Volume 23 Issue 12, December 2020

Volume 23 Issue 12

Focus on neuroscience methods

In this focus issue on neuroscience methods we present a series of reviews, perspectives and commentaries that highlight advances in methods and analytical approaches and provide guidelines and best practices in various areas of neuroscience.

Image: Jennie Vallis. Cover design: Marina Corral Spence.

Editorial

  • Editorial |

    In this special issue, we present a series of reviews, perspectives and commentaries that highlight advances in methods and analytical approaches and provide guidelines and best practices in various areas of neuroscience.

Comment

  • Comment | | Open Access

    • Rafael Yuste
    • , Michael Hawrylycz
    • , Nadia Aalling
    • , Argel Aguilar-Valles
    • , Detlev Arendt
    • , Ruben Armananzas Arnedillo
    • , Giorgio A. Ascoli
    • , Concha Bielza
    • , Vahid Bokharaie
    • , Tobias Borgtoft Bergmann
    • , Irina Bystron
    • , Marco Capogna
    • , Yoonjeung Chang
    • , Ann Clemens
    • , Christiaan P. J. de Kock
    • , Javier DeFelipe
    • , Sandra Esmeralda Dos Santos
    • , Keagan Dunville
    • , Dirk Feldmeyer
    • , Richárd Fiáth
    • , Gordon James Fishell
    • , Angelica Foggetti
    • , Xuefan Gao
    • , Parviz Ghaderi
    • , Natalia A. Goriounova
    • , Onur Güntürkün
    • , Kenta Hagihara
    • , Vanessa Jane Hall
    • , Moritz Helmstaedter
    • , Suzana Herculano
    • , Markus M. Hilscher
    • , Hajime Hirase
    • , Jens Hjerling-Leffler
    • , Rebecca Hodge
    • , Josh Huang
    • , Rafiq Huda
    • , Konstantin Khodosevich
    • , Ole Kiehn
    • , Henner Koch
    • , Eric S. Kuebler
    • , Malte Kühnemund
    • , Pedro Larrañaga
    • , Boudewijn Lelieveldt
    • , Emma Louise Louth
    • , Jan H. Lui
    • , Huibert D. Mansvelder
    • , Oscar Marin
    • , Julio Martinez-Trujillo
    • , Homeira Moradi Chameh
    • , Alok Nath
    • , Maiken Nedergaard
    • , Pavel Němec
    • , Netanel Ofer
    • , Ulrich Gottfried Pfisterer
    • , Samuel Pontes
    • , William Redmond
    • , Jean Rossier
    • , Joshua R. Sanes
    • , Richard Scheuermann
    • , Esther Serrano-Saiz
    • , Jochen F. Steiger
    • , Peter Somogyi
    • , Gábor Tamás
    • , Andreas Savas Tolias
    • , Maria Antonietta Tosches
    • , Miguel Turrero García
    • , Hermany Munguba Vieira
    • , Christian Wozny
    • , Thomas V. Wuttke
    • , Liu Yong
    • , Juan Yuan
    • , Hongkui Zeng
    •  & Ed Lein

News & Views

  • News & Views |

    A new technique developed by Garcia-Marques and colleagues uses CRISPR–Cas9 editing to activate an ordered sequence of fluorescent markers in stem cells and their progeny. These tools represent a new way to probe the spatial and temporal patterns of cell lineage progression.

    • Clayton M. Carey
    •  & James A. Gagnon

  • News & Views |

    Network neuroscientists envision the brain as a network of nodes (regions) linked via edges (connections). A long-held assumption is that node-centric interactions are the primary phenomena of interest. Faskowitz et al. introduce a novel edge-centric framework with the potential to usher in a new era of discovery in connectomics research.

    • Lucina Q. Uddin

Perspectives

Review Articles

  • Review Article |

    In this Primer article, Bijsterbosch and colleagues provide an accessible discussion of the challenges faced in analytical representations of functional brain organization and provide clear recommendations to unite a fractionated field.

