Pore formation in fluctuating membranes

We study the nucleation of a single pore in a fluctuating lipid membrane, specifically taking into account the membrane fluctuations, as well as the shape fluctuations of the pore. For large enough pores, the nucleation free energy is well-described by shifts in the effective membrane surface tension and the pore line tension. Using our framework, we derive the stability criteria for the various pore formation regimes. In addition to the well-known large-tension regime from the classical nucleation theory of pores, we also find a low-tension regime in which the effective line and surface tensions can change sign from their bare values. The latter scenario takes place at sufficiently high temperatures, where the opening of a stable pore of finite size is entropically favorable.Comment: 9 pages, 3 figure

Plasma flows and magnetic field interplay during the formation of a pore

We studied the formation of a pore in AR NOAA 11462. We analysed data obtained with the IBIS at the DST on April 17, 2012, consisting of full Stokes measurements of the Fe I 617.3 nm lines. Furthermore, we analysed SDO/HMI observations in the continuum and vector magnetograms derived from the Fe I 617.3 nm line data taken from April 15 to 19, 2012. We estimated the magnetic field strength and vector components and the LOS and horizontal motions in the photospheric region hosting the pore formation. We discuss our results in light of other observational studies and recent advances of numerical simulations. The pore formation occurs in less than 1 hour in the leading region of the AR. The evolution of the flux patch in the leading part of the AR is faster (< 12 hour) than the evolution (20-30 hour) of the more diffuse and smaller scale flux patches in the trailing region. During the pore formation, the ratio between magnetic and dark area decreases from 5 to 2. We observe strong downflows at the forming pore boundary and diverging proper motions of plasma in the vicinity of the evolving feature that are directed towards the forming pore. The average values and trends of the various quantities estimated in the AR are in agreement with results of former observational studies of steady pores and with their modelled counterparts, as seen in recent numerical simulations of a rising-tube process. The agreement with the outcomes of the numerical studies holds for both the signatures of the flux emergence process (e.g. appearance of small-scale mixed polarity patterns and elongated granules) and the evolution of the region. The processes driving the formation of the pore are identified with the emergence of a magnetic flux concentration and the subsequent reorganization of the emerged flux, by the combined effect of velocity and magnetic field, in and around the evolving structure.Comment: Accepted for publication in Astronomy and Astrophysic

Formation of the postmitotic nuclear envelope from extended ER cisternae precedes nuclear pore assembly

During mitosis, the nuclear envelope merges with the endoplasmic reticulum (ER), and nuclear pore complexes are disassembled. In a current model for reassembly after mitosis, the nuclear envelope forms by a reshaping of ER tubules. For the assembly of pores, two major models have been proposed. In the insertion model, nuclear pore complexes are embedded in the nuclear envelope after their formation. In the prepore model, nucleoporins assemble on the chromatin as an intermediate nuclear pore complex before nuclear envelope formation. Using live-cell imaging and electron microscope tomography, we find that the mitotic assembly of the nuclear envelope primarily originates from ER cisternae. Moreover, the nuclear pore complexes assemble only on the already formed nuclear envelope. Indeed, all the chromatin-associated Nup 107–160 complexes are in single units instead of assembled prepores. We therefore propose that the postmitotic nuclear envelope assembles directly from ER cisternae followed by membrane-dependent insertion of nuclear pore complexes

Pore-scale characterization and modelling of CO2 flow in tight sandstones using X-ray micro-CT; Knorringfjellet formation of the Longyearbyen CO2 lab, Svalbard

Rocks of the Knorringfjellet Formation in Central Spitsbergen form a potential storage reservoir for CO2 below Longyearbyen. They are characterised by a moderate porosity and low permeability. However, water injection tests have shown positive results and fractures are considered to facilitate fluid flow. Therefore, hard data on fracture parameters and pore characteristics schould be analysed to better understand flow characteristics. Consequently, sandstone and conglomerate samples from the Knorringfjellet Formation were sampled and characterised with High Resolution X-ray Computed Tomography (HRXCT) at the Centre for X-ray Tomography at Ghent University, Belgium (UGCT). The dataset includes samples taken from drillholes in the vicinity of Longyearbyen, drilled during the pilot phase at the Longyearbyen CO2 project, as well as from the Knorringfjellet Formation outcrops at Konusdalen and Criocerasdalen. This was done in order to compare micro-fracture and pore parameters in both settings. With HRXCT, the samples were analysed at pore scale and quantitative information of the pore network and fractures were extracted. Pore networks were used for the modelling of CO2 flow in specific samples and information on fracture aperture was obtained at a micrometre scale. The acquired dataset can be directly used for a better understanding of flow in the aquifer

