Branches in the lines of descent: Charles Darwin and the evolution of the species concept

Charles Darwin introduced a novel idea into the concept of species, namely that species are branches in the lines of descent (segments of population lineages). In addition to this novel evolutionary component, Darwin's species concept also retained an older taxonomic component, namely the view that the species category is a taxonomic rank; moreover, he adopted amount of difference as a criterion for ranking lineages as species. Subsequent biologists retained both components of Darwin's species concept, although they replaced Darwin's ranking criterion with ranking criteria that either are more objectively defined or relate more directly to the biological bases of lineage separation and divergence. Numerous alternative ranking criteria were proposed, resulting in a proliferation of species definitions and a controversy concerning the concept of species. That controversy can be resolved by distinguishing more explicitly between the theoretical concept of species and the operational criteria that are used to apply the concept in practice. By viewing the various alternative ranking criteria as operational indicators of lineage separation rather than necessary properties of species, the conflicts among competing species concepts are eliminated, resulting in a unified concept of species. A brief examination of the history of biology reveals that an important shift related to the unified species concept has been emerging ever since Darwin reformulated the concept of species with an evolutionary basis. The species category is effectively being decoupled from the hierarchy of taxonomic ranks and transferred to the hierarchy of biological organization. Published 2011. This article is a US Government work and is in the public domain in the USA. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 19–35.     

Evolutionary recruitment of a flavin-dependent monooxygenase for stabilization of sequestered pyrrolizidine alkaloids in arctiids

Pyrrolizidine alkaloids are secondary metabolites that are produced by certain plants as a chemical defense against herbivores. They represent a promising system to study the evolution of pathways in plant secondary metabolism. Recently, a specific gene of this pathway has been shown to have originated by duplication of a gene involved in primary metabolism followed by diversification and optimization for its specific function in the defense machinery of these plants. Furthermore, pyrrolizidine alkaloids are one of the best-studied examples of a plant defense system that has been recruited by several insect lineages for their own chemical defense. In each case, this recruitment requires sophisticated mechanisms of adaptations, e.g., efficient excretion, transport, suppression of toxification, or detoxification. In this review, we briefly summarize detoxification mechanism known for pyrrolizidine alkaloids and focus on pyrrolizidine alkaloid N-oxidation as one of the mechanisms allowing insects to accumulate the sequestered toxins in an inactivated protoxic form. Recent research into the evolution of pyrrolizidine alkaloid N-oxygenases of adapted arctiid moths (Lepidoptera) has shown that this enzyme originated by the duplication of a gene encoding a flavin-dependent monooxygenase of unknown function early in the arctiid lineage. The available data suggest several similarities in the molecular evolution of this adaptation strategy of insects to the mechanisms described previously for the evolution of the respective pathway in plants.     

Multi-step oxidations catalyzed by cytochrome P450 enzymes: Processive vs. distributive kinetics and the issue of carbonyl oxidation in chemical mechanisms

Catalysis of sequential oxidation reactions is not unusual in cytochrome P450 (P450) reactions, not only in steroid metabolism but also with many xenobiotics. One issue is how processive/distributive these reactions are, i.e., how much do the “intermediate” products dissociate. Our work with human P450s 2E1, 2A6, and 19A1 on this subject has revealed a mixture of systems, surprisingly with a more distributive mechanism with an endogenous substrate (P450 19A1) than for some xenobiotics (P450s 2E1, 2A6). One aspect of this research involves carbonyl intermediates, and the choice of catalytic mechanism is linked to the hydration state of the aldehyde. The non-enzymatic rates of hydration and dehydration of carbonyls are not rapid and whether P450s catalyze the reversible hydration is unknown. If carbonyl hydration and dehydration are slow, the mechanism may be set by the carbonyl hydration status.     

Spectroscopic features of cytochrome P450 reaction intermediates

Cytochromes P450 constitute a broad class of heme monooxygenase enzymes with more than 11,500 isozymes which have been identified in organisms from all biological kingdoms [1]. These enzymes are responsible for catalyzing dozens chemical oxidative transformations such as hydroxylation, epoxidation, N-demethylation, etc., with very broad range of substrates [2] and [3]. Historically these enzymes received their name from ‘pigment 450’ due to the unusual position of the Soret band in UV–vis absorption spectra of the reduced CO-saturated state [4] and [5]. Despite detailed biochemical characterization of many isozymes, as well as later discoveries of other ‘P450-like heme enzymes’ such as nitric oxide synthase and chloroperoxidase, the phenomenological term ‘cytochrome P450’ is still commonly used as indicating an essential spectroscopic feature of the functionally active protein which is now known to be due to the presence of a thiolate ligand to the heme iron [6]. Heme proteins with an imidazole ligand such as myoglobin and hemoglobin as well as an inactive form of P450 are characterized by Soret maxima at 420 nm [7]. This historical perspective highlights the importance of spectroscopic methods for biochemical studies in general, and especially for heme enzymes, where the presence of the heme iron and porphyrin macrocycle provides rich variety of specific spectroscopic markers available for monitoring chemical transformations and transitions between active intermediates of catalytic cycle.     

