How to model DNA replication in stochastic models of synthetic genetic circuits (and why)

Biocircuit modeling sometimes requires explicit tracking of a self-replicating DNA species. The most obvious, straightforward way to model a replicating DNA is structurally unstable and leads to pathological model behavior. We describe a simple, stable replication mechanism with good model behavior and show how to derive it from a mechanistic model of ColE1 replication.

Modified Data Storage and Replication Mechanism with Frequent Use-Case Based Indexing

The real time applications demands high speed and reliable data access from the remote database. An effective logical data management strategy that handles simultaneous connections with better performance negotiation is inevitable. This work considers an e-health care application that proposes MongoDB based modified indexing and performance tuning methods. To cope with certain high frequency use case and its performance mandates, a flexible and efficient logical data management may be preferred. By analysing the data dependency, data decomposition concerns and the performance requirements of the specific use case of the medical application, a logical schema may be customized on an ala-carte basis. This work focused on the flexible logical data modeling schemes and its performance factors of the NoSql DB. The efficiency of unstructured data base management in storing and retrieving the e-health care data was analysed with a web based tool. To enable faster data retrieval and query processing over the distributed nodes, a Spark based storage engine was built on top of the MongoDB based data storage management. With Spark tool, the database has been made distributed as master–slave structures with suitable data replication mechanisms. In such distributed database the fail-over also implemented with the suitable replication mechanism. This work considered MongoDB based flexible schema modeling and Spark based distributed computation with multiple chunks of data. The flexible data modeling scheme with MongoDB with the on-demand Spark based computation framework was proposed. To facilitate the eventual consistency, scalability aspects of the e-health care applications, use case based indexing was proposed. With the effective data management, faster query processing the horizontal scalability has been increased. The overall efficiency and scalability of the proposed logical data management approach was analysed. Through the simulation studies, the proposed approach has been claimed to boost the performance of the bigdata based application to a considerable extent.

A bacteriophage infecting Mesorhizobium species has a prolate capsid and shows similarities to a family of Caulobacter crescentus phages

Mesorhizobium phage vB_MloS_Cp1R7A-A1 was isolated from soil planted with chickpea in Saskatchewan. It is dissimilar in sequence and morphology to previously described rhizobiophages. It is a B3 morphotype virus with a distinct prolate capsid and belongs to the tailed phage family Siphoviridae. Its genome has a GC content of 60.3% and 238 predicted genes. Putative functions were predicted for 57 genes, which include 27 tRNA genes with anticodons corresponding to 18 amino acids. This represents the highest number of tRNA genes reported yet in a rhizobiophage. The gene arrangement shows a partially modular organization. Most of the structural genes are found in one module, whereas tRNA genes are in another. Genes for replication, recombination, and nucleotide metabolism form the third module. The arrangement of the replication module resembles the replication module of Enterobacteria phage T5, raising the possibility that it uses a recombination-based replication mechanism, but there is also a suggestion that a T7-like replication mechanism could be used. Phage termini appear to be long direct repeats of just over 12 kb in length. Phylogenetic analysis revealed that Cp1R7A-A1 is more closely related to PhiCbK-like Caulobacter phages and other B3 morphotype phages than to other rhizobiophages sequenced thus far.

Safety Mechanisms in Relational Database as Part of the IT System of the Enterprise

The work examines the effectiveness of the replication mechanism of the X production company database. In order to extend the functionality of the computer database of the enterprise, a model of its resource flow was created and an intensional and extensional part was created for a test database based on real enterprise resources. The model has been simplified to 3-rd normal form. The implementation was done in the MySQL database system. Two different operating systems were selected for testing: Windows and Linux. The database management system (DBMS) is working under the GPL license. MySQL DBMS offers many security mechanisms, and to secure the database, system of users permissions to objects have been selected and also an encryption of access passwords for users and connections to servers was used. A replication engine based on the binary log and the model “main server and backup server” was used to create a copy of the enterprise data.

Structure–Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System

Plants are sessile organisms, and their DNA is particularly exposed to damaging agents. The integrity of plant mitochondrial and plastid genomes is necessary for cell survival. During evolution, plants have evolved mechanisms to replicate their mitochondrial genomes while minimizing the effects of DNA damaging agents. The recombinogenic character of plant mitochondrial DNA, absence of defined origins of replication, and its linear structure suggest that mitochondrial DNA replication is achieved by a recombination-dependent replication mechanism. Here, I review the mitochondrial proteins possibly involved in mitochondrial DNA replication from a structural point of view. A revision of these proteins supports the idea that mitochondrial DNA replication could be replicated by several processes. The analysis indicates that DNA replication in plant mitochondria could be achieved by a recombination-dependent replication mechanism, but also by a replisome in which primers are synthesized by three different enzymes: Mitochondrial RNA polymerase, Primase-Helicase, and Primase-Polymerase. The recombination-dependent replication model and primers synthesized by the Primase-Polymerase may be responsible for the presence of genomic rearrangements in plant mitochondria.

A Lightweight Collaborative GIS Data Editing Approach to Support Urban Planning

Collaborative geospatial data editing is different from other collaborative editing systems, such as textual editing, owing to its geospatial nature. This paper presents a version-based lightweight collaborative geospatial editing method for urban planning. This method extracts editing data and generates a version for collaborative editing, which reduces the data size and thus allows for a high feedback speed. A replication mechanism is engaged to replicate a version for the client to freely edit, which ensures constraint-free editing in collaboration. Based on this method, realizing the fact that heterogeneous geospatial data and non-professional users are involved, a lightweight architecture, integrating web services, and component technologies, was proposed. This architecture provides a unified data access interface and powerful editing ability and ensures a high feedback speed and constraint-free editing. The result of the application of the proposed approach in a practical project demonstrates the usability of collaborative geospatial editing in urban planning. While this approach has been designed for urban planning, it can be modified for use in other domains.