Depletion of nucleoporins from HeLa nuclear pore complexes to facilitate the production of ghost pores for in vitro reconstitution

During cell division, Nuclear Pore Complexes (NPCs) are broken down into protein subcomplexes that are the basis for reassembly in daughter cells. This is the driving force for the establishment of an in vitro reconstitution system to study aspects of NPC reassembly. In this study, nuclear envelope (NE) was isolated from HeLa cells. NE was treated with increasing concentrations of heparin to extract nucleoporins (Nups) for the production of “ghost pores” which are pores severely deficient in Nups, while still containing Pore Membrane proteins (POM) needed to anchor the NPC. Ghost pores have been subjected to incubation with previously stripped Nups and some re-binding has been shown to occur by western blot analysis. This in vitro assay provides a powerful tool to investigate the protein–protein interactions of NPC reassembly from a human cell line. Through a better understanding of the process of NPC reassembly, we can continue to piece together the puzzle of this macromolecular structure. It is most advantageous to establish a straightforward reconstitution procedure at the mammalian level.     

A multi‐resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand‐binding site

In multi‐resolution simulations, different system components are simultaneously modeled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the active site to capture the chemistry of ligand binding. Global properties of the rest of the protein also play an essential role, determining the structure and fluctuations of the binding site; however, these can be modeled on a coarser level. Similarly, in the most computationally efficient scheme only the solvent hydrating the active site requires atomistic detail. We present a methodology to couple atomistic and coarse‐grained protein models, while solvating the atomistic part of the protein in atomistic water. This allows a free choice of which protein and solvent degrees of freedom to include atomistically. This multi‐resolution methodology can successfully model stable ligand binding, and we further confirm its validity by exploring the reproduction of system properties relevant to enzymatic function. In addition to a computational speedup, such an approach can allow the identification of the essential degrees of freedom playing a role in a given process, potentially yielding new insights into biomolecular function. Proteins 2016; 84:1902–1913. © 2016 Wiley Periodicals, Inc.     

Identifying core habitats and corridors for giant pandas by combining multiscale random forest and connectivity analysis

Habitat loss and fragmentation are widely acknowledged as the main driver of the decline of giant panda populations. The Chinese government has made great efforts to protect this charming species and has made remarkable achievements, such as population growth and habitat expansion. However, habitat fragmentation has not been reversed. Protecting giant pandas in a large spatial extent needs to identify core habitat patches and corridors connecting them. This study used an equal‐sampling multiscale random forest habitat model to predict a habitat suitability map for the giant panda. Then, we applied the resistant kernel method and factorial least‐cost path analysis to identify core habitats connected by panda dispersal and corridors among panda occurrences, respectively. Finally, we evaluated the effectiveness of current protected areas in representing core habitats and corridors. Our results showed high scale dependence of giant panda habitat selection. Giant pandas strongly respond to bamboo percentage and elevation at a relatively fine scale (1 km), whereas they respond to anthropogenic factors at a coarse scale (≥2 km). Dispersal ability has significant effects on core habitats extent and population fragmentation evaluation. Under medium and high dispersal ability scenarios (12,000 and 20,000 cost units), most giant panda habitats in the Qionglai mountain are predicted to be well connected by dispersal. The proportion of core habitats covered by protected areas varied between 38% and 43% under different dispersal ability scenarios, highlighting significant gaps in the protected area network. Similarly, only 43% of corridors that connect giant panda occurrences were protected. Our results can provide crucial information for conservation managers to develop wise strategies to safeguard the long‐term viability of the giant panda population.     

Differential effect of dopamine catabolism and uptake inhibition on dopamine-induced calcium dysregulation and viability loss

