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2,697 results for “Lipids”
Lipidomic datasets for: Transmembrane protein 135 regulates lipid homeostasis through its role in peroxisomal DHA metabolism
<p>Transmembrane protein 135 (TMEM135) is thought to participate in the cellular response to increased intracellular lipids yet no defined molecular function for TMEM135 in lipid metabolism has been identified. In this study, we performed a lipid analysis of tissues from <em>Tmem135</em> mutant mice and found striking reductions of docosahexaenoic acid (DHA) across all <em>Tmem135</em> mutant tissues, indicating a role of TMEM135 in the production of DHA. Since all enzymes required for DHA synthesis remain intact in <em>Tmem135</em> mutant mice, we hypothesized that TMEM135 is involved in the export of DHA from peroxisomes. The <em>Tmem135</em> mutation likely leads to the retention of DHA in peroxisomes, causing DHA to be degraded within peroxisomes by their beta-oxidation machinery. This may lead to generation or alteration of ligands required for the activation of peroxisome proliferator-activated receptor a (PPARa) signaling, which in turn could result in increased peroxisomal number and beta-oxidation enzymes observed in <em>Tmem135</em> mutant mice. We confirmed this effect of PPARa signaling by detecting decreased peroxisomes and their proteins upon genetic ablation of <em>Ppara</em> in <em>Tmem135</em> mutant mice. Using <em>Tmem135</em> mutant mice, we also validated the protective effect of increased peroxisomes and peroxisomal beta-oxidation on the metabolic disease phenotypes of leptin mutant mice which has been observed in previous studies. Thus, we conclude that TMEM135 has a role in lipid homeostasis through its function in peroxisomes.</p>
Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts"
<p>Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts" by Julia R Rogers and Phillip L Geissler (<a href="https://doi.org/10.1371/journal.pcbi.1010992">Rogers, J. R.; Geissler, P. L. <em>PLoS Comput. Biol.</em> <strong>2023</strong>, <em>19</em>, e1010992</a>; bioRxiv DOI: https://doi.org/10.1101/2022.09.10.507427). All input coordinates, topologies, and parameter files in addition to equilibrium simulation trajectories and analysis results are provided.</p>
DPPC lipid bilayer simulation with CHARMM36-LJPME force field using OpenMM
<p>DPPC lipid bilayer simulation (300 ns) with CHARMM36-LJPME force field using OpenMM at 323K.</p> <p>Used in <a href="http://doi.org/10.1021/acs.jctc.1c00951">https://doi.org/10.1021/acs.jctc.1c00951</a></p> <p>The force field parameters were downloaded from <a href="https://terpconnect.umd.edu/%7Ejbklauda/ff.html">https://terpconnect.umd.edu/%7Ejbklauda/ff.html</a>.</p> <p><a href="https://zenodo.org/api/files/1e89f677-91a8-472d-aebb-144fddd58d23/trajCORRECT1-2.dcd?versionId=5317fd88-6b98-4905-b171-53c1cd199cfe">trajCORRECT1-2.dcd </a>has incorrect timestamps. traj1-2.xtc has correct timestamps.<br> </p>
Dataset for: Buckling of lipidic ultrasound contrast agents under quasi-static load
<p>Collapse of lipidic ultrasound contrast agents under high-frequency compressive load has been historically interpreted by the vanishing of surface tension. By contrast, buckling of elastic shells is known to occur when costly compressible stress is released through bending. Through quasi-static compression experiments on lipidic shells, we analyze the buckling events in the framework of classical elastic buckling theory and deduce the mechanical characteristics of these shells. They are then compared to that obtained through acoustic characterization.</p>
Protein-lipid association in lizard chemical signals
