351 research outputs found

    SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes

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    <p>Abstract</p> <p>Background</p> <p>It has been repeatedly observed that gene order is rapidly lost in prokaryotic genomes. However, persistent synteny blocks are found when comparing more or less distant species. These genes that remain consistently adjacent are appealing candidates for the study of genome evolution and a more accurate definition of their functional role. Such studies require visualizing conserved synteny blocks in a large number of genomes at all taxonomic distances.</p> <p>Results</p> <p>After comparing nearly 600 completely sequenced genomes encompassing the whole prokaryotic tree of life, the computed synteny data were assembled in a relational database, SynteBase. SynteView was designed to visualize conserved synteny blocks in a large number of genomes after choosing one of them as a reference. SynteView functions with data stored either in SynteBase or in a home-made relational database of personal data. In addition, this software can compute <it>on-the-fly </it>and display the distribution of synteny blocks which are conserved in pairs of genomes. This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. It is also possible to download sequences of genes belonging to these synteny blocks for further studies. SynteView is accessible through Java Webstart at <url>http://www.synteview.u-psud.fr</url>.</p> <p>Conclusion</p> <p>SynteBase answers queries about gene order conservation and SynteView visualizes the obtained results in a flexible and powerful way which provides a comparative overview of the conserved synteny in a large number of genomes, whatever their taxonomic distances.</p

    Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

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    <p>Abstract</p> <p>Background</p> <p>Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving.</p> <p>Results</p> <p>We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD) using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing <it>bona fide </it>orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs), and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms.</p> <p>Conclusion</p> <p>The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene order conservation in prokaryotes whichever their taxonomic distance. Thus, our approach will make easy the rapid identification of POGS in the next few years as we are expecting to be inundated with thousands of completely sequenced microbial genomes.</p

    Bis(2,2′-bipyridyl-κ2 N,N′)bis­(2-hydroxy­benzoato)-κO 1;κ2 O 1,O 1′-cadmium(II) methanol solvate

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    The title compound, [Cd(C7H5O3)2(C10H8N2)2]·CH3OH, contains one monomeric seven-coordinate cadmium complex and one methanol solvate mol­ecule. The CdII atom is coordinated to two 2,2′-bipyridyl ligands via the N atoms and to two salicylate anions (Hsal−) via the carboxyl­ate O atoms, which act as monodentate ligand for the one and bidentate ligand for the second. The CdII atom exhibits a {6 + 1} environment, approximately described as a distorted capped octa­hedron with the apical positions occupied by one of the two N atoms belonging to one bipyridyl ligand and one of the two carboxyl­ate O atoms from the monodentate Hsal− ligand. Two intra­molecular six-membered hydrogen-bonded rings are present, generated from inter­actions between the carboxyl­ate and hydr­oxy groups of the salicylate ligands. There is one inter­molecular hydrogen-bonding inter­action involving the methanol solvent mol­ecule and the carboxyl­ate group from the monodentate Hsal− ligand. The crystal packing is governed by π–π stacking inter­actions [centroid–centroid distance = 3.783 (4) Å] which occur between bipyridyl ligands, by C—H⋯O and C—H⋯π inter­actions and by numerous van der Waals contacts

    William Lang Dessaint (1930-2013)

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    William Dessaint est né le 6 mars 1930 à Villerupt (Meurthe-et-Moselle) d’un père français et d’une mère américaine. À la fin de la Seconde Guerre mondiale et à la suite de la séparation de ses parents, il quitta la France pour les États-Unis avec sa mère et son frère cadet. Au hasard de ses amitiés et du fait de l’éducation biculturelle qu’il avait reçue, il se découvrit une passion pour l’étude de la géographie et des peuples du monde, et notamment pour l’Europe balkanique et l’Asie. Il s’e..

