《Nature》目录要览：2010-02-18出版
时间：2010-02-19 阅读： 我要评论:
《Nature》目录要览：2010-02-18出版
封面故事：非洲古老部落人的基因组序列
Complete Khoisan and Bantu genomes from southern Africa
本期Nature发表了来自纳米比亚喀拉哈里沙漠的一个土生土长的采猎者和来自南非的一个班图人的完整基因组序列，同时还有来自喀拉哈里沙漠其他三个采猎部落的蛋白编码区域。对可能是已知最古老现代人类分支的遗传变异进行分析，将有助于了解人类多样性，帮助将南部非洲人包括在医学基因组研究项目中。最初观察结果包括这样一个事实：就核苷酸取代而言，“布须曼人”（Bushmen）彼此之间的差异似乎要超过与典型亚洲人和欧洲人的差异。更值得推测的是，这些基因组之间的变异体以及现有数据可能表示，他们的基因为适应农业生活方式而发生了变异。本期封面图片所描绘的是喀拉哈里沙漠南部觅食的“布须曼人”，研究人员获得了该部落人群的完整基因组序列。（Letter p. 943; News & Views; www.nature.com/podcast）封面照片：Stephan C. Schuster
关于癌症基因组研究的两篇论文（Cancer genomics refined）
Signatures of mutation and selection in the cancer genome / The landscape of somatic copy-number alteration across human cancers
本期两篇文章为不断增长的癌症基因组数据增添了更多内容。Bignell等人分析了一组746个可以公开获取的癌症细胞系中大量同型（纯合子）基因删除。结合有关同样基因半合子删除的信息，这些数据表明，癌症中所发现的很多删除反映了一个基因位于基因组中的一个脆弱点，而不是其失去会产生选择性生长优势的隐性癌症基因。Beroukhim等人发表了有关3000多个人类原发癌标本体细胞版本数量变异的迄今最大的数据集。很多改变是多种肿瘤类型共有的。功能实验表明，凋亡基因MCL1 和BCL2L1发挥了致癌基因的作用， 这两个基因与很多癌症中所见的扩散有关。（Articles pp. 893, 899）
导致基因表达随机性的原因（Gene expression differences）
Variability in gene expression underlies incomplete penetrance
1925年，Timoféeff-Ressovsky 和 Romaschoff独立发现，有相同突变体等位基因的个体可以表现出突变表现型或者野生表现型，这个特性被称为“不完全外显率”。自那时以来，人们意识到，在遗传上相同的生物个体即使在相同环境中也会表现出不同特征，而且基因表达也有随机性。近年来，人们对微生物的这种基因表达“噪音”进行了定量研究。现在，Alexander van Oudenaarden及其同事将定量方法延伸到了一种多细胞生物，即线虫。利用单mRNA分子计数技术，他们显示了调控胚胎中小肠细胞生成的基因所发生的突变怎样导致其他基因水平及所产生的表现型出现更大随机性，尽管基因型相同，尽管环境条件也固定不变。这项工作还反映了基因调控网络会怎样使不同突变更加稳定、强健。（Article p. 913; News & Views）
活动星系喷射流的能量来源（Astrophysical jet power）
A change in the optical polarization associated with a γ-ray flare in the blazar 3C 279
少量活动星系是极端现象，其动力来自星系中心超大质量黑洞附近引力能的释放。在内流气体与外流喷射流相互作用的排放区到底发生了什么并不清楚。其中一个这种极端天体是“耀变体”3C 279。利用费米太空望远镜对3C 279所做的多带观测显示了与光偏振角度的巨大变化巧合的一个壮观的伽马射线耀斑。这表明光发射区与伽马射线发射区共空间，并且说明存在一个高度有序的喷射磁场。对这种类型宇宙加速的未来观测，可为将物质加速到接近光速所需的巨大能量是怎样产生的提供线索。（Letter p. 919; News & Views）
Ia-型超新星到底是怎样形成的（Supernova precursors）
An upper limit on the contribution of accreting white dwarfs to the type Ia supernova rate
Ia-型超新星被用作标准烛光，来确定宇宙距离尺度，但它们前身星的精确性质仍不清楚。对此有两个相互竞争的模型，各自都取得不同程度的成功。Ia-型超新星被认为是由白矮星的热核爆炸形成的，这种爆炸要么是由一个双星体系中两颗白矮星的合并触发的，要么是当一颗白矮星由于来自伴星的、逐渐发生的物质吸积而达到临界大小时触发的。按照吸积说法，膨胀中的恒星被预测在X-射线波段会有强烈发射。现在，根据钱德拉卫星对附近星系的X-射线观测结果，Marat Gilfanov 和 Ákos Bogdán估计，吸积说法只能解释年轻星系中大约不到5%的Ia-型超新星，尽管在晚期星系中情况可能会有所不同。（Letter p. 924）
广义相对论预测得到准确验证（Clocking on to relativity）
A precision measurement of the gravitational redshift by the interference of matter waves
广义相对论一个中心预测是，引力场会减慢时钟速度。以前对这种效应（被称为“引力红移”）的测量工作涉及放置在不同高度的时钟，而且此前该参数一直是支持弯曲时空理论的参数中测量最不准确的一个。现在，利用超过10年前在关于自由落体加速的一项研究中进行的实验工作所取得的结果，研究人员以前所未有的准确性确定了这一预测。对实验数据（关于在一个原子喷泉中上下跳跃的单个铯原子的量子干涉的数据）所做分析，提供了一个基于物质波干涉的测量结果，它将准确性提高了10,000倍。（Letter p. 926）
地球早期微化石被证实来自生物（Early, complex life）
Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic deposits
早期古细菌页岩和粉砂岩沉积物中较大的、细胞样结构的发现，为认为非常早的时候地球上就有多样化活生物体的观点增添了新证据。有关这样古老的化石的说法经常存在争议，因为非生物过程可产生生物类微结构和化学特征，与活生物体中的相似。因此，为了排除这些微结构的非生物来源，研究人员进行了广泛努力。它们通过了这种排查，结果表明它们似乎是有有机壁的微化石，来自大型微生物，这些微生物与以前所报告的、生活在距今约32亿年前的地球早期海洋里阳光能够照射到的浅层海水中的微生物垫共生。（Letter p. 934; News & Views）
蝙蝠回声定位能力的形成时间和起源（A bone of echolocation）
A bony connection signals laryngeal echolocation in bats
