Editorials
モントリオール議定書にハイドロフルオロカーボンを組み込めるかどうかは、気候変動問題に対する国際社会の責任感を試す試金石だ。
All together now p.593
Online discussion is an essential aspect of the post-publication review of findings.
doi: 10.1038/502593a
「発表された論文に対するピアレビュー」は科学に役立つ重要な仕組みになる可能性があり、科学者はオンラインでのコメントに積極的に参加して欲しい。
Time to talk p.593
Proposals to bring hydrofluorocarbons under the auspices of the Montreal Protocol provide a simple test of the international community’s commitment to tackling climate change.
doi: 10.1038/502593b
英国の人気SFテレビ番組「Doctor Who」が50周年を迎え、科学の法則に反していても、ストーリーや工夫で科学がドラマになる可能性を示している。
Playful paradoxes p.594
A half-century of Doctor Who has shown the dramatic possibilities of science in the arts.
doi: 10.1038/502594a
News
監視の緩んだヨーロッパに、再びポリオまん延の恐れが。
Polio risk looms over Europe p.601
Cases in Syria highlight vulnerability of nearby countries to the viral disease.
doi: 10.1038/502601a
米国の起業家が、数学的才能のカギとなる遺伝子を探すプロジェクトを。
Root of maths genius sought p.602
Entrepreneur’s ‘Project Einstein’ taps 400 top academics for their DNA.
doi: 10.1038/502602a
ブラックホールの最終的な運命をめぐり、収縮するが消滅はしないという新たな理論が。
Black holes shrink but endure p.603
Theorist’s idea takes on information-preservation problem.
doi: 10.1038/502603a
アフリカで、稲妻を利用する低コストの暴風雨予報システムの試験的運用が。
Lightning network tested out in Guinea p.604
Project to forecast African storms provides cheap alternative to radar-based weather services.
doi: 10.1038/502604a
地球外生命体探査の関心の対象が、再び矮星へ。
Astronomers revisit dwarf stars’ promise p.606
Kepler data spur searches for habitable planets around small, low-temperature stars.
doi: 10.1038/502606a
土壌解析システムの開発で、アフリカ農業の肥料利用状況に改善の期待が。
Farmers dig into soil quality p.607
Analytical technique promises to match fertilizers to soil in bid to boost yields in Africa.
doi: 10.1038/502607a
Features
天文学：南天の星
Astronomy: Southern star p.608
Can the Southern African Large Telescope live up to its potential?
doi: 10.1038/502608a
生態学：湖上の麗人
Ecology: Lady of the lakes p.612
Diane Orihel set her PhD aside to lead a massive protest when Canada tried to shut down its unique Experimental Lakes Area.
doi: 10.1038/502612a
News & Views
生態学：乾燥地域で炭素、窒素、リンの関係を切り離す要因
Ecology: Drivers of decoupling in drylands p.628
乾燥地帯では、乾燥が強まるにつれて土壌中の炭素、窒素とリンのバランスが変化しているという研究結果から、全球的な気候変動が土壌の肥沃性と生態系サービスにどのように影響を及ぼすのかについての手がかりが得られる。
doi: 10.1038/502628a
構造生物学：転写機械についての重要な発見
Structural biology: Pivotal findings for a transcription machine p.629
完全なRNAポリメラーゼI複合体の結晶構造が、今回明らかにされた。この構造が、RNAポリメラーゼI上のDNAが結合するのに使われる裂け目の開閉と転写制御とを結びつけている。
doi: 10.1038/nature12700
量子物理学：フェルミの海から飛び出す単一電子
Quantum physics: Single electrons pop out of the Fermi sea p.630
電子伝導体中の１つ１つの電子の制御が可能になれば、新規な量子技術につながる道が開かれるだろう。ナノスケールの電極中の電子の海から単一の電子を引き出すことが今回可能になった。
doi: 10.1038/nature12699
生物物理：障壁を通る難儀な経路
Biophysics: Rough passage across a barrier p.632
溶液中での化学反応の動態はクラマースの理論によって記述されるが、それに関わるパラメーターは直接測定されたことがなかった。タンパク質の折りたたみについての研究によって、この問題をどのようにしたら克服できるかが示された。
doi: 10.1038/nature12697
水質管理：排水に関するデータのギャップ
Water management: The data gap p.633
包括的な調査によって、排水の産生、処理および使用に関するデータの全球的な不足が明らかになった。この状況が改善されれば、政府が排水というこの貴重な資源の管理に対する法律を制定するのに役立つだろう。
doi: 10.1038/502633a
海洋生物学：動物であるサンゴはストレスに硫黄で立ち向かう
Marine biology: Coral animals combat stress with sulphur p.634
サンゴに共生して光合成を行う藻類は、海洋の水温調節に関わる硫黄化合物を産生している。研究の展開過程で、動物であるサンゴが同じ化合物を産生していることが明らかになった。
doi: 10.1038/nature12698
Articles
細胞：細動脈ニッチは造血幹細胞の休止状態を維持する
Arteriolar niches maintain haematopoietic stem cell quiescence p.637
Immunofluorescence imaging and computational modelling are used to study the spatial distribution of different cell types within the haematopoietic stem cell (HSC) niche; findings show that quiescent HSCs associate specifically with small arterioles that are preferentially found in the endosteal bone marrow and are essential in maintaining this quiescence.
doi: 10.1038/nature12612
構造生物学：14のサブユニットからなるRNAポリメラーゼIの結晶構造
Crystal structure of the 14-subunit RNA polymerase I p.644
RNA polymerase (Pol) I transcribes ribosomal RNA that is critically required for ribosome assembly, and the enzyme is a major determinant of protein biosynthesis and cell growth; here the crystal structure of the complete 14-subunit Pol I from yeast is determined, providing insights into its unique architecture and the possible functional roles of its components.
doi: 10.1038/nature12636
構造生物学：RNAポリメラーゼIの構造と転写調節
RNA polymerase I structure and transcription regulation p.650
The crystal structure of the complete 14-subunit RNA polymerase (Pol) I from yeast is determined, providing insights into its unique architecture and the possible functional roles of its components.
doi: 10.1038/nature12712
Letters
宇宙：ペルセウス座銀河団の銀河間物質における均一な金属分布
A uniform metal distribution in the intergalactic medium of the Perseus cluster of galaxies p.656
Most of the metals (elements heavier than helium) produced by stars in the member galaxies of clusters currently reside within the hot, X-ray-emitting intra-cluster gas. Observations of X-ray line emission from this intergalactic medium have suggested a relatively small cluster-to-cluster scatter outside the cluster centres and enrichment with iron out to large radii, leading to the idea that the metal enrichment occurred early in the history of the Universe. Models with early enrichment predict a uniform metal distribution at large radii in clusters, whereas those with late-time enrichment are expected to introduce significant spatial variations of the metallicity. To discriminate clearly between these competing models, it is essential to test for potential inhomogeneities by measuring the abundances out to large radii along multiple directions in clusters, which has not hitherto been done. Here we report a remarkably uniform iron abundance, as a function of radius and azimuth, that is statistically consistent with a constant value of ZFe = 0.306 ± 0.012 in solar units out to the edge of the nearby Perseus cluster. This homogeneous distribution requires that most of the metal enrichment of the intergalactic medium occurred before the cluster formed, probably more than ten billion years ago, during the period of maximal star formation and black hole activity.
