text:
☰ Menu
Continue Reading →
FeaturedMeeting AnnouncementsNews
Congratulations to the inaugural winners of the SMBE Allan Wilson Award, SMBE Mid-Career Award for Research, SMBE Community Service Award and the SMBE Lifetime Contribution Award!
FeaturedMeeting AnnouncementsNewsSpotlightsUncategorized
SMBE is now calling for proposals for workshops/satellite meetings to be held between Fall 2016 and Fall 2017. Funds will be awarded on a competitive basis to members of the molecular evolution research community to run workshops/satellite meetings on an important, focused, and timely topic of their choice. The deadline for submission of proposals is May 15, 2016.
FeaturedFellowshipsJobsMeeting AnnouncementsNewsSpotlightsUncategorized
Julie Marin and S. Blair Hedges
AbstractChoanoflagellates and filastereans are the closest known single celled relatives of Metazoa within Holozoa and provide insight into how animals evolved from their unicellular ancestors. Codon usage bias has been extensively studied in metazoans, with both natural selection and mutation pressure playing important roles in different species. The disparate nature of metazoan codon usage patterns prevents the reconstruction of ancestral traits. However, traits conserved across holozoan protists highlight characteristics in the unicellular ancestors of Metazoa. Presented here are the patterns of codon usage in the choanoflagellates Monosiga brevicollis and Salpingoeca rosetta, as well as the filasterean Capsaspora owczarzaki. Codon usage is shown to be remarkably conserved. Highly biased genes preferentially use GC-ending codons, however there is limited evidence this is driven by local mutation pressure. The analyses presented provide strong evidence that natural selection, for both translational accuracy and efficiency, dominates codon usage bias in holozoan protists. In particular, the signature of selection for translational accuracy can be detected even in the most weakly biased genes. Biased codon usage is shown to have coevolved with the tRNA species, with optimal codons showing complementary binding to the highest copy number tRNA genes. Furthermore, tRNA modification is shown to be a common feature for amino acids with higher levels of degeneracy and highly biased genes show a strong preference for using modified tRNAs in translation. The translationally optimal codons defined here will be of benefit to future transgenics work in holozoan protists, as their use should maximise protein yields from edited transgenes.
AbstractMultiple sequence alignment is a prerequisite for many evolutionary analyses. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that explicitly accounts for the underlying codon structure of protein-coding nucleotide sequences. Its unique characteristic allows building reliable codon alignments even in the presence of frameshifts. This facilitates downstream analyses such as selection pressure estimation based on the ratio of nonsynonymous to synonymous substitutions. Here, we present MACSE v2, a major update with an improved version of the initial algorithm enriched with a complete toolkit to handle multiple alignments of protein-coding sequences. A graphical interface now provides user-friendly access to the different subprograms.
AbstractNeuropeptides are neurosecretory signaling molecules in protostomes and deuterostomes (together Nephrozoa). Little, however, is known about the neuropeptide complement of the sister group of Nephrozoa, the Xenacoelomorpha, which together form the Bilateria. Because members of the xenacoelomorph clades Xenoturbella, Nemertodermatida, and Acoela differ extensively in their central nervous system anatomy, the reconstruction of the xenacoelomorph and bilaterian neuropeptide complements may provide insights into the relationship between nervous system evolution and peptidergic signaling. Here, we analyzed transcriptomes of seven acoels, four nemertodermatids, and two Xenoturbella species using motif searches, similarity searches, mass spectrometry and phylogenetic analyses to characterize neuropeptide precursors and neuropeptide receptors. Our comparison of these repertoires with previously reported nephrozoan and cnidarian sequences shows that the majority of annotated neuropeptide GPCRs in cnidarians are not orthologs of specific bilaterian neuropeptide receptors, which suggests that most of the bilaterian neuropeptide systems evolved after the cnidarian–bilaterian evolutionary split. This expansion of more than 20 peptidergic systems in the stem leading to the Bilateria predates the evolution of complex nephrozoan organs and nervous system architectures. From this ancient set of neuropeptides, acoels show frequent losses that correlate with their divergent central nervous system anatomy. We furthermore detected the emergence of novel neuropeptides in xenacoelomorphs and their expansion along the nemertodermatid and acoel lineages, the two clades that evolved nervous system condensations. Together, our study provides fundamental insights into the early evolution of the bilaterian peptidergic systems, which will guide future functional and comparative studies of bilaterian nervous systems.
AbstractAmong mammals, several lineages have independently adapted to a subterranean niche and possess similar phenotypic traits for burrowing (e.g., cylindrical bodies, short limbs, and absent pinnae). Previous research on mole-rats has revealed molecular adaptations for coping with reduced oxygen, elevated carbon dioxide, and the absence of light. In contrast, almost nothing is known regarding molecular adaptations in other subterranean lineages (e.g., true moles and golden moles). Therefore, the extent to which the recurrent phenotypic adaptations of divergent subterranean taxa have arisen via parallel routes of molecular evolution remains untested. To address these issues, we analyzed ∼8,000 loci in 15 representative subterranean taxa of four independent transitions to an underground niche for signatures of positive selection and convergent amino acid substitutions. Complementary analyses were performed in nonsubterranean "control" taxa to assess the biological significance of results. We found comparable numbers of positively selected genes in each of the four subterranean groups; however, correspondence in terms of gene identity between gene sets was low. Furthermore, we did not detect evidence of more convergent amino acids among subterranean species pairs compared with levels found between nonsubterranean controls. Comparisons with nonsubterranean taxa also revealed loci either under positive selection or with convergent substitutions, with similar functional enrichment (e.g., cell adhesion, immune response, and coagulation). Given the limited indication that positive selection and convergence occurred in the same loci, we conclude that selection may have acted on different loci across subterranean mammal lineages to produce similar phenotypes.
Joana Isabel Meier, David Alexander Marques, Catherine Elise Wagner, Laurent Excoffier, and Ole Seehausen
AbstractDeep coalescence and introgression make it challenging to infer phylogenetic relationships among closely related species that arose through radiative speciation events. Despite numerous phylogenetic analyses and the availability of whole genomes, the phylogeny in the Anopheles gambiae species complex has not been confidently resolved. Here we extract over 80, 000 coding and noncoding short segments (called loci) from the genomes of six members of the species complex and use a Bayesian method under the multispecies coalescent model to infer the species tree, which takes into account genealogical heterogeneity across the genome and uncertainty in the gene trees. We obtained a robust estimate of the species tree from the distal region of the X chromosome: (A. merus, ((A. melas, (A. arabiensis, A. quadriannulatus)), (A. gambiae, A. coluzzii))), with A. merus to be the earliest branching species. This species tree agrees with the chromosome inversion phylogeny and provides a parsimonious interpretation of inversion and introgression events. Simulation informed by the real data suggest that the coalescent approach is reliable while the sliding-window analysis used in a previous phylogenomic study generates artifactual species trees. Likelihood ratio test of gene flow revealed strong evidence of autosomal introgression from A. arabiensis into A. gambiae (at the average rate of ∼0.2 migrants per generation), but not in the opposite direction, and introgression of the 3 L chromosomal region from A. merus into A. quadriannulatus. Our results highlight the importance of accommodating incomplete lineage sorting and introgression in phylogenomic analyses of species that arose through recent radiative speciation events.
AbstractOverlapping genes in viruses maximize the coding capacity of their genomes and allow the generation of new genes without major increases in genome size. Despite their importance, the evolution and function of overlapping genes are often not well understood, in part due to difficulties in their detection. In addition, most bioinformatic approaches for the detection of overlapping genes require the comparison of multiple genome sequences that may not be available in metagenomic surveys of virus biodiversity. We introduce a simple new method for identifying candidate functional overlapping genes using single virus genome sequences. Our method uses randomization tests to estimate the expected length of open reading frames and then identifies overlapping open reading frames that significantly exceed this length and are thus predicted to be functional. We applied this method to 2548 reference RNA virus genomes and find that it has both high sensitivity and low false discovery for genes that overlap by at least 50 nucleotides. Notably, this analysis provided evidence for 29 previously undiscovered functional overlapping genes, some of which are coded in the antisense direction suggesting there are limitations in our current understanding of RNA virus replication.
