Human nucleolar protein SURF6/RRP14 participates in early steps of pre-rRNA processing

The biogenesis of ribosomes requires tightly controlled transcription and processing of pre-rRNA which comprises ribosomal RNAs forming the core of large and small ribosomal subunits. Early steps of the pre-rRNA processing and assembly of the ribosomal subunits require a large set of proteins that perform folding and nucleolytic cleavage of pre-rRNAs in the nucleoli. Structure and functions of proteins involved in the pre-rRNA processing have been extensively studied in the budding yeast S. cerevisiae. Functional characterization of their human homologues is complicated by the complexity of mammalian ribosomes and increased number of protein factors involved in the ribosomal biogenesis. Homologues of human nucleolar protein SURF6 from yeast and mouse, Rrp14 and Surf6, respectively, had been shown to be involved in the early steps of pre-rRNA processing. Rrp14 works as RNA chaperone in complex with proteins Ssf1 and Rrp15. Human SURF6 knockdown and overexpression were used to clarify a role of SURF6 in the early steps of pre-rRNA processing in human cell lines HeLa and HTC116. By analyzing the abundance of the rRNA precursors in cells with decreased level or overexpression of SURF6, we demonstrated that human SURF6 is involved in the maturation of rRNAs from both small and large ribosomal subunits. Changes in the SURF6 level caused by knockdown or overexpression of the protein do not result in the death of HeLa cells in contrast to murine embryonic fibroblasts, but significantly alter the distribution of cells among the phases of the cell cycle. SURF6 knockdown in both p53 sufficient and p53 deficient HCT116 human cancer cells results in elongation of G0/G1 and shortening of G2/M phase. This surprising result suggests p53 independence of SURF6 effects on the cell cycle and possible multiple functions of SURF6. Our data point to the shift from pathway 1 to pathway 2 of the rRNA biogenesis caused by the SURF6 knockdown and its likely association with p53 pathway.

The children's emotional speech recognition by adults: Cross-cultural study on Russian and Tamil language

The current study investigated the features of cross-cultural recognition of four basic emotions "joy-neutral (calm state)-sad-anger" in the spontaneous and acting speech of Indian and Russian children aged 8-12 years across Russian and Tamil languages. The research tasks were to examine the ability of Russian and Indian experts to recognize the state of Russian and Indian children by their speech, determine the acoustic features of correctly recognized speech samples, and specify the influence of the expert's language on the cross-cultural recognition of the emotional states of children. The study includes a perceptual auditory study by listeners and instrumental spectrographic analysis of child speech. Different accuracy and agreement between Russian and Indian experts were shown in recognizing the emotional states of Indian and Russian children by their speech, with more accurate recognition of the emotional state of children in their native language, in acting speech vs spontaneous speech. Both groups of experts recognize the state of anger via acting speech with the high agreement. The difference between the groups of experts was in the definition of joy, sadness, and neutral states depending on the test material with a different agreement. Speech signals with emphasized differences in acoustic patterns were more accurately classified by experts as belonging to emotions of different activation. The data showed that, despite the universality of basic emotions, on the one hand, the cultural environment affects their expression and perception, on the other hand, there are universal non-linguistic acoustic features of the voice that allow us to identify emotions via speech.

Activity Theory for the De-Structuralized Modernity

The present paper discusses perspectives of Activity Theory (AT) in the context of contemporary globalizing world, describing which we refer to the notion "De-structuralized modernity" (Sorokin and Froumin 2020). Radical changes in everyday life challenge social sciences and humanities. Approaches are in demand, which have the potential to comprehend the changing human étant and éntre. We argue that Activity Theory has the potential to face these challenges. Leontiev's AT grounds on the idea of qualitatively new mental features arising to deal with novel environmental challenges, which is much in line with J.M. Baldwin reasoning on evolution. AT also offers a method to prognosis the upcoming neoplasms. In the same time, applying classics of AT to the current reality, "De-structuralized modernity", entails the need for new theoretical elaborations of the latter, stemming from the radical transformation of the relations between individual and socio-cultural environments. A unique societal context emerges on the global level, which, on the one hand, requires individual to adapt constantly to changing socio-cultural reality, and, on the other hand, dramatically expands his/her potential for proactive actorhood transforming surrounding structures. We argue that the major and novel challenge for the individual is that maintaining the integrity and coherence of the a) Self-identity and b) system of links with the socio-cultural environment - in their dynamics and unity, has become a qualitatively different issue, much more complicated and problematic than ever before. The notion of "culture" has particular relevance and importance in this context because it allows grasping simultaneously two dimensions in their dynamic dialectical interrelations. First, the "internal" ("subjective", "in the minds") and "external" ("objective", material and institutional environment) realities. Second, individual ("micro") and societal ("macro") scales of human activities. Discussing the ways to understand these dynamics, we dispute the popular "constitutive view" on personality and refer to the concept of the "ontological shift" (Mironenko and Sorokin 2018). We also highlight how technological advancements change and "expand" human nature making it capable to deal with the outlined new tasks.

VGsim: Scalable viral genealogy simulator for global pandemic

Accurate simulation of complex biological processes is an essential component of developing and validating new technologies and inference approaches. As an effort to help contain the COVID-19 pandemic, large numbers of SARS-CoV-2 genomes have been sequenced from most regions in the world. More than 5.5 million viral sequences are publicly available as of November 2021. Many studies estimate viral genealogies from these sequences, as these can provide valuable information about the spread of the pandemic across time and space. Additionally such data are a rich source of information about molecular evolutionary processes including natural selection, for example allowing the identification of new variants with transmissibility and immunity evasion advantages. To our knowledge, there is no framework that is both efficient and flexible enough to simulate the pandemic to approximate world-scale scenarios and generate viral genealogies of millions of samples. Here, we introduce a new fast simulator VGsim which addresses the problem of simulation genealogies under epidemiological models. The simulation process is split into two phases. During the forward run the algorithm generates a chain of population-level events reflecting the dynamics of the pandemic using an hierarchical version of the Gillespie algorithm. During the backward run a coalescent-like approach generates a tree genealogy of samples conditioning on the population-level events chain generated during the forward run. Our software can model complex population structure, epistasis and immunity escape.

We develop a fast and flexible simulation software package VGsim for modeling epidemiological processes and generating genealogies of large pathogen samples. The software takes into account host population structure, pathogen evolution, host immunity and some other epidemiological aspects. The computational efficiency of the package allows to simulate genealogies of tens of millions of samples, which is important, e.g., for SARS-CoV-2 genome studies.

Spread of endemic SARS-CoV-2 lineages in Russia before April 2021

In 2021, the COVID-19 pandemic was characterized by global spread of several lineages with evidence for increased transmissibility. Throughout the pandemic, Russia has remained among the countries with the highest number of confirmed COVID-19 cases, making it a potential hotspot for emergence of novel variants. Here, we show that among the globally significant variants of concern that have spread globally by late 2020, alpha (B.1.1.7), beta (B.1.351) or gamma (P.1), none have been sampled in Russia before the end of 2020. Instead, between summer 2020 and spring 2021, the epidemic in Russia has been characterized by the spread of two lineages that were rare in most other countries: B.1.1.317 and a sublineage of B.1.1 including B.1.1.397 (hereafter, B.1.1.397+). Their frequency has increased concordantly in different parts of Russia. On top of these lineages, in late December 2020, alpha (B.1.1.7) emerged in Russia, reaching a frequency of 17.4% (95% C.I.: 12.0%-24.4%) in March 2021. Additionally, we identify three novel distinct lineages, AT.1, B.1.1.524 and B.1.1.525, that have started to spread, together reaching the frequency of 11.8% (95% C.I.: 7.5%-18.1%) in March 2021. These lineages carry combinations of several notable mutations, including the S:E484K mutation of concern, deletions at a recurrent deletion region of the spike glycoprotein (S:Δ140-142, S:Δ144 or S:Δ136-144), and nsp6:Δ106-108 (also known as ORF1a:Δ3675-3677). Community-based PCR testing indicates that these variants have continued to spread in April 2021, with the frequency of B.1.1.7 reaching 21.7% (95% C.I.: 12.3%-35.6%), and the joint frequency of B.1.1.524 and B.1.1.525, 15.2% (95% C.I.: 7.6%-28.2%). Although these variants have been displaced by the onset of delta variant in May-June 2021, lineages B.1.1.317, B.1.1.397+, AT.1, B.1.1.524 and B.1.1.525 and the combinations of mutations comprising them that are found in other lineages merit monitoring.

Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium

Estimating admixture histories is crucial for understanding the genetic diversity we see in present-day populations. Allele frequency or phylogeny-based methods are excellent for inferring the existence of admixture or its proportions. However, to estimate admixture times, spatial information from admixed chromosomes of local ancestry or the decay of admixture linkage disequilibrium (ALD) is used. One popular method, implemented in the programs ALDER and ROLLOFF, uses two-locus ALD to infer the time of a single admixture event, but is only able to estimate the time of the most recent admixture event based on this summary statistic. To address this limitation, we derive analytical expressions for the expected ALD in a three-locus system and provide a new statistical method based on these results that is able to resolve more complicated admixture histories. Using simulations, we evaluate the performance of this method on a range of different admixture histories. As an example, we apply the method to the Colombian and Mexican samples from the 1000 Genomes project. The implementation of our method is available at https://github.com/Genomics-HSE/LaNeta.

We establish a theoretical framework to model 3-locus admixture linkage disequilibrium of an admixed population taking into account the effects of genetic drift, migration and recombination. The theory is used to develop a method for estimating the times of multiple admixtures events. We demonstrate the accuracy of the method on simulated data and we apply it to previously published data from Mexican and Colombian populations to explore the complex history of American populations in the post-Colombian period.

An approach to quantitate maternal transcripts localized in sea urchin egg cortex using RT-qPCR with accurate normalization

The sea urchin egg cortex is a peripheral region of eggs comprising a cell membrane and adjacent cytoplasm, which contains actin and tubulin cytoskeleton, cortical granules and some proteins required for early development. Method for isolation of cortices from sea urchin eggs and early embryos was developed in 1970s. Since then, this method has been reliable tool to study protein localization and cytoskeletal organization in cortex of unfertilized eggs and embryos during first cleavages. This study was aimed to estimate the reliability of RT-qPCR to analyze levels of maternal transcripts that are localized in egg cortex. Firstly, we selected seven potential reference genes, 28S, Cycb, Ebr1, GAPDH, Hmg1, Smtnl1 and Ubb, the transcripts of which are maternally deposited in sea urchin eggs. The candidate reference genes were ranked by five different algorithms (BestKeeper, CV, ΔCt, geNorm and NormFinder) based on calculated level of stability in both eggs as well as isolated cortices. Our results showed that gene ranking differs in total RNA and mRNA samples, though Ubb is most suitable reference gene in both cases. To validate feasibility of comparative analysis of eggs and isolated egg cortices, we selected Daglb-2 as a gene of interest, which transcripts are potentially localized in cortex according to transcriptome analysis, and observed increased level of Daglb-2 in egg cortices by RT-qPCR. This suggests that proposed RNA isolation method with subsequent quantitative RT-qPCR analysis can be used to determine cortical association of transcripts in sea urchin eggs.

Short-term effect of COVID-19 lockdowns on atmospheric CO2, CH4 and PM2.5 concentrations in urban environment

The COVID-19 pandemic has changed all areas of human activity as it forced the authorities around the world to enact unprecedented restrictions such as "lockdowns". The low economic activity reduced the anthropogenic impact on the environment, in particular, greenhouse gases and aerosols emissions were decreased. However, the associated change in air quality is difficult to directly observe and quantify, since concentrations of these components in urban areas are affected by many other factors. In this work statistical analysis of atmospheric CO2, CH4 and PM2.5, measured in 2017-2020 in the city of Ekaterinburg, Russia, are presented. A detailed focus was made on the lockdown period from March 28 to April 30, 2020. A significant decrease in concentrations and inter-hourly variations of all studied components were observed only in the short "self-isolation" period from April 6 to April 8. The anthropogenic origin of this effect, primarily associated with the reduction in vehicular traffic, was concluded from mean diurnal cycles and air temperature correlations of all components. A decrease in the difference between measured and background CO2 and CH4 mole fractions was also found during this period. The difference was 1.3±0.2 ppm for CO2 and 8±4 ppb for CH4, which was many times lower than during any other observed periods, suggesting a short-term effect of lockdown restrictions. Overall, a negative impact on the atmosphere quickly resumed after the recovery of economic activity. The approaches in this study can be used to detect weak fluctuations of atmospheric components in other urban territories.

The SARS-CoV-2 main protease doesn't induce cell death in human cells in vitro

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19) which has extremely rapidly spread worldwide. In order to develop the effective antiviral therapies, it is required to understand the molecular mechanisms of the SARS-CoV-2 pathogenesis. The main protease, or 3C-like protease (3CLpro), plays the essential role in the coronavirus replication that makes the enzyme a promising therapeutic target. Viral enzymes are known to be multifunctional. Particularly, 3CLpro of SARS-CoV was shown to induce apoptosis in addition to its main function. In the present study we analyzed the cytotoxicity of active SARS-CoV-2 3CLpro and its inactivated form upon their individual expression in four human cell lines. For this purpose, we constructed a protein biosensor which allows to detect the proteolytic activity of SARS-CoV-2 3CLpro and confirmed the expression of the active protease in all cell lines used. We studied viability and morphology of the cells and found that both active and inactivated enzyme variants induce no cell death in contrast to the homologous 3CL protease of SARS-CoV. These results indicate that SARS-CoV-2 3CLpro is unlikely contribute to the cytopathic effect observed during viral infection directly.

Transcriptome analysis reveals high tumor heterogeneity with respect to re-activation of stemness and proliferation programs

Significant alterations in signaling pathways and transcriptional regulatory programs together represent major hallmarks of many cancers. These, among all, include the reactivation of stemness, which is registered by the expression of pathways that are active in the embryonic stem cells (ESCs). Here, we assembled gene sets that reflect the stemness and proliferation signatures and used them to analyze a large panel of RNA-seq data from The Cancer Genome Atlas (TCGA) Consortium in order to specifically assess the expression of stemness-related and proliferation-related genes across a collection of different tumor types. We introduced a metric that captures the collective similarity of the expression profile of a tumor to that of ESCs, which showed that stemness and proliferation signatures vary greatly between different tumor types. We also observed a high degree of intertumoral heterogeneity in the expression of stemness- and proliferation-related genes, which was associated with increased hazard ratios in a fraction of tumors and mirrored by high intratumoral heterogeneity and a remarkable stemness capacity in metastatic lesions across cancer cells in single cell RNA-seq datasets. Taken together, these results indicate that the expression of stemness signatures is highly heterogeneous and cannot be used as a universal determinant of cancer. This calls into question the universal validity of diagnostic tests that are based on stem cell markers.

Open-source low-cost cardiac optical mapping system

Fluorescent imaging with voltage- or calcium-sensitive dyes, known as optical mapping, is one of the indispensable modern techniques to study cardiac or neural electrophysiology, unsurpassed by temporal and spatial resolution. High-speed CMOS cameras capable of optical registration of action potential propagation are in general very costly. We present a complete solution priced below US$1,000 (including camera and lens) at the moment of publication with an open-source image acquisition and processing software. We demonstrate that the iDS UI-3130CP rev.2 camera we used in this study is capable of 200x200 977 frames per second (FPS) action potential recordings from rodent hearts, with the signal-to-noise-ratio of a conditioned signal of 16 ± 10. A comparison with a specialized MiCAM Ultimate-L camera has shown that signal-to-noise ratio (SNR) while lower is sufficient for accurate measurements of AP waveform, conduction velocity (± 0.04 m/s) and action potential duration (± 7ms) in mouse and rat hearts. We used 4-aminopyridine to prolong the action potential duration in mouse heart, thus demonstrating that the proposed system is adequate for pharmacological studies.

Assessment on facile Diels-Alder approach of α-pyrone and terpenoquinone for the expedient synthesis of various natural scaffolds

The development of highly facile synthetic procedures for the expedient synthesis of complex natural molecules is always in demand. As this aspect, the Diels-Alder reaction (DAR) has a versatile approach to the synthesis of complex natural compounds and highly regio-/stereoselcetive heterocyclic scaffolds. Additionally, α-pyrone and terpenoquinone are two versatile key intermediates that are prevalent in various bioactive natural compounds for instance, (±)-crinine, (±)-joubertinamine, (±)-pancratistatin, (-)-cyclozonarone, and 8-ephipuupehedione, etc. Hence, the current review summarizes the Diels-Alder reaction application of α-pyrone and terpenoquinone to the constructive synthesis of various natural products over the past two decades (2001-2021). Equally, it serves as a stencil for the invention and development of new synthetic strategies for high-complex molecular structured natural and heterocyclic molecules.

First population norms for the EQ-5D-3L in the Russian Federation

Purpose

The EQ–5D survey instrument is routinely applied to general and patient specific populations in many countries, as a means of measuring Health Related Quality of Life (HRQOL) and/or informing Health Technology Assessment. The instrument is the subject of growing interest in the Russian Federation, as too is Health Technology Assessment. This research is the first to systematically present the EQ–5D–3L nationally representative population norms and to examine the socioeconomic and socio-demographic characteristics of the instrument among a representative sample of the Russian population.

