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Although restriction-modification systems are found in both Eubacterial and Archaeal kingdoms, comparatively less is known about patterns of DNA methylation and genome defense systems in archaea. Here we report the complete closed genome sequence and methylome analysis of Methanococcus aeolicus PL15/Hp, a strain of the CO2-reducing methanogenic archaeon and a commercial source for MaeI, MaeII, and MaeIII restriction endonucleases. The M. aeolicus PL15/Hp genome consists of a 1.68 megabase circular chromosome predicted to contain 1,615 protein coding genes and 38 tRNAs. A combination of methylome sequencing, homology-based genome annotation, and recombinant gene expression identified five restriction-modification systems encoded by this organism, including the methyltransferase and site-specific endonuclease of MaeIII. The MaeIII restriction endonuclease was recombinantly expressed, purified and shown to have site-specific DNA cleavage activity in vitro.

Supplementary Figure 1 Legend from ΔNp63α Up-Regulates the Hsp70 Gene in Human Cancer

HSP70, a stress response protein, is known to be a determinant of cell death and cell transformation. We show that different isoforms of p63 have different transcriptional activities on hsp70 genes. ΔNp63α, an abundantly expressed isoform of p63, activates (in vitro and in vivo), whereas TAp63γ down-regulates the expression of hsp70. We further show that the transactivation domain at the NH2 terminus of p63 represses, whereas the COOH terminus activates hsp70 transcription. In addition, ΔNp63α regulates transcription of the hsp70 gene through its interaction with the CCAAT binding factor and NF-Y transcription factors which are known to form a complex with the CCAAT box located in the hsp70 promoter. Moreover, ΔNp63α expression correlates with HSP70 expression in all head and neck cancer cell lines. Finally, we show colocalization of ΔNp63α and HSP70 in the epithelium and coexpression of both proteins in 41 primary head and neck cancers. Our study provides strong evidence for the physiologic association between ΔNp63α and hsp70 in human cancer, thus further supporting the oncogenic potential of ΔNp63α.

Supplementary Figure 1 from ΔNp63α Up-Regulates the Hsp70 Gene in Human Cancer

The article goes on to describe a solution to the problem of information support for the synthesis of new technical systems. The method consists in organizing the ontology of the subject area and filling it with data from the Russian-language patent array. An algorithm is presented for constructing a graph of elements of technical object structures from previously extracted primary semantic SAO (Subject–Action–Object) structures. The extracted bundles are preprocessed by searching for homogeneous sentence members and generating additional case forms. This is followed by linking the prepared SAO-objects into a single graph. The mechanism consists in sequentially transforming the subject and object actants into a set of anchor points from a common vocabulary of terms, followed by the memorization of the relation (predicate) for the identified points. The evaluation of data extraction by the system is carried out: the value of the F1 metric for a strict evaluation is 63 % and for a non-strict 79 %, respectively. The non-strict evaluation takes into account the correctness of the extraction of SAO root elements only. The extracted data is then converted into a subject domain ontology. The ontology scheme as a concept includes the structural elements of technical objects and the relationship between them, as well as supporting information on the invention. The initial content of the ontology is based on the processing of 11, 200 patent documents for inventions. The existing scheme already allows retrieving useful information about alternatives of structural components and communications between them. For example, searching for all elements of a structure in a given invention or tracking relationships. The results suggest that the proposed approach is promising. The authors see further research direction in improving the existing data extraction method and extending the ontology.

