus. The cells of strain M are straight or curved rods 0.6-0.9 x 1.8-4.2 microm in size. According to the cell wall structure, the bacteria are gram-negative. Chlorosomes are located along the cell periphery. Strain M is an obligate anaerobe capable of photoautotrophic growth on sulfide, thiosulfate, and H2. It utilizes ammonium, urea, casein hydrolysate, and N2 as nitrogen sources and sulfide, thiosulfate, and elemental sulfur as sulfur sources. Bacteriochlorophyll c and the carotenoid chlorobactene are the main pigments. The optimal growth temperature is 25-28 degrees C; the optimal pH is 6.8. The strain does not require NaCl. Vitamin B12 stimulates growth. The content of the G+C base pairs in the DNA of strain M is 58.3 mol %. In the phylogenetic tree constructed on the basis of analysis of nucleotide sequences of 16S rRNA genes, strain M forms a separate branch, which occupies an intermediate position between the phylogenetic cluster containing representatives of the genus Chlorobaculum (94.9-96.8%) and the cluster containing species of the genus Chlorobium (94.1-96.5%). According to the results of analysis of the amino acid sequence corresponding to the fmo gene, strain M represents a branch which, unlike that in the "ribosomal" tree, falls into the cluster of the genus Chlorobaculum (95.8-97.2%). Phylogenetic analysis of the amino acid sequence corresponding to the nifH gene placed species of the genera Chlorobaculum and Chlorobium into a single cluster, whereas strain M formed a separate branch. The results obtained allow us to describe strain M as a new species of the genus Chlorobaculum. Chlorobaculum macestae sp. nov.

Prenatal hyperhomocysteinemia as a model of oxidative stress of the brain.

We found that methionine added to the ration of pregnant rats (1 g/kg body weight) induced sustained hyperhomocysteinemia and led to the formation of sustained oxidative stress in the brain of their progeny. Newborn animals were characterized by lower body weight, SOD deficiency in the brain, increased neuronal death, and desensitization of NMDA receptors. These factors are associated with impaired cognitive capacity in the Morris test.

[Isolation and characterization of nitrogen-fixing bacteria of the genus Azospirillum from the soil of a Sphagnum peat bog].

The presence of nitrogen-fixing bacteria of the genus Azospirillum in the soils of acidic raised Sphagnum bogs is revealed for the first time. Three Azospirillum strains, B2, B21, and B22, were isolated as a component of methane-oxidizing enrichment cultures, whereas attempts to isolate them directly from peat samples have failed. The results of comparative analysis of the nucleotide sequences of 16S rRNA genes, DNA-DNA hybridization, and the analysis of the sequences of the functional genes encoding nitrogenase and ribulose-1, 5-bisphosphate carboxylase reveal that all the newly obtained strains can be classified as Azospirillum lipoferum. Yet, unlike A. lipoferum. the isolates do not require biotin and utilize sucrose, inositol, and glycerol for growth. The cell morphology of strain B2 differs from that of the type strain and strains B21 and B22. The results obtained indicate the variability of morphological, physiological, and biochemical properties in closely related Azospirillum strains and suggest the existence of metabolic relationships between methanotrophic bacteria and the representatives of the genus Azospirillum under peat bog conditions.

[Comparative characterization of cultured methane-oxidizing bacteria by serological and molecular methods].

Three stable methane-oxidizing enrichment cultures, SB26, SB31, and SB31A were analyzed by transmission electron microscopy and by serological and molecular techniques. Electron microscopy revealed the presence of both type I and type II methanotrophs in SB31 and SB31A enrichments; only type II methanotrophs were found in SB26 enrichment. Methylosinus trichosporium was detected in all three enrichments by the application of species-specific antibodies. Additionally, Methylocystis echinoides was found in SB26 culture; Methylococcus capsulatus, in SB31 and SB31A; and Methylomonas methanica, in SB31. The analysis with pmoA and nifH gene sequences as phylogenetic markers revealed the presence of Methylosinus/Methylocystis group in all communities. Moreover, the analysis of pmoA sequences revealed the presence of Methylomonas in SB31. Methylocella was detected in SB31 and SB31A enrichments only by nifH analysis. It was concluded that the simultaneous application of different approaches reveals more reliable information on the diversity of methanotrophs.

[Phylogeny of anoxygenic filamentous phototrophic bacteria of the family Oscillochloridaceae as inferred from comparative analyses of the rrs, cbbL, and nifH genes].

