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Search Results: 1 - 10 of 465 matches for " Quentin Gascuel "
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Transcriptomic analysis of the interaction between Helianthus annuus and its obligate parasite Plasmopara halstedii shows single nucleotide polymorphisms in CRN sequences
Falah As-sadi, Sébastien Carrere, Quentin Gascuel, Thibaut Hourlier, David Rengel, Marie-Christine Le Paslier, Amandine Bordat, Marie-Claude Boniface, Dominique Brunel, Jér?me Gouzy, Laurence Godiard, Patrick Vincourt
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-498
Abstract: A 454 pyrosequencing run of two infected sunflower samples (inbred lines XRQ and PSC8 infected with race 710 of P. halstedii, which exhibit incompatible and compatible interactions, respectively) generated 113,720 and 172,107 useable reads. From these reads, 44,948 contigs and singletons have been produced. A bioinformatic portal, HP, was specifically created for in-depth analysis of these clusters. Using in silico filtering, 405 clusters were defined as being specific to oomycetes, and 172 were defined as non-specific oomycete clusters. A subset of these two categories was checked using PCR amplification, and 86% of the tested clusters were validated. Twenty putative RXLR and CRN effectors were detected using PSI-BLAST. Using corresponding sequences from four races (100, 304, 703 and 710), 22 SNPs were detected, providing new information on pathogen polymorphisms.This study identified a large number of genes that are expressed during H. annuus/P. halstedii compatible or incompatible interactions. It also reveals, for the first time, that an infection mechanism exists in P. halstedii similar to that in other oomycetes associated with the presence of putative RXLR and CRN effectors. SNPs discovered in CRN effector sequences were used to determine the genetic distances between the four races of P. halstedii. This work therefore provides valuable tools for further discoveries regarding the H. annuus/P. halstedii pathosystem.Downy mildew in sunflowers (Helianthus annuus L.) is caused by the oomycete Plasmopara halstedii (Farl.) Berlese et de Toni. Both the host plant and the pathogen species originated in North America, where co-evolution has taken place [1]. As the result of the fast evolution of the pathogen and despite considerable efforts by public research and seed companies, downy mildew remains a major risk for the crop, as new races of the pathogen are bypassing the resistance of sunflower hybrids [2], which is generally based on race-specific Pl genes [3-6]. On
Expression of Odorant Receptor Family, Type 2 OR in the Aquatic Olfactory Cavity of Amphibian Frog Xenopus tropicalis
Tosikazu Amano, Jean Gascuel
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0033922
Abstract: Recent genome wide in silico analyses discovered a new family (type 2 or family H) of odorant receptors (ORs) in teleost fish and frogs. However, since there is no evidence of the expression of these novel OR genes in olfactory sensory neurons (OSN), it remains unknown if type 2 ORs (OR2) function as odorant receptors. In this study, we examined expression of OR2 genes in the frog Xenopus tropicalis. The overall gene expression pattern is highly complex and differs depending on the gene and developmental stage. RT-PCR analysis in larvae showed that all of the OR2η genes we identified were expressed in the peripheral olfactory system and some were detected in the brain and skin. Whole mount in situ hybridization of the larval olfactory cavity confirmed that at least two OR2η genes so far tested are expressed in the OSN. Because tadpoles are aquatic animals, OR2η genes are probably involved in aquatic olfaction. In adults, OR2η genes are expressed in the nose, brain, and testes to different degrees depending on the genes. OR2η expression in the olfactory system is restricted to the medium cavity, which participates in the detection of water-soluble odorants, suggesting that OR2ηs function as receptors for water-soluble odorants. Moreover, the fact that several OR2ηs are significantly expressed in non-olfactory organs suggests unknown roles in a range of biological processes other than putative odorant receptor functions.
