| 1. |
- Mikkelsen, Tarjei S, et al.
(författare)
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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7141, s. 167-177
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Tidskriftsartikel (refereegranskat)abstract
- We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
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| 2. |
- Mikkelsen, D.R, et al.
(författare)
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Assessment of Transport in NCSX
- 2007
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Ingår i: Fusion Science and Technology. ; 51, s. 166-180
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Tidskriftsartikel (refereegranskat)abstract
- We explore whether the energy confinement and planned heating in the National Compact Stellarator Experiment (NCSX) are sufficient to test magnetohydrodynamic (MHD) stability limits, and whether the configuration is sufficiently quasi-axisymmetric to reduce the neoclassical ripple transport to low levels, thereby allowing tokamak-like transport. A zero-dimensional model with fixed profile shapes is related to global energy confinement scalings for stellarators and tokamaks, neoclassical transport properties are assessed with the DKES, NEO, and NCLASS codes, and a power balance code is used to predict temperature profiles. Reaching the NCSX goal of = 4% at low collisionality will require HISS-95 = 3, which is higher than the best achieved in present stellarators. However, this level of confinement is actually ~10% lower than that predicted by the ITER-97P tokamak L-mode scaling. By operating near the stellarator density limit, the required HISS-95 is reduced by 35%. The high degree of quasi-axisymmetry of the configuration and the self-consistent "ambipolar" electric field reduce the neoclassical ripple transport to a small fraction of the neoclassical axisymmetric transport. A combination of neoclassical and anomalous transport models produces pressure profile shapes that are within the range of those used to study the MHD stability of NCSX. We find that = 4% plasmas are "neoclassically accessible" and are compatible with large levels of anomalous transport in the plasma periphery.
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| 3. |
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| 4. |
- Fowler, D., et al.
(författare)
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Atmospheric composition change : Ecosystems-Atmosphere interactions
- 2009
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Ingår i: Atmospheric Environment. - : Elsevier BV. - 1352-2310 .- 1873-2844. ; 43:33, s. 5193-5267
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Forskningsöversikt (refereegranskat)abstract
- Ecosystems and the atmosphere: This review describes the state of understanding the processes involved in the exchange of trace gases and aerosols between the earth's surface and the atmosphere. The gases covered include NO, NO2, HONO, HNO3, NH3, SO2, DMS, Biogenic VOC, O-3, CH4, N2O and particles in the size range 1 nm-10 mu m including organic and inorganic chemical species. The main focus of the review is on the exchange between terrestrial ecosystems, both managed and natural and the atmosphere, although some new developments in ocean-atmosphere exchange are included. The material presented is biased towards the last decade, but includes earlier work, where more recent developments are limited or absent. New methodologies and instrumentation have enabled, if not driven technical advances in measurement. These developments have advanced the process understanding and upscaling of fluxes, especially for particles, VOC and NH3. Examples of these applications include mass spectrometric methods, such as Aerosol Mass Spectrometry (AMS) adapted for field measurement of atmosphere-surface fluxes using micrometeorological methods for chemically resolved aerosols. Also briefly described are some advances in theory and techniques in micrometeorology. For some of the compounds there have been paradigm shifts in approach and application of both techniques and assessment. These include flux measurements over marine surfaces and urban areas using micrometeorological methods and the up-scaling of flux measurements using aircraft and satellite remote sensing. The application of a flux-based approach in assessment of O-3 effects on vegetation at regional scales is an important policy linked development secured through improved quantification of fluxes. The coupling of monitoring, modelling and intensive flux measurement at a continental scale within the NitroEurope network represents a quantum development in the application of research teams to address the underpinning science of reactive nitrogen in the cycling between ecosystems and the atmosphere in Europe. Some important developments of the science have been applied to assist in addressing policy questions, which have been the main driver of the research agenda, while other developments in understanding have not been applied to their wider field especially in chemistry-transport models through deficiencies in obtaining appropriate data to enable application or inertia within the modelling community. The paper identifies applications, gaps and research questions that have remained intractable at least since 2000 within the specialized sections of the paper, and where possible these have been focussed on research questions for the coming decade.
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| 5. |
- Mackey, Abigail L., et al.
(författare)
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The influence of anti-inflammatory medication on exercise-induced myogenic precursor cell responses in humans
- 2007
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Ingår i: Journal of applied physiology. - : American Physiological Society. - 8750-7587 .- 1522-1601. ; 103:2, s. 425-431
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Tidskriftsartikel (refereegranskat)abstract
- The consumption of nonsteroidal anti-inflammatory drugs (NSAIDs) is widespread among athletes when faced with muscle soreness or injury, but the effects of NSAIDs on satellite cell activity in humans are unknown. To investigate this, 14 healthy male endurance athletes (mean peak oxygen consumption 62 ml x kg(-1) x min(-1)) volunteered for the study, which involved running 36 km. They were divided into two groups and received either 100 mg indomethacin per day or placebo. Muscle biopsies collected before the run and on days 1, 3, and 8 afterward were analyzed for satellite cells by immunohistochemistry with the aid of neural cell adhesion molecule (NCAM) and fetal antigen-1 (FA1) antibodies. Muscle biopsies were also collected from untrained individuals for comparison. Compared with preexercise levels, a 27% increase in the number of NCAM+ cells was observed on day 8 postexercise in the placebo group (P < 0.05), while levels remained similar at all time points in the NSAID group. No change was seen in the proportion of FA1+ cells, although lower levels were found in the muscle of endurance-trained athletes compared with untrained individuals (P < 0.05). These results suggest that ingestion of anti-inflammatory drugs attenuates the exercise-induced increase in satellite cell number, supporting the role of the cyclooxygenase pathway in satellite cell activity.
