Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization

Background: Nickel (Ni) and cobalt (Co) are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B12. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. Results: We carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i) transport systems, and (ii) metalloproteomes. Our data show that both metals are widely used in bacteria and archaea. Cbi/NikMNQO is the most common prokaryotic Ni/Co transporter, while Ni-dependent urease and Ni-Fe hydrogenase, and B12-dependent methionine synthase (MetH), ribonucleotide reductase and methylmalonyl-CoA mutase are the most widespread metalloproteins for Ni and Co, respectively. Occurrence of other metalloenzymes showed a mosaic distribution and a new B12-dependent protein family was predicted. Deltaproteobacteria and Methanosarcina generally have larger Ni- and Co-dependent proteomes. On the other hand, utilization of these two metals is limited in eukaryotes, and very few of these organisms utilize both of them. The Ni-utilizing eukaryotes are mostly fungi (except saccharomycotina) and plants, whereas most B12-utilizing organisms are animals. The NiCoT transporter family is the most widespread eukaryotic Ni transporter, and eukaryotic urease and MetH are the most common Ni- and B12-dependent enzymes, respectively. Finally, investigation of environmental and other conditions and identity of organisms that show dependence on Ni or Co revealed that host-associated organisms (particularly obligate intracellular parasites and endosymbionts) have a tendency for loss of Ni/Co utilization. Conclusion: Our data provide information on the evolutionary dynamics of Ni and Co utilization and highlight widespread use of these metals in the three domains of life, yet only a limited number of user proteins

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization

Background: Nickel (Ni) and cobalt (Co) are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B12. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. Results: We carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i) transport systems, and (ii) metalloproteomes. Our data show that both metals are widely used in bacteria and archaea. Cbi/NikMNQO is the most common prokaryotic Ni/Co transporter, while Ni-dependent urease and Ni-Fe hydrogenase, and B12-dependent methionine synthase (MetH), ribonucleotide reductase and methylmalonyl-CoA mutase are the most widespread metalloproteins for Ni and Co, respectively. Occurrence of other metalloenzymes showed a mosaic distribution and a new B12-dependent protein family was predicted. Deltaproteobacteria and Methanosarcina generally have larger Ni- and Co-dependent proteomes. On the other hand, utilization of these two metals is limited in eukaryotes, and very few of these organisms utilize both of them. The Ni-utilizing eukaryotes are mostly fungi (except saccharomycotina) and plants, whereas most B12-utilizing organisms are animals. The NiCoT transporter family is the most widespread eukaryotic Ni transporter, and eukaryotic urease and MetH are the most common Ni- and B12-dependent enzymes, respectively. Finally, investigation of environmental and other conditions and identity of organisms that show dependence on Ni or Co revealed that host-associated organisms (particularly obligate intracellular parasites and endosymbionts) have a tendency for loss of Ni/Co utilization. Conclusion: Our data provide information on the evolutionary dynamics of Ni and Co utilization and highlight widespread use of these metals in the three domains of life, yet only a limited number of user proteins

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of high-quality inferences of transcriptional regulatory interactions have been already accumulated for diverse taxonomic groups of bacteria. The reconstructed regulons include transcription factors, their cognate DNA motifs and regulated genes/operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. The initial release of the database includes ∼11 500 candidate binding sites for ∼400 orthologous groups of transcription factors from over 350 prokaryotic genomes. Majority of these data are represented by genome-wide regulon reconstructions in Shewanella and Streptococcus genera and a large-scale prediction of regulons for the LacI family of transcription factors. Another section in the database represents the results of accurate regulon propagation to the closely related genomes

Design and implementation of adaptive technology for teaching mathematics to school children based on integrated diagnostic approach to subject preparation and competence development

