《Nature》目录要览（2010-10-28出版）

封面故事：“1000基因组项目”发表首篇论文
A map of human genome variation from population-scale sequencing
本期Nature含有“1000基因组项目”(The 1000 Genomes Project)首
次发表的成果，该项目是一个国际合作项目，它将生成
一个庞大的、公开的人类基因变异目录。该项目的计划
是，对大约2000个人进行测序，这些人身份不明，事实
上他们来自全世界20个人群。在本期Nature发表的是该项
目的第一篇论文，它是来自该项目试点阶段的成果，即
测试以高吞吐量平台进行全基因组测序的三个不同策
略：对三个人群的179人按低覆盖率进行全基因组测序；
对两个由“母亲-父亲-孩子”组成的三人组按高覆盖率
进行测序；对来自七个人群的697人进行以外显子为目标
的测序。（Article p. 1061; News & Views）


SLAC1细菌同源物的晶体结构被确定（Structure of stomatal 
anion channel SLAC1）
Homologue structure of the SLAC1 anion channel for closing stomata in 
leaves
SLAC1是一个最近识别出的、存在于植物叶子中的阴离子
通道，在那里它控制膨压(turgor pressure)，从而控制植物
气门响应包括二氧化碳、臭氧和干旱在内的环境因素而
开启。现在，细菌身上相当于SLAC1的一种物质（即来
自“流感嗜血杆菌”的“亚碲酸盐抗性蛋白TehA”）的X-
射线晶体结构已被确定。由结构启发而获得的突变发生
机理被用来分析该通道的导电性质。气孔的静电特性表
明，不同阴离子之间的选择性在很大程度上是离子脱水
的能量成本的一个函数。这项工作以及对该细菌蛋白功
能所做的进一步研究表明，SLAC1 和TehA代表着由环境刺
激控制的一大类选择性阴离子通道。（Article p. 1074; 
News & Views）


迄今发现的质量最大的中子星（Record neutron star mass 
rules out exotics）
A two-solar-mass neutron star measured using Shapiro delay
对双星毫秒脉冲星J1614-2230所做的新的观测工作，识别
出其组成部分之一是精确质量已知的最大质量中子星
——几乎比以前的最高值大近20%。中子星由已知最致密
的物质形式组成，而毫秒脉冲星是转动的中子星。迄今
为止，观察到的中子星质量范围太窄，不能排除对“奇
异”的非核成分的很多预测，但这个脉冲星约为两个太
阳的质量，从而排除了当前提出的涉及奇异“超
子”或“玻色子”凝聚态的几乎全部状态方程。
（Letter p. 1081; News & Views）


半导体中磁性掺杂原子的取向（Attractive variations on 
spintronic qubits）
Detecting excitation and magnetization of individual dopants in a 
semiconductor
一个非磁性半导体基质中孤立的磁性掺杂原子代表着自
旋电子学应用的一个很有希望的体系。这些原子的行为
就像罗盘的指针一样，每个针都可指向不同方向，从而
载有与传统信息技术中的一个“位”相似的信息。此
前，一直没有可能来研究基质本身的原子结构与掺杂原
子磁性之间的相关性。现在，Khajetoorians等人开发出一
种灵敏的扫描探针技术，它能在一个二维半导体系统内
测量单个磁性掺杂原子的自旋激发——实质上，这种方
法能读出原子罗盘指针的取向。他们发现，掺杂原子起
孤立量子自旋的作用，由于较大的磁各向异性效应，这
些自旋被迫朝着表平面的方向——这个结果得到计算结
果的支持。这项工作为对嵌入在半导体中的磁性掺杂进
行原子尺度和单自旋层面的研究提供了一个起点。
（Letter p. 1084）


海洋磷酸盐的地质史（Geological history of marine phosphate）
The evolution of the marine phosphate reservoir
磷被普遍认为是海洋中初级生产力的一种限制营养物，
在调控海洋-大气系统的氧化-还原状态中有重要作用。 
Planavsky等人利用富含氧化铁的沉积岩中磷对铁的比例随
时间的变化来评估海洋磷酸盐库的演化。他们发现，在
地球历史上过去5.42亿年中，磷酸盐浓度相对是恒定
的。这些数据还表明，在距今大约7亿年前发生的所
谓“雪球地球”冰河作用之后，地球上有溶解的高浓度
磷酸盐，它们有可能导致了快速的初级生产活动、有机
碳埋存和大气中氧含量的增加，从而为后生动物的兴起
铺平道路。（Letter p. 1088; News & Views）


