Deep Neural Networks to Register and Annotate the Cells of theC. elegansNervous System DOI Creative Commons
Adam Atanas,

Alicia Kun-Yang Lu,

Jung Soo Kim

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 22, 2024

ABSTRACT Aligning and annotating the heterogeneous cell types that make up complex cellular tissues remains a major challenge in analysis of biomedical imaging data. Here, we present series deep neural networks allow for automatic non-rigid registration identification context nervous system freely-moving C. elegans . A semi-supervised learning approach was used to train network (BrainAlignNet) aligns pairs images bending head with single pixel-level accuracy. When incorporated into an image pipeline, this can link neuronal identities over time 99.6% separate (AutoCellLabeler) trained annotate >100 based on multi-spectral fluorescence genetic markers. This labels different per animal 98% accuracy, exceeding individual human labeler performance by aggregating knowledge across manually labeled datasets. Finally, third (CellDiscoveryNet) perform unsupervised discovery labeling analyzing unlabeled data from many animals. The CellDiscoveryNet matched labelers. These tools will be useful wide range applications research should straightforward generalize other requiring alignment annotation dense tissues.

Language: Английский

Brain-wide representations of behavior spanning multiple timescales and states in C. elegans DOI Creative Commons

Adam A. Atanas,

Jung Soo Kim, Ziyu Wang

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(19), P. 4134 - 4151.e31

Published: Aug. 21, 2023

Changes in an animal's behavior and internal state are accompanied by widespread changes activity across its brain. However, how neurons the brain encode this is impacted poorly understood. We recorded brain-wide diverse motor programs of freely moving C. elegans built probabilistic models that explain each neuron encodes quantitative behavioral features. By determining identities neurons, we created atlas defined classes connectome behavior. Many have conjunctive representations multiple behaviors. Moreover, although many current actions, others integrate recent actions. behavior, identify these flexible nodes connectome. Our results provide a global map cell types

Language: Английский

Citations

47
A line attractor encoding a persistent internal state requires neuropeptide signaling DOI Creative Commons
George Mountoufaris, Aditya Nair, Bin Yang

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(21), P. 5998 - 6015.e18

Published: Aug. 26, 2024

Language: Английский

Citations

9
Discovering motifs to fingerprint multi-layer networks: a case study on the connectome of C. Elegans DOI Creative Commons
Deepak Sharma, Matthias Renz, Philipp Hoevel

et al.

The European Physical Journal B, Journal Year: 2025, Volume and Issue: 98(1)

Published: Jan. 1, 2025

Language: Английский

Citations

1
A single neuron in C. elegans orchestrates multiple motor outputs through parallel modes of transmission DOI Creative Commons
Yung-Chi Huang,

Jinyue Luo,

Wenjia Huang

et al.

Current Biology, Journal Year: 2023, Volume and Issue: 33(20), P. 4430 - 4445.e6

Published: Sept. 27, 2023

Animals generate a wide range of highly coordinated motor outputs, which allows them to execute purposeful behaviors. Individual neurons in the circuits that behaviors have remarkable capacity for flexibility as they exhibit multiple axonal projections, transmitter systems, and modes neural activity. How these multi-functional properties enable generation adaptive remains unknown. Here, we show HSN neuron C. elegans evokes programs over different timescales suite behavioral changes during egg laying. Using activity perturbations vivo calcium imaging, acutely increases laying locomotion while also biasing animals toward low-speed dwelling behavior minutes. The acute effects on high-speed are mediated by separate sets transmitters compartments. long-lasting part release serotonin, is taken up re-released NSM, another serotonergic class directly dwelling. Our results how single allow it induce reveal can borrow serotonin from one control behavior.

Language: Английский

Citations

17
Dorsal raphe neurons integrate the values of reward amount, delay, and uncertainty in multi-attribute decision-making DOI Creative Commons
Yang-Yang Feng, Ethan S. Bromberg-Martin, Ilya E. Monosov

et al.

Cell Reports, Journal Year: 2024, Volume and Issue: 43(6), P. 114341 - 114341

Published: June 1, 2024

The dorsal raphe nucleus (DRN) is implicated in psychiatric disorders that feature impaired sensitivity to reward amount, impulsivity when facing delays, and risk-seeking confronting uncertainty. However, it has been unclear whether how DRN neurons signal delay, uncertainty during multi-attribute value-based decision-making, where subjects consider these attributes make a choice. We recorded as monkeys chose between offers whose attributes, namely expected uncertainty, varied independently. Many signaled offer this population tended integrate the manner reflected monkeys' preferences for After response post-decision feedback, same signed prediction errors, suggesting broader role tracking value across task epochs behavioral contexts. Our data illustrate participates computations, guiding theories about of decision-making disease.

