Prediction of membrane protein types by means of wavelet analysis and cascaded neural networks

In this study, membrane proteins were classified using the information hidden in their sequences. It was achieved by applying the wavelet analysis to the sequences and consequently extracting several features, each of them revealing a proportion of the information content present in the sequence. The resultant features were made normalized and subsequently fed into a cascaded model developed in order to reduce the effect of the existing bias in the dataset, rising from the difference in size of the membrane protein classes. The results indicate an improvement in prediction accuracy of the model in comparison with similar works. The application of the presented model can be extended to other fields of structural biology due to its efficiency, simplicity and flexibility.     

Lineages-through-time plots of neutral models for speciation

Drawing inferences about macroevolutionary processes from phylogenetic trees is a fundamental challenge in evolutionary biology. Understanding stochastic models for speciation is an essential step in solving this challenge. We consider a neutral class of stochastic models for speciation, the constant rate birth-death process. For trees with n extant species - which might be derived from bigger trees via random taxon sampling - we calculate the expected time of the kth speciation event (k=1,...,n-1). Further, for a tree with n extant species, we calculate the density and expectation for the number of lineages at any time between the origin of the process and the present. With the developed methods, expected lineages-through-time (LTT) plots can be drawn analytically. The effect of random taxon sampling on LTT plots is discussed.     

美国东部杜克森林长期定位研究综述

 该文比较系统地综述了美国东部杜克森林76年来植物种类变化、种群动态和森林演替研究的基本情况。重点介绍了该森林内永久性森林样地的 设置和调查规范,以及最近10年来利用永久样地数据进行树木空间格局和自然干扰研究的最新进展,并将杜克森林永久样地监测规范和数据管 理方法与目前主要的森林监测网络进行了一定的比较,旨在对目前国际上蓬勃开展的长期定位植物多样性监测和空间格局研究有所启示和帮助 。     

Thirty‐eight years of change in a tropical forest: plot data from Mpanga Forest Reserve,Uganda

Variations in the composition and structure of mid‐altitude, semi‐deciduous topical forest in a 0.64‐ha plot in Mpanga Forest Reserve, Uganda, are described for a 38‐year period to 2006. Repeat surveys of trees in the plot with a girth ≥30 cm at reference height in 1982, 1993 and 2006, following a baseline survey in 1968, indicate only relatively minor fluctuations in density, Shannon diversity, evenness, basal area (BA) and estimated above ground biomass. The largest trees [diameter at breast height (dbh) > 40 cm] and main canopy taxa (e.g. Celtis mildbraedii) accounted for the largest fraction of BA. Mortality was the highest amongst taxa classed as early seral, understorey and/or in the smallest size category (dbh = 9.5–20 cm), while new recruits were predominantly understorey taxa. Only one tree was recorded as felled for human use between the surveys of 1968 and 1993. In contrast, a considerable increase in anthropogenic disturbance was evident at the time of the 2006 survey, and illegal logging now poses a substantial threat to future resource availability and carbon storage in what was for a time one of the most protected areas of forest in Uganda.     

Forecasting Environmental Responses to Restoration of Rivers Used as Log Floatways: An Interdisciplinary Challenge

Log floating in the 19th to mid 20th centuries has profoundly changed the environmental conditions in many northern river systems of the world. Regulation of flow by dams, straightening and narrowing of channels by various piers and wing dams, and homogenization of bed structure are some of the major impacts. As a result, the conditions for many riverine organisms have been altered. Removing physical constructions and returning boulders to the channels can potentially restore conditions for these organisms. Here we describe the history of log driving, review its impact on physical and biological conditions and processes, and predict the responses to restoration. Reviewing the literature on comparable restoration efforts and building upon this knowledge, using boreal Swedish rivers as an example, we address the last point. We hypothesize that restoration measures will make rivers wider and more sinuous, and provide rougher bottoms, thus improving land-water interactions and increasing the retention capacity of water, sediment, organic matter and nutrients. The geomorphic and hydraulic/hydrologic alterations are supposed to favor production, diversity, migration and reproduction of riparian and aquatic organisms. The response rates are likely to vary according to the types of processes and organisms. Some habitat components, such as beds of very large boulders and bedrock outcrops, and availability of sediment and large woody debris are believed to be extremely difficult to restore. Monitoring and evaluation at several scales are needed to test our predictions.     