Methods

Based on a nationally representative health and well-being survey of the Russian population, conducted in November 2017, we establish the descriptive results, including the EQ-VAS and the EQ-5D Index, by age and gender, examine the correspondence between the EQ–5D health classifications and the separate EQ-VAS scores, and draw on a set of augmented logistic regressions to evaluate the association between the presence of problems in each dimension and various socio-economic and health-related characteristics.

Results

We find strong evidence that the EQ-5D instrument is sensitive to underlying observed and latent health experiences, that it mirrors many of the characteristics familiar from other settings but that there are Russian specificities which merit further research, particularly with respect to the anxiety/depression dimension of the instrument.

Conclusion

This research represents an important landmark for HRQOL studies in Russia as well as for the prospects of continuing to develop the scholarly and practical infrastructure necessary for Russian Health Technology Assessment to advance.

Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat

We present a comprehensive survey of cytogenetic and genomic diversity of the GGA^tA^t genepool of wheat, thereby unlocking these plant genetic resources for wheat improvement. Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite its potential huge value for wheat breeding, the tetraploid GGA^tA^t genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGA^tA^t genepool and its domestication history would further its use for wheat improvement. The paper provides the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGA^tA^t genepool. According to the results obtained, the extant GGA^tA^t genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGA^tA^t wheats, revealed group- and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. The origin and domestication history of the GGA^tA^t lineages is discussed in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGA^tA^t wheat genepool and provide the basis for an increased use of the GGA^tA^t wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.

Selection of reference genes for quantitative analysis of microRNA expression in three different types of cancer

MicroRNAs (miRNAs) are promising biomarkers in cancer research. Quantitative PCR (qPCR), also known as real-time PCR, is the most frequently used technique for measuring miRNA expression levels. The use of this technique, however, requires that expression data be normalized against reference genes. The problem is that a universal internal control for quantitative analysis of miRNA expression by qPCR has yet to be known. The aim of this work was to find the miRNAs with stable expression in the thyroid gland, brain and bone marrow according to NanoString nCounter miRNA quantification data. As a results, the most stably expressed miRNAs were as follows: miR-361-3p, -151a-3p and -29b-3p in the thyroid gland; miR-15a-5p, -194-5p and -532-5p in the brain; miR-140-5p, -148b-3p and -362-5p in bone marrow; and miR-423-5p, -28-5p and -532-5p, no matter what tissue type. These miRNAs represent promising reference genes for miRNA quantification by qPCR.

Modification of thermally expanded graphite and its effect on the properties of the amperometric biosensor

The work considered the properties of a biosensor based on a novel nanomaterial-modified thermally expanded graphite (TEGM). The main focus was on whether the procedure of additional graphite thermal expansion would affect the electrochemical properties of biosensors based on membrane fractions of acetic acid bacteria Gluconobacter oxydans. Raman spectroscopy, scanning electron microscopy and electrochemical analysis were used for the study. Raman spectra showed that the formation of TEGM led to its stratification into smaller particles and a better orderly layered structure with high "graphenization" degree. Modification of TEG led to the formation of additional cavities into which bacterial cells or bacterial membrane fractions could be immobilized and affect the electrical conductivity of the biosensors positively. Calculation of the heterogeneous charge transfer constants showed that processes occurring on the electrodes are quasi-reversible. The limiting stage of these processes is the transfer of an electron from a biological component on the electrode surface, not the diffusion of the analyte from the solution to the active centers of the enzyme. We showed the possibility of developing third-generation mediator-free biosensors for glucose detection based on TEGM, as well as of second-generation mediator biosensors for glucose, ethanol and glycerol detection.

IPSC-Derived Human Neurons with GCaMP6s Expression Allow In Vitro Study of Neurophysiological Responses to Neurochemicals

The study of human neurons and their interaction with neurochemicals is difficult due to the inability to collect primary biomaterial. However, recent advances in the cultivation of human stem cells, methods for their neuronal differentiation and chimeric fluorescent calcium indicators have allowed the creation of model systems in vitro. In this paper we report on the development of a method to obtain human neurons with the GCaMP6s calcium indicator, based on a human iPSC line with the TetON–NGN2 transgene complex. The protocol we developed allows us quickly, conveniently and efficiently obtain significant amounts of human neurons suitable for the study of various neurochemicals and their effects on specific neurophysiological activity, which can be easily registered using fluorescence microscopy. In the neurons we obtained, glutamate (Glu) induces rises in [Ca²⁺]_i which are caused by ionotropic receptors for Glu, predominantly of the NMDA-type. Taken together, these facts allow us to consider the model we have created to be a useful and successful development of this technology.

Bio-zeolite use for metal removal from copper-containing synthetic effluents

The adsorption capacity of biologically modified zeolite with respect to copper-containing effluents (Cu(II)-Fe(III), Cu(II)-Fe(III)-Ni(II), Cu(II)-Fe(II)-Zn(II), and Cu(II)-Fe(II)-Ni(II)-Zn(II)) has been investigated in order to apply it for industrial effluents treatment. Obtained bio-zeolite was characterized using neutron activation analysis, confocal laser scanning microscopy, and scanning electron microscopy. The efficiency of metal ions removal was determined as a function of pH, copper concentration, time, and temperature. The metal sorption in analyzed systems showed to be pH-dependent. The equilibrium adsorption data were interpreted using Freundlich and Langmuir isotherms and the adsorption mechanism was investigated by kinetic studies. The sorption of Cu(II) and Zn(II) fitted well pseudo-first and pseudo-second-order models, while Ni(II) sorption was better described by the Elovich model. The thermodynamic parameters, ∆G°, ∆H°, and ∆S were evaluated to understand the nature of the sorption process. Obtained results show that bio-zeolite is of interest for heavy metal ions removal from industrial effluents.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40201-021-00694-x.

ABCA1 and ABCG1 DNA methylation in epicardial adipose tissue of patients with coronary artery disease

BACKGROUND

Recent studies have focused on the potential role of epicardial adipose tissue (EAT) in the development of coronary artery disease (CAD). ABCA1 and ABCG1 transporters regulate cell cholesterol content and reverse cholesterol transport. We aimed to determine whether DNA methylation and mRNA levels of the ABCA1 and ABCG1 genes in EAT and subcutaneous adipose tissue (SAT) were associated with CAD.

METHODS

Paired EAT and SAT samples were collected from 82 patients undergoing elective cardiac surgery either for coronary artery bypass grafting (CAD group, N = 66) or valve surgery (NCAD group, N = 16). ABCA1 and ABCG1 mRNA levels in EAT and SAT samples were analyzed using real time polymerase chain reaction, ABCA1 protein levels in EAT samples were assessed by western blotting. ABCA1 and ABCG1 DNA methylation analysis was performed in 24 samples from the CAD group and 9 samples from the NCAD group via pyrosequencing.

RESULTS

DNA methylation levels in the ABCA1 promoter and ABCG1 cg27243685 and cg06500161 CpG sites were higher in EAT samples from patients with CAD compared with NCAD (21.92% vs 10.81%, p = 0.003; 71.51% vs 68.42%, p = 0.024; 46.11% vs 37.79%, p = 0.016, respectively). In patients with CAD, ABCA1 and ABCG1 DNA methylation levels were higher in EAT than in SAT samples (p < 0.05). ABCA1 mRNA levels in EAT samples were reduced in the subgroup of patients with CAD and concomitant carotid artery disease or peripheral artery disease compared with the NCAD group (p = 0.024). ABCA1 protein levels in EAT samples tended to be lower in CAD patients than in the NCAD group (p = 0.053). DNA methylation levels at the ABCG1 cg27243685 site positively correlated with plasma triglyceride concentration (r = 0.510, p = 0.008), body mass index (r = 0.556, p = 0.013) and waist-to-hip ratio (r = 0.504, p = 0.012) in SAT samples.

CONCLUSION

CAD is associated with ABCA1 and ABCG1 DNA hypermethylation in EAT. CAD with concomitant carotid artery disease or peripheral artery disease is accompanied by decreased ABCA1 gene expression in EAT. DNA methylation levels at the ABCG1 cg27243685 locus in SAT are associated with hypertriglyceridemia and obesity.

