Biology subjects

Chauhan, N.

Publications and source records attributed to Chauhan, N..

14 recordsLinked to original sources

bioRxiv2026

Agroforestry reshapes soil bacterial communities to enhance Ricinus communis oil quality and bioactivity over monocropping: comparative metagenomics and culture-dependent insights

An agroforestry (AF) system improves crop quality, ecosystem services, and microbial resilience, but its effects on oilseed bioactivity and soil microbiomes are still underexplored. This study compared AF and monocropping systems for castor (Ricinus communis L.) grown in Rajasthan, India, to evaluate plant productivity, seed oil composition, antimicrobial properties, and soil bacterial communities. AF enhanced seed morphology and germination. Castor oil from agroforestry had a 2.4-fold higher phenolic content, 2% more ricinoleic acid, and lower levels of oleic and linoleic acids compared to monocropping, confirmed by infrared spectroscopy and gas chromatography, along with increased expression of the RcDGAT2 gene involved in fatty acid biosynthesis. This led to improved antimicrobial activity against Bacillus mobilis and Pseudomonas fluorescens. Full-length 16S rRNA gene sequencing on the Nanopore platform identified 17 bacterial phyla in soil microbiomes, with Proteobacteria and Firmicutes as the dominant phyla. While alpha diversity was similar, AF soils showed distinct taxonomic shifts, enriching bacteria such as Alkalimonas, Aureimonas, Blastopirellula, Glutamicibacter, Rhizobium, Rhizomicrobium, and Rhodovulum, linked to nutrient cycling and plant growth promotion. Isolated rhizospheric/root endophytic Bacillus safensis and Enterobacter cloacae from AF castor exhibited plant growth-promoting traits via biochemical tests and whole-genome sequencing; their oil biosynthesis genes likely contribute to host oil quality by enhancing precursor supply and phenolic pathways. These isolates enhanced the growth of the model plant Arabidopsis thaliana. In summary, AF enhances the bioactivity of castor oil and microbial functions by modulating plant-soil-microbe interactions, thereby supporting sustainable crop quality and soil health.

microbiology↗

bioRxiv2026

Candida auris can acquire antifungal resistance without selection pressure

The human fungal pathogen Candidozyma auris (formerly Candida auris) can cause prolonged infection outbreaks with high mortality rates in healthcare settings. Treatment failures of patients arise not only from antifungal drug resistance, but also from intra-species variability in pathogenicity as well as induced hypermutation events in response to clinical therapy. Whole genome sequencing was used to identify genetic mutations using the CDC mycoSNPs pipeline. Antifungal susceptibility testing was performed based on Clinical and Laboratory Standards Institute (CLSI) methods. We report here that the interlaboratory exchange of C. auris clinical isolates dried on sterile filter paper, resulted in the emergence of at least three distinct morphotypes following reconstitution. These distinct morphotypes exhibited differences in drug resistance and morphogenesis, linked to the accumulation of mutations in genes associated with azole and echinocandin resistance. Using whole genome sequencing, we identified several variants in TAC1B, MRR1 and FKS2 that correlate with altered drug susceptibilities. Experiments recapitulating filter paper shipment conditions revealed genetic and epigenetic changes, explaining the morphogenetic switching and altered azole resistance. Our findings demonstrate that C. auris can acquire mutations affecting drug resistance traits even in the absence of antifungal exposure, raising concerns about shipment preparation procedures across mycology laboratories. The results are of broad relevance for the medical mycology community, as they call for standardized protocols for exchanging clinical strains, but also experiments to verify phenotypic traits between laboratories. ImportancePathogenesis and antifungal drug resistance traits of Candida auris vary widely across clinical strains and are often attributed to elevated mutation rates. In fungal pathogen research, clinical strains are commonly exchanged between laboratories by transfer on filter paper, a convenient and widely used practice. However, in the case of a C. auris clinical strain received from a collaborating laboratory, we identified multiple acquired mutations. These genetic alterations caused marked changes in morphogenesis and antifungal susceptibility, demonstrating that resistance in C. auris can arise without antifungal selection pressure. Our findings highlight the potential for genetic and phenotypic diversification during routine strain handling and underscore the need for standardized protocols for exchanging clinical C. auris strains across mycology laboratories.

microbiology↗

bioRxiv2025

Increased versican and fibrosis in mesenteric lymph nodes disrupts immune surveillance and drives systemic bacterial dissemination in cirrhosis