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| 6. |
- Markljung, Ellen, et al.
(författare)
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ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth
- 2009
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 7:12, s. e1000256-
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Tidskriftsartikel (refereegranskat)abstract
- A single nucleotide substitution in intron 3 of IGF2 in pigs abrogates a binding site for a repressor and leads to a 3-fold up-regulation of IGF2 in skeletal muscle. The mutation has major effects on muscle growth, size of the heart, and fat deposition. Here, we have identified the repressor and find that the protein, named ZBED6, is previously unknown, specific for placental mammals, and derived from an exapted DNA transposon. Silencing of Zbed6 in mouse C2C12 myoblasts affected Igf2 expression, cell proliferation, wound healing, and myotube formation. Chromatin immunoprecipitation (ChIP) sequencing using C2C12 cells identified about 2,500 ZBED6 binding sites in the genome, and the deduced consensus motif gave a perfect match with the established binding site in Igf2. Genes associated with ZBED6 binding sites showed a highly significant enrichment for certain Gene Ontology classifications, including development and transcriptional regulation. The phenotypic effects in mutant pigs and ZBED6-silenced C2C12 myoblasts, the extreme sequence conservation, its nucleolar localization, the broad tissue distribution, and the many target genes with essential biological functions suggest that ZBED6 is an important transcription factor in placental mammals, affecting development, cell proliferation, and growth.
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| 7. |
- Sun, J, et al.
(författare)
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Structural determination of a low-symmetry surface by low-energy electron diffraction and ab initio calculations: Bi(110)
- 2006
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. ; 74
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Tidskriftsartikel (refereegranskat)abstract
- he surface structure of Bi(110) has been investigated by low-energy electron diffraction (LEED) intensity analysis and by first-principles calculations. Diffraction patterns at a sample temperature of 110 K and normal incidence reveal a bulk truncated (1×1) surface without indication of any structural reconstruction despite the presence of dangling bonds on the surface layer. Good agreement is obtained between the calculated and measured diffraction intensities for this complex, low-symmetry surface containing only one mirror-plane symmetry element. No significant interlayer spacing relaxations are found. The Debye temperature for the surface layer is found to be lower than in the bulk, which is indicative of larger vibrational atomic amplitudes at the surface. Meanwhile, the second layer shows a Debye temperature close to the bulk value. The experimental results for the relaxations agree well with those of our first-principles calculation.
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| 8. |
- Trajkovska, V., et al.
(författare)
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BDNF downregulates 5-HT2A receptor protein levels in hippocampal cultures
- 2009
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Ingår i: Neurochemistry International. - : Elsevier BV. - 0197-0186. ; 55:7, s. 697-702
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Tidskriftsartikel (refereegranskat)abstract
- Both brain-derived neurotrophic factor (BDNF) and the serotonin receptor 2A (5-HT2A) have been related to depression pathology. Specific 5-HT2A receptor changes seen in BDNF conditional mutant mice suggest that BDNF regulates the 5-HT2A receptor level. Here we show a direct effect of BDNF on 5-HT2A receptor protein levels in primary hippocampal neuronal and mature hippocampal organotypic cultures exposed to different BDNF concentrations for either 1, 3, 5 or 7 days. In vivo effects of BDNF on hippocampal 5-HT2A receptor levels were further corroborated in (BDNF +/-) mice with reduced BDNF levels. In primary neuronal cultures, 7 days exposure to 25 and 50 ng/mL BDNF resulted in downregulation of 5-HT2A, but not of 5-HT1A, receptor protein levels. The BDNF-associated downregulation of 5-HT2A receptor levels was also observed in mature hippocampal organotypic cultures, excluding confounding effects of BDNF on immature tissue. BDNF +/- mice showed significant increased 5-HT2A receptor levels in hippocampus confirming the association between 5-HT2A receptor and BDNF levels in vivo. In conclusion, our results point to a regulatory role of BDNF on 5-HT2A receptor levels. This interaction may be an important mechanism in the role of BDNF in affective disorders emphasizing the need for further elucidating the specificity and the mechanism behind this regulation. (C) 2009 Elsevier Ltd. All rights reserved.
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| 9. |
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| 10. |
- Westerström, Rasmus, et al.
(författare)
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Structure and reactivity of a model catalyst alloy under realistic conditions
- 2008
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Ingår i: Journal of Physics: Condensed Matter. - : IOP Publishing. - 1361-648X .- 0953-8984. ; 20:18, s. 6-184018
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Tidskriftsartikel (refereegranskat)abstract
- Using a combined experimental and theoretical approach, we show that a thin RhO2 oxide film forms on a Pt25Rh75(100) surface at elevated oxygen pressures and temperatures prior to the bulk oxidation. By the use of in situ surface x-ray diffraction under realistic CO oxidation reaction conditions, we show that the onset of the growth of thin RhO2 oxide film coincides with an increase in CO2 production. During the reaction, the consumed oxide film is continuously re-grown by oxygen in the gas phase. Our theoretical results strongly suggest that the CO adsorbs on the metallic substrate but reacts with the O in the RhO2 oxide film at the border between the RhO2 oxide film and the metallic substrate. This scenario could explain the experimental observations of oxidation reactions on other late transition metal surfaces as well as on their corresponding nanoparticles under realistic conditions.
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