Fast NJ-like algorithms to deal with incomplete distance matrices
Alexis Criscuolo, Olivier Gascuel
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-166
Abstract: We propose an adaptation to incomplete matrices of three agglomerative algorithms, namely NJ, BIONJ [3] and MVR [4]. Our adaptation generalizes to incomplete matrices the taxon pair selection criterion of NJ (also used by BIONJ and MVR), and combines this generalized criterion with that of ADDTREE [5]. Steps (b) and (c) are also modified, but O(n3) time complexity is kept. The performance of these new algorithms is studied with large scale simulations, which mimic multi-gene phylogenomic datasets. Our new algorithms – named NJ*, BIONJ* and MVR* – infer phylogenetic trees that are as least as accurate as those inferred by other available methods, but with much faster running times. MVR* presents the best overall performance. This algorithm accounts for the variance of the pairwise evolutionary distance estimates, and is well suited for multi-gene studies where some distances are accurately estimated using numerous genes, whereas others are poorly estimated (or not estimated) due to the low number (absence) of sequenced genes being shared by both species.Our distance-based agglomerative algorithms NJ*, BIONJ* and MVR* are fast and accurate, and should be quite useful for large scale phylogenomic studies. When combined with the SDM method [6] to estimate a distance matrix from multiple genes, they offer a relevant alternative to usual supertree techniques [7]. Binaries and all simulated data are downloadable from [8].Phylogeny inference methods can be classified into two main categories: character-based (e.g. maximum-parsimony or maximum-likelihood) and distance-based approaches. The latter have low running times which are quite useful (mandatory in some cases) to perform large-scale studies and bootstrap analyses. A number of computer simulations [9-17] have shown that distance methods are fairly accurate, though not as accurate as likelihood-based methods that are much more time consuming. Using any distance-based method first requires to estimate the pairwise evolut
Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum's relatives infecting great apes
Samuel Blanquart, Olivier Gascuel
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-70
Abstract: To distinguish between these mutually exclusive hypotheses on the origin of Plasmodium falciparum and its great ape infecting relatives, we performed a comprehensive phylogenetic analysis based on a data set of three mitochondrial genes from 33 to 84 malaria parasites. We showed that malarial mitochondrial genes have evolved slowly and are compositionally homogeneous. We estimated their phylogenetic relationships using Bayesian and maximum-likelihood methods. Inferred trees were checked for their robustness to the (i) site selection, (ii) assumptions of various probabilistic models, and (iii) taxon sampling. Our results robustly support a common ancestry of rodent parasites and Plasmodium falciparum's relatives infecting great apes.Our results refute the most common view of the origin of great ape malaria parasites, and instead demonstrate the robustness of a less well-established phylogenetic hypothesis, under which Plasmodium falciparum and its relatives infecting great apes are closely related to rodent parasites. This study sheds light on the evolutionary history of Plasmodium falciparum, a major issue for human health.Malaria is an overwhelming public health problem all over the world. It kills one to three million people annually and infects 200 to 500 million others [1]. Human malaria is induced by infections caused by a range of eukaryotic protists belonging to the phylum Apicomplexa. These organisms possess an endosymbiont of red algal origin [2] derived into an apical organelle, the apicoplast. This organelle is specialized in host cell invasion [3]. Within Apicomplexa, malaria parasites, also called Haemosporidia, are characterized by their infection of vertebrate hosts, haemoglobin digestion, and a complex life cycle involving dipteran vectors feeding from their vertebrate hosts' blood [4].Haemosporidia include the genera Leucocytozoon (bird parasites), Haemoproteus and Parahaemoproteus (Sauria, i.e. bird and reptile parasites), Plasmodium (saurian and m
Inferring ancestral sequences in taxon-rich phylogenies
Olivier Gascuel,Mike Steel
Quantitative Biology , 2010,
Abstract: Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length (e.g. for a gene) although we are often able to sample more taxa, it is useful to consider a dual type of statistical consistency where we increase the number of species, rather than characters. This raises some basic questions: what can we learn about the evolutionary process as we increase the number of species? In particular, does having more species allow us to infer the ancestral state of characters accurately? This question is particularly relevant when sequence site evolution varies in a complex way from character to character, as well as for reconstructing ancestral sequences. In this paper, we assemble a collection of results to analyse various approaches for inferring ancestral information with increasing accuracy as the number of taxa increases.
Predicting the ancestral character changes in a tree is typically easier than predicting the root state
Olivier Gascuel,Mike Steel
Quantitative Biology , 2013,
Abstract: Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show that when the mutation rate become too large, reconstructing the ancestral state at the tree root is no longer feasible. Here, we also study the reconstruction of the ancestral changes that occurred along the tree edges. We show that, depending on the tree and branch length distribution, reconstructing these changes (i.e. reconstructing the ancestral state of all internal nodes in the tree) may be easier or harder than reconstructing the ancestral root state. However, results from information theory indicate that for the standard Yule tree, the task of reconstructing internal node states remains feasible, even for very high substitution rates. Moreover, computer simulations demonstrate that for more complex trees and scenarios, this result still holds. For a large variety of counting, parsimony-based and likelihood-based methods, the predictive accuracy of a randomly selected internal node in the tree is indeed much higher than the accuracy of the same method when applied to the tree root. Moreover, parsimony- and likelihood-based methods appear to be remarkably robust to sampling bias and model mis-specification.