The development of school teaching  systems to enable effective adaptive communication of information requires specific pedagogical solutions to several important theoretical and methodological problems .These include 1) the discernment of basic characteristics needed to diagnose and improve the quality of subject preparation for schoolchildren, 2) clarifying the role of the teacher in the structure of adaptive learning  process, and  3) finding ways to integrate adaptive content into the framework of courses on mathematics. The purpose of our study was to determine theoretical and methodological foundations of teaching mathematics to schoolchildren taking into account their level of ability with the consequent development of appropriate adaptive content. The basic characteristics that underpin the concept of adaptive learning which contributes to both individual profiles of student ability to learn and subsequent success outcomes are: proficiency, motivation to learn and level of mathematical knowledge. The evaluation of individual profile structure of schoolchildren determines the choice of methodologies for presentation of adaptive content in ways allowing development and motivation. The system of educational process management developed in this way includes both content-methodical and procedural-technological components. This makes it possible to automatically evaluate the level of each students' mathematical training (knowledge, motivation, development) and to ensure continuous improvement. This system can also be used by secondary teachers of mathematics as a part of extracurricular activities, or as a distance learning support. In addition, the recommendations for structuring multi-level problem material can be used by mathematics teachers to self-construct adaptive sets tasks at various stages of teaching mathematics. As a result, students have the opportunity to improve their own profile of learning success, particularly by solving a chain of tasks

Activation of students ' activity in the conditions of training in cooperation technology

Competence-based approach, becoming dominant in the system of higher education, marked the transition from traditional methods and means of education to the use of innovative technologies. Modern higher schools under the influence of the requirements of Federal state educational standards seek to optimize their own activities in order to improve the quality of education and seek new ways to build competence. Today, within the framework of the competence-based approach having a practice-oriented focus, technologies of training in cooperation that meet the requirements for modern training of students are becoming more popular. The purpose of the article is to present the experience of using learning technologies in cooperation, activating the students’ performance. A powerful argument in favor of training in cooperation technologies implementation is their wide functionality in the development of professional competence of a specialist. Since the development of student competence takes place within the framework of various activities, we consider the technology of training in cooperation, allowing students to maximize their potential in the process of interaction with classmates. The article identifies such important advantages of the technology under consideration as the development of independence, creative component, skills of effective interaction and the ability to conduct a constructive dialogue. We consider ideas of training in cooperation technology in detail as well as carry the analysis on the example of pedagogical courses. The presented research allowed establishing increase of students’ activity in studying of pedagogical courses at the expense of identification of an average score in studied profiles

Implementation of discussion technologies in a personality-centered professional education

The conditions of modern labor market dictate the need for highly qualified specialists who creatively approach the performance of their professional activities, independently making competent productive decisions. In search of a solution to this problem, higher education institutions resort to the use of modern educational technologies. The article presents the forms of implementation of discussion technologies, their peculiarity, considers their importance and specificity of use in the conditions of personality-centered training and defines the goals of discussion technologies implementation in the course study. The study revealed an increase in the level of students’ training. The use of discussion technologies allowed them to study the topics of the course more deeply

ELEMENTS OF ‘‘FUZZY LOGIC’’ AS A COMPONENT OF PROFESSIONAL AND PEDAGOGICAL TRAINING OF FUTURE MATHEMATICS AND INFORMATICS TEACHERS

Introduction: the article describes the application of fuzzy logic in the teaching of mathematics. This theory has a great creative ability to solve various pedagogical tasks for the implementation of the developing and applied functions of school mathematical education. The purpose of the article is to identify the possibilities of including the theory of fuzzy logic in the composition of professional training for future teachers of mathematics and computer science with the definition of content and methodological features. Materials and Methods: normative and programmatic documents describing the implementation of the training of future teachers of mathematics and computer science were studied during the writing of the article. The authors looked through the results of sociological surveys of students. Theoretical analysis and comparison of domestic and foreign approaches to the study of fuzzy logic were used, as well as analysis of the content and features of the professional training process for future teachers of mathematics and com¬puter science. Pedagogical measurements, generalization of the experience of teaching special subjects at the Penza State University, and pedagogical experiments were involved. Results: the need to study the elements of fuzzy mathematics in the school and the appropriateness of including this subject in the content of professional preparation of future mathematics and computer science teachers was demonstrated. Methodological prerequisites for studying this topic are defined, the Using Elements of Fuzzy Logic to Solve Pedagogical Problems intensive course is developed. Discussion and Conclusions: the fuzzy logic course allows to strengthen the motivational and developing potential of teachers of mathematics and computer science at school and university due to the non-conventionality of the involved thinking techniques and the possibility of connecting diverse subject interrelations. As the main way of preparing future teachers of mathematics and computer science for teaching students the elements of fuzzy mathematics, it is advisable to consider an elective course that includes elements of fuzzy logic and their pedagogical applications. Students used the materials quite effectively in the course of their practical work as teachers of mathematics and computer science in high school

