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Open Access
Featured
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Article
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A multicolor suite for deciphering population coding of calcium and cAMP in vivo
Improved green cAMP and red calcium sensors were developed to facilitate dual-color imaging in vivo. These sensors will allow studying the relationship between calcium and cAMP signaling.
- Tatsushi Yokoyama
- , Satoshi Manita
- & Masayuki Sakamoto
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This Month |
The brown seaweed Ectocarpus
Brown seaweeds are multicellular eukaryotes that have been evolving independently of animals and plants for more than a billion years. The filamentous brown alga Ectocarpus has been used as a model to understand the biology of these enigmatic organisms and to shed light on a range of major questions, from the molecular basis of complex developmental patterns to the evolution of sex.
- Susana M. Coelho
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Article |
Improved green and red GRAB sensors for monitoring spatiotemporal serotonin release in vivo
Deng et al. expand the toolbox of neurotransmitter sensors with high-sensitivity green and red genetically encoded serotonin sensors. These are suitable for in vivo applications, as demonstrated in a variety of applications in mice.
- Fei Deng
- , Jinxia Wan
- & Yulong Li
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Research Highlight |
Predicting neural activity from facial expressions
Facemap tracks keypoints on the mouse face and feeds the information into a deep neural network to predict neural activity.
- Nina Vogt
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Article |
Improved green and red GRAB sensors for monitoring dopaminergic activity in vivo
Next-generation red and green G-protein-coupled receptor-based dopamine sensors with improved properties have been developed. Their performance is demonstrated in cell culture, in brain slices and in vivo in the mouse.
- Yizhou Zhuo
- , Bin Luo
- & Yulong Li
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Article
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Uncovering developmental time and tempo using deep learning
A deep learning-based method that uses microscopy images to stage embryos and analyze developmental time.
- Nikan Toulany
- , Hernán Morales-Navarrete
- & Patrick Müller
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Resource
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Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration
An updated version of the Waxholm Space atlas of the rat brain includes more detailed annotations of several brain regions, including the cortex, striatopallidal region, midbrain and thalamus, expanding the previous version with 112 new and 57 revised structures.
- Heidi Kleven
- , Ingvild E. Bjerke
- & Trygve B. Leergaard
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Article |
Sensitive multicolor indicators for monitoring norepinephrine in vivo
Red and green genetically encoded indicators for norepinephrine have been developed and employed to monitor norepinephrine during locomotion and reward behavior in mice. The strategy used for generating these indicators also produced indicators for other neuromodulators.
- Zacharoula Kagiampaki
- , Valentin Rohner
- & Tommaso Patriarchi
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Article
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Voltage-Seq: all-optical postsynaptic connectome-guided single-cell transcriptomics
Voltage-Seq combines voltage imaging, optogenetics and single-cell RNA-seq for high-throughput analysis of functional and transcriptomic properties of neurons in situ.
- Veronika Csillag
- , Marianne Hiriart Bizzozzero
- & János Fuzik
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This Month |
The cavefish Astyanax mexicanus
Astyanax mexicanus exists in two forms: a surface form that is abundantly distributed throughout freshwater bodies in Middle America and a blind subterranean form endemic to caves in northeastern Mexico. These diverse fish populations have become a vertebrate model for investigating the genetic basis of environmental adaptation.
- Nicolas Rohner
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News & Views |
Lighting up action potentials with fast and bright voltage sensors
Three groundbreaking studies have created a new generation of genetically encoded voltage indicators, empowering us to tackle a host of questions on our path toward understanding the brain.
- Alessio Andreoni
- & Lin Tian
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Article |
A positively tuned voltage indicator for extended electrical recordings in the brain
The ASAP4 family of genetically encoded voltage indicators allows recording of action potentials and subthreshold activity with either one- or two-photon microscopy over extended periods of time.
- S. Wenceslao Evans
- , Dong-Qing Shi
- & Michael Z. Lin
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Article
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Hardwiring tissue-specific AAV transduction in mice through engineered receptor expression
SELECTIV is an efficient method for tissue-specific AAV-mediated transgene expression in mice mediated by AAV receptor overexpression.
- James Zengel
- , Yu Xin Wang
- & Jan E. Carette
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Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development
MISAR-seq combines spatial-ATAC-seq and RNA-seq for spatial profiling of both chromatin accessibility and gene expression, as demonstrated in the developing mouse brain.
- Fuqing Jiang
- , Xin Zhou
- & Guangdun Peng
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Article
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Cross-modality supervised image restoration enables nanoscale tracking of synaptic plasticity in living mice
XTC is a supervised deep-learning-based image-restoration approach that is trained with images from different modalities and applied to an in vivo modality with no ground truth. XTC’s capabilities are demonstrated in synapse tracking in the mouse brain.
- Yu Kang T. Xu
- , Austin R. Graves
- & Jeremias Sulam
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Brief Communication
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High-contrast en bloc staining of mouse whole-brain and human brain samples for EM-based connectomics
For EM-based connectomics applications, a staining protocol for large tissue samples in the range of a centimeter has been developed, which avoids artifacts common with established protocols.
