Nanoscale uniformity of pore architecture in diatomaceous silica: a combined small and wide angle x-ray scattering study

Combined small and wide angle X‐ray scattering (SAXS and WAXS) analysis was applied to purified biogenic silica of cultured diatom frustules and of natural populations sampled on marine tidal flats. The overall WAXS patterns did not reveal crystalline phases (WAXS domain between 0.07 to 0.5 nm) in this biogenic silica, which is in line with previous reports on the amorphous character of the SiO₂ matrix of diatom frustules. One exception was the silica of the pennate species Cylindrotheca fusiformis Reimann et Lewin, which revealed wide peaks in the WAXS spectra. These peaks either indicate the presence of a yet unknown crystalline phase with a repetitive distance (d‐value ≈0.06 nm) or are caused by the ordering of the fibrous silica fragments; numerous girdle bands. The SAXS spectra revealed the size range of pores (diameter d between 3.0 and 65 nm), the presence of distinct pores (slope transitions), and structure factors (oscillation of the spectra). All slopes varied in the range of ?4.0 to ?2.5, with two clear common regions among species: d < 10 nm (slopes –4, denoted as region I and also called the Porod region), and 10.0 < d < 40.0 nm (slopes ?2.9 to ?3.8, denoted as region II). The existence of these common regions suggests the presence of comparable form (region I) and structure (region II) factors, respectively the shape of the primary building units of the silica and the geometry of the pores. Contrast variation experiments using dibromomethane to fill pores in the SiO₂ matrix showed that scattering was caused by pores rather than silica particles. Electron microscopic analysis confirmed the presence of circular, elliptical, and rectangular pores ranging in size from 3 to 65 nm, determining the structure factor. The fine architecture (length/width ratio of pore diameters) and distribution of the pores, however, seemed to be influenced by environmental factors, such as the salinity of and additions of AlCl₃ to the growth medium. The results indicate that diatoms deposit silica with pores <50 nm in size and are highly homologous with respect to geometry. Consequently, it is suggested that in diatoms, whether pennate or centric, the formation of silica at a nanoscale level is a uniform process.     

Range of Variation in the Somatic Infraciliature and Contractile Vacuole Pores of Tetrahymena pyriformis

SYNOPSIS. Meridian ranges and contractile vacuole pore patterns were determined for 36 strains of Tetrahymena pyriformis, including most of the “classic” amicronucleate and micronucleate strains used by many investigators, plus a dozen other strains not previously characterized with respect to these two morphological features. Uniform axenic culturing and staining techniques were employed. Meridian ranges and modes are analyzed with strain-by-strain comparisons to the reports of previous investigators. The overall inclusive range of the 36 strains was 15–25 meridians. Modes for individual strains varied from 16 to 23. Broader ranges and, especially, higher modes and higher limits are recorded than those reported by Corliss (1953) for strains grown in bacterized hay cultures. Two postoral meridians are characteristic, although a single individual having only one and a few having three postorals were observed. Three postorals were found only in those strains having the higher number of total meridians. A few individuals, showing an anterior half or a posterior half of a bipolar meridian missing, indicate a possible explanation of how a single dividing individual could produce a proter and an opisthe differing in the total number of meridians. Meridian ranges of individual strains do not overlap each other in all cases, but they do constitute a progressively overlapping series which does not warrant taxonomic separation of strains at either extreme from each other. Contractile vacuole pores varied from 1 to 3, with 2 pores (1 each in meridians 5 and 6) being characteristic of 22 of the strains. The 2-pore 6-7 pattern was modal for 8 of the strains. Presence of 3 pores (in 5, 6 and 7) was typical of only 2 strains, but 3 pores were found occasionally. Another pattern of 3 pores (in 6, 7 and 8) was observed occasionally in 10 strains. Double pores (in 6 and 7 or 7 and 8) and the triple pore patterns were observed only in the strains having the highest total number of meridians. These variations are not considered adequate justification for taxonomic separation. Strains Ki and Aq are affirmed to be T. pyriformis. Strains V¹ PP and V, formerly regarded as strains of T. vorax, are considered to be T. pyriformis, supporting the view of Shaw and Williams (1963).     

