Membrane Tube Research Articles

Absolute/Convective Instabilities and Front Propagation in Lipid Membrane Tubes

Biological lipid membranes make up the boundary of the cell and many of its internal organelles, and are often found in cylindrical configurations. For example, membrane tethers are pulled along microtubules by various proteins, and axonal flows bring lipids from the growth cone of a neuron to its cell body. Such systems involve lipids flowing in-plane as a two-dimensional fluid, while the membrane bends out-of-plane as an elastic shell. in this work, we investigate the stability of biological membrane tubes that are locally perturbed at a single location, with and without a base flow of lipids.

SNX9: An Unconventional Bar Domain Protein?

BAR domain protein sorting nexin 9 (SNX9) has been reported to play an important role in both clathrin-mediated and clathrin-independent endocytosis. Recent cell biology studies have shown that SNX9 self-assembles at the endocytic (tubular) membrane necks and it was suggested that this assembly of SNX9 can constrict the necks. However, the mechanism underlying the recruitment of SNX9 to the endocytic neck remains unclear. Moreover, a direct observation of SNX9 constricting tubular membranes is still missing. Here, to study the recruitment of SNX9 and its mechanical effect on tubular membranes, we used an in vitro approach where highly curved membrane tubes with controlled radii are pulled from giant unilamellar vesicles in the presence of purified full-length SNX9 injected adjacent to the tubes. We demonstrated that SNX9 can sense positive membrane curvature, thus accounting for the recruitment of SNX9 to endocytic membrane necks. However, we observed that SNX9 does not constrict membrane tubes. This observation is surprising given that in vitro the BAR domain of endophilin and amphiphysin has been shown to sense membrane curvature and constrict membrane tubes, and structurally the BAR domain of SNX9 is similar to that of endophilin and amphiphysin but with a shallower curvature. Our results thus further indicate that SNX9 is not a conventional BAR domain protein.

Membrane Fission: Insights from Reconstituting Organelle Form and Chemistry

The lipid bilayer is highly resilient to rupture and explains why it was selected over the course of evolution to serve a barrier function. Yet fission, or the splitting of a membrane compartment, is a central theme in biology that manifests during cell division, organelle biogenesis and vesicular transport. Fission involves the local application of forces to bend and constrict or thin down a membrane tube. Since bending requires the bilayer to deviate from its preferred planar configuration, fission is energetically unfavorable.

Endocytosis Against High Turgor Pressure is Made Easier by Partial Protein Coating and a Freely Rotating Base

During clathrin-mediated endocytosis, a patch of flat plasma membrane is deformed into a vesicle. in walled cells, such as plants and fungi, the turgor pressure is high and pushes the membrane against the cell wall, thus hindering membrane internalization. Using mathematical modeling, we studied how a patch of membrane is deformed against turgor pressure by a point force. We found that a large amount of force is needed to merely start deforming the membrane and an even larger force is needed to pull a membrane tube.

The Mechanics and Thermodynamics of Tubule Formation in Biological Membranes.

Membrane tubulation is a ubiquitous process that occurs both at the plasma membrane and on the membranes of intracellular organelles. These tubulation events are known to be mediated by forces applied on the membrane either due to motor proteins, by polymerization of the cytoskeleton, or due to the interactions between membrane proteins binding onto the membrane. The numerous experimental observations of tube formation have been amply supported by mathematical modeling of the associated membrane mechanics and have provided insights into the force-displacement relationships of membrane tubes. Recent advances in quantitative biophysical measurements of membrane-protein interactions and tubule formation have necessitated the need for advances in modeling that will account for the interplay of multiple aspects of physics that occur simultaneously. Here, we present a comprehensive review of experimental observations of tubule formation and provide context from the framework of continuum modeling. Finally, we explore the scope for future research in this area with an emphasis on iterative modeling and experimental measurements that will enable us to expand our mechanistic understanding of tubulation processes in cells.

