Commentary

  • Commentary |

    This Commentary discusses the problem of phototoxicity in live imaging and suggests guidelines to improve its assessment and reporting.

    • P Philippe Laissue
    • , Rana A Alghamdi
    • , Pavel Tomancak
    • , Emmanuel G Reynaud
    •  & Hari Shroff
  • Commentary |

    • Jan Van Deun
    • , Pieter Mestdagh
    • , Patrizia Agostinis
    • , Özden Akay
    • , Sushma Anand
    • , Jasper Anckaert
    • , Zoraida Andreu Martinez
    • , Tine Baetens
    • , Els Beghein
    • , Laurence Bertier
    • , Geert Berx
    • , Janneke Boere
    • , Stephanie Boukouris
    • , Michel Bremer
    • , Dominik Buschmann
    • , James B Byrd
    • , Clara Casert
    • , Lesley Cheng
    • , Anna Cmoch
    • , Delphine Daveloose
    • , Eva De Smedt
    • , Seyma Demirsoy
    • , Victoria Depoorter
    • , Bert Dhondt
    • , Tom A P Driedonks
    • , Aleksandra Dudek
    • , Abdou Elsharawy
    • , Ilaria Floris
    • , Andrew D Foers
    • , Kathrin Gärtner
    • , Abhishek D Garg
    • , Edward Geeurickx
    • , Jan Gettemans
    • , Farzaneh Ghazavi
    • , Bernd Giebel
    • , Tom Groot Kormelink
    • , Grace Hancock
    • , Hetty Helsmoortel
    • , Andrew F Hill
    • , Vincent Hyenne
    • , Hina Kalra
    • , David Kim
    • , Joanna Kowal
    • , Sandra Kraemer
    • , Petra Leidinger
    • , Carina Leonelli
    • , Yaxuan Liang
    • , Lien Lippens
    • , Shu Liu
    • , Alessandra Lo Cicero
    • , Shaun Martin
    • , Suresh Mathivanan
    • , Prabhu Mathiyalagan
    • , Támas Matusek
    • , Gloria Milani
    • , Marta Monguió-Tortajada
    • , Liselot M Mus
    • , Dillon C Muth
    • , Andrea Németh
    • , Esther N M Nolte-'t Hoen
    • , Lorraine O'Driscoll
    • , Roberta Palmulli
    • , Michael W Pfaffl
    • , Bjarke Primdal-Bengtson
    • , Erminia Romano
    • , Quentin Rousseau
    • , Susmita Sahoo
    • , Natalia Sampaio
    • , Monisha Samuel
    • , Benjamin Scicluna
    • , Bieke Soen
    • , Anneleen Steels
    • , Johannes V Swinnen
    • , Maarit Takatalo
    • , Safia Thaminy
    • , Clotilde Théry
    • , Joeri Tulkens
    • , Isabel Van Audenhove
    • , Susanne van der Grein
    • , Alan Van Goethem
    • , Martijn J van Herwijnen
    • , Guillaume Van Niel
    • , Nadine Van Roy
    • , Alexander R Van Vliet
    • , Niels Vandamme
    • , Suzanne Vanhauwaert
    • , Glenn Vergauwen
    • , Frederik Verweij
    • , Annelynn Wallaert
    • , Marca Wauben
    • , Kenneth W Witwer
    • , Marijke I Zonneveld
    • , Olivier De Wever
    • , Jo Vandesompele
    •  & An Hendrix
  • Commentary |

    In this Commentary, Ascoli et al. discuss recipes for setting up public data sharing initiatives based on their experiences with NeuroMorpho.Org.

    • Giorgio A Ascoli
    • , Patricia Maraver
    • , Sumit Nanda
    • , Sridevi Polavaram
    •  & Rubén Armañanzas
  • Commentary |

    We convened an ad hoc International Working Group for Antibody Validation in order to formulate the best approaches for validating antibodies used in common research applications and to provide guidelines that ensure antibody reproducibility. We recommend five conceptual 'pillars' for antibody validation to be used in an application-specific manner.