Nucleopores of the giant amoeba,Pelomyxa carolinensis

Summary As shown in tangential sections of Pelomyxa carolinensis nuclei, there are many pores, each with a surrounding annulus. Each annulus is composed of 8 subannuli or satellites, plus one to three central granules. Each satellite is an electron opaque mass (of much smaller opaque particulates) about 25 nm in diameter. The outer diameter of each annulus is about 115 nm while the inner, or pore diameter, is about 65 nm. The pores occur at distances averaging 185 nm from center to center. Frequently, delicate filaments connect adjacent satellites, and the central granule with the satellites. As seen in cross sections of the nucleus, nucleopores are formed by the fusion of the inner and outer nuclear envelope membranes. The pore appears as a gap, spanned by a delicate diaphragm anchored to the nuclear envelope where its two membranes are fused. Possible functions of the pore-annulus complexes are discussed.Work supported by the U.S. Atomic Energy Commission.The authors acknowledge the assistance of Miss Elaine C. Silver, General Electric Co., Philadelphia, and Dr. Robert Wolfgang of Argonne National Laboratory.     

Ionic channels formed byStaphylococcus aureus alpha-toxin: Voltage-dependent inhibition by divalent and trivalent cations

Summary The interaction ofStaphylococcus aureus -toxin with planar lipid membranes results in the formation of ionic channels whose conductance can be directly measured in voltage-clamp experiments. Single-channel conductance depends linearly on the solution conductivity suggesting that the pores are filled with aqueous solution; a rough diameter of 11.4±0.4 Å can be estimated for the pore. The conductance depends asymmetrically on voltage and it is slightly anion selective at pH 7.0, which implies that the channels are asymmetrically oriented into the bilayer and that ion motion is restricted at least in a region of the pore. The pores are usually open in a KCl solution but undergo a dose- and voltage-dependent inactivation in the presence of diand trivalent cations, which is mediated by open-closed fluctuations at the single-channel level. Hill plots indicate that each channel can bind two to three inactivating cations. The inhibiting efficiency follows the sequence Zn²⁺>Tb³⁺>Ca²⁺>Mg²⁺>Ba²⁺. suggesting that carboxyl groups of the protein may be involved in the binding step. A voltage-gated inactivation mechanism is proposed which involves the binding of two polyvalent cations to the channel, one in the open and one in the closed configuration, and which can explain voltage, dose and time dependence of the inactivation.     

Armillaria luteobubalina mycelium develops air pores that conduct oxygen to rhizomorph clusters

Armillaria luteobubalina produces air pores in culture. They consist of two parts: a basal region of tissue elevated to form a mound covered with a rind continuous with that of the colony, but perforated; and an apical region of long parallel hyphae, cemented together by scattered patches of extracellular material. This forms a hydrophobic structure that is elevated above the general level of the mycelial crust and does not easily become waterlogged. Air pores develop near the inoculum plug shortly after inoculation, arising directly from the mycelium, and rhizomorphs are initiated from them. The air pore contains a complex system of gas space connecting the atmosphere with the central canal of each rhizomorph. The tissue beneath the melanised colony crust also contains gas space, especially near air pores. This is also connected with the gas space of each rhizomorph and of each air pore. Measurements with oxygen electrodes show that air pores and their associated rhizomorphs conduct oxygen. The average oxygen conductance of a group of air pores with associated rhizomorphs, within agar blocks, but with rhizomorph apices cut off, was about 700 × 10⁻¹² m³ s⁻¹, equivalent to about 200 × 10⁻¹² m³ s⁻¹ for each air-pore. We conclude that the air pores conduct oxygen into the gas space below the pigmented mycelium of the colony, where the rhizomorphs - which also conduct oxygen - originate. A. luteobubalina thus has a complex aerating system which allows efficient diffusion of oxygen into rhizomorphs, and this is likely to facilitate extension of inoculum into low-oxygen environments.     

