Structural variability and new intermolecular interactions of Z-DNA in crystals of d(pCpGpCpGpCpG).

We have determined the single crystal x-ray structure of the synthetic DNA hexamer d(pCpGpCpGpCpG) in two different crystal forms. The hexamer pCGCGCG has the Z-DNA conformation and in both cases the asymmetric unit contains more than one Z-DNA duplex. Crystals belong to the space group C222(1) with a = 69.73, b = 52.63, and c = 26.21 A, and to the space group P2(1) with a = 49.87, b = 41.26, c = 21.91 A, and gamma = 97.12 degrees. Both crystals show new crystal packing modes. The molecules also show striking new features when compared with previously determined Z-DNA structures: 1) the bases in one duplex have a large inclination with respect to the helical axis, which alters the overall shape of the molecule. 2) Some cytosine nitrogens interact by hydrogen bonding with phosphates in neighbor molecules. Similar base-phosphate interactions had been previously detected in some B-DNA crystals. 3) Basepair stacking between the ends of neighbor molecules is variable and no helical continuity is maintained between contiguous hexamer duplexes.     

Genetic differentiation of charrs in the Russian north and far east

Genetic differences and relationships within charrs Salvelinus alpinus , northern and southern S. malma, S. taranetzi, S. levanidovi and S. leucomaenis , were studied by examination of 31–35 allozyme loci and PCR-RFLP analysis of mtDNA segment (about 2600 bp) including the cytochrome b gene and D-loop. Data for mtDNA were also obtained for samples of S. drjagini, S. albus and for European samples of S. alpinus. Generally allozyme and mtDNA segment analyses produced similar pictures of genetic divergence and relationships. The southern S. malma exhibited the greatest genetic variability (allozyme heterozygosity and mtDNA haplotype diversity). S. alpinus, S. malma, S. levanidovi and S. leucomaenis had fixed differences from one another at various allozyme loci, and differed in fixed (but polymorphic in S. malma ) individual mtDNA haplotypes produced with MspI restrictase. Such genetic individuality is typical of distinct taxa. S. taranetzi is closest genetically to allopatric S. alpinus , but exhibited fixed differences from the northern S. malma in sympatry. In all samples of S. alpinus the only mtDNA haplotype was shared with S. drjagini. S. albus shared its single haplotype with the northern S. malma from the same locality. S. leucomaenis is differentiated from the other species to the greatest extent, possibly reflecting an early evolutionary divergence. Some evolutionary and taxonomic implications of the genetic relationships of charrs studied are discussed.     

Differentiation of chum salmon Oncorhynchus keta Wallbaum populations as revealed with microsatellite and allozyme markers: A comparative study

The features and extent of population differentiation in chum salmon Oncorhynchus keta from Sakhalin and Iturup Islands were studied with 10 microsatellite and 12 allozyme markers. It was demonstrated with the example of allozyme polymorphism at the EstD locus that the effect of an individual locus with one major allele is capable of distorting the total picture of population differentiation. Multiallelic microsatellites were more efficient in revealing the genetic structure of chum salmon populations at the levels of differences between regional populations and between the stocks of individual rivers of the same region.     

Sensitivity of the neurons in the auditory inferior colliculus of mice to the direction of the shift of broadband spectral notch noise

Series of a notch noise with regular shifts of the notch center frequency: one--from low frequencies to high frequencies and the other--from high frequencies to the low, were synthesized. The notch noise series imitated sound source vertical moving. Single neuron's responses of inferior colliculus of the house mouse (Mus musculus) to the notch-noises altered with notch central frequency varying through excitatory and inhibitory frequency response areas in neurones' receptive fields. The neural responses alteration to the notch noise varying depended on the bandwidth of notch. Disinhibition in inhibitory side band could be higher if the notch overlying the inhibitory areas followed the notch overlying the excitatory areas. The data obtained make it possible to consider the excitatory and inhibitory interaction as a mechanism of neural sensitivity to the notch moving direction. Neurones' response set could provide information about sound source moving over auditory space.     

A comparative study of the isocitrate dehydrogenases of Chlorobium limicola forma Chlorobium thiosulfatophilum and Rhodopseudomonas palustris

The carboxylation of 2-oxoglutarate in the reductive tricarboxylic acid cycle in the obligate photolithotroph Chlorobium limicola forma thiosulfatophilum and the oxidation of isocitrate in the tricarboxylic acid cycle in the photoheterotroph Rhodopseudomonas palustris are catalyzed by isocitrate dehydrogenases. A comparative study of these enzymes isolated from the two bacteria showed that they virtually do not differ in the enzymatic and kinetic properties.     