Influence of membrane-cortex linkers on the extrusion of membrane tubes

The cell membrane is an inhomogeneous system composed of phospholipids, sterols, carbohydrates, and proteins that can be directly attached to underlying cytoskeleton. The protein linkers between the membrane and the cytoskeleton are believed to have a profound effect on the mechanical properties of the cell membrane and its ability to reshape. Here, we investigate the role of membrane-cortex linkers on the extrusion of membrane tubes using computer simulations and experiments. In simulations, we find that the force for tube extrusion has a nonlinear dependence on the density of membrane-cortex attachments: at a range of low and intermediate linker densities, the force is not significantly influenced by the presence of the membrane-cortex attachments and resembles that of the bare membrane. For large concentrations of linkers, however, the force substantially increases compared with the bare membrane. In both cases, the linkers provided membrane tubes with increased stability against coalescence. We then pulled tubes from HEK cells using optical tweezers for varying expression levels of the membrane-cortex attachment protein Ezrin. In line with simulations, we observed that overexpression of Ezrin led to an increased extrusion force, while Ezrin depletion had a negligible effect on the force. Our results shed light on the importance of local protein rearrangements for membrane reshaping at nanoscopic scales.

Asymmetric desorption of lipid oxidation products induces membrane bending.

Lipid oxidation, detected in metabolic processes, is induced in excess when the cellular membrane suffers extra oxidative stress. Lipid oxidation can compromise biomembrane function in part through perturbations of lipid packing, membrane permeability, and morphology. Two major types of oxidation products, one with a partially truncated lipid tail with a hydrophilic group at the tail-end, and secondly, a lysolipid (with one of the chains completely truncated) can disturb the membrane bilayer packing significantly. However, they also have an increased tendency to desorb from the membrane. In this study we investigated desorption kinetics of two characteristic lipid oxidation products (PAzePC and 18 : 1 LysoPC) from a model membrane system, and we evaluated the consequences of this process on membrane shape transitions. Using a microfluidic chamber coupled with micropipette aspiration, we observed the incorporation of the two lipids into the membrane of a giant unilamellar vesicle (GUV) and further determined their desorption rates, association rates and flip-flop rates. For both lipids, the desorption is on the time scale of seconds, one to two orders of magnitude faster than their flipping rates. Dilution of the outer solution of the GUVs allowed asymmetric desorption of these two lipids from the GUVs. This process induced lipid number asymmetry and charge asymmetry, specifically for PAzePC containing GUVs, and caused membrane tubulation. Our results indicate that the desorption of lipid oxidation products can alter the local structure of biomembranes and result in morphological changes that may relate to membrane function.

Automatic Semicircular Canal Segmentation of CT Volumes Using Improved 3D U-Net with Attention Mechanism.

The vestibular system is the sensory apparatus that helps the body maintain its postural equilibrium, and semicircular canal is an important organ of the vestibular system. The semicircular canals are three membranous tubes, each forming approximately two-thirds of a circle with a diameter of approximately 6.5 mm, and segmenting them accurately is of great benefit for auxiliary diagnosis, surgery, and treatment of vestibular disease. However, the semicircular canal has small volume, which accounts for less than 1% of the overall computed tomography image. Doctors have to annotate the image in a slice-by-slice manner, which is time-consuming and labor-intensive. To solve this problem, we propose a novel 3D convolutional neural network based on 3D U-Net to automatically segment the semicircular canal. We added the spatial attention mechanism of 3D spatial squeeze and excitation modules, as well as channel attention mechanism of 3D global attention upsample modules to improve the network performance. Our network achieved an average dice coefficient of 92.5% on the test dataset, which shows competitive performance in semicircular canals segmentation task.

Binding of curvature-inducing proteins onto tethered vesicles.

A tethered vesicle, which consists of a cylindrical membrane tube and a spherical vesicle, is produced by a mechanical force that is experimentally imposed by optical tweezers and a micropipette. This tethered vesicle is employed for examining the curvature sensing of curvature-inducing proteins. In this study, we clarify how the binding of proteins with a laterally isotropic spontaneous curvature senses and generates the membrane curvatures of the tethered vesicle using mean-field theory and meshless membrane simulation. The force-dependence curves of the protein density in the membrane tube and the tube curvature are reflection symmetric and point symmetric, respectively, from the force point, in which the tube has a sensing curvature. The bending rigidity and spontaneous curvature of the bound proteins can be estimated from these force-dependence curves. First-order transitions can occur between low and high protein densities in the tube at both low and high force amplitudes. The simulation results of the homogeneous phases agree very well with the theoretical predictions. In addition, beaded-necklace-like tubes with microphase separation are found in the simulation.

