| 21. |
- Barends, Thomas R. M., et al.
(författare)
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Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase
- 2009
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 459, s. 1015-1018
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Tidskriftsartikel (refereegranskat)abstract
- The ability to respond to light is crucial for most organisms. BLUF is a recently identified photoreceptor protein domain that senses blue light using a FAD chromophore. BLUF domains are present in various proteins from the Bacteria, Euglenozoa and Fungi. Although structures of single-domain BLUF proteins have been determined, none are available for a BLUF protein containing a functional output domain; the mechanism of light activation in this new class of photoreceptors has thus remained poorly understood. Here we report the biochemical, structural and mechanistic characterization of a full-length, active photoreceptor, BlrP1 (also known as KPN_01598), from Klebsiella pneumoniae. BlrP1 consists of a BLUF sensor domain and a phosphodiesterase EAL output domain which hydrolyses cyclic dimeric GMP (c-di-GMP). This ubiquitous second messenger controls motility, biofilm formation, virulence and antibiotic resistance in the Bacteria. Crystal structures of BlrP1 complexed with its substrate and metal ions involved in catalysis or in enzyme inhibition provide a detailed understanding of the mechanism of the EAL-domain c-di-GMP phosphodiesterases. These structures also sketch out a path of light activation of the phosphodiesterase output activity. Photon absorption by the BLUF domain of one subunit of the antiparallel BlrP1 homodimer activates the EAL domain of the second subunit through allosteric communication transmitted through conserved domain-domain interfaces.
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| 22. |
- Barthelmy, S D, et al.
(författare)
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An origin for short gamma-ray bursts unassociated with current star formation
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 438, s. 994-996
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Tidskriftsartikel (refereegranskat)abstract
- Two short (< 2 s) gamma-ray bursts (GRBs) have recently been localized(1-4) and fading afterglow counterparts detected(2-4). The combination of these two results left unclear the nature of the host galaxies of the bursts, because one was a star-forming dwarf, while the other was probably an elliptical galaxy. Here we report the X-ray localization of a short burst (GRB 050724) with unusual gamma-ray and X-ray properties. The X-ray afterglow lies off the centre of an elliptical galaxy at a redshift of z = 0.258 (ref. 5), coincident with the position determined by ground-based optical and radio observations(6-8). The low level of star formation typical for elliptical galaxies makes it unlikely that the burst originated in a supernova explosion. A supernova origin was also ruled out for GRB 050709 ( refs 3, 31), even though that burst took place in a galaxy with current star formation. The isotropic energy for the short bursts is 2 - 3 orders of magnitude lower than that for the long bursts. Our results therefore suggest that an alternative source of bursts - the coalescence of binary systems of neutron stars or a neutron star-black hole pair - are the progenitors of short bursts.
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| 23. |
- Belonoshko, Anatoly B., et al.
(författare)
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Stability of the body-centred-cubic phase of iron in the Earth's inner core
- 2003
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 424:6952, s. 1032-1034
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Tidskriftsartikel (refereegranskat)abstract
- Iron is thought to be the main constituent of the Earth's core(1), and considerable efforts(2-14) have therefore been made to understand its properties at high pressure and temperature. While these efforts have expanded our knowledge of the iron phase diagram, there remain some significant inconsistencies, the most notable being the difference between the 'low' and 'high' melting curves(15). Here we report the results of molecular dynamics simulations of iron based on embedded atom models fitted to the results of two implementations of density functional theory. We tested two model approximations and found that both point to the stability of the body-centred-cubic (b.c.c.) iron phase at high temperature and pressure. Our calculated melting curve is in agreement with the 'high' melting curve, but our calculated phase boundary between the hexagonal close packed (h. c. p.) and b.c.c. iron phases is in good agreement with the 'low' melting curve. We suggest that the h.c.p.-b.c.c. transition was previously misinterpreted as a melting transition, similar to the case of xenon(16-18), and that the b.c.c. phase of iron is the stable phase in the Earth's inner core.
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| 24. |
- Bengtsson, Ragnar, et al.
(författare)
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Nuclear physics - A non-disappearing magic trick
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 449:7161, s. 411-411
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Well-established models of nuclei describe properties such as shells and magic numbers. But how do these predictions stand up to scrutiny for exotic, unstable nuclei? Pretty well, according to the latest study.
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| 25. |
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| 26. |
- Bieling, Peter, et al.
(författare)
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Reconstitution of a microtubule plus-end tracking system in vitro
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7172, s. 1100-1105
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Tidskriftsartikel (refereegranskat)abstract
- The microtubule cytoskeleton is essential to cell morphogenesis. Growing microtubule plus ends have emerged as dynamic regulatory sites in which specialized proteins, called plus-end-binding proteins (+TIPs), bind and regulate the proper functioning of microtubules. However, the molecular mechanism of plus-end association by +TIPs and their ability to track the growing end are not well understood. Here we report the in vitro reconstitution of a minimal plus-end tracking system consisting of the three fission yeast proteins Mal3, Tip1 and the kinesin Tea2. Using time-lapse total internal reflection fluorescence microscopy, we show that the EB1 homologue Mal3 has an enhanced affinity for growing microtubule end structures as opposed to the microtubule lattice. This allows it to track growing microtubule ends autonomously by an end recognition mechanism. In addition, Mal3 acts as a factor that mediates loading of the processive motor Tea2 and its cargo, the Clip170 homologue Tip1, onto the microtubule lattice. The interaction of all three proteins is required for the selective tracking of growing microtubule plus ends by both Tea2 and Tip1. Our results dissect the collective interactions of the constituents of this plus-end tracking system and show how these interactions lead to the emergence of its dynamic behaviour. We expect that such in vitro reconstitutions will also be essential for the mechanistic dissection of other plus-end tracking systems.
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| 27. |
- 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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| 28. |
- 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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| 29. |
- Boisvert, Catherine, et al.
(författare)
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The pectoral fin of Panderichthys and the origin of digits
- 2008
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Ingår i: Nature. - London : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 456:7222, s. 636-638
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Tidskriftsartikel (refereegranskat)abstract
- One of the identifying characteristics of tetrapods (limbed vertebrates) is the presence of fingers and toes. Whereas the proximal part of the tetrapod limb skeleton can easily be homologized with the paired fin skeletons of sarcopterygian (lobe-finned) fish, there has been much debate about the origin of digits. Early hypotheses1 interpreted digits as derivatives of fin radials, but during the 1990s the idea gained acceptance that digits are evolutionary novelties without direct equivalents in fish fin skeletons. This was partly based on developmental genetic data2, but also substantially on the pectoral fin skeleton of the elpistostegid (transitional fish/tetrapod) Panderichthys, which appeared to lack distal digit-like radials3. Here we present a CT scan study of an undisturbed pectoral fin of Panderichthys demonstrating that the plate-like 'ulnare' of previous reconstructions is an artefact and that distal radials are in fact present. This distal portion is more tetrapod-like than that found in Tiktaalik 4 and, in combination with new data about fin development in basal actinopterygians5, sharks6 and lungfish7, makes a strong case for fingers not being a novelty of tetrapods but derived from pre-existing distal radials present in all sarcopterygian fish.
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| 30. |
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