Biology subjects

Sutradhar, S.

Publications and source records attributed to Sutradhar, S..

7 recordsLinked to original sources

bioRxiv2025

Neurons exploit stochastic growth to rapidly and economically build dense radially oriented dendritic arbors

Dendrites grow by stochastic branching, elongation, and retraction. A key question is whether such a mechanism is sufficient to form highly branched dendritic morphologies. Alternatively, are signals from other cells or is the topological hierarchy of the growing network necessary for dendrite geometry? To answer these questions, we developed a mean-field model in which branch dynamics is isotropic and homogenous (i.e., no extrinsic instruction) and depends only on the average lengths and densities of branches. Branching is modeled as density-dependent nucleation so there are no tree structures and no network topology. Despite its simplicity, the model predicted several key morphological properties of class IV Drosophila sensory dendrites, including the exponential distribution of branch lengths, the parabolic scaling between dendrite number and length densities, the tight spacing of the dendritic meshwork (which required minimal total branch length), and the radial orientation of branches. Stochastic growth also accelerated the overall expansion rate of the arbor. Therefore, stochastic dynamics is an economical and rapid space-filling mechanism for building dendritic arbors without external guidance or hierarchical branching mechanisms. Our model provides a general theoretical framework for understanding how macroscopic branching patterns emerge from microscopic dynamics.

developmental biology↗

bioRxiv2025

PI(3)P signaling regulates endosomal flux underlying developmental synaptic remodeling via Rab4

Rab4 GTPase, essential for endosomal sorting and trafficking, is implicated in synaptic atrophy and dementia. To uncover the underlying mechanism, we studied the correlation between Rab4 vesicle transport in axons and episodic remodeling of synapses in the central nervous system (CNS) of Drosophila larvae. We found that synapse-bound traffic and presynaptic enrichment of Rab4 vesicles increase during the programmed, transient contraction of synapses in the ventral neuropil region at a specific larval stage. This coincides with the episodic activation of insulin and Vps34-mediated signaling, which elevates phosphatidylinositol-3-phosphate levels on Rab4 vesicles. The presence of this phospholipid on Rab4-associated vesicles recruit a PX-domain-containing motor protein, Klp98A, accelerating synapse-directed traffic. This, in turn, increases presynaptic enrichment of Rab4 during the developmentally programmed synapse contraction phase. Our findings elucidate the molecular mechanism that regulates developmental synaptic plasticity in the CNS via insulin signaling and directed axonal transport of endosomes. Author summaryHealthy brain function relies on the growth and remodeling of synaptic connections between nerve cells. This process involves carefully orchestrated movements of proteins and membranes inside the neurites. For instance, endosome movement in the nerve cell extensions helps guide neuronal growth, recycle parts of the synapse, and alter signal transmissions between neurons. Rab GTPases, a group of small G-proteins, are crucial for these processes. Here, we aimed to understand what triggers these processes and how the supply chain within nerve cell extensions is connected to changes at the synapse. In fruit fly larvae, we observed that the movement of Rab4 vesicles in the nerve cell extensions is inversely related to gross synapse content. A further examination revealed that onset of insulin signaling accelerates the Rab4 vesicles towards synapse through a lipid kinase called Vps34, which makes a signaling lipid called phospatidylinnositol-3-phosphate. Higher levels this lipid molecule on Rab4 vesicles attract a motor protein, Klp98A, speeding up their movement during the synaptic contraction phase. Our findings reveal a new mechanism that regulates Rab4 vesicle transport and its impact on synapse stability. The study further suggests potential targets for controlling age-related dementia likely to be caused by excessive insulin signaling in neurons.

neuroscience↗

bioRxiv2024

Insulin signaling accelerates the anterograde movement of Rab4 vesicles in axons through Klp98a/KIF16B recruitment via Vps34-PI3Kinase

