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This study focused on conditions that allow ferromanganese mineralization in modern aeolian sands along the coastal strip of Lake Baikal – a UNESCO world heritage site. Here, we describe a geochemical barrier that divides two geosystems – swamp and littoral (backwater) zones – included within the largest freshwater reservoir on the Earth – Lake Baikal. In correspondence with this geochemical barrier (identified in swamp waters), there is a change in redox conditions. This induces a sharp decrease in the migration capacity of manganese and iron, contributing to their accumulation. Such a geochemical barrier is one of the main elements determining the unique water composition of Lake Baikal, which is related to the precipitation of manganese and iron oxides. Ferromanganese mineralization, revealed by the presence of manganite and limonite dripstones, is responsible for the cementation of aeolian sand grains, explaining the formation of the recent ore-bearing sandstones observed in the study area. The average manganese oxide and ferric oxide contents in the ore were 5.18 and 3.60%, respectively. Research highlights: Ferromanganese sediments in the modern aeolian sands along Lake Baikal shores. Geochemical barrier on the border between the lake and swamp. Limonite−manganite substance cements aeolian sands turning them into sandstones. Model for the formation of a ferromanganese mineralisation. [ABSTRACT FROM AUTHOR]

Cell functioning is tightly regulated process. For many years, research in the fields of proteomics and functional genomics has been focused on the role of proteins in cell functioning. The advances in science have led to the uncovering that short open reading frames, previously considered non-functional, serve a variety of functions. Short reading frames in polycistronic mRNAs often regulate their stability and translational efficiency of the main reading frame. The improvement of proteomic analysis methods has made it possible to identify the products of translation of short open reading frames in quantities that suggest the existence of functional role of those peptides and short proteins. Studies demonstrating their role unravel a new level of the regulation of cell functioning and its adaptation to changing conditions. This review is devoted to the analysis of functions of recently discovered peptides and short proteins. [ABSTRACT FROM AUTHOR]

Upgrading the properties of diesel fractions is considered one of the crucial processes in the petrochemical industry; and for this purpose in laboratory-scale researching it is studied on the base of the hydroisomerization of n-hexadecane as a main model reaction. Recently, zeolite-based bifunctional catalysts have proven their efficiency due to their remarkable acidity, shape-selectivity and relative resistance to deactivation. In this review, different topological-type zeolite-based catalysts, the mechanism of their catalytic effect in n-C16 isomerization, and the principles of shape-selectivity are reviewed. A comparison of their structural-operational characteristics is made. The impact of some feedstock impurities on the catalyst's performance and deactivation due to carbonaceous deposits as well as various modern eco-friendly cost-effective synthesis techniques are also discussed. [ABSTRACT FROM AUTHOR]

The article is devoted to the analysis of the construction of new system of gender images in the sociopolitical conditions in Russia during the last thirty ages. Based on Kress and Van Leeuwen multisemiotic theory and the ideas A. Dudareva, I.Groshev and M. Petrova, we conducted a research of gender images of women in the Soviet Union and modern Russian advertising. The data comes from 300 images of the Russian men and women in advertising. These 300 images were specifically chosen by the author in order to be acceptable for coding. As the result of the study, we developed the typology of gender images of woman in Russian advertisement. Our conclusion was that economic, political and socio-cultural factors were the main factors in the transformation of gender images in modern Russia. The gender of a woman, her body and figures as shown in the media, very often were object of sexual exploitation, when the impact of using the image and play with human sexual passion forces her to commit certain actions, such as buying goods. This characteristic of our commercialization of gender images turns a person, both men and women, into a commodity. Gender is becoming the object that can be purchased and can be enjoyed. [ABSTRACT FROM AUTHOR]

The problem of the quantitative interpretation of qualitative data is one of the most important in sociological research. Textual analysis has placed emphasis on deep and careful study of texts how personal strategies embodied in the concepts. However, quantitative interpretation has always been problematic. Our paper deals with the corpus-based conceptualization method, which can considered as a method of collecting and organizing data material from linguistic corpora. The corpus-based conceptualization allows us to establish a closer link with the meaning and identify the whole spectrum of meanings. It shows that some sociologists lose essential meanings in the research process because of lack of in-deep immersion in the daily life and speech of the people. We chose the concepts of "altruism" and "mercy" as examples to demonstrate the corpus-based conceptualization and its place in sociological research methodology. Data comes from the Russian National Corpus. The Russian National Corpus consists of 1802 relevant words, with 775 for altruism and 1047 for mercy. Data processing carried out by SPSS 19.0. As the result, we have discussed what difficulties the researcher can meet using this method and have offered SFL and Role and Reference grammar as a way to accurately determine the context. Our suggestions can be used in the preparation of questionnaires, guides, in an analysis of interview transcripts. [ABSTRACT FROM AUTHOR]