<p>Most animal chemical signals comprise a complex mixture of compounds, each with its own chemical properties, which are combined to maximize signal efficacy in a given environment. Such blends forms integrated functional units hypothesized to be shaped by selective forces acting on the functional mixture as a whole, rather than on a single component.</p> <p>Chemical communication plays a pivotal role in lizards, and many species have developed specialized epidermal glands whose secretions are waxy, homogeneous blends of lipids and proteins used for intra- and inter-specific signalling. Lipids are historically considered the main semiochemical source, while proteins provide mere structural support to the lipophilic fraction. Recent discoveries, however, point towards a key signalling role for proteins, as well.</p> <p>The potential signalling functions of both proteins and lipids let use to hypothesise that they should undergo to a certain degree of integration. We tested this hypothesis by comparing the composition and complexity of the lipophilic and proteinaceous fractions of the epidermal gland secretions of 36 lizard species (Lacertidae), and combining quantitative, phylogenetically-informed analysis with tandem mass spectrometry to identify the proteins responsible for such a potential association.</p> <p>We found the composition and complexity of proteins and lipids to be strongly correlated. Protein composition was mostly influenced by the relative proportion of cholestanol, provitamin D<sub>3</sub>, stigmasterol, and tocopherol, while the complexity of the protein pattern increased with that of lipids. Additionally, two identified proteins (carbonic anhydrase and protein disulfide isomerase) increased their concentration as provitamin D<sub>3</sub> became more abundant.</p> <p>Our results validate the hypothesis of an integration between the lipid and protein fractions of lizard secretions. The prevalence of proteins with enzymatic properties suggests the integration to be more complex than previously thought: proteins may serve to modulate the efficacy, stability, and durability of the signal, by dynamically controlling the chemical environment of the blend. Likewise, we cannot exclude that proteins contribute to the semiochemical function of the mixture, maybe forming with lipids an individual-specific chemical profile.</p> <p>Here we present the original data not available from other, already published researches (i.e., protein electrophoretic profiles and lipid composition). Notably:</p> <p>LM8.xls = excel sheet reporting the percentage concentrations of the eight lipids specifically used to characterize the lipophilic fraction</p> <p>MSdata.zip = mass spectrometry raw files (in .mzXML format) obtained from the analysis of the three molecular weight region related to the increase in provitamin D<sub>3</sub> abundance.</p>
Surfactant Proteins SP-B and SP-C in Pulmonary Surfactant Monolayers: Physical Properties Controlled by Specific Protein–Lipid Interactions - Simulation dataset
<p>Simulation data related to the article:</p> <p>Liekkinen, J., Olzynska, A., Cwiklik, L., Bernardino de la Serna, J., Vattulainen, I., & Javanainen, M. Surfactant Proteins SP-B and SP-C in Pulmonary Surfactant Monolayers: Physical Properties Controlled by Specific Protein–Lipid Interactions. <em>bioRxiv</em>, pp.2022-12. (Pre-print available at https://doi.org/10.1101/2022.12.12.520108)</p> <p> </p> <p>DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated in non-equilibrium conditions. The monolayer is compressed or expanded at a constant rate at different temperatures. Surfactant proteins SP-B and SP-C are included in the monolayers for comparison. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum.</p> <p>All trajectories are simulated for 5000 ns with Gromacs 5.1.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index (.ndx) files are also included. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/</p> <p>[1] DOI: 10.1021/jp101759q</p> <p>[2] DOI: 10.1021/jz501780a</p> <p>[3] DOI: 10.1016/j.softx.2015.06.001</p>
Dataset for "Supramolecular design of CO2-responsive lipid nanomaterials"
<p>This dataset provides the raw data supporting the paper: Supramolecular design of CO<sub>2</sub>-responsive lipid nanomaterials. It comprises SAXS data (Figure 4 on the manuscript), cryo-TEM images (Figure 5), Zeta-potential measurment (Table 1) and DLS data (Table1 and Figure S8).</p>
