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Search Results: 1 - 10 of 204564 matches for " Yves Van de Peer "
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The future for plants and plants for the future
Yves Van de Peer
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-7-308
Abstract: The 2007 EMBO Conference on Plant Molecular Biology brought together about 150 plant scientists from 23 different countries in the beautiful town of Ghent in Belgium. This is where, some might say, plant molecular genetics received a major boost, with the work of Marc Van Montagu and Jeff Schell in the 1970s on the Ti plasmid of the plant pathogenic bacterium Agrobacterium tumefaciens. Plant modification with the help of the Ti plasmid of A. tumefaciens is now routine in many laboratories and has helped create genetically modified (GM) crops that are cultivated throughout the world.Marc Van Montagu (Institute of Plant Biotechnology for Developing Countries, Ghent, Belgium) opened the conference by reflecting on both the past and the future of plant science. Contemplating that future, he stressed the importance of transgenic plants not only to further our basic knowledge on the function of genes, but also to cope with problems mankind will have to deal with: feeding an ever-increasing population on shrinking areas of arable land; the attrition of fossil fuels such as coal, oil and gas; and global warming. Van Montagu warned that in order to build a more sustainable economy in the future, it will be absolutely necessary for Europe to embrace the use of GM crops, as has already happened in large parts of the world. The strong reaction of consumer-rights groups and environmentalists against the use of GM crops has probably had a larger impact on plant science in Europe than generally recognized, and has been, at least in part, responsible for the drop in the numbers of students choosing plant research over the past few years.Fortunately, the tide seems to have turned, and plant science is becoming more attractive again, on the one hand because GM plants have been used for almost 15 years without any major health hazards being reported, and on the other hand through the growing awareness that plants might indeed hold the key to some of the most threatening problems of ou
A mystery unveiled
Yves Van de Peer
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-5-113
Abstract: The number of genome duplications uncovered in the evolutionary history of land plants seems to be steadily increasing. In a recent paper in Nature, Jiao et al. [1] provide evidence for two additional, previously unnoticed ancient whole genome duplications (WGDs) in seed plants. More precisely, the authors propose a WGD in the common ancestor of all extant angiosperms, and an even older one in the common ancestor of all extant seed plants. This means, for instance, that adding these to the well-documented and widely accepted hexaploidy event shared by most, if not all, of the eudicots, and the two more recent genome duplications after its divergence with papaya, the small genome of Arabidopsis should carry the traces of at least five WGDs. And although Arabidopsis actually might be an extreme case, it represents only one of many plant lineages that have experienced a number of nested WGDs since the origin of seed and flowering plants (Figure 1).So why have these older events not been detected before? Plant genomes are highly dynamic and usually go through an intense phase of structural rearrangements and gene loss following duplication. Bioinformatics tools to detect within-genome colinearity can be used to find remnants of relatively recent WGDs, but, since colinearity fades with time, old(er) duplication events in plants generally can not be detected this way. In many cases, WGDs can also be detected by building age distributions of paralogs, where the number of paralogs is plotted against their age, which can be approximated by the number of synonymous substitutions per synonymous site (KS). A peak in such a distribution indicates a burst of duplications at about the same time, and is often interpreted as a WGD event. However, due to gene loss and saturation effects, KS age distributions become unreliable for the detection of older duplication events. To see whether they could find evidence for older WGDs in plants, Jiao et al. [1] used a phylogenomic approach an
'Horizontal' plant biology on the rise
Yves Van de Peer
Genome Biology , 2004, DOI: 10.1186/gb-2004-6-1-302
Abstract: The annual meetings on plant genomics, of which Plant-GEMS2OO4 was the third, are now among the most important plant meetings in Europe. This year, almost 600 scientists from more than 30 different countries participated, and the meeting was supported by the national programs in plant genomics in France, Germany, the UK and the Netherlands, and by the French, German, Spanish and British research ministries. This report focuses in particular on the strengths and expectations of comparative genomics in plants, an area that is only now starting to be fully exploited.Comparative genomics is often praised as an extremely powerful way of discovering novel biological features. A well-known example of its power is the identification of conserved elements, such as as cis-acting regulatory elements, in distantly related genomes: because of their conservation over long periods of time, such elements must have some important function. Another merit of comparative genomics is expected to be its ability to uncover the transfer of structural and functional information from one genome to another. This assumption is based on the observation that, although chromosomal rearrangements can be extensive, the genomes of different species still exhibit a certain degree of colinearity. Keynote speaker Steve Tanksley (Cornell University, Ithaca, USA) argued that only through comparative and integrative approaches will the mechanisms of evolution and adaptation be revealed, and he stressed the importance of moving from 'Vertical' biology within a single species to 'horizontal' biology across species. Currently, the genomes of at least 10 plant species are being fully or partially sequenced. They have been selected to complement the two model plants whose genome sequence has already been determined, namely Arabidopsis thaliana (thale cress) and Oryza sativa (rice). Tanksley also reported on the Solanaceae Genome Initiative, which is studying the genomes of tomatoes, potatoes and their relative
Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids
Yves Van de Peer
Genome Biology , 2004, DOI: 10.1186/gb-2004-5-12-250
Abstract: In 1993, Sydney Brenner and colleagues [1] proposed sequencing the pufferfish genome as a cost-effective way to identify and characterize human genes. The genome of the pufferfish is only about one-eighth of the size of that of human but was expected to contain a similar gene repertoire. Ten years later, not only has a draft genome sequence been released for Takifugu rubripes (Fugu, also known as the Japanese or tiger pufferfish) [2], but also for Tetraodon nigroviridis (green spotted pufferfish) [3], a close relative that diverged from Takifugu 18-30 million years ago (Mya). By comparing the two pufferfish genomes with that of human, several hundred novel human genes have already been uncovered, as was predicted by Brenner and colleagues [1]. But the pufferfish genome sequencing projects have also yielded a surprising finding: ray-finned fish (Actinopterygii), such as pufferfish might have more genes than lobe-finned fish (coelacanths and lungfish) and land vertebrates, because of additional gene-duplication events [4]. The recent release of the Tetraodon genome sequence [3] provides overwhelming evidence that a genome-duplication event did indeed occur early in the evolution of ray-finned fish.Some of the first data pointing to a possible genome duplication in fish came from Hox genes and Hox gene clusters. Hox genes encode DNA-binding proteins that specify cell fate along the anterior-posterior axis of bilaterian animal embryos and occur in one or more clusters of up to 13 genes. Whereas lobe-finned fish, amphibians, reptiles, birds and mammals have four clusters, extra Hox gene clusters have been discovered in zebrafish, Medaka, Nile tilapia and pufferfish [4]. The observation that such distantly related species [5] all have seven or eight Hox gene clusters suggested the occurrence of an additional genome-duplication event in the ray-finned fish lineage before the divergence of most teleost (bony fish) species. More recent comparative genomic studies have turned
The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection
Cindy Martens, Yves Van de Peer
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-353
Abstract: Analysis of the complete genomes of three different Phytophthora species, using a newly developed approach, unveiled a large number of small duplicated blocks, mainly consisting of two or three consecutive genes. Further analysis of these duplicated genes and comparison with the known gene and genome duplication history of ten other eukaryotes including parasites, algae, plants, fungi, vertebrates and invertebrates, suggests that the ancestor of P. infestans, P. sojae and P. ramorum most likely underwent a whole genome duplication (WGD). Genes that have survived in duplicate are mainly genes that are known to be preferentially retained following WGDs, but also genes important for pathogenicity and infection of the different hosts seem to have been retained in excess. As a result, the WGD might have contributed to the evolutionary and pathogenic success of Phytophthora.The fact that we find many small blocks of duplicated genes indicates that the genomes of Phytophthora species have been heavily rearranged following the WGD. Most likely, the high repeat content in these genomes have played an important role in this rearrangement process. As a consequence, the paucity of retained larger duplicated blocks has greatly complicated previous attempts to detect remnants of a large-scale duplication event in Phytophthora. However, as we show here, our newly developed strategy to identify very small duplicated blocks might be a useful approach to uncover ancient polyploidy events, in particular for heavily rearranged genomes.Oomycetes or water molds form a diverse group of eukaryotic micro-organisms that have originally been classified as Fungi because of their similarity in growth morphology, propagation through spores and weaponry to infect host organisms [1]. Furthermore, they occupy similar ecological niches and share many cell wall degrading enzymes to weaken host tissues [2,3]. However, biochemical and molecular data have shown that oomycetes have little affinity with "
Angiosperm polyploids and their road to evolutionary success
Jeffrey A. Fawcett,Yves Van de Peer
Trends in Evolutionary Biology , 2010, DOI: 10.4081/eb.2010.e3
Abstract: The abundance of polyploidy among flowering plants has long been recognized, and recent studies have uncovered multiple ancient polyploidization events in the evolutionary history of several angiosperm lineages. Once polyploids are formed they must get locally established and then propagate and survive while adapting to different environments and avoiding extinction. This might ultimately lead to their long-term evolutionary success, where their descendant lineages survive for tens of millions of years. Along this road to evolutionary success, polyploids must overcome several obstacles, to which several genetic and ecological factors are likely to contribute. One recurrent observation, based on present-day polyploids, has been the high frequency of polyploids in harsh environments. Also, recent studies proposed that the success of certain ancient polyploids might be linked to periods of climatic change. Although we are still in the early stages of unraveling the factors that resulted in the long-term evolutionary success of ancient polyploids, the advances in genomic sequencing and molecular dating methods promise to enhance our understanding. It, therefore, seems timely to review our current knowledge of what determines the success of polyploids. Here, we discuss especially how harsh conditions or periods of climatic change might affect the rate of formation, establishment, persistence and long-term evolutionary success of polyploids in angiosperms.
