Biology subjects

Bhatia, T.

Publications and source records attributed to Bhatia, T..

8 recordsLinked to original sources

bioRxiv2026

Evolution of Vesicle Shape Parameters Based on A Deep-Learning Based Image Analysis Framework Over Extended Time Periods

A precise analysis of shape instabilities in cell-sized membrane compartments requires thorough quantification of the shape dynamics of individual components over extended periods. Herein, we have used phase-contrast microscopy to image giant unilamellar membrane vesicles (GUVs), which are widely used as model systems for cellular structures. GUVs were prepared in the fluid lamellar phase of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine with and without cholesterol dissolved within a potato starch solution. The morphological changes and budding dynamics of individual GUVs with different chemical compositions were quantified using a deep-learning based image analysis framework over extended time periods, by using phase-contrast micrographs as input data. This automated framework integrates contour-based detection of the mother vesicle with precise segmentation of daughter compartments, thereby enabling explicit identification and tracking of mother and daughter vesicles at high temporal resolution. These findings further facilitate the measurement of the temporal evolution of vesicle morphometrics including area, and local membrane curvature during budding, that can be used as an input to develop computational models aimed at elucidating curvature-driven membrane remodeling in complex soft materials.

biophysics↗

bioRxiv2026

A Saliva-Inspired Model of Enzymatic Starch Hydrolysis by Alpha Amylase

We demonstrate that the enzymatic activity of alpha-amylase (AA) can serve as an effective physicochemical trigger for membrane remodeling in giant unilamellar vesicles (GUVs). This work provides insight into how primitive protocellular reactions directly translate into the membrane's mechanical responses. Analysis of the potato starch utilized in this work is composed of ~26\% amylose and ~75\% amylopectin. Quantitative DNS analysis revealed time- and concentration-dependent accumulation of reducing sugars during starch degradation by AA. The HPLC-RID chromatograms demonstrated the synthesis of glucose, maltose, maltotriose, maltotetraose, maltopentaose, maltohexaose, and maltoheptaose, with maltose and maltotriose as the major products. The accumulation of these soluble hydrolysis products gradually increases the osmolarity of the extracellular medium surrounding the vesicles, leading to osmotic asymmetry across the membrane. This biochemical framework provides a quantitative basis for understanding membrane deformation, curvature generation, vesicle deflation, and budding. In addition to the specific starch--$\alpha$-amylase system studied here, our work uncovers a general mechanism by which external biochemical reactions control membrane shape transformations via osmotic coupling. Such enzyme-driven remodeling offers a simple yet powerful strategy for inducing dynamic structural changes in artificial cells. It may provide insight into primitive protocellular processes in which metabolic activity and membrane mechanics were inherently coupled.

biophysics↗

bioRxiv2025

Threshold-like transcriptomic responses of European beech to simulated future climates

Beech (Fagus sylvatica) is one of the most important forest tree species in Europe, both in terms of land coverage and ecosystem services. Although it is projected to be strongly affected by climate change, insights into its functional genomic responses to realistic future scenarios are still lacking. We conducted a fully controlled ecotron experiment to examine the transcriptomic responses of 125 young, naturally regenerated beech trees exposed to regionalized dynamic climate series representing a reference period (1987-2016) and two future climate scenarios (Representative Concentration Pathways, RCP2.6 and RCP8.5, for 2071-2100) in Germany. RCPs describe alternative greenhouse gas trajectories established by the IPCC, ranging from strong mitigation (RCP2.6) to high, unmitigated emissions (RCP8.5), the latter representing a worst-case future scenario. Although both scenarios produced substantial transcriptional changes relative to the reference period, RCP8.5 elicited markedly stronger responses than RCP2.6, with nearly twice as many differentially expressed genes and unique transcriptional programs across functional categories that were not predictable from the RCP2.6 transcriptomes. Our study reveals emergent functional responses in European beech under projected late 21st-century climate conditions in Germany and highlights potential biomarkers for monitoring ecosystem responses to climate change.

ecology↗

bioRxiv2024

Shape analysis of biomimetic and plasma membrane vesicles

Giant membrane vesicles (GUVs) and Giant plasma membrane vesicles (GPMVs) are models for examining membrane properties. We attempted to conduct a comparative study of reduced volume of vesicles with different lipid compositions, solution symmetry, solution asymmetry, and membrane charge. The vesicular morphology is studied using three-dimensional visualization techniques. The vesicles may not be exactly similar to spheres, but they may have some fluctuations resulting in changes in their shape. To understand these shape deformations, we visualize them as confocal image stacks. Our experimental observations indicate that the charge of the membrane affects the deflation of the GUVs in the presence of trans-bilayer sugar asymmetries. The lipid bilayers of our GUVs contain a uniform distribution of the lipids in the two leaflets, which implies that the two leaflets have the same lipid composition and there is no asymmetries in this composition. However, they obtain trans-bilayer asymmetries through asymmetric adsorption or desorption layers of different solution compositions adjacent to each leaflet. The deformation of the GPMVs shapes extracted from cells with trans-bilayer buffer asymmetries and the composition asymmetries is also estimated and compared with biomimetic membranes.

