Ion-mediated nucleic acid helix-helix interactions

Salt ions are essential for the folding of nucleic acids. We use the tightly bound ion (TBI) model, which can account for the correlations and fluctuations for the ions bound to the nucleic acids, to investigate the electrostatic free-energy landscape for two parallel nucleic acid helices in the solution of added salt. The theory is based on realistic atomic structures of the helices. In monovalent salt, the helices are predicted to repel each other. For divalent salt, while the mean-field Poisson-Boltzmann theory predicts only the repulsion, the TBI theory predicts an effective attraction between the helices. The helices are predicted to be stabilized at an interhelix distance approximately 26-36 A, and the strength of the attractive force can reach -0.37 k(B)T/bp for helix length in the range of 9-12 bp. Both the stable helix-helix distance and the strength of the attraction are strongly dependent on the salt concentration and ion size. With the increase of the salt concentration, the helix-helix attraction becomes stronger and the most stable helix-helix separation distance becomes smaller. For divalent ions, at very high ion concentration, further addition of ions leads to the weakening of the attraction. Smaller ion size causes stronger helix-helix attraction and stabilizes the helices at a shorter distance. In addition, the TBI model shows that a decrease in the solvent dielectric constant would enhance the ion-mediated attraction. The theoretical findings from the TBI theory agree with the experimental measurements on the osmotic pressure of DNA array as well as the results from the computer simulations.     

Ion-mediated flow changes suppressed by minimal calcium presence in xylem sap in Chrysanthemum and Prunus laurocerasus

After the discovery of ion-mediated changes in xylem hydraulic resistance a few years ago, a number of research papers were published that related ion-mediated flow changes in the xylem to various aspects of whole plant functioning and evolutionary diversification of vascular cells. Ion-mediated changes in xylem hydraulic resistance are commonly quantified as the percentile change in hydraulic resistance, relative to the hydraulic resistance measured using a reference fluid, usually (ultra) pure deionized water. In this research the impact was investigated of the complete absence of all ions in deionized water compared with reference fluids containing a minimal amount of free calcium on the quantification of ion-mediated flow changes in stem segments of Chrysanthemum (Dendranthemaxgrandiflorum Tzvelev) and Prunus L. (Prunus laurocerasus L.). The addition of 10 mM KCl to deionized water significantly increased flow rate in Chrysanthemum (17-24%) and Prunus L. (16%). The addition of 1 mM CaCl(2) to the reference fluid reduced this KCl-mediated increase in flow rate to 1-2% in both species. 1 mM Ca(2+) is within the lower range of Ca(2+)-concentrations normally measured in xylem sap of many plant species, and three times lower than the original Ca(2+)-concentration measured in the xylem sap of Chrysanthemum plants used for the present measurements. The present results indicate that the complete removal of cations from the xylem fluid with deionized water causes the major part of the ion-mediated flow change previously reported in the xylem of plants. It is concluded that the use of deionized water as a reference fluid should be avoided. Earlier proposed relationships between ion-mediated changes and water flow in xylem of plants should be re-evaluated if they were based on deionized water as the reference fluid.     

Ion-mediated RNA structural collapse: effect of spatial confinement

RNAs are negatively charged molecules that reside in cellular environments with macromolecular crowding. Macromolecular confinement can influence the ion effects in RNA folding. In this work, using the recently developed tightly bound ion model for ion fluctuation and correlation, we investigate the effect of confinement on ion-mediated RNA structural collapse for a simple model system. We find that for both Na(+) and Mg(2+), the ion efficiencies in mediating structural collapse/folding are significantly enhanced by the structural confinement. This enhancement of ion efficiency is attributed to the decreased electrostatic free-energy difference between the compact conformation ensemble and the (restricted) extended conformation ensemble due to the spatial restriction.     

Ion-mediated increase in the hydraulic conductivity of Laurel stems: role of pits and consequences for the impact of cavitation on water transport

