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25 results for “Membrane Mechanics”
Data supporting publication: Nanoscale Mechanical Manipulation of Ultrathin SiN Membranes Enabling Infrared Near-Field Microscopy of Liquid-Immersed samples
<p>This repository includes the data corresponding to the figures shown in the journal article entitled Nanoscale Mechanical Manipulation of Ultrathin SiN Membranes Enabling Infrared Near-Field Microscopy of Liquid-Immersed samples, published in small. </p>
Accompanying data for the paper "Accounting for the mechanical response of the cell membrane during the uptake of random nanoparticles"
<h2>Contributions</h2> <ul> <li><strong>Iaquinta Sarah</strong> did contribute to the first draft edition, the development of the theoretical background of the algorithms and their implementation</li> <li><strong>Khazaie Sharam</strong> did contribute to the revision and edition of the draft, and to the development of the theoretical background of the algorithms</li> <li><strong>Jacquemin Frédéric</strong> did contribute to the project management and to the revision of the article.</li> <li><strong>Fréour Sylvain</strong> did contribute to the project management and to the revision of the article.</li> </ul> <h2>Funding sources</h2> <p>i-Site NExT : Grant/Award Number: ANR-16-IDEX-0007, Région Pays de la Loire and CNRS (French National Centre for Scientific Research).</p> <h2>Data structure and information</h2> <ul> <li>code - <code>np_uptake source and data directory</code> <ul> <li>workflow - <code>scripts to reproduce figures</code></li> <li>np_uptake - <code>source code producing results and figures</code> <ul> <li>figures - <code>utility module to produce figures</code></li> <li>model - <code>see detailed description below</code></li> <li>metamodel_implementation - <code>see detailed description below</code></li> <li>sensitivity_analysis - <code>see detailed description below</code></li> </ul> </li> </ul> </li> </ul> <h3>Detailed description</h3> <h4>Abstract</h4> <p>In order to improve the efficiency of the delivery of cancer treatments to cancer cells, the cellular uptake of nanoparticles (NPs), used as drug delivery systems, is numerically investigated through a mechanical approach. The objective is to optimize the NP's mechanical and geometrical properties to enhance their entry into cancer cells while avoiding benign ones. In previous studies, these properties are modeled as constant during the process of cellular uptake. However, recent observations of the displacement of the membrane's constituents towards the region in the cell membrane where the uptake of the NPs takes place show that the mechanical properties of the membrane vary during this process. Reason for writing The important contribution of adhesion to the wrapping process is already well documented in literature. It is therefore crucial to model this parameter properly as the conclusions made with a constant adhesion model may not be accurate compared to reality. Methodology Based on the existing knowledge on the reaction of membrane constituents to interaction with NPs, a 3-parameter sigmoidal function, accounting for the delay, amplitude, and speed of the reaction, has been used to model the evolution of adhesion. A variance-based sensitivity analysis has then been performed in order to quantify the influence of these parameters on the outputs of the model. Results It was found that the introduction of a variable adhesion tends to alter the predictions of endocytosis of NPs. The contribution of the amplitude and delay is respectively 0.32 and 0.43 times as important as that of the NP's aspect ratio, which is the prominent parameter. The influence of the slope of the transition is the least important parameter and does not appear to contribute to endocytosis. Implications Hence, models of the cellular uptake of NPs should use a variable, instead of constant, adhesion in order a representative as possible of the behavior of the cell membrane. The predictions are different from those obtained using a model with constant adhesion.