    • Mathias Uhlen
    • , Anita Bandrowski
    • , Steven Carr
    • , Aled Edwards
    • , Jan Ellenberg
    • , Emma Lundberg
    • , David L Rimm
    • , Henry Rodriguez
    • , Tara Hiltke
    • , Michael Snyder
    •  & Tadashi Yamamoto
  • Commentary |

    Cryo-EM has emerged rapidly as a method for determining high-resolution structures of biological macromolecules. The author of this Commentary discusses just how much better this technology may get and how fast such developments are likely to happen.

    • Robert M Glaeser
  • Commentary |

    Quality control of cell lines used in biomedical research is essential to ensure reproducibility. Although cell line authentication has been widely recommended for many years, misidentification, including cross-contamination, remains a serious problem. We outline a multi-stakeholder, incremental approach and policy-related recommendations to facilitate change in the culture of cell line authentication.

    • Leonard P Freedman
    • , Mark C Gibson
    • , Stephen P Ethier
    • , Howard R Soule
    • , Richard M Neve
    •  & Yvonne A Reid
  • Commentary |

    Scientific animations have tremendous potential as instruments of insight and dissemination. However, audiences are often unable to determine the degree to which visualizations are informed by scientific evidence. By providing a more detailed account of source use, developers can increase the credibility of animations as scientific tools.

    • Stuart G Jantzen
    • , Jodie Jenkinson
    •  & Gaël McGill
  • Commentary |

    The reliability and reproducibility of science are under scrutiny. However, a major cause of this lack of repeatability is not being considered: the wide sample-to-sample variability in the P value. We explain why P is fickle to discourage the ill-informed practice of interpreting analyses based predominantly on this statistic.

    • Lewis G Halsey
    • , Douglas Curran-Everett
    • , Sarah L Vowler
    •  & Gordon B Drummond
  • Commentary |

    Developments in electrical and optical recording technology are scaling up the size of neuronal populations that can be monitored simultaneously. Light-sheet imaging is rapidly gaining traction as a method for optically interrogating activity in large networks and presents both opportunities and challenges for understanding circuit function.

    • Philipp J Keller
    • , Misha B Ahrens
    •  & Jeremy Freeman
  • Commentary |

    In light sheet–based fluorescence microscopy (LSFM), optical sectioning in the excitation process minimizes fluorophore bleaching and phototoxic effects. Because biological specimens survive long-term three-dimensional imaging at high spatiotemporal resolution, LSFM has become the tool of choice in developmental biology.

    • Ernst H K Stelzer
  • Commentary |

    Ten years of development in light-sheet microscopy have led to spectacular demonstrations of its capabilities. The technology is ready to assist biologists in tackling scientific problems, but are biologists ready for it? Here we discuss the interdisciplinary challenges light-sheet microscopy presents for biologists and highlight available resources.

    • Emmanuel G Reynaud
    • , Jan Peychl
    • , Jan Huisken
    •  & Pavel Tomancak
  • Commentary |

    The ability to convert somatic cells to induced pluripotent stem cells has immense potential to further our understanding of development and disease mechanisms, and for cellular therapy. Before researchers can achieve these goals, they must expand current methodology to incorporate animal models and quantitative descriptions of the essential phenomena driving reprogramming.

    • Peter Karagiannis
    •  & Shinya Yamanaka
  • Commentary |

    A decade of advances in genome engineering technologies has enabled the editing of genome sequences much like one edits computer code; many more applications for precisely manipulating genome structure and function are on the horizon.

    • Charles A Gersbach
  • Commentary |

    Our choice, among many candidates, of the ten areas of methods development with the most impact on biological research over the last decade. Visit Methagora to browse Nature Methods papers in some of these areas.

  • Commentary |

    A revolution in DNA sequencing technology has enabled new insights from thousands of genomes sequenced across taxa.

