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Find video protocols related to scientific articles indexed in Pubmed.
Evidence for the persistence of an active endogenous retrovirus (ERVE) in humans.
Genetica
PUBLISHED: 09-06-2014
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Transposable elements (TEs) account for nearly half (44 %) of the human genome. However, their overall activity has been steadily declining over the past 35-50 million years, so that <0.05 % of TEs are presumably still "alive" (potentially transposable) in human populations. All the active elements are retrotransposons, either autonomous (LINE-1 and possibly the endogenous retrovirus ERVK), or non-autonomous (Alu and SVA, whose transposition is dependent on the LINE-1 enzymatic machinery). Here we show that a lineage of the endogenous retrovirus ERVE was recently engaged in ectopic recombination events and may have at least one potentially fully functional representative, initially reported as a novel retrovirus isolated from blood cells of a Chinese patient with chronic myeloid leukemia, which bears signals of positive selection on its envelope region. Altogether, there is strong evidence that ERVE should be included in the short list of potentially active TEs, and we give clues on how to identify human specific insertions of this element that are likely to be segregating in some of our populations.
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A new mountain lizard from Montes de León (NW Iberian Peninsula): Iberolacerta monticola astur ssp. nov. (Squamata: Lacertidae).
Zootaxa
PUBLISHED: 05-16-2014
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Iberolacerta populations from the Northern Montes de Leon (NML) were studied by means of external morphology (scalation and biometry), osteology and genetics (mtDNA and microsatellites), searching for their homogeneity ("intrazonalanalysis") and, once verified, comparing them with Iberolacerta monticola s. str. (from Central Cantabrian Mountains)and/. gal ani (from Southern Montes de Leon) ("extrazonal analysis") from neighboring areas.Our "intrazonal analysis" revealed discordances between the different approaches, especially the patterns of variation of nuclear microsatellites (congruent with external morphology) and mtDNA, namely a very low nuclear differentiation between relatively highly differentiated mtDNA lineages. The morphological approach was unable to discriminate any of the populations as significantly different from the others in the NML. Mitochondrial DNA revealed a haplotype lineage closely related to I. galani (MNL-II in our text) in some specimens of Sierra de Villabandfn and Suspiron, but these populations are morphologically indistinguishable from the main part of the other populations that belong to lineage NML-1,phylogenetically closer to/. monticola. After a separation from I. manti cola ca. 1.8 Mya, the populations in this geographic region must have suffered at least two different waves of gene flow from I. gal ani, the second one not much later than 0.5 Mya. Microsatellite results indicate that all the NML populations are genetically similar in terms of their nuclear genomes,independently of their mitochondrial differentiation (NML-I vs. NML-II haplotype groups). Since all the morphological and microsatellite evidences point towards the fact that, independently of the mitochondrial haplotypes that they bear (NML-1 or NML-II), there is only one taxon in the area, we describe it as: Iberolacerta monticola astur ssp. nov.Concerning the relationships of I. m. astur ssp. nov. with I. monticola s. str. and I. gal ani ("extra zonal analysis"), in the female analyses the new taxon centroid is closer to I. monticola s. str. than to I. gal ani (more similarity with I manticolas.str.), whereas in the male analyses the relationship is just the contrary (closer to I. gal ani, paralleling the direction of the hypothesized past hybridization). Moreover, in both sexes' ANOVA, I. m. astur ssp. nov. results more similar (lessP<0.05 differences) to I. galani than to I. monticola s. str. Osteologically, I. m. astur ssp. nov. is slightly more similar toI. monticola s. str. than to I. galani, especially in the squamosal bone, which is regularly arched (primitive shape). Genetically,as indicated above, the NML populations can be subdivided in two groups according to their mitochondrial DNA,namely NML-I (bearing clearly differentiated haplotypes, phylogenetically closer to I. monticola) and NML-II (whose haplotypes could have been mistaken for those of an I. gal ani population). This mitochondrial subdivision has at most a subtle nuclear correlate, however. According to the nuclear microsatellite markers, all the NML populations belong to a single group(/. m. astur ssp. nov.), which would be more similar to I. gal ani than to I monticola, with NML-II populations lying closer to I. galani than those from the NML-I group and, correspondingly, more distant from I. monticola. The discordant phylogenetic signal of mitochondrial and nuclear markers is discussed in terms of past introgression events and sex-biases in phylopatry and dispersion in these species. Iberolacerta manti cola astur ssp. nov., inhabits the Northern Montes de Leon (Sierra de Gistreo sensu latissimo ): Gistredo,Catoute, Tambaron, Nevadfn, Villabandfn (or Macizo del Alto de Ia Canada), Arcos del Agua (or Fernan Perez),Tiendas and Suspiron, mainly in quartzite and slate rock substrates. Its current distribution, cornered in the NW of theNorthern part of the Montes de Leon, suggests a possible competitive exclusion between this taxon and/. galani, as the galani haplotypes (NML-II) appear cornered in the most harsh and continental areas, speaking also about a, even in the past, very limited presence of this species in the area that probably was soon absorbed by I. m. astur ssp. nov. (with NMLI haplotypes). Variation in watershed limits (especially with l montico/a s. str. in the North) and Pleistocene climatic oscillations(with I. gal ani in the South) probably played a crucial role in isolation of the different Iberolacerta colonizationwaves in this zone. These changes in the boundaries among watersheds limited the contact between the NML and the main Cantabrian Mountains, restricting to narrow points (different along time) the contact between the two ranges, and thus,the areas for possible contact between I. m. astur ssp. nov. and I. monticola s. str. (see Fig. lB). The origin of this tax on dates back to the end of Pliocene or Lower Pleistocene (around 1.8 Mya), according to mtDNA divergence. On the other side, climatic oscillations allowed expansion and contact with the more continental harsh climate-dwelling I. gal ani.