    • Janine Bijsterbosch
    • , Samuel J. Harrison
    • , Saad Jbabdi
    • , Mark Woolrich
    • , Christian Beckmann
    • , Stephen Smith
    •  & Eugene P. Duff

  • Review Article |

    This Review discusses two high-throughput techniques—massively parallel reporter assays (MPRAs) and CRISPR screens—focusing on their potential to validate non-coding genetic risk variants in human stem cell models of complex brain disorders.

    • Kayla G. Townsley
    • , Kristen J. Brennand
    •  & Laura M. Huckins

  • Review Article |

    Behavioral quantification is changing neuroscience. Pereira et al. provide an overview of the latest advances in motion tracking and behavior prediction and discuss how these methods are used to understand the brain in ways not previously possible.

    • Talmo D. Pereira
    • , Joshua W. Shaevitz
    •  & Mala Murthy

Brief Communications

Articles

  • Article |

    Chun et al. find that a severe model of reactive astrocytes overproduces hydrogen peroxide, leading to the development of Alzheimer’s disease-like pathologies, including neurodegeneration, tauopathy and memory impairment.

    • Heejung Chun
    • , Hyeonjoo Im
    • , You Jung Kang
    • , Yunha Kim
    • , Jin Hee Shin
    • , Woojin Won
    • , Jiwoon Lim
    • , Yeonha Ju
    • , Yongmin Mason Park
    • , Sunpil Kim
    • , Seung Eun Lee
    • , Jaekwang Lee
    • , Junsung Woo
    • , Yujin Hwang
    • , Hyesun Cho
    • , Seonmi Jo
    • , Jong-Hyun Park
    • , Daesoo Kim
    • , Doo Yeon Kim
    • , Jeong-Sun Seo
    • , Byoung Joo Gwag
    • , Young Soo Kim
    • , Ki Duk Park
    • , Bong-Kiun Kaang
    • , Hansang Cho
    • , Hoon Ryu
    •  & C. Justin Lee

  • Article |

    Alzheimer’s disease is often considered a disease of neurons. This study reveals that astrocytes are also impaired by the disease and that these cells contribute more to memory deterioration than previously thought.

    • Kevin Richetin
    • , Pascal Steullet
    • , Mathieu Pachoud
    • , Romain Perbet
    • , Enea Parietti
    • , Mathischan Maheswaran
    • , Sabiha Eddarkaoui
    • , Séverine Bégard
    • , Catherine Pythoud
    • , Maria Rey
    • , Raphaëlle Caillierez
    • , Kim Q Do
    • , Sophie Halliez
    • , Paola Bezzi
    • , Luc Buée
    • , Geneviève Leuba
    • , Morvane Colin
    • , Nicolas Toni
    •  & Nicole Déglon

  • Article |

    Uhlmann et al. show that the preclinical phase of Alzheimer’s disease may in fact be a relatively late manifestation of a much earlier pathogenic and targetable process of seed formation and propagation.

    • Ruth E. Uhlmann
    • , Christine Rother
    • , Jay Rasmussen
    • , Juliane Schelle
    • , Carina Bergmann
    • , Emily M. Ullrich Gavilanes
    • , Sarah K. Fritschi
    • , Anika Buehler
    • , Frank Baumann
    • , Angelos Skodras
    • , Rawaa Al-Shaana
    • , Natalie Beschorner
    • , Lan Ye
    • , Stephan A. Kaeser
    • , Ulrike Obermüller
    • , Søren Christensen
    • , Fredrik Kartberg
    • , Jeffrey B. Stavenhagen
    • , Jens-Ulrich Rahfeld
    • , Holger Cynis
    • , Fang Qian
    • , Paul H. Weinreb
    • , Thierry Bussiere
    • , Lary C. Walker
    • , Matthias Staufenbiel
    •  & Mathias Jucker

  • Article |

    Using cryo-electron tomography to detect individual GABAA receptors in hippocampal synapses, we discovered a hierarchical and mesophasic organization of inhibitory postsynaptic density proteins that enables efficient synaptic transmission.