DETERMINATION OF UNIT PARAMETERS WITH SELECTIVE MEMBRANES

The energy complex of Russia is largely based on oil and gas potential. One of the ways to maintain the rate of hydrocarbon production is the use of gas methods. In this regard, inexpensive methods of obtaining pure gases are relevant. One of such approaches is the use of installations with selective membranes, the use of which is ineffective without preliminary modeling. There are currently no models that provide accurate quantitative results. Therefore, the main goal of this article is to develop a detailed mathematical model of the gas separation process in an installation with selective membranes and to determine the technological parameters with its help. The paper deals with the division of air in a membrane unit into pure gases: nitrogen and oxygen. The membrane consists of fibers, their sizes are comparable to the sizes of gas molecules, due to which the gas separation process takes place, since the transmission rate of the components is different. Filtering rate is a function of spatial coordinate and time. The basic system of the mechanics equations of multiphase systems is used for modeling. The developed mathematical model is based for the first time on the most detailed approach, in which the process is considered both inside and outside the membrane. To describe the processes outside the membrane, a system of equations for component fluxes is used, and inside the membrane, the conservation laws of mass and momentum are used. The model is reduced to a dimensionless form in order to get away from dimensional physical quantities and to carry out a criterion analysis to assess the contribution of parameters affecting the gas separation process. The data used for the evaluation correspond to a real membrane plant. By numerically solving the model equations, the distribution of nitrogen concentration inside and outside the membrane tubes is obtained. Analysis of the model in a dimensionless form shows that all factors make a comparable order of magnitude contribution to the final distribution of gas concentration.

Endophilin recruitment drives membrane curvature generation through coincidence detection of GPCR loop interactions and negative lipid charge

Endophilin plays key roles during endocytosis of cellular receptors, including generating membrane curvature to drive internalization. Electrostatic interactions between endophilin’s BIN/Amphiphysin/Rvs domain and anionic membrane lipids have been considered the major driving force in curvature generation. However, the SH3 domain of endophilin also interacts with the proline-rich third intracellular loop (TIL) of various G-protein-coupled receptors (GPCRs), and it is unclear whether this interaction has a direct role in generating membrane curvature during endocytosis. To examine this, we designed model membranes with a membrane density of 1400 receptors per μm2 represented by a covalently conjugated TIL region from the β1-adrenergic receptor. We observed that TIL recruits endophilin to membranes composed of 95 mol% of zwitterionic lipids via the SH3 domain. More importantly, endophilin recruited via TIL tubulates vesicles and gets sorted onto highly curved membrane tubules. These observations indicate that the cellular membrane bending and curvature sensing activities of endophilin can be facilitated through detection of the TIL of activated GPCRs in addition to binding to anionic lipids. Furthermore, we show that TIL electrostatically interacts with membranes composed of anionic lipids. Therefore, anionic lipids can modulate TIL/SH3 domain binding. Overall, our findings imply that an interplay between TIL, charged membrane lipids, BAR domain, and SH3 domain could exist in the biological system and that these components may act in coordination to regulate the internalization of cellular receptors.

Membrane morphologies induced by mixtures of arc-shaped particles with opposite curvature.

Biological membranes are shaped by various proteins that either generate inward or outward membrane curvature. In this article, we investigate the membrane morphologies induced by mixtures of arc-shaped particles with coarse-grained modeling and simulations. The particles bind to the membranes either with their inward, concave side or their outward, convex side and, thus, generate membrane curvature of opposite sign. We find that small fractions of convex-binding particles can stabilize three-way junctions of membrane tubules, as suggested for the protein lunapark in the endoplasmic reticulum of cells. For comparable fractions of concave-binding and convex-binding particles, we observe lines of particles of the same type, and diverse membrane morphologies with grooves and bulges induced by these particle lines. The alignment and segregation of the particles is driven by indirect, membrane-mediated interactions.

Erosion behaviors of membrane tubes in a fluidized bed reactor with hydrogen separation

Based on a hybrid Eulerian-Lagrangian approach, erosion characteristic of membrane tubes in a membrane-assisted fluidized bed reactor is numerically evaluated. The erosion rate of Pd-based membrane is integrated. The influence of hydrogen separation on gas-solid hydrodynamics and erosion characteristics is discussed. The relationship between concentration polarization and membrane tube erosion is examined. The results demonstrate that the maximum wear of Pd-based membrane occurs at the normal angle. The hydrogen separation weakens membrane tube erosion in a fluidized bed. The arrangement of membrane tube locations plays a very important role in tube erosion. The non-uniform hydrogen concentration strengthens the maximum membrane tube wear, especially for the bottom of the fluidized bed reactor.

