Prediction of the packing arrangement of strands in β-sheets of globular proteins

A method is proposed for predicting the adjacency order in which strands pack in a -sheet in a protein, on the basis of its amino acid sequence alone. The method is based on the construction of a predicted contact map for the protein, in which the probability that various residue pairs are close to each other is computed from statistically determined average distances of residue pairs in globular proteins of known structure. Compact regions, i.e., portions of the sequence with many interresidue contacts, are determined on the map by using an objective search procedure. The proximity of strands in a -sheet is predicted from the density of contacts in compact regions associated with each pair of strands. The most probable -sheet structures are those with the highest density of contacts. The method has been tested by computing the probable strand arrangements in a five-strand -sheet in five proteins or protein domains, containing 62–138 residues. Of the theoretically possible 60 strand arrangements, the method selects two to eight arrangements as most probable; i.e., it leads to a large reduction in the number of possibilities. The native strand arrangement is among those predicted for three of the five proteins. For the other two, it would be included in the prediction by a slight relaxation of the cutoff criteria used to analyze the density of contacts.     

The efficiency of water use in water stressed plants is increased due to ABA induced stomatal closure

Gas exchange and abscisic acid content of Digitalis lanata EHRH. have been examined at different levels of plant water stress. Net photosynthesis, transpiration and conductance of attached leaves declined rapidly at first, then more slowly following the withholding of irrigation. The intercellular partial pressure of CO₂ decreased slightly. The concentration of 2-cis(S)ABA increased about eight-fold in the leaves of non-irrigated plants as compared with well-watered controls. A close linear correlation was found between the ABA content of the leaves and their conductance on a leaf area basis. In contrast, the plot of net assimilation versus ABA concentration was curvilinear, leading to an increased efficiency of water use during stress. After rewatering, photosynthesis reached control values earlier than transpiration, leaf conductance and ABA content. From these data it is concluded that transpiration through the stomata is directly controlled by the ABA content, whereas net photosynthesis is influenced additionally by other factors.Possible reasons for the responses of photosynthesis and water use efficiency to different stress and ABA levels are discussed.Abbreviations A net CO₂ assimilation - ABA abscisic acid - C_i intercellular CO₂ concentration - g stomatal conductance - T transpiration - WUE water use efficiency     

Effects of drought on host and endophyte development in mycorrhizal soybeans in relation to water use and phosphate uptake

Bethlenfalvay, G. J., Brown, M. S., Ames, R. N. and Thomas, R. S. 1988. Effects of drought on host and endophyte development in mycorrhizal soybeans in relation to water use and phosphate uptake. - Physiol. Plant. 72: 565–571.
Soybean [ Glycine max (L.) Merr.] plants were grown in pot cultures and inoculated with the vesicular-arbuscular mycorrhizal (VAM) fungus Glomus mosseae (Nicol. & Gerd.) Gerd. and Trappe or provided with P fertilizer (non-VAM plants). After an initial growth period (21 days), plants were exposed to cycles of severe, moderate or no drought stress over a subsequent 28-day period by rewatering at soil water potentials of -1.0, -0.3 or -0.05 MPa. Dry weights of VAM plants were greater at severe stress and smaller at no stress than those of non-VAM plants. Phosphorus fertilization was applied to produce VAM and non-VAM plants of the same size at moderate stress. Root and leaf P concentrations were higher in non-VAM plants at all stress levels. All plants were stressed to permanent wilting prior to harvest. VAM plants had lower soil moisture content at harvest than non-VAM plants. Colonization of roots by G. mosseae did not vary with stress, but the biomass and length of the extraradical mycelium was greater in severely stressed than in non-stressed plants. Growth enhancement of VAM plants relative to P-fertilized non-VAM plants under severe stress was attributed to increased uptake of water as well as to more efficient P uptake. The ability of VAM plants to deplete soil water to a greater extent than non-VAM plants suggests lower permanent wilting potentials for the former.     

