Identification and characterization of key substructures involved in the early folding events of a (beta/alpha)8-barrel protein as studied by experimental and computational methods

A number of studies have examined the structural properties of late folding intermediates of (beta/alpha)8-barrel proteins involved in tryptophan biosynthesis, whereas there is little information available about the early folding events of these proteins. To identify the contiguous polypeptide segments important to the folding of the (beta/alpha)8-barrel protein Escherichia coli N-(5'-phosphoribosyl)anthranilate isomerase, we structurally characterized fragments and circularly permuted forms of the protein. We also simulated thermal unfolding of the protein using molecular dynamics. Our fragmentation experiments demonstrate that the isolated (beta/alpha)(1-4)beta5 fragment is almost as stable as the full-length protein. The far and near-UV CD spectra of this fragment are indicative of native-like secondary and tertiary structures. Structural analysis of the circularly permutated proteins shows that if the protein is cleaved within the two N-terminal betaalpha modules, the amount of secondary structure is unaffected, whereas, when cleaved within the central (beta/alpha)(3-4)beta5 segment, the protein simply cannot fold. An ensemble of the denatured structures produced by thermal unfolding simulations contains a persistent local structure comprised of beta3, beta4 and beta5. The presence of this three-stranded beta-barrel suggests that it may be an important early-stage folding intermediate. Interactions found in (beta/alpha)(3-4)beta5 may be essential for the early events of ePRAI folding if they provide a nucleation site that directs folding.     

Components of ecosystem evaporation in a temperate coniferous rainforest, with canopy transpiration scaled using sapwood density

Here we develop and test a method to scale sap velocity measurements from individual trees to canopy transpiration (E(c)) in a low-productivity, old-growth rainforest dominated by the conifer Dacrydium cupressinum. Further, E(c) as a component of the ecosystem water balance is quantified in relation to forest floor evaporation rates and measurements of ecosystem evaporation using eddy covariance (E(eco)) in conditions when the canopy was dry and partly wet. Thermal dissipation probes were used to measure sap velocity of individual trees, and scaled to transpiration at the canopy level by dividing trees into classes based on sapwood density and canopy position (sheltered or exposed). When compared with ecosystem eddy covariance measurements, E(c) accounted for 51% of E(eco) on dry days, and 22% of E(eco) on wet days. Low transpiration rates, and significant contributions to E(eco) from wet canopy evaporation and understorey transpiration (35%) and forest floor evaporation (25%), were attributable to the unique characteristics of the forest: in particular, high rainfall, low leaf area index, low stomatal conductance and low productivity associated with severe nutrient limitation.     

Sucrose application,soil microbial respiration and evolved carbon dioxide isotope enrichment under contrasting land uses

Heterotrophic decomposition of organic matter dictates that substrate supply rate, including energy and nutrients, can limit soil microbial activity. In New Zealand, soils are naturally deficient in nitrogen and phosphorus. Fertiliser application is a part of pastoral agriculture, the countrys most widespread land use. We postulated that organic soils under grazed pasture and pristine forest would be at the extremes of substrate quality and supply rate, and thus potential microbial response to food opportunities. Soil microbial responses to the addition of fresh energy (sucrose) were determined by laboratory experiments with root-free samples and intact cores including roots. Responses were quantified by respiration and respired carbon (C) isotope (¹³C) enrichment measurements. A supra-trace sucrose dose (0.002 mol kg^–1 (soil)) caused the forest soils microbial respiration rate to nearly double within 2 h. The peak response took 20 h, and saturation occurred beyond a sucrose dose of 0.05 mol kg^–1 (soil). Intact soil cores from the forest had similar respiration rates and responses. For root-free soil samples from the grazed pasture, respiration response to sucrose was nearly immediate, dose dependent, and there was up to a 9-fold increase in the rate. Intact cores from the pasture had much higher respiration rates, but a similar response to sucrose. For both soils, the similarity of sucrose application effects on respiration and relative ¹³C enrichment of the respired carbon was striking.     

五台山林区典型人工林群落物种多样性研究

对山西五台山林区4种典型人工林群落物种多样性特征进行了定量研究,结果表明: 1 4种人工林群落灌木层和草本层的Simpson指数 D 和Shannon-Wienner指数 H′ 差异不显著,物种丰富度指数和均匀度指数 Jsw 差异显著,均匀度指数 Ea 差异极显著,草本层发育明显好于灌木层; 2 各人工群落尚处于演替初期阶段,林下植被发育常以禾本科阳生性植物为主; 3 对4种人工林群落灌草层物种多样性显著性检验结果显示,在灌草层物种多样性特征上,油松林与桦木林、山杨林多样性差异显著 P<0.05 ,其它群落差异不显著.山杨林物种多样性程度较高,油松林最差; 4 不同人工林群落物种总体多样性特征分析表明,桦木和山杨人工林群落总体α多样性与油松林差异显著,且多样性较大,阔叶林更有利于林下植被的发育和更新; 5 对人工生态系统物种多样性研究是退耕还林、天然林保护等生态环境工程的延伸,对于植被恢复后的生物学效果评价有重要意义.     

