《Nature》目录要览：2009-10-08出版
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《Nature》目录要览：2009-10-08出版
封面故事：基因组和转录组随肿瘤转移所发生的变化
Mutational evolution in a lobular breast tumour profiled at single
nucleotide resolution
下一代测序方法被用来研究来自一个患者（而不是来自一个细胞系或异种移植物）的一
种“雌激素-受体-阿尔法-阳性”转移性小叶乳腺癌的基因组和转录组，研究的时段是
从原发肿瘤被诊断出到出现转移之间的9年时间。对同一患者转移肿瘤和原发肿瘤中的
体细胞非同义编码突变所做比较，以及对基因组和转录组数据的组合分析，加深了我们
对会随病情发展出现的突变演化的认识。封面背景图片所示为来自这项研究中所用原发
小叶肿瘤的组织。（Letter p. 809）
与复杂疾病相关的基因突变（Genetics of complex diseases）
Finding the missing heritability of complex diseases
全基因组关联研究（GWAS）发现了数百种与复杂人类疾病相关的基因突变，但这些突变
大部分对增加患病风险的贡献都非常小。遗传性似乎有一大部分无法被检测到。人们对
遗传性中未能检测到的这一部分提出以下可能的解释：影响较小的大量变异体尚未发
现；存在一些当前的基因型分析技术无法检测到的罕见的结构变异或表观遗传变异；以
及存在难以检测到的基因与基因之间和基因与环境之间的相互作用。在一篇“Review”
文章中，Teri Manolio及其同事对最有可能将这些解释和其他可能的解释加以区分的研
究策略进行了分析。（Review p. 747）在一篇“News Feature”文章中，Kelly Rae
Chi介绍了三个相关案例，它们反映了对GWAS研究结果做生物学解释所存在的困难。
（page 715）
几种嗜热菌的Argonaute蛋白的晶体结构被确定（How Argonaute slices mRNA）
Nucleation, propagation and cleavage of target RNAs in Ago silencing
complexes
RNA沉默降低基因表达的手段之一是，通过对一种互补mRNA进行由小RNA引导的解理。
Argonaute家族的蛋白是植物和动物基因表达的必要调控因子。它们通过结合到单链引
导RNA分子上来发挥作用，形成RISC复合物，后者正好在该序列与跟Argonaute结合的
RNA形成互补的地方催化mRNA的解理。现在，发生突变、从而抑制解理活性的几种嗜热
菌Argonaute蛋白的晶体结构已被确定，它们与一个引导RNA和具有不同长度的几个目标
RNA形成复合物。对几种不同结构所做比较显示了随引导和目标RNA成对而出现的构形变
化，也为涉及三个天冬氨酸和两个Mg2+离子的解理提出了一个机制。（Article p.
754; News & Views）
量子混沌体系的实验模拟（Quantum chaos is tops）
Quantum signatures of chaos in a kicked top
混沌在从简单到复杂的体系中都会存在。它存在于原子能级、电子转移、化学反应、神
经网络、人口动态、天气系统以及行星运动中。事实上它几乎在任何地方都存在，但混
沌从根本上来讲似乎与量子力学是相矛盾的，而且物理学家也早就在寻找经典混沌的量
子特征。现在，研究人员通过实验实现了量子混沌模拟工作者所需要的一个预备状态，
即“Kicked Top ”，它提供了一个原子体系，该体系可被用来研究量子混沌，观测在
经典世界有相应混沌体系的量子相空间动态。该体系围绕超冷铯原子建立，这些原子受
到一个磁力作用（这种作用像被踢了一脚），该作用破坏了它们的电子和核自旋。这个
体系有混沌特征，其中包括对扰动敏感、有动态纠缠的证据等。（Letter p. 768;
News & Views）
对流纹岩火山应予以密切监测（Rhyolytic volcanoes: the ones to watch）
Rapid ascent of rhyolitic magma at Chaitén volcano, Chile
智利的Chaitén火山2008年5月1日出乎意料地发生了爆炸性喷发，而且目前仍在喷发。
这次火山喷发已使超过5000人离开了家园，为智利造成了数百万美元的损失。它也为地
球物理学家提供了直接观测由流纹岩岩浆火山喷发（地球上最大的一些爆炸性火山喷发
事件的原因）的难得机会。Jonathan Castro 和 Donald Dingwell所提供的岩石学证据
和实验证据表明，Chaitén的水合流纹岩岩浆上升非常快，其速度约为每秒一米左右。
如此快速的上升（与多数硅酸盐岩浆的行为形成鲜明对比）表明，从岩浆超过5公里的
储存深度处到近地表的过渡时间只有4小时，为这样的喷发几乎没有留下预警时间。这
项工作表明，对在全新世（过去1万年左右）一直活跃的、尤其是那些在主要人口聚居
中心附近的流纹岩火山应予以密切监测。（Letter p. 780）
用基因疗法治疗先天视力缺陷的希望（Gene therapy in colour）
Gene therapy for red–green colour blindness in adult primates
人们经常假设，视力和其他神经能力的发育存在关键时期，这些关键时期在青春期之前
结束。例如，基因疗法对患有先天性视力障碍的成人也许是不可能的。但用成年蜘蛛猿
（它们正常情况下是红绿色盲）所做实验表明，有可能通过基因疗法向它们视网膜细胞
中添加第三种光色素（人的视蛋白），从而使这些蜘蛛猿获得一个新维度的色视觉。这
项工作不仅为人类的一种常见先天性视力缺陷提出了一个可能的疗法（临床试验目前正
在进行当中），而且还表明视觉处理具有极大的神经可塑性，并为三色视觉的形成指出
了可能的路径。（Letter p. 784）
衔接蛋白STING在宿主防卫体系中的作用（Where is thy STING?）
STING regulates intracellular DNA-mediated, type I interferon-dependent
innate immunity
衔接蛋白STING（它是“Stimulator of INterferon Genes”的首字母缩写，亦称MITA
和ERIS）正在成为先天免疫系统对微生物DNA的反应当中的一个重要组成部分。
Ishikawa等人发现，在没有STING时，小鼠对几种DNA 和 RNA病毒感染的敏感度得到增
强。由STING调节的干扰素诱导，要求STING将“TANK-结合激酶-1”从内质网向含有内
体囊的Sec5重新定位。这项工作说明，STING可能是宿主抵抗单纯疱疹病毒等DNA病原体
所必需的。（Letter p. 788）
抑制素延长线虫寿命的方式（Worms need a brake）
