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Search Results: 1 - 10 of 300646 matches for " J. Roman Arguello "
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Gene Duplication and Ectopic Gene Conversion in Drosophila
J. Roman Arguello,Tim Connallon
Genes , 2011, DOI: 10.3390/genes2010131
Abstract: The evolutionary impact of gene duplication events has been a theme of Drosophila genetics dating back to the Morgan School. While considerable attention has been placed on the genetic novelties that duplicates are capable of introducing, and the role that positive selection plays in their early stages of duplicate evolution, much less attention has been given to the potential consequences of ectopic (non-allelic) gene conversion on these evolutionary processes. In this paper we consider the historical origins of ectopic gene conversion models and present a synthesis of the current Drosophila data in light of several primary questions in the field.
Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing
Margarida Cardoso-Moreira, J Roman Arguello, Andrew G Clark
Genome Biology , 2012, DOI: 10.1186/gb-2012-13-12-r119
Abstract: By applying split-read methods to a total of 10x coverage of 454 shotgun sequence across 9 lines of D. melanogaster and by re-examining a previously published dataset of CNVs detected using tiling arrays, we identified the precise breakpoints of more than 600 insertions, deletions and duplications. Contrasting these CNVs with those found in humans showed that in both taxa CNV breakpoints fall into three classes: blunt breakpoints; simple breakpoints associated with microhomology; and breakpoints with additional nucleotides inserted/deleted and no microhomology. In both taxa CNV breakpoints are enriched with non-B DNA sequence structures, which may impair DNA replication and/or repair. However, in contrast to human genomes, Non-Allelic Homologous-Recombination (NAHR) plays a negligible role in CNV formation in Drosophila. In flies, non-homologous repair mechanisms are responsible for simple, recurrent and complex CNVs, including insertions of de novo sequence as large as 60 bp.Humans and Drosophila differ considerably in the importance of homology-based mechanisms for the formation of CNVs, likely as a consequence of the differences in the abundance and distribution of both segmental duplications and transposable elements between the two genomes.
Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila.
Arguello J Roman,Chen Ying,Yang Shuang,Wang Wen
PLOS Genetics , 2006,
Abstract: The formation of chimeric gene structures provides important routes by which novel proteins and functions are introduced into genomes. Signatures of these events have been identified in organisms from wide phylogenic distributions. However, the ability to characterize the early phases of these evolutionary processes has been difficult due to the ancient age of the genes or to the limitations of strictly computational approaches. While examples involving retrotransposition exist, our understanding of chimeric genes originating via illegitimate recombination is limited to speculations based on ancient genes or transfection experiments. Here we report a case of a young chimeric gene that has originated by illegitimate recombination in Drosophila. This gene was created within the last 2-3 million years, prior to the speciation of Drosophila simulans, Drosophila sechellia, and Drosophila mauritiana. The duplication, which involved the B llchen gene on Chromosome 3R, was partial, removing substantial 3' coding sequence. Subsequent to the duplication onto the X chromosome, intergenic sequence was recruited into the protein-coding region creating a chimeric peptide with approximately 33 new amino acid residues. In addition, a novel intron-containing 5' UTR and novel 3' UTR evolved. We further found that this new X-linked gene has evolved testes-specific expression. Following speciation of the D. simulans complex, this novel gene evolved lineage-specifically with evidence for positive selection acting along the D. simulans branch.
