《Nature》目录要览：2009-12-10出版
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《Nature》目录要览：2009-12-10出版
封面故事：“大鼠GluA2受体”的X-射线晶体结构
X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor
中枢神经系统中的大多数兴奋型神经传输（允许神经元彼此沟通的事件）是由离子型谷氨酸盐受体调控的，这些受体通过打开结合谷氨酸盐上的一个跨膜离子通道发挥作用。过去人们对它们的总体结构知之甚少，但现在Eric Gouaux及其同事报告了结合到一个竞争性拮抗剂上的对AMPA敏感的亚型“大鼠GluA2受体”的X-射线晶体结构。该受体（如封面图片所示）具有一个出乎意料的对称性和亚单元排列：总体上为双重对称，细胞外区域按局部二聚体对的形式来组织。离子通道区域表现出四重对称。这种结构（是根据来自定点诱变实验的数据获得的）表明，对NMDA敏感的受体GluN1 和 GluN2A在总体结构上与GluA2相似。从这些结构可以推断出非竞争性拮抗剂和孔阻断分子对离子通道的激发、脱敏和抑制机制。（Article p. 745; News & Views）
磁场对伽马射线暴的贡献程度（A magnetic push for GRBs）
Ten per cent polarized optical emission from GRB 090102
伽马射线暴（宇宙中已知能量最大的爆炸）的性质是非常有争议的话题。其中的一个争议点是，磁场（而不是由重子物质所产生的压力）在加速从不断扩大的火球以相对论速度发射出的物质喷射流中所参与的程度。在这样一个距离观测磁场是困难的，但来自一次伽马射线暴的早期光辐射的偏振将能够指示磁力的参与程度。现在，对来自GRB 090102的早期辐射（2009年1月2日由Swift卫星探测到）所做的观测显示了偏振的广泛存在（约占10%左右），这表明存在大尺度的磁场。（Letter p. 767; News and Views）
宇宙射线的产生与恒星形成之间的联系有了证据（Starburst cosmic rays）
A connection between star formation activity and cosmic rays in the starburst galaxy M82
对来自星爆星系M82（亦称为“雪茄星系”）的甚高能伽马射线的探测，为宇宙射线（质子和核）的产生与恒星形成之间是否存在联系提供了曾被怀疑存在、但以前却未得到证明的证据。VERITAS切伦科夫天文望远镜阵列从M82中心附近一个点状光源记录到能量超过700 GeV的伽马射线，相当于比银河系中的平均密度大约500倍的一个宇宙射线密度。（Letter p. 770）
十二边形准晶体堆积成功（A surprise package）
Disordered, quasicrystalline and crystalline phases of densely packed tetrahedra
目前仍未解决的最紧密堆积排列所采用的最简单的形状之一是正四面体，尽管人们在理论上、计算上和实验上都做了很多努力。利用一个涉及热力学计算机模拟的新方法（该方法可让体系向高密度状态自然发展），Sharon Glotzer及其同事获得了对四面体来说迄今最为紧密的有序堆积结构，堆积率为0.8324。 出乎意料的是，该结构是一种十二边形准晶体，这是从硬颗粒或从非球形构造单元形成一种准晶体的第一例。（Letter p. 773）
地球历史上已知最大的洪灾（Taken at the flood）
Catastrophic flood of the Mediterranean after the Messinian salinity crisis
距今大约560万年前，地中海与世界其他海洋分开，而且在这之后被称为“Messinian salinity crisis”的时期，随着海水蒸发，海平面急剧下降。海水在距今大约530万年前恢复了，但关于这一事件（地球历史上已知最大的洪灾）的细节仍然很不完整。利用钻孔、地震数据和数值模拟所进行的一项研究表明，这是一次灾难性的事件：虽然它是从一个可能持续了数千年的涓涓溪流开始的，但入注的水中多达90%是在不到两年时间里输送到地中海里的。这样一个突发的洪灾可能曾使海平面以超过每天10米的峰值速度上升。（Letter p. 778）
鸟类懂得“男为悦己者容”（Plumage to impress）
Reproductive skew and selection on female ornamentation in social species
很多鸟类雄性颜色鲜艳，而雌性颜色暗淡，鸟类观测者以此来辨别它们，并将这种方式称之为LBJs (‘little brown jobs’)。 对雄性追求很多雌性而雌性对交配对象又很挑剔的物种来说是这样的，也有必要这样，因为这样它们能够最大限度地利用在养育后代上的投入。但对那些雄性和雌性分担养育责任(即所谓的“合作繁育”)的物种情况又是怎么样的呢？在这样的物种中，两性之间往往看起来比较像。传统观点认为雄性的装饰性减弱，但事实未必是这样的，正如对雄性和雌性非洲八哥的装饰水平进行的一项研究所表明的那样。在这一群居物种中，雌性为引起雄性注意而相互竞争，从而变得装饰性更强，可以与雄性相媲美。在不与亲戚生活在一起的物种中，雄性比雌性装饰性更强。（Letter p. 786）
蜗壳螺旋的手性能够逆转（Snails, on the other hand）
Chiral blastomere arrangement dictates zygotic left–right asymmetry pathway in snails
蜗壳螺旋的手性（即镜像不能叠加的一种结构）由一个单一位点在遗传上决定，是由母方遗传的。对此负责的基因一直未被发现。现在，Reiko. Kuroda等人发现，对大蜗牛“静水椎实螺”（Lymnaea stagnalis）8-细胞阶段的胚胎中的细胞进行简单的操纵，能够在成年个体中逆转手性。而且引人注目的是，nodal基因（一个在很多物种中赋予左-右非对称性的基因）的表达也被细胞的重排逆转。他们还发现，在手性决定基因（一个或多个）与在促进主导型分裂球排列的第三次分裂时的手性细胞骨架动态之间有一个强烈的基因联系。这一可以跟踪的实验体系的获得，将使左-右对称性的机制比以前更容易研究。（Letter p. 790; News & Views）
生态酶活性与生态系统的养分供应（Ecoenzymes in balance）
Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil and sediment
能量和养分通过生态系统的流动由代谢限制和养分供应两个因素决定。现在，对由微生物释放到环境中去消化有机质的外部“生态酶”（ecoenzymes）所做的一项研究表明，这些酶的活性遵从一个一致的比例关系，这种关系独立于微生物群落的组成。研究人员在土壤和淡水沉积物中对调控异养微生物群落大部分碳、氮和磷摄取的四种酶进行了测量，在所有这些生境中，碳、氮和磷的吸收活性比都接近1:1:1。生态酶活性可被看作是将两个主要生态理论（化学当量理论和代谢理论）统一起来的一种联系，因为酶的表达是由环境养分供应状态的随机性专门调控的细胞代谢的一个产物。（Letter p. 795）
