Ultrastructure of the mesonephros of whitefishes from the Lake Baikal basin.

The article presents a study of the mesonephros ultrastructure of Baikal omul Coregonus migratorius, Baikal whitefish Coregonus baicalensis, and a cross between Baikal whitefish and humpback whitefish (C. baicalensis × Coregonus pidschian). The mesonephros ultrastructure was studied using electron microscopy methods. The results of the study show that the number of mature granulocytes is a systematic feature and does not depend on the ecology of fish. The quantitative characteristics of blood cells and the ultrastructural features of leukocytes in the mesonephros are associated with the functioning of the nonspecific defence system in fish. Morphological diversity of epithelial cells in nephron tubules is the ancestral characteristic of the modern omul population, associated with geological and climatic events in the history of Lake Baikal. The development of haematopoietic tissue in the mesonephros, the ultrafine structure of ion-transporting interstitial cells, as well as some ultrastructural features found in the nephron, reflect the adaptive capabilities of the species to live in the ultra-deep Lake Baikal.

Antigenic Cartography of SARS-CoV-2.

Antigenic cartography is a tool for interpreting and visualizing antigenic differences between virus variants based on virus neutralization data. This approach has been successfully used in the selection of influenza vaccine seed strains. With the emergence of SARS-CoV-2 variants escaping vaccine-induced antibody response, adjusting COVID-19 vaccines has become essential. This review provides information on the antigenic differences between SARS-CoV-2 variants revealed by antigenic cartography and explores a potential of antigenic cartography-based methods (e.g., building antibody landscapes and neutralization breadth gain plots) for the quantitative assessment of the breadth of the antibody response. Understanding the antigenic differences of SARS-CoV-2 and the possibilities of the formed humoral immunity aids in the prompt modification of preventative vaccines against COVID-19.

Responses of zebra and quagga mussels to copper and tribytiltin exposure: Bioconcentration, metabolic and cardiac biomarkers.

One of the top ecological priorities is to find sensitive indicators for pollution monitoring. This study focuses on the bioconcentration and responses (condition index, survival, oxygen consumption, heart rates, and oxidative stress and neurotoxic effect biomarkers) of mussels from the Volga River basin, Dreissena polymorpha and Dreissena bugensis, to long-term exposure to toxic chemicals such as tributyltin (TBT, 25 and 100 ng/L) and copper (Cu, 100 and 1000 µg/L). We found that TBT was present in the tissues of zebra and quagga mussels in comparable amounts, whereas the bioconcentration factor of Cu varied depending on its concentration in water. Differences in responses between the two species were revealed. When exposed to high Cu concentrations or a Cu-TBT mixture, quagga mussels had a lower survival rate and a longer heart rate recovery time than zebra mussels. TBT treatment caused neurotoxicity (decreased acetylcholinesterase activity) and oxidative stress (increased levels of thiobarbituric acid reactive substances) in both species. TBT and Cu levels in mussel tissues correlated positively with the condition index, but correlated with the level of acetylcholinesterase in the mussel gills. The principal component analysis revealed three main components: the first consists of linear combinations of 14 variables reflecting TBT water pollution, TBT and Cu levels in mussel tissues, and biochemical indicators; the second includes Cu water concentration, cardiac tolerance, and mussel size; and the third combines weight, metabolic rate, and heart rates. Quagga mussels are less tolerable to contaminants than zebra mussels, so they may be used as a sensitive indicator.

Analysis of Predicted Amino Acid Sequences of Diatom Microtubule Center Components.

Diatoms synthesize species-specific exoskeletons inside cells under the control of the cytoskeleton and microtubule center. Previous studies have been conducted with the visualization of the microtubule center; however, its composition has not been studied and reliably established. In the present study, several components of MTOC in diatoms, GCP (gamma complex proteins), Aurora A, and centrins have been identified. Analysis of the predicted amino acid sequences of these proteins revealed structural features typical for diatoms. We analyzed the conserved amino acids and the motives necessary for the functioning of proteins. Phylogenetic analysis of GCP showed that all major groups of diatoms are distributed over phylogenetic trees according to their systematic position. This work is a theoretical study; however, it allows drawing some conclusions about the functioning of the studied components and possible ways to regulate them.

Antigenic Cartography Indicates That the Omicron BA.1 and BA.4/BA.5 Variants Remain Antigenically Distant to Ancestral SARS-CoV-2 after Sputnik V Vaccination Followed by Homologous (Sputnik V) or Heterologous (Comirnaty) Revaccination.

