Biology subjects

Padhi, A.

Publications and source records attributed to Padhi, A..

6 recordsLinked to original sources

bioRxiv2026

Heterotypic FG-Nup98-tau condensates form nested assemblies through stoichiometry-dependent phase transitions

The dysfunction of nucleocytoplasmic transport (NCT) and tau aggregation are emerging as interconnected hallmarks of neurodegenerative tauopathies. However, the molecular basis by which components of the nuclear pore complex and tau interact remains unclear. Here, we combine experimental and computational approaches to elucidate the mechanism of heterotypic phase separation between the FG-repeat domain of nucleoporin Nup98 (FG-Nup98) and tau. In vitro assays revealed that FG-Nup98 and tau undergo coacervation, forming dynamic condensates whose morphology and dynamics depend on stoichiometry, macromolecular crowding, and ionic strength. FRAP indicated reduced tau mobility within FG-Nup98-rich condensates, supporting a scaffold-client model. Complementary computational analyses revealed hierarchical binding energetics: FG-Nup98 self-association is strongest, followed by FG-Nup98-tau and tau-tau interactions. While FG-Nup98 forms stable homotypic networks, tau-tau contacts are transient but energetically favorable, which suggests that elevated tau concentrations may trigger a transition from droplets to tau aggregates. Together, these results establish that multivalent FG-Nup98-tau interactions drive condensate formation that could potentially perturb the permeability barrier of the nuclear pore. This study elucidates the coordinated behaviors of FG-Nup98-tau condensates and provides a framework for understanding NCT defects in tauopathies.

biochemistry↗

bioRxiv2025

Accurate processing of ultra-short immune signals by singlemacrophages

Accurately interpreting short-lived signals is challenging within noisy cellular microenvironments. It is not known if cells can distinguish different signaling molecules under transient exposure. Here, we explored the temporal limits of signal detection by single macrophages. Microfluidic experiments monitoring NF-{kappa}B dynamics showed that macrophages strongly respond even to 1-second pulses of cytokine and pathogen ligands. Information theory showed that short-pulse response is highly specific to the stimulating ligand, comparable to that under long-term stimulation. Macrophages were mainly sensitive to the duration of cytokines, and the dose of pathogen ligands. Stimulus duration altered the ranking of response strengths among different pathogenic ligands. Mathematical modeling showed that receptor cooperativity is crucial for robust responses to transient signals, while receptor pathway variability leads to accurate signaling in fluctuating environments. These findings demonstrate that dynamic transcription factor specificity is preserved across varying signal durations and uncover network-level mechanisms that accurately distinguish transiently encountered threats.

systems biology↗

bioRxiv2022

Deep Learning Enabled Label-free Cell Force Computation in Deformable Fibrous Environments

Cells move within tissues by pulling on and reshaping their fibrous surroundings. Measuring the associated forces has been a fundamental challenge in cell biology. Here, we develop deep-learning-enabled live-cell fiber-force microscopy (DLFM), which computes forces produced by living cells in real time as they interact with tissue-like fiber networks. DLFM combines basic phase microscopy with novel deep learning to simultaneously track cell movement and fiber deformation without disruptive fluorescent labels or chemical modifications. This allowed us to measure forces in real-time situations that were previously impossible to study, revealing an intricate mechanical landscape: cells generate ten-fold changes in force as they change shape during migration, create force-dipoles during cell-cell interactions, and dramatically alter their force patterns during stem cell differentiation. Through integrated experiments and mathematical modeling, we discovered that cells in fibrous environments form force-generating adhesions throughout their body, strikingly different from the edge-only adhesions seen in traditional petri dish experiments. Results clarify cytoskeletal pathways by which cells adapt force-generating machinery to navigate the fibrous architecture of tissues.

biophysics↗

bioRxiv2020

Rational Design of the Remdesivir Binding Site in the RNA-dependent RNA Polymerase of SARS-CoV-2: Implications for Potential Resistance

