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124 results for “phospholipids”
Computational Studies of Substrate Transport and Specificity in a Phospholipid Flippase
<p>MD trajectories of all-atom and CG simulations of PI4P activated E2P state of the Drs2p-Cdc50p complex.</p>
Input Files for Peptide Translocation Across Phospholipid Membranes Using Various Collective Variables and Martini Coarse-Grained Simulations
<p>Input files for publication: Ivo Kabelka, Radim Brožek, and Robert Vácha: Selecting Collective Variables and Free Energy Methods for Peptide Translocation Across Membranes, Journal of Chemical Information and Modeling, submitted</p>
Elevated urine BMP phospholipids in LRRK2 and VPS35 mutation carriers with and without Parkinson's disease
<p><strong>Participant demographic and clinical characteristics, and urine BMP phospholipid levels. </strong></p> <p>For each participant, sample collection site is provided as: BCN (Barcelona), VIE (Vienna), DND (Dundee), or SSB (San Sebastian). Also provided are age at study participation, age at PD diagnosis (where applicable), sex (M, for male, and F, for female), experimental group (control, iPD –idiopathic PD –, LRRK2 G2019S, LRRK2 R1441G/C, VPS35 D620N, GBA, or other), and PD status (NMC for non-manifesting mutation carriers, or PD). Values for all measured BMP species presented as ng of BMP per mg of creatinine are provided. Additionally, urine creatinine (mg/ml) and non-normalized BMP levels are provided. BQL designates BMP levels that were below quantification level and NM designates values that were not measured for a particular individual.</p>
Sachs: Protein and Phospholipids Expressions
<p>The Sachs dataset measures the expression level of different proteins and phospholipids in human cells. It includes the simultaneous measurements of 11 phosphorylated proteins and phospholipids derived from thousands of individual primary immune system cells, subjected to both general and specific molecular interventions.</p> <p> </p> <p><strong>Task: </strong>The dataset can be used to study causal discovery algorithms.</p> <p> </p> <p><strong>Summary: </strong></p> <ul> <li><strong>Size of collection</strong>: 14 datasets on 11 features and 707 to 927 observations</li> <li><strong>Task:</strong> Causal Discovery Problem</li> <li><strong>Data Type:</strong> Continuous Data</li> <li><strong>Dataset Scope:</strong> Collection of Datasets</li> <li><strong>Ground Truth:</strong> Known Graph</li> <li><strong>Temporal Structure:</strong> Static Data</li> <li><strong>License:</strong> CC BY (granted by G. Nolan and D. Lauffenburger)</li> <li><strong>Missing Values:</strong> No Missing Data</li> </ul> <p> </p> <p><strong>Missingness Statement: </strong>There are no missing values.<strong><br></strong></p> <p> </p> <p><strong>Features:</strong></p> <p>Each sample in each dataset consists of quantitative amounts of each of the following 11 phosphorylated molecules, simultaneously measured from single cells:</p> <table> <tbody> <tr> <th>Measured molecule</th> <th>Antibody specificity</th> </tr> </tbody> <tbody> <tr> <td>Raf</td> <td>Phosphorylation at S259</td> </tr> <tr> <td>Erk1 and Erk2</td> <td>Phosphorylation at T202 and Y204</td> </tr> <tr> <td>P38</td> <td>Phosphorylation at T180 and Y182</td> </tr> <tr> <td>Jnk</td> <td>Phosphorylation at T183 and Y185</td> </tr> <tr> <td>Akt.