Biology subjects

Sengupta, T.

Publications and source records attributed to Sengupta, T..

13 recordsLinked to original sources

bioRxiv2025

Neuronal SET1/COMPASS-mediated epigenetic regulation of de novo transcription drives accelerated forgetting with age

Forgetting is a critical component of memory, but its molecular regulation - particularly with age - is not well understood. Epigenetic modifications are a candidate for this regulation and may further drive age-related behavioral decline, as they are dramatically altered in the aging brain. We found that multiple components of the SET1/COMPASS complex, a conserved histone methyltransferase complex associated with active gene transcription, are upregulated with age in the C. elegans nervous system. Neuronal knockdown of the SET1/COMPASS components improves memory in young adult animals and slows memory decline in old animals. By pharmacological and genetic inhibition, optogenetics, and neuronal mRNA and chromatin profiling, we demonstrate that SET1/COMPASS-mediated active transcription promotes forgetting. SET1/COMPASS regulates the de novo activity-dependent transcription and release of a neuropeptidergic signal from the AWC olfactory sensory neuron, which erases the associative memory trace in downstream motor neurons, resulting in forgetting. We further found that increased SET1/COMPASS-dependent chromatin accessibility at these gene loci with age primes these loci for transcription, resulting in accelerated forgetting. Our results reveal the role of active gene transcription in the regulation of forgetting and altered SET1/COMPASS-mediated gene transcription as a mechanism of cognitive decline, implicating increased expression of COMPASS components as a driver of increased forgetting in the aging brain. This mechanism may offer a new target for slowing loss of cognitive function with age.

neuroscience↗

bioRxiv2025

Molecular Requirements for C. elegans Transgenerational Epigenetic Inheritance of Pathogen Avoidance

C. elegans major food source is bacteria, and worms are naturally attracted to many bacterial species, including pathogenic Pseudomonas; in fact, worms prefer PA14 as well as wild bacteria over the lab E. coli strain (OP50) standardly used in the laboratory setting. Many labs have shown that despite this natural attraction to PA14, prior exposure to PA14 causes the worms to instead avoid PA14. This behavioral switch can happen on a relatively fast time scale, even within the duration of the choice assay. Here we show that accurate assessment of the animals true first choice requires the use of a paralytic (azide) to trap the worms at their initial choice, and to prevent the switch from attraction to avoidance of PA14 within the assay period. We previously discovered that exposure of C. elegans to 25{degrees}C plate-grown PA14 at 20{degrees}C for 24hrs not only leads to these animals switching from attraction to avoidance of PA14, but also to their progeny avoiding PA14 in the naive state, and this avoidance persists through the F4 generation. Other types of PA14 training can also cause P0 and/or F1 avoidance, but do not induce transgenerational (F2 and beyond) inheritance. We also previously showed that the transgenerational (P0-F4) learned avoidance is mediated by P11, a small RNA produced by PA14. P11 is both necessary and sufficient for transgenerational epigenetic inheritance of avoidance behavior. P11 is highly expressed in our standard growth conditions (25{degrees}C on surfaces), but not in other conditions, suggesting that reported failure to observe F2-F4 avoidance is most likely due to the absence of P11 expression in PA14 in the experimenters growth conditions. Through mutant analyses, we have tested many genes - including germline regulators, small RNA uptake, RNA interference/processing, chromatin modifiers, and neuronal genes -for their involvement in transgenerational inheritance of learned pathogen avoidance, allowing us to better understand the molecular requirements for this process. We previously found that wild C. elegans strains also show TEI of learned pathogen avoidance, and that at least two other wild bacteria, P. vranovensis and P. fluorescens 15, induce this transgenerational avoidance. The avoidance induced by each Pseudomonas species functions through a specific, distinct small RNA (Pv1 in P. vranovensis and Pfs1 in P. fluorescens 15, respectively) that either directly or indirectly reduce the levels of the gene maco-1, which in turn regulates daf-7 expression in the ASI neuron and subsequent avoidance behavior. The conservation of multiple components of this small RNA TEI mechanism across C. elegans strains and in multiple Pseudomonas species suggests that this transgenerational learned avoidance behavior is likely to be functional and physiologically important in wild conditions.

genetics↗

bioRxiv2024

Absence of Evidence is Not Evidence of Absence: The many flaws in the case against transgenerational epigenetic inheritance of pathogen avoidance in C. elegans

