New method for rapid assessment of the functional composition of herbaceous plant communities

Abstract We propose a rapid sampling method to assess the functional composition of herbaceous plant communities without prior knowledge of the floristic composition. To determine the community‐level value of traits (‘aggregated trait values’) for a plant community, a standardized population‐centred method exists, but requires substantial manpower and reliable botanical knowledge. We tested an alternative method, the trait transect, using four subalpine pastures in the Beaufortain region (Northern French Alps) selected along a fertility gradient. We applied both methods to measure five commonly used ‘soft traits’ known to be responsive to soil nutrient availability: plant vegetative and reproductive height, specific leaf area, leaf dry matter and nitrogen contents. We tested whether the variation of these traits along the gradient detected with the population‐centred method was also detected with the trait transect. Both methods detected expected trends in the traits in response to the fertility gradient. The trait transect method was as efficient as the population‐centred method and is recommended as an appropriate tool for monitoring ecosystem changes in response to environmental conditions and management, especially in species‐rich communities.     

Critical role of helix 12 of the vitamin D(3) receptor for the partial agonism of carboxylic ester antagonists.

The carboxy-terminal alpha-helix of a nuclear receptor ligand-binding domain (LBD), helix 12, contains a critical, ligand-modulated interface for the interaction with coactivator proteins. In this study, using the example of the vitamin D receptor (VDR) and the partial antagonist ZK159222, the role of helix 12 (residues 417-427) for both antagonistic and agonistic receptor actions was investigated. Amino acid residue G423 was demonstrated to be critical for partial agonism of ZK159222, but not for the activity of the natural VDR agonist, 1alpha,25-dihydroxyvitamin D(3) (1alpha,25(OH)(2)D(3)). The amount of partial agonism of ZK159222 increased when helix 12 was truncated by the last four amino acid residues (Delta424-27) and augmented even more, when in addition helix 12 of VDR's dimerization partner, retinoid X receptor (RXR), was truncated. In contrast, the low agonism of a structural derivative of ZK159222, ZK168281, was not affected comparably, whereas other close structural relatives of ZK159222 even demonstrated the same agonistic activity as that of 1alpha,25(OH)(2)D(3). The amount of agonism of ZK159222 and ZK168281 at different variations of helix 12 correlated well with VDR's ability to complex with coactivator proteins and inversely correlated with the strength of the compound's antagonistic action on 1alpha,25(OH)(2)D(3) signalling. Molecular dynamics simulations of the LBD complexed with the two antagonists could explain their different action by demonstrating a more drastic displacement of helix 12 through ZK168281 than through ZK159222. Moreover, the modelling could indicate a kink of helix 12 at amino acid residue G423, which provides the last four amino acid residues of helix 12 with a modulatory role for the partial agonism of some VDR antagonists, such as ZK159222. In conclusion, partial agonism of a VDR antagonist is lower the more it disturbs helix 12 in taking the optimal position for coactivator interaction.     

Roles of non‐native hydrogen‐bonding interaction in helix‐coil transition of a single polypeptide as revealed by comparison between Gō‐like and non‐Gō models

To explore the role of non‐native interactions in the helix‐coil transition, a detailed comparison between a Gō‐like model and a non‐Gō model has been performed via lattice Monte Carlo simulations. Only native hydrogen bonding interactions occur in the Gō‐like model, and the non‐native ones with sequence interval more than 4 is also included into the non‐Gō model. Some significant differences between the results from those two models have been found. The non‐native hydrogen bonds were found most populated at temperature around the helix‐coil transition. The rearrangement of non‐native hydrogen bonds into native ones in the formation of α‐helix leads to the increase of susceptibility of chain conformation, and even two peaks of susceptibility of radius of gyration versus temperature exist in the case of non‐Gō model for a non‐short peptide, while just a single peak exists in the case of Gō model for a single polypeptide chain with various chain lengths. The non‐native hydrogen bonds have complicated the temperature‐dependence of Zimm‐Bragg nucleation constant. The increase of relative probability of non‐native hydrogen bonding for long polypeptide chains leads to non‐monotonous chain length effect on the transition temperature. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

黄土高原丘陵沟壑区小流域植被净第一性生产力模型

构建了机理性植被净第一性生产力模型(Vegetation—Soil—Integrated—Model,VSIM)。该模型将土壤水分动态过程与植被生长过程相耦合,用以分析黄土高原丘陵沟壑区土壤水分对植被生产力的影响。模型考虑了叶片尺度上气孔导度对净光合过程和蒸腾过程的影响,在此基础上通过考虑植被冠层结构和地形因素的影响对模型进行尺度转换,并以位于黄土高原丘陵沟壑区纸坊沟流域的观测数据对模型进行参数化和验证。结果表明对于生物量的模拟草本和半灌木比乔、灌木好．主要植被类型LAI的季节变化与观测结果具有很好的一致性,模型能够反映出流域降雨一产流过程,并且基本上也能够反映土壤水分的时空变化范围。模拟结果表明,刺槐林和苹果林属于高光合一低蒸腾类型,农作物、白羊草群落和达乌里胡枝子群落属于高光合一高蒸腾类型,铁杆蒿群落和茭蒿群落属于低光合一低蒸腾类型,而沙棘灌丛和柠条灌丛的净第一性生产力居中,但蒸腾量较高。流域内土壤水分在多年序列上基本平衡,而在不同的水文年表现出失衡。其中刺槐林、苹果林和沙棘灌丛的多年平均土壤水分在年内存在少量亏缺,铁杆蒿群落和茭蒿群落略有增加,而其它植被类型基本保持平衡。丰水年不同植被类型土壤含水量都明显高于欠水年,土壤水分含量的变化在丰水年表现为盈余,而在欠水年表现为明显的亏缺。     