Origination of an X-Linked Testes Chimeric Gene by Illegitimate Recombination in Drosophila
J. Roman Arguello,Ying Chen,Shuang Yang,Wen Wang ,Manyuan Long
PLOS Genetics , 2006, DOI: 10.1371/journal.pgen.0020077
Abstract: The formation of chimeric gene structures provides important routes by which novel proteins and functions are introduced into genomes. Signatures of these events have been identified in organisms from wide phylogenic distributions. However, the ability to characterize the early phases of these evolutionary processes has been difficult due to the ancient age of the genes or to the limitations of strictly computational approaches. While examples involving retrotransposition exist, our understanding of chimeric genes originating via illegitimate recombination is limited to speculations based on ancient genes or transfection experiments. Here we report a case of a young chimeric gene that has originated by illegitimate recombination in Drosophila. This gene was created within the last 2–3 million years, prior to the speciation of Drosophila simulans, Drosophila sechellia, and Drosophila mauritiana. The duplication, which involved the B?llchen gene on Chromosome 3R, was partial, removing substantial 3′ coding sequence. Subsequent to the duplication onto the X chromosome, intergenic sequence was recruited into the protein-coding region creating a chimeric peptide with ~ 33 new amino acid residues. In addition, a novel intron-containing 5′ UTR and novel 3′ UTR evolved. We further found that this new X-linked gene has evolved testes-specific expression. Following speciation of the D. simulans complex, this novel gene evolved lineage-specifically with evidence for positive selection acting along the D. simulans branch.
Can Yeast (S. cerevisiae) Metabolic Volatiles Provide Polymorphic Signaling?
J. Roman Arguello, Carolina Sellanes, Yann Ru Lou, Robert A. Raguso
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0070219
Abstract: Chemical signaling between organisms is a ubiquitous and evolutionarily dynamic process that helps to ensure mate recognition, location of nutrients, avoidance of toxins, and social cooperation. Evolutionary changes in chemical communication systems progress through natural variation within the organism generating the signal as well as the responding individuals. A promising yet poorly understood system with which to probe the importance of this variation exists between D. melanogaster and S. cerevisiae. D. melanogaster relies on yeast for nutrients, while also serving as a vector for yeast cell dispersal. Both are outstanding genetic and genomic models, with Drosophila also serving as a preeminent model for sensory neurobiology. To help develop these two genetic models as an ecological model, we have tested if - and to what extent - S. cerevisiae is capable of producing polymorphic signaling through variation in metabolic volatiles. We have carried out a chemical phenotyping experiment for 14 diverse accessions within a common garden random block design. Leveraging genomic sequences for 11 of the accessions, we ensured a genetically broad sample and tested for phylogenetic signal arising from phenotypic dataset. Our results demonstrate that significant quantitative differences for volatile blends do exist among S. cerevisiae accessions. Of particular ecological relevance, the compounds driving the blend differences (acetoin, 2-phenyl ethanol and 3-methyl-1-butanol) are known ligands for D. melanogasters chemosensory receptors, and are related to sensory behaviors. Though unable to correlate the genetic and volatile measurements, our data point clear ways forward for behavioral assays aimed at understanding the implications of this variation.
Repetitive Element-Mediated Recombination as a Mechanism for New Gene Origination in Drosophila
Shuang Yang equal contributor,J. Roman Arguello equal contributor,Xin Li,Yun Ding,Qi Zhou,Ying Chen,Yue Zhang,Ruoping Zhao,Frédéric Brunet,Lixin Peng,Manyuan Long ,Wen Wang
PLOS Genetics , 2008, DOI: 10.1371/journal.pgen.0040003
Abstract: Previous studies of repetitive elements (REs) have implicated a mechanistic role in generating new chimerical genes. Such examples are consistent with the classic model for exon shuffling, which relies on non-homologous recombination. However, recent data for chromosomal aberrations in model organisms suggest that ectopic homology-dependent recombination may also be important. Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements. Here we use ~7,000 cDNA probes (~112,000 primary images) to screen eight species within the Drosophila melanogaster subgroup and identify 17 duplicates that were generated through ectopic recombination within the last 12 mys. Most of these are functional and have evolved divergent expression patterns and novel chimeric structures. Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes. Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species.