Prohibitin couples diapause signalling to mitochondrial metabolism during
ageing in C. elegans
抑制素是普遍存在的、在演化过程中保留下来的蛋白，在线粒体内膜上形成一种环状结
构。但我们并不知道它确切的作用是什么。现在，Marta Artal-Sanz 和 Nektarios
Tavernarakis发现，抑制素通过调控线粒体功能和脂肪代谢延长线虫寿命。但在滞育突
变体（即节食的线虫）中，抑制素的存在实际上缩短寿命。本文作者提出，抑制素是通
过控制线虫能量供应（控制脂肪使用和能量生产）来延长其寿命的。但是，在不利的外
部条件下，如在养分供应有限的情况下，能量需求会超过供应，寿命在没有这种限制时
也会延长。（Letter p. 793）
自闭症易感基因被发现（Scanning for links autism）
A genome-wide linkage and association scan reveals novel loci for autism
自闭症是一种具有高度遗传性的神经发育疾病，然而迄今所发现的特定易感基因非常
少。现在，在一组1,031个多元化自闭症家庭中利用50万个全基因组SNP（单核苷酸多态
性）所进行的一次全基因组扫描，显示了与自闭症相关的重要关联。所发现的关联区域
为罕见变异筛选提供了目标，同时研究人员还在染色体5p15上的SEMA5A 和TAS2R1之间
发现了一个新的关联。SEMA5A的表达被发现在自闭症患者脑中减少，从而进一步证实它
是一个自闭症易感基因。（Letter p. 802）
可消除转录组分析偏误的RNA测序技术（A direct line to the transcriptome）
Direct RNA sequencing
了解基因组的功能输出（一个细胞或细胞群中的全部信使RNA，被称为转录组），是生
物学研究过程中的一个必要步骤。当前研究转录组的方法依赖于微阵列和测序方法，它
们需要合成互补DNA，之后再进行多种操作，这样会引入偏误和潜在的人为结果。现
在，螺旋生物科学公司（Helicos BioSciences Corporation）的一个小组开发出一种
直接单分子RNA测序技术，将该技术按比例放大之后，有希望做出无偏误的高通量转录
组分析结果。（Letter p. 814）
JAK2激酶的一个以前不知道的核功能（JAK2 kinase goes nuclear）
JAK2 phosphorylates histone H3Y41 and excludes HP1 from chromatin
JAK2是一种非受体酪氨酸激酶，通过诱导胞质信号级联来调控各种不同细胞过程。现
在，Dawson等人报告了JAK2的一个以前不知道的核功能。由JAK2催化的组蛋白H3的酪氨
酸磷酸化，会导致HP1-阿尔法与染色质的结合被破坏，并导致基因表达的变化。人们对
这一发现之所以特别感兴趣，是因为JAK2抑制因子正在接受治疗骨髓性白血病的临床试
验，在这种白血病中JAK2失控。（Letter p. 819）
----------------------
NEWS AND VIEWS
----------------------
Human genetics: Sharp focus on the variable genome pp735-736
Copy-number variation [mdash] deleted or duplicated regions of DNA - is
widespread in the human genome. A systematic population survey of the
common variants provides an invaluable resource for further studies.
John A. L. Armour
doi:10.1038/461735a
http://www.nature.com/nature/journal/v461/n7265/full/461735a.html
Quantum mechanics: Passage through chaos pp736-737
A quantum system can undergo tunnelling even without a barrier to tunnel
through. The latest experiments visualize this process in exquisite detail,
completely reconstructing the state of the evolving system.
Daniel A. Steck
doi:10.1038/461736a
http://www.nature.com/nature/journal/v461/n7265/full/461736a.html
Vision: Gene therapy in colour pp737-739
Replacing a missing gene in adult colour-blind monkeys restores normal
colour vision. How the new photoreceptor cells produced by this therapy
lead to colour vision is a fascinating question.
Robert Shapley
doi:10.1038/461737a
http://www.nature.com/nature/journal/v461/n7265/full/461737a.html
Cosmology: Dark is the new black pp740-741
Rival experimental methods to determine the Universe's expansion are
contending to become the fashionable face of cosmology. Fresh theoretical
calculations make one of them the hot tip for next season.
Richard Massey
doi:10.1038/461740a
http://www.nature.com/nature/journal/v461/n7265/full/461740a.html
Microbiology: Life on leaves pp741-742
The surface of plant leaves [mdash] the phyllosphere [mdash] is home to
many microbes. A 'community proteogenomics' approach offers a fresh
look at what it takes to survive and thrive in this unique habitat.
