Non-cubic layered structure of Ba(1-x)K(x)BiO3 superconductor

Bismuthate superconductor Ba(1-x)K(x)BiO3 (x=0.27-0.49, Tc=25-32K) grown by an electrolysis technique was studied by electron diffraction and high-resolution electron microscopy. The crystalline structure thereof has been found to be non-cubic, of the layered nature, and non-centrosymmetric, with the lattice parameters a ~ ap, c ~ 2ap (ap is a simple cubic perovskite cell parameter) containing an ordered arrangement of barium and potassium. The evidence for the layered nature of the bismuthate superconductor removes the principal crystallographic contradiction between bismuthate and cuprate high-Tc superconductors.Comment: 4 pages, 3 figures, to be published in Physical Review B as a Rapid Communicatio

Разработка базы данных мотивов регуляции транскрипции у бактерий

O b j e c t i v e s . The amount of data generated by modern methods of high-throughput sequencing is such that their analysis is performed mainly in automatic mode. In particular, the use of newly decoded genomic sequences is possible only after the annotation of functional elements of the genome, which, as a rule, is performed by automatic pipelines. Such annotation pipelines do a good job to identify the genes, but none of them annotate regulatory elements. Without these elements it is not possible to understand when and how genes can be expressed. Information on the regulatory elements of bacteria is collected in several specialized databases (RegulonDB, CollecTF, Prodoric2, etc.), however, only a part of this information can be used for annotation of regulatory elements, and only for a very limited range of bacteria. Previously, we proposed a clear formal criterion for applying regulatory information to any bacterial genome. Such a criterion is the CR tag, a sequence of amino acid residues of a transcriptional regulator that specifically contacts the nitrogenous bases of regulatory element in genomic DNA. The mathematical model of a regulatory element (motif) associated with a CR tag can be correctly applied to annotate similar elements in any genomes encoding a transcriptional regulator with an identical CR tag. The accumulation of motifs associated with CR tags raised the question of their ordered storage for the convenience of subsequent use in the annotation of genomic sequences. Since no one of well-known databases uses the concept of CR tags, a new database ought to be developed. Thus, the goal of this work is to create a database with information about bacterial transcription factors and DNA sequences recognized by them, suitable for annotation of regulatory sequences in bacterial genomes.M e t h o d s .  Infological  modeling  of  the  subject  area  was  carried  out  using  the  IDEF1X  methodology. The database was developed using the Microsoft SQL Server DBMS. A cross-platform application for importing data into a database is written in C++ using Qt technology.Re s u l t s . As a result of the study of the subject area, a relational data model was developed and implemented in the Microsoft SQL Server DBMS, which allows holistic storage of information about accumulated transcription regulation motifs in bacteria, including information about the publications confirming their correctness. To automate the process of entering accumulated data, a cross-platform application was developed for importing structured data on transcription factors.Co n c l u s i o n .  The  main difference of  the  developed database is  the  use  of  CR-tag  concept. Records of mathematical models of regulatory elements (motifs) in the database are associated with a CR tag and, therefore, can be correctly used to annotate similar elements in any genomes encoding a transcriptional regulator with an identical CR tag. The developed database will provide structured and holistic data storage, as well as their quick search when used in the pipeline for automatic annotation of regulatory elements in bacterial genomic sequences.Ц е л и. Объемы данных, генерируемые современными методами высокопроизводительного секвенирования, таковы, что их анализ выполняется преимущественно в автоматическом режиме. В частности, использование вновь расшифрованных геномных последовательностей возможно только после аннотации функциональных элементов генома, которая, как правило, выполняется автоматическими конвейерами. Такие конвейеры аннотации успешно справляются с идентификацией генов, но ни один из них не аннотирует регуляторные элементы, без которых нельзя понять, когда и как гены могут экспрессироваться. Информация о регуляторных элементах бактерий собрана в нескольких специализированных базах данных (RegulonDB, CollecTF, Prodoric2 и др.), однако только часть этой информации можно использовать для аннотации регуляторных элементов и только у очень ограниченного круга бактерий. Ранее авторами был предложен четкий формальный критерий для применения регуляторной информации к любым бактериальным геномам. Таким критерием стал CR-тег – последовательность аминокислотных остатков транскрипционного регулятора, специфически контактирующих с азотистыми основаниями регуляторного элемента в геномной ДНК. Связанная с CR-тегом математическая модель регуляторного элемента (мотив) может быть корректно применена для аннотации подобных элементов в любых геномах, кодирующих транскрипционный регулятор с идентичным CR-тегом. Накопление связанных с CR-тегами мотивов поставило вопрос об их упорядоченном хранении для удобства последующего применения при аннотации геномных последовательностей. Поскольку ни одна из известных баз данных не использует концепцию CR-тегов, потребовалась разработка новой базы данных. Таким образом, целью работы является создание базы данных с информацией о бактериальных транскрипционных факторах и распознаваемых ими последовательностях ДНК, пригодной для аннотации регуляторных последовательностей в бактериальных геномах.М е то д ы .  Инфологическое моделирование предметной области производилось с помощью методологии IDEF1X. Разработка базы данных выполнялась посредством СУБД Microsoft SQL Server. Кроссплатформенное приложение по импорту данных в базу данных написано на языке C++ с использованием технологии Qt.Р е з у л ь т а т ы . В результате проведенного исследования предметной области была разработана и реализована в СУБД Microsoft SQL Server реляционная модель данных, позволяющая целостное хранение информации  о  накопленных  мотивах  регуляции  транскрипции  у  бактерий,  включая  и  информацию о публикациях, подтверждающих корректность этих мотивов. Для автоматизации процесса ввода накопленных данных разработано кроссплатформенное приложение для импорта структурированных данных о транскрипционных факторах.З а к л ю ч е н и е .  Основным отличием разработанной базы данных является использование концепции CR-тега. Записи математических моделей регуляторных элементов (мотивов) в базе данных связаны с CR-тегом и поэтому могут быть корректно применены для аннотации подобных элементов в любых геномах, кодирующих транскрипционный регулятор с идентичным CR-тегом. Разработанная база данных обеспечит структурированное и целостное хранение данных, а также их быстрый поиск при использовании в конвейере автоматической аннотации регуляторных элементов в бактериальных геномных последовательностях