- Kun Song
- , Zhihui Feng
- & Moritz Helmstaedter
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Article
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Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission
iGluSnFR variants with improved signal-to-noise ratios and targeting to postsynaptic sites have been developed, enabling the analysis of glutamatergic neurotransmission in vivo as illustrated in the mouse visual and somatosensory cortex.
- Abhi Aggarwal
- , Rui Liu
- & Kaspar Podgorski
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Article
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Engineering of NEMO as calcium indicators with large dynamics and high sensitivity
The NEMO series of genetically encoded calcium indicators report calcium activity in neuronal and non-neuronal cells with high signal-to-baseline ratio, which is shown in neuronal culture, slice preparations, in vivo and in planta.
- Jia Li
- , Ziwei Shang
- & Youjun Wang
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Article |
Neural engineering with photons as synaptic transmitters
PhAST is a technology for establishing de novo or modulating synaptic transmission in a light-dependent manner in C. elegans. By combining a calcium-dependent luciferase on pre-synapses with channelrhodopsin on post-synapses, light serves as a synthetic neurotransmitter.
- Montserrat Porta-de-la-Riva
- , Adriana Carolina Gonzalez
- & Michael Krieg
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Article
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Rapid detection of neurons in widefield calcium imaging datasets after training with synthetic data
DeepWonder removes background signals from widefield calcium recordings and enables accurate and efficient neuronal segmentation with high throughput.
- Yuanlong Zhang
- , Guoxun Zhang
- & Qionghai Dai
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Article
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High-resolution line-scan Brillouin microscopy for live imaging of mechanical properties during embryo development
Line-scan Brillouin microscopy enables fast 3D imaging of mechanical properties with low phototoxicity, as shown for Drosophila and mouse embryos, as well as ascidians.
- Carlo Bevilacqua
- , Juan Manuel Gomez
- & Robert Prevedel
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Article |
High-speed low-light in vivo two-photon voltage imaging of large neuronal populations
A suite of tools including positive-going voltage indicators, a high-speed two-photon microscope, and denoising software enables prolonged imaging of electrical activity in neurons with limited toxicity.
- Jelena Platisa
- , Xin Ye
- & Jerry L. Chen
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Brief Communication |
mScarlet3: a brilliant and fast-maturing red fluorescent protein
Two mScarlet variants with high brightness and fast maturation times have been evolved. These variants behave favorably as fusion tags and Förster resonance energy transfer acceptors.
- Theodorus W. J. Gadella Jr.
- , Laura van Weeren
- & Antoine Royant
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Brief Communication |
In vivo photopharmacology with a caged mu opioid receptor agonist drives rapid changes in behavior
CNV-Y-DAMGO enables photopharmacological manipulations of mu opioid receptor signaling in behaving mice with high temporal resolution.
- Xiang Ma
- , Desiree A. Johnson
- & Matthew R. Banghart
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Article |
Femtosecond laser microdissection for isolation of regenerating C. elegans neurons for single-cell RNA sequencing
Femtosecond laser microdissection enables transcriptomic analyses of single neurons based on their phenotype.
- Peisen Zhao
- , Sudip Mondal
- & Adela Ben-Yakar
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News & Views |
Linking connectome with transcriptome using a self-inactivating rabies virus
A self-inactivating rabies virus tracer allows long-term monitoring and transcriptomic profiling of synaptically connected cells.
- Shenqin Yao
- & Boaz P. Levi
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Brief Communication |
A modular architecture for organizing, processing and sharing neurophysiology data
A modular architecture for managing and sharing electrophysiology, behavior, colony management and other data has been built to support individual laboratories or large consortia.
- Luigi Acerbi
- , Valeria Aguillon-Rodriguez
- & Miles J. Wells
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Article |
Combining long-term circuit mapping and network transcriptomics with SiR-N2c
A self-inactivating variant of the CVS-N2c rabies virus enables both retrograde viral tracing and transcriptomic analyses, thereby allowing a combination of circuit mapping and molecular studies.
- Hassal Lee
- , Ernesto Ciabatti
- & Marco Tripodi
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Article |
Miniature three-photon microscopy maximized for scattered fluorescence collection
A three-photon miniature microscope with optimized light-collection efficiency facilitates imaging of neuronal activity throughout the cortex, as well as in the hippocampus, in freely moving mice.
- Chunzhu Zhao
- , Shiyuan Chen
- & Heping Cheng
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Article
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A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice
A lightweight three-photon miniature microscope allows imaging neuronal activity throughout the cortex in freely moving mice.
- Alexandr Klioutchnikov
- , Damian J. Wallace
- & Jason N. D. Kerr
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This Month |
The red harvester ant
Harvester ants live in desert grasslands and eat seeds. Colonies manage water stress by regulating foraging using olfactory interactions between outgoing and returning foragers. A long-term study in New Mexico shows how this collective behavior is evolving in drought conditions.
