Biological synthesis of circular polypeptides

Here, we review the use of different biochemical approaches for biological synthesis of circular or backbone-cyclized proteins and peptides. These methods allow the production of circular polypeptides either in vitro or in vivo using standard recombinant DNA expression techniques. Protein circularization can significantly impact protein engineering and research in protein folding. Basic polymer theory predicts that circularization should lead to a net thermodynamic stabilization of a folded protein by reducing the entropy associated with the unfolded state. Protein cyclization also provides a valuable tool for exploring the effects of topology on protein folding kinetics. Furthermore, the biological production of cyclic polypeptides makes possible the production of cyclic polypeptide libraries. The generation of such libraries, which was previously restricted to the domain of synthetic chemists, now offers biologists access to highly diverse and stable molecular libraries for probing protein structure and function.     

A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization

We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa-Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation of polypeptide folding starting from a fully unfolded state. We compare our results with available native state structures from Protein Data Bank (PDB) for a few de-novo proteins and two natural proteins, Ubiquitin and Lysozyme. Based on our simulations we are able to draw the energy landscape for a small de-novo protein, Chignolin. We also use two well known protein structure prediction software, MODELLER and GROMACS to compare our results. In the end, we show how a modification of normal elastic network model can lead to higher accuracy and lower time required for simulation.     

森林生态系统土壤保持价值的年内动态

以定位观测数据位基础,选用日雨量模型和通用土壤流失方程,研究了5种森林生态系统土壤保持价值的年内动态。研究表明,季节雨林、次生林、人工橡胶林、阔叶红松林和次生白桦林的土壤保持价值分别为570.29、347.87、174.65、14.31元.hm-.2a-1和8.76元.hm-.2a-1。土壤保持价值各月分配不均,5-10月的土壤保持价值占全年土壤保持价值的80%以上。西双版纳3种森林生态系统土壤保持价值构成中,保持土壤养分的价值高达60%以上。长白山2种森林生态系统的土壤保持价值构成有所不同,阔叶红松林以减少泥沙淤积价值为主,而次生白桦林以保持土壤养分价值为主。土壤保持价值构成中,减少废弃地价值的不足总价值的10%。     

江西九连山常绿阔叶林优势种群的年龄结构与分布格局

以江西九连山常绿阔叶林为研究对象,用"空间序列代替时间变化"的方法,应用统计软件对该地区常绿阔叶林群落优势种群的年龄结构特征和分布格局进行线性回归分析。结果表明:润楠的存活曲线表现为极显著的线性关系,罗浮栲与赤楠等种群的存活曲线表现为显著的线性关系;种群的年龄结构既有稳定型或增长型,也有衰退波动型,如木荷、润楠等种群的年龄结构为稳定增长型,拟赤杨、枫香等种群的年龄结构为衰退型,丝线吊芙蓉、罗浮槭、鹿角栲等种群的年龄结构由稳定型趋向衰退型。应用聚集度指标、方差和均值比率、负二项式分布等方法研究各主要优势种群的分布格局,结果为构成群落乔木层的12个主要优势种群的分布格局均属聚集分布,并符合负二项式分布。     

云南普洱季风常绿阔叶林演替系列植物和土壤C、N、P化学计量特征

通过测定中国西南季风常绿阔叶林不同演替阶段(演替15a,演替30a及原始林)群落中植物叶片与土壤中C、N、P含量,探索了季风常绿阔叶林不同演替阶段群落C、N、P化学计量特征及其与物种丰富度及多度的相关性。结果表明:土壤及植物中全N、全P含量及土壤中C含量均为演替30a群落中最低,而植物中C含量在不同演替阶段群落间无显著性差异。在不同演替阶段共有种中,40%的物种N含量原始林中最高,40%的物种P含量演替15a群落中最高,而80%的物种C含量无显著性差异。土壤中C:N比在不同演替阶段间无显著变化,而N:P及C:P比则随演替呈减小趋势。植物中C:N及C:P比均为演替30a群落最高,而N:P比则随演替呈增加趋势。不同演替阶段共有种的C:N比中,40%的物种原始林中最低,40%的物种无差异,而C:P与N:P比中则均有60%物种无显著性差异,但70%物种在演替15a群落中N:P小于14,演替30a群落中50%物种N:P在14—16,原始林中则有80%物种N:P大于16。群落物种丰富度及个体多度均与C:N、N:P、C:P无显著的相关性,但植物中的N、P与土壤的N、P分别具有显著的线性正相关,说明土壤中N、P供应量影响植物体中的N、P含量。     

The Greater Cape Floristic Region

Aim The Cape Floristic Region (CFR) (Cape Floristic Kingdom) is currently narrowly delimited to include only the relatively mesic Cape fold mountains and adjacent intermontane valleys and coastal plains. We evaluate the floristic support for expanding the delimitation to include the whole winter‐rainfall area (arid and mesic climates) into a Greater CFR. Location Southern Africa, particularly the south‐western tip. Methods The initial divisive hierarchical classification analysis twinspan used the presence/absence of vascular plant genera to obtain major floristic groupings in southern Africa. For the more detailed analyses, we scored the flora as present/absent within a set of centres, among which the floristic relationships were investigated (agglomerative methods, upgma and minimum spanning trees). These analyses were conducted with species, genera and families separately. The centres were grouped into five regions. The species richness and endemism was calculated for the centres, regions and combination of regions. The dominant floristic components of each region were sought by calculating the percentage contribution of each family to the flora. Results The divisive method showed that the winter‐rainfall areas are floristically distinct from the rest of southern Africa. The species‐ and generic‐level analyses revealed five regions: CFR, Karoo Region, Hantam‐Tanqua‐Roggeveld Region, Namaqualand Region and Namib‐Desert Region. The CFR has the highest endemism and richness. However, the combination of the CFR, the Hantam‐Tanqua‐Roggeveld Region and the Namaqualand Region results in a higher total endemism. Combined, these three regions almost match the region delimited by the twinspan analysis, and together constitute the Greater CFR. Main conclusions The CFR constitutes a valid floristic region. This is evident from the endemism and the distinctive composition of the flora. However, the total endemism is higher for the whole winter‐rainfall area, and this supports the recognition of the larger unit. If floristic regions are to be delimited only on endemism, then the Greater CFR is to be preferred. If floristic regions are delimited on the composition of their floras at family level, then the support for such a grouping is weaker.     