非洲类人猿的早期多样性（Early diversity in African 
anthropoids）
Late middle Eocene epoch of Libya yields earliest known radiation of 
African anthropoids
类人猿（包括猴子、猿和人类在内的高等灵长类）的起
源充满了神秘。来自非洲始新世的化石曾表明，它们起
源于该大陆，但这个观点受到亚洲相关发现的挑战。现
在，这个游戏又被始新世时期利比亚的几个类人猿灵长
类物种的发现所改变，其中每个物种都属于一个不同的
类别。这表明，灵长类是早期分化的（可能是在亚
洲），然后与其他种类的哺乳动物一起向非洲迁移。
（Letter p. 1095）


重组图显示性别差异（Recombination maps reveal differences 
between the sexes）
Fine-scale recombination rate differences between sexes, populations 
and individuals
高分辨率重组图在遗传研究中有很多用途。现有的这种
重组图（它们利用来自HapMap项目的高密度SNP（单核苷酸
多态性）数据的联系失衡模式）已被证明非常有用。但
它们有一些局限性，如不能提供关于不同性别之间和同
一性别之内重组特征之差别的信息。在冰岛从事deCODE遗
传研究的一个小组，利用来自超过15000个“父母-子女
对”的全基因组SNP数据来首次构建基于直接观察到的重
组事件的重组图，其分辨率达到10kb。他们的数据显
示，不同性别之间存在有趣的重组差别。例如，在男性
中，重组倾向于对外显子进行“洗牌”，而在女性中它
则产生附近基因的新组合。将这些重组图与基于联系失
衡的重组图进行对比，显示了在欧洲、非洲和美国的人
群之间以前没有被发现的差别。（Letter p. 1099）


一种大脑-机器视觉接口（A visual brain–machine interface）
On-line, voluntary control of human temporal lobe neurons
大脑必须不断在大量外界感觉刺激之间进行选择，以便
专注并处理其中少数一些刺激。“内侧颞叶”(MTL)中的
神经元对特定视觉目标有选择性响应，它们的活动已知
由认知效应调控。Cerf等人构建了一个新的大脑-机器接
口，在该接口中，当观看叠加的电脑图像的神经外科手
术患者被要求让一个图像渐现或渐隐时，迅速学会了调
控他们位于不同子区域和不同半球的MTL神经元的神经活
动，从而增加某些细胞的激发速度，同时降低其他细胞
的激发速度，并控制组合图像的内容。这项工作提供了
人类可以控制他们自己大脑内的视觉神经元的神经活
动、而且这种活动还可以被解码来控制设备的直接证
据。希望这样的接口装置今后有一天将能帮助有各种各
样神经损伤（如“闭锁综合征”或运动神经元疾病）的
患者进行沟通。（Letter p. 1104）


胰腺癌从初发到转移的时间线（A timeline for pancreatic 
cancer）
The patterns and dynamics of genomic instability in metastatic 
pancreatic cancer / Distant metastasis occurs late during the genetic 
evolution of pancreatic cancer
Christine Iacobuzio-Donahue及其同事利用全基因组“外显子
组”测序来分析来自相同患者的原发胰腺癌和一种或多
种转移肿瘤。他们发现肿瘤由截然不同的亚克隆组成，
确定了转移性癌症克隆在原发肿瘤内演化的演化图，并
且估计了肿瘤发展的时间尺度。基于这些数据他们估
计，在胰腺肿瘤发生的开始和原发的、非转移性肿瘤的
形成之间的平均时间为11.8年，而指示性转移克隆的出
现另需6.8年。这些数据表明存在一个潜在很大的机会窗
口，在此时段内也许有可能相对较早地检测出癌症
来。Peter Campbell及其同事利用下一代测序方法检测了13
名胰腺癌患者的染色体重排。结果显示患者间存在相当
大的异质性，表明在转移的发生过程中基因组不稳定和
演化是持续存在的。但对所研究的大部分患者来说，所
发现的基因重排中超过一半存在于所有转移肿瘤和原发
肿瘤中，从而使其成为在这种疾病的早期和晚期进行治
疗干预的潜在目标。（Letters pp. 1109, 1114）



