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591.
Kimberly A. Selkoe Oscar E. Gaggiotti Brian W. Bowen Robert J. Toonen 《Molecular ecology》2014,23(12):3064-3079
What shapes variation in genetic structure within a community of codistributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the archipelago's stepping stone configuration, isolation by distance was the least common type of genetic structure, detected in four species. Regional structuring (i.e. division of sites into genetically and spatially distinct regions) was most common, detected in 20 species and nearly in all endemics and habitat specialists. Seven species displayed chaotic (spatially unordered) structuring, and all were nonendemic generalist species. Chaotic structure also associated with relatively high global FST. Pelagic larval duration (PLD) was not a strong predictor of variation in population structure (R2 = 0.22), but accounting for higher FST values of chaotic and invertebrate species, compared to regionally structured and fish species, doubled the power of PLD to explain variation in global FST (adjusted R2 = 0.50). Multivariate correlation of eight species traits to six genetic traits highlighted dispersal ability, taxonomy (i.e. fish vs. invertebrate) and habitat specialization as strongest influences on genetics, but otherwise left much variation in genetic traits unexplained. Considering that the study design controlled for many sampling and geographical factors, the extreme interspecific variation in spatial genetic patterns observed for Hawaìi marine species may be generated by demographic variability due to species‐specific abundance and migration patterns and/or seascape and historical factors. 相似文献
592.
Eric Elguero Céline Arnathau Patrick Durand Sylvain Brisse Laure Diancourt Agnes Aubouy Pierre Becquart Umberto D'Alessandro Didier Fontenille Dionicia Gamboa Amanda Maestre Didier Ménard Lise Musset Oscar Noya Vincent Veron Albina Wide Bernard Carme Eric Legrand Christine Chevillon Francisco J. Ayala Franck Prugnolle 《Molecular ecology》2014,23(8):1979-1993
Pathogens, which have recently colonized a new host species or new populations of the same host, are interesting models for understanding how populations may evolve in response to novel environments. During its colonization of South America from Africa, Plasmodium falciparum, the main agent of malaria, has been exposed to new conditions in distinctive new human populations (Amerindian and populations of mixed origins) that likely exerted new selective pressures on the parasite's genome. Among the genes that might have experienced strong selective pressures in response to these environmental changes, the eba genes (erythrocyte‐binding antigens genes), which are involved in the invasion of the human red blood cells, constitute good candidates. In this study, we analysed, in South America, the polymorphism of three eba genes (eba‐140, eba‐175, eba‐181) and compared it to the polymorphism observed in African populations. The aim was to determine whether these genes faced selective pressures in South America distinct from what they experienced in Africa. Patterns of genetic variability of these genes were compared to the patterns observed at two housekeeping genes (adsl and serca) and 272 SNPs to separate adaptive effects from demographic effects. We show that, conversely to Africa, eba‐140 seemed to be under stronger diversifying selection in South America than eba‐175. In contrast, eba‐181 did not show any sign of departure from neutrality. These changes in the patterns of selection on the eba genes could be the consequence of changes in the host immune response, the host receptor polymorphisms and/or the ability of the parasite to silence or express differentially its invasion proteins. 相似文献
593.
Joan Font-Burgada Oscar Reina David Rossell Fernando Azorín 《Nucleic acids research》2014,42(4):2126-2137
Development of tools to jointly visualize the genome and the epigenome remains a challenge. chroGPS is a computational approach that addresses this question. chroGPS uses multidimensional scaling techniques to represent similarity between epigenetic factors, or between genetic elements on the basis of their epigenetic state, in 2D/3D reference maps. We emphasize biological interpretability, statistical robustness, integration of genetic and epigenetic data from heterogeneous sources, and computational feasibility. Although chroGPS is a general methodology to create reference maps and study the epigenetic state of any class of genetic element or genomic region, we focus on two specific kinds of maps: chroGPSfactors, which visualizes functional similarities between epigenetic factors, and chroGPSgenes, which describes the epigenetic state of genes and integrates gene expression and other functional data. We use data from the modENCODE project on the genomic distribution of a large collection of epigenetic factors in Drosophila, a model system extensively used to study genome organization and function. Our results show that the maps allow straightforward visualization of relationships between factors and elements, capturing relevant information about their functional properties that helps to interpret epigenetic information in a functional context and derive testable hypotheses. 相似文献
594.
