Biology subjects

Kulkarni, S. S.

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

14 recordsLinked to original sources

bioRxiv2026

Chemical Synthesis of Thrombostasin: An Anticoagulant Protein Produced by the Horn Fly Haematobia irritans

Thrombostasin is a cysteine-free anticoagulant protein produced by the horn fly Haematobia irritans, featuring an unusual stretch of seven consecutive aspartate residues within the polypeptide sequence. Here, we report the first chemical synthesis of native thrombostasin and a hepta-glutamate analogue, together with assessment of their thrombin inhibitory and anticoagulant activity.

molecular biology↗

bioRxiv2026

Signaling by a tyrosine-sulfated peptide balances growth and osmotic stress response in rice

Peptide hormone signaling coordinates plant growth and osmotic stress responses, yet how the transition between these responses is regulated remains poorly understood. Here, we investigated the function of the rice PLANT PEPTIDES CONTAINING SULFATED TYROSINE 8 (OsPSY8) peptide in osmotic stress responses. OsPSY8 was predominantly expressed in root tissues under non-stress conditions, with preferential expression in lateral roots where it promoted root growth. Osmotic stress rapidly reduced OsPSY8 expression in roots through the OsWRKY24 transcription factor. Loss-of-function ospsy8 mutants exhibited enhanced osmotic stress tolerance, whereas OsPSY8 overexpression increased osmotic stress susceptibility. Transcriptomic analyses revealed that disruption of OsPSY8 activated stress-responsive pathways, including those associated with lignin biosynthesis, compatible solute production, cell wall remodeling, and reactive oxygen species (ROS) scavenging, and was accompanied by increased lignin accumulation in roots. In contrast, overexpression of OsPSY8 resulted in maintenance of growth-associated transcriptional programs while suppressing stress-responsive pathways under osmotic stress. Together, these findings identify OsPSY8 as an important regulator of the transition from growth to stress adaptation in rice and suggest that stress-induced repression of PSY signaling is required to disengage growth programs and activate adaptive responses during osmotic stress. Significance StatementCrop survival during drought depends on the ability to transition from growth to stress adaptation. Plant peptide hormones have emerged as important regulators of this critical transition, highlighting the importance of investigating their roles and potential for improving crop resilience. We show that a rice peptide hormone regulates this transition. Under non-stress conditions, this peptide hormone, predominantly expressed in rice roots, promotes root growth while suppressing stress responses. During osmotic stress, expression of the peptide hormone decreases, resulting in activation of stress-responsive pathways, such as lignin biosynthesis and reactive oxygen species scavenging. These findings demonstrate that a peptide hormone coordinates the balance between growth and stress adaptation in rice, with broader implications for understanding and improving crop resilience.

plant biology↗

bioRxiv2026

Comparative genomics of the unusual arachnid order Solifugae spotlight the molecular and genetic basis for adaptations to arid habitats

The evolutionary transition to terrestrial life required overcoming several physiological hurdles; however, such challenges were amplified in desert environments. While several xeric-adapted arachnids utilize permanent burrows or "sit-and-wait" foraging strategies as possible energy conservation adaptations in harsh habitats, camel spiders exhibit a counterintuitive, high-energy lifestyle. To investigate the molecular underpinnings distinguishing Solifugae within Chelicerata, we utilized a comparative genomics framework that incorporates a newly sequenced, previously unpublished solifuge genome. We identified lineage-specific expanded orthogroups and evaluated selective pressures acting upon paralogous sequences within our ingroup solifuge species. Additionally, we also focused on fatty acid-associated proteins and heat shock proteins to elucidate how Solifugae may have evolved such anomalous behaviors compared to their arachnid relatives. Our analyses revealed significant signatures of positive selection within key gene families across the solifuge lineage. Notably, paralogs within the cytochrome P450 and biotinidase families showed consistent evidence of selection across all three taxa, suggesting specialized metabolic or detoxification requirements. Furthermore, we identified candidate loci implicated in axonal guidance and lipid metabolism, and a specialized fatty acid enzyme repertoire. While subsequent research is required to determine whether some of the genomic signatures unveiled here are shared across a broader phylogenetic distribution within Solifugae, we establish a critical baseline for future functional validation.

evolutionary biology↗

bioRxiv2026

No silver bullet: Patterns of macrosynteny recapitulate systemic conflicts in the higher-level relationships of the arachnids

