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2,697 results for “Lipids”
Dataset for "Diets supplemented with Saccharina latissima influence the expression of genes related to lipid metabolism and oxidative stress modulating rainbow trout (Oncorhynchus mykiss) fillet composition" (doi.org/10.1016/j.fct.2020.111332)
<p>Dataset corresponding to the following article:</p> <p>Ferreira, M., Larsen, B.K., Granby, K., Cunha, S.C., Monteiro, C., Fernandes, J.O., Nunes, M.L., Marques, A., Dias, J., Cunha, I., Castro, L.F.C., Valente, L.M.P., 2020. Diets supplemented with <em>Saccharina latissima </em>influence the expression of genes related to lipid metabolism and oxidative stress modulating rainbow trout (<em>Oncorhynchus mykiss</em>) fillet composition. Food Chem. Toxicol. 140, 111332. <a href="https://doi.org/10.1016/j.fct.2020.111332">https://doi.org/10.1016/j.fct.2020.111332</a></p>
Diverse arsenic-containing lipids in the surface ocean
<p>Arsenic is present at nanomolar levels throughout the ocean, and microbes assimilate this potentially toxic element due to its similarity to inorganic phosphorus. Although dissolved arsenic has been a focus of several oceanographic studies, the size and chemical character of the particulate arsenic pool is poorly understood. We measured particulate arsenic in five samples from the open ocean and determined the contribution of arsenic-containing lipids to this pool. Here we show that the accumulation of arsenic into lipids is a widespread phenomenon in the surface ocean. Particulate arsenic concentrations were 15 to 42 pmol L<sup><span>−</span>1</sup> with 7–20% of the particulate arsenic pool within arsenolipids. We found that arsenosugar phospholipids dominated the arsenolipid pools in our samples with a minor component of arsenohydrocarbons and other unidentified lipids. A significant portion of the arsenosugar phospholipids (up to 35%) were present as previously undescribed mixed acyl ether lipids, suggesting a bacterial source.</p>
Text-fig. 9. Lusitanispermum choffatii gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, orthoslices). a) Longitudinal orthoslice (yz0769) through the median plane of the seed (S174345) showing expanded exotestal cells (ex, arrow head) in the hilar region and well-preserved cellular nutritive tissue with an embedded tiny embryo (asterisk markes the margin of the embryo); note well-developed mesotesta (me) on the raphal side of seed. b) Longitudinal orthoslice (yz0750) in the median plane showing detail of micropylar part of seed with well-preserved exotesta (ex) and mesotesta (me) and tiny embryo with two rudimentary cotyledons (asterisks mark the margin of the cotyledons); note numerous granular bodies in the cellular nutritive tissue that are probably the remains of protein and lipid bodies. c) Transverse orthoslice (xy0311) through seed below hilum showing the bulging exotesta (arrow heads) (S174472); note that the exotestal cells in this region have thinner walls (arrows). d) Transverse orthoslice (xy0900) through the middle of a seed showing the uneven thickening of the anticlinal walls of the exotestal cells (ex), which are thicker towards the outside and very thin towards the inside; note also mesotesta (me) and the well-preserved cellular nutritive tissue (S174472). Scale bars = 500 µm (a, d); 250 µm (b, c). in Extinct Taxa Of Exotestal Seeds Close To Austrobaileyales And Nymphaeales From The Early Cretaceous Of Portugal
Text-fig. 9. Lusitanispermum choffatii gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, orthoslices). a) Longitudinal orthoslice (yz0769) through the median plane of the seed (S174345) showing expanded exotestal cells (ex, arrow head) in the hilar region and well-preserved cellular nutritive tissue with an embedded tiny embryo (asterisk markes the margin of the embryo); note well-developed mesotesta (me) on the raphal side of seed. b) Longitudinal orthoslice (yz0750) in the median plane showing detail of micropylar part of seed with well-preserved exotesta (ex) and mesotesta (me) and tiny embryo with two rudimentary cotyledons (asterisks mark the margin of the cotyledons); note numerous granular bodies in the cellular nutritive tissue that are probably the remains of protein and lipid bodies. c) Transverse orthoslice (xy0311) through seed below hilum showing the bulging exotesta (arrow heads) (S174472); note that the exotestal cells in this region have thinner walls (arrows). d) Transverse orthoslice (xy0900) through the middle of a seed showing the uneven thickening of the anticlinal walls of the exotestal cells (ex), which are thicker towards the outside and very thin towards the inside; note also mesotesta (me) and the well-preserved cellular nutritive tissue (S174472). Scale bars = 500 µm (a, d); 250 µm (b, c).