The effectiveness and safety of intensive lipid-lowering with different Rosuvastatin-based regimens in patients at high risk: A nonblind, randomized, controlled trial
<p><span><strong>Background</strong>:</span> <span>Statin alone or nonstatins as add-ons have been introduced to intensive low-density lipoprotein cholesterol (LDL-C) </span><span>lowering</span><span> therapy in patients at high cardiovascular disease (CVD) risk. The purpose of this study was to evaluate the effectiveness and safety of different statin-based regimens for patients at high risk</span><span>.</span></p> <p><span><strong>Methods</strong>:</span> <span>Three hundred patients at high CVD risk were randomly assigned to the statin group</span><span> (Rosuvastatin 20mg/d</span><span>), statin_EZ group</span> <span>(Rosuvastatin 10mg/d + ezetimibe </span><span>10mg/d</span><span>), statin_pcsk group (Rosuvastatin </span><span>10mg/d</span><span> + alirocumab </span><span>75mg/2</span><span>weeks) or combine3 group (Rosuvastatin 10mg/d + ezetimibe 10mg/d + alirocumab 75mg/2weeks)</span><span>.</span> <span>The primary outcome measure was cholesterol levels </span><span>(LDL-C, total cholesterol (TC) triglycerides (TGs), and high-density lipoprotein cholesterol (HDL-C))</span><span> after 24</span><span> weeks of</span><span> follow-up. The secondary outcome measures were safety markers and the proportion of patients who achieved the < 70 mg/dL (1.8 mmol/L) LDL-C target. </span><span>A logistic</span><span> regression model was performed to explore the factors affecting lipid target achievement.</span></p> <p><span><strong>Results</strong>:</span> <span>The TC and LDL-C levels after treatment were significantly different among the four groups</span> <span>(p < 0.05). The levels in both the combine3 group and </span><span>the </span><span>statin_pcsk9 group were significantly lower than </span><span>those in </span><span>the statin group and the statin_EZ group (</span><span>p < 0.05</span><span>), but there was no significant difference between</span><span> the</span><span> combine3 group and </span><span>the </span><span>statin_pcsk9 group. The incidence of adverse events in the four groups was low.</span><span> Body mass index (BMI) and hypertensive status were related to target achievement.</span></p> <p><span><strong>Conclusion</strong>:</span><span> The combination of a statin</span><span> and a PCSK9 inhibitor was safe and more effective for the treatment of high-risk CVD patients, while the addition of </span><span>ezetimibe was</span><span> unable to significantly lower lipid levels any further. The rate of achieving </span><span>the </span><span>target was higher in patients </span><span>with</span><span> hypertension and a low BMI.</span></p>
Movies of oxidized lipids PoxnoPC and PazePC in POPC bilayers
<p>Movies showing the last 100 ns from 1 microsecond simulations of PoxnoPC-POPC and PazePC-POPC systems. <br> </p> <ul> <li>POPC: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphochol</li> <li>PoxnoPC: 1-palmitoyl-2-(9’-oxo-nonanoyl)-sn-glycero-3-phosphocholin</li> <li>PazePC: 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholin</li> </ul> <p><strong>Reference:</strong></p> <ul> <li><em><strong>Effect of oxidation on POPC lipid bilayers: Anionic carboxyl group plays a major role</strong></em>, Behnaz Bagheri, Phansiri Boonnoy, <a href="https://www.researchgate.net/profile/Jirasak-Wong-Ekkabut">Jirasak Wong-ekkabut</a> and <a href="https://www.researchgate.net/profile/Mikko-Karttunen-2">Mikko Karttunen</a>, PCCP (2023). DOI: <a href="https://doi.org/10.1039/D3CP01692G">https://doi.org/10.1039/D3CP01692G</a> </li> </ul> <p> </p>
PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis thaliana Plasma Membrane and Inserts a Lipid
