Pore dimensions for accumulating biomass. II. Microbes that form spores and exhibit mycelial growth

The relationship between the dimensions of a spore and the accumulation of that microbe in a porous, inorganic structure has been determined. In order to achieve high accumulation of mycelial growth, at least 70% of the pores of an inorganic carrier should have pore diameters in the range of one times the smallest dimension of the fungal spore but less than about 16 times the largest dimension of that spore. This relationship was established by varying the physical parameters of the carriers as well as their chemical composition.     

The influence of red cell mechanical properties on flow through single capillary-sized pores

The resistive pulse technique was used to study the influence of specific mechanical properties of the red cell on its ability to enter and flow through single capillary-sized pores with diameters of 3.6, 5.0 and 6.3 micron and lengths of 11 micron. A two-fold increase in membrane shear elasticity resulted in a 40 percent increase in the cell's transit time through a 3.6 micron pore but produced no change in transit time through a 6.3 micron pore. A two-fold increase in membrane shear viscosity produced a 40 percent increase in transit time through the 3.6 micron pore and small but significant increases in transit times through the larger pores. Osmotically dehydrated cells showed no increase in transit time through a 6.3 micron pore, but showed increases in transit times of 50 to 70 percent through 5.0 and 3.6 micron pores. Dense red cells showed increased transit times through both 5.0 micron and 6.0 micron pores. These results indicate that for cells with normal geometric properties, the membrane's shear viscosity and elasticity only influence the cell's transit through pores of 5 micron or less in diameter. However, alterations in the cell's geometric properties can extend the influence of membrane shear properties to larger diameter pores.     

Membrane mechanics can account for fusion pore dilation in stages.

Once formed, fusion pores rapidly enlarge to semi-stable conductance values. The membranes lining the fusion pore are continuous bilayer structures, so variations of conductance in time reflect bending and stretching of membranes. We therefore modeled the evolution of fusion pores using the theory of the mechanics of deforming homogeneous membranes. We calculated the changes in length and width of theoretical fusion pores according to standard dynamical equations of motion. Theoretical fusion pores quickly achieve semi-stable dimensions, which correspond to energy minima located in a canyon between energy barriers. The height of the barrier preventing pore expansion diminishes along the dimensions of length and width. The bottom of the canyon slopes gently downward along increasing length. As a consequence, theoretical fusion pores slowly lengthen and widen as the dimensions migrate along the bottom of the canyon, until the barrier vanishes and the pore rapidly enlarges. The dynamics of growth is sensitive to tension, spontaneous curvature, bending elasticity, and mobilities. This sensitivity can account for the quantitative differences in pore evolution observed in two experimental systems: HA-expressing cells fusing to planar bilayer membranes and beige mouse mast cell degranulation. We conclude that the mechanics of membranes could cause the phenomenon of stagewise growth of fusion pores.     

DIFFUSION THROUGH STOMATES

Ting, Irwin P., and Walter E. Loomis. (Iowa State U., Ames.) Diffusion through stomates. Amer. Jour. Bot. 50(9): 866–872. Illus. 1963.—It is shown that the rule that diffusion through isolated, small pores is proportional to the diameter rather than the area of the pores is valid for pores of diameters as small as 20 μ, and that the curve extends to the origin at zero diameters, indicating that the law is effective throughout the range of stomatal sizes. Suggestions that an elliptical pore will be relatively more effective in diffusion than a circular one and that diffusion is concentrated at the periphery of the pore are not supported by experimental evidence and are physically improbable. Brown and Escombe's conclusion that there is no interference in the diffusion through the individual pores of a multiperforate membrane if the pores are spaced 10 diameters apart is not valid for diffusion through the stomates of a leaf. With pores of 200 μ and less spaced 10 diameters apart, interference increases rapidly with a smaller size and larger number of pores. As a result, the diffusion through a membrane with pores 19 μ in diameter and 190 μ apart was the same as that through a membrane with pores 132 μ in diameter and 1.32 mm apart, although the calculated capacity of the first membrane was 7 times that of the second. The diffusion of water vapor through multiperforate membranes with pores spaced 10 diameters apart has an apparent maximum of 65–70% of the diffusion through an open tube. Calculations of the effect of partial closing of stomates, using Verduin's equation for interference between pores, indicate that the theoretical diffusion capacity of 10 μ stomates spaced at 10 diameters would be increased several times by closing to an average diameter of 5 μ. This increase illustrates the dominant effect of interference in diffusion through small, closely spaced pores. Calculated diffusion through these stomates would not be decreased until they were more than 95% closed. It is concluded that stomatal opening will have no important effect on diffusion from or into a leaf until the stomates are essentially closed.     

