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2510 Janelia Publications

Showing 1-10 of 2510 results
07/16/24 | Closing the Experiment-Modeling-Perturbation Loop in Whole-Brain Neuroscience.
Ahrens MB
Neurosci Bull. 2024 Jul 16:. doi: 10.1007/s12264-024-01253-8
07/11/24 | Molecular and cellular mechanisms of teneurin signaling in synaptic partner matching.
Xu C, Li Z, Lyu C, Hu Y, McLaughlin CN, Wong KK, Xie Q, Luginbuhl DJ, Li H, Udeshi ND, Svinkina T, Mani DR, Han S, Li T, Li Y, Guajardo R, Ting AY, Carr SA, Li J, Luo L
Cell. 2024 Jul 03:. doi: 10.1016/j.cell.2024.06.022

In developing brains, axons exhibit remarkable precision in selecting synaptic partners among many non-partner cells. Evolutionarily conserved teneurins are transmembrane proteins that instruct synaptic partner matching. However, how intracellular signaling pathways execute teneurins' functions is unclear. Here, we use in situ proximity labeling to obtain the intracellular interactome of a teneurin (Ten-m) in the Drosophila brain. Genetic interaction studies using quantitative partner matching assays in both olfactory receptor neurons (ORNs) and projection neurons (PNs) reveal a common pathway: Ten-m binds to and negatively regulates a RhoGAP, thus activating the Rac1 small GTPases to promote synaptic partner matching. Developmental analyses with single-axon resolution identify the cellular mechanism of synaptic partner matching: Ten-m signaling promotes local F-actin levels and stabilizes ORN axon branches that contact partner PN dendrites. Combining spatial proteomics and high-resolution phenotypic analyses, this study advanced our understanding of both cellular and molecular mechanisms of synaptic partner matching.

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07/04/24 | iTome Volumetric Serial Sectioning Apparatus for TEM
Peale DR, Hess H, Lee PR, Cardona A, Bock DD, Schneider-Mizell C, Fetter RD, Lee W, Robinson CG, Iyer N, Managan C
bioRxiv. 2024 Jul 07:. doi: 10.1101/2024.07.02.601671

An automated ultra-microtome capable of sectioning thousands of ultrathin sections onto standard TEM slot grids was developed and used to section: a complete Drosophila melanogaster first-instar larva, three sections per grid, into 4,866 34-nm-thick sections with a cutting and pickup success rate of 99.74%; 30 microns of mouse cortex measuring roughly 400 um x 2000 um at 40 nm per slice; and a full adult Drosophila brain and ventral nerve column into 9,300 sections with a pickup success rate of 99.95%. The apparatus uses optical interferometers to monitor a reference distance between the cutting knife and multiple sample blocks. Cut sections are picked up from the knife-boat water surface while they are still anchored to the cutting knife. Blocks without embedded tissue are used to displace tissue-containing sections away from the knife edge so that the tissue regions end up in the grid slot instead of on the grid rim.

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07/05/24 | LarvaTagger: Manual and automatic tagging of drosophila larval behaviour.
Laurent F, Blanc A, May L, Gándara L, Cocanougher BT, Jones BM, Hague P, Barre C, Vestergaard CL, Crocker J, Zlatic M, Jovanic T, Masson J
Bioinformatics. 2024 Jul 05:. doi: 10.1093/bioinformatics/btae441

MOTIVATION: As more behavioural assays are carried out in large-scale experiments on Drosophila larvae, the definitions of the archetypal actions of a larva are regularly refined. In addition, video recording and tracking technologies constantly evolve. Consequently, automatic tagging tools for Drosophila larval behaviour must be retrained to learn new representations from new data. However, existing tools cannot transfer knowledge from large amounts of previously accumulated data.We introduce LarvaTagger, a piece of software that combines a pre-trained deep neural network, providing a continuous latent representation of larva actions for stereotypical behaviour identification, with a graphical user interface to manually tag the behaviour and train new automatic taggers with the updated ground truth.

RESULTS: We reproduced results from an automatic tagger with high accuracy, and we demonstrated that pre-training on large databases accelerates the training of a new tagger, achieving similar prediction accuracy using less data.

AVAILABILITY: All the code is free and open source. Docker images are also available. See

SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.

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06/27/24 | Lattice light sheet microscopy reveals 4D force propagation dynamics and leading-edge behaviors in an embryonic epithelium in Drosophila.
Vanderleest TE, Xie Y, Budhathoki R, Linvill K, Hobson C, Heddleston J, Loerke D, Blankenship JT
Curr Biol. 2024 Jun 27:. doi: 10.1016/j.cub.2024.06.017

How pulsed contractile dynamics drive the remodeling of cell and tissue topologies in epithelial sheets has been a key question in development and disease. Due to constraints in imaging and analysis technologies, studies that have described the in vivo mechanisms underlying changes in cell and neighbor relationships have largely been confined to analyses of planar apical regions. Thus, how the volumetric nature of epithelial cells affects force propagation and remodeling of the cell surface in three dimensions, including especially the apical-basal axis, is unclear. Here, we perform lattice light sheet microscopy (LLSM)-based analysis to determine how far and fast forces propagate across different apical-basal layers, as well as where topological changes initiate from in a columnar epithelium. These datasets are highly time- and depth-resolved and reveal that topology-changing forces are spatially entangled, with contractile force generation occurring across the observed apical-basal axis in a pulsed fashion, while the conservation of cell volumes constrains instantaneous cell deformations. Leading layer behaviors occur opportunistically in response to favorable phasic conditions, with lagging layers "zippering" to catch up as new contractile pulses propel further changes in cell topologies. These results argue against specific zones of topological initiation and demonstrate the importance of systematic 4D-based analysis in understanding how forces and deformations in cell dimensions propagate in a three-dimensional environment.

