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2,697 results for “Lipids”
Graphical abstract in Novel Media for Lipid Production of Chlorococcum oleofaciens: A RSM Approach
Graphical abstract
The expressivity of rare coding variants for blood lipids in over a million individuals
<p>The supplemental data and codes for Koyama et al. "The expressivity of rare coding variants for blood lipids in over a million individuals"</p>
Data supporting: "Interaction of MRI Contrast Agent [Gd(DOTA)]− with Lipid Membranes: A Molecular Dynamics Study"
Open the record for dataset details and reuse information.
Biochemical and biophysical drivers of the hydrogen isotopic composition of carbohydrates and acetogenic lipids
<p>The hydrogen isotopic composition (δ2H) of plant compounds is increasingly used as a hydro-climatic proxy, however, the interpretation of δ2H values is hampered by potential co-effecting biochemical and biophysical processes. Here, we studied δ2H values of water and carbohydrates in leaves and roots, and of leaf n-alkanes, in two distinct tobacco (Nicotiana sylvestris) experiments. Large differences in plant performance and biochemistry resulted from (a) soil fertilization with varying nitrogen (N) species ratios and (b) knockout-induced starch deficiency. We observed a strong 2H-enrichment in sugars and starch with a decreasing performance induced by increasing NO3-/NH4+ ratios and starch deficiency, and from leaves to roots. However, δ2H values of cellulose and n-alkanes were less affected. We show that relative concentrations of sugars and starch, interlinked with leaf gas-exchange, shape δ2H values of carbohydrates. We thus provide novel insights into drivers of hydrogen isotopic composition of plant compounds and the mechanistic modelling of plant cellulose δ2H values.</p>
Supplementary Material 1: Phylogenetic tree from Unraveling an unknown diversity of archaeal and bacterial tetraether membrane lipid producers in a euxinic marine system
<p>Phylogenetic tree (Black Sea MAGs)</p>
Supplementary Information for "Biocatalytic Ether Lipid Synthesis by an Archaeal Glycerolprenylase" - Computational Data
<p>This is part of the external Supplementary Information covering the molecular dynamics simulations section for our publication "Biocatalytic Ether Lipid Synthesis by an Archaeal Glycerolprenylase" by Felix Kaspar et al., freely available as a preprint from ChemRxiv ( ).</p> <p>The .zip file contains raw data, processed data and metadata for the <strong>computational results</strong>. This includes files for the MD simulations and the preparations of the structures. </p> <p>Raw data regarding the experimental results are stored in a separate zenodo entry (<a href="../doi/10.5281/zenodo.10559443">https://zenodo.org/doi/10.5281/zenodo.10559443</a>) by Felix Kaspar. This includes UV, flourescence, NMR data, as well as data results of crystallization screens and reports on MPLC runs. </p>
Lipid extraction alters amino acid composition and bulk, but not amino acid, carbon and nitrogen isotope values
<p>Rationale: Concerns exist over observed shifts in value and variance of nitrogen isotopes following physicochemical extraction of lipids from organic matter. The mechanisms behind these apparent changes in bulk tissue δ15N values are not fully understood yet have major implications for analytical costs and integrity of data interpretations.</p> <p>Methods: Changes in proximate analysis, amino acid composition, C:N ratios, bulk tissue and amino acid δ13C and δ15N values, and resulting isotope‐based food web metrics were compared between lipid‐intact and lipid‐extracted muscle tissue of fishes spanning <1% to >20% muscle fat content to identify mechanisms of nitrogen isotope fractionation associated with physicochemical lipid extraction.</p> <p>Results: Bulk δ13C and δ15N values increased and %N, C:N ratios and crude protein content decreased following lipid extraction. Resulting bulk isotope niche spacing and overlap varied significantly between lipid‐intact and lipid‐extracted tissues. While amino acid composition significantly changed during lipid extraction, particularly for lipid‐associated amino acids (e.g., Glu, Lys, Ser), individual amino acid δ13C and δ15N values, and their associated compound‐specific isotope analysis of amino acids (CSIA‐AA)‐based food web metrics, did not.</p> <p>Conclusions: Physicochemical lipid extraction caused significant tissue composition changes (e.g., leaching of amino acids and 15N‐deplete nitrogenous waste) that affected δ13C and δ15N values and tissue %C and %N beyond simply removing lipids. However, lipid extraction did not alter individual amino acid δ13C or δ15N values or their associated CSIA‐AA‐based food web metrics.</p>
Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes? - additional data
<p>CaM_Data_Repository_Revision:<br>This folder contains the experimental raw data, analysis and source for the final figures reported in the paper after revision (Open Biology): "Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?". It is divided into five (1-3) folders, named as the technique used to obtain the data. Each of them, where applicable, consists of three different subfolders (raw data, analysed data, final graph). Read below for more details. </p> <p>1) ConfocalMicroscopy</p> <p> 1a) Raw_Data: the raw images are reported as .dat and .bmp formats, divided into folders (according date first yymmdd, and within the same day according to composition). Each folder contains a .txt file reporting the experimental details </p> <p> 1b) Final_Graph<br> - Figure_1E.csv is the new source file x-y of the bar plot shown in figure 1E (% of GUVs which showed adsorption of CaM over the total amount of measured GUVs) in the revised version of the manuscript<br> <br>2) DLS</p> <p> 2a) Raw Data: <br> - DLS_lipid 0.4mM_1.7uM CaM_10mM CaCl2 contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder <br> - DLS_lipid 0.4mM_10mM CaCl2_1.7uM CaM contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder </p> <p> 2b) Final_Graph: <br> - Fig.S4B.xlsx contains the x-y source file for the figure S4B<br> - Fig.S5A.xlsx contains the x-y source file for the figure S5A </p> <p>3) Z-potential</p> <p> 3a) Raw Data: <br> - ZetaPotential_lipid 0.4mM_1.7uM CaM_10mM CaCl2 contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder <br> - ZetaPotential_lipid 0.4mM_10mM CaCl2_1.7uM CaM contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder </p> <p> 3b) Final_Graph: <br> - Fig.S4C.xlsx contains the x-y source file for the figure S4C<br> - Fig.S5B.xlsx contains the x-y source file for the figure S5B </p> <p> </p> <p> </p>
Raw data Lipid measurement
<p><span>Variants in </span><em><span>GBA1</span></em><span> result in dysregulated sphingolipids. </span><span>We investigated five CSF d18:1 sphingolipid species in a multicenter cohort comprising people with </span><span>Parkinson’s Disease </span><span>and Dementia with Lewy bodies with and without <em>GBA1</em> variants and healthy controls. We found no increase of d18:1 sphingolipid species in heterozygous <em>GBA1</em> variant participants. Sphingolipid levels had no effect on development of cognitive impairment.We conclude that CSF d18:1 sphingolipids seem not suitable to be used as a state marker in </span><span>Parkinson’s Disease</span><span>.</span></p>
200 ns simulation of a DMPC bilayer using Gromos 53A6 + Berger lipids
<p><strong>MD simulation of a DMPC bilayer: 200 ns </strong></p> <ul> <li>Gromos 53A6 force field and Berger lipids (lipid.itp)</li> <li>128 DMPC lipids and 3655 SPC waters. Total number of atoms: 16853.</li> <li>This simulation: 200 ns. The systems was equilibrated for 52 ns before this run.</li> <li>Simulation details: <ul> <li>Temperature: 323 K</li> <li>Times step: 2 fs</li> <li>V-rescale thermostat, Parrinello-Rahman barostat, P-LINCS for constraints</li> <li>The run was done using a laptop with GTX980M. Performance: ~105ns/day</li> </ul> </li> <li>Area per lipid and thickness (P-P distance) are provided.</li> </ul>
Lipid-polymer nanoparticles to probe the native-like environment of intra-membrane rhomboid protease GlpG and its activity
<p><span>Polymers can facilitate detergent-free extraction of membrane proteins into nanodiscs (e.g., SMALPs, DIBMALPs), incorporating both integral membrane proteins as well as co-extracted native membrane lipids. Lipid-only SMALPs and DIBMALPs have been shown to possess a unique property; the ability to exchange lipids through ‘collisional lipid mixing’<em>.</em> Here we expand upon this mixing to include protein-containing DIBMALPs, using the rhomboid protease GlpG. Through lipidomic analysis before and after incubation with DMPC or POPC DIBMALPs, we show that lipids are rapidly exchanged between protein and lipid-only DIBMALPs, and can be used to identify bound or associated lipids through ‘washing-in’ exogenous lipids. Additionally, through the requirement of rhomboid proteases to cleave intra-membrane substrates, we show that this mixing can be performed for two protein-containing DIBMALP populations, assessing the native function of intramembrane proteolysis and demonstrating that this mixing has no deleterious effects on protein stability or structure</span></p>
Data for publication: Pixelated High-Q Metasurfaces for in Situ Biospectroscopy and Artificial Intelligence-Enabled Classification of Lipid Membrane Photoswitching Dynamics
Open the record for dataset details and reuse information.
