| | | Volume 507 Number 7492 | | | | nature | | The science that matters. Every week. | | | | | | | | | | |  | | | GAME OF CLONES: 20% off Monoclonal Projects
In 2014, Rockland Immunochemicals will be forming alliances with researchers, clients and customers, to highlight special products and promotions throughout the year. Each House represents a large range of Rockland's products, all designed with high-quality and ease-of-use in mind...Because research shouldn't feel like you're at a Red Wedding. | | | | | | | | Jump to the content that matters to you | | | | | | | | | | | | | | | A fully photonics-based coherent radar system | | The next generation of radar systems will need to be highly automated and use software-defined signal generation and detection for flexible operation in surveillance and wireless communications. Photonic radar, using lasers to generate and detect radiofrequency signals, might fit the bill. Until now photonics-based generation and detection of radio signals have generally been studied separately. But now Paolo Ghelfi et al. have combined the individual components to produce a functioning, complete photonic radar system. The system's effectiveness and precision are demonstrated in a field-trial involving the detection of passing aircraft. | | | | | | | | | | | | | Sulphide oxidation and carbonate dissolution as a source of CO2 over geological timescales | | It is thought that mountain uplift stimulated carbon dioxide consumption by silicate mineral weathering during the Cenozoic, roughly the past 66 million years, but there are no signs of a corresponding increase in volcanic carbon dioxide emissions that could balance the carbon budget. This paper suggests that some of the missing carbon dioxide could have been produced by coupled sulphide oxidation and carbonate dissolution, a process that may also have been accelerated in response to uplift. This hypothesis is consistent with isotopic records and may help explain the interactions between the long-term carbon cycle, tectonics, and Earth's climate. | | | | | | | | | | | | | The genomic landscape of Neanderthal ancestry in present-day humans | | The modern human genome contains tantalizing traces of Neanderthal ancestry. Sriram Sankararaman et al. show that Neanderthal genes are found at a high frequency in regions that affect skin and hair characteristics, which may have helped modern humans adapt to a chilly non-African environment. Yet some genetic regions are devoid of Neanderthal DNA, suggesting that certain genes were not tolerated and were swept away. The 'lost' genes include a number expressed in the testis and on the X chromosome, implying that Neanderthal DNA reduced fertility when expressed in a modern human genetic environment. | | | | | | | | | | | |  | | | Speed. Resolution. Clarity. Accuracy. The Hamamatsu NanoZoomer Series delivers all of this and more. The ultimate digital whole-slide scanner and virtual microscopy tool, the NanoZoomer delivers reliable, robust scanning 24/7/365. Features include high sensitivity, fast scanning, flexible fluorescence capabilities, and a Z-stack feature to accommodate thicker tissue samples. | | | | | | | | | | | | | | | | | In this week's podcast: how a mother's vitamin A deficiency impacts her baby's immunity, why scientists are taking acting classes, a new brain implant that listens as well as talks to the brain, and what happened at the beginning of the Universe. In our latest video feature, scientists from the Centre for Astrophysics have found evidence of gravitational waves created mere moments after the dawn of the Universe. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | What lies beneath ▶ | | | | A focus on specific biological targets rather than constellations of symptoms heralds a more scientific approach to the treatment of neuropsychiatric disorders. | | | | | | | | | | | | How to get ahead ▶ | | | | The success of the $1,000 genome programme offers lessons for fostering innovation. | | | | | | | | | | | | Past wisdom ▶ | | | | The recent Nature PastCast series is instructive as well as entertaining. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Neuroscience: Tuning the brain ▶ | | | | Deep brain stimulation has shown promise in treating conditions such as Parkinson's disease. Now scientists are using the technology to eavesdrop on problem neural circuits. | | | | | | | | | | | | Technology: The $1,000 genome ▶ | | | | With a unique programme, the US government has managed to drive the cost of genome sequencing down towards a much-anticipated target. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |  | | | A special, fully-funded event exclusively for early-career plant scientists. Free registration includes: access to talks and sessions, meals, and accommodation. Poster session, high-profile speakers, social events. Limited places available - apply early to avoid disappointment. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Diversity and dynamics of the Drosophila transcriptome OPEN ▶ | | | | James B. Brown, Nathan Boley, Robert Eisman et al. | | | | A large-scale transcriptome analysis in Drosophila melanogaster, across tissues, cell types and conditions, provides insights into global patterns and diversity of transcription initiation, splicing, polyadenylation and non-coding RNA expression. | | | | | | | | | | | | REST and stress resistance in ageing and Alzheimer’s disease ▶ | | | | Tao Lu, Liviu Aron, Joseph Zullo et al. | | | | REST, a developmental regulator, is markedly induced in human neurons during ageing but is lost in Alzheimer’s disease; REST represses genes that promote neurodegeneration, is neuroprotective in animal models, and is associated with cognitive preservation and longevity in humans. | | | | | | | | | | | | Structural basis for translocation by AddAB helicase–nuclease and its arrest at χ sites ▶ | | | | Wojciech W. Krajewski, Xin Fu, Martin Wilkinson et al. | | | | A dual-function helicase–nuclease, typified by RecBCD in Escherichia coli, acts on free DNA ends during bacterial double-stranded break repair until it reaches a χ sequence at which it pauses before continuing with modified enzymatic properties; here several crystal structures of the related AddAB enzyme from Bacillus subtilis bound to χ-containing DNA are presented, offering insight into χ recognition and its effect on DNA translocation. | | | | | | | | | | | | miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis ▶ | | | | Kate M. Creasey, Jixian Zhai, Filipe Borges et al. | | | | The generation of widespread epigenetically activated short interfering RNAs by the targeting of microRNAs to transposon transcripts in Arabidopsis thaliana is shown to be a latent mechanism that only becomes active when the transcripts are epigenetically reactivated, for example, during reprogramming of the germ line. | | | | | | | | | | | | Nectar secretion requires sucrose phosphate synthases and the sugar transporter SWEET9 ▶ | | | | I Winnie Lin, Davide Sosso, Li-Qing Chen et al. | | | | Although nectar is known to be important, for example in plant–insect interactions, little has been known about the mechanism of its secretion; sucrose phosphate synthases are now reported to be essential for the synthesis of the sucrose component of nectar and the transporter protein SWEET9 is shown to mediate sucrose export into the extracellular space of the nectary. | | | | | | | | | | | | Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant ▶ | | | | Nicholas D. Bonawitz, Jeong Im Kim, Yuki Tobimatsu et al. | | | | Disruption of lignin biosynthesis has been proposed as a way to improve forage and bioenergy crops, but it can result in stunted growth and developmental abnormalities; here, the undesirable features of one such manipulation are shown to depend on the transcriptional co-regulatory complex Mediator. | | | | | | | | | | | | Metabolic determinants of cancer cell sensitivity to glucose limitation and biguanides ▶ | | | | Kıvanç Birsoy, Richard Possemato, Franziska K. Lorbeer et al. | | | | New apparatus is used to maintain proliferating cancer cells in low-glucose conditions, demonstrating that mitochondrial oxidative phosphorylation (OXPHOS) is essential for optimal proliferation in these conditions; the most sensitive cell lines are defective in OXPHOS upregulation and may therefore be sensitive to current antidiabetic drugs that inhibit OXPHOS. | | | | | | | | | | | | Reconciliation of the carbon budget in the ocean’s twilight zone ▶ | | | | Sarah L. C. Giering, Richard Sanders, Richard S. Lampitt et al. | | | | The discrepancy between the components of the oceanic carbon budget — export of carbon from the surface and its conversion into carbon dioxide by water-column biota at depth — is reconciled using field data and a steady-state model which indicates that synergy between microbes and zooplankton is an important factor. | | | | | | | | | | | | Identification of genomic alterations in oesophageal squamous cell cancer ▶ | | | | Yongmei Song, Lin Li, Yunwei Ou et al. | | | | Using whole-genome and whole-exome sequencing, this study identifies eight significantly mutated genes in oesophageal squamous cell cancer, including two genes, ADAM29 and FAM135B, not previously associated with this cancer type. | | | | | | Methane fluxes show consistent temperature dependence across microbial to ecosystem scales ▶ | | | | Gabriel Yvon-Durocher, Andrew P. Allen, David Bastviken et al. | | | | This study shows that the emission of CH4 and the ratio of CH4 to CO2 emissions increase markedly with seasonal increases in temperature. Global warming may have a large impact on the relative contributions of CO2 and CH4 to total greenhouse gas emissions from aquatic ecosystems, terrestrial wetlands and rice paddies. | | | | | | Maternal retinoids control type 3 innate lymphoid cells and set the offspring immunity ▶ | | | | Serge A. van de Pavert, Manuela Ferreira, Rita G. Domingues et al. | | | | Maternal levels of dietary retinoids control the size of secondary