《Nature》目录：2010-06-24出版

封面故事：具有高唤回效率的量子记忆体
Efficient quantum memory for light
存取由光脉冲传输的量子信息的能力对于量子通信网络的建设必不可少。以前报道的量子记忆体（以原子蒸气为存储媒介）的唤回效率不到17%。 现在Morgan Hedges及其同事介绍了一种低噪音固态量子记忆体，在其中，信息存储在一个“原硅酸钇”晶体中的镨离子的光跃迁中，唤回效率高达69%。 在光强度低时，这种量子记忆体的表现超过经典记忆装置。如果对所采用材料的光学性能做一些改进，这样的记忆体也许可用于实用的量子信息应用中。（Letter p. 1052）


酰胺的新合成路径（New synthetic route to amides）
Umpolung reactivity in amide and peptide synthesis
酰胺键作为天然肽和蛋白的骨干普遍存在，也存在于很多具有疗效的小分子中。这种键的传统实验合成主要依赖于碳-氮键形成过程中的脱水方法，碳和氮仍分别保持亲电子和亲核特点。Shen等人介绍了酰胺合成的一个新路径，涉及通过胺和硝基烷的碘激发来使反应物极性发生逆转（这个过程被称为“极性反转”）。它与当前所采用的方法相比有几个优势，如比较方便，且有很多不同起始化合物可供利用，并且它还有可能发展成为肽和含酰胺小分子的一种高效的对映选择性合成方法。（Article p. 1027; News & Views）


假基因所起的作用（A role for pseudogenes）
A coding-independent function of gene and pseudogene mRNAs regulates tumour biology
微RNA已知通过与一个目标信使RNA中的不完全互补序列相互作用来调控基因表达。但真实情况是否相反呢？即mRNA表达是否会影响微RNA的分布呢？一项新的研究表明，一个假基因（肿瘤抑制因子假基因PTENP1）的3΄未翻译区域(UTR)能与相关的蛋白编码基因PTEN结合相同的微RNA。这表明，假基因具有一个作为“诱饵”的生物功能：螯合微RNA，从而影响它们对所表达的基因的调控。（Article p. 1033; News & Views）


“DNA聚合酶η”的结构被确定（DNA polymerase structures）
Structural basis for the suppression of skin cancers by DNA polymerase η / Structure and mechanism of human DNA polymerase η
紫外线的穿透辐射诱导皮肤细胞中的DNA病灶，它们会阻止DNA复制和引起能发展成癌症的突变。身体应对这种损伤的一种方式涉及专门化的DNA聚合酶，以此来绕过这样的病灶。“DNA聚合酶η” (Polη)通过复制含有胸腺嘧啶二聚物的DNA来做这件事，而这种酶的失活导致被称为“着色性干皮病”的皮肤病的一个变种和皮肤癌的高发病率。现在，两个小组确定了Polη的晶体结构。这些结构（一个是酵母酶的结构，一个是人体酶的催化区域的结构）显示了尺寸较大的胸腺嘧啶二聚物在一个异常大的活性点上是怎样被容纳的、以及病灶是怎样通过在其他聚合酶中不存在的相互作用来稳定的。“着色性干皮病”患者的“错义突变”被发现会破坏聚合酶在正常B形式中维持受损DNA的能力。在配发的News & Views文章中，Suse Broyde 和 Dinshaw Patel讨论了Polη的结构与所报道的其他Y-家族DNA聚合酶结构的相符性问题。（Articles pp. 1039, 1044; News & Views）


“热木星”HD 209458b的质量被确定（An exoplanet's mass）
The orbital motion, absolute mass and high-altitude winds of exoplanet HD 209458b
大多数已知太阳系外星球是用“径向速度法”发现的，即测量它们沿轨道运行的伴星在主星中所诱导的“摆动”。如果行星的轨道速度也可以被确定，那么就有可能在不需要做进一步假设或不需要依靠模型的情况下来计算恒星及其太阳系外行星的质量。现在，这一点对被研究得非常透彻的“热木星”HD 209458b已经做到了，所依据的是对一氧化碳分子吸收线的变化“多普勒偏移”的光谱测量结果，而这些分子吸收线是在该行星经过其主星与地球之间时观测到的。主星（恒星）和行星的质量分别为1.00±0.22太阳质量和0.64±0.09木星质量。结果还显示，作为一氧化碳信号相对于主星速度的“蓝移”，有一股强风从该行星有光照的白天一边的高纬度处向其无光照的夜晚一边流动。（Letter p. 1049; News & Views）


