Simple combined explicit/implicit water model

A simple combined water model (SCW model) for the calculation of the hydration free energy is presented. In the frame of the model a solute is placed in the centre of the spherical cavity with explicit water molecules, which are considered at the atomistic level. Rigid wall potential at the boundary of the cavity restricts the moving of the explicit water molecules. Water outside the sphere is considered as the conducting continuum (implicit part of the model). Simulation is performed in the frame of the NVT ensemble (constant number of particles, volume and temperature), density of water is fixed and equal to experimental value 1 g/cm³. The energy of electrostatic interaction of atomic point charges of the explicit water molecules with conducting continuum is calculated analytically by means of the image charges method. It provides high computational efficiency of the SCW model. For the averaging of the calculated thermodynamic and structural values over microstates of the system the thermodynamic integration method is used. The possible using of SCW for the docking problem is discussed.     

Lengthy unilateral EEG changes in alert rabbits after a spreading single depressed wave

Effects of a single wave of the cortical spreading depression (SD) on the ECoG of a waking rabbit was studied with chronically implanted intracortical calomel and silverball epidural electrodes. DC potential shifts and integral electrical activity were recorded monopolary in reference to a nasal-bone electrode. ECoG spectral analysis (FFT) showed that an SD wave was accompanied by a suppression of the neocortical activity in a broad frequency range (0.25-80 Hz). However, the SD-related ECoG depression was a rather short phenomenon (5-7 min) as compared to a following rebound effect, i.e., persistent (1.5-2 h) unilateral exaltation of bioelectrical activity. The spectral power in the delta (6-14 fold) and beta bands (2-6-fold) increased, whereas the high-frequency activity (40-80 Hz) remained suppressed. Similar changes in the contralateral neocortex were poorly pronounced or absent; this resulted in a strong interhemispheric asymmetry. It is suggested that (1) exaltation of the delta activity after SD wave is related not only to a dendrite swelling and changes in the extracellular space structure but to increase in synaptic transmission efficiency, probably, by the type of anoxic potentiation, (2) activation of some subcortical structures by the mechanism of their release from the inhibitory neocortical control is an additional factor of the augmentation of the delta and spindle-like beta activity after an SD wave, and (3) the long-term attenuation of the high-frequency gamma activity is a result of its strong suppression during the SD and its reciprocal relations with the exalted delta activity.     

Immunochemical study of the antigenic structure of microbes of the genus Bordetella. 5. Fractionation of the extracts of the parapertussis microbes and the study of the immunochemical and biochemical properties of the isolated fractions]

Fractions responsible for the main part of the serological and immunogenic activity differing by the set of antigens were isolated from the salt extracts of parapertussis microbes by gel-filtration on Sephadex G-100, ion exchange chromatography on DEAE-cellulose, and preparative electrophoresis in agar. Fractions, disclosing a sufficiently high serological activity and possessing the immunological properties, but containing the minimal set (2--3 out of 7) antigens, which were included in the initial extract, were isolated in the agar gel in the use of the preparative electrophoresis method.     

Isolation of fractions from Bordetella parapertussis extracts and their use for preparing an erythrocyte diagnostic preparation]

Soluble parapertusis antigen, serologically active, having hemosensitive properties and containing only 2 antigenic components was obtained by the method of ethanol fractionation of microbial extracts. This method is simple and convenient for production purposes. The antigen thus obtained was used for the production of a highly specific erythrocytic diagnostic preparation (formalinized, liquid). When tested in reaction with animal and human sera, the new diagnostic preparation proved to be sufficiently active and species specific.     

Cholinergic pyramidal neurons of the motor region of human neocortex

By means of histochemical methods for revealing +choline acetyltransferase (ChAT) and acetylcholinesterase (AChE) cytoarchitectonic of the field 4 of the motor cortex of the cerebrum has been studied in 5 persons at the age of 33-65 years. An essential part of neurons at revealing AChE and most of them at revealing ChAT do not react. Among giant pyramidal neurons (Bets) according to ChAT activity, 4 types are distinguished: neurons with low, middle, high and very high activity. The presence of ChAT is ascertained in middle and large pyramidal neurons of the III layer. Presence of ChAT-positive synapses is demonstrated in apical dendrites. A conclusion is made that less part of the pyramidal in the III, V layers are cholinergic ones.     

3-D Golgi and image analysis of the olfactory tubercle in schizophrenia

OBJECTIVE: To examine morphologic changes in the olfactory tubercle (OT) spiny neurons and astrocytes in schizophrenia (Sch) by means of quantitative 3-D Golgi and immunocytochemical studies. STUDY DESIGN: Free-floating vibrotome sections of postmortem brain tissue from 10 controls and 12 Sch cases were used for Golgi study and glial fibrillary acidic protein (GFAP) immunocytochemistry. A gray level image analysis was applied for quantitative estimation of GFAP-positive astrocytes on uniform, randomly sampled sections. This method is effective for low-contrast objects on an uneven background. Golgi-impregnated OT spiny neurons were analyzed both qualitatively and quantitatively in three dimensions with a semiautomated microscope-computer system. From digitized image of the neurons, various metric parameters were estimated to characterize the dendritic tree. RESULTS: In cases of Sch, degenerative changes in the dendrites of OT spiny neurons were revealed. A decrease in the maximal radius of the dendritic tree and total length of dendrites were accompanied by an increase in the length density of dendrites. Hypertrophy and a more-intensive GFAP reaction of astrocytes were found in OT of Sch. CONCLUSION: Based on these results, one can hypothesize that OT spiny neurons in Sch are involved in the process of dendritic reorganization, including degenerative changes in dendrites.     

Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

Background

Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos taurus taurus more adapted to temperate climates and the tropically adapted Bos taurus indicus. After domestication, human selection exponentially intensified these differences. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 770,000 SNP across the genome and compared using smoothed F_ST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds.

Results

Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal components analyses and unsupervised clustering confirmed the well-characterized main division of domestic cattle. The top 1% smoothed F_ST, potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top F_ST signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:~50 Mb and BTA14:~25 Mb; both regions harboring candidate genes and different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. The bottom 1% of the smoothed F_ST values, potentially associated to balancing selection, included 24 regions across 13 chromosomes. These regions often overlap with copy number variants, including the highly variable region at BTA23:~24 Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated with a significant overrepresentation of immune related pathways.

Conclusions

Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-876) contains supplementary material, which is available to authorized users.     

Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

Background

Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns.

Methods

By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation.

Results

For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1.

Conclusions

The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance.