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Agribiotechnology: Blue-sky rice

Nature - Wed, 10/29/2014 - 00:00

Agribiotechnology: Blue-sky rice

Nature. doi:10.1038/514S52a

Author: Leigh Dayton

Rice is a staple food, but production is not keeping pace with the rise in global population. So scientists are dreaming big and aiming high to change the future for this crucial grain.

Categories: Literature

Biotechnology: Against the grain

Nature - Wed, 10/29/2014 - 00:00

Biotechnology: Against the grain

Nature. doi:10.1038/514S55a

Author: Michael Eisenstein

Golden rice could help to end a nutritional crisis — but only if researchers can overcome some daunting technical and political hurdles.

Categories: Literature

Domestication: The birth of rice

Nature - Wed, 10/29/2014 - 00:00

Domestication: The birth of rice

Nature. doi:10.1038/514S58a

Author: Ewen Callaway

From a wild Asian grass to a refined crop that is the staple diet of half the world's population, the domestication of Oryza sativa spans centuries, but the grain's ancestry is hotly contested.

Categories: Literature

Yield: The search for the rice of the future

Nature - Wed, 10/29/2014 - 00:00

Yield: The search for the rice of the future

Nature. doi:10.1038/514S60a

Author: Felix Cheung

Scientists are hoping to make the world's most successful crop even better.

Categories: Literature

Contamination: The toxic side of rice

Nature - Wed, 10/29/2014 - 00:00

Contamination: The toxic side of rice

Nature. doi:10.1038/514S62a

Author: Emily Sohn

Around the world, researchers are looking for ways to rid rice of a troublesome companion.

Categories: Literature

Agriculture: The next frontier

Nature - Wed, 10/29/2014 - 00:00

Agriculture: The next frontier

Nature. doi:10.1038/514S64a

Author: Karen Ravn

Africa's newfound taste for an old grain has experienced problems — drought, low yields and costly imports. But new projects are driving the continent towards self-sufficiency.

Categories: Literature

Perspective: Time to unleash rice

Nature - Wed, 10/29/2014 - 00:00

Perspective: Time to unleash rice

Nature. doi:10.1038/514S66a

Author: Robert Zeigler

Corporate inefficiency and government meddling are curbing production of the vital crop in the countries that need it most, says Robert Zeigler.

Categories: Literature

Correction

Nature - Wed, 10/29/2014 - 00:00

Correction

Nature 514, 7524 (2014). http://www.nature.com/doifinder/10.1038/514548b

The News Feature ‘The ethics squad’ (Nature514, 418–420; 2014) misspelled Susan Kornetsky’s name.

Categories: Literature

Evolutionary developmental biology: Ghost locus appears

Nature - Wed, 10/29/2014 - 00:00

Evolutionary developmental biology: Ghost locus appears

Nature 514, 7524 (2014). doi:10.1038/514570a

Authors: James O. McInerney & Mary J. O'Connell

The sequences of two sponge genomes provide evidence that the ParaHox developmental genes are older than previously thought. This has implications for animal taxonomy and for developmental and evolutionary biology. See Letter p.620

Categories: Literature

Structural biology: Enzyme–chromatin complex visualized

Nature - Wed, 10/29/2014 - 00:00

Structural biology: Enzyme–chromatin complex visualized

Nature 514, 7524 (2014). doi:10.1038/514572a

Authors: Jürg Müller & Christoph W. Müller

The structure of an enzyme that is bound to a nucleosome — a protein complex around which DNA is wrapped — reveals how contacts between the two orient the enzyme so that it can modify a specific amino-acid residue. See Article p.591

Categories: Literature

Materials science: Radicals promote magnetic gel assembly

Nature - Wed, 10/29/2014 - 00:00

Materials science: Radicals promote magnetic gel assembly

Nature 514, 7524 (2014). doi:10.1038/514574a

Authors: Christopher B. Rodell & Jason A. Burdick

Engineering complex tissues requires high-throughput, three-dimensional patterning of materials and cells. A method to assemble small gel components using magnetic forces from encapsulated free radicals could be just the ticket.