To solve the problem of information support for the synthesis of new technical solutions, a method of extracting structured data from an array of Russian-language patents is presented. The key features of the invention, such as the structural elements of the technical object and the relationships between them, are considered as information support. The data source addresses the main claim of the invention in the device patent. The unit of extraction is the semantic structure Subject-Action-Object (SAO), which semantically describes the constructive elements. The extraction method is based on shallow parsing and claim segmentation, taking into account the specifics of writing patent texts. Often the excessive length of the claim sentence and the specificity of the patent language make it difficult to efficiently use off-the-shelf tools for data extracting. All processing steps include: segmentation of the claim sentences; extraction of primary SAO structures; construction of the graph of the construct elements f the invention; integration of the data into the domain ontology. This article deals with the first two stages. Segmentation is carried out according to a number of heuristic rules, and several natural language processing tools are used to reduce analysis errors. The primary SAO elements are extracted considering the valences of the predefined semantic group of verbs, as well as information about the type of processed segment. The result of the work is the organization of the domain ontology, which can be used to find alternative designs for nodes in a technical object. In the second part of the article, an algorithm for constructing a graph of structural elements of a separate technical object, an assessment of the effectiveness of the system, as well as ontology organization and the result are considered.

The effect of polymer binders on the thermal behavior, combustion, and composition of condensed gasification products of model boron-containing compositions was studied to determine the optimal fuel composition for the gas generator of a ducted rocket engine. The physicochemical transformations of boron particles during combustion wave propagation in a solid propellant and during the interaction with the decomposition products of oxidizer and binder were investigated. The binder components were oligodiene urethane and polyether urethane rubbers plasticized with various substances: phthalic acid dimethyl ester, transformer oil, and dioctyl sebacate. Samples of successively complicated composition with the same rubber-to-plasticizer ratio were studied. After thermal analysis of plasticizers and rubbers, plasticized binders and compositions of these binders with boron were investigated and the combustion parameters of model compositions obtained by adding a third component—ammonium perchlorate—were determined. It was found that the thermal decomposition of the more heat-resistant binder and the melt formation of boron oxide largely overlapped and proceeded simultaneously. Features of the combustion of compositions with various binders were identified by high-speed video recording. The composition and microstructure of condensed gasification products collected from the gas phase directly from the burning surface and those remaining in the form of a porous framework after combustion were studied in detail by electron microscopy and thermogravimetry. Based on a comparative analysis of experimental data, it is concluded that it is preferable to use plasticizers and rubbers with reduced thermal stability in inert binders for compositions with amorphous boron designed for gas generators of ducted rocket engines. The possibility of the formation of boron suboxide (B6O) crystals during combustion of boron-containing compositions is shown for the first time.

Suspension cell culture of camel’s thorn Alhagi persarum Boiss. et Buhse was produced for the first time and its characteristics were determined under different growing conditions (flasks and bubble bioreactors with useful volume of 15 L). The obtained culture was notable for an intense growth (accumulation of dry biomass of 15–20 g/L, growth index of 11–16, and specific growth rate of 0.15 ± 0.01 d–1), with growth characteristics in bioreactors close to parameters observed in flasks. Qualitative composition of secondary metabolites in biomass of this cell culture grown in flasks was preliminarily examined by means of ultra-performance liquid chromatography coupled with mass spectrometry (UPLC-ESI-MS). Isoflavones from different structural groups were detected: free isoflavones (an isomer of afrormosin), glycosides of isoflavones (glycosides of calycosin and formononetin), and acylated glycosides of isoflavones (malonyl glycosides of calycosin, formononetin, genistein, and the isomer of afrormosin). Extracts from biomass of A. рersarum suspension cell culture grown in flasks were tested for antimicrobial activity. Staphylococcus aureus АТСС 25923 and Pseudomonas aeruginosa АТСС 27853 were used as test cultures. Extracts showed a specific antimicrobial activity in respect to S. aureus but were inactive to P. aeruginosa. Thus, the obtained cell culture of A. persarum is a promising object for further examination with a potential of using as an alternative raw material and a source of biologically active compounds characteristic of this species.

This article reveals the connection between the "policy of memory", which was developed in the post-war Germany, and the modern practice of repentance to the peoples of the former colonies, which is characteristic of Western countries. It is concluded that the "policy of memory", originally aimed at the inadmissibility of the repetition of the Holocaust in the future, has become part of the identity in the countries of the West.

The conditions for carrying out molecular dynamics calculations of adsorption isotherms of gases and vapors in micropores of active carbons providing a quantitative coincidence of the calculated and experimental isotherms are considered.

The review examines the principles in formation of cell culture and tissue collections of higher plants in vitro as a variant of genetic collections, the modern state and perspective of using collections in studies of the peculiarities and patterns of synthesis of biologically active substances of higher plants, the important role of collections in biotechnological production of substances for medicinal preparations, and methods for maintaining the stability of cell cultures during long-term cultivation. Particular attention is paid to the retrospective and current state of the All-Russia Collection of Cell Cultures of Higher Plants, the founder of which was Russian Academy of Sciences Corresponding Member R.G. Butenko.

Herein we report a comprehensive laboratory synthesis of a series of energetic azidonitrate derivatives (ANDP, SMX, AMDNNM, NIBTN, NPN, 2-nitro-1,3-dinitro-oxypropane) starting from the readily available nitroisobutylglycerol. This simple protocol allows obtaining the high-energy additives from the available precursor in yields higher than those reported using safe and simple operations not presented in previous works. A detailed characterization of the physical, chemical, and energetic properties including impact sensitivity and thermal behavior of these species was performed for the systematic evaluation and comparison of the corresponding class of energetic compounds.

The article is devoted to an important event in the political history of post-Soviet Russia, namely the first parliamentary elections in its history. The aim of the work was to determine the specifics of the results of the first elections of deputies of the Russian Parliament after the collapse of the USSR in the Nizhny Novgorod region. The tasks of the work are related to the study of the elections of deputies of the State Duma (both by single-mandate districts and by party lists), and the Federation Council. A number of conclusions are drawn regarding the political sympathies of residents of different administrative-territorial units of the Nizhny Novgorod region in the first half of the last decade. A kind of Nizhny Novgorod «red belt» is defined geographically, consisting of the southern districts of the region, as well as several districts of the north and east of the region, where voters mostly supported the left. It is revealed that the level of political activity in the elections is quite high, which is not surprising in view of the intense political life during the perestroika period in Gorky, and then in Nizhny Novgorod

Phosphorothioation (PT), in which a non-bridging oxygen is replaced by a sulfur, is one of the rare modifications discovered in bacteria and archaea that occurs on the sugar-phosphate backbone as opposed to the nucleobase moiety of DNA. While PT modification is widespread in the prokaryotic kingdom, how PT modifications are distributed in the genomes and their exact roles in the cell remain to be defined. In this study, we developed a simple and convenient technique called EcoWI-seq based on a modification-dependent restriction endonuclease to identify genomic positions of PT modifications. EcoWI-seq shows similar performance than other PT modification detection techniques and additionally, is easily scalable while requiring little starting material. As a proof of principle, we applied EcoWI-seq to map at base resolution the PT modifications in the genomes of both the Salmonella enterica cerro 87 and E. coli expressing the dnd+ gene cluster. Specifically, we address whether the partial establishment of modified PT positions is a stochastic or deterministic process. EcoWI-seq reveals a systematic usage of the same subset of target sites in clones for which the PT modification has been independently established.

The article describes the process of developing an automated intelligent search system based on physical effects. The developed system performs descriptor, full-text search, logging of search queries, displaying physical effects and other functions.

As an addition to previously obtained data, it has been shown that the adsorption isotherms calculated by the molecular dynamics method for components of light hydrocarbon mixtures in micropores of active carbons and on graphene surfaces are quantitatively described by equations of lattice models with well-coordinated equation parameters.

Bridged 1,2,4,5-tetraoxanes were prepared using available acidic ion exchange resin with high yields despite the possibility of peroxide decomposition under heterogeneous conditions. The bridged tetraoxanes demonstrated high cytotoxicity against HeLa cancer cells in vitro, which in some cases was higher than that of cisplatin, artesunate, and dihydroartemisinin.