----------------------
NEWS & VIEWS
----------------------
Genomics: In search of rare human variants pp1050-1051
The 1000 Genomes Project has completed its pilot phase, sequencing the 
whole genomes of 179 individuals and characterizing all the protein-
coding sequences of many others. Welcome to the third phase of human 
genomics. See Article p.1061
Rasmus Nielsen
doi:10.1038/4671050a
http://www.nature.com/nature/journal/v467/n7319/full/4671050a.html

Drug development: Longer-lived proteins pp1051-1052
Short residence times in the bloodstream reduce the effectiveness of 
protein drugs. Application of an approach that combines protein and 
polymer engineering prolongs circulation time and increases drug 
uptake by tumours.
Jeffrey A. Hubbell
doi:10.1038/4671051a
http://www.nature.com/nature/journal/v467/n7319/full/4671051a.html

Biogeochemistry: Phosphorus and the gust of fresh air pp1052-1053
Evidence of intense phosphorus weathering following 'snowball Earth' 
glaciations raises a further possibility [mdash] that this revved-up 
nutrient cycle drove conditions for the explosion of animal life. See 
Letter p.1088
Gabriel M. Filippelli
doi:10.1038/4671052a
http://www.nature.com/nature/journal/v467/n7319/full/4671052a.html

Cancer: Genomic evolution of metastasis pp1053-1055
Prognosis for patients with pancreatic cancer is bleak, often owing to 
late diagnosis. The estimate that at least 15 years pass from tumour 
initiation to malignancy offers hope for early detection and 
prevention. See Letters p.1109 &  p.1114
E. Georg Luebeck
doi:10.1038/4671053a
http://www.nature.com/nature/journal/v467/n7319/full/4671053a.html

Stem cells: The intestinal-crypt casino pp1055-1056
Stem cells can renew themselves indefinitely [mdash] a feature that is 
often attributed to asymmetrical cell division. Fresh experimental and 
mathematical models of the intestine provide evidence that begs to 
differ.
Michael P. Verzi and Ramesh A. Shivdasani
doi:10.1038/4671055a
http://www.nature.com/nature/journal/v467/n7319/full/4671055a.html

Astrophysics: Weighing in on neutron stars pp1057-1058
The more massive a neutron star is, the greater the constraints it 
places on the nature of the matter at its core. The discovery of a new 
mass record holder has strengthened those constraints considerably. 
See Letter p.1081
M. Coleman Miller
doi:10.1038/4671057a
http://www.nature.com/nature/journal/v467/n7319/full/4671057a.html

Structural biology: A peep through anion channels pp1058-1059
The crystal structure of a protein channel provides clues about the 
mechanisms that control the closure of pores found in the epidermis of 
plant leaves. Excitingly, the protein channel folds in a way never 
seen before. See Article p.1074
Sebastien Thomine and Helene Barbier-Brygoo
doi:10.1038/4671058a
http://www.nature.com/nature/journal/v467/n7319/full/4671058a.html

----------------------
ARTICLES
----------------------
A map of human genome variation from population-scale sequencing
pp1061-1073
The goal of the 1000 Genomes Project is to provide in-depth 
information on variation in human genome sequences. In the pilot phase 
reported here, different strategies for genome-wide sequencing, using 
high-throughput sequencing platforms, were developed and compared. The 
resulting data set includes more than 95% of the currently accessible 
variants found in any individual, and can be used to inform 
association and functional studies.

doi:10.1038/nature09534
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09534.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09534.html

Homologue structure of the SLAC1 anion channel for closing stomata in 
leaves pp1074-1080
SLAC1 is a plant ion channel that controls turgor pressure in the 
guard cells of plant stomata, thereby regulating the exchange of water 
vapour and photosynthetic gases in response to environmental signals. 
Here, the X-ray crystal structure of a bacterial homologue of SLAC1 
has been solved, and structure-inspired mutagenesis has been used to 
analyse the conductance properties of the channel. The findings 
indicate that selectivity among different anions is largely a function 
of the energetic cost of ion dehydration.
Yu-hang Chen et al.
doi:10.1038/nature09487
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09487.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09487.html

----------------------
LETTERS
----------------------
A two-solar-mass neutron star measured using Shapiro delay pp1081-1083
Neutron stars comprise the densest form of matter known to exist in 
our Universe, but their composition and properties are uncertain. 
Measurements of their masses and radii can constrain theoretical 
predictions of their composition, but so far it has not been possible 
to rule out many predictions of 'exotic' non-nucleonic components. 
Here, radio timing observations of the binary millisecond pulsar 
J1614-2230 are presented, allowing almost all currently proposed 
hyperon or boson condensate equations of state to be ruled out.
P. B. Demorest et al.
doi:10.1038/nature09466
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09466.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09466.html