蝙蝠是高度专业化的哺乳动物，它们都能飞，而且很多还能用回声定位来沟通和寻找猎物。对一种名为“Onchonycteris finneyi”的原始蝙蝠化石所做研究表明，虽然它能飞，但却不能进行回声定位。现在，对26个蝙蝠物种所做的一项显微计算机断层扫描研究（显微CT研究）显示，在利用喉部产生的“咔嗒”声进行回声定位的蝙蝠身上，喉部的茎突舌骨与头颅耳朵区域的鼓膜骨相连。这种条件也见于“Onchonycteris finneyi”，从而再次开启了关于在蝙蝠早期演化中飞行和回声定位能力的形成时间和起源的基础性问题。（Letter p. 939）
幼鸟学习鸣唱过程中身体的解剖变化（Growing for a song）
Rapid spine stabilization and synaptic enhancement at the onset of behavioural learning
以前的研究表明，脑部结构变化和感官体验之间有一个关联，但类似变化是否也伴随着学习却并不确定。对正在学习成鸟鸣叫模式的斑胸草雀幼鸟的声音控制核HVC（higher vocal centre）中的单个神经元所做的高分辨率双光子活体成像表明，学习的确涉及这样的变化。在学习它们第一首歌的24小时内，斑胸草雀幼鸟HVC中在正常情况下处于动态的树状脊会变得更大、更稳定，突触活动得到增强。（Letter p. 948）
神经冠异常与“CHARGE综合症”（Neural crest abnormalities）
CHD7 cooperates with PBAF to control multipotent neural crest formation
“CHARGE综合症”是一种罕见的先天性症候，其特征是颅面结构、周围神经系统、耳朵、眼睛和心脏畸形。它是由为CHD7（一种依赖于ATP的染色质重塑蛋白）编码的基因所发生的杂合突变引起的。人们在25年前假设，“CHARGE综合症”由神经冠的异常发育导致。这一假设一直未能得到验证，但现在Bajpai等人发现，CHD7是多能迁移性神经冠的形成所必需的，是激发神经冠转录回路所必需的。另外，CHD7还被发现与另一染色质重塑复合物PBAF共同作用，来促进神经冠基因表达和细胞迁移。（Letter p. 958）
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NEWS AND VIEWS
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Early life: Ancient acritarchs pp885-886
Big and beautiful microfossils have been extracted from rocks that are
more than 3 billion years old. They offer tantalizing hints about the
antiquity of the eukaryote lineage of organisms that includes ourselves.
Roger Buick
doi:10.1038/463885a
http://www.nature.com/nature/journal/v463/n7283/full/463885a.html
Astrophysics: Cosmic jet engines pp886-887
In some galaxies, matter falling onto a supermassive black hole is
ejected in narrow jets moving at close to the speed of light. New
observations provide insight into the workings of these cosmic accelerators.
Andy Young
doi:10.1038/463886a
http://www.nature.com/nature/journal/v463/n7283/full/463886a.html
Gene regulation: A chromatin thermostat pp887-888
When environmental temperatures rise, plants seek help from their core
molecular mechanisms to adapt. The chromatin protein H2A.Z, which
regulates gene expression, is one such rescue molecule.
Roger B. Deal and Steven Henikoff
doi:10.1038/463887a
http://www.nature.com/nature/journal/v463/n7283/full/463887a.html
Animal behaviour: An ill wind for finches p888
Tim Lincoln
doi:10.1038/463888a
http://www.nature.com/nature/journal/v463/n7283/full/463888a.html
Structural biology: Transformative encounters pp889-890
Researchers have met the challenge of capturing transient states of
the SUMO E1 activating enzyme. Their pictures show radically different
crystal structures for two of the steps in this enzyme's activity.
Brenda A. Schulman and Arthur L. Haas
doi:10.1038/463889a
http://www.nature.com/nature/journal/v463/n7283/full/463889a.html
Quantum measurement: A light touch pp890-891
A technique used primarily to study fundamental issues in quantum
mechanics has now been shown to have promise as a powerful practical
tool for making ultra-precise measurements.
Aephraim M. Steinberg
doi:10.1038/463890a
http://www.nature.com/nature/journal/v463/n7283/full/463890a.html
Genetics: Random expression goes binary pp891-892
The production of intestinal cells in a worm embryo is regulated by
a network of transcription factors. Studies of these networks in
mutant worms provide evidence for stochastic effects in gene expression.