• Cellulose microfibers were modified with Fe 3 O 4 nanoparticles in a tunable way. • Adsorption of lauric acid onto Fe 3 O 4 -modified fibers leads to shape-stable PCM. • Magnetic PCM composites can store thermal energy under alternating magnetic field. • Magnetite nanoparticles improves light-to-thermal conversion of PCM composites. Fe 3 O 4 -modified cellulose microfibers containing 7, 16, and 31 wt% of magnetite were prepared via co-precipitation of Fe2+ and Fe3+ salts. The magnetic phase-change composites were synthesized by adsorption of lauric acid onto the modified fibers with the highest saturation magnetization (23 emu/g) and magnetic-to-thermal conversion. The resulted composites demonstrated the saturation magnetization of 11.2 emu/g and latent heat storage capacity of 90 J/g corresponding to the loading efficiency of lauric acid of 49–51 wt%. The IR-imaging revealed the efficient accumulation of latent heat in the phase-change composite under the simulated sunlight and high frequency alternating magnetic field along with the excellent shape stability of the composites during the melting of lauric acid. [ABSTRACT FROM AUTHOR]

A nanoarchitectural approach for synthesis of highly crystalline zeolites based on natural aluminosilicate nanotubes with adjustable silica to alumina ratio has been developed. A double template technique was proposed for synthesis of zeolite microcrystals with geometric morphology defined by the initial aluminosilicate nanotubes (halloysite). Remarkable and unique zeolite microcrystal shapes (submicron spheres, pompon-like systems and coffin-shaped prisms) possessing different internal structures (sodalite, analcime, mordenite, mordenite framework inverted) were obtained from halloysite by hydrothermal method. Halloysite Si/Al adjustments (acid etching, addition of extra silica or alumina) significantly affected crystalline structure and morphology of the obtained materials, while changing organic templates did not have a considerable effect. [Display omitted] • A novel approach for zeolites synthesis from aluminosilicate nanotubes was proposed. • Zeolites morphology is defined by the initial aluminosilicate nanotubes. • SOD, ANA, MOR, and MFI microstructures were synthesized from natural nanoclay. [ABSTRACT FROM AUTHOR]

Telomere length is associated with the proliferative potential of cells. Telomerase is an enzyme that elongates telomeres throughout the entire lifespan of an organism in stem cells, germ cells, and cells of constantly renewed tissues. It is activated during cellular division, including regeneration and immune responses. The biogenesis of telomerase components and their assembly and functional localization to the telomere is a complex system regulated at multiple levels, where each step must be tuned to the cellular requirements. Any defect in the function or localization of the components of the telomerase biogenesis and functional system will affect the maintenance of telomere length, which is critical to the processes of regeneration, immune response, embryonic development, and cancer progression. An understanding of the regulatory mechanisms of telomerase biogenesis and activity is necessary for the development of approaches toward manipulating telomerase to influence these processes. The present review focuses on the molecular mechanisms involved in the major steps of telomerase regulation and the role of post-transcriptional and post-translational modifications in telomerase biogenesis and function in yeast and vertebrates. [ABSTRACT FROM AUTHOR]

Flow-seq is a method that combines fluorescently activated cell sorting and next-generation sequencing to deduce a large amount of data about translation efficiency from a single experiment. Here, we constructed a library of fluorescent protein-based reporters preceded by a set of 648 natural 5′-untranslated regions (5′-UTRs) of Escherichia coli genes. Usually, Flow-seq libraries are constructed using uniform-length sequence elements, in contrast to natural situations, where functional elements are of heterogenous lengths. Here, we demonstrated that a 5′-UTR library of variable length could be created and analyzed with Flow-seq. In line with previous Flow-seq experiments with randomized 5′-UTRs, we observed the influence of an RNA secondary structure and Shine–Dalgarno sequences on translation efficiency; however, the variability of these parameters for natural 5′-UTRs in our library was smaller in comparison with randomized libraries. In line with this, we only observed a 30-fold difference in translation efficiency between the best and worst bins sorted with this factor. The results correlated with those obtained with ribosome profiling. [ABSTRACT FROM AUTHOR]

Demonstrates that the 5'-untranslated region (UTR) of human heat shock protein Hsp70 mRNA represents an internal ribosome entry site (IRES) with the relative activity similar to that of the classical picornaviral IRES. Expression of a downstream reporter gene directed by the 5'-UTR of Hsp70 mRNA in a dicistronic vector; Variance in the effect of small deletions within the 5'-UTR of Hsp70 mRNA on the IRES activity.