</p> <h4>Code</h4> <p>This repository is divided into 4 folders:</p> <ul> <li> <p><em>model</em>: contains the code used to compute the total variation of energy of the interface between a circular NP and a membrane by accounting for the mechanical accommodation of the latter. This folder also contains the routine to determine the final wrapping phase of the system.</p> </li> <li> <p><em>metamodel_implementation</em>: contains a script to check for the representativeness of the dataset used to create a metamodel, a script to create Kriging and PCE metamodels using the Openturns opensource library, and a routine to validate the metamodel that has just been created;</p> </li> <li> <p><em>sensitivity_analysis</em>: contains a script that allows to create samples based on the Kriging metamodels that have been created and exported as .pkl files in the metamodel folder. These samples are then used to the apply sensitivity algorithms. The user can choose among the various sensitivity algorithms provided by Openturns. For PCE metamodels, a routine is implemented to directly get the Sobol indices from the coefficients of the PCE metamodel. The indices can be plotted through plot routines;</p> </li> <li> <p><em>figures</em>: contains a utils script to display the graphs and save them as PNG files with consistency.</p> </li> </ul>
trajectories for: Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations
<p>Coarse-grained trajectories produced and analysed for publication: </p> <p>----------------------</p> <p>Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations</p> <p>Andreas Haahr Larsen*, Lilya Tata*, Laura John & Mark S.P. Sansom</p> <p>Department of Biochemistry, University of Oxford, Oxford, United Kingdom, OX1 3QU</p> <p>PLOS comp biol (in press) </p> <p>-------------------------</p> <p> </p> <p>** file overview**</p> <p>md_X.xtc: (X=0..14) 15 repeated CG simulations (1500 ns each) of the FYVE domain from EEA1 binding to POPC:POP1 bilayer. The repeats differ in the rotation of the initial frame.<br> </p> <p>final_cg2at_aligned.pdb: initial frame for AT (after CG2AT)</p> <p>prod_cym_cent_repX.xtc (X=1,2,3) 3 repeated AT sims (500 ns each) of the FYVE domain from EEA1 binding to POPC:POP1 bilayer. </p> <p>** scripts for reproduction at GitHub**</p> <p>scripts and files for reproduction are available at: https://github.com/andreashlarsen/Larsen-Tata2021-FYVE</p>
Data for publication "Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism"
<p>The data provided refer to our published article:</p> <p>T. John,* S. Piantavigna, T. J. A. Dealey, B. Abel, H. J. Risselada, L. L. Martin*, Lipid oxidation controls peptide self-assembly near<br>membranes through a surface attraction mechanism, Chem. Sci. 14 (2023), 3730-3741. <a href="https://doi.org/10.1039/d3sc00159h">https://doi.org/10.1039/d3sc00159h</a>.</p>
Membrane interaction and mechanism of LC3 lipidation machinery in autophagy raw GUV data
<p>Raw GUV data of fluorescent protein imaged on a Nikon A1 confocal microscope with a 63 × Plan 359 Apochromat 1.4 NA objective. Three biological replicates were performed for each experimental 360 condition. Identical laser power and gain settings were used during the course of all conditions.</p>
All-atom simulations elucidate the molecular mechanism underlying RNA-membrane interactions
<p>Topology files and frames extracted from the minimum of the free energy profile F(d_z) (or F(d_min) for single-stranded RNAs), within 2.5kBT. These files can be used to reproduce the hydrogen bond analyses in the manuscript.</p> <p>Scripts which were used to extract hydrogen bond information are available on <a href="https://github.com/salvatoredimarco/rna-membrane">https://github.com/salvatoredimarco/rna-membrane</a></p> <p><strong>Systems:</strong></p> <p>4xN: nucleosides</p> <p>4xN2: dinucleotides</p> <p>4xN3: trinucleotides</p> <p>4xN_OPC: nucleosides simulated with OPC water model. Energy threshold is here 1.0*kBT, because of weaker binding.</p> <p>1xGA, 1xGU, 1xGC, 1xCU</p> <p>1xGGC, 1xGCG</p> <p>1xquadruplex: G-quadruplex</p> <p>1xstrand: 19-mer RNA strand</p> <p>1xhairpin: 16-mer folded hairpin</p> <p>1x16mer_elong: 16-mer unfolded, restrained</p> <p>2x16mer_loose1/2: 16-mer unfolded, unrestrained</p>
Molecular mechanism underlying SNARE-mediated membrane fusion enlightened by all-atom molecular dynamics simulations
Open the record for dataset details and reuse information.
