The Force-Biased Algorithm for the Irregular Close Packing of Equal Hard Spheres

Abstract

We present a “force-biased” algorithm for generating the irregular close packing of hard spheres. The algorithm is partly based on Jodrey and Tory's ideas [9] and incorporates methods from Molecular Dynamics. Packings generated by means of the two algorithms are consistent up to final packing fraction of 0.65, which seems to be the limit density of Jodrey and Tory's method. Significantly higher densities (up to 0.71) can be achieved for small numbers of spheres by the force-biased algorithm. However the shape of the radial and angle distribution functions implies that a partial short-range ordering occurs in packings of those densities.     

Solute exchange between the plasma and epithelial lining fluid of rat lungs.

Although the transport of solutes from air spaces to plasma has been extensively studied, comparatively little information is available concerning solute equilibration between the plasma and the epithelial lining fluid (ELF) of air-filled lungs. In the present study, 11 lipophobic indicators varying in molecular mass between 22 and 80,000 Da were injected intravenously and/or intramuscularly into anesthetized rats in a manner designed to keep blood concentrations constant. The animals were killed by rapid lavage of their lungs at various intervals up to 120 min after the injections had been made. Indicator concentrations in the bronchoalveolar lavage (BAL) fluid and plasma were determined, and BAL-to-plasma concentration ratios were calculated for indicators that were injected (exogenous: [14C]urea, 22Na+, [3H]mannitol, 99mTc-diethylenetriaminepentaacetate (a chelate), 51Cr-(ethylene dinitrilo)tetraacetate (a chelate), 113mIn-transferrin, human albumin, and Evans blue-labeled rat albumin) and those that were already present from the plasma and ELF (unlabeled urea, rat albumin, and rat transferrin). Leakage of exogenous indicators in the blood into the BAL fluid was observed during the lavage procedure. Leakage of [14C]urea, 22Na+, and [3H]mannitol exceeded that of the heavier solute molecules. Diffusion of proteins and the labeled chelates into the ELF before lavage occurred at similar rates, suggesting vesicular transport. Use of rapidly diffusible solutes such as urea for determining dilution of ELF by BAL should be accompanied by intravascular injections of labeled solutes to correct for diffusion from the blood during lavage. Alternatively, labeled chelates or serum proteins can be used to estimate dilution of ELF by BAL. Interstitial sampling may be inevitable if the epithelium has been injured before lavage.     

Effects of metal ion and solute conformation change on hydration of small amino acid

The effects of metal ion and solute conformation change on the structures, energetic and dynamics of water molecules in the first hydration shell of amino acid were studied, using three forms of alanine (Ala) and Li(+)/Ala as model molecules. The theoretical investigations were started with construction of the test-particle model (T-model) potentials for all molecules involved and followed by molecular dynamics (MD) simulations of [Ala](aq) and [Li(+)/Ala](aq) at 298 K. The MD results showed that the hydrogen bond (H-bond) networks of water at the functional groups of Ala are strengthened by the metal ion binding, whereas the rotation of the N-C(alpha) bond from the angle phi=0 degrees to 180 degrees brings about smaller effects which cannot be generalized. It was also shown that the dynamics of water molecule in the first hydration shell of amino acid could be estimated from the total-average potential energy landscapes and the water exchange diagrams. The MD results suggested inclusion of an additional dynamic step in the water exchange process, in which water molecule moves inside a channel within the first hydration shell of solute, before leaving the channel at some point. The theoretical results reported in the present work iterated the necessity to include explicit water molecules in the model calculations.     

Effects of acute hyperoxic exposure on solute fluxes across the blood-gas barrier in rat lungs

Zheng, Lu P., Rui Sheng Du, and Barbara E. Goodman.Effects of acute hyperoxic exposure on solute fluxes across the blood-gas barrier in rat lungs. J. Appl.Physiol. 82(1): 240-247, 1997.We investigatedeffects of acute hyperoxia on solute transport from air space tovascular space in isolated rat lungs. Air spaces were filled withKrebs-Ringer bicarbonate solution containing fluoresceinisothiocyanate-labeled dextran (FD-20; mol wt 20,000) and either²²Na⁺and [¹⁴C]sucrose, orD-[¹⁴C]glucoseandL-[³H]glucose.Apparent permeability-surface area products for tracers over time (upto 120 min) were calculated for isolated perfused lungs from controlrats (room air) and rats exposed to >95%O₂ for 48 or 60 h immediatelypostexposure. After O₂ exposures,mean fluxes for[¹⁴C]sucrose and FD-20were significantly higher than in room-air control lungs. However,amiloride-sensitive Na⁺ and activeD-glucose fluxes were unchangedafter hyperoxic exposure. Therefore, it is unlikely that decreases innet solute transport in this lung-injury model contributed to pulmonaryedema resulting from O₂ toxicity.Increased net solute transport shown to help resolve pulmonary edemaafter acute hyperoxic exposure must therefore begin during the recoveryperiod. In summary, our data show increases in passive solute fluxesbut no changes in active solute fluxes immediately after acutehyperoxic lung injury.

