Analysis of peptides from known proteins: Clusterization in sequence space

A combinatorial sequence space (CSS) model was introduced to represent sequences as a set of overlapping k-tuples of some fixed length which correspond to points in the CSS. The aim was to analyze clusterization of protein sequences in the CSS and to test various hypotheses about the possible evolutionary basis of this clusterization. The authors developed an easy-to-use technique which can reveal and analyze such a clusterization in a multidimensional CSS. Application of the technique led to an unexpectedly high clusterization of points in the CSS corresponding to k-tuples from known proteins. The clusterization could not be inferred from nonuniform amino acid frequencies or be explained by the influence of homologous data. None of the tested possible evolutionary and structural factors could explain the clusterization observed either. It looked as if certain protein sequence variations occurred and were fixed in the early course of evolution. Subsequent evolution (predominantly neutral) allowed only a limited number of changes and permitted new variants which led to preservation of certain k-tuples during the course of evolution. This was consistent with the theory of exon shuffling and protein block structure evolution. Possible applications of sequence space features found were also discussed.Correspondence to: H.A. Lim     

Psychophysiologic parameters of reproducing emotions in healthy subjects and patients during the first episode of depression

We analyzed the spectral power of EEG rhythms and some psychological features in patients with depression (first episode) and in healthy subjects. In the control group, the distributions of the spectral power of the alpha3 and gamma rhythms was symmetrical. In reproducing joy, the power of the alpha3 rhythm increased in the occipital and that of the gamma rhythm increased in the temporal areas of the left hemisphere. In depressive patients, predominant activation of the left posterior cortical quadrant in the alpha3 band was observed both in the baseline activity and during reproducing emotions of both valences. In these patients, the gamma rhythm predominated in the anterior regions of the right hemisphere during rest. The mental reproduction of joy and grief in depressive patients shifted the maximal gamma rhythm spectral power to the occipital cortical regions. Thus, in depressive patients, any emotional load, regardless of its valence, results in a decrease in the pathologic gamma activity and makes the distribution of cortical electric activity more close to that of healthy subjects.     

Properties and clinical application of quasi-liquid form of lysozyme

The course of transendoscopic quasi-liquid form of lysozyme treatment of the relapse of peptic ulcer was microbiologically and clinically substantiated. A high antimicrobial and sorption activity of the quasi-liquid form of lysozyme with respect to the microflora isolated from the mucous membrane of the stomach and the duodenum was shown. The transendoscopic introduction of this form of lysozyme significantly reduces the time of the cicatrization of ulcers and the stay of patients in the hospital.     

Temporal characteristics of the initial stage of the verbal information processing in healthy subjects and in schizophrenia

The study aimed to investigate the early coding of visually presented words and pseudowords using event-related potentials (ERP). We conducted comparative analysis of the characteristics of P100 and N170 in healthy controls and in patients with the first episode of schizophrenia during passive perception of verbal stimuli as well as under conditions of relevant words and pseudowords. The latency of early ERP components P100 and N170 appeared to be shorter in comparison with healthy subjects in the temporal, parietal and occipital areas. The latency of P100 in patients was significantly shorter in the temporal, parietal and occipital areas, whereas the latency of N170 was shorter in the parietal and occipital areas than in controls. The latency of N170 in healthy subjects was significantly longer to words than to pseudowords and in patients - vice versa. The latencies of N170 in all TPO areas were equal in healthy subjects during word processing, and this equality was upset during non-word processing. In patients with schizophrenia the equality was upset, but, opposite to healthy patients, the upset of equality was more expressed during words processing. Thus, the early stage of verbal information processing in schizophrenic patients is insufficient in time. The time deficit of the automatic processes may lead to defective processing of overall information.     

Perception of consonant and dissonant chords: changes in the power of the EEG evoked activity

Human perception of dissonant and consonant chords was studied by analyzing brain evoked activity. It was found that the perception of dissonant chords was accompanied by activation of the right frontal lobe, which controls negative emotions. Consonant chords activated the left frontal region, which controls positive emotions.     

Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps

The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds. Here, we present an overview of the importance of cytogenetic maps to Drosophila biology and to the concepts of chromosomal evolution. Physical and genetic markers were used to anchor the genome assembly scaffolds to the polytene chromosomal maps for each species. In addition, a computational approach was used to anchor smaller scaffolds on the basis of the analysis of syntenic blocks. We present the chromosomal map data from each of the 11 sequenced non-Drosophila melanogaster species as a series of sections. Each section reviews the history of the polytene chromosome maps for each species, presents the new polytene chromosome maps, and anchors the genomic scaffolds to the cytological maps using genetic and physical markers. The mapping data agree with Muller's idea that the majority of Drosophila genes are syntenic. Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement events.     

Comparative EEG study in normal and autistic children

The work represents the results of a comparative study of spectral power as well as averaged coherence in alpha, beta and gamma EEG bands in 5-to-7-year-old autistic and healthy boys in the state of rest and under cognitive load (mental calculation). The mean age of the examined children was 6 years 4 months. In both healthy and autistic children, there was a clear-cut baseline frontal-occipital gradient of the alpha activity. Performance of the cognitive task led to enhancement of spectral power in the alpha1 band and shifting its maximum to the left hemisphere, did not change the activity in the alpha2 band, and considerably increased the spectral power in the alpha3 band. In healthy children, the spectral power and average coherence of the fast rhythms increased in the central and frontal areas of the left hemisphere. The right-side dominance of the spectral power of the alpha band was revealed in autistic children both in the baseline and during cognitive task. The spectral power of the gamma band was higher in autistic children than in healthy children in the baseline. The cognitive task did not change this fast activity in autistic children.     

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.     

Activation of brain structures by fMRI data when viewing the video clips and recall of shown actions

In 10 healthy volunteers, brain tomograms were recorded using an fMRI scanner with a 3T-field magnet. Emotionally neutral and emotionally involving videos were used for stimulation. Registration consisted of seven series: two series of viewing a fixation point and two kinds of video clips, one series of viewing of a succession of two types of video clips, two series of watching videos with subsequent recall, and two series of viewing the fixation point followed by recall of content online. Viewing content online caused the greatest degree of metabolism increase localized in the visual cortex. This activation was more pronounced during the presentation of an emotionally involving video clip. In addition to the occipital lobe, it actively involved the temporal, parietal and, to a lesser extent, the frontal cortex. Activation of the motor cortex was detected only in some subjects. The "interference" effect in which the increase in metabolism was minimal was observed during a consequent demonstration of video-clips. Immediate recall of video-clips after viewing caused the greatest activation of the posterior frontal and motor cortex. Delayed recall activated mostly the anterior frontal cortex. There was a decrease of metabolism in the visual cortex during the recall. The greatest reduction in the visual cortex was observed during immediate recall. Immediate and delayed recall activated the structures associated with the maintenance of consciousness, memory and a system of mirror neurons.