A Target Restricted Assembly Method (TRAM) for Phylogenomics

While next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are still prohibitive steps for many phylogenomics applications. Here we describe a method of Target Restricted Assembly (TRAM) of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes. This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon

The molecular sensory machinery of a Chagas disease vector: expression changes through imaginal moult and sexually dimorphic features

The triatomine bug Rhodnius prolixus is a main vector of Chagas disease, which affects several million people, mostly in Latin-America. Host searching, pheromone communication, and microclimatic preferences are aspects of its behaviour that depend on multimodal sensory inputs. The molecular bases of these sensory processes are largely unknown. The expression levels of genes transcribed in antennae were compared between 5th instar larvae, and female and male adults by means of RNA-Seq. The antennae of R. prolixus showed increased expression of several chemosensory-related genes in imaginal bugs, while both sexes had similar expression patterns for most target genes. Few cases suggest involvement of target genes in sexually dimorphic functions. Most odorant and ionotropic receptor genes seemed to be expressed in all libraries. OBPs and CSPs showed very high expression levels. Other sensory-related genes such as TRPs, PPKs and mechanoreceptors had consistent levels of expression in all libraries. Our study characterises most of the sensory gene repertoire of these insects, opening an avenue for functional genetics studies. The increase in expression of chemosensory genes suggests an enhanced role in adult bugs. This knowledge allows developing new behaviour interfering strategies, increasing the options for translational research in the vector control field.Centro Regional de Estudios Genómico

Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression

Citation: Meyers, P. J., Powell, T. H. Q., Walden, K. K. O., Schieferecke, A. J., Feder, J. L., Hahn, D. A., . . . Ragland, G. J. (2016). Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression. Journal of Experimental Biology, 219(17), 2613-2622. doi:10.1242/jeb.140566The duration of dormancy regulates seasonal timing in many organisms and may be modulated by day length and temperature. Though photoperiodic modulation has been well studied, temperature modulation of dormancy has received less attention. Here, we leverage genetic variation in diapause in the apple maggot fly, Rhagoletis pomonella, to test whether gene expression during winter or following spring warming regulates diapause duration. We used RNAseq to compare transcript abundance during and after simulated winter between an apple-infesting population and a hawthorn-infesting population where the apple population ends pupal diapause earlier than the hawthorn-infesting population. Marked differences in transcription between the two populations during winter suggests that the 'early' apple population is developmentally advanced compared with the 'late' hawthorn population prior to spring warming, with transcripts participating in growth and developmental processes relatively up-regulated in apple pupae during the winter cold period. Thus, regulatory differences during winter ultimately drive phenological differences that manifest themselves in the following summer. Expression and polymorphism analysis identify candidate genes in the Wnt and insulin signaling pathways that contribute to population differences in seasonality. Both populations remained in diapause and displayed a pattern of up-and then down-regulation (or vice versa) of growth-related transcripts following warming, consistent with transcriptional repression. The ability to repress growth stimulated by permissive temperatures is likely critical to avoid mismatched phenology and excessive metabolic demand. Compared with diapause studies in other insects, our results suggest some overlap in candidate genes/pathways, though the timing and direction of changes in transcription are likely species specific

Beta-delayed deuteron emission from 11Li: decay of the halo

The deuteron-emission channel in the beta-decay of the halo-nucleus 11Li was measured at the ISAC facility at TRIUMF by implanting post-accelerated 11Li ions into a segmented silicon detector. The events of interest were identified by correlating the decays of 11Li with those of the daughter nuclei. This method allowed the energy spectrum of the emitted deuterons to be extracted, free from contributions from other channels, and a precise value for the branching ratio B_d = 1.30(13) x 10-4 to be deduced for E(c.m.) > 200 keV. The results provide the first unambiguous experimental evidence that the decay takes place essentially in the halo of 11Li, and that it proceeds mainly to the 9Li + d continuum, opening up a new means to study of the halo wave function of 11Li.Comment: 4 pages, 3 figure

