Water-filled Cavities Research Articles

Quasi-droplet microbubbles for high resolution sensing applications

Optical properties and sensing capabilities of fused silica microbubbles were studied numerically using a finite element method. Mode characteristics, such as quality factor (Q) and effective refractive index, were determined for different bubble diameters and shell thicknesses. For sensing applications with whispering gallery modes (WGMs), thinner shells yield improved sensitivity. However, the Q-factor decreases with reduced thickness and this limits the final resolution. Three types of sensing applications with microbubbles, based on their optimized geometrical parameters, were studied. Herein the so-called quasi-droplet regime is defined and discussed. It is shown that best resolution can be achieved when microbubbles act as quasi-droplets, even for water-filled cavities at the telecommunications C-band.

Using ground penetrating radar in levee assessment to detect small scale animal burrows

Abstract Levees are civil engineering structures built to protect human lives, property, and agricultural lands during flood events. To keep these important structures in a safe condition, continuous monitoring must be performed regularly and thoroughly. Small rodent burrows are one of the major defects within levees; however, their early detection and repair helps in protecting levees during flooding events. A set of laboratory experiments was conducted to analyze the polarity change in GPR signals in the presence of subsurface voids and water-filled cavities. Ground Penetrating Radar (GPR) surveys using multi frequency antennas (400 MHz and 900 MHz) were conducted along an 875 meter section of the Lollie Levee near Conway, Arkansas, USA, to assess the levee's structural integrity. Many subsurface animal burrows, water-filled cavities, clay clasts, and metallic objects were investigated and identified. These anomalies were located at different depths and have different sizes. To ground truth the observations, hand dug trenches were excavated to confirm several anomalies. Results show an excellent match between GPR interpreted anomalies and the observed features. In-situ dielectric constant measurements were used to calculate the feature depths. The results of this research show that the 900 MHz antenna has more advantages over the 400 MHz antenna.

Structural features important for differences in protein partitioning in aqueous dextran–polyethylene glycol two-phase systems of different ionic compositions

Partitioning of 15 proteins in dextran–70-polyethylene glycol (PEG)-8000 aqueous two-phase systems (ATPSs) in the presence of 0.01M sodium phosphate buffer, pH7.4 was studied. The effect of salt additives (NaCl, CsCl, Na2SO4, NaClO4 and NaSCN) at different concentrations on the protein partition behavior was examined. The salt effects on protein partitioning were analyzed by using the Collander solvent regression relationship between the protein partition coefficients in ATPSs with and without salt additives. The results obtained show that the presence and concentration of salt additives affect the protein partition behavior. Analysis of ATPSs in terms of the differences between the relative hydrophobicity and electrostatic properties of the phases does not explain the protein partition behavior. The differences between protein partitioning could not be explained by the protein size. The structural signatures for the proteins were constructed from partition coefficient values in four ATPSs with different salt additives, and the structural distances were calculated using cytochrome c as the reference structure. The structural distances for all the examined proteins (except lysozyme) were found to be interrelated. Analysis of about 50 different descriptors of the protein structures revealed that the partition behavior of proteins is determined by the peculiarities of their surfaces (e.g., the number of water-filled cavities and the averaged hydrophobicity of the surface residues) and by the intrinsic flexibility of the protein structure measured in terms of the B-factor (or temperature factor).

Mapping groundwater conditions in different geological environments in the northern area of UAE using 2D earth resistivity imaging survey

A water resources database was developed and used to characterize the geological and hydrogeological settings of groundwater aquifers in the northern part of the United Arab Emirates. An intensive 2D Earth Resistivity Imaging (ERI) survey was conducted in selected areas to assess the available groundwater resources and delineate the salt-water intrusion. Drilling information of the existing monitoring wells as well as their records of water table elevations and groundwater salinity were used to measure the horizontal and vertical variations in lithology, degree of saturation, and groundwater salinity and thus to improve the interpretation of ERI data. The results of the chemical analyses of water samples collected from the wells along with the 2D ERI survey profiles were used to obtain an empirical relationship between the inferred earth resistivity and the amount of total dissolved solids. This relationship was used along with the true resistivity sections resulting from the inversion of 2D ERI data to identify and map three zones of water-bearing formation (fresh, brackish, and salt-water zones) in the coastal areas. The results indicated that the depth to the fresh-brackish interface exceeded 50 m at the upstream of the wadies and was in the order of 10 m or less in the vicinity of shoreline. Because of the high resistivity contrast between dry and water saturated fractured rocks; this method was very successful in detecting water-filled fractures and cavities in the carbonate aquifer. The application of this method was unsuccessful in clayey aquifers as it was not possible to isolate lenses of gravel and/or saturated with saline or brackish water from the surrounding clayey materials.