Rare genomic changes have long been sought by phylogeneticists for their potential to resolve obdurate nodes in the tree of life. Recently, patterns of macrosynteny have been proffered as a breakthrough for challenging relationships within invertebrates. One taxon that stands to benefit from the application of this approach is Chelicerata (the sister group to the rest of Arthropoda), whose radiation has long defied resolution, despite intensive investigations using morphological characters, molecular sequence data, and a combination thereof. Challenges to the resolution of chelicerate phylogeny include an ancient rapid radiation, the incidence of several fast-evolving lineages prone to long-branch attraction artifacts, and extinction of multiple ordinal level lineages that cannot be sampled for breaking long branches. At present, only a subset of nodes has been stably resolved. To break this impasse, we brought to bear multiple classes of phylogenetically informative rare genomic changes, including the sequencing of the first genomes for Ricinulei and Palpigradi. Here, we show that an ancient, shared whole genome duplication event is restricted to Arachnopulmonata (the most recent common ancestor of spiders and scorpions), disfavoring traditional placements of either Ricinulei or Palpigradi as close relatives of tetrapulmonates. Intriguingly, investigation of fusion-with-mixing events identified equal support for mutually exclusive placements for Acariformes, the least stable of the arachnid orders. Our results suggest that fusion-with-mixing, far from being a silver bullet, likely exhibits the same emergent property as all character systems, in that it is prone to homoplasy and conflicting signal stemming from ancient rapid radiations.

evolutionary biology↗

bioRxiv2026

Microtubule-templated actin assembly by septin9 drives apical expansion of epithelial cells

Cells dynamically regulate the size of their apical domain during epithelial morphogenesis. Multiciliated cells (MCCs) represent an extreme case, undergoing massive apical expansion to accommodate hundreds of basal bodies that generate an array of motile cilia. While actin-generated forces drive this expansion, the molecular mechanisms that govern actin assembly and organization remain poorly understood. We show that in Xenopus, depletion of Septin9 results in failure of filamentous actin assembly, apical domain expansion, and ciliogenesis. Notably, human Septin9 (SEPT9) localizes to cortical microtubules rather than actin filaments. Live-cell imaging and pharmacological studies reveal that SEPT9 and microtubules form a mutually stabilizing scaffold that directs actin assembly. Using isoform-specific depletion and rescue experiments that genetically separate the microtubule from its actin-bound functions of SEPT9, we demonstrate that SEPT9 association with microtubules is required for actin assembly. These results provide the first in vivo demonstration that microtubule-templated actin assembly via Septin9 drives apical surface expansion during epithelial morphogenesis.

cell biology↗

bioRxiv2026

Physiological, Histological, and Cognitive Characterization of a Macaque Model of Presbycusis

Age-related hearing loss (ARHL), or presbycusis, is one of the most prevalent sensory deficits in older adults and has been increasingly implicated in cognitive decline and dementia. This study characterizes ARHL in a rhesus macaque model by combining histological, physiological, and cognitive assessments. Aged macaques exhibited progressive cochlear degeneration, with marked outer hair cell loss at mid-to-high frequencies, elevated auditory thresholds, reduced distortion product otoacoustic emissions, and impaired auditory brainstem responses including amplitude reduction, latency prolongation, and diminished temporal precision. Despite modest reductions in inner hair cell ribbon synapse counts, hypertrophic changes were observed. These auditory deficits correlated with subtle impairments in visual working memory, as measured by a delayed match-to-sample task, underscoring a potential sensory-cognitive link. By capturing cross-domain aging markers in a translationally relevant primate model, this work lays a foundation for mechanistic studies and therapeutic interventions targeting both hearing and cognition in aging populations.

neuroscience↗

bioRxiv2025

Patient-informed CRISPR Screen Identifies FLNB as a Novel Congenital Heart Disease and Ciliopathy Gene

Heterotaxy (HTX) syndrome is a congenital disorder characterized by abnormal left-right organ placement, often leading to severe congenital heart defects (CHD). Despite advances in sequencing, many CHD/HTX-associated genes remain functionally unvalidated, hindering effective clinical diagnosis and management. Here, we leveraged a high-throughput CRISPR/Cas9 screening approach in the Xenopus model to rapidly evaluate candidate genes identified from whole-exome sequencing of human CHD patients. Our screen identified Filamin B (FLNB), an actin-binding protein previously linked to skeletal disorders but not to ciliopathies or CHD. We identified 5 probands with CHD/HTX, 3 with recessive, and 2 with damaging heterozygous mutations in FLNB. Disrupting FLNB in Xenopus reproduced key features of the human HTX phenotype, including defects in cardiac development and impaired motile cilia function. Rescue experiments confirmed the functional conservation of human FLNB, directly implicating actin cytoskeletal disruption in ciliogenesis and left-right patterning defects. Our results provide crucial evidence linking human FLNB dysfunction to ciliopathies and CHD/HTX.

genetics↗

bioRxiv2025

Integrative Functional Genomics Identifies ARHGAP10 in the 4q31.2 Locus as a Novel Congenital Heart Disease and Ciliopathy Gene.