Data set for "On the interplay between lipids and asymmetric dynamics of an NBS degenerate ABC transporter"
<p>Supplementary data from molecular dynamics simulations performed on different states of bMRP1 (IF apo, IF ATP- and/or LTX-bound, as well as OF ATP-bound states) and embedded in different lipid bilayer membranes (namely POPC, POPE, POPC:POPE (3:1), POPC-Chol (3:1) and POPC:POPE:Chol (2:1:1).</p> <p>Are included:</p> <p>- Initial and postMD data</p> <p>- MD inputs used</p> <p>- Raw source data used for plot (ABC structural parameters, H-bond and non-covalent analyses, lipid order parameters, and efficiencies from Allopath tool)</p> <p>- PCA supplementary movies (PC1)</p>
Data for publication "Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism"
<p>The data provided refer to our published article:</p> <p>T. John,* S. Piantavigna, T. J. A. Dealey, B. Abel, H. J. Risselada, L. L. Martin*, Lipid oxidation controls peptide self-assembly near<br>membranes through a surface attraction mechanism, Chem. Sci. 14 (2023), 3730-3741. <a href="https://doi.org/10.1039/d3sc00159h">https://doi.org/10.1039/d3sc00159h</a>.</p>
Data from: Balanced replacement of fish meal with Hermetia illucens meal allows efficient hepatic nutrient metabolism and increased fillet lipid quality in gilthead sea bream (Sparus aurata) juveniles
<p>In the present study, gilthead sea bream (<em>Sparus aurata</em>) juveniles were reared using sustainable feeds containing insect meal from <em>Hermetia illucens</em> larvae and poultry by-products meal. Proteomics and Proton Nuclear Magnetic Resonance-based metabolomics analysis were used to assess the metabolic impact of tested dietary formulations in sea bream liver, whereas the composition of muscle fillet was characterized by means of metabolomics and gas chromatography of fatty acids methyl esters. Replacing fish meal with insect meal in a 5% fish meal diet did not substantially alter metabolism of dietary nutrients, leading to small but statistically detectable effects solely on lauric acid content of sea bream fillet, and few alterations in some markers of immune response, such as leukocyte elastase inhibitor-like, granzyme B (G,H)-like, and two associated ortholog groups namely serpin B, and chymase). Liver morphology confirmed the absence of structural damage or inflammation in the insect meal-fed group, which showed a lower amount of hepatic lipid deposition and accumulation, too.</p>
Simulation data and code used for the publication in Magn. Reson. "Time-domain proton-detected local-field NMR for molecular structure determination in complex lipid membranes"
<p>Simulation data used in the publication Magn. Reson. "Time-domain proton-detected local-field NMR for molecular structure determination in complex lipid membranes". The simulation data set, and the code developed to generate such data, are included. Details in the published paper </p>
Data from: Human atlastin-3 is a constitutive ER fusion catalyst (lipid mixing data)
<p>Homotypic membrane fusion catalyzed by the atlastin (ATL) GTPase sustains the branched endoplasmic reticulum (ER) network in metazoans. Our recent discovery that two of three human ATL paralogs (ATL1/2) are C-terminally autoinhibited implied that relief of autoinhibition would be integral to the ATL fusion mechanism. An alternative hypothesis is that the third paralog ATL3 promotes constitutive ER fusion with relief of ATL1/2 autoinhibition used conditionally. However, published studies suggest ATL3 is a weak fusogen at best. Contrary to expectations, we demonstrate here that purified human ATL3 catalyzes efficient membrane fusion in vitro and is sufficient to sustain the ER network in triple knockout cells. Strikingly, ATL3 lacks any detectable C-terminal autoinhibition, like the invertebrate <em>Drosophila</em> ATL orthologue. Phylogenetic analysis of ATL C-termini indicates that C-terminal autoinhibition is a recent evolutionary innovation. We suggest that ATL3 is a constitutive ER fusion catalyst and that ATL1/2 autoinhibition likely evolved in vertebrates as a means of upregulating ER fusion activity on demand.</p>
