Mechanistic aspects of chiral discrimination by surface‐immobilized α1‐acid glycoprotein

The immobilization of the globular protein α‐1‐acid glycoprotein (AGP) onto silica gel led to the commercial availability of an AGP column, which has a high enantioselectivity. The enantioselectivity of AGP columns has been demonstrated in numerous applications. Due to potential AGP structural changes occurring upon its immobilization, the interaction between particular pairs of enantiomers and the stationary phase is very difficult to assess. Therefore, in this paper we report a mechanistic study that probes the nature of these types of interactions. As model ligands, we employed two LTD₄ antagonists (L‐708, 738, MK0476, and their enantiomers) which have a rigid backbone consisting of a conjugated aromatic region and a side chain which is terminated with a carboxylic functional group. The difference between the two compounds is a two‐fluorine versus one‐chlorine substituent in the aromatic region of the molecule. To study the interaction between the two homologues and the AGP stationary phase, several parameters were varied, including pH, ionic strength, organic modifier, and temperature. van't Hoff plots were constructed and found to be nonlinear. They could, however, be divided into two linear regions, one from 0°C to ∼30°C, and another from 39°C to 50°C. The region at lower temperature implied that the separation was entropy‐dominated while the separation at higher temperature was enthalpically driven. The transition from the entropic to the enthalpically driven separation region suggested that bound AGP undergoes a conformational change. Fluorescence spectroscopy performed on the AGP stationary phase found evidence for a limited conformational transition at a similar temperature, consistent with this hypothesis. Chirality 11:224–232, 1999. © 1999 Wiley‐Liss, Inc.     

Anion induced conformational preference of CαNN motif residues in functional proteins

Among different ligand binding motifs, anion binding C^αNN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C^αNN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C^αNN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion.     

A method of factor analysis for shape coordinates

Currently the most common reporting style for a geometric morphometric (GMM) analysis of anthropological data begins with the principal components of the shape coordinates to which the original landmark data have been converted. But this focus often frustrates the organismal biologist, mainly because principal component analysis (PCA) is not aimed at scientific interpretability of the loading patterns actually uncovered. The difficulty of making biological sense of a PCA is heightened by aspects of the shape coordinate setting that further diverge from our intuitive expectations of how morphometric measurements ought to combine. More than 50 years ago one of our sister disciplines, psychometrics, managed to build an algorithmic route from principal component analysis to scientific understanding via the toolkit generally known as factor analysis. This article introduces a modification of one standard factor‐analysis approach, Henry Kaiser's varimax rotation of 1958, that accommodates two of the major differences between the GMM context and the psychometric context for these approaches: the coexistence of “general” and “special” factors of form as adumbrated by Sewall Wright, and the typical loglinearity of partial warp variance as a function of bending energy. I briefly explain the history of principal components in biometrics and the contrast with factor analysis, introduce the modified varimax algorithm I am recommending, and work three examples that are reanalyses of previously published cranial data sets. A closing discussion emphasizes the desirability of superseding PCA by algorithms aimed at anthropological understanding rather than classification or ordination.     

Conspecific density dependence and community structure: Insights from 11 years of monitoring in an old‐growth temperate forest in Northeast China

Forest community structure may be influenced by seedling density dependence, however, the effect is loosely coupled with population dynamics and diversity in the short term. In the long term the strength of conspecific density dependence may fluctuate over time because of seedling abundance, yet few long‐term studies exist. Based on 11 years of seedling census data and tree census data from a 25‐ha temperate forest plot in Northeast China, we used generalized linear mixed models to test the relative effects of local neighborhood density and abiotic factors on seedling density and seedling survival. Spatial point pattern analysis was used to determine if spatial patterns of saplings and juveniles, in relation to conspecific adults, were in accordance with patterns uncovered by conspecific negative density dependence at the seedling stage. Our long‐term results showed that seedling density was mainly positively affected by conspecific density, suggesting dispersal limitation of seedling development. The probability of seedling survival significantly decreased over 1 year with increasing conspecific density, indicating conspecific negative density dependence in seedling establishment. Although there was variation in conspecific negative density dependence at the seedling stage among species and across years, a dispersed pattern of conspecific saplings relative to conspecific adults at the local scale (<10 m) was observed in four of the 11 species examined. Overall, sapling spatial patterns were consistent with the impacts of conspecific density on seedling dynamics, which suggests that conspecific negative density dependence is persistent over the long term. From the long‐term perspective, conspecific density dependence is an important driver of species coexistence in temperate forests.     

Long‐term after‐effects of fertilisation on the restoration of calcareous grasslands

Question: What are the long‐term implications of former fertilisation for the ecological restoration of calcareous grasslands? Location: Gerendal, Limburg, The Netherlands. Methods: In 1970, ten permanent plots were established in just abandoned agricultural calcareous grassland under a regime of annual mowing in August. From 1971 to 1979, two different fertiliser treatments were applied twice a year to a subset of the plots (artificial fertiliser with different proportions of nitrogen and phosphorus). The vegetation of the plots was recorded yearly and vegetation biomass samples were taken for peak standing crop and total amounts of nitrogen, phosphorus and potassium. Species composition and floristic diversity were analysed over the research period (1970–2006) and between the treatments, including the use of multivariate techniques (Detrended Correspondence Analysis). Results: In terms of species number, there is a clear optimum 10 to 20 years after fertilisation has been terminated. Afterwards, there is a slow decrease; no new species appear and species of more nutrient‐rich conditions gradually disappear. For the fertilised plots that received a relatively high proportion of N, effects are found only in the first years, whereas, for the plots that received a relatively high proportion of P, long‐term after‐effects are found in species composition, peak standing crop, total amounts of phosphorus in biomass, and in soil phosphorus data. Conclusions: The effect of artificial fertiliser with a large amount of nitrogen disappears in less than ten years when mown in August, including removal of the hay. This is a promising result for restoration of N‐enriched calcareous grasslands, as the applied dose of nitrogen in this experiment largely exceeds the extra input of nitrogen via atmospheric deposition. Application of fertiliser with a large amount of phosphorus, however, has effects even more than 25 years after the last addition. There are no prospects that this effect will become reduced in the near future under the current mowing management.     

