PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions

As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF's classification performance in 12-species _Drosophila_ genome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues, and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE

Is anxiety associated with negative interpretations of ambiguity in children and adolescents? A systematic review and meta-analysis

Background The tendency to interpret ambiguity as threat (‘negative interpretation’) has been implicated in cognitive models of anxiety. A significant body of research has examined the association between anxiety and negative interpretation, and reviews suggest there is a robust positive association in adults. However, evidence with children and adolescents has been inconsistent. This study aimed to provide a systematic quantitative assessment of the association between anxiety and negative interpretation in children and adolescents. Methods Following systematic searches and screening for eligibility, 345 effects sizes from 77 studies were meta-analysed. Results Overall a medium positive association was found between anxiety and negative interpretation in children and adolescents (d ̂ = 0.62). Two variables significantly moderated this effect. Specifically, the association increased in strength with increasing age and when the content of ambiguous scenarios matched the anxiety subtype under investigation. Conclusions Results extend findings from adult literature by demonstrating an association in children and adolescents with evidence for content specificity in the association. Age effects imply a role for development. Results raise considerations for when and for whom clinical treatments for anxiety focusing on interpretation bias are appropriate. The vast majority of studies included in the review have used correlational designs and there are a limited number of studies with you ng children. The results should be considered with these limitations in mind

The atmospheric parameters and spectral interpolator for the stars of MILES

Context. Empirical libraries of stellar spectra are used for stellar classification and synthesis of stellar populations. MILES is a medium spectral-resolution library in the optical domain covering a wide range of temperatures, surface gravities and metallicities. Aims. We re-determine the atmospheric parameters of these stars in order to improve the homogeneity and accuracy. We build an interpolating function that returns a spectrum as a function of the three atmospheric parameters, and finally, we characterize the precision of the wavelength calibration and stability of the spectral resolution. Methods. We use the ULySS program with the ELODIE library as a reference and compare the results with literature compilations. Results. We obtain precisions of 60 K, 0.13 and 0.05 dex respectively for Teff, log g and [Fe/H] for the FGK stars. For the M stars, the mean errors are 38 K, 0.26 and 0.12 dex, and for the OBA 3.5%, 0.17 and 0.13 dex. We construct an interpolator that we test against the MILES stars themselves. We test it also by measuring the atmospheric parameters of the CFLIB stars with MILES as reference and find it to be more reliable than the ELODIE interpolator for the evolved hot stars, like in particular those of the blue horizontal branch.Comment: A&A accepted, 29 pages, 6 figure

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Stressful life events are related to more negative interpretations, but not under acute stress

Studies have identified deleterious effects of stress on multiple cognitive processes such as memory and attention. Little is known about the impact of stress on interpretation. We investigated how an induced acute stress and more long-term stress related to life events were associated with interpretations of ambiguous stimuli. Fifty participants answered a questionnaire indexing the number of stressful life events. A median split was used to compare those reporting few or more events. Half of participants performed an arithmetic task that induced acute stress; they were compared to a control group performing a less stressful task. We measured the interpretation of ambiguous visual stimuli, which participants had to judge as “negative” or “positive”. We found a significant interaction between the number of stressful life events and the induced acute stress on the proportion of positive interpretations. In the control group, participants reporting more stressful events produced less positive interpretations than those reporting few events. In the induced stress condition, no significant difference was found. Life events tend to influence interpretation in the absence of an acute stressor, which seems to be more influent in the short term

Preparation of anti-vicinal amino alcohols: asymmetric synthesis of D-erythro-Sphinganine, (+)-spisulosine and D-ribo-phytosphingosine

Two variations of the Overman rearrangement have been developed for the highly selective synthesis of anti-vicinal amino alcohol natural products. A MOM-ether directed palladium(II)-catalyzed rearrangement of an allylic trichloroacetimidate was used as the key step for the preparation of the protein kinase C inhibitor D-erythro-sphinganine and the antitumor agent (+)-spisulosine, while the Overman rearrangement of chiral allylic trichloroacetimidates generated by asymmetric reduction of an alpha,beta-unsaturated methyl ketone allowed rapid access to both D-ribo-phytosphingosine and L-arabino-phytosphingosine

A systematic review of the effectiveness and cost-effectiveness of peer education and peer support in prisons.