Changes in hydraulic conductivity (K(h)) were measured in stems of Laurus nobilis L. during perfusion with KCl, NaCl or sucrose solutions. Ionic solutes induced marked increase of K(h) with respect to deionized water but sucrose had no effect. The kinetics of KCl-induced K(h) increase was measured together with changes in [K(+)] of the perfused solution. K(h) increases were paralleled by increases in the [K(+)](out)/[K(+)](in) ratio. Samples of different lengths or with increasing percentage loss of conductivity (PLC) due to xylem cavitation were tested, with the aim of increasing radial flow through intervessel pits. KCl solutions enhanced the K(h) of 12-cm-long samples with a concentration-dependent effect up to 100 mm KCl. DeltaK(h) increased from 3 to 30% in 1.5- and 12-cm-long samples, respectively and remained constant for longer samples. Increasing PLC induced an exponential increase in DeltaK(h). PLC measured with KCl solutions was significantly less than that measured with deionized water, suggesting that measurements of PLC can be affected by the composition of the perfused solution. Experiments support the hypothesis that the 'ionic effect' is mediated by physico-chemical changes of pectins of the pit membranes and raise the possibility that plants might alter the ionic composition of the xylem sap to alleviate the hydraulic impact of cavitation.     

Ion-mediated resistance to osmotic changes of ram spermatozoa: the role of amiloride and ouabain

The aim of this study was to evaluate whether the Na+/K+ and Na+/H+ exchange can maintain the function of fresh ram spermatozoa. We analyzed the quality parameters of spermatozoa from fresh ram ejaculates incubated in iso- (about 300 mOsm), hypo- (about 100 mOsm) and hyperosmotic (about 900 mOsm) media in the presence of ouabain a specific inhibitor of the Na+/K+ ATP-ase or amiloride, a specific inhibitor of the Na+/H+ antiporter. Ouabain increased the percentage of morphologically altered acrosomes in isoosmotic media (from about 10% to 15% in control to about 30% with 10(-4) M ouabain) and decreased the percentage of total motility (from about 80% in control to about 50% to 55% with 10(-4) M ouabain). Ouabain decreased the mean linearity component of motility and decreased the frequency of head displacement. The addition of ouabain increased the percentage of altered acrosomes in the hypo- and hyperosmotic media, although it did not modify viability in either media. Ouabain also increased the percentage of swollen tails in the hypoosmotic medium at higher concentrations of the inhibitor. Amiloride increased the percentage of altered acrosomes in all media although its effect was less intense than that of ouabain. In isoosmotic media, total motility was decreased from about 80% in control to about 65% with 10(-4) M amiloride. Motile spermatozoa incubated with amiloride showed a clear decrease of mean velocity and mean linearity and increased frequency of head displacement. In the hyperosmotic medium, adding amiloride decreased the percentage of viability and altered tails at concentrations as low as 10(-6) to 10(-5) M. Our results indicate that the active mechanisms which control Na+ transport play a significant role in the maintenance of function in ram spermatozoa subjected to different osmotic environments. These mechanisms may be important in maintaining ram sperm function both "in vivo" and "in vitro".     

Cell determinants of vasopressin-stimulated water flow

I present a technique that permits evaluation of the permeability to water of the luminal membrane of the toad urinary bladder, independently of constraints to water flow imposed by the remainder of the tissue. This technique essentially depends on fixation of the luminal membrane with 1% glutaraldehyde for 5 min, and subsequent elimination of cytosolic constraints by decreasing the tonicity of the serosal bath to 1/2 normal strength. The increased hydraulic conductivity found with serosal hypotonicity is readily reversible, as the bladder returns to an isotonic serosal bath. By evaluating water flow in luminally fixed bladders during bathing in normal and hypotonic bath, one may identify the relative contribution of the luminal membrane and the "cytosol" on water flow. Using this technique, I found that the effect of the prostaglandin inhibitor Naproxen to increase vasopressin-stimulated water flow is due to increased luminal membrane permeability. The effect of histidine to increase vasopressin-stimulated water flow, however, depends on increased permeability of both the luminal membrane as well as the underlying structures. The action of serosal hypertonicity to induce water flow is due to an increased luminal permeability. However, serosal hypertonicity decreases "cytosolic" permeability, so that its overall function is a composite effect of its action at the luminal membrane and the "cytosolic" level.     

