| 1. |
- Arnlund, David, et al.
(författare)
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Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser
- 2014
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 11:9, s. 923-926
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Tidskriftsartikel (refereegranskat)abstract
- We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions.
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| 2. |
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| 3. |
- Basaiawmoit, R V, et al.
(författare)
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SAXS Models of TGFBIp Reveal a Trimeric Structure and Show That the Overall Shape Is Not Affected by the Arg124His Mutation
- 2011
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Ingår i: JOURNAL OF MOLECULAR BIOLOGY. - : Elsevier Science B.V., Amsterdam. - 0022-2836. ; 408:3, s. 503-513
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Tidskriftsartikel (refereegranskat)abstract
- Human transforming growth factor beta induced protein (TGFBIp) is composed of 683 residues, including an N-terminal cysteine-rich (EMI) domain, four homologous fasciclin domains, and an Arg-Gly-Asp (RGD) motif near the C-terminus. The protein is of interest because mutations in the TGFBI gene encoding TGFBIp lead to corneal dystrophy (CD), a condition where protein aggregates within the cornea compromise transparency. The complete three-dimensional structure of TGFBIp is not yet available, with the exception of a partial X-ray structure of the archetype FAS1 domain derived from Drosophila fasciclin-1. In this study, small-angle X-ray scattering (SAXS) models of intact wild-type (WT) human TGFBIp and a mutant (R124H) are presented. The mutation R124H leads to a variant of granular CD. The deduced structure of the TGFBIp monomer consists of four FAS1 domains in a simple "beads-on-a-string" arrangement, constructed by the superimposition of four consecutive Drosophila fasciclin domains. The SAXS-based model of the TGFBIp R124H mutant displayed no structural differences from WT. Both WT TGFBIp and the R124H mutant formed trimers at higher protein concentrations. The similar association properties and three-dimensional shape of the two proteins suggest that the mutation does not induce any major structural rearrangements, but points towards the role of other corneal-specific factors in the formation of corneal R124H deposits.
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| 4. |
- Claesson, Per M., et al.
(författare)
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Bottle-brush polymers : Adsorption at surfaces and interactions with surfactants
- 2010
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Ingår i: Advances in Colloid and Interface Science. - : Elsevier BV. - 0001-8686 .- 1873-3727. ; 155:1-2, s. 50-57
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Tidskriftsartikel (refereegranskat)abstract
- Solution and adsorption properties of both charged and uncharged bottle-brush polymers have been investigated. The solution conformation and interactions in solution have been investigated by small-angle scattering techniques. The association of the bottle-brush polymers with anionic surfactants has also been studied. Surfactant binding isotherm measurements, NMR, surface tension measurements, as well as SAXS, SANS and light scattering techniques were utilized for understanding the association behaviour in bulk solutions. The adsorption of the bottle-brush polymers onto oppositely charged surfaces has been explored using a battery of techniques, including reflectometry, ellipsometry, quartz crystal microbalance, and neutron reflectivity. The combination of these techniques allowed determination of adsorbed mass, layer thickness, water content, and structural changes occurring during layer formation. The adsorption onto mica was found to be very different to that on silica, and an explanation for this was sought by employing a lattice mean-field theory. The model was able to reproduce a number of salient experimental features characterizing the adsorption of the bottle-brush polymers over a wide range of compositions, spanning from uncharged bottle-brushes to linear polyelectrolytes. This allowed us to shed light on the importance of electrostatic surface properties and non-electrostatic surface-polymer affinity for the adsorption. The interactions between bottle-brush polymers and anionic surfactants in adsorbed layers have also been elucidated using ellipsometry, neutron reflectivity and surface force measurements.
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| 5. |
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| 6. |
- Hammond, Philip S., et al.