After examining the data and methods presented in Gainey, et al., bioRxiv, 20241 we conclude that the authors did not use an experimental paradigm that would have allowed them to replicate our results on transgenerational epigenetic inheritance (TEI) of learned avoidance that we regularly observe2-5. That is, we agree with the authors that their experiments show no evidence of TEI. However, there are substantial differences in their execution of every step of the work that also make it impossible for the authors to claim that they are replicating our experiments or protocols. Based on these differences, we do not believe there is an issue of "robustness" and "reliability" in our TEI findings, but rather that Hunter and colleagues have in fact not tested the central condition of TEI - that is, small RNA production by bacteria and subsequent uptake by C. elegans - nor have they carried out proper behavioral and imaging assays to assess this behavior. Our subsequent work shows that indeed this example of transgenerational epigenetic inheritance is not just observed in laboratory settings with PA14, but is also induced by wild strains of Pseudomonas, exhibiting its robustness. Just as we offered advice and training to Hunter and colleagues, we are happy to advise anyone who wishes to learn this assay. We have now performed the experiments in the absence of azide, a deviation from our protocol that Hunter and colleagues deliberately made, and found that this omission may account for most if not all of the differences from our results. It is disingenuous for the authors to have presented their work as if they have used our protocol, given the fact that they chose to not use the same conditions for the most basic assay used in the work, the chemotaxis assay, which would have been necessary to replicate in order to reproduce our work. Therefore, Gainey et al.s claims that our protocol or results are "irreproducible" are not supported by their evidence.

genetics↗

bioRxiv2023

Programmed Cell Death Modifies Neural Circuits and Tunes Intrinsic Behavior

Programmed cell death (PCD) is a common feature of animal development. During development of the C. elegans hermaphrodite, programmed cell death eliminates 131 cells in stereotyped positions in the cell lineage, mostly in neuronal lineages. Blocking cell death results in supernumerary "undead" neurons. We find that undead neurons can be wired into circuits, can display activity, and can modify specific behaviors. The two undead RIM-like neurons participate in the RIM-containing circuit that computes movement. The presence of these two extra neurons results in animals that initiate fewer reversals and lengthens the duration of those reversals that do occur. We describe additional behavioral alterations of cell-death mutants, including in locomotory turning angle and pharyngeal pumping. These findings indicate that physiological or evolutionary variations in PCD might reveal latent neuronal elements that the nervous system can incorporate to modify nervous system function and animal behavior.

neuroscience↗

bioRxiv2023

A small RNA from a natural bacterial pathogen of C. elegans induces transgenerational inheritance of learned avoidance

Previously, we discovered that a small RNA from a clinical isolate of Pseudomonas aeruginosa, PA14, induces learned avoidance and its transgenerational inheritance in C. elegans. Pseudomonas aeruginosa is an important human pathogen, and there are other Pseudomonads in C. elegans natural habitat, but it is unclear whether C. elegans ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in C. elegans natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we found that a pathogenic Pseudomonas vranovensis strain isolated from the C. elegans microbiota, GRb0427, like PA14, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure to GRb0427, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. Using bacterial small RNA sequencing, we identified Pv1, a small RNA from GRb0427, that matches the sequence of C. elegans maco-1. We find that Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, P. mendocina; this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance are functional in C. elegans natural environment, and that different bacterial small RNA-mediated regulation systems evolved independently but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.

genetics↗

bioRxiv2023

Enhanced Branched-Chain Amino Acid Metabolism Improves Age-related Reproductive Function

Reproductive aging is one of the earliest human aging phenotypes, and mitochondrial dysfunction has been linked to oocyte quality decline. However, it is not known which mitochondrial metabolic processes are critical for oocyte quality maintenance with age. To understand how mitochondrial processes contribute to C. elegans oocyte quality, we characterized the mitochondrial proteomes of young and aged wild-type and long-reproductive daf-2 mutants. Here we show that the mitochondrial proteomic profiles of young wild-type and daf-2 worms are similar and share upregulation of branched-chain amino acid (BCAA) metabolism pathway enzymes. Reduction of the BCAA catabolism enzyme BCAT-1 shortens reproduction, elevates mitochondrial reactive oxygen species levels, and shifts mitochondrial localization. Moreover, bcat-1 knockdown decreases oocyte quality in daf-2 worms and reduces reproductive capability, indicating the role of this pathway in the maintenance of oocyte quality with age. Importantly, oocyte quality deterioration can be delayed, and reproduction can be extended in wild-type animals both by bcat-1 overexpression and by supplementing with Vitamin B1, a cofactor needed for BCAA metabolism.

cell biology↗

bioRxiv2022

Acute sleep deprivation induces synaptic remodeling at the soleus muscle neuromuscular junction in rats