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Isolation and characterization of two satellite DNAs in some Iberian rock lizards (Squamata, Lacertidae).
J. Exp. Zool. B Mol. Dev. Evol.
PUBLISHED: 04-08-2013
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Satellite DNAs represent a large portion of all high eukaryotic genomes. They consist of numerous very similar repeated sequences, tandemly arranged in large clusters up to 100 million base pairs in length, usually located in the heterochromatic parts of chromosomes. The biological significance of satDNAs is still under discussion, but most of their proposed functions are related to heterochromatin and/or centromere formation and function. Because information about the structure of reptilian satDNA is far from exhaustive, we present a molecular and cytogenetic characterization of two satDNA families in four lacertid species. Two families of tandemly repeated DNAs, namely TaqI and HindIII satDNAs, have been cloned and sequenced from four species belonging to the genus Iberolacerta. These satDNAs are characterized by a monomer length of 171-188 and 170-172?bp, and by an AT content of 60.5% and 58.1%, respectively. FISH experiments with TaqI satDNA probe produced bright signals in pericentromeric regions of a subset of chromosomes whereas all the centromeres were marked by HindIII probe. The results obtained in this study suggest that chromosome location and abundance of satDNAs influence the evolution of these elements, with centromeric families evolving tenfold faster than interstitial/pericentromeric ones. Such different rates render different satellites useful for phylogenetic investigation at different taxonomic ranks. J. Exp. Zool. (Mol. Dev. Evol.) 322B: 13-26, 2014. © 2013 Wiley Periodicals, Inc.
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Causes and evolutionary consequences of population subdivision of an Iberian mountain lizard, Iberolacerta monticola.
PLoS ONE
PUBLISHED: 01-01-2013
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The study of the factors that influence population connectivity and spatial distribution of genetic variation is crucial for understanding speciation and for predicting the effects of landscape modification and habitat fragmentation, which are considered severe threats to global biodiversity. This dual perspective is obtained from analyses of subalpine mountain species, whose present distribution may have been shaped both by cyclical climate changes over ice ages and anthropogenic perturbations of their habitats. Here, we examine the phylogeography, population structure and genetic diversity of the lacertid lizard Iberolacerta monticola, an endemism considered to be facing a high risk of extinction in several populations.
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Evolutionary dynamics of the Ty3/gypsy LTR retrotransposons in the genome of Anopheles gambiae.
PLoS ONE
PUBLISHED: 01-24-2011
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Ty3/gypsy elements represent one of the most abundant and diverse LTR-retrotransposon (LTRr) groups in the Anopheles gambiae genome, but their evolutionary dynamics have not been explored in detail. Here, we conduct an in silico analysis of the distribution and abundance of the full complement of 1045 copies in the updated AgamP3 assembly. Chromosomal distribution of Ty3/gypsy elements is inversely related to arm length, with densities being greatest on the X, and greater on the short versus long arms of both autosomes. Taking into account the different heterochromatic and euchromatic compartments of the genome, our data suggest that the relative abundance of Ty3/gypsy LTRrs along each chromosome arm is determined mainly by the different proportions of heterochromatin, particularly pericentric heterochromatin, relative to total arm length. Additionally, the breakpoint regions of chromosomal inversion 2La appears to be a haven for LTRrs. These elements are underrepresented more than 7-fold in euchromatin, where 33% of the Ty3/gypsy copies are associated with genes. The euchromatin on chromosome 3R shows a faster turnover rate of Ty3/gypsy elements, characterized by a deficit of proviral sequences and the lowest average sequence divergence of any autosomal region analyzed in this study. This probably reflects a principal role of purifying selection against insertion for the preservation of longer conserved syntenyc blocks with adaptive importance located in 3R. Although some Ty3/gypsy LTRrs show evidence of recent activity, an important fraction are inactive remnants of relatively ancient insertions apparently subject to genetic drift. Consistent with these computational predictions, an analysis of the occupancy rate of putatively older insertions in natural populations suggested that the degenerate copies have been fixed across the species range in this mosquito, and also are shared with the sibling species Anopheles arabiensis.
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Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.
Science
PUBLISHED: 10-09-2010
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Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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