种子中的非编码反义RNA转录体（Regulatory RNAs go to seed）
Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target
“春化”是植物继寒冬之后在春天获得根据环境提示来开花的能力的过程，是植物的一个关键适应性特征，对农业生产有较大影响。拟南芥开花抑制因子FLC在由Polycomb调控蛋白调节的一个过程中被“春化”关闭。现在，FLC的非编码反义RNA转录体被发现存在于冷处理的种子中，并对温度变化有响应，这说明它们在低温感应和FLC沉默中有可能扮演一个角儿。这种类型的反义转录事件（源自基因的3´端）也许是调控相应“正义”转录的一个普遍机制。（Letter p. 799）
丙氨酰tRNA合成酶的疑点被揭开（Editorial changes）
Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma
丙氨酰tRNA合成酶有时能结合一个甘氨酸或一个丝氨酸，而不是丙胺酸。如果一个“错误的”氨基酸随后被从合成酶活性点转移到一个生长中的多肽链上的话，这样便会引起翻译错误。Guo等人利用晶体结构、突变酶和动力学分析发现了为什么这种酶具有这样一个混乱的特异性，也发现了这个问题是怎样通过编辑蛋白AlaXps的演化被克服的。（Letter p. 808）
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NEWS AND VIEWS
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Developmental biology: Asymmetry with a twist pp727-728
In snails, manipulating the orientation of cells in the early embryo
alters the left--right asymmetry of the shell and body. These findings
refine the search for the symmetry-breaking event in this and other animals.
Nipam H. Patel
doi:10.1038/462727a
http://www.nature.com/nature/journal/v462/n7274/full/462727a.html
Gamma-ray bursts: Magnetism in a cosmic blast pp728-729
Astronomers know little about γ-ray bursts other than that they
are the most energetic explosions in the Universe. The latest observations
indicate that large-scale magnetism contributes to their power.
Maxim Lyutikov
doi:10.1038/462728a
http://www.nature.com/nature/journal/v462/n7274/full/462728a.html
50 & 100 years ago p729
doi:10.1038/462729b
http://www.nature.com/nature/journal/v462/n7274/full/462729b.html
Neuroscience: Excitatory view of a receptor pp729-731
Ion channels opened by glutamate mediate fast cell-to-cell information
transfer in the nervous system. The structure of a full-length tetrameric
glutamate receptor is both confirmatory and revelatory.
Lonnie P. Wollmuth and Stephen F. Traynelis
doi:10.1038/462729a
http://www.nature.com/nature/journal/v462/n7274/full/462729a.html
Earth science: The enigma of D'' pp731-732
A phase transition of Earth's most abundant mineral occurs at pressures
and temperatures corresponding to those thought to exist just above
Earth's core. New experiments shed light on this enigmatic D'' region.
Kanani K. M. Lee
doi:10.1038/462731a
http://www.nature.com/nature/journal/v462/n7274/full/462731a.html
Immunology: Dendritic-cell genealogy pp732-733
The differing origins of gut dendritic cells ― white blood cells that
modulate immune responses ― may explain how the intestinal immune system
manages to destroy harmful pathogens while tolerating beneficial bacteria.
Sophie Laffont and Fiona Powrie
doi:10.1038/462732a
http://www.nature.com/nature/journal/v462/n7274/full/462732a.html
Structural biology: Molecular coin slots for urea pp733-734
Membrane-bound protein channels that allow only urea to pass
through are vital to the kidney's ability to conserve water.
Crystal structures show that the channels select urea molecules
by passing them through thin slots.