Language: Английский

Citations

5
Building and integrating brain-wide maps of nervous system function in invertebrates DOI Creative Commons
Talya S. Kramer, Steven W. Flavell

Current Opinion in Neurobiology, Journal Year: 2024, Volume and Issue: 86, P. 102868 - 102868

Published: April 3, 2024

The selection and execution of context-appropriate behaviors is controlled by the integrated action neural circuits throughout brain. However, how activity coordinated across brain regions, nervous system structure enables these functional interactions, remain open questions. Recent technical advances have made it feasible to build brain-wide maps function, such as maps, connectomes, cell atlases. Here, we review recent progress in this area, focusing on C. elegans D. melanogaster, work has produced global systems. We also describe circuit motifs elucidated studies specific networks, which highlight complexities that must be captured accurate models whole-brain function.

Language: Английский

Citations

4
fmo-4 promotes longevity and stress resistance via ER to mitochondria calcium regulation in C. elegans DOI Open Access
Angela M. Tuckowski, Safa Beydoun,

Elizabeth S Kitto

et al.

Published: Jan. 27, 2025

Flavin-containing monooxygenases (FMOs) are a conserved family of xenobiotic enzymes upregulated in multiple longevity interventions, including nematode and mouse models. Previous work supports that C. elegans fmo-2 promotes longevity, stress resistance, healthspan by rewiring endogenous metabolism. However, there five FMOs mammalian FMOs, it is not known whether promoting health benefits role this gene family. Here, we report expression fmo-4 lifespan extension paraquat resistance downstream both dietary restriction inhibition mTOR. We find overexpression just the hypodermis sufficient for these benefits, significantly modifies transcriptome. By analyzing changes expression, genes related to calcium signaling altered expression. Highlighting importance homeostasis pathway, overexpressing animals sensitive thapsigargin, an ER stressor inhibits flux from cytosol lumen. This calcium/ interaction solidified data showing modulating intracellular with either small molecules or genetics can change and/or interact affect resistance. Further analysis pathway where modulates activating transcription factor-6 ( atf-6 ), whose knockdown induces requires Together, our identify as longevity-promoting actions pathways homeostasis.

Language: Английский

Citations

0
Dimorphic Neural Network Architecture Prioritizes Sexual-related Behaviors in Male C. elegans DOI Open Access
Xuebin Wang, Hanli Liu, Wenjing Yang

et al.

Published: Feb. 27, 2025

Neural network architecture determines its functional output. However, the detailed mechanisms are not well characterized. In this study, we focused on neural architectures of male and hermaphrodite C. elegans association with sexually dimorphic behaviors. We applied graph theory computational neuroscience methods to systematically discern features these two networks. Our findings revealed that a small percentage sexual-specific neurons exerted dominance throughout entire net-work, suggesting male’s prioritized sexual-related behavior outputs. Based structural dynamical characteristics complete networks, sub-networks containing sex-specific their immediate neighbors, or exclusively comprising sex-shared neurons, predicted behavioral outcomes for males hermaphrodites. To verify prediction, performed calcium imaging experiments dissected circuit is specific increased spontaneous local search in mate-searching. research sheds light circuits underlie behaviors elegans, provides significant insights into inter-connected relationship between at whole-brain level.

Language: Английский

Citations

0
Dimorphic Neural Network Architecture Prioritizes Sexual-related Behaviors in Male C. elegans DOI Open Access
Xuebin Wang, Hanli Liu, Wenjing Yang

et al.

Published: Feb. 27, 2025

Neural network architecture determines its functional output. However, the detailed mechanisms are not well characterized. In this study, we focused on neural architectures of male and hermaphrodite C. elegans association with sexually dimorphic behaviors. We applied graph theory computational neuroscience methods to systematically discern features these two networks. Our findings revealed that a small percentage sexual-specific neurons exerted dominance throughout entire net-work, suggesting male’s prioritized sexual-related behavior outputs. Based structural dynamical characteristics complete networks, sub-networks containing sex-specific their immediate neighbors, or exclusively comprising sex-shared neurons, predicted behavioral outcomes for males hermaphrodites. To verify prediction, performed calcium imaging experiments dissected circuit is specific increased spontaneous local search in mate-searching. research sheds light circuits underlie behaviors elegans, provides significant insights into inter-connected relationship between at whole-brain level.

Language: Английский

Citations

0
C. elegans wired and wireless connectome: insights into principles of nervous system structure and function DOI
Keertana Venkatesh, Lidia Ripoll-Sánchez, Isabel Beets

et al.

Journal of Biosciences, Journal Year: 2025, Volume and Issue: 50(1)

Published: March 12, 2025

Language: Английский

Citations

0