Adrian Streit and Ralf J. Sommer
doi:10.1038/463891a
http://www.nature.com/nature/journal/v463/n7283/full/463891a.html
50 & 100 years ago p892
doi:10.1038/463892a
http://www.nature.com/nature/journal/v463/n7283/full/463892a.html
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ARTICLES
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Signatures of mutation and selection in the cancer genome pp893-898
Homozygous gene deletions in cancer cells occur over recessive cancer
genes (where they can confer selective growth advantage) or over genes
at fragile sites of the genome (where they are thought to reflect
increased DNA breakage). Here, a large number of homozygous deletions
in a collection of cancer cell lines are identified and analysed to
derive structural signatures for the two different types of deletion.
More deletions are found in inherently fragile regions, and fewer
overlying recessive genes.
Graham R. Bignell et al.
doi:10.1038/nature08768
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08768.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08768.html
The landscape of somatic copy-number alteration across human cancers
pp899-905
One way of discovering genes with key roles in cancer development is to
identify genomic regions that are frequently altered in human cancers.
Here, high-resolution analyses of somatic copy-number alterations (SCNAs)
in numerous cancer specimens provide an overview of regions of focal SCNA
that are altered at significant frequency across several cancer types.
An oncogenic function is also found for the anti-apoptosis genes MCL1
and BCL2L1, which reside in amplified genome regions in many cancers.
Rameen Beroukhim et al.
doi:10.1038/nature08822
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08822.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08822.html
Active site remodelling accompanies thioester bond formation in the SUMO E1
pp906-912
The post-translational modification of cellular proteins by ubiquitin (Ub)
and ubiquitin-like (Ubl) proteins - such as SUMO - regulates a
broad array of cellular processes. E1 enzymes activate Ub and Ubl in two
steps, by carboxy-terminal adenylation and thioester bond formation to a
catalytic cysteine, but the structural basis for the intermediates remains
unknown. Crystal structures for SUMO E1 in complex with SUMO adenylate
and tetrahedral intermediate analogues are now reported and analysed.
Shaun K. Olsen et al.
doi:10.1038/nature08765
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08765.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08765.html
Variability in gene expression underlies incomplete penetrance pp913-918
Even genetically identical organisms in homogeneous environments vary,
indicating that randomness in developmental processes such as gene expression
may generate phenotypic diversity. Intestinal specification in the nematode
Caenorhabditis elegans, in which wild-type cell fate is invariant and controlled
by a small transcriptional network, is now studied. The results demonstrate
that mutations in developmental networks can expose stochastic variability
in gene expression, leading to phenotypic variation.
Arjun Raj, Scott A. Rifkin, Erik Andersen and Alexander van Oudenaarden
doi:10.1038/nature08781
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08781.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08781.html
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LETTERS
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A change in the optical polarization associated with a [ggr]-ray flare in
the blazar 3C[thinsp]279 pp919-923
It is widely accepted that strong and variable radiation detected over all
accessible energy bands in a number of active galaxies arises from a relativistic,
Doppler-boosted jet pointing close to our line of sight. However, the size of
the emitting zone and the location of this region relative to the central
supermassive black hole are poorly understood. Here, the coincidence of a
[gamma]-ray flare with a dramatic change of optical polarization angle is
reported, providing evidence for co-spatiality of optical and [gamma]-ray
emission regions and indicating a highly ordered jet magnetic field.
doi:10.1038/nature08841
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08841.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08841.html
An upper limit on the contribution of accreting white dwarfs to the
type[thinsp]Ia supernova rate pp924-925
Type Ia supernovae are thought to be associated with the thermonuclear
explosions of white dwarf stars, but the nuclear runaway that leads to the
explosion could occur through two different pathways with different X-ray
signatures. The X-ray flux from six nearby elliptical galaxies and galaxy
bulges is now observed to reveal that it is a factor of about 30-50 less
than predicted by the accretion scenario, where a white dwarf accumulates
material from a companion star.
Marat Gilfanov and Akos Bogdan
doi:10.1038/nature08685
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08685.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08685.html
A precision measurement of the gravitational redshift by the interference
of matter waves pp926-929
One of the central predictions of general relativity is that a clock in a
gravitational potential well runs more slowly than a similar clock outside
the well. This effect, known as gravitational redshift, has been measured
using clocks on a tower, an aircraft and a rocket, but here, laboratory
experiments based on quantum interference of atoms are shown to produce a
much more precise measurement.
Holger Muller, Achim Peters and Steven Chu
doi:10.1038/nature08776
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08776.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08776.html
Upside-down differentiation and generation of a /`primordial/' lower mantle
pp930-933
For the first billion years or so of the Earth's history, there may have been
whole-mantle convection, but after this period differentiation of the Earth's
mantle has been controlled by solid-state convection. Many trace elements -
known as 'incompatible elements' - preferentially partition into low-density
melts and are concentrated into the crust, but half of these incompatible
elements should be hidden in the Earth's interior. It is now suggested that a
by-product of whole-mantle convection is deep and hot melting, resulting in
the generation of dense liquids that sank into the lower mantle.
Cin-Ty A. Lee et al.
doi:10.1038/nature08824
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08824.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08824.html
Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic
deposits pp934-938
Claims that life existed on Earth in the early Archaean eon (3.2 billion years
ago) are often controversial, as non-biological processes can produce life-like
microstructures and chemical signatures that mimic those of the remains of
living organisms. Now, however, the discovery of relatively large, carbonaceous
spheroidal microstructures - interpreted as organic-walled microfossils - in
early Archaean deposits adds further evidence that life existed, thrived and
survived on Earth at a very early date.
