封面故事：5500万年前全球变暖的原因
大约5500万年前，地球经历了一场极端全球变暖。造成这次全球变暖的原因可能是大量温室气体释放进了大气中，类似于今天化石燃料燃烧所引起的问题。难以设想什么事件会如此剧烈，足以产生这样的效应，但在挪威海下面的岩石中超过700个大型管状结构的发现，为当时可能发生的事件提供了线索。沉积物中火山喷发物的侵入，可能引起有机物质的迅速分解和爆炸性管状结构的形成。本期封面图片（courtesy Audun Groth, Norsk Hydro）所示为挪威中部大陆边缘沉积序列中一个具有管状结构的火山物质群，占地面积超过2500平方公里。
Nature 429, 542 - 545 (
Release of methane from a volcanic basin as a mechanism for initial Eocene global warming
A 200,000-yr interval of extreme global warming marked the start of the Eocene epoch about 55 million years ago. Negative carbon- and oxygen-isotope excursions in marine and terrestrial sediments show that this event was linked to a massive and rapid (<ぐ颵ᇏ芻ꨀ봀text>
神经元获得并保持自身功能身份及特性的奥秘
神经科学家所面临的一个有趣的问题是，神经元是怎样获得并保持它们的功能身份和特性的，包括对神经传输物质的选择。对Xenopus胚胎的脊髓所做的一项研究显示，不同神经元类型产生不同的电活性和Ca2+离子流入模式，这种模式可改变由神经元表达的传输物质，而不影响细胞身份的其他标记。这似乎是一个动态平衡问题：抑制Ca2+的活性，会增加激发性传输物质乙酰胆碱和谷氨酸盐的表达，减少抑制性物质氨基乙酸和GABA的表达；当增强活性时，会发生相反的过程。Nature 429, 523 - 530 (
Activity-dependent homeostatic specification of transmitter expression in embryonic neurons
Neurotransmitters are essential for interneuronal signalling, and the specification of appropriate transmitters in differentiating neurons has been related to intrinsic neuronal identity and to extrinsic signalling proteins. Here we show that altering the distinct patterns of Ca2+ spike activity spontaneously generated by different classes of embryonic spinal neurons in vivo changes the transmitter that neurons express without affecting the expression of markers of cell identity. Regulation seems to be homeostatic: suppression of activity leads to an increased number of neurons expressing excitatory transmitters and a decreased number of neurons expressing inhibitory transmitters; the reverse occurs when activity is enhanced. The imposition of specific spike frequencies in vitro does not affect labels of cell identity but again specifies the expression of transmitters that are inappropriate for the markers they express, during an early critical period. The results identify a new role of patterned activity in development of the central nervous system.
三维光子晶体的制造
光子晶体可以光波长本身的长度尺度来控制光，所以它们有用在各种各样的微型光学和电子装置中作为“集成光路”的潜力。但是，材料科学家首先需要开发出具有人为设计的微腔和波导以及制造光学装置所需的建造单元的三维光子晶体的制造方法来。现在，随着具有人为缺陷的三维光子晶体的制造成功，我们离这个目标更近了一步。这种晶体是用一种逐层印刷的平板印刷术制造成的，人为设计出的缺陷，具有在适合电信应用的波长将共振签名引入材料中的效果。Nature 429, 538 - 542 (
A three-dimensional optical photonic crystal with designed point defects
Photonic crystals offer unprecedented opportunities for miniaturization and integration of optical devices. They also exhibit a variety of new physical phenomena, including suppression or enhancement of spontaneous emission, low-threshold lasing, and quantum information processing. Various techniques for the fabrication of three-dimensional (3D) photonic crystals—such as silicon micromachining, wafer fusion bonding, holographic lithography, self-assembly, angled-etching, micromanipulation, glancing-angle deposition and auto-cloning—have been proposed and demonstrated with different levels of success. However, a critical step towards the fabrication of functional 3D devices, that is, the incorporation of microcavities or waveguides in a controllable way, has not been achieved at optical wavelengths. Here we present the fabrication of 3D photonic crystals that are particularly suited for optical device integration using a lithographic layer-by-layer approach. Point-defect microcavities are introduced during the fabrication process and optical measurements show they have resonant signatures around telecommunications wavelengths (1.3–1.5 µm). Measurements of reflectance and transmittance at near-infrared are in good agreement with numerical simulations.
