| 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. |
- Franz, P, et al.
(författare)
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Tomographic imaging of resistive mode dynamics in the Madison Symmetric Torus reversed-field pinch
- 2006
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Ingår i: Physics of Plasmas. - : AIP Publishing. - 1070-664X .- 1089-7674. ; 13:1, s. 012510-
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Tidskriftsartikel (refereegranskat)abstract
- A detailed study of the dynamics and magnetic topological effects of resistive-tearing modes is presented for different operational regimes in the Madison Symmetric Torus reversed-field pinch [R. N. Dexter , Fusion Technol. 19, 131 (1991)]. Soft-x-ray tomography and magnetic measurements, along with numerical reconstruction of magnetic-field lines with the ORBIT code [R. B. White and M. S. Chance, Phys. Fluids 27, 2455 (1984)], have been employed. Magnetic-mode dynamics has been investigated in standard plasmas during the transition to the quasi-single helicity state, in which a single mode dominates the mode spectrum. Single helical soft-x-ray structures are studied with tomography in these cases. These structures are associated with magnetic islands, indicating that helical flux surfaces appear in the plasma. Mode dynamics has also been examined during auxiliary inductive current drive, the goal of which is to reduce the tearing-mode amplitudes. In this case the phenomenology of the soft-x-ray structures appearing in the plasma is more complex. In fact, when a quasi-single helicity spectrum occurs, a single island bigger than in the standard case is usually found. On the other hand, when all modes decrease, two helical soft-x-ray structures are observed, with the same helicity as the two innermost resonant modes. This constitutes the first direct evidence of magnetic-chaos reduction during auxiliary inductive current drive, which is responsible for the achievement of the best confinement in the reversed-field pinch configuration up to now.
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| 3. |
- Frassinetti, Lorenzo, et al.
(författare)
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Soft X-ray pulses in the reversed-field pinch
- 2005
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Ingår i: IEEE Transactions on Plasma Science. - 0093-3813 .- 1939-9375. ; 33:2, s. 462-463
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Tidskriftsartikel (refereegranskat)abstract
- Data obtained in the Madison Symmetric Torus reversed-field pinch with a soft X-ray diagnostic will be presented. They have been used to study transient transport events in this device. Fast thermal relaxation events are associated to bursts of magnetohydrodynamic fluctuations.
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| 4. |
- Graves, Genevieve J. M., et al.
(författare)
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Limits from the Hubble Space Telescope on a Point Source in SN 1987A
- 2005
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 629, s. 944-959
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Tidskriftsartikel (refereegranskat)abstract
- We observed supernova 1987A (SN 1987A) with the Space Telescope Imaging Spectrograph (STIS) on the Hubble Space Telescope (HST) in 1999 September and again with the Advanced Camera for Surveys (ACS) on the HST in 2003 November. Our spectral observations cover ultraviolet (UV) and optical wavelengths from 1140 to 10266 Å, and our imaging observations cover UV and optical wavelengths from 2900 to 9650 Å. No point source is observed in the remnant. We obtain a limiting flux of Fopt<=1.6×10-14 ergs s-1 cm-2 in the wavelength range 2900-9650 Å for any continuum emitter at the center of the supernova remnant (SNR). This corresponds to an intrinsic luminosity of Lopt<=5×1033 ergs s-1. It is likely that the SNR contains opaque dust that absorbs UV and optical emission, resulting in an attenuation of ~35% due to dust absorption in the SNR. Correcting for this level of dust absorption would increase our upper limit on the luminosity of a continuum source by a factor of 1.54. Taking into account dust absorption in the remnant, we find a limit of Lopt<=8×1033 ergs s-1. We compare this upper bound with empirical evidence from point sources in other supernova remnants and with theoretical models for possible compact sources. We show that any survivor of a possible binary system must be no more luminous than an F6 main-sequence star. Bright young pulsars such as Kes 75 or the Crab pulsar are excluded by optical and X-ray limits on SN 1987A. Other nonplerionic X-ray point sources have luminosities similar to the limits on a point source in SN 1987A; RCW 103 and Cas A are slightly brighter than the limits on SN 1987A, while Pup A is slightly fainter. Of the young pulsars known to be associated with SNRs, those with ages <=5000 yr are all too bright in X-rays to be compatible with the limits on SN 1987A. Examining theoretical models for accretion onto a compact object, we find that spherical accretion onto a neutron star is firmly ruled out and that spherical accretion onto a black hole is possible only if there is a larger amount of dust absorption in the remnant than predicted. In the case of thin-disk accretion, our flux limit requires a small disk, no larger than 1010 cm, with an accretion rate no more than 0.3 times the Eddington accretion rate. Possible ways to hide a surviving compact object include the removal of all surrounding material at early times by a photon-driven wind, a small accretion disk, or very high levels of dust absorption in the remnant. It will not be easy to improve substantially on our optical-UV limit for a point source in SN 1987A, although we can hope that a better understanding of the thermal infrared emission will provide a more complete picture of the possible energy sources at the center of SN 1987A.