Emmanuelle J. Javaux, Craig P. Marshall and Andrey Bekker
doi:10.1038/nature08793
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08793.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08793.html
A bony connection signals laryngeal echolocation in bats pp939-942
Echolocation is usually associated with bats. Many echolocating bats produce
signals in the larynx, but a few species produce tongue clicks. Here, studies
show that in all bats that use larynx-generated clicks, the stylohyal bone is
connected to the tympanic bone. Study of the stylohyal and tympanic bones of a
primitive fossil bat indicates that this species may have been able to
echolocate, despite previous evidence to the contrary, raising the question
of when and how echolocation evolved in bats.
Nina Veselka et al.
doi:10.1038/nature08737
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08737.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08737.html
Complete Khoisan and Bantu genomes from southern Africa pp943-947
Until now, fully sequenced human genomes of the indigenous hunter-gatherer
peoples of southern Africa have been limited to recently diverged populations.
The complete genome sequences of an indigenous hunter-gatherer from the
Kalahari Desert and of a Bantu from southern Africa are now presented. The
extent of whole-genome and exome diversity is characterized; the observed
genomic differences may help to pinpoint genetic adaptations to an agricultural lifestyle.
Stephan C. Schuster et al.
doi:10.1038/nature08795
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08795.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08795.html
Rapid spine stabilization and synaptic enhancement at the onset of behavioural
learning pp948-952
The brain's capacity to respond to instructive capacity underlies behavioural
learning, but how instructive experience acts on the juvenile brain, a period
in which learning is often enhanced, remains unknown. Here, two-photon in
vivo imaging is used to study the brains of zebra finches as they learn to
sing. The results indicate that behavioural learning results when instructive
experience is able to rapidly stabilize and strengthen synapses on the
sensorimotor neurons that control the learned behaviour.
Todd F. Roberts, Katherine A. Tschida, Marguerita E. Klein and Richard Mooney
doi:10.1038/nature08759
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08759.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08759.html
Rere controls retinoic acid signalling and somite bilateral symmetry
pp953-957
The vertebrate body plan shows marked bilateral symmetry, although this can
be disrupted in conditions such as scoliosis. Here, a mutation in Rere is
found that leads to the formation of asymmetrical somites in mouse embryos;
furthermore, Rere is shown to control retinoic acid signalling, which is
required to maintain somite symmetry by interacting with Fgf8. The results
provide insight into how bilateral symmetry is maintained.
Goncalo C. Vilhais-Neto et al.
doi:10.1038/nature08763
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08763.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08763.html
CHD7 cooperates with PBAF to control multipotent neural crest formation
pp958-962
Heterozygous mutations in the gene encoding CHD7, an ATP-dependent
chromatin-remodelling protein, result in CHARGE syndrome - a disorder
characterized by malformations of the craniofacial structures, peripheral
nervous system, ears, eyes and heart. In humans and Xenopus, CHD7 is now
shown to be essential for the formation of multipotent migratory neural
crest and for activating the transcriptional circuitry of the neural crest;
shedding light on the pathoembryology of CHARGE syndrome.
Ruchi Bajpai et al.
doi:10.1038/nature08733
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08733.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08733.html
TCR-peptide-MHC interactions in situ show accelerated kinetics and increased
affinity pp963-967
T lymphocytes, which are an integral part of most adaptive immune responses,
recognize foreign antigens through the binding of antigenic peptide-major
histocompatibility complex (pMHC) molecules on other cells to specific T-cell
antigen receptors (TCRs). Using single-molecule microscopy and fluorescence
resonance energy transfer, the kinetics of TCR-pMHC binding are now measured
in situ, revealing accelerated kinetics and increased affinity when compared
with solution measurements.
Johannes B. Huppa et al.
doi:10.1038/nature08746
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08746.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08746.html
Enzyme-inhibitor-like tuning of Ca2+ channel connectivity with calmodulin
pp968-972
Ca2+ channels and calmodulin (CaM) are two prominent hubs of biological
ignalling networks, affecting functions such as cardiac excitability and gene
transcription. The prevailing view has been that the ultrastrong affinity of
channels for the Ca2+-free form of calmodulin (apoCaM) ensures their saturation
with CaM and yields a form of concentration independence between Ca2+ channels
and CaM. Here, however, significant exceptions to this autonomy are shown to exist.
Xiaodong Liu, Philemon S. Yang, Wanjun Yang and David T. Yue
doi:10.1038/nature08766
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08766.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08766.html
----------------------
TECHNOLOGY FEATURES
----------------------
Whole-animal imaging: The whole picture pp977-980
As the techniques for imaging whole animals become more sophisticated,
researchers are able to get a clearer picture of what is going on inside.
Monya Baker looks at the options available.
Monya Baker
doi:10.1038/463977a
http://www.nature.com/nature/journal/v463/n7283/full/463977a.html
Whole-animal imaging: Probe progress p979
doi:10.1038/463979a
http://www.nature.com/nature/journal/v463/n7283/full/463979a.html
Whole-animal imaging: Table of suppliers p981
doi:10.1038/463981a
http://www.nature.com/nature/journal/v463/n7283/full/463981a.html
----------------------
FUTURES
----------------------
Unfinished business p990
In cold storage.
