A glimpse into the active site of a group II intron and maybe the spliceosome, too

The X-ray crystal structure of an excised group II self-splicing intron was recently solved by the Pyle group. Here we review some of the notable features of this structure and what they may tell us about the catalytic active site of the group II ribozyme and potentially the spliceosome. The new structure validates the central role of domain V in both the structure and catalytic function of the ribozyme and resolves several outstanding puzzles raised by previous biochemical, genetic and structural studies. While lacking both exons as well as the cleavage sites and nucleophiles, the structure reveals how a network of tertiary interactions can position two divalent metal ions in a configuration that is ideal for catalysis.     

Extinction vulnerability of coral reef fishes

With rapidly increasing rates of contemporary extinction, predicting extinction vulnerability and identifying how multiple stressors drive non-random species loss have become key challenges in ecology. These assessments are crucial for avoiding the loss of key functional groups that sustain ecosystem processes and services. We developed a novel predictive framework of species extinction vulnerability and applied it to coral reef fishes. Although relatively few coral reef fishes are at risk of global extinction from climate disturbances, a negative convex relationship between fish species locally vulnerable to climate change vs. fisheries exploitation indicates that the entire community is vulnerable on the many reefs where both stressors co-occur. Fishes involved in maintaining key ecosystem functions are more at risk from fishing than climate disturbances. This finding is encouraging as local and regional commitment to fisheries management action can maintain reef ecosystem functions pending progress towards the more complex global problem of stabilizing the climate.     

Indices of plant N availability in an alpine grassland under elevated atmospheric CO2

The objective of this study was to estimate whether elevated atmospheric [CO₂] alters plant N availability in a native high-elevation grassland in the Swiss Alps using two integrative, relatively non-disruptive methods. Estimates based on seasonal net plant N uptake, and those based on the amounts of NH ₄ ⁺ -N plus NO ₃ ^– -N captured by ion exchange resin (IER) bags, did not differ in plots treated with ambient (355 L L^–1) and elevated (680 L L^–1) [CO₂] in either the second (1993) or third (1994) growing season under treatment with elevated [CO₂]. The results of this study suggest that the effects of rising atmospheric [CO₂] on plant N availability may be negligible in this grassland. The results also contrast the relatively large effects of elevated atmospheric [CO₂] (increases and decreases) reported for highly disturbed artificial systems.     

湖北九宫山成熟常绿落叶阔叶混交林 3种优势种的邻域效应研究

以最近邻株距离统计研究了湖北九宫山成熟常绿落叶阔叶混交林3种优势种青冈栎(Cyclobalanopsis glauca)、甜槠(Castanopsis eyrei)和短柄枹栎(Quercus serrata var.brevipetiolata)的邻域效应,进而探讨了局域尺度上的竞争/帮促关系与物种共存格局。结果显示,青冈栎、甜槠和短柄枹栎的最近邻株距离不存在下限;青冈栎的胸径大小与其种内最近邻株距离存在正相关(p= 0.029),甜槠的胸径大小与种内、种间最近邻株距离均无相关性(p≥ 0.360),而短柄枹栎的胸径大小与种间最近邻株距离为负相关(p= 0.040);3树种中任意一个的种内与种间最近邻株距离都没有显著差异(p≥ 0.122)。这些结果表明,九宫山成熟常绿落叶阔叶混交林内邻域尺度上的竞争排斥并未充分激化,但是青冈栎的种内竞争仍然在起作用,而甜槠的竞争效应不明显,短柄枹栎则依赖种间帮促甚于相互竞争。同种和异种之间的排斥效果没有差异表明局域尺度的物种共存格局可能出于随机过程而非负密度制约过程。     

Characterization of an unusual folding pattern in a catalytically active guanine quadruplex structure

In the presence of certain metal ions, DNA and RNA can form guanine quadruplex structures, which have been proposed to play a functional role in a variety of biological processes. An 18-nucleotide DNA oligomer, PS2.M, d(GTG3TAG3CG3T2G2), was previously reported to bind hemin and the resulting complex exhibited peroxidase activity. It was proposed that PS2.M folds unimolecularly into an antiparallel quadruplex with unusual, single-base loops and terminal guanines positioned in adjacent quartets. Here we describe structural and stability properties of PS2.M alone in different buffers and metal ions, using gel electrophoresis, circular dichroism (CD), ultraviolet (UV)-visible spectroscopies, and one-dimensional 1H nuclear magnetic resonance (NMR). Native gel behavior of PS2.M in the presence of either Na+ or Pb2+ suggests the formation of unimolecular structures but, in the presence of K+, both unimolecular and multistranded structures are observed. In the presence of Pb2+ ions, PS2.M forms a unimolecular quadruplex containing three guanine quartets. CD titrations reveal that binding of Pb2+ ions to PS2.M is stoichiometric, and a single lead cation suffices to fully fold PS2.M. The PS2.M-Na+ system also forms a similar unimolecular quadruplex. In the presence of K+, the PS2.M-K+ system forms mixed species. With increasing time and PS2.M concentration, the contribution of unimolecular species decreases while that of multimolecular species increases, and this behavior is independent of buffer media. These results suggest that the catalytically active form, studied in the presence of K+, may be a parallel, multistranded quadruplex rather than an antiparallel, unimolecular quadruplex.     

