Vesicle Dynamics Research Articles

P–648 In-vitro Evaluation of SCF and StxBP1 in Polycystic Ovary Syndrome (PCOS)

Abstract Study question Is the interaction between intrafollicular cells in PCOS, impaired by the change of vesicular fusion and/or exocytosis in granulosa cells (GCs)? Summary answer StxBP1 expression leves impared in GCs of PCOS. What is known already PCOS characterised as follicular arrest on antral follicles, cystic follicle formation, and follicular development failure. GCs secretes wide variety of factors via exocytosis, and plays critical role during folliculogenesis. Secretory vesicles are transported to cellular membrane. This process requires local concentrations of SNAREs consisting of tSNARE, vSNARE, and other vesicle fusion associated proteins. SNARE proteins are involved in vesicle fusion, exocytosis, and intracellular trafficking. GCs secretes KITL which provides follicular activation and growth. Syntaxins are one of the members of SNARE complex. StxBP1 is a protein which has a crucial role in secretory vesicle fusion that provides fusion of syntaxins. Study design, size, duration Granulosa cells (GCs) were collected for primary cell culture, since 2019 from both PCOS (n = 10) and healthy (male factor infertility) (n = 10) women undergoing ART. Each GCs from participant divided into two groups as in-vitro stimulated group and in-vitro nonstimulated group. Participants/materials, setting, methods GCs have been isolated from follicular fluid taken from patients during oocyte pick-up at Hacettepe University In-Vitro Fertilization Unit. nGCs were cultured at most secod subcultures after the isolation. The stimulated groups of both PCOS and control groups were stimulated by hCG(10IU/ml) ve FSH(0.5IU/ml) for 24 hours. Vesicle fusion proteins (Stx6, StxBP1, and SNAP25), KITL, and FSHr expressions were analyzed on granulosa cells from each group via immunofluorescent (IF) labeling and cyto-ELISA. Main results and the role of chance FSHr were compared in both control and PCOS before and after stimulation. There was no difference between FSHr expression levels in both groups. Indirect IF is widely considered for SNAP25, Stx6, StxBP1 proteins in all groups of GCs screening with/without stimulation. Expression of SNAP25, StxBP1 mainly scattered through all cytoplasmic area,s and membranous localization was observed. Stx6 expressions were particularly distinguished at perinuclear area of cytoplasm. However, stimulated cells of control appeared more peripherally Stx6 expression. This pattern caused by stimulation wasn’t observed in PCOS. Expressions of SNAP25, Stx6, StxBP1 were observed with less expression in PCOS. Also, the response to stimulation was lower than the control group. The differences in Stx6, SNAP25, StxBP1 and KITL levels before and after stimulation was evaluated for both control and PCOS in Cyto-ELISA. However, both SNAP25 and Stx6 expressions in GCs of both groups were similar in response to stimulation. The expression levels of StxBP1 in response to stimulation were significantly lesser than control at PCOS. KITL expressions were lower in the PCOS as expected furthermore similar to StxBP1 in response to stimulation. According to our findings, the highest response to stimulation in GCs occurred for StxBP1 and KITL in the control. Limitations, reasons for caution Since human cells were used in the study and the cells of each patient do not exhibit the same characteristics, the lowest number of patient samples identified in the statistical power analysis were included in the study. Wider implications of the findings: Our view to the disruption in the secretion of signal molecules in terms of vesicle dynamics will offer a new perspective in female infertility or cross-talks in folliclar cells of the ovary. Trial registration number TSA–2019–18196

Stiffening Effect of the [Bmim][Cl] Ionic Liquid on the Bending Dynamics of DMPC Lipid Vesicles

The elastic properties of the cellular lipid membrane play a crucial role for life. Their alteration can lead to cell malfunction, and in turn, being able to control them holds the promise of effective therapeutic and diagnostic approaches. In this context, due to their proven strong interaction with lipid bilayers, ionic liquids (ILs)—a vast class of organic electrolytes—may play an important role. This work focuses on the effect of the model imidazolium-IL [bmim][Cl] on the bending modulus of DMPC lipid vesicles, a basic model of cellular lipid membranes. Here, by combining small-angle neutron scattering and neutron spin–echo spectroscopy, we show that the IL, dispersed at low concentrations at the bilayer–water interface, (i) diffuses into the lipid region, accounting for five IL-cations for every 11 lipids, and (ii) causes an increase of the lipid bilayer bending modulus, up to 60% compared to the neat lipid bilayer at 40 °C.