Osmotic water flow in leaky epithelia

I review three currently unsolved and controversial problems in understanding solute-linked water transport in epithelia. 1. Values of osmotic water permeability (Posm) calculated from steady-state osmotic flow in response to a gradient of a probe molecule tend to be underestimates, because of three unstirred-layer (USL) effects. These are: dissipation of the probe's gradient by diffusion in USL's; reduction of the probe's gradient, due to the sweeping-away effect of water flow generated by the probe itself; and solute polarization (creation of an opposing gradient of an initially symmetrically distributed solute by the sweeping-away effect). These errors increase with probe permeability, USL thickness, Posm, and concentration ratio of symmetrically distributed solute to probe, and vary inversely as the fractional area available for water flow (e.g., lateral intercellular space width). The form of an osmotic transient, and the possibility of extracting a true Posm value from the transient, depend on the relative values of three time constants: those for solute diffusion in USL's, for solute polarization by water flow in USL's and for measuring water flow. Sweeping-away effects cause major underestimates (by one or more orders of magnitude) in epithelial Posm determinations, as shown by apparent streaming potentials during osmotic flow and by transiently reversed flows after removal of the proble. True Posm values for leaky epithelia probably exceed 10(-3) or 10(-2) cm/sec.osm. The necessary conditions for resolving osmotic transients are set out. 2. I illustrate the difficulties in deciding what fraction of transepithelial water flow is via the cells, and what fraction via the junctions. There is no existing method for answering this question. 3. Controversies about the validity, or need for modification, of the standing-gradient theory are discussed. Progress in this field requires new methods: to resolve osmotic transients; to separate transcellular and transjunctional water flows; and to measure solute concentrations in lateral intercellular spaces directly.     

Modeling water flow through arterial tissue

A simple model of, water flow through deformable porous media has been developed with emphasis on application to arterial walls. The model incorporates a strain-dependent permeability function into Darcy's Law which is coupled, to the force balance for the bulk material. A simple analytical expression relating water flux (volume flux) to pressure differential is developed which shows how strain-dependent permeability can lead to a reduction in hydraulic conductivity with increasing differential pressure as observed in experiments with arteries. The variation of permeability with position in the wall, which may influence the convective diffusion of macromolecules, is determined for both cylindrical and planar segments and a marked influence of geometry is noted.     

The flow of water into fruit trees. I. Resistances to water flow through roots and stems

Relative conductivity (K) to water in healthy apple trees ranged from maximum values of 18.2 cm³.100 s^-1.cm length.0.001 Pas.kPa^-1.cm^-2 xylem area, for major suberized roots to values of 1.6 for 1-yr-old twigs. The values for equivalent parts of healthy cherry trees were 26.3 and 3.3. Trees with roots affected by the larvae of the fruit tree root weevil (Leptopius squalidus) which causes either chronic growth decline or sudden wilting and death, had values as low as 1% of healthy trees, in those parts of the tree showing wilting and lack of growth. Water flow under pressure into the root systems of healthy apple trees increased linearly with increases in pressure from 200 to 800 kPa. Flows into dormant and active root systems respectively were 0.6 and 1.7 cm³.100 s^-1. 100 cm² root surface area. 100 kPa^-1.     

Modeling tree water flow as an unsaturated flow through a porous medium

The electric circuit analogy has had a profound influence on how tree physiologists measure, model and think about tree water flow. For example, previous models that attempt to account for changes in saturation use the electric circuit analogy to define capacitance as the change in saturation per change in pressure. Given that capacitance is constant, this relationship implies that subjecting a block of wood to a pressure of -2.5 MPa for 2 min results in the same change in saturation as subjecting the same block to the same pressure for 2 days. Given the definition of capacitance, it is unclear how the electric circuit analogy could be used to predict changes in saturation separately from changes in pressure. The inadequacies in the electric circuit analogy discussed in this paper necessitate a new theory of tree water flow that recognizes the sapwood as being a porous medium and explicitly deals with the full implications of the unsaturated flow occurring in the sapwood. The theory proposed in this paper combines the Cohesion theory with a mathematical theory of multiphase flow through porous media. Based on this theory, both saturated and unsaturated tree water flow models are presented. Previous partial differential equation models of tree water flow based on the electric circuit analogy are shown to be mathematically equivalent to the model of saturated porous flow. The unsaturated model of tree water flow explicitly models the pressure profile and the rates of change in saturation and specific interfacial area (a measure of how the water in the unsaturated sapwood is partitioned between mobile and immobile components). The unsaturated model highlights the differences between saturated and unsaturated flow and the need to measure the variables governing tree water flow at higher spatial and temporal resolutions.     

