Systems biology articles within Nature

Featured

  • Letter |

    Saccharomyces cerevisiae is engineered to produce high concentrations of artemisinic acid, a precursor of the artemisinin used in combination therapies for malaria treatment; an efficient and practical chemical process to convert artemisinic acid to artemisinin is also developed.

    • C. J. Paddon
    • , P. J. Westfall
    •  & J. D. Newman

  • Article |

    A global view of the genetic networks regulating the differentiation of TH17 cells is presented, based on temporal expression profiling, computational network reconstruction and validation of predicted interactions by nanowire-mediated siRNA perturbation.

    • Nir Yosef
    • , Alex K. Shalek
    •  & Aviv Regev

  • Letter |

    A mathematical method, known as ergodic rate analysis, has been developed and used to study the rates of molecular events from single time measurements of large populations of fixed cells; this new method is able to overcome some of the previous limitations with regards to studying cell-size control.

    • Ran Kafri
    • , Jason Levy
    •  & Marc W. Kirschner

  • Letter |

    A high-throughput mutagenesis study in a PDZ domain shows that biochemical function and adaptation primarily originate from a collectively evolving amino acid network within the structure termed a protein sector.

    • Richard N. McLaughlin Jr
    • , Frank J. Poelwijk
    •  & Rama Ranganathan

  • Letter |

    Although zebrafish is an important animal model for basic vertebrate biology and human disease modelling, rapid targeted genome modification has not been possible in this species; here a technique based on improved artificial transcription activator-like effector nucleases (TALENs) allows precise sequence modifications at pre-determined genomic locations.

    • Victoria M. Bedell
    • , Ying Wang
    •  & Stephen C. Ekker

  • Article
    | Open Access

    A description is given of the ENCODE consortium’s efforts to examine the principles of human transcriptional regulatory networks; the results are integrated with other genomic information to form a hierarchical meta-network where different levels have distinct properties.

    • Mark B. Gerstein
    • , Anshul Kundaje
    •  & Michael Snyder

  • News & Views |

    The small genomes of some bacteria could provide the first complete understanding of a biological system. A new computer model brings this goal closer, by calculating every process in a dividing Mycoplasma cell.

    • Mark Isalan

  • Review Article |

    Over the past ten years, protein engineering has established biocatalysis as a practical and environmentally friendly alternative to traditional forms of catalysis both in the laboratory and in industry.

    • U. T. Bornscheuer
    • , G. W. Huisman
    •  & K. Robins

  • News & Views |

    A stepwise process of mutation and structural analysis has modulated a flexible binding interface of an immune-cell signalling protein, interleukin-2, and generated mutant proteins with enhanced anticancer activity. See Article p.529

    • Eric T. Boder

  • News & Views |

    Molecular machines containing related protein subunits are common in cells. Reconstruction of ancient proteins suggests that this type of complexity can evolve in the absence of any initial selective advantage. See Letter p.360

    • W. Ford Doolittle

  • Outlook |

    Systems science can provide guidance in capturing the complementary approaches to healthcare, says Jan van der Greef.

    • Jan van der Greef

  • News & Views |

    Scientists have begun to overhaul a yeast's genome to make it more stable, engineerable and evolvable. Remarkably, the part-natural, part-synthetic yeast cells function and reproduce without obvious ill effects. See Letter p.471

    • Peter J. Enyeart
    •  & Andrew D. Ellington

  • News & Views |

    Even during effective treatment with antiretroviral drugs, low levels of HIV persist. In part, this could be due to cell-to-cell transfer of multiple virions and the drugs' inability to inhibit replication when virus levels are high. See Letter p.95

    • Steven G. Deeks

  • News & Views |

    The idea that artificial neural networks could be based on molecular components is not new, but making such a system has been difficult. A network of four artificial neurons made from DNA has now been created. See Letter p.368

    • Anne Condon

  • News |

    DNA square-root solver is biggest molecular computer yet.

    • Zoë Corbyn

  • Technology Feature |

    Biologists have copied an existing genetic code, but haven't yet commercialized it or written their own. What will it take for a tour de force to reach industrial force?