Congenital heart disease (CHD) remains a major cause of pediatric morbidity and mortality, yet its genetic underpinnings are not fully understood. Two studies independently identified rare deletions in ARHGAP10 (GAP10), a Rho GTPase-activating protein located at 4q31.2 in individuals with heterotaxy and atrial septal defects (n=2 rare copy number variants (CNVs)), highlighting GAP10 as a new candidate CHD gene. While the 4q31.2 locus is implicated in CHD, the function of GAP10 has not been investigated. Here, using Xenopus tropicalis as a model, we demonstrate that gap10 deletion disrupts morphogenetic movements critical for body axis extension, left-right organizer (LRO) formation, and ciliogenesis, leading to severe cardiac looping defects that closely mirror human CHD phenotypes. Moreover, gap10 localizes to basal bodies of motile cilia in multiciliated cells, where it regulates basal body organization and apical actin enrichment by recruiting focal adhesion kinase (FAK) to specialized ciliary adhesion complexes. In summary, our findings implicate GAP10 as a clinically relevant, genetically supported, and functionally validated regulator of CHD and ciliogenesis, underscoring the power of integrative functional genomics in the discovery of rare disease genes.

developmental biology↗

bioRxiv2025

Multiciliated cells adapt the mechanochemical Piezo1-Erk1/2-Yap1 cell proliferation axis to fine-tune centriole number.

Multiciliated cells (MCCs) are specialized epithelial cells that undergo massive amplification of centrioles, constructing several motile cilia to propel fluid flow. The abundance of cilia is critical for efficient fluid flow, yet how MCCs regulate centriole/cilia numbers remains a major knowledge gap. We have shown that mechanical tension plays a central role in regulating apical area and centriole number in MCCs. Here, we demonstrate that centriole amplification is controlled by a mechanochemical pathway essential for cell proliferation in cycling cells. Specifically, MCCs under tension use Piezo1-mediated calcium signaling to drive Erk[1/2] phosphorylation via PKC and subsequent Yap1 activation. Remarkably, MCCs use this pathway to activate a cilia-specific transcription program, influencing the expression of Foxj1, a master regulator of motile ciliogenesis. Our work is the first to identify a novel function for an important mechanochemical pathway in centriole amplification in MCCs, offering new insights into ciliopathies and cancer, where aberrant centriole numbers are implicated. TeaserThis study demonstrates that multiciliated cells utilize the mechanochemical Piezo1-Erk1/2-Yap1 cell proliferation axis to activate the cilia-specific transcriptional factor Foxj1 and amplify centrioles in a tension- dependent manner.

cell biology↗

bioRxiv2023

Mechanisms of cilia regeneration in Xenopus multiciliated epithelium in vivo.

Cilia regeneration is a physiological event, and while studied extensively in unicellular organisms, it remains poorly understood in vertebrates. In this study, using Xenopus multiciliated cells (MCCs) as a model, we demonstrate that, unlike unicellular organisms, deciliation removes the transition zone (TZ) and the ciliary axoneme. While MCCs immediately begin the regeneration of the ciliary axoneme, surprisingly, the assembly of TZ is delayed. However, ciliary tip proteins, Sentan and Clamp, localize to regenerating cilia without delay. Using cycloheximide (CHX) to block new protein synthesis, we show that the TZ protein B9d1 is not a component of the cilia precursor pool and requires new transcription/translation, providing insights into the delayed repair of TZ. Moreover, MCCs in CHX treatment assemble fewer ([~] 10 vs. [~]150 in controls) but near wild-type length (ranging between 60 to 90%) cilia by gradually concentrating ciliogenesis proteins like IFTs at a select few basal bodies. Using mathematical modeling, we show that cilia length compared to cilia number influences the force generated by MCCs more. In summary, our results question the requirement of TZ in motile cilia assembly and provide insights into how cells determine organelle size and number.

cell biology↗

bioRxiv2022

The rediscovery of a relict unlocks the first global phylogeny of whip spiders (Amblypygi)