Rice cultivar evaluation for phosphorus use efficiency

Phosphorus deficiency is one of the most growth-limiting factors in acid soils in various parts of the world. The objective of this study was to screen 25 rice cultivars (Oryza sativa L.) at low, medium, and high levels of soil P. Number of tillers, root length, plant height, root dry weight and shoot dry weight were related to tissue P concentrations, P uptake and P-use efficiency. Shoot weight was found to be the plant parameter most sensitive to P deficiency. Significant cultivar differences in P use efficiency were found. Phosphorus use efficiency was higher in roots than shoots and decreased with increasing levels of soil P. Positive correlations were found among growth parameters such as plant height, tillers, root and shoot weight, and P content of roots and shoots. These results indicate selection of rice cultivars for satisfactory performance under low P availability can be carried out using shoot and root dry weight as criteria.     

The response ofPlantago lanceolata L. andP. major L. spp.major to nitrate depletion

To study aspects of the ecology of grassland species, in a comparative experiment, plants ofP. lanceolata andP. major were grown in pots in a greenhouse, and subjected to a gradual nitrate depletion for several weeks. Control plants were weekly supplied with nitrate. Growth, leaf appearance and disappearance, concentrations of cations and inorganic anions, soluble and insoluble reduced nitrogen concentrations,in vivo nitrate reductase activity (NRA) and the concentration of non-structural carbohydrates in several parts of the plants were followed. Depletion of nitrate caused a reduction of shoot growth, both in biomass and number of leaves. Withering of leaves increased. Accumulation of root dry matter was little (P. lanceolata), or not (P. major) affected. The concentration of reduced nitrogen in all tissues also decreased, both that of the soluble and that of the insoluble fraction. As a result, nitrogen use efficiency (NUE, g dry matter produced per mmol N incorporated) increased by nitrate depletion. NRA was higher in the roots than in the leaves, and decreased with increasing nitrate depletion. In control plants, nitrate became also limiting. This resulted in decreasing nitrate concentrations in leaves and roots. In the leaves, the decrease in nitrate concentration was preceded by a decrease in NRA. The decrease of the nitrate concentration was parallelled by an increase in the concentration of soluble sugar. No major differences in the response towards nitrate depletion were observed between the two species. Grassland Species Research Group, publication no. 129     

Development of tool use in a macaque and a gorilla

The development of the capacity to use a stick as a tool was tested in a macaque (Macaca fuscata) and a gorilla (Gorilla gorilla gorilla) infants that had previously shown to be able to use strings and supports as dragging tools. Subjects were tested between 15 and 38 months of age. Different levels of competence between the subjects emerged over testing. The macaque developed a stereotyped strategy to cope with the problem, only getting random successes, whilst the gorilla developed a flexible strategy and revealed to be able to mentally represent the solution of the problem. In fact, when not successful using the stick, the gorilla thought out an alternative strategy, choosing and adapting a new object to use it as a tool.     

Activity budgets and use of enclosed space by wild boars (Sus scrofa) in captivity

This research was conducted on a captive group of eight wild boars: Four wildborn adults (one male and three females) and four piglets (one male and three females), born in captivity two months before the beginning of the study. They were housed in the Rome Zoo in a 1,000 sq m enclosure furnished with trees, mud pools, a water basin, and two small barns. Data on eight behavioral states (sleeping, resting, rooting, eating, walking, standing, scratching, and nursing) were collected by instantaneous sampling at 10-minute intervals. The spatial location of each subject was also noted, as well as closeness to conspecifics. Results showed that adults and piglets differed in their activity budgets. Activity patterns showed a significant correlation with the mean temperatures. Furthermore, there was a significant difference in the use of the exhibit areas between adults and piglets. This study suggests a social structure in which the core is constituted by females and their yearlings. The nonbreeding female has a more marginal position than the breeding ones. Finally, the male tends to be even more peripheral and solitary. Our results are partly consistent with the data obtained in studies on free-ranging wild boars (Mauget, 1980; Dardaillon, 1984).     

The osmotic/calcium stress theory of brain damage: Are free radicals involved?