    • John D McPherson
  • Commentary |

    Much of our knowledge about biological systems has been obtained by examining ensembles of molecules. However, this has begun to change because of the unprecedented precision and clarity afforded by single-molecule measurements. The last decade has seen amazing advances in the resolution and complexity of these methods, making it possible to ask and answer entirely new types of biological questions.

    • Taekjip Ha
  • Commentary |

    The optogenetic revolution is transforming neuroscience. The dramatic recent progress in using light to both control and read out neural activity has highlighted the need for better probes, improved light delivery and more careful interpretation of results, which will all be required for optogenetics to fully realize its remarkable potential.

    • Michael Häusser
  • Commentary |

    We argue that standard thermodynamic considerations and scaling laws show that a single cell cannot substantially raise its temperature by endogenous thermogenesis. This statement seriously questions the interpretations of recent work reporting temperature heterogeneities measured in single living cells.

    • Guillaume Baffou
    • , Hervé Rigneault
    • , Didier Marguet
    •  & Ludovic Jullien
  • Commentary |

    'Irreproducibility' is symptomatic of a broader challenge in measurement in biomedical research. From the US National Institute of Standards and Technology (NIST) perspective of rigorous metrology, reproducibility is only one aspect of establishing confidence in measurements. Appropriate controls, reference materials, statistics and informatics are required for a robust measurement process. Research is required to establish these tools for biological measurements, which will lead to greater confidence in research results.

    • Anne L Plant
    • , Laurie E Locascio
    • , Willie E May
    •  & Patrick D Gallagher
  • Commentary |

    Authors discuss how synthetic biology approaches could be applied to assemble synthetic quasibiological systems able to replicate and evolve, illuminating universal properties of life and the search for its origins.

    • James Attwater
    •  & Philipp Holliger
  • Commentary |

    Single-molecule super-resolution techniques emerged only several years ago but have revolutionized fluorescence microscopy of cellular structures. We discuss some key principles of these techniques, point out pitfalls, highlight recent developments and identify opportunities for the future.

    • Ulrike Endesfelder
    •  & Mike Heilemann
  • Commentary |

    Individual cells of the same phenotype are commonly viewed as identical functional units of a tissue or organ. However, the deep sequencing of DNA and RNA from single cells suggests a more complex ecology of heterogeneous cell states that together produce emergent system-level function. Continuing development of high-content, real-time, multimodal single-cell measurement technologies will lead to the ultimate goal of understanding the function of an individual cell in the context of its microenvironment.

    • James Eberwine
    • , Jai-Yoon Sul
    • , Tamas Bartfai
    •  & Junhyong Kim
  • Commentary |

    Emerging technologies are bringing single-cell genome sequencing into the mainstream; this field has already yielded insights into the genetic architecture and variability between cells that highlight the dynamic nature of the genome.

    • Paul C Blainey
    •  & Stephen R Quake
  • Commentary |

    Recent technical advances have enabled RNA sequencing (RNA-seq) in single cells. Exploratory studies have already led to insights into the dynamics of differentiation, cellular responses to stimulation and the stochastic nature of transcription. We are entering an era of single-cell transcriptomics that holds promise to substantially impact biology and medicine.

    • Rickard Sandberg
  • Commentary |

    Two surveys of over 1,700 publications whose authors use quantitative real-time PCR (qPCR) reveal a lack of transparent and comprehensive reporting of essential technical information. Reporting standards are significantly improved in publications that cite the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, although such publications are still vastly outnumbered by those that do not.

