利用秆维管束进行中国散生竹类的聚类分析

本文是应用模糊聚类分析方法研究中国散生竹类分类的一次尝试。分类特征采用了竹秆上、中、下三段各类型维管束数,方法上使用了模糊(Fuzzy)直接聚类分析进行综合分析。经电子计算机运算后,不仅取得了与传统分类基本一致的分类结果,同时也表明这种方法较之其它一些植物数量分类方法简便易行,此外还讨论了一些中国散生竹类分类上的问题。     

Bird communities in traditional wood-pastures with changing management in Eastern Europe

Wood-pastures are fragile ecosystems because they were formed by, and depend on specific, low-intensity multifunctional management. Although their ecological and cultural significance is high, wood-pastures are rapidly deteriorating all over Europe, mainly due to changing land use. We still lack a basic understanding of the ecological value of wood-pastures, and in which features they differ from other landscape elements. In this paper we investigated the ecological value of wood-pastures for passerine birds by (i) comparing bird assemblages of wood-pastures with those of closed forests and open pastures and (ii) exploring the relationships between variables describing wood-pastures and species traits of the bird assemblages. Our study region (Southern Transylvania, Romania) provides a unique opportunity to understand the importance of a traditional cultural and ecological environment for many different organisms. Wood-pastures had a higher overall number of bird species, and a higher spatial turnover in bird community composition than closed forests and open pastures. We found significant associations between bird species traits and habitat structural elements in wood-pastures such as large trees, oak- and pear trees and shrubs. Our findings suggest that traditional wood-pastures in Southern Transylvania have distinct and rich passerine bird communities. This richness is inextricably linked to the multifunctional, low-intensity land use traditionally applied in the wood-pastures that promotes high niche diversity. For effective conservation of the biodiversity of wood-pastures, a detailed understanding is needed of how different management regimes may influence the key structural elements of wood-pastures relevant for biodiversity and these should be protected.     

Vitamin D effective ultraviolet wavelengths due to scattering in shade

Solar UVB radiation (280–320 nm) is an initiator of Vitamin D₃ production in the human skin. While numerous studies have been conducted in relation to the biological impact of UV exposure in full sun, less research has investigated the irradiances in shade. The purpose of this study was to determine the levels of UV radiation in relation to Vitamin D₃ induction with six commonly encountered shade environments for the larger solar zenith angles observed during autumn and winter. Spectral UV irradiance measurements were made under relatively clear sky conditions at a sub-tropical Southern Hemisphere site for six specific shade environments and solar zenith angle between 35° and 60° to investigate the biologically effective UV irradiances for pre-Vitamin D₃ production. Data from this research indicates that pre-Vitamin D₃ effective UV wavelengths in the shade were most significant for tree shade and a shade umbrella. Compared to that in full sun, pre-Vitamin D₃ effective UV wavelengths were at levels of approximately 52 and 55%, respectively, beneath the shade umbrella and in tree shade. UVB irradiance levels in the shade of a northern facing covered veranda and in a car with windows closed were significantly less than those beneath the shade umbrella, with levels of approximately 11 and 0%, respectively, of those in full sun. Shade is important as a UV minimisation strategy; however, it may also play an important role in providing the human body with adequate levels of UVB radiation for pre-Vitamin D₃ production without experiencing the relatively higher levels of UVA irradiances present in full sun.     

Tight clustering: a resampling-based approach for identifying stable and tight patterns in data

In this article, we propose a method for clustering that produces tight and stable clusters without forcing all points into clusters. The methodology is general but was initially motivated from cluster analysis of microarray experiments. Most current algorithms aim to assign all genes into clusters. For many biological studies, however, we are mainly interested in identifying the most informative, tight, and stable clusters of sizes, say, 20-60 genes for further investigation. We want to avoid the contamination of tightly regulated expression patterns of biologically relevant genes due to other genes whose expressions are only loosely compatible with these patterns. "Tight clustering" has been developed specifically to address this problem. It applies K-means clustering as an intermediate clustering engine. Early truncation of a hierarchical clustering tree is used to overcome the local minimum problem in K-means clustering. The tightest and most stable clusters are identified in a sequential manner through an analysis of the tendency of genes to be grouped together under repeated resampling. We validated this method in a simulated example and applied it to analyze a set of expression profiles in the study of embryonic stem cells.     

Monte Carlo-based assessment of the trade-off between spatial resolution,field-of-view and scattered radiation in the variable resolution X-ray CT scanner

ObjectiveThe purpose of this work is to evaluate the impact of optimization of magnification on performance parameters of the variable resolution X-ray (VRX) CT scanner.MethodsA realistic model based on an actual VRX CT scanner was implemented in the GATE Monte Carlo simulation platform. To evaluate the influence of system magnification, spatial resolution, field-of-view (FOV) and scatter-to-primary ratio of the scanner were estimated for both fixed and optimum object magnification at each detector rotation angle. Comparison and inference between these performance parameters were performed angle by angle to determine appropriate object position at each opening half angle.ResultsOptimization of magnification resulted in a trade-off between spatial resolution and FOV of the scanner at opening half angles of 90°–12°, where the spatial resolution increased up to 50% and the scatter-to-primary ratio decreased from 4.8% to 3.8% at a detector angle of about 90° for the same FOV and X-ray energy spectrum. The disadvantage of magnification optimization at these angles is the significant reduction of the FOV (up to 50%). Moreover, magnification optimization was definitely beneficial for opening half angles below 12° improving the spatial resolution from 7.5 cy/mm to 20 cy/mm. Meanwhile, the FOV increased by more than 50% at these angles.ConclusionIt can be concluded that optimization of magnification is essential for opening half angles below 12°. For opening half angles between 90° and 12°, the VRX CT scanner magnification should be set according to the desired spatial resolution and FOV.     