AbstractTransposable elements (TEs) contribute to a large fraction of the expansion of many eukaryotic genomes due to the capability of TEs duplicating themselves through transposition. A first step to understanding the roles of TEs in a eukaryotic genome is to characterize the population-wide variation of TE insertions in the species. Here, we present a maximum-likelihood (ML) method for estimating allele frequencies and detecting selection on TE insertions in a diploid population, based on the genotypes at TE insertion sites detected in multiple individuals sampled from the population using paired-end (PE) sequencing reads. Tests of the method on simulated data show that it can accurately estimate the allele frequencies of TE insertions even when the PE sequencing is conducted at a relatively low coverage (=5X). The method can also detect TE insertions under strong selection, and the detection ability increases with sample size in a population, although a substantial fraction of actual TE insertions under selection may be undetected. Application of the ML method to genomic sequencing data collected from a natural Daphnia pulex population shows that, on the one hand, most (>90%) TE insertions present in the reference D. pulex genome are either fixed or nearly fixed (with allele frequencies >0.95); on the other hand, among the nonreference TE insertions (i.e., those detected in some individuals in the population but absent from the reference genome), the majority (>70%) are still at low frequencies (<0.1). Finally, we detected a substantial fraction (∼9%) of nonreference TE insertions under selection.
AbstractUnderstanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. The essential function of many proteins that fold into a specific structure is their ability to bind to a ligand, which can be assayed for thousands of mutated variants. However, binding assays do not distinguish whether mutations affect the stability of the binding interface or the overall fold. Here, we introduce a statistical method to infer a detailed energy landscape of how a protein folds and binds to a ligand by combining information from many mutated variants. We fit a thermodynamic model describing the bound, unbound, and unfolded states to high quality data of protein G domain B1 binding to IgG-Fc. We infer distinct folding and binding energies for each mutation providing a detailed view of how mutations affect binding and stability across the protein. We accurately infer the folding energy of each variant in physical units, validated by independent data, whereas previous high-throughput methods could only measure indirect changes in stability. While we assume an additive sequence–energy relationship, the binding fraction is epistatic due its nonlinear relation to energy. Despite having no epistasis in energy, our model explains much of the observed epistasis in binding fraction, with the remaining epistasis identifying conformationally dynamic regions.
AbstractThe rate of recombination impacts on rates of protein evolution for at least two reasons: it affects the efficacy of selection due to linkage and influences sequence evolution through the process of GC-biased gene conversion (gBGC). We studied how recombination, via gBGC, affects inferences of selection in gene sequences using comparative genomic and population genomic data from the collared flycatcher (Ficedula albicollis). We separately analyzed different mutation categories ("strong"-to-"weak," "weak-to-strong," and GC-conservative changes) and found that gBGC impacts on the distribution of fitness effects of new mutations, and leads to that the rate of adaptive evolution and the proportion of adaptive mutations among nonsynonymous substitutions are underestimated by 22–33%. It also biases inferences of demographic history based on the site frequency spectrum. In light of this impact, we suggest that inferences of selection (and demography) in lineages with pronounced gBGC should be based on GC-conservative changes only. Doing so, we estimate that 10% of nonsynonymous mutations are effectively neutral and that 27% of nonsynonymous substitutions have been fixed by positive selection in the flycatcher lineage. We also find that gene expression level, sex-bias in expression, and the number of protein–protein interactions, but not Hill–Robertson interference (HRI), are strong determinants of selective constraint and rate of adaptation of collared flycatcher genes. This study therefore illustrates the importance of disentangling the effects of different evolutionary forces and genetic factors in interpretation of sequence data, and from that infer the role of natural selection in DNA sequence evolution.
AbstractThe Shine–Dalgarno (SD) sequence motif facilitates translation initiation and is frequently found upstream of bacterial start codons. However, thousands of instances of this motif occur throughout the middle of protein coding genes in a typical bacterial genome. Here, we use comparative evolutionary analysis to test whether SD sequences located within genes are functionally constrained. We measure the conservation of SD sequences across Enterobacteriales, and find that they are significantly less conserved than expected. Further, the strongest SD sequences are the least conserved whereas we find evidence of conservation for the weakest possible SD sequences given amino acid constraints. Our findings indicate that most SD sequences within genes are likely to be deleterious and removed via selection. To illustrate the origin of these deleterious costs, we show that ATG start codons are significantly depleted downstream of SD sequences within genes, highlighting the constraint that these sequences impose on the surrounding nucleotides to minimize the potential for erroneous translation initiation.
AbstractGene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique functional interactions. Phylogenetic analysis of the catalytic region indicates positive selection on one paralog following duplication, consistent with retention via neofunctionalization. Positive selection on residue pairs that are predicted to interact between subunits suggests that paralogous subunits have evolved specific assembly partners. Additional Pol subunits as well as Pol-interacting proteins also possess grass-specific paralogs, supporting the hypothesis that a novel Pol complex with distinct function has evolved in the grass family, Poaceae.
AbstractViral genome integration provides a complex route to biological innovation that has rarely but repeatedly occurred in one of the most diverse lineages of organisms on the planet, parasitoid wasps. We describe a novel endogenous virus in braconid wasps derived from pathogenic alphanudiviruses. Limited to a subset of the genus Fopius, this recent acquisition allows an unprecedented opportunity to examine early endogenization events. Massive amounts of virus-like particles (VLPs) are produced in wasp ovaries. Unlike most endogenous viruses of parasitoid wasps, the VLPs do not contain DNA, translating to major differences in parasitism-promoting strategies. Rapid changes include genomic rearrangement, loss of DNA processing proteins, and wasp control of viral gene expression. These events precede the full development of tissue-specific viral gene expression observed in older associations. These data indicate that viral endogenization can rapidly result in functional and evolutionary changes associated with genomic novelty and adaptation in parasitoids.
AbstractThe multispecies coalescent provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories. The Bayesian program BPP includes a full-likelihood implementation of the multispecies coalescent, using transmodel Markov chain Monte Carlo to calculate the posterior probabilities of different species trees. BPP is suitable for analyzing multilocus sequence data sets and it accommodates the heterogeneity of gene trees (both the topology and branch lengths) among loci and gene tree uncertainties due to limited phylogenetic information at each locus. Here, we provide a practical guide to the use of BPP in species tree estimation. BPP is a command-line program that runs on linux, macosx, and windows. This protocol shows how to use both BPP 3.4 (http://abacus.gene.ucl.ac.uk/software/) and BPP 4.0 (https://github.com/bpp/).
AbstractExpression of transposable elements (TE) is transiently activated during human preimplantation embryogenesis in a developmental stage- and cell type-specific manner and TE-mediated epigenetic regulation is intrinsically wired in developmental genetic networks in human embryos and embryonic stem cells. However, there are no systematic studies devoted to a comprehensive analysis of the TE transcriptome in human adult organs and tissues, including human neural tissues. To investigate TE expression in the human Dorsolateral Prefrontal Cortex (DLPFC), we developed and validated a straightforward analytical approach to chart quantitative genome-wide expression profiles of all annotated TE loci based on unambiguous mapping of discrete TE-encoded transcripts using a de novo assembly strategy. To initially evaluate the potential regulatory impact of DLPFC-expressed TE, we adopted a comparative evolutionary genomics approach across humans, primates, and rodents to document conservation patterns, lineage-specificity, and colocalizations with transcription factor binding sites mapped within primate- and human-specific TE. We identified 654,665 transcripts expressed from 477,507 distinct loci of different TE classes and families, the majority of which appear to have originated from primate-specific sequences. We discovered 4,687 human-specific and transcriptionally active TEs in DLPFC, of which the prominent majority (80.2%) appears spliced. Our analyses revealed significant associations of DLPFC-expressed TE with primate- and human-specific transcription factor binding sites, suggesting potential cross-talks of concordant regulatory functions. We identified 1,689 TEs differentially expressed in the DLPFC of Schizophrenia patients, a majority of which is located within introns of 1,137 protein-coding genes. Our findings imply that identified DLPFC-expressed TEs may affect human brain structures and functions following different evolutionary trajectories. On one side, hundreds of thousands of TEs maintained a remarkably high conservation for ∼8 My of primates' evolution, suggesting that they are likely conveying evolutionary-constrained primate-specific regulatory functions. In parallel, thousands of transcriptionally active human-specific TE loci emerged more recently, suggesting that they could be relevant for human-specific behavioral or cognitive functions.