Phylogeny of anoxygenic filamentous phototrophic bacteria (AFPB) of the family Oscillochloridaceae (Oscillochloris trichoides DG6T and the recently isolated strains Oscillochloris sp. R and C6) was studied based on comparative analyses of the genes coding for 16S rRNA (rrs), ribulose- 1,5-bisphosphate carboxylase/oxygenase (cbbL), and nitrogenase (nifH). The sequences of the genes studied proved to be identical in the three strains, which is in agreement with data obtained earlier that showed lack of differentiating phenotypic distinctions between these strains; therefore, it is proposed that the new strains should be identified as representatives of the species O. trichoides. Using an earlier designed system of oligonucleotide primers and a specially designed additional primer, fragments of the cbbL genes of the "red-like" form I RuBPC were amplified and sequenced for all of the O. trichoides strains. Analysis of the cbbL genes suggested a separate position of the bacteria studied in the phylogenetic tree, where O. trichoides strains formed an independent branch, which, apart from this species, also included the only studied species of gram-positive facultatively chemoautotrophic bacteria, Sulfobacillus acidophilus. In the phylogenetic tree inferred from the analysis of nifH genes, the bacteria under study also formed a new separate branch, deviating near the root, which indicated lack of relatedness between them and other phototrophic bacteria. The data obtained support the conclusion that AFPB has an ancient origin and their identification as one of the main evolutionary lineages of eubacteria, which was made based on the analysis of ribosomal genes.

Ontogeny of facial dimorphism and patterns of individual development within one human population.

Based on a longitudinal study of radiographs of the Denver Growth Study, we investigated the morphological development of individual and gender differences in the anterior neurocranium, face, and basicranium. In total, 500 X-rays of 14 males and 14 females, each with 18 landmarks and semilandmarks, were digitized and analyzed using geometric morphometric methods. Sexual dimorphism in shape and form is already present at the earliest age stage included in the analysis. However, the nature of dimorphism changes with age. Four factors apper to contribute to cranial sexual dimorphism in human postnatal development: 1) initial, possibly prenatal, differences in shape; 2) differences in the association of size and shape; 3) male hypermorphosis; and 4) some degree of difference in the direction of male and female growth trajectories. Studying changes in individuals, we find a low correlation between newborn and adult morphology, while 3-year-olds already show a high correlation with their adult form. We conclude that the adult pattern of interindividual difference in facial form in a single human population is established within the first few years of life.

[Method for rapid DNA extraction from bacterial communities of different soils].

A method for indirect DNA extraction from various soils significantly differing in their physicochemical properties has been developed. The proposed method is based on cell desorption from soil particles using a Tris-EDTA (TE) buffer supplemented with polyvinylpolypyrrolydone (PVPP) and sodium dodecylsulfate (SDS). Subsequent cell lysis and purification of DNA preparations methods based on alkaline lysis followed by chromatography on ion-exchange resins were described by us earlier. The purity of the DNA preparations obtained did not depend on the type of soil. It was shown that the DNA preparations can be used for the amplification of rather large fragments, e.g., sequences spanning the complete 16S rRNA gene.

Na-K-ATPase in rat cerebellar granule cells is redox sensitive.

Redox-induced regulation of the Na-K-ATPase was studied in dispersed rat cerebellar granule cells. Intracellular thiol redox state was modulated using glutathione (GSH)-conjugating agents and membrane-permeable ethyl ester of GSH (et-GSH) and Na-K-ATPase transport and hydrolytic activity monitored as a function of intracellular reduced thiol concentration. Depletion of cytosolic and mitochondrial GSH pools caused an increase in free radical production in mitochondria and rapid ATP deprivation with a subsequent decrease in transport but not hydrolytic activity of the Na-K-ATPase. Selective conjugation of cytosolic GSH did not affect free radical production and Na-K-ATPase function. Unexpectedly, overloading of cerebellar granule cells with GSH triggered global free radical burst originating most probably from GSH autooxidation. The latter was not followed by ATP depletion but resulted in suppression of active K(+) influx and a modest increase in mortality. Suppression of transport activity of the Na-K-ATPase was observed in granule cells exposed to both permeable et-GSH and impermeable GSH, with inhibitory effects of external and cytosolic GSH being additive. The obtained data indicate that redox state is a potent regulator of the Na-K-ATPase function. Shifts from an "optimal redox potential range" to higher or lower levels cause suppression of the Na-K pump activity.

[Geoalkalibacter ferrihydriticus gen. nov., sp. nov., the first alkaliphilic representative of the family Geobacteraceae, isolated from a soda lake].

Investigation of iron reduction in bottom sediments of alkaline soda lakes resulted in the isolation of a new obligately anaerobic iron-reducing bacterium, strain Z-0531, from Lake Khadyn (Tuva Republic, Russia) sediment samples. The cells of strain Z-0531 are short (1.0-1.5 by 0.3-0.5 microm), motile, non-spore-forming, gram-negative rods. The isolate is an obligate alkaliphile, developing in the pH range of 7.8-10.0, with an optimum at pH 8.6. It does not require NaCl but grows at NaCl concentrations of 0-50 g/1l. It can oxidize acetate with such electron acceptors as amorphous Fe(llI) hydroxide (AFH), EDTA-Fe(III), anthraquinone-2,6-disulfonate (quinone), Mn(IV), and S(0). On media with EDTA-Fe(III), the isolate can oxidize, apart from acetate, ethanol, pyruvate, oxalate, arginine, tartrate, lactate, propionate, and serine. H2 is not utilized. The reduced products formed during growth with AFH are siderite or magnetite, depending on the growth conditions. The isolate is incapable of fermenting sugars, peptides, and amino acids. Yeast extract or vitamins are required as growth factors. The organism is capable of dinitrogen fixation and harbors the nifH gene. The DNA G+C content is 55.3 mol %. 16S rRNA analysis places strain Z-0531 into the family Geobacteraceae. Its closest relative (93% similarity) is Desulfuromonas palmitatis. Based on phenotypic distinctions and phylogenetic position, it is proposed that strain Z-0531 be assigned to the new genus and species Geoalkalibacter ferrihydriticus gen. nov., sp. nov.