Reconstitution of phase-separated signaling clusters and actin polymerization on supported lipid bilayers
<p>Liquid–liquid phase separation driven by weak interactions between multivalent molecules contributes to the cellular organization by promoting the formation of biomolecular condensates. At membranes, phase separation can promote the assembly of transmembrane proteins with their cytoplasmic binding partners into micron-sized membrane-associated condensates. For example, phase separation promotes clustering of nephrin, a transmembrane adhesion molecule, resulting in increased Arp2/3 complex-dependent actin polymerization. In vitro reconstitution is a powerful approach to understanding phase separation in biological systems. With a bottom-up approach, we can determine the molecules necessary and sufficient for phase separation, map the phase diagram by quantifying de-mixing over a range of molecular concentrations, assess the material properties of the condensed phase using fluorescence recovery after photobleaching (FRAP), and even determine how phase separation impacts downstream biochemical activity. Here, we describe a detailed protocol to reconstitute nephrin clusters on supported lipid bilayers with purified recombinant protein. We also describe how to measure Arp2/3 complex-dependent actin polymerization on bilayers using fluorescence microscopy. These different protocols can be performed independently or combined as needed. These general techniques can be applied to reconstitute and study phase-separated signaling clusters of many different receptors or to generally understand how actin polymerization is regulated at membranes.</p>
Lipid membrane simulations with flat-bottom and double-bilayer setups, part 2/2
<p>To cite: Biriukov, D. and Javanainen, M. Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints. J. Chem. Theory Comput. 2023, 19 (18), 6332–6341. DOI: <a href="https://doi.org/10.1021/acs.jctc.3c00614">10.1021/acs.jctc.3c00614</a></p> <p>Gromacs molecular dynamics simulations to compare membrane and solvent properties from lipid membrane simulations with flat-bottom and double-bilayer setups. CHARMM36 force field was used except for simulations with peptides, where a prosECCo model was used [Nencini et al., Biophys. J. 121, 157a (2022)]</p> <p>This dataset contains only double-bilayer simulations. The flat-bottom simulations together with all topologies and mdp files can be found in part 1 : DOI: <a href="https://zenodo.org/record/7973838">10.5281/zenodo.7973838</a></p> <p>Abbreviations in the names of simulation files:</p> <ul> <li>"fb" - simulations with a flat-bottom setup</li> <li>"2m" - simulations with two lipid membranes, i.e., a double-bilayer setup</li> <li>"popc" - membrane is modeled as a POPC lipid bilayer</li> <li>"mix" - a realistic membrane with various lipids is modeled, resembling the composition from [Lorent et al., Nat. Methods 16, 644–652 (2020)]</li> <li>"nak" - only sodium and potassium cations, together with chloride anions, are present in the system</li> <li>"ext" - as "nak", but also calcium and magnesium cations are added</li> <li>"r9" - as "nak" but also R9 (nona-arginine) peptides are added on both sides of the membrane</li> <li>"r9k" - as "nak" but also R9 (nona-arginine) peptides are added on the extracellular side of the membrane</li> <li>"one" - ions are present only on one side of a lipid membrane</li> <li>"freecl" - flat-bottom simulations but without restraints on chloride anions</li> <li>"s" - simulations were performed using the scaled-charge prosECCo75 force field based on CHARMM [Nencini et al., Biophys. J. 121, 157a (2022)]</li> <li>"restr" - restraint .gro file with ionic/peptide <em>z</em> coordinates set to zero</li> </ul>
Lipid membrane simulations with flat-bottom and double-bilayer setups, part 1/2