Mark A. Knepper and Joseph A. Mindell
doi:10.1038/462733a
http://www.nature.com/nature/journal/v462/n7274/full/462733a.html
Obituary: Qian Xuesen (1911--2009) p735
Founder of China's missile and space programme.
Jane Qiu
doi:10.1038/462735a
http://www.nature.com/nature/journal/v462/n7274/full/462735a.html
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NEWS AND VIEWS Q&A
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Systems chemistry: Molecular networks come of age pp736-738
The advent of sophisticated analytical tools enables the collective
behaviour of networks of interacting molecules to be studied. The
emerging field of systems chemistry promises to allow such networks
to be designed to perform complex functions, and might even shed
light on the origins of life.
Jonathan R. Nitschke
doi:10.1038/462736a
http://www.nature.com/nature/journal/v462/n7274/full/462736a.html
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ARTICLES
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Cancer-associated IDH1 mutations produce 2-hydroxyglutarate pp739-744
Mutations in the enzyme cytosolic isocitrate dehydrogenase 1 (IDH1)
are commonly found in glioblastomas, a major subset of primary human
brain cancers. However, only a single copy of the gene is mutated,
suggesting that the mutation does not result in a simple loss of
function. Here, IDH1 mutations are shown to act in a gain-of-function
manner, resulting in a new ability of the enzyme to catalyse [alpha]-
ketoglutarate to R(-)-2-hydroxyglutarate, an onco-metabolite.
Lenny Dang et al.
doi:10.1038/nature08617
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08617.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08617.html
X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate
receptor pp745-756
The majority of excitatory neurotransmission in the central nervous
system is mediated by ionotropic glutamate receptors, which function by
opening a transmembrane ion channel upon binding of glutamate. However,
despite this crucial role in neurobiology, the architecture and atomic
structure of an intact isotropic glutamate receptor are unknown. The X-ray
crystal structure of the rat GluA2 receptor in complex with a competitive
antagonist is now reported and analysed.
Alexander I. Sobolevsky, Michael P. Rosconi and Eric Gouaux
doi:10.1038/nature08624
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08624.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08624.html
Crystal structure of a bacterial homologue of the kidney urea transporter
pp757-761
Specialized urea transporters have evolved to achieve rapid and selective
urea permeation in the mammalian kidney, a process ultimately necessary for
water re-absorption. Here, the X-ray crystal structure of a functional urea
transporter from the bacterium Desulfovibrio vulgaris is presented and
analysed; the results establish that the urea transporter operates by a
channel-like mechanism and reveal the physical and chemical basis of urea selectivity.
Elena J. Levin, Matthias Quick and Ming Zhou
doi:10.1038/nature08558
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08558.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08558.html
Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme
pp762-766
In living systems, the repair of genotoxic damage requires that the lesion
first be detected in an excess of undamaged DNA. A base-excision DNA repair
enzyme, MutM, is now captured and structurally elucidated at the stage of
initial encounter with a damaged nucleobase within a DNA duplex. By combining
structural biology and computational modelling, the pathway by which this
encounter causes the damaged nucleobase to be extruded from the DNA duplex is defined.
Yan Qi et al.
doi:10.1038/nature08561
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08561.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08561.html
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LETTERS
----------------------
Ten per cent polarized optical emission from GRB[thinsp]090102 pp767-769
The nature of the jets and the role of magnetic fields in gamma-ray bursts
(GRBs) remain unclear. There are two possible models, one of which suggests
that magnetic fields are critical; to distinguish between these models the
degree of polarization in early-time emission must be measured. The early
optical emission from GRB 090102 is now reported to be polarized at 10
[plusmn] 1 per cent, indicating the presence of large-scale fields
originating in the expanding fireball.
I. A. Steele et al.
doi:10.1038/nature08590
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08590.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08590.html
A connection between star formation activity and cosmic rays in the starburst
galaxy M82 pp770-772
Cosmic rays are believed to be mainly accelerated by the winds and supernovae
of massive stars, although definite evidence for this is lacking. The active
regions of starburst galaxies have exceptionally high rates of star formation,
and therefore should produce cosmic rays that interact with interstellar gas
and radiation to produce diffuse γ-rays. The detection and analysis of >700-GeV
γ-rays from M82, the prototype small starburst galaxy, now links cosmic-ray
acceleration to star formation activity.
V. A. Acciari et al.
doi:10.1038/nature08557
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08557.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08557.html
Disordered, quasicrystalline and crystalline phases of densely packed
tetrahedra pp773-777
All hard, convex shapes pack more densely than spheres, although for
tetrahedra this was demonstrated only very recently. Here, tetrahedra are
shown to pack even more densely than previously thought. Thermodynamic
computer simulations allow the system to evolve naturally towards high-density
states, showing that a fluid of hard tetrahedra undergoes a first-order phase
transition to a dodecagonal quasicrystal, and yielding the highest packing
fractions yet observed for tetrahedra.