This overview presents data showing that glucose use increases and that excitatory amino acids (i.e., glutamate, aspartate), taurine and ascorbate increase in the extracellular fluid during seizures. During the cellular hyperactive state taurine appears to serve as an osmoregulator and ascorbate may serve as either an antioxidant or as a pro-oxidant. Finally, a unifying hypothesis is given for seizure-induced brain damage. This unifying hypothesis states that during seizures there is a release of excitatory amino acids which act on glutamatergic receptors, increasing neuronal activity and thereby increasing glucose use. This hyperactivity of cells causes an influx, of calcium (i.e. calcium stress) and water movements (i.e., osmotic stress) into the cells that culminate in brain damage mediated by reactive oxygen species.Special issue dedicated to Dr. Frederick E. Samson     

CO2 and water vapour exchange in four alpine herbs at two altitudes and under varying light and temperature conditions

CO₂ and water vapour exchange rates of four alpine herbs namely: Rheum emodi, R. moorcroftianum, Megacarpaea polyandra and Rumex nepalensis were studied under field conditions at 3600 m (natural habitat) and 550 m altitudes. The effect of light and temperature on CO₂ and water vapour exchange was studied in the plants grown at lower altitude. In R. moorcroftianum and R. nepalensis, the average photosynthesis rates were found to be about three times higher at 550 m as compared to that under their natural habitat. However, in M. polyandra, the CO₂ exchange rates were two times higher at 3600 m than at 550 m but in R. emodi, there were virtually no differences at the two altitudes. These results indicate the variations in the CO₂ exchange rates are species specific. The change in growth altitude does not affect this process uniformly.The transpiration rates in R. emodi and M. polyandra were found to be very high at 3600 m compared to 550 m and are attributed to overall higher stomatal conductance in plants of these species, grown at higher altitude. The mid-day closure of stomata and therefore, restriction of transpirational losses of water were observed in all the species at 550 m altitude. In addition to the effect of temperature and relative humidity, the data also indicate some endogenous rhythmic control of stomatal conductance.The temperature optima for photosynthesis was close to 30°C in M. polyandra and around 20°C in the rest of the three species. High temperature and high light intensity, as well as low temperature and high light intensity, adversely affect the net rate of photosynthesis in these species.Both light compensation point and dark respiration rate increased with increasing temperature.The effect of light was more prominent on photosynthesis than the effect of temperature, however, on transpiration the effect of temperature was more prominent than the effect of light intensity.No definite trends were found in stomatal conductance with respect to light and temperature. Generally, the stomatal conductance was highest at 20°C.The study reveals that all these species can easily be cultivated at relatively lower altitudes. However, proper agronomical methodology will need to be developed for better yields.     

The influence of habitat use and foraging on the replacement of one introduced wasp species by another in New Zealand

Abstract.

• 1 New Zealand was colonized by the German wasp, Vespula germanica (F.), in the 1940s and it subsequently became established throughout the country. The common wasp, V.vulgaris (L), colonized in the late 1970s and is still spreading.
• 2 The common wasp has replaced the German wasp in some habitats in New Zealand. Samples from a nationwide postal survey indicate that the common wasp is now the more abundant species in honeydew beech forests (Nothofagus spp.), and to a lesser extent in other native forests. The German wasp is still the more abundant wasp in rural areas (excluding forest). The two species are at present co-dominant in urban areas, although this may be a transient phase.
• 3 In honeydew beech forest the two species show different foraging patterns that provide the potential for local coexistence. Although both species are generalist feeders, the German wasp is more commonly found foraging for protein amongst the forest litter, whereas the common wasp forages more on shrubs and tree saplings. Despite this difference, the common wasp can still replace the German wasp in honeydew beech forest within a few years of invasion.
• 4 In honeydew beech forests in which the German wasp is the more abundant species it dominates honeydew trunks (sugar resource), whereas the common wasp dominates honeydew trunks in areas where it is the more abundant species. The change from German to common wasp domination of honeydew trunks is more rapid than the change in dominance in other microhabitats. Aggressive interactions may be taking place on this high quality, potentially defensible sugar resource.