Transcriptome profiling helps to identify potential and true molecular switches of stealth to brute force behavior in Pectobacterium atrosepticum during systemic colonization of tobacco plants

© 2018, Koninklijke Nederlandse Planteziektenkundige Vereniging. In the present study, we have monitored the process of systemic plant colonization by the plant pathogenic bacterium Pectobacterium atrosepticum (Pba) using RNA-Seq analysis in order to compare bacterial traits under in planta and in vitro conditions and to reveal potential players that participate in switching from stealth to brute force strategy of the pathogen. Two stages of tobacco plant colonization have been assayed: i) the initial one associated with visually symptomless spread of bacteria throughout the host body via primary xylem vessels where bacterial emboli were formed (stealth strategy), and ii) the advanced stage coupled with an extensive colonization of core parenchyma and manifestation of soft rot symptoms (brute force strategy). Plant-inducible genes in Pba and potential players switching the pathogen’s behavior were revealed. Genes from the cfa locus responsible for the production of coronafacic acid displayed the strongest induction in the asymptomatic zone relative to the symptomatic one and were shown experimentally to act as the true strategy “switchers” of Pba behavior in planta. Surprisingly, cfa genes appeared to be unnecessary for establishment of the asymptomatic stage of plant colonization but were required for the transition to soft-rot-associated symptomatic stage coupled with over-induction of jasmonate-mediated pathway in the plant

ANALYSIS OF THE METHODS OF PREVENTION OF BURNING-IN ON THE SURFACE OF STEEL AND CAST IRON MOULDINGS

The known theories and approaches explaining the nature of formation process of a metal penetration (burning-in) on a surface of steel and iron castings are described in the article. The methods and materials which are applied in antistick coatings and in the molding sand mixtures for prevention of defect formation is also given in the paper

RESEARCH OF THE INFLUENCE NANOMODIFICATION ON THE STRUCTURE AND PROPERTIES OF ZINC ANTIFRICTION ALLOYS

This article describes technology of producing of antifriction alloys of zinc–aluminum–copper composition. The effect of modification by nanostructured materials in forming structures of antifriction alloys in the manufacture of heavy-duty plain bearing liners was examined

The PhoPQ Two-Component System Is the Major Regulator of Cell Surface Properties, Stress Responses and Plant-Derived Substrate Utilisation During Development of Pectobacterium versatile-Host Plant Pathosystems