    • Stephen A Bustin
    • , Vladimir Benes
    • , Jeremy Garson
    • , Jan Hellemans
    • , Jim Huggett
    • , Mikael Kubista
    • , Reinhold Mueller
    • , Tania Nolan
    • , Michael W Pfaffl
    • , Gregory Shipley
    • , Carl T Wittwer
    • , Peter Schjerling
    • , Philip J Day
    • , Mónica Abreu
    • , Begoña Aguado
    • , Jean-François Beaulieu
    • , Anneleen Beckers
    • , Sara Bogaert
    • , John A Browne
    • , Fernando Carrasco-Ramiro
    • , Liesbeth Ceelen
    • , Kate Ciborowski
    • , Pieter Cornillie
    • , Stephanie Coulon
    • , Ann Cuypers
    • , Sara De Brouwer
    • , Leentje De Ceuninck
    • , Jurgen De Craene
    • , Hélène De Naeyer
    • , Ward De Spiegelaere
    • , Kato Deckers
    • , Annelies Dheedene
    • , Kaat Durinck
    • , Margarida Ferreira-Teixeira
    • , Annelies Fieuw
    • , Jack M Gallup
    • , Sandra Gonzalo-Flores
    • , Karen Goossens
    • , Femke Heindryckx
    • , Elizabeth Herring
    • , Hans Hoenicka
    • , Laura Icardi
    • , Rolf Jaggi
    • , Farzad Javad
    • , Michael Karampelias
    • , Frederick Kibenge
    • , Molly Kibenge
    • , Candy Kumps
    • , Irina Lambertz
    • , Tim Lammens
    • , Amelia Markey
    • , Peter Messiaen
    • , Evelien Mets
    • , Sofia Morais
    • , Alberto Mudarra-Rubio
    • , Justine Nakiwala
    • , Hilde Nelis
    • , Pal A Olsvik
    • , Claudina Pérez-Novo
    • , Michelle Plusquin
    • , Tony Remans
    • , Ali Rihani
    • , Paulo Rodrigues-Santos
    • , Pieter Rondou
    • , Rebecca Sanders
    • , Katharina Schmidt-Bleek
    • , Kerstin Skovgaard
    • , Karen Smeets
    • , Laura Tabera
    • , Stefan Toegel
    • , Tim Van Acker
    • , Wim Van den Broeck
    • , Joni Van der Meulen
    • , Mireille Van Gele
    • , Gert Van Peer
    • , Mario Van Poucke
    • , Nadine Van Roy
    • , Sarah Vergult
    • , Joris Wauman
    • , Marina Tshuikina-Wiklander
    • , Erik Willems
    • , Sara Zaccara
    • , Fjoralba Zeka
    •  & Jo Vandesompele
  • Commentary |

    Optimism about biomedicine is challenged by the increasingly complex ethical, legal and social issues it raises. Reporting of scientific methods is no longer sufficient to address the complex relationship between science and society. To promote 'ethical reproducibility', we call for transparent reporting of research ethics methods used in biomedical research.

    • James A Anderson
    • , Marleen Eijkholt
    •  & Judy Illes
  • Commentary |

    We present a summary of the scientific deliberations and major conclusions that arose from a workshop on the BRAIN Initiative.

    • Aravi Samuel
    • , Herbert Levine
    •  & Krastan B Blagoev
  • Commentary |

    Much of what is known about mammalian cell regulation has been achieved with the aid of transiently transfected cells. However, overexpression can violate balanced gene dosage, affecting protein folding, complex assembly and downstream regulation. To avoid these problems, genome engineering technologies now enable the generation of stable cell lines expressing modified proteins at (almost) native levels.

    • Toby J Gibson
    • , Markus Seiler
    •  & Reiner A Veitia
  • Commentary |

    New methods for mapping synaptic connections and recording neural signals generate rich and complex data on the structure and dynamics of brain networks. Making sense of these data will require a concerted effort directed at data analysis and reduction as well as computational modeling.

    • Olaf Sporns
  • Commentary |

    Opinions diverge on whether mapping the synaptic connectivity of the brain is a good idea. Here we argue that albeit their limitations, such maps will reveal essential characteristics of neural circuits that would otherwise be inaccessible.