Mass transfer at the outer surface of a spiral tube heat exchanger in a stirred tank reactor and possible applications

Mass transfer at the external surface of a horizontal spiral tube exchanger placed at the bottom of a stirred tank was investigated by using the dissolution of copper in acidified dichromate technique under different considerations of (i) reactor configuration (i.e., presence of baffles, spiral tube distance from the tank bottom, spiral tube diameter and pitch, impeller geometry), (ii) acidified dichromate solution properties, and (iii) mixing intensity (i.e., impeller rotational speed). It is revealed that mass transfer increases with increasing mixing intensity, spiral tube pitch, and with the presence of baffles. The larger the spiral tube diameter, the lower the mass transport. The results, for spiral tube placed at the tank bottom, in case of axial- and radial-flow impellers were correlated by dimensionless correlations with an average deviation of 11% and 9%, respectively. Applications of the current results include (i) design of a spiral tube heat exchangers in agitated vessels, (ii) design of catalytic heat exchanger/reactor suitable for exothermic reactions involving heat-sensitive materials, and (iii) design of semi-continuous spiral tube membrane equipment suitable for processes such as dialysis and ultrafiltration.

Are endoplasmic reticulum subdomains shaped by asymmetric distribution of phospholipids? Evidence from a C. elegans model system.

Physical contact between organelles are widespread, in part to facilitate the shuttling of protein and lipid cargoes for cellular homeostasis. How do protein-protein and protein-lipid interactions shape organelle subdomains that constitute contact sites? The endoplasmic reticulum (ER) forms extensive contacts with multiple organelles, including lipid droplets (LDs) that are central to cellular fat storage and mobilization. Here, we focus on ER-LD contacts that are highlighted by the conserved protein seipin, which promotes LD biogenesis and expansion. Seipin is enriched in ER tubules that form cage-like structures around a subset of LDs. Such enrichment is strongly dependent on polyunsaturated and cyclopropane fatty acids. Based on these findings, we speculate on molecular events that lead to the formation of seipin-positive peri-LD cages in which protein movement is restricted. We hypothesize that asymmetric distribution of specific phospholipids distinguishes cage membrane tubules from the bulk ER.

Phosphatidylinositol-4-kinase IIα licenses phagosomes for TLR4 signaling and MHC-II presentation in dendritic cells

Toll-like receptor (TLR) recruitment to phagosomes in dendritic cells (DCs) and downstream TLR signaling are essential to initiate antimicrobial immune responses. However, the mechanisms underlying TLR localization to phagosomes are poorly characterized. We show herein that phosphatidylinositol-4-kinase IIα (PI4KIIα) plays a key role in initiating phagosomal TLR4 responses in murine DCs by generating a phosphatidylinositol-4-phosphate (PtdIns4P) platform conducive to the binding of the TLR sorting adaptor Toll-IL1 receptor (TIR) domain-containing adaptor protein (TIRAP). PI4KIIα is recruited to maturing lipopolysaccharide (LPS)-containing phagosomes in an adaptor protein-3 (AP-3)-dependent manner, and both PI4KIIα and PtdIns4P are detected on phagosomal membrane tubules. Knockdown of PI4KIIα-but not the related PI4KIIβ-impairs TIRAP and TLR4 localization to phagosomes, reduces proinflammatory cytokine secretion, abolishes phagosomal tubule formation, and impairs major histocompatibility complex II (MHC-II) presentation. Phagosomal TLR responses in PI4KIIα-deficient DCs are restored by reexpression of wild-type PI4KIIα, but not of variants lacking kinase activity or AP-3 binding. Our data indicate that PI4KIIα is an essential regulator of phagosomal TLR signaling in DCs by ensuring optimal TIRAP recruitment to phagosomes.

A novel CFD simulation of H2 separation by Pd-based helical and straight membrane tubes

A novel three-dimensional CFD simulation of H2 gas permeation through dense palladium (Pd) membrane was developed. Due to discontinuity of flow in a membrane, usually, gas diffusion process is simulated by introducing source and sink terms. In a novel approach, an analogy between heat and mass transfer is considered. The most important advantage of this approach is that there is no need to define sink and source terms, and the membrane thickness is considered as a solution domain without separating the geometry adjacent to the membrane. Also, it allows the modeling of multilayer membranes with different mechanisms of diffusion, separately. The effect of membrane geometry on the hydrogen separation was investigated using the straight and helical modules by defining user-defined function (UDF) and user-defined scalars (UDS). The results showed an average flux and H2 recovery enhancement of 20% and 13% for helical configuration, respectively. The influence of the feed gas and sweep gas flow rates, helix pitch, coil diameter, pressure difference, and module temperature on hydrogen separation was also investigated. The proposed simulation model was validated using the experimental data. The results indicated that this method has a maximum error of about 10% for H2 flux.

