Biology subjects

Pradhan, D.

Publications and source records attributed to Pradhan, D..

5 recordsLinked to original sources

bioRxiv2025

NF-κB mediates transactivation of HNRNPD, resulting in PTEN destabilization and constitutive activation of the PI3K-AKT pathway in oral cancer cells

Heterogeneous Ribonucleoprotein D (hnRNPD), an RNA binding protein transcriptionally upregulated by NF-{kappa}B transcription factor, is associated with poor outcome of Oral Squamous Cell Carcinoma (OSCC). However, the role of hnRNPD in OSCC remains elusive. This study reveals that hnRNPD positively affects the proliferation, migration, invasion, and survival of OSCC cells. Transcriptome profiling in hnRNPD knockout cells identified significant upregulation of PTEN and inhibition of the PI3K/AKT/mTOR axis. HnRNPD mediates the destabilization of PTEN mRNA by binding to the class II AU-Rich Element (ARE) in 3UTR of PTEN. The expression of hnRNPD and PTEN are strongly negatively correlated in OSCC tissue specimens, further corroborating hnRNPD-mediated PTEN destabilization. The hnRNPD knockout inhibited autophagy, evident by an accumulation of autophagic vesicles and decreased autophagic flux. Mechanistically, the hnRNPD knockout reduced the expression of NF-{kappa}B, eventually downregulating its transcriptional target LC3b, a key mediator of autophagy. SA-{beta}-Galactosidase staining in hnRNPD KO cells conclusively demonstrated the onset of cellular senescence. The present study demonstrates hnRNPD-driven positive modulation of autophagy via NF-{kappa}B, independent of the PI3K/AKT/mTOR axis, highlighting it as a novel therapeutic target for treating oral cancer. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/631360v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@11f6844org.highwire.dtl.DTLVardef@f65124org.highwire.dtl.DTLVardef@1492571org.highwire.dtl.DTLVardef@13931dd_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIHnRNPD mediates oral cancer cell proliferation, migration, invasion, and survival. C_LIO_LIHnRNPD acts as a novel regulator of the PI3K/AKT/mTOR axis by destabilization of PTEN. C_LIO_LINF-{kappa}B/RelA downregulated on knockout of HNRNPD, inhibiting autophagy through downregulating its transcriptional target LCB-II. C_LIO_LIHnRNPD mediates cellular senescence in oral cancer cells. C_LI

cancer biology↗

bioRxiv2024

Vocal species are more central in Eastern Himalayan Mixed-Species bird flocks

Mixed-species flocks (MSF) represent an important form of social organisation in bird communities worldwide. Despite its likely importance in flock formation and cohesion, the role of vocal communication in the formation and maintenance of MSF in birds is hitherto understudied. In this study, we examine if a species centrality within a mixed-species flock is influenced by its vocal behaviour during the dawn chorus, i.e., the time of MSF formation. Using acoustic sampling and field observations, we studied the bird species found in MSF in the Eastern Himalayas. Our results show differential vocal activity patterns among MSF-forming bird species and suggest a positive correlation between calling rates and closeness centrality (species importance in a flock) in understory MSFs. We also found a more synchronised vocalisation pattern in the understory MSFs, with a consistent peak in vocal activity in the early morning hours, whereas no consistent vocal pattern was found for canopy flocks. Overall, our results suggest a potential mechanism that drives MSF formation wherein the vocal activity of central species precedes and likely attracts participation from other attendant species.

ecology↗

bioRxiv2023

Bird communities in a selectively logged tropical montane forest are dominated by small, low-elevation species

Tropical montane forests are critical centres of terrestrial biodiversity and endemism, and face a range of threats, including selective logging and climate change. However, few studies have explored the joint influence of these threats, particularly in tropical mountains, despite how crucial it is to understand the cumulative impact of forest loss and climate change on biodiversity. We used mist-netting and bird ringing data from a long-term (10-year) community and population monitoring program to examine how the composition of the mid-elevation Eastern Himalayan understorey bird community changed in the mid-elevation primary and logged forest. Because logged forest is warmer than primary forest, we hypothesised that the bird community would shift towards lower elevation species, with a faster transition in logged forest. Further, because logged forest has lower arthropod abundance, we hypothesised that the primary forest community would have larger species than the logged forest community. Our study shows that the bird community in the logged forest shifted towards lower-elevation species than in the primary forest (although this was not statistically significant). Moreover, we found that smaller species were better able to colonise warmer logged forest, whereas larger species reached higher densities in primary forest. These trends are likely to be driven by climate change causing upslope range shifts and logged forest selecting for species that are likely to tolerate the consequently altered abiotic (higher temperatures) and biotic (lower resources) environment. These findings have significant implications for understanding the impacts of forest loss and climate change on biodiversity, particularly in tropical montane forests.

ecology↗

bioRxiv2022

Toroidal displacement of Klebsiella pneumoniae by Pseudomonas aeruginosa is a unique mechanism to avoid competition for iron

Competition for resources is one of the major drivers for evolution and retention of new traits in microbial communities. Quorum-dependent traits of opportunistic human pathogen Pseudomonas aeruginosa allow it to survive and thrive in nature. Here, we report a unique surfactant-driven pushing mechanism that P. aeruginosa employs specifically against Klebsiella pneumoniae. The pushing is accomplished in a manner that is dependent on nutrient limitation and quorum sensing. We find that P. aeruginosa employs neither proteases nor toxic secondary metabolites against K. pneumoniae. Rhamnolipid biosurfactant appears to be the only factor required to displace Klebsiella effectively. Both rhamnolipid production and the pushing ability of P. aeruginosa are suppressed by iron supplementation. We show that both these bacteria produce several siderophores in minimal medium and rapidly deplete iron. Under these conditions, P. aeruginosa pushes Klebsiella away from the substratum using rhamnolipid, reducing the competition for iron. Our study describes a unique quorum and iron-responsive mechanism in P. aeruginosa to support its own growth during resource competition.

microbiology↗

bioRxiv2019

Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models.

Flux coupling identifies sets of reactions whose fluxes are \"coupled\" or correlated in genome-scale models. By identified sets of coupled reactions, modelers can 1.) reduce the dimensionality of genome-scale models, 2.) identify reactions that must be modulated together during metabolic engineering, and 3.) identify sets of important enzymes using high-throughput data. We present three computational tools to improve the efficiency, applicability, and biological interpretability of flux coupling analysis.\n\nThe first algorithm (cachedFCF) uses information from intermediate solutions to decrease the runtime of standard flux coupling methods by 10-100 fold. Importantly, cachedFCF makes no assumptions regarding the structure of the underlying model, allowing efficient flux coupling analysis of models with non-convex constraints.\n\nWe next developed a mathematical framework (FALCON) that incorporates enzyme activity as continuous variables in genome-scale models. Using data from gene expression and fitness assays, we verified that enzyme sets calculated directly from FALCON models are more functionally coherent than sets of enzymes collected from coupled reaction sets.\n\nFinally, we present a method (delete-and-couple) for expanding enzyme sets to allow redundancies and branches in the associated metabolic pathways. The expanded enzyme sets align with known biological pathways and retain functional coherence. The expanded enzyme sets allow pathway-level analyses of genome-scale metabolic models.\n\nTogether, our algorithms extend flux coupling techniques to enzymatic networks and models with transcriptional regulation and other non-convex constraints. By expanding the efficiency and flexibility of flux coupling, we believe this popular technique will find new applications in metabolic engineering, microbial pathogenesis, and other fields that leverage network modeling.

systems biology↗