    Dibromidobis­(4-hydr­oxy-1,5-dimethyl-2-phenyl-3-pyrazolone)zinc(II)

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    In the title compound, [ZnBr2(C11H12N2O2)2], the Zn(II) ion is coordinated by two Br atoms and two O atoms from two 4-hydroxy­anti­pyrine mol­ecules via the carbonyl O atoms, which act as monodentate ligands, giving rise to a distorted tetra­hedral geometry. The values of the bond angles at the Zn atom are in the range 99.4 (1) to 113.2 (1)°. The presence of O—H⋯O and O—H⋯Br intra­molecular hydrogen bonds can explain the difference between the two Zn—O [1.961 (3)/2.015 (3) Å] and the two Zn—Br [2.350 (1)/2.378 (1) Å] bond lengths. The crystal structure is governed by C—H⋯O, C—H⋯Br and Zn—Br⋯Cg(π-ring) inter­actions

    Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma

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    International audienceThe mechanisms of gene amplification in tumour cells are poorly understood and the relationship between extrachromosomal DNA molecules, named double minutes (dmins), and intrachromosomal homogeneously staining regions (hsr) is not documented at nucleotide resolution. Using fluorescent in situ hybridization and whole genome sequencing, we studied a xenografted human oligodendroglioma where the co-amplification of the EGFR and MYC loci was present in the form of dmins at early passages and of an hsr at later passages. The amplified regions underwent multiple rearrangements and deletions during the formation of the dmins and their transformation into hsr. In both forms of amplification, non-homologous end-joining and microhomology-mediated end-joining rather than replication repair mechanisms prevailed in fusions. Small fragments, some of a few tens of base pairs, were associated in contigs. They came from clusters of breakpoints localized hundreds of kilobases apart in the amplified regions. The characteristics of some pairs of junctions suggest that at least some fragments were not fused randomly but could result from the concomi-tant repair of neighbouring breakpoints during the interaction of remote DNA sequences. This characterization at nucleotide resolution of the transition between extra-and intrachromosome amplifications highlights a hitherto uncharacterized organization of the amplified regions suggesting the involvement of new mechanisms in their formation

    Neutron powder diffraction and Mössbauer spectroscopy (119Sn and 155Gd) studies of the CeScSi-type GdMgSn and GdMgPb compounds

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    International audienceThe magnetic structures of the CeScSi-type GdMgSn and GdMgPb compounds have been studied by both neutron powder diffraction and Mössbauer spectroscopy (119Sn and 155Gd). The neutron diffraction results show that the two compounds adopt incommensurate antiferromagnetic structures at 5.4 K with propagation vectors k⃗ =[0.910,0.077,0] for GdMgSn and k⃗ =[0.892,0,0] for GdMgPb. The magnetic moments lie in the basal plane, which is confirmed by both 119Sn and 155Gd Mössbauer spectroscopy. Mössbauer spectroscopy refinements and simulations reveal that the magnetic structure of GdMgSn is cycloidal at low temperature and undergoes a transition to a modulated magnetic structure above T∼40 K. A similar magnetic transition is inferred for GdMgPb. The magnetic structures of GdMgSn and GdMgPb are compared with those of other CeScSi-type compounds

    Dichloridobis[(S)-2-hydroxy­propion­amide-κ2 O,O′]manganese(II)

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    In the title compound, [MnCl2(C3H7NO2)2], the MnII ion is bound to two Cl atoms and to four O atoms from two lacta­mide mol­ecules which act as bidentate ligands, giving rise to a highly distorted octa­hedral coordination geometry. The axial positions are occupied by one Cl atom and one O (hydr­oxy) atom. The values of the cis bond angles at the Mn atom are in the range 72.33 (5)–100.17 (6)°. Of the two possible coordination modes (N,O- or O,O-bidentate) in metal complexes with lacta­mide or its derivatives described in the literature, the title compound exhibits the O,O-bidentate mode. In the crystal structure, monomeric manganese(II) complexes are linked by several N—H⋯Cl, O—H⋯Cl and O—H⋯O hydrogen bonds, generating a three-dimensional network
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