基于遥感和GIS的天津建成区扩张特征及驱动力

城市地域时空扩张特征是表征城市化水平的重要测量指标.利用1987-2006年4期TM(或ETM)影像资料,获取了天津市市内六区和环城四区近20年的土地利用变化数据.结合社会经济统计数据,应用GIS空间分析方法和空间重心转移模型,分析了天津市建成区的扩张过程、扩张方向及其驱动力.结果表明:2006年天津市中心城区基本上被建设用地所占据,建设用地达到全区面积的82.0%,而环城四区建设用地也占到了24.9%;1987-2006年,天津市建成区扩张非常明显,近20年来建设用地面积增加了19.1%,2001-2006年是天津市建成区扩张最明显时期,建设用地的增加主要来自耕地和水域;1987-2006年天津建成区主要以市内六区为中心呈外向型方式扩张,但总体上空间重心转移方向为东南;经济增长是建成区扩张最重要的因素,主要源于GDP的快速增长和产业结构的调整;交通的发展对城市用地的扩展有明显的促进作用,对城市空间扩张有指向性作用;人口增加也加剧了建成区扩张,但主要通过经济的发展对建成区扩张起作用;宏观政策在很大程度上决定了天津市扩张的格局和规模.     

The molecular mechanisms of interactions between bioactive peptides and angiotensin-converting enzyme

The ability of milk protein derived Ile-Pro-Ala (IPA), Phe-Pro (FP) and Gly-Lys-Pro (GKP) peptides to inhibit angiotensin I-converting enzyme (ACE), a protein with an important role in blood-pressure regulation, were verified in vitro and in vivo. This work elucidates the modes and molecular mechanisms of the interaction of IPA, FP and GKP with ACE, including mechanisms that bind the peptides to the cofactor Zn²⁺. It was observed that the best docking poses obtained for IPA, FP and GKP were at the ACE catalytic site with very similar modes of interaction, including the interaction with Zn²⁺. The interactions, including H-bonds, hydrophobic, hydrophilic, and electrostatic interactions, as well as the interaction with Zn²⁺, were responsible for the binding between the bioactive peptides and ACE.     

Loop‐loop interactions govern multiple steps in indole‐3‐glycerol phosphate synthase catalysis

Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole‐3‐glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active‐site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady‐state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate‐determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps‐ns and µs‐ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active‐site β1α1 and β2α2 loops of indole‐3‐glycerol phosphate synthase results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent interactions with nearby structural elements.     

垃圾填埋场N2O排放通量及测定方法研究进展

氧化亚氮(N₂O)是第三大温室气体和最主要的臭氧层破坏气体.填埋是目前城市生活垃圾处理处置的主要方式,而垃圾填埋场是N₂O的排放源之一.实验室研究和现场测定均表明,生活垃圾填埋场可以有高的N₂O释放通量,但不同填埋场测定数据差异很大.目前,对生活垃圾填埋场N₂O排放量的原位准确测定以及排放机理和重要性的认识仍有很多不足.本文概述了生活垃圾填埋场N₂O排放研究现状,从垃圾堆体和覆土层两部分探讨了传统厌氧卫生填埋场的N₂O产生和排放机理,并就此对新型脱氮型生物反应器填埋场做了相应探讨.最后,就静态箱法、涡度相关法等N₂O通量测定方法在填埋场的适用性进行了讨论,并展望了填埋场N₂O排放的研究方向.     

Light‐Induced Degradation of Polymer:Fullerene Photovoltaic Devices: An Intrinsic or Material‐Dependent Failure Mechanism?

Although degradation mechanisms in organic photovoltaic devices continue to receive increased attention, it is only recently that the initial light‐induced failure, or so‐called burn‐in effect, has been considered. Both prototypical polythiophene:fullerene and polycarbazole:fullerene systems exhibit an exponential performance loss of ≈40% upon 150 h of continuous solar illumination. While the decrease in both the short‐circuit current (J_SC) and open‐circuit voltage (V_OC) is the origin of performance loss in poly(3‐hexylthiophene):[6,6]‐phenyl‐C61‐butyric acid methyl ester (P3HT:PC₆₀BM), in poly(N‐9′‐hepta‐decanyl‐2,7‐carbazole‐alt‐5,5‐(4′,7′‐di‐2‐thienyl‐2′,1′,3′‐benzothiadiazole)):[6,6]‐phenyl‐C71‐butyric acid methyl ester (PCDTBT:PC₇₀BM) the decline of the fill factor dominates. By systematic variation of the interface layers, active layer thickness, and acceptor in polythiophene:fullerene cells, the loss in J_SC is ascribed to a degradation in the bulk of the P3HT:PC₆₀BM, while the drop in V_OC is reversible and arises from charge trapping at the contact interfaces. By replacing the C₆₀ fullerene derivative with a C₇₀ derivative, or by modifying the electron transport layer, the J_SC or V_OC, respectively, are stabilized. These insights prove that the burn‐in process stems from multiple concurrent failure mechanisms. Comparing the ageing and recovery processes in P3HT and PCDTBT blends results in the conclusion that their interface failures differ in nature and that burn‐in is a material dependent, rather than an intrinsic, failure mechanism.