Tracking of fluorescently labeled polymer particles reveals surface effects during shear-controlled aggregation

Surface chemistry is believed to be the key parameter affecting the aggregation and breakage of colloidal suspensions when subjected to shear. To date, only a few works dealt with the understanding of the role of the physical and chemical properties of the particles’ surface upon aggregation under shear. Previous studies suggested that surface modifications strongly affect polymer particles’ adhesion, but it was very challenging to demonstrate this effect and monitor these alterations upon prolonged exposure to shear forces. More importantly, the mechanisms leading to these changes remain elusive. In this work, shear-induced aggregation experiments of polymer colloidal particles have been devised with the specific objective of highlighting material transfer and clarifying the role of the softness of the particle’s surface. To achieve this goal, polymer particles with a core–shell structure comprising fluorescent groups have been prepared so that the surface’s softness could be tuned by the addition of monomer acting as a plasticizer and the percentage of fluorescent particles could be recorded over time via confocal microscopy to detect eventual material transfer among different particles. For the first time, material exchange occurring on the soft surface of core–shell polymer microparticles upon aggregation under shear was observed and proved. More aptly, starting from a 50% labeled/nonlabeled mixture, an increase in the percentage of particles showing a fluorescent signature was recorded over time, reaching a fraction of 70% after 5 h

Supporting data for: "Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles" by Ewa Sitarska, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, Aline Tschanz, Christer Ejsing, Yannick Schwab, Jan Kosinski, Michael Sixt, Anna Kreshuk, Anna Erzberger and Alba Diz-Muñoz

This repository contains the supporting data for the paper:  "Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles" by Ewa Sitarska, Silvia Dias Almeida, Marianne Sandvold Beckwith,  Julian Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, Aline  Tschanz, Christer Ejsing, Yannick Schwab, Jan Kosinski, Michael Sixt,  Anna Kreshuk, Anna Erzberger and Alba Diz-Muñoz 1) Data for Coarse-Grained MD Simulations This repository contains scripts, jupyter notebooks and files to  reproduce the simulation results presented in this work and to generate  the accompanying figures. !! Important note: these files are provided as is! scripts and top files include original file names and need to be adapted by the user to their system!! !! tpr files should work for gromacs 2021 out of the box !! TPR files for each step in the setup from minimization -> equilibation -> production _pp.tpr is without water for processing and visualization purposes. the .tpr files can be run to reproduce the trajectories from the paper. Note that due to numerical inaccuracies over long periods of time results might diverge from the exact results in the paper. However, the time averages will be the same. Files with _275 are presented in the main text and have less curvature than files with _575 with higher curvature (SI figure). the itp files are renamed to be used with the scaled martini force field (alpha=0.7) (see methods of paper) the setup can be followed in setup_curvature.sh and setup.system.ipynb analysis code as reported in the methods can be found in postprocessing_curvature.ipynb and postprocessing_contacts.ipynb 2) Scripts for TIRFM Images analysis (in zip file)  time_area_space.py is a simple script that performs some shape and intensity calculations on images You will need: 1) time framed movies of moving cells, where correspondent membrane proteins are also seen 2) Cell segmentation masks 3) Protein segmentation masks It reads the cells' segmentation (channel 3) and binary erodes the segmentation. Then, subtracts from the original membrane mask, in order to have a border area of the perimeter of the cell. Then, calculates the percentage of proteins in that area (proteins area / border area) and the ratio of number of proteins in the border versus the total number of proteins Finally, performs a number of calculations regarding the shape (elongation, eccentricity, etc) </p

bio-phys/MDBenchmark: Release 1.3.3

This is the last release before we introduce a new command-line interface for mdbenchmark plot and some changes for mdbenchmark generate with version 2.0.0. Bugfixes Users were unable to generate a plot when running mdbenchmark analyze --plot. (#86

MDBenchmark: A Toolkit to Optimize the Performance of Molecular Dynamics Simulations

Molecular dynamics simulations resolve biomolecular processes and material properties with incomparable detail. As a result, they consume a significant fraction of worldwide supercomputing resources. With our open source benchmarking software MDBenchmark, expert and novice users alike can easily determine the optimal settings for their specific simulation system, MD engine, software environment, and hardware configuration. Ultimately, saving computation time, energy, and money at essentially no additional cost will produce better science.<br /

FAM134B-RHD protein clustering drives spontaneous budding of asymmetric membranes

Living cells constantly remodel the shape of their lipid membranes. In the endoplasmic reticulum (ER), the reticulon homology domain (RHD) of the reticulophagy regulator 1 (RETR1/FAM134B) forms dense autophagic puncta that are associated with membrane removal by ER-phagy. In molecular dynamics (MD) simulations, we find that FAM134B-RHD spontaneously forms clusters, driven in part by curvature-mediated attractions. At a critical size, as in a nucleation process, the FAM134B-RHD clusters induce the formation of membrane buds. The kinetics of budding depends sensitively on protein concentration and bilayer asymmetry. Our MD simulations shed light on the role of FAM134B-RHD in ER-phagy and show that membrane asymmetry can be used to modulate the kinetic barrier for membrane remodeling

Séminaire sur les mesures d'incitation et leur informatisation

Réunion: Séminaire sur les mesures d'incitation et leur informatisation, mars 1990, Ouagadougou, B

Artificial intelligence reveals nuclear pore complexity

Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport. Their intricate 120 MDa architecture remains incompletely understood. Here, we report a near-complete structural model of the human NPC scaffold with explicit membrane and in multiple conformational states. We combined AI-based structure prediction with in situ and in cellulo cryo-electron tomography and integrative modeling. We show that linker Nups spatially organize the scaffold within and across subcomplexes to establish the higher-order structure. Microsecond-long molecular dynamics simulations suggest that the scaffold is not required to stabilize the inner and outer nuclear membrane fusion, but rather widens the central pore. Our work exemplifies how AI-based modeling can be integrated with in situ structural biology to understand subcellular architecture across spatial organization levels

Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles

Abstract To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment

Social micro-siting : increasing acceptance through local adaption

The establishment of land-based wind-farms often requires large land areas affecting a number of contradictory interests including the individual interests of citizens. In Sweden consultation is statutory, prescribed by Swedish Environmental Code including all individuals affected by the project. Projectors often invite to consultative process in a stage where the project has made some progress and where a site-plan is more or less established. From the citizen perspective, wind farm projects affecting the local area might seem threatening. For instance, for people living in rural areas, the characteristics of the surrounding environment are closely connected to their way of life. Thereby, “threats” towards the local environment might pose a threat to their entire outlook on life. Often this leads to frustration and rage towards the projector. This presentation introduces the basic features of a consultative process more thoroughly involving and adjusting to citizens and their local community and the distinguishing characteristics of their local physical and social environment, Social Micro-Siting. Social Micro-Siting has the potential to create added value to the participating community and to the projector, increasing the general acceptance of wind-farm localization. As the process is based on ongoing dialogue with the local citizens, it might also provide solutions to complex local issues of a more practical character.Godkänd; 2012; 20121218 (andbra)</p