네이처 컨텐츠

Editorial

Home-brew tests need regulation p.5

A US proposal to regulate medical diagnostics from individual labs reflects the tests’ growing complexity. Such guidance should be welcomed, not resisted.

doi: 10.1038/512005a

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News

News Features

THE ROBO-CHEMIST p.20

The race is on to build a machine that can synthesize any organic compound. It could transform chemistry.

Mark Peplow

doi: 10.1038/512020a

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News & Views

Seeds of selective nanotube growth p.30

'Seed' molecules have been made that enable synthesis of just one kind of single-walled carbon nanotube, rather than a mixture of species. This paves the way for the preparation of pure samples of any nanotube species. See Letter p.61

James M. Tour

doi: 10.1038/512030a

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Directions for the drivers p.31

A comparison of colorectal cancer and normal cells from 103 patients identifies dozens of genes that are differently expressed in tumour cells as a result of altered regulation of transcription. See Letter p.87

Greg Gibson

doi: 10.1038/nature13649

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Alzheimer's disease under strain p.32

Two studies of amyloid-β protein aggregates, which cause Alzheimer's disease, find that different conformations of the aggregates can define different strains of the disorder, drawing parallels with prion diseases.

Adriano Aguzzi

doi: 10.1038/512032a

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Portrait of a doomed star p.34

Some stars explode in thermonuclear supernovae, but understanding of why this occurs comes mainly from indirect clues. Now, the progenitor of a member of a strange class of such explosions may have been detected directly. See Letter p.54

Stephen Justham

doi: 10.1038/512034a

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Early treatment may not be early enough p.35

Giving monkeys antiretroviral therapy from just three days after exposure to simian immunodeficiency virus does not prevent a subsequent rebound of viral replication, suggesting that viral reservoirs are established early. See Letter p.74

Kai Deng & Robert F. Siliciano

doi: 10.1038/nature13647

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Tooth structure re-engineered p.36

Mice deficient in the EDA protein lack normal tooth features. Restoring EDA in embryonic teeth at increasing doses has now been found to recover these dental features in a stepwise pattern that mimics evolution. See Article p.44

Zhe-Xi Luo

doi: 10.1038/nature13651

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Articles

Convergence of terrestrial plant production across global climate gradients p.39

Net primary production is affected by temperature and precipitation, but whether this is a direct kinetic effect on plant metabolism or an indirect ecological effect mediated by changes in plant age, plant biomass or growing season length is unclear — this study develops metabolic scaling theory to be able to answer this question and applies it to a global data set of plant productivity, concluding that it is indirect effects that explain the influence of climate on productivity, which is characterized by a common scaling relationship across climate gradients.

Sean T. Michaletz, Dongliang Cheng, Andrew J. Kerkhoff & Brian J. Enquist

doi: 10.1038/nature13470

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Replaying evolutionary transitions from the dental fossil record p.44

Gradual changes that occur to mammalian tooth morphology across evolutionary time were modeled in vitro and in vivo by modulation of signalling pathways in the mouse, and computer modelling was used to provide further analysis of the parameters influencing tooth morphology.

doi: 10.1038/nature13613

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Structure of the DDB1–CRBN E3 ubiquitin ligase in complex with thalidomide p.49

The crystal structures of thalidomide and its derivatives bound to the E3 ligase subcomplex DDB1–CRBN are shown; these drugs are found to have dual functions, interfering with the binding of certain cellular substrates to the E3 ligase but promoting the binding of others, thereby modulating the degradation of cellular proteins.

Eric S. Fischer, Kerstin Böhm, John R. Lydeard, Haidi Yang, Michael B. Stadler, Simone Cavadini, Jane Nagel, Fabrizio Serluca, Vincent Acker, Gondichatnahalli M. Lingaraju + et al.

doi: 10.1038/nature13527

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Letters

A luminous, blue progenitor system for the type Iax supernova 2012Z p.54

The detection of the luminous, blue progenitor system of the type Iax supernova 2012Z suggests that this supernova was the explosion of a white dwarf accreting material from a helium-star companion.

Curtis McCully, Saurabh W. Jha, Ryan J. Foley, Lars Bildsten, Wen-fai Fong, Robert P. Kirshner, G. H. Marion, Adam G. Riess & Maximilian D. Stritzinger

doi: 10.1038/nature13615

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Tunable spin–spin interactions and entanglement of ions in separate potential wells p.57

The ability of individual ions trapped in separate potential wells to simulate spin–spin interactions is demonstrated by tuning the Coulomb interaction between two ions, independently controlling their local wells and entangling their internal states with a fidelity of approximately 0.82.

A. C. Wilson, Y. Colombe, K. R. Brown, E. Knill, D. Leibfried & D. J. Wineland

doi: 10.1038/nature13565

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Controlled synthesis of single-chirality carbon nanotubes p.61

Present preparation methods fail to meet fully the demand for structurally pure single-walled carbon nanotubes; surface-catalysed cyclodehydrogenation reactions are now shown to convert precursor molecules deposited on a platinum(111) surface into ultrashort nanotube seeds that can then be grown further into defect-free and structurally pure single-walled carbon nanotubes of single chirality.

doi: 10.1038/nature13607

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Rapid seeding of the viral reservoir prior to SIV viraemia in rhesus monkeys p.74

Reservoirs of virus infection represent the most important reason why HIV-1 cannot be cured with current antiretroviral drugs; now the refractory viral reservoir is shown to be seeded as early as 3 days after infection in a monkey model, even before the virus is detected in the blood.