Amir Haji-Akbari et al.
doi:10.1038/nature08641
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08641.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08641.html
Catastrophic flood of the Mediterranean after the Messinian salinity crisis
pp778-781
5.33 million years ago, in an event known as the Zanclean flood, Atlantic
waters refilled a mostly desiccated Mediterranean Sea which had become
disconnected from the world's oceans; however, the nature, abruptness and
evolution of this flood remain poorly constrained. Using borehole and seismic
data and a model study, it is now suggested that 90 per cent of the water was
transferred in a short period of a few months to two years, with peak rates of
sea level rise in the Mediterranean possibly reaching more than 10 metres per day.
D. Garcia-Castellanos et al.
doi:10.1038/nature08555
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08555.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08555.html
Thickness and Clapeyron slope of the post-perovskite boundary pp782-785
Seismic detectability of the boundaries and convection in the mantle is
strongly influenced by the thicknesses and Clapeyron slopes of mantle phase
boundaries. The unusually large positive Clapeyron slope found for the boundary
between perovskite and post-perovskite (the 'pPv boundary') would destabilize
high-temperature anomalies in the lowermost mantle, in disagreement with the
seismic observations. Here, new studies of the thickness and Clapeyron slope
of the pPv boundary shed light on this matter.
Krystle Catalli, Sang-Heon Shim and Vitali Prakapenka
doi:10.1038/nature08598
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08598.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08598.html
Reproductive skew and selection on female ornamentation in social species
pp786-789
Male animals are typically more elaborately ornamented than females, probably
because females make more of an energetic investment in raising young. However,
this generality may not apply in cooperatively breeding vertebrates, where the
energetic load is similar in males and females. The socially diverse African
starlings are now used to study this issue, revealing that where intrasexual
competition among females may be intense, female trait elaboration is selected for.
Dustin R. Rubenstein and Irby J. Lovette
doi:10.1038/nature08614
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08614.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08614.html
Chiral blastomere arrangement dictates zygotic left--right asymmetry pathway in
snails pp790-794
Most animals display internal and/or external left-right asymmetry. The gastropod
Lymnaea stagnalis has both sinistral and dextral snails within a species; the
chirality is hereditary, but the gene(s) and mechanisms for handedness-
determination are not yet identified. In L. stagnalis, the chiral blastomere
arrangement at the eight-cell stage is now shown to determine left-right
asymmetry throughout development, acting upstream of the Nodal signalling pathway.
Reiko Kuroda, Bunshiro Endo, Masanori Abe and Miho Shimizu
doi:10.1038/nature08597
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08597.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08597.html
Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil
and sediment pp795-798
The atomic ratio of carbon:nitrogen:phosphorus can be used to describe biota in
terms of elemental composition, and this stoichiometry is fundamental for
understanding the production dynamics and biogeochemical cycles of ecosystems.
Heterotrophic microbial communities from terrestrial soils and fresh-water
sediments are now shown to share a common functional stoichiometry in relation
to organic nutrient acquisition, reflecting the similar scaling relationships
of four key ecoenzymes.
Robert L. Sinsabaugh, Brian H. Hill and Jennifer J. Follstad Shah
doi:10.1038/nature08632
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08632.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08632.html
Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb
target pp799-802
Here, the link between non-coding RNA and chromatin regulation is investigated
through analysis of FLC - a regulator of flowering time in Arabidopsis
and a target of several chromatin pathways. FLC is silenced by prolonged cold
in a Polycomb-mediated process called vernalization. Upregulation of long
non-coding antisense transcripts covering the entire FLC locus are now
suggested to have an early role in the cold-induced silencing mechanism.
Szymon Swiezewski, Fuquan Liu, Andreas Magusin and Caroline Dean
doi:10.1038/nature08618
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08618.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08618.html
Long-range oncogenic activation of Igh--c-myc translocations by the Igh 3'
regulatory region pp803-807
Lymphomas often contain translocations that link c-myc to the immunoglobulin
heavy chain locus (encoded by Igh), but the nature of the elements that activate
oncogenes within such translocations is unknown. Transgenic mice with Igh 3'
regulatory region (Igh3' RR) sequences fused to c-myc are predisposed to B
lymphomas. Here, the oncogenic role of the Igh3' RR is investigated by
inactivating it in two distinct mouse models for B-cell lymphoma with
Igh-c-myc translocations.
Monica Gostissa et al.
doi:10.1038/nature08633
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08633.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08633.html
Paradox of mistranslation of serine for alanine caused by AlaRS recognition
dilemma pp808-812
Alanyl-tRNA synthetases (AlaRSs) may confuse glycine or serine with alanine,
potentially causing mistranslation and thus profound functional consequences,
with serine posing a bigger challenge than glycine. AlaXps - free-standing,
genome-encoded editing proteins - represent one editing checkpoint to prevent
this from occurring. Nine crystal structures, together with kinetic and
mutational analysis, now show how AlaXps solve the serine misactivation problem.
Min Guo et al.
doi:10.1038/nature08612
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08612.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08612.html
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FUTURES
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In the recovery room p818
The advance of science.