A Mutational and Computational Study of Water and Ion Movement through the S6 Bundle-Crossing of CaV1.2 Channel

How exactly voltage-gated calcium and sodium channels open their physical gate formed by the S6 TM segments is not clear yet. To study this, we modeled the pore-forming region of CaV1.2 channel using a combination of homology-based modeling and abinitio Rosetta algorithm. The obtained fold was stable during 100-200 ns long molecular dynamics runs with implicit membrane and solvent. In explicit membrane/water systems, it remained stable during multiple 40-50 ns runs. When tested with the ZDOCK protein-docking algorithm, the fold binds toxin Calcicludine at a site that incorporates residues, which previously were shown to be involved in binding of the toxin. Molecular dynamics with SWM4-NDP water and polarizable ions reveals the presence of novel water-filled cavities on the intracellular side of the channel. We mutated the principal residues that form them and show their critical role in channel gating.According to molecular dynamics calculations, water polarizability appears to be important for the filling of channel. We observe that water molecules form stable structures (an enthalpy stabilized ice-like phase) inside the channel. We mutated the principal residues that are predicted to alter water structures in the pore and confirm their role in channel gating. Overall, our findings further elaborate previously proposed involvement of water in channel gating and uncover a novel molecular view on the final steps of channel opening. Supported by NIH R01 MH079406.

Basic Biology and Host Use Patterns of Tephritid Flies (Phytalmiinae: Acanthonevrini, Dacinae: Gastrozonini) Breeding in Bamboo (Poaceae: Bambusoidea)

AbstractWe report results of field collections, laboratory rearing, and behavioral observations of tephritids belonging to the tribes Acanthonevrini and Gastrozonini in Malaysia and Thailand. The focus of the study was on general biology, seasonal history, mating, oviposition, larval biology, larval habits, and microhabitats. Host association with bamboo was unequivocally established for 31 species. Adult flies fed on liquids oozing from plants or other sources. Most species developed in the rainy season, when bamboo shoots were available. In Thailand, adult flies gathered along streams in the dry season. Observed sexual behavior patterns appeared to be simple in Gastrozonini, whereas in some Acanthonevrini, the males produced a foamy “nuptial gift,” which was offered to females during courtship. Eggs were laid under sheaths or in injuries to the bamboo surface. The main obstacle to oviposition and penetration of shoots appeared to be the hard culm sheaths.Thelarvae entered feeding substrates via injuries, holes created by other insects, or by squeezing in between culm sheaths and bamboo walls. Larvae of Gastrozonini and Rioxoptilona (Acanthonevrini) fed on living or dead bamboo shoots. Larvae of other Acanthonevrini developed in water-filled internode cavities, scraping particles from walls or collecting them from the water surface. Bamboo growth stages and degree of protection by culm sheaths were used to classify microhabitats. These determined to a large extent which guilds of flies could be found. While larvae of some bamboo tephritids destroyed thin bamboo shoots or branches, most acted as secondary pests and did not cause substantial economic losses.