     

The effects of salt depletion on blood and tissue ion concentrations in the freshwater mussel,Ligumia subrostrata (Say)

Summary The extracellular and intracellular fluid volumes of pondwater acclimatedLigumia subrostrata are equal (3.9 ml/g dry tissue). Total blood solute is 47 mOsm and is composed primarily of Na (19.1 mM), Cl (10.6 mM), HCO₃ (12.7 mM), Ca (4.3 mM), and K (0.5 mM). Major intracellular solutes are K (14.0 mM), Na (7.0 mM) and Cl (2.4 mM).L. subrostrata continuously exposed to deionized water at 20°C exhibit a maximum decrease of 23% in extracellular fluid total solute within 30 days. The maximum [Na] and [Cl] losses are 40% and 76% respectively, while [Ca] and [HCO₃] increase by 44% and 37% respectively. No apparent change in extracellular [K] occurs. Intracellular [Na] decreases 53% and [Cl] decreases 79%, but [K] declines only 15%. Intracellular fluid volume, extracellular fluid volume, and total body water decrease 17%, 31%, and 22% respectively. Inulin clearance is 0.41 ml/g dry tissue·h for pondwater acclimated mussels and declines to 0.24 ml/g dry tissue·h during salt depletion. When salt depleted mussels are returned to solutions containing Na or Cl, they experience a net uptake of salt. The accumulated ions are about equally distributed in the extra- and intracellular compartments.     

Movement of zymosterol, a precursor of cholesterol, among three membranes in human fibroblasts

Where examined, cholesterol is synthesized in the endoplasmic reticulum; however, its precursor, zymosterol, is found mostly in the plasma membrane. The novel implication of these disparate findings is that zymosterol circulates within the cell. In tracing its movements, we have now established the following: (a) in human fibroblasts, zymosterol is converted to cholesterol solely in the rough ER. (b) Little or no zymosterol or cholesterol accumulates in the rough ER in vivo. (c) Newly synthesized zymosterol moves to the plasma membrane without a detectable lag and with a half-time of 9 min, about twice as fast as cholesterol. (d) The pool of radiolabeled zymosterol in the plasma membrane turns over rapidly, faster than does intracellular cholesterol. Thus, plasma membrane zymosterol is not stagnant. (e) [3H]Zymosterol pulsed into intact cells is initially found in the plasma membrane. It is rapidly internalized and is then converted to [3H] cholesterol. Half of the [3H]cholesterol produced returns to the plasma membrane within 30 min of the initial [3H]zymosterol pulse. (f) Nascent zymosterol accumulates in a buoyant sterol-rich intracellular membrane before it reaches the plasma membrane. This membrane also acquires nascent cholesterol, exogenous [3H]zymosterol pulsed into intact cells, and [3H]cholesterol synthesized from the exogenous [3H] zymosterol. These results suggest that at least one sterol moves rapidly and in both directions among the rough endoplasmic reticulum, a sterol-rich intracellular membrane bearing nascent cholesterol, and the plasma membrane.     

不同土壤采样设计下土壤表层微生物α多样性的差异分析

【背景】土壤采样是土壤研究的基础,采样方案的不同可能会对土壤微生物多样性的研究结果产生一定影响。【目的】研究不同的土壤采样设计方案对土壤样品16S rRNA基因高通量测序结果的影响。【方法】对2个不同生境样地的土壤进行网格化采样,对采集的18个土壤样品进行16S rRNA基因测序分析,通过模拟5种常见土壤采样方法,对比不同采样方式所获得的测序结果。【结果】不同采样方式会产生不同的测序结果。在测序深度有效的情况下,细菌总物种数随着采样数的增加而逐渐增长,增长速度在采样数大于5以后趋于平缓;样品中的优势物种(序列数200以上)只需很少的采样数(1-3)即可观察到全部物种;Shannon-Wiener指数与Simpson指数的变化较相似,当采样数由1到3时两指数均有较大增长,之后变化放缓。【结论】土壤细菌微生物测序研究中,土壤样地采样数量低于3个会影响测序结果的可靠性,采样方案选择梅花形采样法或蛇形采样法较为适宜。     