<p>Harvest yields depend on the plant's ability to fix carbon and deal with changing environmental conditions. Especially during seasonal and diurnal cycles, the plant must constantly adjust its metabolism according to available resources or external stressors. The metabolic changes that a plant undergoes in response to stress are well understood, but the long-distance signaling mechanisms that facilitate communication throughout the plant are less studied. The phloem is considered the predominant conduit for the bidirectional transport of these signals through metabolites, nucleic acids, proteins, and lipids. Lipid trafficking through the phloem in particular attracted our attention due to its reliance on soluble lipid-binding proteins (LBP) that generate and solubilize otherwise membrane-associated lipids. The Phloem Lipid-Associated Family Protein (PLAFP) from <em>Arabidopsis thaliana </em>is generated in response to abiotic stress as is its lipid-ligand phosphatidic acid (PA). PLAFP is proposed to transport PA through the phloem in response to drought stress. To understand the interactions between PLAFP and PA, almost 100 independent systems comprised of the protein and one PA, or a plasma membrane containing varying amounts of PA, were simulated. In the simulations, PLAFP does bind to the plasma membrane independent of the PA concentration, and it adopts a binding pose, where W41 and R82 penetrate the membrane surface and anchor PLAFP. This triggers a separation of the two loop regions containing W41 and R82. Subsequently, PA does insert into PLAFP's beta-sandwich and multiple amino acids besides W41 and R82 are identified that drive the insertion. Fine-tuning the protein-membrane and protein-PA interface by mutating a selection of these amino acids could allow modulating the signaling sensitivity to the climate the plant is supposed to grow in.</p>
Data from: A correlation between seasonally changing photoperiod, whole body lipid, and condition factor in juvenile spring Chinook Salmon (Oncorhynchus tshawytscha)
<p><span></span></p> <p>The regulation of lipid stores is a central process for the physiology and ecology of fishes. Seasonal variation in lipid stores has been directly linked to survival of fishes across periods of food deprivation. We assessed whether a seasonally changing photoperiod was correlated to seasonal changes in energetic status to help better understand these important processes. Groups of first-feeding Chinook salmon fry were introduced to a seasonal photoperiod cycle, but the point of entrance into the seasonal cycle varied from near the winter solstice (December), to either side of the spring equinox (February & May). Temperature and feeding rate were similar for all treatments. Subsequently, condition factor and whole-body lipid content were assessed through a seasonal progression. Throughout most of the experiment, length and weight did not differ between the different photoperiod treatments, however whole body lipid and Fulton's condition factor did. Furthermore, changes in both whole body lipid and Fulton's condition factor in all treatment groups followed a similar seasonal pattern that was inversely related to day length (highest K and lipid levels found during days with the least light). These results suggest that regardless of age or size, there is a correlation between seasonal changes in photoperiod and changes in body composition in juvenile Chinook salmonids.</p>
Lipid analysis of S.c. cells expressing ProtA-ScNdc1 (261-655), ProtA-AHNdc1-ProtA, or ProtA-ScHmg1
<p>Nuclear pore complexes (NPCs) are embedded in the nuclear envelope and built from <span>∼</span>30 different nucleoporins (Nups) in multiple copies, and few are integral membrane proteins. One of these transmembrane nucleoporins, Ndc1, is thought to function in NPC assembly at the fused inner and outer nuclear membranes. Here, we show a direct interaction of Ndc1<span>'</span>s transmembrane domain with Nup120 and Nup133, members of the pore membrane coating Y-complex. We identify an amphipathic helix in Ndc1<span>'</span>s C-terminal domain binding highly curved liposomes. Upon overexpression, this amphipathic motif is toxic and dramatically alters the intracellular membrane organization in yeast. Ndc1<span>'</span>s amphipathic motif functionally interacts with related motifs in the C-terminus of the nucleoporins Nup53 and Nup59, important for pore membrane binding and interconnecting NPC modules. The essential function of Ndc1 can be suppressed by deleting the amphipathic helix from Nup53. Our data indicate that nuclear membrane and presumably NPC biogenesis depends on a balanced ratio between amphipathic motifs in diverse nucleoporins.</p>
