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Search Results: 1 - 10 of 234 matches for " Antonis Rokas "
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Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade
Leonidas Salichos,Antonis Rokas
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0018755
Abstract: Accurate identification of orthologs is crucial for evolutionary studies and for functional annotation. Several algorithms have been developed for ortholog delineation, but so far, manually curated genome-scale biological databases of orthologous genes for algorithm evaluation have been lacking. We evaluated four popular ortholog prediction algorithms (MultiParanoid; and OrthoMCL; RBH: Reciprocal Best Hit; RSD: Reciprocal Smallest Distance; the last two extended into clustering algorithms cRBH and cRSD, respectively, so that they can predict orthologs across multiple taxa) against a set of 2,723 groups of high-quality curated orthologs from 6 Saccharomycete yeasts in the Yeast Gene Order Browser.
Evaluating Rare Amino Acid Substitutions (RGC_CAMs) in a Yeast Model Clade
Kenneth Polzin, Antonis Rokas
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0092213
Abstract: When inferring phylogenetic relationships, not all sites in a sequence alignment are equally informative. One recently proposed approach that takes advantage of this inequality relies on sites that contain amino acids whose replacement requires multiple substitutions. Identifying these so-called RGC_CAM substitutions (after Rare Genomic Changes as Conserved Amino acids-Multiple substitutions) requires that, first, at any given site in the amino acid sequence alignment, there must be a minimum of two different amino acids; second, each amino acid must be present in at least two taxa; and third, the amino acids must require a minimum of two nucleotide substitutions to replace each other. Although theory suggests that RGC_CAM substitutions are expected to be rare and less likely to be homoplastic, the informativeness of RGC_CAM substitutions has not been extensively evaluated in biological data sets. We investigated the quality of RGC_CAM substitutions by examining their degree of homoplasy and internode certainty in nearly 2.7 million aligned amino acid sites from 5,261 proteins from five species belonging to the yeast Saccharomyces sensu stricto clade whose phylogeny is well-established. We identified 2,647 sites containing RGC_CAM substitutions, a number that contrasts sharply with the 100,887 sites containing RGC_non-CAM substitutions (i.e., changes between amino acids that require only a single nucleotide substitution). We found that RGC_CAM substitutions had significantly lower homoplasy than RGC_non-CAM ones; specifically RGC_CAM substitutions showed a per-site average homoplasy index of 0.100, whereas RGC_non-CAM substitutions had a homoplasy index of 0.215. Internode certainty values were also higher for sites containing RGC_CAM substitutions than for RGC_non-CAM ones. These results suggest that RGC_CAM substitutions possess a strong phylogenetic signal and are useful markers for phylogenetic inference despite their rarity.
Bushes in the Tree of Life
Antonis Rokas,Sean B. Carroll
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0040352
Abstract:
Bushes in the Tree of Life
Antonis Rokas ,Sean B Carroll
PLOS Biology , 2006, DOI: 10.1371/journal.pbio.0040352
Abstract:
Two Different Secondary Metabolism Gene Clusters Occupied the Same Ancestral Locus in Fungal Dermatophytes of the Arthrodermataceae
Han Zhang, Antonis Rokas, Jason C. Slot
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0041903
Abstract: Background Dermatophyte fungi of the family Arthrodermataceae (Eurotiomycetes) colonize keratinized tissue, such as skin, frequently causing superficial mycoses in humans and other mammals, reptiles, and birds. Competition with native microflora likely underlies the propensity of these dermatophytes to produce a diversity of antibiotics and compounds for scavenging iron, which is extremely scarce, as well as the presence of an unusually large number of putative secondary metabolism gene clusters, most of which contain non-ribosomal peptide synthetases (NRPS), in their genomes. To better understand the historical origins and diversification of NRPS-containing gene clusters we examined the evolution of a variable locus (VL) that exists in one of three alternative conformations among the genomes of seven dermatophyte species. Results The first conformation of the VL (termed VLA) contains only 539 base pairs of sequence and lacks protein-coding genes, whereas the other two conformations (termed VLB and VLC) span 36 Kb and 27 Kb and contain 12 and 10 genes, respectively. Interestingly, both VLB and VLC appear to contain distinct secondary metabolism gene clusters; VLB contains a NRPS gene as well as four porphyrin metabolism genes never found to be physically linked in the genomes of 128 other fungal species, whereas VLC also contains a NRPS gene as well as several others typically found associated with secondary metabolism gene clusters. Phylogenetic evidence suggests that the VL locus was present in the ancestor of all seven species achieving its present distribution through subsequent differential losses or retentions of specific conformations. Conclusions We propose that the existence of variable loci, similar to the one we studied, in fungal genomes could potentially explain the dramatic differences in secondary metabolic diversity between closely related species of filamentous fungi, and contribute to host adaptation and the generation of metabolic diversity.