Johan Leveau
doi:10.1038/461741a
http://www.nature.com/nature/journal/v461/n7265/full/461741a.html
Structural biology: Tracing Argonaute binding pp743-744
Argonaute proteins inhibit gene expression by binding to messenger RNA
via a small nucleic-acid guide. Structures of the Argonaute complex
bound to target RNA reveal snapshots of a silencing machine at work.
Samir Bouasker and Martin J. Simard
doi:10.1038/461743a
http://www.nature.com/nature/journal/v461/n7265/full/461743a.html
Photonics: One-way road for light pp744-745
The transmission of information from one place to another by light waves
sent through waveguides is hampered by light attenuation and scattering
loss. Magnetic photonic crystals could provide a solution to such problems.
Eli Yablonovitch
doi:10.1038/461744a
http://www.nature.com/nature/journal/v461/n7265/full/461744a.html
----------------------
REVIEW
----------------------
Finding the missing heritability of complex diseases pp747-753
Teri A. Manolio et al.
doi:10.1038/nature08494
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08494.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08494.html
----------------------
ARTICLES
----------------------
Nucleation, propagation and cleavage of target RNAs in Ago silencing
complexes pp754-761
The Argonaute (Ago) family of proteins provides the slicer activity of
the RNA-induced silencing complex, with the Ago component of the complex
providing the catalytic residues governing guide-strand mediated
site-specific
cleavage of target RNA. Here, the crystal structures of ternary complexes
of Thermus thermophilus Ago catalytic mutants are reported and analysed.
Yanli Wang et al.
doi:10.1038/nature08434
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08434.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08434.html
Role of the polycomb protein EED in the propagation of repressive histone
marks pp762-767
Polycomb group proteins are involved in the epigenetic maintenance of
repressive chromatin states, with the gene-silencing activity of the
Polycomb
repressive complex 2 (PRC2) dependent on its ability to trimethylate lysine
27 of histone H3. The carboxy-terminal domain of the EED subunit of the
complex is now shown to specifically bind to histone tails carrying
trimethyl-lysine residues associated with repressive chromatin marks,
leading to activation of the methyltransferase activity of PRC2.
Raphael Margueron et al.
doi:10.1038/nature08398
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08398.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08398.html
----------------------
LETTERS
----------------------
Quantum signatures of chaos in a kicked top pp768-771
There has been a long-standing search for quantum signatures of classical
chaos. Here, an atomic system that can be used to study quantum chaos - the
quantum kicked top - is experimentally realized and directly observed to
reveal dynamics in quantum phase space that have a chaotic classical
counterpart.
Clear differences are noted in the sensitivity to perturbation in chaotic
versus regular regimes and dynamical entanglement is proposed as a signature
of chaos.
S. Chaudhury et al.
doi:10.1038/nature08396
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08396.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08396.html
Observation of unidirectional backscattering-immune topological
electromagnetic
states pp772-775
The quantum Hall effect arises in two-dimensional electron systems and is
characterized by current being carried by electrons along the edges of the
system, in so-called chiral edge states (CESs), as a consequence of
nontrivial
topological properties of the bulk electronic band structure. Recently, it
was
theoretically predicted that electromagnetic analogues of CESs could be
observed in photonic crystals; here, this is experimentally demonstrated.
Zheng Wang, Yidong Chong, J. D. Joannopoulos and Marin Soljacic
doi:10.1038/nature08293
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08293.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08293.html
Early Palaeogene temperature evolution of the southwest Pacific
Ocean pp776-779
About 34 million years ago, the first major Antarctic ice sheets appeared,
suggesting that major cooling had taken place; however, the global
transition
into this icehouse climate remains poorly constrained. A new, continuous
record
of sea surface temperature (SST) from an ocean sediment core in the East
Tasman Plateau now suggests that there was almost no latitudinal SST
gradient
between subequatorial and subpolar regions during the Early Eocene age
(55-50 million years ago).
Peter K. Bijl et al.
doi:10.1038/nature08399
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08399.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08399.html
Rapid ascent of rhyolitic magma at Chaiten volcano, Chile pp780-783
Although rhyolite magma has fuelled some of the Earth's largest explosive
volcanic eruptions, our understanding of these events is incomplete due to
the previous lack of direct observation of these eruptions. On 1 May 2008,
Chaiten volcano in Chile erupted rhyolite magma unexpectedly and
explosively.
Here, petrological and experimental data are presented that indicate that
the
hydrous rhyolite magma at Chaiten ascended very rapidly from storage depth
to near-surface, with velocities of the order of one metre per second.
Jonathan M. Castro and Donald B. Dingwell
doi:10.1038/nature08458
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08458.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08458.html
Gene therapy for red--green colour blindness in adult primates pp784-787
Red-green colour blindness is the most common single locus genetic disorder.
Gene therapy is now used in adult monkeys, colour blind since birth, to
provide
the receptoral basis for trichromatic colour vision. Despite the expectation
from classic visual deprivation experiments that neural connections
established
during development are incapable of processing an input not present from
birth,
treated monkeys displayed trichromatic colour vision behaviour.
