| 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. |
- Lindblad-Toh, Kerstin, et al.
(författare)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Tidskriftsartikel (refereegranskat)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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| 3. |
- Moschos, Sterghios Athanasios, et al.
(författare)
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Lung delivery studies using siRNA conjugated to TAT(48-60) and penetratin reveal peptide induced reduction in gene expression and induction of innate immunity
- 2007
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Ingår i: Bioconjugate Chemistry. - : American Chemical Society (ACS). - 1520-4812 .- 1043-1802. ; 18:5, s. 1450-1459
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Tidskriftsartikel (refereegranskat)abstract
- The therapeutic application of siRNA shows promise as an alternative approach to small-molecule inhibitors for the treatment of human disease. However, the major obstacle to its use has been the difficulty in delivering these large anionic molecules in vivo. In this study, we have investigated whether siRNA-mediated knockdown of p38 MAP kinase mRNA in mouse lung is influenced by conjugation to the nonviral delivery vector cholesterol and the cell penetrating peptides (CPP) TAT(48-60) and penetratin. Initial studies in the mouse fibroblast L929 cell line showed that siRNA conjugated to cholesterol, TAT(48-60), and penetratin, but not siRNA alone, achieved a limited reduction of p38 MAP kinase mRNA expression. Intratracheal administration of siRNA resulted in localization within macrophages and scattered epithelial cells and produced a 30-45% knockdown of p38 MAP kinase mRNA at 6 h. As with increasing doses of siRNA, conjugation to cholesterol improved upon the duration but not the magnitude of mRNA knockdown, while penetratin and TAT(48-60) had no effect. Importantly, administration of the penetratin or TAT(48-60) peptides alone caused significant reduction in p38 MAP kinase mRNA expression, while the penetratin-siRNA conjugate activated the innate immune response. Overall, these studies suggest that conjugation to cholesterol may extend but not increase siRNA-mediated p38 MAP kinase mRNA knockdown in the lung. Furthermore, the use of CPP may be limited due to as yet uncharacterized effects upon gene expression and a potential for immune activation.
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| 4. |
- Richards, Stephen, et al.
(författare)
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The genome of the model beetle and pest Tribolium castaneum.
- 2008
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Ingår i: Nature. - 1476-4687. ; 452:7190, s. 949-55
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Tidskriftsartikel (refereegranskat)abstract
- Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
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| 5. |
- Szatmari, Peter, et al.
(författare)
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Mapping autism risk loci using genetic linkage and chromosomal rearrangements.
- 2007
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 39:3, s. 319-328
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Tidskriftsartikel (refereegranskat)abstract
- Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,168 families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.
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| 6. |
- Binner, Jane M., et al.
(författare)
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Admissible monetary aggregates for the euro area
- 2009
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Ingår i: Journal of International Money and Finance. - : Elsevier BV. - 0261-5606. ; 28:1, s. 99-114
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Tidskriftsartikel (refereegranskat)abstract
- We use the Fleissig and Whitney [Fleissig, A.R., Whitney, G.A., 2003. A new PC-based test for Varian's weak separability conditions. Journal of Business and Economics Statistics 21 (1), 133-144] weak separability test to determine admissible levels of monetary aggregation for the Euro area. We find that the Euro area monetary assets in M2 and M3 are weakly separable and construct admissible Divisia monetary aggregates for these assets. We show that real growth of the admissible Divisia aggregates enters the Euro area IS curve positively and significantly for the period from 1980 to 2005. Out of sample, we show that Divisia M2 and M3 appear to contain useful information for forecasting Euro area inflation. (c) 2008 Elsevier Ltd. All rights reserved.
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| 7. |
- Dahlquist, Erik, et al.
(författare)
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Presentation of a dry black liquor gasification process with direct causticization
- 2005
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Ingår i: TAPPI Journal. ; 4:6, s. 15-19
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Tidskriftsartikel (refereegranskat)abstract
- In a new black liquor gasification process, black liquor is injected into a circulating fluidized bed, with sodium titanate (Na 2O· (TiO 2) 3) as the fluidizing medium.The organics are gasified mainly by steam reforming because the temperature is relatively low (below 870°C) and the water content of the black liquor is relatively high (>20% water).The black liquor inorganics consist mainly of sodium carbonate and sodium sulfate. In the reactor, sodium carbonate is converted into Na 2O·TiO 2, which is removed from the bed and dissolved in water to give 4 NaOH + Na 2O·(TiO 2)3. After dewatering, this material is reinjected into the fluidized bed.The sulfate is reduced to Na 2S, and most of the sulfur is evaporated as H 2S after Na 2S reacts with CO 2 + H 2O. In a scrubber, the H 2S is selectively absorbed without CO 2. The direct causticization makes the lime kiln unnecessary. The gas is reheated after dust is removed and then combusted in a gas turbine/steam turbine cycle, to produce 2-3 times more electricity than produced in steam cycles with conventional recovery boilers.
