Lack of conservation of bacterial type promoters in plastids of Streptophyta

<p>Abstract</p> <p/> <p>We demonstrate the scarcity of conserved bacterial-type promoters in plastids of Streptophyta and report widely conserved promoters only for genes <it>psaA, psbA, psbB, psbE, rbcL</it>. Among the reasonable explanations are: evolutionary changes of sigma subunit paralogs and phage-type RNA polymerases possibly entailing the loss of corresponding nuclear genes, <it>de novo </it>emergence of the promoters, their loss together with plastome genes; functional substitution of the promoter boxes by transcription activation factor binding sites.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Arcady Mushegian, and by Dr. Alexander Bolshoy and Dr. Yuri Wolf (both nominated by Dr. Purificación López-García).</p

Modeling RNA polymerase competition: the effect of σ-subunit knockout and heat shock on gene transcription level

<p>Abstract</p> <p>Background</p> <p>Modeling of a complex biological process can explain the results of experimental studies and help predict its characteristics. Among such processes is transcription in the presence of competing RNA polymerases. This process involves RNA polymerases collision followed by transcription termination.</p> <p>Results</p> <p>A mathematical and computer simulation model is developed to describe the competition of RNA polymerases during genes transcription on complementary DNA strands. E.g., in the barley <it>Hordeum vulgare </it>the polymerase competition occurs in the locus containing plastome genes <it>psbA</it>, <it>rpl23</it>, <it>rpl2 </it>and four bacterial type promoters. In heat shock experiments on isolated chloroplasts, a twofold decrease of <it>psbA </it>transcripts and even larger increase of <it>rpl23</it>-<it>rpl2 </it>transcripts were observed, which is well reproduced in the model. The model predictions are in good agreement with virtually all relevant experimental data (knockout, heat shock, chromatogram data, etc.). The model allows to hypothesize a mechanism of cell response to knockout and heat shock, as well as a mechanism of gene expression regulation in presence of RNA polymerase competition. The model is implemented for multiprocessor platforms with MPI and supported on Linux and MS Windows. The source code written in C++ is available under the GNU General Public License from the laboratory website. A user-friendly GUI version is also provided at <url>http://lab6.iitp.ru/en/rivals</url>.</p> <p>Conclusions</p> <p>The developed model is in good agreement with virtually all relevant experimental data. The model can be applied to estimate intensities of binding of the holoenzyme and phage type RNA polymerase to their promoters using data on gene transcription levels, as well as to predict characteristics of RNA polymerases and the transcription process that are difficult to measure directly, e.g., the intensity (frequency) of holoenzyme binding to the promoter in correlation to its nucleotide composition and the type of σ-subunit, the amount of transcription initiation aborts, etc. The model can be used to make functional predictions, e.g., heat shock response in isolated chloroplasts and changes of gene transcription levels under knockout of different σ-subunits or RNA polymerases or due to gene expression regulation.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Anthony Almudevar, Dr. Aniko Szabo, Dr. Yuri Wolf (nominated by Dr. Peter Olofsson) and Prof. Marek Kimmel.</p

Mediation as an alternative dispute resolution: world experience

The present paper is devoted to the application of mediation as an alternative dispute resolution procedure. It defines features of the legal regulation of mediation procedures in different countries and legal systems, such as United States, European Union, China, and Russian Federation. In addition, the main principles of mediation and their implementation in different legal systems are analyzed in this pape

Вычислительные методы для решения задачи комбинирования секторов воздушного пространства