Nanofluidics for Simultaneous Size and Charge Profiling of Extracellular Vesicles.

Extracellular vesicles (EVs) are cell-derived membrane structures that circulate in body fluids and show considerable potential for noninvasive diagnosis. EVs possess surface chemistries and encapsulated molecular cargo that reflect the physiological state of cells from which they originate, including the presence of disease. In order to fully harness the diagnostic potential of EVs, there is a critical need for technologies that can profile large EV populations without sacrificing single EV level detail by averaging over multiple EVs. Here we use a nanofluidic device with tunable confinement to trap EVs in a free-energy landscape that modulates vesicle dynamics in a manner dependent on EV size and charge. As proof-of-principle, we perform size and charge profiling of a population of EVs extracted from human glioblastoma astrocytoma (U373) and normal human astrocytoma (NHA) cell lines.

Vesicle dynamics during the egress of malaria gametocytes from the red blood cell

Malaria parasites are obligate intracellular pathogens that live in human red blood cells harbored by a parasitophorous vacuole. The parasites need to exit from the red blood cell to continue life-cycle progression and ensure human-to-mosquito transmission. Two types of blood stages are able to lyse the enveloping red blood cell to mediate egress, the merozoites and the gametocytes. The intraerythrocytic parasites exit the red blood cell via an inside-out mode during which the membrane of the parasitophorous vacuole ruptures prior to the red blood cell membrane. Membrane rupture is initiated by the exocytosis of specialized secretory vesicles following the perception of egress triggers. The molecular mechanisms of red blood cell egress have particularly been studied in malaria gametocytes. Upon activation by external factors, gametocytes successively discharge at least two types of vesicles, the osmiophilic bodies needed to rupture the parasitophorous vacuole membrane and recently identified egress vesicles that are important for the perforation of the erythrocyte membrane. In recent years, important components of the signaling cascades leading to red blood cell egress have been investigated and several proteins of the osmiophilic bodies have been identified. We here report on the newest findings on the egress of gametocytes from the red blood cell. We further focus on the content and function of the egress-related vesicles and discuss the molecular machinery that might drive vesicle discharge.

Secreted C-type lectin regulation of neuromuscular junction synaptic vesicle dynamics modulates coordinated movement.

The synaptic cleft manifests enriched glycosylation, with structured glycans coordinating signaling between presynaptic and postsynaptic cells. Glycosylated signaling ligands orchestrating communication are tightly regulated by secreted glycan-binding lectins. Using the Drosophila neuromuscular junction (NMJ) as a model glutamatergic synapse, we identify a new Ca2+-binding (C-type) lectin, Lectin-galC1 (LGC1), which modulates presynaptic function and neurotransmission strength. We find that LGC1 is enriched in motoneuron presynaptic boutons and secreted into the NMJ extracellular synaptomatrix. We show that LGC1 limits locomotor peristalsis and coordinated movement speed, with a specific requirement for synaptic function, but not NMJ architecture. LGC1 controls neurotransmission strength by limiting presynaptic active zone (AZ) and postsynaptic glutamate receptor (GluR) aligned synapse number, reducing both spontaneous and stimulation-evoked synaptic vesicle (SV) release, and capping SV cycling rate. During high-frequency stimulation (HFS), mutants have faster synaptic depression and impaired recovery while replenishing depleted SV pools. Although LGC1 removal increases the number of glutamatergic synapses, we find that LGC1-null mutants exhibit decreased SV density within presynaptic boutons, particularly SV pools at presynaptic active zones. Thus, LGC1 regulates NMJ neurotransmission to modulate coordinated movement.