Katherine Mancuso et al.
doi:10.1038/nature08401
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08401.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08401.html
STING regulates intracellular DNA-mediated, type I interferon-dependent
innate
immunity pp788-792
Although the innate immune system is known to be critical for the early
detection
of invading pathogens and for initiating host defence systems, little is
known
about how it is galvanized to respond to DNA-based microbes. STING
(stimulator
of interferon genes) is now shown to be necessary for the initiation of
effective
type I interferon production and, accordingly, there is an increase in the
susceptibility of Sting-knockout mice to infection by the DNA virus HSV-1.
Hiroki Ishikawa, Zhe Ma and Glen N. Barber
doi:10.1038/nature08476
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08476.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08476.html
Prohibitin couples diapause signalling to mitochondrial metabolism during
ageing
in C.[thinsp]elegans pp793-797
Prohibitins are ubiquitous, evolutionarily conserved proteins, which form a
ring-like complex at the inner membrane of the mitochondria. Here, the
mitochondrial
prohibitin complex is shown to promote longevity by modulating mitochondrial
function and fat metabolism in the nematode Caenorhabditis elegans, with its
deficiency shortening the lifespan of otherwise wild-type animals. However,
under conditions of dietary restriction, knockdown of prohibitin promotes
longevity.
Marta Artal-Sanz and Nektarios Tavernarakis
doi:10.1038/nature08466
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08466.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08466.html
Genetic variation in IL28B and spontaneous clearance of hepatitis C virus
There are approximately 170 million people infected with hepatitis C virus
(HCV)
worldwide. About 30% of individuals with persistent HCV infection develop
chronic
liver disease, with various epidemiological, viral and host factors having
been
implicated in the differences in HCV clearance or persistence. Here, a
single
nucleotide polymorphism recently shown to be strongly associated with a
difference
in response to HCV drug treatment is also shown to be associated with viral
clearance.
David L. Thomas et al.
doi:10.1038/nature08463
Abstract:
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08463.html
Article:
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08463.html
A genome-wide linkage and association scan reveals novel loci for
autism pp802-808
Autism is a highly heritable neurodevelopmental disorder, and yet few
specific
susceptibility genes have been identified to date. A linkage and association
mapping study using half a million genome-wide single nucleotide
polymorphisms
is now described in a common set of 1,031 multiplex autism families. The
linkage
regions identified provide targets for rare variation screening whereas the
discovery of a single novel association, SEMA5A, demonstrates the action of
common variants.
Lauren A. Weiss and Dan E. Arking
doi:10.1038/nature08490
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08490.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08490.html
Mutational evolution in a lobular breast tumour profiled at single
nucleotide
resolution pp809-813
Advances in next generation sequencing have made it possible to precisely
characterize the coding mutations that occur during the development and
progression
of individual cancers. Here, this technique is used to sequence the genomes
and
transcriptomes of an oestrogen-receptor-[alpha]-positive metastatic lobular
breast
cancer; significant evolution is found to occur with disease progression.
Sohrab P. Shah et al.
doi:10.1038/nature08489
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08489.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08489.html
Direct RNA sequencing pp814-818
Understanding the functional output of the genome - the transcriptome - is
an
essential step on the way to understanding human biology and disease.
Current
transcriptome analysis methods are indirect, typically requiring RNA to be
converted to complementary DNA (cDNA) before measurements. Single molecule
RNA
sequencing without prior conversion of RNA to cDNA is now reported.
Fatih Ozsolak et al.
doi:10.1038/nature08390
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08390.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08390.html
JAK2 phosphorylates histone H3Y41 and excludes HP1[agr] from
chromatin pp819-822
The activation of Janus kinase 2 (JAK2), a non-receptor tyrosine kinase that
regulates several cellular processes by inducing cytoplasmic signalling
cascades,
is a frequent event in haematological malignancies. Here, human JAK2 is
shown to
be present in the nucleus of haematopoietic cells, where it directly
phosphorylates
Tyr 41 on histone H3, thus preventing the binding of heterochromatin protein
I[alpha].
Mark A. Dawson et al.
doi:10.1038/nature08448
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08448.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08448.html
Structural insights into mechanisms of the small RNA methyltransferase
HEN1 pp823-827
Some of the small RNAs involved in RNA silencing require the addition of a 2
[prime]-O-methyl group on the 3[prime] terminal nucleotide in order for the
precursor RNA to be correctly processed. This modification is performed by
the
HEN1 RNA methyltransferase, the crystal structure of which - from
Arabidopsis- is now solved.
Ying Huang et al.
doi:10.1038/nature08433
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08433.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08433.html
----------------------
ERRATA
----------------------
Dense packings of the Platonic and Archimedean solids p828
S. Torquato and Y. Jiao
doi:10.1038/nature08492
http://www.nature.com/nature/journal/v461/n7265/full/nature08492.html
Stable single-unit-cell nanosheets of zeolite MFI as active and long-lived
catalysts p828
Minkee Choi et al.
doi:10.1038/nature08493
http://www.nature.com/nature/journal/v461/n7265/full/nature08493.html
----------------------
CORRIGENDUM
----------------------
Genotypic sex determination enabled adaptive radiations of extinct marine
reptiles p828
Chris L. Organ, Daniel E. Janes, Andrew Meade and Mark Pagel
doi:10.1038/nature08523
http://www.nature.com/nature/journal/v461/n7265/full/nature08523.html
----------------------
FUTURES
----------------------
Life in a monastic lab p836
A vocational career.