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| 5. |
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| 6. |
- 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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| 7. |
- 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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| 8. |
- Baker-Austin, Craig, et al.
(författare)
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Extreme arsenic resistance by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.
- 2007
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Ingår i: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 11:3, s. 425-34
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Tidskriftsartikel (refereegranskat)abstract
- 'Ferroplasma acidarmanus' Fer1 is an arsenic-hypertolerant acidophilic archaeon isolated from the Iron Mountain mine, California; a site characterized by heavy metals contamination. The presence of up to 10 g arsenate per litre [As(V); 133 mM] did not significantly reduce growth yields, whereas between 5 and 10 g arsenite per litre [As(III); 67-133 mM] significantly reduced the yield. Previous bioinformatic analysis indicates that 'F. acidarmanus' Fer1 has only two predicted genes involved in arsenic resistance and lacks a recognizable gene for an arsenate reductase. Biochemical analysis suggests that 'F. acidarmanus' Fer1 does not reduce arsenate indicating that 'F. acidarmanus' Fer1 has an alternative resistance mechanism to arsenate other than reduction to arsenite and efflux. Primer extension analysis of the putative ars transcriptional regulator (arsR) and efflux pump (arsB) demonstrated that these genes are co-transcribed, and expressed in response to arsenite, but not arsenate. Two-dimensional polyacrylamide gel electrophoresis analysis of 'F. acidarmanus' Fer1 cells exposed to arsenite revealed enhanced expression of proteins associated with protein refolding, including the thermosome Group II HSP60 family chaperonin and HSP70 DnaK type heat shock proteins. This report represents the first molecular and proteomic study of arsenic resistance in an acidophilic archaeon.
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| 9. |
- Butts, Craig P, et al.
(författare)
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Structure-based rationale for selectivity in the asymmetric allylic alkylation of cycloalkenyl esters employing the Trost 'Standard Ligand' (TSL): isolation, analysis and alkylation of the monomeric form of the cationic eta(3)-cyclohexenyl complex [(eta(3)-c-C6H9)Pd(TSL)]+.
- 2009
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 131:29, s. 9945-57
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Tidskriftsartikel (refereegranskat)abstract
- The solution-phase structures of the monomeric forms of the cationic Pd-eta(3)-allyl and Pd-eta(3)-cyclohexenyl complexes [Pd(R,R)-1(eta(3)-C(3)H(5))](+) (7(+)) and [Pd(R,R)-1(eta(3)-C(6)H(9))](+) (8(+)) bearing the trans-cyclohexylenediamine-based Trost 'Standard Ligand' (R,R)-1 have been elucidated by NMR, isotopic labeling and computation. In both complexes, (R,R)-1 is found to adopt a C(1)-symmetric conformation, leading to a concave shape in the 13-membered chelate in which one amide group in the chiral scaffold projects its NH unit out of the concave surface in close vicinity to one allyl terminus. The adjacent amide has a reversed orientation and projects its carbonyl group out of the concave face in the vicinity of the opposite allyl terminus. Stoichiometric and catalytic asymmetric alkylations of [8(+)][X(-)] by MCHE(2) (E = ester, M = 'escort' counterion, X = Pd allyl counterion) show the same selectivities and trends as have been reported for in situ-generated catalysts, and a new model for the enantioselectivity has been explored computationally. Three factors are found to govern the regioselectivity (pro-S vs pro-R) of attack of nucleophiles on the eta(3)-C(6)H(9) ring in 8(+) and thus the ee of the alkylation product: (i) a pro-R torquoselective bias is induced by steric interaction of the eta(3)-C(6)H(9) moiety with one phenyl ring of the ligand; (ii) pro-S delivery of the nucleophile can be facilitated by hydrogen-bonding with the concave orientated amide N-H; and (iii) pro-R delivery of the nucleophile can be facilitated by escort ion (M) binding to the concave orientated amide carbonyl. The latter two opposing interactions lead to the selectivity of the alkylation being sensitive to the identities of X(-) and M(+). The generation of 8(+) from cyclohexenyl ester substrate has also been explored computationally. The concave orientated amide N-H is able to activate the leaving group of the allylic ester by hydrogen bonding to its carbonyl group. However, this interaction is only feasible for the (S)-enantiomer of substrate, leading to the prediction of a powerful kinetic resolution (k(S) >> k(R)), as is found experimentally. This new model involving two regiochemically distinct (NH) and (CO) locations for nucleofuge or nucleophile binding, may prove of broad utility for the interpretation of the selectivity in asymmetric allylic alkylation reactions catalyzed by Pd complexes of (R,R)-1 and related ligands.
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| 10. |
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