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Arhondakis S.,TEAM Informatics | Auletta F.,Stazione Zoologica Anton Dohrn | Bernardi G.,Stazione Zoologica Anton Dohrn | Bernardi G.,Rome 3 University
Genome Biology and Evolution | Year: 2011

It is well established that changes in the phenotype depend much more on changes in gene expression than on changes in protein-coding genes, and that cis-regulatory sequences and chromatin structure are two major factors influencing gene expression. Here, we investigated these factors at the genome-wide level by focusing on the trinucleotide patterns in the 0.1- to 25-kb regions flanking the human genes that are present in the GC-poorest L1 and GC-richest H3 isochore families, the other families exhibiting intermediate patterns. We could show 1) that the trinucleotide patterns of the 25-kb gene-flanking regions are representative of the very different patterns already reported for the whole isochores from the L1 and H3 families and, expectedly, identical in upstream and downstream locations; 2) that the patterns of the 0.1- to 0.5-kb regions in the L1 and H3 isochores are remarkably more divergent and more specific when compared with those of the 25-kb regions, as well as different in the upstream and downstream locations; and 3) that these patterns fade into the 25-kb patterns around 5kb in both upstream and downstream locations. The 25-kb findings indicate differences in nucleosome positioning and density in different isochore families, those of the 0.1- to 0.5-kb sequences indicate differences in the transcription factors that bind upstream and downstream of genes. These results indicate differences in the regulation of genes located in different isochore families, a point of functional and evolutionary relevance. © The Author(s) 2010. Source

Takeda H.,TEAM Informatics
Methods in molecular biology (Clifton, N.J.) | Year: 2010

We have designed a novel high-throughput (HTP) kinase assay using an array-based surface plasmon resonance (SPR) apparatus. For high flexibility and performance, the kinase assay procedure is divided into an in vitro phosphorylation part and a phospho-detection part on a sensor chip. Not only biotinylated peptides but also recombinant proteins fused with FLAG-GST tandem tag can be used as native substrates. The substrate is selectively captured by a capture antibody immobilized on a sensor chip, and phospho-tyrosine (pTyr) residues are detected by an anti-pTyr antibody. The level of tyrosine phosphorylation is calculated from the capture level of the substrates and the binding level of the anti-pTyr antibody monitored by SPR. A wide dynamic range and real-time monitoring of SPR contribute to improved data reliability, and optimization of the procedure for an array-based apparatus achieved multiple sample processing (1,000 samples/day). Source

Koumandou V.L.,TEAM Informatics | Kossida S.,TEAM Informatics
PLoS Computational Biology | Year: 2014

Bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. Apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation and reduction, sulfate reduction, and methanogenesis. Most bioenergetic pathways have a similar general structure, with an electron transport chain composed of protein complexes acting as electron donors and acceptors, as well as a central cytochrome complex, mobile electron carriers, and an ATP synthase. While each pathway has been studied in considerable detail in isolation, not much is known about their relative evolutionary relationships. Wanting to address how this metabolic diversity evolved, we mapped the distribution of nine bioenergetic modes on a phylogenetic tree based on 16S rRNA sequences from 272 species representing the full diversity of prokaryotic lineages. This highlights the patchy distribution of many pathways across different lineages, and suggests either up to 26 independent origins or 17 horizontal gene transfer events. Next, we used comparative genomics and phylogenetic analysis of all subunits of the F0F1 ATP synthase, common to most bacterial lineages regardless of their bioenergetic mode. Our results indicate an ancient origin of this protein complex, and no clustering based on bioenergetic mode, which suggests that no special modifications are needed for the ATP synthase to work with different electron transport chains. Moreover, examination of the ATP synthase genetic locus indicates various gene rearrangements in the different bacterial lineages, ancient duplications of atpI and of the beta subunit of the F0 subcomplex, as well as more recent stochastic lineage-specific and species-specific duplications of all subunits. We discuss the implications of the overall pattern of conservation and flexibility of the F0F1 ATP synthase genetic locus. © 2014 Koumandou, Kossida. Source

The Classical Swine Fever virus (CSFV) is a major pathogen of livestock and belongs to the flaviviridae viral family. Even though there aren't any verified zoonosis cases yet, the outcomes of CSFV epidemics have been devastating to local communities. In an effort to shed light to the molecular mechanisms underlying the structural and drug design potential of the viral helicase, the three dimensional structure of CSFV helicase has been modeled using conventional homology modeling techniques and the crystal structure of the Hepatitis C virus (HCV) as a template. The established structure of the CSFV helicase has been in silico evaluated for its viability using a repertoire of in silico tools. The ultimate goal of this study is to introduce the 3D conformation of the CSFV helicase as a reliable structure that may be used as the designing platform for de novo, structure-based drug design experiments. In this direction using the modeled structure of CSVF helicase, a 3D pharmacophore was designed. The pharmacophore comprises of a series of key characteristics that molecular inhibitors must satisfy in order to achieve maximum predicted affinity for the given enzyme. Overall, invaluable insights and conclusions are drawn fromthis structural study of the CSFV helicase, which may provide the scientific community with the founding plinth in the fight against CSFV infections through the perspective of the CSFV helicase as a potential pharmacological target. Notably, to date no antiviral agent is available against the CSFV nor is expected soon. Subsequently, there is urgent need for new modern and state-of-the-art antiviral strategies to be developed. © 2013 Vlachakis and Kossida. Source

Vlachakis D.,TEAM Informatics | Kossida S.,TEAM Informatics
Computational and Mathematical Methods in Medicine | Year: 2013

Antibodies appear to be the first line of defence in the adaptive immune response of vertebrates and thereby are involved in a multitude of biochemical mechanisms, such as regulation of infection, autoimmunity, and cancer. It goes without saying that a full understanding of antibody function is required for the development of novel antibody-interacting drugs. These drugs are the Antibody Drug Conjugates (ADCs), which are a new type of targeted therapy, used for example for cancer. They consist of an antibody (or antibody fragment such as a single-chain variable fragment [scFv]) linked to a payload drug (often cytotoxic). Because of the targeting, the side effects should be lower and give a wider therapeutic window. Overall, the underlying principle of ADCs is to discern the delivery of a drug that is cytotoxic to a target that is cancerous, hoping to increase the antitumoural potency of the original drug by reducing adverse effects and side effects, such as toxicity of the cancer target. This is a pioneering field that employs state-of-the-art computational and molecular biology methods in the fight against cancer using ADCs. © 2013 Dimitrios Vlachakis and Sophia Kossida. Source

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