Dependence of the mouse inferior colliculus neurons activity on position and direction of movement of the spectral contrast

Response variability of the single neurons of the inferior colliculus of mouse (Mus musculus) to series of noise bands and of notch noises with regular 1/12 octave steps of the band/notch center frequency and width of noise band/notch 1/3 octave, was studied. Neurons with strong inhibitory influence in excitatory response area (inhibitory-dominated) show low impulse activity when noise band exceeded excitatory response area. Spectral contrasts crossing the center of excitatory response area (at CF or nearly CF) were found to be the most efficient stimuli for such neurons. Neuron responses to spectral contrasts derived both from noise band and noise notch were identical. Approaching of inhibitory and excitatory inputs is expected to sharpen the auditory neurons frequency tuning to position of spectral contrasts, similar to neuronal processing in visual system. Neuron selectivity to the direction of spectral contrasts movement was determined in neuron response differences when the noise band or notch shifted from excitatory area to inhibitory areas as compared with shift in the opposite direction. Functional role of contrast mechanism for sound localization on the base spectral cues related to external ear transfer characteristics is discussed.     

Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

The majority of structural efforts addressing RNA's catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a lambda-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions.     

Genome-wide study identifies two loci associated with lung function decline in mild to moderate COPD

Accelerated lung function decline is a key COPD phenotype; however, its genetic control remains largely unknown. We performed a genome-wide association study using the Illumina Human660W-Quad v.1_A BeadChip. Generalized estimation equations were used to assess genetic contributions to lung function decline over a 5-year period in 4,048 European American Lung Health Study participants with largely mild COPD. Genotype imputation was performed using reference HapMap II data. To validate regions meeting genome-wide significance, replication of top SNPs was attempted in independent cohorts. Three genes (TMEM26, ANK3 and FOXA1) within the regions of interest were selected for tissue expression studies using immunohistochemistry. Two intergenic SNPs (rs10761570, rs7911302) on chromosome 10 and one SNP on chromosome 14 (rs177852) met genome-wide significance after Bonferroni. Further support for the chromosome 10 region was obtained by imputation, the most significantly associated imputed SNPs (rs10761571, rs7896712) being flanked by observed markers rs10761570 and rs7911302. Results were not replicated in four general population cohorts or a smaller cohort of subjects with moderate to severe COPD; however, we show novel expression of genes near regions of significantly associated SNPS, including TMEM26 and FOXA1 in airway epithelium and lung parenchyma, and ANK3 in alveolar macrophages. Levels of expression were associated with lung function and COPD status. We identified two novel regions associated with lung function decline in mild COPD. Genes within these regions were expressed in relevant lung cells and their expression related to airflow limitation suggesting they may represent novel candidate genes for COPD susceptibility.     

Perception of approaching and withdrawing sound sources after exposure to broadband noise: The importance of spatial domain

The existence of space-specific differences in auditory aftereffects has been tested under short-term (5 s) exposure to broadband noise (20–20000 Hz). Adapting stimuli were emitted as constant-amplitude noise sequences. Test stimuli could be of constant and changing amplitude: increasing amplitude of noise pulses in a sequence mimicked an approaching sound source, whereas a decrease in amplitude was perceived as withdrawal. The experiments were done in an anechoic chamber. Auditory aftereffects were assessed under the following conditions: (a) adapting and test stimuli were emitted through a loudspeaker mounted at a distance of 1.1 m from the listener (i.e., subjectively near); (b) both stimuli were emitted from a distance of 4.5 m (subjectively far); (c) adapting and test stimuli were emitted from different distances. The results showed that the characteristics of perception of the imitated sound source motion were similar in proximity and remoteness, which was observed both in the control (without adaptation) and after adaptation to noise. In the absence of adaptation, the psychophysical curves were asymmetrical: the listeners reported approaching of test stimuli more often for both spatial domains. However, the overestimation of test stimuli as drawing closer was more pronounced when they were emitted from the distance of 1.1 m, i.e., from near the listener. After the adaptation to noise, the aftereffects showed spatial specificity and were observed only when adapting and test stimuli belonged to the same spatial domain. These aftereffects were similar in their pattern and strength both in proximity and remoteness: the listeners reported withdrawal of test stimuli more frequently as compared with the control. As a result of these aftereffects, the symmetry of psychometric curves was restored, and the estimation of the direction of sound source motion in the experiment became equiprobable.