</td> <td>Phosphorylation at S473</td> </tr> <tr> <td>Mek 1 and Mek2</td> <td>Phosphorylation at S217 and S221</td> </tr> <tr> <td>PKA substrates</td> <td>Detects proteins and peptides containing a phospho-Ser/Thr residue with arginine at the -3 position</td> </tr> <tr> <td>PKC</td> <td>Detects phosphorylated PKC-α, -βI, -βII, -δ, -ϵ, -η, and -θ isoforms only at C-terminal residue homologous to S660 of PKC-βII</td> </tr> <tr> <td>Plcg</td> <td>Phosphorylation at Y783</td> </tr> <tr> <td>PIP2</td> <td>Detects PIP2</td> </tr> <tr> <td>PIP3</td> <td>Detects PIP3</td> </tr> </tbody> </table> <p> </p> <p><strong>Files:</strong></p> <p>The datasets were collected after a series of stimulatory cues and inhibitory interventions, with cell reactions stopped at 15 minutes after stimulation by fixation, to profile the effects of each condition on the intracellular signaling networks of human primary naïve CD4+ T cells, downstream of CD3, CD28, and LFA-1 activation. The following conditions were used:</p> <table> <tbody> <tr> <th>File</th> <th>Stimulation</th> <th>Description</th> </tr> </tbody> <tbody> <tr> <td>cd3cd28.csv</td> <td>CD3, CD28</td> <td>T cell activation</td> </tr> <tr> <td>cd3cd28icam2.csv</td> <td>CD3, CD28, ICAM-2</td> <td>LFA-1 signaling induction</td> </tr> <tr> <td>cd3cd28_aktinhib.csv</td> <td>CD3, CD28, akt-inhibitor</td> <td>PKA activation</td> </tr> <tr> <td>cd3cd28_g0076.csv</td> <td>CD3, CD28, G0076</td> <td>AKT inhibition</td> </tr> <tr> <td>cd3cd28_psitect.csv</td> <td>CD3, CD28, Psitectorigenin</td> <td>MEK1/MEK2 inhibition</td> </tr> <tr> <td>cd3cd28_u0126.csv</td> <td>CD3, CD28, U0126</td> <td>PKC activation</td> </tr> <tr> <td>cd3cd28_ly.csv</td> <td>CD3, CD28, LY294002</td> <td>PKC inhibition</td> </tr> <tr> <td>pma.csv</td> <td>PMA</td> <td>PIP2 production inhibition</td> </tr> <tr> <td>b2camp.csv</td> <td>β2camp</td> <td>AKT inhibition</td> </tr> <tr> <td>cd3cd28icam2_aktinhib.csv</td> <td>CD3, CD28, ICAM-2, akt-inhib</td> <td>simulated dataset</td> </tr> <tr> <td>cd3cd28icam2_g0076.csv</td> <td>CD3, CD28, ICAM-2, G0076</td> <td>simulated dataset</td> </tr> <tr> <td>cd3cd28icam2_psit.csv</td> <td>CD3, CD28, ICAM-2, Psitectorigenin</td> <td>simulated dataset</td> </tr> <tr> <td>cd3cd28icam2_u0126.csv</td> <td>CD3, CD28, ICAM-2, U0126</td> <td>simulated dataset</td> </tr> <tr> <td>cd3cd28icam2_ly.csv</td> <td>CD3, CD28, ICAM-2, LY294002</td> <td>simulated dataset</td> </tr> </tbody> </table> <ul> <li><strong>Ground_Truth.csv:</strong> Directed Graph derived in Sachs et al. (2005) through multiple interventional experiments.</li> </ul>
Microbiome, mixotrophic algae, zooplankton, and fish amino acid and phospholipid fatty acid content in terrestrial and plastic carbon treatments
<p>Data includes amino acid (µg AA mg DW<sup>-1</sup>) and phospholipid fatty acid content (µg FA mg DW<sup>-1</sup>) of the microbiome, mixotrophic algae, zooplankton, and fish<em> </em>from the four-trophic level experiment. The experiment included control (no addition), 13.5% <sup>13</sup>C-labelled beech leaves (<em>Fagus sylvatica</em>), 97% <sup>13</sup>C-labelled lignin-hemicellulose extracted from wheat (<em>Triticum aestivum</em>, ~80% lignin, 13% hemicellulose), and 99% <sup>13</sup>C-labelled polystyrene (microplastic). Incubation time in humic lake water was 14 days in the control, leaf, and lignin experiment but 56 days for polystyrene, which after mixotrophic algae (<em>Cryptomonas </em>sp.) was introduced to the bottles. In the next step, herbivorous zooplankton (<em>Daphnia magna</em>) consumed microbes, mixotrophic algae, and particles for five days which after they were used as the diet to zebrafish (<em>Danio rerio</em>) during a five-day experiment.</p>
