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3582 Publications

Showing 111-120 of 3582 results
07/20/22 | Transcription factor Acj6 controls dendrite targeting via a combinatorial cell-surface code.
Xie Q, Li J, Li H, Udeshi ND, Svinkina T, Orlin D, Kohani S, Guajardo R, Mani DR, Xu C, Li T, Han S, Wei W, Shuster SA, Luginbuhl DJ, Quake SR, Murthy SE, Ting AY, Carr SA, Luo L
Neuron. 07/2022;110(14):2299-2314.e8. doi: 10.1016/j.neuron.2022.04.026

Transcription factors specify the fate and connectivity of developing neurons. We investigate how a lineage-specific transcription factor, Acj6, controls the precise dendrite targeting of Drosophila olfactory projection neurons (PNs) by regulating the expression of cell-surface proteins. Quantitative cell-surface proteomic profiling of wild-type and acj6 mutant PNs in intact developing brains, and a proteome-informed genetic screen identified PN surface proteins that execute Acj6-regulated wiring decisions. These include canonical cell adhesion molecules and proteins previously not associated with wiring, such as Piezo, whose mechanosensitive ion channel activity is dispensable for its function in PN dendrite targeting. Comprehensive genetic analyses revealed that Acj6 employs unique sets of cell-surface proteins in different PN types for dendrite targeting. Combined expression of Acj6 wiring executors rescued acj6 mutant phenotypes with higher efficacy and breadth than expression of individual executors. Thus, Acj6 controls wiring specificity of different neuron types by specifying distinct combinatorial expression of cell-surface executors.

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07/15/22 | Binding partners regulate unfolding of myosin VI to activate the molecular motor.
Dos Santos Á, Fili N, Hari-Gupta Y, Gough RE, Wang L, Martin-Fernandez M, Arron J, Wait E, Chew TL, Toseland C
The Biochemical Journal. 2022 Jul 15;479(13):1409-1428. doi: 10.1042/BCJ20220025

Myosin VI is the only minus-end actin motor and is coupled to various cellular processes ranging from endocytosis to transcription. This multi-potent nature is achieved through alternative isoform splicing and interactions with a network of binding partners. There is a complex interplay between isoforms and binding partners to regulate myosin VI. Here, we have compared the regulation of two myosin VI splice isoforms by two different binding partners. By combining biochemical and single-molecule approaches, we propose that myosin VI regulation follows a generic mechanism, independently of the spliced isoform and the binding partner involved. We describe how myosin VI adopts an autoinhibited backfolded state which is released by binding partners. This unfolding activates the motor, enhances actin binding and can subsequently trigger dimerization. We have further expanded our study by using single molecule imaging to investigate the impact of binding partners upon myosin VI molecular organisation and dynamics.

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07/14/22 | Using Simulated Training Data of Voxel-Level Generative Models to Improve 3D Neuron Reconstruction.
Liu C, Wang D, Zhang H, Wu W, Sun W, Zhao T, Zheng N
IEEE Transactions on Medical Imaging. 2022 Jul 14;PP:. doi: 10.1109/TMI.2022.3191011

Reconstructing neuron morphologies from fluorescence microscope images plays a critical role in neuroscience studies. It relies on image segmentation to produce initial masks either for further processing or final results to represent neuronal morphologies. This has been a challenging step due to the variation and complexity of noisy intensity patterns in neuron images acquired from microscopes. Whereas progresses in deep learning have brought the goal of accurate segmentation much closer to reality, creating training data for producing powerful neural networks is often laborious. To overcome the difficulty of obtaining a vast number of annotated data, we propose a novel strategy of using two-stage generative models to simulate training data with voxel-level labels. Trained upon unlabeled data by optimizing a novel objective function of preserving predefined labels, the models are able to synthesize realistic 3D images with underlying voxel labels. We showed that these synthetic images could train segmentation networks to obtain even better performance than manually labeled data. To demonstrate an immediate impact of our work, we further showed that segmentation results produced by networks trained upon synthetic data could be used to improve existing neuron reconstruction methods.

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07/08/22 | Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle
Navaneetha Krishnan Bharathan , William Giang , Jesse S. Aaron , Satya Khuon , Teng-Leong Chew , Stephan Preibisch , Eric T. Trautman , Larissa Heinrich , John Bogovic , Davis Bennett , David Ackerman , Woohyun Park , Alyson Petruncio , Aubrey V. Weigel , Stephan Saalfeld , COSEM Project Team , A. Wayne Vogl , Sara N. Stahley , Andrew P. Kowalczyk
bioRxiv. 2022 Jul 08:. doi: 10.1101/2022.07.07.499185

The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.

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07/08/22 | Melding Synthetic Molecules and Genetically Encoded Proteins to Forge New Tools for Neuroscience.
Kumar P, Lavis LD
Annual Review Neuroscience. 2022 Jul 08;45:131-150. doi: 10.1146/annurev-neuro-110520-030031

Unraveling the complexity of the brain requires sophisticated methods to probe and perturb neurobiological processes with high spatiotemporal control. The field of chemical biology has produced general strategies to combine the molecular specificity of small-molecule tools with the cellular specificity of genetically encoded reagents. Here, we survey the application, refinement, and extension of these hybrid small-molecule:protein methods to problems in neuroscience, which yields powerful reagents to precisely measure and manipulate neural systems.