Combined effect of virus infection and water stress on water flow and water economy in grapevines

Water limitation is one of the major threats affecting grapevine production. Thus, improving water‐use efficiency (WUE) is crucial for a sustainable viticulture industry in Mediterranean regions. Under field conditions, water stress (WS) is often combined with viral infections as those are present in major grape‐growing areas worldwide. Grapevine leafroll‐associated virus 3 (GLRaV‐3) is one of the most important viruses affecting grapevines. Indeed, the optimization of water use in a real context of virus infection is an important topic that needs to be understood. In this work, we have focused our attention on determining the interaction of biotic and abiotic stresses on WUE and hydraulic conductance (K_h) parameters in two white grapevine cultivars (Malvasia de Banyalbufar and Giró Ros). Under well‐watered (WW) conditions, virus infection provokes a strong reduction (P < 0.001) in K_petiole in both cultivars; however, K_leaf was only reduced in Malvasia de Banyalbufar. Moreover, the presence of virus also reduced whole‐plant hydraulic conductance (K_hplant) in 2013 and 2014 for Malvasia de Banyalbufar and in 2014 for Giró Ros. Thus, the effect of virus infection on water flow might explain the imposed stomatal limitation. Under WS conditions, the virus effect on K_plant was negligible, because of the bigger effect of WS than virus infection. Whole‐plant WUE (WUE_WP) was not affected by the presence of virus neither under WW nor under WS conditions, indicating that plants may adjust their physiology to counteract the virus infection by maintaining a tight stomatal control and by sustaining a balanced carbon change.     

Assessing water scarcity by simultaneously considering environmental flow requirements,water quantity,and water quality

Water scarcity is a widespread problem in many parts of the world. Most previous methods of water scarcity assessment only considered water quantity, and ignored water quality. In addition, the environmental flow requirement (EFR) was commonly not explicitly considered in the assessment. In this study, we developed an approach to assess water scarcity by considering both water quantity and quality, while at the same time explicitly considering EFR. We applied this quantity–quality-EFR (QQE) approach for the Huangqihai River Basin in Inner Mongolia, China. We found that to keep the river ecosystem health at a “good” level (i.e., suitable for swimming, fishing, and aquaculture), 26% of the total blue water resources should be allocated to meet the EFR. When such a “good” level is maintained, the quantity- and quality-based water scarcity indicators were 1.3 and 14.2, respectively; both were above the threshold of 1.0. The QQE water scarcity indicator thus can be expressed as 1.3(26%)|14.2, indicating that the basin was suffering from scarcity problems related to both water quantity and water quality for a given rate of EFR. The current water consumption has resulted in degradation of the basin's river ecosystems, and the EFR cannot be met in 3 months of a year. To reverse this situation, future policies should aim to reduce water use and pollution discharge, meet the EFR for maintaining healthy river ecosystems, and substantially improve pollution treatment.     

An analysis of water flow in tube-living animals

Water flow has been studied in six tube-dwelling animals that have different pumping mechanisms and layout of their tube systems. The characteristics of the pumping mechanisms and the resistance of the tube systems have been found. Cilia act as impeller pumps and can produce large rates of flow when arranged in parallel, but may produce sufficient flow for small, long thin bodied animals when arranged in series. Larger vermiform animals must use piston mechanism to produce sufficient rates of flow and the high pressures they can produce do not seem to be of use to the animals during normal pumping. Animals with rigid limbs can use these to impel water and produce high rates of flow. Echinocardium, which has a globular body, must match the flow at the inflow and outflow points on the test to the flow over the circumference and has special ciliated spines at these sites to boost flow.     

Enhancement of water flow across a carbon nanotube

It is important to investigate how to enhance the flow rate of single-file water molecules across nanochannels. To our knowledge, all the existing methods are based on pressure gradients, external point charges or uniform/graded electric fields. Accordingly, these methods are all based on exogenous tools, and thus bring challenges for both energy-saving and miniaturisation. In contrast, here we manage to reveal an endogenously determined mechanism of flow enhancement. On the basis of molecular dynamics simulations, we investigate water permeation across a single-walled carbon nanotube (SWCNT A) in the presence of another SWCNT (SWCNT B). We find that the flow rate of the single-file water molecules across SWCNT A is enhanced for the case of unblocked SWCNT B compared with the rate for the case of blocked SWCNT B, and that this flow rate is determined by the separation between the two SWCNTs and the diameter of SWCNT B.     

Mechanism of pressure-induced water flow across plant roots

Summary Pressure-induced non-linear water flow across plant roots was analyzed theoretically. The double-canal model of radial water transport shown lately explained accurately the observed non-linear water flow in maize roots. The driving force rather than the hydraulic permeability caused the non-linear flow of water. The conclusion was drawn that non-linearity in pressure-induced water flow was an inherent property of the apoplast canal system in roots. Net solute transport plays a primary part for water transport.