MD data for Ionizable cationic lipids and helper lipids synergistically contribute to RNA packing and protection in lipid-based nanomaterials
<p>The data stored in this repository is part of the journal article: Zimmer, D. N., Schmid, F., & Settanni, G. (2024). Ionizable Cationic Lipids and Helper Lipids Synergistically Contribute to RNA Packing and Protection in Lipid-Based Nanomaterials. <em>The Journal of Physical Chemistry B</em> <a href="https://doi.org/10.1021/acs.jpcb.4c05057" target="_blank" rel="noopener">https://doi.org/10.1021/acs.jpcb.4c05057</a></p> <p> </p> <p>Data of multiscale simulations of DLinDMA:DOPE:Cholesterol, DLinDMA:DSPC:Cholesterol, DLinDAP:DOPE:Cholesterol and DLinDAP:DSPC:Cholesterol in the presence of RNA. For each formulation, data is provided with different coarse-grained parameterizations (generic, adapted) and differents treatments of the RNA (ELN, noELN). Provided are the first and the final frame of each run, the associated topologies, and the respective gromacs input files.</p> <p><strong>> M_PE, M_PC, P_PE, P_PC</strong></p> <p>DLinDMA:DOPE:Cholesterol, DLinDMA:DSPC:Cholesterol, DLinDAP:DOPE:Cholesterol and DLinDAP:DSPC:Cholesterol in presence of a 40mer RNA fragment. </p> <ul> <li>cg_<strong>generic</strong>+aa: <ul> <li>cg: 2 microsecond production run based on a generic MARTINI parametrization <ul> <li>md_0.gro: first frame</li> <li>md_10.gro: final frame </li> <li>cg_rna_bilayer.top: Topology of the system</li> <li>cg_DLD{M/P}_lipid.itp: generic MARTINI topology of DLinDMA/DLinDAP</li> <li>martini_v2.0_CHOL_02.itp, martini_v2.0_DSPC_01.itp, martini_v2.0_ions, martini_v2.1.itp, martini_v2.1-dna.itp: Several MARTINI topology files for molecules not included in MARTINI</li> <li>Nucleic_A.itp or Nucleic_A_eln.itp: Topology of the RNA fragment for MARTINI</li> </ul> </li> <li>aa: 300/600 nanosecond production run based on CHARMM36 <ul> <li>md_0.gro: first frame</li> <li>md_60.gro: final frame </li> <li>backmapped.top: Topology of the system (including the parametrization of DLinDMA/DLinDAP)</li> <li>CHOL.itp, DOPE.itp, DSPC.itp, 40mer_autopsf.itp: topology files for Cholesterol, DOPE, DSPC and RNA fragment as they are not part of the standard molecules in CHARMM36.</li> </ul> </li> <li>ELN and noELN indicate presence or absence of an elastic network to fix the structure of the RNA during the cg runs. </li> <li>cgmdp: Gromacs input files for the cg runs</li> <li>aamdp: Gromacs input files for the aa runs</li> </ul> </li> <li>cg_<strong>adapted</strong>+aa: <ul> <li>cg: starting and ending frame of a 2 microsecond production run based on an adapted MARTINI parametrization <ul> <li>md_0.gro: first frame</li> <li>md_10.gro: final frame </li> <li>cg_rna_bilayer.top: Topology of the system</li> <li>martini_v2.0_DIDMA_20 or martini_v2.0_DIDAP_20: generic MARTINI topology of DLinDMA/DLinDAP</li> <li>martini_v2.0_CHOL_02.itp, martini_v2.0_DSPC_01.itp, martini_v2.0_ions, martini_v2.1-dna_cr1_POL_NACL.itp: Several MARTINI topology files for molecules not included in MARTINI</li> <li>Nucleic_A.itp or Nucleic_A_eln.itp: Topology of the RNA fragment for MARTINI</li> </ul> </li> <li>aa: 300/600 nanosecond production run based on CHARMM36 <ul> <li>md_0.gro: first frame</li> <li>md_60.gro: final frame </li> <li>backmapped.top: Topology of the system (including the parametrization of DLinDMA/DLinDAP)</li> <li>CHOL.itp, DOPE.itp, DSPC.itp, 40mer_autopsf.itp: topology files for Cholesterol, DOPE, DSPC and RNA fragment as they are not part of the standard molecules in CHARMM36.</li> </ul> </li> <li>ELN and noELN indicate presence or absence of an elastic network to fix the structure of the RNA during the cg runs. </li> <li>cgmdp: Gromacs input files for the cg runs</li> <li>aamdp: Gromacs input files for the aa runs</li> </ul> </li> </ul>
Effects of Pleurotus ferulae water extract (PWE) or Pleurotus ferulae ethanol extract (PEE) on lipid accumulation in 3T3-L1 cells.