Rab4 GTPase organizes endosomal sorting essential for maintaining the balance between recycling and degradative pathways. Rab4 localizes to many cargos whose transport in neurons is critical for regulating neurotransmission and neuronal health. Furthermore, elevated Rab4 levels in the CNS are associated with synaptic atrophy and neurodegeneration in Drosophila and humans, respectively. However, how the transport of Rab4-associated vesicles is regulated in neurons remains unknown. Using in vivo time-lapse imaging of Drosophila larvae, we show that activation of insulin signaling via Dilp2 and dInR increases the anterograde velocity, run length, and flux of Rab4 vesicles in the axons. Molecularly, we show that activation of neuronal insulin signaling further activates Vps34, elevates the levels of PI(3)P on Rab4-associated vesicles, recruits Klp98A (a PI(3)P-binding kinesin-3 motor) and activates their anterograde transport. Together, these observations delineate the role of insulin signaling in regulating axonal transport and synaptic homeostasis. HighlightsO_LIDilp2-mediated insulin signaling activates anterograde transport of Rab4 vesicles C_LIO_LIVps34 regulates anterograde velocity, run length and flux of Rab4 vesicles C_LIO_LILocal PI(3)P signaling on Rab4 vesicles regulates their motility in the axons C_LIO_LIPI(3)P production upon acute insulin stimulation recruits Klp98A on Rab4 vesicles C_LI

cell biology↗

bioRxiv2022

Dynamic microtubules slow down during their shrinkage phase

Microtubules are dynamic polymers that undergo stochastic transitions between growing and shrinking phases. The structural and chemical properties of these phases remain poorly understood. The transition from growth to shrinkage, termed catastrophe, is not a first-order reaction but is rather a multi-step process whose frequency increases with the growth time: the microtubule ages as the older microtubule tip becomes more unstable. Aging shows that the growing phase is not a single state but comprises several substates of increasing instability. To investigate whether the shrinking phase is also multi-state, we characterized the kinetics of microtubule shrinkage following catastrophe using an in vitro reconstitution assay with purified tubulins. We found that the shrinkage speed is highly variable across microtubules and that the shrinkage speed of individual microtubules slows down over time by as much as several fold. The shrinkage slowdown was observed in both fluorescently labeled and unlabeled microtubules as well as in microtubules polymerized from tubulin purified from different species, suggesting that the shrinkage slowdown is a general property of microtubules. These results indicate that microtubule shrinkage, like catastrophe, is time-dependent and that the shrinking microtubule tip passes through a succession of states of increasing stability. We hypothesize that the shrinkage slowdown is due to destabilizing events that took place during growth which led to multi-step catastrophe. This suggests that the aging associated with growth is also manifest during shrinkage with the older, more unstable growing tip being associated with a faster depolymerizing shrinking tip. Statement of SignificanceThe dynamics of the microtubule cytoskeleton is crucial for several functions in eukaryotic cells. Microtubule dynamics is traditionally described by constant growth and shrinkage speeds with first order transitions between the growth and shrinkage phases. However, catastrophe, the transition from growth to shrinkage, increases with microtubule age and is not a first order process. In contrast to the common assumption that microtubules shrink with constant speed, here we show that shrinking microtubule tips undergo step-wise slowdown during depolymerization. Our results suggest that microtubule shrinkage, like catastrophe, is a multi-step process. This finding is important for understanding the molecular nature of microtubule dynamic instability and how microtubule shrinkage can be modulated by microtubule associated proteins.

biophysics↗

bioRxiv2022

Scaled-expansion of the membrane associated cytoskeleton requires conserved kinesin adaptors

A periodic lattice of actin rings and spectrin tetramers scaffolds the axonal membrane. How spectrin is delivered to this structure to scale its size to that of the growing axon is unknown. We found that endogenous spectrin, visualized with singe axon resolution in vivo, is delivered to hotspots in the lattice that support its expansion at rates set by axon stretch-growth. Unlike other cytoskeletal proteins, whose apparent slow movement consists of intermittent bouts of fast movements, spectrin moves slowly and processively. We identified a pair of coiled coil proteins that mediate this slow movement and the expansion of the lattice by linking spectrin to kinesin-1. Thus, processive slow transport and local lattice incorporation support scaled cytoskeletal expansion during axon stretch-growth. One-Sentence SummaryKinesin adaptors control spectrin transport and expansion of the membrane periodic skeleton.

