Entropy effects on the ion-diffusion rate in transmembrane protein channels

We treat the transport of univalent cations through pore-like protein channels in biological membranes analytically, using two models (A + B) for the channel and the ion-channel interaction. A Lennard-Jones-type repulsion between the ions and the pore wall is introduced. We also include Van der Waals- and coulomb-type interactions between polar ligands of the pore-forming protein (e.g., carbonyl groups directed towards the axis of the channel) and the migrating particles. In model A, the polar groups are assumed to occur in pairs of dipoles pointing in opposite directions (as in the gramicidin A channel), while in model B the channel is treated as a pore with a radially isotropic charge distribution. In both models the ion-channel interaction leads to the occurrence of periodic potentials, corresponding to quasi-equilibrium and transition state sites of the ion in the pore. The diffusion rate can be calculated employing rate-theoretical concepts on the basis of microscopic parameters. It is demonstrated that the anomaly (inversion of the normal mass effect) for the transport rates of different ions can be related to differences in the activation entropy. The latter quantity is estimated analytically for both models. As a test, we performed numerical calculations with parameters based on the gramicidin A model. The results are in good agreement with experimental data and data from computer simulations. This shows that simple analytic expressions are well suited for predicting trends in the ionic conductivity of protein channels on the basis of microscopic interactions.     

Ion-specific diffusion rates through transmembrane protein channels. A molecular dynamics study

The migration of different alkali metal cations through a transmembrane model channel is simulated by means of the molecular dynamics technique. The parameters of the model are chosen in close relation to the gramicidin A channel. Coulomb- and van der Waals-type potentials between the ions and flexible carbonyl groups of the pore-forming molecule are used to describe the ion channel interaction. The diffusion properties of the ions are obtained from three-dimensional trajectory calculations. The diffusion rates for the different ions Li+, Na+, K+ and Rb+ are affected not only by the mass of the particles but also very strongly by their size. The latter effect is more pronounced for rigid channels, i.e., for binding vibrational frequencies of the CO groups with v greater than 400 cm-1. In this range the selectivity sequence for the diffusion rates is the inverse of that expected from normal rate theory but agrees with that found in experiments for gramicidin A.     

Stomatal response to humidity in sugarcane and soybean: effect of vapour pressure difference on the kinetics of the blue light response

Abstract. The effect of atmospheric humidity on the kinetics of stomatal responses was quantified in gas exchange experiments using sugarcane ( Saccharum spp. hybrid) and soybean ( Glycine max ). Pulses of blue light were used to elicit pulses of stomatal conductance that were mediated by the specific blue light response of guard cells. Kinetic parameters of the conductance response were more closely related to leaf-air vapour pressure difference (VPD) than to relative humidity or transpiration. Increasing VPD significantly accelerated stomatal opening in both sugarcane and soybean, despite an approximately five-fold faster response in sugarcane. In contrast, the kinetics of stomatal recovery (closure) following the pulse were similar in the two species. Acceleration of opening by high VPD was observed even under conditions where soybean exhibited a feedforward response of decreasing transpiration (E) with increasing evaporative demand (VPD). This result suggests that epidermal, rather than bulk leaf, water status mediates the VPD effect on stomatal kinetics. The data are consistent with the hypothesis that increased cpidermal water loss at high VPD decreases the backpressure exerted by neighbouring cells on guard cells. allowing more rapid stomatal opening per unit of guard cell metabolic response to blue light.     

Geochemistry of aquatic humic substances in the Lake Fryxell Basin, Antarctica

Dissolved organic carbon (DOC) in Lake Fryxell, 10 streams flowing into the lake, and the moat surrounding the lake was studied to determine the influence of sources and biogeochemical processes on its distribution and chemical nature. Lake Fryxell is an amictic, permanently ice-covered lake in the McMurdo Dry Valleys which contains benthic and planktonic microbial populations, but receives essentially no input of organic material from the ahumic soils of the watershed. Biological activity in the water column does not appear to influence the DOC depth profile, which is similar to the profiles for conservative inorganic constituents. DOC values for the streams varied with biomass in the stream channel, and ranged from 0.2 to 9.7 mg C/L. Fulvic acids in the streams were a lower percentage of the total DOC than in the lake. These samples contain recent carbon and appear to be simpler mixtures of compounds than the lake samples, indicating that they have undergone less humification. The fulvic acids from just above the sediments of the lake have a high sulfur content and are highly aliphatic. The main transformations occurring as these fractions diffuse upward in the water column are 1) loss of sulfur groups through the oxycline and 2) decrease in aliphatic carbon and increase in the heterogeneity of aliphatic moieties. The fraction of modem¹⁴C content of the lake fulvic acids range from a minimum of 0.68 (approximately 3000 years old) at 15m depth to 0.997 (recent material) just under the ice. The major processes controlling the DOC in the lake appear to be: 1) The transport of organic matter by the inflow streams resulting in the addition of recent organic material to the moat and upper waters of the lake; 2) The diffusion of organic matter composed of relict organic material and organic carbon resulting from the degradation of algae and bacteria from the bottom waters or sediments of the lake into overlying glacial melt water, 3) The addition of recent organic matter to the bottom waters of the lake from the moat.     