Predicción de la estructura secundaria de proteínas usando Máquinas de soporte Vectorial
Delgado,D. J; Arguello,H; Torres,R;
Revista Colombiana de Biotecnología , 2012,
Abstract: among the computational methods used for predicting secondary structure proteins highlights the use of support vector machines. this research shows the predicted secondary structure of protein from its primary amino acid sequence using support vector machines. as inputs, in the proposed methodology, features are used from different structural motifs or text strings associated with the primary structure which represents the secondary structure, such as r-group and the probability that the amino acid at position adopts a central particular secondary structure. for feature extraction method is used coding of sequences in which each symbol in the primary structure is associated with each symbol in the secondary structure. the use of this encoding method reduces the dimensionality of the data of thousands of characteristics only 220 of these. the results obtained are comparable to those reported in the literature, taking about 70% accuracy. furthermore, it is possible to reduce computational cost in the construction of classifiers because this work models the problem of multi classification as a group of binary classifiers.
The Influence of Artificial Rearing and Live Weight at Slaughter on Kid Carcass Characteristics
A. Arguello,N. Castro,J. Capote,M.B. Solomon
Journal of Animal and Veterinary Advances , 2012,
Abstract: The objective of this research was to study the effects of natural suckling vs a milk replacer diet and two slaughter weights (6 vs 10 kg) on carcass characteristics of kids. Forty male twins, Canary Caprine kids were randomly allocated to one of four treatments. Two groups were reared With their Dams (WD) while the other two were reared using a Milk Replacer (MR). Two end point live weights (LWS; 6 and 10 kg) were used for each feeding system. WD Kids grew faster (32%) than MR. The empty body weight, hot carcass weight and Cold Carcass Weight (CCW) were higher in the 10-kg compared to the 6-kg kids. In relation to carcass conformation measures and indices, there were differences (p<0.01) between the two diets for carcass length and leg length measurements. No effects of diet or LWS were observed for the percentage of primal cuts. WD kids were fatter than MR kids. The kids slaughtered at 10 kg LWS were fatter and less bony than 6 kg kids. The results showed that suckling method had few effects on carcass quality, but increasing slaughter weight substantially improved carcass quality.
Healthy Eating Vital Sign: A New Assessment Tool for Eating Behaviors
Jessica L. J. Greenwood,Junji Lin,Danita Arguello,Trever Ball
ISRN Obesity , 2012, DOI: 10.5402/2012/734682
Abstract:
A Rank-Order Procedure Applied to an Ethoexperimental Behavior Model—The Multivariate Concentric Square FieldTM (MCSF) Test  [PDF]
Bengt J. Meyerson, Betty Jurek, Erika Roman
Journal of Behavioral and Brain Science (JBBS) , 2013, DOI: 10.4236/jbbs.2013.34035
Abstract: Designing relevant animal models in order to investigate the neurobiological basis for human mental disorders is an important challenge. The need for new tests to be developed and traditional tests to be improved has recently been em-phasized. The authors propose a multivariate test approach, the multivariate concentric square fieldTM (MCSF) test. To measure and evaluate variation in the behavioral traits, we here put forward a statistical procedure of which the working title is “trend analysis”. Low doses of the benzodiazepine agonist diazepam (DZP; 1.0, 1.5, or 2.0 mg/kg) were used for exploring the use of the trend analysis in combination with multivariate data analysis for assessment of MCSF per-formance in rats. The commonly used elevated plus maze (EPM) test was used for comparison. The trend analysis comparing vehicle and the DZP1.5 groups revealed significantly higher general activity and risk-taking behavior in the DZP1.5 rats relative to vehicle rats. This finding was supported by multivariate data analysis procedures. It is concluded that the trend analysis together with multivariate data analysis procedures offers possibilities to extract information and illustrates effects obtained in the MCSF test. Diazepam in doses that have no apparent increase in open arm activity in the EPM was effective to alter the behavior in the MCSF test. The MCSF test and the use of multivariate data analysis and the proposed trend analysis may be useful alternatives to behavioral test batteries and traditionally used tests for the understanding of mechanisms underlying various mental states. Finally, the impact of an ethological reasoning and multivariate measures enabling behavioral profiling of animals may be a useful complementary methodology when phenotyping animals in behavioral neuroscience.

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