Pectobacterium versatile (formerly P. carotovorum) is a recently defined species of soft rot enterobacteria capable of infecting many plant hosts and damaging different tissues. Complex transcriptional regulation of virulence properties can be expected for such a versatile pathogen. However, the relevant information is available only for related species and is rather limited. The PhoPQ two-component system, originally described in pectobacteria as PehRS, was previously shown to regulate a single gene, pehA. Using an insertional phoP mutant of Pectobacterium versatile (earlier—P. carotovorum), we demonstrate that PhoP regulates at least 115 genes with a majority of them specific for pectobacteria. The functions performed by PhoP-controlled genes include degradation, transport and metabolism of plant-derived carbon sources (polygalacturonate, arabinose-containing polysaccharides and citrate), modification of bacterial cell envelope and stress resistance. We also demonstrated PhoP involvement in establishing the order of plant cell wall decomposition and utilisation of the corresponding breakdown products. Based on experimental data and in silico analysis, we defined a PhoP binding site motif and provided proof for its universality in enteric bacteria. Scanning P. versatile genome for the locations of this motif suggested a much larger PhoP regulon enriched with the genes important for a plant pathogen, which makes PhoP a global virulence regulator. Potential PhoP targets include many regulatory genes and PhoP control over one of them, expI, was confirmed experimentally, highlighting the link between the PhoPQ two-component and quorum sensing systems. High concentrations of calcium and magnesium ions were found to abolish the PhoPQ-dependent transcription activation but did not relieve repression. Reduced PhoP expression and minimisation of PhoP dependence of regulon members’ expression in P. versatile cells isolated from potato tuber tissues suggest that PhoPQ system is a key switch of expression levels of multiple virulence-related genes fine-tuned to control the development of P. versatile-host plant pathosystem

Complete genome sequence of the abscisic acid-utilizing strain Novosphingobium sp. P6W

© 2019, King Abdulaziz City for Science and Technology. The phytohormone abscisic acid (ABA) plays multiple roles in plant survival and fitness. Significant quantities of ABA are constantly introduced into soil via root exudation, root turnover and incorporation of abscised shoot tissues. In addition, some phytopathogenic fungi synthesize ABA in the course of plant–microbe interactions. The accumulation of soil ABA can inhibit seed germination and root growth but despite this observation, the biochemical pathways of ABA conversion by microorganisms and genetic determinants of the process remain unknown. Here we report on the complete genome sequence of strain P6W, an ABA-utilizing isolate of the genus Novosphingobium. Strain P6W was isolated from the rhizosphere of rice (Oryza sativa L.) seedlings using a selective ABA-supplemented medium. The genome of strain P6W consists of 6,606,532 bp, which includes two chromosomes and two plasmids. It comprises of 5663 protein-coding genes and 80 RNA genes. ANI values calculated based on the analysis of nine previously sequenced genomes of members of the genus Novosphingobium ranged from 77 to 92%, which suggests that strain P6W is potentially a new species of the genus Novosphingobium. Functional annotation of genes in the genome of strain P6W revealed a number genes that could be potentially responsible for ABA degradation

Complete genome sequence of the abscisic acid-utilizing strain Novosphingobium sp. P6W

© 2019, King Abdulaziz City for Science and Technology. The phytohormone abscisic acid (ABA) plays multiple roles in plant survival and fitness. Significant quantities of ABA are constantly introduced into soil via root exudation, root turnover and incorporation of abscised shoot tissues. In addition, some phytopathogenic fungi synthesize ABA in the course of plant–microbe interactions. The accumulation of soil ABA can inhibit seed germination and root growth but despite this observation, the biochemical pathways of ABA conversion by microorganisms and genetic determinants of the process remain unknown. Here we report on the complete genome sequence of strain P6W, an ABA-utilizing isolate of the genus Novosphingobium. Strain P6W was isolated from the rhizosphere of rice (Oryza sativa L.) seedlings using a selective ABA-supplemented medium. The genome of strain P6W consists of 6,606,532 bp, which includes two chromosomes and two plasmids. It comprises of 5663 protein-coding genes and 80 RNA genes. ANI values calculated based on the analysis of nine previously sequenced genomes of members of the genus Novosphingobium ranged from 77 to 92%, which suggests that strain P6W is potentially a new species of the genus Novosphingobium. Functional annotation of genes in the genome of strain P6W revealed a number genes that could be potentially responsible for ABA degradation

Complete genome sequence of abscisic acid-metabolizing rhizobacterium rhodococcus sp. strain P1Y

© 2019 Gogoleva et al. Mechanisms of microbial catabolism of phytohormone abscisic acid (ABA) are still unknown. Here, we report the complete genome sequence of ABAutilizing Rhodococcus sp. strain P1Y, isolated from the rice (Oryza sativa L.) rhizosphere. The sequence was obtained using an approach combining Oxford Nanopore Technologies MinION and Illumina MiSeq sequence data

Complete genome sequence of abscisic acid-metabolizing rhizobacterium rhodococcus sp. strain P1Y

© 2019 Gogoleva et al. Mechanisms of microbial catabolism of phytohormone abscisic acid (ABA) are still unknown. Here, we report the complete genome sequence of ABAutilizing Rhodococcus sp. strain P1Y, isolated from the rice (Oryza sativa L.) rhizosphere. The sequence was obtained using an approach combining Oxford Nanopore Technologies MinION and Illumina MiSeq sequence data