The present study was aimed at evaluating of the effects of dopamine (DA) toxicity on PC12 cells' calcium homeostasis, cellular viability, and free radical levels. Moreover, the effect of receptor inhibition, and DA metabolism and reuptake antagonism on all parameters was also evaluated. Acute treatment with DA impaired the ability of PC12 cells to buffer excess calcium after K+-depolarization, decreased cellular viability by approximately 35%, and increased free radical levels by about 10% in a dose dependent manner. Pretreatment with both active and inactive pargyl monoamine oxidase inhibitors (MAOi) protected PC12 cells from DA toxicity on cellular viability and free radical levels, regardless of the presence or absence of their target enzymes in PC12 cells. These results suggest a lack of specific involvement of DA metabolism by MAO in dopamine's effects on cellular viability and production of free radicals. However, DA-induced dysregulation of calcium homeostasis seems to be more specifically mediated by DA metabolism by MAO. Results indicate that, in order for toxicity to occur the DA must be taken up into the cells. DA receptors do not mediate dopamine cytoxicity, and the D2 receptor plays a modest role in DA-induced calcium dysregulation and generation of free radicals. Moreover, DA-induced cell viability loss is not mediated by calcium, nor by caspase-3 enzyme, but is prevented by inhibition of mitochondrial permeability transition pores.     

The effect of temperature on membrane hydraulic conductivity

The objective of this study was to use the temperature dependence of water permeability to suggest the physical mechanisms of water transport across membranes of osmotically slowly responding cells and to demonstrate that insight into water transport mechanisms in these cells may be gained from easily performed experiments using an electronic particle counter. Osmotic responses of V-79W Chinese hamster fibroblast cells were measured in hypertonic solutions at various temperatures and the membrane hydraulic conductivity was determined. The results were fit with the general Arrhenius equation with two free parameters, and also fit with two specific membrane models each having only one free parameter. Data from the literature including that for human bone marrow stem cells, hamster pancreatic islets, and bovine articular cartilage chondrocytes were also examined. The results indicated that the membrane models could be used in conjunction with measured permeability data at different temperatures to investigate the method of water movement across various cell membranes. This approach for slower responding cells challenges the current concept that the presence of aqueous pores is always accompanied by an osmotic water permeability value, P(f)>0.01 cm/s. The possibility of water transport through aqueous pores in lower-permeability cells is proposed.     

A High‐Performance Supercapacitor Based on KOH Activated 1D C70 Microstructures

Fullerenes are of tremendous interest from fundamental researches to applied perspectives in the past decades. However, their application in supercapacitors has been underdeveloped for a long time. Here, the KOH activation of C₇₀ microtubes is reported at high temperatures, which provides activated samples exhibiting excellent capacitive properties. The improved capacitive performance can be attributed to three aspects: the generation of macropores and micropores, the introduction of oxygen functionalities, and the formation of graphitic carbons from ellipsoidal fullerenes. The optimum activated state for supercapacitor application is achieved at 600 °C, at which the product exhibits the best electrochemical behavior with a gravimetric capacitance of 362.0 F g^?1 at 0.1 A g^?1 and excellent cycling stability with capacitance retention of 92.5% over 5000 cycles at 1 A g^?1.     

pH modulation of transport properties of alamethicin oligomers inserted in zwitterionic-based artificial lipid membranes

Electric features of biological membranes are major determinants of the function and physiological manifestation of membrane-penetrating peptides, and such features are prone to be modulated by the properties of the surrounding aqueous medium. In this work, we demonstrate that pH plays crucial roles in modulating electric characteristics of zwitterionic-based artificial lipid membranes. The effect of pH on electrical properties of such membranes was probed by evaluating the transport properties of embedded alamethicin oligomers over a wide range of pH values (i.e., 0.65, 2.08, 2.94, 7 and 10.1). Our data strongly support the paradigm of a pH-dependent variation of the surface and membrane dipole potential which, in conjunction with possible lateral pressure effects within the lipid membrane, lead to a non-monotonic modulation of the electrical conductance of alamethicin oligomers. As expected, pH modulation of transport properties through the alamethicin oligomer is more visible for narrower pores (that is, the 1st conductive state) with slightly better cation selectivity as compared to larger oligomers.     