Telomerase is a ribonucleoprotein complex that maintains the lengths of telomeres. Most studies of telomerase function have focused on the involvement of telomerase activation in the immortalization of cancer cells and cellular rejuvenation. However, some studies demonstrated that the results do not meet expectations for telomerase action in telomere maintenance. Recent results give reason to think that major telomerase components—the reverse transcriptase protein subunit and telomerase RNA—may participate in many cellular processes, including the regulation of apoptosis and autophagy, cell survival, pro-proliferative effects, regulation of gene expression, and protection against oxidative stress. However, the difficulties faced by scientist when researching telomerase component functions often reduce confidence in the minor effects observed in experiments. In this review, we focus on the analysis of the functions of telomerase components (paying more attention to the telomerase RNA component), both as a complex and as independent components, providing effects that are not associated with telomerase activity and telomere length maintenance. Despite the fact that the data on alternative roles of telomerase components look illusory, it would be wrong to completely reject the possibility of their involvement in other biological processes excluded from research/discussion. Investigations to improve the understanding of every aspect of the functioning of telomerase components will provide the basis for a more precise development of approaches to regulate cellular homeostasis, which is important for carcinogenesis and aging. [ABSTRACT FROM AUTHOR]

[Display omitted] • A new bizeolite Pt/ZSM-5:ZSM-12/Al 2 O 3 catalyst was designed for C-8 aromatics isomerization. • ZSM-5/ZSM-12 based Pt catalyst allows both intra- and intermolecular isomerization routes. • Ethylbenzene and m -xylene conversions over ZSM-5+ZSM-12 based catalyst are higher than over an industrial counterpart. A bizeolite catalyst based on ZSM-5 and ZSM-12 was designed to maximize the yield of valuable aromatics from ethylbenzene (EB) rich feedstocks for the first time. The catalyst Pt/ZSM-5:ZSM-12/Al 2 O 3 was characterized by X-ray diffraction (XRD), nitrogen physisorption, temperature-programmed desorption of ammonia (TPD-NH 3), transmission and scanning electron microscopy (TEM and SEM), X-ray fluorescence analysis (XRF), Fourier-transformed infrared spectroscopy (FTIR) and 27Al magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy. The catalyst and its components were tested in isomerization of an industrial C-8 aromatic cut (C8-Ar) and feedstocks with high EB content. The catalyst demonstrated higher conversion of EB and m -xylene (MX) compared with an industrial catalyst and higher selectivity to dealkylation products. [ABSTRACT FROM AUTHOR]

Ribosome biogenesis is essential for the functioning of living cells. In higher eukaryotes, this multistep process is tightly controlled and involves a variety of specialized proteins and RNAs. This pool of so-called ribosome biogenesis factors includes diverse proteins with enzymatic and structural functions. Some of them have homologs in yeast S. cerevisiae, and their function can be inferred from the structural and biochemical data obtained for the yeast counterparts. The functions of human proteins RPF1 and ESF1 remain largely unclear, although RPF1 has been recently shown to participate in 60S biogenesis. Both proteins have drawn our attention since they contribute to the early stages of ribosome biogenesis, which are far less studied than the later stages. In this study, we employed the loss-of-function shRNA/siRNA-based approach to the human cell line HEK293 to determine the role of RPF1 and ESF1 in ribosome biogenesis. Downregulating RPF1 and ESF1 significantly changed the pattern of RNA products derived from 47S pre-rRNA. Our findings demonstrate that RPF1 and ESF1 are associated with different pre-ribosomal particles, pre-60S, and pre-40S particles, respectively. Our results allow for speculation about the particular steps of pre-rRNA processing, which highly rely on the RPF1 and ESF1 functions. We suggest that both factors are not directly involved in pre-rRNA cleavage but rather help pre-rRNA to acquire the conformation favoring its cleavage. [ABSTRACT FROM AUTHOR]