John Gilbey
doi:10.1038/463990a
http://www.nature.com/nature/journal/v463/n7283/full/463990a.html
Complete Khoisan and Bantu genomes from southern Africa
本期Nature发表了来自纳米比亚喀拉哈里沙漠的一个土生土长的采猎者和来自南非的一个班图人的完整基因组序列，同时还有来自喀拉哈里沙漠其他三个采猎部落的蛋白编码区域。对可能是已知最古老现代人类分支的遗传变异进行分析，将有助于了解人类多样性，帮助将南部非洲人包括在医学基因组研究项目中。最初观察结果包括这样一个事实：就核苷酸取代而言，“布须曼人”（Bushmen）彼此之间的差异似乎要超过与典型亚洲人和欧洲人的差异。更值得推测的是，这些基因组之间的变异体以及现有数据可能表示，他们的基因为适应农业生活方式而发生了变异。本期封面图片所描绘的是喀拉哈里沙漠南部觅食的“布须曼人”，研究人员获得了该部落人群的完整基因组序列。（Letter p. 943; News & Views; www.nature.com/podcast）封面照片：Stephan C. Schuster
关于癌症基因组研究的两篇论文（Cancer genomics refined）
Signatures of mutation and selection in the cancer genome / The landscape of somatic copy-number alteration across human cancers
本期两篇文章为不断增长的癌症基因组数据增添了更多内容。Bignell等人分析了一组746个可以公开获取的癌症细胞系中大量同型（纯合子）基因删除。结合有关同样基因半合子删除的信息，这些数据表明，癌症中所发现的很多删除反映了一个基因位于基因组中的一个脆弱点，而不是其失去会产生选择性生长优势的隐性癌症基因。Beroukhim等人发表了有关3000多个人类原发癌标本体细胞版本数量变异的迄今最大的数据集。很多改变是多种肿瘤类型共有的。功能实验表明，凋亡基因MCL1 和BCL2L1发挥了致癌基因的作用， 这两个基因与很多癌症中所见的扩散有关。（Articles pp. 893, 899）
导致基因表达随机性的原因（Gene expression differences）
Variability in gene expression underlies incomplete penetrance
1925年，Timoféeff-Ressovsky 和 Romaschoff独立发现，有相同突变体等位基因的个体可以表现出突变表现型或者野生表现型，这个特性被称为“不完全外显率”。自那时以来，人们意识到，在遗传上相同的生物个体即使在相同环境中也会表现出不同特征，而且基因表达也有随机性。近年来，人们对微生物的这种基因表达“噪音”进行了定量研究。现在，Alexander van Oudenaarden及其同事将定量方法延伸到了一种多细胞生物，即线虫。利用单mRNA分子计数技术，他们显示了调控胚胎中小肠细胞生成的基因所发生的突变怎样导致其他基因水平及所产生的表现型出现更大随机性，尽管基因型相同，尽管环境条件也固定不变。这项工作还反映了基因调控网络会怎样使不同突变更加稳定、强健。（Article p. 913; News & Views）
活动星系喷射流的能量来源（Astrophysical jet power）
A change in the optical polarization associated with a γ-ray flare in the blazar 3C 279
少量活动星系是极端现象，其动力来自星系中心超大质量黑洞附近引力能的释放。在内流气体与外流喷射流相互作用的排放区到底发生了什么并不清楚。其中一个这种极端天体是“耀变体”3C 279。利用费米太空望远镜对3C 279所做的多带观测显示了与光偏振角度的巨大变化巧合的一个壮观的伽马射线耀斑。这表明光发射区与伽马射线发射区共空间，并且说明存在一个高度有序的喷射磁场。对这种类型宇宙加速的未来观测，可为将物质加速到接近光速所需的巨大能量是怎样产生的提供线索。（Letter p. 919; News & Views）
Ia-型超新星到底是怎样形成的（Supernova precursors）
An upper limit on the contribution of accreting white dwarfs to the type Ia supernova rate
Ia-型超新星被用作标准烛光，来确定宇宙距离尺度，但它们前身星的精确性质仍不清楚。对此有两个相互竞争的模型，各自都取得不同程度的成功。Ia-型超新星被认为是由白矮星的热核爆炸形成的，这种爆炸要么是由一个双星体系中两颗白矮星的合并触发的，要么是当一颗白矮星由于来自伴星的、逐渐发生的物质吸积而达到临界大小时触发的。按照吸积说法，膨胀中的恒星被预测在X-射线波段会有强烈发射。现在，根据钱德拉卫星对附近星系的X-射线观测结果，Marat Gilfanov 和 Ákos Bogdán估计，吸积说法只能解释年轻星系中大约不到5%的Ia-型超新星，尽管在晚期星系中情况可能会有所不同。（Letter p. 924）
广义相对论预测得到准确验证（Clocking on to relativity）
A precision measurement of the gravitational redshift by the interference of matter waves
广义相对论一个中心预测是，引力场会减慢时钟速度。以前对这种效应（被称为“引力红移”）的测量工作涉及放置在不同高度的时钟，而且此前该参数一直是支持弯曲时空理论的参数中测量最不准确的一个。现在，利用超过10年前在关于自由落体加速的一项研究中进行的实验工作所取得的结果，研究人员以前所未有的准确性确定了这一预测。对实验数据（关于在一个原子喷泉中上下跳跃的单个铯原子的量子干涉的数据）所做分析，提供了一个基于物质波干涉的测量结果，它将准确性提高了10,000倍。（Letter p. 926）
地球早期微化石被证实来自生物（Early, complex life）
Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic deposits
早期古细菌页岩和粉砂岩沉积物中较大的、细胞样结构的发现，为认为非常早的时候地球上就有多样化活生物体的观点增添了新证据。有关这样古老的化石的说法经常存在争议，因为非生物过程可产生生物类微结构和化学特征，与活生物体中的相似。因此，为了排除这些微结构的非生物来源，研究人员进行了广泛努力。它们通过了这种排查，结果表明它们似乎是有有机壁的微化石，来自大型微生物，这些微生物与以前所报告的、生活在距今约32亿年前的地球早期海洋里阳光能够照射到的浅层海水中的微生物垫共生。（Letter p. 934; News & Views）
蝙蝠回声定位能力的形成时间和起源（A bone of echolocation）
A bony connection signals laryngeal echolocation in bats