Great Vasyugan Mire: How the world's largest peatland helps addressing the world's largest problems

Peatlands cover 3% of the land, occur in 169 countries, and have-by sequestering 600 Gt of carbon-cooled the global climate by 0.6 °C. After a general review about peatlands worldwide, this paper describes the importance of the Great Vasyugan Mire and presents suggestions about its protection and future research. The World's largest peatland, the Great Vasyugan Mire in West-Siberia, forms the border between the Taiga and the Forest-Steppe biomes and harbours rare species and mire types and globally unique self-organizing patterns. Current oil and gas exploitation may arguably be largely phased out by 2050, which will pave the way for a stronger focus on the mire's role in buffering climate change, maintaining ecosystem diversity, and providing other ecosystem services. Relevant new research lines will benefit from the extensive data sets that earlier studies have gathered for other purposes. Its globally unique character as the 'largest life form on land' qualifies the Great Vasyugan Mire in its entirety to be designated as a UNESCO World Heritage Site and a Ramsar Wetland of International Importance.

Thawing permafrost and methane emission in Siberia: Synthesis of observations, reanalysis, and predictive modeling

Permafrost has been warming in the last decade at rates up to 0.39 °C 10 year-1, raising public concerns about the local and global impacts, such as methane emission. We used satellite data on atmospheric methane concentrations to retrieve information about methane emission in permafrost and non-permafrost environments in Siberia with different biogeochemical conditions in river valleys, thermokarst lakes, wetlands, and lowlands. We evaluated the statistical links with air temperature, precipitation, depth of seasonal thawing, and freezing and developed a statistical model. We demonstrated that by the mid-21st century methane emission in Siberian permafrost regions will increase by less than 20 Tg year-1, which is at the lower end of other estimates. Such changes will lead to less than 0.02 °C global temperature rise. These findings do not support the "methane bomb" concept. They demonstrate that the feedback between thawing Siberian wetlands and the global climate has been significantly overestimated.

Perspectives of climate change: A comparison of scientific understanding and local interpretations by different Western Siberian communities

We present a study of social effects of climate change as experienced by local communities, based on field research and analysis in Western Siberia, from southern taiga to tundra. The results of field anthropological research reveal different attitudes of local residents to climate change. We compare the key trends of climate change with the perspectives of local residents, based on memories, subjective experiences, and local environmental knowledge. Our results highlight a significant divergence of the subjective assessments of residents from objective data on the dynamics of changes in certain environmental elements. We explore how the human subjective perception of natural processes, their consequences and impacts, are influenced by such factors as: type of settlement, age, gender, level of education and how collective stereotypes and judgments merge information in attitude formation. We also address the need to reconcile observed climate change impacts and perceptions to enable decision-makers to engage more constructively with the local population to develop and implement adaptation.

Connecting biodiversity and human dimensions through ecosystem services: The Numto Nature Park in West Siberia

An assessment of the socio-ecological system of the Nature Park "Numto" in West Siberia was carried out based on ecosystem services (ES) mapping, applying a "cascade approach" which was modified according to the specific conditions of low commercial land-use by Indigenous Peoples and adopted with a focus on making it practicable and understandable by decision-makers. The ES values were defined through stakeholder analysis, while the mapping was based on the biophysical traits of the ecosystems and related spatial distribution of ecosystem functions. The mapped ecosystem values differ from the perceived ones. The assessment identified conflicting land uses and groups of stakeholders, including Indigenous Peoples vulnerable to future climate change-induced deficits in access to ES. The ES that are important for climate change mitigation and adaptation are not valued highly by Indigenous Peoples. ES mapping is suggested as an appropriate method for the development of straightforward recommendations for Nature Park management.

Fossil birds from the Roof of the World: The first avian fauna from High Asia and its implications for late Quaternary environments in Eastern Pamir

The Eastern Pamir (eastern Tajikistan) is a high-mountain plateau with elevations up to 7000 m, currently characterized by extremely severe environmental conditions and harboring a specialized montane fauna, which in part is shared with that of the Tibetan Plateau. The modern bird fauna of High Asia comprises a diversity of both ancient and recently diverged endemics, and thus is of general importance for historical biogeography and understanding the origin of modern high mountain ecosystems. However, the past history of the Central Asian highland avian communities remains practically unknown, as no fossil bird assemblages from high elevation areas were previously reported. In particular, it remains completely unexplored how birds responded to late Quaternary climatic fluctuations. Here we report the first fossil bird fauna from the High Asia and the first fossil birds from Tajikistan. An assemblage from the late Pleistocene through middle Holocene of Istykskaya cave (4060 m) in Eastern Pamir surprisingly comprises a remarkable diversity of waterbirds, including a few species that are completely absent from High Asia today and that were not reported globally from such high altitudes. The diversity of waterbirds incudes taxa of various ecological preferences (shorebirds, underwater and surface feeders, both zoophagous and phytophagous), strongly indicating the presence of a productive waterbody at the vicinity of the site in the past. These observations correspond to recent palaeoclimatic data, implying increased water availability in this region, currently occupied by high mountain semi-deserts. Our findings for the first time show that milder environmental conditions of late Quaternary attracted lowland species to the Central Asian highland wetlands. The reported assemblage yet contains several characteristic highland taxa, indicating a long-time persistence of some Central Asian montane faunistic elements. In particular, it includes the Tibetan Sandgrouse (Syrrhaptes tibetanus), a highly-specialized montane dweller, which is for the first time found in the fossil record.

Dynamic Foot Stimulations During Short-Term Hindlimb Unloading Prevent Dysregulation of the Neurotransmission in the Hippocampus of Rats

Spaceflight and simulated microgravity both affect learning and memory, which are mostly controlled by the hippocampus. However, data about molecular alterations in the hippocampus in real or simulated microgravity conditions are limited. Adult Wistar rats were recruited in the experiments. Here we analyzed whether short-term simulated microgravity caused by 3-day hindlimb unloading (HU) will affect the glutamatergic and GABAergic systems of the hippocampus and how dynamic foot stimulation (DFS) to the plantar surface applied during HU can contribute in the regulation of hippocampus functioning. The results demonstrated a decreased expression of vesicular glutamate transporters 1 and 2 (VGLUT1/2) in the hippocampus after 3 days of HU, while glutamate decarboxylase 67 (GAD67) expression was not affected. HU also significantly induced Akt signaling and transcriptional factor CREB that are supposed to activate the neuroprotective mechanisms. On the other hand, DFS led to normalization of VGLUT1/2 expression and activity of Akt and CREB. Analysis of exocytosis proteins revealed the inhibition of SNAP-25, VAMP-2, and syntaxin 1 expression in DFS group proposing attenuation of excitatory neurotransmission. Thus, we revealed that short-term HU causes dysregulation of glutamatergic system of the hippocampus, but, at the same time, stimulates neuroprotective Akt-dependent mechanism. In addition, most importantly, we demonstrated positive effect of DFS on the hippocampus functioning that probably depends on the regulation of neurotransmitter exocytosis.

Effect of stimulus orientation and intensity on short-interval intracortical inhibition (SICI) and facilitation (SICF): A multi-channel transcranial magnetic stimulation study

Besides stimulus intensities and interstimulus intervals (ISI), the electric field (E-field) orientation is known to affect both short-interval intracortical inhibition (SICI) and facilitation (SICF) in paired-pulse transcranial magnetic stimulation (TMS). However, it has yet to be established how distinct orientations of the conditioning (CS) and test stimuli (TS) affect the SICI and SICF generation. With the use of a multi-channel TMS transducer that provides electronic control of the stimulus orientation and intensity, we aimed to investigate how changes in the CS and TS orientation affect the strength of SICI and SICF. We hypothesized that the CS orientation would play a major role for SICF than for SICI, whereas the CS intensity would be more critical for SICI than for SICF. In eight healthy subjects, we tested two ISIs (1.5 and 2.7 ms), two CS and TS orientations (anteromedial (AM) and posteromedial (PM)), and four CS intensities (50, 70, 90, and 110% of the resting motor threshold (RMT)). The TS intensity was fixed at 110% RMT. The intensities were adjusted to the corresponding RMT in the AM and PM orientations. SICI and SICF were observed in all tested CS and TS orientations. SICI depended on the CS intensity in a U-shaped manner in any combination of the CS and TS orientations. With 70% and 90% RMT CS intensities, stronger PM-oriented CS induced stronger inhibition than weaker AM-oriented CS. Similar SICF was observed for any CS orientation. Neither SICI nor SICF depended on the TS orientation. We demonstrated that SICI and SICF could be elicited by the CS perpendicular to the TS, which indicates that these stimuli affected either overlapping or strongly connected neuronal populations. We concluded that SICI is primarily sensitive to the CS intensity and that CS intensity adjustment resulted in similar SICF for different CS orientations.