An investigation of particle flow through capillary models with the resistive pulse technique

The use of the resistive pulse technique for the measurement of microsphere and red cell transit times through single-pore "Nuclepore" membranes (with pore diameters of 3.5 to 7.0 microns and pore length of approximately 11 microns) is described. The investigation of the fluid mechanics and electrical characteristics of the experimental system provides methods for the determination of particle and cell size, and entrance and transit times. Experimental measurement of the position dependent velocity of spherical particles through the pore shows close agreement with theoretical models. Red cell size and transit time through different sized pores at physiological shear stresses is also measured.     

The permeability of the wall fabric of Escherichia coli and Bacillus subtilis.

To study the overall structure of the peptidoglycan fabric of the sacculi of gram-negative and gram-positive walls, actively growing cultures of Escherichia coli and Bacillus subtilis were treated with boiling sodium dodecyl sulfate solutions. The sacculi were then treated with enzymes to eliminate proteins and nucleic acids. These intact saccoli were probed with fluorescein-labeled dextrans with a range of known molecular weights. The penetration of the probes could be monitored by the negative-staining appearance in the fluorescence microscope. At several chosen times, the molecular weight fraction that allowed barely observable entry of the fluorescein-labeled probe and the molecular weight fraction that penetrated to achieve almost, but not quite, the concentration of probe in the solution external to the sacculi were determined. From three pairs of times and molecular weights that met one or the other of these two criteria, the effective pore size could be calculated. The minimum size of protein molecule that could diffuse through the pores was also calculated. Two mathematical models, which gave essentially the same results, were used to interpret the experimental data: one for the permeation of random coils through a surface containing holes and the other for rigid spheres diffusing through water-filled cylindrical pores. The mean estimate of the effective hole radius in walls from E. coli is 2.06 nm, and that of the effective hole size in walls from B. subtilis is 2.12 nm. These results are supported by experiments in which the loss of preloaded cells was monitored. Various fluorescein-labeled dextran samples were mixed with samples of intact cell walls, held for a long time, and then diluted. The efflux of the dextrans was monitored. Neither large nor small dextrans stained under these conditions. Only with dextran samples of a sufficiently small size were the sacculi filled during the preincubation period, and only with the largest of these could the probe not escape quickly. From the pore (or mesh) size, it can be concluded that the wall fabric of both organisms has few imperfections and that the major passageway is through the smallest possible pore, or "tessera," formed by the maximal cross-linking of the peptides from glycan chain to glycan chain compatible with the degree of rotational flexibility of the chains of repeating disaccharides of N-acetyl muramic acid and N-acetyl glucosamine. A tessera is composed of two chains of eight saccharides cross-linked by two octapeptides. The size of a globular hydrophilic molecule, if it did not bind to wall components, that could pass freely through the meshwork of an unstretched sacculus of either organism is roughly 25 kDa. We stress that this is only a rough estimate, and it may be possible for proteins of less than 50 kDa to pass through the native wall during normal growth conditions.     

Immobilized microbes and a high-rate, continuous waste processor for the production of high Btu gas and the reduction of pollutants

Microbes capable of degrading organic wastes (sewage) are densely packed (immobilized) within the pores of controlled-pore ceramics. When the ceramic displays the optimum pore range for the reproduction of these microbes, the minimum volume for a very efficient reactor is required. A two-stage, anaerobic, immobilized microbe reactor has been designed, and laboratoryscale units have been constructed. A few of these units have been operated continuously for two years. These reactors were designed for the efficent conversion of carbon to methane in biodegradable molecules and for the effective transfer of that gas. The reactors were operated at 20, 30, and 40 degrees C at residence times of 2-5.5 h. The total chemical oxygen demand (COD) of the sewage varied from 800-2600 mg/L. The resulting gas contained greater than 90% methane and less than 5% CO(2). Approximately 32-54% of the influent total carbon was recovered as methane. The reduction in COD varied from 63 to 89%.     