分布区扩张的群体遗传学后果:类型与过程,以栎瘿蜂为模型系统
graham,n.,stone,rachel,j.,atkinson,gordon,brown,antonis,rokas
生物多样性 , 2002,
Abstract: ?生物入侵是不均衡世界的一个永恒话题,尤其是当人类有意或无意地引入物种后。很多引入显然是无害的,但另外一些则有着严重的后果,会给入侵地的生物以至于整个生物群落造成影响。本文总结了分布区扩张的常见模式,概述了它们对遗传多样性和种群结构式样所造成的影响。描述了如何根据以一批遗传标记所得到的遗传多样性式样来推断入侵途径,来揭示伴随扩张选择和漂变在形成种群遗传样式中的作用。本文对日益增多的群体遗传学方法进行了总结,这些技术可以用来在不同的时间尺度上推断种群规模所发生的巨大变化(瓶颈效应及种群扩张)。最后,我们以欧洲栎瘿蜂(膜翅目,瘿蜂科,瘿蜂族)一系列入侵的数据为例对一些方法进行了说明。从500~10000年的时间尺度上,多态的等位酶位点上等位基因频率的数据表明:1)遗传多样性沿入侵路线呈不断下降的趋势,支持了冰河期避难所作为遗传多样性中心的作用;2)入侵地区的种群与该物种原产地的种群相比,遗传上的分化更为强烈。这种种群结构在空间上的变异可能是被栎瘿蜂开发的资源尤其是栎树寄主在斑块上出现变异的反映。
The population genetic consequences of range expansion:a review of pattern and process,and the value of oak gallwasps as a model system
分布区扩张的群体遗传学后果:类型与过程,以栎瘿蜂为模型系统(英)

Graham NStone,Rachel JAtkinson,Gordon Brown,Antonis Rokas,
Graham N. Stone
,Rachel J. Atkinson,Gordon Brown,Antonis Rokas

生物多样性 , 2002,
Abstract: Biological invasions are a continuous feature of a non-equilibrium world,ever more so as a result of accidental and deliberate introductions by mankind.While many of these introductions are apparently harmless,others have significant consequences for organisms native to the invaded range,and entire communities may be affected.Here we provide a survey of common models of range expansion,and outline the consequences these models have for patterns in genetic diversity and population structure.We describe how patterns of genetic diversity at a range of markers can be used to infer invasion routes,and to reveal the roles of selection and drift in shaping population genetic patterns that accompany range expansion.We summarise a growing range of population genetic techniques that allow large changes in population size (bottlenecks and population expansions) to be inferred over a range of timescales.Finally,we illustrate some of the approaches described using data for a suite of invasions by oak gallwasps (Hymenoptera,Cynipidae,Cynipini) in Europe.We show that over timescales ranging from 500~10000 years,allele frequency data for polymorphic allozymes reveal (a) a consistent loss of genetic diversity along invasion routes,confirming the role of glacial refugia as centres of genetic diversity over these timescales,and (b) that populations in the invaded range are more subdivided genetically than those in the native range of each species.This spatial variation in population structure may be the result of variation in the patchiness of resources exploited by gallwasps,particularly host oak plants.