Testing four candidate barcoding markers in temperate woody bamboos (Poaceae: Bambusoideae)

Abstract Bambusoideae is an important subfamily of the grass family Poaceae that has considerable economic, ecologic and cultural value. In addition, Bambusoideae species are important constituents of the forest vegetation in China. Because of the paucity of flower‐bearing specimens and homoplasies of morphological characters, it is difficult to identify species of Bambusoideae using morphology alone, especially in the case of temperate woody bamboos (i.e. Arundinarieae). To this end, DNA barcoding has shown great potential in identifying species. The present study is the first attempt to test the feasibility of four proposed DNA barcoding markers (matK, rbcL, trnH–psbA, and internal transcribed spacer [ITS]) in identifying 27 species of the temperate woody bamboos. Three plastid markers showed high levels of universality, whereas the universality of ITS was comparatively low. A single plastid marker provided low levels of discrimination success at both the genus and species levels (<12%). Among the combinations of plastid markers, the highest discriminatory power was obtained using the combination of rbcL+matK (14.8%). Using a combination of three markers did not increase species discrimination. The nuclear region ITS alone could identify 66.7% of species, although fewer taxa were included in the ITS analyses than in the plastid analyses. When ITS was integrated with a single or combination of plastid markers, the species discriminatory power was significantly improved. We suggest that a combination of rbcL+ ITS, which exhibited the highest species identification power of all combinations in the present study, could be used as a potential DNA barcode for temperate woody bamboos.     

Noninvasive online biomass detector system for cultivation in shake flasks

A novel online sensor system for noninvasive and continuous monitoring of cell growth in shake flasks is described. The measurement principle is based on turbidity measurement by detecting 180°‐scattered light and correlation to OD by nonlinear calibration models. The sensor system was integrated into a commercial shaking tablar to read out turbidity from below the shake flasks bottom. The system was evaluated with two model microorganisms, Escherichia coli K12 as prokaryotic and Saccharomyces cerevisiae as eukaryotic model. The sensor allowed an accurate monitoring of turbidity and correlation with OD₆₀₀ ≤ 30. The determination of online OD showed relative errors of about 7.5% for E. coli K12 and 12% for S. cerevisiae. This matches the errors of the laborious offline OD and thus facilitates to overcome the drawbacks of the classical method as risk of contamination and decreasing volumes through sampling. One major challenge was to ensure a defined, nonvarying measurement zone as the rotating suspension in the shake flask forms a liquid sickle which circulates round the flasks inner bottom wall. The resulting alteration of liquid height above the sensor could be compensated by integration of an acceleration sensor into the tablar to synchronize the sensor triggering.     

武夷山五种竹子叶、枝、秆碳氮磷化学计量对生长阶段和海拔的响应

探究竹子化学计量特征对生长阶段和海拔的响应对于了解其生理生态特征及生长适应策略至关重要。对武夷山沿海拔分布的五种典型竹子叶、枝、秆的碳(C)、氮(N)、磷(P)含量及化学计量内稳态指数(H)进行两个生长阶段的测定。结果显示不论生长阶段的变化,各器官N、P含量的变异系数均显著大于C含量,且秆的N、P含量变异系数要显著大于叶片和竹枝,但不同生长阶段并未改变秆的N∶P (12∶1)。毛竹4月份枝和8月份叶的N、P含量均随海拔增加而降低,而箬竹叶的N、P含量均随海拔增加而增加。海拔和生长阶段的交互作用显著提高了竹秆N含量对生长阶段变化的响应。竹叶N和秆的N、P含量在不同生长阶段具有明显的内稳性调控机制,但竹枝N、P的内稳性特征表现不明显。总而言之,这些结果一方面反映了武夷山五种竹子偏向于选择维持叶N含量的内稳态机制,另一方面调节秆N、P含量的协变来应对海拔和生长阶段变化中养分的利用策略。     

Carbon dioxide emission from bamboo culms

Bamboos are one of the fastest growing plants on Earth, and are widely considered to have high ability to capture and sequester atmospheric carbon, and consequently to mitigate climate change. We tested this hypothesis by measuring carbon dioxide (CO₂) emissions from bamboo culms and comparing them with their biomass sequestration potential. We analysed diurnal effluxes from Bambusa vulgaris culm surface and gas mixtures inside hollow sections of various bamboos using gas chromatography. Corresponding variations in gas pressure inside the bamboo section and culm surface temperature were measured. SEM micrographs of rhizome and bud portions of bamboo culms were also recorded. We found very high CO₂ effluxes from culm surface, nodes and buds of bamboos. Positive gas pressure and very high concentrations of CO₂ were observed inside hollow sections of bamboos. The CO₂ effluxes observed from bamboos were very high compared to their carbon sequestration potential. Our measurements suggest that bamboos are net emitters of CO₂ during their lifespan.