| 1. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 2. |
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| 3. |
- Rohmer, Laurence, et al.
(författare)
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Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains
- 2007
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Ingår i: Genome Biology. - : BioMed Central. - 1465-6906 .- 1474-760X. ; 8:6
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Francisella tularensis subspecies tularensis and holarctica are pathogenic to humans, whereas the two other subspecies, novicida and mediasiatica, rarely cause disease. To uncover the factors that allow subspecies tularensis and holarctica to be pathogenic to humans, we compared their genome sequences with the genome sequence of Francisella tularensis subspecies novicida U112, which is nonpathogenic to humans. RESULTS: Comparison of the genomes of human pathogenic Francisella strains with the genome of U112 identifies genes specific to the human pathogenic strains and reveals pseudogenes that previously were unidentified. In addition, this analysis provides a coarse chronology of the evolutionary events that took place during the emergence of the human pathogenic strains. Genomic rearrangements at the level of insertion sequences (IS elements), point mutations, and small indels took place in the human pathogenic strains during and after differentiation from the nonpathogenic strain, resulting in gene inactivation. CONCLUSION: The chronology of events suggests a substantial role for genetic drift in the formation of pseudogenes in Francisella genomes. Mutations that occurred early in the evolution, however, might have been fixed in the population either because of evolutionary bottlenecks or because they were pathoadaptive (beneficial in the context of infection). Because the structure of Francisella genomes is similar to that of the genomes of other emerging or highly pathogenic bacteria, this evolutionary scenario may be shared by pathogens from other species.
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| 4. |
- Namjou, Bahram, et al.
(författare)
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High-density genotyping of STAT4 reveals multiple haplotypic associations with systemic lupus erythematosus in different racial groups
- 2009
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Ingår i: Arthritis and Rheumatism. - : Wiley. - 0004-3591 .- 1529-0131. ; 60:4, s. 1085-1095
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: Systemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disorder, with complex etiology and a strong genetic component. Recently, gene products involved in the interferon pathway have been under intense investigation in terms of the pathogenesis of SLE. STAT-1 and STAT-4 are transcription factors that play key roles in the interferon and Th1 signaling pathways, making them attractive candidates for involvement in SLE susceptibility. METHODS: Fifty-six single-nucleotide polymorphisms (SNPs) across STAT1 and STAT4 on chromosome 2 were genotyped using the Illumina platform, as part of an extensive association study in a large collection of 9,923 lupus patients and control subjects from different racial groups. DNA samples were obtained from the peripheral blood of patients with SLE and control subjects. Principal components analyses and population-based case-control association analyses were performed, and the P values, false discovery rate q values, and odds ratios with 95% confidence intervals were calculated. RESULTS: We observed strong genetic associations with SLE and multiple SNPs located within STAT4 in different ethnic groups (Fisher's combined P = 7.02 x 10(-25)). In addition to strongly confirming the previously reported association in the third intronic region of this gene, we identified additional haplotypic association across STAT4 and, in particular, a common risk haplotype that is found in multiple racial groups. In contrast, only a relatively weak suggestive association was observed with STAT1, probably due to its proximity to STAT4. CONCLUSION: Our findings indicate that STAT4 is likely to be a crucial component in SLE pathogenesis in multiple racial groups. Knowledge of the functional effects of this association, when they are revealed, might improve our understanding of the disease and provide new therapeutic targets.
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| 5. |
- Birney, Ewan, et al.
(författare)
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Prepublication data sharing
- 2009
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 461:7261, s. 168-170
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Tidskriftsartikel (refereegranskat)abstract
- Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.
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| 6. |
- Sjöling, Sara, et al.
(författare)
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Metagenomics : microbial community genomes revealed
- 2008
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Ingår i: Psychrophiles. - Berlin, Heidelberg : Springer. - 9783540743347 - 9783540743354 ; , s. 313-330
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- The rapidly expanding field of metagenomics has revolutionized the ability to analyzemicrobial communities by providing access to ‘true’ microbial diversity. This field has a broad range of applications in the areas of biodiversity, systems biology and biotechnology (Handelsman et al. 2002). As most microbial communities in soil, sediment or aquatic environments are highly complex, consisting of hundreds oreven thousands of species of which only a few have been cultured, the approaches collectively described as metagenomics, community genomics or environmental genomics have been developed to help to unlock this thus far hidden diversity. Metagenomics is therefore the application of modern genomic tools used to analyze the collective genomes of whole microbial communities (the metagenome) in an environmental sample, thereby bypassing the need for isolation or cultivation (Béjà et al. 2000; Riesenfeld et al. 2004b). Even though the tip of the microbial ice-berg has barely been scratched, this approach is rapidly increasing our knowledge of microbial genetic and functional diversity through gene/pathway discovery either by sequencing or activity-based screening strategies (Handelsman 2005).
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| 7. |
- Stanton, Neville A., et al.