Water in a polymeric electrolyte membrane: Sorption/desorption and freezing phenomena

Nafion® is a perfluorosulphonated polymer, widely used in Proton Exchange Membrane Fuel Cells. This polymer adopts a complex structural organisation resulting from the microsegregation between hydrophobic backbones and hydrophilic sulfonic acid groups. Upon hydration water-filled channels and cavities appear, in which the acidic protons are released to form a solution of hydronium ions in water embedded in the polymer matrix. Below 273K, a phenomenon of water sorption/desorption occurs, whose origin is still an open question. Performing neutron diffraction, we monitored the quantity of ice formed during the sorption/desorption as a function of temperature down to 180K. Upon cooling, we observe that ice forms outside of the membrane and crystallises in the hexagonal form (Ih). Simultaneously, the membrane shrinks and dehydrates, leading to an increase of the hydronium ions concentration inside the matrix. Reversibly, the ice melts and the membrane re-hydrates upon heating. A model of solution, whose freezing point varies with the hydronium concentration, is proposed to calculate the quantity of ice formed as a function of temperature. The quantitative agreement between the model and experimental data explains the smooth and reversible behaviour observed during the sorption or desorption of water, pointing out the origin of the phenomena. The proposed picture reconciles both confinement and entropic effects. Other examples of water filled electrolyte nano-structures are eventually discussed, in the context of clarifying the conditions for water transport at low temperature.

Deep icequakes: What happens at the base of Alpine glaciers?

AbstractBasal seismicity cannot be attributed exclusively to glacier stick‐slip motion. As shown by previous studies on temperate Alpine glaciers, there also exist basal seismic sources, which are not due to pure shear mechanisms. Their moment tensors have substantial, if not dominant, isotropic components. Based on first motion data of high‐quality seismic records from Gornergletscher and Triftgletscher, Switzerland, we argue that the observed isotropic components can be explained by tensile faulting. The implied coseismic volumetric change can be both positive (fracture opening) and negative (fracture collapse). We attribute these observations to hydraulic processes near water‐filled cavities, whose connectivity to the subglacial drainage system changes over time. Thus, our proposed icequake source mechanisms cannot be reconciled with pure shear sources at the glacier bed, which would be expected for basal stick‐slip motion. This sliding mode has recently been proposed as a “realitively common” mechanism, which can substantially enhance subglacial erosion. The existence of several seismic source mechanisms (tensile, shear, or some combination of the two) of basal icequakes implies that a solid understanding about the nature of these events is indispensible if conclusions about glacier sliding, subglacial erosion, and other basal processes are to be drawn from observed seismicity.

Dimensionless Correlating-Equations for Predicting the Optimal Tilting Angle of Water-Filled Square and Shallow Enclosures Differentially Heated at Sides

Laminar natural convection heat transfer inside water-filled, tilted square and shallow cavities heated at one side and cooled at the opposite side, is studied numerically. A computational code based on the SIMPLE-C algorithm is used to solve the system of the mass, momentum and energy transfer governing equations. Simulations are performed using the Rayleigh number based on the length of the heated and cooled sides, the height-to-width aspect ratio of the enclosure, and the positive tilting angle with respect to the gravity vector (which corresponds to configurations with the heated wall facing upwards), as independent variables. It is found that the heat transfer performance has a peak at an optimal tilting angle which increases as the Rayleigh number is decreased and the aspect ratio is increased. On the basis of the results obtained, a set of dimensionless correlations is developed.

The cardiac Na + -Ca 2+ exchanger has two cytoplasmic ion permeation pathways

The Na(+)-Ca(2+) exchanger (NCX) is a ubiquitously expressed plasma membrane protein. It plays a fundamental role in Ca(2+) homeostasis by moving Ca(2+) out of the cell using the electrochemical gradient of Na(+) as the driving force. Recent structural studies of a homologous archaebacterial exchanger, NCX_Mj, revealed its outward configuration with two potential ion permeation pathways exposed to the extracellular environment. Based on the symmetry of NCX_Mj structure, an atomic model of an inward-facing conformation was generated showing similar pathways but directed to the cytoplasm. The presence of these water-filled cavities has yet to be confirmed experimentally, and it is unknown if the mammalian exchanger adopts the same structure. In this study, we mutated multiple residues within transmembrane segments 2 and 7 of NCX1.1 (cardiac isoform) to cysteines, allowing us to investigate their sensitivity to membrane-impermeable sulfhydryl reagents as exchanger current block. By trapping NCX1.1 in the inward-facing configuration, we have mapped two differently sized cytoplasmic aqueous cavities, the access of which is modified during exchange. This data reveals movements of the protein associated with ion transport. Electrophysiological characterization shows that the conserved residues within transmembrane segments 2 and 7, coordinating Na(+) and Ca(2+) ions in NCX_Mj, play a fundamental role in NCX1.1. Our results suggest a similar architecture between the mammalian and archaebacterial exchangers.

