<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gabaldón, T.</style></author><author><style face="normal" font="default" size="100%">Peretó, J.</style></author><author><style face="normal" font="default" size="100%">Montero, F.</style></author><author><style face="normal" font="default" size="100%">Gil, R.</style></author><author><style face="normal" font="default" size="100%">Latorre, A.</style></author><author><style face="normal" font="default" size="100%">Moya, A.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Structural analyses of a hypothetical minimal metabolism</style></title><secondary-title><style face="normal" font="default" size="100%">Philos Trans R Soc Lond B Biol Sci</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">*Cell Physiological Phenomena Cells/*metabolism Cluster Analysis *Computer Simulation *Metabolic Networks and Pathways *Models</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Models</style></keyword><keyword><style  face="normal" font="default" size="100%">Statistical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=17510022</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">1486</style></number><volume><style face="normal" font="default" size="100%">362</style></volume><pages><style face="normal" font="default" size="100%">1751-62</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">By integrating data from comparative genomics and large-scale deletion studies, we previously proposed a minimal gene set comprising 206 protein-coding genes. To evaluate the consistency of the metabolism encoded by such a minimal genome, we have carried out a series of computational analyses. Firstly, the topology of the minimal metabolism was compared with that of the reconstructed networks from natural bacterial genomes. Secondly, the robustness of the metabolic network was evaluated by simulated mutagenesis and, finally, the stoichiometric consistency was assessed by automatically deriving the steady-state solutions from the reaction set. The results indicated that the proposed minimal metabolism presents stoichiometric consistency and that it is organized as a complex power-law network with topological parameters falling within the expected range for a natural metabolism of its size. The robustness analyses revealed that most random mutations do not alter the topology of the network significantly, but do cause significant damage by preventing the synthesis of several compounds or compromising the stoichiometric consistency of the metabolism. The implications that these results have on the origins of metabolic complexity and the theoretical design of an artificial minimal cell are discussed.</style></abstract><notes><style face="normal" font="default" size="100%">Gabaldon, Toni Pereto, Juli Montero, Francisco Gil, Rosario Latorre, Amparo Moya, Andres Research Support, Non-U.S. Gov’t England Philosophical transactions of the Royal Society of London. Series B, Biological sciences Philos Trans R Soc Lond B Biol Sci. 2007 Oct 29;362(1486):1751-62.</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Elena, S. F.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author><author><style face="normal" font="default" size="100%">de la Pena, M.</style></author><author><style face="normal" font="default" size="100%">Flores, R.</style></author><author><style face="normal" font="default" size="100%">Diener, T. O.</style></author><author><style face="normal" font="default" size="100%">Moya, A.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment</style></title><secondary-title><style face="normal" font="default" size="100%">J Mol Evol</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular *Phylogeny Plant Viruses/*genetics RNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Satellite/*genetics RNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Viral/genetics Viroids/*genetics</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2001</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=11479686</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">2</style></number><volume><style face="normal" font="default" size="100%">53</style></volume><pages><style face="normal" font="default" size="100%">155-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The proposed monophyletic origin of a group of subviral plant pathogens (viroids and viroid-like satellite RNAs), as well as the phylogenetic relationships and the resulting taxonomy of these entities, has been recently questioned. The criticism comes from the (apparent) lack of sequence similarity among these RNAs necessary to reliably infer a phylogeny. Here we show that, despite their low overall sequence similarity, a sequence alignment manually adjusted to take into account all the local similarities and the insertions/deletions and duplications/rearrangements described in the literature for viroids and viroid-like satellite RNA, along with the use of an appropriate estimator of genetic distances, constitutes a data set suitable for a phylogenetic reconstruction. When the likelihood-mapping method was applied to this data set, the tree-likeness obtained was higher than that corresponding to a sequence alignment that does not take into consideration the local similarities. In addition, bootstrap analysis also supports the major groups previously proposed and the reconstruction is consistent with the biological properties of this RNAs.</style></abstract><notes><style face="normal" font="default" size="100%">Elena, S F Dopazo, J de la Pena, M Flores, R Diener, T O Moya, A Letter Research Support, Non-U.S. Gov’t United States Journal of molecular evolution J Mol Evol. 2001 Aug;53(2):155-9.</style></notes></record></records></xml>