doi: 10.1038/nature12646
量子物理学：レビトンを用いた電子量子光学のための最小励起状態
Minimal-excitation states for electron quantum optics using levitons p.659
The on-demand generation of pure quantum excitations is important for the operation of quantum systems, but it is particularly difficult for a system of fermions. This is because any perturbation affects all states below the Fermi energy, resulting in a complex superposition of particle and hole excitations. However, it was predicted nearly 20 years ago that a Lorentzian time-dependent potential with quantized flux generates a minimal excitation with only one particle and no hole. Here we report that such quasiparticles (hereafter termed levitons) can be generated on demand in a conductor by applying voltage pulses to a contact. Partitioning the excitations with an electronic beam splitter generates a current noise that we use to measure their number. Minimal-excitation states are observed for Lorentzian pulses, whereas for other pulse shapes there are significant contributions from holes. Further identification of levitons is provided in the energy domain with shot-noise spectroscopy, and in the time domain with electronic Hong–Ou–Mandel noise correlations. The latter, obtained by colliding synchronized levitons on a beam splitter, exemplifies the potential use of levitons for quantum information: using linear electron quantum optics in ballistic conductors, it is possible to imagine flying-qubit operation in which the Fermi statistics are exploited to entangle synchronized electrons emitted by distinct sources. Compared with electron sources based on quantum dots, the generation of levitons does not require delicate nanolithography, considerably simplifying the circuitry for scalability. Levitons are not limited to carrying a single charge, and so in a broader context n-particle levitons could find application in the study of full electron counting statistics. But they can also carry a fraction of charge if they are implemented in Luttinger liquids or in fractional quantum Hall edge channels; this allows the study of Abelian and non-Abelian quasiparticles in the time domain. Finally, the generation technique could be applied to cold atomic gases, leading to the possibility of atomic levitons.
doi: 10.1038/nature12713
物理：単一電子とボース・アインシュタイン凝縮体を結合させる
Coupling a single electron to a Bose–Einstein condensate p.664
The coupling of electrons to matter lies at the heart of our understanding of material properties such as electrical conductivity. Electron–phonon coupling can lead to the formation of a Cooper pair out of two repelling electrons, which forms the basis for Bardeen–Cooper–Schrieffer superconductivity. Here we study the interaction of a single localized electron with a Bose–Einstein condensate and show that the electron can excite phonons and eventually trigger a collective oscillation of the whole condensate. We find that the coupling is surprisingly strong compared to that of ionic impurities, owing to the more favourable mass ratio. The electron is held in place by a single charged ionic core, forming a Rydberg bound state. This Rydberg electron is described by a wavefunction extending to a size of up to eight micrometres, comparable to the dimensions of the condensate. In such a state, corresponding to a principal quantum number of n = 202, the Rydberg electron is interacting with several tens of thousands of condensed atoms contained within its orbit. We observe surprisingly long lifetimes and finite size effects caused by the electron exploring the outer regions of the condensate. We anticipate future experiments on electron orbital imaging, the investigation of phonon-mediated coupling of single electrons, and applications in quantum optics.
doi: 10.1038/nature12592
気候：ミシシッピ川流域に記録された薄いローレンタイド氷床南部の緩やかな消滅
Gradual demise of a thin southern Laurentide ice sheet recorded by Mississippi drainage p.668
At the Last Glacial Maximum (LGM), about 21,000 years before present, land-based ice sheets held enough water to reduce global mean sea level by 130 metres. Yet after decades of study, major uncertainties remain as to the distribution of that ice. Here we test four reconstructions of North American deglacial ice-sheet history by quantitatively connecting them to high-resolution oxygen isotope (δ18O) records from the Gulf of Mexico using a water mixing model. For each reconstruction, we route meltwater and seasonal runoff through the time-evolving Mississippi drainage basin, which co-evolves with ice geometry and changing topography as ice loads deform the solid Earth and produce spatially variable sea level in a process known as glacial isostatic adjustment. The δ18O records show that the Mississippi-drained southern Laurentide ice sheet contributed only 5.4 ± 2.1 metres to global sea level rise, of which 0.66 ± 0.07 metres were released during the meltwater pulse 1A event 14,650–14,310 years before present, far less water than previously thought. In contrast, the three reconstructions based on glacial isostatic adjustment overpredict the δ18O-based post-LGM meltwater volume by a factor of 1.6 to 3.6. The fourth reconstruction, which is based on ice physics, has a low enough Mississippi-routed meltwater discharge to be consistent with δ18O constraints, but also contains the largest LGM North American ice volume. This suggests that modelling based on ice physics may be the best way of matching isotopic records while also sequestering enough water in the North American ice sheets to match the observed LGM sea level fall.
