Alexey A. Morozov

High-frequency oscillatory response to illusory contour in typically developing boys and boys with autism spectrum disorders

Illusory contour (IC) perception, a fruitful model for studying the automatic contextual integration of local image features, can be used to investigate the putative impairment of such integration in children with autism spectrum disorders (ASD). We used the illusory Kanizsa square to test how the phase-locked (PL) gamma and beta electroencephalogram (EEG) responses of typically developing (TD) children aged 3-7 years and those with ASD were modulated by the presence of IC in the image. The PL beta and gamma activity strongly differentiated between IC and control figures in both groups of children (IC effect). However, the timing, topography, and direction of the IC effect differed in TD and ASD children. Between 40 msec and 120 msec after stimulus onset, both groups demonstrated lower power of gamma oscillations at occipital areas in response to IC than in response to the control figure. In TD children, this relative gamma suppression was followed by relatively higher parieto-occipital gamma and beta responses to IC within 120-270 msec after stimulus onset. This second stage of IC processing was absent in children with ASD. Instead, their response to IC was characterized by protracted (40-270 msec) relative reduction of gamma and beta oscillations at occipital areas. We hypothesize that children with ASD rely more heavily on lower-order processing in the primary visual areas and have atypical later stage related to higher-order processes of contour integration.

Inverted event-related potentials response to illusory contour in boys with autism

We examined the hypothesis of lower-level processing abnormalities related to perceptual grouping in boys with autism aged 3–6 years. We investigated event-related potentials response to visual elements that either formed perceptually coherent illusory contour or were arranged in a noncoherent way. The results showed that in healthy boys the illusory contour as compared with control stimulus elicited enhanced negativity of N1 peak (C effect), which has been previously found in adults. Autistic boys demonstrated the reliable inverted illusory contour effect, that is, more positive N1 amplitude to illusory contour. We hypothesized that boys with autism were sensitive to difference between illusory contour and control figures basing on collinearity processing mechanisms implemented in neural circuitry of primary visual cortex.

Evolutionary history of the chitin synthases of eukaryotes

Chitin synthases are widespread among eukaryotes and known to have a complex evolutionary history in some of the groups. We have reconstructed the chitin synthase phylogeny using the most taxonomically comprehensive dataset currently available and have shown the presence of independently formed paralogous groups in oomycetes, ciliates, fungi, and all diatoms except raphid pennates. There were also two cases of horizontal gene transfer (HGT): transfer from fungus to early diatoms gave rise to diatom paralogous group, while transfer from raphid pennate diatom to Acantamoeba ancestor is, to our knowledge, restricted to a single gene in amoeba. Early evolution of chitin synthases is heavily obscured by paralogy, and further sequencing effort is necessary.

Annual variations in hepatic antioxidant defenses and lipid peroxidation in a temperate fish, common bream Abramis brama (L.)

Alternation of physiological states during the annual cycle (pre-spawning mobilization, spawning energy loss, post-spawning accumulation of energy reserve, declined metabolic activity during the wintering) occurring in the wide temperature range requires high plasticity of fish defense systems. The article presents a 2-year study of hepatic antioxidant defenses and lipid peroxidation in the temperate cyprinid fish, common bream Abramis brama (L.), in relation to basic annual rhythms, such as photoperiodic and temperature cycling, reproduction and feeding activity. The objective of the study was to evaluate the plasticity of antioxidant defenses in bream under normal conditions throughout the annual cycle, by measuring hepatic antioxidants (superoxide dismutase, catalase, glutathione-S-transferase activities and reduced glutathione concentrations) and products of lipid peroxidation (thiobarbituric acid reactive substances concentrations). The results suggested that hepatic levels of antioxidants in bream varied dramatically during the annual cycle allowing bream to develop necessary adaptation and implement reproduction program. The lowest values of all studied antioxidants were witnessed in the middle of winter. In early spring, antioxidant enzyme activities increased rapidly reaching their maxima in late spring and summer. Toward the end of autumn, enzyme activities were declining toward the levels observed before the ice breakup. Spring–summer up-regulation of antioxidant defenses along with increased lipid peroxidation indicated bream to be experiencing mild oxidative stress.

Pneumatic Video Tactile Sensor for Laparoscopic Surgery

The main purpose of the study is design of the innovative tool for determination of mechanical properties of soft biological tissues during minimally invasive surgical operations. This applied problem is closely related with fundamental problems of diagnostics of pathological conditions of soft biological tissues by means of the tactile sensor. In this paper, the contact interaction between the tactile sensor and the soft biological tissue is studied. The analysis of the stress-strain state of soft tissue is carried out using the solution of boundary value problem of contact mechanics. As a first approximation, the linear elastic model of biological tissue is used in formulation of the problem of contact interaction between biological tissues and the artificial tactile sensor. A method is proposed for determination of mechanical characteristics of the studied tissue basing on measurement of the air pressure in pneumatic chamber of the sensor and on processing of images of the contact area between the sensor head and the tissue. An approach is developed for measuring the axial displacement of the central point of the sensor head and using this information in the procedure of estimation of tissue properties, which extends the potential of the proposed method. The prototype of the miniature video pneumotactile sensor is constructed and tested. Results of these experiments are in good agreement with results of numerical simulations.