Joost Uitdehaag
doi:10.1038/461836a
http://www.nature.com/nature/journal/v461/n7265/full/461836a.html
Mutational evolution in a lobular breast tumour profiled at single
nucleotide resolution
下一代测序方法被用来研究来自一个患者（而不是来自一个细胞系或异种移植物）的一
种“雌激素-受体-阿尔法-阳性”转移性小叶乳腺癌的基因组和转录组，研究的时段是
从原发肿瘤被诊断出到出现转移之间的9年时间。对同一患者转移肿瘤和原发肿瘤中的
体细胞非同义编码突变所做比较，以及对基因组和转录组数据的组合分析，加深了我们
对会随病情发展出现的突变演化的认识。封面背景图片所示为来自这项研究中所用原发
小叶肿瘤的组织。（Letter p. 809）
与复杂疾病相关的基因突变（Genetics of complex diseases）
Finding the missing heritability of complex diseases
全基因组关联研究（GWAS）发现了数百种与复杂人类疾病相关的基因突变，但这些突变
大部分对增加患病风险的贡献都非常小。遗传性似乎有一大部分无法被检测到。人们对
遗传性中未能检测到的这一部分提出以下可能的解释：影响较小的大量变异体尚未发
现；存在一些当前的基因型分析技术无法检测到的罕见的结构变异或表观遗传变异；以
及存在难以检测到的基因与基因之间和基因与环境之间的相互作用。在一篇“Review”
文章中，Teri Manolio及其同事对最有可能将这些解释和其他可能的解释加以区分的研
究策略进行了分析。（Review p. 747）在一篇“News Feature”文章中，Kelly Rae
Chi介绍了三个相关案例，它们反映了对GWAS研究结果做生物学解释所存在的困难。
（page 715）
几种嗜热菌的Argonaute蛋白的晶体结构被确定（How Argonaute slices mRNA）
Nucleation, propagation and cleavage of target RNAs in Ago silencing
complexes
RNA沉默降低基因表达的手段之一是，通过对一种互补mRNA进行由小RNA引导的解理。
Argonaute家族的蛋白是植物和动物基因表达的必要调控因子。它们通过结合到单链引
导RNA分子上来发挥作用，形成RISC复合物，后者正好在该序列与跟Argonaute结合的
RNA形成互补的地方催化mRNA的解理。现在，发生突变、从而抑制解理活性的几种嗜热
菌Argonaute蛋白的晶体结构已被确定，它们与一个引导RNA和具有不同长度的几个目标
RNA形成复合物。对几种不同结构所做比较显示了随引导和目标RNA成对而出现的构形变
化，也为涉及三个天冬氨酸和两个Mg2+离子的解理提出了一个机制。（Article p.
754; News & Views）
量子混沌体系的实验模拟（Quantum chaos is tops）
Quantum signatures of chaos in a kicked top
混沌在从简单到复杂的体系中都会存在。它存在于原子能级、电子转移、化学反应、神
经网络、人口动态、天气系统以及行星运动中。事实上它几乎在任何地方都存在，但混
沌从根本上来讲似乎与量子力学是相矛盾的，而且物理学家也早就在寻找经典混沌的量
子特征。现在，研究人员通过实验实现了量子混沌模拟工作者所需要的一个预备状态，
即“Kicked Top ”，它提供了一个原子体系，该体系可被用来研究量子混沌，观测在
经典世界有相应混沌体系的量子相空间动态。该体系围绕超冷铯原子建立，这些原子受
到一个磁力作用（这种作用像被踢了一脚），该作用破坏了它们的电子和核自旋。这个
体系有混沌特征，其中包括对扰动敏感、有动态纠缠的证据等。（Letter p. 768;
News & Views）
对流纹岩火山应予以密切监测（Rhyolytic volcanoes: the ones to watch）
Rapid ascent of rhyolitic magma at Chaitén volcano, Chile
智利的Chaitén火山2008年5月1日出乎意料地发生了爆炸性喷发，而且目前仍在喷发。
这次火山喷发已使超过5000人离开了家园，为智利造成了数百万美元的损失。它也为地
球物理学家提供了直接观测由流纹岩岩浆火山喷发（地球上最大的一些爆炸性火山喷发
事件的原因）的难得机会。Jonathan Castro 和 Donald Dingwell所提供的岩石学证据
和实验证据表明，Chaitén的水合流纹岩岩浆上升非常快，其速度约为每秒一米左右。
如此快速的上升（与多数硅酸盐岩浆的行为形成鲜明对比）表明，从岩浆超过5公里的
储存深度处到近地表的过渡时间只有4小时，为这样的喷发几乎没有留下预警时间。这
项工作表明，对在全新世（过去1万年左右）一直活跃的、尤其是那些在主要人口聚居
中心附近的流纹岩火山应予以密切监测。（Letter p. 780）
用基因疗法治疗先天视力缺陷的希望（Gene therapy in colour）
Gene therapy for red–green colour blindness in adult primates
人们经常假设，视力和其他神经能力的发育存在关键时期，这些关键时期在青春期之前
结束。例如，基因疗法对患有先天性视力障碍的成人也许是不可能的。但用成年蜘蛛猿
（它们正常情况下是红绿色盲）所做实验表明，有可能通过基因疗法向它们视网膜细胞
中添加第三种光色素（人的视蛋白），从而使这些蜘蛛猿获得一个新维度的色视觉。这
项工作不仅为人类的一种常见先天性视力缺陷提出了一个可能的疗法（临床试验目前正
在进行当中），而且还表明视觉处理具有极大的神经可塑性，并为三色视觉的形成指出
了可能的路径。（Letter p. 784）
衔接蛋白STING在宿主防卫体系中的作用（Where is thy STING?）
STING regulates intracellular DNA-mediated, type I interferon-dependent
innate immunity
衔接蛋白STING（它是“Stimulator of INterferon Genes”的首字母缩写，亦称MITA
和ERIS）正在成为先天免疫系统对微生物DNA的反应当中的一个重要组成部分。
Ishikawa等人发现，在没有STING时，小鼠对几种DNA 和 RNA病毒感染的敏感度得到增
强。由STING调节的干扰素诱导，要求STING将“TANK-结合激酶-1”从内质网向含有内
体囊的Sec5重新定位。这项工作说明，STING可能是宿主抵抗单纯疱疹病毒等DNA病原体
所必需的。（Letter p. 788）
抑制素延长线虫寿命的方式（Worms need a brake）