Phenology of Ficus racemosa in Xishuangbanna,Southwest China1

Leaf and fig phenology (including leafing, flowering, and fruiting) and syconium growth of Ficus racemosa were studied in Xishuangbanna, China. Leaffall and flushing of F. racemosa occurred twice yearly: in mid‐dry season (December to March) and mid‐rainy season (July to September). The adult leaf stage of the first leaf production was remarkably longer than that of the second. F. racemosa bears syconia throughout the year, producing 4.76 crops annually. Asynchronous fig production was observed at a population level. Fig production was independent of leafing. Fig production peaks were not evident, but fluctuation was clear. Diameter growth rates of syconium were normally higher in early developmental stages than in later stages, and reached a peak coinciding with the female flower phase. The mean ± SD of syconium diameter of the female flower phase was 2.19 ± 0.36 cm, and reached 3.67 ± 0.73 cm of the male flower phase. Syconium diameter and receptacle cavity quickly enlarged at the female and male flower phases. Monthly diameter increment of the syconium was primarily affected by average monthly temperature, rather than rainfall or relative humidity.     

Lightning-caused disturbance in the Peruvian Amazon

We surveyed seven lightning strike sites in the northern Peruvian Amazon. An average of 17.3 trees were damaged per strike; large trees (> 60 cm diameter) were disproportionately affected. The results contribute to a growing body of evidence that lightning is an important agent of disturbance pantropically. Abstract in Spanish is available with online material.     

地形异质性对云南普洱季风常绿阔叶林物种多样性的影响

地形异质性通过调控树木生长所需的养分、水分和光照等而成为亚热带森林结构与物种组成的重要驱动因子。但是, 地形异质性对季风常绿阔叶林物种多样性及其分布影响的研究还相对较少。该文基于云南普洱30 hm²森林动态监测样地(大样地) 750个20 m × 20 m的样方调查数据, 以海拔、坡度、凹凸度和坡向4个地形因子为变量, 采用C均值模糊聚类分析大样地的地形类型, 进而分析不同地形条件下的群落物种组成及群落物种多样性; 采用Torus转换检验法, 探讨物种与地形关联性, 为季风常绿阔叶林生物多样性保护提供科学依据。研究结果表明, 大样地可分为山脊、陡坡、缓坡、高谷和沟谷等5类地形, 地形面积分别是8.00、6.04、7.68、2.76和5.52 hm²。大样地中胸径(DBH) ≥ 1 cm的木本植物个体153 418株, 分属79科179属271种。5类地形中, 物种丰富度、不同径级的植株密度和比例明显不同, 多样性及优势物种多度分布具有较大差异。种-面积曲线表明, 同等面积条件下, 随着取样面积增加, 山脊的物种丰富度始终最小, 高谷次之, 沟谷的物种丰富度始终最大。种-个体数累积曲线表明, 随着个体数增加, 山脊物种丰富度的累积速率最小, 种丰富度增加缓慢, 高谷次之。在被检验的123个物种中, 与地形相关的物种有83个, 高达67.5%的物种与至少一类地形存在显著相关关系。山脊和缓坡中与地形具有显著负相关关系的物种数超过显著正相关的物种数; 而与陡坡、高谷和沟谷显著正相关的物种数高于显著负相关的物种数。普洱大样地地形异质性对物种多样性维持的贡献率为7.8%。     

Evaluation of major Acacia species in the nursery towards apicultural landscape restoration around Southwestern Saudi Arabia

Southwestern Saudi Arabia is described by a unique ecosystem and composed of apicultural landscapes where nearly 70% of the beekeeping activities are concentrated. However, this economically important resource is under continuous degradation threat urging restoration. Besides, profound information on the possible major biological components of future restoration; nursery level performances of the native plants, Acacia species is lacking. Hence, the study was aimed at evaluating performances of selected native Acacia species at nursery level as candidate biological tool for apicultural landscape restoration. For this, nine native Acacia species’ seedlings were prepared in accordance to appropriate techniques of nursery operations recommended for arid areas. Meanwhile, species were evaluated and compared based on some performance parameters. Accordingly, significant (P < 0.005) variations were observed among the species in shoot height, collar diameter, height to collar diameter ratio, number of leaves and seedling survival. Acacia origena Hunde, A. gerrardii Benth., and A. johnwoodii Boulos. were superior over the others in most parameters while A. etbaica Schiweinf. and A. asak (Forssk.) willd. were less vulnerable to chanced pathogens. Generally, nursery level performances of all Acacia species under experimentation were within the acceptable range and showed a remarkable score which may lead them to be considered as competent biological tools in the incorporation of the genotypes in apicultural landscape restoration efforts.