Fabrication of Industrial-Scale Porous Stainless Steel Membrane Tubes and Their Applications

A series of industrial-scale 316L stainless steel membrane tubes (Φ60 mm × 1000 mm) was fabricated by wet spray coating three membrane powders (20 μm; 12 μm; 4 μm) onto a pre-sintered 316L stainless steel support tube, followed by sintering. The influence of the membrane powder size and spray coating times or number of spray coating layers on the structure and permeability of the as-sintered membrane tubes was analyzed in detail. A permeability model has been formulated according to the resistance-in-series model based on Darcy’s law. It is shown that the model can reasonably describe the permeability of as-sintered stainless steel membranes. A good balance between the filtration accuracy and the permeability can be achieved by fabricating an ultra-thin metallic membrane structure on the surface of a pre-sintered stainless steel support tube. The gas separation efficiency of the as-fabricated 316L stainless steel membrane reached 99.8% for the 0.3-μm dust particles. The as-sintered porous 316L membrane (Φ60 mm × 1000 mm) was used to filter hot gas mixtures of CO and C4NiO4 in continuous industrial operations for 4 months and demonstrated outstanding performance.

Dynamics and spectral stability of soliton-like structures in fluid-filled membrane tubes

This survey presents results on the stability of elevation solitary waves in axisymmetric elastic membrane tubes filled with a fluid. The elastic tube material is characterized by an elastic potential (elastic energy) that depends non-linearly on the principal deformations and describes the compliant elastic media. Our survey uses a simple model of an inviscid incompressible fluid, which nevertheless makes it possible to trace the main regularities of the dynamics of solitary waves. One of these regularities is the spectral stability (linear stability in form) of these waves. The basic equations of the ‘axisymmetric tube – ideal fluid’ system are formulated, and the equations for the fluid are averaged over the cross-section of the tube, that is, a quasi-one-dimensional flow with waves whose length significantly exceeds the radius of the tube is considered. The spectral stability with respect to axisymmetric perturbations is studied by constructing the Evans function for the system of basic equations linearized around a solitary wave type solution. The Evans function depends only on the spectral parameter , is analytic in the right-hand complex half-plane , and its zeros in coincide with unstable eigenvalues. The problems treated include stability of steady solitary waves in the absence of a fluid inside the tube (the case of constant internal pressure), together with the case of local inhomogeneity (thinning) of the tube wall, the presence of a steady fluid filling the tube (the case of zero mean flow) or a moving fluid (the case of non-zero mean flow), and also the problem of stability of travelling solitary waves propagating along the tube with non-zero speed. Bibliography: 83 titles.

Application of bioactive hydrogels combined with dental pulp stem cells for the repair of large gap peripheral nerve injuries

Due to the limitations in autogenous nerve grafting or Schwann cell transplantation, large gap peripheral nerve injuries require a bridging strategy supported by nerve conduit. Cell based therapies provide a novel treatment for peripheral nerve injuries. In this study, we first experimented an optimal scaffold material synthesis protocol, from where we selected the 10% GFD formula (10% GelMA hydrogel, recombinant human basic fibroblast growth factor and dental pulp stem cells (DPSCs)) to fill a cellulose/soy protein isolate composite membrane (CSM) tube to construct a third generation of nerve regeneration conduit, CSM-GFD. Then this CSM-GFD conduit was applied to repair a 15-mm long defect of sciatic nerve in a rat model. After 12 week post implant surgery, at histologic level, we found CSM-GFD conduit could regenerate nerve tissue like neuron and Schwann like nerve cells and myelinated nerve fibers. At physical level, CSM-GFD achieved functional recovery assessed by a sciatic functional index study. In both levels, CSM-GFD performed like what gold standard, the nerve autograft, could do. Further, we unveiled that almost all newly formed nerve tissue at defect site was originated from the direct differentiation of exogeneous DPSCs in CSM-GFD. In conclusion, we claimed that this third-generation nerve regeneration conduit, CSM-GFD, could be a promising tissue engineering approach to replace the conventional nerve autograft to treat the large gap defect in peripheral nerve injuries.