<p><span>Lipid accumulation was measured in 3T3-L1 adipocytes following Oil Red O staining, both with and without PWE or PEE treatment. Results are expressed as the mean ± standard deviation (SD) (n = 3). Different letters indicate significant differences (p < 0.05), as determined by one-way analysis of variance (ANOVA) followed by Tukey’s post hoc test.</span></p>
APOE4 is associated with elevated blood lipids and lower levels of innate immune biomarkers in a tropical Amerindian subsistence population
<p>In post-industrial settings, <i>APOE4</i> is associated with increased cardiovascular and neurological disease risk. However, the majority of human evolutionary history occurred in environments with higher pathogenic diversity and low cardiovascular risk. We hypothesize that in high-pathogen and energy-limited contexts, the <i>APOE4</i> allele confers benefits by reducing innate inflammation when uninfected, while maintaining higher lipid levels that buffer costs of immune activation during infection. Among Tsimane forager-farmers of Bolivia (N=1266), <i>APOE4</i> is associated with 30% lower C-reactive protein, and higher total cholesterol and oxidized-LDL. Blood lipids were either not associated, or negatively associated with inflammatory biomarkers, except for associations of oxidized-LDL and inflammation which were limited to high BMI adults. Further, <i>APOE4</i> carriers maintain higher levels of total and LDL cholesterol at low BMIs. These results suggest the relationship between <i>APOE4</i> and lipids may be beneficial for pathogen-driven immune responses, and unlikely to increase cardiovascular risk in an active subsistence population.</p>
Pigment, fatty acid and lipid data of the sea slug Elysia crispata in two habitat depths
<p>Sacoglossan sea slugs are the only animals able to sequester functional chloroplasts from the algae they feed on and keep them functional for more than a month. Here, we characterized <em>Elysia crispata</em> distributed in a coral reef from Southern Gulf of Mexico at two depths: 0-4 m and 8-12 m. We provide information on the concentrations of 12 pigments, 27 fatty acids, and total lipid, glycolipid and phospholipid amounts. </p>
Research data supporting: "A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields"
<p>This repository contains the data used in the paper of Capelli <em>et al. </em>"A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields", published on Journal of Physical Chemistry B (DOI: 0.1021/acs.jpcb.1c02503).<br> <br> The archive traj_processed.tar.gz contains the trajectories converted in xyz format with the dimensions of the box.</p> <p>The archive trajectories_xtc.tar.gz contains the raw trajectories (of the membranes without solvent) in gromacs xtc format with a .tpr binary file. <br> </p>
Molecular dynamics simulation of the permeation of 5ALA across the lipid bilayers of the stratum corneum
<p>Input and output files for US-REST3 MD simulations of the permeation of 5ALA across a lipid bilayer representative of the lipid bilayers of the stratum corneum. Each folder corresponds to US-REST3 and conventional US calculations performer at different distances between the permeant and the centre of mass of the lipid bilayer.</p>
Molecular dynamics simulation of the permeation of Me-5ALA across the lipid bilayers of the stratum corneum
<p>Input and output files for US-REST3 MD simulations of the permeation of Me-5ALA across a lipid bilayer representative of the lipid bilayers of the stratum corneum. Each folder corresponds to US-REST3 and conventional US calculations performer at different distances between the permeant and the centre of mass of the lipid bilayer.</p>
Lipid metabolism, fatty acid composition and meat quality in broilers supplemented with increasing levels of defrosted black soldier fly larvae
<p>Dataset for the experiment to evaluate the effects of increasing levels of whole black soldier fly larvae (BSFL) in broiler diets on lipid metabolism, fatty acid composition, and meat quality of birds. Chicks received the whole BSFL at 10%, 20%, or 30% of the feed intake of control chickens that received no BSFL but only age-specific diets. <a href="https://doi.org/10.3920/JIFF2022.0125">https://doi.org/10.3920/JIFF2022.0125</a></p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.