The catalyst H3+x PMo12-x +6 Mox +5 O40 supported on SiO2 was developed for peroxidation of 1,3- and 1,5-diketones with hydrogen peroxide with the formation of bridged 1,2,4,5-tetraoxanes and bridged 1,2,4-trioxolanes (ozonides) with high yield based on isolated products (up to 86 and 90 %, respectively) under heterogeneous conditions. Synthesis of peroxides under heterogeneous conditions is a rare process and represents a challenge for this field of chemistry, because peroxides tend to decompose on the surface of a catalyst . A new class of antifungal agents for crop protection, that is, cyclic peroxides: bridged 1,2,4,5-tetraoxanes and bridged ozonides, was discovered. Some ozonides and tetraoxanes exhibit a very high antifungal activity and are superior to commercial fungicides, such as Triadimefon and Kresoxim-methyl. It is important to note that none of the fungicides used in agricultural chemistry contains a peroxide fragment.

The article is devoted to the activities of corresponding member of the USSR Academy of Sciences V. S. Troitskiy stayed against the launch of the Gorky nuclear power plant for heat supply. V. S. Troitskiy’s arguments against starting this object are indicated. The reasons for the significance of his actions against GAST for the development of informal politicized organizations in Gorky are revealed. The influence of V. S. Troitskiy on the position of the scientific community on significant socio-political issues is indicated

It has been demonstrated that adsorption isotherms on microporous activated carbons calculated by the method of molecular dynamics at temperatures higher than critical for adsorbents quantitatively coincide with experimental isotherms at calculations in micropores of finite sizes, with the micropore width being chosen in accordance with the theory of micropore volume filling and properly selected force field.

The authors examine the main problems regarding the development of international legal framework in the area of fighting terrorism, including the elaboration of the universal definition of the phenomenon of “terrorism” and “international terrorism”. The analysis of legal systems of the leading countries indicates the differences in national legislations in the sphere of fighting terrorism, which creates difficulties on the global scale, since each state has the own representation on this phenomenon, and thus, the means of counteraction. Such gaps in the international law is beneficial for the United State to ensure national interests. The main conclusions lie in the thesis that the global community is currently incapable of developing the unified normative-legal base in the area of fighting terrorism, namely in pertains to consolidation of the universal definition of this phenomenon within the framework of the United Nations. Among the main reasons, the authors highlight the problem of cooperation of the national legal systems on the global scale in this sphere, as well as unwillingness of some countries to fulfill prior commitments.

Recent evidence shows that small open reading frame (smORF

Understanding mechanisms that shape horizontal exchange in prokaryotes is a key problem in biology. A major limit on DNA entry is imposed by restriction-modification (RM) processes that depend on the pattern of DNA modification at host-specified sites. In classical RM, endonucleolytic DNA cleavage follows detection of unprotected sites on entering DNA. Recent investigation has uncovered BREX systems, RM-like activities that employ host protection by DNA modification but replication arrest without evident nuclease action on unmodified phage DNA. We show that the historical stySA RM locus of Salmonella enterica sv Typhimurium is a BREX homolog. The stySA29 allele of the hybrid strain LB5000 carries a mutated version of the ancestral LT2 BREX system. Surprisingly, both a restriction and a methylation defect are observed for this lineage despite lack of mutations in brxX, the modification gene homolog. Instead, flanking genes pglZ and brxC each carry multiple mutations (μ) in C-terminal domains. To avoid plasmid artifacts and potential stoichiometric interference, we chose to investigate this system in situ, replacing the mutated pglZμ and brxCμ genes with wild type (WT). PglZ-WT supports methylation in the presence of either BrxCμ or BrxC-WT but not in the presence of a deletion/insertion allele, ΔbrxC::cat. Restriction of phage L requires both BrxC-WT and PglZ-WT, implicating the BrxC C-terminus specifically in restriction activity. Disruption of four other CDS with cat cassettes still permitted modification, suggesting that BrxC, PglZ and BrxX are principal components of the modification activity. BrxL is required for restriction only. A partial disruption of brxL disrupts transcription globally.

Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and “Candidatus Thiothrix anitrata” sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation. Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.