Hippocampal alpha-synuclein mediates depressive-like behaviors

Alpha-synuclein (α-syn) which encoded by SNCA plays a critical role in the neurotransmission, vesicle dynamics, and neuroplasticity. Alteration to SNCA expression is associated with major depressive disorder. However, the pathogenic mechanism of SNCA in depression remains unknown. Herein, we reported that SNCA was up-regulated in the peripheral blood of major depressive disorder (MDD) patients and the depressive mice. Chronic restraint stress (CRS) also up-regulated the SNCA expression in the hippocampus. Moreover, over-expression of SNCA in the hippocampus triggered spontaneous depressive-like behaviors under the non-stressed conditions in mice, and knockout of SNCA could reverse CRS-induced depressive-like behaviors. SNCA led to synapse loss and neuronal cell death in the hippocampus possibly via complement-mediated microglial engulfment and inflammation, and thus contributed to the pathogenesis of depressive disorder. Overall, hippocampal SNCA and complement system are involved in the pathogenesis of depressive disorder and it provides a new perspective for the occurrence of depressive disorder.

Caveolin-1 deficiency impairs synaptic transmission in hippocampal neurons

In addition to providing structural support, caveolin-1 (Cav1), a component of lipid rafts, including caveolae, in the plasma membrane, is involved in various cellular mechanisms, including signal transduction. Although pre-synaptic membrane dynamics and trafficking are essential cellular processes during synaptic vesicle exocytosis/synaptic transmission and synaptic vesicle endocytosis/synaptic retrieval, little is known about the involvement of Cav1 in synaptic vesicle dynamics. Here we demonstrate that synaptic vesicle exocytosis is significantly impaired in Cav1–knockdown (Cav1–KD) neurons. Specifically, the size of the synaptic recycled vesicle pool is modestly decreased in Cav1–KD synapses and the kinetics of synaptic vesicle endocytosis are somewhat slowed. Notably, neurons rescued by triple mutants of Cav1 lacking palmitoylation sites mutants show impairments in both synaptic transmission and retrieval. Collectively, our findings implicate Cav1 in activity-driven synaptic vesicle dynamics—both exocytosis and endocytosis—and demonstrate that palmitoylation of Cav1 is important for this activity.

Role of ATP in Extracellular Vesicle Biogenesis and Dynamics.

Adenosine triphosphate (ATP) is among the molecules involved in the immune response. It acts as danger signal that promotes inflammation by activating both P2X and P2Y purinergic receptors expressed in immune cells, including microglia, and tumor cells. One of the most important receptors implicated in ATP-induced inflammation is P2X7 receptor (P2X7R). The stimulation of P2X7R by high concentration of ATP results in cell proliferation, inflammasome activation and shedding of extracellular vesicles (EVs). EVs are membrane structures released by all cells, which contain a selection of donor cell components, including proteins, lipids, RNA and ATP itself, and are able to transfer these molecules to target cells. ATP stimulation not only promotes EV production from microglia but also influences EV composition and signaling to the environment. In the present review, we will discuss the current knowledge on the role of ATP in the biogenesis and dynamics of EVs, which exert important functions in physiology and pathophysiology.

Unbiased proteomic profiling of host cell extracellular vesicle composition and dynamics upon HIV‐1 infection

Cells release diverse types of extracellular vesicles (EVs), which transfer complex signals to surrounding cells. Specific markers to distinguish different EVs (e.g. exosomes, ectosomes, enveloped viruses like HIV) are still lacking. We have developed a proteomic profiling approach for characterizing EV subtype composition and applied it to human Jurkat T cells. We generated an interactive database to define groups of proteins with similar profiles, suggesting release in similar EVs. Biochemical validation confirmed the presence of preferred partners of commonly used exosome markers in EVs: CD81/ADAM10/ITGB1, and CD63/syntenin. We then compared EVs from control and HIV‐1‐infected cells. HIV infection altered EV profiles of several cellular proteins, including MOV10 and SPN, which became incorporated into HIV virions, and SERINC3, which was re‐routed to non‐viral EVs in a Nef‐dependent manner. Furthermore, we found that SERINC3 controls the surface composition of EVs. Our workflow provides an unbiased approach for identifying candidate markers and potential regulators of EV subtypes. It can be widely applied to in vitro experimental systems for investigating physiological or pathological modifications of EV release.

