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| 2. |
- Carninci, P, et al.
(författare)
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The transcriptional landscape of the mammalian genome
- 2005
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 309:5740, s. 1559-1563
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Tidskriftsartikel (refereegranskat)abstract
- This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5′ and 3′ boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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| 3. |
- Ahrens, J, et al.
(författare)
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Intermediate resonance excitation in the gamma p -> p pi(0)pi(0) reaction
- 2005
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 624:3-4, s. 173-180
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Tidskriftsartikel (refereegranskat)abstract
- The helicity dependence of the total cross section for the (gamma) over right arrow(p) over right arrow -> p pi(0)pi(0) reaction has been measured for the first time at incident photon energies from 400 to 800 MeV. The measurement, performed at the tagged photon beam facility of the MAMI accelerator in Mainz, used the large acceptance detector DAPHNE and a longitudinally polarized frozen-spin target. This channel is found to be excited predominantly when the photon and proton have a parallel spin orientation, most likely due to the intermediate production of the D-13(1520) resonance. However, the contribution of the antiparallel spin configuration, arising from other reaction mechanisms, is also not negligible. This result gives important new information to resolve the existing model discrepancies in the identification of the nucleon resonances contributing to this channel.
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| 6. |
- 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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| 7. |
- Han, Shizhong, et al.
(författare)
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Evaluation of imputation-based association in and around the integrin-alpha-M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE)
- 2009
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 18:6, s. 1171-1180
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Tidskriftsartikel (refereegranskat)abstract
- We recently identified a novel non-synonymous variant, rs1143679, at exon 3 of the ITGAM gene associated with systemic lupus erythematosus (SLE) susceptibility in European-Americans (EAs) and African-Americans. Using genome-wide association approach, three other studies also independently reported an association between SLE susceptibility and ITGAM or ITGAM-ITGAX region. The primary objectives of this study are to assess whether single or multiple causal variants from the same gene or any nearby gene(s) are involved in SLE susceptibility and to confirm a robust ITGAM association across nine independent data sets (n = 8211). First, we confirmed our previously reported association of rs1143679 (risk allele 'A') with SLE in EAs (P = 1.0 x 10(-8)) and Hispanic-Americans (P = 2.9 x 10(-5)). Secondly, using a comprehensive imputation-based association test, we found that ITGAM is one of the major non-human leukocyte antigen susceptibility genes for SLE, and the strongest association for EA is the same coding variant rs1143679 (log(10)Bayes factor=20, P = 6.17 x 10(-24)). Thirdly, we determined the robustness of rs1143679 association with SLE across three additional case-control samples, including UK (P = 6.2 x 10(-8)), Colombian (P = 3.6 x 10(-7)), Mexican (P = 0.002), as well as two independent sets of trios from UK (P(TDT) = 1.4 x 10(-5)) and Mexico (P(TDT) = 0.015). A meta-analysis combing all independent data sets greatly reinforces the association (P(meta) = 7.1 x 10(-50), odds ratio = 1.83, 95% confidence interval = 1.69-1.98, n = 10 046). However, this ITGAM association was not observed in the Korean or Japanese samples, in which rs1143679 is monomorphic for the non-risk allele (G). Taken together along with our earlier findings, these results demonstrate that the coding variant, rs1143679, best explains the ITGAM-SLE association, especially in European- and African-derived populations, but not in Asian populations.
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| 8. |
- Mancusi, Davide, 1980, et al.
(författare)
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Calculation of Energy-Deposition Distributions and Microdosimetric Estimation of the Biological Effect of a 9C Beam
- 2009
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Ingår i: Radiation and Environmental Biophysics. - 1432-2099 .- 0301-634X. ; 48:2, s. 135-143
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Tidskriftsartikel (refereegranskat)abstract
- Among the alternative beams being recently considered for external cancer radiotherapy, C-9 has received some attention because it is expected that its biological effectiveness could be boosted by the beta-delayed emission of two alpha particles and a proton that takes place at the ion-stopping site. Experiments have been performed to characterise this exotic beam physically and models have been developed to estimate quantitatively its biological effect. Here, the particle and heavy-ion transport code system (PHITS ) is used to calculate energy-deposition and linear energy transfer distributions for a C-9 beam in water and the results are compared with published data. Although PHITS fails to reproduce some of the features of the distributions, it suggests that the decay of C-9 contributes negligibly to the energy-deposition distributions, thus contradicting the previous interpretation of the measured data. We have also performed a microdosimetric calculation to estimate the biological effect of the decay, which was found to be negligible; previous microdosimetric Monte-Carlo calculations were found to be incorrect. An analytical argument, of geometrical nature, confirms this conclusion and gives a theoretical upper bound on the additional biological effectiveness of the decay. However, no explanation can be offered at present for the observed difference in the biological effectiveness between C-9 and C-12; the reproducibility of this surprising result will be verified in coming experiments.
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| 10. |
- Sihver, Lembit, 1962, et al.
(författare)
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Recent developments and benchmarking of the PHITS code
- 2007
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Ingår i: Advances in Space Research. - : Elsevier BV. - 1879-1948 .- 0273-1177. ; 40:9, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- Many new options have recently been included in PHITS, e.g., to calculate LET distributions of particles in matter or energy-deposition distributions event by event and correlations between energy depositions in different regions. This makes it possible to calculate the effects of particle radiation on biological and non-biological materials, e.g., risk for single event upsets in electronic devices. As a part of an extensive ongoing benchmarking of PHITS, we have compared calculated partial projectile fragmentation cross sections with accelerator-based measurements from the reactions of 200-1000 MeV/n He-4, C-12, N-14, O-16, Ne-20, Si-28, Ar-40, and Fe-56 on polyethylene, carbon, aluminum, copper, tin and lead, with different thicknesses, using different total reaction cross section models in PHITS. We have compared simulated and measured Bragg and attenuation curves of 200 MeV/n C-12 in water, and neutron energy spectra, at different angles, from 100 to 400 MeV/n C-12 stopped in water. Bragg curves for 110, 140, 170, 190 and 225 MeV/n He-3 in water have been studied, as well as gamma-ray dose decay curves of activated Cu target bombarded by 400 and 800 MeV/n Ar-40. When using the default total reaction cross section model developed by Tripathi et al. (1996,1997 and 1999) [Tripathi, R.K., Cucinotta, F.A., Wilson, J.W. Accurate universal parameterization of absorption cross sections, Nucl. Instr. Methods B117, 347, 1996; Tripathi, R.K., Wilson, J.W., Cucinotta, F.A. Accurate universal parameterization of absorption cross sections II - neutron absorption cross sections. Nucl. Instr. Methods B129, 11, 1997; Tripathi, R.K., Cucinotta, F.A., Wilson, J.W. Accurate universal parameterization of absorption cross sections III - light systems. Nucl. Instr. Methods B155, 349, 1999.] the partial fragmentation cross sections appear to be systematically slightly underestimated by a factor which is independent on the fragment species within the same data set, and so do the simulated neutron energy spectra from selected heavy ion reactions; especially in the forward direction. The simulated attenuation and Bragg curves, however, show good agreement with measured ones. These observations stimulate further benchmarking to confirm the accuracy of the code and gives directions on possible improvements to be applied to the code in the near future. (C) 2007 Published by Elsevier Ltd on behalf of COSPAR.
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