Eric Brown
doi:10.1038/462818a
http://www.nature.com/nature/journal/v462/n7274/full/462818a.html
X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor
中枢神经系统中的大多数兴奋型神经传输（允许神经元彼此沟通的事件）是由离子型谷氨酸盐受体调控的，这些受体通过打开结合谷氨酸盐上的一个跨膜离子通道发挥作用。过去人们对它们的总体结构知之甚少，但现在Eric Gouaux及其同事报告了结合到一个竞争性拮抗剂上的对AMPA敏感的亚型“大鼠GluA2受体”的X-射线晶体结构。该受体（如封面图片所示）具有一个出乎意料的对称性和亚单元排列：总体上为双重对称，细胞外区域按局部二聚体对的形式来组织。离子通道区域表现出四重对称。这种结构（是根据来自定点诱变实验的数据获得的）表明，对NMDA敏感的受体GluN1 和 GluN2A在总体结构上与GluA2相似。从这些结构可以推断出非竞争性拮抗剂和孔阻断分子对离子通道的激发、脱敏和抑制机制。（Article p. 745; News & Views）
磁场对伽马射线暴的贡献程度（A magnetic push for GRBs）
Ten per cent polarized optical emission from GRB 090102
伽马射线暴（宇宙中已知能量最大的爆炸）的性质是非常有争议的话题。其中的一个争议点是，磁场（而不是由重子物质所产生的压力）在加速从不断扩大的火球以相对论速度发射出的物质喷射流中所参与的程度。在这样一个距离观测磁场是困难的，但来自一次伽马射线暴的早期光辐射的偏振将能够指示磁力的参与程度。现在，对来自GRB 090102的早期辐射（2009年1月2日由Swift卫星探测到）所做的观测显示了偏振的广泛存在（约占10%左右），这表明存在大尺度的磁场。（Letter p. 767; News and Views）
宇宙射线的产生与恒星形成之间的联系有了证据（Starburst cosmic rays）
A connection between star formation activity and cosmic rays in the starburst galaxy M82
对来自星爆星系M82（亦称为“雪茄星系”）的甚高能伽马射线的探测，为宇宙射线（质子和核）的产生与恒星形成之间是否存在联系提供了曾被怀疑存在、但以前却未得到证明的证据。VERITAS切伦科夫天文望远镜阵列从M82中心附近一个点状光源记录到能量超过700 GeV的伽马射线，相当于比银河系中的平均密度大约500倍的一个宇宙射线密度。（Letter p. 770）
十二边形准晶体堆积成功（A surprise package）
Disordered, quasicrystalline and crystalline phases of densely packed tetrahedra
目前仍未解决的最紧密堆积排列所采用的最简单的形状之一是正四面体，尽管人们在理论上、计算上和实验上都做了很多努力。利用一个涉及热力学计算机模拟的新方法（该方法可让体系向高密度状态自然发展），Sharon Glotzer及其同事获得了对四面体来说迄今最为紧密的有序堆积结构，堆积率为0.8324。 出乎意料的是，该结构是一种十二边形准晶体，这是从硬颗粒或从非球形构造单元形成一种准晶体的第一例。（Letter p. 773）
地球历史上已知最大的洪灾（Taken at the flood）
Catastrophic flood of the Mediterranean after the Messinian salinity crisis
距今大约560万年前，地中海与世界其他海洋分开，而且在这之后被称为“Messinian salinity crisis”的时期，随着海水蒸发，海平面急剧下降。海水在距今大约530万年前恢复了，但关于这一事件（地球历史上已知最大的洪灾）的细节仍然很不完整。利用钻孔、地震数据和数值模拟所进行的一项研究表明，这是一次灾难性的事件：虽然它是从一个可能持续了数千年的涓涓溪流开始的，但入注的水中多达90%是在不到两年时间里输送到地中海里的。这样一个突发的洪灾可能曾使海平面以超过每天10米的峰值速度上升。（Letter p. 778）
鸟类懂得“男为悦己者容”（Plumage to impress）
Reproductive skew and selection on female ornamentation in social species
很多鸟类雄性颜色鲜艳，而雌性颜色暗淡，鸟类观测者以此来辨别它们，并将这种方式称之为LBJs (‘little brown jobs’)。 对雄性追求很多雌性而雌性对交配对象又很挑剔的物种来说是这样的，也有必要这样，因为这样它们能够最大限度地利用在养育后代上的投入。但对那些雄性和雌性分担养育责任(即所谓的“合作繁育”)的物种情况又是怎么样的呢？在这样的物种中，两性之间往往看起来比较像。传统观点认为雄性的装饰性减弱，但事实未必是这样的，正如对雄性和雌性非洲八哥的装饰水平进行的一项研究所表明的那样。在这一群居物种中，雌性为引起雄性注意而相互竞争，从而变得装饰性更强，可以与雄性相媲美。在不与亲戚生活在一起的物种中，雄性比雌性装饰性更强。（Letter p. 786）
蜗壳螺旋的手性能够逆转（Snails, on the other hand）
Chiral blastomere arrangement dictates zygotic left–right asymmetry pathway in snails
蜗壳螺旋的手性（即镜像不能叠加的一种结构）由一个单一位点在遗传上决定，是由母方遗传的。对此负责的基因一直未被发现。现在，Reiko. Kuroda等人发现，对大蜗牛“静水椎实螺”（Lymnaea stagnalis）8-细胞阶段的胚胎中的细胞进行简单的操纵，能够在成年个体中逆转手性。而且引人注目的是，nodal基因（一个在很多物种中赋予左-右非对称性的基因）的表达也被细胞的重排逆转。他们还发现，在手性决定基因（一个或多个）与在促进主导型分裂球排列的第三次分裂时的手性细胞骨架动态之间有一个强烈的基因联系。这一可以跟踪的实验体系的获得，将使左-右对称性的机制比以前更容易研究。（Letter p. 790; News & Views）
生态酶活性与生态系统的养分供应（Ecoenzymes in balance）
Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil and sediment
能量和养分通过生态系统的流动由代谢限制和养分供应两个因素决定。现在，对由微生物释放到环境中去消化有机质的外部“生态酶”（ecoenzymes）所做的一项研究表明，这些酶的活性遵从一个一致的比例关系，这种关系独立于微生物群落的组成。研究人员在土壤和淡水沉积物中对调控异养微生物群落大部分碳、氮和磷摄取的四种酶进行了测量，在所有这些生境中，碳、氮和磷的吸收活性比都接近1:1:1。生态酶活性可被看作是将两个主要生态理论（化学当量理论和代谢理论）统一起来的一种联系，因为酶的表达是由环境养分供应状态的随机性专门调控的细胞代谢的一个产物。（Letter p. 795）
