4.4 Article

Methods for analyzing neuronal structure and activity in Caenorhabditis elegans

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans

Eviatar Yemini et al.

Summary: NeuroPAL is a multicolor transgene that helps resolve neuronal identities in C. elegans. It can be used with various reporters of gene expression or neuronal dynamics and has been utilized in studies related to metabotropic receptor expression, cell fate changes, and brainwide activity in response to chemosensory cues.
Article Genetics & Heredity

A nervous system-specific subnuclear organelle in Caenorhabditis elegans

Kenneth Pham et al.

Summary: We have identified a novel subnuclear organelle, NUN bodies, in the nematode Caenorhabditis elegans, which are highly cell type specific and only present in neuronal, glial, and neuron-like cells. The formation of NUN bodies is independent of transcription factors and their remodeling in canal-associated neurons depends on the Prd-type homeobox gene ceh-10. This unique subnuclear organelle raises questions about the biochemical processes in the nucleus that differentiate nervous system-associated cells from other cell types.

GENETICS (2021)

Article Multidisciplinary Sciences

Structural and developmental principles of neuropil assembly in C. elegans

Mark W. Moyle et al.

Summary: Neuropil is a fundamental tissue organization in the brain, where densely packed neurons form precise circuit architecture. Through a diffusion condensation algorithm, nested circuit structures within the nerve ring of Caenorhabditis elegans were identified, revealing a stratified architecture that segregates sensory information and motor outputs. Using high resolution microscopy and cell-tracking algorithms, the study uncovered principles of cell position, migration, and outgrowth that guide the organization of the layered neuropil.

NATURE (2021)

Article Multidisciplinary Sciences

A multi-scale brain map derived from whole-brain volumetric reconstructions

Christopher A. Brittin et al.

Summary: The organization of the animal nervous system is crucial for body functions, relying on features across different scales. The research successfully presented a structure-function model of the main neuropil in the nematode Caenorhabditis elegans, revealing the internal organization and connectivity patterns within the nerve ring.

NATURE (2021)

Article Biology

Graphical-model framework for automated annotation of cell identities in dense cellular images

Shivesh Chaudhary et al.

Summary: This article introduces a probabilistic-graphical-model framework, CRF_ID, based on Conditional Random Fields, for unbiased and automated cell identification. CRF_ID achieves higher accuracy and better robustness against challenging noise conditions in experimental data compared to existing methods. Additionally, it can boost accuracy by efficiently building atlases from annotated data and easily adding new features.
Article Neurosciences

The connectome of the Caenorhabditis elegans pharynx

Steven J. Cook et al.

JOURNAL OF COMPARATIVE NEUROLOGY (2020)

Article Neurosciences

Soma-Targeted Imaging of Neural Circuits by Ribosome Tethering

Yiming Chen et al.

NEURON (2020)

Review Biochemistry & Molecular Biology

Imaging voltage and brain chemistry with genetically encoded sensors and modulators

Akash Pal et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2020)

Article Neurosciences

Brain-wide representations of ongoing behavior: a universal principle?

Harris S. Kaplan et al.

CURRENT OPINION IN NEUROBIOLOGY (2020)

Article Biochemical Research Methods

NuSeT: A deep learning tool for reliably separating and analyzing crowded cells

Linfeng Yang et al.

PLOS COMPUTATIONAL BIOLOGY (2020)

Article Multidisciplinary Sciences

Whole-animal connectomes of both Caenorhabditis elegans sexes

Steven J. Cook et al.

NATURE (2019)

Article Multidisciplinary Sciences

Rhodopsin-based voltage imaging tools for use in muscles and neurons of Caenorhabditis elegans

Negin Azimi Hashemi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Bright and photostable chemigenetic indicators for extended in vivo voltage imaging

Ahmed S. Abdelfattah et al.

SCIENCE (2019)

Article Biochemical Research Methods

Real-time volumetric microscopy of in vivo dynamics and large-scale samples with SCAPE 2.0

Venkatakaushik Voleti et al.

NATURE METHODS (2019)

Article Biochemistry & Molecular Biology

Ultrafast Two-Photon Imaging of a High-Gain Voltage Indicator in Awake Behaving Mice

Vincent Villette et al.

Article Biochemistry & Molecular Biology

A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster

Zhihao Zheng et al.

Correction Biochemistry & Molecular Biology

A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters (vol 14, pg 352, 2018)

Kiryl D. Piatkevich et al.

NATURE CHEMICAL BIOLOGY (2018)

Article Multidisciplinary Sciences

Measurement of intracellular concentration of fluorescently-labeled targets in living cells

Volodymyr Cherkas et al.