Cryo-transmission electron tomography of native casein micelles from bovine milk

Caseins are the principal protein components in milk and an important ingredient in the food industry. In liquid milk, caseins are found as micelles of casein proteins and colloidal calcium nanoclusters. Casein micelles were isolated from raw skim milk by size exclusion chromatography and suspended in milk protein-free serum produced by ultrafiltration (molecular weight cut-off of 3 kDa) of raw skim milk. The micelles were imaged by cryo-electron microscopy and subjected to tomographic reconstruction methods to visualize the 3-dimensional and internal organization of native casein micelles. This provided new insights into the internal architecture of the casein micelle that had not been apparent from prior cryo-transmission electron microscopy studies. This analysis demonstrated the presence of water-filled cavities (∼20 to 30nm in diameter), channels (diameter greater than ∼5nm), and several hundred high-density nanoclusters (6 to 12nm in diameter) within the interior of the micelles. No spherical protein submicellar structures were observed.

Trace and minor element variations and sulfur isotopes in crystalline and colloform ZnS: Incorporation mechanisms and implications for their genesis

Various models have been proposed to explain the formation mechanism of colloform sphalerite, but the origin is still under debate. In order to decipher influences on trace element incorporation and sulfur isotope composition, crystalline and colloform sphalerite from the carbonate-hosted Mississippi-Valley Type (MVT) deposit near Wiesloch, SW Germany, were investigated and compared to sphalerite samples from 52 hydrothermal vein-type deposits in the Schwarzwald ore district, SW Germany to study the influence of different host rocks, formation mechanisms and fluid origin on trace element incorporation. Trace and minor element incorporation in sphalerite shows some correlation to their host rock and/or origin of fluid, gangue, paragenetic minerals and precipitation mechanisms (e.g., diagenetic processes, fluid cooling or fluid mixing). Furthermore, crystalline sphalerite is generally enriched in elements like Cd, Cu, Sb and Ag compared to colloform sphalerite that mainly incorporates elements like As, Pb and Tl. In addition, sulfur isotopes are characterized by positive values for crystalline and strongly negative values for colloform sphalerite. The combination of trace element contents, typical minerals associated with colloform sphalerite from Wiesloch, sulfur isotopes and thermodynamic considerations helped to evaluate the involvement of sulfate-reducing bacteria in water-filled karst cavities. Sulfate-reducing bacteria cause a sulfide-rich environment that leads in case of a metal-rich fluid supply to a sudden oversaturation of the fluid with respect to galena, sphalerite and pyrite. This, however, exactly coincides with the observed crystallization sequence of samples involving colloform sphalerite from the Wiesloch MVT deposit.

Packing of the Extracellular Domain Hydrophobic Core Has Evolved to Facilitate Pentameric Ligand-gated Ion Channel Function

Protein function depends on conformational flexibility and folding stability. Loose packing of hydrophobic cores is not infrequent in proteins, as the enhanced flexibility likely contributes to their biological function. Here, using experimental and computational approaches, we show that eukaryotic pentameric ligand-gated ion channels are characterized by loose packing of their extracellular domain β-sandwich cores, and that loose packing contributes to their ability to rapidly switch from closed to open channel states in the presence of ligand. Functional analyses of GABA(A) receptors show that increasing the β-core packing disrupted GABA-mediated currents, with impaired GABA efficacy and slowed GABA current activation and desensitization. We propose that loose packing of the hydrophobic β-core developed as an evolutionary strategy aimed to facilitate the allosteric mechanisms of eukaryotic pentameric ligand-gated ion channels.