The rapid emergence of evasive SARS-CoV-2 variants is an ongoing challenge for COVID-19 vaccinology. Traditional virus neutralization tests provide detailed datasets of neutralization titers against the viral variants. Such datasets are difficult to interpret and do not immediately inform of the sufficiency of the breadth of the antibody response. Some of these issues could be tackled using the antigenic cartography approach. In this study, we created antigenic maps using neutralization titers of sera from donors who received the Sputnik V booster vaccine after primary Sputnik V vaccination and compared them with the antigenic maps based on serum neutralization titers of Comirnaty-boosted donors. A traditional analysis of neutralization titers against the WT (wild-type), Alpha, Beta, Delta, Omicron BA.1, and BA.4/BA.5 variants showed a significant booster humoral response after both homologous (Sputnik V) and heterologous (Comirnaty) revaccinations against all of the studied viral variants. However, despite this, a more in-depth analysis using antigenic cartography revealed that Omicron variants remain antigenically distant from the WT, which is indicative of the formation of insufficient levels of cross-neutralizing antibodies. The implications of these findings may be significant when developing a new vaccine regimen.

Histology and Ultrastructure of the Nephron and Kidney Interstitial Cells in the Atlantic Salmon (Salmo salar Linnaeus 1758) at Different Stages of Life Cycle.

This article presents data on the mesonephros histology and ultrastructure in the Atlantic salmon from the Baltic Sea and Barents Sea populations, with an emphasis on comparisons between the following ontogenetic stages: parr, smolting, adult life at sea, the adults' return to their natal river to spawn, and spawning. The ultrastructural changes in the renal corpuscle and cells of the proximal tubules of the nephron occurred as early as the smolting stage. Such changes reflect fundamental alterations during the pre-adaptation to life in saltwater. In the Barents Sea population, the adult salmon sampled in the sea had the smallest diameters of the renal corpuscle and proximal and distal tubules, the most narrow urinary space, and the thickest basement membrane. In the group of salmon that entered the mouth of the river and spent less than 24 h in freshwater, the structural rearrangements occurred only in the distal tubules. Better development of the smooth endoplasmic reticulum and a greater abundance of mitochondria in the tubule cells were observed in the adult salmon from the Barents Sea compared to those from the Baltic Sea. Cell-immunity activation was initiated during the parr-smolt transformation. Another pronounced innate-immunity response was registered in the adults returning to the river to spawn.

Taxifolin Modulates Transcriptomic Response to Heat Stress in Rainbow Trout, Oncorhynchus mykiss.

Taxifolin is a natural flavonoid known for its antioxidant, anti-inflammatory, and antiproliferative effects on animals. In this work, we have studied the effect of this compound on rainbow trout, Oncorhynchus mykiss, a major object of aquaculture, under slowly increasing ambient temperature and Gyrodactylus flatworm infection. Transcriptomic profiling of liver samples performed by using the Illumina HiSeq 2500 sequencing platform shows that a combined taxifolin/heat treatment, unlike heat treatment alone, downregulates the production of isopentenyl diphosphate, likely affecting the production of cholesterol and other sterols. Taxifolin treatment also modulates multiple apoptosis regulators and affects the expression of HSPs in response to increasing temperature. On the other hand, the expression of antioxidant enzymes in response to heat is not significantly affected by taxifolin. As for the Gyrodactylus infection, the parasite load is not affected by taxifolin treatment, although it was lower in the high-temperature group. Parasite load also did not induce a statistically significant transcriptomic response within the no heat/no taxifolin group.

Proteomics Analysis in Japanese Medaka Oryzias latipes Exposed to Humic Acid Revealed Suppression of Innate Immunity and Coagulation Proteins.

Humic acids (HA), one of the major components of dissolved organic matter, can interfere with different metabolic pathways in aquatic animals, causing various biological effects. This study aimed to provide a molecular basis for HA-related responses in fish by analyzing changes in the blood plasma proteome following short-term exposure to environmentally relevant HA concentrations using the Japanese medaka Oryzias latipes Hd-rR strain as a model organism. Proteomics data were obtained by high-performance liquid chromatography with tandem mass spectrometry analysis employing a label-free quantification approach. HA caused dysregulation of proteins involved in various biological processes, including protein folding, signaling, transport, metabolism, regulation, immune response, and coagulation. The majority of the differentially abundant proteins were down-regulated, including those involved in humoral immunity and coagulation. HA caused the decrease of the complement cascade and membrane attack complex proteins abundance, as well as proteins participating in activation and regulation of secondary hemostasis. The most pronounced suppression was observed at the highest tested HA concentration.