Mechanism for Vipp1 spiral formation, ring biogenesis and membrane repair
<p><span><span>Here</span><span>,</span><span> we collect </span><span>an image dat</span><span>aset</span><span> of Vipp1 polymerization dynamics on supported lipid bilayers </span><span>using atomic force microscopy (</span><span>AFM</span><span>)</span><span>. A JPK </span><span>NanoWizard</span> <span>Ultraspeed</span><span> AFM (Bruker and JPK </span><span>BioAFM</span><span>) equipped with USC-F0.3-k0.3-10 cantilevers with spring constant of 0.3N nm−1, resonance frequency of about 300 kHz (Nanoworld), was </span><span>employed </span><span>for image acquisition. The AFM was </span><span>operated</span><span> in tapping mode</span><span> with a</span><span> cantilever </span><span>oscil</span><span>l</span><span>ation </span><span>frequency </span><span>near </span><span>to 150kHz. </span><span>Both</span><span> topographic and phase images </span><span>were analysed </span><span>using</span><span> JPKSPM Data Processing, ImageJ, and </span><span>WSxM</span><span> software</span></span>.</p>
A novel mechanism that maintains outer membrane lipid asymmetry in Pseudomonas aeruginosa
<p>Newick file the PA2800 phylogenetic tree in "A novel mechanism that maintains outer membrane lipid asymmetry in Pseudomonas aeruginosa"</p>
Mechanism of Nitric Oxide on Ventilator-induced Diaphragm Dysfunction with Extracorporeal Membrane Lung Assistance
ClinicalTrials.gov study NCT06660784. IPD Sharing: NO. Countries: 1. Publications: 43.
Data from: Stationary quantum entanglement between a massive mechanical membrane and a low frequency LC circuit
<p>Source data for figures.</p>
Mechanical behavior of silicone membranes for adipose tissue synthesis in clinical and theatrical prosthesis
<p>Supplimentary data and figures</p>
Supplement data_A plasma membrane-penetrating mackerel teterapeptide showing a unique algicidal mechanism against Alexandrium fundyense
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ArsR transcriptional regulator mediated attenuated mechanism by regulating self and outer membrane protein in Brucella
<p><span>The ArsR family transcriptional regulators are widely distributed in microorganisms, including in the important intracellular pathogen <i>Brucella</i>. ArsR proteins are implicated in numerous biological processes. However, the specific roles of ArsR family members in <i>Brucella</i> remain obscure. Here we show that ArsR3 (BSS2_RS07325) is required for <i>Brucella</i> survival both under stress <i>in vitro</i> conditions and in a murine infection model<i> in vivo</i>. ArsR3 autoregulate its own expression to maintain metal ion homeostasis to benefit bacterial survival. Moreover, ArsR3 also regulates the production of virulence factor outer membrane protein 25D (Omp25D) which is key for the survival of <i>Brucella</i> under stress conditions. Significantly, ArsR3 deletion strain attenuated in a murine infection model<i> in vivo</i>. Altogether, our findings reveal a unique mechanism in which the ArsR family member ArsR3 autoregulates its expression and also modulates Omp25D expression to maintain metal ion homeostasis and virulence in <i>Brucella</i>.</span></p>
ArsR transcriptional regulator mediated attenuated mechanism by regulating self and outer membrane protein in Brucella
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Morphological and genetic screens reveal mechanisms of BiDAC-induced plasma membrane protein degradation
GEO Series GSE291219. Homo sapiens. 4 samples. Type: Other.
Beyond the plasma membrane disruption: Novel antifungal mechanism of Neosartorya (Aspergillus) fischeri antifungal protein 2 in Candida albicans
GEO Series GSE290357. Candida albicans. 12 samples. Type: Expression profiling by high throughput sequencing.
Mechanical Properties of the Internal Limiting Membrane and Intraoperative Utility of Brilliant Blue g (Bbg) and Indocyanine Green (Icg) Assisted Chromovitrectomy
ClinicalTrials.gov study NCT01485575. IPD Sharing: UNDECIDED. Countries: 2. Publications: 0.
" a Randomized Pilot Study of the Benefit of Nebulized Amikacin in the Treatment of Gram-negative Bacillus Pneumonia Acquired During Mechanical Ventilation in Patients Receiving Extracorporeal Membran
ClinicalTrials.gov study NCT06602557. IPD Sharing: YES. Countries: 0. Publications: 0.
Mechanical Cardiopulmonary Resuscitation During Treatment of Acute Respiratory Failure Through Extracorporeal Membrane Oxygenation.
ClinicalTrials.gov study NCT05342363. IPD Sharing: NO. Countries: 1. Publications: 0.
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International Brain Laboratory public data
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OpenNeuro
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