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| 2. |
- 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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| 3. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 4. |
- Hibbett, D. S., et al.
(författare)
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A higher-level phylogenetic classification of the Fungi
- 2007
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Ingår i: Mycological Research. - : Elsevier BV. - 0953-7562 .- 1469-8102. ; 111, s. 509-547
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Tidskriftsartikel (refereegranskat)abstract
- A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecarioromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotiria. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella. (c) 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.
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| 6. |
- Arimoto, M., et al.
(författare)
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Performance assessment study of the balloon-borne astronomical soft gamma-ray polarimeter PoGOLite
- 2007
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Ingår i: Physica. E, Low-Dimensional systems and nanostructures. - : Elsevier BV. - 1386-9477 .- 1873-1759. ; 40:2, s. 438-441
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Tidskriftsartikel (refereegranskat)abstract
- Measurements of polarization play a crucial role in the understanding of the dominant emission mechanism of astronomical sources. Polarized Gamma-ray Observer-Light version (PoGOLite) is a balloon-borne astronomical soft gamma-ray polarimeter at the 25-80 keV band. The PoGOLite detector consists of a hexagonal close-packed array of 217 Phoswich detector cells (PDCs) and side anti-coincidence shields (SASs) made of BGO crystals surrounding PDCs. Each PDC consists of a slow hollow scintillator, a fast scintillator and a BGO crystal that connects to a photomultiplier tube at the end. To examine the PoGOLite's capability and estimate the performance, we conducted experiments with the PDC using radioisotope 241Am. In addition, we compared this result with performance expected by Monte Carlo simulation with Geant4. As a result, we found that the actual PDC has the capability to detect a 100 m Crab source until 80 keV.
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| 7. |
- Jallow, Muminatou, et al.
(författare)
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Genome-wide and fine-resolution association analysis of malaria in West Africa.
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; , s. 657-665
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Tidskriftsartikel (refereegranskat)abstract
- We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 x 10(-7) to P = 4 x 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations.
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| 8. |
- Kanai, Y., et al.
(författare)
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Beam test of a prototype phoswich detector assembly for the PoGOLite astronomical soft gamma-ray polarimeter
- 2007
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 570:1, s. 61-71
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Tidskriftsartikel (refereegranskat)abstract
- We report about the beam test on a prototype of the balloon-based astronomical soft gamma-ray polarimeter, PoGOLite (Polarized Gamma-ray Observer-Light Version) conducted at KEK Photon Factory, a synchrotron radiation facility in Japan. The synchrotron beam was set at 30, 50, and 70 keV and its polarization was monitored by a calibrated polarimeter. The goal of the experiment was to validate the flight design of the polarimeter. PoGOLite is designed to measure polarization by detecting a Compton scattering and the subsequent photo-absorption in an array of 217 well-type phoswich detector cells (PDCs). The test setup included a first flight model PDC and a front-end electronics to select and reconstruct valid Compton scattering events. The experiment has verified that the flight PDC can detect recoil electrons and select valid Compton scattering events down to 30 keV from background. The measure azimuthal modulations (34.4%, 35.8% and 37.2% at 30, 50, and 70 keV, respectively) agreed within 10% (relative) with the predictions by Geant4 implemented with dependence on the initial and final photon polarizations.
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