Unique and ancestral features in trunk kidney microanatomy and ultrastructure of omul Coregonus migratorius.

This study presents novel data on the microanatomy and ultrastructure of the omul Coregonus migratorius trunk kidney. Adult individuals of C. migratorius were sampled in the Barguzin Bay of Lake Baikal. Active leuko- and erythropoiesis were found in the interstitium of the mesonephros. For the first time, cells with radially arranged vesicles have been described in the renal interstitium of C. migratorius. The quantitative characteristics of blood cells and ultrastructural parameters of leukocytes reflected the functioning of the non-specific defence system in the organism. The share of the renal interstitium, morphological diversity of the epithelial cells of the nephron tubules, the ultrastructural features of the renal corpuscles and nephron tubules and the number of mitochondria in leukocytes and ion-transporting cells were typical for representatives of the whitefish Coregonus lavaretus complex and thus considered ancestral features of the present-day C. migratorius population reflecting its adaptive potential to living in an ultra-deep Lake Baikal.

Dataset on the effects of environmentally relevant humic acid concentrations on the liver protein profile in Japanese medaka (Oryzias latipes).

The data were obtained by a label-free quantification approach from a shotgun proteomics experiment, using STrap sample processing technique for protein digestion and high-performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS) for peptide analysis. MaxQuant data processing was used to obtain proteomics data. The dataset reflects changes in the liver protein profile of Japanese medaka exposed to 0, 5, 40 and 80 mg/L nominal concentrations of Sigma-Aldrich humic acid for 96 h. Actual concentrations of humic acid were measured using the potassium dichromate photometric method and reported in mg organic carbon/L. These proteomics data are relevant for further insights into fish stress responses to humic substances-related challenge.

Biochemical and respiratory parameters in a gastropod Radix balthica exposed to diclofenac.

Diclofenac, an anti-inflammatory drug, is often detected in natural waters in the ng/L to µg/L range, posing a threat to aquatic organisms. The study focused on the effects of diclofenac in a gastropod mollusk Radix balthica. A 72-h exposure to environmentally relevant concentrations of diclofenac caused deviations from the baseline activities of the studied enzymes in the digestive gland of snails. Acetylcholinesterase activity was induced by the end of exposure, with the most pronounced increase at 3 µg/L. Results on glutathione-S-transferase activity were nonuniform, and no significant variations were observed in thiobarbituric acid reactive substances concentrations, indicating that diclofenac did not cause oxidative stress in the digestive gland of R. balthica at 0.04-4 µg/L range. Diclofenac lowered the oxygen consumption rate in snails in a concentration-dependent manner. At concentrations ≥0.9 µg/L, animals attempted to switch aquatic respiration to breathing air to regulate their metabolic needs. The study showed that diclofenac at environmentally relevant concentrations affected the fitness of R. balthica.

Data on length-weight relationships and mean condition factor for Abramis brama and Perca fluviatilis.

Data on total weight and standard length of freshwater bream and perch, two of the most abundant fish species in the Volga River basin, were collected monthly from April 2016 to May 2017. Fish were caught using gill-nets with 50 and 80 mm mesh sizes. Linear regression analysis of log-transformed values was performed. Regression slope and intercept were used to obtain length-weight relationships and mean condition factors. The data can be used for calculation of the relative weights of given species and further efforts to develop a mathematical model for the Volga River ecosystem.

Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal.

We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers 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.

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.

Interpretation of time-of-flight distributions for neutral particles under pulsed laser evaporation using direct Monte Carlo simulation.

A theoretical study of the time-of-flight (TOF) distributions under pulsed laser evaporation in vacuum has been performed. A database of TOF distributions has been calculated by the direct simulation Monte Carlo (DSMC) method. It is shown that describing experimental TOF signals through the use of the calculated TOF database combined with a simple analysis of evaporation allows determining the irradiated surface temperature and the rate of evaporation. Analysis of experimental TOF distributions under laser ablation of niobium, copper, and graphite has been performed, with the evaluated surface temperature being well agreed with results of the thermal model calculations. General empirical dependences are proposed, which allow indentifying the regime of the laser induced thermal ablation from the TOF distributions for neutral particles without invoking the DSMC-calculated database.

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.