A problem of combining elementary sectors of an airspace region is considered, in which a minimum number of combined sectors must be obtained with restrictions on their load and feasibility of combinations such as the requirement of the space connectivity or the membership of a given set of permissible combinations. Computational methods are proposed and tested to be used for solution  of general problems of airspace sectorization. In particular, two types of combinatorial algorithms are proposed for constructing partitions of a finite set with specified element weights and graph-theoretical relationships between the elements. Partitions are constructed by use of a branch and bound method to minimize the number of subsets in the final partition, while limiting the total weight of elements in the subset. In the first type algorithm, ready-made components of the final partition are formed in each node of the branch and bound tree. The remaining part of the original set is further divided at the lower nodes. In the second type algorithm, the entire current partition is formed in each node, the components of which are supplemented at the lower nodes. When comparing algorithms performance, the problems are divided into two groups, one of which contains a connectivity requirement, and the other does not. Several integer programming formulations are also presented. Computational complexity of two problem variants is established: a bin packing type problem with restrictions on feasible combinations, and covering type problem.Рассматривается задача комбинирования секторов региона воздушного пространства, при которой должно быть получено минимальное количество секторов при ограничении на их нагрузку. Предлагаются вычислительные методы, которые могут быть применены в более общих моделях решения задачи. Предлагается алгоритм построения разбиений конечного множества, а также формулировка задачи целочисленного линейного программирования, используется также терминология теории графов

МЕТОДЫ ПОИСКА НЕСКОЛЬКИХ РЕШЕНИЙ СИСТЕМЫ РАЗНОСТНЫХ И ИНТЕРВАЛЬНЫХ ОГРАНИЧЕНИЙ

We develop two methods of solving DBM system. One method is based on Fourier – Motskinelimination scheme, it has complexity O(n3) for finding initial solve and complexity O(n3) for finding solve by changing one of variable value for some cases. The other method is based on the network of constraints approach, it has complexity O(n3) for finding initial solve and  O(n) or approximately for finding solve by changing one of variable value if it is limited by special bounds.  Рассматриваются методы поиска решений систем линейных неравенств специального вида, состоящих из разностных неравенств с двумя переменными и интервальных ограничений с одной переменной. Для решения таких систем предлагаются два подхода, с помощью которых могут быть найдены два экстремальных («максимальное» и «минимальное») решения, а также некоторые другие решения. Первый подход основан на методе Фурье – Моцкина, второй – на представлении системы в виде сети ограничений

МОДЕЛИРОВАНИЕ ДВИЖЕНИЯ ОБЪЕКТОВ БЕЗ ОСТАНОВОК ПО СЕТИ ПЕРЕСЕКАЮЩИХСЯ МАРШРУТОВ

Modeling of movement of objects without stops in a network of crossing routes is studied. The problem is formulated in terms of disjunctive linear programming, mixed integer linear programming and graph theory. Several variants for representing constraints on convergence of objects are considered. NP-completeness of the problem in the strong sense is proved.Рассматривается задача моделирования движения объектов по сети пересекающихся маршрутов. Задача формулируется в терминах дизъюнктивного линейного программирования, смешанного целочисленного линейного программирования и теории графов. Рассматривается несколько вариантов задания ограничений на сближение объектов. Доказывается NP-полнота задачи в сильном смысле

Activity and understanding : structure of action and orientated linguistics

x, 300 p. : ill. ; 23 cm

Activity and understanding : structure of action and orientated linguistics

x, 300 p. : ill. ; 23 cm

Computational methods for airspace sectorisation

A problem of combining elementary sectors of an airspace region is considered, in which a minimum number of combined sectors must be obtained with restrictions on their load and feasibility of combinations such as the requirement of the space connectivity or the membership of a given set of permissible combinations. Computational methods are proposed and tested to be used for solution  of general problems of airspace sectorization. In particular, two types of combinatorial algorithms are proposed for constructing partitions of a finite set with specified element weights and graph-theoretical relationships between the elements. Partitions are constructed by use of a branch and bound method to minimize the number of subsets in the final partition, while limiting the total weight of elements in the subset. In the first type algorithm, ready-made components of the final partition are formed in each node of the branch and bound tree. The remaining part of the original set is further divided at the lower nodes. In the second type algorithm, the entire current partition is formed in each node, the components of which are supplemented at the lower nodes. When comparing algorithms performance, the problems are divided into two groups, one of which contains a connectivity requirement, and the other does not. Several integer programming formulations are also presented. Computational complexity of two problem variants is established: a bin packing type problem with restrictions on feasible combinations, and covering type problem

Activity and understanding : structure of action and orientated linguistics

x, 300 p. : ill. ; 23 cm