doi: 10.1038/nature12609
地球：世界の乾燥地域の乾燥度の関数としての土壌栄養素循環の分離
Decoupling of soil nutrient cycles as a function of aridity in global drylands p.672
The biogeochemical cycles of carbon (C), nitrogen (N) and phosphorus (P) are interlinked by primary production, respiration and decomposition in terrestrial ecosystems. It has been suggested that the C, N and P cycles could become uncoupled under rapid climate change because of the different degrees of control exerted on the supply of these elements by biological and geochemical processes. Climatic controls on biogeochemical cycles are particularly relevant in arid, semi-arid and dry sub-humid ecosystems (drylands) because their biological activity is mainly driven by water availability. The increase in aridity predicted for the twenty-first century in many drylands worldwide may therefore threaten the balance between these cycles, differentially affecting the availability of essential nutrients. Here we evaluate how aridity affects the balance between C, N and P in soils collected from 224 dryland sites from all continents except Antarctica. We find a negative effect of aridity on the concentration of soil organic C and total N, but a positive effect on the concentration of inorganic P. Aridity is negatively related to plant cover, which may favour the dominance of physical processes such as rock weathering, a major source of P to ecosystems, over biological processes that provide more C and N, such as litter decomposition. Our findings suggest that any predicted increase in aridity with climate change will probably reduce the concentrations of N and C in global drylands, but increase that of P. These changes would uncouple the C, N and P cycles in drylands and could negatively affect the provision of key services provided by these ecosystems.
doi: 10.1038/nature12670
生態：サンゴ動物個体によるDMSP生合成と、それがサンゴの熱ストレス応答に果たす役割
DMSP biosynthesis by an animal and its role in coral thermal stress response p.677
Globally, reef-building corals are the most prolific producers of dimethylsulphoniopropionate (DMSP), a central molecule in the marine sulphur cycle and precursor of the climate-active gas dimethylsulphide. At present, DMSP production by corals is attributed entirely to their algal endosymbiont, Symbiodinium. Combining chemical, genomic and molecular approaches, we show that coral juveniles produce DMSP in the absence of algal symbionts. DMSP levels increased up to 54% over time in newly settled coral juveniles lacking algal endosymbionts, and further increases, up to 76%, were recorded when juveniles were subjected to thermal stress. We uncovered coral orthologues of two algal genes recently identified in DMSP biosynthesis, strongly indicating that corals possess the enzymatic machinery necessary for DMSP production. Our results overturn the paradigm that photosynthetic organisms are the sole biological source of DMSP, and highlight the double jeopardy represented by worldwide declining coral cover, as the potential to alleviate thermal stress through coral-produced DMSP declines correspondingly.
doi: 10.1038/nature12677
生化学：マグネトクロムが介在する磁鉄鉱生体鉱物化作用の構造的手がかり
Structural insight into magnetochrome-mediated magnetite biomineralization p.681
Magnetotactic bacteria align along the Earth’s magnetic field using an organelle called the magnetosome, a biomineralized magnetite (Fe(ii)Fe(iii)2O4) or greigite (Fe(ii)Fe(iii)2S4) crystal embedded in a lipid vesicle. Although the need for both iron(ii) and iron(iii) is clear, little is known about the biological mechanisms controlling their ratio. Here we present the structure of the magnetosome-associated protein MamP and find that it is built on a unique arrangement of a self-plugged PDZ domain fused to two magnetochrome domains, defining a new class of c-type cytochrome exclusively found in magnetotactic bacteria. Mutational analysis, enzyme kinetics, co-crystallization with iron(ii) and an in vitro MamP-assisted magnetite production assay establish MamP as an iron oxidase that contributes to the formation of iron(iii) ferrihydrite eventually required for magnetite crystal growth in vivo. These results demonstrate the molecular mechanisms of iron management taking place inside the magnetosome and highlight the role of magnetochrome in iron biomineralization.