Asymmetrical rates of cladogenesis and extinction abound in the Tree of Life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or "living fossils" when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi ("whip spiders"), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous "whips"). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits, but is survived by a single living species, Paracharon caecus Hansen, 1921, that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report several individuals of a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of "dark taxa", and especially phylogenetic relicts in tropical and subtropical habitats.

genomics↗

bioRxiv2018

UNC-16/JIP3 inhibits the function of the regeneration promoting isoform of DLK-1

Neuronal regeneration after injury depends on the intrinsic growth potential of neurons. UNC-16, a C. elegans JIP3 homologue, inhibits axonal regeneration by regulating regrowth initiation and rate of regrowth. UNC-16/JIP3 inhibits the regeneration promoting activity of DLK-1 long but acts additively to and independently of inhibitory DLK-1 short isoform. UNC-16/JIP3 promotes DLK-1 punctate localization in a concentration dependent manner limiting DLK-1 long availability at the cut site minutes after injury. UNC-16 negatively regulates actin dynamics dependent on DLK-1 and microtubule dynamics independent of DLK-1. The faster regeneration seen in unc-16 does not lead to functional recovery. We propose a model where UNC-16/JIP3 plays its inhibitory role through tight temporal and spatial control of DLK-1 function. The dual inhibitory control by both UNC-16 and DLK-1 short calibrate the intrinsic growth promoting function of DLK-1 long in vivo.

neuroscience↗

bioRxiv2018

The Heterotaxy Gene, CCDC11, is Essential for Cytokinesis and Cell-Cell Adhesion Via RhoA Regulation

Mutations in CCDC11 have been identified in multiple patients with heterotaxy (Htx), a disorder of left-right (LR) patterning of the internal organs. In Xenopus, depletion of Ccdc11 causes defects in LR patterning, recapitulating the patient phenotype. Upon Ccdc11 depletion, normally monociliated cells of the Left-Right Organizer (LRO) exhibit multiple cilia per cell. Unexpectedly, we found that Ccdc11 is necessary for successful cytokinesis, and the multiciliation observed in Ccdc11-depleted cells was due to failed cytokinesis. Furthermore, CCDC11 depletion alters cell-cell adhesion with reduction in junctional localization of adhesion molecules. The small GTPase RhoA is critical for cytokinesis and cell-cell adhesion. Because the CCDC11 depletion phenotypes are reminiscent of RhoA loss of function, we investigated a possible connection to regulation of RhoA signaling. We demonstrate that CCDC11 is localized to the cytokinetic contractile ring overlapping with RhoA during cytokinesis and regulates total RhoA protein levels. Our results suggest that CCDC11 connects cytokinesis and LR patterning via RhoA regulation, providing a potential mechanism for heterotaxy disease pathogenesis.

cell biology↗

bioRxiv2017

WDR5 stabilizes actin architecture to promote multiciliated cell formation

HIGHLIGHTS O_LIWDR5 has an H3K4 independent role in the formation of multiciliated cells.\nC_LIO_LIWDR5 controls apical cell expansion, basal body patterning, and ciliogenesis in multiciliated cells.\nC_LIO_LIWDR5 localizes near the ciliary base where it connects basal bodies to F-actin.\nC_LIO_LIWDR5 stabilizes the apical actin network in multiciliated cells.\nC_LI\n\nSUMMARYThe actin cytoskeleton is critical to shape cells and pattern intracellular organelles to drive tissue morphogenesis. In multiciliated cells (MCCs), apical actin forms a lattice that drives expansion of the cell surface necessary to host hundreds of cilia. The actin lattice also uniformly distributes basal bodies across this surface. This apical actin network is dynamically remodeled, but the molecules that regulate its architecture remain poorly understood. We identify the chromatin modifier, WDR5, as a regulator of apical F-actin in multiciliated cells. Unexpectedly, WDR5 functions independently of chromatin modification in MCCs. Instead, we discover a scaffolding role for WDR5 between the basal body and F-actin. Specifically, WDR5 binds to basal bodies and migrates apically, where F-actin organizes around WDR5. Using a monomer trap for G-actin, we show that WDR5 stabilizes F-actin to maintain apical lattice architecture. In summary, we identify a novel, non-chromatin role for WDR5 in stabilizing F-actin in multiciliated cells.\n\nIN BRIEFKulkarni et al discover a chromatin independent function for WDR5 in multiciliated cell formation. WDR5 localizes to the base of cilia and functions as a scaffold between the basal bodies and the apical actin lattice. There, WDR5 stabilizes the actin lattice that allows multiciliated cells to expand their apical surface, pattern basal bodies, and generate hundreds of cilia.

developmental biology↗