Blocking effect of benzene-like fluid transport in nanoscale block-pores

Abstract

The flux through nanoscale pore is one of the key quantities in many processes including membrane applications and fluid separation. Whereas many efforts have been dedicated to the investigation of the fluid flux in nano-channels, the fluid transport behaviours in the block-pores, which contain distinct parts with different geometries or interactions with fluid, are still poorly understood. In this work, by combining both non-equilibrium dynamics simulation and density functional theory, we developed an efficient method for investigating the fluid flux in the block-pores, with which the fluxes of benzene in graphene block slit pores containing a hydrophobic and a hydrophilic region are thereafter investigated. We demonstrate that a region with a stronger interaction with fluid generates a bottleneck for the fluid flow, which greatly suppresses the flux in the pore even though there is no geometrical variation. By tuning the fluid-substrate interaction, the flux inside can be controlled. This study gives clues for the practical application of membrane design.     

Annulate lamellae and single pore complexes in normal, SV40-transformed and tumor cells in vitro : A semiquantitative analysis

The frequency with which annulate lamellae (AL) and single cytoplasmic pore complexes appeared in selected groups (normal cell lines, SV40-, Rous sarcoma-, and 6/94 virus-infected cell lines, SV40-transformed cell lines, and both human and mouse tumor cell lines) was observed during standard electron microscopy techniques.All cell lines tested contained single pore complexes in the rough endoplasmic reticulum (RER). Further, it was found that at early passages WI38 cells have more single pore complexes than at later passages. In SV40-infected CV1 cells, the number of pore complexes increased during the infectious cycle, which indicates that the formation of these complexes may not be dependent on nuclear membrane remnants from mitosis. No pore complexes were found during mitosis, i.e., the formation of cytoplasmic pore complexes is by new synthesis or reformation. We speculate that all proliferating cells and germ cells generate pore complexes (similar to nuclear pore complexes) in their cytoplasmic membrane systems. With respect to annulate lamellae, it was found that:

1. (1) In cell lines where AL could be observed, not all cells exhibited AL stacks.

2. (2) “Normal” cells—such as human fetal lung (WI38) and monkey kidney (CV1) cells, mouse macrophages and fibroblasts, and cells from chicken explants—did not have AL stacks, but AL stacks could be induced by exposure to vinblastine.

3. (3) SV40-infected cells did not generate stacks of AL in the cell lines tested.

4. (4) SV40-transformed cells had AL stacks in a few cells or in many, depending on the cell line.

5. (5) The introduction of the SV40-containing chromosome 7 of human transformed LN-SV cells into a cell type that did not express AL formation caused it to form AL.

6. (6) AL were present up to 48 h after enucleation of mouse L cells, that is until the cells show signs of degeneration (which indicates that cellular upkeep of AL may not be dependent on the presence of the nucleus, as was suggested by the simultaneous disappearance of AL at mitosis).

7. (7) All tumor cell lines investigated were found to have AL stacks.

     

THE CELL WALL OF COSMARIUM BOTRYTIS12

The cell wall of Cosmarium botrytis was studied through the use of the freeze-etch technique. The cell wall consists of many thin layers. Fracturing along one layer reveals the positioning of the wall sculpturing, wall pores, and wall microfibrils. The individual microfibrils are grouped together in bands of parallel oriented fibrils. The different bands of parallel microfibrils were apparently arranged at random angles with regard to each other. Small particles may also be present in the cell walls. The cell wall pore unit of Cosmarium botrytis was studied through the use of scanning, freeze-etching, and thin sectioning techniques. The pore sheaths, on the outside of the cell wall, form a collar around the mouth of each pore. The pore sheath is composed of needle-like fibrils radiating outward from the pore. A pore channel traverses the cell wall and leads to a complex pore bulb region between the cell wall and the plasmalemma. The pore bulb contains many small fibrils which radiate toward the plasmalemma from a number of net-like fibril layers which in turn merge into a very electron dense region near the base of the pore.     

