Biology subjects

Chaudhury, D.

Publications and source records attributed to Chaudhury, D..

10 recordsLinked to original sources

bioRxiv2026

Force Induces a Collective Inactivity in Dyneins to Auto-Regulate Bidirectional Transport of Vesicles

The back-and-forth (bidirectional) motion of Endosomes and Phagosomes along microtubules is fundamentally important for nutrient absorption, receptor recycling, pathogen degradation and many other downstream cellular pathways. Bidirectional motion requires opposing force from the kinesin and dynein motors, causing intermittent Tug-of-Wars (ToWs) followed by runs where winning motors drive their cargo until the next ToW. Dynein displays a counter-intuitive behaviour of catch bonding tightly to the microtubule against opposing force, but why such a response is needed remains unknown. Here we force dynein to catch-bond using an optical trap when dynein-teams are transporting phagosomes in-vitro and inside cells. An unexpected form of collective inactivity emerges, where larger dynein-teams remain inactive for longer after they have been catch-bonded. Kinesin exhibits a high probability of reversing the cargo during such periods of inactivity of dyneins. Therefore, the inactivity of dyneins allows cells to auto-regulate the effect of opposing molecular forces for the purpose of achieving bidirectional motion of endosomes/phagosomes. We propose that an inactivating conformational change is induced when dynein detaches against strain from its catch-bonded state. Collective inactivity follows because each inactive dynein exerts an entropic force on the other to delay the entire team from being activated. We capture the dynamics of this process through a statistical model of Entropically Constrained Reactivation, obtaining predictions in excellent agreement with experimental data. The emergent behaviour observed here possibly prevents a runaway dynein situation inside cells, its simple entropic origin suggesting broader relevance to catch-bonded receptor ligand interactions operating under conditions of cellular crowding.

cell biology↗

bioRxiv2026

Rhythmic expression of a cAMP phosphodiesterase switches neuronal excitability states in the mammalian suprachiasmatic nucleus

How the transcriptome of a neuron determines its electrophysiological properties and how this change in different contexts are major questions in neurobiology. The intracellular molecular clocks in the circadian pacemaker neurons in the mammalian suprachiasmatic nucleus (SCN) drive 24hr rhythms in clock gene expression via a transcriptional-translational feedback loop1,2. These molecular clocks also control 24hr rhythms in the firing of SCN neurons3-5 - a subset of which enter a silent depolarized state around midday6. We used single-cell RNA sequencing and identified that the Avp / Nms and Vip / Nms are the SCN neurons that undergo daytime silencing. We also found high level and rhythmic expression of the Pde10a phosphodiesterase in these Nms SCN neurons. Acutely inhibiting Pde10a activity or elevating intracellular cAMP - to bypass high Pde10a levels - specifically shifts these Nms+ SCN neurons into a depolarized silent state hours ahead of schedule. A similar mechanism may occur in other neurons that switch to silent depolarized states.

neuroscience↗

bioRxiv2025

Distinct depressive-like behavioural phenotypes in mice exhibit unique patterns of transcriptional perturbations across habenular cell subtypes

Major depressive disorder arises from diverse neurobiological mechanisms, yet how specific habenular cell types contribute to distinct depressive-like behaviours remains unclear. Using chronic social defeat stress, behavioural phenotyping, and single-cell RNA sequencing, we mapped stress-induced transcriptional changes across habenular cell types and lateral habenula (LHb) subregions. Our findings reveal that each behavioural phenotype is marked by its own transcriptional profile. These subregion-specific patterns across the LHb suggest that different cellular circuits contribute uniquely to depressive-like states.

neuroscience↗

bioRxiv2023

Molecular signature of primate astrocytes reveals pathways and regulatory changes contributing to the human brain evolution

Astrocytes contribute to the development and regulation of the higher-level functions of the brain, the critical targets of evolution. However, the molecular signature of foetal astrocyte evolution in primates is unknown. Here, to address this question, we use human, chimpanzee, and macaque induced pluripotent stem cell-derived foetal astrocytes (iAstrocytes). Human iAstrocytes are bigger and more complex than the non-human primate iAstrocytes. We find loci related to the regulation of cell size with increased expression in the human lineage. Likewise, we uncover that genes and mechanisms implicated in long-range intercellular signalling are activated in the human iAstrocytes. Strikingly, loci downregulated in the human lineage frequently relate to intellectual disability raising new questions on the trade-offs associated with the evolution of the human mind. Using our system, through a multilevel regulome analysis and machine learning, we uncover that functional activation of enhancers coincides with a previously unappreciated, pervasive gain of binding sites of stripe transcription factors. In summary, we shed new light on a mechanism driving the acquisition of the regulatory potential of enhancers.