Sleep is important for cognitive and physical performance. Sleep deprivation not only affects neural functions but also results in muscular fatigue. A good nights sleep reverses these functional derangements caused by sleep deprivation. The role of sleep in brain function has been extensively studied. However, its role in neuromuscular junction or skeletal muscle morphology is sparsely addressed although skeletal muscle atonia and suspended thermoregulation during rapid eye movement sleep possibly provides a conducive environment for the muscle to rest and repair; somewhat similar to slow-wave sleep for synaptic downscaling. In the present study, we have investigated the effect of 24 h sleep deprivation on the neuromuscular junction morphology and neurochemistry using electron microscopy and immunohistochemistry in the rat soleus muscle. Acute sleep deprivation altered synaptic ultra-structure viz. mitochondria, synaptic vesicle, synaptic proteins, basal lamina, and junctional folds needed for neuromuscular transmission. Further acute sleep deprivation showed the depletion of the neurotransmitter acetylcholine and the overactivity of its degrading enzyme acetylcholine esterase at the neuromuscular junction. The impact of sleep deprivation on synaptic homeostasis in the brain has been extensively reported recently. The present evidence from our studies shows new information on the role of sleep on neuromuscular junction homeostasis and its functioning. Statement of significanceSleep causes synaptic downscaling in the brain, and allows the brain to carry out various housekeeping functions. Here we have reported that the function of the sleep-wake cycle on the synaptic homeostasis extends beyond the brain. Acute sleep deprivation caused significant alteration at ultra and macrostructure of antigravity muscle and the neuromuscular junction along with adaptation to new fiber type in rats. These morpho-functional changes were well correlated with the biochemical assessment of the acetylcholine at the neuromuscular junction. These changes were partially recovered when the rats were allowed to recover from sleep deprivation. The findings suggest a new avenue for a sleep study; employing the neuromuscular junction for exploring the effect of sleep at energy and synaptic homeostasis levels.

neuroscience↗

bioRxiv2022

Incorporating the image formation process into deep learning improves network performance in deconvolution applications

We present Richardson-Lucy Network (RLN), a fast and lightweight deep learning method for 3D fluorescence microscopy deconvolution. RLN combines the traditional Richardson-Lucy iteration with a fully convolutional network structure, improving network interpretability and robustness. Containing only [~]16 thousand parameters, RLN enables 4- to 50-fold faster processing than purely data-driven networks with many more parameters. By visual and quantitative analysis, we show that RLN provides better deconvolution, better generalizability, and fewer artifacts than other networks, especially along the axial dimension. RLN outperforms Richardson-Lucy deconvolution on volumes contaminated with severe out of focus fluorescence or noise and provides 4- to 6-fold faster reconstructions of large, cleared tissue datasets than classic multi-view pipelines. We demonstrate RLNs performance on cells, tissues, and embryos imaged with widefield-, light sheet-, and structured illumination microscopy.

biophysics↗

bioRxiv2021

Multiview super-resolution microscopy

We enhance the performance of confocal microscopy over imaging scales spanning tens of nanometers to millimeters in space and milliseconds to hours in time, improving volumetric resolution more than 10-fold while simultaneously reducing phototoxicity. We achieve these gains via an integrated, four-pronged approach: 1) developing compact line-scanners that enable sensitive, rapid, diffraction-limited imaging over large areas; 2) combining line-scanning with multiview imaging, developing reconstruction algorithms that improve resolution isotropy and recover signal otherwise lost to scattering; 3) adapting techniques from structured illumination microscopy, achieving super-resolution imaging in densely labeled, thick samples; 4) synergizing deep learning with these advances, further improving imaging speed, resolution and duration. We demonstrate these capabilities on more than twenty distinct fixed and live samples, including protein distributions in single cells; nuclei and developing neurons in Caenorhabditis elegans embryos, larvae, and adults; myoblasts in Drosophila wing imaginal disks; and mouse renal, esophageal, cardiac, and brain tissues.

bioengineering↗

bioRxiv2020

Effect of Variations in the Conserved Residues E371 and S359 on the Structural Dynamics of Protein Z Dependent Protease Inhibitor (ZPI): A Molecular Dynamic Simulation Study