zt: A Sofware Tool for Simple and Partial Mantel Tests
Eric Bonnet,Yves Van de Peer
Journal of Statistical Software , 2002,
Abstract:
A helicoidal transfer matrix model for inhomogeneous DNA melting
Tom Michoel,Yves Van de Peer
Quantitative Biology , 2005, DOI: 10.1103/PhysRevE.73.011908
Abstract: An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically stressed DNA with a fixed linking number constraint. Without loss of accuracy, the continuous degrees of freedom can be discretized using a minimal number of discretization points, yielding an effective transfer matrix model of modest dimension (d=36). The resulting algorithms to compute DNA melting profiles are both simple and efficient.
Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics
Klaas Vandepoele, Tineke Casneuf, Yves Van de Peer
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-11-r103
Abstract: Here, we applied a detection strategy that combines features of classic motif overrepresentation approaches in co-regulated genes with general comparative footprinting principles for the identification of biologically relevant regulatory elements and modules in Arabidopsis thaliana, a model system for plant biology. In total, we identified 80 TFBSs and 139 regulatory modules, most of which are novel, and primarily consist of two or three regulatory elements that could be linked to different important biological processes, such as protein biosynthesis, cell cycle control, photosynthesis and embryonic development. Moreover, studying the physical properties of some specific regulatory modules revealed that Arabidopsis promoters have a compact nature, with cooperative TFBSs located in close proximity of each other.These results create a starting point to unravel regulatory networks in plants and to study the regulation of biological processes from a systems biology point of view.Regulation of gene expression plays an important role in a variety of biological processes such as development and responses to environmental stimuli. In plants, transcriptional regulation is mediated by a large number (>1,500) of transcription factors (TFs) controlling the expression of tens or hundreds of target genes in various, sometimes intertwined, signal transduction cascades [1,2]. Transcription factor binding sites (TFBSs; or DNA sequence motifs, or motifs for short) are the functional elements that determine the timing and location of transcriptional activity. In plants and other higher eukaryotes, these elements are primarily located in the long non-coding sequences upstream of a gene, although functional elements in introns and untranslated regions have been described as well [3,4]. Moreover, regulatory motifs organize into separable cis-regulatory modules (CRMs; modules for sort), each defining the cooperation of several TFs required for a specific spatio-temporal expression pattern
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
Tineke Casneuf, Yves Van de Peer, Wolfgang Huber
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-461
Abstract: We demonstrate a positive relation between off-target reporter alignment strength and expression correlation in data from oligonucleotide genechips. Furthermore, we describe a method that allows the identification, from their expression data, of individual probe sets affected by off-target hybridization.The effects of off-target hybridization on expression correlation coefficients can be substantial, and can be alleviated by more accurate mapping between microarray reporters and the target transcriptome. We recommend attention to the mapping for any microarray analysis of gene expression patterns.Microarrays are a valuable tool in functional genomics research. The breadth of their applications is reflected by the myriad of computational methods that have been developed for their analysis in the last decade. One popular practice is to compare expression patterns of genes by calculating correlation coefficients on expression level estimates across a set of conditions. Many downstream analysis tools are based on the presence or absence of correlation in the expression profiles of genes, like the inference of co-expression [1-5], gene regulatory [6] and Bayesian networks [7-10] and the study of gene family evolution [11,12]. From a biological point of view, these approaches are useful and informative, but here we show that if care has not been taken as to how these correlations are calculated and how the reporters for each transcript are selected, incorrect conclusions can be drawn.A gene is represented on a microarray by one or more reporters, i. e. nucleotide sequences that are designed to uniquely match its transcript, or transcripts if different splice variants exist [13]. Affymetrix GeneChips are the most widely used microarray platform, and a wealth of data measured on these arrays is publicly available. Affymetrix reporters are 25-mer oligonucleotides whose sequence is complementary to the intended target. Each target is represented by a set of reporters, called
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