<p>To cite: Biriukov, D. and Javanainen, M. Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints. J. Chem. Theory Comput. 2023, 19 (18), 6332–6341. DOI: <a href="https://doi.org/10.1021/acs.jctc.3c00614">10.1021/acs.jctc.3c00614</a></p> <p>Gromacs molecular dynamics simulations to compare membrane and solvent properties from lipid membrane simulations with flat-bottom and double-bilayer setups. CHARMM36 force field was used except for simulations with peptides, where a prosECCo model was used [Nencini et al., Biophys. J. 121, 157a (2022)]</p> <p>This dataset contains all the topologies and flat-bottom simulation files. The double-bilayer simulation files can be found in part 2: DOI: <a href="https://zenodo.org/record/7974633">10.5281/zenodo.7974633</a></p> <p>Abbreviations in the names of simulation files:</p> <ul> <li>"fb" - simulations with a flat-bottom setup</li> <li>"2m" - simulations with two lipid membranes, i.e., a double-bilayer setup</li> <li>"popc" - membrane is modeled as a POPC lipid bilayer</li> <li>"mix" - a realistic membrane with various lipids is modeled, resembling the composition from [Lorent et al., Nat. Methods 16, 644–652 (2020)]</li> <li>"nak" - only sodium and potassium cations, together with chloride anions, are present in the system</li> <li>"ext" - as "nak", but also calcium and magnesium cations are added</li> <li>"r9" - as "nak" but also R9 (nona-arginine) peptides are added on both sides of the membrane</li> <li>"r9k" - as "nak" but also R9 (nona-arginine) peptides are added on the extracellular side of the membrane</li> <li>"one" - ions are present only on one side of a lipid membrane</li> <li>"freecl" - flat-bottom simulations but without restraints on chloride anions</li> <li>"s" - simulations were performed using the scaled-charge prosECCo75 force field based on CHARMM [Nencini et al., Biophys. J. 121, 157a (2022)]</li> <li>"restr" - restraint .gro file with ionic/peptide <em>z</em> coordinates set to zero</li> </ul> <p> </p>
Membrane interaction and mechanism of LC3 lipidation machinery in autophagy raw GUV data
<p>Raw GUV data of fluorescent protein imaged on a Nikon A1 confocal microscope with a 63 × Plan 359 Apochromat 1.4 NA objective. Three biological replicates were performed for each experimental 360 condition. Identical laser power and gain settings were used during the course of all conditions.</p>
Resurrecting Ancient Antibiotics: Unveiling the Origins of Modern Lipid II Targeting Glycopeptides
<p>Data supporting the publication "Resurrecting Ancient Antibiotics: Unveiling the Origins of Modern Lipid II Targeting Glycopeptides"</p>
Study of Semaglutide for Non-Alcoholic Fatty Liver Disease (NAFLD), a Metabolic Syndrome With Insulin Resistance, Increased Hepatic Lipids, and Increased Cardiovascular Disease Risk (The SLIM LIVER St
ClinicalTrials.gov study NCT04216589. IPD Sharing: YES. Countries: 2. Publications: 2.
Safety, Tolerability, and Effect of Alirocumab in High Cardiovascular Risk Patients With Severe Hypercholesterolemia Not Adequately Controlled With Conventional Lipid-modifying Therapies (ODYSSEY APPR
ClinicalTrials.gov study NCT02476006. IPD Sharing: YES. Countries: 16. Publications: 1.
Efficacy and Safety of Inclisiran as Monotherapy in Patients With Primary Hypercholesterolemia Not Receiving Lipid-lowering Therapy.
ClinicalTrials.gov study NCT05763875. IPD Sharing: YES. Countries: 5. Publications: 1.
Study of Efficacy, Safety, Tolerability and Quality of Life of Inclisiran (KJX839) vs Placebo, on Top of Ongoing Individually Optimized Lipid-lowering Therapy, in Participants With Hypercholesterolemi
ClinicalTrials.gov study NCT05192941. IPD Sharing: YES. Countries: 8. Publications: 1.
Gene expression plasticity, genetic variation and fatty acid remodelling in divergent populations of a tropical bivalve species: lipid profiles
Open the record for dataset details and reuse information.
Transcriptional determinants of lipid mobilization in human adipocytes
Open the record for dataset details and reuse information.
Algal lipid distributions and hydrogen isotope ratios reflect phytoplankton community dynamics in Rotsee (Switzerland)
Open the record for dataset details and reuse information.
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