种子中的非编码反义RNA转录体（Regulatory RNAs go to seed）
Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target
“春化”是植物继寒冬之后在春天获得根据环境提示来开花的能力的过程，是植物的一个关键适应性特征，对农业生产有较大影响。拟南芥开花抑制因子FLC在由Polycomb调控蛋白调节的一个过程中被“春化”关闭。现在，FLC的非编码反义RNA转录体被发现存在于冷处理的种子中，并对温度变化有响应，这说明它们在低温感应和FLC沉默中有可能扮演一个角儿。这种类型的反义转录事件（源自基因的3´端）也许是调控相应“正义”转录的一个普遍机制。（Letter p. 799）
丙氨酰tRNA合成酶的疑点被揭开（Editorial changes）
Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma
丙氨酰tRNA合成酶有时能结合一个甘氨酸或一个丝氨酸，而不是丙胺酸。如果一个“错误的”氨基酸随后被从合成酶活性点转移到一个生长中的多肽链上的话，这样便会引起翻译错误。Guo等人利用晶体结构、突变酶和动力学分析发现了为什么这种酶具有这样一个混乱的特异性，也发现了这个问题是怎样通过编辑蛋白AlaXps的演化被克服的。（Letter p. 808）
----------------------
NEWS AND VIEWS
----------------------
Developmental biology: Asymmetry with a twist pp727-728
In snails, manipulating the orientation of cells in the early embryo
alters the left--right asymmetry of the shell and body. These findings
refine the search for the symmetry-breaking event in this and other animals.
Nipam H. Patel
doi:10.1038/462727a
http://www.nature.com/nature/journal/v462/n7274/full/462727a.html
Gamma-ray bursts: Magnetism in a cosmic blast pp728-729
Astronomers know little about γ-ray bursts other than that they
are the most energetic explosions in the Universe. The latest observations
indicate that large-scale magnetism contributes to their power.
Maxim Lyutikov
doi:10.1038/462728a
http://www.nature.com/nature/journal/v462/n7274/full/462728a.html
50 & 100 years ago p729
doi:10.1038/462729b
http://www.nature.com/nature/journal/v462/n7274/full/462729b.html
Neuroscience: Excitatory view of a receptor pp729-731
Ion channels opened by glutamate mediate fast cell-to-cell information
transfer in the nervous system. The structure of a full-length tetrameric
glutamate receptor is both confirmatory and revelatory.
Lonnie P. Wollmuth and Stephen F. Traynelis
doi:10.1038/462729a
http://www.nature.com/nature/journal/v462/n7274/full/462729a.html
Earth science: The enigma of D'' pp731-732
A phase transition of Earth's most abundant mineral occurs at pressures
and temperatures corresponding to those thought to exist just above
Earth's core. New experiments shed light on this enigmatic D'' region.
Kanani K. M. Lee
doi:10.1038/462731a
http://www.nature.com/nature/journal/v462/n7274/full/462731a.html
Immunology: Dendritic-cell genealogy pp732-733
The differing origins of gut dendritic cells ― white blood cells that
modulate immune responses ― may explain how the intestinal immune system
manages to destroy harmful pathogens while tolerating beneficial bacteria.
Sophie Laffont and Fiona Powrie
doi:10.1038/462732a
http://www.nature.com/nature/journal/v462/n7274/full/462732a.html
Structural biology: Molecular coin slots for urea pp733-734
Membrane-bound protein channels that allow only urea to pass
through are vital to the kidney's ability to conserve water.
Crystal structures show that the channels select urea molecules
by passing them through thin slots.
Mark A. Knepper and Joseph A. Mindell
doi:10.1038/462733a
http://www.nature.com/nature/journal/v462/n7274/full/462733a.html
Obituary: Qian Xuesen (1911--2009) p735
Founder of China's missile and space programme.