    • Joshua L Morgan
    •  & Jeff W Lichtman
  • Commentary |

    By delivering precise, reproducible quantification of proteins of interest in biological samples, targeted proteomics approaches are allowing researchers to apply the scientific method using mass spectrometry.

    • Paola Picotti
    • , Bernd Bodenmiller
    •  & Ruedi Aebersold
  • Commentary |

    Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems.

    • Anel Mahmutovic
    • , David Fange
    • , Otto G Berg
    •  & Johan Elf
  • Commentary |

    Widely used behavioral assays need re-evaluation and validation against their intended use. We focus here on measures of chronic anxiety in mouse models and posit that widely used assays such as the open-field test are performed at the wrong time, for inadequate durations and using inappropriate mouse strains. We propose that behavioral assays be screened for usefulness on the basis of their replicability across laboratories.

    • Ehud Fonio
    • , Ilan Golani
    •  & Yoav Benjamini
  • Commentary |

    Many scholars claim there is a consensus on broad consent for biobanking. We analyzed the literature in PubMed and found no evidence for consensus. Public perception studies report mixed findings on consent, but many biobanks adopt broad consent. A belief in consensus may stem from knowledge of biobank consent practices.

    • Zubin Master
    • , Erin Nelson
    • , Blake Murdoch
    •  & Timothy Caulfield
  • Commentary |

    Driven by the importance of spatial and physical factors in cellular processes and the size and complexity of modern image data, computational analysis of biological imagery has become a vital emerging sub-discipline of bioinformatics and computer vision.

    • Gene Myers
  • Commentary |

    We discuss the advantages and challenges of the open-source strategy in biological image analysis and argue that its full impact will not be realized without better support and recognition of software engineers' contributions to the biological sciences and more support of this development model from funders and institutions.

    • Albert Cardona
    •  & Pavel Tomancak
  • Commentary |

    Bioimaging software developed in a research setting often is not widely used by the scientific community. We suggest that, to maximize both the public's and researchers' investments, usability should be a more highly valued goal. We describe specific characteristics of usability toward which bioimaging software projects should aim.

    • Anne E Carpenter
    • , Lee Kamentsky
    •  & Kevin W Eliceiri
  • Commentary |

    Informatics has driven mass spectrometry–based protein analysis to create large-scale methods for proteomics. As software algorithms have developed, comparisons between algorithms are inevitable. We outline steps for fair and objective comparisons that will make true innovations apparent.

    • John R Yates III
    • , Sung Kyu Robin Park
    • , Claire M Delahunty
    • , Tao Xu
    • , Jeffrey N Savas
    • , Daniel Cociorva
    •  & Paulo Costa Carvalho
  • Commentary |

    Engineered nucleases have advanced the field of gene therapy with the promise of targeted genome modification as a treatment for human diseases. Here we discuss why engineered nucleases are an exciting research tool for gene editing and consider their applications to a range of biological questions.

    • Moira A McMahon
    • , Meghdad Rahdar
    •  & Matthew Porteus
  • Commentary |

    Bioorthogonal chemistry allows a wide variety of biomolecules to be specifically labeled and probed in living cells and whole organisms. Here we discuss the history of bioorthogonal reactions and some of the most interesting and important advances in the field.

    • Michael Boyce
    •  & Carolyn R Bertozzi
  • Commentary |

    A diverse array of small molecule–based fluorescent probes is available for many different types of biological experiments. Here we examine the history of these probes and discuss some of the most interesting applications.

    • Tasuku Ueno
    •  & Tetsuo Nagano
  • Commentary |

    In recent years, single-molecule force spectroscopy techniques have been used to study how inter- and intramolecular interactions control the assembly and functional state of biomolecular machinery in vitro. Here we discuss the problems and challenges that need to be addressed to bring these technologies into living cells and to learn how cellular machinery is controlled in vivo.

    • Yves F Dufrêne
    • , Evan Evans
    • , Andreas Engel
    • , Jonne Helenius
    • , Hermann E Gaub
    •  & Daniel J Müller