Location of a constriction in the lumen of a transmembrane pore by targeted covalent attachment of polymer molecules

Few methods exist for obtaining the internal dimensions of transmembrane pores for which 3-D structures are lacking or for showing that structures determined by crystallography reflect the internal dimensions of pores in lipid bilayers. Several approaches, involving polymer penetration and transport, have revealed limiting diameters for various pores. But, in general, these approaches do not indicate the locations of constrictions in the channel lumen. Here, we combine cysteine mutagenesis and chemical modification with sulfhydryl-reactive polymers to locate the constriction in the lumen of the staphylococcal alpha-hemolysin pore, a model protein of known structure. The rates of reaction of each of four polymeric reagents (MePEG-OPSS) of different masses towards individual single cysteine mutants, comprising a set with cysteines distributed over the length of the lumen of the pore, were determined by macroscopic current recording. The rates for the three larger polymers (1.8, 2.5, and 5.0 kD) were normalized with respect to the rates of reaction with a 1.0-kD polymer for each of the seven positions in the lumen. The rate of reaction of the 5.0-kD polymer dropped dramatically at the centrally located Cys-111 residue and positions distal to Cys-111, whether the reagent was applied from the trans or the cis side of the bilayer. This semi-quantitative analysis sufficed to demonstrate that a constriction is located at the midpoint of the pore lumen, as predicted by the crystal structure, and although the constriction allows a 2.5-kD polymer to pass, transport of a 5.0-kD molecule is greatly restricted. In addition, PEG chains gave greater reductions in pore conductance when covalently attached to the narrower regions of the lumen, permitting further definition of the interior of the pore. The procedures described here should be applicable to other pores and to related structures such as the vestibules of ion channels.     

Reconstruction and morphometry of silkmoth olfactory hairs: A comparative study of sensilla trichodea on the antennae of male Antheraea polyphemus and Antheraea pernyi (Insecta,Lepidoptera)

Summary Olfactory trichoid hairs on the antennae of male Antheraea silkmoths were reconstructed with respect to the following parameters: number, shape, course, and dimensions of outer dendritic segments as well as the numbers of their microtubules; inner and outer dimensions of the cuticular hair shafts; and number and distribution of pores and pore tubules in the hair walls. The smallest distances between dendritic membranes and inner hair surfaces were determined with respect to the possibility of pore tubule contacts. It was shown that most hairs contain one thick and one, or frequently two, thin dendrites. The number of microtubules in the dendrites is correlated with dendrite diameter, which decreases towards the hair tip. The dendrites form numerous swellings and constrictions: this beading occurs especially along the thin dendrites. The dendrites do not run straight, but rather follow a sinuous course in the hairs. The density of wall pores is lowest in the basal region of the hairs. Only in relatively few places do the dendritic membranes get near enough the hair walls to come into the probable range of the pore tubules. In the sensilla trichodea of A. polyphemus, the hairs as well as the dendrites have markedly smaller diameters than in A. pernyi.     

Lipid II-mediated pore formation by the peptide antibiotic nisin: a black lipid membrane study

The antibiotic peptide nisin is the first known lantibiotic that uses a docking molecule within the bacterial cytoplasmic membrane for pore formation. Through specific interaction with the cell wall precursor lipid II, nisin forms defined pores which are stable for seconds and have pore diameters of 2 to 2.5 nm.     

Comparison of transient and successful fusion pores connecting influenza hemagglutinin expressing cells to planar membranes

Time-resolved admittance measurements were used to investigate the evolution of fusion pores formed between cells expressing influenza virus hemagglutinin (HA) and planar bilayer membranes. The majority of fusion pores opened in a stepwise fashion to semistable conductance levels of several nS. About 20% of the pores had measurable rise times to nS conductances; some of these opened to conductances of approximately 500 pS where they briefly lingered before opening further to semistable conductances. The fall times of closing were statistically similar to the rise times of opening. All fusion pores exhibited semistable values of conductance, varying from approximately 2-20 nS; they would then either close or fully open to conductances on the order of 1 microS. The majority of pores closed; approximately 10% fully opened. Once within the semistable stage, all fusion pores, even those that eventually closed, tended to grow. Statistically, however, before closing, transient fusion pores ceased to grow and reversed their conductance pattern: conductances decreased with a measurable time course until a final drop to closure. In contrast, pore enlargement to the fully open state tended to occur from the largest conductance values attained during a pore's semistable stage. This final enlargement was characterized by a stepwise increase in conductance. The density of HA on the cell surface did not strongly affect pore dynamics. But increased proteolytic treatment of cell surfaces did lead to faster growth within the semistable range. Transient pores and pores that fully opened had indistinguishable initial conductances and statistically identical time courses of early growth, suggesting they were the same upon formation. We suggest that transient and fully open pores evolved from common structures with stochastic factors determining their fate.     

