Petri net-based model of the human DNA base excision repair pathway.

Cellular DNA is daily exposed to several damaging agents causing a plethora of DNA lesions. As a first aid to restore DNA integrity, several enzymes got specialized in damage recognition and lesion removal during the process called base excision repair (BER). A large number of DNA damage types and several different readers of nucleic acids lesions during BER pathway as well as two sub-pathways were considered in the definition of a model using the Petri net framework. The intuitive graphical representation in combination with precise mathematical analysis methods are the strong advantages of the Petri net-based representation of biological processes and make Petri nets a promising approach for modeling and analysis of human BER. The reported results provide new information that will aid efforts to characterize in silico knockouts as well as help to predict the sensitivity of the cell with inactivated repair proteins to different types of DNA damage. The results can also help in identifying the by-passing pathways that may lead to lack of pronounced phenotypes associated with mutations in some of the proteins. This knowledge is very useful when DNA damage-inducing drugs are introduced for cancer therapy, and lack of DNA repair is desirable for tumor cell death

Distribution and frequencies of post-transcriptional modifications in tRNAs

<div><p>Functional tRNA molecules always contain a wide variety of post-transcriptionally modified nucleosides. These modifications stabilize tRNA structure, allow for proper interaction with other macromolecules and fine-tune the decoding of mRNAs during translation. Their presence in functionally important regions of tRNA is conserved in all domains of life. However, the identities of many of these modified residues depend much on the phylogeny of organisms the tRNAs are found in, attesting for domain-specific strategies of tRNA maturation. In this work we present a new tool, tRNAmodviz web server (http://genesilico.pl/trnamodviz) for easy comparative analysis and visualization of modification patterns in individual tRNAs, as well as in groups of selected tRNA sequences. We also present results of comparative analysis of tRNA sequences derived from 7 phylogenetically distinct groups of organisms: Gram-negative bacteria, Gram-positive bacteria, cytosol of eukaryotic single cell organisms, Fungi and Metazoa, cytosol of Viridiplantae, mitochondria, plastids and Euryarchaeota. These data update the study conducted 20 y ago with the tRNA sequences available at that time.</p></div

RNAcentral: a comprehensive database of non-coding RNA sequences: a comprehensive database of non-coding RNA sequences

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/

RNAcentral:A comprehensive database of non-coding RNA sequences

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/