AbstractTranscriptome-based exon capture methods provide an approach to recover several hundred markers from genomic DNA, allowing for robust phylogenetic estimation at deep timescales. We applied this method to a highly diverse group of venomous marine snails, Conoidea, for which published phylogenetic trees remain mostly unresolved for the deeper nodes. We targeted 850 protein coding genes (678,322 bp) in ca. 120 samples, spanning all (except one) known families of Conoidea and a broad selection of non-Conoidea neogastropods. The capture was successful for most samples, although capture efficiency decreased when DNA libraries were of insufficient quality and/or quantity (dried samples or low starting DNA concentration) and when targeting the most divergent lineages. An average of 75.4% of proteins was recovered, and the resulting tree, reconstructed using both supermatrix (IQ-tree) and supertree (Astral-II, combined with the Weighted Statistical Binning method) approaches, are almost fully supported. A reconstructed fossil-calibrated tree dates the origin of Conoidea to the Lower Cretaceous. We provide descriptions for two new families. The phylogeny revealed in this study provides a robust framework to reinterpret changes in Conoidea anatomy through time. Finally, we used the phylogeny to test the impact of the venom gland and radular type on diversification rates. Our analyses revealed that repeated losses of the venom gland had no effect on diversification rates, while families with a breadth of radula types showed increases in diversification rates, thus suggesting that trophic ecology may have an impact on the evolution of Conoidea.
AbstractBats are excellent models for studying the molecular basis of sensory adaptation. In Chiroptera, a sensory trade-off has been proposed between the visual and auditory systems, though the extent of this association has yet to be fully examined. To investigate whether variation in visual performance is associated with echolocation, we experimentally assayed the dim-light visual pigment rhodopsin from bat species with differing echolocation abilities. While spectral tuning properties were similar among bats, we found that the rate of decay of their light-activated state was significantly slower in a nonecholocating bat relative to species that use distinct echolocation strategies, consistent with a sensory trade-off hypothesis. We also found that these rates of decay were remarkably slower compared with those of other mammals, likely indicating an adaptation to dim light. To examine whether functional changes in rhodopsin are associated with shifts in selection intensity upon bat Rh1 sequences, we implemented selection analyses using codon-based likelihood clade models. While no shifts in selection were identified in response to diverse echolocation abilities of bats, we detected a significant increase in the intensity of evolutionary constraint accompanying the diversification of Chiroptera. Taken together, this suggests that substitutions that modulate the stability of the light-activated rhodopsin state were likely maintained through intensified constraint after bats diversified, being finely tuned in response to novel sensory specializations. Our study demonstrates the power of combining experimental and computational approaches for investigating functional mechanisms underlying the evolution of complex sensory adaptations.
AbstractViral evolutionary pathways are determined by the fitness landscape, which maps viral genotype to fitness. However, a quantitative description of the landscape and the evolutionary forces on it remain elusive. Here, we apply a biophysical fitness model based on capsid folding stability and antibody binding affinity to predict the evolutionary pathway of norovirus escaping a neutralizing antibody. The model is validated by experimental evolution in bulk culture and in a drop-based microfluidics that propagates millions of independent small viral subpopulations. We demonstrate that along the axis of binding affinity, selection for escape variants and drift due to random mutations have the same direction, an atypical case in evolution. However, along folding stability, selection and drift are opposing forces whose balance is tuned by viral population size. Our results demonstrate that predictable epistatic tradeoffs between molecular traits of viral proteins shape viral evolution.
AbstractManaging the emergence and spread of crop pests and pathogens is essential for global food security. Understanding how organisms have adapted to their native climate is key to predicting the impact of climate change. The potato cyst nematodes Globodera pallida and G. rostochiensis are economically important plant pathogens that cause yield losses of up to 50% in potato. The two species have different thermal optima that may relate to differences in the altitude of their regions of origin in the Andes. Here, we demonstrate that juveniles of G. pallida are less able to recover from heat stress than those of G. rostochiensis. Genome-wide analysis revealed that while both Globodera species respond to heat stress by induction of various protective heat-inducible genes, G. pallida experiences heat stress at lower temperatures. We use C. elegans as a model to demonstrate the dependence of the heat stress response on expression of Heat Shock Factor-1 (HSF-1). Moreover, we show that hsp-110 is induced by heat stress in G. rostochiensis, but not in the less thermotolerant G. pallida. Sequence analysis revealed that this gene and its promoter was duplicated in G. rostochiensis and acquired thermoregulatory properties. We show that hsp-110 is required for recovery from acute thermal stress in both C. elegans and in G. rostochiensis. Our findings point towards an underlying molecular mechanism that allows the differential expansion of one species relative to another closely related species under current climate change scenarios. Similar mechanisms may be true of other invertebrate species with pest status.
AbstractThe mutation rate of an organism is influenced by the interaction of evolutionary forces such as natural selection and genetic drift. However, the mutation spectrum (i.e., the frequency distribution of different types of mutations) can be heavily influenced by DNA repair. Using mutation-accumulation lines of the extremophile bacterium Deinococcus radiodurans ΔmutS1 and the model soil bacterium Pseudomonas fluorescens wild-type and MMR− (Methyl-dependent Mismatch Repair-deficient) strains, we report the mutational features of these two important bacteria. We find that P. fluorescens has one of the highest MMR repair efficiencies among tested bacteria. We also discover that MMR of D. radiodurans preferentially repairs deletions, contrary to all other bacteria examined. We then, for the first time, quantify genome-wide efficiency and specificity of MMR in repairing different genomic regions and mutation types, by evaluating the P. fluorescens and D. radiodurans mutation data sets, along with previously reported ones of Bacillus subtilis subsp. subtilis, Escherichia coli, Vibrio cholerae, and V. fischeri. MMR in all six bacteria shares two general features: 1) repair efficiency is influenced by the neighboring base composition for both transitions and transversions, not limited to transversions as previously reported; and 2) MMR only recognizes indels <4 bp in length. This study demonstrates the power of mutation accumulation lines in quantifying DNA repair and mutagenesis patterns.
AbstractThe heterochromatic genome compartment mediates strictly conserved cellular processes such as chromosome segregation, telomere integrity, and genome stability. Paradoxically, heterochromatic DNA sequence is wildly unconserved. Recent reports that many hybrid incompatibility genes encode heterochromatin proteins, together with the observation that interspecies hybrids suffer aberrant heterochromatin-dependent processes, suggest that heterochromatic DNA packaging requires species-specific innovations. Testing this model of coevolution between fast-evolving heterochromatic DNA and its packaging proteins begins with defining the latter. Here we describe many such candidates encoded by the Heterochromatin Protein 1 (HP1) gene family across Diptera, an insect Order that encompasses dramatic episodes of heterochromatic sequence turnover. Using BLAST, synteny analysis, and phylogenetic tree building across 64 Diptera genomes, we discovered a staggering 121 HP1 duplication events. In contrast, we observed virtually no gene duplication in gene families that share a common "chromodomain" with HP1s, including Polycomb and Su(var)3-9. The remarkably high number of Dipteran HP1 paralogs arises from distant clades undergoing convergent HP1 family amplifications. These independently derived, young HP1s span diverse ages, domain structures, and rates of molecular evolution, including episodes of positive selection. Moreover, independently derived HP1s exhibit convergent expression evolution. While ancient HP1 parent genes are transcribed ubiquitously, young HP1 paralogs are transcribed primarily in male germline tissue, a pattern typical of young genes. Pervasive gene youth, rapid evolution, and germline specialization implicate heterochromatin-encoded selfish elements driving recurrent HP1 gene family expansions. The 121 young genes offer valuable experimental traction for elucidating the germline processes shaped by Diptera's many dramatic episodes of heterochromatin turnover.
Nature provides countless examples of evolutionary arms races, in which species develop adaptations and counter-adaptations in a struggle for survival and reproduction. Such arms races are common between predator and prey or between parasite and host. Understanding this coevolutionary process can aid in our ability to develop necessary countermeasures, such as overcoming bacterial resistance to antibiotics.
AbstractGene duplication and loss contribute to gene content differences as well as phenotypic divergence across species. However, the extent to which gene content varies among closely related plant species and the factors responsible for such variation remain unclear. Here, using the Solanaceae family as a model and Pfam domain families as a proxy for gene families, we investigated variation in gene family sizes across species and the likely factors contributing to the variation. We found that genes in highly variable families have high turnover rates and tend to be involved in processes that have diverged between Solanaceae species, whereas genes in low-variability families tend to have housekeeping roles. In addition, genes in high- and low-variability gene families tend to be duplicated by tandem and whole genome duplication, respectively. This finding together with the observation that genes duplicated by different mechanisms experience different selection pressures suggest that duplication mechanism impacts gene family turnover. We explored using pseudogene number as a proxy for gene loss but discovered that a substantial number of pseudogenes are actually products of pseudogene duplication, contrary to the expectation that most plant pseudogenes are remnants of once-functional duplicates. Our findings reveal complex relationships between variation in gene family size, gene functions, duplication mechanism, and evolutionary rate. The patterns of lineage-specific gene family expansion within the Solanaceae provide the foundation for a better understanding of the genetic basis underlying phenotypic diversity in this economically important family.