Positive selection in extra cellular domains in the diversification of Strigamia maritima chemoreceptors

The recent publication of a centipede (Strigamia maritima) genome has revealed that most members of the chemosensory gene families of ionotropic (IR) and gustatory (GR) receptors do not have identifiable orthologs in insect species. In other words, the diversity of these chemoreceptors in centipedes appears to have evolved after its split from other arthropod lineages. Here we investigate the role of adaptive evolution in S. maritima chemoreceptor diversification using an approach that allows us to discuss functional aspects of such diversification. We applied codon substitution models in a phylogenetic framework to obtain the distribution of selective constraints across the different domains in the IR and GR proteins, and to assess the impact of positive selection in the evolution of these chemoreceptors. We found low selective constraints in most IR and GR duplicates and significant evidence for the presence of positively selected amino acids in 2 of the 4 IR, and in 6 of the GR recent specific expansions. Mapping the sites with high posterior probability of positive selection in protein structure revealed a remarkable uneven distribution of fast-evolving sites across protein domains. Most of these sites are located in extracellular fragments of these receptors, which likely participate in ligand recognition. We hypothesize that adaptive evolution in ligand-binding domains was a major force driving the functional diversification of centipede chemoreceptors

Nuclear Orthologs Derived from Whole Genome Sequencing Indicate Cryptic Diversity in the Bemisia tabaci (Insecta: Aleyrodidae) Complex of Whiteflies

The Bemisia tabaci complex of whiteflies contains globally important pests thought to contain cryptic species corresponding to geographically structured phylogenetic clades. Although mostly morphologically indistinguishable, differences have been shown to exist among populations in behavior, plant virus vector capacity, ability to hybridize, and DNA sequence divergence. These differences allow for certain populations to become invasive and cause great economic damage in a monoculture setting. Although high mitochondrial DNA divergences have been reported between putative conspecifics of the B. tabaci species complex, there is limited data that exists across the whole genome for this group. Using data from 2184 orthologs obtained from whole genome sequencing (Illumina), a phylogenetic analysis using maximum likelihood and coalescent methodologies was completed on ten individuals of the B. tabaci complex. In addition, automatic barcode gap discovery methods were employed, and results suggest the existence of five species. Although the divergences of the mitochondrial cytochrome oxidase I gene are high among members of this complex, nuclear divergences are much lower in comparison. Single-copy orthologs from whole genome sequencing demonstrate divergent population structures among members of the B. tabaci complex and the sequences provide an important resource to aid in future genomic studies of the group

On the Security Cost of Using a Free and Open Source Component in a Proprietary Product

The work presented in this paper is motivated by the need to estimate the security effort of consuming Free and Open Source Software (FOSS) components within a proprietary software supply chain of a large European software vendor. To this extent we have identified three different cost models: centralized (the company checks each component and propagates changes to the different product groups), distributed (each product group is in charge of evaluating and fixing its consumed FOSS components), and hybrid (only the least used components are checked individually by each development team). We investigated publicly available factors (\eg, development activity such as commits, code size, or fraction of code size in different programming languages) to identify which one has the major impact on the security effort of using a FOSS component in a larger software product

The Epidemiology of First-Episode Psychosis in Early Intervention in Psychosis Services: Findings From the Social Epidemiology of Psychoses in East Anglia [SEPEA] Study

