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Volume 463 Issue 7279, 21 January 2010

The genome sequence of the giant panda (of the female Beijing Olympics mascot Jingjing in fact) has been determined using short-read sequencing technology, an achievement that should pave the way for the use of next-generation sequencing for de novo assembly of large eukaryotic genomes. The sequence reveals considerable genomic diversity and a full set of the genes needed for a carnivorous digestion. Yet there are no digestive cellulase genes, so the panda appears to depend on its gut microbes to handle its bamboo diet. Photo by Jianjun Wen, Chengdu Panda Base, November 2009.

Authors

Editorial

  • Editorial |

    With climate-change sceptics waiting to pounce on any scientific uncertainties, researchers need a sophisticated strategy for communication.

  • Editorial |

    Contributions to and from basic science are the part of synthetic biology that most deserves celebration.

  • Editorial |

    The autocratic actions of an institute's founder could destroy a centre of excellence for brain research.

Research Highlights

Journal Club

News

News Feature

  • News Feature |

    Like any other field, research on climate change has some fundamental gaps, although not the ones typically claimed by sceptics. Quirin Schiermeier takes a hard look at some of the biggest problem areas.

    • Quirin Schiermeier
  • News Feature |

    Can engineering approaches tame the complexity of living systems? Roberta Kwok explores five challenges for the field and how they might be resolved.

    • Roberta Kwok

Column

  • Column |

    Quantitative research assessment is a bad idea whose time has come, argues Colin Macilwain.

    • Colin Macilwain

Correspondence

Correction

Opinion

  • Opinion |

    There are mathematically advanced ways to weigh and pool scientific advice. They should be used more to quantify uncertainty and improve decision-making, says Willy Aspinall.

    • Willy Aspinall
  • Opinion |

    People's grasp of scientific debates can improve if communicators build on the fact that cultural values influence what and whom we believe, says Dan Kahan.

    • Dan Kahan

Books & Arts

News & Views

  • News & Views |

    By synchronizing clocks, humans make more efficient use of their time and orchestrate their activities in different places. Bacteria have now been engineered that similarly coordinate their molecular timepieces.

    • Martin Fussenegger
  • News & Views |

    The use of magnetic fields to assemble particles into membranes provides a powerful tool for exploring the physics of self-assembly and a practical method for synthesizing functional materials.

    • Jack F. Douglas
  • News & Views |

    The giant-panda genome is the first reported de novo assembly of a large mammalian genome achieved using next-generation sequencing methods. The feat reflects a trend towards ever-decreasing genome-sequencing costs.

    • Kim C. Worley
    • Richard A. Gibbs
  • News & Views |

    Asteroids are weakly bound piles of rubble, and if one comes close to Earth, tides can cause the object to undergo landslides and structural rearrangement. The outcome of this encounter is a body with meteorite-like colours.

    • Clark R. Chapman
  • News & Views |

    Biologists have assumed that natural selection shapes larger patterns of evolution through interactions such as competition and predation. These patterns may instead be determined by rare, stochastic speciation.

    • Michael J. Benton
  • News & Views |

    Springtime ozone levels in the lower atmosphere over western North America are rising. The source of this pollution may be Asia, a finding that reaffirms the need for international air-quality control.

    • Kathy Law
  • News & Views |

    Physics provides new approaches to difficult biological problems: a plausible mathematical model of how cilia and flagella beat has been formulated, but it needs to be subjected to rigorous experimental tests.

    • T. J. Mitchison
    • H. M. Mitchison

Correction

Article

  • Article | | Open Access

    Here, a draft sequence of the giant panda genome is assembled using next-generation sequencing technology alone. Genome analysis reveals a low divergence rate in comparison with dog and human genomes and insights into panda-specific traits; for example, the giant panda's bamboo diet may be more dependent on its gut microbiome than its own genetic composition.

    • Ruiqiang Li
    • Wei Fan
    • Jun Wang
  • Article |

    A mesenchymal phenotype is the hallmark of tumour aggressiveness in human malignant glioma, but the regulatory programs responsible for implementing the associated molecular signature are largely unknown. Reverse-engineering and an unbiased interrogation of a glioma-specific regulatory network now reveal the transcription factors that activate expression of mesenchymal genes in malignant glioma.

    • Maria Stella Carro
    • Wei Keat Lim
    • Antonio Iavarone
  • Article |

    A defining focus of synthetic biology is the engineering of genetic circuits with predictive functionality in living cells. Here, a decade after the first synthesized genetic toggle switch and oscillator, an engineered gene network with global intercellular coupling is designed that is capable of generating synchronized oscillations in a growing population of cells.

    • Tal Danino
    • Octavio Mondragón-Palomino
    • Jeff Hasty

Letter

  • Letter |

    Telescopic measurements of asteroids' colours rarely match laboratory reflectance spectra of meteorites owing to a 'space weathering' process that rapidly reddens asteroid surfaces. 'Unweathered' asteroids, however, with spectra matching ordinary chondrite meteorites, are seen only among small bodies with orbits that cross inside the orbits of Mars and Earth. Such unweathered asteroids are now shown to have experienced orbital intersections closer than the Earth–Moon distance within the past half-million years.

    • Richard P. Binzel
    • Alessandro Morbidelli
    • Alan T. Tokunaga
  • Letter |

    Although deformation twinning in crystals controls the mechanical behaviour of many materials, its size-dependence has not been explored. Using micro-compression and in situ nano-compression experiments, the stress required for deformation twinning is now found to increase drastically with decreasing sample size of a titanium alloy single crystal, until the sample size is reduced to one micrometre; below this point, deformation twinning is replaced by dislocation plasticity.

