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Search Results: 1 - 10 of 337044 matches for " Andrés Moya "
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Obsolescence and Intervention: On Synthetic-Biological Entities
Andrés Moya
Frontiers in Bioengineering and Biotechnology , 2014, DOI: 10.3389/fbioe.2014.00059
Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data
Miguel Pignatelli,Andrés Moya
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019984
Abstract: A frequent step in metagenomic data analysis comprises the assembly of the sequenced reads. Many assembly tools have been published in the last years targeting data coming from next-generation sequencing (NGS) technologies but these assemblers have not been designed for or tested in multi-genome scenarios that characterize metagenomic studies. Here we provide a critical assessment of current de novo short reads assembly tools in multi-genome scenarios using complex simulated metagenomic data. With this approach we tested the fidelity of different assemblers in metagenomic studies demonstrating that even under the simplest compositions the number of chimeric contigs involving different species is noticeable. We further showed that the assembly process reduces the accuracy of the functional classification of the metagenomic data and that these errors can be overcome raising the coverage of the studied metagenome. The results presented here highlight the particular difficulties that de novo genome assemblers face in multi-genome scenarios demonstrating that these difficulties, that often compromise the functional classification of the analyzed data, can be overcome with a high sequencing effort.
Estimating the extent of horizontal gene transfer in metagenomic sequences
Javier Tamames, Andrés Moya
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-136
Abstract: We have created two different methods that are suitable for the study of HGT in metagenomic samples. The methods are based on phylogenetic and DNA compositional approaches, and have allowed us to assess the extent of possible HGT events in metagenomes for the first time. The methods are shown to be compatible and quite precise, although they probably underestimate the number of possible events. Our results show that the phylogenetic method detects HGT in between 0.8% and 1.5% of the sequences, while DNA compositional methods identify putative HGT in between 2% and 8% of the sequences. These ranges are very similar to these found in complete genomes by related approaches. Both methods act with a different sensitivity since they probably target HGT events of different ages: the compositional method mostly identifies recent transfers, while the phylogenetic is more suitable for the detections of older events. Nevertheless, the study of the number of HGT events in metagenomic sequences from different communities shows a consistent trend for both methods: the lower amount is found for the sequences of the Sargasso Sea metagenome, while the higher quantity is found in the whale fall metagenome from the bottom of the ocean. The significance of these observations is discussed.The computational approaches that are used to find possible HGT events in complete genomes can be adapted to work with metagenomic samples, where a level of high performance is shown in different metagenomic samples. The percentage of possible HGT events that were observed is close to that found for complete genomes, and different microbiomes show diverse ratios of putative HGT events. This is probably related with both environmental factors and the composition in the species of each particular community.Horizontal gene transfer (HGT) is believed to be a very important phenomenon in prokaryotic evolution, as it enables the acquisition of new genes or sets of genes that can accelerate evolution and adap
Intelligibility in microbial complex systems: Wittgenstein and the score of life
Fernando Baquero,Andrés Moya
Frontiers in Cellular and Infection Microbiology , 2012, DOI: 10.3389/fcimb.2012.00088
Abstract: Knowledge in microbiology is reaching an extreme level of diversification and complexity, which paradoxically results in a strong reduction in the intelligibility of microbial life. In our days, the “score of life” metaphor is more accurate to express the complexity of living systems than the classic “book of life.” Music and life can be represented at lower hierarchical levels by music scores and genomic sequences, and such representations have a generational influence in the reproduction of music and life. If music can be considered as a representation of life, such representation remains as unthinkable as life itself. The analysis of scores and genomic sequences might provide mechanistic, phylogenetic, and evolutionary insights into music and life, but not about their real dynamics and nature, which is still maintained unthinkable, as was proposed by Wittgenstein. As complex systems, life or music is composed by thinkable and only showable parts, and a strategy of half-thinking, half-seeing is needed to expand knowledge. Complex models for complex systems, based on experiences on trans-hierarchical integrations, should be developed in order to provide a mixture of legibility and imageability of biological processes, which should lead to higher levels of intelligibility of microbial life.