Generation of Shear Waves from Explosions in Water-Filled Cavities

Abstract We analyze shear waves from a 27 kiloton nuclear explosion at 597 m depth in salt at Azgir, Kazakhstan, and four subsequent small nuclear explosions in the water-filled cavity of the original explosion. We use local recordings on a common set of radial and vertical component instruments to identify the source of these shear waves. These small explosions caused minimal damage to the cavity walls and so are similar in some important ways to cavity decoupled explosions; however, the signal size is comparable to a tamped explosion. The shear wave amplitudes relative to P generated by the water-filled cavity explosions are comparable to each other and to the tamped explosion. Comparison of the water-filled cavity explosions’ P spectra with a distinct bubble pulse peak and two distinct S phases, which lack that spectral peak, indicates that the S phases are not scattered from P . The initial S -waves’ travel-time curve, impulsiveness, and compactness are consistent with generation at or very near the source and are inconsistent with significant scattering much outside the source volume. We estimate that the S waves are consistent with an S -wave source at the same depth and with the same moment as the spherical component of the explosion source. Nonlinear axisymmetric numerical modeling of the nonlinear deformation of the salt medium indicates that neither fracturing nor asphericity of the nonlinear region outside of the cavity, for a variety of source asymmetries, would produce the observed shear waves for any of the water-filled cavity explosions. Oscillations of the cavity itself due to variations in the amplitude and timing of the pressure around the cavity wall can, however, produce shear waves at the frequencies observed. Both offset of the source and asphericity of the cavity lead to such variations in pressure.

Small, specialised and highly mobile? The tree-hole breeding frog, Phrynobatrachus guineensis, lacks fine-scale population structure

Data on population dynamics and distribution are of primary interest to biologists because they reveal information about the species' ecology and evolution and are thus essential for conservation efforts. Patchily distributed species are especially interesting for conservation studies, because of their sometimes very specific environmental requirements. An example of a highly specialised species is the leaf litter frog Phrynobatrachus guineensis. This small species (<20 mm) is short lived, presumably weakly mobile and highly specialised because it uses tree-holes and other small water-filled cavities with very particular abiotic and biotic characteristics for breeding. Previous field studies revealed that P. guineensis exhibited a clumped distribution in Taï National Park (TNP), Ivory Coast, suggesting that the park's population might be subdivided into several (sub)populations. We therefore investigated the population genetic structure of the park using four microsatellite loci, which are the first described microsatellite markers for any African anuran in general and for a species of the family Phrynobatrachidae in particular. In contrast to our expectations, we detected only a slightly significant genetic differentiation based on allele frequencies. We found no correlation between the geographic and genetic distances (isolation by distance) and Bayesian clustering revealed no genetic substructure. We did, however, detect small but significant genetic differentiation between subsequent seasons. The most probable explanation for the lack of population structure is that P. guineensis is more mobile than expected. Adults, most likely females but possibly also juveniles, are able to traverse matrix habitats in which no breeding activities were detected. The temporal genetic differentiation may be the consequence of genetic drift due to high mortality rates and/or non-random mating. Both explanations would be consistent with our field data.

Study of the gel films of Acetobacter Xylinum cellulose and its modified samples by 1H NMR cryoporometry and small-angle X-ray scattering

Gel films of Acetobacter Xylinum cellulose and its modified samples have been investigated by 1H nuclear magnetic resonance (NMR) cryoporometry and small-angle X-ray scattering. The joint use of these two methods made it possible to characterize the sizes of aqueous pores in gel films and estimate the sizes of structural inhomogeneities before and after the sorption of polyvinylpyrrolidone and Se0 nanoparticles (stabilized by polyvinylpyrrolidone) into the films. According to small-angle X-ray scattering data, the sizes of inhomogeneities in a gel film change only slightly upon the sorption of polyvinylpyrrolidone and nanoparticles. The impregnated material is sorbed into water-filled cavities that are present in the gel film. 1H NMR cryoporometry allowed us to reveal the details of changes in the sizes of small aqueous pores during modifications.