Altered network properties in C9ORF72 repeat expansion cortical neurons are due to synaptic dysfunction

BackgroundPhysiological disturbances in cortical network excitability and plasticity are established and widespread in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) patients, including those harbouring the C9ORF72 repeat expansion (C9ORF72RE) mutation – the most common genetic impairment causal to ALS and FTD. Noting that perturbations in cortical function are evidenced pre-symptomatically, and that the cortex is associated with widespread pathology, cortical dysfunction is thought to be an early driver of neurodegenerative disease progression. However, our understanding of how altered network function manifests at the cellular and molecular level is not clear.MethodsTo address this we have generated cortical neurons from patient-derived iPSCs harbouring C9ORF72RE mutations, as well as from their isogenic expansion-corrected controls. We have established a model of network activity in these neurons using multi-electrode array electrophysiology. We have then mechanistically examined the physiological processes underpinning network dysfunction using a combination of patch-clamp electrophysiology, immunocytochemistry, pharmacology and transcriptomic profiling.ResultsWe find that C9ORF72RE causes elevated network burst activity, associated with enhanced synaptic input, yet lower burst duration, attributable to impaired pre-synaptic vesicle dynamics. We also show that the C9ORF72RE is associated with impaired synaptic plasticity. Moreover, RNA-seq analysis revealed dysregulated molecular pathways impacting on synaptic function. All molecular, cellular and network deficits are rescued by CRISPR/Cas9 correction of C9ORF72RE. Our study provides a mechanistic view of the early dysregulated processes that underpin cortical network dysfunction in ALS-FTD.ConclusionThese findings suggest synaptic pathophysiology is widespread in ALS-FTD and has an early and fundamental role in driving altered network function that is thought to contribute to neurodegenerative processes in these patients. The overall importance is the identification of previously unidentified defects in pre and postsynaptic compartments affecting synaptic plasticity, synaptic vesicle stores, and network propagation, which directly impact upon cortical function.

Calcium-vesicles perform active diffusion in the sea urchin embryo during larval biomineralization.

Biomineralization is the process by which organisms use minerals to harden their tissues and provide them with physical support. Biomineralizing cells concentrate the mineral in vesicles that they secret into a dedicated compartment where crystallization occurs. The dynamics of vesicle motion and the molecular mechanisms that control it, are not well understood. Sea urchin larval skeletogenesis provides an excellent platform for investigating the kinetics of mineral-bearing vesicles. Here we used lattice light-sheet microscopy to study the three-dimensional (3D) dynamics of calcium-bearing vesicles in the cells of normal sea urchin embryos and of embryos where skeletogenesis is blocked through the inhibition of Vascular Endothelial Growth Factor Receptor (VEGFR). We developed computational tools for displaying 3D-volumetric movies and for automatically quantifying vesicle dynamics. Our findings imply that calcium vesicles perform an active diffusion motion in both, calcifying (skeletogenic) and non-calcifying (ectodermal) cells of the embryo. The diffusion coefficient and vesicle speed are larger in the mesenchymal skeletogenic cells compared to the epithelial ectodermal cells. These differences are possibly due to the distinct mechanical properties of the two tissues, demonstrated by the enhanced f-actin accumulation and myosinII activity in the ectodermal cells compared to the skeletogenic cells. Vesicle motion is not directed toward the biomineralization compartment, but the vesicles slow down when they approach it, and probably bind for mineral deposition. VEGFR inhibition leads to an increase of vesicle volume but hardly changes vesicle kinetics and doesn’t affect f-actin accumulation and myosinII activity. Thus, calcium vesicles perform an active diffusion motion in the cells of the sea urchin embryo, with diffusion length and speed that inversely correlate with the strength of the actomyosin network. Overall, our studies provide an unprecedented view of calcium vesicle 3D-dynamics and point toward cytoskeleton remodeling as an important effector of the motion of mineral-bearing vesicles.