萨德伯里陨石坑对当地岩石组成的影响
加拿大安大略省的萨德伯里结构，是作为世界上最大的、暴露最彻底的陨石坑之一的萨德伯里陨石坑的所在地，多年来存在争议，争论的问题是它是怎么形成的。科学家提出各种不同的地质事件，但到上个世纪60年代，它被肯定地认为是一个碰撞结构。今天，萨德伯里盆地是一个椭圆形的结构，约60公里长，27公里宽，但该结构最初的直径超过200公里，是在18.5亿年前由一颗直径约10公里的陨石撞击形成的。不过该陨石坑结构仍是一个有争议的话题，因为地质学家试图解释陨石碰撞对该地区的岩石组成有什么影响。这场争论中的最新观点是由Mungall等人提出的，他们认为，陨石在萨德伯里的超高速撞击，有可能引起大陆壳层的部分倒置。Nature 429, 546 - 548 (
Geochemical evidence from the
Deformation and melting of the crust during the formation of large impact craters must have been important during the Earth's early evolution, but such processes remain poorly understood. The 1.8-billion-year-old
林冠中生物质的分布
地球的生物质中90%通过林冠与大气发生相互作用。林冠是地球上最丰富和最濒危的环境，但我们对其中生物质的分布却几乎一无所知。在一项独特的实验中（之所以独特，是因为在该实验中，研究人员从婆罗洲的森林中的树顶上取了200公斤的植物样本），研究人员获得了对雨林树冠中无脊椎动物生物质的数量的新的估计值，这个数字是以前的数字的两倍。在东南亚的雨林中，鸟类筑巢的蕨类植物是作为附生植物生长的（即用森林中的树木作为支撑，但不将其作为营养来源）。在这些蕨类植物更大的样本中，发现含有昆虫和其他无脊椎动物的生物质，与蕨类植物在其中生长的树冠中其他所有地方所发现的类似。这项工作说明，附生植物在雨林生态系统中所扮演的角色可能要比以前所想的重要得多，这也使它们成为生态保护工作的主要目标。Doubling the estimate of invertebrate biomass in a rainforest canopy
人们一般假设，在多数动物中，交配选择采取某种较为固定的形式：雌性为挑选方，而雄性之间相互竞争进行求偶。在少数物种中，性别角色是逆转的。现在，对有两个斑点的虾虎鱼的一个野生种群所做的一项研究显示，在单独一个物种中，雌雄角色可随时间改变。在较短的繁殖季节的早期，雄性是最有竞争力的性别。而在后期，也许是由于雄性的死亡率较高，雄性强烈的求偶行为被雌性积极的求偶行为所取代，雌性之间的竞争加剧。这意味着，根据不同性别的行为将物种称为“传统的”或“角色逆转的”可能都是误导的。对一个物种性别角色的判断可能取决于是在何时何地对其行为进行观察的。Nature 429, 551 - 554 (
Unusually dynamic sex roles in a fish
Sex roles are typically thought of as being fixed for a given species. In most animals males compete for females, whereas the females are more reluctant to mate. Therefore sexual selection usually acts most strongly on males. This is explained by males having a higher potential reproductive rate than females, leading to more males being sexually active (a male-biased operational sex ratio). However, what determines sex roles and the strength of sexual selection is a controversial and much debated question. In this large-scale field study, we show a striking temporal plasticity in the mating competition of a fish (two-spotted goby, Gobiusculus flavescens). Over the short breeding season fierce male–male competition and intensive courtship behaviour in males were replaced by female–female competition and actively courting females. Hence, sex role reversal occurred rapidly. This is the first time that a shift in sex roles has been shown in a vertebrate. The shift might be explained by a large decline in male abundance, strongly skewing the sex ratio towards females. Notably, the sex role reversal did not occur at an equal operational sex ratio, contrary to established sex role theory.