James B. Whitney, Alison L. Hill, Srisowmya Sanisetty, Pablo Penaloza-MacMaster, Jinyan Liu, Mayuri Shetty, Lily Parenteau, Crystal Cabral, Jennifer Shields, Stephen Blackmore + et al.

doi: 10.1038/nature13594

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Neuropathy of haematopoietic stem cell niche is essential for myeloproliferative neoplasms p.78

Myeloproliferative neoplasms are caused by mutations in the haematopoietic stem cell (HSC) compartment, and here the authors show that the HSC niche contributes to the pathogenesis; sympathetic innervation of mesenchymal stem cells (MSCs) is reduced in the bone marrow of patients, which leads to reduced MSC numbers and increased mutant HSC expansion, and restoring sympathetic regulation of MSCs with neuroprotective/sympathomimetic drugs prevents mutant HSC expansion.

Lorena Arranz, Abel Sánchez-Aguilera, Daniel Martín-Pérez, Joan Isern, Xavier Langa, Alexandar Tzankov, Pontus Lundberg, Sandra Muntión, Yi-Shiuan Tzeng, Dar-Ming Lai + et al.

doi: 10.1038/nature13383

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PVT1 dependence in cancer with MYC copy-number increase p.82

Pvt1 overexpression in mice contributes to high Myc levels due to 8q24.21 gain and to MYC-driven tumorigenesis.

Yuen-Yi Tseng, Branden S. Moriarity, Wuming Gong, Ryutaro Akiyama, Ashutosh Tiwari, Hiroko Kawakami, Peter Ronning, Brian Reuland, Kacey Guenther, Thomas C. Beadnell + et al.

doi: 10.1038/nature13311

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Putative cis-regulatory drivers in colorectal cancer p.87

Examination of allele-specific expression identifies 71 genes with excess somatic cis-regulatory effects in colorectal cancer (CRC), and 1,693 and 948 expression quantitative trait loci (eQTLs) in normal samples and tumours, respectively (with 36% of tumour eQTLs exclusive to CRC); tumour-specific eQTLs are more enriched for low CRC genome-wide association study P values and accumulate more somatic mutations than shared eQTLs, suggesting a role as germline-derived cancer regulatory drivers.

doi: 10.1038/nature13602

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Genome-scale functional characterization of Drosophila developmental enhancers in vivo p.91

Systematically assaying the activity of 7,705 candidate enhancers during Drosophila embryogenesis shows that nearly half are active in the embryo and display dynamic spatial patterns during development; enhancer activity is matched to expression patterns of putative target genes and predictive cis-regulatory motifs are identified.

Evgeny Z. Kvon, Tomas Kazmar, Gerald Stampfel, J. Omar Yáñez-Cuna, Michaela Pagani, Katharina Schernhuber, Barry J. Dickson & Alexander Stark

doi: 10.1038/nature13395

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Enhancer loops appear stable during development and are associated with paused polymerase p.96

A high-resolution map of enhancer three-dimensional contacts during Drosophila embryogenesis shows that although local regulatory interactions are frequent, long-range interactions are also very common; unexpectedly, most interactions appear unchanged between tissues and across development and are formed prior to gene expression, indicating that transcription initiates from preformed enhancer–promoter loops, which are associated with paused polymerase.

Yad Ghavi-Helm, Felix A. Klein, Tibor Pakozdi, Lucia Ciglar, Daan Noordermeer, Wolfgang Huber & Eileen E. M. Furlong

doi: 10.1038/nature13417

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Visualizing the kinetic power stroke that drives proton-coupled zinc(ii) transport p.101

The proton gradient is a principal energy source for respiration-dependent active transport, but the structural mechanisms of proton-coupled transport processes are poorly understood. YiiP is a proton-coupled zinc transporter found in the cytoplasmic membrane of Escherichia coli. Its transport site receives protons from water molecules that gain access to its hydrophobic environment and transduces the energy of an inward proton gradient to drive Zn(ii) efflux. This membrane protein is a well-characterized member of the family of cation diffusion facilitators that occurs at all phylogenetic levels. Here we show, using X-ray-mediated hydroxyl radical labelling of YiiP and mass spectrometry, that Zn(ii) binding triggers a highly localized, all-or-nothing change of water accessibility to the transport site and an adjacent hydrophobic gate. Millisecond time-resolved dynamics reveal a concerted and reciprocal pattern of accessibility changes along a transmembrane helix, suggesting a rigid-body helical re-orientation linked to Zn(ii) binding that triggers the closing of the hydrophobic gate. The gated water access to the transport site enables a stationary proton gradient to facilitate the conversion of zinc-binding energy to the kinetic power stroke of a vectorial zinc transport. The kinetic details provide energetic insights into a proton-coupled active-transport reaction.

Sayan Gupta, Jin Chai, Jie Cheng, Rhijuta D’Mello, Mark R. Chance & Dax Fu

doi: 10.1038/nature13382

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