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2,697 results for “Lipids”
MD simulation trajectory of a lipid bilayer: Pure POPC in water. SLIPIDS, Gromacs 4.6.3. 2016.
<p>MD simulation trajectory files, for fully hydrated POPC bilayer [512 POPC, 23943 WAT]. The SLIPIDS force field was used with Gromacs 4.6.3. Conditions: T=298K. 170 ns each trajectory, last 100 ns analyzed.</p>
POPC/Cholesterol (50:50) lipid membrane, 303K, Charmm36 force field, simulation files and 100 ns trajectory for GROMACS simulation engine v5
<p>All runs were performed with GROMACS simulation engine v5 and CHARMM36 additive force field parameters obtained from MacKerell lab website (http://mackerell.umaryland.edu/charmm_ff.shtml, also available at</p> <p>https://doi.org/10.5281/zenodo.209080). Conditions: T=303, 80 POPC and 80 Cholesterol molecules, 7200 tip3p waters, 100ns trajectory (preceded with equilibration). </p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M CsCl, Berger force field for lipids, Dang's for Cs+ and ffgmx for Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M CsCl (102 POPC, 26 POPS, 4290 WAT, 106 Cs+, 80 Cl-). Additional Cs+ cations added to neutralize the negative charge of POPS. Berger force field for lipids, Dang's for Cs+ (), ffgmx for Cl- are employed. Gromacs 4.0.7, T=310K, 200 ns trajectories were calculated with the last 50 ns stored here).<br> K+ nonbonding parameters (from Dang's Cs+ from JPC B 1999, 103, 8195):<br> sig=0.383086, eps=0.41840</p> <p>Used in:</p> <p>P. Jurkiewicz, L. Cwiklik, A. Vojtiskova, P. Jungwirth, M. Hof, Structure, Dynamics, and Hydration of POPC/POPS Bilayers Suspended in NaCl, KCl, and CsCl <br> <em>BBA Biomembranes </em>2012<em>, 1818, 609-616.</em><br> DOI: 10.1016/j.bbamem.2011.11.033</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M KCl, Berger force field for lipids, Dang's for K+ and ffgmx for Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M KCl (102 POPC, 26 POPS, 4290 WAT, 106 K+, 80 Cl-). Additional K+ cations added to neutralize the negative charge of POPS. Berger force field for lipids, Dang's for K+ (), ffgmx for Cl- are employed. Gromacs 4.0.7, T=310K, 200 ns trajectories were calculated with the last 50 ns stored here).K+ nonbonding parameters (from Dang's JPC B 1999, 103, 8195 based on Vacha et al. Biophys. J 2009, 96, 4493.):<br> sig=0.3048655 eps=0.418400</p> <p>Used in:</p> <p>P. Jurkiewicz, L. Cwiklik, A. Vojtiskova, P. Jungwirth, M. Hof, Structure, Dynamics, and Hydration of POPC/POPS Bilayers Suspended in NaCl, KCl, and CsCl <br> <em>BBA Biomembranes </em>2012<em>, 1818, 609-616.</em><br> DOI: 10.1016/j.bbamem.2011.11.033</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M NaCl, Berger force field for lipids and ffgmx for ions
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M NaCl (102 POPC, 26 POPS, 4290 WAT, 106 Na+, 80 Cl-). Additional Na+ cations added to neutralize the negative charge of POPS. Berger force field for lipids and ffgmx for ions are employed. Gromacs 4.0.7, T=310K, 200 ns trajectories were calculated with the last 50 ns stored here.</p> <p>Used in:</p> <p>P. Jurkiewicz, L. Cwiklik, A. Vojtiskova, P. Jungwirth, M. Hof, Structure, Dynamics, and Hydration of POPC/POPS Bilayers Suspended in NaCl, KCl, and CsCl <br> <em>BBA Biomembranes </em>2012<em>, 1818, 609-616.</em><br> DOI: 10.1016/j.bbamem.2011.11.033</p> <p> </p>
Germline proliferation trades off with lipid metabolism in Drosophila
<p>Little is known about the metabolic basis of life-history trade-offs but lipid stores seem to play a pivotal role. During reproduction, an energetically highly costly process, animals mobilize fat reserves. Conversely, reduced or curtailed reproduction promotes lipid storage in many animals. Systemic signals from the gonad seem to be involved: <em>C. elegans</em> lacking germline stem cells display endocrine changes, have increased fat stores and are long-lived. Similarly, germline-ablated <em>D. melanogaster </em>exhibit major somatic physiological changes, but whether and how germline loss affects lipid metabolism remains largely unclear. Here we show that germline-ablated flies have profoundly altered energy metabolism at the transcriptional level and store excess fat as compared to fertile flies. Germline activity thus constrains or represses fat accumulation, and this effect is conserved between flies and worms. More broadly, our findings confirm that lipids represent a major energetic currency in which costs of reproduction are paid.</p>
Coordinate files from LipIDens: Simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.