OBJECTIVE: Few studies have characterized the epidemiology of first-episode psychoses in rural or urban settings since the introduction of early intervention psychosis services. To address this, the authors conducted a naturalistic cohort study in England, where such services are well established. METHOD: All new first-episode psychosis cases, 16-35 years old, presenting to early intervention psychosis services in the East of England were identified during 2 million person-years follow-up. Presence of ICD-10 F10-33 psychotic disorder was confirmed using OPCRIT [operational criteria for psychotic illness]. Incidence rate ratios were estimated following multivariable Poisson regression, adjusting for age, sex, ethnicity, socioeconomic status, neighborhood-level deprivation, and population density. RESULTS: Of 1,005 referrals, 687 participants (68.4%) fulfilled epidemiological and diagnostic criteria for first-episode psychosis (34.0 new cases per 100,000 person-years; 95% CI=31.5-36.6). Median age at referral was similar for men (22.5 years; interquartile range: 19.5-26.7) and women (23.4 years; interquartile range: 19.5-29.1); incidence rates were highest for men and women before 20 years of age. Rates increased for ethnic minority groups (incidence rate ratio: 1.4; 95% CI=1.1-1.6), as well as with lower socioeconomic status (incidence rate ratio: 1.3; 95% CI=1.2-1.4) and in more urban (incidence rate ratio: 1.4;95%CI=1.0-1.8) and deprived (incidence rate ratio: 2.1; 95% CI=1.3-3.3) neighborhoods, after adjustment for confounders. CONCLUSIONS: Pronounced variation in psychosis incidence, peaking before 20 years old, exists in populations served by early intervention psychosis services. Excess rates were restricted to urban and deprived communities, suggesting that a threshold of socioenvironmental adversity may be necessary to increase incidence. This robust epidemiology can inform service development in various settings about likely population-level need

Influence of the Soret effect on convection of binary fluids

Convection in horizontal layers of binary fluids heated from below and in particular the influence of the Soret effect on the bifurcation properties of extended stationary and traveling patterns that occur for negative Soret coupling is investigated theoretically. The fixed points corresponding to these two convection structures are determined for realistic boundary conditions with a many mode Galerkin scheme for temperature and concentration and an accurate one mode truncation of the velocity field. This solution procedure yields the stable and unstable solutions for all stationary and traveling patterns so that complete phase diagrams for the different convection types in typical binary liquid mixtures can easily be computed. Also the transition from weakly to strongly nonlinear states can be analyzed in detail. An investigation of the concentration current and of the relevance of its constituents shows the way for a simplification of the mode representation of temperature and concentration field as well as for an analytically manageable few mode description.Comment: 30 pages, 12 figure

Ethnic Minority Status, Age-at-Immigration and Psychosis Risk in Rural Environments: Evidence From the SEPEA Study.

Objective: Several ethnic minority groups experience elevated rates of first-episode psychosis (FEP), but most studies have been conducted in urban settings. We investigated whether incidence varied by ethnicity, generation status, and age-at-immigration in a diverse, mixed rural, and urban setting. Method: We identified 687 people, 16-35 years, with an ICD-10 diagnosis of FEP, presenting to Early Intervention Psychosis services in the East of England over 2 million person-years. We used multilevel Poisson regression to examine incidence variation by ethnicity, rural-urban setting, generation status, and age-at-immigration, adjusting for several confounders including age, sex, socioeconomic status, population density, and deprivation. Results: People of black African (incidence rate ratio: 4.06; 95% confidence interval [CI]: 2.63-6.25), black Caribbean (4.63; 95% CI: 2.38-8.98) and Pakistani (2.31; 95% CI: 1.35-3.94) origins were at greatest FEP risk relative to the white British population, after multivariable adjustment. Non-British white migrants were not at increased FEP risk (1.00; 95% CI: 0.77-1.32). These patterns were independently present in rural and urban settings. For first-generation migrants, migration during childhood conferred greatest risk of psychotic disorders (2.20; 95% CI: 1.33-3.62). Conclusions: Elevated psychosis risk in several visible minority groups could not be explained by differences in postmigratory socioeconomic disadvantage. These patterns were observed across rural and urban areas of our catchment, suggesting that elevated psychosis risk for some ethnic minority groups is not a result of selection processes influencing rural-urban living. Timing of exposure to migration during childhood, an important social and neurodevelopmental window, may also elevate risk