Modular organization in the reductive evolution of protein-protein interaction networks
Javier Tamames, Andrés Moya, Alfonso Valencia
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-5-r94
Abstract: We have studied the reduction in genome size of Buchnera compared to its close relative Escherichia coli. In this well defined evolutionary scenario, we found that among all the properties of the protein interaction networks, it is the organization of networks into modules that seems to be directly related to the evolutionary process of genome reduction.In Buchnera, the apparently non-random reduction of the modular structure of the networks and the retention of essential characteristics of the interaction network indicate that the roles of proteins within the interaction network are important in the reductive process.Bacterial endosymbionts of insects, such as Buchnera aphidicola [1,2], Blochmannia floridanus [3] and Wigglesworthia glossinidia [4], are paradigms of reductive evolution. These bacteria live in a stable and isolated environment, the bacteriocyte of insects, where the host provides most of their nutritional requirements. As a consequence, the genomes of these bacteria have undergone a process of reduction, losing around 90% of their ancestral genes. These endosymbionts also fail to acquire new genes due to their incapacity to incorporate DNA via lateral gene transfer and their isolated environment. Nevertheless, although their genomes represent a subset of the genome of their ancestors, these gamma-proteobacteria remain closely related to Escherichia coli (98% of the genes in Buchnera have clear orthologues in E. coli). Accordingly, the process of genome shrinkage that these species have undergone has been well documented in terms of the evolution of the corresponding protein families [1,2].Recent research indicates that the capacity of an organism for adaptation depends not only on the properties of its individual molecular components, but also on the structure and organization of its underlying network of molecular interactions. Indeed, it was recently proposed that the modular organization of the network of interactions is necessary to adapt to chan
What Symbionts Teach us about Modularity
Manuel Porcar,Amparo Latorre,Andrés Moya
Frontiers in Bioengineering and Biotechnology , 2013, DOI: 10.3389/fbioe.2013.00014
Abstract: The main goal of Synthetic Biology (SB) is to apply engineering principles to biotechnology in order to make life easier to engineer. These engineering principles include modularity: decoupling of complex systems into smaller, orthogonal sub-systems that can be used in a range of different applications. The successful use of modules in engineering is expected to be reproduced in synthetic biological systems. But the difficulties experienced up to date with SB approaches question the short-term feasibility of designing life. Considering the “engineerable” nature of life, here we discuss the existence of modularity in natural living systems, particularly in symbiotic interactions, and compare the behavior of such systems, with those of engineered modules. We conclude that not only is modularity present but it is also common among living structures, and that symbioses are a new example of module-like sub-systems having high similarity with modularly designed ones. However, we also detect and stress fundamental differences between man-made and biological modules. Both similarities and differences should be taken into account in order to adapt SB design to biological laws.
Metabolic Networks of Sodalis glossinidius: A Systems Biology Approach to Reductive Evolution
Eugeni Belda, Francisco J. Silva, Juli Peretó, Andrés Moya
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0030652
Abstract: Background Genome reduction is a common evolutionary process affecting bacterial lineages that establish symbiotic or pathogenic associations with eukaryotic hosts. Such associations yield highly reduced genomes with greatly streamlined metabolic abilities shaped by the type of ecological association with the host. Sodalis glossinidius, the secondary endosymbiont of tsetse flies, represents one of the few complete genomes available of a bacterium at the initial stages of this process. In the present study, genome reduction is studied from a systems biology perspective through the reconstruction and functional analysis of genome-scale metabolic networks of S. glossinidius. Results The functional profile of ancestral and extant metabolic networks sheds light on the evolutionary events underlying transition to a host-dependent lifestyle. Meanwhile, reductive evolution simulations on the extant metabolic network can predict possible future evolution of S. glossinidius in the context of genome reduction. Finally, knockout simulations in different metabolic systems reveal a gradual decrease in network robustness to different mutational events for bacterial endosymbionts at different stages of the symbiotic association. Conclusions Stoichiometric analysis reveals few gene inactivation events whose effects on the functionality of S. glossinidius metabolic systems are drastic enough to account for the ecological transition from a free-living to host-dependent lifestyle. The decrease in network robustness across different metabolic systems may be associated with the progressive integration in the more stable environment provided by the insect host. Finally, reductive evolution simulations reveal the strong influence that external conditions exert on the evolvability of metabolic systems.
Bioinformatic flowchart and database to investigate the origins and diversity of Clan AA peptidases
Carlos Llorens, Ricardo Futami, Gabriel Renaud, Andrés Moya
Biology Direct , 2009, DOI: 10.1186/1745-6150-4-3