(författare)
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Predicting pilot error: Testing a new methodology and a multi-methods and analysts approach
- 2009
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Ingår i: Applied Ergonomics. - : Elsevier BV. - 1872-9126 .- 0003-6870. ; 40:3, s. 464-471
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Tidskriftsartikel (refereegranskat)abstract
- The Human Error Template (HET) is a recently developed methodology for predicting design-induced pilot error. This article describes a validation study undertaken to compare the performance of HET against three contemporary Human Error Identification (HEI) approaches when used to predict pilot errors for an approach and landing task and also to compare analyst error predictions to an approach to enhancing error prediction sensitivity: the multiple analysts and methods approach, whereby multiple analyst predictions using a range of HEI techniques are pooled. The findings indicate that, of the four methodologies used in isolation, analysts using the HET methodology offered the most accurate error predictions, and also that the multiple analysts and methods approach was more successful overall in terms of error prediction sensitivity than the three other methods but not the HET approach. The results suggest that when predicting design-induced error, it is appropriate to use a toolkit of different HEI approaches and multiple analysts in order to heighten error prediction sensitivity. (c) 2008 Elsevier Ltd. All rights reserved.
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| 8. |
- VandenBerg, Don A., et al.
(författare)
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A Constraint on Zsolar from Fits of Isochrones to the Color-Magnitude Diagram of M67
- 2007
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 666:2, s. L105-L108
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Tidskriftsartikel (refereegranskat)abstract
- The mass at which a transition is made between stars that have radiative or convective cores throughout the core H burning phase is a fairly sensitive function of Z (particularly, the CNO abundances). As a consequence, the ~4 Gyr, open cluster M67 provides a constraint on Zsolar (and the solar heavy-element mixture) because (1) high-resolution spectroscopy indicates that this system has virtually the same metal abundances as the Sun, and (2) its turnoff stars have masses just above the lower limit for sustained core convection on the main sequence. In this study, evolutionary tracks and isochrones using the latest MARCS model atmospheres as boundary conditions have been computed for 0.6-1.4 Msolar on the assumption of a metals mix (implying Zsolar~0.0125) based on the solar abundances derived by M. Asplund and collaborators using 3D model atmospheres. These calculations do not predict a turnoff gap where one is observed in M67. No such difficulty is found if the analysis uses isochrones for Zsolar=0.0165, assuming the Grevesse and Sauval mix of heavy elements. Our findings, like the inferences from helioseismology, indicate a problem with the abundances of Asplund and collaborators. However, it is possible that low-Z models with diffusive processes taken into account will be less problematic.
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| 9. |
- Vandenberg, Don A., et al.
(författare)
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On Stellar Models with Blanketed Atmospheres as Boundary Conditions
- 2007
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Ingår i: Stellar Populations as Building Blocks of Galaxies. ; , s. 23-27
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The impact on the predicted Teff scale of using the latest MARCS model atmospheres, instead of a fixed atmospheric structure (e.g., the gray T–τ relation) is examined. The former were fitted to stellar interior models at both the photosphere and at τ = 100 to determine the sensitivity of evolutionary tracks and isochrones for [Fe/H] = 0.0 and −2.0 to the chosen fitting point. In the case of solar abundances, the Teff of the giant branch varied by up to 100–150 K, depending on how the outer layers were treated. Much smaller variations were found for metal-poor giants (or main-sequence stars). Interestingly, models for the low solar Z favored by Asplund et al. (Z=0.0125) were unable to reproduce the gap near the turnoff in the C-M diagram of the old open cluster M 67, in contrast to models that assume Z=0.0188.
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| 10. |
- VandenBerg, Don A., et al.
(författare)
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On the use of blanketed atmospheres as boundary conditions for stellar evolutionary models
- 2008
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 675:1, s. 746-763
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Tidskriftsartikel (refereegranskat)abstract
- Stellarmodels have been computed for stars having [Fe/H] = 0.0 (assuming both the Grevesse & Sauval and Asplund et al. heavy-element mixtures) and -2.0 to determine the effects on the predicted T-eff scale of using boundary conditions derived from the latest MARCS model atmospheres. The latter were fitted in a fully consistent way to the interior models at the photosphere and at tau = 100: the resultant evolutionary sequences on the H-R diagram were found to be nearly independent of the chosen fitting point. Tracks were also computed in which the pressure at T = T-eff was obtained by integrating the hydrostatic equation together with either the classical gray T(tau, T-eff) relation or that derived by Krishna Swamy from an empirical solar atmosphere. Due to the effects of differences in the solar-calibrated values of the mixing-length parameter, alpha(MLT), very similar tracks were obtained for the different treatments of the atmosphere, except at solar abundances, where the models based on the Krishna Swamy T(tau, T-eff) relationship predicted similar to 150 K hotter giant branches than the others, in good agreement with the inferred temperatures of giants in the open cluster M67 from recent (V - K) -T-eff relations. Tracks that used new "scaled solar, differentially corrected'' MARCS atmospheres were found to agree well with those that employed the Krishna Swamy T(tau, T-eff) relationship, independently of the assumed metal abundance. (Gray atmospheres are quite different from MARCS models.) Fits of isochrones for [Fe/H] = -2.0 to the CMD of the globular cluster M68, as well as the possibility that alpha(MLT) varies with stellar parameters, are also discussed.
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