lymphoid organs and the efficiency of immune responses in the adult offspring. This study reveals a molecular link between maternal nutrients and the formation of immune structures required for resistance to infection in the offspring. | | | | | | | | | | | | | | | | Comprehensive molecular characterization of urothelial bladder carcinoma OPEN ▶ | | | | This paper reports integrative molecular analyses of urothelial bladder carcinoma at the DNA, RNA, and protein levels performed as part of The Cancer Genome Atlas project; recurrent mutations were found in 32 genes, including those involved in cell-cycle regulation, chromatin regulation and kinase signalling pathways; chromatin regulatory genes were more frequently mutated in urothelial carcinoma than in any other common cancer studied so far. | | | | | | Coupling of angiogenesis and osteogenesis by a specific vessel subtype in bone ▶ | | | | Anjali P. Kusumbe, Saravana K. Ramasamy & Ralf H. Adams | | | | Bone homeostasis and repair declines with ageing and the mechanisms regulating the relationship between bone growth and blood vessel formation have remained unknown; this mouse study identifies the endothelial cells that promote the formation of new bone, a small microvessel subtype that can be identified by high CD31 and high Emcn expression. | | | | | | Unexpected link between an antibiotic, pannexin channels and apoptosis ▶ | | | | Ivan K. H. Poon, Yu-Hsin Chiu, Allison J. Armstrong et al. | | | | The pannexin 1 channel on the plasma membrane of apoptotic cells mediates the release of find-me molecular signals to attract phagocytic cells for clearance of the apoptotic cells; here the quinolone antibiotic trovafloxacin is identified as a direct inhibitor of pannexin 1, which results in dysregulated fragmentation of apoptotic cells and may partly explain quinolone toxicity. | | | | | | | | | | | | Melanosome evolution indicates a key physiological shift within feathered dinosaurs ▶ | | | | Quanguo Li, Julia A. Clarke, Ke-Qin Gao et al. | | | | Sampling of extant and fossil amniotes reveals that the diversity of melanosome morphologies increased sharply around the time of the origin of pinnate feathers in maniraptoran dinosaurs (the lineage leading to birds) and independently in mammals; lizard, turtle and crocodilian skin as well as archosaur filamentous body covering shows a limited diversity of melanosome forms, a pattern consistent with convergent changes in the melanocortin system of endothermic animals. | | | | | | | | | | | | The genomic landscape of Neanderthal ancestry in present-day humans ▶ | | | | Sriram Sankararaman, Swapan Mallick, Michael Dannemann et al. | | | | In the modern human genome, elevated Neanderthal ancestry is found at genes affecting keratin filaments, suggesting that gene flow with Neanderthals helped modern humans to adapt to non-African environments; deficiencies of Neanderthal ancestry are also found, particularly on the X chromosome and in genes expressed highly in testes, suggesting that some Neanderthal mutations were not tolerated on a modern human genetic background as they reduced male fertility. | | | | | | | | | | | | | | | | | | | | | | | | Obesity-associated variants within FTO form long-range functional connections with IRX3 ▶ | | | | Scott Smemo, Juan J. Tena, Kyoung-Han Kim et al. | | | | Obesity-associated noncoding sequences within FTO are functionally connected with IRX3, and long-range enhancers in this region recapitulate aspects of IRX3 expression, suggesting that the obesity-associated interval is part of IRX3 regulation; Irx3-deficient mice have lower body weight and are resistant to diet-induced obesity, suggesting IRX3 as a novel determinant of body mass and composition. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Download the new NatureJournals app and gain access to Nature and all Nature-branded research and review journals. All news content and open access articles are free. Subscribe to additional journals in the app for just $35.99*. *Apple exchange rates apply. Limited time offer available on all journals except Scientific Reports. iPad, iPhone and iPod touch are trademarks of Apple Inc. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Metabolic determinants of cancer cell sensitivity to glucose limitation and biguanides ▶ | | | | Kıvanç Birsoy, Richard Possemato, Franziska K. Lorbeer et al. | | | | New apparatus is used to maintain proliferating cancer cells in low-glucose conditions, demonstrating that mitochondrial oxidative phosphorylation (OXPHOS) is essential for optimal proliferation in these conditions; the most sensitive cell lines are defective in OXPHOS upregulation and may therefore be sensitive to current antidiabetic drugs that inhibit OXPHOS. | | | | | | | | | | | | | | | | | | | | Comprehensive molecular characterization of urothelial bladder carcinoma OPEN ▶ | | | | This paper reports integrative molecular analyses of urothelial bladder carcinoma at the DNA, RNA, and protein levels performed as part of