<p>Coordinate files from the first and last frame of coarse-grained (CG) and atomistic (AT) molecular dynamics (MD) simulations used throughout the LipIDens pipeline.</p><p>CG simulations were run for HHAT, OTOP1, ELIC, MscS, TRPV6, ChRmine, Ste2, Connexin-50, NPC1 and the PAT complex. All CG simulations were run for 10 x 15 μs with the exception of NPC1 which was simulated for 10 x 30 μs.</p><p>AT simulations were run for HHAT (5 x 200 ns) and ELIC (3 x 200 ns) in apo configurations.</p><p><strong>File description:</strong></p><p>Directories for each protein are listed with the suffix CG or AT used to indicate the simulation resolution. </p><p>md_fit_firstframe_<i>X</i>.gro - GROMACS structure file for the first frame of replicate <i>X</i>. </p><p>md_fit_lastframe_<i>X</i>.gro - GROMACS structure file for the last frame of replicate <i>X</i>. </p>
3-(4-Hydroxy-3-methoxyphenyl) propionic acid contributes to improved hepatic lipid metabolism via GPR41
<p class="MsoNormal"><span>3-(4-hydroxy-3-methoxyphenyl) propionic acid (HMPA) is a metabolite produced by the gut microbiota through the conversion of 4-hydroxy-3-methoxycinnamic acid (HMCA), which is a widely distributed hydroxycinnamic acid-derived metabolite found abundantly in plants. Several beneficial effects of HMPA have been suggested, such as antidiabetic properties, anticancer activities, and cognitive function improvement, in animal models and human studies. However, the intricate molecular mechanisms underlying the bioaccessibility and bioavailability profile following HMPA intake and the substantial modulation of metabolic homeostasis by HMPA require further elucidation. In this study, we effectively identified and characterized HMPA-specific GPR41 receptor, with greater affinity than HMCA. The activation of this receptor plays a crucial role in the anti-obesity effects and improvement of hepatic steatosis by stimulating the lipid catabolism pathway. For the improvement of metabolic disorders, our results provide insights into the development of functional foods, including HMPA, and preventive pharmaceuticals targeting GPR41.</span></p>
Increased Drp1 acetylation by lipid overload induces cardiomyocyte death and heart dysfunction
<p>Metabolic syndrome is a cluster of abnormalities characterized by obesity and insulin resistance, which compromise energy metabolism, damage mitochondria, cause cardiomyocyte death, and eventually impair heart contraction and relaxation performance. Despite the increasing prevalence of heart complications in obese and diabetic patients, our knowledge on how obese and diabetes mellitus impair heart function is very limited. In this study, we used animal and cell culture models in rodents or monkeys and generated lipid overload models to mimic obesity conditions. We found that excessive lipid supply decreased nicotinamide adenine dinucleotide (oxidized) levels and increased the acetylation of a fission protein Drp1 at a specific lysine residue (K642). Drp1 acetylation at K642 activated Drp1 through phosphorylation, mitochondrial translocation, and oligomerization. The excessively activated Drp1 had higher GTPase activity, bound with VDAC1 on mitochondria, induced mitochondrial fission, and caused cardiomyocyte death. These findings provide new information regarding how lipid overload regulates redox environment, protein acetylation, and the function of mitochondrial fission protein Drp1 in the heart.</p>
Data from: An insight into vitamin E and lipid nutrition of the plains-wanderer Pedionomus torquatus
<p>Vitamin E, as α-tocopherol, is an essential antioxidant protecting the body from free radicals. The vitamin E requirement of managed wildlife species is known to be greater than their wild counterparts, predominantly due to higher dietary lipid content and potentially stressful environments. The plains-wanderer (<em>Pedionomus torquatus</em>, Family Pedionomidae [monotypical]) is a critically endangered, superficially quail-like bird that is the focus of an ongoing captive breeding program in Australia. It is estimated that plains-wanderers have a high vitamin E requirement (compared to domestic poultry species) to offset a high lipid diet and their