Manipulating Phospholipid Vesicles at the Nanoscale: A Transformation from Unilamellar to Multilamellar by an n-Alkyl-poly(ethylene oxide).

We investigated the influence of an n-alkyl-PEO polymer on the structure and dynamics of phospholipid vesicles. Multilayer formation and about a 9% increase in the size in vesicles were observed by cryogenic transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS), and small-angle neutron/X-ray scattering (SANS/SAXS). The results indicate a change in the lamellar structure of the vesicles by a partial disruption caused by polymer chains, which seems to correlate with about a 30% reduction in bending rigidity per unit bilayer, as revealed by neutron spin echo (NSE) spectroscopy. Also, a strong change in lipid tail relaxation was observed. Our results point to opportunities using synthetic polymers to control the structure and dynamics of membranes, with possible applications in technical materials and also in drug and nutraceutical delivery.

Quantification of Insulin Vesicle Dynamics, Fusion Events and Calcium Activity in Intact Mouse Islets

Proper regulation of glucose homeostasis requires the controlled secretion of insulin and glucagon by β- and α-cells, respectively, in the pancreatic islets. The secretion profiles of insulin and glucagon track in opposition to each other with respect to glucose stimulation. These two hormones work as counterregulatory partners to maintain blood glucose homeostasis and the misregulation of both is implicated in the onset of diabetes. Therefore, it is crucial to understand the mechanistic pathways that drive the regulation of both insulin and glucagon release in pancreatic islets. For this, we adopt a multi-pronged approach to investigate the dynamics and fusion events of insulin vesicles, and intracellular Ca2+ activity in β- and α-cells of mouse pancreatic islets. The dynamics of insulin vesicle motion and release were monitored by 2D confocal and 3D dual-view inverted selective plane illumination microscopy (diSPIM) time-lapse imaging on c-peptide-EGFP labeled MIN6 cells and intact islets of transgenic ins1 promoter driven c-peptide-superfolder GFP (c-peptide-sfGFP) expressing mice under different glucose conditions. insulin vesicle fusion events were also quantified with pH-sensitive Vamp2-pHluorin labeled vesicles in MIN6 cells using total internal reflection fluorescence (TIRF) microscopy. Quantification of α- and β-cell Ca2+ activities under glucose stimulation and various conditions were conducted in intact islets of transgenic GCG-iCre and INS-Cre-GCaMP6 mice, respectively, utilizing confocal and diSPIM imaging. in addition, we examine the effects of Complexin 2, a protein kinase A (PKA)-dependent SNARE binding protein, on the regulation of glucagon secretion, along with α-cell intracellular Ca2+ activity, in Complexin2 knockout mice islets. by stepwise delineation of the various mechanistic pathways, we aim to decipher the intricate coordination between the intrinsic, paracrine and juxtacrine mechanisms within individual islet cells for proper islet function.

Rho-kinase inhibition by fasudil modulates pre-synaptic vesicle dynamics.

The Rho kinase (ROCK) signaling pathway is an attractive therapeutic target in neurodegenerationsince it has beenlinked to the prevention of neuronal death and neurite regeneration.The isoquinoline derivative fasudil is apotent ROCK inhibitor, which isalready approved for chronic clinical treatment in humans. However, theeffectsof chronic fasudil treatments on neuronal function are still unknown. We analyzedhere chronicfasudil treatment in primary rat hippocampal cultures. Neurons were stimulated with 20Hz field stimulation and we investigated pre-synaptic mechanisms and parameters regulating synaptic transmission after fasudil treatment by super resolution stimulated emission depletion (STED) microscopy, live-cell fluorescence imaging, and western blotting. Fasudil did not affectbasic synaptic function or the amount ofseveral synaptic proteins, but italtered the chronic dynamics of the synaptic vesicles. Fasudil reduced theproportion of the actively recycling vesicles, and shortened the vesiclelifetime, resulting overall in areduction of the synaptic response uponstimulation. We conclude that fasudil does not alter synapticstructure, acceleratesvesicle turnover, and decreases the number of released vesicles. This broadenstheknown spectrum of effects of this drug, and suggests new potential clinical uses.