AbstractEndogenous viral sequences in eukaryotic genomes, such as those derived from plant pararetroviruses (PRVs), can serve as genomic fossils to study viral macroevolution. Many aspects of viral evolutionary rates are heterogeneous, including substitution rate differences between genes. However, the evolutionary dynamics of this viral gene rate heterogeneity (GRH) have been rarely examined. Characterizing such GRH may help to elucidate viral adaptive evolution. In this study, based on robust phylogenetic analysis, we determined an ancient endogenous PRV group in Oryza genomes in the range of being 2.41–15.00 Myr old. We subsequently used this ancient endogenous PRV group and three younger groups to estimate the GRH of PRVs. Long-term substitution rates for the most conserved gene and a divergent gene were 2.69 × 10−8 to 8.07 × 10−8 and 4.72 × 10−8 to 1.42 × 10−7 substitutions/site/year, respectively. On the basis of a direct comparison, a long-term GRH of 1.83-fold was identified between these two genes, which is unexpectedly low and lower than the short-term GRH (>3.40-fold) of PRVs calculated using published data. The lower long-term GRH of PRVs was due to the slightly faster rate decay of divergent genes than of conserved genes during evolution. To the best of our knowledge, we quantified for the first time the long-term GRH of viral genes using paleovirological analyses, and proposed that the GRH of PRVs might be heterogeneous on time scales (time-dependent GRH). Our findings provide special insights into viral gene macroevolution and should encourage a more detailed examination of the viral GRH.
AbstractVitellogenin (Vtg) is a glycolipophosphoprotein produced by oviparous and ovoviviparous species and is the precursor protein of the yolk, an essential nutrient reserve for embryonic development and early larval stages. Vtg is encoded by a family of paralog genes whose number varies in the different vertebrate lineages. Its evolution has been the subject of considerable analyses but it remains still unclear. In this work, microsyntenic and phylogenetic analyses were performed in order to increase our knowledge on the evolutionary history of this gene family in vertebrates. Our results support the hypothesis that the vitellogenin gene family is expanded from two genes both present at the beginning of vertebrate radiation through multiple independent duplication events occurred in the diverse lineages.
AbstractIt is often unavoidable to combine data from different sequencing centers or sequencing platforms when compiling data sets with a large number of individuals. However, the different data are likely to contain specific systematic errors that will appear as SNPs. Here, we devise a method to detect systematic errors in combined data sets. To measure quality differences between individual genomes, we study pairs of variants that reside on different chromosomes and co-occur in individuals. The abundance of these pairs of variants in different genomes is then used to detect systematic errors due to batch effects. Applying our method to the 1000 Genomes data set, we find that coding regions are enriched for errors, where ∼1% of the higher frequency variants are predicted to be erroneous, whereas errors outside of coding regions are much rarer (<0.001%). As expected, predicted errors are found less often than other variants in a data set that was generated with a different sequencing technology, indicating that many of the candidates are indeed errors. However, predicted 1000 Genomes errors are also found in other large data sets; our observation is thus not specific to the 1000 Genomes data set. Our results show that batch effects can be turned into a virtue by using the resulting variation in large scale data sets to detect systematic errors.
AbstractChlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.0–3.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesize themselves. The Chlamydiae is a phylum with a very wide host range spanning mammals, birds, fish, invertebrates, and unicellular protists. This ecological and phylogenetic diversity offers ongoing opportunities to study intracellular survival and metabolic pathways and adaptations. Of particular evolutionary significance are Chlamydiae from the recently proposed Ca. Parilichlamydiaceae, the earliest diverging clade in this phylum, species of which are found only in aquatic vertebrates. Gill extracts from three Chlamydiales-positive Australian aquaculture species (Yellowtail kingfish, Striped trumpeter, and Barramundi) were subject to DNA preparation to deplete host DNA and enrich microbial DNA, prior to metagenome sequencing. We assembled chlamydial genomes corresponding to three Ca. Parilichlamydiaceae species from gill metagenomes, and conducted functional genomics comparisons with diverse members of the phylum. This revealed highly reduced genomes more similar in size to the terrestrial Chlamydiaceae, standing in contrast to members of the Chlamydiae with a demonstrated cosmopolitan host range. We describe a reduction in genes encoding synthesis of nucleotides and amino acids, among other nutrients, and an enrichment of predicted transport proteins. Ca. Parilichlamydiaceae share 342 orthologs with other chlamydial families. We hypothesize that the genome reduction exhibited by Ca. Parilichlamydiaceae and Chlamydiaceae is an example of within-phylum convergent evolution. The factors driving these events remain to be elucidated.
AbstractPrediction of evolutionary trajectories has been an elusive goal, requiring a deep knowledge of underlying mechanisms that relate genotype to phenotype plus understanding how phenotype impacts organismal fitness. We tested our ability to predict molecular regulatory evolution in a bacteriophage (T7) whose RNA polymerase (RNAP) was altered to recognize a heterologous promoter differing by three nucleotides from the wild-type promoter. A mutant of wild-type T7 lacking its RNAP gene was passaged on a bacterial strain providing the novel RNAP in trans. Higher fitness rapidly evolved. Predicting the evolutionary trajectory of this adaptation used measured in vitro transcription rates of the novel RNAP on the six promoter sequences capturing all possible one-step pathways between the wild-type and the heterologous promoter sequences. The predictions captured some of the regulatory evolution but failed both in explaining 1) a set of T7 promoters that consistently failed to evolve and 2) some promoter evolution that fell outside the expected one-step pathways. Had a more comprehensive set of transcription assays been undertaken initially, all promoter evolution would have fallen within predicted bounds, but the lack of evolution in some promoters is unresolved. Overall, this study points toward the increasing feasibility of predicting evolution in well-characterized, simple systems.
AbstractThe Lennoaceae, a small monophyletic plant family of root parasites endemic to the Americas, are one of the last remaining independently evolved lineages of parasitic angiosperms lacking a published plastome. In this study, we present the assembled and annotated plastomes of two species spanning the crown node of Lennoaceae, Lennoa madreporoides and Pholisma arenarium, as well as their close autotrophic relative from the sister family Ehretiaceae, Tiquilia plicata. We find that the plastomes of L. madreporoides and P. arenarium are similar in size and gene content, and substantially reduced compared to T. plicata, consistent with trends seen in other holoparasitic lineages. In particular, most plastid genes involved in photosynthesis function have been lost, whereas housekeeping genes (ribosomal protein-coding genes, rRNAs, and tRNAs) are retained. One notable exception is the persistence of a rbcL open reading frame in P. arenarium but not L. madreporoides suggesting a nonphotosynthetic function for this gene. Of the retained coding genes, dN/dS ratios indicate that some remain under purifying selection, whereas others show relaxed selection. Overall, this study supports the mounting evidence for convergent plastome evolution in flowering plants following the shift to heterotrophy.
AbstractFeather diversity is striking in many aspects. Although the development of feather has been studied for decades, genetic and genomic studies of feather diversity have begun only recently. Many questions remain to be answered by multidisciplinary approaches. In this review, we discuss three levels of feather diversity: Feather morphotypes, intraspecific variations, and interspecific variations. We summarize recent studies of feather evolution in terms of genetics, genomics, and developmental biology and provide perspectives for future research. Specifically, this review includes the following topics: 1) Diversity of feather morphotype; 2) feather diversity among different breeds of domesticated birds, including variations in pigmentation pattern, in feather length or regional identity, in feather orientation, in feather distribution, and in feather structure; and 3) diversity of feathers among avian species, including plumage color and morph differences between species and the regulatory differences in downy feather development between altricial and precocial birds. Finally, we discussed future research directions.
