Search results for "Sequence analysis"
showing 10 items of 1349 documents
Temporal and spatial diversification of the African disjunct genus Androcymbium (Colchicaceae)
2009
Abstract The genus Androcymbium (Colchicaceae) includes 57 species that are distributed in the extreme northern and southern portions of Africa, mainly in regions with a Mediterranean climate. We present the first phylogeographic analysis of the genus with species from all five of its distribution areas (North Africa, Horn of Africa, Namibia, western South Africa, and eastern South Africa). We used sequence data from six chloroplast regions and one nuclear region. Phylogeographic reconstructions were conducted using both parsimony and Bayesian inference methods. Molecular dating estimates using a Bayesian approach suggest a middle Miocene (13.4 ± 1.5 mya) origin of the genus; this approach …
New insights into the gut microbiome in loggerhead sea turtles Caretta caretta stranded on the Mediterranean coast
2019
Caretta caretta is the most common sea turtle species in the Mediterranean Sea. The species is threatened by anthropomorphic activity that causes thousands of deaths and hundreds of strandings along the Mediterranean coast. Stranded turtles are often cared for in rehabilitation centres until they recover or die. The objective of this study was to characterize the gut microbiome of nine sea turtles stranded along the Sicilian coast of the Mediterranean Sea using high-throughput sequencing analysis targeting V3–V4 regions of the bacterial 16S rRNA gene. Stool samples were collected from eight specimens hosted in the recovery centre after a few days of hospitalization (under 7) and from one ho…
Phylogeographic patterns of decapod crustaceans at the Atlantic-Mediterranean transition.
2012
9 páginas, 4 figuras, 3 tablas.
The Pillars of Hercules as a bathymetric barrier to gene flow promoting isolation in a global deep-sea shark (Centroscymnus coelolepis).
2015
Catarino, Diana ... et. al.-- 19 pages, 5 figures, 4 tables, data accessibility http://dx.doi.org/10.5061/dryad.ss368, supporting information http://dx.doi.org/10.1111/mec.13453
Molecular and morphological identification of larval opecoelids (Digenea: Opecoelidae) parasitising prosobranch snails in a Western Mediterranean lag…
2012
In a study of the digeneans parasitising molluscs in the Els Alfacs lagoon (Ebro Delta, Western Mediterranean) we found heavy infections with sporocysts emitting two types of cotylocercous cercariae in the prosobranch trochid gastropod Gibbula adansonii and with metacercariae in the prosobranch nassariid gastropod Cyclope neritea. A comparative analysis using ITS ribosomal DNA sequences from these larval stages and published sequences of 17 larval and adult opecoelid stages allowed us to elucidate the life-cycle of Macvicaria obovata and to confirm the identification of Cainocreadium labracis based on cercarial morphology. We provide molecular evidence for the identification and the first d…
Genetic architecture of the marbled goby Pomatoschistus marmoratus (Perciformes, Gobiidae) in the Mediterranean Sea
2011
The marbled goby Pomatoschistus marmoratus, a species inhabiting coastal Mediterranean lagoons, has been studied by measuring its mitochondrial DNA variation. This analysis revealed a Mediterranean west vs east split and, subsequently, an eastern differentiation among the Libyan–Tunisian Gulf, the Adriatic Sea and the Aegean Sea. The high cohesion between the samples collected in the vast area of western Mediterranean contrasts with the genetic mosaic of the more sub-structured eastern Mediterranean. This western homogeneity can not yet be fully explained even if a human-mediated migratory flow, due to a maritime traffic, has been posited. The pattern in the eastern basin revealed a genetic…
A Common Genetic Origin for Early Farmers from Mediterranean Cardial and Central European LBK Cultures
2015
Olalde, Iñigo et al.
Speciation of the Paradeontacylix spp. (Sanguinicolidae) of Seriola dumerili. Two new species of the genus Paradeontacylix from the Mediterranean.
2008
Abstract Two new species of teleost blood fluke belonging to the sanguinicolid genus Paradeontacylix are described from the greater amberjack, Seriola dumerili , i.e. Paradeontacylix ibericus n. sp. from the Iberian Peninsula and Paradeontacylix balearicus n. sp. from the Balearic Islands. P. ibericus n. sp. and P. balearicus n. sp. show morphological similarities with Paradeontacylix kampachi and Paradeontacylix grandispinus respectively, which occur in mixed infection in S. dumerili from Japan. Multivariate analysis of morphometrical data provided statistical evidence for the separation of four species. However, component by component analysis did not show statistically significant differ…
Origin of metazoan stem cell system in sponges: first approach to establish the model (Suberites domuncula).
2003
Abstract It is established that Porifera (sponges) represent the earliest phylum which branched off from the common ancestor of all multicellular animals, the Urmetazoa. In the present study, the hypothesis is tested if, during this transition, pluripotent stem cells were formed which are provided—similar to the totipotent cells (archaeocytes/germ cells)—with a self-renewal capacity. As a model system, primmorphs from the sponge Suberites domuncula were used. These 3D-cell aggregates were cultivated in medium (RPMI 1640/seawater) either lacking silicate and ferric iron or in medium which was supplemented with these ‘morphogenetic’ factors. As molecular markers for the potential existence of…
DeepSRE: Identification of sterol responsive elements and nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network anal…
2021
SREBP1 and 2, are cholesterol sensors able to modulate cholesterol-related gene expression responses. SREBPs binding sites are characterized by the presence of multiple target sequences as SRE, NFY and SP1, that can be arranged differently in different genes, so that it is not easy to identify the binding site on the basis of direct DNA sequence analysis. This paper presents a complete workflow based on a one-dimensional Convolutional Neural Network (CNN) model able to detect putative SREBPs binding sites irrespective of target elements arrangements. The strategy is based on the recognition of SRE linked (less than 250 bp) to NFY sequences according to chromosomal localization derived from …