Prohibitin couples diapause signalling to mitochondrial metabolism during
ageing in C. elegans
抑制素是普遍存在的、在演化过程中保留下来的蛋白，在线粒体内膜上形成一种环状结
构。但我们并不知道它确切的作用是什么。现在，Marta Artal-Sanz 和 Nektarios
Tavernarakis发现，抑制素通过调控线粒体功能和脂肪代谢延长线虫寿命。但在滞育突
变体（即节食的线虫）中，抑制素的存在实际上缩短寿命。本文作者提出，抑制素是通
过控制线虫能量供应（控制脂肪使用和能量生产）来延长其寿命的。但是，在不利的外
部条件下，如在养分供应有限的情况下，能量需求会超过供应，寿命在没有这种限制时
也会延长。（Letter p. 793）
自闭症易感基因被发现（Scanning for links autism）
A genome-wide linkage and association scan reveals novel loci for autism
自闭症是一种具有高度遗传性的神经发育疾病，然而迄今所发现的特定易感基因非常
少。现在，在一组1,031个多元化自闭症家庭中利用50万个全基因组SNP（单核苷酸多态
性）所进行的一次全基因组扫描，显示了与自闭症相关的重要关联。所发现的关联区域
为罕见变异筛选提供了目标，同时研究人员还在染色体5p15上的SEMA5A 和TAS2R1之间
发现了一个新的关联。SEMA5A的表达被发现在自闭症患者脑中减少，从而进一步证实它
是一个自闭症易感基因。（Letter p. 802）
可消除转录组分析偏误的RNA测序技术（A direct line to the transcriptome）
Direct RNA sequencing
了解基因组的功能输出（一个细胞或细胞群中的全部信使RNA，被称为转录组），是生
物学研究过程中的一个必要步骤。当前研究转录组的方法依赖于微阵列和测序方法，它
们需要合成互补DNA，之后再进行多种操作，这样会引入偏误和潜在的人为结果。现
在，螺旋生物科学公司（Helicos BioSciences Corporation）的一个小组开发出一种
直接单分子RNA测序技术，将该技术按比例放大之后，有希望做出无偏误的高通量转录
组分析结果。（Letter p. 814）
JAK2激酶的一个以前不知道的核功能（JAK2 kinase goes nuclear）
JAK2 phosphorylates histone H3Y41 and excludes HP1 from chromatin
JAK2是一种非受体酪氨酸激酶，通过诱导胞质信号级联来调控各种不同细胞过程。现
在，Dawson等人报告了JAK2的一个以前不知道的核功能。由JAK2催化的组蛋白H3的酪氨
酸磷酸化，会导致HP1-阿尔法与染色质的结合被破坏，并导致基因表达的变化。人们对
这一发现之所以特别感兴趣，是因为JAK2抑制因子正在接受治疗骨髓性白血病的临床试
验，在这种白血病中JAK2失控。（Letter p. 819）
----------------------
NEWS AND VIEWS
----------------------
Human genetics: Sharp focus on the variable genome pp735-736
Copy-number variation [mdash] deleted or duplicated regions of DNA - is
widespread in the human genome. A systematic population survey of the
common variants provides an invaluable resource for further studies.
John A. L. Armour
doi:10.1038/461735a
http://www.nature.com/nature/journal/v461/n7265/full/461735a.html
Quantum mechanics: Passage through chaos pp736-737
A quantum system can undergo tunnelling even without a barrier to tunnel
through. The latest experiments visualize this process in exquisite detail,
completely reconstructing the state of the evolving system.
Daniel A. Steck
doi:10.1038/461736a
http://www.nature.com/nature/journal/v461/n7265/full/461736a.html
Vision: Gene therapy in colour pp737-739
Replacing a missing gene in adult colour-blind monkeys restores normal
colour vision. How the new photoreceptor cells produced by this therapy
lead to colour vision is a fascinating question.
Robert Shapley
doi:10.1038/461737a
http://www.nature.com/nature/journal/v461/n7265/full/461737a.html
Cosmology: Dark is the new black pp740-741
Rival experimental methods to determine the Universe's expansion are
contending to become the fashionable face of cosmology. Fresh theoretical
calculations make one of them the hot tip for next season.
Richard Massey
doi:10.1038/461740a
http://www.nature.com/nature/journal/v461/n7265/full/461740a.html
Microbiology: Life on leaves pp741-742
The surface of plant leaves [mdash] the phyllosphere [mdash] is home to
many microbes. A 'community proteogenomics' approach offers a fresh
look at what it takes to survive and thrive in this unique habitat.