AbstractAphids are a diverse group of taxa that contain agronomically important species, which vary in their host range and ability to infest crop plants. The genome evolution underlying agriculturally important aphid traits is not well understood. We generated draft genome assemblies for two aphid species: Myzus cerasi (black cherry aphid) and the cereal specialist Rhopalosiphum padi. Using a de novo gene prediction pipeline on both these, and three additional aphid genome assemblies (Acyrthosiphon pisum, Diuraphis noxia, and Myzus persicae), we show that aphid genomes consistently encode similar gene numbers. We compare gene content, gene duplication, synteny, and putative effector repertoires between these five species to understand the genome evolution of globally important plant parasites. Aphid genomes show signs of relatively distant gene duplication, and substantial, relatively recent, gene birth. Putative effector repertoires, originating from duplicated and other loci, have an unusual genomic organization and evolutionary history. We identify a highly conserved effector pair that is tightly physically linked in the genomes of all aphid species tested. In R. padi, this effector pair is tightly transcriptionally linked and shares an unknown transcriptional control mechanism with a subset of ∼50 other putative effectors and secretory proteins. This study extends our current knowledge on the evolution of aphid genomes and reveals evidence for an as-of-yet unknown shared control mechanism, which underlies effector expression, and ultimately plant parasitism.
AbstractThe frequency of horizontal transfers of transposable elements (HTTs) varies among the types of elements according to the transposition mode and the geographical and temporal overlap of the species involved in the transfer. The drosophilid species of the genus Zaprionus and those of the melanogaster, obscura, repleta, and virilis groups of the genus Drosophila investigated in this study shared space and time at some point in their evolutionary history. This is particularly true of the subgenus Zaprionus and the melanogaster subgroup, which overlapped both geographically and temporally in Tropical Africa during their period of origin and diversification. Here, we tested the hypothesis that this overlap may have facilitated the transfer of retrotransposons without long terminal repeats (non-LTRs) between these species. We estimated the HTT frequency of the non-LTRs BS and Helena at the genome-wide scale by using a phylogenetic framework and a vertical and horizontal inheritance consistence analysis (VHICA). An excessively low synonymous divergence among distantly related species and incongruities between the transposable element and species phylogenies allowed us to propose at least four relatively recent HTT events of Helena and BS involving ancestors of the subgroup melanogaster and ancestors of the subgenus Zaprionus during their concomitant diversification in Tropical Africa, along with older possible events between species of the subgenera Drosophila and Sophophora. This study provides the first evidence for HTT of non-LTRs retrotransposons between Drosophila and Zaprionus, including an in-depth reconstruction of the time frame and geography of these events.
AbstractPlastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even between close relatives, the presence and location of these elements is widely variable when viewed in a phylogenetic context. We characterize these elements and refer to them collectively as Mobile Open Reading Frames in Fern Organelles (MORFFO). We further note that the presence of MORFFO is not restricted to Pteridaceae, but is found across ferns and other plant clades. MORFFO elements are regularly associated with inversions, intergenic expansions, and changes to the inverted repeats. They likewise appear to be present in mitochondrial and nuclear genomes of ferns, indicating that they can move between genomic compartments with relative ease. The origins and functions of these mobile elements are unknown, but MORFFO appears to be a major driver of structural genome evolution in the plastomes of ferns, and possibly other groups of plants.
AbstractThe transcriptome of the venom duct of the Atlantic piscivorous cone species Chelyconus ermineus (Born, 1778) was determined. The venom repertoire of this species includes at least 378 conotoxin precursors, which could be ascribed to 33 known and 22 new (unassigned) protein superfamilies, respectively. Most abundant superfamilies were T, W, O1, M, O2, and Z, accounting for 57% of all detected diversity. A total of three individuals were sequenced showing considerable intraspecific variation: each individual had many exclusive conotoxin precursors, and only 20% of all inferred mature peptides were common to all individuals. Three different regions (distal, medium, and proximal with respect to the venom bulb) of the venom duct were analyzed independently. Diversity (in terms of number of distinct members) of conotoxin precursor superfamilies increased toward the distal region whereas transcripts detected toward the proximal region showed higher expression levels. Only the superfamilies A and I3 showed statistically significant differential expression across regions of the venom duct. Sequences belonging to the alpha (motor cabal) and kappa (lightning-strike cabal) subfamilies of the superfamily A were mainly detected in the proximal region of the venom duct. The mature peptides of the alpha subfamily had the α4/4 cysteine spacing pattern, which has been shown to selectively target muscle nicotinic-acetylcholine receptors, ultimately producing paralysis. This function is performed by mature peptides having a α3/5 cysteine spacing pattern in piscivorous cone species from the Indo-Pacific region, thereby supporting a convergent evolution of piscivory in cones.
AbstractThis work presents a systematic approach to study the conservation of genes between fruit flies and mammals. We have listed 971 Drosophila genes involved in female reproduction at the ovarian level and systematically looked for orthologs in the Ciona, zebrafish, coelacanth, lizard, chicken, and mouse. Depending on the species, the percentage of these Drosophila genes with at least one ortholog varies between 69% and 78%. In comparison, only 42% of all the Drosophila genes have an ortholog in the mouse genome (P < 0.0001), suggesting a dramatically higher evolutionary conservation of ovarian genes. The 177 Drosophila genes that have no ortholog in mice and other vertebrates correspond to genes that are involved in mechanisms of oogenesis that are specific to the fruit fly or the insects. Among 759 genes with at least one ortholog in the zebrafish, 73 have an expression enriched in the ovary in this species (RNA-seq data). Among 760 genes that have at least one ortholog in the mouse; 76 and 11 orthologs are reported to be preferentially and exclusively expressed in the mouse ovary, respectively (based on the UniGene expressed sequence tag database). Several of them are already known to play a key role in murine oogenesis and/or to be enriched in the mouse/zebrafish oocyte, whereas others have remained unreported. We have investigated, by RNA-seq and real-time quantitative PCR, the exclusive ovarian expression of 10 genes in fish and mammals. Overall, we have found several novel candidates potentially involved in mammalian oogenesis by an evolutionary approach and using the fruit fly as an animal model.


text:
Nick Piggott (Chairperson, RadioDNS, Bristol, UK)
Michael Hill (Managing Director, UK Radioplayer, London, UK)
Andy Buckingham (Creative Technologist, Global Radio, Bristol, UK)
Sebastian Kett (Consulting Engineer, SWR, Germany)
Tobias Wallerius (Hardware Architect, Visteon, Germany)
With hybrid radio, your radio is getting cleverer. From additional visuals in the kitchen to cars that never lose the signal of your station, we look at the future of how your radio looks: and discover broadcasters who are doing hybrid radio now on a variety of devices.
Scooped by
Nicolas Moulard - Actuonda
onto Radio 2.0 (En & Fr)

subset: commoncrawl


text:
Expedia-Verified Reviews
Don't miss out on a lower price on this hotel
Get an overview of this hotelFamily-friendly hotel with 2 restaurants and full-service spa
Popular property highlights
This family-friendly Beverly Hills hotel is located in the historical district, within 1 mi (2 km) of Rodeo Drive and Century City. Melrose Avenue and Whiskey a Go Go are also within 2 mi (3 km).
Hotel Features
2 restaurants, a full-service spa, and an outdoor pool are available at this hotel. Free WiFi in public areas and a free area shuttle are also provided. Additionally, a 24-hour fitness center, a bar/lounge, and a poolside bar are onsite.
Room Amenities
All 208 soundproofed rooms feature free WiFi and MP3 docks. Plasma TVs with satellite channels and DVD players provide a bit of entertainment, and guests will also appreciate thoughtful touches like bathrobes and slippers.
Languages Spoken
- English
The Beverly Hills Hotel
Hotel Amenities
Hotel Amenities
In addition to a full-service spa, The Beverly Hills Hotel features an outdoor pool and a spa tub. Dining is available at one of the hotel's 2 restaurants and guests can grab coffee at the coffee shop/café. Guests can unwind with a drink at one of the hotel's bars, which include a poolside bar and a bar/lounge. A computer station is located on site and wireless Internet access is complimentary.
Business amenities at this 5-star property consist of a 24-hour business center, limo/town car service, and meeting rooms. Event facilities measuring 22000 square feet (2044 square meters) include a conference center. This Art Deco hotel also offers a 24-hour fitness center, a sauna, and spa services. A complimentary area shuttle within 5.00 mi is available for guests. Parking is available onsite for a surcharge.