biophysics↗

bioRxiv2024

TECPR2 is a Rab5 effector that regulates endosomal cargo recycling

Small GTP-binding (G) proteins of the Rabs, Arfs, and Arls (Arf-like) family mediate the recruitment of their effectors to subcellular membrane-bound compartments, which in turn mediates vesicle budding, motility, and tethering. Here, we report that Tectonin-{beta}-propeller repeat containing protein 2 (TECPR2), a protein mutated in a form of hereditary sensory and autonomic neuropathy (HSAN), is an effector of early endosomal Rab protein, Rab5, and interacts with Rab5 via its C-terminal TECPR repeats. The HSAN-associated TECPR2 (R1336W) missense variant was deficient in Rab5-binding and, consequently, in membrane recruitment. TECPR2-depletion led to perinuclear collapse of recycling endosomes and increased overlap of sorting and degradative subdomain markers on early endosomes. Consistent with a possible role in endocytic recycling, we observed impaired recycling and increased lysosomal degradation of 5{beta}1 integrin receptors upon TECPR2 knockdown. TECPR2 regulates the early endosomal localization of the cargo adaptor for {beta}1 integrins, SNX17, and its-associated protein complex WASH, which mediates actin polymerization on early endosomes. Finally, TECPR2 depletion in the zebrafish model resulted in delayed motility and changes in the neuromuscular junction. Our study supports an early endosomal role for TECPR2 in cargo recycling and provides insights into how its loss-of- function results in a neurodegenerative genetic disorder.

cell biology↗

bioRxiv2022

Redefining the structure of tip-links in hair-cells

Tip-link, the gating-spring in hearing, modulates the mechanoelectrotransduction process and protects the hearing sensory machineries from overexcited auditory inputs. Tip-links are formed by two exceptionally long cadherins, cadherin-23 and protocadherin-15. It is proposed that both the cadherins first independently form cis-dimers through lateral interactions and finally, engage in trans-interactions to form the heterotetrameric assembly in tip-links. In fact, the molecular details of the protocadherin cis-dimers are well-understood. However, little structural and molecular details are known for independent cis-dimer of cadherin-23. Using photo-induced cross-linking of unmodified proteins in solution and on lipid-membranes, we observed no trace of cadherin-23 cis-dimers, rather we captured trans-homodimers of cadherin-23. We thus, redefine the tip-link structure where protocadherin-15 remains as cis-dimers, however, two individual cadherin-23 binds to protocadherin-15 cis-dimer for tip linking.

biochemistry↗

bioRxiv2020

Super-elasticity of plasma- and synthetic membranes by coupling of membrane asymmetry and liquid-liquid phase separation

Biological cells are contained by a fluid lipid bilayer (plasma membrane, PM) that allows for large deformations, often exceeding 50% of the initial (or projected) PM area. Biochemically isolated lipids self-organize into membranes, but the extraordinary deformability of the plasma membrane is lost. Pure lipid bilayers are prone to rupture at small (<2-4%) area strains and this limits progress for synthetic reconstitution of cellular features such as migration, phagocytosis and division. Here, we show that by preserving PM structure and composition during isolation from cells, vesicles with cell-like elasticity are obtained. We found that these plasma membrane vesicles store significant area in the form of nanotubes in their lumen. These are recruited by mechanical tension applied to the outer vesicle membrane showing an apparent elastic response. This "super-elastic" response emerges from the interplay of lipid liquid-liquid phase separation and membrane asymmetry. This finding allows for bottom-up engineering of synthetic vesicles that appear over one magnitude softer and with three fold larger deformability than conventional lipid vesicles.

biophysics↗

bioRxiv2019

Oligogenic rare variant contributions in schizophrenia and their convergence with genes harboring de novo mutations in schizophrenia, autism, and intellectual disability: Evidence from multiplex families

Clinical and genetic heterogeneity has been documented extensively in schizophrenia, a common behavioural disorder with heritability estimates of about 80%. Common and rare de novo variant based studies have provided notable evidence for the likely involvement of a range of pathways including glutamatergic, synaptic signalling and neurodevelopment. To complement these studies, we sequenced exomes of 11 multimember affected schizophrenia families from India. Variant prioritisation performed based on their rarity (MAF <0.01), shared presence among the affected individuals in the respective families and predicted deleterious nature, yielded a total of 785 inherited rare protein sequence altering variants in 743 genes among the 11 families. These showed an enrichment of genes involved in the extracellular matrix and cytoskeleton components, synaptic and neuron related ontologies and neurodevelopmental pathways, consistent with major etiological hypotheses. We also noted an overrepresentation of genes from previously reported gene sets with de novo protein sequence altering variants in schizophrenia, autism, intellectual disability; FMRP target and loss of function intolerant genes. Furthermore, a minimum of five genes known to manifest behavioural/neurological and nervous system abnormalities in rodent models had deleterious variants in them shared among all affected individuals in each of the families. Majority of such variants segregated within and not across families providing strong suggestive evidence for the genetically heterogeneous nature of disease. More importantly, study findings unequivocally support the classical paradigm of cumulative contribution of multiple genes, notably with an apparent threshold effect for disease manifestation and offer a likely explanation for the unclear mode of inheritance in familial schizophrenia.

genetics↗