PLOS ONE (2018)

Article Biochemistry & Molecular Biology

C. elegans AWA Olfactory Neurons Fire Calcium-Mediated All-or-None Action Potentials

Qiang Liu et al.

Article Biology

Sensorimotor integration in Caenorhabditis elegans: a reappraisal towards dynamic and distributed computations

Harris S. Kaplan et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2018)

Article Biochemical Research Methods

Fast, in vivo voltage imaging using a red fluorescent indicator

Madhuvanthi Kannan et al.

NATURE METHODS (2018)

Review Neurosciences

An Inconvenient Truth: Calcium Sensors Are Calcium Buffers

Shane M. McMahon et al.

TRENDS IN NEUROSCIENCES (2018)

Article Neurosciences

A Pipeline for Volume Electron Microscopy of the Caenorhabditis elegans Nervous System

Ben Mulcahy et al.

FRONTIERS IN NEURAL CIRCUITS (2018)

Article Biochemical Research Methods

Pneumatic stimulation of C. elegans mechanoreceptor neurons in a microfluidic trap

Adam L. Nekimken et al.

LAB ON A CHIP (2017)

Article Biochemical Research Methods

Automated and controlled mechanical stimulation and functional imaging in vivo in C. elegans

Yongmin Cho et al.

LAB ON A CHIP (2017)

Article Multidisciplinary Sciences

A global brain state underlies C. elegans sleep behavior

Annika L. A. Nichols et al.

SCIENCE (2017)

Article Biochemical Research Methods

Automatically tracking neurons in a moving and deforming brain

Jeffrey P. Nguyen et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Multidisciplinary Sciences

Sex-specific pruning of neuronal synapses in Caenorhabditis elegans

Meital Oren-Suissa et al.

NATURE (2016)

Article Biochemical Research Methods

Quantitative assessment of fluorescent proteins

Paula J. Cranfill et al.

NATURE METHODS (2016)

Review Neurosciences

Genetically encoded indicators of neuronal activity

Michael Z. Lin et al.

NATURE NEUROSCIENCE (2016)

Review Behavioral Sciences

Comparative Connectomics

Martijn P. van den Heuvel et al.

TRENDS IN COGNITIVE SCIENCES (2016)

Article Biochemical Research Methods

Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space

Yu Toyoshima et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Global Brain Dynamics Embed the Motor Command Sequence of Caenorhabditis elegans

Saul Kato et al.

Article Biochemistry & Molecular Biology

Saturated Reconstruction of a Volume of Neocortex

Narayanan Kasthuri et al.

Article Neurosciences

Serotonin differentially modulates Ca2+ transients and depolarization in a C-elegans nociceptor

Jeffrey A. Zahratka et al.

JOURNAL OF NEUROPHYSIOLOGY (2015)

Article Biochemical Research Methods

Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics

Kenneth J. Hayworth et al.

NATURE METHODS (2015)

Article Computer Science, Interdisciplinary Applications

BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies

Yinan Wan et al.

NEUROINFORMATICS (2015)

Article Cell Biology

A Circuit for Gradient Climbing in C. elegans Chemotaxis

Johannes Larsch et al.

CELL REPORTS (2015)

Article Biochemical Research Methods

Automated detection and tracking of many cells by using 4D live-cell imaging data

Terumasa Tokunaga et al.

BIOINFORMATICS (2014)

Review Multidisciplinary Sciences

The present and future role of microfluidics in biomedical research

Eric K. Sackmann et al.

NATURE (2014)

Article Biochemical Research Methods

Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes

Thomas Thestrup et al.

NATURE METHODS (2014)

Article Biochemical Research Methods

Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy

Robert Prevedel et al.

NATURE METHODS (2014)

Article Multidisciplinary Sciences

Inducible and titratable silencing of Caenorhabditis elegans neurons in vivo with histamine-gated chloride channels

Navin Pokala et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Bright and fast multicoloured voltage reporters via electrochromic FRET

Peng Zou et al.

NATURE COMMUNICATIONS (2014)

Article Biochemistry & Molecular Biology

Modular Control of Glutamatergic Neuronal Identity in C. elegans by Distinct Homeodomain Proteins

Esther Serrano-Saiz et al.

Article Biochemistry & Molecular Biology

Serotonin and the Neuropeptide PDF Initiate and Extend Opposing Behavioral States in C. elegans

Steven W. Flavell et al.

Article Biochemistry & Molecular Biology

System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes

Daniel J. Bumbarger et al.

Article Neurosciences

O2-Sensing Neurons Control CO2 Response in C. elegans

Mayra A. Carrillo et al.