- Express check-in
- Bar/lounge
- Elevator/lift
- 24-hour front desk
- Poolside bar
- Porter/bellhop
- Express check-out
- Dry cleaning/laundry service
- Outdoor pool
- Limo or Town Car service available
- Valet parking (surcharge)
- Computer station
- Conference space size (meters) - 2044
- Terrace
- Luggage storage
- Hair salon
- ATM/banking
- Concierge services
- Gift shops or newsstand
- Conference center
- Shopping on site
- Pool umbrellas
- Total number of rooms - 208
- Number of floors - 4
- Fireplace in lobby
- Full-service spa
- Conference space
- Spa treatment room(s)
- Tours/ticket assistance
- Meeting rooms 5
- Pool cabanas (surcharge)
- Year Built 1912
- Coffee shop or café
- Free WiFi
- Pool sun loungers
- Steam room
- Babysitting or childcare (free)
- Sauna
- Safe-deposit box at front desk
- Free area shuttle
- Spa services on site
- Breakfast available (surcharge)
- Number of restaurants - 2
- 24-hour business center
- Conference space size (feet) - 22000
- Laundry facilities
- Spa tub
- 24-hour fitness facilities
- Wedding services
- Garden
- Multilingual staff
Available in all rooms: Free WiFi
Available in some public areas: Free WiFi
Languages Spoken
- English
- Filipino
- French
- German
- Italian
- Portuguese
- Spanish
Valet parking (surcharge)
Room Amenities
- Premium TV channels
- DVD player
- Pay movies
- Video-game console
- Premium bedding
- Hypo-allergenic bedding available
- Air conditioning
- Free newspaper
- In-room climate control (air conditioning)
- Soundproofed rooms
- Phone
- Minibar
- Free bottled water
- Microwave (on request)
- Refrigerator (on request)
- Daily housekeeping
- Turndown service
- Private bathroom
- Bathrobes
- Free toiletries
- Hair dryer
- Separate bathtub and shower
- In-room massage available
- Slippers
- In-room childcare (surcharge)
- Satellite TV service
- Iron/ironing board
- In-room safe
- Desk
- Number of bathrooms -
- Free WiFi
- MP3 docking station
- Blackout drapes/curtains
- Room service (24 hours)
- Connecting/adjoining rooms available
- Free cribs/infant beds
- Individually furnished
- Individually decorated
- Plasma TV
Where to Eat
Full breakfasts are available for a surcharge and are served each morning between 6 AM and 10:30 AM.
The Polo Lounge - Overlooking the garden, this restaurant specializes in American cuisine and serves breakfast, brunch, lunch, and dinner. Guests can order drinks at the bar and enjoy alfresco dining (weather permitting). A children's menu is available. Open daily.
The Cabana Café - This poolside restaurant specializes in American cuisine and serves breakfast, brunch, lunch, and light fare. Guests can order drinks at the bar and enjoy alfresco dining (weather permitting). A children's menu is available. Open daily.
Bar Nineteen12 - Overlooking the garden, this bar serves dinner and light fare. Guests can enjoy alfresco dining (weather permitting). Open select days.
Fountain Coffee Room - This diner specializes in American cuisine and serves breakfast, brunch, lunch, and light fare. A children's menu is available. Open daily.
24-hour room service is available.
Nearby Things to Do
An outdoor pool and a spa tub are on site. Other recreational amenities include a sauna and a 24-hour fitness center.
The recreational activities listed below are available either on site or nearby; fees may apply.
- Game viewing nearby
- Water skiing nearby
- Golfing nearby
- Snorkeling nearby
- Rock climbing nearby
- Surfing/boogie boarding nearby
- Mountain biking nearby
- Skydiving nearby
- Windsurfing nearby
- Bicycle rentals nearby
- Boat tours nearby
- Segway rental/tour nearby
- Hiking/biking trails nearby
- Golf lessons available nearby
- Kayaking nearby
- Sailing nearby
- Scooter/moped rentals nearby
Spa Services
Beverly Hills Hotel Spa has 6 treatment rooms including rooms for couples and outdoor treatment areas. Services include deep-tissue massages, hot stone massages, sports massages, and Swedish massages. A variety of treatment therapies are provided, including aromatherapy. The spa is equipped with a sauna and a steam room.
The spa is open daily. Children under 18 years old are not allowed in the spa without adult supervision. Guests under 12 years old are not allowed in the spa.
- Number of treatment rooms 6
- Outdoor treatment areas
- Couples treatment rooms
- Manicures and pedicures
- Body wraps
- Body treatments
- Body scrubs
- Facial treatments
- Aromatherapy treatments
- Hot stone massage
- Deep tissue massage
- Swedish massage
- Prenatal massage
- Sauna in spa
- Steam room in spa
- Minimum age to access spa is 12
- Sports massage
- Detoxification wrap
- Massages
If you have requests for specific accessibility needs, please note them at check-out when you book your room.
- Accessible bathroom
- Roll-in shower
- In-room accessibility
Hotel Policies
Check-in time ends at 11 PM
Check-in time starts at 3 PM
Check-out time is noon
Payment types
Children and extra beds
- Children are welcome.
- Kids stay free! Children 12 years old and younger stay free when using existing bedding.
- Free cribs (infant beds)!
- Pets allowed for an extra charge of USD 35 per pet, per night
- Up to 35 lb
- Specific rooms only, restrictions apply
- Pet-friendly rooms can be requested by contacting the property at the number on the booking confirmation
You need to know
Extra-person charges may apply and vary depending on property policy.
Optional extras
- Breakfast fee: between USD 16 and USD 40 per person (approximately)
- Valet parking fee: USD 48.00 per night (in/out privileges)
- Pet fee: USD 35 per pet, per night
Hotel Name
- Beverly Hills Hotel
- Hotel Beverly Hills
- The Beverly Hills
- The Hotel Beverly Hills
We should mention
Reservations are required for massage services and spa treatments. Reservations can be made by contacting the hotel prior to arrival, using the contact information on the booking confirmation. Children 12 years old and younger stay free when occupying the parent or guardian's room, using existing bedding. The property has connecting/adjoining rooms, which are subject to availability and can be requested by contacting the property using the number on the booking confirmation. The property allows pets in specific rooms only and has other pet restrictions (surcharges apply and can be found in the Fees section). Guests can arrange to bring pets by contacting the property directly, using the contact information on the booking confirmation.
Awards & Affiliations
- The Beverly Hills Hotel is listed in the 2016 Condé Nast Traveler Top 100 List.


text:
I've started a massive SPAM purge, any accounts that have spammed are being removed, also for a short period new user signups are disallowed until the SPAM cleaning is finished.
Graphics and Design
Share Graphic and Design Suggestions
Discuss any issues with Dreamweaver
- Discussions:
- 25
Latest: Which do you like? Flash or Dreamweaver?? rajdeep, Sep 4, 2016
- Messages:
- 173
Website Design
Share any thoughts or ideas for Designs
- Discussions:
- 398
Latest: Need reliable Graphic design and Technical Support services Woodstock, Dec 5, 2017
- Messages:
- 1,768
Page 4 of 26
Thread Display Options
Page 4 of 26


text:
Fisher Cats rained out in Pa.
July 12. 2013 10:21PM
The Fisher Cats and the Reading Fightin' Phils were rained out in their attempt to play the second game of a four-game series at FirstEnergy Stadium on Friday night.
The game will be made up as part of a day-night, split-admission doubleheader on Saturday, Aug. 24, in Reading.
The teams will try again Saturday night at 7:05. Deck McGuire (4-7, 5.51) pitches for the Fisher Cats against Reading's Brody Colvin (3-2, 7.13).


text:
Dear Answer Angel: I really, really want to wear blue jeans to work. There's no prohibition against it, but on the other hand, no one does. Any thoughts on when/if they're appropriate?
Dear J.T.: OK, you "really, really want to wear blue jeans to work," but do you also really, really want to get promoted? Then don't wear jeans to the office. Just because there are no rules against it, if nobody is wearing them, then you shouldn't either — not if you want to advance at your company.
Remember that old adage that you should dress for the job you want, not the job you have. So check out your boss and dress up at least as much as he/she does. A lot of people are confused by "workplace casual," and with good reason. For some offices that does mean jeans are OK, but for others it means nice slacks or a dress/skirt for women; pressed trousers and a business shirt for men (in short, everything but a jacket and tie).
How to tell what's appropriate? Look around at the people who are getting ahead. Copy them.
Dear Answer Angel: I would like some advice on how to shop at an outlet mall.
Dear L.T.: Short answer: Cautiously. I love outlet mall shopping. But I think our usual tendency is to buy things that we don't need because they're a bargain. That is not a good way to save money.
Have you wondered if the stuff in the outlets is the leftovers that didn't sell at the regular retail shops? The answer is sometimes. But increasingly, the merchandise in outlets is created for those stores and was never sold in full-price places. The recession has changed our shopping habits, says expert David Ober, the president of an outlet mall trade group, the Council of Developers of Outlet Centers and Retailers. He says surveys show more than ever that those who formerly shopped only at department stores are also shopping the outlets.