Adsorption of organic phase-change materials (PCMs) by the porous matrix of microfibrillar cellulose (MFC) is a simple and versatile way to prepare shape-stable phase-change composites, which are promising as sustainable thermoregulating additives to construction materials. However, due to MFC inherent morphology, the resulting composites have relatively low poured density that complicates their introduction in sufficient amounts, for instance, into mortar mixes. Unlike MFC, fungal mycelium has, by an order, less fibrils thickness and, thus, possesses significantly higher poured density. Herein, we studied the feasibility of fungal mycelium-based matrices as alternative biopolymeric porous supports for preparation of sustainable and shape-stable phase-change composites. Two methods were employed to prepare the porous mycelium-based supports. The first one was the solid-state fermentation, which resulted in partial biotransformation of MFCs to mycelium hyphae, while the second one was the liquid-state surface fermentation, used to cultivate the reference matrix of Trametes hirsuta hyphae. The phase-change composites were prepared by adsorption of model organic PCMs on porous biopolymer matrices. The mass ratio of support/PCM was 40/60 wt%. The composites were studied with respect to their structure, composition, poured density, latent heat storage properties, and thermal and shape stability. The employment of the partially transformed to mycelium-hyphae MFC fibers was found to be a suitable way to prepare phase-change composites with improved poured density while preserving a reasonable latent heat capacity and shape stability as compared to the MFC/PCM composites. [ABSTRACT FROM AUTHOR]

Organic phase-change materials (PCMs) hold promise in developing advanced thermoregulation and responsive energy systems owing to their high latent heat capacity and thermal reliability. However, organic PCMs are prone to leakages in the liquid state and, thus, are hardly applicable in their pristine form. Herein, we encapsulated organic PCM n-Octadecane into polyurethane capsules via polymerization of commercially available polymethylene polyphenylene isocyanate and polyethylene glycol at the interface oil-in-water emulsion and studied how various n-Octadecane feeding affected the shell formation, capsule structure, and latent heat storage properties. The successful shell polymerization and encapsulation of n-Octadecane dissolved in the oil core was verified by confocal microscopy and Fourier-transform infrared spectroscopy. The mean capsule size varied from 9.4 to 16.7 µm while the shell was found to reduce in thickness from 460 to 220 nm as the n-Octadecane feeding increased. Conversely, the latent heat storage capacity increased from 50 to 132 J/g corresponding to the growth in actual n-Octadecane content from 25% to 67% as revealed by differential scanning calorimetry. The actual n-Octadecane content increased non-linearly along with the n-Octadecane feeding and reached a plateau at 66–67% corresponded to 3.44–3.69 core-to-monomer ratio. Finally, the capsules with the reasonable combination of structural and thermal properties were evaluated as a thermoregulating additive to a commercially available paint. [ABSTRACT FROM AUTHOR]

Ribosomal protein S6 in Escherichia coli is modified by ATP-dependent glutamate ligase RimK. Up to four glutamate residues are added to the C-terminus of S6 protein. In this work we demonstrated that unlike the majority of ribosome modifications in E. coli , oligoglutamylation of S6 protein is regulated and happens only in the stationary phase of bacterial culture. Only S6 protein incorporated into assembled small ribosomal subunits, but not newly made free S6 protein is a substrate for RimK protein. Overexpression of the rimK gene leads to the modification of S6 protein even in the exponential phase of bacterial culture. Thus, it is unlikely that any stationary phase specific factor is needed for the modification. We propose a model that S6 modification is regulated solely via the rate of ribosome biosynthesis at limiting concentration of RimK enzyme. • E. coli ribosomal protein S6 is oligoglutamylated by RimK. • Modification happens only in the stationary phase. • Assembled 30S subunit but not free S6 protein is modified. • A model is proposed for the regulation of S6 modification. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Purpose: High- and medium-throughput assays are now routine methods for drug screening and toxicology investigations on mammalian cells. However, a simple and cost-effective analysis of cytotoxicity that can be carried out with commonly used laboratory equipment is still required.Procedures: The developed cytotoxicity assays are based on human cell lines stably expressing eGFP, tdTomato, mCherry, or Katushka2S fluorescent proteins. Red fluorescent proteins exhibit a higher signal-to-noise ratio, due to less interference by medium autofluorescence, in comparison to green fluorescent protein. Measurements have been performed on a fluorescence scanner, a plate fluorimeter, and a camera photodocumentation system.Results: For a 96-well plate assay, the sensitivity per well and the measurement duration were 250 cells and 15 min for the scanner, 500 cells and 2 min for the plate fluorimeter, and 1000 cells and less than 1 min for the camera detection. These sensitivities are similar to commonly used MTT (tetrazolium dye) assays. The used scanner and the camera had not been previously applied for cytotoxicity evaluation. An image processing scheme for the high-resolution scanner is proposed that significantly diminishes the number of control wells, even for a library containing fluorescent substances. The suggested cytotoxicity assay has been verified by measurements of the cytotoxicity of several well-known cytotoxic drugs and further applied to test a set of novel bacteriotoxic compounds in a medium-throughput format.Conclusion: The fluorescent signal of living cells is detected without disturbing them and adding any reagents, thus allowing to investigate time-dependent cytotoxicity effects on the same sample of cells. A fast, simple and cost-effective assay is suggested for cytotoxicity evaluation based on mammalian cells expressing fluorescent proteins and commonly used laboratory equipment. [ABSTRACT FROM AUTHOR]