doi: 10.1038/nature12573
生物物理：単一分子の蛍光を使って障壁通過の動態を調べる
Single-molecule fluorescence probes dynamics of barrier crossing p.685
Kramers developed the theory on how chemical reaction rates are influenced by the viscosity of the medium. At the viscosity of water, the kinetics of unimolecular reactions are described by diffusion of a Brownian particle over a free-energy barrier separating reactants and products. For reactions in solution this famous theory extended Eyring’s transition state theory, and is widely applied in physics, chemistry and biology, including to reactions as complex as protein folding. Because the diffusion coefficient of Kramers’ theory is determined by the dynamics in the sparsely populated region of the barrier top, its properties have not been directly measured for any molecular system. Here we show that the Kramers diffusion coefficient and free-energy barrier can be characterized by measuring the temperature- and viscosity-dependence of the transition path time for protein folding. The transition path is the small fraction of an equilibrium trajectory for a single molecule when the free-energy barrier separating two states is actually crossed. Its duration, the transition path time, can now be determined from photon trajectories for single protein molecules undergoing folding/unfolding transitions. Our finding of a long transition path time with an unusually small solvent viscosity dependence suggests that internal friction as well as solvent friction determine the Kramers diffusion coefficient for α-helical proteins, as opposed to a breakdown of his theory, which occurs for many small-molecule reactions. It is noteworthy that the new and fundamental information concerning Kramers’ theory and the dynamics of barrier crossings obtained here come from experiments on a protein rather than a much simpler chemical or physical system.
doi: 10.1038/nature12649
植物：シロイヌナズナの概日時計の光合成による同調
Photosynthetic entrainment of the Arabidopsis thaliana circadian clock p.689
Circadian clocks provide a competitive advantage in an environment that is heavily influenced by the rotation of the Earth, by driving daily rhythms in behaviour, physiology and metabolism in bacteria, fungi, plants and animals. Circadian clocks comprise transcription–translation feedback loops, which are entrained by environmental signals such as light and temperature to adjust the phase of rhythms to match the local environment. The production of sugars by photosynthesis is a key metabolic output of the circadian clock in plants. Here we show that these rhythmic, endogenous sugar signals can entrain circadian rhythms in Arabidopsis thaliana by regulating the gene expression of circadian clock components early in the photoperiod, thus defining a ‘metabolic dawn’. By inhibiting photosynthesis, we demonstrate that endogenous oscillations in sugar levels provide metabolic feedback to the circadian oscillator through the morning-expressed gene PSEUDO-RESPONSE REGULATOR 7 (PRR7), and we identify that prr7 mutants are insensitive to the effects of sucrose on the circadian period. Thus, photosynthesis has a marked effect on the entrainment and maintenance of robust circadian rhythms in A. thaliana, demonstrating that metabolism has a crucial role in regulation of the circadian clock.
doi: 10.1038/nature12603
代謝工学：人工的な非酸化的解糖は炭素の完全な保存を可能にする
Synthetic non-oxidative glycolysis enables complete carbon conservation p.693
Glycolysis, or its variations, is a fundamental metabolic pathway in life that functions in almost all organisms to decompose external or intracellular sugars. The pathway involves the partial oxidation and splitting of sugars to pyruvate, which in turn is decarboxylated to produce acetyl-coenzyme A (CoA) for various biosynthetic purposes. The decarboxylation of pyruvate loses a carbon equivalent, and limits the theoretical carbon yield to only two moles of two-carbon (C2) metabolites per mole of hexose. This native route is a major source of carbon loss in biorefining and microbial carbon metabolism. Here we design and construct a non-oxidative, cyclic pathway that allows the production of stoichiometric amounts of C2 metabolites from hexose, pentose and triose phosphates without carbon loss. We tested this pathway, termed non-oxidative glycolysis (NOG), in vitro and in vivo in Escherichia coli. NOG enables complete carbon conservation in sugar catabolism to acetyl-CoA, and can be used in conjunction with CO2 fixation and other one-carbon (C1) assimilation pathways to achieve a 100% carbon yield to desirable fuels and chemicals.
