Recent changes in mountain grasslands: a vegetation resampling study

Understanding how land‐use changes affect different facets of plant biodiversity in seminatural European grasslands is of particular importance for biodiversity conservation. As conclusions of previous experimental or synchronic observational studies did not converge toward a general agreement, assessing the recent trends in vegetation change in various grassland systems using a diachronic approach is needed. In this resurvey study, we investigated the recent changes in grassland vegetation of the French Jura Mountains, a region with a long tradition of pastoralism. We compared the floristic composition of 150 grassland plots recorded between 1990 and 2000 with new relevés made in 2012 on the same plots. We considered taxonomic, phylogenetic and functional diversity as well as ecological characteristics of the plant communities derived from ecological indicator values and life strategies of the species. PCA of the floristic composition revealed a significant general trend linked to the sampling year. Wilcoxon paired tests showed that contemporary communities were generally more dominated by grass species and presented a higher tolerance to defoliation, a higher pastoral value, and a higher nutrient indicator value. Comparisons revealed a decrease in phylogenetic and functional diversity. By contrast, local species richness has slightly increased. The intensity of change in species composition, measured by Hellinger distance between pairs of relevés, was dependent on neither the time lag between the two surveys, the author of the first relevé nor its location or elevation. The most important changes were observed in grasslands that previously presented low pastoral value, low grass cover, low tolerance to defoliation, and high proportion of stress‐tolerant species. This trend was likely linked to the intensification of grassland management reported in the region, with a parallel increase in mowing frequency, grazing pressure, and fertilization level. More restrictive specifications should be applied to agricultural practices to avoid overexploitation of mountain species‐rich grasslands and its negative consequences on their biodiversity and resilience.     

Biological screening of rain forest plot trees from Palawan Island (Philippines)

Study plots totaling 0.2 Ha were established in primary forest in the highlands of central Palawan Island, Philippines. Samples of various anatomical parts [typically leaf + twig (If/tw), stem bark (sb), and root (rt)] were collected from all tree species represented within the plots by individuals having a diameter at breast height > or = 10 cm. In all, 211 distinct samples were obtained from 68 tree species, representing 35 families (not including samples from 4 indeterminate species). Methanol extracts of these samples were tested in in vitro antiplasmodial, brine shrimp toxicity, and cytotoxicity assays. The following samples showed an IC50 < or = 10 microg/mL against either chloroquine-sensitive or chloroquine-resistant clones of Plasmodium falciparum: Acronychia laurifolia (sb), Agathis celebica (lf/tw), Aglaia sp. 1 (sb), Aglaia sp. 2 (lf/tw, rt), Bhesa sp. 1 (rt), Cinnamomum griffithii (lf/tw), Croton leiophyllus (rt), Dysoxylum cauliflorum (rt), Garcinia macgregorii (sb), Lithocarpus sp. 1 (rt, sb), Meliosma pinnata ssp. macrophylla (lf/tw, rt), Myristica guatteriifolia (lf/tw), Ochrosia glomerata (rt, sb), Swintonia foxworthyi (lf/tw), Syzygium sp. 1 (rt), Turpinia pomifera (rt), and Xanthophyllum flavescens (sb). Secondly, those samples which displayed > or = 50% immobilization of brine shrimp at 100 microg/mL were: Acronychia laurifolia (lf/tw/fruit, rt, sb), Agathis celebica (lf/tw, sb), Aglaia sp. 1 (lf/tw), Alphonsea sp. 1 (rt), Ardisia iwahigensis (lf/tw), Arthrophyllum ahernianum (lf/tw, rt, sb), Castanopsis cf. evansii (rt), Cinnamomum griffithii (lf/tw, rt), Croton argyratus (lf/tw), C. leiophyllus (lf/tw, rt), Dysoxylum cauliflorum (fruit, lf/tw, rt), Euonymus javanicus (rt), Glochidion sp. 1 (rt), Polyosma sp. 1 (rt), Symplocos polyandra (rt), Timonius gammillii (sb), and Xanthophyllum flavescens (rt). Lastly, samples which exhibited an IC50 < or = 20 microg/mL against one or more of the cancer cell lines employed (LU1, KB, KB-V1, P-388, LNCaP, or ZR-75-1) include: Acronychia laurifolia (lf/tw/fruit, rt, sb), Aglaia sp. 1 (sb), Aglaia sp. 2 (rt), Alphonsea sp. 1 (rt), Ardisia iwahigensis (lf/tw, rt, sb), Astronia cumingiana (sb), Croton argyratus (lf/tw, rt, sb), C. leiophyllus (lf/tw, rt), Dimorphocalyx murina (lf/tw, rt, sb), Lithocarpus caudatifolius (rt, sb), Litsea cf. sibuyanensis (rt), Syzygium cf. attenuatum (rt, sb), S. confertum (sb), Ternstroemia gitingensis (rt), and Ternstroemia sp. 1 (rt, sb).     