A global LC-MS2-based methodology to identify and quantify anionic phospholipids in plant samples
<p>This table contains peaks aera values from LC-MS used to develop a method for identification and quantification of anionic lipid in plant sample: Genva et al. 2023: “A global LC-MS2-based methodology to identify and quantify anionic phospholipids in plant samples”</p>
Chemokines kill bacteria without triggering antimicrobial resistance by binding anionic phospholipids
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Chemokines kill bacteria by binding anionic phospholipids without triggering antimicrobial resistance
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Phospholipid Fatty Acid Profiles of Bacteria and Fungi in Peat Exposed to Experimentally Increased N Deposition, 2015
Development of the oil sands has led to increasing atmospheric N deposition, with values as high as 17 kg N ha-1 yr-1; regional background levels <2 kg N ha-1 yr-1. Bogs, being ombrotrophic, may be especially susceptible to increasing N deposition. To examine responses to N deposition, over five years, we experimentally applied N (as NH4NO3) to a bog near Mariana Lakes, Alberta, at rates of 0, 5, 10, 15, 20, and 25 kg N ha-1 yr-1, plus controls (no water or N addition). In July of 2015 we measured PLFA markers in two depths in each plot. For the most part, microbial group abundances were not affected by increasing N input (Fig. 16). However, actinomycete abundance decreased with increasing N deposition at rates that were similar in 0-5 and 5-10 cm peat. Gram-negative bacteria increased slightly with increasing N input and were more abundant in 0-5 cm than in 5-10 cm peat; correspondingly the Gram-positive to Gram-negative bacterial ratio decreased with increasing N input and was lower in 0-5 cm than in 5-10 cm peat. Total microbial abundance and total bacterial abundance were significantly higher in 0-5 cm peat than in 5-10 cm peat. It may be that more sensitive/targeted techniques, such as high-throughput pyrosequencing, 16s RNA clone library analysis and rRNA-targeted fluorescence in situ hybridization (FISH) or whole genome shotgun sequencing may be required to reveal bog microbial community responses to N loading.
Phospholipid Fatty Acid Profiles of Bacteria and Fungi in Poor Fen Peat Exposed to Experimentally Increased N Deposition, 2015
Development of the oil sands has led to increasing atmospheric N deposition, with values as high as 17 kg N ha-1 yr-1; regional background levels <2 kg N ha-1 yr-1. To examine responses to N deposition, over five years, we experimentally applied N (as NH4NO3) to a poor fen near Mariana Lake, Alberta, at rates of 0, 5, 10, 15, 20, and 25 kg N ha-1 yr-1, plus controls (no water or N addition). In July of 2015 we measured PLFA markers in two depths in each plot. Fungal abundance increased at N addition levels above 16.6 kg N ha-1 yr-1 and total bacterial abundance also increased at N addition levels above 17.1 kg N ha-1 yr-1, such that the fungal:bacterial ratio was not significantly affected by N addition. Total microbial, gram-negative bacterial, and actinomycete abundance also showed an apparent threshold responses to N addition at 16-17 kg N ha-1 yr-1 addition levels.It may be that more sensitive/targeted techniques, such as high-throughput pyrosequencing, 16s RNA clone library analysis and rRNA-targeted fluorescence in situ hybridization (FISH) or whole genome shotgun sequencing may be required to reveal detailed fen microbial community responses to N loading.