硅中杂质原子的量子操纵（Atom manipulation in silicon）
Coherent control of Rydberg states in silicon
当一个原子被激发到一种“Rydberg”状态时，其电子波动函数可以从不到0.1纳米延伸到几个纳米或更多。这个过程可被用来诱导和相干控制两个相距足够远、在其正常状态下不会发生相互作用的两个原子之间的相互作用。Thornton Greenland及其同事利用这一现象实现了与以前利用激光冷却束缚的原子所做到的结果可以相比的量子操纵，但却是在固体状态、在硅中的磷杂质（掺杂）原子上。该方法有可能经过改造来控制少量在已知位置上的、可独立寻址的杂质原子，如量子逻辑门的实施所要求的那样。（Letter p. 1057）


深水中的溶解硝酸盐向海洋表面输送（Ocean nitrates on the up）
Nitrate supply from deep to near-surface waters of the North Pacific subtropical gyre
溶解的无机碳的季节性（春季和夏季）消耗发生在世界海洋中大多数无生产力的或寡营养的区域的表面混合层中。消失的溶解无机碳被认为被光合作用转化成了颗粒性碳，然而显然没有足够的溶解营养物来支持所需的植物生长数量。现在，一个可能的营养供应机制已在一项在北太平洋进行的研究中被识别出来。短期运输事件（持续不到10天）将缺营养的表面海水与深水中的溶解硝酸盐联系了起来。当从表面到250米深处的水柱被当成一个整体时，营养供应和需求近乎相等。（Letter p. 1062）


捕食模式随猎物丰富程度的变化（Patterns of predation）
Environmental context explains Lévy and Brownian movement patterns of marine predators
在一个食物来源不集中、不可预测的生境中找到食物的最好方式是什么？理论表明，觅食的生物应采取一种“Lévy-flight”搜索策略，它是“随机行走”的一个变异形式，在这种形式的行走中，短距离的探索性蹦蹦跳跳与偶尔较长距离的行走相间。但当捕食者发现它们自己周围有丰足的食物时，简单的不规则运动或“布朗”运动就应当足够了。事实证明，野生动物中有关真正的“Lévy-flight”式觅食的明显证据难以获得，但是现在，对包括鲨鱼、大马林鱼（枪鱼）和金枪鱼在内的14个海洋捕食者物种构成的一个大型数据集所做的一项分析证明了这一点。电子标记显示，当在生产力较低、猎物稀少的水域游动时，鱼类采取Lévy行为；而在生产力较高的生活环境中时，它们则采用“布朗”运动方式。（Letter p. 1066; News & Views）


一个神经控制中心（A centre for neural control）
Activity-dependent relocation of the axon initial segment fine-tunes neuronal excitability / Presynaptic activity regulates Na+ channel distribution at the axon initial segment
位于每个神经纤维根部的“轴突起始段” (AIS)（在那里，成簇的钠通道产生动作势，后者随后沿轴突传播），是从事神经可激发性之性质研究的神经科学家的关注焦点。作为一个神经脉冲的来源，它似乎是调控神经活动的一个逻辑点。本期Nature上两篇论文证实，AIS是一个内在的神经弹性来源。Matthew Grubb 和 Juan Burrone发现，电活动可逆地改变AIS在培养的海马神经元中的位置。他们提出，由此所导致的内在可激发性的增加在发育过程中可能会微调神经可激发性，同时也为癫痫的控制指出了潜在目标。Hiroshi Kuba、Yuki Oichi 和Harunori Ohmori发现，在消除了声音刺激的鸟听觉神经元中，AIS的尺寸增加。同样，内在可激发性会增加、并且可能有助于听觉通道的维持。这样的神经弹性也许可补偿某些形式的失聪。（Letters pp. 1070; 1075; News & Views）