A 'stochastic safety radius' for distance-based tree reconstruction
Olivier Gascuel,Mike Steel
Quantitative Biology , 2014,
Abstract: A variety of algorithms have been proposed for reconstructing trees that show the evolutionary relationships between species by comparing differences in genetic data across present-day taxa. If the leaf-to-leaf distances in a tree can be accurately estimated, then it is possible to reconstruct this tree from these estimated distances, using polynomial-time methods such as the popular `Neighbor-Joining' algorithm. There is a precise combinatorial condition under which distance-based methods are guaranteed to return a correct tree (in full or in part) based on the requirement that the input distances all lie within some `safety radius' of the true distances. Here, we explore a stochastic analogue of this condition, and mathematically establish upper and lower bounds on this `stochastic safety radius' for distance-based tree reconstruction methods. Using simulations, we show how this notion provides a new way to compare the performance of distance-based tree reconstruction methods. This may help explain why Neighbor-Joining performs so well, as its stochastic safety radius appears close to optimal (while its more classical safety radius is the same as many other less accurate methods).
Estrogen-induced DNA synthesis in vascular endothelial cells is mediated by ROS signaling
Quentin Felty
BMC Cardiovascular Disorders , 2006, DOI: 10.1186/1471-2261-6-16
Abstract: The effect of estrogen on the production of intracellular oxidants and the role of estrogen-induced ROS on cell growth was studied in human umbilical vein endothelial cells. ROS were measured by monitoring the oxidation of 2'7'-dichlorofluorescin by spectrofluorometry. Endothelial cell growth was measured by a colorimetric immunoassay based on BrdU incorporation into DNA.Physiological concentrations of estrogen (367 fmol and 3.67 pmol) triggered a rapid 2-fold increase in intracellular oxidants in endothelial cells. E2-induced ROS formation was inhibited to basal levels by cotreatment with the mitochondrial inhibitor rotenone (2 μM) and xanthine oxidase inhibitor allopurinol (50 μM). Inhibitors of NAD(P)H oxidase, apocynin and DPI, did not block E2-induced ROS formation. Furthermore, the NOS inhibitor, L-NAME, did not prevent the increase in E2-induced ROS. These findings indicate both mitochondria and xanthine oxidase are the source of ROS in estrogen treated vascular endothelial cells. E2 treated cells showed a 2-fold induction of BrdU incorporation at 18 h which was not observed in cells exposed to vehicle alone. Cotreatment with ebselen (20 μM) and NAC (1 mM) inhibited E2-induced BrdU incorporation without affecting the basal levels of DNA synthesis. The observed inhibitory effect of NAC and ebselen on E2-induced DNA synthesis was also shown to be dose dependent.We have shown that estrogen exposure stimulates the rapid production of intracellular ROS and they are involved in growth signaling of endothelial cells. It appears that the early estrogen signaling does not require estrogen receptor genomic signaling because we can inhibit estrogen-induced DNA synthesis by antioxidants. Findings of this study may further expand research defining the underlying mechanism of how estrogen may promote vascular lesions. It also provides important information for the design of new antioxidant-based drugs or new antioxidant gene therapy to protect the cardiovascular health of
The Metaphysical Necessity of Natural Laws.
Quentin Smith
Philosophica , 2001,
Abstract:
La libertad de las repúblicas: un tercer concepto de libertad?
Skinner, Quentin
Isegoría , 2005,
Abstract: In this article the author tries to show that there is a third concept of liberty beyond the two coined by Isaiah Berlin. In order to do that he embarks himself in a historical reconstruction of both hobbesian liberty and liberty before liberalism. He concludes that although liberty as non-interference was a feasible ideal in post-war western societies there are other concepts of liberty equally valuable depending on what account we believe should be given of the normative character of human nature. En este artículo se quiere mostrar que hay un tercer concepto de libertad aparte de los dos descritos por Isaiah Berlin. Para llevar a cabo su propósito el autor realiza una reconstrucción histórica del concepto hobbesiano de libertad y del concepto de libertad al que éste se opuso. Se concluye se alando que, aunque el concepto de libertad como no interferencia pudo se un ideal valioso en el mundo occidental de la posguerra, hay otros conceptos de libertad que son igualmente valiosos en relación a la concepción que tengamos del carácter normativo de la naturaleza humana.
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