Biology subjects

S, S. K.

Publications and source records attributed to S, S. K..

5 recordsLinked to original sources

bioRxiv2026

A parsimonious murburn model for microbial motility connects metabolic water ejection to observable mechanical outcomes

The classical model of bacterial flagellar motility posits a rotary engine driven by proton motive force (pmf), with torque generated by stator-rotor interactions and transmitted through a flexible hook to a helical filament. Despite decades of acceptance, this model faces fundamental challenges in thermodynamics, structural mechanics, evolutionary parsimony, and direct observational evidence. We develop and quantitatively test the murburn model, a new paradigm for bacterial motility in which water, produced as an inevitable byproduct of metabolic redox activity, is ejected via the basal secretory module and channelled along the spiral grooves of the flagellar filament. The ejected flow creates a local shear field that induces a transverse bending wave; the precession of this wave is observed as apparent rotation and generates thrust through anisotropic viscous drag, without any rotary motor, ion gradient, or axial rotation. The principal contribution of this work is a self-contained, first-principles treatment of this mechanism: for a unipolar flagellated cell we derive the governing low-Reynolds-number elastohydrodynamic relations from slender-body theory and show that physiologically realistic rates of metabolic water production reproduce the observed swimming speeds and apparent-rotation frequencies at a small fraction of the cellular energy budget, while direct jet propulsion is quantitatively excluded. Building on this derivation, we provide a force-balance comparison of the competing propulsion mechanisms, obtain a set of falsifiable predictions that distinguish the murburn model from the rotary motor, and report a structural analysis of cryo-EM flagellar-hook architectures that reveals solvent-accessible radial canals consistent with lateral water transport. The same single principle accounts for swimming, tumbling, gliding, spirochete undulation, and archaeal motility, without requiring rotating shafts, ion-gradient coupling, or complex switching mechanisms.

biophysics↗

bioRxiv2025

Structure-based discovery of Saponarin as a broad-spectrum allosteric inhibitor of banana viral coat proteins

Banana (Musa spp.), a globally significant staple crop, suffers substantial yield losses from persistent viral infections caused by Banana Bunchy Top Virus (BBTV), Banana Streak Virus (BSV), Banana Bract Mosaic Virus (BBrMV), and Banana Mosaic Virus (BMoV). Given the critical role of viral coat proteins (CPs) in genome encapsidation, movement, and host infectivity, these capsid components represent attractive targets for antiviral intervention. Here, we report a comprehensive in silico pipeline integrating homology modeling, structure-based molecular docking, pharmacokinetic profiling, and 100-ns all-atom molecular dynamics (MD) simulations to identify potential CP inhibitors from a curated phytochemical library. High-confidence structural models of the CPs were generated using SWISS-MODEL and AlphaFold3 and validated via Ramachandran analysis, ERRAT, and Verify3D. Virtual screening of 100 plant-derived compounds revealed Saponarin, a flavonoid glucoside, as the top-scoring molecule across all viral targets, with docking scores ranging from -13.33 to -8.75 kcal/mol. Binding interactions were dominated by extensive hydrogen bonds and {pi}-based stacking with conserved aromatic and polar residues within the capsid interface pockets. ADMET predictions indicated Saponarin possesses favorable physicochemical properties, high aqueous compatibility, low clearance, and minimal ecotoxicological risk. MD simulations confirmed stable binding, persistent hydrogen bonding, and conserved protein compactness, supporting an allosteric inhibition mechanism. These findings establish Saponarin as a structurally and pharmacologically viable broad-spectrum antiviral candidate for banana virus control, warranting experimental validation for translational deployment in sustainable crop protection strategies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=44 SRC="FIGDIR/small/662402v2_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@44d761org.highwire.dtl.DTLVardef@1982aa5org.highwire.dtl.DTLVardef@117eabeorg.highwire.dtl.DTLVardef@13495d9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Schematic representation of the structure-based virtual screening workflow for identifyin broad-spectrum inhibitors targeting coat proteins (CPs) of BBTV, BSV, BBrMV, and BMoV. Homology models of CPs were constructed, followed by binding site prediction, ligand retrieval, and molecular docking of 100 phytochemicals. Saponarin emerged as the top candidate, showing strong binding at conserved allosteric sites. ADMET profiling confirmed favorable pharmacokinetics and low toxicity. Molecular dynamics simulations validated the stability of Saponarin-CP complexes, supporting its potential as a broad-spectrum antiviral agent against multiple banana viruses. C_FIG

plant biology↗

bioRxiv2024

Hydrogen sulfide (H2S) coordinates redox balance, carbon metabolism, and mitochondrial bioenergetics to suppress SARS-CoV-2 infection.

Viruses exploit host metabolism for replication and immune-regulation. Understanding how SARS-CoV-2 alters the host metabolism may lead to treatments for COVID-19. We report that a ubiquitous gaseous molecule, hydrogen sulfide (H2S), regulates redox, metabolism, and mitochondrial bioenergetics to control SARS-CoV-2. Virus replication is associated with down-regulation of the H2S-producing enzymes cystathionine-{beta}-synthase (CBS), cystathionine-{gamma}-lyase (CTH), and 3-mercaptopyruvate sulfurtransferase (3-MST), resulting in diminished endogenous H2S levels. Inhibition of CTH resulted in SARS-CoV-2 proliferation. A slow-releasing H2S donor, GYY4137, diminished virus replication by inducing Nrf2/Keap1 pathway, restoring redox balance and mitochondrial bioenergetics. Treatment of SARS-CoV-2-infected animals with GYY4137 suppressed viral replication, ameliorated respiratory pathology, and restored antioxidant gene expression. Notably, whole-body plethysmography showed improved pulmonary function variables, including pulmonary obstruction and end-expiratory pause upon GYY4137 treatment in vivo. Data extend our understanding of H2S-mediated regulation of viral-infections, and open new avenues for investigating the pathogenic mechanisms and therapeutic opportunities for coronavirus-associated disorders.

microbiology↗

bioRxiv2023

Aeroplane wing, a new recessive autosomal phenotypic marker in malaria vector, Anopheles stephensi Liston

A novel and distinct mutant, with an aeroplane wing (ae) phenotype, is reported for the first time in the urban malaria vector, Anopheles stephensi. The mutant mosquitoes exhibit extended wings that are easily visible to naked eyes in both sexes. This mutant was first observed in a nutritionally stressed experimental isofemale line and characterized for its genetic inheritance and other related parameters. Meticulous and strategic genetic crosses revealed that the ae gene is an autosomal, recessive, non-sex-linked and monogenic trait with full penetrance and uniform expression in the adult stage. Cytogenetic study of the ovarian polytene chromosome revealed an inversion on the 3L chromosome (3Li) in both the ae mutant and its parent line. No significant differences in wing venation and other parameters were observed in ae mutants compared to their normal parental lines. This ae mutant would be an excellent marker that can be used by researchers to study the function of related genes within the genome. Author summaryIn the present study, we have established and describe the inheritance of an unusual novel aeroplane (ae) winged mutant in Anopheles stephensi, an urban malaria vector in India. The ae mutant lines exhibit three open-wing orientations in both the sexes of adults viz. left (LW), right (RW) and double wing (DW) during its resting phase. Through various inbreeding crosses we demonstrated the mode of inheritance of the ae gene to be autosomal, recessive and monogenic in nature. The morphometric studies of eggs and wings revealed that mutant lines are on par with their parental lines. Cytogenetic study of polytene chromosome of ae mutant revealed the presence of heterogenic inversion on the 3L chromosome arm, which might help in adaptation mechanism. We strongly believe that ae phenotypic markers have great applications bridging both basic and applied genetic research such as constructing linkage maps, identifying loci of quantitative and/or qualitative traits and as guides for insect transformation studies.

genetics↗

bioRxiv2021

Behavioral context shapes vocal sequences in two anuran species with different repertoire sizes

Acoustic signals in animals serve to convey context-dependent information to receivers. Birds and mammals combine diverse sounds into complex sequences to communicate, but these sequences largely remain understudied in other taxa. Anuran vocalizations are a prominent feature of their life history, and function in defense of territories and to attract mates. However, despite the spectacular diversity of anurans in tropical regions of the world, vocal diversity and communication strategies remain relatively poorly studied. Specifically, studies of vocal sequences and context-dependent vocal patterns in frogs remain few. Here, we investigated the context-dependent vocal repertoire and the use of vocal sequences by two anuran species belonging to different lineages, both endemic to the hyper-diverse Western Ghats of India. By recording vocal sequences both when frogs were alone and in the presence of a territorial rival, we present evidence that both species modify their vocal repertoire according to context. Specifically, one species appends notes to generate more complex sequences, whereas the other shifts to different note types, resulting in different sequences for different contexts. Thus, despite differences in repertoire size, both frog species are capable of adjusting the temporal sequence of vocalizations to communicate in different contexts. This study highlights the need for further studies of insular frogs, to understand how diversification across these continental islands has influenced the evolution of vocal repertoires, vocal sequence patterns and communication systems. Lay SummaryAnimals employ complex sequences of acoustic signals to communicate in diverse behavioral contexts. Here, we demonstrate that two frog species with different vocal repertoires both modify the sequence of note emissions in the presence of a territorial rival. These patterns demonstrate that anurans are capable of complex shifts in the patterns of their vocalization, to communicate different messages to different receivers. Our findings demonstrate the value of studying behavioral diversity in tropical regions.

animal behavior and cognition↗