An immersed boundary projection method for incompressible interface simulations in 3D flows

In this paper, we extend our previous immersed boundary (IB) projection method for 2D inextensible vesicle in unsteady Stokes flow (Ong and Lai, 2020 [23]) to 3D incompressible interface as a prototype of vesicles. In spite of similar numerical algorithm to the 2D case, the present 3D numerical implementation is far from straightforward. An incompressible interface immersed in Newtonian fluid must ensure both conservative constraints associated with local fluid volume and local interfacial area. To accomplish this, we triangulate the incompressible interface, whereby the unknown elastic tension is defined on the triangles, while the associated tension force term is defined at vertices (Lagrangian markers). Consistent approximations of surface differential operators on a triangulated interface are developed accordingly. An extra scalar field is introduced in the IB projection approach so that the fluid pressure and interfacial elastic tension are efficiently solved in a divide-and-conquer manner. As a result, the local interfacial and volumetric incompressibilities can be ideally satisfied simultaneously. A series of numerical tests on the present scheme is performed to verify the robustness and applicability of the method. We first carry out the convergence study of the solution variables defined on the fluid and interface. We then study the shear-induced deformations of incompressible interface for various initial configurations. At last, the bending force and the penalty force for improved volume conservation are further incorporated into our method to simulate an oblate vesicle dynamics in quiescent flow.

The mRNA-Binding Protein RBM3 Regulates Activity Patterns and Local Synaptic Translation in Cultured Hippocampal Neurons.

The activity and the metabolism of the brain change rhythmically during the day/night cycle. Such rhythmicity is also observed in cultured neurons from the suprachiasmatic nucleus, which is a critical center in rhythm maintenance. However, this issue has not been extensively studied in cultures from areas less involved in timekeeping, as the hippocampus. Using neurons cultured from the hippocampi of newborn rats (both male and female), we observed significant time-dependent changes in global activity, in synaptic vesicle dynamics, in synapse size, and in synaptic mRNA amounts. A transcriptome analysis of the neurons, performed at different times over 24 h, revealed significant changes only for RNA-binding motif 3 (Rbm3). RBM3 amounts changed, especially in synapses. RBM3 knockdown altered synaptic vesicle dynamics and changed the neuronal activity patterns. This procedure also altered local translation in synapses, albeit it left the global cellular translation unaffected. We conclude that hippocampal cultured neurons can exhibit strong changes in their activity levels over 24 h, in an RBM3-dependent fashion.SIGNIFICANCE STATEMENT This work is important in several ways. First, the discovery of relatively regular activity patterns in hippocampal cultures implies that future studies using this common model will need to take the time parameter into account, to avoid misinterpretation. Second, our work links these changes in activity strongly to RBM3, in a fashion that is independent of the canonical clock mechanisms, which is a very surprising observation. Third, we describe here probably the first molecule (RBM3) whose manipulation affects translation specifically in synapses, and not at the whole-cell level. This is a key finding for the rapidly growing field of local synaptic translation.

Systematic Comparison of Vesicular Targeting Signals Leads to the Development of Genetically Encoded Vesicular Fluorescent Zn2+ and pH Sensors.

Genetically encoded fluorescent sensors have been widely used to illuminate secretory vesicle dynamics and the vesicular lumen, including Zn2+ and pH, in living cells. However, vesicular sensors have a tendency to mislocalize and are susceptible to the acidic intraluminal pH. In this study, we performed a systematic comparison of five different vesicular proteins to target the fluorescent protein mCherry and a Zn2+ Förster resonance energy transfer (FRET) sensor to secretory vesicles. We found that motifs derived from vesicular cargo proteins, including chromogranin A (CgA), target vesicular puncta with greater efficacy than transmembrane proteins. To characterize vesicular Zn2+ levels, we developed CgA-Zn2+ FRET sensor fusions with existing sensors ZapCY1 and eCALWY-4 and characterized subcellular localization and the influence of pH on sensor performance. We simultaneously monitored Zn2+ and pH in individual secretory vesicles by leveraging the acceptor fluorescent protein as a pH sensor and found that pH influenced FRET measurements in situ. While unable to characterize vesicular Zn2+ at the single-vesicle level, we were able to monitor Zn2+ dynamics in populations of vesicles and detected high vesicular Zn2+ in MIN6 cells compared to lower levels in the prostate cancer cell line LnCaP. The combination of CgA-ZapCY1 and CgA-eCALWY-4 allows for measurement of Zn2+ from pM to nM ranges.