Experimental data of "Elevated concentrations cause upright alpha-synuclein conformation at lipid interfaces" (NatComm)
<p>The experimental data in this dataset is the basis of the article entitled "Elevated concentrations cause upright alpha-synuclein conformation at lipid interfaces", which will hopefully be published in NatComm soon. We will add a DOI then. It contains the vibrational sum-frequency generation (VSFG), atomic-force microscopy (AFM) and surface-pressure datasets of alpha-synuclein interacting with 1,2-Dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) monolayers, at various alpha-synuclein concentrations.</p>
Potentiation of endocannabinoids and other lipid amides prevents hyperalgesia and inflammation in a pre-clinical model of migraine
<p>This dataset comprises the findings obtained in the study aimed at investigating the anti-migraine effects of two URB597 analogs with improved solubility and bioavailability – ARN14633 ([4-fluoro-3-[3-(methylcarbamoyl)phenyl]phenyl] N-cyclohexylcarbamate) and ARN14280 ([3-(3-carbamoylphenyl)-4-(difluoromethoxy)phenyl] N-cyclohexylcarbamate), in the migraine rat model based by nitroglycerin (NTG) administration. Two compounds significantly attenuated the nocifensive behavior induced by NTG compared with original URB597 administered in the same conditions. Additionally, both inhibitors reverted the neurobiological changes induced by NTG in specific peripheral and central areas. Although the precise mechanism underlying these effects remains to be elucidated, our results support further investigational studies of FAAH blockade as a potential therapeutic strategy to treat migraine conditions.</p> <p>ARN14633 (1 mg/kg, i.p.), ARN14280 (3 mg/kg, i.p.) and URB597 (2mg/kg, i.p.) were administered to adult male Sprague-Dawley rats 3 hours after NTG injection. One hour after the administration of either compound, rats were subjected to the orofacial formalin test and compared. In addition, the anti-migraine effects of two URB597 analogs were evaluated by neuronal nitric oxide synthase, pain mediators peptides, pro-inflammatory cytokines gene expression and lipid amides levels in specific areas.</p> <p><strong>The in vivo and ex vivo assessments were:</strong></p> <p>1) mRNA expression levels: CGRP, SP, interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-alpha) and IL-1beta in cervical spinal cord, medulla-pons and trigeminal ganglia. mRNA levels were measured by rt-PCR. All samples were assayed in triplicate and gene expression levels were calculated according to 2−∆∆Ct = 2− (∆Ct gene − ∆Ct housekeeping gene) formula by using Ct (cycle threshold) values.</p> <p>2) Central and peripheral Endocannabinoids levels: Lipid amides levels were measured using a Xevo TQ UPLC-MS/MS system equipped with a reversed-phase BEH C18 column (2.1 × 50 mm, 1.7 μm particle size) (Waters, Milford, USA). The mobile phase consisted of 0.1% formic acid in water as solvent A and 0.1% formic acid in acetonitrile as solvent B. A linear gradient was used: 0.0–0.5 min 20% B; 0.5–2.5 min 20 to 100% B; and 2.5–3.0 min maintained at 100% B. The column was reconditioned to 20% B for 1 min. Analysis time was 4 min and the injection volume was 5 μL.</p> <p><strong>Results in brief</strong></p> <p>ARN14633 and ARN14280 attenuated NTG-induced nocifensive behavior compared with URB597. Additionally, the new FAAH inhibitors reduced transcription of genes encoding neuronal nitric oxide synthase, pain mediators peptides (calcitonin gene-related peptide, substance P) and pro-inflammatory cytokines (tumor necrosis factor-alpha, interleukin-1beta and 6) in the trigeminal ganglion, cervical spinal cord and medulla. Finally, both compounds strongly elevated levels of endocannabinoids and/or other FAAH substrates in cervical spinal cord and medulla, and, to a lesser extent, in the trigeminal ganglia.</p>