Estimation of effective population size and detection of a recent population decline coinciding with habitat fragmentation in a ground beetle

We assess the impact of habitat fragmentation on the effective size (N(e)) of local populations of the flightless ground beetle Carabus violaceus in a small (<25 ha) and a large (>80 ha) forest fragment separated by a highway. N(e) was estimated based on the temporal variation of allele frequencies at 13 microsatellite loci using two different methods. In the smaller fragment, N(e) estimates ranged between 59 and a few hundred, whereas values between 190 and positive infinity were estimated for the larger fragment. In both samples, we detected a signal of population decline, which was stronger in the small fragment. The estimated time of onset of this N(e) reduction was consistent with the hypothesis that recent road constructions have divided a continuous population into several isolated subpopulations. In the small fragment, N(e) of the local population may be so small that its long-term persistence is endangered.     

Growth inhibition and induction of differentiation and apoptosis mediated by sodium butyrate in caco-2 cells with algal glycolipids

Summary Glycolipids should have potential effects as antitumor agents. However, very few studies have examined this property of digalactosyl diacylglycerol (DGDG) and sulfoquinovosyl diacylglycerol (SQDG) on colon cancer cells. Cell viability was determined every 24 h with sodium 2-(4-iodophenyl)-3-(4-nitrophenyl)-5-(2, 4-disulfophenyl)-2H-tetrazolium dye reduction assay up to 72 h. Alkaline phosphatase activity was measured for assessing cell differentiation. Apoptosis was tested with enzyme-linked immunosorbent assay analysis. Growth of Caco-2 cells was inhibited apparently at 48 h after addition of SQDG and at 72 h with DGDG. Alkaline phosphatase activity of Caco-2 cells obviously increased in combination with DGDG or SQDG and sodium butyrate (NaBT) at 72 h, indicating that DGDG and SQDG enhanced cell differentiation induced with NaBT. An increased enrichment factor was found when the cell was treated in combination with DGDG or SQDG and NaBT. These results strongly suggest that DGDG and SQDG should be considered as the leading compounds of potentially useful colon cancer chemotherapy agents when NaBT is combined.     

Abundance of two threatened woodpecker species in relation to the proportion of spruce plantations in native pine forests of western Norway

In a comparative study we investigated woodpecker abundance in forest landscapes with different proportion of native pine forest and spruce plantations in western Norway. In 100 circular study plots of 100ha each we recorded 38 white-backed –Dendrocopos leucotos, 22 grey-headed –Picus canus, 13 great spotted –Dendrocopos major, 6 green –Picus viridis, and 2 lesser spotted –Dendrocopos minor woodpeckers in the breeding season. The mean number of recorded woodpecker species peaked at 20–40% spruce plantations. The two most common species in the study, the white-backed and the grey-headed woodpeckers are both Red-listed species in Norway and among the rarest woodpeckers in Europe. The white-backed woodpecker preferred plots with higher than average proportions of standing dead trees and deciduous trees, and low proportions of spruce plantations in the plots. The grey-headed woodpecker preferred plots in the western (coastal) parts of the study area with presence of large aspen Populus tremula trees. Logistic regression models did not reveal any clear threshold values with respect to proportion of spruce plantations in plots, although both woodpecker species were extremely rare in plots with >60% spruce plantations. We recommend spruce plantations to be kept at moderate levels to ensure viable populations of woodpeckers in western Norway.     

Diversity of dung and carrion beetles in a disturbed Mexican tropical montane cloud forest and on shade coffee plantations

This paper analyzes the diversity of dung and carrion beetles (Scarabaeinae and Silphidae) in four human-induced habitats of a disturbed tropical montane cloud forest: polyspecific shade coffee plantations, monospecific shade coffee plantations, tropical montane cloud forest fragments, and clear cuts. The four habitats had similar richness, species composition, and assemblage structure of dung and carrion beetles. Differences were found in abundance and biomass levels for the four dominant species in the landscape. Dung beetles were more abundant than carrion beetles, but the biomass was higher for the latter. Carrion beetles were seasonal, while dung beetles were clearly not. When forest fragments and shade coffee plantations were compared to other similar habitats in the region, the same general pattern was observed. However, forests with high disturbance and monospecific shade coffee plantations had lower species richness than forests with low and medium disturbance and polyspecific shade coffee plantations. Thus shade coffee plantations maintain connectivity between patches of cloud forest in a landscape that is strongly affected by human activities. Protecting landscape diversity appears to ensure high species richness.     

Have recent changes in forest structure reduced the Estonian black stork <Emphasis Type="Italic">Ciconia nigra</Emphasis> population?

The black stork Ciconia nigra is listed as a focal species for guiding forest management in Estonia, where forestry has recently intensified and the stork population has suffered a twofold decline. We explored a possible link between the decline of the population and man-induced changes in forest structure, by analysing nesting of the species in relation to forest cover, edge effects and stand structure. Although the storks had distinct habitat preferences (old remote stands near rivers and a certain distance far from ecotones in well-forested landscapes), these were hardly reflected in site re-occupancy and productivity. Therefore, changes in forest structure are probably not responsible for the population decline, although preferences for specific forest environments may limit the range of potential nest sites. The results indicated that edge avoidance cannot be considered a species-specific feature over large areas and clear habitat preferences are not necessarily related with the present success of a population. We also suggest that lists of focal species should be regularly updated and validated in the field.