Evidence for calcium-mediated perception of plant symbiotic signals in aequorin-expressing Mesorhizobium loti

Background  

During the interaction between rhizobia and leguminous plants the two partners engage in a molecular conversation that leads to reciprocal recognition and ensures the beginning of a successful symbiotic integration. In host plants, intracellular Ca²⁺ changes are an integral part of the signalling mechanism. In rhizobia it is not yet known whether Ca²⁺ can act as a transducer of symbiotic signals.     

Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infection

Background  

The extraction of biological knowledge from genome-scale data sets requires its analysis in the context of additional biological information. The importance of integrating experimental data sets with molecular interaction networks has been recognized and applied to the study of model organisms, but its systematic application to the study of human disease has lagged behind due to the lack of tools for performing such integration.     

Homologous illegitimate random integration of foreign DNA into the X chromosome of a transgenic mouse line

Background  

It is not clear how foreign DNA molecules insert into the host genome. Recently, we have produced transgenic mice to investigate the role of the fad2 gene in the conversion of oleic acid to linoleic acid. Here we describe an integration mechanism of fad2 transgene by homologous illegitimate random integration.     

STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

Background  

The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user.     

Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy

Background  

Molecular networks represent the backbone of molecular activity within cells and provide opportunities for understanding the mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of these networks. Dilated cardiomyopathy is a leading cause of heart failure. Although previous studies have identified putative biomarkers or therapeutic targets for heart failure, the underlying molecular mechanism of dilated cardiomyopathy remains unclear.     

An integrated approach to the prediction of domain-domain interactions

Background  

The development of high-throughput technologies has produced several large scale protein interaction data sets for multiple species, and significant efforts have been made to analyze the data sets in order to understand protein activities. Considering that the basic units of protein interactions are domain interactions, it is crucial to understand protein interactions at the level of the domains. The availability of many diverse biological data sets provides an opportunity to discover the underlying domain interactions within protein interactions through an integration of these biological data sets.     

BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies

Background  

Understanding of immune response mechanisms of pathogen-infected host requires multi-scale analysis of genome-wide data. Data integration methods have proved useful to the study of biological processes in model organisms, but their systematic application to the study of host immune system response to a pathogen and human disease is still in the initial stage.     

Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates

Background  

The knowledge about proteins with specific interaction capacity to the protein partners is very important for the modeling of cell signaling networks. However, the experimentally-derived data are sufficiently not complete for the reconstruction of signaling pathways. This problem can be solved by the network enrichment with predicted protein interactions. The previously published in silico method PAAS was applied for prediction of interactions between protein kinases and their substrates.     

Semantic integration to identify overlapping functional modules in protein interaction networks

Background  

The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module detection algorithms.     

Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information

Background  

Protein-protein interactions play essential roles in protein function determination and drug design. Numerous methods have been proposed to recognize their interaction sites, however, only a small proportion of protein complexes have been successfully resolved due to the high cost. Therefore, it is important to improve the performance for predicting protein interaction sites based on primary sequence alone.     

Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution

Background  

Plant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. Most of them, with the exception of virus-like sequences, do not allow us to trace their origins nor to follow the process of their integration into the host genome. Recent discoveries of virus-like sequences in plant genomes led us to set the objective of elucidating the origin of the repetitive sequences. Endogenous rice tungro bacilliform virus (RTBV)-like sequences (ERTBVs) have been found throughout the rice genome. Here, we reconstructed putative virus structures from RTBV-like sequences in the rice genome and characterized to understand evolutionary implication, integration manner and involvements of endogenous virus segments in the corresponding disease response.     

DASMiner: discovering and integrating data from DAS sources

Background  

DAS is a widely adopted protocol for providing syntactic interoperability among biological databases. The popularity of DAS is due to a simplified and elegant mechanism for data exchange that consists of sources exposing their RESTful interfaces for data access. As a growing number of DAS services are available for molecular biology resources, there is an incentive to explore this protocol in order to advance data discovery and integration among these resources.     

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes

Background  

Although many genomic features have been used in the prediction of protein-protein interactions (PPIs), frequently only one is used in a computational method. After realizing the limited power in the prediction using only one genomic feature, investigators are now moving toward integration. So far, there have been few integration studies for PPI prediction; one failed to yield appreciable improvement of prediction and the others did not conduct performance comparison. It remains unclear whether an integration of multiple genomic features can improve the PPI prediction and, if it can, how to integrate these features.     

Stringent and reproducible tetracycline-regulated transgene expression by site-specific insertion at chromosomal loci with pre-characterised induction characteristics

Background  

The ability to regulate transgene expression has many applications, mostly concerning the analysis of gene function. Desirable induction characteristics, such as low un-induced expression, high induced expression and limited cellular heterogeneity, can be seriously impaired by chromosomal position effects at the site of transgene integration. Many clones may therefore need to be screened before one with optimal induction characteristics is identified. Furthermore, such screens must be repeated for each new transgene investigated, and comparisons between clones with different transgenes is complicated by their different integration sites.     

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data forDrosophila

Background  

Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis. One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to many existing and emerging data sets.     

Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis

Background  

High-throughput genetic screening approaches have enabled systematic means to study how interactions among gene mutations contribute to quantitative fitness phenotypes, with the aim of providing insights into the functional wiring diagrams of genetic interaction networks on a global scale. However, it is poorly known how well these quantitative interaction measurements agree across the screening approaches, which hinders their integrated use toward improving the coverage and quality of the genetic interaction maps in yeast and other organisms.     

REEF: searching REgionally Enriched Features in genomes

Background  

In Eukaryotic genomes, different features including genes are not uniformly distributed. The integration of annotation information and genomic position of functional DNA elements in the Eukaryotic genomes opened the way to test novel hypotheses of higher order genome organization and regulation of expression.     

Mining protein networks for synthetic genetic interactions

Background  

The local connectivity and global position of a protein in a protein interaction network are known to correlate with some of its functional properties, including its essentiality or dispensability. It is therefore of interest to extend this observation and examine whether network properties of two proteins considered simultaneously can determine their joint dispensability, i.e., their propensity for synthetic sick/lethal interaction. Accordingly, we examine the predictive power of protein interaction networks for synthetic genetic interaction in Saccharomyces cerevisiae, an organism in which high confidence protein interaction networks are available and synthetic sick/lethal gene pairs have been extensively identified.