Transmembrane Segment II of NhaA Na+/H+ Antiporter Lines the Cation Passage, and Asp65 Is Critical for pH Activation of the Antiporter

The crystal structure of Escherichia coli NhaA determined at pH 4 has provided insights into the mechanism of activity of a pH-regulated Na+/H+ antiporter. However, because NhaA is activated at physiological pH (pH 5.5-8.5), many questions related to the active state of NhaA have remained elusive. Our experimental results at physiological pH and computational analyses reveal that amino acid residues in transmembrane segment II contribute to the cation pathway of NhaA and its pH regulation: 1) transmembrane segment II is a highly conserved helix and the conserved amino acid residues are located on one side of the helix facing either the cytoplasmic or periplasmic funnels of NhaA structure. 2) Cys replacements of the conserved residues and measuring their antiporter activity in everted membrane vesicles showed that D65C, L67C, E78C, and E82C increased the apparent K(m) to Na+ and Li+ and changed the pH response of the antiporter. 3) Introduced Cys replacements, L60C, N64C, F71C, F72C, and E78C, were significantly alkylated by [14C]N-ethylmaleimide implying the presence of water-filled cavities in NhaA. 4) Several Cys replacements were modified by MTSES and/or MTSET, membrane impermeant, negatively and positively charged reagents, respectively, that could reach Cys replacements from the periplasm only via water-filled funnel(s). Remarkably, the reactivity of D65C to MTSES increased with increasing pH and chemical modification by MTSES but not by MTSET, decreased the apparent K(m) of the antiporter at pH 7.5 (10-fold) but not at pH 8.5, implying the importance of Asp(65) negative charge for pH activation of the antiporter.

Osmotic cavitation of elastomeric intraocular lenses

In recent years, traditional rigid materials have been replaced with softer elastomers in intraocular lenses to minimize the size of the required surgical incision, thereby reducing patient recuperation time. However, water-filled cavities that may impact visual acuity are found in many of these new implants. We demonstrate that the cavitation observed in vivo can occur due to an osmotic pressure difference between the aqueous solution within the cavity and the external media in which the lens is immersed. By reducing the osmolarity of the external solution from 300 to 0mM, we observe an increase in cavity volume of almost a factor of 30. Further, we have developed a model for cavity growth assuming the controlling factor is diffusion of hydrophilic molecules from the polymer matrix into the cavity. We find that the experimental observations are consistent with the model and suggest that oligomeric species generated during polymerization are responsible for the observed cavitation.

A multi-analytical study of degradation of lignin in archaeological waterlogged wood

Historical or archaeological wooden objects are generally better conserved in wet environments than in other contexts. Nevertheless, anaerobic erosion bacteria can slowly degrade waterlogged wood, causing a loss of cellulose and hemicellulose and leading to the formation of water-filled cavities. During this process, lignin can also be altered. The result is a porous and fragile structure, poor in polysaccharides and mainly composed of residual lignin, which can easily collapse during drying and needs specific consolidation treatments. For this reason, the chemical characterization of archaeological lignin is of primary importance in the diagnosis and conservation of waterlogged wood artifacts. Current knowledge of the lignin degradation processes in historical and archaeological wood is extremely inadequate. In this study lignin extracted from archaeological waterlogged wood was examined using both Py-GC/MS, NMR spectroscopy and GPC analysis. The samples were collected from the Site of the Ancient Ships of San Rossore (Pisa, Italy), where since 1998 31 shipwrecks, dating from 2nd century BC to 5th century AD, have been discovered. The results, integrated by GPC analysis, highlight the depolymerization of lignin with cleavage of ether bonds, leading to an higher amount of free phenol units in the lignin from archaeological waterlogged wood, compared to sound lignin from reference wood of the same species.

Water-filled Cavities in the Voltage-Sensing Domain of a Potassium Channel Embedded in Lipid Bilayers

S1-S4 voltage-sensing domains (VSD) are conserved structural modules found in a large variety of voltage-sensitive membrane proteins. We investigated the topology, hydration properties and protein-lipid interactions of the VSD from KvAP in lipid membranes using neutron diffraction and solid-state NMR techniques. Neutron diffraction experiments demonstrate that the VSD changes the water distribution and profiles of POPC:POPG bilayers. To explore the topology of the VSD in the membrane, we uniformly deuterated the protein and incorporated it into lipid bilayers. A significant fraction of the protein scattering length density is observed in the head-group region of the bilayer. The protein density and water distribution within the bilayer largely overlap, suggesting a high degree of protein hydration within the membrane. Solid-state NMR magnetization transfer data are consistent with deep penetration of water molecules into bilayer-embedded VSDs. We hypothesize that VSDs have water filled cavities, which may be essential for VSD function.