Categories: Literature

Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome

Nature - Wed, 10/29/2014 - 00:00

Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome

Nature 514, 7524 (2014). doi:10.1038/nature13890

Authors: Robert K. McGinty, Ryan C. Henrici & Song Tan

The Polycomb group of epigenetic enzymes represses expression of developmentally regulated genes in many eukaryotes. This group includes the Polycomb repressive complex 1 (PRC1), which ubiquitylates nucleosomal histone H2A Lys 119 using its E3 ubiquitin ligase subunits, Ring1B and Bmi1, together with an E2 ubiquitin-conjugating enzyme,

Categories: Literature

Possible planet formation in the young, low-mass, multiple stellar system GG Tau A

Nature - Wed, 10/29/2014 - 00:00

Possible planet formation in the young, low-mass, multiple stellar system GG Tau A

Nature 514, 7524 (2014). doi:10.1038/nature13822

Authors: Anne Dutrey, Emmanuel Di Folco, Stéphane Guilloteau, Yann Boehler, Jeff Bary, Tracy Beck, Hervé Beust, Edwige Chapillon, Fredéric Gueth, Jean-Marc Huré, Arnaud Pierens, Vincent Piétu, Michal Simon & Ya-Wen Tang

The formation of planets around binary stars may be more difficult than around single stars. In a close binary star (with a separation of less than a hundred astronomical units), theory predicts the presence of circumstellar disks around each star, and an outer circumbinary disk surrounding a gravitationally cleared inner cavity around the stars. Given that the inner disks are depleted by accretion onto the stars on timescales of a few thousand years, any replenishing material must be transferred from the outer reservoir to fuel planet formation (which occurs on timescales of about one million years). Gas flowing through disk cavities has been detected in single star systems. A circumbinary disk was discovered around the young low-mass binary system GG Tau A (ref. 7), which has recently been shown to be a hierarchical triple system. It has one large inner disk around the single star, GG Tau Aa, and shows small amounts of shocked hydrogen gas residing within the central cavity, but other than a single weak detection, the distribution of cold gas in this cavity or in any other binary or multiple star system has not hitherto been determined. Here we report imaging of gas fragments emitting radiation characteristic of carbon monoxide within the GG Tau A cavity. From the kinematics we conclude that the flow appears capable of sustaining the inner disk (around GG Tau Aa) beyond the accretion lifetime, leaving time for planet formation to occur there. These results show the complexity of planet formation around multiple stars and confirm the general picture predicted by numerical simulations.

Categories: Literature

Possible planet formation in the young, low-mass, multiple stellar system GG Tau A

Nature - Wed, 10/29/2014 - 00:00

Possible planet formation in the young, low-mass, multiple stellar system GG Tau A

Nature 514, 7524 (2014). doi:10.1038/nature13822

Authors: Anne Dutrey, Emmanuel Di Folco, Stéphane Guilloteau, Yann Boehler, Jeff Bary, Tracy Beck, Hervé Beust, Edwige Chapillon, Fredéric Gueth, Jean-Marc Huré, Arnaud Pierens, Vincent Piétu, Michal Simon & Ya-Wen Tang

The formation of planets around binary stars may be more difficult than around single stars. In a close binary star (with a separation of less than a hundred astronomical units), theory predicts the presence of circumstellar disks around each star, and an outer circumbinary disk surrounding a gravitationally cleared inner cavity around the stars. Given that the inner disks are depleted by accretion onto the stars on timescales of a few thousand years, any replenishing material must be transferred from the outer reservoir to fuel planet formation (which occurs on timescales of about one million years). Gas flowing through disk cavities has been detected in single star systems. A circumbinary disk was discovered around the young low-mass binary system GG Tau A (ref. 7), which has recently been shown to be a hierarchical triple system. It has one large inner disk around the single star, GG Tau Aa, and shows small amounts of shocked hydrogen gas residing within the central cavity, but other than a single weak detection, the distribution of cold gas in this cavity or in any other binary or multiple star system has not hitherto been determined. Here we report imaging of gas fragments emitting radiation characteristic of carbon monoxide within the GG Tau A cavity. From the kinematics we conclude that the flow appears capable of sustaining the inner disk (around GG Tau Aa) beyond the accretion lifetime, leaving time for planet formation to occur there. These results show the complexity of planet formation around multiple stars and confirm the general picture predicted by numerical simulations.