Skeletal morphogenesis in some living collosphaerid Radiolaria

Two major patterns of shell morphogenesis occurring in varying proportions among species were identified by examining skeletons from five species of living collosphaerid, colonial Radiolaria: Collosphaera huxleyi, Acrosphaera cyrtodon, Acrosphaera spinosa, Siphonosphaera tubulosa and Siphonosphaera socialis. Skeletons possessing large open-lattice structures characterized by ellipsoidal to polygonal pores separated by narrow bars are produced by repeated subdivision of large pores into smaller pores. A bridge-like bar grows across the pore and subdivides it into two or more smaller pores. In skeletons with small, nearly circular pores and occasionally elongated tubular rims, the pores appear to be developed by rim thickening. Silica is deposited at the perimeter of the pore, thus decreasing its diameter and increasing the bar width between pores. In some species exhibiting intermediate types of skeletal morphology, there appears to be varying amounts of both bridge growth and rim growth. These data are used to explore possible phylogenetic pathways for a variety of collosphaerid species and to elucidate the processes of skeletal deposition in Radiolaria.     

On the existence of a hysteresis loop in open and closed end pores

We have studied the adsorption of argon at 87 K in slit pores of finite length with a smooth graphitic potential, open at both ends or closed at one end. Simulations were carried out using conventional GCMC (grand canonical Monte Carlo) or kMC (kinetic Monte Carlo) in the canonical ensemble with extremely long Markov chain, of at least 2 × 10⁸ configurations; selected simulations with much longer Markov chains do not show any change in the results. When the pore width is in the micropore range (0.65 nm), type I isotherms are obtained for both pore models and for both simulation methods. However, wider pores (1, 2 and 3 nm in width) all exhibit hysteresis loops in the GCMC simulations, while in the canonical ensemble simulations, the isotherms pass through a sigmoid van der Waals type loop in the transition region. This loop locates the true equilibrium transition. For the pores with one closed end, this transition is close to, or coincides with, the adsorption branch of the GCMC hysteresis loop, but for the open-ended pores, it is more closely associated with the desorption branch. In a separate study of adsorption hysteresis in an infinitely long slit pore, using both simulation techniques, the van der Waals loop follows the adsorption branch of the GCMC isotherm to the transition, then reverts to a long vertical section that falls midway between the two hysteresis branches and finally moves to the desorption transition close to the evaporation pressure. An examination of molecular distributions inside the pores reveals two coexisting phases in the canonical simulations, whereas in the grand canonical simulations, the molecules are uniformly distributed along the length of the pores.     

The correct position of flagellar insertion in Prorocentrum and description of Prorocentrum rhathymum sp. nov. (Pyrrhophyta)

For three Prorocentrum species, P. minimum (Pavillard) Schiller,P. rhathymum sp. nov., and P. triestinum Schiller, we have foundthat both flagella emerge from a single large pore. This arrangementis contrary to previous observations which suggested they arosefrom separate pores. Prorocentrum triestinum has only one anteriorpore, whereas P. minimum and P. rhathymum sp. nov. have an additionalauxiliary pore. The pores in all three species are formed bya series of small plates. The left and right valves on eachspecies can be identified by ornamentation unique to each valve.Prorocentrum rhathymum sp. nov., isolated from the planktonof Cinnamon Bay, Virgin Islands, is described. ² The Biological Laboratories, Harvard University, Cambridge,Massachusetts 02138 ³ Department of Botany, Duke University, Durham, North Carolina27706     

GCEMC Simulations of “Swiss Cheese” Ion Exchange Membranes in Dilute Solutions of Primitive Model 1:1 Electrolytes with Different Sizes of Ions or 2:1 Electrolytes with Different Bjerrum Parameters

