Adaptive significance of facultative paedomorphosis in Triturus alpestris (Amphibia, Caudata): resource partitioning in an alpine lake

1. Facultative paedomorphosis is a polymorphism that has important evolutionary implications in promoting morphological differentiation and variation in habitat use. It occurs in several urodele species throughout the world. Several hypotheses based on life-history theory have been proposed to explain the wide range of habitats in which facultative paedomorphosis occurs, suggesting multifactorial causes.
2. In harsh habitats, such as mountain lakes, paedomorphosis might promote niche partitioning between morphs. This hypothesis was tested by comparing micro-habitat use and diet of two coexisting morphs in an alpine lake.
3. Paedomorphs occupied all microhabitats in the lake while metamorphs occurred only along the shoreline or at the water surface. Paedomorphic newts were frequent in deep water, where they foraged mainly on plankton. Plankton was poorly exploited by metamorphic newts, which fed mainly on terrestrial insects. Difference between morphs in microhabitat use, and consequently in the diet, were consistent in both sexes and in juveniles.
4. In adults, the mass and energy value of stomach contents did not differ between morphs, suggesting a similar food availability in the habitats occupied.
5. This study indicates habitat partitioning between morphs involving dietary differences. Specific benefits and costs of each ontogenetic pathway may allow their coexistence in this deep and fishless lake. Paedomorphosis benefits individual newts by making new food resources available and presumably reducing competition at the shore of the lake. However, the proximate causes of such an ontogenetic switch remain unclear.     

氧敏感蛋白空间晶体生长的研究

为适应固氮酶蛋白等厌氧蛋白质空间晶体生长的要求,应在地面用简易而适用的厌氧加样装置以优化这类蛋白的结晶条件。用塑料袋或简易箱代替固氮酶实验室常用的笨重厌氧箱,获得了缺失nifZ因氮菌（Azotobacter vinelandii Lipmann）突变种的MoFe蛋白和含锰固氮培养基中生物的UW3的MnFe蛋白晶体,并在远离固氮酶实验室的地方,使用由小仪器塑料袋和急求用的氩气袋组成的更轻便的厌氧装置,用坐滴法也能使这两种蛋白结晶出来。结果表明,利用上述简易厌氧装置有望达到以上2种厌氧蛋白空间晶体生长的要求。     

Quantitative metrics of overlaps in Grinnellian niches: advances and possible drawbacks

Aim Studies of environmental niche shift/niche conservatism that are based on species distribution modelling require a quantification of niche purity and potential overlap. Although various metrics have been proposed for this task, no comparisons of their performance are available yet that express the linearity of range shifts and error‐proneness. Herein, we assess the performance of six niche overlap metrics using three sister pairs of plethodontid salamanders as well as artificial species to test for linearity of overlap curves, impacts of varying potential distribution sizes and study area sizes. Location North America, artificial environments. Methods Species distribution models for the salamanders were performed with Maxent , and artificial species were created in the R environment. Potential distributions of species with varying range sizes and extents of the study area were compared using the Bray–Curtis distance BC, Schoener's D, two different modifications of the Hellinger distance I_mod, I_cor, Pianka's O and Horn's R. Niche overlaps in ecological space were compared using linear discriminant analyses based on principal components. Results Simulations of niche overlaps revealed strong variations in the performance of the niche overlap metrics. In artificial species, BC and D performed best, followed by O, R and I_cor, but the modified Hellinger distance I_mod showed a nonlinear slope and a truncated range. Furthermore, the simulations suggest that, in proportionally small potential distributions on large grids, an inclusion of a high proportion of grid cells with low occurrence probabilities representing background noise may bias assessments of niche overlaps. Main conclusions Both the salamander examples and simulations suggest that Schoener's D and the Bray–Curtis distance BC are best suited to compute niche overlaps from potential distributions derived from species distribution models. However, like all analysed metrics, both D and BC are seriously affected by the inclusion of high numbers of grid cells where the species are probably absent, i.e. with low occurrence probabilities. Therefore, pre‐processing to eliminate background noise in the potential distribution grids is highly recommended.     

城市绿地的生态环境效应研究进展

工业化的快速发展和城市化进程的加剧,使得城市生态环境的破坏和污染愈来愈严重,加速了城市的“生态环境危机”.城市绿地能够通过植被的光合作用、吸收作用、隔离阻挡作用、蒸腾以及蒸散作用改善城市的生态环境.目前研究主要集中在降温、增湿、固碳释氧、降噪、抗污染、生物多样性保护等6个方面.关于城区绿地对6种生态环境要素的改善程度、影响范围、机理问题以及不同植被种类生态环境效应的差异情况等,国内外学者都进行了大量详细的研究.基于传统实地观测数据进行城市绿地的生态环境效应研究是目前主要使用的研究方法,部分学者开始使用遥感技术手段研究城区绿地的降温增湿效应.在总结和分析前人研究成果的基础上,从研究内容的不同着手,主要总结并系统评估了目前关于城市绿地6种生态环境效应的研究,为今后相关研究提供参考.     