neuroscience↗

bioRxiv2023

Phosphatidic Acid Dependent Recruitment of Microtubule Motors to Spherical Supported Lipid Bilayers for In-vitro Motility Assays

A variety of membrane-bound vesicles are transported by the kinesin and dynein motor proteins respectively towards plus and minus ends of microtubules inside cells. How specific lipids, particularly rare lipids, bind and activate motors on the vesicle membrane and the biological consequences thereof are poorly understood. Here we prepare spherical supported lipid bilayers (SLBs) consisting of a latex bead enclosed within a membrane that contains phosphatidic acid (PA). When incubated with motor-protein enriched fractions from Dictyostelium or from Rat brain, PA-coated SLBs exhibit robust motion along in-vitro polymerized microtubules. We quantify the activity of SLB-bound motors by measuring their force generation against an Optical trap on polarity-labelled microtubules. Such experiments reveal that PA recruits dynein-dynactin from Dictyostelium, but kinesin-1 from rat brain fractions to drive SLB motion. Kinesin-1 is able to dominate over dynein when dynactin, an activator of dynein, is deficient on SLBs. We demonstrate how inhibiting only kinesin can block both kinesin and dynein activity on a cargo, thus providing an explanation for the long-standing "paradox of co-dependence" in the field of intracellular transport. We also find that as the size of a motor-driven SLB increases, the SLB is able to reverse direction more easily along a microtubule. This observation provides clues as to how micron-sized cargoes are efficiently able to navigate the crowded cytoskeletal space inside cells.

cell biology↗

bioRxiv2023

Nighttime-specific gene expression changes in suprachiasmatic nucleus and habenula are associated with resiliency to chronic social stress

The molecular mechanisms that link stress and circadian rhythms still remain unclear. The habenula (Hb) is a key brain region involved in regulating diverse types of emotion-related behaviours while the suprachiasmatic nucleus (SCN) is the bodys central clock. To investigate the effects of chronic social stress on transcription patterns, we performed gene expression analysis in the Hb and SCN of stress naive and stress exposed mice. Our analysis revealed a large number of differentially expressed genes and enrichment of synaptic and cell signalling pathways between resilient and stress-naive mice at ZT16 in both the Hb and SCN. This transcriptomic signature was nighttime-specific and observed only in stress-resilient mice. In contrast, there were relatively few differences between the stress-susceptible and stress-naive groups across timepoints. Our results reinforce the functional link between diurnal gene expression patterns and differential responses to stress, thereby highlighting the importance of temporal expression patterns in homeostatic stress responses.

neuroscience↗

bioRxiv2023

Chronic social stress blunts core body temperature and molecular rhythms of Cirbp and Rbm3 in mice lateral habenula

Chronic social stress in mice causes behavioral and physiological changes that result in perturbed rhythms of body temperature, activity and sleep-wake cycle. To further understand the link between mood disorders and temperature rhythmicity in mice that are resilient or susceptible to stress, we measured core body temperature (Tcore) before and after exposure to chronic social defeat stress (CSDS). We found that Tcore amplitudes of stress-resilient and susceptible mice are dampened during exposure to CSDS. However, following CSDS, resilient mice recovered temperature amplitude faster than susceptible mice. Furthermore, the interdaily stability (IS) of temperature rhythms was fragmented in stress-exposed mice during CSDS, which recovered to control levels following stress. There were minimal changes in locomotor activity after stress exposure which correlates with regular rhythmic expression of Prok2 - an output signal of the suprachiasmatic nucleus. We also determined that expression of thermosensitive genes Rbm3 and Cirbp in the lateral habenula (LHb) were blunted 1-day after CSDS. Rhythmic expression of these genes recovered 10 days later. Overall, we show that CSDS blunts Tcore and thermosensitive gene rhythms. Tcore rhythm recovery is faster in stress-resilient mice, but Rbm3 and Cirbp recovery is uniform across the phenotypes.

neuroscience↗

bioRxiv2020

What it takes to be at the top: The interrelationship between chronic social stress and social dominance