Categories: Literature

Quantum tomography of an electron

Nature - Wed, 10/29/2014 - 00:00

Quantum tomography of an electron

Nature 514, 7524 (2014). doi:10.1038/nature13821

Authors: T. Jullien, P. Roulleau, B. Roche, A. Cavanna, Y. Jin & D. C. Glattli

The complete knowledge of a quantum state allows the prediction of the probability of all possible measurement outcomes, a crucial step in quantum mechanics. It can be provided by tomographic methods which have been applied to atomic, molecular, spin and photonic states. For optical or microwave photons, standard tomography is obtained by mixing the unknown state with a large-amplitude coherent photon field. However, for fermions such as electrons in condensed matter, this approach is not applicable because fermionic fields are limited to small amplitudes (at most one particle per state), and so far no determination of an electron wavefunction has been made. Recent proposals involving quantum conductors suggest that the wavefunction can be obtained by measuring the time-dependent current of electronic wave interferometers or the current noise of electronic Hanbury-Brown/Twiss interferometers. Here we show that such measurements are possible despite the extreme noise sensitivity required, and present the reconstructed wavefunction quasi-probability, or Wigner distribution function, of single electrons injected into a ballistic conductor. Many identical electrons are prepared in well-controlled quantum states called levitons by repeatedly applying Lorentzian voltage pulses to a contact on the conductor. After passing through an electron beam splitter, the levitons are mixed with a weak-amplitude fermionic field formed by a coherent superposition of electron–hole pairs generated by a small alternating current with a frequency that is a multiple of the voltage pulse frequency. Antibunching of the electrons and holes with the levitons at the beam splitter changes the leviton partition statistics, and the noise variations provide the energy density matrix elements of the levitons. This demonstration of quantum tomography makes the developing field of electron quantum optics with ballistic conductors a new test-bed for quantum information with fermions. These results may find direct application in probing the entanglement of electron flying quantum bits, electron decoherence and electron interactions. They could also be applied to cold fermionic (or spin-1/2) atoms.

Categories: Literature

Room-temperature magnetic order on zigzag edges of narrow graphene nanoribbons

Nature - Wed, 10/29/2014 - 00:00

Room-temperature magnetic order on zigzag edges of narrow graphene nanoribbons

Nature 514, 7524 (2014). doi:10.1038/nature13831

Authors: Gábor Zsolt Magda, Xiaozhan Jin, Imre Hagymási, Péter Vancsó, Zoltán Osváth, Péter Nemes-Incze, Chanyong Hwang, László P. Biró & Levente Tapasztó

The possibility that non-magnetic materials such as carbon could exhibit a novel type of s–p electron magnetism has attracted much attention over the years, not least because such magnetic order is predicted to be stable at high temperatures. It has been demonstrated that atomic-scale structural defects of graphene can host unpaired spins, but it remains unclear under what conditions long-range magnetic order can emerge from such defect-bound magnetic moments. Here we propose that, in contrast to random defect distributions, atomic-scale engineering of graphene edges with specific crystallographic orientation—comprising edge atoms from only one sub-lattice of the bipartite graphene lattice—can give rise to a robust magnetic order. We use a nanofabrication technique based on scanning tunnelling microscopy to define graphene nanoribbons with nanometre precision and well-defined crystallographic edge orientations. Although so-called ‘armchair’ ribbons display quantum confinement gaps, ribbons with the ‘zigzag’ edge structure that are narrower than 7 nanometres exhibit an electronic bandgap of about 0.2–0.3 electronvolts, which can be identified as a signature of interaction-induced spin ordering along their edges. Moreover, upon increasing the ribbon width, a semiconductor-to-metal transition is revealed, indicating the switching of the magnetic coupling between opposite ribbon edges from the antiferromagnetic to the ferromagnetic configuration. We found that the magnetic order on graphene edges of controlled zigzag orientation can be stable even at room temperature, raising hopes of graphene-based spintronic devices operating under ambient conditions.