植物茎干细胞的控制（Control of shoot stem cells）
Hormonal control of the shoot stem-cell niche
植物在其顶端分生组织中不断保持着干细胞，植物的茎系统和根系统就是从顶端分生组织产生的。在经典植物模型拟南芥中，茎顶端分生组织中的干细胞命运由植物生长素和细胞分裂素等激素来控制。现在，对这些激素之间的交流所做的一项研究表明，两个A-型“拟南芥响应调控因子”基因对细胞分裂素和植物生长素信号进行集成，并将这些输入与茎顶端分生组织中的核心调控机制联系起来。这项工作为植物生长素和细胞分裂素在设置茎干细胞小生境中的协同活动提出了一个机制性框架，并且突显了根和茎干细胞系统在对植物激素响应方面的差别。（Letter p. 1089）




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NEWS AND VIEWS
----------------------
Gene-expression forum: Decoy for microRNAs pp1016-1017
Pseudogenes are considered to be defunct relatives of known genes. But there
is some surprising news: pseudogenes are functional and could have a role in
the control of cancer. Two experts discuss the significance of these findings
for understanding the regulation of gene expression and cancer biology.
Isidore Rigoutsos and Frank Furnari
doi:10.1038/4651016a
http://www.nature.com/nature/journal/v465/n7301/full/4651016a.html

Astronomy: Exoplanet caught speeding pp1017-1018
The masses of exoplanets have so far been inferred from the tiny gravitational
pull they exert on the host stars. It is now possible to measure them from
shifts in spectral lines arising from the planets' atmospheres.
Mercedes Lo'pez-Morales
doi:10.1038/4651017a
http://www.nature.com/nature/journal/v465/n7301/full/4651017a.html

Ecology: Fish in Le'vy-flight foraging pp1018-1019
Le'vy flights are a theoretical construct that has attracted wide interdisciplinary
interest. Empirical evidence shows that the principle applies to the foraging
of marine predators.
Gandhimohan M. Viswanathan
doi:10.1038/4651018a
http://www.nature.com/nature/journal/v465/n7301/full/4651018a.html

Evolutionary biology: Expanding islands of speciation pp1019-1020
Speciation can occur even when the incipient species coexist and can interbreed.
An extensive analysis of two fruitfly strains suggests that many genomic regions
contribute to speciation in such cases.
Erin S. Kelleher and Daniel A. Barbash
doi:10.1038/4651019a
http://www.nature.com/nature/journal/v465/n7301/full/4651019a.html

Organic chemistry: Amide bonds made in reverse pp1020-1022
Amide bonds connect the amino acids in proteins and occur in many other useful
molecules. An amide-forming reaction that turns the conventional approach on
its head offers a practical way of making these bonds.
Karl Scheidt
doi:10.1038/4651020a
http://www.nature.com/nature/journal/v465/n7301/full/4651020a.html

Neuroscience: A plastic axonal hotspot pp1022-1023
Neurons generate their output signal ― the action potential ― in a distinct
region of the axon called the initial segment. The location and extent of this
trigger zone can be modified by neural activity to control excitability.
Jan Gru"ndemann and Michael Ha"usser
doi:10.1038/4651022a
http://www.nature.com/nature/journal/v465/n7301/full/4651022a.html

DNA repair: How to accurately bypass damage pp1023-1024
Ultraviolet radiation can cause cancer through DNA damage ― specifically, by
linking adjacent thymine bases. Crystal structures show how the enzyme DNA
polymerase [eta] accurately bypasses such lesions, offering protection.
Suse Broyde and Dinshaw J. Patel
doi:10.1038/4651023a
http://www.nature.com/nature/journal/v465/n7301/full/4651023a.html

Obituary: Cecil Terence Ingold (1905-2010) p1025
A leading light in the twentieth-century study of fungi.
Nicholas P. Money
doi:10.1038/4651025a
http://www.nature.com/nature/journal/v465/n7301/full/4651025a.html

----------------------
ARTICLES
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Umpolung reactivity in amide and peptide synthesis pp1027-1032
The backbones of all natural peptides and proteins are composed of amide bonds.
In the laboratory, the construction of such bonds generally relies on dehydrative
approaches, although there are alternatives. It is now shown that the activation
of amines and nitroalkanes with an electrophilic iodine source can lead directly
to amide products.
Bo Shen, Dawn M. Makley and Jeffrey N. Johnston
doi:10.1038/nature09125
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09125.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09125.html