The weapon potential of a microbe

The designation of a microbe as a potential biological weapon poses the vexing question of how such a decision is made given the many pathogenic microbes that cause disease. Analysis of the properties of microbes that are currently considered biological weapons against humans revealed no obvious relationship to virulence, except that all are pathogenic for humans. Notably, the weapon potential of a microbe rather than its pathogenic properties or virulence appeared to be the major consideration when categorizing certain agents as biological weapons. In an effort to standardize the assessment of the risk that is posed by microbes as biological warfare agents using the basic principles of microbial communicability (defined here as a parameter of transmission) and virulence, a simple formula is proposed for estimating the weapon potential of a microbe.     

Passage of inulin and p-aminohippuric acid through artificial membranes: implications for measurement of renal function.

Diffusion of inulin and p-aminohippuric acid (PAH) in combined aqueous solution through artificial membranes was measured at room temperature and atmospheric pressure. The membranes had pore diameters of 26, 50, 100, 200, 250, 350, 510 or 990 A. The diffusion of PAH was only restricted with a pore size of 26 A, but inulin diffusion was restricted at 100 A. When diffusion of both solutes was unrestricted (pore diameter greater than or equal to 200 A), PAH diffused four times faster than inulin, and in restricted situations this ratio was even greater. The results of these diffusion studies allow the major and minor molecular dimensions of the solutes to be estimated. Filtration of the two solutes was studied in slowly flowing situations and also with increased temperature and pressure. Pore sizes required for unrestricted filtration were the same as for unrestricted diffusion but the passage ratio was reduced from 4 to 2. These results suggest strongly that two conditions are necessary if the glomerular filtration rate (GFR) of inulin is to equal the true GFR: membrane pore size must be at least 200 A and passage through the membranes must be by bulk transport.     

Protein-sodium dodecyl sulfate complexes: determination of molecular weight, size and shape by controlled pore glass chromatography

The peak position vs log molecular weight curves of protein-SDS complexes chromatographed on controlled pore glass of narrow pore size distribution is linear over a molecular weight range of 17,000–385,000. A glass with a pore size of approximately 500 Å allows the inclusion of all complexes in this range. Peak position curves on glasses with broad pore distributions show decreased resolution and deviate from linearity at low elution coefficients.Exclusion size analysis of the elution coefficients of individual complexes from different columns with pore diameters ranging from 197 to 650 Å gives from 120 to 423 Å as their longest dimension. Assuming constant hydration and SDS-to-protein ration, the found dimension suggests the shape of a football, rather than a sphere or rigid rod.     

Temperature effect on the sulfur isotope fractionation during sulfate reduction by two strains of the hyperthermophilic Archaeoglobus fulgidus

Sulfur isotope fractionation during dissimilatory sulfate reduction by two strains of the thermophilic archaeon Archaeoglobus fulgidus (strains VC‐16 and Z) was explored over the entire temperature range of growth. The optimal cell‐specific sulfate reduction rate (14 fmol cell^?1 h^?1) was found at 82–84°C but growth was measured as low as 54°C. The fractionation ranged between 0.52‰ and 27‰, with largest fractionations were found at intermediate temperatures and the smallest fractionations at the lowest and highest temperatures. There was an inverse relationship between the cell‐specific sulfate reduction rate and fractionation, and the cell‐specific rate was a good indicator of the expected fractionations regardless of whether temperature or substrate concentrations controlled the rate. Comparison of the fractionation trend found in this study with similar measurements for seven other sulfate‐reducers showed that sulfate‐reducing organisms respond to temperature in three different ways and this correlated with their maximum fractionation value, but not with the cell‐specific sulfate reduction rate. A sulfur isotope model was used to reproduce the observed variation of fractionation with temperature. This approach predicted the rate of internal sulfur transformations as having the major influence on the observed fractionations in the intermediate temperature range, whereas the exchange of sulfate across the cell membrane controls fractionation at low and high temperatures.     

Molecular simulation of size-selective gas adsorption in idealised carbon nanotubes

Molecular simulations were used to examine the adsorption of diatomic molecules (nitrogen and oxygen) and similarly sized gases (argon and methane) in pores with van der Waals diameters similar in size to the gas diameters. Idealised carbon nanotubes were used to model generic pores, to better understand the effect of pore diameter on guest adsorption in the absence of defects, specific adsorption sites, or variations in pore diameter that often complicate studies of gas adsorption in other porous materials. Molecular dynamics simulations of open nanotubes show that argon and methane are able to enter tubes whose diameters are slightly smaller than the gas diameters. Diatomic gases are able to enter tubes that are significantly smaller than their kinetic diameters with the molecular axis aligned parallel to the nanotube. The results indicate that size-selective adsorption of these gases is theoretically possible, although differences in pore diameters of only a few tenths of an Angstrom are required. Grand canonical Monte Carlo simulations of a 3.38 Å nanotube indicate significant uptake by argon and oxygen, but not nitrogen or methane. The adsorption of nitrogen and methane gradually increases as the nanotube diameter approaches 4.07 Å, and all gases fully saturate a 4.54 Å nanotube. Of the nanotubes studied, the largest adsorption enthalpy for any gas corresponds to the 4.54 Å nanotube, with significantly lower enthalpies seen in the 5.07 Å nanotube. These results suggest an ideal pore diameter for each gas based on the gas–pore van der Waals interaction energies. Trends in the ideal diameter correlate with the minimum tube diameter accessible to each gas.     

Altered nuclear pore diameters in G1-arrested cells of the yeast Saccharomyces cerevisiae.

Nuclear pores in cells of the yeast Saccharomyces cerevisiae were examined by using the freeze-fracture technique. Nuclear pore diameters in actively growing cells appear to be exclusively of the normal diameter (75 to 115 nm), whereas some pore diameters in abnormally small G1-arrested cells produced by nitrogen starvation are unusually wide (120 to 160 nm). There may be a correlation between nuclear pore size and nuclear envelope size, the larger pores tending to occur in the smaller envelopes. The finding suggests that nuclear pore diameter may not function in regulating the flow of informational molecules from nucleus to cytoplasm, but may be implicated in regulating the flow of substrates into the nucleus.     

Octagonal nuclear pores

Negative staining of isolated nuclear envelopes by phosphotungstate shows that the nuclear pores are octagonal rather than circular. Pores of the same shape and approximately the same width, 663 ± 5 A, were demonstrated in the newt, Triturus, the frog, Rana, and the starfish, Henricia. The outer and inner diameters of the annulus associated with each pore are respectively greater and less than the width of the pore itself. For this reason surface views of the envelope, unless negatively stained, fail to show the true dimensions of the pores.     

The Prevalence of Pores and Canals in Leaf Cuticular Membranes. 2. Supplemental Studies

Evidence is presented for the existence of discrete, naturalcuticular pores concomitant with anticlinally-oriented transcuticularcanals found in the mature leaf surfaces of 26 out of 37 taxaamong 19 families. This investigation is an extension of earlierobservations made on 32 other taxa among 14 families. Dewaxed,chemically isolated, adaxial and abaxial cuticular membranesin conjunction with transverse leaf sections were examined usingordinary staining techniques. The ubiquitous pores occur randomlywith no evidence of clustering. Pore and canal diameters averageapprox. 1 µm. Canal lengths are directly related to cuticlethickness. No correlations were found between cuticle thicknessesand either pore frequencies or pore and canal diameters. Evidenceis provided by light microscopy photomicrographs. Leaf cuticles, cuticular membranes, cuticular pores, transcuticular canals, cuticular flanges     

Nanometer-Scale Pore Characteristics of Lacustrine Shale,Songliao Basin,NE China

In shale, liquid hydrocarbons are accumulated mainly in nanometer-scale pores or fractures, so the pore types and PSDs (pore size distributions) play a major role in the shale oil occurrence (free or absorbed state), amount of oil, and flow features. The pore types and PSDs of marine shale have been well studied; however, research on lacustrine shale is rare, especially for shale in the oil generation window, although lacustrine shale is deposited widely around the world. To investigate the relationship between nanometer-scale pores and oil occurrence in the lacustrine shale, 10 lacustrine shale core samples from Songliao Basin, NE China were analyzed. Analyses of these samples included geochemical measurements, SEM (scanning electron microscope) observations, low pressure CO₂ and N₂ adsorption, and high-pressure mercury injection experiments. Analysis results indicate that: (1) Pore types in the lacustrine shale include inter-matrix pores, intergranular pores, organic matter pores, and dissolution pores, and these pores are dominated by mesopores and micropores; (2) There is no apparent correlation between pore volumes and clay content, however, a weak negative correlation is present between total pore volume and carbonate content; (3) Pores in lacustrine shale are well developed when the organic matter maturity (Ro) is >1.0% and the pore volume is positively correlated with the TOC (total organic carbon) content. The statistical results suggest that oil in lacustrine shale mainly occurs in pores with diameters larger than 40 nm. However, more research is needed to determine whether this minimum pore diameter for oil occurrence in lacustrine shale is widely applicable.