疟疾感染靠的是寄主帮忙
很多病原体已经学会了通过抗原变异来延长它们的感染时间。这一策略获得成功的一个关键是，在免疫上截然不同的变种是先后、而不是同时出现的。抗原变异总被看作是寄生虫逃避寄主防卫系统的一种适应性行为，但用数学模拟方法做的一次新的尝试表明，具有讽刺意味的是，抗原变异所需要的协调工作可能是由寄主本身来完成的。疟疾寄生虫“镰刀形疟原虫”感染红血球的模型表明，短时间的交叉反应响应也可产生一系列前后出现的显性抗原变种。这一结果可解释在疟疾病人中所观察到的一些不好理解的现象，因为有较强交叉反应免疫响应的患者属于这种情况，他们更可能变成慢性感染。Transient cross-reactive immune responses can orchestrate antigenic variation in malaria
The malaria parasite Plasmodium falciparum has evolved to prolong its duration of infection by antigenic variation of a major immune target on the surface of the infected red blood cell. This immune evasion strategy depends on the sequential, rather than simultaneous, appearance of immunologically distinct variants. Although the molecular mechanisms by which a single organism switches between variants are known in part, it remains unclear how an entire population of parasites within the host can synchronize expression to avoid rapidly exhausting the variant repertoire. Here we show that short-lived, partially cross-reactive immune responses to parasite-infected erythrocyte surface antigens can produce a cascade of sequentially dominant antigenic variants, each of which is the most immunologically distinct from its preceding types. This model reconciles several previously unexplained and apparently conflicting epidemiological observations by demonstrating that individuals with stronger cross-reactive immune responses can, paradoxically, be more likely to sustain chronic infections. Antigenic variation has always been seen as an adaptation of the parasite to evade host defence: we show that the coordination necessary for the success of this strategy might be provided by the host.
在生物进化过程中所发生的遗传变异并非都是达尔文的自然选择的结果，实际上绝大多数的基因序列变化是近乎中性的突变的随机漂移的结果。自然选择与随机变异所占的比重是一个几十年来有过很多讨论的话题。现在，大鼠和小鼠的基因组序列数据已经出来了，同时又有人类基因组数据作为参考，Bazykin等人对涉及9390个等价基因的360万个小鼠和大鼠密码子之间的核苷取代模式进行了分析研究，发现了一个复杂的变异模式。总体上，由积极的选择引起的碱基取代所占的比例在 0.5%-1%左右。令人吃惊的是，在大鼠祖先中由积极的选择（而不是随机的漂移）所引起的取代几乎是在小鼠祖先中的频度的两倍。Nature 429, 558 - 562 (
Positive selection at sites of multiple amino acid replacements since rat–mouse divergence
New alleles become fixed owing to random drift of nearly neutral mutations or to positive selection of substantially advantageous mutations. After decades of debate, the fraction of fixations driven by selection remains uncertain. Within 9,390 genes, we analysed 28,196 codons at which rat and mouse differ from each other at two nucleotide sites and 1,982 codons with three differences. At codons where rat–mouse divergence involved two non-synonymous substitutions, both of them occurred in the same lineage, either rat or mouse, in 64% of cases; however, independent substitutions would occur in the same lineage with a probability of only 50%. All three non-synonymous substitutions occurred in the same lineage for 46% of codons, instead of the 25% expected. Furthermore, comparison of 12 pairs of prokaryotic genomes also shows clumping of multiple non-synonymous substitutions in the same lineage. This pattern cannot be explained by correlated mutation or episodes of relaxed negative selection, but instead indicates that positive selection acts at many sites of rapid, successive amino acid replacement.
果蝇（Drosophila melanogaster）的胰岛素信号通道的突变，可产生长寿命的成年个体。例如，类胰岛素受体或其基质的同型接合子，可延迟蛹变成成虫的时间、减少生殖和延长寿命。这些突变在所有生命阶段都表达，所以不清楚什么时候必须减少胰岛素信号来延长寿命，也不清楚胰岛素是直接产生这些效应的还是通过二级荷尔蒙产生这些效应的。类胰岛素受体还控制dFOXO（一种转录因子，等同于哺乳动物的FOXO3a和线虫的daf-16，二者都与调节寿命有关）的磷酸化。现在，研究发现，在果蝇体内，当将dFOXO只在成年阶段激活时，当dFOXO只在头部的脂肪体中表达时，它调节果蝇的衰老过程。它只减少类胰岛素肽DILP-2的表达。这项工作表明，类胰岛素信号可能影响衰老过程，因为它们控制组织衰老和一个在全身施加其影响的调节系统。Nature 429, 562 - 566 (
Drosophila dFOXO controls lifespan and regulates insulin signalling in brain and fat body
In Drosophila melanogaster, ageing is slowed when insulin-like signalling is reduced: life expectancy is extended by more than 50% when the insulin-like receptor (InR) or its receptor substrate (
Nature 429, 571 - 574 (
Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene
