Targeted Gene Mutations in the Forest Pathogen Dothistroma septosporum Using CRISPR/Cas9.

Dothistroma needle blight, caused by Dothistroma septosporum, has increased in incidence and severity over the last few decades and is now one of the most important global diseases of pines. Disease resistance breeding could be accelerated by knowledge of pathogen virulence factors and their host targets. However, this is hindered due to inefficient targeted gene disruption in D. septosporum, which is required for virulence gene characterisation. Here we report the first successful application of CRISPR/Cas9 gene editing to a Dothideomycete forest pathogen, D. septosporum. Disruption of the dothistromin pathway regulator gene AflR, with a known phenotype, was performed using nonhomologous end-joining repair with an efficiency of > 90%. Transformants with a range of disruption mutations in AflR were produced. Disruption of Ds74283, a D. septosporum gene encoding a secreted cell death elicitor, was also achieved using CRISPR/Cas9, by using a specific donor DNA repair template to aid selection where the phenotype was unknown. In this case, 100% of screened transformants were identified as disruptants. In establishing CRISPR/Cas9 as a tool for gene editing in D. septosporum, our research could fast track the functional characterisation of candidate virulence factors in D. septosporum and helps set the foundation for development of this technology in other forest pathogens.Published onlin

Cultural modulation of face and gaze scanning in young children

Previous research has demonstrated that the way human adults look at others’ faces is modulated by their cultural background, but very little is known about how such a culture-specific pattern of face gaze develops. The current study investigated the role of cultural background on the development of face scanning in young children between the ages of 1 and 7 years, and its modulation by the eye gaze direction of the face. British and Japanese participants’ eye movements were recorded while they observed faces moving their eyes towards or away from the participants. British children fixated more on the mouth whereas Japanese children fixated more on the eyes, replicating the results with adult participants. No cultural differences were observed in the differential responses to direct and averted gaze. The results suggest that different patterns of face scanning exist between different cultures from the first years of life, but differential scanning of direct and averted gaze associated with different cultural norms develop later in life

The SEGUE Stellar Parameter Pipeline. I. Description and Initial Validation Tests

We describe the development and implementation of the SEGUE (Sloan Extension for Galactic Exploration and Understanding) Stellar Parameter Pipeline (SSPP). The SSPP derives, using multiple techniques, radial velocities and the fundamental stellar atmospheric parameters (effective temperature, surface gravity, and metallicity) for AFGK-type stars, based on medium-resolution spectroscopy and $ugriz$ photometry obtained during the course of the original Sloan Digital Sky Survey (SDSS-I) and its Galactic extension (SDSS-II/SEGUE). The SSPP also provides spectral classification for a much wider range of stars, including stars with temperatures outside of the window where atmospheric parameters can be estimated with the current approaches. This is Paper I in a series of papers on the SSPP; it provides an overview of the SSPP, and initial tests of its performance using multiple data sets. Random and systematic errors are critically examined for the current version of the SSPP, which has been used for the sixth public data release of the SDSS (DR-6).Comment: 64 pages, 8 tables, 12 figures, submitted to the Astronomical Journa

The SEGUE Stellar Parameter Pipeline. II. Validation with Galactic Globular and Open Clusters

We validate the performance and accuracy of the current SEGUE (Sloan Extension for Galactic Understanding and Exploration) Stellar Parameter Pipeline (SSPP), which determines stellar atmospheric parameters (effective temperature, surface gravity, and metallicity) by comparing derived overall metallicities and radial velocities from selected likely members of three globular clusters (M 13, M 15, and M 2) and two open clusters (NGC 2420 and M 67) to the literature values. Spectroscopic and photometric data obtained during the course of the original Sloan Digital Sky Survey (SDSS-I) and its first extension (SDSS-II/SEGUE) are used to determine stellar radial velocities and atmospheric parameter estimates for stars in these clusters. Based on the scatter in the metallicities derived for the members of each cluster, we quantify the typical uncertainty of the SSPP values, sigma([Fe/H]) = 0.13 dex for stars in the range of 4500 K < Teff < 7500 K and 2.0 < log g < 5.0, at least over the metallicity interval spanned by the clusters studied (-2.3 < [Fe/H] < 0). The surface gravities and effective temperatures derived by the SSPP are also compared with those estimated from the comparison of the color-magnitude diagrams with stellar evolution models; we find satisfactory agreement. At present, the SSPP underestimates [Fe/H] for near-solar-metallicity stars, represented by members of M 67 in this study, by about 0.3 dex.Comment: 56 pages, 8 Tables, 15 figures, submitted to the Astronomical Journa

A Bayesian method for evaluating and discovering disease loci associations

Background: A genome-wide association study (GWAS) typically involves examining representative SNPs in individuals from some population. A GWAS data set can concern a million SNPs and may soon concern billions. Researchers investigate the association of each SNP individually with a disease, and it is becoming increasingly commonplace to also analyze multi-SNP associations. Techniques for handling so many hypotheses include the Bonferroni correction and recently developed Bayesian methods. These methods can encounter problems. Most importantly, they are not applicable to a complex multi-locus hypothesis which has several competing hypotheses rather than only a null hypothesis. A method that computes the posterior probability of complex hypotheses is a pressing need. Methodology/Findings: We introduce the Bayesian network posterior probability (BNPP) method which addresses the difficulties. The method represents the relationship between a disease and SNPs using a directed acyclic graph (DAG) model, and computes the likelihood of such models using a Bayesian network scoring criterion. The posterior probability of a hypothesis is computed based on the likelihoods of all competing hypotheses. The BNPP can not only be used to evaluate a hypothesis that has previously been discovered or suspected, but also to discover new disease loci associations. The results of experiments using simulated and real data sets are presented. Our results concerning simulated data sets indicate that the BNPP exhibits both better evaluation and discovery performance than does a p-value based method. For the real data sets, previous findings in the literature are confirmed and additional findings are found. Conclusions/Significance: We conclude that the BNPP resolves a pressing problem by providing a way to compute the posterior probability of complex multi-locus hypotheses. A researcher can use the BNPP to determine the expected utility of investigating a hypothesis further. Furthermore, we conclude that the BNPP is a promising method for discovering disease loci associations. © 2011 Jiang et al

The Case for the Dual Halo of the Milky Way

Carollo et al. have recently resolved the stellar population of the Milky Way halo into at least two distinct components, an inner halo and an outer halo. This result has been criticized by Schoenrich et al., who claim that the retrograde signature associated with the outer halo is due to the adoption of faulty distances. We refute this claim, and demonstrate that the Schoenrich et al. photometric distances are themselves flawed because they adopted an incorrect main-sequence absolute magnitude relationship from the work of Ivezi\'c et al. When compared to the recommended relation from Ivezi\'c et al., which is tied to a Milky Way globular cluster distance scale and accounts for age and metallicity effects, the relation adopted by Schoenrich et al. yields up to 18% shorter distances for stars near the main-sequence turnoff (TO). Use of the correct relationship yields agreement between the distances assigned by Carollo et al. and Ivezi\'{c} et al. for low-metallicity dwarfs to within 6-10%. Schoenrich et al. also point out that intermediate-gravity stars (3.5 <= log g <= 4.0) with colors redder than the TO region are likely misclassified, with which we concur. We implement a new procedure to reassign luminosity classifications for the TO stars that require it. New derivations of the rotational behavior demonstrate that the retrograde signature and high velocity dispersion of the outer-halo population remains. We summarize additional lines of evidence for a dual halo, including a test of the retrograde signature based on proper motions alone, and conclude that the preponderance of evidence strongly rejects the single-halo interpretation.Comment: 46 pages, 2 tables, 15 figures, Accepted for publication in the Astrophysical Journa

Cross-sectional survey of users of internet depression communities

Background: Internet-based depression communities provide a forum for individuals to communicate and share information and ideas. There has been little research into the health status and other characteristics of users of these communities. Methods: Online cross-sectional survey of Internet depression communities to identify depressive morbidity among users of Internet depression communities in six European countries; to investigate whether users were in contact with health services and receiving treatment; and to identify user perceived effects of the communities. Results: Major depression was highly prevalent among respondents (varying by country from 40% to 64%). Forty-nine percent of users meeting criteria for major depression were not receiving treatment, and 35% had no consultation with health services in the previous year. Thirty-six percent of repeat community users who had consulted a health professional in the previous year felt that the Internet community had been an important factor in deciding to seek professional help. Conclusions: There are high levels of untreated and undiagnosed depression in users of Internet depression communities. This group represents a target for intervention. Internet communities can provide information and support for stigmatizing conditions that inhibit more traditional modes of information seeking