Jane Qiu
doi:10.1038/462735a
http://www.nature.com/nature/journal/v462/n7274/full/462735a.html
----------------------
NEWS AND VIEWS Q&A
----------------------
Systems chemistry: Molecular networks come of age pp736-738
The advent of sophisticated analytical tools enables the collective
behaviour of networks of interacting molecules to be studied. The
emerging field of systems chemistry promises to allow such networks
to be designed to perform complex functions, and might even shed
light on the origins of life.
Jonathan R. Nitschke
doi:10.1038/462736a
http://www.nature.com/nature/journal/v462/n7274/full/462736a.html
----------------------
ARTICLES
----------------------
Cancer-associated IDH1 mutations produce 2-hydroxyglutarate pp739-744
Mutations in the enzyme cytosolic isocitrate dehydrogenase 1 (IDH1)
are commonly found in glioblastomas, a major subset of primary human
brain cancers. However, only a single copy of the gene is mutated,
suggesting that the mutation does not result in a simple loss of
function. Here, IDH1 mutations are shown to act in a gain-of-function
manner, resulting in a new ability of the enzyme to catalyse [alpha]-
ketoglutarate to R(-)-2-hydroxyglutarate, an onco-metabolite.
Lenny Dang et al.
doi:10.1038/nature08617
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08617.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08617.html
X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate
receptor pp745-756
The majority of excitatory neurotransmission in the central nervous
system is mediated by ionotropic glutamate receptors, which function by
opening a transmembrane ion channel upon binding of glutamate. However,
despite this crucial role in neurobiology, the architecture and atomic
structure of an intact isotropic glutamate receptor are unknown. The X-ray
crystal structure of the rat GluA2 receptor in complex with a competitive
antagonist is now reported and analysed.
Alexander I. Sobolevsky, Michael P. Rosconi and Eric Gouaux
doi:10.1038/nature08624
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08624.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08624.html
Crystal structure of a bacterial homologue of the kidney urea transporter
pp757-761
Specialized urea transporters have evolved to achieve rapid and selective
urea permeation in the mammalian kidney, a process ultimately necessary for
water re-absorption. Here, the X-ray crystal structure of a functional urea
transporter from the bacterium Desulfovibrio vulgaris is presented and
analysed; the results establish that the urea transporter operates by a
channel-like mechanism and reveal the physical and chemical basis of urea selectivity.
Elena J. Levin, Matthias Quick and Ming Zhou
doi:10.1038/nature08558
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08558.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08558.html
Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme
pp762-766
In living systems, the repair of genotoxic damage requires that the lesion
first be detected in an excess of undamaged DNA. A base-excision DNA repair
enzyme, MutM, is now captured and structurally elucidated at the stage of
initial encounter with a damaged nucleobase within a DNA duplex. By combining
structural biology and computational modelling, the pathway by which this
encounter causes the damaged nucleobase to be extruded from the DNA duplex is defined.
Yan Qi et al.
doi:10.1038/nature08561
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08561.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08561.html
----------------------
LETTERS
----------------------
Ten per cent polarized optical emission from GRB[thinsp]090102 pp767-769
The nature of the jets and the role of magnetic fields in gamma-ray bursts
(GRBs) remain unclear. There are two possible models, one of which suggests
that magnetic fields are critical; to distinguish between these models the
degree of polarization in early-time emission must be measured. The early
optical emission from GRB 090102 is now reported to be polarized at 10
[plusmn] 1 per cent, indicating the presence of large-scale fields
originating in the expanding fireball.
I. A. Steele et al.
doi:10.1038/nature08590
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08590.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08590.html
A connection between star formation activity and cosmic rays in the starburst
galaxy M82 pp770-772
Cosmic rays are believed to be mainly accelerated by the winds and supernovae
of massive stars, although definite evidence for this is lacking. The active
regions of starburst galaxies have exceptionally high rates of star formation,
and therefore should produce cosmic rays that interact with interstellar gas
and radiation to produce diffuse γ-rays. The detection and analysis of >700-GeV
γ-rays from M82, the prototype small starburst galaxy, now links cosmic-ray
acceleration to star formation activity.
V. A. Acciari et al.
doi:10.1038/nature08557
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08557.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08557.html
Disordered, quasicrystalline and crystalline phases of densely packed
tetrahedra pp773-777
All hard, convex shapes pack more densely than spheres, although for
tetrahedra this was demonstrated only very recently. Here, tetrahedra are
shown to pack even more densely than previously thought. Thermodynamic
computer simulations allow the system to evolve naturally towards high-density
states, showing that a fluid of hard tetrahedra undergoes a first-order phase
transition to a dodecagonal quasicrystal, and yielding the highest packing
fractions yet observed for tetrahedra.
Amir Haji-Akbari et al.
doi:10.1038/nature08641
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08641.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08641.html
Catastrophic flood of the Mediterranean after the Messinian salinity crisis
pp778-781
5.33 million years ago, in an event known as the Zanclean flood, Atlantic
waters refilled a mostly desiccated Mediterranean Sea which had become
disconnected from the world's oceans; however, the nature, abruptness and
evolution of this flood remain poorly constrained. Using borehole and seismic
data and a model study, it is now suggested that 90 per cent of the water was
transferred in a short period of a few months to two years, with peak rates of
sea level rise in the Mediterranean possibly reaching more than 10 metres per day.