The response of giant phospholipid vesicles to pore-forming peptide melittin

The interaction between the pore-forming peptide melittin (MLT) and giant phospholipid vesicles was explored experimentally. Micromanipulation and direct optical observation of a vesicle (loaded with sucrose solution and suspended in isomolar glucose solution) enabled the monitoring of a single vesicle response to MLT. Time dependences of the vesicle size, shape and the composition of the inner solution were examined at each applied concentration of MLT (in the range from 1 to 60 μg/ml). The response varied with MLT concentration from slight perturbation of the membrane to disintegration of the vesicle. A model for MLT-vesicle interaction is proposed that explains the observed phenomena in the entire span of MLT concentrations and is consistent with deduced underlying mechanisms of MLT action: trans-membrane positioning and dimerization of MLT, the lipid flow from the outer to the inner membrane leaflet induced by MLT translocation, formation of pores and the consequent transport of small molecules through the membrane. The results of the theoretical analysis stress the role of dimers in the MLT-membrane interaction and demonstrate that the MLT-induced membrane permeability for sugar molecules in this experimental set-up depends on both MLT concentration and time.     

Mechanism of plasmid delivery by hydrodynamic tail vein injection. I. Hepatocyte uptake of various molecules

BACKGROUND: The hydrodynamic tail vein (HTV) injection of naked plasmid DNA is a simple yet effective in vivo gene delivery method into hepatocytes. It is increasingly being used as a research tool to elucidate mechanisms of gene expression and the role of genes and their cognate proteins in the pathogenesis of disease in animal models. A greater understanding of its mechanism will aid these efforts and has relevance to macromolecular and nucleic acid delivery in general. METHODS: In an attempt to explore how naked DNA enters hepatocytes the fate of a variety of molecules and particles was followed over a 24-h time frame using fluorescence microscopy. The uptake of some of these compounds was correlated with marker gene expression from a co-injected plasmid DNA. In addition, the uptake of the injected compounds was correlated with the histologic appearance of hepatocytes. RESULTS: Out of the large number of nucleic acids, peptides, proteins, inert polymers and small molecules that we tested, most were efficiently delivered into hepatocytes independently of their size and charge. Even T7 phage and highly charged DNA/protein complexes of 60-100 nm in size were able to enter the cytoplasm. In animals co-injected with an enhanced yellow fluorescent protein (EYFP) expression vector and fluorescently labeled immunoglobulin (IgG), hepatocytes flooded with large amounts of IgG appeared permanently damaged and did not express EYFP-Nuc. Hepatocytes expressing EYFP had only slight IgG uptake. In contrast, when an EYFP expression vector was co-injected with a fluorescently labeled 200-bp linear DNA fragment, both were mostly (in 91% of the observed cells) co-localized to the same hepatocytes 24 h later. CONCLUSIONS: The appearance of permanently damaged cells with increased uptake of some molecules such as endogenous IgG raised the possibility that a molecule could be present in a hepatocyte but its transport would not be indicative of the transport process that can lead to foreign gene expression. The HTV procedure enables the uptake of a variety of molecules (as previous studies also found), but the uptake process for some of these molecules may be associated with a more disruptive process to the hepatocytes that is not compatible with successful gene delivery.     

Forms and Functions of Meso and Micro-niches of Carbon within Soil Aggregates

Soil aggregates include sand/silt/clay, water, ion and organic matter contents combined with natural dry/wet (D/W) cycling alters both the formation and function of intra-aggregate pore continuity, connectivity, dead-end storage volumes, and tortuosity. Surface aggregates in the 0-5 cm depths of most soils experience from 34 to 57 D/W cycles that exceed differences in water contents >10%. Both the rates of drying or wetting, (intensity) and the D/W range of soil water contents (severity) alter the transport of water, C and N through micro and mesofaunal habitats among multiple size domains. This report identifies micro-niche locations of accumulating soil C within soil aggregate regions that may affect nematode residence sites and migration pathways. Recent advances in X-ray microtomography enable the examination of intact pore networks within soil aggregates at resolutions as small as 4 microns. Geostatistical and multi-fractal methods provide concise characteristics of pore spatial distributions within the aggregates and are useful for comparing these alterations among soils. Aggregates subjected to multiple D/W cycles developed greater spatial correlations that parallel increases in the (13)C sorption within aggregate interiors were compared with locations of soil microbial communities. Past research indicates microbial activities within the soil aggregate matrix are spatially heterogeneous due to complex pore geometries within aggregates. Illumination of the "blackbox" interiors of soil aggregates includes a discussion of natural and anthropogenic alterations of solution flow and carbon sequestration by soil aggregates containing biophysical gradients.