INFLUENCE OF THE INDIRECT EFFECTS OF GUPPIES ON LIFE‐HISTORY EVOLUTION IN RIVULUS HARTII

Early theories of life‐history evolution predict that increased predation on young/small individuals selects for delayed maturation and decreased reproductive effort, but such theory only considers changes in mortality. Predators reduce prey abundance and increase food to survivors. Theory that incorporates such indirect effects yields different predictions. Trinidadian killifish, Rivulus hartii, inhabit communities with and without guppies. Guppies prey on young Rivulus and Rivulus densities decline and growth rates increase when guppies are present. Prior work showed that Rivulus phenotypes from communities with guppies matured earlier and had higher fecundity, consistent with theories that incorporate indirect effects. Here we examined the genetic basis of these differences by rearing 2nd generation, laboratory‐born Rivulus from sites with and without guppies under two food levels that match natural differences in growth. Many locality × food interactions were significant, often reversing the relationship between communities. Such interactions imply that there are fitness trade‐offs associated with adaptation to high or low resource environments. On high food, Rivulus from localities with guppies matured earlier, produced many small eggs, and exhibited increased reproductive investment; these differences reversed on low food. Our results suggest that indirect effects mold Rivulus evolution and thereby highlight connections between community processes and evolutionary change.     

Colorimetric detection of oxalate in aqueous solution by a pyrogallol red‐based Cu2+ complex

The pyrogallol red (PR)‐based Cu²⁺ complex was proven to be an effective and selective colorimetric chemosensing ensemble for recognition of oxalate over other anions in a perfect aqueous solution. The addition of oxalate to the PR–Cu²⁺ complex resulted in a colour change from purple to orange colour due to the regeneration of PR by the chelation of oxalate with Cu²⁺, while other anions did not induce any significant colour change. Moreover, it was revealed that no obvious interference was observed during the titrations with oxalate into each other anion. Therefore, the PR–Cu²⁺ complex can be used as a simple and practical colorimetric chemosensor for detecting oxalate.     

Simple rules describe bottom-up and top-down control in food webs with alternative energy pathways

Many human influences on the world's ecosystems have their largest direct impacts at either the top or the bottom of the food web. To predict their ecosystem-wide consequences we must understand how these impacts propagate. A long-standing, but so far elusive, problem in this endeavour is how to reduce food web complexity to a mathematically tractable, but empirically relevant system. Simplification to main energy channels linking primary producers to top consumers has been recently advocated. Following this approach, we propose a general framework for the analysis of bottom-up and top-down forcing of ecosystems by reducing food webs to two energy pathways originating from a limiting resource shared by competing guilds of primary producers (e.g. edible vs. defended plants). Exploring dynamical models of such webs we find that their equilibrium responses to nutrient enrichment and top consumer harvesting are determined by only two easily measurable topological properties: the lengths of the component food chains (odd-odd, odd-even, or even-even) and presence vs. absence of a generalist top consumer reconnecting the two pathways (yielding looped vs. branched webs). Many results generalise to other looped or branched web structures and the model can be easily adapted to include a detrital pathway.     

云南纵向岭谷区道路网络对生态系统影响的尺度效应

云南纵向岭谷区具有复杂的生态系统,其生物多样性在全球中具有重要地位,但是由于人类活动的影响,尤其是道路网络的发展及其导致的土地利用变化,使得该地区生态系统退化日益严重.选取2km×2km、4km×4km、6km×6km、… \,20km×20km网格进行多尺度相关分析和方差分析,研究云南纵向岭谷区道路网络与生态系统分布的相关性及其独立和交互作用,分析道路网络对生态系统影响的尺度效应.然后又进一步研究了道路网络和地形因子(比如海拔、坡度和坡向等)对生态系统的独立和交互作用.研究结果表明,道路网络与生态系统分布的相关性与路网等级有关,其相关程度与路网等级呈反比,随着尺度的变化,道路网络与生态系统分布的相关性表现为增强型、减弱型、质变型和无尺度效应这4种类型.在大多数尺度下,道路网络和地形因子对生态系统分布既有独立作用,也有交互作用.其中,高等级路网的独立作用比较显著,而低等级路网的独立作用不太显著.但是,随着尺度的增大,县乡路网、乡村路网和小路网对生态系统分布的独立和交互作用均显著,且表现出高度的相似性,表明地形对低等级道路具有明显的干扰或屏蔽效应.