Protein Z (PZ) dependent protease inhibitor (ZPI) is a natural anticoagulant inhibiting blood coagulation proteases fXa and fXIa. Despite being a member of the serpin superfamily, it possesses unique structural features such as activation by PZ that regulate its inhibitory function. It is well known that effecient protease inhibition by serpins is dependent on the dynamics of its reactive center loop (RCL). In order to understand the RCL dynamics of ZPI, we performed Molecular Dynamics (MD) simulation on ZPI and its E371 and S359 variants located at important conserved functional sites. Unexpectedly, the RCL of E371 variants, such as E371K, E371R, and E371Q, were shown to be very stable due to compensatory interactions at the proximal end of RCL. Interestingly, RCL flexibility was shown to be enhanced in the double mutant K318-E371 due to the repulsive effect of increased negative charge on top of the breach region. Principal component analysis (PCA) coupled with residue wise interaction network (RIN) revealed correlated motion between the RCL and the PZ binding regions in the WT. Whereas the analysis revealed a loss of regulation in correlated motion between RCL and PZ binding hotspot Tyr240 in the double mutant. Additionally, the S359F and S359I mutations also resulted in increased RCL flexibility owing to the disruption of stabilizing hydrogen bonding interaction at the N terminal end of S5A. Thus, the current study proposes that the overall stabilizing interactions of S5A is a major regulator of proper loop movement of ZPI for protease inhibition and therefore its activity. The results would be beneficial to engineer activity compromised ZPI mutants as a prophylactic agent for the treatment of hemophilia.

biophysics↗

bioRxiv2020

A neurite-zippering mechanism, mediated by layer-specific expression of IgCAMs, regulates synaptic laminar specificity in the C. elegans nerve ring neuropil

During development, neurites and synapses segregate into specific neighborhoods or layers within nerve bundles. The developmental programs guiding placement of neurites in specific layers, and hence their incorporation into specific circuits, are not well understood. We implement novel imaging methods and quantitative models to document the embryonic development of the C. elegans brain neuropil, and discover that differential adhesion mechanisms control precise placement of single neurites onto specific layers. Differential adhesion is orchestrated via developmentally-regulated expression of the IgCAM SYG-1, and its partner ligand SYG-2. Changes in SYG-1 expression across neuropil layers result in changes in adhesive forces, which sort SYG-2-expressing neurons. Sorting to layers occurs, not via outgrowth from the neurite tip, but via an alternate mechanism of retrograde zippering, involving interactions between neurite shafts. Our study indicates that biophysical principles from differential adhesion govern neurite placement and synaptic specificity in vivo in developing neuropil bundles.

neuroscience↗

bioRxiv2020

Structural and developmental principles of neuropil assembly in C. elegans

Neuropil is a fundamental form of tissue organization within brains1. In neuropils, densely packed neurons synaptically interconnect into precise circuit architecture2,3, yet the structural and developmental principles governing nanoscale precision in bundled neuropil assembly remain largely unknown4-6. Here we use diffusion condensation, a coarse-graining clustering algorithm7, to identify nested circuit structures within the C. elegans cerebral neuropil (called the nerve ring). We determine that the nerve ring neuropil is organized into four tightly bundled strata composed of related behavioral circuits. We demonstrate that the stratified architecture of the neuropil is a geometrical representation of the functional segregation of sensory information and motor outputs, with specific sensory organs and muscle quadrants mapping onto particular neuropil strata. We identify groups of neurons with unique morphologies that integrate information across strata and that create a sophisticated honeycomb-shaped scaffold that encases the strata within the nerve ring. We resolve the developmental sequence leading to stratified neuropil organization through the integration of lineaging and cell tracking algorithms with high resolution light-sheet microscopy, and reveal principles of cell position, migration and hierarchical outgrowth that guide neuropil organization. Our results uncover conserved design principles underlying nerve ring neuropil architecture and function, and a pioneer neuron-based, temporal progression of outgrowth that guides the hierarchical development of the layered neuropil. Our findings provide a blueprint for using structural and developmental approaches to systematically understand neuropil organization within brains.

neuroscience↗

bioRxiv2018

Cholesterol depletion by MβCD enhances membrane tension, its heterogeneity and affects cellular integrity.

Cholesterol depletion in cells by M{beta}CD remodels the plasma membranes mechanics and its interactions with the underlying cytoskeleton. Decoupling the two effects and studying various alterations to the membranes mechanical parameters is important for understanding cholesterols role in cellular response to stress. By mapping membrane height fluctuations in single cells, we report that M{beta}CD treatment reduces temporal fluctuations and flattens out the membrane - but does not supress activity-driven fluctuations. We find that membrane tension increase contributes most to the altered fluctuations, among the multiple mechanical parameters computed. Maps also reveal an enhanced long-range heterogeneity within single cells, both in amplitude of fluctuations and membrane tension on cholesterol depletion. To check if this alters the tenacity of membrane to mechanical stress we use hypo-osmotic shock. We find that on M{beta}CD treatment, cells are more prone to rupture than control cells, and this is not hindered by actomyosin perturbations. We report increased rupture sizes on cholesterol depletion and argue that, together, this indicates decreased lysis and line tension. Therefore, we show that cholesterol depletion directly affects cell membranes not only by enhancing membrane-cytoskeleton interactions, but also by increasing membrane tension while reducing lysis tension - hence making cells prone to rupture.

biophysics↗