Root,shoot and soil parameters required for process-oriented models of crop growth limited by water or nutrients

A review is given of the prospects for using process-oriented models of water and nutrient uptake in improving integrated agriculture. Government-imposed restrictions on the use of external inputs will increase the likelihood of (temporary) nutrient or water stress in crop production in NW Europe and thus a better understanding is required of shoot-root-soil interactions than presently available. In modelling nutrient and water uptake, three approaches are possible: 1) models-without-roots, based on empirically derived efficiency ratios for uptake of available resources, 2) models evaluating the uptake potential of root systems as actually found in the field and 3) models which also aim at a prediction of root development as influenced by interactions with environmental factors. For the second type of models the major underlying processes are known and research can concentrate on model refinement on the one hand and practical application on the other. The main parameters required for such models are discussed and examples are given of practical applications. For the third type of models quantification of processes known only qualitatively is urgently needed.     

Diffusivity of Cu2+ in calcium alginate gel beads

The diffusivity of Cu(2+) in calcium alginate beads calculated by the shrinking core model (SCM) was reevaluated in this work. The results obtained in this work were significantly different than those by the original authors. There were excellent agreements between the results obtained by the SCM in this work and those by the more rigorous linear absorption model (LAM) by the original authors. (c) 1994 John Wiley & Sons, Inc.     

The Wageningen Rhizolab — a facility to study soil-root-shoot-atmosphere interactions in crops

A research facility is described for the integrated study of soil-root-shoot-atmosphere relationships in crops. The Wageningen Rhizolab has been in use since 1990, and consists of two rows, each with eight below-ground compartments aligned along a corridor. A rain shelter automatically covers the experimental area at the start of rainfall. Compartments are 125 cm × 125 cm and 200 cm deep. Each compartment has a separate drip irrigation system. Crop canopy photosynthesis, respiration, and transpiration can be measured simultaneously and continuously on four out of eight compartments at a time. Each compartment can be filled with a selected soil material (repacked soil) and is accessible from the corridor over its full depth. Multiple sensors for measuring soil moisture status, electrical conductivity, temperature, soil respiration, trace gases and oxygen are installed in spatial patterns in accordance with the requirements of the experiments. Sensors are connected to control and data-acquisition devices. Likewise, provisions have been made to sample manually the soil solution and soil atmosphere. Root observation tubes (minirhizotrons) are installed horizontally at depth intervals ranging from 5 cm (upper soil layers) to 25 cm (below 1 m). The facility is at present in use to study growth and development of vegetation (crops) in relation to drought, nutrient status, soil-borne diseases, and underground root competition. One important application is the study of elevated CO₂ concentration and climate change and the way they affect crops and their carbon economy. Growth and development of field grown vegetables and winter cover crops are also evaluated. The common aspect of those studies is to gain a better understanding of crop growth under varying environmental conditions, and to collect datasets that may help to improve mechanistic crop growth simulation models that can address suboptimal growth conditions.     

Direct assessment of symbiotically fixed nitrogen in the rhizosphere of alfalfa

Rhizodeposition has been proposed as one mechanism for the accumulation of significant amounts of N in soil during legume growth. The objective of this experiment was to directly quantify losses of symbiotically fixed N from living alfalfa (Medicago sativa L.) roots to the rhizosphere. We used ¹⁵N-labeled N₂ gas to tag recently fixed N in three alfalfa lines [cv. Saranac, Ineffective Saranac (an ineffectively nodulated line), and an unnamed line in early stages of selection for apparent N excretion] growing in 1-m long polyvinylchloride drainage lysimeters in loamy sand soil in a greenhouse. Plants were in the late vegetative to flowering growth stage during the 2-day labelling period. We determined the fate of this fixed N in various plant organs and soil after a short equilibration period (2 to 4 days) and after one regrowth period (35 to 37 days). Extrapolated N₂ fixation rates (46 to 77g plant^–1 h^–1) were similar to rates others have measured in the field. Although there was significant accretion of total N in rhizosphere compared to bulk soil, less than 1% was derived from newly fixed N and there were no differences between the excreting line and Saranac. Loss of N in percolate water was small. These results provide the first direct evidence that little net loss of symbiotically-fixed N occurs from living alfalfa roots into surrounding soil. In addition, these results confirm our earlier findings, which depended on indirect ¹⁵N labelling techniques. Net N accumulation in soil during alfalfa growth is likely due to other processes, such as decomposition of roots, nodules, and above ground litter, rather than to N excretion from living roots and nodules.     

Some rumen ciliates have endosymbiotic methanogens

Abstract Most of the small ciliate protozoa, including Dasytricha ruminantium and Entodinium spp. living in the rumen of sheep, were found to have intracellular bacteria. These bacteria were not present in digestive vacuoles. They showed characteristic coenzyme F₄₂₀ autofluorescence and they were detected with a rhodamine-labelled Archaea-specific oligonucleotide probe. The measured volume percent of autofluorescing bacteria (1%) was close to the total volume of intracellular bacteria estimated from TEM stereology. Thus it is likely that all of the bacteria living in the cytoplasm of these ciliates were endosymbiotic methanogens, using H₂ evolved by the host ciliate to form methane. Intracellular methanogens appear to be much more numerous than those attached to the external cell surface of ciliates.     

Tansley Review No. 59 Leaf boundary layers

Studies of heat and mass exchange between leaves and their local environment are central to our understanding of plant-atmosphere interactions. The transfer across aerodynamic leaf boundary layers is generally described by non-dimensional expressions which reflect largely empirical adaptations of engineering models derived for flat plates. This paper reviews studies on leaves, and leaf models with varying degrees of abstraction, in free and forced convection. It discusses implecations of finding for leaf morphology as it affects – and is affected by – the local microclimate. Predictions of transfer from many leaves in plant communities are complicated by physical and physiological feedback mechanisms between leaves and their environment. Some common approaches, and the current challenge of integrating leaf-atmosphere interactions into models of global relevance, are also briefly addressed.