naturally flighty temperament. This study therefore aims to gain a greater understanding of the nutritional status and vitamin E requirements of plains-wanderers in managed environments. Total lipid and α-tocopherol intake were quantified for 26 zoo-managed plains-wanderers over a series of diet intake trials in addition to measurement of plasma α-tocopherol and cholesterol concentrations. Plains-wanderers that consumed higher portions of dietary fat had significantly lower circulating α-tocopherol concentrations than birds that consumed lower total dietary fat (p < 0.001). Additionally, plasma cholesterol concentrations of managed plains-wanderers were found to be significantly greater than all other bird species reviewed, irrespective of Family or feeding type. We also present the first published data quantifying the nutritional makeup of stomach contents of a wild plains-wanderer for use as a potential guide for diet formulation. This study forms a vital foundational insight into the nutritional management of plains-wanderers, but further research is required to understand their dietary habits and cholesterol metabolism. </p>
Experimentally probing the effect of confinement geometry on lipid diffusion
<p>Dataset accompanying the J. Phys. Chem. B paper: "<span>Experimentally probing the effect of confinement geometry on lipid diffusion". Contains raw and processed FCS data, processed FRAP data, and VCell simulations, and Jupyter notebooks to generate the figures in the associated manuscript.</span></p>
Target for lipid to carbohydrate intake minimizes cost of growth
<p>Many theoretical treatments of foraging use energy as currency, with carbohydrates and lipids considered interchangeable as energy sources. However, herbivores must often synthesize lipids from carbohydrates since they are in short supply in plants, theoretically increasing the cost of growth. We tested whether a generalist insect herbivore (<em>Locusta migratoria</em>) can improve their growth efficiency by consuming lipids, and whether these locusts have a preferred intake target caloric ratio of carbohydrate to lipid (C:L). Locusts fed pairs of isocaloric, isoprotein diets differing in C and L consistently selected a 2C:1L target. Locusts reared on isocaloric, isoprotein 3C:0L diets attained similar final body masses and lipid contents as locusts fed the 2C:1L diet but ate more and had a ~12% higher metabolic rate—indicating an energetic cost for lipogenesis. These results demonstrate that some animals can selectively regulate carbohydrate to lipid intake and that consumption of dietary lipid can improve growth efficiency.</p>
Fig. 3 in Novel Media for Lipid Production of Chlorococcum oleofaciens: A RSM Approach
Fig. 3. Comparison of algal growth in CFTRI and AM medium
A bottom-up coarse-grained model for interactions of lipids with TiO2 nanoparticles
<p>Supplemetary information data to the paper:</p> <p>M.Ivanov and A.P.Lyubartsev, "Development of a bottom-up coarse-grained model for interactions of lipids with TiO<br> nanoparticles", J. Comput. Chem.m 2024. Doi: <a href="https://doi.org/10.1002/jcc.27310">10.1002/jcc.27310</a></p>
Re-charging your fats: Charmm36 parameters for neutral lipids triacylglycerol and diacylglycerol
<p>Dataset containing files required to run the simulations and reproduce the Figures appearing in "Re-charging your fats: Charmm36 parameters for neutral lipids triacylglycerol and diacylglycerol"</p>
Correlations between bulk and surface properties of meibomian lipids with alteration of wax- to-sterol esters content
<p>These are the surface pressure/area isotherms and the stress relaxations of the transient dilatational elasticity modulus used in the study "Correlations between bulk and surface properties of meibomian lipids with alteration of wax- to-sterol esters content" in Chemistry and Physics of Lipids https://www.sciencedirect.com/science/article/pii/S000930842100116X</p> <p>The measurements are performed with by Langmuir surface balance µ Trough XS, area 135 cm<sup>2</sup>, volume 100 mL (Kibron, Helsinki, Finland), via the Wilhelmy wire probe method (instrumental accuracy 0.01 mN/m). Physiological saline solution buffer (PBS, pH 7.4) was utilized as trough subphase.</p> <p> </p> <p> </p>