Detecting excitation and magnetization of individual dopants in a 
semiconductor pp1084-1087
Isolated magnetic atoms doped into a semiconductor represent an 
interesting system for spintronics applications and a possible means 
of constructing quantum bits. So far, however, it has not been 
possible to study the correlation between the local atomic structure 
and the dopant's magnetic properties. Here, sensitive scanning probe 
techniques have been developed that allow the spin excitations of 
individual magnetic dopants within a two-dimensional semiconductor 
system to be measured.
Alexander A. Khajetoorians et al.
doi:10.1038/nature09519
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09519.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09519.html

The evolution of the marine phosphate reservoir pp1088-1090
Phosphorus is a biolimiting nutrient that is important in regulating 
the redox state of the ocean-atmosphere system. Here, the ratio of 
phosphorus to iron in iron-oxide-rich sedimentary rocks through time 
has been used to evaluate the evolution of the marine phosphate 
reservoir. Phosphate concentrations have been relatively constant over 
the past 542 million years of Earth's history, but were high in the 
aftermath of the 'snowball Earth' glaciations some 750 to 635 million 
years ago, with implications for the rise of metazoan life.
Noah J. Planavsky et al.
doi:10.1038/nature09485
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09485.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09485.html

Deformation of the lowermost mantle from seismic anisotropy pp1091-1094
Here, the seismic anisotropy of the Earth's lowermost mantle between 
North and Central America has been measured, using shallow and deep 
earthquakes to increase the azimuthal coverage. The findings show that 
the previously assumed vertical transverse isotropy [mdash] where wave 
speed should show no azimuthal variation [mdash] is not possible, and 
that more complicated mechanisms must be involved.
Andy Nowacki, James Wookey and J-Michael Kendall
doi:10.1038/nature09507
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09507.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09507.html

Late middle Eocene epoch of Libya yields earliest known radiation of 
African anthropoids pp1095-1098
The origin of the anthropoids (higher primates, including monkeys, 
apes and humans) is mysterious. Fossils from the Eocene epoch in 
Africa have suggested that the anthropoids originated there, but this 
has been challenged by findings in Asia. Here, the discovery is 
reported of the oldest known diverse assemblage of African 
anthropoids, from the Eocene of Libya. The diversity of species found 
suggests either a long interval of anthropoid evolution in Africa, or 
the nearly synchronous colonization of Africa by several anthropoid 
clades.
Jean-Jacques Jaeger et al.
doi:10.1038/nature09425
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09425.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09425.html

Fine-scale recombination rate differences between sexes, populations 
and individuals pp1099-1103
Here, human genome-wide single-nucleotide polymorphism (SNP) data from 
more than 15,000 parent-offspring pairs have been used to construct 
the first recombination maps that are based on directly observed 
recombination events. The data reveal interesting differences between 
the sexes: for instance, in males recombination tends to shuffle 
exons, whereas in females it generates new combinations of nearby 
genes. Comparison of these maps with others also reveals population 
differences.
Augustine Kong et al.
doi:10.1038/nature09525
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09525.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09525.html

On-line, voluntary control of human temporal lobe neurons pp1104-1108
Neurons in the medial temporal lobe are selectively responsive to 
particular visual objects, but their activity is modulated by internal 
cognitive effects. Here it is shown that humans can regulate the 
activity of their MTL neurons to alter the outcome of the contest 
between external images and their internal representation. Using a 
brain-machine interface, subjects looked at a hybrid superposition of 
two images and had to enhance one image at the expense of the other, 
using cognitive strategies such as attention and imagery.
Moran Cerf et al.
doi:10.1038/nature09510
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09510.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09510.html

The patterns and dynamics of genomic instability in metastatic 
pancreatic cancer pp1109-1113
Pancreatic cancer is highly aggressive, usually because of widespread 
metastasis. Here, next-generation DNA sequencing has been used to 
detect genomic rearrangements in 13 patients with pancreatic cancer 
and to explore clonal relationships among metastases. The results 
reveal not only considerable inter-patient heterogeneity, but also 
ongoing genomic instability and evolution during the development of 
metastases.
Peter J. Campbell et al.
doi:10.1038/nature09460
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09460.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09460.html