Maria Rosa Garcia-Silva Julia Sanguinetti Florencia Cabrera-Cabrera Oscar Franzén Alfonso Cayota 《Gene》2014
The study of small RNAs and Argonaute proteins in eukaryotes that are deficient in functional RNA interference could provide insights into novel functions of small RNAs. In this study we describe small non-coding RNAs bound to a distinctive Argonaute protein of Trypanosoma cruzi, TcPIWI-tryp. Co-immunoprecipitation of TcPIWI-tryp followed by deep sequencing of isolated RNA identified abundant small RNAs derived from rRNAs and tRNAs. The small RNA repertoire differed from that of the canonical Argonaute in organisms with functional RNA interference, which could indicate novel biological functions for TcPIWI-tryp in T. cruzi and other members of the trypanosomatid clade. 相似文献
595.
Silke Roedder Tara Sigdel Nathan Salomonis Sue Hsieh Hong Dai Oriol Bestard Diana Metes Andrea Zeevi Albin Gritsch Jennifer Cheeseman Camila Macedo Ram Peddy Mara Medeiros Flavio Vincenti Nancy Asher Oscar Salvatierra Ron Shapiro Allan Kirk Elaine Reed Minnie M. Sarwal 《PLoS medicine》2014,11(11)
BackgroundDevelopment of noninvasive molecular assays to improve disease diagnosis and patient monitoring is a critical need. In renal transplantation, acute rejection (AR) increases the risk for chronic graft injury and failure. Noninvasive diagnostic assays to improve current late and nonspecific diagnosis of rejection are needed. We sought to develop a test using a simple blood gene expression assay to detect patients at high risk for AR.ConclusionsThe kSORT blood QPCR assay is a noninvasive tool to detect high risk of AR of renal transplants.Please see later in the article for the Editors'' Summary 相似文献
596.
A. E. Ruiz‐Contreras K. Carrillo‐Sánchez I. Ortega‐Mora M. A. Barrera‐Tlapa T. V. Román‐López C. B. Rosas‐Escobar L. Flores‐Barrera U. Caballero‐Sánchez Z. Muñoz‐Torres S. Romero‐Hidalgo S. Hernández‐Morales J. A. González‐Barrios F. Vadillo‐Ortega M. Méndez‐Díaz R. Aguilar‐Roblero O. Prospéro‐García 《Genes, Brain & Behavior》2014,13(2):173-178
Individual differences in cognitive performance are partly dependent, on genetic polymporhisms. One of the single‐nucleotide polymorphisms (SNP) of the CNR1 gene, which codes for cannabinoid receptor 1 (CB1R), is the rs2180619, located in a regulatory region of this gene (6q14–q15). The alleles of the rs2180619 are A > G; the G allele has been associated with addiction and high levels of anxiety (when the G allele interacts with the SS genotype of the 5‐HTTLPR gene). However, GG genotype is observed also in healthy subjects. Considering G allele as risk for ‘psychopathological conditions’, it is possible that GG healthy subjects do not be addicted or anxious, but would have reduced performance, compared to AA subjects, in attentional control and working memory processing. One hundred and sixty‐four healthy young Mexican‐Mestizo subjects (100 women and 64, men; mean age: 22.86 years, SD=2.72) participated in this study, solving a task where attentional control and working memory were required. GG subjects, compared to AA subjects showed: (1) a general lower performance in the task (P = 0.02); (2) lower performance only when a high load of information was held in working memory (P = 0.02); and (3) a higher vulnerability to distractors (P = 0.03). Our results suggest that, although the performance of GG subjects was at normal levels, a lower efficiency of the endocannabinoid system, probably due to a lowered expression of CB1R, produced a reduction in the performance of these subjects when attentional control and working memory processing is challenged . 相似文献
597.
Jeroen Siebring Matthijs JH Elema Fátima Drubi Vega ákos T Kovács Patsy Haccou Oscar P Kuipers 《The ISME journal》2014,8(1):77-87
Bacillus subtilis sporulation is a last-resort phenotypical adaptation in response to starvation. The regulatory network underlying this developmental pathway has been studied extensively. However, how sporulation initiation is concerted in relation to the environmental nutrient availability is poorly understood. In a fed-batch fermentation set-up, in which sporulation of ultraviolet (UV)-mutagenized B. subtilis is repeatedly triggered by periods of starvation, fitter strains with mutated tagE evolved. These mutants display altered timing of phenotypical differentiation. The substrate for the wall teichoic acid (WTA)-modifying enzyme TagE, UDP-glucose, has recently been shown to be an intracellular proxy for nutrient availability, and influences the timing of cell division. Here we suggest that UDP-glucose also influences timing of cellular differentiation. 相似文献
598.
599.
600.
Oscar Ramirez I?igo Olalde Jonas Berglund Belen Lorente-Galdos Jessica Hernandez-Rodriguez Javier Quilez Matthew T Webster Robert K Wayne Carles Lalueza-Fox Carles Vilà Tomas Marques-Bonet 《BMC genomics》2014,15(1)