Search results for "Sequence analysi"
showing 10 items of 1351 documents
A systems biology perspective on cholangiocellular carcinoma development: focus on MAPK-signaling and the extracellular environment.
2008
Background/Aims Multiple genes have been implicated in cholangiocellular carcinoma (CCC) development. However, the overall neoplastic risk is likely associated with a much lower number of critical physiological pathways. Methods To investigate this hypothesis, we extracted all published genetic associations for the development of CCC from PubMed (genetic association studies, but also studies associating genes and CCC in general, i.e. functional studies in cell lines, genetic studies in humans, knockout mice etc.) and integrated CCC microarray data. Results We demonstrated the MAPK pathway was consistently enriched in CCC. Comparing our data to genetic associations in HCC often successfully …
Neuroglobin, cytoglobin, and myoglobin contribute to hypoxia adaptation of the subterranean mole rat Spalax.
2010
The subterranean mole rat Spalax is an excellent model for studying adaptation of a mammal toward chronic environmental hypoxia. Neuroglobin (Ngb) and cytoglobin (Cygb) are O 2 -binding respiratory proteins and thus candidates for being involved in molecular hypoxia adaptations of Spalax . Ngb is expressed primarily in vertebrate nerves, whereas Cygb is found in extracellular matrix-producing cells and in some neurons. The physiological functions of both proteins are not fully understood but discussed with regard to O 2 supply, the detoxification of reactive oxygen or nitrogen species, and apoptosis protection. Spalax Ngb and Cygb coding sequences are strongly conserved. However, mRNA and …
Molecular phylogenetics and historical biogeography of the west-palearctic common toads (Bufo bufo species complex)
2012
In most pan-Eurasiatic species complexes, two phenomena have been traditionally considered key processes of their cladogenesis and biogeography. First, it is hypothesized that the origin and development of the Central Asian Deserts generated a biogeographic barrier that fragmented past continuous distributions in Eastern and Western domains. Second, Pleistocene glaciations have been proposed as the main process driving the regional diversification within each of these domains. The European common toad and its closest relatives provide an interesting opportunity to examine the relative contributions of these paleogeographic and paleoclimatic events to the phylogeny and biogeography of a wide…
Description, microhabitat selection and infection patterns of sealworm larvae (Pseudoterranova decipiens species complex, nematoda: ascaridoidea) in …
2013
Third-stage larvae of the Pseudoterranova decipiens species complex (also known as sealworms) have been reported in at least 40 marine fish species belonging to 21 families and 10 orders along the South American coast. Sealworms are a cause for concern because they can infect humans who consume raw or undercooked fish. However, despite their economic and zoonotic importance, morphological and molecular characterization of species of Pseudoterranova in South America is still scarce. Methods: A total of 542 individual fish from 20 species from the Patagonian coast of Argentina were examined for sealworms. The body cavity, the muscles, internal organs, and the mesenteries were examined to dete…
The age and evolution of sociality in Stegodyphus spiders: a molecular phylogenetic perspective
2006
Social, cooperative breeding behaviour is rare in spiders and generally characterized by inbreeding, skewed sex ratios and high rates of colony turnover, processes that when combined may reduce genetic variation and lower individual fitness quickly. On these grounds, social spider species have been suggested to be unstable in evolutionary time, and hence sociality a rare phenomenon in spiders. Based on a partial molecular phylogeny of the genus Stegodyphus , we address the hypothesis that social spiders in this genus are evolutionary transient. We estimate the age of the three social species, test whether they represent an ancestral or derived state and assess diversification relative to s…
Proteomic analysis of the acid-soluble nacre matrix of the bivalve Unio pictorum: detection of novel carbonic anhydrase and putative protease inhibit…
2010
10 pages; International audience; The matrix extracted from mollusc shell nacre is a mixture of proteins and glycoproteins that is thought to play a major role in controlling biomineral synthesis and in increasing its mechanical properties. We investigated the nacreous shell of the freshwater mussel Unio pictorum, to which we applied a proteomics approach adapted to mollusc shell proteins. On one hand, the acid-soluble nacre matrix was fractionated by SDS-PAGE and the five main protein bands (P95, P50, P29, P16, and P12) were digested with trypsin and analyzed by nanoLC-MS/MS followed by de novo sequencing. On the other hand, the acid-soluble nacre matrix was analyzed in a similar manner, w…
Reconfigurable Accelerator for the Word-Matching Stage of BLASTN
2013
BLAST is one of the most popular sequence analysis tools used by molecular biologists. It is designed to efficiently find similar regions between two sequences that have biological significance. However, because the size of genomic databases is growing rapidly, the computation time of BLAST, when performing a complete genomic database search, is continuously increasing. Thus, there is a clear need to accelerate this process. In this paper, we present a new approach for genomic sequence database scanning utilizing reconfigurable field programmable gate array (FPGA)-based hardware. In order to derive an efficient structure for BLASTN, we propose a reconfigurable architecture to accelerate the…
Pythium regulare sp. nov., Isolated from the Canary Islands, Its Taxonomy, Its Region of rDNA, and Comparison with Related Species
2003
Pythium regulare (CI-34) was isolated from some soil samples taken in the Canary Islands (Spain). This new species is very closely related to P. irregulare isolated from pea roots in The Netherlands by Buisman in 1927. The species of Pythium are members of the kingdom Chromista. Pythium regulare is characterized by its ornamented oogonia bearing blunt or digitate spines, and its non-sporulating type of sporangia or hyphal bodies, its aplerotic oospores, its monoclinous and diclinous antheridia that at times crowd around the oogonia. The taxonomic description of this oomycete, the PCR of the internal transcribed region (spacers ITS1, ITS2, and the gene 5.8 S) of its ribosomal nuclear DNA as …
BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures
2018
Abstract Motivation Modern bioinformatics tools for analyzing large-scale NGS datasets often need to include fast implementations of core sequence alignment algorithms in order to achieve reasonable execution times. We address this need by presenting the BGSA toolkit for optimized implementations of popular bit-parallel global pairwise alignment algorithms on modern microprocessors. Results BGSA outperforms Edlib, SeqAn and BitPAl for pairwise edit distance computations and Parasail, SeqAn and BitPAl when using more general scoring schemes for pairwise alignments of a batch of sequence reads on both standard multi-core CPUs and Xeon Phi many-core CPUs. Furthermore, banded edit distance perf…
CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
2020
Motivation Numerous sequencing studies, including transcriptomics of host-pathogen systems, sequencing of hybrid genomes, xenografts, mixed species systems, metagenomics and meta-transcriptomics, involve samples containing genetic material from divergent organisms. A crucial step in these studies is identifying from which organism each sequencing read originated, and the experimental design should be directed to minimize biases caused by cross-mapping of reads to incorrect source genomes. Additionally, pooling of sufficiently different genetic material into a single sequencing library could significantly reduce experimental costs but requires careful planning and assessment of the impact of…