Volume 9 Issue 8, August 2012

Volume 9 Issue 8

An Escherichia coli 'community' gene regulatory network, made by combining the predictions of several network inference methods tested in the DREAM5 challenge. Cover by Erin Dewalt, based on a design and image provided by Daniel Marbach and Gustavo Stolovitzky.

Editorial

  • Editorial |

    Peer review is an essential part of scientific discourse, and referees deserve formal recognition for the service they provide.

This Month

Correspondence

Research Highlights

Methods in Brief

Tools in Brief

Research Highlights

Technology Feature

  • Technology Feature |

    Rapidly maturing techniques reveal messengers within cells.

    • Monya Baker

News and Views

  • News & Views |

    A precomputed database of lineage-restricted reference genes yields a fast and accurate tool that uses sequence similarity alone to compute clade abundances from shotgun metagenomic data sets.

    • Daniel H Haft
    •  & Andrey Tovchigrechko
  • News & Views |

    An experimental infrastructure consisting of environmentally controlled and spatially linked habitat patches permits studies on terrestrial animal dispersal at an unprecedented scale for an experiment with such strict control.

    • Nick M Haddad

Analysis

  • Analysis |

    This analysis comprehensively compares methods for gene regulatory network inference submitted through the DREAM5 challenge. It demonstrates that integration of predictions from multiple methods shows the most robust performance across data sets.

    • Daniel Marbach
    • , James C Costello
    • , Robert Küffner
    • , Nicole M Vega
    • , Robert J Prill
    • , Diogo M Camacho
    • , Kyle R Allison
    • , The DREAM5 Consortium
    • , Andrej Aderhold
    • , Kyle R Allison
    • , Richard Bonneau
    • , Diogo M Camacho
    • , Yukun Chen
    • , James J Collins
    • , Francesca Cordero
    • , James C Costello
    • , Martin Crane
    • , Frank Dondelinger
    • , Mathias Drton
    • , Roberto Esposito
    • , Rina Foygel
    • , Alberto de la Fuente
    • , Jan Gertheiss
    • , Pierre Geurts
    • , Alex Greenfield
    • , Marco Grzegorczyk
    • , Anne-Claire Haury
    • , Benjamin Holmes
    • , Torsten Hothorn
    • , Dirk Husmeier
    • , Vân Anh Huynh-Thu
    • , Alexandre Irrthum
    • , Manolis Kellis
    • , Guy Karlebach
    • , Robert Küffner
    • , Sophie Lèbre
    • , Vincenzo De Leo
    • , Aviv Madar
    • , Subramani Mani
    • , Daniel Marbach
    • , Fantine Mordelet
    • , Harry Ostrer
    • , Zhengyu Ouyang
    • , Ravi Pandya
    • , Tobias Petri
    • , Andrea Pinna
    • , Christopher S Poultney
    • , Robert J Prill
    • , Serena Rezny
    • , Heather J Ruskin
    • , Yvan Saeys
    • , Ron Shamir
    • , Alina Sîrbu
    • , Mingzhou Song
    • , Nicola Soranzo
    • , Alexander Statnikov
    • , Gustavo Stolovitzky
    • , Nicci Vega
    • , Paola Vera-Licona
    • , Jean-Philippe Vert
    • , Alessia Visconti
    • , Haizhou Wang
    • , Louis Wehenkel
    • , Lukas Windhager
    • , Yang Zhang
    • , Ralf Zimmer
    • , Manolis Kellis
    • , James J Collins
    •  & Gustavo Stolovitzky

Brief Communications

  • Brief Communication |

    Due to an unexpected cell-penetrating property, zinc-finger nucleases (ZFNs) can be delivered to several mammalian cell types as proteins. Dose-dependent disruption of an endogenous gene was achieved with reduced activity at known off-target sites.