Abstract

Monte Carlo simulations using a Markov process corresponding to a (generalized) Grand Canonical Ensemble have been performed for a number of spherical micropores in equilibrium with dilute external bulk solutions of primitive model electrolytes. Dilute solutions of 1:1 electrolytes with a Bjerrum parameter B = 1.546 with cations three times larger than the anions have been simulated. Also, dilute solutions of 2:1 electrolytes with ions of equal size and reduced Bjerrum parameters B_r = 1.546 and 3 have been simulated. The pores are primitive pores with hard walls and the same dielectric permittivity in the wall and in the pore solution. They range from a pore radius = 5 times the mean ionic diameter to 35 times this diameter, and they carry a fixed charge equal to + 5,0 and ?5 elementary charges. The fixed charge is modelled as smoothly distributed on the pore-wall interface. In addition to the electric potential of the interfacial charge and the electric potential of the spherical double layer, a potential Δ between the pore solution and the bulk solution may be deliberately added. For single pores we may take Δ = 0, but then the pore is generally not electroneutral. In a “Swiss cheese” membrane with a lot of (equally sized) pores, the membrane phase has to approach electroneutrality for growing size of the phase. This is approximated by means of a membrane generated potential Δ in each pore (from the electrostatic interactions with the other pores). The potential A so chosen to obtain electroneutrality is the GCEMC Donnan potential. These non-ideal Donnan potentials are compared to the ideal values (with activity coefficients equal to zero). From the mean occupation numbers of cations and anions in the pores, the average pore values of the mean ionic and the single ionic activity coefficients of the ions are calculated. These are very dependent on pore sizes and on the potential in the pore. The excess energy and the electrostatic Helmholtz free energy of the ions in the pores are also simulated directly. The electrostatic entropy is found as the difference.     

Brownian dynamics study of flux ratios in sodium channels

Measurements of unidirectional fluxes in ion channels provide one of the experimental methods for studying the steps involved in ion permeation in biological pores. Conventionally, the number of ions in the pore is inferred by fitting the ratio of inward and outward currents to an exponential function with an adjustable parameter known as the flux ratio exponent. Here we investigate the relationship between the number of ions in the pore and the flux ratio exponent in a model sodium channel under a range of conditions. Brownian dynamics simulations enable us to count the precise number of ions in the channel and at the same time measure the currents flowing across the pore in both directions. We show here that the values of the flux ratio exponent n′ ranges between 1 and 3 and is highly dependent on the ionic concentrations in which measurements are made. This is a consequence of the fact that both inward and outward currents are susceptible to saturation with increasing concentration. These results indicate that measurements of the flux ratio exponent cannot be directly related to the number of ions in the pore and that interpretation of such experimental measurements requires careful consideration of the conditions in which the study is made.     

Effects of Spontaneous Bilayer Curvature on Influenza Virus–mediated Fusion Pores

Cells expressing the hemagglutinin protein of influenza virus were fused to planar bilayer membranes containing the fluorescent lipid probes octadecylrhodamine (R18) or indocarbocyanine (DiI) to investigate whether spontaneous curvature of each monolayer of a target membrane affects the growth of fusion pores. R18 and DiI lowered the transition temperatures for formation of an inverted hexagonal phase, indicating that these probes facilitate the formation of negative curvature structures. The probes are known to translocate from one monolayer of a bilayer membrane to the other in a voltage-dependent manner. The spontaneous curvature of the cis monolayer (facing the cells) or the trans monolayer could therefore be made more negative through control of the polarity of voltage across the planar membrane. Electrical admittance measurements showed that the open times of flickering fusion pores were shorter when probes were in trans monolayers and longer when in cis monolayers compared with times when probe was symmetrically distributed. Open times were the same for probe symmetrically distributed as when probes were not present. Thus, open times were a function of the asymmetry of the spontaneous curvature between the trans and cis monolayers. Enriching the cis monolayer with a negative curvature probe reduced the probability that a small pore would fully enlarge, whereas enriching the trans monolayer promoted enlargement. Lysophosphatidylcholine has positive spontaneous curvature and does not translocate. When lysophosphatidylcholine was placed in trans leaflets of planar membranes, closing of fusion pores was rare. The effects of the negative and positive spontaneous curvature probes do not support the hypothesis that a flickering pore closes from an open state within a hemifusion diaphragm (essentially a “flat” structure). Rather, such effects support the hypothesis that the membrane surrounding the open pore forms a three-dimensional hourglass shape from which the pore flickers shut.     