Phase-change materials (PCMs) attract much attention with regard to their capability of mitigating fossil fuel-based heating in in-building applications, due to the responsive accumulation and release of thermal energy as a latent heat of reversible phase transitions. Organic PCMs possess high latent heat storage capacity and thermal reliability. However, bare PCMs suffer from leakages in the liquid form. Here, we demonstrate a reliable approach to improve the shape stability of organic PCM n-octadecane by encapsulation via interfacial polymerization at an oil/water interface of Pickering emulsion. Cellulose nanocrystals are employed as emulsion stabilizers and branched oligo-polyol with high functionality to crosslink the polyurethane shell in reaction with polyisocyanate dissolved in the oil core. This gives rise to a rigid polyurethane structure with a high density of urethane groups. The formation of a polyurethane shell and successful encapsulation of n-octadecane is confirmed by FTIR spectroscopy, XRD analysis, and fluorescent confocal microscopy. Electron microscopy reveals the formation of non-aggregated capsules with an average size of 18.6 µm and a smooth uniform shell with the thickness of 450 nm. The capsules demonstrate a latent heat storage capacity of 79 J/g, while the encapsulation of n-octadecane greatly improves its shape and thermal stability compared with bulk paraffin. [ABSTRACT FROM AUTHOR]

Following nanoarchitectural approach, mesoporous halloysite nanotubes with internal surface composed of alumina were loaded with 5-6 nm RuCo nanoparticles by sequential loading/ reduction procedure. Ruthenium nanoclusters were loaded inside clay tube by microwaveassisted method followed by cobalt ions electrostatic attraction to ruthenium during wetness impregnation step. Developed nanoreactors with bimetallic RuCo nanoparticles were investigated as catalysts for the Fischer-Tropsch process. The catalyst with 14.3 wt.% of Co and 0.15 wt.% of Ru showed high activity (CO conversion reached 24.6%), low selectivity to methane (11.9%), CO2 (0.3%), selectivity to C5+ hydrocarbons of 79.1% and chain growth index (α) = 0.853. Proposed nanoreactors showed better selectivity to target products combined with high activity in comparison to the similar bimetallic systems supported on synthetic porous materials. It was shown that reducing agent (NaBH4 or H2) used to obtain Ru nanoclusters at first synthesis step played a very important role in the reducibility and selectivity of resulting RuCo catalysts. [ABSTRACT FROM AUTHOR]

Wehave synthesized and characterized a panel of new binuclearmixed valence Cu(I,II) complexes containing substituted 2-alkylthio-5-arylmethylene-4H-imidazolin-4-ones with unusual structure. These complexesare shown to be cytotoxic for various cell lines. We have found thatthese compounds did not intercalate DNA, inhibited number of polymerases(telomerase predominantly), accumulated in the cell nucleus, and causedDNA degradation. Preliminary studies revealed that lead compound inhibitedhuman breast adenocarcinoma growth in mice model. [ABSTRACT FROM AUTHOR]