(författare)
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Cetacean abundance and distribution in European Atlantic shelf waters to inform conservation and management
- 2013
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Ingår i: Biological Conservation. - : Elsevier BV. - 0006-3207 .- 1873-2917. ; 164, s. 107-122
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Tidskriftsartikel (refereegranskat)abstract
- The European Union (EU) Habitats Directive requires Member States to monitor and maintain at favourable conservation status those species identified to be in need of protection, including all cetaceans. In July 2005 we surveyed the entire EU Atlantic continental shelf to generate robust estimates of abundance for harbour porpoise and other cetacean species. The survey used line transect sampling methods and purpose built data collection equipment designed to minimise bias in estimates of abundance. Shipboard transects covered 19,725 km in sea conditions <= Beaufort 4 in an area of 1,005,743 km(2). Aerial transects covered 15,802 km in good/moderate conditions (<= Beaufort 3) in an area of 364,371 km(2). Thirteen cetacean species were recorded; abundance was estimated for harbour porpoise (375,358; CV = 0.197), bottlenose dolphin (16,485; CV = 0.422), white-beaked dolphin (16,536; CV = 0.303), short-beaked common dolphin (56,221; CV = 0.234) and minke whale (18,958; CV = 0.347). Abundance in 2005 was similar to that estimated in July 1994 for harbour porpoise, white-beaked dolphin and minke whale in a comparable area. However, model-based density surfaces showed a marked difference in harbour porpoise distribution between 1994 and 2005. Our results allow EU Member States to discharge their responsibilities under the Habitats Directive and inform other international organisations concerning the assessment of conservation status of cetaceans and the impact of bycatch at a large spatial scale. The lack of evidence for a change in harbour porpoise abundance in EU waters as a whole does not exclude the possibility of an impact of bycatch in some areas. Monitoring bycatch and estimation of abundance continue to be essential. (C) 2013 The Authors.
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| 7. |
- Jacobsen, L, et al.
(författare)
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The effect of turbidity and prey fish density on consumption rates of piscivorous Eurasian perch Perca fluviatili
- 2014
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Ingår i: Journal of limnology. - Pavia : Pagepress. - 1129-5767 .- 1723-8633. ; 73:1, s. 187-190
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Tidskriftsartikel (refereegranskat)abstract
- Predator-prey interaction strengths in variable environments constitute a fundamental link to the understanding of aquatic ecosystem responses to environmental change. The present study investigates the effects of visibility conditions and prey fish density on predation rates of visually oriented piscivorous Eurasian perch Perca fluviatilis L. This was done in outdoor mesocosm (16 m2) experiments with clear water and two levels of turbidity (25 and 105 NTU) and two prey fish densities [3.1 and 12.5 roach Rutilus rutilus (L.) individuals m–2]. Perch consumption rates were affected by visibility less than expected, while they were highly affected by increased prey fish density. Perch responded to high prey density in all visibility conditions, indicating that prey density is more crucial for consumption than visibility in turbid lakes.
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| 8. |
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| 9. |
- Kivekäs, Niku, et al.
(författare)
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Contribution of ship traffic to aerosol particle concentrations downwind of a major shipping lane
- 2014
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 14:16, s. 8255-8267
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Tidskriftsartikel (refereegranskat)abstract
- Particles in the atmosphere are of concern due to their toxic properties and effects on climate. In coastal areas, ship emissions can be a significant anthropogenic source. In this study we investigated the contribution from ship emissions to the total particle number and mass concentrations at a remote location. We studied the particle number concentration (12 to 490 nm in diameter), the mass concentration (12 to 150 nm in diameter) and number and volume size distribution of aerosol particles in ship plumes for a period of 4.5 months at Hovsore, a coastal site on the western coast of Jutland in Denmark. During episodes of western winds, the site is about 50 km downwind of a major shipping lane and the plumes are approximately 1 hour old when they arrive at the site. We have used a sliding percentile-based method for separating the plumes from the measured background values and to calculate the ship plume contribution to the total particle number and PM0.15 mass concentration (mass of particles below 150 nm in diameter, converted from volume assuming sphericity) at the site. The method is not limited to particle number or volume concentration, but can also be used for different chemical species in both particle and gas phase. The total number of analyzed ship plumes was 726, covering on average 19% of the time when air masses were arriving at the site over the shipping lane. During the periods when plumes were present, the particle concentration exceeded the background values on average by 790 cm(-3) by number and 0.10 gm(-3) by mass. The corresponding daily average values were 170 cm-3 and 0.023 gm-3, respectively. This means that the ship plumes contributed between 11 and 19% to the particle number concentration and between 9 and 18% to PM0.15 during days when air was arriving over the shipping lane. The estimated annual contribution from ship plumes, where all wind directions were included, was in the range of 5-8% in particle number concentration and 4-8% in PM0.15.
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