Search results for "Sequence analysi"
showing 10 items of 1351 documents
Evolution of arginine deiminase (ADI) pathway genes
2002
We have analyzed the evolution of the three genes encoding structural enzymes of the arginine deiminase (ADI) pathway, arginine deiminase (ADI), ornithine transcarbamoylase (OTC), and carbamate kinase (CK) in a wide range of organisms, including Archaea, Bacteria, and Eukarya. This catabolic route was probably present in the last common ancestor to all the domains of life. The results obtained indicate that these genes have undergone a complex evolutionary history, including horizontal transfer events, duplications, and losses. Therefore, these genes are not adequate to infer organismal relationships at deep branching levels, but they provide an insight into how catabolic genes evolved and …
Analysis of DNA sequence variation within marine species using Beta-coalescents
2013
We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially due to extreme reproductive behaviour, e.g. via Hedgecock's "reproduction sweepstakes". Besides the data analysis, in particular the inference of mutation rates and the estimation of the (real) time to the most recent common ancestor, we briefly address the question whether the genealogies might be adequately described by so-called Beta coalescents (as opposed to Kingman's coalescent), allowing multiple mergers of genealogies. The choice of the underlying…
Multiple overseas dispersal in amphibians
2003
Amphibians are thought to be unable to disperse over ocean barriers because they do not tolerate the osmotic stress of salt water. Their distribution patterns have therefore generally been explained by vicariance biogeography. Here, we present compelling evidence for overseas dispersal of frogs in the Indian Ocean region based on the discovery of two endemic species on Mayotte. This island belongs to the Comoro archipelago, which is entirely volcanic and surrounded by sea depths of more than 3500 m. This constitutes the first observation of endemic amphibians on oceanic islands that did not have any past physical contact to other land masses. The two species of frogs had previously been tho…
UNCLES: Method for the identification of genes differentially consistently co-expressed in a specific subset of datasets
2015
Background Collective analysis of the increasingly emerging gene expression datasets are required. The recently proposed binarisation of consensus partition matrices (Bi-CoPaM) method can combine clustering results from multiple datasets to identify the subsets of genes which are consistently co-expressed in all of the provided datasets in a tuneable manner. However, results validation and parameter setting are issues that complicate the design of such methods. Moreover, although it is a common practice to test methods by application to synthetic datasets, the mathematical models used to synthesise such datasets are usually based on approximations which may not always be sufficiently repres…
Virally Infected Mouse Liver Endothelial Cells Trigger CD8+ T-Cell Immunity
2009
Background & Aims Dendritic cell activation through ligation of pattern recognition receptors leading to full functional maturation causes induction of CD8 + T-cell immunity through increased delivery of costimulatory signals instead of tolerance. Here we investigate whether organ-resident antigen-presenting cells, such as liver sinusoidal endothelial cells (LSECs), also switch from tolerogenic to immunogenic CD8 + T-cell activation upon such stimulation. Methods Murine LSECs were isolated by immunomagnetic separation and analyzed for functional maturation upon triggering pattern recognition receptors or viral infection employing gene expression analysis and T cell coculture assays. In vivo…
Hidden Mediterranean diversity: Assessing species taxa by molecular phylogeny within the opilionid family Trogulidae (Arachnida, Opiliones)
2009
This is the first comprehensive study to evaluate the relationships between the western palearctic harvestman families Dicranolasmatidae, Trogulidae and Nemastomatidae with focus on the phylogeny and systematics of Trogulidae, using combined sequence data of the nuclear 28S rRNA and the mitochondrial cytochrome b gene. Bayesian analysis and Maximum parsimony do not reliably resolve Dicranolasma as distinct family but place it on a similar phylogenetic level as several lineages of Trogulidae. Nemastomatidae and Trogulidae turned out to be monophyletic, as did genera Anelasmocephalus and Trogulus within the Trogulidae. The genera Calathocratus, Platybessobius and Trogulocratus each appeared p…
Defining the role of common variation in the genomic and biological architecture of adult human height
2014
Item does not contain fulltext Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated approximately 2,000, approximately 3,700 and approximately 9,500 SNPs explained approximately 21%, approximately 24% and approximately 29% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes…
Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma
2013
Background Tumor models are critical for our understanding of cancer and the development of cancer therapeutics. Here, we present an integrated map of the genome, transcriptome and immunome of an epithelial mouse tumor, the CT26 colon carcinoma cell line. Results We found that Kras is homozygously mutated at p.G12D, Apc and Tp53 are not mutated, and Cdkn2a is homozygously deleted. Proliferation and stem-cell markers, including Top2a, Birc5 (Survivin), Cldn6 and Mki67, are highly expressed while differentiation and top-crypt markers Muc2, Ms4a8a (MS4A8B) and Epcam are not. Myc, Trp53 (tp53), Mdm2, Hif1a, and Nras are highly expressed while Egfr and Flt1 are not. MHC class I but not MHC class…
Peptidases specific for proline-containing peptides and their unusual peptide-dependent regulation in Oenococcus oeni
2009
International audience; Growth of the lactic acid bacterium (LAB) Oenococcus oeni, which is involved in malolactic fermentation during the winemaking process, is stimulated by peptides originating from yeast. In this study, we investigated the impact of peptides on O. oeni growth, peptidase activity and the expression of genes encoding the studied peptidases. Low levels of PepN activity and very high levels of PepI activity were observed in O. oeni, whereas levels of PepX activity were intermediate. The level of biosynthesis of these O. oeni peptidases was shown to depend on peptides present in the culture medium. These results were confirmed by transcriptional analyses of putative pep gene…
Sequence features and evolutionary mechanisms in the chicken avidin gene family
2001
The chicken avidin gene family comprises the avidin gene (avd) and several homologous avidin-related genes (avrs). The sequences of the avr genes are nearly identical to each other but exhibit nonrandomly distributed, frequently nonsynonymous nucleotide substitutions compared to avd. In this study, we determined the genetic distances and the phylogeny of the avd and avr genes and found differences between different exons and introns. Our results suggest the involvement of biased gene conversion in the evolution of the genes. Furthermore, one of the genes was identified as a putative fusion gene. The occurrence of both gene conversion and recombination supports the models suggesting a common…