Mohanty, S. S. | bioRxiv Science

bioRxiv2026

Switchgrass Root Cell Wall Composition and Anatomy Vary with Depth, Suggesting Approaches for Trait Enhancement

Plant root cellular architecture and cell wall composition influence plant productivity, stress resilience, biotic interactions, and potentially soil carbon accumulation. This study establishes comprehensive compositional parameters for roots of a lowland switchgrass genotype, DVR3. Root traits were analyzed in 12.5 cm depth segments, from Zone 1 near the surface to Zone 4 down to 50 cm. Mean abundance (g/mg) for major cell wall components included cellulose 470 {+/-} 20, xylose 250 {+/-} 20, lignin 170 {+/-} 15, and total suberin 35 {+/-} 5. Composition and cellular anatomy varied with depth, in a partially coordinated manner. Cross sections showed extensive aerenchyma in mature root regions despite greater root mass density, corresponding to abundant lignin and cellulose. Deep roots were enriched for pectin-associated traits, including arabinogalactan II, homogalacturonan, and arabinose-associated linkages. Suberin content did not vary significantly, though Casparian strip formation, endoderm and exoderm thickening, and suberin surface staining progressed with development. Similar trends in root lignin and specific root length were observed for another lowland switchgrass genotype, AP13. These results suggest that it may be possible to genetically enhance native switchgrass root chemistry to promote soil penetration and below-ground carbon accumulation by reducing variability with development, potentially via cell-type specific adjustments.

plant biology↗

bioRxiv2025

Molecular docking of Pyocyanin from Pseudomonas aeruginosa with NADPH oxidase and Toll-like receptor 4 : Exploring the Link Between Oral Microbiome and Oral Cancer Pathogenesis

Oral cancer is among the leading cancers in India, with its progression influenced not only by genetic and environmental factors but also by dysbiosis in the oral microbiome. Pseudomonas aeruginosa, an opportunistic Gram-negative bacterium, has been implicated in oral carcinogenesis through the action of its virulence factor, pyocyanin--a redox-active phenazine that induces reactive oxygen species (ROS), promoting oxidative stress, immune dysregulation, and inflammation. Despite evidence linking pyocyanin to ROS-related pathways, its molecular interaction with key host proteins like NADPH oxidase and Toll-like receptor 4 (TLR4) remains unexplored. The present study aims to investigate the molecular interactions of pyocyanin with NADPH oxidase and TLR4 through molecular docking, aiming to elucidate its role in oxidative and inflammatory mechanisms associated with oral cancer pathogenesis. The structures of pyocyanin and the NADPH oxidase (NOX2) and TLR4 target proteins were retrieved from PubChem and RCSB PDB, respectively. CASTp was used to identify potential binding pockets. Molecular docking was performed using the HADDOCK server. The docked complexes were analyzed based on HADDOCK scores, binding energies, RMSD, and buried surface area. Interaction profiles were visualized using BIOVIA Discovery Studio. Among the docking clusters, Cluster 6 for the NOX2-pyocyanin complex showed a favorable HADDOCK score (84.4 {+/-} 2.9), low RMSD (0.2 {+/-} 0.0), and substantial buried surface area (456.1 {+/-} 13.2 [A]2). For the TLR4-pyocyanin complex, Cluster 1 exhibited the most favorable interaction profile with a HADDOCK score of 25.0 {+/-} 5.5 and a Z-score of -2.3. Binding site prediction and hydropathy analysis supported the structural feasibility of pyocyanin interaction with both targets. This study provides structural insights into the potential interaction of pyocyanin with NADPH oxidase and TLR4, supporting its role in modulating oxidative stress and inflammatory signaling pathways. These findings enhance our understanding of oral microbiome-host interactions and their contribution to oral cancer pathogenesis.

bioinformatics↗