[Obtaining of intrapopulational dissociants of some bacilli and the use of DIR-PCR for their identification]. / Poluchenie vnutripopuliatsionnykh dissotsiantov nekotorykh batsill i primenenie metoda DIR-PTSP dlia ikh identifikatsii.

The paper is the first to suggest methods for rapid obtaining and genotypic identification of phenotypic (colonial-morphological) dissociants of bacterial cultures. For revelation of the potential dissociation ability and obtaining of dissociants, the use of bacterial cyst-like refractile cells (CRC) is recommended. These cells are characterized by enhanced variability; upon their first passage, an abrupt increase in the dissociation index is observed as a result of the emergence of cells that form morphologically different types of colonies. The approaches elaborated were tested with Bacillus cereus, B. subtilis, and B. licheniformis, for which colonial-morphological dissociants of various types were obtained after the first passage of CRC (both of those formed in the developmental cycle of bacteria and of those arising as a result of artificial increase of the concentration of anabiosis autoinducers in the cultivation medium). The genomic distinctions between dissociants of B. cereus and B. subtilis were estimated using polymerase chain reaction with a primer system designed based on the analysis of nucleotide sequences of complete prokaryotic genomes available in the GenBank database (DIR-PCR). The application of the suggested method allowed distinctions between the genomes of dissociants of Bacillus cereus and B. subtilis to be revealed, which is in agreement with the hypothesis that suggests reversible intragenomic rearrangements to be the basis of bacterial dissociation into subpopulations.

Functional relationship between Na/K-ATPase and NMDA-receptors in rat cerebellum granule cells.

Activation of rat cerebellum granule cells by N-methyl-D-aspartate (NMDA, 10(-4)-10(-3) M) results in progressive increase in reactive oxygen species (ROS) and suppression of the ouabain-sensitive part of Na/K-ATPase activity. When Na/K-ATPase was inhibited by high ouabain concentrations (10(-5)-5 x 10(-4) M), an increase in stationary ROS level in neuronal cells was noted, this effect being attenuated by NMDA antagonists, MK-801 and D-AP5. It is concluded that in cerebellum neurons, ouabain-resistant Na/K-ATPase is responsible for suppression of intracellular level of ROS, which, in turn, inhibit ouabain-sensitive Na/K-ATPase.

Glutamate receptors modulate oxidative stress in neuronal cells. A mini-review.

Multiple lines of evidence demonstrate that reactive oxygen species (ROS) are involved in regulation of normal cell metabolism as second messengers. Under extreme conditions, these molecules induce oxidative stress, which may stimulate (or accompany) a number of neurodegenerative processes. In the glutamatergic system, ROS levels are under control of ionotropic and metabotropic glutamate receptors, which modulate ion fluxes through the neuronal membrane. The Na+/K(+)-pump is also one of the important participants affecting stationary ROS levels through several distinct mechanisms. This review describes the involvement of the Na+/K(+)-pump in intracellular signaling mechanisms via cross-talk between the pump and glutamate receptors in cerebellum granule cells. Selective dysfunction of mGlu II receptors may also lead to abnormal protein phosphorylation (i.e., tau phosphorylation), culminating in neurodegenerative disorders (i.e., Alzheimer disease). Also, unregulated production of intracellular ROS resulting from an imbalance of ionotropic and metabotropic receptors may activate one or more protein kinases. In summary, Glu receptor dysfunction, leading to a deficit in glutamate-mediated signal transduction may represent one of the earliest stages of neurodegenerative disorders. The Na+/K(+)-pump is able to prevent over-production of intracellular ROS, thus increasing oxidative stability of neuronal cells.

[Cellulose decomposition under nitrogen deficiency by bacteria isolated from the intestines of phytophagous vertebrates]. / Rasshcheplenie tsellulozy pri defitsite azota bakteriiami, vydelennymi iz kishechnika rastitel'noiadnykh pozvonochnykh.

A nitrogen-fixing strain identified as Klebsiella pneumonia 402-2 and two endoglucanase-synthesizing Bacillus strains were isolated from the intestines of phytophagous animals. One of the Bacillus strains was identified as Bacillus subtilis GL. Klebsiella pneumoniae 402-2 increased the endoglucanase activity of both Bacillus strains in mixed cultures. The data on the taxonomic position of strains 402-2 and GL and on the nitrogen-fixing capacity of strain 402-2 were confirmed by sequencing and analyzing their 16S rRNA genes and by amplifying the nitrogenase gene nifH.