蝙蝠是高度专业化的哺乳动物，它们都能飞，而且很多还能用回声定位来沟通和寻找猎物。对一种名为“Onchonycteris finneyi”的原始蝙蝠化石所做研究表明，虽然它能飞，但却不能进行回声定位。现在，对26个蝙蝠物种所做的一项显微计算机断层扫描研究（显微CT研究）显示，在利用喉部产生的“咔嗒”声进行回声定位的蝙蝠身上，喉部的茎突舌骨与头颅耳朵区域的鼓膜骨相连。这种条件也见于“Onchonycteris finneyi”，从而再次开启了关于在蝙蝠早期演化中飞行和回声定位能力的形成时间和起源的基础性问题。（Letter p. 939）
幼鸟学习鸣唱过程中身体的解剖变化（Growing for a song）
Rapid spine stabilization and synaptic enhancement at the onset of behavioural learning
以前的研究表明，脑部结构变化和感官体验之间有一个关联，但类似变化是否也伴随着学习却并不确定。对正在学习成鸟鸣叫模式的斑胸草雀幼鸟的声音控制核HVC（higher vocal centre）中的单个神经元所做的高分辨率双光子活体成像表明，学习的确涉及这样的变化。在学习它们第一首歌的24小时内，斑胸草雀幼鸟HVC中在正常情况下处于动态的树状脊会变得更大、更稳定，突触活动得到增强。（Letter p. 948）
神经冠异常与“CHARGE综合症”（Neural crest abnormalities）
CHD7 cooperates with PBAF to control multipotent neural crest formation
“CHARGE综合症”是一种罕见的先天性症候，其特征是颅面结构、周围神经系统、耳朵、眼睛和心脏畸形。它是由为CHD7（一种依赖于ATP的染色质重塑蛋白）编码的基因所发生的杂合突变引起的。人们在25年前假设，“CHARGE综合症”由神经冠的异常发育导致。这一假设一直未能得到验证，但现在Bajpai等人发现，CHD7是多能迁移性神经冠的形成所必需的，是激发神经冠转录回路所必需的。另外，CHD7还被发现与另一染色质重塑复合物PBAF共同作用，来促进神经冠基因表达和细胞迁移。（Letter p. 958）
----------------------
NEWS AND VIEWS
----------------------
Early life: Ancient acritarchs pp885-886
Big and beautiful microfossils have been extracted from rocks that are
more than 3 billion years old. They offer tantalizing hints about the
antiquity of the eukaryote lineage of organisms that includes ourselves.
Roger Buick
doi:10.1038/463885a
http://www.nature.com/nature/journal/v463/n7283/full/463885a.html
Astrophysics: Cosmic jet engines pp886-887
In some galaxies, matter falling onto a supermassive black hole is
ejected in narrow jets moving at close to the speed of light. New
observations provide insight into the workings of these cosmic accelerators.
Andy Young
doi:10.1038/463886a
http://www.nature.com/nature/journal/v463/n7283/full/463886a.html
Gene regulation: A chromatin thermostat pp887-888
When environmental temperatures rise, plants seek help from their core
molecular mechanisms to adapt. The chromatin protein H2A.Z, which
regulates gene expression, is one such rescue molecule.
Roger B. Deal and Steven Henikoff
doi:10.1038/463887a
http://www.nature.com/nature/journal/v463/n7283/full/463887a.html
Animal behaviour: An ill wind for finches p888
Tim Lincoln
doi:10.1038/463888a
http://www.nature.com/nature/journal/v463/n7283/full/463888a.html
Structural biology: Transformative encounters pp889-890
Researchers have met the challenge of capturing transient states of
the SUMO E1 activating enzyme. Their pictures show radically different
crystal structures for two of the steps in this enzyme's activity.
Brenda A. Schulman and Arthur L. Haas
doi:10.1038/463889a
http://www.nature.com/nature/journal/v463/n7283/full/463889a.html
Quantum measurement: A light touch pp890-891
A technique used primarily to study fundamental issues in quantum
mechanics has now been shown to have promise as a powerful practical
tool for making ultra-precise measurements.
Aephraim M. Steinberg
doi:10.1038/463890a
http://www.nature.com/nature/journal/v463/n7283/full/463890a.html
Genetics: Random expression goes binary pp891-892
The production of intestinal cells in a worm embryo is regulated by
a network of transcription factors. Studies of these networks in
mutant worms provide evidence for stochastic effects in gene expression.