A coupled map lattice model for spontaneous pore formation in anodic oxidation

We construct a coupled map lattice model for the spontaneous pore formation in anodic oxidation in two dimensions and perform numerical simulations, after we explain steady flat solutions, their linear stability and a single pore solution for a model of Parkhutik and Shershulsky.Comment: 7 pages, 7 figure

Coupling between pore formation and phase separation in charged lipid membranes

We investigated the effect of charge on the membrane morphology of giant unilamellar vesicles (GUVs) composed of various mixtures containing charged lipids. We observed the membrane morphologies by fluorescent and confocal laser microscopy in lipid mixtures consisting of a neutral unsaturated lipid [dioleoylphosphatidylcholine (DOPC)], a neutral saturated lipid [dipalmitoylphosphatidylcholine (DPPC)], a charged unsaturated lipid [dioleoylphosphatidylglycerol (DOPG$^{\scriptsize{(-)}}$)], a charged saturated lipid [dipalmitoylphosphatidylglycerol (DPPG$^{\scriptsize{(-)}}$)], and cholesterol (Chol). In binary mixtures of neutral DOPC/DPPC and charged DOPC/DPPG$^{\scriptsize{(-)}}$, spherical vesicles were formed. On the other hand, pore formation was often observed with GUVs consisting of DOPG$^{\scriptsize{(-)}}$ and DPPC. In a DPPC/DPPG$^{\scriptsize{(-)}}$/Chol ternary mixture, pore-formed vesicles were also frequently observed. The percentage of pore-formed vesicles increased with the DPPG$^{\scriptsize{(-)}}$ concentration. Moreover, when the head group charges of charged lipids were screened by the addition of salt, pore-formed vesicles were suppressed in both the binary and ternary charged lipid mixtures. We discuss the mechanisms of pore formation in charged lipid mixtures and the relationship between phase separation and the membrane morphology. Finally, we reproduce the results seen in experimental systems by using coarse-grained molecular dynamics simulations.Comment: 34 pages, 10 figure

Single-channel electrophysiology reveals a distinct and uniform pore complex formed by α-synuclein oligomers in lipid membranes.

Synucleinopathies such as Parkinson's disease, multiple system atrophy and dementia with Lewy bodies are characterized by deposition of aggregated α-synuclein. Recent findings indicate that pathological oligomers rather than fibrillar aggregates may represent the main toxic protein species. It has been shown that α-synuclein oligomers can increase the conductance of lipid bilayers and, in cell-culture, lead to calcium dyshomeostasis and cell death. In this study, employing a setup for single-channel electrophysiology, we found that addition of iron-induced α-synuclein oligomers resulted in quantized and stepwise increases in bilayer conductance indicating insertion of distinct transmembrane pores. These pores switched between open and closed states depending on clamped voltage revealing a single-pore conductance comparable to that of bacterial porins. Pore conductance was dependent on transmembrane potential and the available cation. The pores stably inserted into the bilayer and could not be removed by buffer exchange. Pore formation could be inhibited by co-incubation with the aggregation inhibitor baicalein. Our findings indicate that iron-induced α-synuclein oligomers can form a uniform and distinct pore species with characteristic electrophysiological properties. Pore formation could be a critical event in the pathogenesis of synucleinopathies and provide a novel structural target for disease-modifying therapy

Rising methane gas bubbles form massive hydrate layers at the seafloor

Extensive methane hydrate layers are formed in the near-surface sediments of the Cascadia margin. An undissociated section of such a layer was recovered at the base of a gravity core (i.e. at a sediment depth of 120 cm) at the southern summit of Hydrate Ridge. As a result of salt exclusion during methane hydrate formation, the associated pore waters show a highly elevated chloride concentration of 809 mM. In comparison, the average background value is 543 mM. A simple transport-reaction model was developed to reproduce the Cl- observations and quantify processes such as hydrate formation, methane demand, and fluid flow. From this first field observation of a positive Cl- anomaly, high hydrate formation rates (0.15–1.08 mol cm-2 a-1) were calculated. Our model results also suggest that the fluid flow rate at the Cascadia accretionary margin is constrained to 45–300 cm a-1. The amount of methane needed to build up enough methane hydrate to produce the observed chloride enrichment exceeds the methane solubility in pore water. Thus, most of the gas hydrate was most likely formed from ascending methane gas bubbles rather than solely from CH4 dissolved in the pore water