Categories: Literature

Stochastic transport through carbon nanotubes in lipid bilayers and live cell membranes

Nature - Wed, 10/29/2014 - 00:00

Stochastic transport through carbon nanotubes in lipid bilayers and live cell membranes

Nature 514, 7524 (2014). doi:10.1038/nature13817

Authors: Jia Geng, Kyunghoon Kim, Jianfei Zhang, Artur Escalada, Ramya Tunuguntla, Luis R. Comolli, Frances I. Allen, Anna V. Shnyrova, Kang Rae Cho, Dayannara Munoz, Y. Morris Wang, Costas P. Grigoropoulos, Caroline M. Ajo-Franklin, Vadim A. Frolov & Aleksandr Noy

There is much interest in developing synthetic analogues of biological membrane channels with high efficiency and exquisite selectivity for transporting ions and molecules. Bottom-up and top-down methods can produce nanopores of a size comparable to that of endogenous protein channels, but replicating their affinity and transport properties remains challenging. In principle, carbon nanotubes (CNTs) should be an ideal membrane channel platform: they exhibit excellent transport properties and their narrow hydrophobic inner pores mimic structural motifs typical of biological channels. Moreover, simulations predict that CNTs with a length comparable to the thickness of a lipid bilayer membrane can self-insert into the membrane. Functionalized CNTs have indeed been found to penetrate lipid membranes and cell walls, and short tubes have been forced into membranes to create sensors, yet membrane transport applications of short CNTs remain underexplored. Here we show that short CNTs spontaneously insert into lipid bilayers and live cell membranes to form channels that exhibit a unitary conductance of 70–100 picosiemens under physiological conditions. Despite their structural simplicity, these ‘CNT porins’ transport water, protons, small ions and DNA, stochastically switch between metastable conductance substates, and display characteristic macromolecule-induced ionic current blockades. We also show that local channel and membrane charges can control the conductance and ion selectivity of the CNT porins, thereby establishing these nanopores as a promising biomimetic platform for developing cell interfaces, studying transport in biological channels, and creating stochastic sensors.

Categories: Literature

Stochastic transport through carbon nanotubes in lipid bilayers and live cell membranes

Nature - Wed, 10/29/2014 - 00:00

Stochastic transport through carbon nanotubes in lipid bilayers and live cell membranes

Nature 514, 7524 (2014). doi:10.1038/nature13817

Authors: Jia Geng, Kyunghoon Kim, Jianfei Zhang, Artur Escalada, Ramya Tunuguntla, Luis R. Comolli, Frances I. Allen, Anna V. Shnyrova, Kang Rae Cho, Dayannara Munoz, Y. Morris Wang, Costas P. Grigoropoulos, Caroline M. Ajo-Franklin, Vadim A. Frolov & Aleksandr Noy

There is much interest in developing synthetic analogues of biological membrane channels with high efficiency and exquisite selectivity for transporting ions and molecules. Bottom-up and top-down methods can produce nanopores of a size comparable to that of endogenous protein channels, but replicating their affinity and transport properties remains challenging. In principle, carbon nanotubes (CNTs) should be an ideal membrane channel platform: they exhibit excellent transport properties and their narrow hydrophobic inner pores mimic structural motifs typical of biological channels. Moreover, simulations predict that CNTs with a length comparable to the thickness of a lipid bilayer membrane can self-insert into the membrane. Functionalized CNTs have indeed been found to penetrate lipid membranes and cell walls, and short tubes have been forced into membranes to create sensors, yet membrane transport applications of short CNTs remain underexplored. Here we show that short CNTs spontaneously insert into lipid bilayers and live cell membranes to form channels that exhibit a unitary conductance of 70–100 picosiemens under physiological conditions. Despite their structural simplicity, these ‘CNT porins’ transport water, protons, small ions and DNA, stochastically switch between metastable conductance substates, and display characteristic macromolecule-induced ionic current blockades. We also show that local channel and membrane charges can control the conductance and ion selectivity of the CNT porins, thereby establishing these nanopores as a promising biomimetic platform for developing cell interfaces, studying transport in biological channels, and creating stochastic sensors.