Mild phenotype of knockouts of the major apurinic/apyrimidinic endonuclease APEX1 in a non-cancer human cell line

The major human apurinic/apyrimidinic (AP) site endonuclease, APEX1, is a central player in the base excision DNA repair (BER) pathway and has a role in the regulation of DNA binding by transcription factors. In vertebrates, APEX1 knockouts are embryonic lethal, and only a handful of knockout cell lines are known. To facilitate studies of multiple functions of this protein in human cells, we have used the CRISPR/Cas9 system to knock out the APEX1 gene in a widely used non-cancer hypotriploid HEK 293FT cell line. Two stable knockout lines were obtained, one carrying two single-base deletion alleles and one single-base insertion allele in exon 3, another homozygous in the single-base insertion allele. Both mutations cause a frameshift that leads to premature translation termination before the start of the protein's catalytic domain. Both cell lines totally lacked the APEX1 protein and AP site-cleaving activity, and showed significantly lower levels of the APEX1 transcript. The APEX1-null cells were unable to support BER on uracil- or AP site-containing substrates. Phenotypically, they showed a moderately increased sensitivity to methyl methanesulfonate (MMS; ~2-fold lower EC50 compared with wild-type cells), and their background level of natural AP sites detected by the aldehyde-reactive probe was elevated ~1.5-2-fold. However, the knockout lines retained a nearly wild-type sensitivity to oxidizing agents hydrogen peroxide and potassium bromate. Interestingly, despite the increased MMS cytotoxicity, we observed no additional increase in AP sites in knockout cells upon MMS treatment, which could indicate their conversion into more toxic products in the absence of repair. Overall, the relatively mild cell phenotype in the absence of APEX1-dependent BER suggests that mammalian cells possess mechanisms of tolerance or alternative repair of AP sites. The knockout derivatives of the extensively characterized HEK 293FT cell line may provide a valuable tool for studies of APEX1 in DNA repair and beyond.

Spectral and time-resolved photoluminescence of human platelets doped with platinum nanoparticles

This paper describes a detailed study of spectral and time-resolved photoprocesses in human platelets and their complexes with platinum (Pt) nanoparticles (NPs). Fluorescence, quantum yield, and platelet amino acid lifetime changes in the presence and without femtosecond ablated platinum NPs have been studied. Fluorescence spectroscopy analysis of main fluorescent amino acids and their residues (tyrosine (Tyr), tryptophan (Trp), and phenylalanine (Phe)) belonging to the platelet membrane have been performed. The possibility of energy transfer between Pt NPs and the platelet membrane has been revealed. Förster Resonance Energy Transfer (FRET) model was used to perform the quantitative evaluation of energy transfer parameters. The prospects of Pt NPs usage deals with quenching-based sensing for pathology's based on platelet conformations as cardiovascular diseases have been demonstrated.

A strategy for mapping biophysical to abstract neuronal network models applied to primary visual cortex

A fundamental challenge for the theoretical study of neuronal networks is to make the link between complex biophysical models based directly on experimental data, to progressively simpler mathematical models that allow the derivation of general operating principles. We present a strategy that successively maps a relatively detailed biophysical population model, comprising conductance-based Hodgkin-Huxley type neuron models with connectivity rules derived from anatomical data, to various representations with fewer parameters, finishing with a firing rate network model that permits analysis. We apply this methodology to primary visual cortex of higher mammals, focusing on the functional property of stimulus orientation selectivity of receptive fields of individual neurons. The mapping produces compact expressions for the parameters of the abstract model that clearly identify the impact of specific electrophysiological and anatomical parameters on the analytical results, in particular as manifested by specific functional signatures of visual cortex, including input-output sharpening, conductance invariance, virtual rotation and the tilt after effect. Importantly, qualitative differences between model behaviours point out consequences of various simplifications. The strategy may be applied to other neuronal systems with appropriate modifications.

A hierarchy of theoretical approaches to study a neuronal network depends on a tradeoff between biological fidelity and mathematical tractibility. Biophysically-detailed models consider cellular mechanisms and anatomically defined synaptic circuits, but are often too complex to reveal insights into fundamental principles. In contrast, increasingly abstract reduced models facilitate analytical insights. To better ground the latter to the underlying biology, we describe a systematic procedure to move across the model hierarchy that allows understanding how changes in biological parameters—physiological, pathophysiological, or because of new data—impact the behaviour of the network. We apply this approach to mammalian primary visual cortex, and examine how the different models in the hierarchy reproduce functional signatures of this area, in particular the tuning of neurons to the orientation of a visual stimulus. Our work provides a navigation of the complex parameter space of neural network models faithful to biology, as well as highlighting how simplifications made for mathematical convenience can fundamentally change their behaviour.

Thermal remodelling of Alternanthera mosaic virus virions and virus-like particles into protein spherical particles

The present work addresses the thermal remodelling of flexible plant viruses with a helical structure and virus-like particles (VLPs). Here, for the first time, the possibility of filamentous Alternanthera mosaic virus (AltMV) virions' thermal transition into structurally modified spherical particles (SP) has been demonstrated. The work has established differences in formation conditions of SP from virions (SPV) and VLPs (SPVLP) that are in accordance with structural data (on AltMV virions and VLPs). SP originate from AltMV virions through an intermediate stage. However, the same intermediate stage was not detected during AltMV VLPs' structural remodelling. According to the biochemical analysis, AltMV SPV consist of protein and do not include RNA. The structural characterisation of AltMV SPV/VLP by circular dichroism, intrinsic fluorescence spectroscopy and thioflavin T fluorescence assay has been performed. AltMV SPV/VLP adsorption properties and the availability of chemically reactive surface amino acids have been analysed. The revealed characteristics of AltMV SPV/VLP indicate that they could be applied as protein platforms for target molecules presentation and for the design of functionally active complexes.

E/Z isomerization of astaxanthin and its monoesters in vitro under the exposure to light or heat and in overilluminated Haematococcus pluvialis cells

Thermo- and photoisomerization of astaxanthin was investigated in a model system (solutions in methanol and chloroform), and the dynamics of astaxanthin isomers and esters content was analyzed in Haematococcus pluvialis green algal cells exposed to factors inducing astaxanthin accumulation. In both systems, the astaxanthin isomerization process seems to be defined by a) the action of light (or heat), and b) the dielectric constant of the surrounding medium. Upon heating, the accumulation of Z-isomers occurred in a model system during the entire incubation period. For the first 5 h of illumination, both Z-isomers accumulated in the solutions up to 5%, and then their content decreased. The accumulated amount of the Z-isomers in the cells of H. pluvialis was found to reach 42% of the total content of astaxanthin initially, and then it decreased during the experiment. The results lead to a conclusion that both cultivation of H. pluvialis culture in specific conditions and heat treatment of the resulting extracts from it might be efficient for obtaining large amounts of economically useful astaxanthin Z-isomer.

Replacement of Arg in the conserved N-terminal RLFDQxFG motif affects physico-chemical properties and chaperone-like activity of human small heat shock protein HspB8 (Hsp22)

The small heat shock protein (sHsp) called HspB8 (formerly, Hsp22) is one of the least typical sHsp members, whose oligomerization status remains debatable. Here we analyze the effect of mutations in a highly conservative sequence located in the N-terminal domain of human HspB8 on its physico-chemical properties and chaperone-like activity. According to size-exclusion chromatography coupled to multi-angle light scattering, the wild type (WT) HspB8 is present as dominating monomeric species (~24 kDa) and a small fraction of oligomers (~60 kDa). The R29A amino acid substitution leads to the predominant formation of 60-kDa oligomers, leaving only a small fraction of monomers. Deletion of the 28–32 pentapeptide (Δ mutant) results in the formation of minor quantities of dimers (~49 kDa) and large quantities of the 24-kDa monomers. Both the WT protein and its Δ mutant efficiently bind a hydrophobic probe bis-ANS and are relatively rapidly hydrolyzed by chymotrypsin, whereas the R29A mutant weakly binds bis-ANS and resists chymotrypsinolysis. In contrast to HspB8 WT and its Δ mutant, which are well phosphorylated by cAMP-dependent and ERK1 protein kinases, the R29A mutant is poorly phosphorylated. R29A mutation affects the chaperone-like activity of HspB8 measured in vitro. It is concluded that the irreplaceable Arg residue located in the only highly conservative motif in the N-terminal domain of all sHsp proteins affects the oligomeric structure and key properties of HspB8.