Esterification of exogenously derived free cholesterol by cultured fibroblasts

The incorporation and esterification by cultured human fibroblasts of vesicle- or low density lipoprotein-derived free [3H]cholesterol was examined. The rate of the cellular uptake of free [3H]cholesterol from lipid vesicles was similar in both LDL-receptor positive lung fibroblasts and in LDL-receptor negative fibroblasts. When human LDL was used as the carrier of free [3H]cholesterol, however, the LDL-receptor positive lung fibroblasts incorporated significantly more [3H]cholesterol than did the LDL-receptor negative cells. The exchangeable free [3H]cholesterol was available for intracellular esterification. The formation of [3H]cholesteryl esters was markedly inhibited by lysosomotropic drugs, either indicating a partly lysosomal esterification reaction, or implying that free [3H]cholesterol moves through the lysosomal compartment on its way to intracellular esterification sites. Either way, the lysosomes appear to have a metabolic role in the metabolism of exchangeable free [3H]cholesterol.     

Transport and metabolism of xylem cytokinins during lateral bud release in decapitated chickpea (Cicer arietinum) seedlings

Although cytokinins (CKs) are widely thought to have a role in promoting shoot branching, there is little data supporting a causative or even a correlative relationship between endogenous CKs and timing of bud outgrowth. We previously showed that lateral bud CK content increased rapidly following shoot decapitation. However, it is not known whether roots are the source of this CK. Here, we have used shoot decapitation to instantaneously induce lateral bud release in chickpea seedlings. This treatment rapidly alters rate and direction of solvent and solute (including CK) trafficking, which may be a passive signalling mechanism central to initiation of lateral bud release. To evaluate changes in xylem transport, intact and decapitated plants were infiltrated with [³H]zeatin riboside ([³H]ZR), a water‐soluble blue dye or [³H]H₂O by injection into the hypocotyl. All three tracers were recovered in virtually all parts of the shoot within 1 h of injection. In intact plants, solute accumulation in the lateral bud at node 1 was significantly less than in the adjacent stipule and nodal tissue. In decapitated plants, accumulation of [³H]ZR and of blue dye in the same bud position was increased 3‐ to 10‐fold relative to intact plants, whereas content of [³H]H₂O was greatly reduced indicating an increased solvent throughput. The stipule and cut stem, predicted to have high evapotranspiration rates, also showed increased solute content accompanied by enhanced depletion of [³H]H₂O. To assess whether metabolism modifies quantities of active CK reaching the buds, we followed the metabolic fate of [³H]ZR injected at physiological concentrations. Within 1 h, 80–95% of [³H]ZR was converted to other active CKs (mainly zeatin riboside‐5′phosphate (ZRMP) and zeatin (Z)), other significant, but unconfirmed metabolites some of which may be active (O‐acetylZR, O‐acetylZRMP and a compound correlated with sites of high CK‐concentrations) and inactive catabolites (adenosine, adenine, 5′AMP and water). Despite rapid metabolic degradation, the total active label, which was indicative of CK concentration in buds, increased rapidly following decapitation. It can be inferred that xylem sap CKs represent one source of active CKs appearing in lateral buds after shoot decapitation.     

On the Distribution of a Permeable Solute during Poiseuille Flow in Capillary Tubes

Equations are derived describing the dispersion of a permeable solute during Poiseuille flow in a capillary model. It is shown that for the normal range of physiological parameters such as capillary radius, capillary length, blood flow, permeability coefficients, and diffusion constants, the center of mass of a bolus of solute moves at a speed very close to the mean speed of flow and that the solute leaves the capillary with an exponential time course depending on the permeability but not on the diffusion constant. There is no appreciable difference in the dispersion of the solute or in its rate of permeation from the capillary whether one considers piston flow or Poiseuille flow. A bolus of arbitrary radial shape tends to become radially uniform very close to the arterial end of the capillary.     

Patterns of accumulation resulting from Taxes and changes in motility of micro-organisms

Summary An analysis is made of the development of patterns of accumulation of micro-organisms, as governed by tactic responses, changes in motility, and the effects of diffusion.When a soluble crystal is placed in a suspension of micro-organisms, the first manifestation is the development of a clear zone surrounding the crystal. This effect is a physical one, produced by a transfer of momentum from the solute molecules to the organisms.As the solute spreads and its boundary moves more slowly, the organisms are distributed in patterns which depend upon the occurrence of tactic responses and the influence of the solute upon motility. A congregation in the zone occupied by the solute can correspond either to a positive chemotaxis or to an inhibition of motility by the solute. Conversely, a withdrawal from the solute can signal either a negative chemotaxis or an enhancement of motility by the solute.The proper interpretation of the patterns described in Figs. 10 and 11 requires a microscopic study of individual organisms, in which the effect of the reagent upon motility is noted.     