Intensive research activity alters short-term seedling dynamics in a tropical forest

Researchers can have unintentional, yet significant effects on their study systems. We tested for the effects of an intensive tree census on seedling dynamics in a 50-ha permanent forest plot on Barro Colorado Island, Panama. At the community level, and for different shade-tolerance guilds, we found no significant differences in seedling recruitment or survival inside compared to controls outside the plot. However, among growth forms, canopy trees and lianas exhibited significantly lower seedling survival inside the plot. Results suggest that intense researcher activity impacts short-term vegetation dynamics, but effects do not accumulate over time.     

Ants accelerate succession from mountain grassland towards spruce forest

Question: What is the role of mound‐building ants (Lasius flavus) in successional changes of a grassland ecosystem towards a spruce forest? Location: Slovenské Rudohorie Mountains, Slovakia; ca. 950 m a.s.l. near the Obrubovanec point (1020 m a.s.l.; 48°41′N, 19°39′E). Methods: Both chronosequence data along a successional gradient and temporal data from long‐term permanent plots were collected on ants, spruce establishment, and vegetation structure, together with additional data on spruce growth. Results: There are more spruce seedlings on ant mounds (4.72 m^?2) than in the surrounding vegetation (0.81 m^?2). Spruce seedlings grow faster on these mounds compared to surrounding areas. The first colonization wave of seedlings was rapid and probably occurred when grazing prevailed over mowing. Ant colony presence, mound volume, and plant species composition change along the successional gradient. Mounds become bigger when partly shaded but shrink in closed forest, when ant colonies disappear. Shade‐tolerant acidophylic species replace grassland plants both on the mounds and in surrounding areas. Conclusions: The massive occurrence of Lasius flavus anthills contributes to a runaway feedback process that accelerates succession towards forest. The effect of ants as ecosystem engineers is scale‐dependent: although they stabilize the system at the scale of an individual mound, they may destabilize the whole grassland system over a longer time scale if combined with changes in mowing regime.     

Luminescent sensor for Cd2+, Hg2+ and Ag+ in water based on a sulphur‐containing receptor: quantitative binding–softness relationship

A water‐soluble, high‐output fluorescent sensor, based on a lumazine ligand with a thiophene substituent for Cd²⁺, Hg²⁺ and Ag⁺ metal ions, is reported. The sensor displays fluorescence enhancement upon Cd²⁺ binding (log  β = 2.79 ± 0.08) and fluorescence quenching by chelating with Ag⁺ and Hg²⁺ (log β = 4.31 ± 0.15 and 5.42 ± 0.1, respectively). The mechanism of quenching is static and occurs by formation of a ground‐state non‐fluorescent complex followed by rapid intersystem crossing. The value of the Stern–Volmer quenching rate constant (k_q) by Ag⁺ ions is close to 6.71 × 10¹² mol/L/s at 298 K. The thermodynamic parameters (ΔG, ΔH and ΔS) were also evaluated and indicated that the complexation process is spontaneous, exothermic and entropically favourable. The quantitative linear relationship between the softness values of Klopman (σ_K) or Ahrland (σ_A) and the experimental binding constants (β) being in the order of Hg²⁺ > Ag⁺ > Cd²⁺ suggests that soft–soft interactions are the key for the observed sensitivity and selectivity in the presence of other metal ions, such as: Pb²⁺, Ni²⁺, Mn²⁺, Cu²⁺, Co²⁺, Zn²⁺ and Mg²⁺ ions. Copyright © 2008 John Wiley & Sons, Ltd.     

古田山24 ha森林动态监测样地常绿阔叶林群落结构和组成动态: 探讨2008年冰雪灾害的影响

常绿阔叶林是我国亚热带地区的地带性植被, 其中最为典型而且分布最广泛的是中亚热带常绿阔叶林。为探讨2008年初我国南方发生的冰雪灾害对中亚热带常绿阔叶林的影响, 以浙江省古田山国家级自然保护区24 ha森林动态监测样地内的中亚热带常绿阔叶林为例, 研究了该森林在冰雪灾害前后(2005-2010年)的群落结构及物种组成动态。结果表明, 群落径级结构变化较小, 但群落整体补员不足且死亡率较高; 多个粒度上的群落动态显示出一致的衰退特征, 但不同生境间的群落动态存在差异; 物种多度和胸高截面积多呈减小趋势, 但频度和重要值变化不明显。同时, 物种的多度、胸高截面积、频度和重要值等次序均无明显变化。这说明2008年发生的冰雪灾害对古田山中亚热带常绿阔叶林群落的短期动态产生了较大的负面影响, 且其影响程度与植物胸径和地形等因素密切相关; 同时也反映了古田山中亚热带常绿阔叶林群落结构对冰雪灾害干扰具有一定的抵抗力。