    • Monya Baker

  • Books & Arts |

    Anthony King explores a Dublin exhibition that exposes the controversies of synthetic biology.

    • Anthony King

  • Books & Arts |

    George Ellis reminds us that Brian Greene's beguiling book on parallel worlds is more theory than fact.

    • George Ellis

  • News & Views |

    Protein engineering of an enzyme that catalytically detoxifies organophosphate compounds in the body opens up fresh opportunities in the search for therapeutic protection against nerve agents used in chemical warfare.

    • Frank M. Raushel

  • News & Views |

    Cellular compartmentalization is an effective way to build gene circuits capable of complex logic operations, in which binary inputs are converted into binary outputs according to user-defined rules. See Letters p.207 & p.212

    • Bochong Li
    •  & Lingchong You

  • News & Views |

    Computers use transistor-based logic gates as the basis of their functions, but molecular logic gates would make them much faster. A report of DNA-based logic gates could be a first step towards molecular computing.

    • Thomas Carell

  • Comment |

    Biologists and engineers should work together: synthetic biology reveals how organisms develop and function, argue Michael Elowitz and Wendell A. Lim.

    • Michael Elowitz
    •  & Wendell A. Lim

  • News |

    Biologists join physicists in a bid to map the workings of the human organ at all scales.

    • Alison Abbott

  • Letter |

    For synthetic biologists' creativity to be unleashed, basic circuits must become truly interchangeable, that is, modular and scalable. This study, one of two linked papers, has harnessed bacterial 'quorum sensing' to achieve complex computation through communication between individual cells performing simple logic functions. Such extracellular 'chemical wiring' is one promising way to get around intracellular noise when building more complex genetic circuitry.

    • Alvin Tamsir
    • , Jeffrey J. Tabor
    •  & Christopher A. Voigt

  • Article |

    The central amygdala relies on inhibitory circuitry to encode fear memories, but how this information is acquired and expressed in these connections is unknown. Two new papers use a combination of cutting-edge technologies to reveal two distinct microcircuits within the central amygdala, one required for fear acquisition and the other critical for conditioned fear responses. Understanding this architecture provides a strong link between activity in a specific circuit and particular behavioural consequences.

    • Wulf Haubensak
    • , Prabhat S. Kunwar
    •  & David J. Anderson

  • News & Views |

    Short residence times in the bloodstream reduce the effectiveness of protein drugs. Application of an approach that combines protein and polymer engineering prolongs circulation time and increases drug uptake by tumours.

    • Jeffrey A. Hubbell

  • News & Views |

    The ratio of nutrient elements in marine subsurface waters is much the same everywhere, even though biogeochemically distinct ocean biomes exist. A modelling study that includes mixing solves this conundrum. See Article p.550

    • Raymond N. Sambrotto

  • News & Views |

    Theory suggests that the risk of critical transitions in complex systems can be revealed by generic indicators. A lab study of extinction in plankton populations provides experimental support for that principle. See Letter p. 456

    • Marten Scheffer

  • News & Views |

    Noise in biochemical processes can compromise precision in cellular functions. An analysis involving information theory suggests that there is a strict limit to how far noise can be suppressed by feedback.

    • Li Sun
    •  & Attila Becskei

  • News & Views |

    The means by which supermassive black holes form and grow have remained largely unclear. Numerical simulations show that the collision of massive galaxies can naturally lead to the creation of these objects.

    • Marta Volonteri

  • News & Views |

    Approaches that abandon traditional speech categories offer promise for developing statistical descriptions that encapsulate how speech conveys information. Grandparents would be among the beneficiaries.

    • Michael S. Lewicki

  • News & Views |

    A simple model highlights the pros and cons of chasing — and escaping — in groups. It shows that, for a given number of prey animals, an optimal number of predators exists that maximizes the success of the catch.

    • Tamás Vicsek

  • News & Views |

    Unexpected chlorine chemistry in the lowest part of the atmosphere can affect the cycling of nitrogen oxides and the production of ozone, and reduce the lifetime of the greenhouse gas methane.

    • Roland von Glasow

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