Coarse-grained implicit solvent lipid force field with a compatible resolution to the Cα protein representation.

Biological membranes have been prominent targets for coarse-grained (CG) molecular dynamics simulations. While minimal CG lipid models with three beads per lipid and quantitative CG lipid models with >10 beads per lipid have been well studied, in between them, CG lipid models with a compatible resolution to residue-level CG protein models are much less developed. Here, we extended a previously developed three-bead lipid model into a five-bead model and parameterized it for two phospholipids, POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine). The developed model, iSoLF, reproduced the area per lipid, hydrophobic thickness, and phase behaviors of the target phospholipid bilayer membranes at the physiological temperature. The model POPC and DPPC membranes were in liquid and gel phases, respectively, in accordance with experiments. We further examined the spontaneous formation of a membrane bilayer, the temperature dependence of physical properties, the vesicle dynamics, and the POPC/DPPC two-component membrane dynamics of the CG lipid model, showing some promise. Once combined with standard Cα protein models, the iSoLF model will be a powerful tool to simulate large biological membrane systems made of lipids and proteins.

Dynamics of Vesicles Driven Into Closed Constrictions by Molecular Motors.

We study the dynamics of a model of membrane vesicle transport into dendritic spines, which are bulbous intracellular compartments in neurons driven by molecular motors. We reduce the lubrication model proposed in Fai et al. (Phys Rev Fluids 2:113601, 2017) to a fast-slow system, yielding an analytically and numerically tractable equation equivalent to the original model in the overdamped limit. The model's key parameters include: (1) the ratio of motors that prefer to push toward the head of the dendritic spine to the motors that prefer to push in the opposite direction, and (2) the viscous drag exerted on the vesicle by the spine constriction. We perform a numerical bifurcation analysis in these parameters and find that steady-state vesicle velocities appear and disappear through several saddle-node bifurcations. This process allows us to identify the region of parameter space in which multiple stable velocities exist. We show by direct calculations that there can only be unidirectional motion for sufficiently close vesicle-to-spine diameter ratios. Our analysis predicts the critical vesicle-to-spine diameter ratio, at which there is a transition from unidirectional to bidirectional motion, consistent with experimental observations of vesicle trajectories in the literature.

The divergence-conforming immersed boundary method: Application to vesicle and capsule dynamics

We extend the recently introduced divergence-conforming immersed boundary (DCIB) method [1] to fluid-structure interaction (FSI) problems involving closed co-dimension one solids. We focus on capsules and vesicles, whose discretization is particularly challenging due to the higher-order derivatives that appear in their formulations. In two-dimensional settings, we employ cubic B-splines with periodic knot vectors to obtain discretizations of closed curves with C2 inter-element continuity. In three-dimensional settings, we use analysis-suitable bi-cubic T-splines to obtain discretizations of closed surfaces with at least C1 inter-element continuity. Large spurious changes of the fluid volume inside closed co-dimension one solids are a well-known issue for IB methods. The DCIB method results in volume changes orders of magnitude lower than conventional IB methods. This is a byproduct of discretizing the velocity-pressure pair with divergence-conforming B-splines, which lead to negligible incompressibility errors at the Eulerian level. The higher inter-element continuity of divergence-conforming B-splines is also crucial to avoid the quadrature/interpolation errors of IB methods becoming the dominant discretization error. Benchmark and application problems of vesicle and capsule dynamics are solved, including mesh-independence studies and comparisons with other numerical methods.