A coding-independent function of gene and pseudogene mRNAs regulates tumour
biology pp1033-1038
The canonical role of messenger RNA (mRNA) is in protein coding and synthesis.
But could mRNAs also have a role that is related to their ability to compete for
microRNA binding? Here, the functional relationship between the mRNAs produced by
the PTEN tumour suppressor gene and its pseudogene PTENP1 is investigated. The
results suggest that pseudogenes have a biological function, in sequestering
microRNAs and so affecting their regulation of gene expression.
Laura Poliseno et al.
doi:10.1038/nature09144
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09144.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09144.html

Structural basis for the suppression of skin cancers by DNA polymerase [eegr]
pp1039-1043
Ultraviolet radiation causes damage to DNA in skin cells, blocking DNA replication
and causing mutations that can lead to cancer. One way in which the cell deals
with such damage involves specialized DNA polymerases, such as Pol[eta], that
can bypass lesions. Here the crystal structure is presented of Pol? in complex
with a thymine-thymine dimer and with undamaged DNA. The bulky thymine dimer is
accommodated in an atypically large active site, and stabilized by interactions
not found in other polymerases.
Timothy D. Silverstein et al.
doi:10.1038/nature09104
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09104.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09104.html

Structure and mechanism of human DNA polymerase [eegr] pp1044-1048
Ultraviolet radiation causes damage to DNA in skin cells, blocking DNA replication
and causing mutations that can lead to cancer. One way in which the cell deals
with such damage involves specialized DNA polymerases, such as Pol[eta], that
can bypass lesions. Here the crystal structure of Pol[eta] is presented at four
consecutive steps during DNA synthesis through thymine dimers. Pol[eta] acts
like a 'molecular splint' to stabilize damaged DNA, and accommodates the thymine
dimer in an atypically large active site.
Christian Biertu"mpfel et al.
doi:10.1038/nature09196
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09196.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09196.html

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LETTERS
----------------------
The orbital motion, absolute mass and high-altitude winds of exoplanet HD[thinsp]
209458b pp1049-1051
If the orbital velocity of an extrasolar planet could be determined, the masses
of both the planet and its host star could be calculated using Newton's law of
gravity. Here, high-dispersion ground-based spectroscopy of a transit of the
extrasolar planet HD 209458b is reported. This allowed the radial component of
the planet's orbital velocity to be calculated, and thus the masses of star and
planet. Moreover, a strong wind flowing from the irradiated dayside to the
non-irradiated nightside of the planet is suggested.
Ignas A. G. Snellen, Remco J. de Kok, Ernst J. W. de Mooij and Simon Albrecht
doi:10.1038/nature09111
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09111.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09111.html

Efficient quantum memory for light pp1052-1056
A quantum memory would enable storage and retrieval of a quantum state of light
without corrupting the information it carries. Previous devices have had low
efficiencies of less than 17 per cent, and used weak quantum states with an
average photon number of around one. Now a solid-state quantum memory is
described with an efficiency of up to 69 per cent, which performs better
than a classical device for bright states of up to 500 photons.
Morgan P. Hedges, Jevon J. Longdell, Yongmin Li and Matthew J. Sellars
doi:10.1038/nature09081
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09081.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09081.html

Coherent control of Rydberg states in silicon pp1057-1061
When an atom is excited into a Rydberg state, its electronic wavefunction can
extend to several nanometres. This process can be used to induce and coherently
control interactions between atoms that are far enough apart to be non-interacting
in their normal states. Now, such behaviour has been realized in a solid-state
context, by demonstrating coherent control of the wavefunctions of phosphorus
dopant atoms in silicon.
P. T. Greenland et al.
doi:10.1038/nature09112
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09112.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09112.html

Nitrate supply from deep to near-surface waters of the North Pacific subtropical
gyre pp1062-1065
Concentrations of dissolved inorganic carbon (DIC) decrease in the surface mixed
layers during spring and summer in most of the oligotrophic ocean. The missing
DIC is thought to be converted to particulate carbon by photosynthesis, but known
mechanisms do not seem to supply enough nutrients for the photosynthesis. Here
it is shown that short-lived transport events connect deep-water nitrate stocks
with nutrient-poor surface waters.
Kenneth S. Johnson, Stephen C. Riser and David M. Karl
doi:10.1038/nature09170
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09170.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09170.html

