The living library of The Cotapata National Park in Bolivia: an example of application of Bolivian law on the access to genetic resources

Developing countries with a rich biodiversity want to control the use of this natural patrimony, especially in the research of natural compounds of pharmaceutical interest. Here we present the organization of six permanent plots in a mountain tropical forest on the east side of the Andean Cordillera in Bolivia, and their role in the discovery of plants with antiplasmodial or antileishmanial activities. Permanent plots are widely used in ecological survey, but rarely in bioprospecting. This set-up allows Bolivian authorities to control the bioprospecting, and facilitates further chemical studies on the bioactive plants. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Lucia Acebey and Amira Apaza have contributed equally to this work.     

Biodiversity conservation,yield, and alternative products in coffee agroecosystems in Sumatra,Indonesia

Agroecology and conservation must overlap to protect biodiversity and farmer livelihoods. Coffee agroecosystems with complex shade canopies protect biodiversity. Yet, few have examined biodiversity in coffee agroecosystems in Asia relative to the Americas and many question whether coffee agroecosystems can play a similar role for conservation. We examined vegetation, ant and bird diversity, coffee yields and revenues, and harvest of alternative products in coffee farms and forests in SW Sumatra, Indonesia near Bukit Barisan Selatan National Park (BBS). BBS is among the last habitats for large mammals in Sumatra and >15,000 families illegally cultivate coffee inside of BBS. As a basis for informing management recommendations, we compared the conservation potential and economic outputs from farms inside and outside of BBS. Forests had higher canopy cover, canopy depth, tree height, epiphyte loads, and more emergent trees than coffee farms. Coffee farms inside BBS had more epiphytes and trees and fewer coffee plants than farms outside BBS. Tree, ant, and bird richness was significantly greater in forests than in coffee farms, and richness did not differ in coffee farms inside and outside of BBS. Species similarity of forest and coffee trees, ants, and birds was generally low (<50%). Surprisingly, farms inside the park were significantly older, but farm size, coffee yields, and revenues from coffee did not depend on farm location. Farmers outside BBS received higher prices for their coffee and also more often produced other crops in their coffee fields such that incentives could be created to draw illegal farmers out of the park. We also discuss these results with reference to similar work in Chiapas, Mexico to compare the relative contribution of coffee fields to conservation in the two continents, and discuss implications for working with farmers in Sumatra towards conservation plans incorporating sustainable coffee production.     

Functional divergence of the duplicated AtKIN14a and AtKIN14b genes: critical roles in Arabidopsis meiosis and gametophyte development

Gene duplication is important for gene family evolution, allowing for functional divergence and innovation. In flowering plants, duplicated genes are widely observed, and functional redundancy of closely related duplicates has been reported, but few cases of functional divergence of close duplicates have been described. Here, we show that the Arabidopsis AtKIN14a and AtKIN14b genes encoding highly similar kinesins are two of the most closely related Arabidopsis paralogs, which were formed by a duplication event that occurred after the split of Arabidopsis and poplar. In addition, AtKIN14a and AtKIN14b exhibit varying degrees of coding sequence divergence. Further genetic studies of plants carrying atkin14a and/or atkin14b mutations indicate that, although these two genes have similar functions, there is clear evidence for functional divergence. Although both genes are important for male and female meiosis, AtKIN14a plays a more critical role in male meiosis than AtKIN14b . Moreover, either one of these two genes is necessary and sufficient for gametophyte development, indicating that they are redundant for this function. Therefore, AtKIN14a and AtKIN14b together play important roles in controlling plant reproductive development. Our results suggest that the AtKIN14a and AtKIN14b genes have retained similar functions in gametophyte development and female meiosis, but have evolved partially distinct functions in male meiosis, with AtKIN14a playing a more substantive role.     

虚拟筛选与新药发现

虚拟筛选是创新药物研究的新方法和新技术,近年来引起了研究机构和制药公司的高度重视,并且已经成为一种与高通量筛选互补的实用化工具,加入到了创新药物研究的工作流程(pipeline)中。本文介绍国际上虚拟筛选及其在创新药物发现中应用的研究进展,特别介绍了我国这方面研究的状况。     

Effects of habitat complexity on forest beetle diversity: do functional groups respond consistently?

We examined the responses of a beetle assemblage to habitat complexity differences within a single habitat type, Sydney sandstone ridgetop woodland, using pitfall and flight‐intercept trapping. Six habitat characters (tree canopy cover, shrub canopy cover, ground herb cover, soil moisture, amount of leaf litter, and amount of logs, rocks and debris) were scored between 0 and 3 using ordinal scales to reflect habitat complexity at survey sites. Pitfall trapped beetles were more species rich and of different composition in high complexity sites, compared with low complexity sites. Species from the Staphylinidae (Aleocharinae sp. 1 and sp. 2), Carabidae (Pamborus alternans Latreille), Corticariidae (Cartodere Thomson sp. 1) and Anobiidae (Mysticephala Ford sp. 1) were most clearly responsible for the compositional differences, preferring high complexity habitat. Affinities between general functional groupings of pitfall‐trapped beetles and habitat variables were not clear at a low taxonomic resolution (family level). The composition and species richness of flight‐intercept‐trapped beetles were similar in high and low complexity sites. Our study demonstrates that discrete responses of the various functional groups of beetles are strongly associated with their feeding habits, indicated by differing habitat components from within overall composite habitat complexity measures. Although habitat preferences by beetle species may often reflect their foraging habits, clarification of the causal mechanisms underpinning the relationships between habitat complexity and beetles are critical for the development of general principles linking habitat, functional roles and diversity.     

Facilitative interactions rather than resource partitioning drive diversity-functioning relationships in laboratory fungal communities

We manipulated the number of saprotrophic fungi in either a complex multi-resource substratum (sterilized forest soil), or a single-resource substratum (powdered cellulose). The substrates were inoculated with five common species of soil fungi in all possible combinations (from monocultures to five species in combination). In both substrates, the rate of organic matter decomposition was positively associated with species richness. The effect of fungal diversity was much stronger in the uniform single-resource substrate ( r ² = 0.455, P  < 0.0001) than in soil ( r ² = 0.154, P  < 0.0001). The results document that species richness of microbial decomposers strongly affects decomposition processes, at least at the species poor end of the diversity gradient. Both, 'sampling effect' and 'species complementarity effect' contributed to the community response with the latter being much more pronounced in uniform substrate than in soil. This indicates that facilitative interactions are more important than resource partitioning for positive effects of species richness.     

Patch dynamics in grazed subtropical native pastures in south‐east Queensland

Abstract Patch formation is common in grazed grasslands but the mechanisms involved in the formation and maintenance of patches are not clear. To increase our knowledge on this subject we examined possible reasons for patch formation and the influence of management on changes between patch states in three experiments in native pasture communities in the Crows Nest district, south‐east Queensland. In these communities, small‐scale patches (tall grassland (dominated by large and medium tussock grasses), short swards (dominated by short tussock grasses and sedges), and lawns (dominated by stoloniferous and/or rhizomatous grasses)) are readily apparent. We hypothesized that the formation of short sward and lawn patches in areas of tall grassland was due to combinations of grazing and soil fertility effects. This was tested in Experiment 1 by applying a factorial combination of defoliation, nutrient application and transplants of short tussock and stoloniferous species to a uniform area of tall grassland. Total species density declined during the experiment, was lower with high nutrient applications, but was not affected by defoliation. There were significant changes in abundance of species that provided support for our hypotheses. With light defoliation and low nutrients, the tall grassland remained dominated by large tussock grasses and contained considerable amounts of forbs. With heavy defoliation, the pastures were dominated by medium tussock grasses and there were significant decreases in forbs and increases in sedges (mainly with low nutrients) and stoloniferous grasses (mainly with high nutrients). Total germinable seed densities and those of most species groups were significantly lower in the heavy defoliation than the light defoliation plots. Total soil seed numbers were not affected by nutrient application but there were fewer seeds of the erect forbs and more sedge seeds in plots with high nutrients. The use of resting from grazing and fire to manage transitions between patches was tested. In Experiment 2 , changes in species density and abundance were measured for 5 years in the three patch types with and without grazing. Experiment 3 examined the effects of fire, grazing and resting on short sward patches over 4 years. In Experiment 2 , total species density was lower in lawn than short sward or tall grassland patches, and there were more species of erect forbs than other plant groups in all patch types. The lawn patches were originally dominated by Cynodon spp. This dominance continued with grazing but in ungrazed patches the abundance of Cynodon spp. declined and that of forbs increased. In the short sward patches, dominance of short tussock grasses continued with grazing but in ungrazed plots their abundance declined while that of large tussock grasses increased. The tall grassland patches remained dominated by large and medium tussock species. In Experiment 3 , fire had no effect on species abundance. On the grazed plots the short tussock grasses remained dominant but where the plots were rested from grazing the small tussock grasses declined and the large tussock grasses increased in abundance. The slow and relatively small changes in these experiments over 4 or 5 years showed how stable the composition of these pastures is, and that rapid changes between patch types are unlikely.     