Inferring Phylogenetic Networks from Gene Order Data

Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary), sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm). Binary encoding can also be useful, but only when the methods mentioned above cannot be used.

A family of silicon transporter structural genes in a pennate diatom Synedra ulna subsp. danica (Kütz.) Skabitsch

Silicon transporters (SIT) are the proteins, which capture silicic acid in the aquatic environment and direct it across the plasmalemma to the cytoplasm of diatoms. Diatoms utilize silicic acid to build species-specific ornamented exoskeletons and make a significant contribution to the global silica cycle, estimated at 240 ±40 Tmol a year. Recently SaSIT genes of the freshwater araphid pennate diatom Synedra acus subsp. radians are found to be present in the genome as a cluster of two structural genes (SaSIT-TD and SaSIT-TRI) encoding several concatenated copies of a SIT protein each. These structural genes could potentially be transformed into “mature” SIT proteins by means of posttranslational proteolytic cleavage. In the present study, we discovered three similar structural SuSIT genes in the genome of a closely related freshwater diatom Synedra ulna subsp. danica. Structural gene SuSIT1 is identical to structural gene SuSIT2, and the two are connected by a non-coding nucleotide DNA sequence. All the putative “mature” SITs contain conserved amino acid motifs, which are believed to be important in silicon transport. The data obtained suggest that the predicted “mature” SIT proteins may be the minimal units necessary for the transport of silicon is S. ulna subsp. danica. The comparative analysis of all available multi-SITs has allowed us to detect two conservative motifs YQXDXVYL and DXDID, located between the “mature” proteins. Aspartic acid-rich DXDID motif can, in our opinion, serve as a proteolysis site during the multi-SIT cleavage. The narrow distribution of the distances between CMLD and DXDID motifs can serve as additional evidence to the conservation of their function.

Seasonal changes in hepatic antioxidant enzyme activities of the perch Perca fluviatilis in the Upper Volga basin, Russia

Seasonal changes in several physiological endpoints of the perch Perca fluviatilis in the temperate climatic conditions were examined. Hepatic antioxidant enzyme activities (superoxide dismutase, catalase, and glutathione-S-transferase) varied dramatically throughout the annual cycle. Driven by internal and external factors, the greatest values of the studied characteristics were timed to the periods of spawning and elevated water temperature. The results of this study showed high plasticity of the fish’s antioxidant system, which allows the perch to bear naturally occurring oxidative stress.

Intra-annual variability of hepatic ethoxyresorufin-O-deethylase activity in freshwater bream Abramis brama

ABSTRACT This study presents the dynamics of hepatic ethoxyresorufin-O-deethylase activity levels in bream, Abramis brama L., with an emphasis on between-sex differences, over a year-long sampling period. Seasonal changes in ethoxyresorufin-O-deethylase activity were observed, possibly related to both internal and external factors. Significant fluctuations were witnessed in spring and summer in males and females, likely determined by changes in sex hormone levels and water temperature. Almost invariable enzyme activity was seen in bream in autumn. Two peaks in ethoxyresorufin-O-deethylase activity were registered in females in winter and early spring, while males demonstrated a gradual increase. Such marked variability manifested in females during an ice-cover period might be associated with the endogenous control of oocyte maturation by the endocrine system. Present study provides a basis for more accurate interpretation of ethoxyresorufin-O-deethylase induction in bream when using this endpoint in the field studies.This study presents the dynamics of hepatic ethoxyresorufin-O-deethylase activity levels in bream, Abramis brama L., with an emphasis on between-sex differences, over a year-long sampling period. S...

DISTANT JOINING: A SEQUENCE SAMPLING METHOD FOR COMPLEX EVOLUTIONARY HISTORIES

Motivation: Massive parallel phylogenetic analyses allow to reconstruct phylogenetic trees for every gene in genome, typically using the set of potential homologues detected via BLAST or analogue. However, if the amount of hits is too high, the dataset should be reduced to tractable size, preferably without human intervention. Currently available methods are error-prone on at least some datasets and some of them also depend on additional data which may not be available. Results: We propose a distance-based algorithm, termed Distant Joining, for phylogenetic dataset reduction that does not require any input besides sequences themselves. It was shown to be robust to both complex evolutionary histories and large data sets. We also discuss the assumptions and limitations of different sequence sampling approaches, and provide guidelines to selection of the method for a phylomic pipeline. Availability: Proof-of-concept Python implementation is available at https://github.com/SynedraAcus/sampler under the terms of CC-BY-4.0 license. Please check README for dependencies. Supplementary information: Supplementary data are available at Journal of Bioinformatics and Genomics online.