Raw data for: Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity
<p>This repository contains raw data and code related to "Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity" by Goretzki et al.</p> <p>Included are molecular dynamics parameter files, initial structures after system equilibration, production trajectories, and final structures of simulations of:<br> 1. coarse-grained IDRs on membrane, and force and position data for restrained c-termini. Trajectories are subsampled with one frame every 50 ns.<br> 2. The tetrameric TRPV4 core in a POPC in atomistic resolution. Trajectories are sampled with one frame every 1 ns. <br> 3. The isolated ARD in solution in atomistic resolution. Trajectories are subsampled with one frame every 1 ns.</p> <p>Contact information:<br> Name: Stefan L. Schaefer<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: stefan.schaefer@biophys.mpg.de</p> <p>Name: Ainara Claveras Cabezudo<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: ainara.claveras@biophys.mpg.de</p>
MD simulations: Conditions for the stable adsorption of lipid monolayers to solid surfaces
<p>Essential files for Gromacs used in the study "Conditions for the stable adsorption of lipid monolayers to solid surfaces."</p> <p>Systems: DLPC bilayer, SAM+DLPC pulling, SAM with water droplets</p>
Trajectories of simulated lipid membranes interacting with antimicrobial peptidomimetic AMC-109 and simulation setup files
<p>Trajectories of simulated lipid membranes with antimicrobial peptidomimetic AMC-109.<br> Trajectories are in GROMACS format ".xtc", the frame rate is 10 ns, and water and NaCl ions were omitted from the trajectory deposit to reduce the size to acceptable limits.</p> <p>The molecules are described using MARTINI 3 coarse grained force field.<br> This repository contains a set of simulations with varying ratio of POPC:POPG lipids from<br> 100% POPC, 0% POPG (denoted as "pg000p..") to<br> 0% POPC, 100% POPG (denoted as "pg100p..").<br> Ratios between these two extremes go in steps of 10%,<br> e.g. "pg060p.." denotes 40% POPC, 60% POPG.</p> <p> </p> <p>The files with ".out" or ".xvg" suffix are properties analyzed from the simulation. Namely, they are:<br> - "thickness" : thickness of the membrane<br> - "apl" : area per lipid of the lipid membrane<br> - "numcont" : number of contacts between the peptidomimetic AMC-109 and the lipids<br> - "ordPars" : order parameters of the end tail segments of the sn-1 tail of POPC lipids.</p> <p>More details about how these properties were generated can be found in the attached scripts (".sh" files) in this repository.</p> <p>Sample topology files in GROMACS format (binary ".tpr" and ASCII ".itp") are provided to complete the description of the molecular topologies used to generate the presented simulations.</p> <p> </p> <p>This repository was created as a Supporting Information to a scientific paper at Nature Communications,</p> <p>Lateral membrane organization as target of an antimicrobial peptidomimetic compound, 2023.</p>
Single lipid component membrane bilayer MD with CHARMM36 force field, simulated with the CHARMM program
<p>Data for ten single component lipid bilayer simulations, with 3 files per lipid: a DCD file with coordinates, a PSF file describing the system, and a .zip file containing the starting coordinate set (CHARMM COOR format) and the other inputs used for the CHARMM simulations. Only the POPG system includes ions: Na+ to neutralize the lipids, and ca. 0.15 M NaCl.</p> <p>The DCD trajectory files contain coordinate sets stored at 0.1 ns intervals, <br> and are in the original CHARMM binary format.