Volatiles and Refractories in Surface-Bounded Exospheres in the Inner Solar System

Volatiles and refractories represent the two end-members in the volatility range of species in any surface-bounded exosphere. Volatiles include elements that do not interact strongly with the surface, such as neon (detected on the Moon) and helium (detected both on the Moon and at Mercury), but also argon, a noble gas (detected on the Moon) that surprisingly adsorbs at the cold lunar nighttime surface. Refractories include species such as calcium, magnesium, iron, and aluminum, all of which have very strong bonds with the lunar surface and thus need energetic processes to be ejected into the exosphere. Here we focus on the properties of species that have been detected in the exospheres of inner Solar System bodies, specifically the Moon and Mercury, and how they provide important information to understand source and loss processes of these exospheres, as well as their dependence on variations in external drivers.

Myosin 1C isoform A is a novel candidate diagnostic marker for prostate cancer

Early diagnosis of prostate cancer is a challenging issue due to the lack of specific markers. Therefore, a sensitive diagnostic marker that is expressed or upregulated exclusively in prostate cancer cells would facilitate diagnostic procedures and ensure a better outcome. We evaluated the expression of myosin 1C isoform A in 5 prostate cell lines, 41 prostate cancer cases, and 11 benign hyperplasias. We analyzed the expression of 12 surface molecules on prostate cancer cells by flow cytometry and analyzed whether high or low myosin 1C isoform A expression could be attributed to a distinct phenotype of prostate cancer cells. Median myosin 1C isoform A expression in prostate cancer samples and cancer cell lines was 2 orders of magnitude higher than in benign prostate hyperplasia. Based on isoform A expression, we could also distinguish clinical stage 2 from clinical stage 3. Among cell lines, PC-3 cells with the highest myosin 1C isoform A level had diminished numbers of CD10/CD13-positive cells and increased numbers of CD29 (integrin β1), CD38, CD54 (ICAM1) positive cells. The surface phenotype of clinical samples was similar to prostate cancer cell lines with high isoform A expression and could be described as CD10-/CD13- with heterogeneous expression of other markers. Both for cell lines and cancer specimens we observed the strong correlation of high myosin 1C isoform A mRNA expression and elevated levels of CD29 and CD54, suggesting a more adhesive phenotype for cells with high isoform A expression. Compared to normal tissue, prostate cancer samples had also reduced numbers of CD24- and CD38-positive cells. Our data suggest that a high level of myosin 1C isoform A is a specific marker both for prostate cancer cells and prostate cancer cell lines. High expression of isoform A is associated with less activated (CD24/CD38 low) and more adhesive (CD29/CD54 high) surface phenotype compared to benign prostate tissue.

Hsp70 affects memory formation and behaviorally relevant gene expression in Drosophila melanogaster

Heat shock proteins, in particular Hsp70, play a central role in proteostasis in eukaryotic cells. Due to its chaperone properties, Hsp70 is involved in various processes after stress and under normal physiological conditions. In contrast to mammals and many Diptera species, inducible members of the Hsp70 family in Drosophila are constitutively synthesized at a low level and undergo dramatic induction after temperature elevation or other forms of stress. In the courtship suppression paradigm used in this study, Drosophila males that have been repeatedly rejected by mated females during courtship are less likely than naive males to court other females. Although numerous genes with known function were identified to play important roles in long-term memory, there is, to the best of our knowledge, no direct evidence implicating Hsp70 in this process. To elucidate a possible role of Hsp70 in memory formation, we used D. melanogaster strains containing different hsp70 copy numbers, including strains carrying a deletion of all six hsp70 genes. Our investigations exploring the memory of courtship rejection paradigm demonstrated that a low constitutive level of Hsp70 is apparently required for learning and the formation of short and long-term memories in males. The performed transcriptomic studies demonstrate that males with different hsp70 copy numbers differ significantly in the expression of a few definite groups of genes involved in mating, reproduction, and immunity in response to rejection. Specifically, our analysis reveals several major pathways that depend on the presence of hsp70 in the genome and participate in memory formation and consolidation, including the cAMP signaling cascade.

Plant CSR types in the north: comparing the morphological and morpho-physiological approaches

Grime's competition-stress-ruderal (CSR) theory is widely used to study plant species' responses to multiple environmental factors. We compared two models to allocate CSR types the global "StrateFy" model (Pierce et al. Funct Ecol, 31:444-457, 2017) and a locally developed morpho-physiological model (Novakovskiy et al. Int J Ecol, p e1323614, 2016). The "StrateFy" model is based on three morphological leaf traits: leaf area (LA), leaf dry matter content (LDMC) and specific leaf area (SLA). The morpho-physiological model additionally uses plant height (PH), leaf dry weight (LDW), photosynthetic capacity (PN) and respiration rate (RD), leaf nitrogen, and carbon concentration (LNC, LCC). We applied both models to 74 plant species, the traits of which were measured at mountain (Northern Urals) and plane (Komi Republic, Russia) landscapes of European Northeast. The comparison of the calculated C, S, and R scores showed two groups of species with large and unidirectional differences. The first group consists of species with a shift from S (morpho-physiological model) to CR (StrateFy model) strategy. Species of this group are typical for deep shaded habitats and characterized by low LDMC (10-25%) and high SLA (30-60 mm² mg^-1). The second group consists of C species (morpho-physiological model) which were classified as S (StrateFy model) strategy. This group includes mainly tall shrubs, graminoids, and forbs with relatively small leaves (300-2000 mm²). In our opinion, the CSR strategies obtained by the morpho-physiological model showed better agreement with the basic principles underlying Grime's theory. The use of a limited number of morphological traits (LA, LDMC, SLA) in the StrateFy model does not always allow to determine the life strategy correctly. For example, these traits are insufficient for a clear separation of deeply shaded stress-tolerant species and ruderals. On the other hand, the use of the morpho-physiological model requires a large number of field measurements, which makes it difficult to use this model to allocate CSR strategies for a large number of species.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00973-9.

Influence of Bacillus thuringiensis and avermectins on gut physiology and microbiota in Colorado potato beetle: Impact of enterobacteria on susceptibility to insecticides

Gut physiology and the bacterial community play crucial roles in insect susceptibility to infections and insecticides. Interactions among Colorado potato beetle Leptinotarsa decemlineata (Say), its bacterial associates, pathogens and xenobiotics have been insufficiently studied. In this paper, we present our study of the survival, midgut histopathology, activity of digestive enzymes and bacterial communities of L. decemlineata larvae under the influence of Bacillus thuringiensis var. tenebrionis (morrissoni) (Bt), a natural complex of avermectins and a combination of both agents. Moreover, we estimated the impact of culturable enterobacteria on the susceptibility of the larvae to Bt and avermectins. An additive effect between Bt and avermectins was established regarding the mortality of the larvae. Both agents led to the destruction of midgut tissues, a decrease in the activity of alpha-amylases and alkaline proteinases, a decrease in the Spiroplasma leptinotarsae relative abundance and a strong elevation of Enterobacteriaceae abundance in the midgut. Moreover, an elevation of the enterobacterial CFU count was observed under the influence of Bt and avermectins, and the greatest enhancement was observed after combined treatment. Insects pretreated with antibiotics were less susceptible to Bt and avermectins, but reintroduction of the predominant enterobacteria Enterobacter ludwigii, Citrobacter freundii and Serratia marcescens increased susceptibility to both agents. We suggest that enterobacteria play an important role in the acceleration of Bt infection and avermectin toxicoses in L. decemlineata and that the additive effect between Bt and avermectin may be mediated by alterations in the bacterial community.

Wear patterns and dental functioning in an Early Cretaceous stegosaur from Yakutia, Eastern Russia

Isolated stegosaurian teeth from the Early Cretaceous high-latitude (palaeolatitude estimate of N 62°- 66.5°) Teete locality in Yakutia (Eastern Siberia, Russia) are characterized by a labiolingually compressed, slightly asymmetrical and mesiodistally denticulated (9-14 denticles) crown, a pronounced ring-like cingulum, as well as a "complex network of secondary ridges". The 63 teeth (found during on-site excavation in 2012, 2017-2019 and screen-washing in 2017-2019) most likely belong to one species of a derived (stegosaurine) stegosaur. Most of the teeth exhibit a high degree of wear and up to three wear facets has been observed on a single tooth. The prevalence of worn teeth with up to three wear facets and the presence of different types of facets (including steeply inclined and groove-like) indicate the tooth-tooth contact and precise dental occlusion in the Teete stegosaur. The microwear pattern (mesiodistally or slightly obliquely oriented scratches; differently oriented straight and curved scratches on some wear facets) suggest a complex jaw mechanism with palinal jaw motion. Histological analysis revealed that the Teete stegosaur is characterized by relatively short tooth formation time (95 days) and the presence of a "wavy enamel pattern". Discoveries of a "wavy enamel pattern" in the Teete stegosaur, in a Middle Jurassic stegosaur from Western Siberia, and in the basal ceratopsian Psittacosaurus, suggest that this histological feature is common for different ornithischian clades, including ornithopods, marginocephalians, and thyreophorans. A juvenile tooth in the Teete sample indicates that stegosaurs were year-round residents and reproduced in high latitudes. The combination of high degree of tooth wear with formation of multiple wear facets, complex jaw motions, relatively short tooth formation time and possibly high tooth replacement rates is interpreted as a special adaptation for a life in high-latitude conditions or, alternatively, as a common stegosaurian adaptation making stegosaurs a successful group of herbivorous dinosaurs in the Middle Jurassic-Early Cretaceous and enabeling them to live in both low- and high-latitude ecosystems.