Prediction of protease types in a hybridization space

Regulating most physiological processes by controlling the activation, synthesis, and turnover of proteins, proteases play pivotal regulatory roles in conception, birth, digestion, growth, maturation, ageing, and death of all organisms. Different types of proteases have different functions and biological processes. Therefore, it is important for both basic research and drug discovery to consider the following two problems. (1) Given the sequence of a protein, can we identify whether it is a protease or non-protease? (2) If it is, what protease type does it belong to? Although the two problems can be solved by various experimental means, it is both time-consuming and costly to do so. The avalanche of protein sequences generated in the post-genetic era has challenged us to develop an automated method for making a fast and reliable identification. By hybridizing the functional domain composition and pseudo-amino acid composition, we have introduced a new method called "FunD-PseAA predictor" that is operated in a hybridization space. To avoid redundancy and bias, demonstrations were performed on a dataset where none of the proteins has >or=25% sequence identity to any other. The overall success rate thus obtained by the jackknife cross-validation test in identifying protease and non-protease was 92.95%, and that in identifying the protease type was 94.75% among the following six types: (1) aspartic, (2) cysteine, (3) glutamic, (4) metallo, (5) serine, and (6) threonine. Demonstration was also made on an independent dataset, and the corresponding overall success rates were 98.36% and 97.11%, respectively, suggesting the FunD-PseAA predictor is very powerful and may become a useful tool in bioinformatics and proteomics.     

经寰枕间隙侧方穿刺移植人脐血单个核细胞对难治性神经系统疾病的疗效分析

目的探讨寰枕间隙侧方穿刺术移植人脐血单个核细胞治疗难治性神经系统疾病的可行性和安全性。 方法应用寰枕间隙侧方穿刺术对230例患者进行450次人脐血单个核细胞治疗,观察治疗中及治疗后有无不良反应和并发症,对比治疗前后血液分析、血沉、生化全项、出凝血机制和肿瘤标记物数值,同时观察患者治疗前后病情转归,采用配对比较t检验进行统计学分析。 结果所有患者治疗后均无头痛、感染、皮疹、血肿形成等不良反应和其它移植并发症出现。32例（7.1%）治疗后出现一过性血压升高,8例（1.8%）出现一过性发热,10例（2.2%）穿刺时诉穿刺处深部软组织胀痛,拔针后疼痛消失。患者白细胞计数治疗前（7.9±1.1）×10⁹个/?L和治疗后3个月（8.0±1.3）×10⁹个/L相比差异无统计学意义（t =?0.891,P?=?0.374）,谷丙转氨酶治疗前（31.9±5.8）U/L和治疗后3个月（32.4±6.2）U/L相比差异无统计学意义（t?=?0.893,P?=?0.372）,球蛋白治疗前（22.1±1.7）g/L和治疗后3个月（21.8±1.8）g/L相比差异无统计学意义（t?=?0.838,P?=?0.066）,AFP治疗前（9.9±1.6）μg/L和治疗后3个月（10.1±1.7）μg/L相比差异无统计学意义（t?=?1.299,P?=?0.195）,患者血液学指标（血常规+血沉、生化全项、全身肿瘤标记物、病毒筛查、出凝血机制）在治疗前后无统计学差异。183例患者治疗有效,有效率79.6%。 结论寰枕间隙侧方穿刺术移植人脐血单个核细胞治疗难治性神经系统疾病是安全可行并可能有效的。     

Analysis of peptides from known proteins: Clusterization in sequence space

A combinatorial sequence space (CSS) model was introduced to represent sequences as a set of overlapping k-tuples of some fixed length which correspond to points in the CSS. The aim was to analyze clusterization of protein sequences in the CSS and to test various hypotheses about the possible evolutionary basis of this clusterization. The authors developed an easy-to-use technique which can reveal and analyze such a clusterization in a multidimensional CSS. Application of the technique led to an unexpectedly high clusterization of points in the CSS corresponding to k-tuples from known proteins. The clusterization could not be inferred from nonuniform amino acid frequencies or be explained by the influence of homologous data. None of the tested possible evolutionary and structural factors could explain the clusterization observed either. It looked as if certain protein sequence variations occurred and were fixed in the early course of evolution. Subsequent evolution (predominantly neutral) allowed only a limited number of changes and permitted new variants which led to preservation of certain k-tuples during the course of evolution. This was consistent with the theory of exon shuffling and protein block structure evolution. Possible applications of sequence space features found were also discussed.Correspondence to: H.A. Lim     

Structure of Hepatitis B Surface Antigen from Subviral Tubes Determined by Electron Cryomicroscopy

Hepatitis B virus consists of an icosahedral core containing the double-stranded DNA genome, enveloped by a membrane with embedded surface proteins. The crystal structure of the core protein has been solved but little information about the structure of the surface proteins has so far been available. There are three sizes of surface protein, small (S), medium (M) and large (L), which form disulfide-bonded homo- and heterodimers. The three proteins, expressed from different start sites in the coding sequence, share the common C-terminal S region; the M protein contains an additional preS2 sequence N-terminal to S, and the L protein a further preS1 sequence N-terminal to M. In infected individuals, the surface proteins are produced in huge excess over the amount needed for viral envelopment and are secreted as a heterogeneous mixture of isometric and tubular subviral particles. We have used electron cryomicroscopy to study tubular particles extracted from human serum. Helical Fourier-Bessel analysis was used to calculate a low-resolution map, although it showed that the tubes were quite disordered. From the symmetry derived from this analysis, we used single-particle methods to improve the resolution. We found that the tubes had a diameter of approximately 250 Å, with spike-like features projecting from the membrane. In the plane of the membrane the proteins appear to be close packed. We propose a model for the packing arrangement of surface protein dimers in the tubes.