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism in bacteria is diverse and involves FNR-like transcription factors HcpR, DNR, and NnrR; two-component systems NarXL and NarQP; NO-responsive activator NorR; and nitrite-sensitive repressor NsrR. Using comparative genomics approaches, we predict DNA-binding motifs for these transcriptional factors and describe corresponding regulons in available bacterial genomes. Within the FNR family of regulators, we observed a correlation of two specificity-determining amino acids and contacting bases in corresponding DNA recognition motif. Highly conserved regulon HcpR for the hybrid cluster protein and some other redox enzymes is present in diverse anaerobic bacteria, including Clostridia, Thermotogales, and delta-proteobacteria. NnrR and DNR control denitrification in alpha- and beta-proteobacteria, respectively. Sigma-54-dependent NorR regulon found in some gamma- and beta-proteobacteria contains various enzymes involved in the NO detoxification. Repressor NsrR, which was previously known to control only nitrite reductase operon in Nitrosomonas spp., appears to be the master regulator of the nitric oxides' metabolism, not only in most gamma- and beta-proteobacteria (including well-studied species such as Escherichia coli), but also in Gram-positive Bacillus and Streptomyces species. Positional analysis and comparison of regulatory regions of NO detoxification genes allows us to propose the candidate NsrR-binding motif. The most conserved member of the predicted NsrR regulon is the NO-detoxifying flavohemoglobin Hmp. In enterobacteria, the regulon also includes two nitrite-responsive loci, nipAB (hcp-hcr) and nipC (dnrN), thus confirming the identity of the effector, i.e. nitrite. The proposed NsrR regulons in Neisseria and some other species are extended to include denitrification genes. As the result, we demonstrate considerable interconnection between various nitrogen-oxides-responsive regulatory systems for the denitrification and NO detoxification genes and evolutionary plasticity of this transcriptional network

Федеральный закон о Национальной электронной библиотеке и начало его реализации

There is considered the Federal Law of the Russian Federation of 03.07.2016 no. 342-FZ “On the Amendments to the Federal Law ‘On Librarianship’ in part of creation of the Federal State Infor-mation System ‘National Electronic Library’ ” (NEL). This law creates the legal basis for the functioning of the new state information system NEL. There are analyzed the provisions of the Federal law defining the notion of the “Federal State Information System ‘National Electronic Library’ ”, Regulations on the NEL objects, NEL participants, NEL online catalogue, etc. Separately considered the functions and authority of the operator of NEL - the Russian State Library. Statistics on the current phase of NEL operation is provided.Рассматривается Федеральный закон Российской Федерации от 03.07.2016 г. № 342-ФЗ «О внесении изменений в Федеральный закон “О библиотечном деле” в части создания федеральной государственной информационной системы “Национальная электронная библиотека”» (НЭБ). Этот закон создает правовую основу для функционирования новой государственной информационной системы НЭБ. Анализируются нормы закона, определяющие понятие «федеральная государственная информационная система “Национальная электронная библиотека”», положение об объектах НЭБ, участниках НЭБ, электронном каталоге НЭБ и др. Отдельно рассматриваются функции и полномочия оператора НЭБ - Российской государственной библиотеки. Приводится статистика о современном этапе функционирования НЭБ