Development of ordered arrays of cell wall pores in desmids : a nucleation model

Two-dimensional arrays of pores on cell walls of Micrasterias rotata and Cosmarium botrytis show a high degree of order. We review various measures of order and choose to analyze the data in terms of Clark & Evans' (1954) R parameter. The experimental R values are high, but not high enough to demand the precise ordering abilities of a morphogen wave mechanism. Following Claxton (1964), we show that the patterns are compatible with random and continuous nucleation of pore initials, each of which inactivates a circular inhibitory field around it against further nucleation. We discuss several versions of a model in which inhibition is produced by depletion of a substance, needed both for growth and for nucleation, below a critical concentration for the latter. This critical behaviour is probably analogous to the critical micelle concentration in detergent solutions, not the critical supersaturation of classical nucleation theory in phase transitions. The growing nuclei must rapidly reach constant radius. The size of the inhibitory fields requires diffusion to be in two (not three) dimensions.     

Optimal pursuit times: How long should predators pursue their prey?

Data suggest that the length of time that a predator pursues a given prey is both variable and adjustable. We present an extension of the optimal diet model that incorporates adjustable pursuit times to predict how long a predator should pursue their prey. The model makes three significant contributions.

1. 1. When the density of good prey is increased, poor prey should gradually disappear from the diet.

2. 2. Depending on how the encounter rates with prey are varied, the model generates patterns of frequency-dependent and inverse frequency-dependent foraging.

3. 3. The density of poor prey can influence the proportion captured of more valuable prey.

     

The effects of heparin on endogenous DNA polymerase activity of rat liver nuclei and chromatin fractions

1. 1. Heparin activates endogenous DNA polymerase activity in isolated rat hepatic nuclei to a synthesis rate two to three times the control values, when added in amounts as small as 10% of total nuclear DNA.

2. 2. Cations such as polylysine, polyornithine and unfractionated histones form insoluble complexes with heparin and reverse its effect in either order of addition.

3. 3. Autoradiography demonstrates many apparent new sites of DNA synthesis in heparin-treated nuclei, both in previously inactive and in previously active nuclei.

4. 4. Electron microscopy shows a dramatic change in the chromatin pattern upon treatment with heparin; fiber diameters are significantly decreased, probably indicating loss of supercoiling.

5. 5. The response to heparin of the endogenous polymerase activity in three chromatin fractions is examined. Two of the three fractions show patterns similar to whole nuclei; the third, a high specific activity fraction, has a distinctively different pattern of response to heparin.

6. 6. The kinetic data combined with the behavior of the high specific activity chromatin fraction indicate that the heparin effect on endogenous DNA synthesis may have more than one component.

     

Minimum Membrane Bending Energies of Fusion Pores

Membranes fuse by forming highly curved intermediates, culminating in structures described as fusion pores. These hourglass-like figures that join two fusing membranes have high bending energies, which can be estimated using continuum elasticity models. Fusion pore bending energies depend strongly on shape, and the present study developed a method for determining the shape that minimizes bending energy. This was first applied to a fusion pore modeled as a single surface and then extended to a more realistic model treating a bilayer as two monolayers. For the two-monolayer model, fusion pores were found to have metastable states with energy minima at particular values of the pore diameter and bilayer separation. Fusion pore energies were relatively insensitive to membrane thickness but highly sensitive to spontaneous curvature and membrane asymmetry. With symmetrical bilayers and monolayer spontaneous curvatures of ?0.1 nm^?1 (a typical value) separated by 6 nm (closest distance determined by repulsive hydration forces), fusion pore formation required 43–65 kT. The pore radius of ~2.25 nm fell within the range estimated from conductance measurements. With bilayer separation >6 nm, fusion pore formation required less energy, suggesting that protein scaffolds can promote fusion by bending membranes toward one another. With nonzero spontaneous monolayer curvature, the shape that minimized the energy change during fusion pore formation differed from the shape that minimized its energy after it formed. Thus, a nascent fusion pore will relax spontaneously to a new shape, consistent with the experimentally observed expansion of nascent fusion pores during viral fusion.