doi: 10.1038/nature12575
生化学：構造とゲノムの文脈を用いることによる新規な酵素と代謝経路の発見
Discovery of new enzymes and metabolic pathways by using structure and genome context p.698
Assigning valid functions to proteins identified in genome projects is challenging: overprediction and database annotation errors are the principal concerns. We and others are developing computation-guided strategies for functional discovery with ‘metabolite docking’ to experimentally derived or homology-based three-dimensional structures. Bacterial metabolic pathways often are encoded by ‘genome neighbourhoods’ (gene clusters and/or operons), which can provide important clues for functional assignment. We recently demonstrated the synergy of docking and pathway context by ‘predicting’ the intermediates in the glycolytic pathway in Escherichia coli. Metabolite docking to multiple binding proteins and enzymes in the same pathway increases the reliability of in silico predictions of substrate specificities because the pathway intermediates are structurally similar. Here we report that structure-guided approaches for predicting the substrate specificities of several enzymes encoded by a bacterial gene cluster allowed the correct prediction of the in vitro activity of a structurally characterized enzyme of unknown function (PDB 2PMQ), 2-epimerization of trans-4-hydroxy-l-proline betaine (tHyp-B) and cis-4-hydroxy-d-proline betaine (cHyp-B), and also the correct identification of the catabolic pathway in which Hyp-B 2-epimerase participates. The substrate-liganded pose predicted by virtual library screening (docking) was confirmed experimentally. The enzymatic activities in the predicted pathway were confirmed by in vitro assays and genetic analyses; the intermediates were identified by metabolomics; and repression of the genes encoding the pathway by high salt concentrations was established by transcriptomics, confirming the osmolyte role of tHyp-B. This study establishes the utility of structure-guided functional predictions to enable the discovery of new metabolic pathways.
doi: 10.1038/nature12576
分子生物学：減数分裂時の染色体構造は乗換え部位の指定を制約するとともにそれに反応する
Meiotic chromosome structures constrain and respond to designation of crossover sites p.703
Crossover recombination events between homologous chromosomes are required to form chiasmata, temporary connections between homologues that ensure their proper segregation at meiosis I. Despite this requirement for crossovers and an excess of the double-strand DNA breaks that are the initiating events for meiotic recombination, most organisms make very few crossovers per chromosome pair. Moreover, crossovers tend to inhibit the formation of other crossovers nearby on the same chromosome pair, a poorly understood phenomenon known as crossover interference. Here we show that the synaptonemal complex, a meiosis-specific structure that assembles between aligned homologous chromosomes, both constrains and is altered by crossover recombination events. Using a cytological marker of crossover sites in Caenorhabditis elegans, we show that partial depletion of the synaptonemal complex central region proteins attenuates crossover interference, increasing crossovers and reducing the effective distance over which interference operates, indicating that synaptonemal complex proteins limit crossovers. Moreover, we show that crossovers are associated with a local 0.4–0.5-micrometre increase in chromosome axis length. We propose that meiotic crossover regulation operates as a self-limiting system in which meiotic chromosome structures establish an environment that promotes crossover formation, which in turn alters chromosome structure to inhibit other crossovers at additional sites.
doi: 10.1038/nature12577
構造生物学：海洋性シアノバクテリア内部でのウイルス粒子組み立て中間体の画像化
Visualizing virus assembly intermediates inside marine cyanobacteria p.707
Cyanobacteria are photosynthetic organisms responsible for ∼25% of organic carbon fixation on the Earth. These bacteria began to convert solar energy and carbon dioxide into bioenergy and oxygen more than two billion years ago. Cyanophages, which infect these bacteria, have an important role in regulating the marine ecosystem by controlling cyanobacteria community organization and mediating lateral gene transfer. Here we visualize the maturation process of cyanophage Syn5 inside its host cell, Synechococcus, using Zernike phase contrast electron cryo-tomography (cryoET). This imaging modality yields dramatic enhancement of image contrast over conventional cryoET and thus facilitates the direct identification of subcellular components, including thylakoid membranes, carboxysomes and polyribosomes, as well as phages, inside the congested cytosol of the infected cell. By correlating the structural features and relative abundance of viral progeny within cells at different stages of infection, we identify distinct Syn5 assembly intermediates. Our results indicate that the procapsid releases scaffolding proteins and expands its volume at an early stage of genome packaging. Later in the assembly process, we detected full particles with a tail either with or without an additional horn. The morphogenetic pathway we describe here is highly conserved and was probably established long before that of double-stranded DNA viruses infecting more complex organisms.
doi: 10.1038/nature12604