Johan Leveau
doi:10.1038/461741a
http://www.nature.com/nature/journal/v461/n7265/full/461741a.html
Structural biology: Tracing Argonaute binding pp743-744
Argonaute proteins inhibit gene expression by binding to messenger RNA
via a small nucleic-acid guide. Structures of the Argonaute complex
bound to target RNA reveal snapshots of a silencing machine at work.
Samir Bouasker and Martin J. Simard
doi:10.1038/461743a
http://www.nature.com/nature/journal/v461/n7265/full/461743a.html
Photonics: One-way road for light pp744-745
The transmission of information from one place to another by light waves
sent through waveguides is hampered by light attenuation and scattering
loss. Magnetic photonic crystals could provide a solution to such problems.
Eli Yablonovitch
doi:10.1038/461744a
http://www.nature.com/nature/journal/v461/n7265/full/461744a.html
----------------------
REVIEW
----------------------
Finding the missing heritability of complex diseases pp747-753
Teri A. Manolio et al.
doi:10.1038/nature08494
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08494.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08494.html
----------------------
ARTICLES
----------------------
Nucleation, propagation and cleavage of target RNAs in Ago silencing
complexes pp754-761
The Argonaute (Ago) family of proteins provides the slicer activity of
the RNA-induced silencing complex, with the Ago component of the complex
providing the catalytic residues governing guide-strand mediated
site-specific
cleavage of target RNA. Here, the crystal structures of ternary complexes
of Thermus thermophilus Ago catalytic mutants are reported and analysed.
Yanli Wang et al.
doi:10.1038/nature08434
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08434.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08434.html
Role of the polycomb protein EED in the propagation of repressive histone
marks pp762-767
Polycomb group proteins are involved in the epigenetic maintenance of
repressive chromatin states, with the gene-silencing activity of the
Polycomb
repressive complex 2 (PRC2) dependent on its ability to trimethylate lysine
27 of histone H3. The carboxy-terminal domain of the EED subunit of the
complex is now shown to specifically bind to histone tails carrying
trimethyl-lysine residues associated with repressive chromatin marks,
leading to activation of the methyltransferase activity of PRC2.
Raphael Margueron et al.
doi:10.1038/nature08398
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08398.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08398.html
----------------------
LETTERS
----------------------
Quantum signatures of chaos in a kicked top pp768-771
There has been a long-standing search for quantum signatures of classical
chaos. Here, an atomic system that can be used to study quantum chaos - the
quantum kicked top - is experimentally realized and directly observed to
reveal dynamics in quantum phase space that have a chaotic classical
counterpart.
Clear differences are noted in the sensitivity to perturbation in chaotic
versus regular regimes and dynamical entanglement is proposed as a signature
of chaos.
S. Chaudhury et al.
doi:10.1038/nature08396
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08396.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08396.html
Observation of unidirectional backscattering-immune topological
electromagnetic
states pp772-775
The quantum Hall effect arises in two-dimensional electron systems and is
characterized by current being carried by electrons along the edges of the
system, in so-called chiral edge states (CESs), as a consequence of
nontrivial
topological properties of the bulk electronic band structure. Recently, it
was
theoretically predicted that electromagnetic analogues of CESs could be
observed in photonic crystals; here, this is experimentally demonstrated.
Zheng Wang, Yidong Chong, J. D. Joannopoulos and Marin Soljacic
doi:10.1038/nature08293
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08293.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08293.html
Early Palaeogene temperature evolution of the southwest Pacific
Ocean pp776-779
About 34 million years ago, the first major Antarctic ice sheets appeared,
suggesting that major cooling had taken place; however, the global
transition
into this icehouse climate remains poorly constrained. A new, continuous
record
of sea surface temperature (SST) from an ocean sediment core in the East
Tasman Plateau now suggests that there was almost no latitudinal SST
gradient
between subequatorial and subpolar regions during the Early Eocene age
(55-50 million years ago).
Peter K. Bijl et al.
doi:10.1038/nature08399
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08399.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08399.html
Rapid ascent of rhyolitic magma at Chaiten volcano, Chile pp780-783
Although rhyolite magma has fuelled some of the Earth's largest explosive
volcanic eruptions, our understanding of these events is incomplete due to
the previous lack of direct observation of these eruptions. On 1 May 2008,
Chaiten volcano in Chile erupted rhyolite magma unexpectedly and
explosively.
Here, petrological and experimental data are presented that indicate that
the
hydrous rhyolite magma at Chaiten ascended very rapidly from storage depth
to near-surface, with velocities of the order of one metre per second.
Jonathan M. Castro and Donald B. Dingwell
doi:10.1038/nature08458
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08458.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08458.html
Gene therapy for red--green colour blindness in adult primates pp784-787
Red-green colour blindness is the most common single locus genetic disorder.
Gene therapy is now used in adult monkeys, colour blind since birth, to
provide
the receptoral basis for trichromatic colour vision. Despite the expectation
from classic visual deprivation experiments that neural connections
established
during development are incapable of processing an input not present from
birth,
treated monkeys displayed trichromatic colour vision behaviour.
Katherine Mancuso et al.
doi:10.1038/nature08401
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08401.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08401.html
STING regulates intracellular DNA-mediated, type I interferon-dependent
innate
immunity pp788-792
Although the innate immune system is known to be critical for the early
detection
of invading pathogens and for initiating host defence systems, little is
known
about how it is galvanized to respond to DNA-based microbes. STING
(stimulator
of interferon genes) is now shown to be necessary for the initiation of
effective
type I interferon production and, accordingly, there is an increase in the
susceptibility of Sting-knockout mice to infection by the DNA virus HSV-1.