Brownian dynamics simulation of protofilament relaxation during rapid freezing

Electron cryo-microscopy (Cryo-EM) is a powerful method for visualizing biological objects with up to near-angstrom resolution. Instead of chemical fixation, the method relies on very rapid freezing to immobilize the sample. Under these conditions, crystalline ice does not have time to form and distort structure. For many practical applications, the rate of cooling is fast enough to consider sample immobilization instantaneous, but in some cases, a more rigorous analysis of structure relaxation during freezing could be essential. This difficult yet important problem has been significantly under-reported in the literature, despite spectacular recent developments in Cryo-EM. Here we use Brownian dynamics modeling to examine theoretically the possible effects of cryo-immobilization on the apparent shapes of biological polymers. The main focus of our study is on tubulin protofilaments. These structures are integral parts of microtubules, which in turn are key elements of the cellular skeleton, essential for intracellular transport, maintenance of cell shape, cell division and migration. We theoretically examine the extent of protofilament relaxation within the freezing time as a function of the cooling rate, the filament's flexural rigidity, and the effect of cooling on water's viscosity. Our modeling suggests that practically achievable cooling rates are not rapid enough to capture tubulin protofilaments in conformations that are incompletely relaxed, suggesting that structures seen by cryo-EM are good approximations to physiological shapes. This prediction is confirmed by our analysis of curvatures of tubulin protofilaments, using samples, prepared and visualized with a variety of methods. We find, however, that cryofixation may capture incompletely relaxed shapes of more flexible polymers, and it may affect Cryo-EM-based measurements of their persistence lengths. This analysis will be valuable for understanding of structures of different types of biopolymers, observed with Cryo-EM.

Structure Investigations of Islands with Atomic-Scale Boron-Carbon Bilayers in Heavily Boron-Doped Diamond Single Crystal: Origin of Stepwise Tensile Stress

The detailed studies of the surface structure of synthetic boron-doped diamond single crystals using both conventional X-ray and synchrotron nano- and microbeam diffraction, as well as atomic force microscopy and micro-Raman spectroscopy, were carried out to clarify the recently discovered features in them. The arbitrary shaped islands towering above the (111) diamond surface are formed at the final stage of the crystal growth. Their lateral dimensions are from several to tens of microns and their height is from 0.5 to 3 μm. The highly nonequilibrium conditions of crystal growth enhance the boron solubility and, therefore, lead to an increase of the boron concentrations in the islands on the surface up to 10²² cm^-3, eventually generating significant stresses in them. The stress in the islands is found to be the volumetric tensile stress. This conclusion is based on the stepwise shift of the diamond Raman peak toward lower frequencies from 1328 to 1300 cm^-1 in various islands and on the observation of the shift of three low-intensity reflections at 2-theta Bragg angles of 41.468°, 41.940° and 42.413° in the X-ray diffractogram to the left relative to the (111) diamond reflection at 2theta = 43.93°. We believe that the origin of the stepwise tensile stress is a discrete change in the distances between boron-carbon layers with the step of 6.18 Å. This supposition explains also the stepwise (step of 5 cm^-1) behavior of the diamond Raman peak shift. Two approaches based on the combined application of Raman scattering and X-ray diffraction data allowed determination of the values of stresses both in lateral and normal directions. The maximum tensile stress in the direction normal to the surface reaches 63.6 GPa, close to the fracture limit of diamond, equal to 90 GPa along the [111] crystallographic direction. The presented experimental results unambiguously confirm our previously proposed structural model of the boron-doped diamond containing two-dimensional boron-carbon nanosheets and bilayers.

Simultaneous bidirectional hindlimb locomotion in decerebrate cats

We show that epidural spinal cord stimulation can elicit stable bidirectional locomotion of decerebrate cats on a split-belt treadmill. The stepping pattern of one limb was similar to unidirectional forward walking and, the other-was similar to unidirectional backward walking. This confirms that spinal and brainstem circuitry are sufficient to control such complex and extraordinary motor tasks driven by somatosensory input. Interlimb coordination during forward and backward walking was preserved in 2 out of 4 animals during 'extreme' conditions when one of the treadmill belts was stopped. Bidirectional locomotion worsened but was still possible after temporary spinalization by cooling the spinal cord on a low thoracic level. These present evidence for the great degree of the automatism for this stepping mode defined by the spinal neuronal networks.

The effect of some antiseptic drugs on the energy transfer in chromatophore photosynthetic membranes of purple non-sulfur bacteria Rhodobacter sphaeroides

Chromatophores of purple non-sulfur bacteria (PNSB) are invaginations of the cytoplasmic membrane that contain a relatively simple system of light-harvesting protein-pigment complexes, a photosynthetic reaction center (RC), a cytochrome complex, and ATP synthase, which transform light energy into the energy of synthesized ATP. The high content of negatively charged phosphatidylglycerol (PG) and cardiolipin (CL) in PNSB chromatophore membranes makes these structures potential targets that bind cationic antiseptics. We used the methods of stationary and kinetic fluorescence spectroscopy to study the effect of some cationic antiseptics (chlorhexidine, picloxydine, miramistin, and octenidine at concentrations up to 100 μM) on the spectral and kinetic characteristics of the components of the photosynthetic apparatus of Rhodobacter sphaeroides chromatophores. Here we present the experimental data on the reduced efficiency of light energy conversion in the chromatophore membranes isolated from the photosynthetic bacterium Rb. sphaeroides in the presence of cationic antiseptics. The addition of antiseptics did not affect the energy transfer between the light-harvesting LH1 complex and reaction center (RC). However, it significantly reduced the efficiency of the interaction between the LH2 and LH1 complexes. The effect was maximal with 100 μM octenidine. It has been proved that molecules of cationic antiseptics, which apparently bind to the heads of negatively charged cardiolipin molecules located in the rings of light-harvesting pigments on the cytoplasmic surface of the chromatophores, can disturb the optimal conditions for efficient energy migration in chromatophore membranes.

Rutting vocal display in male impala (Aepyceros melampus) and overlap with alarm context

BACKGROUND

The rutting vocal display of male impala Aepyceros melampus is unique for its complexity among ruminants. This study investigates bouts of rutting calls produced towards potential mates and rival males by free-ranging male impala in Namibia. In particular, a comparison of male rutting and alarm snorts is conducted, inspired by earlier findings of mate guarding by using alarm snorts in male topi Damaliscus lunatus.

RESULTS

Rutting male impala produced 4-38 (13.5 ± 6.5) rutting calls per bout. We analyzed 201 bouts, containing in total 2709 rutting calls of five types: continuous roars produced within a single exhalation-inhalation cycle; interrupted roars including few exhalation-inhalation cycles; pant-roars distinctive by a pant-phase with rapidly alternating inhalations and exhalations; usual snorts lacking any roar part; and roar-snorts starting with a short roar part. Bouts mostly started and ended with usual snorts. Continuous roars were the shortest roars. The average duration of the exhalatory phase was longest in the continuous roars and shortest in the pant-roars. The average fundamental frequency (49.7-51.4 Hz) did not differ between roar types. Vocal tract length, calculated by using measurements of the first four vocal tract resonances (formants), ranged within 381-382 mm in all roar types. In the studied male impala, rutting snorts within bouts of rutting calls were longer and had higher values of the upper quartile in the call spectra than alarm snorts produced towards potential danger.

CONCLUSIONS

Additional inhalations during the emission of the interrupted and pant-roars prolong their duration compared to the continuous roars but do not affect the fundamental frequency or the degree of larynx retraction while roaring. Alarm snorts are separated from one another by large intervals, whereas the intervals between rutting snorts within bouts are short. Sometimes, rutting snorts alternate with roars, whereas alarm snorts do not. Therefore, it is not the acoustic structure of individual snorts but the temporal sequence and the occasional association with another call type that defines snorts as either rutting or alarm snorts. The rutting snorts of male impala may function to attract the attention of receptive females and delay their departure from a male's harem or territory.