Adrian Streit and Ralf J. Sommer
doi:10.1038/463891a
http://www.nature.com/nature/journal/v463/n7283/full/463891a.html
50 & 100 years ago p892
doi:10.1038/463892a
http://www.nature.com/nature/journal/v463/n7283/full/463892a.html
----------------------
ARTICLES
----------------------
Signatures of mutation and selection in the cancer genome pp893-898
Homozygous gene deletions in cancer cells occur over recessive cancer
genes (where they can confer selective growth advantage) or over genes
at fragile sites of the genome (where they are thought to reflect
increased DNA breakage). Here, a large number of homozygous deletions
in a collection of cancer cell lines are identified and analysed to
derive structural signatures for the two different types of deletion.
More deletions are found in inherently fragile regions, and fewer
overlying recessive genes.
Graham R. Bignell et al.
doi:10.1038/nature08768
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08768.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08768.html
The landscape of somatic copy-number alteration across human cancers
pp899-905
One way of discovering genes with key roles in cancer development is to
identify genomic regions that are frequently altered in human cancers.
Here, high-resolution analyses of somatic copy-number alterations (SCNAs)
in numerous cancer specimens provide an overview of regions of focal SCNA
that are altered at significant frequency across several cancer types.
An oncogenic function is also found for the anti-apoptosis genes MCL1
and BCL2L1, which reside in amplified genome regions in many cancers.
Rameen Beroukhim et al.
doi:10.1038/nature08822
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08822.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08822.html
Active site remodelling accompanies thioester bond formation in the SUMO E1
pp906-912
The post-translational modification of cellular proteins by ubiquitin (Ub)
and ubiquitin-like (Ubl) proteins - such as SUMO - regulates a
broad array of cellular processes. E1 enzymes activate Ub and Ubl in two
steps, by carboxy-terminal adenylation and thioester bond formation to a
catalytic cysteine, but the structural basis for the intermediates remains
unknown. Crystal structures for SUMO E1 in complex with SUMO adenylate
and tetrahedral intermediate analogues are now reported and analysed.
Shaun K. Olsen et al.
doi:10.1038/nature08765
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08765.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08765.html
Variability in gene expression underlies incomplete penetrance pp913-918
Even genetically identical organisms in homogeneous environments vary,
indicating that randomness in developmental processes such as gene expression
may generate phenotypic diversity. Intestinal specification in the nematode
Caenorhabditis elegans, in which wild-type cell fate is invariant and controlled
by a small transcriptional network, is now studied. The results demonstrate
that mutations in developmental networks can expose stochastic variability
in gene expression, leading to phenotypic variation.
Arjun Raj, Scott A. Rifkin, Erik Andersen and Alexander van Oudenaarden
doi:10.1038/nature08781
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08781.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08781.html
----------------------
LETTERS
----------------------
A change in the optical polarization associated with a [ggr]-ray flare in
the blazar 3C[thinsp]279 pp919-923
It is widely accepted that strong and variable radiation detected over all
accessible energy bands in a number of active galaxies arises from a relativistic,
Doppler-boosted jet pointing close to our line of sight. However, the size of
the emitting zone and the location of this region relative to the central
supermassive black hole are poorly understood. Here, the coincidence of a
[gamma]-ray flare with a dramatic change of optical polarization angle is
reported, providing evidence for co-spatiality of optical and [gamma]-ray
emission regions and indicating a highly ordered jet magnetic field.
doi:10.1038/nature08841
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08841.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08841.html
An upper limit on the contribution of accreting white dwarfs to the
type[thinsp]Ia supernova rate pp924-925
Type Ia supernovae are thought to be associated with the thermonuclear
explosions of white dwarf stars, but the nuclear runaway that leads to the
explosion could occur through two different pathways with different X-ray
signatures. The X-ray flux from six nearby elliptical galaxies and galaxy
bulges is now observed to reveal that it is a factor of about 30-50 less
than predicted by the accretion scenario, where a white dwarf accumulates
material from a companion star.
Marat Gilfanov and Akos Bogdan
doi:10.1038/nature08685
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08685.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08685.html
A precision measurement of the gravitational redshift by the interference
of matter waves pp926-929
One of the central predictions of general relativity is that a clock in a
gravitational potential well runs more slowly than a similar clock outside
the well. This effect, known as gravitational redshift, has been measured
using clocks on a tower, an aircraft and a rocket, but here, laboratory
experiments based on quantum interference of atoms are shown to produce a
much more precise measurement.
Holger Muller, Achim Peters and Steven Chu
doi:10.1038/nature08776
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08776.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08776.html
Upside-down differentiation and generation of a /`primordial/' lower mantle
pp930-933
For the first billion years or so of the Earth's history, there may have been
whole-mantle convection, but after this period differentiation of the Earth's
mantle has been controlled by solid-state convection. Many trace elements -
known as 'incompatible elements' - preferentially partition into low-density
melts and are concentrated into the crust, but half of these incompatible
elements should be hidden in the Earth's interior. It is now suggested that a
by-product of whole-mantle convection is deep and hot melting, resulting in
the generation of dense liquids that sank into the lower mantle.
Cin-Ty A. Lee et al.
doi:10.1038/nature08824
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08824.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08824.html
Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic
deposits pp934-938
Claims that life existed on Earth in the early Archaean eon (3.2 billion years
ago) are often controversial, as non-biological processes can produce life-like
microstructures and chemical signatures that mimic those of the remains of
living organisms. Now, however, the discovery of relatively large, carbonaceous
spheroidal microstructures - interpreted as organic-walled microfossils - in
early Archaean deposits adds further evidence that life existed, thrived and
survived on Earth at a very early date.