• MFC was modified with Ag nanoparticles with a mass content of 13% • Adsorption of SA onto AgMFC fibers results in shape stable PCM composites. • Ag nanoparticles do not affect the phase transitions of SA on the fiber surface. • SA/AgMFC composites have improved heating and cooling rate comparing to SA/MFC ones. • The improved heat transfer in SA/AgMFC composites reduces their thermal stability. Composite phase change material was prepared via adsorption of stearic acid onto cellulose microfibrils modified with Ag nanoparticles. The latent heat storage capacity, cycling performance, thermal stability, and heating/cooling rate of the composites were studied with differential scanning calorimetry, thermogravimetric analysis, and thermal imaging and compared to those of the composite prepared by adsorption of stearic acid onto pure microfibrillar cellulose. The modification of cellulose with Ag nanoparticles improves the heating and cooling rate of the composites and promotes latent heat release during the solidification of stearic acid on the fiber surface. [ABSTRACT FROM AUTHOR]

Hydrogenation of CO2 relative to valuable chemical compounds such as methanol or dimethyl ether (DME) is an attractive route for reducing CO2 emissions in the atmosphere. In the present work, the hydrogenation of CO2 into DME over CuO-In2O3, supported on halloysite nanotubes (HNT) was investigated in the temperature range 200–300 °C at 40 atm. HNT appears to be novel promising support for bifunctional catalysts due to its thermal stability and the presence of acidic sites on its surface. CuO-In2O3/HNT catalysts demonstrate higher CO2 conversion and DME selectivity compared to non-indium CuO/HNT catalysts. The catalysts were investigated by N2 adsorption, X-ray diffraction, hydrogen-temperature programmed reduction and transition electron microscopy. The acid sites were analyzed by temperature programmed desorption of ammonia. It was shown that CuO/HNT was unstable under reaction conditions in contrast to CuO-In2O3/HNT. The best CuO-In2O3/HNT catalyst provided CO2 conversion of 7.6% with 65% DME selectivity under P = 40 atm, T = 250 °C, gas hour space velocity 12,000 h−1 and H2:CO2 = 3:1. [ABSTRACT FROM AUTHOR]

A method of analysis of translation initiation complexes by toeprinting has recently acquired a wide application to investigate molecular mechanisms of translation initiation in eukaryotes. So far, this very fruitful approach was used when researchers did not aim to discriminate between patterns of toeprints for 48S and 80S translation initiation complexes. Here, using cap-dependent and internal ribosomal entry site (IRES)-dependent mRNAs, we show that the toeprint patterns for 48S and 80S complexes are distinct whether the complexes are assembled in rabbit reticulocyte lysate or from fully purified individual components. This observation allowed us to demonstrate for the first time a delay in the conversion of the 48S complex into the 80S complex for β-globin and encephalomyocarditis virus (EMCV) RNAs, and to assess the potential of some 80S antibiotics to block polypeptide elongation. Besides, additional selection of the authentic initiation codon among three consecutive AUGs that follow the EMCV IRES was revealed at steps subsequent to the location of the initiation codon by the 40S ribosomal subunit. [Copyright &y& Elsevier]

Purpose: Liver cancers are among the deadliest malignancies due to a limited efficacy of early diagnostics, the lack of appropriate biomarkers and insufficient discrimination of different types of tumors by classic and molecular methods. In this study, we searched for novel long non-coding RNA (lncRNA) as well as validated several known candidates suitable as probable biomarkers for primary liver tumors of various etiology. Methods: We described a novel lncRNA HELIS (aka "HEalthy LIver Specific") and estimated its expression by RT-qPCR in 82 paired tissue samples from patients with hepatocellular carcinoma (HCC), cholangiocarcinoma (CCA), combined HCC-CCA, pediatric hepatoblastoma (HBL) and non-malignant hepatocellular adenoma (HCA) and focal nodular hyperplasia (FNH). Additionally, we examined expression of cancer-associated lncRNAs HULC, MALAT1, UCA1, CYTOR, LINC01093 and H19, which were previously studied mainly in HCC. Results: We demonstrated that down-regulation of HELIS strongly correlates with carcinogenesis; whereas in tumors with non-hepatocyte origin (HBL, CCA) or in a number of poorly differentiated HCC, this lncRNA is not expressed. We showed that recently discovered LINC01093 is dramatically down-regulated in all malignant liver cancers; while in benign tumors LINC01093 expression is just twice decreased in comparison to adjacent samples. Conclusion: Our study revealed that among all measured biomarkers only down-regulated HELIS and LINC01093, up-regulated CYTOR and dysregulated HULC are perspective for differential diagnostics of liver cancers; whereas others demonstrated discordant results and cannot be considered as potential universal biomarkers for this purpose. [ABSTRACT FROM AUTHOR]