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| 8. |
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| 9. |
- Fahlman, Andreas, et al.
(författare)
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Metabolic costs of foraging and the management of O2 and CO2 stores in Steller sea lions
- 2008
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Ingår i: The Journal of Experimental Biology. - Cambridge : The Company of Biologists. - 0022-0949 .- 1477-9145. ; 211, s. 3573-3580
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Tidskriftsartikel (refereegranskat)abstract
- The metabolic costs of foraging and the management of O2 and CO2 stores during breath-hold diving was investigated in three female Steller sea lions (Eumetopias jubatus) trained to dive between 10 and 50 m (N=1142 dives). Each trial consisted of two to eight dives separated by surface intervals that were determined by the sea lion (spontaneous trials) or by the researcher (conditioned trials). During conditioned trials, surface intervals were long enough for O2 to return to pre-dive levels between each dive. The metabolic cost of each dive event (dive+surface interval; DMR) was measured using flow-through respirometry. The respiratory exchange ratio (O2/CO2) was significantly lower during spontaneous trials compared with conditioned trials. DMR was significantly higher during spontaneous trials and decreased exponentially with dive duration. A similar decrease in DMR was not as evident during conditioned trials. DMR could not be accurately estimated from the surface interval (SI) following individual dives that had short SIs (<50 s), but could be estimated on a dive by dive basis for longer SIs (>50 s). DMR decreased by 15%, but did not differ significantly from surface metabolic rates (MRS) when dive duration increased from 1 to 7 min. Overall, these data suggest that DMR is almost the same as MRS, and that Steller sea lions incur an O2 debt during spontaneous diving that is not repaid until the end of the dive bout. This has important consequences in differentiating between the actual and `apparent' metabolic rate during diving, and may explain some of the differences in metabolic rates reported in pinniped species.
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| 10. |
- Haas, Gabriel P, et al.
(författare)
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Needle biopsies on autopsy prostates: sensitivity of cancer detection based on true prevalence
- 2007
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 99:19, s. 1484-1489
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: It is difficult to estimate the diagnostic accuracy of biopsy for prostate cancer because men with negative biopsy do not undergo radical prostatectomy and thus have no confirmation of biopsy findings. METHODS: We performed 18-core needle biopsies on autopsy prostates from 164 men who had no history of prostate cancer. Six-core biopsies were taken from each of the mid peripheral zone (MPZ), the lateral peripheral zone (LPZ), and the central zone (CZ). We tested associations between age and tumor characteristics and analyzed the sensitivity of biopsies at each site. All statistical tests were two-sided. RESULTS: Prostate cancer was present in 47 (29%) prostates. Of the 47 cancers detected, 20 were clinically significant according to histologic criteria. Tumor volume was associated with tumor grade (P = .012) and with age (P<.001). The biopsies from the CZ did not detect any cancer that was not present in biopsies of either the MPZ or LPZ. The sensitivity of the biopsies taken from the MPZ and LPZ together (53%, 95% confidence interval [CI] = 38% to 68%) was therefore the same as that of 18-core biopsies and was superior to that of biopsies of the MPZ alone (30%, 95% CI = 17% to 45%) (P = .003). The sensitivities of biopsies from the MPZ for clinically significant and insignificant cancer were 55% (95% CI = 32% to 77%) and 11% (95% CI = 2% to 29%), respectively, compared with 80% (95% CI = 56% to 94%) and 33% (95% CI = 17% to 54%) for those from the MPZ and LPZ combined. CONCLUSIONS: The ability to detect prostate cancer was more related to the biopsy site than to the number of biopsy cores taken. The 12-core biopsies, six cores each from the MPZ and LPZ, were most likely to detect the majority of clinically significant cancers but also detected many insignificant cancers. When the six-core biopsies from the CZ were added, no increase in sensitivity was observed.
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