褐飞虱迁飞参数的数值模拟

迁飞性害虫褐飞虱对中国和亚洲其它国家和地区的水稻有着十分严重的危害,其迁飞参数的时空变化是种群迁飞这一生态行为的重要体现。应用目前国际上先进的中尺度数值预报模式MM5 (V3.2 )对我国褐飞虱北迁、南返的过程进行了数值模拟,根据模拟结果对害虫的迁出虫源地、迁飞路径、降落区、空中迁飞速率、迁飞高度、迁飞历时和迁飞距离等迁飞参数进行了一系列的数值计算和客观分析,得到了与实际虫情普查和雷达观测资料相当吻合的结果,从而比较精确地阐明了褐飞虱迁出起飞、空中定向飞行、降落迁入等迁飞行为的动力学机制。     

Modeling Historical Ecology, Thinking about Contemporary Systems

One way to make archaeological trajectories compelling to contemporary audiences is through detailed computer simulation with graphical interfaces that allow students or researchers to explore historical sequences and ask "what if" questions of them. We discuss progress on modeling coupled human systems and ecosystems over long periods in the Mesa Verde region of the U.S. Southwest, a project developed with both research and educational products in mind. The project has many foci, but here we concentrate on fuel-wood availability and its pre-Hispanic use in the pygmy forests of this region. Our preliminary results tend to indicate that wood for fuels became sufficiently limited in this sequence to become a factor of considerable importance in decisions about where to live, how to build, and even whether to remain in the region. The same logic of modeling can be used to study problems of contemporary forest use in other parts of the world.     

Uncertainty Analysis in Life Cycle Assessment (LCA): Case Study on Plant-Protection Products and Implications for Decision Making (9 pp + 3 pp)

Goal, Scope, and Background Uncertainty analysis in LCA is important for sound decision support. Nevertheless, the actual influence of uncertainty on decision making in specific LCA case-studies has only been little studied so far. Therefore, we assessed the uncertainty in an LCA comparing two plant-protection products.Methods Uncertainty and variability in LCI flows and characterization factors (CML-baseline method) were expressed as generic uncertainty factors and subsequently propagated into impact scores using Monte-Carlo simulation. Uncertainty in assumptions on production efficiency for chemicals, which is of specific interest for the case study, was depicted by scenarios. Results and Discussion Impact scores concerning acidification, eutrophication, and global warming display relatively small dispersions. Differences in median impact scores of a factor of 1.6 were sufficient in the case study for a significant distinction of the products. Results of toxicity impact-categories show large dispersions due to uncertainty in characterization factors and in the composition of sum parameters. Therefore, none of the two products was found to be significantly environmentally preferable to the other. Considering the case study results and inherent characteristics of the impact categories, a tentative rule of thumb is put forward that quantifies differences in impact scores necessary to obtain significant results in product comparisons.Conclusion Published LCA case-studies may have overestimated the significance of results. It is therefore advisable to routinely carry out quantitative uncertainty analyses in LCA. If this is not feasible, for example due to time restrictions, the rule of thumb proposed here may be helpful to evaluate the significance of results for the impact categories of global warming, acidification, eutrophication, and photooxidant creation.     

马铃薯干物质分配与器官建成的动态模拟研究

根据多年不同保护地栽培田间试验的结果,利用Origin软件结合马铃薯生长发育的基本特点,提出了以发育生理日为驱动变量的光合产物在不同器官间分布的数值模型,方法简便,机理明确,模拟精度高.研究还给出了不同发育时期马铃薯不同器官的干物率变化模型,并依此推导出器官的鲜重模型,进行了马铃薯块茎产量的模拟,结果表明模拟值与实测值具有良好的一致性。     

Simulation of the N-terminus of HIV-1 glycoprotein 41000 fusion peptide in micelles.

In this paper, the N-terminus of glycoprotein-41, the HIV-1 fusion peptide, was studied by molecular dynamics simulations in an explicit sodium dodecyl sulfate micelle. The simulation provides a detailed picture of the equilibrium structure and peptide stability as it interacts with the micelle. The equilibrium location of the peptide shows the peptide at the surface of the micelle with hydrophobic residues interacting with the micelle's core. At equilibrium, the peptide adopts an alpha-helical structure from residues 5-16 and a type-1 beta-turn from 17-20 with the other residues exhibiting more flexible conformations. The primary hydrophobic interactions with the micelle are from the leucine and phenylalanine residues (Leu-7, Phe-8, Leu-9, Phe-11, Leu-12) while the alanine and glycine residues (Ala-1, Gly-3, Gly-5, Ala-6, Gly-10, Gly-13, Ala-14, Ala-15, Gly-16, Gly-10, Ala-21) interact favorably with water molecules. The results suggest that Phe-8, part of the highly conserved FLG motif of the fusion peptide, plays a key role in the interaction of the peptide with membranes. Our simulations corroborate experimental investigations of the fusion peptide in SDS micelles, providing a high-resolution picture that explains the experimental findings.