Summary: Translation efficiency contributes several orders of magnitude difference in the overall yield of exogenous gene expression in bacteria. In diverse bacteria, the translation initiation site, whose sequence is the primary determinant of the translation performance, is comprised of the start codon and the Shine–Dalgarno box located upstream. Here, we have examined how the sequence of a spacer between these main components of the translation initiation site contributes to the yield of synthesized protein. We have created a library of reporter constructs with the randomized spacer region, performed fluorescently activated cell sorting and applied next‐generation sequencing analysis (the FlowSeq protocol). As a result, we have identified sequence motifs for the spacer region between the Shine–Dalgarno box and AUG start codon that may modulate the translation efficiency in a 100‐fold range. [ABSTRACT FROM AUTHOR]

Genes coding for small peptides have been frequently misannotated as long noncoding RNA (lncRNA) genes. Here we have demonstrated that one such transcript is translated into a 56-aminoacid- long peptide conserved in chordates, corroborating the work published while this manuscript was under review. The Mtln peptide could be detected in mitochondria of mouse cell lines and tissues. In line with its mitochondrial localization, lack of the Mtln decreases the activity of mitochondrial respiratory chain complex I. Unlike the integral components and assembly factors of NADH: ubiquinone oxidoreductase, Mtln does not alter its enzymatic activity directly. Interaction of Mtln with NADH-dependent cytochrome b5 reductase stimulates complex I functioning most likely by providing a favorable lipid composition of the membrane. Study of Mtln illuminates the importance of small peptides, whose genes might frequently be misannotated as lncRNAs, for the control of vitally important cellular processes. [ABSTRACT FROM AUTHOR]

Microbiome spectra serve as critical clues to elucidate the evolutionary biology pathways, potential pathologies, and even behavioral patterns of the host organisms. Furthermore, exotic sources of microbiota represent an unexplored niche to discover microbial secondary metabolites. However, establishing the bacterial functionality is complicated by an intricate web of interactions inside the microbiome. Here we apply an ultrahigh-throughput (uHT) microfluidic droplet platform for activity profiling of the entire oral microbial community of the Siberian bear to isolate Bacillus strains demonstrating antimicrobial activity against Staphylococcus aureus. Genome mining allowed us to identify antibiotic amicoumacin A (Ami) as responsible for inhibiting the growth of S. aureus. Proteomics and metabolomics revealed a unique mechanism of Bacillus selfresistance to Ami, based on a subtle equilibrium of its deactivation and activation by kinase AmiN and phosphatase AmiO, respectively. We developed uHT quantitative single-cell analysis to estimate antibiotic efficacy toward different microbiomes and used it to determine the activity spectra of Ami toward human and Siberian bear microbiota. Thus, uHT microfluidic droplet platform activity profiling is a powerful tool for discovering antibiotics and quantifying external influences on a microbiome. [ABSTRACT FROM AUTHOR]

During a cell's lifespan, DNA break formation is a common event, associated with many processes, from replication to apoptosis. Most of DNA breaks are readily repaired, but some are meant to persist in time, such as the chromosome ends, protected by telomeres. Besides them, eukaryotic genomes comprise shorter stretches of interstitial telomeric repeats. We assumed that the latter may also be associated with the formation of DNA breaks meant to persist in time. In zebrafish and mouse embryos, cells containing numerous breakage foci were identified. These breaks were not associated with apoptosis or replication, nor did they seem to activate DNA damage response machinery. Unlike short-living, accidental sparse breaks, the ones we found seem to be closely associated, forming discrete break foci. A PCR-based method was developed, allowing specific amplification of DNA regions located between inverted telomeric repeats associated with breaks. The cloning and sequencing of such DNA fragments were found to denote some specificity in their distribution for different tissue types and development stages. [ABSTRACT FROM PUBLISHER]