Abstract: In this paper, we describe in-progress database and bioinformatic flowchart designed to characterize the clan AA protein domain based on all possible protein families through ancestral reconstructions, sequence logos, and hidden markov models (HMMs). The flowchart includes the characterization of a major consensus sequence based on 6 amino acid patterns with correspondence with Andreeva's model, the structural template describing the clan AA peptidase fold. The set of tools is work in progress we have organized in a database within the GyDB project, referred to as Clan AA Reference Database http://gydb.uv.es/gydb/phylogeny.php?tree=caard webcite.The pre-existing classification combined with the evolutionary history of LTR retroelements permits a consistent taxonomical collection of sequence logos and HMMs. This set is useful for gene annotation but also a reference to evaluate the diversity of, and the relationships among, the different families. Comparisons among HMMs suggest a common ancestor for all dimeric clan AA peptidases that is halfway between single-domain nonviral peptidases and those coded by Ty3/Gypsy LTR retroelements. Sequence logos reveal how all clan AA families follow similar protein domain architecture related to the peptidase fold. In particular, each family nucleates a particular consensus motif in the sequence position related to the flap. The different motifs constitute a network where an alanine-asparagine-like variable motif predominates, instead of the canonical flap of the HIV-1 peptidase and closer relatives.This article was reviewed by Daniel H. Haft, Vladimir Kapitonov (nominated by Jerry Jurka), and Ben M. Dunn (nominated by Claus Wilke).Clan AA of the aspartic peptidases (CAPs) [1] is a group of proteolytic enzymes that use an aspartate dyad and a molecule of water to hydrolyze a peptide bond [2]. There are 2 major forms of this enzyme; the single domain aspartic peptidase (LTRCAP) encoded by eukaryotic LTR retroelements, which dimeri
Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies
Eugeni Belda, Andrés Moya, Stephen Bentley, Francisco J Silva
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-449
Abstract: A detailed characterization of mobile genetic elements and pseudogenes reveals a massive presence of different types of prophage elements together with five different families of IS elements that have proliferated across the genome of Sodalis glossinidius at different levels. In addition, a detailed survey of intergenic regions allowed the characterization of 1501 pseudogenes, a much higher number than the 972 pseudogenes described in the original annotation. Pseudogene structure reveals a minor impact of mobile genetic element proliferation in the process of gene inactivation, with most of pseudogenes originated by multiple frameshift mutations and premature stop codons. The comparison of metabolic profiles of Sodalis glossinidius and tsetse fly primary endosymbiont Wiglesworthia glossinidia based on their whole gene and pseudogene repertoires revealed a novel case of pathway inactivation, the arginine biosynthesis, in Sodalis glossinidius together with a possible case of metabolic complementation with Wigglesworthia glossinidia for thiamine biosynthesis.The complete re-analysis of the genome sequence of Sodalis glossinidius reveals novel insights in the evolutionary transition from a free-living ancestor to a host-dependent lifestyle, with a massive proliferation of mobile genetic elements mainly of phage origin although with minor impact in the process of gene inactivation that is taking place in this bacterial genome. The metabolic analysis of the whole endosymbiotic consortia of tsetse flies have revealed a possible phenomenon of metabolic complementation between primary and secondary endosymbionts that can contribute to explain the co-existence of both bacterial endosymbionts in the context of the tsetse host.Symbiotic associations between bacteria and insects are widespread in nature, being postulated as one of the key factors of their evolutionary success. Bacterial endosymbionts allow insects to colonize novel ecological niches characterized by unbalanced n
Patrones de distribución espacial de ensambles de macroinvertebrados bentónicos de un sistema fluvial Andino Patagónico Spatial distribution patterns of benthic macroinvertebrates assemblages in an Andean Patagonian fluvial system
Revista chilena de historia natural , 2009,
Abstract: En enero de 2006 se estudiaron los patrones espaciales de distribución de comunidades de macroinvertebrados bentónicos de la cuenca hidrográfica del río Baker (45°50' O y 47°55' S) y los principales factores controladores, intentando cubrir la mayor variedad de ecosistemas lóticos. Para llevar a cabo el estudio se seleccionaron 27 estaciones de muestreo ubicadas en las diferentes subcuencas del río. En cada estación se realizó una caracterización fisicoquímica del agua (conductividad, oxígeno disuelto, pH, temperatura y turbidez), y se documentaron las características del tramo de río (e.g. ancho del cauce y tipo de sedimento) e información cartográfica utilizando un sistema de información geográfica (SIG). Se identificaron un total de 51 taxa que correspondieron en su mayoría a larvas de insectos (80 %). Los grupos con mayor riqueza fueron los órdenes Ephemeroptera (15 taxa), Plecoptera (8 taxa) y Trichoptera (8 taxa). Los análisis de clasificación y ordenación realizados con los datos de abundancia, permitieron reconocer siete grupos de estaciones diferentes (A-F) que fueron estadísticamente significativos (P < 0.05). El análisis de regresión múltiple, muestra que la variable ambiental que mejor explica los patrones biológicos observados, fue el porcentaje de cobertura de bolones, explicando el 44 % de la varianza de los datos biológicos (r2 = 0.44 P < 0.05). In January of 2006 we studied the distributional patterns of benthic macroinvertebrate communities of the Baker river basin (45°50' O and 47°55' S) and their main controlling factors trying to cover the greater variety of the lotic ecosystems. To carry out the study, 27 sampling stations were located in the different sub basins of the river. In each station, physical-chemical parameters of the column of water were quantified (conductivity, dissolved oxygen, pH, temperature and turbidity), and documented characteristics of the segment (e.g. wide of the channel and sediment type) and cartographic information using a geographic information system (GIS) and complemented with cartographic information using GIS. Identified a total of 51 taxa, are mostly insect larvae (80 %). The groups most richness were orders Ephemeroptera (15 taxa), Plecoptera (8 taxa) and Trichoptera (8 taxa). The classification and ordination analyses carried out with the data of abundance, allowed to recognize seven groups stations (A-F) statistically significant (P < 0.05). The múltiple regression analysis, showed that the environmental variable that accounts for the observed biological patterns, was coverage cobble, explaining
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