Categories: Literature

Centennial-scale changes in the global carbon cycle during the last deglaciation

Nature - Wed, 10/29/2014 - 00:00

Centennial-scale changes in the global carbon cycle during the last deglaciation

Nature 514, 7524 (2014). doi:10.1038/nature13799

Authors: Shaun A. Marcott, Thomas K. Bauska, Christo Buizert, Eric J. Steig, Julia L. Rosen, Kurt M. Cuffey, T. J. Fudge, Jeffery P. Severinghaus, Jinho Ahn, Michael L. Kalk, Joseph R. McConnell, Todd Sowers, Kendrick C. Taylor, James W. C. White & Edward J. Brook

Global climate and the concentration of atmospheric carbon dioxide (CO2) are correlated over recent glacial cycles. The combination of processes responsible for a rise in atmospheric CO2 at the last glacial termination (23,000 to 9,000 years ago), however, remains uncertain. Establishing the timing and rate of CO2 changes in the past provides critical insight into the mechanisms that influence the carbon cycle and helps put present and future anthropogenic emissions in context. Here we present CO2 and methane (CH4) records of the last deglaciation from a new high-accumulation West Antarctic ice core with unprecedented temporal resolution and precise chronology. We show that although low-frequency CO2 variations parallel changes in Antarctic temperature, abrupt CO2 changes occur that have a clear relationship with abrupt climate changes in the Northern Hemisphere. A significant proportion of the direct radiative forcing associated with the rise in atmospheric CO2 occurred in three sudden steps, each of 10 to 15 parts per million. Every step took place in less than two centuries and was followed by no notable change in atmospheric CO2 for about 1,000 to 1,500 years. Slow, millennial-scale ventilation of Southern Ocean CO2-rich, deep-ocean water masses is thought to have been fundamental to the rise in atmospheric CO2 associated with the glacial termination, given the strong covariance of CO2 levels and Antarctic temperatures. Our data establish a contribution from an abrupt, centennial-scale mode of CO2 variability that is not directly related to Antarctic temperature. We suggest that processes operating on centennial timescales, probably involving the Atlantic meridional overturning circulation, seem to be influencing global carbon-cycle dynamics and are at present not widely considered in Earth system models.

Categories: Literature

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

Nature - Wed, 10/29/2014 - 00:00

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

Nature 514, 7524 (2014). doi:10.1038/nature13881

Authors: Sofia A. V. Fortunato, Marcin Adamski, Olivia Mendivil Ramos, Sven Leininger, Jing Liu, David E. K. Ferrier & Maja Adamska

Sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors, including homeobox genes belonging to the Antennapedia (ANTP) class, which in bilaterians encompass Hox, ParaHox and NK genes. In the genome of the demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians. It has been proposed that Hox and ParaHox genes originated from NK cluster genes after divergence of sponges from the lineage leading to cnidarians and bilaterians. On the other hand, synteny analysis lends support to the notion that the absence of Hox and ParaHox genes in Amphimedon is a result of secondary loss (the ghost locus hypothesis). Here we analysed complete suites of ANTP-class homeoboxes in two calcareous sponges, Sycon ciliatum and Leucosolenia complicata. Our phylogenetic analyses demonstrate that these calcisponges possess orthologues of bilaterian NK genes (Hex, Hmx and Msx), a varying number of additional NK genes and one ParaHox gene, Cdx. Despite the generation of scaffolds spanning multiple genes, we find no evidence of clustering of Sycon NK genes. All Sycon ANTP-class genes are developmentally expressed, with patterns suggesting their involvement in cell type specification in embryos and adults, metamorphosis and body plan patterning. These results demonstrate that ParaHox genes predate the origin of sponges, thus confirming the ghost locus hypothesis, and highlight the need to analyse the genomes of multiple sponge lineages to obtain a complete picture of the ancestral composition of the first animal genome.

Categories: Literature

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