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07/04/24 | CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells.
Yang L, Min Y, Liu Y, Gao B, Liu X, Huang Y, Wang H, Yang L, Liu ZJ, Chen L
Nat Methods. 2024 Jul 04:. doi: 10.1038/s41592-024-02333-3

Dynamic imaging of genomic loci is key for understanding gene regulation, but methods for imaging genomes, in particular non-repetitive DNAs, are limited. We developed CRISPRdelight, a DNA-labeling system based on endonuclease-deficient CRISPR-Cas12a (dCas12a), with an engineered CRISPR array to track DNA location and motion. CRISPRdelight enables robust imaging of all examined 12 non-repetitive genomic loci in different cell lines. We revealed the confined movement of the CCAT1 locus (chr8q24) at the nuclear periphery for repressed expression and active motion in the interior nucleus for transcription. We uncovered the selective repositioning of HSP gene loci to nuclear speckles, including a remarkable relocation of HSPH1 (chr13q12) for elevated transcription during stresses. Combining CRISPR-dCas12a and RNA aptamers allowed multiplex imaging of four types of satellite DNA loci with a single array, revealing their spatial proximity to the nucleolus-associated domain. CRISPRdelight is a user-friendly and robust system for imaging and tracking genomic dynamics and regulation.

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07/10/24 | Multi-day neuron tracking in high-density electrophysiology recordings using earth mover’s distance
Augustine Xiaoran Yuan , Jennifer Colonell , Anna Lebedeva , Adam Charles , Timothy Harris
eLife. 2024-07-10:. doi: 10.7554/eLife.92495.3

Accurate tracking of the same neurons across multiple days is crucial for studying changes in neuronal activity during learning and adaptation. Advances in high-density extracellular electrophysiology recording probes, such as Neuropixels, provide a promising avenue to accomplish this goal. Identifying the same neurons in multiple recordings is, however, complicated by non-rigid movement of the tissue relative to the recording sites (drift) and loss of signal from some neurons. Here, we propose a neuron tracking method that can identify the same cells independent of firing statistics, that are used by most existing methods. Our method is based on between-day non-rigid alignment of spike-sorted clusters. We verified the same cell identity in mice using measured visual receptive fields. This method succeeds on datasets separated from 1 to 47 days, with an 84% average recovery rate.

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06/02/24 | Dynamic assemblies of parvalbumin interneurons in brain oscillations.
Huang Y, Chen H, Lin Y, Lin S, Zheng Q, Abdelfattah AS, Lavis LD, Schreiter ER, Lin B, Chen T
Neuron. 2024 Jun 02:. doi: 10.1016/j.neuron.2024.05.015

Brain oscillations are crucial for perception, memory, and behavior. Parvalbumin-expressing (PV) interneurons are critical for these oscillations, but their population dynamics remain unclear. Using voltage imaging, we simultaneously recorded membrane potentials in up to 26 PV interneurons in vivo during hippocampal ripple oscillations in mice. We found that PV cells generate ripple-frequency rhythms by forming highly dynamic cell assemblies. These assemblies exhibit rapid and significant changes from cycle to cycle, varying greatly in both size and membership. Importantly, this variability is not just random spiking failures of individual neurons. Rather, the activities of other PV cells contain significant information about whether a PV cell spikes or not in a given cycle. This coordination persists without network oscillations, and it exists in subthreshold potentials even when the cells are not spiking. Dynamic assemblies of interneurons may provide a new mechanism to modulate postsynaptic dynamics and impact cognitive functions flexibly and rapidly.

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06/28/24 | Exploration and exploitation are flexibly balanced during local search in flies
Goldschmidt D, Guo Y, Chitnis SS, Christoforou C, Turner-Evans D, Ribeiro C, Hermundstad AM, Jayaraman V, Haberkern H
bioRxiv. 2024 Jun 28:. doi: 10.1101/2024.06.26.600764

After finding food, a foraging animal must decide whether to continue feeding, or to explore the environment for potentially better options. One strategy to negotiate this tradeoff is to perform local searches around the food but repeatedly return to feed. We studied this behavior in flies and used genetic tools to uncover the underlying mechanisms. Over time, flies gradually expand their search, shifting from primarily exploiting food sources to exploring the environment, a change that is likely driven by increases in satiety. We found that flies’ search patterns preserve these dynamics even as the overall scale of the search is modulated by starvation-induced changes in metabolic state. In contrast, search induced by optogenetic activation of sugar sensing neurons does not show these dynamics. We asked what navigational strategies underlie local search. Using a generative model, we found that a change in locomotor pattern after food consumption could account for repeated returns to the food, but failed to capture relatively direct, long return trajectories. Alternative strategies, such as path integration or sensory taxis could allow flies to return from larger distances. We tested this by individually silencing the fly’s head direction system, olfaction and hygrosensation, and found that the only substantial effect was from perturbing hygrosensation, which reduced the number of long exploratory trips. Our study illustrates that local search is composed of multiple behavioral features that evolve over time based on both internal and external factors, providing a path towards uncovering the underlying neural mechanisms.

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06/01/24 | Resolution in super-resolution microscopy - definition, trade-offs and perspectives.
Prakash K, Baddeley D, Eggeling C, Fiolka R, Heintzmann R, Manley S, Radenovic A, Smith C, Shroff H, Schermelleh L
Nat Rev Mol Cell Biol. 2024 Jul 01:. doi: 10.1038/s41580-024-00755-7

Super-resolution microscopy (SRM) is gaining popularity in biosciences; however, claims about optical resolution are contested and often misleading. In this Viewpoint, experts share their views on resolution and common trade-offs, such as labelling and post-processing, aiming to clarify them for biologists and facilitate deeper understanding and best use of SRM.

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