Mechanism of the historical and the ongoing Vulcanian eruptions of Ebeko volcano, Northern Kuriles

Ebeko is one of the most active volcanoes of the Kurile island arc, producing frequent mild Vulcanian explosions with eruption clouds up to 5 km high. The volcano poses a serious threat to the Severo-Kurilsk town with a population of around 2500 inhabitants, located at a distance of only 7 km on a fan of the volcano's laharic deposits. Here, we report an overview of the activity of the volcano in the 20th-21st centuries and the results of our geological and petrological investigations of the ongoing Vulcanian eruption that started in 2016. We have found that eruptions of Ebeko span a range of mechanisms from purely magmatic to phreatic/hydrothermal. Three of its historical eruptions (the 1934-1935, 1987-1991, and the 2016-ongoing) involved fresh magma, while during the others (1967-1971, 2009-2011) fresh magma was not erupted. Juvenile material of the ongoing eruption represents highly crystalline and highly viscous (more than 10⁸ pa s) low-silica (56-58 wt% SiO₂) andesite. Historical data and our observations of the ongoing eruption allowed us to suggest a functional model of the volcano where Vulcanian explosions are caused by shallow intrusions of small diapir-like batches of strongly crystallized and highly viscous andesitic magma ascending into water-saturated, hydrothermally altered rocks composing the volcano summit. We suggest that the diapir's ascent is governed by their positive buoyancy. Some of the diapirs reach and breach the ground surface producing magmatic eruptions of Ebeko, while the others are stuck at the shallow subsurface level and feed intensive hydrothermal activity as well as phreatic eruptions of the volcano. Positive buoyancy of the diapirs is too weak to allow them to extrude high above the ground surface to form lava domes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00445-020-01426-z.

Multinuclear MRI Research

The presented data clearly demonstrate that multinuclear MRI has a great potential in research and clinical fields. The biomedical value of many heavy nuclei that are part of drugs, contrast agents, and molecular complexes in live tissues emphasizes the need for creating and using MRI scanners tuned to the Larmor frequencies of such nuclei. This article discusses a number of specific problems solved with the use of multinuclear MRI. Since the sensitivity of the MRI on heavy nuclei, as a rule, is insufficient for obtaining images of satisfactory quality, it is proposed to use hyperpolarization techniques for preparing objects for the MRI diagnostics. However, bearing in mind the high cost of hyperpolarization techniques, alternative approaches using contrast agents normally absent in tissues can be more suitable in certain situations. For instance, due to the absence of fluorine in the body, ¹⁹F MRI allows for successful diagnostics of the respiratory tract and lungs filled with fluorine-containing gas, detecting the location of the blood substitute Perftoran® in the body, monitoring the transport along the gastrointestinal tract of a capsule filled with a preparation containing fluorine-19 nuclei, etc. The possibility of non-invasive local measurements of the concentration of sodium-23 in the body, which, in case of a deviation from the norm, is linked to such pathologies as diabetes, hypertension, renal failure, and many others, is also demonstrated. Reported as well is the creation of transmitting and receiving infrastructure that makes possible effective MRI measurements at low fields (of about 0.5 T) at 10 Larmor frequencies corresponding to the nuclei of hydrogen, deuterium, fluorine, boron, chlorine, sodium, carbon, phosphorus, silicon and oxygen.

A new approach to estimating the prevalence of hereditary hearing loss: An analysis of the distribution of sign language users based on census data in Russia

The absence of comparable epidemiological data challenges the correct estimation of the prevalence of congenital hearing loss (HL) around the world. Sign language (SL) is known as the main type of communication of deaf people. We suggest that the distribution of SL can be interpreted as an indirect indicator of the prevalence of congenital HL. Since a significant part of congenital HL is due to genetic causes, an assessment of the distribution of SL users can reveal regions with an extensive accumulation of hereditary HL. For the first time, we analyzed the data on the distribution of SL users that became available for the total population of Russia by the 2010 census. Seventy-three out of 85 federal regions of Russia were ranked into three groups by the 25th and 75th percentiles of the proportion of SL users: 14 regions-"low proportion"; 48 regions-"average proportion"; and 11 regions-"high proportion". We consider that the observed uneven prevalence of SL users can reflect underlying hereditary forms of congenital HL accumulated in certain populations by specific genetic background and population structure. At least, the data from this study indicate that the highest proportions of SL users detected in some Siberian regions are consistent with the reported accumulation of specific hereditary HL forms in indigenous Yakut, Tuvinian and Altaian populations.

Bacillus-infecting bacteriophage Izhevsk harbors thermostable endolysin with broad range specificity

Several bacterial species belonging to the Bacillus cereus group are known to be causative agents of food poisoning and severe human diseases. Bacteriophages and their lytic enzymes called endolysins have been widely shown to provide for a supplemental or primary means of treating bacterial infections. In this work we present a new broad-host-range phage Izhevsk, which infects the members of the Bacillus cereus group. Transmission electron microscopy, genome sequencing and comparative analyses revealed that Izhevsk is a temperate phage with Siphoviridae morphology and belongs to the same genus as the previously described but taxonomically unclassified bacteriophages Tsamsa and Diildio. The Ply57 endolysin of Izhevsk phage has broad-spectrum activity against B. cereus sensu lato. The thermolability of Ply57 is higher than that of the PlyG of Wβ phage. This work contributes to our current understanding of phage biodiversity and may be useful for further development of efficient antimicrobials aimed at diagnosing and treating infectious diseases and food contaminations caused by the Bacillus cereus group of bacteria.

High genetic diversity of ancient horses from the Ukok Plateau

A growing number of researchers studying horse domestication come to a conclusion that this process happened in multiple locations and involved multiple wild maternal lines. The most promising approach to address this problem involves mitochondrial haplotype comparison of wild and domestic horses from various locations coupled with studies of possible migration routes of the ancient shepherds. Here, we sequenced complete mitochondrial genomes of six horses from burials of the Ukok plateau (Russia, Altai Mountains) dated from 2.7 to 1.4 thousand years before present and a single late Pleistocene wild horse from the neighboring region (Denisova cave). Sequencing data indicates that the wild horse belongs to an extinct pre-domestication lineage. Integration of the domestic horse data with known Eurasian haplotypes of a similar age revealed two distinct groups: the first one widely distributed in Europe and presumably imported to Altai, and the second one specific for Altai Mountains and surrounding area.

Stylostome formation by parasitic larvae of Allothrombium fuliginosum (Trombidiformes: Trombidiidae): morphology of feeding tubes and factors affecting their size

The morphology and formation of stylostomes (feeding tubes) in hosts' body during the parasitic phase of Allothrombium fuliginosum (Hermann) larvae were studied for the first time with light microscopy (LM) and transmission electron microscopy (TEM). The stylostomes were observed in three aphids species-Acyrthosiphon pisum (Harris), Elatobium abietinum (Walker), and Macrosiphum rosae (L.)-parasitized by mites under laboratory conditions. They consisted of 2-6 main branches, preliminarily unbranched, then producing secondary and sometimes also tertiary branches as finally formed structures. Their walls were uniformly electron-dense, without any longitudinal and transverse stratifications and showed rather irregular outlines. Distally, the stylostome branches revealed transparent pores and cavities in their walls, connecting the stylostome canal with surrounding haemocoelic space. The total length of stylostomes at the end of the parasitic phase was on average 16× greater than that recorded in the youngest stylostomes. No differences in the overall shape of feeding tubes between host species were stated. The stylostomes formed in different host species did not differ significantly, except their total length, which attained the highest value in tissues of Ac. pisum.

A plant-based transient expression system for the rapid production of highly immunogenic Hepatitis E virus-like particles

OBJECTIVE

Hepatitis E virus (HEV) infection is a major cause of acute hepatitis worldwide. The aim of the study is the development of plant expression system for the production of virus-like particles formed by HEV capsid and the characterization of their immunogenicity.

RESULTS

Open reading frame (ORF) 2 encodes the viral capsid protein and possesses candidate for vaccine production. In this study, we used truncated genotype 3 HEV ORF 2 consisting of aa residues 110 to 610. The recombinant protein was expressed in Nicotiana benthamiana plants using the self-replicating potato virus X-based vector pEff up to 10% of the soluble protein fraction. The yield of HEV 110-610 after purification was 150-200 µg per 1 g of green leaf biomass. The recombinant protein formed nanosized virus-like particles. The immunization of mice with plant-produced HEV 110-610 protein induced high levels of HEV-specific serum antibodies.

CONCLUSIONS

HEV ORF 2 (110-610 aa) can be used as candidate for the development of a plant-produced vaccine against Hepatitis E.