Background and ObjectiveMesenteric lymph nodes (MLN) are immunological barriers against bacterial translocation (BT). Enhanced gut BT through MLN facilitates bacterial spread and higher mortality in cirrhosis. We aimed to elucidate mechanisms underlying MLN failure to effectively contain BT during advanced cirrhosis. DesignBT and immune cells were analyzed in lymphoid organs and circulation of control and CCl4 models, with and without MLN (MLNx). MLN proteomics identified versican (VCAN) as major upregulated protein in cirrhosis, whose immunomodulatory function was examined in vitro and in vivo in CCl and (Bile duct ligation) BDL models. Plasma VCAN were measured in end-stage cirrhosis patients and analyzed as mortality predictor. ResultsIn control rats, bacteria were confined to MLN, whereas cirrhotics showed BT to MLN, lymph, and portal blood. Compared to control, CCl4 rats had increased activated Th-cells in MLN but reduced in circulation. In control-MLNx rats, activated Th-cells were reduced in circulation vs controls. In BDL models, MLN CFU correlated with VCAN level. In vitro, VCAN enhanced T cell suppression and impaired migration which was reversed by CD44 blockade. In vivo VCAN knockdown reduced fibrosis and bacterial burden in MLN, while restoring Th-cell activation locally and systemically. Clinically, plasma VCAN levels were elevated in advanced cirrhosis patients and remained an independent predictor of 28-day sepsis-related mortality. ConclusionIncreased VCAN impairs T cell activation and migration in MLN, fostering immune suppression and bacterial persistence. Plasma VCAN levels serve as promising biomarker for MLN dysfunction and prognostic factor for predicting sepsis-related mortality in end-stage cirrhosis. What is already known on this topic - Enhanced gut bacterial translocation through mes-enteric lymph nodes (MLN) facilitates systemic bacterial spread and increases mortality in cirrhosis. The mechanisms underlying MLN failure to effectively contain bacterial spread during advanced cirrhosis remain largely unknown. What this study adds - The study unveils a critical role of lymph node fibrosis and elevated versican (VCAN) expression in causing deranged immune responses and bacterial clearance in MLN, increasing systemic bacterial load and immunosuppression. Most importantly, high plasma VCAN emerges as a prognostic biomarker for functional failure of MLN and 28-day mortality predictor in critically ill patients with cirrhosis. How this study might affect research, practice or policy - VCAN, representing enhanced MLN fibrosis and dysfunction, emerges as a predictive biomarker of adverse clinical out-comes in patients with advanced cirrhosis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/690350v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@369f4eorg.highwire.dtl.DTLVardef@14c232org.highwire.dtl.DTLVardef@d99b21org.highwire.dtl.DTLVardef@57ac95_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

Targeting a novel chloroquine derivative to lysosomes induces massive and irreversible damage to lysosomes and suppresses autophagosomes and lysosomes assembly in cancer

Pancreatic ductal adenocarcinoma (PDAC) exhibits profound therapy resistance driven by lysosome dependent nutrient recycling, metabolic adaptation, and stress tolerance. Current lysosome-targeting agents such as chloroquine (CQ) and hydroxychloroquine (HCQ) show limited efficacy due to transient activity and dose-limiting toxicities. To overcome these limitations, we developed Lysostilbenes, a new class of hybrid small molecules combining the CQ pharmacophore with lysosome-disrupting trans-4,4'-dihydroxystilbene. Lysostilbene-4 emerged as the lead candidate, demonstrating [~]30-40-fold greater cytotoxicity against PDAC cells than parental compounds, while sparing non-malignant cells. At nanomolar concentrations, Lysostilbene-4 induced rapid, irreversible lysosomal membrane permeabilization (LMP), initiating a lysosome mitochondria apoptotic cascade via cathepsin-B release, BID cleavage, BAX activation, and caspase-mediated apoptosis. In parallel, it abrogated lysosomal recovery by impairing repair, lysophagy, autophagosome maturation, and uncoupling TFEB-driven transcriptional programs from effective lysosome biogenesis. TFEB knockout further sensitized PDAC cells, underscoring TFEB as a key determinant of lysosomal resilience and a potential predictive biomarker. Importantly, Lysostilbene-4 was well tolerated in preclinical mouse models at supra-therapeutic doses without systemic toxicity. These findings position Lysostilbene-4 as a first-in-class lysosome-targeting therapeutic that enforces sustained lysosomal collapse while disabling adaptive recovery mechanisms, providing a mechanistically precise and safe strategy against PDAC.

cancer biology↗

bioRxiv2024

CHK1-mediated regulation of TOP1 catalytic activity suppresses replication and transcription-associated genomic instability

The Topoisomerase 1 (TOP1) catalytic cycle involves a TOP1-DNA-covalent-complex (TOP1cc), which, if stabilized, can induce rapid accumulation of potentially lethal DNA double strand breaks (DSBs). Although TOP1cc are critically associated with genome instability, it is not yet precisely known how cells regulate TOP1cc level, under unperturbed physiological-condition, to prevent its accumulation and lethal consequences. We discovered a key role of CHK1 in phosphorylating TOP1 at Serine-320 and stimulating TOP1-catalytic cycle to minimise genome wide accumulation of TOP1cc in cancers. Pharmacological or genetic ablation of CHK1-mediated TOP1-phosphorylation leads to stalled replication forks and generates copious amounts of replication/transcription-associated DSBs, R-loops and transcription-replication collisions, eventually leading to chromosomal instability. Further, TOP1ccs stabilized due to CHK1 inhibition are not efficiently targeted by cellular TOP1cc-removal machineries. Since multiple patient clinical trials are ongoing with TOP1- and CHK1-targeting drugs, current finding of CHK1-mediated regulation of TOP1cc may help in better understanding the therapeutic outcomes.