Dominance hierarchies of social animal groups are influenced by complex factors such as stress. Stress experienced by an animal prior to social interactions with a conspecific may be a determinant of their future social dynamics. Additionally, long-term occupancy of a specific hierarchical rank can have psychophysiological effects, leading to vulnerability to future stress. The current study aimed to delineate differential effects of stress acting before or after hierarchy formation. Using the chronic social defeat stress (CSDS) paradigm we performed behavioural investigations to determine whether exposure to CSDS before hierarchy formation predicted the new dominance status. Moreover, in another study we investigated whether social rank predicted stress vulnerability. We found that CSDS did not impede the establishment of dominance in new hierarchies as both stress-susceptible (socially avoidant) and -resilient (social) mice were able to attain dominant ranks. In contrast, within newly established hierarchies of stress-naive mice, the subordinate, but not dominant, mice exhibit significantly greater avoidance of novel social targets. However, following exposure to CSDS, both lowest- and highest-ranked mice exhibit strong susceptibility to stress as measured by decreased interactions with a novel social target. These results suggest that the response to chronic social stress did not determine social rank in new cohorts, but low-status mice in newly established groups exhibited lower sociability to novel social targets. Interestingly, exposure of a hierarchical social group to chronic social stress led to stress-susceptibility in both high- and low-status mice as measured by social interaction. HighlightsO_LIStress susceptibility to chronic social defeat did not impede the establishment of dominance in new hierarchies. C_LIO_LISubordinate mice exhibit reduced social preference after hierarchy formation. C_LIO_LIFollowing chronic social defeat stress, both subordinate and dominant mice exhibit susceptible-like reduction in social interaction, but dominant mice exhibit the greater decrease in social preference as compared to baseline. C_LI

neuroscience↗

bioRxiv2020

Larger active site in an ancestral hydroxynitrile lyase increases catalytically promiscuous esterase activity

Hydroxynitrile lyases (HNLs) belonging to the /{beta}-hydrolase-fold superfamily evolved from esterases approximately 100 million years ago. Reconstruction of an ancestral hydroxynitrile lyase in the /{beta}-hydrolase fold superfamily yielded a catalytically active hydroxynitrile lyase, HNL1. Several properties of HNL1 differ from the modern HNL from rubber tree (HbHNL). HNL1 favors larger substrates as compared to HbHNL, is two-fold more catalytically promiscuous for ester hydrolysis (p-nitrophenyl acetate) as compared to mandelonitrile cleavage, and resists irreversible heat inactivation to 35 {degrees}C higher than for HbHNL. We hypothesized that the x-ray crystal structure of HNL1 may reveal the molecular basis for the differences in these properties. The x-ray crystal structure solved to 1.96-[A] resolution shows the expected /{beta}-hydrolase fold, but a 60% larger active site as compared to HbHNL. This larger active site echoes its evolution from esterases since related esterase SABP2 from tobacco also has a 38% larger active site than HbHNL. The larger active site in HNL1 likely accounts for its ability to accept larger hydroxynitrile substrates. Site-directed mutagenesis of HbHNL to expand the active site increased its promiscuous esterase activity 50-fold, consistent with the larger active site in HNL1 being the primary cause of its promiscuous esterase activity. Urea-induced unfolding of HNL1 indicates that it unfolds less completely than HbHNL (m-value = 0.63 for HNL1 vs 0.93 kcal/ mol{middle dot}M for HbHNL), which may account for the ability of HNL1 to better resist irreversible inactivation upon heating. The structure of HNL1 shows changes in hydrogen bond networks that may stabilize regions of the folded structure.

biochemistry↗

bioRxiv2020

Blunted Diurnal Firing in Lateral Habenula Projections to Dorsal Raphe Nucleus and Delayed Photoentrainment in Stress-Susceptible Mice.

Daily rhythms are disrupted in patients suffering from mood disorders. The lateral habenula (LHb) and dorsal raphe nucleus (DRN) contribute to circadian timekeeping and regulate mood. Thus, pathophysiology in these nuclei may be responsible for aberrations in daily rhythms during mood disorders. Using the chronic social defeat stress (CSDS) paradigm and in-vitro slice electrophysiology we measured the effects of stress on diurnal rhythms in firing of LHb cells projecting to the DRN (cellsLHb[->]DRN) and DRN cells alone. We also performed optogenetic experiments to investigate if increased firing in cellsLHb[->]DRN during exposure to subthreshold social defeat stress (SSDS), induces stress-susceptibility. Last we investigated whether exposure to CSDS affected the ability of mice to phototentrain to a new LD cycle. The cellsLHb[->]DRN and DRN cells alone of stress-susceptible mice express greater blunted diurnal firing compared to stress-naive (control) and stress-resilient mice. Day-time optogenetic activation of cellsLHb[->]DRN during SSDS induces stress-susceptibility which shows the direct correlation between increased activity in this circuit and putative mood disorders. Finally, we found that stress-susceptible mice are slower, while stress-resilient mice are faster, at photoentraining to a new LD cycle. Our findings suggest that CSDS induces blunted daily rhythms in firing in cellsLHb[->]DRN and slow rate of photoentrainment in susceptible-mice. In contrast, resilientmice may undergo homeostatic adaptations that maintain daily rhythms in firing in cellsLHb[->]DRN and also show rapid photoentrainment to a new LD-cycle.

neuroscience↗