Emmanuelle J. Javaux, Craig P. Marshall and Andrey Bekker
doi:10.1038/nature08793
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08793.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08793.html
A bony connection signals laryngeal echolocation in bats pp939-942
Echolocation is usually associated with bats. Many echolocating bats produce
signals in the larynx, but a few species produce tongue clicks. Here, studies
show that in all bats that use larynx-generated clicks, the stylohyal bone is
connected to the tympanic bone. Study of the stylohyal and tympanic bones of a
primitive fossil bat indicates that this species may have been able to
echolocate, despite previous evidence to the contrary, raising the question
of when and how echolocation evolved in bats.
Nina Veselka et al.
doi:10.1038/nature08737
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08737.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08737.html
Complete Khoisan and Bantu genomes from southern Africa pp943-947
Until now, fully sequenced human genomes of the indigenous hunter-gatherer
peoples of southern Africa have been limited to recently diverged populations.
The complete genome sequences of an indigenous hunter-gatherer from the
Kalahari Desert and of a Bantu from southern Africa are now presented. The
extent of whole-genome and exome diversity is characterized; the observed
genomic differences may help to pinpoint genetic adaptations to an agricultural lifestyle.
Stephan C. Schuster et al.
doi:10.1038/nature08795
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08795.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08795.html
Rapid spine stabilization and synaptic enhancement at the onset of behavioural
learning pp948-952
The brain's capacity to respond to instructive capacity underlies behavioural
learning, but how instructive experience acts on the juvenile brain, a period
in which learning is often enhanced, remains unknown. Here, two-photon in
vivo imaging is used to study the brains of zebra finches as they learn to
sing. The results indicate that behavioural learning results when instructive
experience is able to rapidly stabilize and strengthen synapses on the
sensorimotor neurons that control the learned behaviour.
Todd F. Roberts, Katherine A. Tschida, Marguerita E. Klein and Richard Mooney
doi:10.1038/nature08759
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08759.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08759.html
Rere controls retinoic acid signalling and somite bilateral symmetry
pp953-957
The vertebrate body plan shows marked bilateral symmetry, although this can
be disrupted in conditions such as scoliosis. Here, a mutation in Rere is
found that leads to the formation of asymmetrical somites in mouse embryos;
furthermore, Rere is shown to control retinoic acid signalling, which is
required to maintain somite symmetry by interacting with Fgf8. The results
provide insight into how bilateral symmetry is maintained.
Goncalo C. Vilhais-Neto et al.
doi:10.1038/nature08763
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08763.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08763.html
CHD7 cooperates with PBAF to control multipotent neural crest formation
pp958-962
Heterozygous mutations in the gene encoding CHD7, an ATP-dependent
chromatin-remodelling protein, result in CHARGE syndrome - a disorder
characterized by malformations of the craniofacial structures, peripheral
nervous system, ears, eyes and heart. In humans and Xenopus, CHD7 is now
shown to be essential for the formation of multipotent migratory neural
crest and for activating the transcriptional circuitry of the neural crest;
shedding light on the pathoembryology of CHARGE syndrome.
Ruchi Bajpai et al.
doi:10.1038/nature08733
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08733.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08733.html
TCR-peptide-MHC interactions in situ show accelerated kinetics and increased
affinity pp963-967
T lymphocytes, which are an integral part of most adaptive immune responses,
recognize foreign antigens through the binding of antigenic peptide-major
histocompatibility complex (pMHC) molecules on other cells to specific T-cell
antigen receptors (TCRs). Using single-molecule microscopy and fluorescence
resonance energy transfer, the kinetics of TCR-pMHC binding are now measured
in situ, revealing accelerated kinetics and increased affinity when compared
with solution measurements.
Johannes B. Huppa et al.
doi:10.1038/nature08746
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08746.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08746.html
Enzyme-inhibitor-like tuning of Ca2+ channel connectivity with calmodulin
pp968-972
Ca2+ channels and calmodulin (CaM) are two prominent hubs of biological
ignalling networks, affecting functions such as cardiac excitability and gene
transcription. The prevailing view has been that the ultrastrong affinity of
channels for the Ca2+-free form of calmodulin (apoCaM) ensures their saturation
with CaM and yields a form of concentration independence between Ca2+ channels
and CaM. Here, however, significant exceptions to this autonomy are shown to exist.
Xiaodong Liu, Philemon S. Yang, Wanjun Yang and David T. Yue
doi:10.1038/nature08766
Abstract: http://www.nature.com/nature/journal/v463/n7283/abs/nature08766.html
Article: http://www.nature.com/nature/journal/v463/n7283/full/nature08766.html
----------------------
TECHNOLOGY FEATURES
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Whole-animal imaging: The whole picture pp977-980
As the techniques for imaging whole animals become more sophisticated,
researchers are able to get a clearer picture of what is going on inside.
Monya Baker looks at the options available.
Monya Baker
doi:10.1038/463977a
http://www.nature.com/nature/journal/v463/n7283/full/463977a.html
Whole-animal imaging: Probe progress p979
doi:10.1038/463979a
http://www.nature.com/nature/journal/v463/n7283/full/463979a.html
Whole-animal imaging: Table of suppliers p981
doi:10.1038/463981a
http://www.nature.com/nature/journal/v463/n7283/full/463981a.html
----------------------
FUTURES
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Unfinished business p990
In cold storage.
John Gilbey
doi:10.1038/463990a
http://www.nature.com/nature/journal/v463/n7283/full/463990a.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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