JOURNAL OF NEUROSCIENCE (2013)

Article Neurosciences

The Rich Club of the C. elegans Neuronal Connectome

Emma K. Towlson et al.

JOURNAL OF NEUROSCIENCE (2013)

Article Multidisciplinary Sciences

Ultrasensitive fluorescent proteins for imaging neuronal activity

Tsai-Wen Chen et al.

NATURE (2013)

Article Biochemical Research Methods

Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light

Tina Schrodel et al.

NATURE METHODS (2013)

Review Neurosciences

Computational methods and challenges for large-scale circuit mapping

Moritz Helmstaedter et al.

CURRENT OPINION IN NEUROBIOLOGY (2012)

Article Neurosciences

Imaging neural circuit dynamics with a voltage-sensitive fluorescent protein

Walther Akemann et al.

JOURNAL OF NEUROPHYSIOLOGY (2012)

Article Neurosciences

Optimization of a GCaMP Calcium Indicator for Neural Activity Imaging

Jasper Akerboom et al.

JOURNAL OF NEUROSCIENCE (2012)

Article Multidisciplinary Sciences

Compartmentalized calcium dynamics in a C. elegans interneuron encode head movement

Michael Hendricks et al.

NATURE (2012)

Article Biochemical Research Methods

Elastic volume reconstruction from series of ultra-thin microscopy sections

Stephan Saalfeld et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Fiji: an open-source platform for biological-image analysis

Johannes Schindelin et al.

NATURE METHODS (2012)

Article Neurosciences

Tonic signaling from O2 sensors sets neural circuit activity and behavioral state

Karl Emanuel Busch et al.

NATURE NEUROSCIENCE (2012)

Review Neurosciences

The economy of brain network organization

Edward T. Bullmore et al.

NATURE REVIEWS NEUROSCIENCE (2012)

Article Multidisciplinary Sciences

TrakEM2 Software for Neural Circuit Reconstruction

Albert Cardona et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

Photo-inducible cell ablation in Caenorhabditis elegans using the genetically encoded singlet oxygen generating protein miniSOG

Yingchuan B. Qi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

The Connectome of a Decision-Making Neural Network

Travis A. Jarrell et al.

SCIENCE (2012)

Article Neurosciences

C-elegans multi-dendritic sensory neurons: Morphology and function

Adi Albeg et al.

MOLECULAR AND CELLULAR NEUROSCIENCE (2011)

Article Multidisciplinary Sciences

Network anatomy and in vivo physiology of visual cortical neurons

Davi D. Bock et al.

NATURE (2011)

Article Biochemical Research Methods

High-content behavioral analysis of Caenorhabditis elegans in precise spatiotemporal chemical environments

Dirk R. Albrecht et al.

NATURE METHODS (2011)

Article Multidisciplinary Sciences

Transfer characteristics of a thermosensory synapse in Caenorhabditis elegans

Anusha Narayan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Optogenetic analysis of synaptic transmission in the central nervous system of the nematode Caenorhabditis elegans

Theodore H. Lindsay et al.

NATURE COMMUNICATIONS (2011)

Article Multidisciplinary Sciences

Neural coding in a single sensory neuron controlling opposite seeking behaviours in Caenorhabditis elegans

Atsushi Kuhara et al.

NATURE COMMUNICATIONS (2011)

Article Biochemical Research Methods

Structural Properties of the Caenorhabditis elegans Neuronal Network

Lav R. Varshney et al.

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biochemical Research Methods

Conditions for dye-filling of sensory neurons in Caenorhabditis elegans

Yong-Guang Tong et al.

JOURNAL OF NEUROSCIENCE METHODS (2010)

Article Biochemical Research Methods

Automated imaging of neuronal activity in freely behaving Caenorhabditis elegans

Juliette Ben Arous et al.

JOURNAL OF NEUROSCIENCE METHODS (2010)

Article Biochemical Research Methods

Imaging brain electric signals with genetically targeted voltage-sensitive fluorescent proteins

Walther Akemann et al.

NATURE METHODS (2010)

Article Neurosciences

Complex network measures of brain connectivity: Uses and interpretations

Mikail Rubinov et al.

NEUROIMAGE (2010)

Article Multidisciplinary Sciences

The Fusogen EFF-1 Controls Sculpting of Mechanosensory Dendrites

Meital Oren-Suissa et al.

SCIENCE (2010)

Article Biochemical Research Methods

Efficient Physical Embedding of Topologically Complex Information Processing Networks in Brains and Computer Circuits

Danielle S. Bassett et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Article Biochemical Research Methods

CATMAID: collaborative annotation toolkit for massive amounts of image data

Stephan Saalfeld et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans

Xiao Liu et al.