</p> <p>Lipid Nlpd Nwat ns<br> DLPC 648 25920 200<br> DMPC 648 16632 100<br> DOPC 648 21681 350<br> DOPE 648 21681 350<br> DPPC 648 19701 300<br> POPC 648 20178 200<br> POPE 720 23049 100<br> POPG 648 29160 200<br> PSM 648 18828 200<br> SDPE 648 25920 100</p> <p>"Mechanical properties of lipid bilayers from molecular dynamics simulation",<br> R. M. Venable, F. L. Brown and R. W. Pastor,<br> Chemistry and Physics of Lipids, 192 pp. 60-74 (2015). </p> <p>https://pubmed.ncbi.nlm.nih.gov/26238099/<br> https://www.sciencedirect.com/science/article/pii/S0009308415300190?via%3Dihub</p> <p> See also:</p> <p>"Identifying systematic errors in a power spectral analysis of simulated<br> lipid membranes"<br> Muhammed F. Ergüder, Markus Deserno<br> J. Chem. Phys. 154, 214103 (2021); doi: 10.1063/5.0049448<br> </p> <p> </p>
Lipids of different phytoplankton groups differ in sensitivity to degradation: implications for carbon export
<p>Data were collected on seven cruises on a monthly basis from February to August in 2010 in the northern Adriatic Sea (RV001 (N 45°04.8', E 013°36.6'), SJ107 (N 45°02.9', E 013°19.0'), SJ105 (N 45°02.0', E 0.13°09.3'), SJ103 (N 45°01.0', E 012°59.6'), SJ101 (N 44°59.9', E 012°50.3'), and SJ108 (N 44°48.7', E 012°45.0')). </p> <p>A CTD probe (Seabird SBE25, Sea–Bird Electronics Inc., Bellevue, Washington, USA) was used to measure temperature and salinity. Total phosphorus, dissolved inorganic orthophosphates (PO<sub>4</sub><sup>3-</sup>), total inorganic nitrogen (TIN), including nitrates (NO<sub>3</sub>¯), nitrites (NO<sub>2</sub>¯), and ammonium (NH<sub>4</sub><sup>+</sup>)), were determined by spectrophotometric methods (Parsons et al., 1984) on board and immediately after sampling using Shimadzu UV-Mini 1240 spectrophotometer with 10 cm quartz cuvettes. Organic phosphorus concentration was calculated as the difference between total and inorganic phosphorus concentrations. Subsamples for the determination of chlorophyll <em>a</em> (Chl <em>a</em>) were filtered on Whatman GF/C filters and stored frozen at -20°C until further processing. Chl <em>a</em> concentrations were determined following 3 h extraction in 90% acetone (in the dark, with grinding), on a Turner TD–700 fluorimeter (Parsons et al., 1984).</p> <p>We preserved 200 mL of seawater with 2% neutralized formaldehyde (final concentration) and performed nano- and microphytoplankton determination and enumeration within one month of sampling. The stored sample was homogenized by gentle shaking, and a subsample was added to the Utermöhl sedimentation chamber (volume: 50 mL; Hydro-Bios Apparatebau, Altenholz, Germany), where it settled for ~30 h. We performed the analysis on a Zeiss Axiovert 200 (Zeiss, Jena, Germany) following the inverted microscope method (Utermöhl, 1958, Hasle 1978). Total phytoplankton included all species counted in the microphytoplankton (20–200 µm) and nanophytoplankton (2-20 µm) groups (Sieburth et al., 1978). Taxa were identified to species level and subsequently grouped to diatoms, dinoflagellates, and nanophytoplankton coccolithophores and phytoflagellates (which included chlorophytes, chrysophytes, cryptophytes and prasinophytes) according to Tomas (1997).</p> <p>For POC determination, 1 L of seawater was filtered on board through 0.7 mm Whatman GF/F filters precombusted at 450 °C/5h. After filtration, the filters were rinsed with Milli-Q water to remove salts and stored in liquid nitrogen on board and at -80 <sup>o</sup>C in the laboratory until analysis. POC was analyzed using an SSM–5000A solid sample module connected to a Shimadzu TOC–V<sub>CPH</sub> carbon analyzer calibrated with glucose (Sugimura and Suzuki, 1988). POC concentrations were corrected based on filter blank measurements. The average filter blank value including the instrument blank value corresponded to 5 mg C L<sup>-1</sup>. The reproducibility obtained for the glucose standard was 3%.