Functional response of a parasitoid Ganaspidium utilis （Hymenoptera： Eucoilidae） on the leafminer Liriomyza trifolii （Diptera： Agromyzidae）

Functional response of a solitary, larval-pupal endoparasitoid of Liriomyza leafminers, Ganaspidium utilis Beardsley, was estimated on Liriomyza trifolii Burgess at three temperatures （17℃, 25℃, 29℃ ） and host densities. A type Ⅱ random parasitoid equation （RPE） was used to estimate instantaneous search rate and handling time. The instantaneous search rate increased as temperature increased. All of the RPE regressions obtained for functional response of G. utilis at different temperatures were significant （P〈0.01）. The slope of RPE regression lines was lower across the temperatures. At 29±2℃, the maximum number of larvae parasitized was 7.8 per day. It decreased to 7.2 larvae parasitized at 25±2℃. At 17±2℃, no significant increment of parasitization was observed due to the host density increments. The estimated handling time was lowest at 17±2℃ and highest at 25 ± 2℃, respectively. The ability of G. utilis to find and parasitize L. trifolii over a wide range of temperatures makes them a good candidate for biological control of Liriomyza leafminers.     

Variations in the Volatile Organic Compound Emission Potential of Plant Functional Groups in the Temperate Grassland Vegetation of Inner Mongolia, China

The biogenic volatile organic compounds (VOC) emitted by the vegetation of a terrestrial ecosystem play a key role in both regional air quality and tropospheric chemistry. To describe the general emission properties of VOC of different plant functional groups (PFG) in a typical temperate grassland in Inner Mongolia, China, we randomly selected 175 plant species and measured the quantities of isoprene and monoterpene in situ. Results showed that most plants had low VOC emission potential at the species level,especially for some dominant plants, such as Leymus chinensis Tzvel., Stipa grandis Smirn., and Agropyron cristatum Gaertn. At the PFG level, the lowest VOC emission potential was found for perennial rhizome grasses, a major PFG in a typical temperate grassland ecosystem. The effects of overgrazing and subsequent vegetation succession on the emission of VOC by different plant life form functional groups (PLFG)were also discussed.     

Red/ET 同源重组介导细菌人工染色体的快速修饰

随着基因组测序工程的实施与完成,如何对包含完整基因信息的特定细菌人工染色体 (BAC) 进行有目的修饰,已成为功能基因组学研究的一个重要环节 . 应用新近优化的 Red/ET 同源重组技术对目标 BAC 进行修饰,以 pSC101-BAD-gbaA 为依托质粒,采用 rpsL-neo 为正 / 反向筛选系统,可以快速、高效地对 BAC 进行剪切、插入、替换等操作,其中能够进行抗性筛选的一步 BAC 修饰只需一周时间,以插入非抗性标记基因 Cre 为代表的两步 BAC 修饰在两周内即可完成 . 通过阿拉伯多糖诱导调控和简单地变化培养温度,能使 pSC101-BAD-gbaA 依托质粒在发挥完 Red/ET 同源重组作用后自然消失,最终获得完整而纯净的修饰后 BAC ,为加快功能基因组学研究提供了一个可靠的实验平台 .