The Cancer Genome Atlas project; recurrent mutations were found in 32 genes, including those involved in cell-cycle regulation, chromatin regulation and kinase signalling pathways; chromatin regulatory genes were more frequently mutated in urothelial carcinoma than in any other common cancer studied so far. | | | | | | | | | | | | Obesity-associated variants within FTO form long-range functional connections with IRX3 ▶ | | | | Scott Smemo, Juan J. Tena, Kyoung-Han Kim et al. | | | | Obesity-associated noncoding sequences within FTO are functionally connected with IRX3, and long-range enhancers in this region recapitulate aspects of IRX3 expression, suggesting that the obesity-associated interval is part of IRX3 regulation; Irx3-deficient mice have lower body weight and are resistant to diet-induced obesity, suggesting IRX3 as a novel determinant of body mass and composition. | | | | | | Coupling of angiogenesis and osteogenesis by a specific vessel subtype in bone ▶ | | | | Anjali P. Kusumbe, Saravana K. Ramasamy & Ralf H. Adams | | | | Bone homeostasis and repair declines with ageing and the mechanisms regulating the relationship between bone growth and blood vessel formation have remained unknown; this mouse study identifies the endothelial cells that promote the formation of new bone, a small microvessel subtype that can be identified by high CD31 and high Emcn expression. | | | | | | Unexpected link between an antibiotic, pannexin channels and apoptosis ▶ | | | | Ivan K. H. Poon, Yu-Hsin Chiu, Allison J. Armstrong et al. | | | | The pannexin 1 channel on the plasma membrane of apoptotic cells mediates the release of find-me molecular signals to attract phagocytic cells for clearance of the apoptotic cells; here the quinolone antibiotic trovafloxacin is identified as a direct inhibitor of pannexin 1, which results in dysregulated fragmentation of apoptotic cells and may partly explain quinolone toxicity. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Coherent control of the waveforms of recoilless γ-ray photons ▶ | | | | Farit Vagizov, Vladimir Antonov, Y. V. Radeonychev et al. | | | | The resonant interaction between γ-ray photons and an ensemble of nuclei with a periodically modulated resonant transition frequency can be used to control the waveforms of the photons coherently; for example, individual γ-ray photons can be converted into a coherent, ultrashort pulse train or into a double pulse. | | | | | | | | | | | | | | | | The remnant of a merger between two dwarf galaxies in Andromeda II ▶ | | | | N. C. Amorisco, N. W. Evans, G. van de Ven | | | | At the lowest galactic mass scales, evidence of a merger between two galaxies is provided by the kinematic detection of a stellar stream — indicative of an accretion event — in the dwarf spheroidal galaxy Andromeda II, one of the satellite galaxies of Andromeda. | | | | | | | | | | | | Rotationally driven ‘zebra stripes’ in Earth’s inner radiation belt ▶ | | | | A. Y. Ukhorskiy, M. I. Sitnov, D. G. Mitchell et al. | | | | The distributions of energetic electrons across the entire spatial extent of Earth’s inner radiation belt are found to be organized in regular, highly structured and unexpected ‘zebra stripes’, produced by Earth’s rotation. | | | | | | | | | | | | A fully photonics-based coherent radar system ▶ | | | | Paolo Ghelfi, Francesco Laghezza, Filippo Scotti et al. | | | | The next generation of radar systems must be photonic to obtain frequency flexibility and improved performance; here both generation and detection of radio signals are demonstrated in a successful field trial of a photonic-based radar system using aeroplanes. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Reconciliation of the carbon budget in the ocean’s twilight zone ▶ | | | | Sarah L. C. Giering, Richard Sanders, Richard S. Lampitt et al. | | | | The discrepancy between the components of the oceanic carbon budget — export of carbon from the surface and its conversion into carbon dioxide by water-column biota at depth — is reconciled using field data and a steady-state model which indicates that synergy between microbes and zooplankton is an important factor. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Nature Clinical Collection on Hepatocellular carcinoma (HCC)
This Clinical Collection covers key aspects of the pathogenesis and treatment of HCC, including insights into disease pathways and possible future therapeutic targets. This activity is supported by an educational grant from Lilly. | | | | | | | | | | | | | | | | | | | | | | | | Retractions: A clean slate ▶ | | | | Mistakes are part of science. But setting the record straight promptly and clearly can help to avoid a career blot. | | | | | | | | | | | | | | | | Strapped students ▶ | | | | Graduate students face myriad financial challenges — some more obvious than others, says Susie Crowe. | | | | | | | | | | | | Careers related news & comment | | | | | | | | | | | | | | | | | | | | | | 
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