Hiroki Ishikawa, Zhe Ma and Glen N. Barber
doi:10.1038/nature08476
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08476.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08476.html
Prohibitin couples diapause signalling to mitochondrial metabolism during
ageing
in C.[thinsp]elegans pp793-797
Prohibitins are ubiquitous, evolutionarily conserved proteins, which form a
ring-like complex at the inner membrane of the mitochondria. Here, the
mitochondrial
prohibitin complex is shown to promote longevity by modulating mitochondrial
function and fat metabolism in the nematode Caenorhabditis elegans, with its
deficiency shortening the lifespan of otherwise wild-type animals. However,
under conditions of dietary restriction, knockdown of prohibitin promotes
longevity.
Marta Artal-Sanz and Nektarios Tavernarakis
doi:10.1038/nature08466
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08466.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08466.html
Genetic variation in IL28B and spontaneous clearance of hepatitis C virus
There are approximately 170 million people infected with hepatitis C virus
(HCV)
worldwide. About 30% of individuals with persistent HCV infection develop
chronic
liver disease, with various epidemiological, viral and host factors having
been
implicated in the differences in HCV clearance or persistence. Here, a
single
nucleotide polymorphism recently shown to be strongly associated with a
difference
in response to HCV drug treatment is also shown to be associated with viral
clearance.
David L. Thomas et al.
doi:10.1038/nature08463
Abstract:
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08463.html
Article:
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08463.html
A genome-wide linkage and association scan reveals novel loci for
autism pp802-808
Autism is a highly heritable neurodevelopmental disorder, and yet few
specific
susceptibility genes have been identified to date. A linkage and association
mapping study using half a million genome-wide single nucleotide
polymorphisms
is now described in a common set of 1,031 multiplex autism families. The
linkage
regions identified provide targets for rare variation screening whereas the
discovery of a single novel association, SEMA5A, demonstrates the action of
common variants.
Lauren A. Weiss and Dan E. Arking
doi:10.1038/nature08490
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08490.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08490.html
Mutational evolution in a lobular breast tumour profiled at single
nucleotide
resolution pp809-813
Advances in next generation sequencing have made it possible to precisely
characterize the coding mutations that occur during the development and
progression
of individual cancers. Here, this technique is used to sequence the genomes
and
transcriptomes of an oestrogen-receptor-[alpha]-positive metastatic lobular
breast
cancer; significant evolution is found to occur with disease progression.
Sohrab P. Shah et al.
doi:10.1038/nature08489
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08489.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08489.html
Direct RNA sequencing pp814-818
Understanding the functional output of the genome - the transcriptome - is
an
essential step on the way to understanding human biology and disease.
Current
transcriptome analysis methods are indirect, typically requiring RNA to be
converted to complementary DNA (cDNA) before measurements. Single molecule
RNA
sequencing without prior conversion of RNA to cDNA is now reported.
Fatih Ozsolak et al.
doi:10.1038/nature08390
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08390.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08390.html
JAK2 phosphorylates histone H3Y41 and excludes HP1[agr] from
chromatin pp819-822
The activation of Janus kinase 2 (JAK2), a non-receptor tyrosine kinase that
regulates several cellular processes by inducing cytoplasmic signalling
cascades,
is a frequent event in haematological malignancies. Here, human JAK2 is
shown to
be present in the nucleus of haematopoietic cells, where it directly
phosphorylates
Tyr 41 on histone H3, thus preventing the binding of heterochromatin protein
I[alpha].
Mark A. Dawson et al.
doi:10.1038/nature08448
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08448.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08448.html
Structural insights into mechanisms of the small RNA methyltransferase
HEN1 pp823-827
Some of the small RNAs involved in RNA silencing require the addition of a 2
[prime]-O-methyl group on the 3[prime] terminal nucleotide in order for the
precursor RNA to be correctly processed. This modification is performed by
the
HEN1 RNA methyltransferase, the crystal structure of which - from
Arabidopsis- is now solved.
Ying Huang et al.
doi:10.1038/nature08433
Abstract:
http://www.nature.com/nature/journal/v461/n7265/abs/nature08433.html
Article:
http://www.nature.com/nature/journal/v461/n7265/full/nature08433.html
----------------------
ERRATA
----------------------
Dense packings of the Platonic and Archimedean solids p828
S. Torquato and Y. Jiao
doi:10.1038/nature08492
http://www.nature.com/nature/journal/v461/n7265/full/nature08492.html
Stable single-unit-cell nanosheets of zeolite MFI as active and long-lived
catalysts p828
Minkee Choi et al.
doi:10.1038/nature08493
http://www.nature.com/nature/journal/v461/n7265/full/nature08493.html
----------------------
CORRIGENDUM
----------------------
Genotypic sex determination enabled adaptive radiations of extinct marine
reptiles p828
Chris L. Organ, Daniel E. Janes, Andrew Meade and Mark Pagel
doi:10.1038/nature08523
http://www.nature.com/nature/journal/v461/n7265/full/nature08523.html
----------------------
FUTURES
----------------------
Life in a monastic lab p836
A vocational career.
Joost Uitdehaag
doi:10.1038/461836a
http://www.nature.com/nature/journal/v461/n7265/full/461836a.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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