Association between prenatal provision of lipid‐based nutrient supplements and cesarean delivery: Findings from a randomized controlled trial in Malawi
<p>Data set for a published manuscript on Maternal & Child Nutrition.</p> <p><strong>ABSTRACT:</strong> In populations with a high prevalence of childhood and adolescent undernutrition, supplementation during pregnancy aiming at improving maternal nutritional status and preventing fetal growth restriction might theoretically lead to cephalopelvic disproportion and delivery complications. We investigated whether the prenatal provision of small-quantity lipid-based nutrient supplements (SQ-LNS) was associated with an increased risk of caesarean section (CS) or other delivery complications. Pregnant Malawian women were randomised to receive daily i) iron–folic acid (IFA) capsule (control), ii) multiple micronutrient (MMN) capsule of 18 micronutrients (second control), or iii) SQ-LNS with similar micronutrients as MMN, plus four minerals and macronutrients contributing 118 kcal. We analysed the associations of SQ-LNS, CS, and other delivery complications using log-binomial regressions. Among 1391 women enrolled, 1255 had delivery information available. The incidence of CS and delivery complications was 6.3% and 8.2%, respectively. The incidence of CS was 4.0%, 6.0%, and 8.9% (p = 0.017) in the IFA, MMN, and LNS groups, respectively. Compared to the IFA group, the relative risk (95% confidence interval) of CS was 2.2 (1.3–3.8) (p = 0.006) in the LNS group and 1.5 (0.8–2.7) (p = 0.200) in the MMN group. We found no significant differences for other delivery complications. Provision of SQ-LNS to pregnant women may have increased the incidence of CS. The baseline rate was, however, lower than recommended. It is unclear if the higher CS incidence in the SQ-LNS group resulted from increased obstetric needs or more active health seeking and a better supply of services. Trial registered at clinicaltrials.gov, NCT01239693.</p>
Fish resist temptation from junk food: State-dependent diet choice in reproductive Atlantic cod (Gadus morhua) facing seasonal fluxes of lipid-rich prey
<p>In ecological sciences, animal diets are often simplified to "resources" or "caloric quantities". However, in the present study, we investigated the optimal foraging strategy of Atlantic cod (Gadus morhua) when both macro- and micro-nutritional requirements are accounted for. Proteins cannot be synthesized from fatty acids, so the proteins for gonad development must come from other dietary sources. In addition, micronutrients are required in smaller quantities. For example, for cod, arachidonic acid (ARA) acts as a micronutrient precursor for prostaglandins, which is important for reproduction. We formulated a dynamic state-dependent model to make predictions about optimal diet choice and foraging behavior. We applied the model to a case study in the strait between Denmark and Sweden. The model predicted that energy acquired from dietary protein should be twice that acquired from lipids, with a small increase in the lipid requirements when gonads are growing. The model also predicted that the "energy sparing effect of lipids" made it beneficial to engage in risky foraging activity to supplement a lean diet with a little bit of fat. When we re-constructing the model to also optimize ARA uptake, the cod consumed relatively more ARA-rich crabs in the months prior to spawning, despite the otherwise poor energetic value of this prey. In support of the model predictions, field observations indicated that lipid stores reached a peak shortly after the arrival of the lipid-rich migrating herring and the fatty acid signal of these herring were evident in the liver of nearly all cod. Three month later, only half of the cod contained the herring-derived fatty acid signal, supporting the predicted shift in prey type prior to spawning. From these model predictions and field observations, we conclude that, also in the wild, nutritional requirements can be at least as important as pure energy acquisition.</p>
Amines and lipids metabolites in blood plasma and saliva samples in pigs.