Bottom line: If you see something you like at an outlet store, don't presume you can buy more later at a department store. And a savings tip: Before you start shopping — whether at a full-price or outlet mall — always go to the customer service desk and ask if they're offering any coupons or daily deals.
Dear Answer Angel: I have bought my last pair of prescription sunglasses. I just lost another pair, and I just can't afford the $400 it costs to replace them. What are my options? I'm blind without my prescription glasses.
— Glasses-less
Dear Glasses-less: A man I know lost one too many pairs of sunglasses over the years while out fishing. Now he buys sun flip-ups at clipons.com for $19.95. They come in many different lens colors and sizes to fit your regular clear prescription glasses. The downside is they look a little nerdy. The website also sells sun lenses that use four little clips to attach to most regular lenses. These are a little better looking and cost $24.95. A detailed measuring chart helps get the size right.
Dear Answer Angel: I've been working out a lot and couldn't figure out why I developed ugly back fat. I realized I went up a bra size because of developing my back muscles, and the fat was just the result of being squeezed into too-tight bras. So now I'm stuck with a collection of expensive sports bras and regular bras that don't fit. Is there a way to stretch them a little?
— Fitness Queen
Dear F.Q.: This is an easy, cheap fix. Type "bra extender" into your browser and you'll find a wide array of inexpensive two, three or four-hook gizmos that will enable you to add several inches to your bra band. I've tried them and they even stay on in the washing machine. Problem solved.
Dear Answer Angel: My son and his girlfriend were visiting me from out of town and went shopping. She purchased a dress and when she got home she realized the security tag was still on it. There's no branch of the store in her small town. What to do?
— Anne
Dear Anne: I had this precise problem a few years back. Since I wanted to wear the garment right away, I had to waste time going to several stores (with my receipt) trying to find a place that used the same sort of security tags (and therefore had the machinery to remove them). I did find a store that could remove the tag. But the other option is to call the place where she bought the dress, talk to a manager and arrange to send it back (asking the store to pay shipping since it wasn't her fault). Enclose a copy of the receipt (but keep the original). If no receipt, this will complicate things, but the store manager should be able to either trust you or tell you how to get a duplicate. Moral of the story: Always check that the security tag has been removed and save those receipts.
Reader rant
I'm confused and angry about the sizes of women's clothes! I am a 35-year-old woman who has remained the same weight for the past 15 years. But in the last few years, I have found that clothing brands that used to fit me well in a size small or extra-small now are too big on me. With all the vanity sizing I'm seeing now, it's impossible to tell what size I am. I used to wear size 10 pants and now sometimes I'm a 2. It's infuriating to go shopping these days. I have to take four sizes of the same thing into the dressing room just to make sure I'll have the right one to try on. And it's even worse ordering online and having to guess what size I am in this or that catalog. Is it the obesity epidemic that has led clothing makers to call a 10 a size 2 now? Why aren't sizes standard?
— Meg
Anybody besides me agree with Meg?


text:
yep pretty much ^^
The All American Rejects are bomb and u kno it!
ugh i hate waiting...
The Girl In Black.
Yeah... waiting is really such a troublesome task. But hey... there's a saying that 'good comes to those who wait', neh? XDD And now here's your monthly dose of YumePati manga.
Phoenix haven't translated recettes 24-26 because of her work but, she'll definitely get into it once she's free. So please wait for it people. And also... just take note: IF YOU HAVE NO IDEA WHAT HAPPENED BEFORE THIS CHAPTER, PLEASE CLICK PAGE 1 AND 2 OF THIS FORUM AND READ MY POSTS ABOUT THE OTHER CHAPTERS.
If you had paid attention to all the details up to recette 30, then continue reading to find out what happened in recette 31. ^^
Spoiler Alert! Click to show or hide
Alrighty then... so in the previous chapter, we had witnessed Amano's confession that she actually likes Kashino all this time, (finally, after so many chapters of denying >.>) though it wasn't said in front of Kashino. And that Vanilla actually has a boyfriend but she was separated from him because he was assigned somewhere else. It was quite surprising, right? No? Well, maybe my spoilers were at fault. XDD
Anyway, before recette 30 ended, the judges for the Salon de Marie competition came. Henri-sensei, Ameya-sensei, the chairman, the blue-haired male teacher (which I forgot what his name was) and the chairman of the France branch of St. Marie. Well, at least, that's what we all thought... ;)
This chapter started pretty normally. Andou and Hanabusa first doubted if they could really come inside, since they're outsiders. But, they eventually came inside anyway. When they came in, the judges were already tasting the sweets. The judges were very impressed with the taste and all that, but all throughout, only one guy didn't really became so happy. And do you know who that was?
That was the "chairman" of the France branch. He has black shaggy-looking hair with quite a curly mustache. He does resemble what the men used to look like in France in the old days. Ahem... >.> And his name is 'Arazan'. Hmm...
So, after awhile, the judges finally came to the last sweet which was: Amano's 'Lemon Moon'. The chairman thought it was very unique, Henri-sensei was quite intrigued by it, Ameya-sensei first thought that it only has an attractive appearance and the blue-haired teacher said that it fits the "has a fresh taste" criteria. And what about Arazan, you ask? Well, obviously, he didn't do much reaction. Instead, he insulted the abilities of the students, saying that they were very low leveled. Chocolat got mad at his statement. Cafe stopped her from doing anything violent and told her that he has seen that man somewhere before. And well... what do you know? Arazan was actually part of the Sweets Kingdom! A cabinet minister, in fact!
And so, since he was so disappointed with the level of the students, he decided to do something very horrible: FORCE (take note of that word) all the Sweets Spirits to return back to the Sweets Kingdom. Why? Well, to train all of the Sweets Spirits AGAIN, of course. And, as expected, the students doesn't want this to happen, especially Amano. Julian, being the prince of the Sweets Kingdom, ordered Arazan to stop but Arazan shove him away and created a magic white hole to take in ALL the Sweets Spirits in the area. For some strange reason, before all the Sweets Spirits disappeared, all of their magic spoons/forks and etc. were given to their individual human partners. And after that ordeal, Arazan just walked away. Heh... to think that he could SHOVE a PRINCE like that... what a rude man, eh?
SO... with all their Sweets Spirits gone, the students of St. Marie Academy became so gloomy. The school wasn't so fun for them anymore and they couldn't make any sweet.
What do you think happened to Amano and the Sweets Oujis then? Well... while the Sweets Oujis were busy "sulking" (especially Andou since he was so sad at Caramel's sudden "departure"), Amano was actually "offering" many sweets to the Queen (yeah, to the Queen's statue) everyday and was praying and pleading to the Queen to give the Sweets Spirits another chance. The Sweets Oujis noticed that Amano was doing this so they followed her and helped her make sweets. In the final page of this chapter, it was stated that it was actually the 'Lemon Moon month'. Do you remember the legend of the Lemon Moon? Well, Vanilla told Amano something about that in the previous chapter so, if you have no idea or you don't remember, refer to my recette 30 post. That'll give you an idea on what might happen. :)
Well, that's all that happened in this chapter. Quite normal and... quite a horrible punishment for the humans. Aww...
So... will Amano and the Sweets Oujis go to the Sweets Kingdom to get their Sweets Spirits back?? OR will the Queen just grant their wish and she'll state a condition in the next chapter?? LET'S ALL FIND OUT NEXT MONTH!! XDDD
I'm Reborn... a Hitman... an assassin... a KILLAH. XDD
aww man she finally realized her feelings and then BAM! a drama mini-sode had to happen xD
hopefully the spirits can come back or maybe Ichigo is going to the spirit world to talk to someone O:
cant wait for next month(:
and again THANK YOU~!
'One day your life will Flash before your eyes, Make sure it's worth watching'
aww. that sucks. I hope they get their sweet spirits back D:
i wish the manga would come out sooner~!!!!!!!!!!!!!!!!!!!!!!!! >_< i hate waiting.
I want to read chapters 21-however many there are yet! Where can I find them?!
hey, does anyone know if Yumeiro Patissiere's mangaka (Natsumi Matsumoto) survived the tsunami/earthquake? I don't see her name on any of the magakas that are safe list, so does anyone here no for certain? I hope she's okay DDDDDDDDD:
Sorry I meant to put this up a while ago, but I've been busy with university stuff. So here's chapter 24 and Chapter 25.
Spoiler Alert! Click to show or hide
Chapter 24
Well actually not much happened in chapter 24, it was mostly Ichigo centric and about Ichigo gaining experience about working the floor (waitressing) and how to package sweets fast and still making it pretty. The Sweet Princes only appeared once too.