- Deborah M. Gordon
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Article |
Sensitive genetically encoded sensors for population and subcellular imaging of cAMP in vivo
cAMPFIREs are genetically encoded cAMP sensors that are suitable for in vivo imaging of cAMP signaling, as demonstrated in Drosophila larvae and behaving mice.
- Crystian I. Massengill
- , Landon Bayless-Edwards
- & Haining Zhong
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Resource
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Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain
This Resource presents a serial block-face EM dataset of the whole larval zebrafish brain, including automated segmentation of neurons, detection of synapses and reconstruction of circuitry for visual motion processing.
- Fabian Svara
- , Dominique Förster
- & Herwig Baier
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Brief Communication
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SyConn2: dense synaptic connectivity inference for volume electron microscopy
SyConn2 is a machine learning-based framework for inferring and analyzing the connectomes contained in a volume electron microscopy dataset of brain tissue, for example from the zebra finch.
- Philipp J. Schubert
- , Sven Dorkenwald
- & Joergen Kornfeld
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Article
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Estimation of skeletal kinematics in freely moving rodents
Pose estimation in combination with an anatomically constrained model allows inferring skeletal kinematics in rodents.
- Arne Monsees
- , Kay-Michael Voit
- & Jason N. D. Kerr
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This Month |
The turquoise killifish
A naturally short-lived fish opens the gates for rapid exploration of vertebrate aging.
- Itamar Harel
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Article
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A fluorescent sensor for real-time measurement of extracellular oxytocin dynamics in the brain
A fluorescent sensor for oxytocin called MTRIAOT has been developed. The sensor’s capabilities are demonstrated in fiber photometry measurements in freely behaving mice.
- Daisuke Ino
- , Yudai Tanaka
- & Masaaki Nishiyama
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This Month |
The crustacean Parhyale
Parhyale hawaiensis comes from tropical intertidal shores and mangroves. In research, it is used to explore topics ranging from embryonic development and regeneration, to tidal rhythms and environmental pollution.
- Michalis Averof
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Comment |
The EQIPD framework for rigor in the design, conduct, analysis and documentation of animal experiments
The EQIPD framework for rigor in animal experiments aims to unify current recommendations based on evidence behind their rationale and was prospectively tested for feasibility in multicenter animal experiments.
- Jan Vollert
- , Malcolm Macleod
- & Andrew S. C. Rice
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Article |
De novo construction of T cell compartment in humanized mice engrafted with iPSC-derived thymus organoids
Engraftment of human thymic organoids supports de novo development of a functional human T cell compartment in a humanized mouse model.
- Ann Zeleniak
- , Connor Wiegand
- & Yong Fan
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Editorial |
Creatures galore
In this issue, we are delighted to launch a new regular feature: the Creature Column.
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This Month |
Tardigrades
Tardigrades are everywhere. They’re tiny — usually under a millimeter long — and they’re mostly transparent, so they’re easy to miss. But you probably walk by them every day. We’ve been grooming them as emerging models for studying how body forms evolve and how biological materials can survive extreme conditions.
- Bob Goldstein
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Article
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Functional ultrasound localization microscopy reveals brain-wide neurovascular activity on a microscopic scale
Functional ultrasound localization microscopy monitors cerebrovascular blood flow by detecting the flow of injected microbubbles, providing access to brain activity at high spatiotemporal resolution.
- Noémi Renaudin
- , Charlie Demené
- & Mickael Tanter
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Directed evolution of adeno-associated virus for efficient gene delivery to microglia
Recombinant adeno-associated virus tools for enhanced microglial transduction in mice are reported. These viruses can be used to express functional reporters or genome editing tools with high microglial specificity, with the help of microglia-specific Cre lines.
- Rui Lin
- , Youtong Zhou
- & Minmin Luo
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Research Highlight |
FlipFlop of the T cell immune system
FlipFlop mice harbor functionally reversed T cells due to a switch in CD4 and CD8 expression.
- Nina Vogt
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Research Highlight |
Two-photon imaging in freely behaving mice
The MINI2P is a two-photon miniscope that enables robust calcium imaging during mouse behavior.
- Nina Vogt
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Article |
NeuroMechFly, a neuromechanical model of adult Drosophila melanogaster
NeuroMechFly enables simulations of adult Drosophila melanogaster. The platform combines a biomechanical representation of the fly body, models of the muscles, a neural controller and a physics-based simulation of the environment.
- Victor Lobato-Rios
- , Shravan Tata Ramalingasetty
- & Pavan Ramdya
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News & Views |
Tracking together: estimating social poses
Two new toolkits that leverage deep-learning approaches can track the positions of multiple animals and estimate poses in different experimental paradigms.
- Sena Agezo
- & Gordon J. Berman
RoboEM: automated 3D flight tracing for synaptic-resolution connectomics