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124 results for “phospholipids”
SGS-LTER Graduate Student Research: Phospholipid fatty acid (PFLA) as Biochemical Responses of US Great Plains Grasslands to Regional and Interannual Variability in Precipitation (1999-2001)
This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/85531. Carbon (C) sequestration potential in grasslands is thought to be high due to the large soil organic carbon pools characteristic of these ecosystems. Inputs of C (aboveground net primary productivity) are highly correlated to precipitation across the Great Plains region; however, changes in C pool size at a specific site are governed by the relative input and output rates across time. Our objective was to quantify the ecosystem C response of three grassland community types (shortgrass steppe, mixed grass and tallgrass prairie) to interannual variation in precipitation. At five sites across a precipitation gradient in the Great Plains, we measured net primary production (NPP), soil respiration (SRESP), and litter decomposition rates for three consecutive years. NPP, SRESP, and litter decomposition increased from shortgrass steppe (175, 454, and 47 g C m-2 yr-1) to tallgrass prairie (408, 1221, and 348 g C m-2 yr-1 for NPP, SRESP, and litter decomposition respectively). Increased growing season precipitation between study years resulted in increased NPP, SRESP, and litter decomposition at almost all sites. However, the regional patterns of the interannual NPP, SRESP, and lit
Data from: Mitochondrial membranes in cardiac muscle from Antarctic notothenioid fishes vary in phospholipid composition and membrane fluidity
Antarctic notothenioid fishes are highly stenothermal, yet their tolerance for warming is species-dependent. Because a body of literature points to the loss of cardiac function as underlying thermal limits in ectothermic animals, we investigated potential relationships among properties of ventricular mitochondrial membranes in notothenioids with known differences in both cardiac mitochondrial metabolism and organismal thermal tolerance. Fluidity of mitochondrial membranes was quantified by fluorescence depolarization for the white-blooded Chaenocephalus aceratus and the red-blooded Notothenia coriiceps. In these same membranes, lipid compositions and products of lipid peroxidation, the latter of which can disrupt membrane order, were analyzed in both species and in a second icefish, Pseudochaenichthys georgianus. Mitochondrial membranes from C. aceratus were significantly more fluid than those of the more thermotolerant species N. coriiceps (P < .0001). Consistent with this, ratios of total phosphatidylethanolamine (PE) to total phosphatidylcholine (PC) were lower in membranes from both species of icefishes, compared to those of N. coriiceps (P < .05). However, membranes of N. coriiceps displayed a greater unsaturation index (P < .0001). No differences among species were found in membrane products of lipid peroxidation. With rising temperatures, greater contents of PC in mitochondrial membranes from ventricles of icefishes are likely to promote membrane hyperfluidization at a lower temperature than for cardiac mitochondrial membranes from the red-blooded notothenioid. We propose that physical and chemical properties of the mitochondrial membranes may contribute to some of the observed differences in thermal sensitivity of physiological function among these species.
Simulations of Na+ and Ca2+ binding to phospholipid membranes
<p>Simulations of various bilayers together with ions. A DOPC bilayer in the liquid disordered phase (310 K) and a DPPC bilayer in the gel phase (293 K), both formed of 200 lipids, were simulated with the presence of either 130 mM of NaCl or 450 mM of CaCl_2. The Slipids model [1–3] is employed for lipids, tip3p model for water, the ion parameters by Smith and Dang for NaCl [4] and the ion parameters by Kohagen et al. for CaCl_2 [5]. Trajectories with NaCl are 200 ns long, while with CaCl_2 they were either 500 ns (DOPC) or 800 ns (DPPC) long.</p> <p>Additionally, a ternary mixture of DPPC, DOPC, and cholesterol was simulated with the presence of 150 mM or 1 M of NaCl [4] at 310 K. The membrane was pre-assembled to contain Ld/Lo coexistence with a well-defined boundary. The Lo side consisted of 205 DPPC and 52 cholesterol molecules, while the Ld side consisted of 166 DOPC molecules. Trajectories are 200 ns long.</p> <p>The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ and the ion parameters are available at https://bitbucket.org/hseara/ions/<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format. Trajectories (.xtc) are saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file except for the varying temperatures (md.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p> <p>[4] Computer simulations of NaCl association in polarizable water. David E. Smith and Liem X. Dang, The Journal of Chemical Physics 1994 100, 3757-3766, DOI: 10.1063/1.466363</p> <p>[5] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions. Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth, The Journal of Physical Chemistry B 2014 118 (28), 7902-7909, DOI: 10.1021/jp5005693</p>
Figure S1 Chemical structures of the phospholipids used in the present study.