Distant metastasis occurs late during the genetic evolution of 
pancreatic cancer pp1114-1117
Here, whole-genome sequencing has been used to analyse primary 
pancreatic tumours and one or more metastases from the same patients. 
The findings show that tumours are composed of several geographically 
distinct subclones, and allow maps to be produced showing how 
metastatic cancer clones evolve within the primary tumour. Moreover, a 
quantitative analysis of the timing of the genetic evolution of 
pancreatic cancer has been performed.
Shinichi Yachida et al.
doi:10.1038/nature09515
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09515.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09515.html

Structural basis of semaphorin-plexin signalling pp1118-1122
Semaphorin proteins mediate signal transduction by interacting with 
plexin receptors; they have key roles in neuronal development and many 
other biological processes. Here, crystal structures are presented of 
the semaphorin-binding regions of plexin B1 and plexin A2 with their 
cognate semaphorin ectodomains. On the basis of these structures, a 
signalling mechanism is proposed.
Bert J. C. Janssen et al.
doi:10.1038/nature09468
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09468.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09468.html

Structural basis for semaphorin signalling through the plexin receptor
pp1123-1127
Semaphorin proteins mediate signal transduction by interacting with 
plexin receptors; they have key roles in neuronal development and many 
other biological processes. Here, crystal structures are presented of 
the semaphorin 6A receptor-binding fragment and the plexin A2 ligand-
binding fragment in their pre-signalling and signalling states. On the 
basis of these structures, a signalling mechanism is proposed.
Terukazu Nogi et al.
doi:10.1038/nature09473
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09473.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09473.html

Maternal mRNA deadenylation and decay by the piRNA pathway in the 
early Drosophila embryo pp1128-1132
Piwi-associated RNAs (piRNAs) are small RNAs with several functions in 
the germline, such as repressing transposable elements and helping to 
maintain germline stem cells. Now, a function for piRNAs has been 
discovered outside the germline, in the fruitfly embryo. Specifically, 
piRNAs are required for the decay of the messenger RNA encoding the 
posterior morphogen Nanos. When piRNA-induced regulation is impaired, 
this mRNA is stabilized and developmental defects ensue.
Christel Rouget et al.
doi:10.1038/nature09465
Abstract: http://www.nature.com/nature/journal/v467/n7319/abs/nature09465.html
Article: http://www.nature.com/nature/journal/v467/n7319/full/nature09465.html

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TECHNOLOGY FEATURES
----------------------
Genomics: The search for association pp1135-1138
The list of human genetic variations is expanding; but an 
understanding of how they contribute to disease is still patchy.
Monya Baker
doi:10.1038/4671135a
http://www.nature.com/nature/journal/v467/n7319/full/4671135a.html

Genomics: The tough new variants p1136
doi:10.1038/4671136a
http://www.nature.com/nature/journal/v467/n7319/full/4671136a.html

Genomics: Seeing more SNPs p1138
doi:10.1038/4671138a
http://www.nature.com/nature/journal/v467/n7319/full/4671138a.html

Genomics: Table of suppliers pp1139-1140
doi:10.1038/4671139a
http://www.nature.com/nature/journal/v467/n7319/full/4671139a.html

----------------------
FUTURES
----------------------
The greatest science-fiction story ever written p1146
A real page-turner.
Eric James Stone
doi:10.1038/4671146a
http://www.nature.com/nature/journal/v467/n7319/full/4671146a.html

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Advance Online Publication
----------------------
27 October 2010
Quantum tunnelling of the magnetization in a monolayer of oriented 
single-molecule magnets
M. Mannini et al.
doi:10.1038/nature09478
Abstract: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09478.html
Article: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09478.html

Bottom-up effects of plant diversity on multitrophic interactions in a 
biodiversity experiment
Christoph Scherber et al.
doi:10.1038/nature09492
Abstract: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09492.html
Article: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09492.html

Climate-driven population divergence in sex-determining systems
Ido Pen et al.
doi:10.1038/nature09512
Abstract: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09512.html
Article: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09512.html

24 October 2010
Structure and mechanism of the S component of a bacterial ECF 
transporter
Peng Zhang, Jiawei Wang and Yigong Shi
doi:10.1038/nature09488
Abstract: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09488.html
Article: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09488.html

Support for a synaptic chain model of neuronal sequence generation
Michael A. Long, Dezhe Z. Jin and Michale S. Fee
doi:10.1038/nature09514
Abstract: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09514.html
Article: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09514.html

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