Background: In the course of replication of eukaryotic chromosomes, the telomere length is maintained due to activity of telomerase, the ribonucleoprotein reverse transcriptase. Abolishing telomerase function causes progressive shortening of telomeres and, ultimately, cell cycle arrest and replicative senescence. To better understand the cellular response to telomerase deficiency, we performed a transcriptomic study for the thermotolerant methylotrophic yeast Hansenula polymorpha DL-1 lacking telomerase activity. Results: Mutant strain of H. polymorpha carrying a disrupted telomerase RNA gene was produced, grown to senescence and analyzed by RNA-seq along with wild type strain. Telomere shortening induced a transcriptional response involving genes relevant to telomere structure and maintenance, DNA damage response, information processing, and some metabolic pathways. Genes involved in DNA replication and repair, response to environmental stresses and intracellular traffic were up-regulated in senescent H. polymorpha cells, while strong down-regulation was observed for genes involved in transcription and translation, as well as core histones. Conclusions: Comparison of the telomerase deletion transcription responses by Saccharomyces cerevisiae and H. polymorpha demonstrates that senescence makes different impact on the main metabolic pathways of these yeast species but induces similar changes in processes related to nucleic acids metabolism and protein synthesis. Up-regulation of a subunit of the TORC1 complex is clearly relevant for both types of yeast. [ABSTRACT FROM AUTHOR]

Ultrahigh-throughput screening (uHTS) techniques can identify unique functionality from millions of variants. To mimic the natural selection mechanisms that occur by compartmentalization in vivo, we developed a technique based on single-cell encapsulation in droplets of a monodisperse microfluidic double water-in-oil-in-water emulsion (MDE). Biocompatible MDE enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography- mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. This platform was probed with uHTS for biocatalysts anchored to yeast with enrichment close to the theoretically calculated limit and cell-tocell interactions. MDE-FACS allowed the identification of human butyrylcholinesterase mutants that undergo self-reactivation after inhibition by the organophosphorus agent paraoxon. The versatility of the platform allowed the identification of bacteria, including slowgrowing oral microbiota species that suppress the growth of a common pathogen, Staphylococcus aureus, and predicted which genera were associated with inhibitory activity. [ABSTRACT FROM AUTHOR]

The biodiversity of microorganisms is maintained by intricate nets of interactions between competing species. Impaired functionality of human microbiomes correlates with their reduced biodiversity originating from aseptic environmental conditions and antibiotic use. Microbiomes of wild animals are free of these selective pressures. Microbiota provides a protecting shield from invasion by pathogens in the wild, outcompeting their growth in specific ecological niches. We applied ultrahigh-throughput microfluidic technologies for functional profiling of microbiomes of wild animals, including the skin beetle, Siberian lynx, common raccoon dog, and East Siberian brown bear. Single-cell screening of the most efficient killers of the common human pathogen Staphylococcus aureus resulted in repeated isolation of Bacillus pumilus strains. While isolated strains had different phenotypes, all of them displayed a similar set of biosynthetic gene clusters (BGCs) encoding antibiotic amicoumacin, siderophore bacillibactin, and putative analogs of antimicrobials including bacilysin, surfactin, desferrioxamine, and class IId cyclical bacteriocin. Amicoumacin A (Ami) was identified as a major antibacterial metabolite of these strains mediating their antagonistic activity. Genome mining indicates that Ami BGCs with this architecture subdivide into three distinct families, characteristic of the B. pumilus, B. subtilis, and Paenibacillus species. While Ami itself displays mediocre activity against the majority of Gram-negative bacteria, isolated B. pumilus strains efficiently inhibit the growth of both Gram-positive S. aureus and Gram-negative E. coli in coculture. We believe that the expanded antagonistic activity spectrum of Ami-producing B. pumilus can be attributed to the metabolomic profile predetermined by their biosynthetic fingerprint. Ultrahigh-throughput isolation of natural probiotic strains from wild animal microbiomes, as well as their metabolic reprogramming, opens up a new avenue for pathogen control and microbiome remodeling in the food industry, agriculture, and healthcare. [ABSTRACT FROM AUTHOR]

Abstract: Telomeres are the nucleoprotein complexes that cap the linear chromosome ends. Telomerase is a ribonucleoprotein that maintains telomere length in stem, embryonic and cancer cells. Somatic cells don't contain active telomerase and telomere function as mitotic clock and telomere length determines the number of cell divisions. Telomerase RNA (TER) contains the template for telomere synthesis and serves as a structural scaffold for holoenzyme assembly. We compared different oligonucleotide based methods for telomerase RNA inhibition, such as antisense oligonucleotides, knockdown by transient siRNA transfection and silencing by miRNA derived from short expressed RNA hairpin in HEK293 cells. All of these methods were applied to different TER regions. Our results revealed that CR2/CR3 domain of TER is accessible in vitro and in vivo and could serve as an optimal site for oligonucleotide-based telomerase silencing. [Copyright &y& Elsevier]