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Simulation data for the article ,,Filling the gap with long n-alkanes: incorporation of C20 and C30 into phospholipid membranes" - Set3
<p>First set of simulation trajectories and input files for the manuscript ,,Filling the gap with long n-alkanes: incorporation of C20 and C30 into phospholipid membranes".</p> <p>System: DPPC + n-triacontane (CHARMM36); 288 DPPC, 19 water molecules per lipid, 343K</p> <p>Numbers of n-triacontane molecules are given in the file names.</p> <p>Simulations consisted of three 100ns runs, an .xtc trajectory is only included for the final run. Trajectories were created with -dt 10(ps) and -pbc nojump, as used for analysis in the manuscript. Solvent molecules were removed from the trajectories for file size reduction.</p>
Simulation data for the article ,,Filling the gap with long n-alkanes: incorporation of C20 and C30 into phospholipid membranes" - Set1
<p>First set of simulation trajectories and input files for the manuscript ,,Filling the gap with long n-alkanes: incorporation of C20 and C30 into phospholipid membranes".</p> <p>Systems: DPPC + n-decane (CHARMM36); 72 DPPC, 7 water molecules per lipid, 333K unless otherwise noted in the file names.</p> <p>Numbers of n-decane molecules are given in the file names.</p> <p>Simulations consisted of three 100ns runs, an .xtc trajectory is only included for the final run. Trajectories were created with -dt 10(ps) and -pbc nojump, as used for analysis in the manuscript. Solvent molecules were removed from the trajectories for file size reduction.</p>
Simulation data for the article ,,Filling the gap with long n-alkanes: incorporation of C20 and C30 into phospholipid membranes" - Set2
<p>First set of simulation trajectories and input files for the manuscript ,,Filling the gap with long n-alkanes: incorporation of C20 and C30 into phospholipid membranes" (submitted to Langmuir, under peer-review).</p> <p>System: DPPC + n-eicosane (CHARMM36); 72 DPPC, 18 water molecules per lipid, 333K, unless otherwise noted in the file name.</p> <p>Numbers of n-eicosane molecules are given in the file names.</p> <p>Simulations consisted of three 100ns runs, an .xtc trajectory is only included for the final run. Trajectories were created with -dt 10(ps) and -pbc nojump, as used for analysis in the manuscript. Solvent molecules were removed from the trajectories for file size reduction.</p>
The force field, parameters and configurations from the paper "Dispersion of hydrophilic nanoparticles in natural rubber with phospholipids"
<p>The force field, parameters and configurations from the paper "Dispersion of hydrophilic nanoparticles in natural rubber with phospholipids"</p>
MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"
<p>Input files and trajectories of n-alkane/lipid systems used in the article: ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids".</p> <p>Equilibrated starting configurations were created using CHARMM36. Otherwise, filenames specifiy the force field used (C36 or SL), Temperature and system composition.</p> <p>.xtc trajectories were created using gmx trjconv with options -pbc nojump -dt 10. run2 equals simulations from 100-200ns, run3 equals 200-300ns. The first 100ns were excluded from the analysis and are not included in this dataset.</p> <p>Exemplary .mdp files have been included for both force-fields. Please refer to the manuscript for the force field sources and additional information.</p>
Interferon-inducible phospholipids govern IFITM3-dependent endosomal antiviral immunity
<p>Raw data from indicated Figures of our work entitled "Interferon-inducible phospholipids govern IFITM3-dependent endosomal antiviral immunity" by Unali et al., published as Open Access in EMBO J.</p> <p> </p> <p> </p>
Input Files for Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase
<p>Input files for simulations in publication: Helene Jahn, Ladislav Bartoš, Grace I. Dearden, Jeremy S. Dittman, Joost C. M. Holthuis, Robert Vácha, Anant K. Menon: Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase</p>
Phospholipid Absorption of a Milk Phospholipid
ClinicalTrials.gov study NCT01327430. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Effect of Omega-3 Phospholipids on Perceptual-cognitive Training
ClinicalTrials.gov study NCT01856829. IPD Sharing: Not stated. Countries: 1. Publications: 9.
Determine How Consumption of Dairy Fat Fractions Rich in Phospholipids and Proteins Influence Inflammation in the Fed State-Phase 1
ClinicalTrials.gov study NCT01811329. IPD Sharing: Not stated. Countries: 1. Publications: 11.
Effect of Dietary Phospholipids on Atopic Dermatitis
ClinicalTrials.gov study NCT01326520. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Register of Patients With Anti-Phospholipids Syndrome (APS) and/or Systemic Lupus Erythematosus (SLE)
ClinicalTrials.gov study NCT02782039. IPD Sharing: NO. Countries: 1. Publications: 3.
Ranger Resilience and Improved Performance on Phospholipid Bound Omega-3's
ClinicalTrials.gov study NCT02908932. IPD Sharing: NO. Countries: 1. Publications: 33.
Phospholipid Hypothesis of Depression: From Molecular Biology, Neuroimaging to Behaviour
ClinicalTrials.gov study NCT02615405. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Observational Study of Choline, Its Metabolites, and Phospholipids in Preterm Infants
ClinicalTrials.gov study NCT02027584. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Mitochondrial membranes in cardiac muscle from Antarctic notothenioid fishes vary in phospholipid composition and membrane fluidity
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