BACKGROUND: Prisoners experience significantly worse health than the general population. This review examines the effectiveness and cost-effectiveness of peer interventions in prison settings. METHODS: A mixed methods systematic review of effectiveness and cost-effectiveness studies, including qualitative and quantitative synthesis was conducted. In addition to grey literature identified and searches of websites, nineteen electronic databases were searched from 1985 to 2012. Study selection criteria were: Population: Prisoners resident in adult prisons and children resident in Young Offender Institutions (YOIs). INTERVENTION: Peer-based interventions Comparators: Review questions 3 and 4 compared peer and professionally led approaches. OUTCOMES: Prisoner health or determinants of health; organisational/ process outcomes; views of prison populations. STUDY DESIGNS: Quantitative, qualitative and mixed method evaluations. RESULTS: Fifty-seven studies were included in the effectiveness review and one study in the cost-effectiveness review; most were of poor methodological quality. Evidence suggested that peer education interventions are effective at reducing risky behaviours, and that peer support services are acceptable within the prison environment and have a positive effect on recipients, practically or emotionally. Consistent evidence from many, predominantly qualitative, studies, suggested that being a peer deliverer was associated with positive effects. There was little evidence on cost-effectiveness of peer-based interventions. CONCLUSIONS: There is consistent evidence from a large number of studies that being a peer worker is associated with positive health; peer support services are also an acceptable source of help within the prison environment and can have a positive effect on recipients. Research into cost-effectiveness is sparse. SYSTEMATIC REVIEW REGISTRATION: PROSPERO ref: CRD42012002349

The Caenorhabditis elegans Gene mfap-1 Encodes a Nuclear Protein That Affects Alternative Splicing

RNA splicing is a major regulatory mechanism for controlling eukaryotic gene expression. By generating various splice isoforms from a single pre–mRNA, alternative splicing plays a key role in promoting the evolving complexity of metazoans. Numerous splicing factors have been identified. However, the in vivo functions of many splicing factors remain to be understood. In vivo studies are essential for understanding the molecular mechanisms of RNA splicing and the biology of numerous RNA splicing-related diseases. We previously isolated a Caenorhabditis elegans mutant defective in an essential gene from a genetic screen for suppressors of the rubberband Unc phenotype of unc-93(e1500) animals. This mutant contains missense mutations in two adjacent codons of the C. elegans microfibrillar-associated protein 1 gene mfap-1. mfap-1(n4564 n5214) suppresses the Unc phenotypes of different rubberband Unc mutants in a pattern similar to that of mutations in the splicing factor genes uaf-1 (the C. elegans U2AF large subunit gene) and sfa-1 (the C. elegans SF1/BBP gene). We used the endogenous gene tos-1 as a reporter for splicing and detected increased intron 1 retention and exon 3 skipping of tos-1 transcripts in mfap-1(n4564 n5214) animals. Using a yeast two-hybrid screen, we isolated splicing factors as potential MFAP-1 interactors. Our studies indicate that C. elegans mfap-1 encodes a splicing factor that can affect alternative splicing.National Natural Science Foundation (China) (Grant 30971639)United States. National Institutes of Health (Grant GM24663

Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish

Sexual dimorphism is a fascinating subject in evolutionary biology and mostly results from sex-biased expression of genes, which have been shown to evolve faster in gonochoristic species. We report here genome and sex-specific transcriptome sequencing of Sparus aurata, a sequential hermaphrodite fish. Evolutionary comparative analysis reveals that sex-biased genes in S. aurata are similar in number and function, but evolved following strikingly divergent patterns compared with gonochoristic species, showing overall slower rates because of stronger functional constraints. Fast evolution is observed only for highly ovary-biased genes due to female-specific patterns of selection that are related to the peculiar reproduction mode of S. aurata, first maturing as male, then as female. To our knowledge, these findings represent the first genome-wide analysis on sex-biased loci in a hermaphrodite vertebrate species, demonstrating how having two sexes in the same individual profoundly affects the fate of a large set of evolutionarily relevant genes.European Union KBBE.2013.1.2-10 European Community 311920 Fondazione Cassa di Risparmio Padova e Rovigo FCT - Foundation for Science and Technology research grant SPARCOMP under the Call ARISTEIA I of the National Strategic Reference Framework - by the EU 36 Hellenic Republic through the European Social Fundinfo:eu-repo/semantics/publishedVersio

Adapting effects of emotional expression in anxiety: evidence for an enhanced late positive potential

An adaptation paradigm was used to investigate the influence of a previously experienced visual context on the interpretation of ambiguous emotional expressions. Affective classification of fear-neutral ambiguous expressions was performed following repeated exposure to either fearful or neutral faces. There was a shift in the behavioural classification of morphs towards ‘fear’ following adaptation to neutral compared to adaptation to fear with a non-significant trend towards the high anxiety group compared to the low being more influenced by the context. The event-related potential (ERP) data revealed a more pronounced late positive potential (LPP), beginning at ~400 ms post-stimulus onset, in the high but not the low anxiety group following adaptation to neutral compared to fear. In addition, as the size of the behavioural adaptation increased there was a linear increase in the magnitude of the late-LPP. However, context-sensitivity effects are not restricted to trait anxiety, with similar effects observed with state anxiety and depression. These data support the proposal that negative moods are associated with increased sensitivity to visual contextual influences from top-down elaborative modulations, as reflected in an enhanced late positive potential deflection