    • Thomas Gaj
    • , Jing Guo
    • , Yoshio Kato
    • , Shannon J Sirk
    •  & Carlos F Barbas III
  • Brief Communication |

    Genotyping based on restriction site7ndash;associated (RAD) sequencing around type IIB enzyme recognition sites is reported. The streamlined reduced-representation approach features even and tunable genome coverage and enables large-scale genotyping studies by maximizing the amount of genotypic information that can be obtained from individuals for a given amount of sequencing.

    • Shi Wang
    • , Eli Meyer
    • , John K McKay
    •  & Mikhail V Matz
  • Brief Communication |

    This method achieves simultaneous and spatially colocalized excitation of three fluorophores with distinct spectra, doing so via two-photon microscopy using a femtosecond laser and an optical parametric oscillator and by temporally overlapping the beams. Imaging of 'Brainbow'-labeled mouse and chicken nervous tissue and of developing fly embryos is shown.

    • Pierre Mahou
    • , Maxwell Zimmerley
    • , Karine Loulier
    • , Katherine S Matho
    • , Guillaume Labroille
    • , Xavier Morin
    • , Willy Supatto
    • , Jean Livet
    • , Delphine Débarre
    •  & Emmanuel Beaurepaire
  • Brief Communication |

    A rare cutting protease that creates large peptides is well suited for differentiating protein isoforms and detecting combinations of post-translational modifications by tandem mass spectrometry.

    • Cong Wu
    • , John C Tran
    • , Leonid Zamdborg
    • , Kenneth R Durbin
    • , Mingxi Li
    • , Dorothy R Ahlf
    • , Bryan P Early
    • , Paul M Thomas
    • , Jonathan V Sweedler
    •  & Neil L Kelleher
  • Brief Communication |

    This paper reports a fluorescence imaging method based on interference contrast in which the incidence angle of the excitation light is actively scanned. The high axial precision and temporal resolution are used for dynamic nanoscale imaging of cytoskeleton and adhesion proteins in living cells.

    • Matthew J Paszek
    • , Christopher C DuFort
    • , Matthew G Rubashkin
    • , Michael W Davidson
    • , Kurt S Thorn
    • , Jan T Liphardt
    •  & Valerie M Weaver

Articles

  • Article |

    A flexible, environmentally controlled experimental setup for the study of terrestrial animal dispersal is reported. Its unprecedented scale should enable studies in spatial ecology and permit tests of conservation strategies in the face of environmental change.

    • Delphine Legrand
    • , Olivier Guillaume
    • , Michel Baguette
    • , Julien Cote
    • , Audrey Trochet
    • , Olivier Calvez
    • , Susanne Zajitschek
    • , Felix Zajitschek
    • , Jane Lecomte
    • , Quentin Bénard
    • , Jean-François Le Galliard
    •  & Jean Clobert
  • Article |

    The combination of cell-free protein expression and combinatorial dual labeling–aided NMR analysis allows for the rapid backbone structure assessment of human membrane proteins.

    • Christian Klammt
    • , Innokentiy Maslennikov
    • , Monika Bayrhuber
    • , Cédric Eichmann
    • , Navratna Vajpai
    • , Ellis Jeremy Chua Chiu
    • , Katherine Y Blain
    • , Luis Esquivies
    • , June Hyun Jung Kwon
    • , Bartosz Balana
    • , Ursula Pieper
    • , Andrej Sali
    • , Paul A Slesinger
    • , Witek Kwiatkowski
    • , Roland Riek
    •  & Senyon Choe
  • Article |

    Two large-scale resources for studying microRNA function are presented: one is a library of fluorescent sensors with a corresponding assay for global profiling of microRNA activity in different cell types; the other is a decoy library for suppressing microRNA activity individually or in pooled loss-of-function screens.

    • Gavriel Mullokandov
    • , Alessia Baccarini
    • , Albert Ruzo
    • , Anitha D Jayaprakash
    • , Navpreet Tung
    • , Benjamin Israelow
    • , Matthew J Evans
    • , Ravi Sachidanandam
    •  & Brian D Brown