Phospholipid fatty acids (PFLA) on decomposed litter: An evolutionary perspective on functional diversity in co-occuring willow(salix) species
Thirteen willow (Salix) species occur in southeastern Minnesota and often co-occur within the same wetlands. This high local diversity is challenging to explain since closely related species are often functionally similar and density-dependent interactions such as competition and susceptibility to pests and pathogens should limit their co-occurrence. However, if willow species are partitioning resources, or if they are phylogenetically structured so that closely related species rarely co-occur, then the impact of these density-dependent processes could be reduced. In this study, I examined the role of niche partitioning in maintaining local willow diversity by comparing species physiology in a greenhouse.
Input files for publication: Binding of DEP Domain to Phospholipid Membranes: More Than Just Electrostatics
<p>Input files for publication: Francesco L. Falginella, Marek Kravec, Martina Drabinová, Petra Paclíková, Vítězslav Bryja, and Robert Vácha: Binding of DEP Domain to Phospholipid Membranes: More Than Just Electrostatics</p>
Aligning of water molecules into proton-conducing transmembrane water wires by oxygen atoms of phospholipid ester linkers
<p>A media AVI file that shows how oxygen atoms of ester linkers of the two converging phospholipid molecules form an "oxygen passage" along which water molecules align in a proton-conducting wire. Further details could be found in our article</p>
SAXS Data of Phospholipid Mixtures forming the Inverted Hexagonal Phase
<h1>Lipids and Experimental Info</h1>
Effect of Natural Food on Gut Microbiome and Phospholipid Spectrum of Immune Cells in COVID-19 Patients
ClinicalTrials.gov study NCT05970861. IPD Sharing: Not stated. Countries: 1. Publications: 2.
PET/CT Evaluation of Primary and Metastatic Brain Tumors With a Novel Radioiodinated Phospholipid Ether Analogue I-NM404
ClinicalTrials.gov study NCT01540513. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ATLANTIS Trial: Phospholipid Omega-3 Versus Conventional Omega-3
ClinicalTrials.gov study NCT07394517. IPD Sharing: NO. Countries: 1. Publications: 1.
The flexible stalk domain of sTREM2 modulates its interactions with brain-based phospholipids
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PEMT-mediated phospholipid imbalance promotes age-associated metabolic dysfunction-associated steatotic liver disease progression
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Phospholipid fatty acids (PFLA) on decomposed litter: Nitrogen limitation in decomposition
Modern agriculture and fossil fuel combustion contribute to the transfer of N from largely inert pools (atmospheric N2, fossil fuel reserves) to biologically reactive forms that can be transported downwind from agricultural or industrial areas to ecosystems that historically may have experienced low levels of N inputs. Understanding how increased N inputs alter the cycling of another biologically important element, C, has been impeded by uncertainties about N effects on the process of decomposition. To date, ecologists remain unable to predict when, where, and in what forms N addition stimulates rates of decomposition. For example, recent work showed that in eight low-N sites in Central Minnesota, litter N was positively correlated with decomposition, suggesting N limitation of decomposition, yet addition of inorganic N fertilizer increased decomposition in only two of eight sites. These paradoxical results call into question the assumption that the often-observed correlation between substrate N concentration and decomposition arises because N limits decomposition. Research is addressing three interrelated questions:* (1) Why do litter N and externally supplied N have contrasting effects on decomposition in low-N ecosystems? (2) Do different forms of N (organic vs. inorganic; substrate vs. externally supplied) affect the activity, function and composition of the decomposer community differently, and, if so, what are the consequences for decomposition? (3) What are temporal dynamics of the activity, function, and composition of the decomposer community and do these dynamics depend upon the amount and forms of N supplied to the decomposer community?* These questions will be addressed using a 4-y decomposition experiment manipulating the quantity and form of N available to decomposers via use of substrates ranging in N concentrations and of inorganic (ammonium nitrate) and organic (amino acids) N fertilizers. The response of microbial biomass, stoichiometry, efficiency
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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)
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.