Biology subjects

Chodankar, A.

Publications and source records attributed to Chodankar, A..

4 recordsLinked to original sources

bioRxiv2026

Aging associated RNA loss impairs the dynamics of RNA and protein condensates

Altered biomolecular condensate dynamics are increasingly implicated in age-associated neurodegenerative disorders, yet the molecular principles governing these changes remain incompletely understood. Here, we demonstrate that aged cells across diverse cellular and organismal models harbor pre-formed, viscous, and persistent stress granules (SGs), which we term alt-SGs. These persistent condensates confer protection to senescent cells under fluctuating stress conditions. Comparative analyses reveal that alt-SGs exhibit elevated RNA-binding protein (RBP)-to-RNA ratios, underscoring a shift in condensate stoichiometry. By quantifying SG composition and dynamics in live cells and in vitro, we establish that RNA concentration is a key determinant of condensate material properties, molecular composition, and dissolution capacity. Importantly, aging cells display diminished absolute RNA concentrations due to reduced RNA metabolic activity. Reactivation of RNA metabolism restores RNA/RBP ratios within SGs and alleviates aging-associated phenotypes. Together, our findings highlight RNA metabolism as a central regulator of condensate stoichiometry and function, linking metabolic decline to altered phase behavior and cellular aging. Key findingsO_LIAging and senescence have Alt-SGs with increased protein/RNA Ratio C_LIO_LIAlt-SGs are persistent after stress removal in aging C_LIO_LIAging is associated with reduced total cellular RNA C_LIO_LIReactivating RNA metabolism rescues SG phenotypes C_LIO_LIAlt-SGs are protective for senescent cell C_LI

cell biology↗

bioRxiv2025

Spatial Expression Pattern and Cellular Organisation of Gap Junctions in Third Instar Wing Imaginal Discs of Drosophila melanogaster

The Drosophila wing imaginal disc serves as a powerful model to study intercellular communication during development. In our study, we report and discuss the expression pattern and cellular distribution of innexin-1, innexin-2 and innexin-3 in the cells of the wing imaginal discs. Our immunohistochemical data show that all three innexins are broadly expressed across the membranes of both the disc proper and peripodial epithelial cells of the wing disc. The stainings further reveal that, within the disc proper epithelium, junctional proteins are arranged in a clear apico-basal hierarchy: cadherins at the apical surface, followed by septate junction proteins, with innexins localised sub-apically beneath these components. All three innexins are enriched within this sub-apical domain, and are additionally detected at mid-and baso-lateral sites in varying levels. Notably, innexin-2 exhibits partial colocalization with coracle, a septate junction-associated protein, suggesting a functional association. In the peripodial epithelium, innexins are detected in distinct punctate patterns across cell membranes, implying heterogeneity in their molecular characteristics. To validate these expression patterns, we carried out tissue-specific RNAi-mediated knockdowns using the pannier-Gal4 driver targeting the notum, a structurally and functionally important but underexplored region in innexin research. Knockdown of innexin-2 and innexin-3 led to complete loss of their expression within this region. Notably, silencing of innexin-2 also affected the expression of septate junction associated proteins and innexin-3 knockdown was accompanied by a significant reduction in disc size and altered morphology. These findings depict and confirm the presence of innexins in the notum region and also indicate that individual innexins may have distinct or shared functional roles within the same tissue domain of expression. Their localization to specific membrane domains is likely to underlie their differential modes of action. Although previous studies have demonstrated the functional involvement of gap junctions in various aspects of normal wing development in Drosophila, a description of the arrangement of innexins on the third instar wing discs is required for better understanding of their roles. Our study addresses this gap by providing a comprehensive analysis of the cellular localisation and organisation of gap junctions, specifically innexin-1,-2 and-3, within the third instar wing discs, thereby supporting and extending existing knowledge.

cell biology↗

bioRxiv2024

EFFICIENT RIBOSOMAL RNA DEPLETION FROM DROSOPHILA TOTAL RNA FOR NEXT-GENERATION SEQUENCING APPLICATIONS

We developed a cost-effective enzyme-based rRNA-depletion method tailored for Drosophila melanogaster, addressing the limitations of existing commercial kits and the lack of peer-reviewed alternatives. Our method employs single-stranded DNA probes complementary to Drosophila rRNA, forming DNA-RNA hybrids. These hybrids are then degraded using the RNase H enzyme, effectively removing rRNA and enriching all non-ribosomal RNAs, including mRNA, lncRNA and small RNA. When compared to a commercial rRNA removal kit, our approach demonstrated superior rRNA removal efficiency and mapping percentage, confirming its effectiveness. Additionally, our method successfully enriched the non-coding transcriptome, making it a valuable tool for studying ncRNA in Drosophila. The probe sequences and rRNA-depletion protocol are made freely available, offering a reliable alternative for rRNA-depletion experiments.

molecular biology↗

bioRxiv2021

A DROSOPHILA CIRCUIT FOR HABITUATION OVERRIDE

Habituated animals retain a latent capacity for robust engagement with familiar stimuli. In most instances, the ability to override habituation is best explained by postulating that habituation arises from the potentiation of inhibitory inputs onto stimulus-encoding assemblies and that habituation override occurs through disinhibition. Previous work has shown that inhibitory plasticity contributes to specific forms of olfactory and gustatory habituation in Drosophila. Here we analyze how exposure to a novel stimulus causes override of gustatory (proboscis-extension reflex or "PER") habituation. While brief sucrose contact with tarsal hairs causes naive Drosophila to extend their proboscis, persistent exposure reduces PER to subsequent sucrose stimuli. We show that in so habituated animals, either brief exposure of the proboscis to yeast or direct thermogenetic activation of sensory neurons restores PER response to tarsal sucrose stimulation. Similar override of PER habituation can also be induced by brief thermogenetic activation of a population of TH (Tyrosine-Hydroxylase) positive neurons, a subset of which send projections to the subesophagial zone (SEZ). Significantly, sensory-neuron induced habituation override requires transmitter release from these TH-positive cells. Treatments that cause override specifically influence the habituated state, with no effect on the naive sucrose response across a range of concentrations. Taken together with other findings, these observations in female flies are consistent with a model in which novel taste stimuli trigger activity in dopaminergic neurons which, directly or indirectly, inhibit GABAergic cells that drive PER habituation. The implications of these findings for general mechanisms of attentional and sensory override of habituation are discussed.

neuroscience↗