Environmental context explains Le'vy and Brownian movement patterns of marine
predators pp1066-1069
What is the best way for predators to find food when prey is sparse and distributed
unpredictably? Theory predicts that in such circumstances predators should adopt
a Le-flight strategy, in which short exploratory hops are occasionally interspersed
with longer trips. When prey is abundant, simple Brownian motion should suffice.
Now, analysis of a large data set of marine predators establishes that animals
do indeed adopt Levy-flight foraging when prey is sparse, and Brownian episodes
when prey is abundant.
Nicolas E. Humphries et al.
doi:10.1038/nature09116
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09116.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09116.html

Activity-dependent relocation of the axon initial segment fine-tunes neuronal
excitability pp1070-1074
A nerve cell sends signals to others through action potentials, which begin at
the 'initial segment' of the neuron's axon. It is now shown that changes in
electrical activity can alter the position of this initial segment in cultured
rat hippocampal neurons. The resulting increase in intrinsic excitability - the
tendency to fire action potentials [mdash] represents a new form of neuronal
plasticity and could provide a new target in the control of epilepsy.
Matthew S. Grubb and Juan Burrone
doi:10.1038/nature09160
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09160.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09160.html

Presynaptic activity regulates Na+ channel distribution at the axon initial
segment pp1075-1078
A nerve cell sends signals to others through action potentials, which begin at
the 'initial segment' of the neuron's axon. Here it is shown that the length
of this initial segment increases in bird auditory neurons that have been deprived
of auditory stimulation. The resulting increase in intrinsic excitability - the
tendency to fire action potentials [mdash] represents a new form of neuronal
plasticity and might contribute to the maintenance of the auditory pathway
after hearing loss.
Hiroshi Kuba, Yuki Oichi and Harunori Ohmori
doi:10.1038/nature09087
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09087.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09087.html

Subcapsular sinus macrophages prevent CNS invasion on peripheral infection
with a neurotropic virus pp1079-1083
Macrophages that populate the lymph nodes are known to clear viruses from the
lymph and to initiate antiviral humoral immune responses. It is now shown that
these macrophages also have another function: they prevent lymph-borne neurotropic
viruses from entering the central nervous system. The mechanism is dependent on
the production of type I interferon.
Matteo Iannacone et al.
doi:10.1038/nature09118
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09118.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09118.html

Sphingosine-1-phosphate is a missing cofactor for the E3 ubiquitin ligase TRAF2
pp1084-1088
Engagement of the tumour-necrosis factor (TNF) receptor results in the assembly
of multi-component signalling complexes by adaptor proteins that include TNF
receptor-associated factor 2 (TRAF2). Genetic evidence indicates that TRAF2 is
needed for the polyubiquitination of receptor interacting protein 1 (RIP1), but
direct evidence has been lacking. Here it is shown that the lipid
sphingosine-1-phosphate is a co-factor needed for this ubiquitination activity of TRAF2.
Sergio E. Alvarez et al.
doi:10.1038/nature09128
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09128.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09128.html

Hormonal control of the shoot stem-cell niche pp1089-1092
Zhong Zhao et al.
doi:10.1038/nature09126
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09126.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09126.html

Activation of autophagy during cell death requires the engulfment receptor Draper
pp1093-1096
Christina K. McPhee, Mary A. Logan, Marc R. Freeman and Eric H. Baehrecke
doi:10.1038/nature09127
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09127.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09127.html

Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of
transcription pp1097-1101
Small regulatory RNAs function both in the cytoplasm, inhibiting expression from
messenger RNAs, and in the nucleus, silencing heterochromatin and preventing
genome rearrangement. Now a new protein involved in RNA interference in the
nucleus has been characterized. This protein, NRDE-2, associates with NRDE-3
and short interfering RNAs on nascent transcripts. This association prevents
elongation of the transcripts by RNA polymerase II, making this a co-transcriptional
form of gene silencing.
Shouhong Guang et al.
doi:10.1038/nature09095
Abstract: http://www.nature.com/nature/journal/v465/n7301/abs/nature09095.html
Article: http://www.nature.com/nature/journal/v465/n7301/full/nature09095.html

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