    • Yun-Tao Liu
    • , Chang-Lu Tao
    • , Xiaokang Zhang
    • , Wenjun Xia
    • , Dong-Qing Shi
    • , Lei Qi
    • , Cheng Xu
    • , Rong Sun
    • , Xiao-Wei Li
    • , Pak-Ming Lau
    • , Z. Hong Zhou
    •  & Guo-Qiang Bi

  • Article |

    When people are isolated, they crave social interactions. Midbrain craving regions were activated by food in hungry people, and by social interactions in people mandated to be isolated.

    • Livia Tomova
    • , Kimberly L. Wang
    • , Todd Thompson
    • , Gillian A. Matthews
    • , Atsushi Takahashi
    • , Kay M. Tye
    •  & Rebecca Saxe

Resources

Technical Reports

  • Technical Report |

    Garcia-Marques et al. present CLADES, an innovative approach to study neuronal lineages based on CRISPR. Inspired by synthetic biology, CLADES relies on a system of genetic switches to activate and inactivate reporter genes in a predetermined order.

    • Jorge Garcia-Marques
    • , Isabel Espinosa-Medina
    • , Kai-Yuan Ku
    • , Ching-Po Yang
    • , Minoru Koyama
    • , Hung-Hsiang Yu
    •  & Tzumin Lee

    Collection:

  • Technical Report |

    This study describes a series of new gene-regulatory sequences that restrict expression of viral transgenes to specific interneuron subtypes, allowing for selective monitoring and manipulation of their activity from mice to humans.

    • Douglas Vormstein-Schneider
    • , Jessica D. Lin
    • , Kenneth A. Pelkey
    • , Ramesh Chittajallu
    • , Baolin Guo
    • , Mario A. Arias-Garcia
    • , Kathryn Allaway
    • , Sofia Sakopoulos
    • , Gates Schneider
    • , Olivia Stevenson
    • , Josselyn Vergara
    • , Jitendra Sharma
    • , Qiangge Zhang
    • , Tom P. Franken
    • , Jared Smith
    • , Leena A. Ibrahim
    • , Kevin J. M astro
    • , Ehsan Sabri
    • , Shuhan Huang
    • , Emilia Favuzzi
    • , Timothy Burbridge
    • , Qing Xu
    • , Lihua Guo
    • , Ian Vogel
    • , Vanessa Sanchez
    • , Giuseppe A. Saldi
    • , Bram L. Gorissen
    • , Xiaoqing Yuan
    • , Kareem A. Zaghloul
    • , Orrin Devinsky
    • , Bernardo L. Sabatini
    • , Renata Batista-Brito
    • , John Reynolds
    • , Guoping Feng
    • , Zhanyan Fu
    • , Chris J. McBain
    • , Gord Fishell
    •  & Jordane Dimidschstein

  • Technical Report |

    Kuan, Phelps, et al. used synchrotron X-ray imaging and deep learning to map dense neuronal wiring in fly and mouse tissue, enabling examination of individual cells and connectivity in circuits governing motor control and perceptual decision-making.

    • Aaron T. Kuan
    • , Jasper S. Phelps
    • , Logan A. Thomas
    • , Tri M. Nguyen
    • , Julie Han
    • , Chiao-Lin Chen
    • , Anthony W. Azevedo
    • , John C. Tuthill
    • , Jan Funke
    • , Peter Cloetens
    • , Alexandra Pacureanu
    •  & Wei-Chung Allen Lee

  • Technical Report |

    A method for parameterizing electrophysiological neural power spectra into periodic and aperiodic components is introduced, addressing limitations of common approaches. The method is validated in simulation and demonstrated on real data applications.

    • Thomas Donoghue
    • , Matar Haller
    • , Erik J. Peterson
    • , Paroma Varma
    • , Priyadarshini Sebastian
    • , Richard Gao
    • , Torben Noto
    • , Antonio H. Lara
    • , Joni D. Wallis
    • , Robert T. Knight
    • , Avgusta Shestyuk
    •  & Bradley Voytek

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