<p>The dataset presented in here is generated in a project named "<strong>Effects of sanitary and health status on amino acid and energy metabolism of growing-finishing pigs.</strong>" The metabolomics data from two samples types in pigs were generated in collaboration with Metabolomics Facility Leiden, The Netherlands and Wageningen Livestock Research, The Netherlands. This collaboration was realized and funded by Enabling Technology Hotels programme, ZonMW, NWO, The Netherlands (<strong>project number: 435005015</strong>). </p> <p>Targeted quantification of metabolites in two metabolomic platforms covering amines and oxidative stress metabolites in the blood and saliva samples in pigs. The samples were collected from a feeding trial. Briefly, After weaning, i.e., at week 4, pigs were fed a starter (4-9 weeks), grower (9-14 weeks), and finisher (14-22 weeks) diet containing either starch or fat as an energy source. At week 9, before the pigs were fed the grower diet, blood plasma and saliva samples were collected from the pigs (n=6) and the animals were stratified according to different hygiene conditions. At week 14, i.e., before the pigs received the finisher diet, and at week 22, i.e., at the end of this experiment, blood plasma and saliva samples were collected from the pigs (n=6) in the cohort receiving a diet with a different energy source under contrasting sanitary status. </p> <p>Targeted quantification of metabolites in two metabolomic platforms covering amines and oxidative stress metabolites in the blood and saliva samples in pigs. The number of identified metabolites are shown in Table 1.</p> <p><strong>Table 1</strong>: <strong>Number of identified amines and lipids metabolites in blood plasma and saliva samples in pigs.</strong> </p> <table> <tbody> <tr> <td> <table align="center"> <tbody> <tr> <td> <p> </p> </td> <td> <p>Data reported as</p> </td> </tr> <tr> <td> </td> <td> <p>Peak areas<sup>1</sup></p> </td> <td> <p>Relative response ratios<sup>4</sup></p> </td> </tr> <tr> <td> <p> </p> </td> <td> <p>Confidence<sup>2</sup></p> </td> <td> <p>Caution<sup>3</sup></p> </td> <td> <p>Confidence</p> </td> <td> <p>Caution</p> </td> </tr> <tr> <td> <p><em>Amines</em></p> </td> <td> </td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td> <p>Blood plasma</p> </td> <td> <p>not required</p> </td> <td> <p>not required</p> </td> <td> <p>58</p> </td> <td> <p>2</p> </td> </tr> <tr> <td> <p>Saliva</p> </td> <td> <p>not required</p> </td> <td> <p>not required</p> </td> <td> <p>52</p> </td> <td> <p>5</p> </td> </tr> <tr> <td> <p><em>Lipids </em></p> <p><em>(low pH)</em></p> </td> <td> </td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td> <p>Blood plasma</p> </td> <td> <p>47</p> </td> <td> <p>17</p> </td> <td> <p>47</p> </td> <td> <p>17</p> </td> </tr> <tr> <td> <p>Saliva</p> </td> <td> <p>18</p> </td> <td> <p>34</p> </td> <td> <p>52</p> </td> <td> <p>11</p> </td> </tr> <tr> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td> <p><em>Lipids </em></p> <p><em>(High pH)</em></p> </td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td> <p>Blood plasma</p> </td> <td> <p>24</p> </td> <td> <p>25</p> </td> <td> <p>24</p> </td> <td> <p>25</p> </td> </tr> <tr> <td> <p>Saliva</p> </td> <td> <p>28</p> </td> <td> <p>17</p> </td> <td> <p>28</p> </td> <td> <p>17</p> </td> </tr> </tbody> </table> <p> </p> </td> </tr> </tbody> </table> <p></p> <p><sup>1</sup> For the lipid platform, large variations in internal standard were observed between study samples. This could be due to the difference in matrix effect between the study samples, i.e., blood plasma and saliva. It is known that the matrix effect varies significantly depending on the origin of the samples and is influenced by phenotypic characteristics such as species, age, and gender. Therefore, peak areas were provided as an additional data set that can be used as input data for downstream metabolomics analysis.</p> <p><sup>2</sup> Metabolite signaling complied with the acceptance criteria of RSDqc <15%.</p> <p><sup>3</sup> Metabolite signaling did not comply with the acceptance criteria of our quality control i.e. of RSDqc <15%, but they present RSDs up to 30%.</p> <p><em><sup>4</sup> </em>target area/ISTD area; unit free<em>.</em> </p> <p>Available data-set:</p> <p>-Four different signaling lipids data-set: 1) peak areas for plasma samples, 2) peak area ratios (metabolite to ISTD) for plasma samples, 3) peak areas for saliva samples, and 4) peak area ratios (metabolite to ISTD) for saliva samples.</p> <p> - Two signalling amine data-set: 1) peak area ratios (metabolite to ISTD) for plasma samples, and 2) peak area ratios (metabolite to ISTD) for saliva samples.</p> <p> </p>
Tables S1 and S2. Structural Diversity, Biosynthesis, and Function of Plant Falcarin-type Polyactylenic Lipids
<p>Table S1. Compounds and structures used to generate structural similarity network in Figure 2.</p> <p>Table S2. List of functional FAD2s used to generate Figures 4 and 5.</p>
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