Importance of sites of tracer administration and blood sampling in relation to leucine metabolism. Practical considerations.

For the same infusion site of L-[1-14C]leucine, sampling downstream of arterial blood underestimates leucine turnover, whereas sampling of venous blood overestimates turnover. Further, the lungs release a small but consistent amount of leucine into the blood. Unlabelled leucine also is produced by the portal-drained viscera, and some is removed immediately by the liver. These sources of leucine should thus be considered in turnover calculations.     

Ubiquitin-Directed Antibodies Inhibit Neuronal Transporters in Rat Brain Synaptosomes

Affinity-purified antibodies specific for ubiquitin were found to inhibit the sodium-dependent uptake of [3H]choline, gamma-[3H]aminobutyric acid [( 3H]GABA), [3H]glutamate, [3H]norepinephrine, [3H]aspartate, and [3H]serotonin in rat cerebral cortical synaptosomes at a low concentration (10 micrograms/ml). These antibodies (termed anti-Ub) had no effect on the sodium-independent uptake of these substances or their calcium-dependent efflux. Synaptosomal [3H]deoxyglucose uptake was not affected in normal Krebs Ringer buffer containing 10 mM glucose, but was inhibited in glucose-free medium. Other nonneuronal sodium-dependent transport processes were found to be unaffected by 10 micrograms/ml anti-Ub, suggesting that anti-Ub does not bind indiscriminantly to sodium-binding sites on sodium-dependent organic solute transporters. Finally, anti-Ub inhibited sodium-dependent [3H]GABA and [3H]glutamate uptake in plasma membrane ghosts, devoid of membrane potential, which were derived from rat cerebral cortical synaptosomes. These results suggest that neuronal transporters or sites proximal to them may be ubiquitinylated on the plasma membrane surface.     

Solutes Involved in Osmotic Adjustment to Increasing Salinity in Suspension Cells of Alternanthera philoxeroides Griseb

Cell recovery from osmotic stress was studied in suspension cell cultures from Alternanthera philoxeroides [Mart.] Griseb. Changes in different classes of cellular solutes were measured after cells were transferred from 0 to 200 mM NaCl (high salt) to obtain an integrated picture of the solute pools involved in osmotic adjustment. By 2 h, cellular [Na⁺] and [Cl⁻] had increased several-fold, potentially accounting for the osmotic adjustment that produced a rapid recovery of cell turgor. There was a four-fold increase in the concentration of quaternary ammonium compounds (QAC) by 12 h and a slower increase for several days afterward. Betaine aldehyde dehydrogenase (BADH) is required for synthesis of glycine betaine, a QAC produced by a range of organisms in response to osmotic stress. Western-blot analysis for BADH suggested that glycine betaine was a significant component of the QAC solutes. The amount of BADH was generally similar at different sampling times for control and high salt cells, unlike previous reports of stimulation by osmotic stress in intact plants of some species. Between 3 and 7 days after cell transfer to high salt, other organic solutes increased in concentration and [Na⁺] and [Cl⁻] decreased. In A. philoxeroides, high [Na⁺] and [Cl⁻] produce rapid osmotic adjustment but organic solutes apparently replace these potentially harmful inorganic ions after the recovery of turgor.     

Rapid Response of the Yield Threshold and Turgor Regulation during Adjustment of Root Growth to Water Stress in Zea mays

Responses of cortical cell turgor (P) following rapid changes in osmotic pressure ([pi]m) were measured throughout the elongation zone of maize (Zea mays L.) roots using a cell pressure probe and compared with simultaneously measured root elongation to evaluate: yield threshold (Y) (minimum P for growth), wall extensibility, growth-zone radial hydraulic conductivity (K), and turgor recovery rate. Small increases in [pi]m (0.1 MPa) temporarily decreased P and growth, which recovered fully in 5 to 10 min. Under stronger [pi]m (up to 0.6 MPa), elongation stopped for up to 30 min and then resumed at lower rates. Recoveries in P through solute accumulation and lowering of Y enabled growth under water stress. P recovery was as much as 0.3 MPa at [pi]m = 0.6 MPa, but recovery rate declined as water stress increased, suggesting turgor-sensitive solute transport into the growth zone. Under strong [pi]m, P did not recover in the basal part of the growth zone, in conjunction with a 30% shortening of the growth zone. Time courses showed Y beginning to decrease within several minutes after stress imposition, from about 0.65 MPa to a minimum of about 0.3 MPa in about 15 min. The data concerning Y were not confounded significantly by elastic shrinkage. K was high (1.3 x 10-10 m2 s-1 MPa-1), suggesting very small growth-induced water potential gradients.     