Structural and functional aspects of the respiratory chain of synaptic and nonsynaptic mitochondria derived from selected brain regions

Studies on brain mitochondria are complicated by the regional, cellular, and subcellular heterogeneity of the central nervous system. This study was performed using synaptic and nonsynaptic mitochondria obtained from cortex, hippocampus, and striatum of male Sprague-Dawley rats (3 months old). Ubiquinone content, detected by HPLC analysis, was about 1.5 nmol/mg protein with an approximate CoQ₉/CoQ₁₀ molecular ratio of 2:1. The activities of several respiratory chain complexes were also studied (succinate-cyt.c reductase, NADH-cyt.c reductase, succinate-DCIP, ubiquinol₂-cyt.c reductase, and cytochrome oxidase), and generally found to be higher in mitochondria from cortex than from other regions. Study of the activities of some of these enzymes vs. 1/T (Arrhenius plots) showed a straight line with an activation energy between 7 and 10 kcal/mol in all the three areas considered. Only CoQ₂H₂-cyt.c reductase activity revealed a biphasic temperature dependence. Also anisotropy (as fluorescence polarization) of the hydrophobic probe DPH showed a deviation from linearity; the break points for both enzymatic activity and anisotropy were found at about 23–24°C.     

Comparison of the regeneration after burning,cutting and ploughing in a Cistus ladanifer shrubland

The recovery of a Cistus shrubland after experimental treatments (cutting, burning and ploughing) was studied to determine qualitative and quantitative differences in the secondary succession. The study was carried out in three experimental plots of 100 m² each, in which five 1 m² sampling units were fixed and surveyed for five years, estimating cover percentage of each plant species. The data were analysed by means of affinity indexes (Sorensen and Steinhaus Indexes). The results indicated that the cover of the woody species increased progressively, but the degree of recovery depended on the treatment, as well as on the time afterwards. The number of these species remained almost constant throughout the whole period. The herbaceous species diversity was higher in the two first years in all treatments. When treatments were compared, the greatest diversity occurred after cutting. The regeneration of the community occurred by autosuccession in which the diversity decreased when the dominance of Cistus increased, unlike the general trend of the classical theories. The recovery was very quick after all three treatments, which can be interpreted as a great resilience of this ecosystem.     

Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation

In this paper, we intend to predict protein structural classes (α, β, α+β, or α/β) for low-homology data sets. Two data sets were used widely, 1189 (containing 1092 proteins) and 25PDB (containing 1673 proteins) with sequence homology being 40% and 25%, respectively. We propose to decompose the chaos game representation of proteins into two kinds of time series. Then, a novel and powerful nonlinear analysis technique, recurrence quantification analysis (RQA), is applied to analyze these time series. For a given protein sequence, a total of 16 characteristic parameters can be calculated with RQA, which are treated as feature representation of protein sequences. Based on such feature representation, the structural class for each protein is predicted with Fisher's linear discriminant algorithm. The jackknife test is used to test and compare our method with other existing methods. The overall accuracies with step-by-step procedure are 65.8% and 64.2% for 1189 and 25PDB data sets, respectively. With one-against-others procedure used widely, we compare our method with five other existing methods. Especially, the overall accuracies of our method are 6.3% and 4.1% higher for the two data sets, respectively. Furthermore, only 16 parameters are used in our method, which is less than that used by other methods. This suggests that the current method may play a complementary role to the existing methods and is promising to perform the prediction of protein structural classes.     

108 years of change in spatial pattern following selective harvest of a Pinus ponderosa stand in northern Arizona,USA

Questions: How did an initial tree harvest in 1894 influence the spatial and temporal patterns of Pinus ponderosa recruitment? How do these patterns compare to our understanding of P. ponderosa stand dynamics prior to Euro‐American settlement? How might spatial pattern information, particularly with respect to patch characteristics, inform current restoration and management practices? Location: A 2.59‐ha permanent sample plot in the Fort Valley Experimental Forest, Flagstaff, Arizona. The plot was selectively harvested in 1894 and measured in 1909 and 2002. Methods: We used historical stem‐map and ledger data, contemporary data, and dendrochronological techniques to reconstruct stand structure (tree size, age, location) in three scenarios: (1) unharvested (1909), (2) harvested (1909), and (3) contemporary (2002). We used Clark and Evans' R, Ripley's K(t) univariate analysis, and correlogram analysis to assess the spatial pattern in each scenario. We also used Ripley's K₁₂(t) bivariate analysis and tree age data to examine spatial and temporal recruitment patterns as observed in the contemporary scenario. Results and Conclusions: The unharvested stand was aggregated at scales up to 28 m. The selective harvest accentuated the spatial patchiness of the stand in 1909 and changed spatial patterns by homogenizing tree size within patches. By 2002, the stand was a single patch dominated by small trees. Post‐harvest recruitment patterns were not spatially random; Pinus seedlings initially established in natural grass openings and then proceeded to fill‐in stump patches created by harvesting. Knowledge of spatial pattern should be explicitly incorporated into restoration activities in these forests.