    • Qian Yu
    • Zhi-Wei Shan
    • Evan Ma
  • Letter |

    In the search to reduce our dependency on fossil-fuel energy, new plastic materials that are less dependent on petroleum are being developed, with water-based gels — hydrogels — representing one possible solution. Here, a mixture of water, 3% clay and a tiny amount of a special organic binder is shown to form a transparent hydrogel that can be moulded into shape-persistent, free-standing objects and that rapidly and completely self-heals when damaged.

    • Qigang Wang
    • Justin L. Mynar
    • Takuzo Aida
  • Letter |

    High concentrations of ozone in the troposphere are toxic and act as a greenhouse gas. Anthropogenic emissions of ozone precursors have caused widespread increases in ozone concentrations since the late 1800s, with the fastest-growing ozone precursor emissions currently coming out of east Asia. Much of the springtime east Asian pollution is exported towards western North America; a strong increase in springtime ozone mixing ratios is now found in the free troposphere over this region.

    • O. R. Cooper
    • D. D. Parrish
    • M. A. Avery
  • Letter |

    The Red Queen metaphor has species accumulating small changes to keep up with a continually changing environment, with speciation occurring at a constant rate. This constant-rate claim is now tested against four competing models, using 101 phylogenies of animal, plant and fungal taxa. The results provide a new interpretation of the Red Queen; a view linking speciation to rare stochastic events that cause reproductive isolation.

    • Chris Venditti
    • Andrew Meade
    • Mark Pagel
  • Letter |

    If robustness is the opposite of evolvability, we might expect that a robust population would have difficulty adapting to environmental change; however, some studies have suggested that genetic robustness facilitates adaptation. Here, using a general population genetics model, mutational robustness is found to either impede or facilitate adaptation depending on the population size, the mutation rate and the structure of the fitness landscape.

    • Jeremy A. Draghi
    • Todd L. Parsons
    • Joshua B. Plotkin
  • Letter |

    Evidence from animal studies shows that testosterone can induce aggressive behaviour, but whether this extrapolates to humans is an area of debate. The sublingual administration of a single dose of testosterone in women is now shown to cause a substantial increase in fair bargaining behaviour, although subjects who believed they received testosterone behaved much more unfairly than those who thought they received a placebo.

    • C. Eisenegger
    • M. Naef
    • E. Fehr
  • Letter |

    Clear cell renal carcinoma, the most common form of adult kidney cancer, is often characterized by the presence of inactivating mutations in the VHL gene. A large survey for somatic mutations now identifies inactivating mutations in two genes encoding enzymes involved in histone modification, highlighting the role of mutations in components of the chromatin modification machinery in human cancer.

    • Gillian L. Dalgliesh
    • Kyle Furge
    • P. Andrew Futreal
  • Letter |

    Expression of the embryonic M2 isoform of pyruvate kinase (PKM2) by tumour cells promotes aerobic glycolysis, whereas the normal adult isoform, PKM1, promotes oxidative phosphorylation. Expression of these isoforms is regulated by alternative splicing; here, aberrant expression of three heterogeneous nuclear ribonucleoprotein splicing factors, which are themselves regulated by the c-Myc oncogene, is shown to be responsible for the M1 to M2 switch in cancer.

    • Charles J. David
    • Mo Chen
    • James L. Manley
  • Letter |

    Antimicrobial peptides (AMPs) are an important class of immune effector molecules which fight pathogen infections. AMP induction in Drosophila is regulated through the activation of the Toll and immune deficiency pathways; it is now shown that AMP activation can be achieved independently of these pathways by the transcription factor FOXO. In non-infected animals, AMP genes are activated in response to nuclear FOXO activity when induced by starvation.

    • Thomas Becker
    • Gerrit Loch
    • Michael Hoch
  • Letter |

    Although cyclin D1 is frequently overexpressed in human cancers, the full range of its functions in normal development and oncogenesis is unclear. Here, tagged cyclin D1 knock-in mouse strains are developed to allow a search for cyclin D1-binding proteins in different mouse organs using high-throughput mass spectrometry. The results show that, in addition to its established cell cycle roles, cyclin D1 has an in vivo transcriptional function in mouse development.

    • Frédéric Bienvenu
    • Siwanon Jirawatnotai
    • Piotr Sicinski
  • Letter |

    Group II chaperonins are present in eukaryotes and archaea and are essential mediators of cellular protein folding. This process is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis, but the structural rearrangements and molecular events leading to lid closure are unknown. Using cryo-electron microscopy, the structures of an archaeal group II chaperonin in the open and closed states are now reported, providing details of this mechanism.

    • Junjie Zhang
    • Matthew L. Baker
    • Wah Chiu

Erratum

Corrigendum

Erratum

Corrigendum

Careers Q&A

  • Careers Q&A |

    Jon Gluyas of Durham University, UK, is the country's first professor of carbon capture and storage and geoenergy.

    • Virginia Gewin

Career Brief

  • Career Brief |

    NIH stipend increase not enough, says US National Postdoctoral Association.

  • Career Brief |

    Biotech firms raise much more money in 2009, buoyed by big pharma partnerships

Careers and Recruitment

  • Careers and Recruitment |

    The drug and biotech industries are not always easy to break into. Developing a diverse skill set could be the key to success, Karen Kaplan reports.

    • Karen Kaplan

Futures

Brief Communications Arising

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