It starts with the Salon about to open up and Ichigo is mopping the floors and then she says something to the Chief (I can't really understand it), but shortly after that the shop opens and customers come rushing in. Of course Tennouji's Angel Pudding is a best sellers and Ichigo comments on the customers smiles. Then an old woman comes up asking her to wrap her sweets, Ichigo tries, but she can't get it done fast enough, so Yamane steps in and does it for her and then scolds Ichigo, Ichigo gets depressed. Later on, the Sweet Princes gives her some of their new creations to taste and Ichigo starts feeling that she is still so far away from their level.
It's closing time at the Salon and as Ichigo is getting ready to leave, she notices Yamane practicing with cream and asks Cross if she can do it too, but when she's about to start the Chief comes in and scolds her work, Ichigo gets upset and then runs away and stuffs her face with cake at a Patissiere. As she buys some cake she notices the workers and how fast they wrap their cakes. At the dorm, Ichigo starts practicing over the next few days by timing Yamane's wrapping and wrapping various cakes and her books until she does it right for a customer. The chapter ends with Yamane scolding Ichigo about something and the chief tells them to behave.
Chapter 25
It's been about 3 months since Ichigo has started working at the Salon. Ichigo comments that she is still meeting up with Andou and Hanabusa even though they are in the High School Division and Kashino has managed to skip another grade (so he's in his 2nd year of High School).
The chapter starts off with Ichigo and the Salon Chief are tasting one of Kurosu's (Cross) new creations, apparently the chief didn't think it was ready to be put on the menu. The chief then calls everyone together and announces that the new staff is allowed to practice in the kitchen (I'm not really sure about the translation) and Ichigo sees it as a chance to prove herself. So she tries to make custard, but it's not at that level yet.
Later on, Rumi and Ichigo are walking and they see lots of people gathering around a display with candy art done by the Sweet Princes and they comment on how far they have come. Ichigo realizes that she has a long way to go.
It's a really busy day at the Salon, and Cross and the other kitchen staff are really busy and need help, so Ichigo volunteers but she messes up and ends up crying. So later that night, Ichigo is seen practicing really hard and the Sweet Princes show up and end up helping her. Kashino comments that he can't see her clumsiness every day, as it is irritating. But, when Ichigo tries to stir it Kashino helps her by holding her hand and showing her how its done. (I love this Kashigo moment!)
The next day, Ichigo is at the salon, and she asks to try and make the custard again, and Yamane complains again (the one from chapter 23), but Cross agrees to let Ichigo has a go. Ichigo starts making the custard; however, Ichigo ends up burning her wrist.
End of Chapter.
Ah, I wonder when chapter 21 will be avaliable for us to read in english...
wooo thanks Phoenix_tears!! its almost complete :3
'One day your life will Flash before your eyes, Make sure it's worth watching'
chapter 21?
Um... sorry guys. I won't be able to post the translation for recette 32 until I get the newest chapter for this month which is recette 33. I might be able to post again at about early May. (To those who care,) I was actually watching a very important episode of iCarly and I got distracted so much that I wasn't able to translate. And also... something came up in school and... I got extremely busy.
Though I can't give you the FULL summary of the chapter (YET), I could give you just a few spoilers. Here are some of them:
Spoiler Alert! Click to show or hide
1) Amano and the Sweets Oujis were sent to the Sweets Kingdom.
2) They met four other patissieres that were from the France branch of St. Marie Academy.
3) Of course, since this is a manga about cakes and sweets, we get to have a little showdown between our main four and those four patissieres I've mentioned above.
4) We get to see that Arazan again [look at my post about recette 31 if you don't know him].
5) And well... to those who want to know, our main four reunited with their fellow Sweets Spirits.
Now... to answer questions:
@Dayse502: Er... chapter 21 would be released by the translators soon. Just wait patiently like the rest. And please don't ask me. I'm sorry to disappoint you, but I'm not a member of the translator team. I'm just a free man giving you fellow fans some bits and spoilers about the upcoming chapters.
@Everliferulz7769: I saw one article before (a few weeks ago before I saw your post, to be exact) and I found that Natsumi-san is safe. Don't worry.
@gamegirl2099: Same as my reply to Dayse, just please be patient. I'm sure the life of those translators doesn't really revolve around translating the YumePati manga. In other words, they're busy.
@animelovergirl111: Because of my memory, I'm not so sure what you're talking about... but, if you're talking about that hole in episode 11 of the anime, then no. The cliff in episode 11 and the cliff in chapter 30 are not the same. Well, at least, I don't think so.
@cupcake_love: You didn't ask anything but... I just want to thank you for actually "tuning in" everytime I post a new spoiler for the upcoming chapter. I appreciate your praises.
I'm Reborn... a Hitman... an assassin... a KILLAH. XDD
Thank you for answering me! I'm sorry if I was impatient, and I didn't mean to pressure anyone (really, sorry ), it's because I'm nor used to read manga online, so I didn't know well the time the translators take to release a new chapter (and I'm very grateful to them for having that work!). again, i'm sorry.
Oh, and thank you for your spoilers too! They really make my day happier!
Yay reunited once again
@TennisNoHaou: aw you're making me blush , but really I should be thanking you and Phoenix_tears for doing this for us. I can imagine how much work it involves translating every chapter. So thank YOU(: And unlike some people I don't mind waiting so don't feel pressured to update when you're supposed to, because just getting this information is like a gift! So take your time, like you said every translator out there has their own life also.
'One day your life will Flash before your eyes, Make sure it's worth watching'


text:
My friend Pat Jones is a cartoonist who writes a comic she calls "Rock Garden," whose main character - a middle aged woman named Rose - offers sage advice and insights in her running commentary on life. Recently she had one which was especially good. The thirty-something daughter asks Rose "how can I have a happier life?" Rose replies "that's easy - only remember the good stuff."
Our life is like a garden. We plant the things we want to see, but we know that if we don't tend that garden, it will become overrun with weeds, varmints and insects which will destroy the beauty we have painstakingly created.
Negative thoughts are weeds in our garden our life. They will surely find their way into our garden, and they are persistent. Good thoughts require nurturing, like the things we plant in our garden, the ones we want to see come to fruition. We can plant all the good thoughts we want, but those weed-like negative thoughts take root easily and won't go away unless you pull them up by the roots or otherwise kill them.
This battle between the good things we seek to build in our life and the negative things which constantly encroach upon it is never ending. It is a daily engagement, and like those pesky weeds, negative thoughts don't need much nourishment. They don't need tilling and planting. They barely need sunshine and water. They grow where we can't get positive thoughts to grow.
I began writing this column in 2006, and one of the reasons I did it was to redirect my own life. I had become too immersed in negative thoughts and commentaries. I watched the twenty four news channels all the time. I constantly inundated myself with the endless interviews and panel discussion bemoaning every aspect of life. It became like hanging out with a sour bunch of people.
It has been said that we become like the five people we spend the most time with. That's probably an oversimplification, but at its core that thought is correct. If you want to be positive, surround yourself with positive people. If you surround yourself with negative, toxic, caustic people, their attitudes will leach into your own, and you will find yourself bogged down in negativity.
Every life has good things and bad things to remember. I am blessed with a good memory, but sometimes it works too well. Sometimes it won't let go of a memory and the hurt that memory has attached to it. The thought becomes like a visitor who stops by one day, and you look up a month later, and they're still living with you, a constant companion in your life.
You have to roust that freeloading negativity out of your life. You have to decide to "accentuate the positive, eliminate the negative," as the lyric from the 1944 popular tune "Ac-Cent-Tchu-Ate the Positive" taught us. Choose to remember the good. Choose to eschew the negative. Tell it what the bartenders tell their lingering patrons at closing time: "you don't have to go home, but you have to get on up out of here."
© 2013, Jim "Pappy" Moore, All Rights Reserved.
See the cartoon referred to in this column at http://www.webcomicsnation.com/patjones/rockgardencomics/series.php?view=archive&chapt er=52930&name=rockgardencomics


text:
HAGERSTOWN, Md. (AP) — The federal Centers for Disease Control and Prevention says a rabies death in Maryland was caused by an organ transplant.
The agency said Friday that three other people in Florida, Georgia and Illinois who got organs from the same donor are getting anti-rabies shots.
The donor died of rabies in Florida in 2011 after moving there from North Carolina.
The CDC says it's working with public health officials and health care facilities in all five states to identify people who were in close contact with the initial donor or the four organ recipients. The agency says those people might need rabies post-exposure treatment.