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Romani LabSvoboda Lab
07/08/22 | Neural Algorithms and Circuits for Motor Planning.
Inagaki HK, Chen S, Daie K, Finkelstein A, Fontolan L, Romani S, Svoboda K
Annual Review Neuroscience. 2022 Jul 08;45:249-271. doi: 10.1146/annurev-neuro-092021-121730

The brain plans and executes volitional movements. The underlying patterns of neural population activity have been explored in the context of movements of the eyes, limbs, tongue, and head in nonhuman primates and rodents. How do networks of neurons produce the slow neural dynamics that prepare specific movements and the fast dynamics that ultimately initiate these movements? Recent work exploits rapid and calibrated perturbations of neural activity to test specific dynamical systems models that are capable of producing the observed neural activity. These joint experimental and computational studies show that cortical dynamics during motor planning reflect fixed points of neural activity (attractors). Subcortical control signals reshape and move attractors over multiple timescales, causing commitment to specific actions and rapid transitions to movement execution. Experiments in rodents are beginning to reveal how these algorithms are implemented at the level of brain-wide neural circuits.

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07/06/22 | Taste quality interactions and transformations in a sensorimotor circuit
Philip K. Shiu , Gabriella R. Sterne , Stefanie Engert , Barry J. Dickson , Kristin Scott
eLife. 2022 Jul 06:. doi: 10.1101/2022.03.06.483180

Taste detection and hunger state dynamically regulate the decision to initiate feeding. To study how context-appropriate feeding decisions are generated, we combined synaptic resolution circuit reconstruction with targeted genetic access to specific neurons to elucidate a gustatory sensorimotor circuit for feeding initiation in Drosophila melanogaster. This circuit connects gustatory sensory neurons to proboscis motor neurons through three intermediate layers. Most of the neurons in this pathway are necessary and sufficient for proboscis extension, a feeding initiation behavior, and respond selectively to sugar taste detection. Hunger signals act at select second-order neurons to increase feeding initiation in food-deprived animals. In contrast, a bitter taste pathway inhibits premotor neurons, illuminating a central mechanism that weighs sugar and bitter tastes to promote or inhibit feeding. Together, these studies reveal the neural circuit basis for the integration of external taste detection and internal nutritive state to flexibly execute a critical feeding decision.

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07/04/22 | Visualizing Synaptic Dopamine Efflux with a 2D Nanofilm.
Chandima Bulumulla , Andrew T. Krasley , Deepika Walpita , Abraham G. Beyene
eLife. 2022 Jul 04:. doi: 10.7554/eLife.78773

Chemical neurotransmission constitutes one of the fundamental modalities of communication between neurons. Monitoring release of these chemicals has traditionally been difficult to carry out at spatial and temporal scales relevant to neuron function. To understand chemical neurotransmission more fully, we need to improve the spatial and temporal resolutions of measurements for neurotransmitter release. To address this, we engineered a chemi-sensitive, two-dimensional nanofilm that facilitates subcellular visualization of the release and diffusion of the neurochemical dopamine with synaptic resolution, quantal sensitivity, and simultaneously from hundreds of release sites. Using this technology, we were able to monitor the spatiotemporal dynamics of dopamine release in dendritic processes, a poorly understood phenomenon. We found that dopamine release is broadcast from a subset of dendritic processes as hotspots that have a mean spatial spread of ≈3.2 µm (full width at half maximum) and are observed with a mean spatial frequency of 1 hotspot per ≈7.5 µm of dendritic length. Major dendrites of dopamine neurons and fine dendritic processes, as well as dendritic arbors and dendrites with no apparent varicose morphology participated in dopamine release. Remarkably, these release hotspots colocalized with Bassoon, suggesting that Bassoon may contribute to organizing active zones in dendrites, similar to its role in axon terminals.

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07/03/22 | Multifunctional fluorophores for live-cell imaging and affinity capture of proteins
Kumar P, Jason D. Vevea , Edwin R. Chapman , Luke D. Lavis
bioRxiv. 2022 Jul 03:. doi: 10.1101/2022.07.02.498544

The development of enzyme-based self-labeling tags allow the labeling of proteins in living cells with synthetic small-molecules. Use of a fluorophore-containing ligand enables the visualization of protein location inside cells using fluorescence microscopy. Alternatively, deployment of a biotin-containing ligand allows purification of tagged protein using affinity resins. Despite these various applications of self-labeling tags, most ligands serve a single purpose. Here, we describe self-labeling tag ligands that allow both visualization and subsequent capture of a protein. A key design principle is exploiting the chemical properties and size of a rhodamine fluorophore to optimize cell-permeability of the ligand and the capture efficiency of the biotin conjugate. This work generates useful “multifunctional” fluorophores with generalizable design principles that will allow the construction of new tools for biology.

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07/01/22 | Kinetic principles underlying pioneer function of GAGA transcription factor in live cells.
Tang X, Li T, Liu S, Wisniewski J, Zheng Q, Rong Y, Lavis LD, Wu C
Nature Structural and Molecular Biology. 2022 Jul 01;29(7):665-676. doi: 10.1038/s41594-022-00800-z

How pioneer factors interface with chromatin to promote accessibility for transcription control is poorly understood in vivo. Here, we directly visualize chromatin association by the prototypical GAGA pioneer factor (GAF) in live Drosophila hemocytes. Single-particle tracking reveals that most GAF is chromatin bound, with a stable-binding fraction showing nucleosome-like confinement residing on chromatin for more than 2 min, far longer than the dynamic range of most transcription factors. These kinetic properties require the full complement of GAF's DNA-binding, multimerization and intrinsically disordered domains, and are autonomous from recruited chromatin remodelers NURF and PBAP, whose activities primarily benefit GAF's neighbors such as Heat Shock Factor. Evaluation of GAF kinetics together with its endogenous abundance indicates that, despite on-off dynamics, GAF constitutively and fully occupies major chromatin targets, thereby providing a temporal mechanism that sustains open chromatin for transcriptional responses to homeostatic, environmental and developmental signals.

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