Immobilization of Xylan-Degrading Enzymes from Scytalidium thermophilum on Eudragit L-100

Summary Xylanase from Scytalidium thermophilum was immobilized on Eudragit L-100, a pH sensitive copolymer of methacrylic acid and methyl methacrylate. The enzyme was non-covalently immobilized and the system expressed 70% xylanase activity. The immobilized preparation had broader optimum temperature of activity between 55 and 65 °C as compared to 65 °C in case of free enzyme and broader optimum pH between 6.0 and 7.0 as compared to 6.5 in case of free enzyme. Immobilization increased the t_1/2 of enzyme at 60 °C from 15 to 30 min with a stabilization factor of 2. The K_m and V_max values for the immobilized and free xylanase were 0.5% xylan and 0.89 μmol/ml/min and 0.35% xylan and 1.01 μmol/ml/min respectively. An Arrhenius plot showed an increased value of activation energy for immobilized xylanase (227 kcal/mol) as compared to free xylanase (210 kcal/mol) confirming the higher temperature stability of the free enzyme. Enzymatic saccharification of xylan was also improved by xylanase immobilization.     

Multi-scale comparisons of cliff vegetation in Colorado

We developed a nested vegetation sampling protocol to sample the plant diversity on south-facing cliffs and cliff bases in Jefferson County, Colorado. The multi-scale plots included three nested spatial scales, 1 m², 20 m², and 40 m². We compared plant species richness and species diversity among large cliffs, medium cliffs, small cliffs, and non-cliff sites using Hill's diversity numbers (N ₀, N ₁, and N ₂) for the 1-m² quadrats. Species richness (N ₀) was calculated for the 20-m² and 40-m² plots. Our results indicate that plant species diversity on the cliff faces did not increase with increasing cliff area. This pattern was consistent at all three sampling scales. A model selection was run to determine if plant species diversity values on the cliff faces were associated with cliff variables. None of the cliff variables measured were good predictors of diversity at the 1-m² scale. However, at the 20-m² scale, canyon differences and a positive relationship with increasing cliff surface roughness explained 70% of the variability in species richness. Although most plant species sampled on the cliff faces were also found in the base plots, 13 species were sampled only on the cliff faces. Additionally, dry south facing cliffs support a mix of xeric and mesic plants indicating that cliffs may provide unique microenvironments for plant establishment. This revised version was published online in August 2006 with corrections to the Cover Date.     

A combined method for determining inhibition type, kinetic parameters, and inhibition coefficients for aerobic cometabolism of 1,1,1-trichloroethane by a butane-grown mixed culture.

A combined method for determining inhibition type, kinetic parameters, and inhibition coefficients is developed and presented. The method was validated by applying it to data obtained from batch kinetics of the aerobic cometabolism of 1,1,1-trichloroethane (1,1,1-TCA) by a butane-grown mixed culture. The maximum degradation rates (k(max)) and half-saturation coefficients (K(s)) were independently determined in single compound tests, and compared with those obtained from inhibition tests. The inhibition type was determined using direct linear plots at various substrate and inhibitor concentrations. Kinetic parameters (k(max) and K(s)) and inhibition coefficients (K(ic) and K(iu)) were determined by nonlinear least squares regression (NLSR) fits of the inhibition model determined from the direct linear plots. Initial guesses of the kinetic parameters for NLSR were determined from linearized inhibition equations that were derived from the correlations between apparent maximum degradation rates (k(app)(max)) and/or the apparent half-saturation coefficient (K(app)(s)) and the k(max), K(s), and inhibitor concentration (I(L)) for each inhibition equation. Two different inhibition types were indicated from the direct linear plots: competitive inhibition of 1,1,1-TCA on butane degradation, and mixed inhibition of 1,1,1-TCA transformation by butane. Good agreement was achieved between independently measured k(max) and K(s) values and those obtained from both NLSR and the linearized inhibition equations. The initial guesses of all the kinetic parameters determined from linear plots were in the range of the values estimated from NLSR analysis. Overall the results show that use of the direct linear plot method to identify the inhibition type, coupled with initial guesses from linearized plots for NLSR analysis, results in an accurate method for determining inhibition types and coefficients. Detailed studies with pure cultures and purified enzymes are needed to further demonstrate the utility of this method.     