</p> <p>For particulate lipid analysis, we collected 3 L of seawater prefiltered through a 200 μm stainless steel screen to remove larger particles including microzooplankton. Lipids were collected on through precombusted (450 °C/5h) 47 mm GF/F filters and stored in liquid nitrogen until lipid extraction. It was performed using a modified one-phase solvent mixture of dichloromethane-methanol-water procedure (Bligh and Dyer, 1959; Vrana et al., 2023). In short, in order to assess recoveries in later stages of sample analysis we added 5 µg of standard methyl stearate to the sliced filters together with 10 mL of a one-phase solvent mixture (dichloromethane/methanol/deionized water (1:2:0.8 v/v/v)). This was then subjected to an ultrasonic treatment for three minutes and stored overnight in the refrigerator, afterwards we filtered the extracts through a sinter funnel into a separatory funnel, washed once with a the one-phase solvent mixture (10 mL), once with dichloromethane (5 mL) and 0.73% NaCl (5 mL) (1:1 v/v), and once with 10 mL dichloromethane. The dichloromethane extracts were concentrated by rotary evaporation under a nitrogen atmosphere and kept at -20 °C until measurements were made. To prepare the lipid extracts for analysis, the dichloromethane extracts were evaporated to dryness under nitrogen flow and then dissolved in 20 µL dichloromethane prior to analysis.</p> <p>Lipid classes were separated on Chromarods SIII and quantified with external calibration using a mixture of standard lipids by a thin-layer chromatograph-flame ionization detector (TLC-FID) Iatroscan Mark-VI (Iatron), using a hydrogen flow of 160 mL min<sup>-1</sup> and an air flow of 2000 mL min<sup>-1</sup>. This method identify eighteen lipid classes: hydrocarbons (HC), steryl esters (SE), fatty acid methyl esters (ME), fatty ketone (KET), triacylglycerols (TG), free fatty acids (FFA), fatty alcohols (ALC), 1,3-diacylglycerols (1,3DG), sterols (ST), 1,2-diacylglycerols (1,2DG), pigments (PIG), monoacylglycerols (MG), three glycolipids (GL) including monogalactosyl-, digalactosyl-, and sulfoquinovosyl- diacylglycerol (MGDG, DGDG, and SQDG, respectively), and three phospholipids (PL) (phosphatidylglycerols (PG), phosphatidylethanolamines (PE), and phosphatidylcholines (PC)). Total lipid concentration is calculated by summing all detected classes. Full details can be found in Gašparović et al. (2015; 2017). In this article we focused on lipid degradation indices trough the lipolysis index (Goutx et al., 2003), which characterize the degree of lipid degradation in seawater. Lipolysis index is calculated as the ratio of the sum of lipid degradation indices (ALC+FFA+MG+DG) to the sum of cell lipids TG, WE, and glyco- and phospho-lipids (Goutx et al., 2003).</p>
Data for: Lipid biomarkers recording marine microbial community structure changes through the Frasnian‐Famennian mass extinction event
<p>This dataset contains data for a research article published on Geobiology. The article is entitled " <span class="Dummy">Lipid biomarkers recording marine microbial community structure changes through the </span><span class="fc">Frasnian‐Famennian</span><span class="Dummy"> mass extinction event</span>". <span class="Dummy"><span class="Dummy">This study aims to reconstruct changes in the marine microbial community structure through the Late Devonian Frasnian‐Famennian (F‐F) transition. We performed a multiproxy investigation on a drill core of the Upper Devonian New Albany Shale from the Illinois Basin (western Kentucky, USA). </span><span class="Dummy">Detailed information regarding the data collection, analysis, and interpretation can be found in the </span></span><span class="Dummy"><span class="Dummy">following paper:<br></span></span></p> <p class="MsoNormal">Chen J., Hogancamp<sup> </sup>N., Lu<sup> </sup>M., Ikejiri T., Malina N., Ojeda<sup> </sup>A., Sun Y., Lu Y. 2023. Lipid Biomarkers Recording Marine Microbial Community Structure Changes Through the Frasnian‐Famennian Mass Extinction Event. Geobiology <a href="https://doi.org/10.1111/gbi.12568"><span>https://doi.org/10.1111/gbi.12568</span></a></p>
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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)
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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.