GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae

Motivation: Multi-scale modeling of biological systems requires integration of various information about genes and proteins that are connected together in networks. Spatial, temporal and functional information is available; however, it is still a challenge to retrieve and explore this knowledge in an integrated, quick and user-friendly manner.Results: We present GEMMER (GEnome-wide tool for Multi-scale Modeling data Extraction and Representation), a web-based data-integration tool that facilitates high quality visualization of physical, regulatory and genetic interactions between proteins/genes in Saccharomyces cerevisiae. GEMMER creates network visualizations that integrate information on function, temporal expression, localization and abundance from various existing databases. GEMMER supports modeling efforts by effortlessly gathering this information and providing convenient export options for images and their underlying data.Availability and implementation: GEMMER is freely available at http://gemmer.barberislab.com. Source code, written in Python, JavaScript library D3js, PHP and JSON, is freely available at https://github.com/barberislab/GEMMER.<br/

DGT-induced copper flux predicts bioaccumulation and toxicity to bivalves in sediments with varying properties

Many regulatory frameworks for sediment quality assessment include consideration of contaminant bioavailability. However, the “snap-shots” of metal bioavailability provided by analyses of porewaters or acid-volatile sulfidesimultaneously extractable metal (AVS-SEM) relationships do not always contribute sufficient information. The use of inappropriate or inadequate information for assessing metal bioavailability in sediments may result in incorrect assessment decisions. The technique of diffusive gradients in thin films (DGT) enables the in situ measurement of metal concentrations in waters and fluxes from sediment porewaters. We utilized the DGT technique to interpret the bioavailability of copper to the benthic bivalve Tellina deltoidalis in sediments of varying properties contaminated with copper-based antifouling paint particles. For a concentration series of copper-paint contaminated sandy, silty-sand, and silty sediment types, DGTprobes were used to measure copper fluxes to the overlying water, at the sedimentwater interface, and in deeper sediments. The overlying water copper concentrations and DGT-Cu fluxes were shown to provide excellent exposure concentration−response relationships in relation to lethal effects occurring to the copper-sensitive benthic bivalve, T. deltoidalis. The study demonstrates the strength of the DGT technique, which we expect will become frequently used for assessing metal bioavailability in sediments

HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein

The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.Animal science

Parallel Expansions of Sox Transcription Factor Group B Predating the Diversifications of the Arthropods and Jawed Vertebrates

Group B of the Sox transcription factor family is crucial in embryo development in the insects and vertebrates. Sox group B, unlike the other Sox groups, has an unusually enlarged functional repertoire in insects, but the timing and mechanism of the expansion of this group were unclear. We collected and analyzed data for Sox group B from 36 species of 12 phyla representing the major metazoan clades, with an emphasis on arthropods, to reconstruct the evolutionary history of SoxB in bilaterians and to date the expansion of Sox group B in insects. We found that the genome of the bilaterian last common ancestor probably contained one SoxB1 and one SoxB2 gene only and that tandem duplications of SoxB2 occurred before the arthropod diversification but after the arthropod-nematode divergence, resulting in the basal repertoire of Sox group B in diverse arthropod lineages. The arthropod Sox group B repertoire expanded differently from the vertebrate repertoire, which resulted from genome duplications. The parallel increases in the Sox group B repertoires of the arthropods and vertebrates are consistent with the parallel increases in the complexity and diversification of these two important organismal groups

Caractérisation de la famille des gènes sox chez drosophila melanogaster

MONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Understanding principles of the dynamic biochemical networks of life through systems biology

Systems Biology brings the potential to discover fundamental principles of Life that cannot be discovered by considering individual molecules. This chapter discusses a number of early, more recent, and upcoming discoveries of such network principles. These range from the balancing of fluxes through metabolic networks, the potential of those networks for truly individualized medicine, the time dependent control of fluxes and concentrations in metabolism and signal transduction, the ways in which organisms appear to regulate metabolic processes vis-à-vis limitations therein, tradeoffs in robustness and fragility, and a relation between robustness and time dependences in the cell cycle. The robustness considerations will lead to the issue whether and how evolution has been able to put in place design principles of control engineering such as infinite robustness and perfect adaptation in the hierarchical biochemical networks of cell biology © 2014 Elsevier Inc. All rights reserved