Vegetation change in a man‐made salt marsh affected by a reduction in both grazing and drainage

Abstract. In order to restore natural salt marsh in a 460‐ha nature reserve established in man‐made salt marsh in the Dollard estuary, The Netherlands, the artificial drainage system was neglected and cattle grazing reduced. Vegetation changes were traced through two vegetation surveys and monitoring of permanent plots over 15 yr after the management had been changed. Exclosure experiments were started to distinguish grazing effects from effects of increased soil waterlogging caused by the neglect of the drainage system. Both vegetation surveys and permanent plots demonstrated a dichotomy in vegetation succession. The incidence of secondary pioneer vegetation dominated by Salicornia spp. and Suaeda maritima increased from 0 to 20%, whereas the late‐successional (Phragmites australis) vegetation from 10 to 15%. Grazing intensity decreased towards the sea. The grazed area contracted landward, which allowed vegetation dominated by tall species to increase seaward. Grazing and increased waterlogging interacted in several ways. The impact of trampling increased, and in the intensively grazed parts soil salinity increased. This can probably be explained by low vegetation cover in spring. Framework Ordination, an indirect‐gradient‐analysis technique, was used to infer the importance of environmental factors in influencing changes in species composition. Many changes were positively or negatively correlated with soil aeration and soil salinity, whereas elevation was of minor importance. Grazing accounted for only a few changes in species frequency. Changes in permanent plots were greater during the first than during the second half of the study period. In exclosures that were installed halfway through the study period, there was a relatively rapid recovery of previously dominant species that had decreased during the first half of the study period. Species richness per unit area in the reserve increased. At the seaward side of the marsh, the altered management allowed succession to proceed leading to establishment of stands of Phragmites australis, whereas on the landward side, the combination of moderate grazing with neglect of the drainage system appeared an effective measure in maintaining habitats for a wider range of halophytic species.     

Vegetation of ant-hills in a mountain grassland:effects of mound history and of dominant ant species

Vegetation in grasslands with well-developed long-lastingant-hills in the Slovenské Rudohorie Mts., Slovakia, was studiedin relation to (i) position on the mound, (ii) ant speciesforming the mound, and (iii) history of the mound. Permanent plotrecordings of mound size and dominant ant species started fifteen years priorthe study began provided information on the history of individual mounds.The mound vegetation bears a striking similarity to vegetation insimilar habitats across a large part of Europe due to presence of species suchas Agrostis capillaris, Dianthusdeltoides, Polytrichum commune agg.,Thymus pulegioides, and Veronicaofficinalis. Out of the three major ant species-groups presentat the site (Lasius flavus, Tetramoriumcaespitum and Formica spp.), L.flavus had the most pronounced and the most lasting effect on themound vegetation. The dominance of the plant species listed above increased withthe time span over which the mound was inhabited by L.flavus. The effects of other species on vegetation composition,though discernible from short-term observation, disappeared over severalyears. The mounds proper did not differ from the undisturbed grassland in theproportion of myrmecochorous plants or plants with specific seed size ordormancy type. However, there was a highly significant concentration ofmyrmecochorous plants in the grassland patches immediately neighbouring themounds; this is likely to be due to seeds deposited there by the workers fromthe nest after the elaiosomes had been consumed. The mound vegetation wascomposed mainly of species with long stolons or rhizomes; however, there was nosignificant difference in formation type or length of stolons/rhizomesbetween mounds and the rest of the grassland or among mounds formed by differentant species.