Article Multidisciplinary Sciences

Natural variation in a neural globin tunes oxygen sensing in wild Caenorhabditis elegans

Annelie Persson et al.

NATURE (2009)

Article Biochemical Research Methods

A 3D digital atlas of C. elegans and its application to single-cell analyses

Fuhui Long et al.

NATURE METHODS (2009)

Letter Neurosciences

First report of action potentials in a C. elegans neuron is premature

Shawn R. Lockery et al.

NATURE NEUROSCIENCE (2009)

Article Neurosciences

The quest for action potentials in C. elegans neurons hits a plateau

Shawn R. Lockery et al.

NATURE NEUROSCIENCE (2009)

Review Neurosciences

Complex brain networks: graph theoretical analysis of structural and functional systems

Edward T. Bullmore et al.

NATURE REVIEWS NEUROSCIENCE (2009)

Article Multidisciplinary Sciences

Graded synaptic transmission at the Caenorhabditis elegans neuromuscular junction

Qiang Liu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Editorial Material Neurosciences

Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling

Graham Knott et al.

JOURNAL OF NEUROSCIENCE (2008)

Article Biochemical Research Methods

Improving membrane voltage measurements using FRET with new fluorescent proteins

Hidekazu Tsutsui et al.

NATURE METHODS (2008)

Article Biochemical Research Methods

Automated on-chip rapid microscopy, phenotyping and sorting of C. elegans

Kwanghun Chung et al.

NATURE METHODS (2008)

Article Biochemical Research Methods

A genetically encoded calcium indicator for chronic in vivo two-photon imaging

Marco Mank et al.

NATURE METHODS (2008)

Article Neurosciences

Action potentials contribute to neuronal signaling in C-elegans

Jerry E. Mellem et al.

NATURE NEUROSCIENCE (2008)

Review Neurosciences

Noise in the nervous system

A. Aldo Faisal et al.

NATURE REVIEWS NEUROSCIENCE (2008)

Article Multidisciplinary Sciences

Dissecting a circuit for olfactory behaviour in Caenorhabditis elegans

Sreekanth H. Chalasani et al.

NATURE (2007)

Article Biochemical Research Methods

Microfluidics for in vivo imaging of neuronal and behavioral activity in Caenorhabditis elegans

Nikos Chronis et al.

NATURE METHODS (2007)

Article Multidisciplinary Sciences

Targeted cell killing by reconstituted caspases

Dattananda S. Chelur et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Modularity and community structure in networks

M. E. J. Newman

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Cell Biology

Regulation of synaptic transmission by RAB-3 and RAB-27 in Caenorhabditis elegans

Timothy R. Mahoney et al.

MOLECULAR BIOLOGY OF THE CELL (2006)

Article Multidisciplinary Sciences

Wiring optimization can relate neuronal structure and function

BL Chen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Multidisciplinary Sciences

Imaging cellular signals in the heart in vivo:: Cardiac expression of the high-signal Ca2+ indicator GCaMP2

YN Tallini et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Multidisciplinary Sciences

Automated cell lineage tracing in Caenorhabditis elegans

ZR Bao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Multidisciplinary Sciences

MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision

RJ Johnston et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

In vivo imaging of C-elegans ASH neurons:: cellular response and adaptation to chemical repellents

MA Hilliard et al.

EMBO JOURNAL (2005)

Article Biochemistry & Molecular Biology

Genetically encoded indicators of cellular calcium dynamics based on troponin C and green fluorescent protein

N Heim et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2004)

Article Biochemistry & Molecular Biology

The C. elegans thermosensory neuron AFD responds to warming

KD Kimura et al.

CURRENT BIOLOGY (2004)

Article Multidisciplinary Sciences

Expanded dynamic range of fluorescent indicators for Ca2+ by circularly permuted yellow fluorescent proteins

T Nagai et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Computer Science, Software Engineering

Combining hierarchy and energy for drawing directed graphs

L Carmel et al.

IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS (2004)

Article Multidisciplinary Sciences

Network motifs: Simple building blocks of complex networks

R Milo et al.

SCIENCE (2002)

Article Biochemistry & Molecular Biology

C-elegans responds to chemical repellents by integrating sensory inputs from the head and the tail

MA Hilliard et al.

CURRENT BIOLOGY (2002)

Article Biotechnology & Applied Microbiology

A high signal-to-noise Ca2+ probe composed of a single green fluorescent protein

J Nakai et al.

NATURE BIOTECHNOLOGY (2001)

Article Biochemistry & Molecular Biology

WormBase: network access to the genome and biology of Caenorhabditis elegans

L Stein et al.

NUCLEIC ACIDS RESEARCH (2001)