| 1. |
- 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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| 2. |
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| 3. |
- Gambardella, P., et al.
(författare)
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Supramolecular control of the magnetic anisotropy in two-dimensional high-spin Fe arrays at a metal interface
- 2009
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Ingår i: Nature Materials. - 1476-4660 .- 1476-1122. ; 8:3, s. 189-193
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Tidskriftsartikel (refereegranskat)abstract
- Magnetic atoms at surfaces may provide the ultimate paradigm of a solid-state magnetic memory exhibiting either classical , or quantum , behaviour. Individual atoms, however, are difficult to arrange in regular patterns1,2,3,4, . Moreover, their magnetic properties are dominated by interaction with the substrate, which, as in the case of Kondo systems, often leads to a decrease or quench of their local magnetic moment , . Here we show that the supramolecular assembly of Fe and 1,4-benzenedicarboxylic acid molecules on a Cu surface results in ordered arrays of high-spin mononuclear Fe centres on a 1.5 nm square grid. Lateral coordination with the molecular ligands yields unsaturated yet stable coordination bonds, which allow for the chemical modification of the electronic and magnetic properties of the Fe atoms independently from the substrate. The easy magnetization direction of the Fe centres can be switched by oxygen adsorption, thus opening a way to control the magnetic anisotropy in supramolecular layers akin to that employed in metallic thin films , , , .
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| 4. |
- Haas, Brian J., et al.
(författare)
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Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
- 2009
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 461:7262, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
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| 5. |
- Hreinsdottir, S, et al.
(författare)
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A complex earthquake sequence captured by the continuous GPS network in SW Iceland
- 2009
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Ingår i: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 36:12, s. L12309-
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Tidskriftsartikel (refereegranskat)abstract
- A complex sequence of earthquakes struck the western part of the South Iceland Seismic Zone (SISZ) on 29 May 2008. The sequence initiated with a M(w)6.3 (NEIC) earthquake in the western part of the SISZ. Aftershocks from the earthquake delineate two parallel N-S trending structures 4 km apart, in addition to activity along an E-W zone further westward. Continuous GPS measurements can best be explained by right-lateral strike-slip motion on two parallel N-S trending faults, with little slip occurring on other structures illuminated by earthquake activity. We estimate a total moment release of M(w)6.2, with M(w)6.1 on the first rupture and M(w)6.0 on the second rupture. High rate (1 Hz) CGPS data from a near-field station suggest that the main asperity on the Kross fault ruptured within 3 s of the initial mainshock on the Ingolfsfjall fault. Citation: Hreinsdottir, S., T. Amadottir, J. Decriem, H. Geirsson, A. Tryggvason, R. A. Bennett, and P. LaFemina (2009), A complex earthquake sequence captured by the continuous GPS network in SW Iceland, Geophys. Res. Lett., 36, L12309, doi: 10.1029/2009GL038391.
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| 6. |
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| 7. |
- Jónsdóttir, Kristín, et al.
(författare)
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Habits of a glacier-covered volcano : Seismicity patterns and velocity structure of Katla volcano, Iceland
- 2007
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Ingår i: Annals of Glaciology. - : International Glaciological Society. - 0260-3055 .- 1727-5644. ; 45, s. 169-177
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Tidskriftsartikel (refereegranskat)abstract
- The Katla volcano, overlain by the Mýrdalsjökull glacier, is one of the most active and hazardous volcanoes in Iceland. Earthquakes show anomalous magnitude-frequency behaviour and mainly occur in two distinct areas: within the oval caldera and around Goðabunga, a bulge on its western flank. The seismicity differs between the areas; earthquakes in Goðabunga are low frequency and shallow whereas those beneath the caldera occur at greater depths and are volcano-tectonic. The seismicity shows seasonal variations but the rates peak at different times in the two areas. A snow budget model, which gives an estimate of the glacial loading, shows good correlation with seismic activity on an annual scale. Data recorded by the permanent network South Iceland Lowland (SIL), as well as by a temporary network, are used to invert for a 3D seismic velocity model underneath Eyjafjallajökull, Goðabunga and the Katla caldera. The tomography resolves a 15 km wide, aseismic, high-velocity structure at a depth of more than 4 km between the Eyjafjallajökull volcano in the west and the Katla volcano in the east. Anomalously low velocities are observed beneath the Katla caldera, which is interpreted as being a significantly fractured area of anomalously high temperature.
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| 8. |
- Margulies, Elliott H, et al.
(författare)
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- 2007
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 17:6, s. 760-774
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Tidskriftsartikel (refereegranskat)abstract
- A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
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| 9. |
- Moya-Cessa, H., et al.
(författare)
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Degree of polarization and quantum-mechanical purity
- 2008
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Ingår i: Journal of the European Optical Society-Rapid Publications. - : European Optical Society. - 1990-2573. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- The purity parameter is used in quantum mechanics to discriminate pure states from mixed states. We employ this concept to define a degree of polarization for general, three-dimensional, classical random electric fields. Our approach leads to a result that is identical with a recent definition obtained by a decomposition of the polarization matrix in terms of the Gell-Mann matrices. We also give an expression for this degree of polarization based on the constituent two-dimensional subsystems. [DOI: 10.2971/jeos.2008.08014]
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| 10. |
- Sigmundsson, Freyr Gauti, 1972-, et al.
(författare)
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Árangur agera á slitinni fjærsin upphandleggsvöva á FSA 1986-2006 [Repair of distal biceps brachii tendon ruptures : long term retrospective follow-up for two-incision technique]
- 2009
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Ingår i: Laeknabladid. - : Laeknafelag Islands. - 0023-7213 .- 1670-4959. ; 95:1, s. 19-24
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: Rupture of the distal tendon of the biceps muscle is a rare injury. If unrepaired the patient will be left with weakness of supination of the arm and flexion in the elbow. Long term results for the 2-incision approach for tendon reinsertion are few but in this study we describe the long term, clinical, functional, and subjective results of surgical repair using the 2-incision method described by Boyd and Anderson.MATERIAL AND METHODS: All patients who were operated at FSA hospital during the years 1986-2000 because of rupture of the distal tendon of the biceps muscle were asked to participate in the study. Twelve of 16 patients accepted and answered the DASH questionnaire. Strength was tested with handheld dynamometer and ROM where measured. Radiograph was taken of the affected arm.RESULTS: From 1986 through 2006 we operated on 16 patients because of rupture of the distal biceps tendon, one female and 15 male. Mean age at the time of rupture was 46 years (24-53).The average follow up were seven years (1-17). Ten of 12 patients were operated within two weeks from the injuries. No difference in strength was found between operated and non-operated arms. Late repair was associated with high DASH score and poor subjective results. Six patients developed heterotopic ossification but none of them developed radioulnar synostosis. One reoperation because entrapment of the median nerve was done.CONCLUSIONS: Despite heterotopic ossification and a small ROM deficit the Boyd and Anderson technique for repair of distal biceps ruptures yields good long term results in a low volume rural hospital. Early diagnosis and tendon reinsertion is of great importance to avoid persistent anterior elbow pain and poor subjective results.
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