This article describes the application of relatively high-density foamed cement for cementing wells in the Volga and Urals region. Good cementing practices with high density or conventional density cement slurry is required to ensure mud displacement in fluid saturated intervals of reservoir formations (Benge et al; 1982). With this requirement met, the cement column should circumferentially cover the annulus at this very interval which is exposed to the highest loads. However, due to limited physical and mechanical properties of conventional cement slurries in both liquid and solid state, in certain cases conventional slurries do not solve the problems encountered by the Customer, namely elimination of annular flow between the casing and cement sheath. High-density foamed cement is considered as an improved alternative to conventional cement slurries, and results in a high quality and durable sealing of gas and oil saturated production zones for the life of the well. Proprietary software and process equipment are used for the mixing of the foamed cement slurry with a variety of foaming properties. This process enables the use of a base cement slurry with higher density (up to 2.1 g/cm3) for delivering foamed cement slurries in a wide range of densities. To avoid possible cross flows behind the casing, pilot tests were conducted, where a conventional cement slurry (1.80–1.90 g/cm3) was replaced with a high-density foamed cement slurry with equivalent density with a foam quality of approx. 10% making the cement sheath elastic with improved adhesion to both the casing string and the formation (Spaulding et al; 2018). Pilot tests, incorporating the cementing of several production casings, were conducted where only foamed cement slurries with various foam quality were used in the entire cementing interval. No conventional (non-foamed) cement systems were used in these cases.

Over 85 EUV scanners are installed at customer factories and being used in high volume manufacturing (HVM) of leading semiconductor devices. The latest generation of EUV sources are operating at 250W with 92% availability, while meeting all performance requirements. Future EUV scanners are projected to require even higher power to meet throughput requirements. In this paper, we provide an overview of a the latest advances in the laboratory for tin laser-produced-plasma (LPP) extreme-ultraviolet (EUV) sources at 13.5nm enabling HVM at the N5 node and beyond, highlighting crucial EUV source technology developments needed to meet future requirements for EUV power and stability. This includes the performance of subsystems designed for critical source functions such as collector protection and continuous tin droplet supply.

The genome of halophilic archaeon Haloarcula sinaiiensis ATCC 33800 was sequenced and assembled and comprises seven replicons. Four m6A and one m4C modified motifs and their responsible methyltransferase genes have been identified in the genome by single-molecule real-time (SMRT) sequencing and bioinformatic analysis.

Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and “Candidatus Thiothrix anitrata” sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation. Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.

BisI is a sequence-specific and 5-methylcytosine (m5C)-dependent restriction endonuclease (REase), that cleaves the modified DNA sequence Gm5CNGC (G indicates that the cytosine opposite to G is modified). We expressed and purified a number of BisI homologs from sequenced bacterial genomes and used Illumina sequencing to determine the Pam7902I (Esp638I-like) cleavage sites in phage Xp12 DNA. One BisI homolog KpnW2I is EcoBLMcrX-like, cleaving GCNGC/RCNGY/RCNRC sites with m5C. We also cloned and expressed three BisI homologs from metagenome sequences derived from thermophilic sources. One enzyme EsaTMI is active at 37 to 65°C. EsaHLI cleaves GCNGC sites with three to four m5C and is active up to 50°C. In addition, we determined the number and position of m5C in BisI sites for efficient cleavage. BisI cleavage efficiency of GCNGC site is as following: Gm5CNGC (two internal m5C) > Gm5CNGC (one internal m5C) > GCNGm5C (one external m5C) > > GCNGC (unmodified). Three or four m5C in GCNGC site also supports BisI cleavage although partial inhibition was observed on duplex oligos with four m5C. BisI can be used to partially cleave a desired GCNGC site targeted with a complementary oligonucleotide (hemi-methylated). The m5C-dependent BisI variants will be useful for epigenetic research.

Based on a numerical experiment, it is proven that the Dubinin theory of micropore filling can be extended to adsorption equilibria at supercritical temperatures. The temperature dependences of the main parameters of the theory are refined.

HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5′-GCG↓C-3′ in duplex DNA and cleaves (‘↓’) to produce fragments with 2-base, 3′-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 Å. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded β sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the ‘PD-D/EXK’ superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G↓CGC) and MspI (C↓CGG), which produce fragments with 5′-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.