The Molecular Evolution of the p120-Catenin Subfamily and Its Functional Associations
Robert H. Carnahan,Antonis Rokas,Eric A. Gaucher,Albert B. Reynolds
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015747
Abstract: p120-catenin (p120) is the prototypical member of a subclass of armadillo-related proteins that includes δ-catenin/NPRAP, ARVCF, p0071, and the more distantly related plakophilins 1–3. In vertebrates, p120 is essential in regulating surface expression and stability of all classical cadherins, and directly interacts with Kaiso, a BTB/ZF family transcription factor.
Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding
R Pitts, David C Rinker, Patrick L Jones, Antonis Rokas, Laurence J Zwiebel
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-271
Abstract: We compared chemosensory tissue transcriptomes to whole body transcriptomes of each sex to identify chemosensory enhanced genes. In the six data sets analyzed, we detected expression of nearly all known chemosensory genes and found them to be highly enriched in both olfactory tissues of males and females. While the maxillary palps of both sexes demonstrated strict chemosensory gene expression overlap, we observed acute differences in sensory specialization between male and female antennae. The relatively high expression levels of chemosensory genes in the female antennae reveal its role as an organ predominately assigned to chemosensation. Remarkably, the expression of these genes was highly conserved in the male antennae, but at much lower relative levels. Alternatively, consistent with a role in mating, the male antennae displayed significant enhancement of genes involved in audition, while the female enhancement of these genes was observed, but to a lesser degree.These findings suggest that the chemoreceptive spectrum, as defined by gene expression profiles, is largely similar in female and male An. gambiae. However, assuming sensory receptor expression levels are correlated with sensitivity in each case, we posit that male and female antennae are perceptive to the same stimuli, but possess inverse receptive prioritizations and sensitivities. Here we have demonstrated the use of RNA-seq to characterize the sensory specializations of an important disease vector and grounded future studies investigating chemosensory processes.Insects rely heavily upon chemosensation, the ability to detect and react to environmental chemical cues, in virtually every aspect of their life cycle [1]. Chemosensation is critical to food source identification, predator avoidance, oviposition site selection, kin recognition, mate choice, and toxic compound avoidance. In insects, chemosensory neurons are contained within distinct tissues on many parts of the body, most conspicuously on the
The Fumagillin Gene Cluster, an Example of Hundreds of Genes under veA Control in Aspergillus fumigatus
Sourabh Dhingra, Abigail L. Lind, Hsiao-Ching Lin, Yi Tang, Antonis Rokas, Ana M. Calvo
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0077147
Abstract: Aspergillus fumigatus is the causative agent of invasive aspergillosis, leading to infection-related mortality in immunocompromised patients. We previously showed that the conserved and unique-to-fungi veA gene affects different cell processes such as morphological development, gliotoxin biosynthesis and protease activity, suggesting a global regulatory effect on the genome of this medically relevant fungus. In this study, RNA sequencing analysis revealed that veA controls the expression of hundreds of genes in A. fumigatus, including those comprising more than a dozen known secondary metabolite gene clusters. Chemical analysis confirmed that veA controls the synthesis of other secondary metabolites in this organism in addition to gliotoxin. Among the secondary metabolite gene clusters regulated by veA is the elusive but recently identified gene cluster responsible for the biosynthesis of fumagillin, a meroterpenoid known for its anti-angiogenic activity by binding to human methionine aminopeptidase 2. The fumagillin gene cluster contains a veA-dependent regulatory gene, fumR (Afu8g00420), encoding a putative C6 type transcription factor. Deletion of fumR results in silencing of the gene cluster and elimination of fumagillin biosynthesis. We found expression of fumR to also be dependent on laeA, a gene encoding another component of the fungal velvet complex. The results in this study argue that veA is a global regulator of secondary metabolism in A. fumigatus, and that veA may be a conduit via which chemical development is coupled to morphological development and other cellular processes.
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