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- Darre, L., et al.
(författare)
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Molecular Dynamics Simulations and Neutron Reflectivity as an Effective Approach To Characterize Biological Membranes and Related Macromolecular Assemblies
- 2015
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 11:10, s. 4875-4884
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Tidskriftsartikel (refereegranskat)abstract
- In combination with other spectroscopy, microscopy, and scattering techniques, neutron reflectivity is a powerful tool to characterize biological systems. Specular reflection of neutrons provides structural information at the nanometer and subnanometer length scales, probing the composition and organization of layered materials. Currently, analysis of neutron reflectivity data involves several simplifying assumptions about the structure of the sample under study, affecting the extraction and interpretation of information from the experimental data. Computer simulations can be used as a source of structural and dynamic data with atomic resolution. We present a novel tool to compare the structural properties determined by neutron reflectivity experiments with those obtained from molecular simulations. This tool allows benchmarking the ability of molecular dynamics simulations to reproduce experimental data, but it also promotes unbiased interpretation of experimentally determined quantities. Two application examples are presented to illustrate the capabilities of the new tool. The first example is the generation of reflectivity profiles for a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer from molecular dynamics simulations using data from both atomistic and coarse-grained models, and comparison with experimentally measured data. The second example is the calculation of lipid volume changes with temperature and composition from all atoms simulations of single and mixed 1,2-di-palmitoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC) bilayers.
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- Domene, HM, et al.
(författare)
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Human acid-labile subunit deficiency: clinical, endocrine and metabolic consequences
- 2009
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Ingår i: Hormone research. - : S. Karger AG. - 1423-0046. ; 72:3, s. 129-141
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Tidskriftsartikel (refereegranskat)abstract
- The majority of insulin-like growth factor (IGF)-I and IGF-II circulate in the serum as a complex with the insulin-like growth factor binding protein (IGFBP)-3 or IGFBP-5, and an acid-labile subunit (ALS). The function of ALS is to prolong the half-life of the IGF-I-IGFBP-3/IGFBP-5 binary complexes. Fourteen different mutations of the human <i>IGFALS</i> gene have been identified in 17 patients, suggesting that ALS deficiency may be prevalent in a subset of patients with extraordinarily low serum levels of IGF-I and IGFBP-3 that remain abnormally low upon growth hormone stimulation. Postnatal growth was clearly affected. Commonly, the height standard deviation score before puberty was between –2 and –3, and approximately 1.4 SD shorter than the midparental height SDS. Pubertal delay was found in 50% of the patients. Circulating IGF-II, IGFBP-1, -2 and -3 levels were reduced, with the greatest reduction observed for IGFBP-3. Insulin insensitivity was a common finding, and some patients presented low bone mineral density. Human ALS deficiency represents a unique condition in which the lack of ALS proteins results in the disruption of the entire IGF circulating system. Despite a profound circulating IGF-I deficiency, there is only a mild impact on postnatal growth. The preserved expression of locally produced IGF-I might be responsible for the preservation of linear growth near normal limits.
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- Fernandez-Martinez, M., et al.
(författare)
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Nitrate pollution reduces bryophyte diversity in Mediterranean springs
- 2020
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697. ; 705
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Tidskriftsartikel (refereegranskat)abstract
- Anthropogenic activities and intensive farming arc causing nitrate pollution in groundwater bodies. These aquifers are drained by springs which, in the Mediterranean region, act as refugia for preserving biodiversity of species that need continuous water. Some springs are also used for drinking water for wild animals, livestock and humans, so if their water quality is compromised it can become a threat to public health. However, the impact of nitrate pollution on these biotic communities remains unknown. We sampled 338 assemblages of aquatic and semi-aquatic bryophytes (i.e., hygrophytic mosses and liverworts) growing in springs in a gradient of water conductivity, nitrate concentration and climate and distributed across the north-east of the Iberian Peninsula to investigate the impact of nitrate pollution on the diversity of bryophytes and moss functional traits in Mediterranean springs. Based on previous literature suggesting that increased nitrogen load decreases biodiversity in grasslands and freshwater ecosystems, we hypothesised that water nitrate pollution in springs decreases bryophyte diversity at the local and regional scales. Our results indicated that, at the local scale (spring), nitrate pollution reduced the number and the likelihood of finding a rare species in springs. Rare species were found in 4% of the springs with nitrate above 50 mg but in 32% of the springs with nitrate below 50 mg L-1. Moss, liv- erwort and overall bryophyte diversity were not directly affected by nitrate at the local scale but nitrate consistently decreased diversity of mosses, liverworts and rare bryophyte species at the regional scale. We also found that warmer and drier springs presented fewer bryophyte species. Our results show that the combination of nitrate pollution, increasing temperature and drought could severely threaten bryophyte diversity Mediterranean springs. Our results indicate that the absence of rare bryophytes could be used as a bioindicator of nitrate pollution in springs.
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- Lind, Tania, et al.
(författare)
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Antimicrobial peptide dendrimer interacts with phosphocholine membranes in a fluidity dependent manner: a neutron reflection study combined with molecular dynamics simulations.
- 2015
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Ingår i: Biochimica et Biophysica Acta. - : Elsevier BV. - 0006-3002 .- 0005-2736 .- 1878-2434. ; 1848:10, s. 2075-2084
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Tidskriftsartikel (refereegranskat)abstract
- The interaction mechanism of a novel amphiphilic antimicrobial peptide dendrimer, BALY, with model lipid bilayers was explored through a combination of neutron reflection and molecular dynamics simulations. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dipalmitoyl-sn-glycero-3-phos-phocholine (DPPC) lipid bilayers were examined at room temperature to extract information on the interaction of BALY with fluid and gel phases, respectively. Furthermore, a 1:4 mixture of POPC and DPPC was used as a model of a phase-separated membrane. Upon interaction with fluid membranes, BALY inserted in the distal leaflet and caused thinning and disordering of the headgroups. Membrane thinning and expansion of the lipid cross-sectional area was observed for gel phase membranes, also with limited insertion to the distal leaflet. However, dendrimer insertion through the entire lipid tail region was observed upon crossing the lipid phase transition temperature of DPPC and in phase separated membranes. The results show clear differences in the interaction mechanism of the dendrimer depending on the lipid membrane fluidity, and suggest that a role for lipid phase separation in promoting its antimicrobial activity.
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