cell biology↗

bioRxiv2021

Dynamic Instability of Dendrite Tips Generates the Highly Branched Morphologies of Sensory Neurons

The highly ramified arbors of neuronal dendrites provide the substrate for the high connectivity and computational power of the brain. Altered dendritic morphology is associated with neuronal diseases. Many molecules have been shown to play crucial roles in shaping and maintaining dendrite morphology. Yet, the underlying principles by which molecular interactions generate branched morphologies are not understood. To elucidate these principles, we visualized the growth of dendrites throughout larval development of Drosophila sensory neurons and discovered that the tips of dendrites undergo dynamic instability, transitioning rapidly and stochastically between growing, shrinking, and paused states. By incorporating these measured dynamics into a novel, agent-based computational model, we showed that the complex and highly variable dendritic morphologies of these cells are a consequence of the stochastic dynamics of their dendrite tips. These principles may generalize to branching of other neuronal cell-types, as well as to branching at the subcellular and tissue levels.

biophysics↗

bioRxiv2021

Focal Laser Stimulation of Fly Nociceptors Activates Distinct Axonal and Dendritic Ca2+ Signals

Drosophila Class IV neurons are polymodal nociceptors that detect noxious mechanical, thermal, optical and chemical stimuli. Escape behaviors in response to attacks by parasitoid wasps are dependent on Class IV cells, whose highly branched dendritic arbors form a fine meshwork that is thought to enable detection of the wasps needle-like ovipositor barb. To understand how mechanical stimuli trigger cellular responses, we used a focused 405-nm laser to create highly local lesions to probe the precise position needed in evoke responses. By imaging calcium signals in dendrites, axons, and soma in response to stimuli of varying positions, intensities and spatial profiles, we discovered that there are two distinct nociceptive pathways. Direct stimulation to dendrites (the contact pathway) produces calcium responses in axons, dendrites and the cell body whereas stimulation adjacent to the dendrite (the non-contact pathway) produces calcium responses in the axons only. We interpret the non-contact pathway as damage to adjacent cells releasing diffusible molecules that act on the dendrites. Axonal responses have higher sensitivities and shorter latencies. In contrast, dendritic responses have lower sensitivities and longer latencies. Stimulation of finer, distal dendrites leads to smaller responses than stimulation of coarser, proximal dendrites, as expected if the contact response depends on the geometric overlap of the laser profile and the dendrite diameter. Because the axon signals to the CNS to trigger escape behaviors, we propose that the density of the dendritic meshwork is high not only to enable direct contact with the ovipositor, but also to enable neuronal activation via diffusing signals from damaged surrounding cells. Dendritic contact evokes responses throughout the dendritic arbor, even to regions distant and distal from the stimulus. These dendrite-wide calcium signals may facilitate hyperalgesia or cellular morphological changes following dendritic damage. Statement of SignificanceAnimals encounter a wide range of noxious stimuli in the natural world. Nociceptive neurons are specialized cells that sense harmful stimuli and trigger avoidance responses. Class IV cells, located under the cuticle in Drosophila larvae, are polymodal nociceptors that respond to noxious mechanical, thermal, optical, and chemical stimuli. To investigate the spatial requirements of mechanoreception in Class IV neurons, we measured calcium signals evoked by a focused laser beam that creates highly localized tissue damage. We discovered that different cellular compartments - axons and dendrites - responded differentially depending on whether the stimulus makes direct contact with the neuron or not. This provides evidence that mechanical nociception in Class IV cells occurs via two distinct pathways.

neuroscience↗