ABSTRACTSARS-CoV-2 is rapidly evolving with the continuous emergence of new mutations. There is no specific antiviral therapy for COVID-19, and the use of Remdesivir for treating COVID-19 will likely continue before clinical trials are completed. Due to the lengthening pandemic and evolving nature of the virus, predicting potential residues prone to mutations is crucial for the management of Remdesivir resistance. We used a rational ligand-based interface design complemented with mutational mapping to generate a total of 100,000 mutations and provide insight into the functional outcome of mutations in the Remdesivir-binding site in nsp12. After designing 56 residues in the Remdesivir binding site of nsp12, the designs retained 96-98% sequence identity, which suggests that SARS-CoV-2 attains resistance and develops further infectivity with very few mutations in the nsp12. We also identified affinity-attenuating Remdesivir binding designs of nsp12. Several mutants acquired decreased binding affinity with Remdesivir, which suggested drug resistance. These hotspot residues had a higher probability of undergoing selective mutations in the future to develop Remdesivir and related drug-based resistance. A comparison of 21 nsp12 Remdesivir-bound designs to the 13 EIDD-2801-bound nsp12 designs suggested that EIDD-2801 would be more effective in preventing the emergence of resistant mutations and against Remdesivir-resistance strains due to the restricted mutational landscape. Combined with the availability of more genomic data, our information on mutation repertoires is critical to guide scientists to rational structure-based drug discovery. Knowledge of the potential residues prone to mutation improves our understanding and management of drug resistance and disease pathogenesis.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

bioRxiv2019

Nano-twines to twine-bridges: Role of force exerting perpendicular lateral protrusions in fibroblastic cell contraction

Aligned extracellular matrix fibers enable fibroblasts to undergo myofibroblastic activation and lead to elongated cell morphology. The fibroblasts in turn contract to cause alignment of the extracellular matrix. This feedback process is critical in pathological occurrences such as desmoplasia and is not well understood. Using engineered fiber networks that serve as force sensors, we identify lateral protrusions with specific functions and morphology that are induced by elongated fibroblastic cells and which apply extracellular fiber-deflecting contractile forces. Lateral projections, named twines, produce twine bridges upon interacting with neighboring parallel fibers. These mature into \"perpendicular lateral protrusions\" (PLPs) that enable cells to spread laterally and effectively contract. Using quantitative microscopy, we show that the twines originate from the stratification of cyclic actin waves traversing the entire length of the cell. The primary twines swing freely in 3D and engage neighboring extracellular fibers. Once engaged, a lamellum extends from the primary twine and forms a second twine, which also engages with the neighboring fiber. As the lamellum fills in the space between the two twines, a sheet-like PLP is formed to contract effectively. By controlling the geometry of extracellular networks we confirm that anisotropic fibrous environments enable PLP formation, and these force-generating PLPs are oriented perpendicular to the parent cell body. PLP formation kinetics indicated mechanisms analogous to other/known actin-based structures. Our identification of force-exerting PLPs in anisotropic fibrous environments suggests an explanation for cancer-associated desmoplastic expansion at single-cell resolution, providing possible new clinical intervention opportunities.

cell biology↗

bioRxiv2017

Mycobacterium tuberculosis LprE enhances bacterial persistence by inhibiting cathelicidin and autophagy in macrophages

Mycobacterium tuberculosis(Mtb) lipoproteins are known to facilitate bacterial survival by manipulating the host immune responses. Here, we have characterized a novel Mtb lipoprotein LprE(LprEMtb), and demonstrated its role in mycobacterial survival. LprEMtb acts by down-regulating the expression of cathelicidin, Cyp27B1, VDR and p38-MAPK via TLR-2 signaling pathway. Deletion of lprEMtb resulted in induction of cathelicidin and decreased survival in the host. Interestingly, LprEMtb was also found to inhibit autophagy mechanism to dampen host immune response. Episomal expression of LprEMtb in non-pathogenic Mycobacterium smegmatis(Msm) increased bacillary persistence by down-regulating the expression of cathelicidin and autophagy, while deletion of LprEMtb orthologue in Msm, had no effect on cathelicidin and autophagy expression. Moreover, LprEMtb blocked phago-lysosome fusion by suppressing the expression of EEA1, Rab7 and LAMP-1 endosomal markers by down-regulating IL-12 and IL-22 cytokines. Our results indicate that LprEMtb plays an important role in mycobacterial pathogenesis in the context of innate immunity.

physiology↗