D. Garcia-Castellanos et al.
doi:10.1038/nature08555
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08555.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08555.html
Thickness and Clapeyron slope of the post-perovskite boundary pp782-785
Seismic detectability of the boundaries and convection in the mantle is
strongly influenced by the thicknesses and Clapeyron slopes of mantle phase
boundaries. The unusually large positive Clapeyron slope found for the boundary
between perovskite and post-perovskite (the 'pPv boundary') would destabilize
high-temperature anomalies in the lowermost mantle, in disagreement with the
seismic observations. Here, new studies of the thickness and Clapeyron slope
of the pPv boundary shed light on this matter.
Krystle Catalli, Sang-Heon Shim and Vitali Prakapenka
doi:10.1038/nature08598
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08598.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08598.html
Reproductive skew and selection on female ornamentation in social species
pp786-789
Male animals are typically more elaborately ornamented than females, probably
because females make more of an energetic investment in raising young. However,
this generality may not apply in cooperatively breeding vertebrates, where the
energetic load is similar in males and females. The socially diverse African
starlings are now used to study this issue, revealing that where intrasexual
competition among females may be intense, female trait elaboration is selected for.
Dustin R. Rubenstein and Irby J. Lovette
doi:10.1038/nature08614
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08614.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08614.html
Chiral blastomere arrangement dictates zygotic left--right asymmetry pathway in
snails pp790-794
Most animals display internal and/or external left-right asymmetry. The gastropod
Lymnaea stagnalis has both sinistral and dextral snails within a species; the
chirality is hereditary, but the gene(s) and mechanisms for handedness-
determination are not yet identified. In L. stagnalis, the chiral blastomere
arrangement at the eight-cell stage is now shown to determine left-right
asymmetry throughout development, acting upstream of the Nodal signalling pathway.
Reiko Kuroda, Bunshiro Endo, Masanori Abe and Miho Shimizu
doi:10.1038/nature08597
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08597.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08597.html
Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil
and sediment pp795-798
The atomic ratio of carbon:nitrogen:phosphorus can be used to describe biota in
terms of elemental composition, and this stoichiometry is fundamental for
understanding the production dynamics and biogeochemical cycles of ecosystems.
Heterotrophic microbial communities from terrestrial soils and fresh-water
sediments are now shown to share a common functional stoichiometry in relation
to organic nutrient acquisition, reflecting the similar scaling relationships
of four key ecoenzymes.
Robert L. Sinsabaugh, Brian H. Hill and Jennifer J. Follstad Shah
doi:10.1038/nature08632
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08632.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08632.html
Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb
target pp799-802
Here, the link between non-coding RNA and chromatin regulation is investigated
through analysis of FLC - a regulator of flowering time in Arabidopsis
and a target of several chromatin pathways. FLC is silenced by prolonged cold
in a Polycomb-mediated process called vernalization. Upregulation of long
non-coding antisense transcripts covering the entire FLC locus are now
suggested to have an early role in the cold-induced silencing mechanism.
Szymon Swiezewski, Fuquan Liu, Andreas Magusin and Caroline Dean
doi:10.1038/nature08618
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08618.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08618.html
Long-range oncogenic activation of Igh--c-myc translocations by the Igh 3'
regulatory region pp803-807
Lymphomas often contain translocations that link c-myc to the immunoglobulin
heavy chain locus (encoded by Igh), but the nature of the elements that activate
oncogenes within such translocations is unknown. Transgenic mice with Igh 3'
regulatory region (Igh3' RR) sequences fused to c-myc are predisposed to B
lymphomas. Here, the oncogenic role of the Igh3' RR is investigated by
inactivating it in two distinct mouse models for B-cell lymphoma with
Igh-c-myc translocations.
Monica Gostissa et al.
doi:10.1038/nature08633
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08633.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08633.html
Paradox of mistranslation of serine for alanine caused by AlaRS recognition
dilemma pp808-812
Alanyl-tRNA synthetases (AlaRSs) may confuse glycine or serine with alanine,
potentially causing mistranslation and thus profound functional consequences,
with serine posing a bigger challenge than glycine. AlaXps - free-standing,
genome-encoded editing proteins - represent one editing checkpoint to prevent
this from occurring. Nine crystal structures, together with kinetic and
mutational analysis, now show how AlaXps solve the serine misactivation problem.
Min Guo et al.
doi:10.1038/nature08612
Abstract: http://www.nature.com/nature/journal/v462/n7274/abs/nature08612.html
Article: http://www.nature.com/nature/journal/v462/n7274/full/nature08612.html
----------------------
FUTURES
----------------------
In the recovery room p818
The advance of science.
Eric Brown
doi:10.1038/462818a
http://www.nature.com/nature/journal/v462/n7274/full/462818a.html
| 《Nature》目录要览 — 2011-04-28出版 |
| 《Nature》目录要览：2011-01-20出版 |
| 《Nature》目录要览：2010-12-23出版 |
| 《Nature》目录要览：2010-12-16出版 |
| 《Nature》目录要览：2010-12-09出版 |
| 《Nature》目录要览：2010-12-02出版 |
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