Stabilization of the water oxidizing polypeptide assembly on Photosystem II membranes by osmolytes and other solutes

The integrity of Photosystem II membranes isolated from chloroplast thylakoids is profoundly affected by the solute environment. Examples are given for stabilizing effects various solutes have on the binding of the 17 and 23 kDa extrinsic polypeptides under conditions conductive to their dissociation. It is concluded that these and many other solute effects on Photosystem II membranes can be accommodated readily in a concept developed by Timasheff and his coworkers according to which the responses of proteins to their solute environment are consequences of interaction preferences among the constituents of the solvent-protein-solute systems.Abbreviations Chl chlorophyll - MES 2-(N-morpholino)ethanesulfonic acid - MOPS (3-[N-morpholino]propanesulfonic acid) - PS II Photosystem II     

Differential Solute Regulation in Leaf Blades of Various Ages in Salt-Sensitive Wheat and a Salt-Tolerant Wheat x Lophopyrum elongatum (Host) A. Love Amphiploid

Leaf blades of different ages from a salt-tolerant wheat x Lophopyrum elongatum (Host) A. Love (syn. Agropyron elongatum Host) amphiploid and its salt-sensitive wheat parent (Triticum aestivum L.cv Chinese Spring) were compared for their ionic relations, organic solute accumulation, and sap osmotic potential ([pi]sap). The plants were grown for 18 d in nonsaline (1.25 mM Na+) and salinized (200 mM NaCl) nutrient solutions. The response of leaf blades to NaCl salinity depended greatly on their age or position on the main stem. Na and proline levels were highest in the oldest leaf blade and progressively lower in younger ones. Glycine betaine and asparagine levels were highest in the youngest blade. The [pi]sap was similar for corresponding leaf blades of both genotypes, but contributions of various solutes to the difference in [pi]sap between blades from control and 200 mM NaCl treatments differed greatly. The NaCl-induced decline in [pi]sap of the youngest leaf blade of Chinese Spring was predominately due to the accumulation of Na and to a lesser extent asparagine; in the amphiploid, it was due to a combination of glycine betaine, K, Na, and asparagine. Proline contributed little in the youngest blade of either genotype. In the older blades Na was the major solute contributing to the decline in [pi]sap. Thus, the maintenance of low Na and high K levels and the accumulation of glycine betaine in the young leaf tissues contributed to the NaCl tolerance of the amphiploid. No such role was evident for proline.     

Determination of deoxycholic acid pool size and input rate using [24-13C]deoxycholic acid and serum sampling

We have developed an isotope dilution method for determination of deoxycholic acid pool size and input rate which employs oral administration of 50 mg of [24-13C]deoxycholic acid and serum sampling. The method has been validated by classical isotope dilution technique using [24-14C]deoxycholic acid and bile sampling in five patients with colonic adenomas. Excellent agreement between pool sizes and input rates determined with 13C/12C isotope ratio measurements in serum and 14C measurements in bile was obtained when isotope ratios were measured in the conjugated fraction of deoxycholic acid in serum. We conclude that pool size and input rate of deoxycholic acid can accurately be determined by blood sampling after oral administration of [24-13C]deoxycholic acid, therewith eliminating the use of radioactive tracers and the need for bile sampling.     

The separation of peptide hormone diastereoisomers by reverse phase high pressure liquid chromatography. Factors affecting separation of oxytocin and its diastereoisomers--structural implications.

Experimental conditions and parameters involved in high performance liquid chromatography (HPLC) separations of the peptide hormone oxytocin and seven of its diastereoisomers, namely [1-hemi-D-cystine]-, [2-D-tyrosine]-, [4-D-glutamine]-, [5-D-asparagine]-, [6-hemi-D-cystine-], [7-D-proline]-, and [8-D-leucine]-oxytocin, on reverse phase columns were investigated. The effects of solvent, pH, and salt concentration were studied. Using the solvent systems 10% tetrahydrofuran-ammonium acetate buffer or 18% acetonitrile-ammonium acetate buffer and the muBondapak C18 support, oxytocin was separated from each of its diastereoisomers under all conditions studied, but the order of elution of diastereoisomers was highly dependent on solvent and to a lesser extent on pH. Separations of the hormone and its diastereoisomers on reverse phase HPLC and on classical partition chromatography on Sephadex G-25 were compared. The results are discussed in terms of the interactions of the solute with the reverse phase column and the solvent system. Implications of these findings in terms of the different solution conformations of the peptides are discussed.