cancer biology↗

bioRxiv2024

The Candida auris Hog1 MAP kinase is essential for the colonization of murine skin and intradermal persistence

Candida auris, a multidrug-resistant human fungal pathogen, was first identified in 2009 in Japan. Since then, systemic C. auris infections have now been reported in more than 50 countries, with mortality rates of 30-60%. A major contributing factor to its high inter- and intrahospital clonal transmission is that C. auris, unlike most Candida species, displays unique skin tropism and can stay on human skin for a prolonged period. However, the molecular mechanisms responsible for C. auris skin colonization, intradermal persistence, and systemic virulence are poorly understood. Here, we report that C. auris Hog1 mitogen-activated protein kinase (MAPK) is essential for efficient skin colonization, intradermal persistence, as well as systemic virulence. RNA-seq analysis of wildtype parental and hog1{Delta} mutant strains revealed marked down-regulation of genes involved in processes such as cell adhesion, cell-wall rearrangement, and pathogenesis in hog1{Delta} mutant compared to the wildtype parent. Consistent with these data, we found a prominent role for Hog1 in maintaining cell-wall architecture, as the hog1{Delta} mutant demonstrated a significant increase in cell-surface {beta}-glucan exposure and a concomitant reduction in chitin content. Additionally, we observed that Hog1 was required for biofilm formation in vitro and fungal survival when challenged with primary murine macrophages and neutrophils ex vivo. Collectively, these findings have important implications for understanding the C. auris skin adherence mechanisms and penetration of skin epithelial layers preceding bloodstream infections. ImportanceCandida auris is a World Health Organization (WHO) fungal priority pathogen and an urgent public health threat recognized by the Centers for Disease Control and Prevention (CDC). C. auris has a unique ability to colonize human skin. It also persists on abiotic surfaces in healthcare environments for an extended period of time. These attributes facilitate the inter- and intrahospital clonal transmission of C. auris. Therefore, understanding C. auris skin colonization mechanisms are critical for infection control, especially in hospitals and nursing homes. However, despite its profound clinical relevance, the molecular and genetic basis of C. auris skin colonization mechanisms are poorly understood. Herein, we present data on the identification of the Hog1 MAP kinase as a key regulator of C. auris skin colonization. These findings lay foundation for further characterization of unique mechanisms that promote fungal persistence on human skin.

microbiology↗

bioRxiv2024

A BODIPY-naphtholimine-BF2 dyad for precision photodynamic therapy, targeting and dual imaging of endoplasmic reticulum and lipid droplets in cancer

Currently effective therapeutic modalities for pancreatic ductal adenocarcinoma (PDAC) is not available, leading to gloomy prognosis and ~6-months median patient survival. Recent advances showed the promise of photodynamic therapy (PDT) for PDAC patients. Next generation photosensitizers (PS) are based on "organelle-targeted-PDT" and provides new paradigm in the field of precision medicines to address the current challenge for treating PDAC. In this investigation, we have constructed a novel PS, named as NbB, for precise targeting of endoplasmic reticulum (ER) and lipid droplets (LD) in PDAC, as malignant PDAC cells are heavily relying on ER for hormone synthesis. Our live cell imaging and fluorescence recovery after photobleaching (FRAP) experiments revealed that NbB is instantly targeted to ER and LD and show simultaneous dual fluorescence colour due to polar and non-polar milieu of ER and LD. Interestingly, the same molecule generates triplet state and singlet oxygen efficiently and cause robust ER stress and apoptosis in two different PDAC cells in the presence of light. Together, we present, for the first time, a potential next generation precision medicine for ER-LD organelle specific imaging and PDT of pancreatic cancer.

cancer biology↗

bioRxiv2023

Human O-linked Glycosylation Site Prediction Using Pretrained Protein Language Model

O-linked glycosylation of proteins is an essential post-translational modification process in Homo sapiens, where the attachment of a sugar moiety occurs at the oxygen atom of serine and/or threonine residues. This modification plays a pivotal role in various biological and cellular functions. While threonine or serine residues in a protein sequence are potential sites for O-linked glycosylation, not all threonine or serine residues are O-linked glycosylated. Furthermore, the modification is reversible. Hence, it is of vital importance to characterize if and when O-linked glycosylation occurs. We propose a multi-layer perceptron-based approach termed OglyPred-PLM which leverages the contextualized embeddings produced from the ProtT5-XL-UniRef50 protein language model that significantly improves the prediction performance of human O-linked glycosylation sites. OglyPred-PLM surpassed the performance of other indispensable O-linked glycosylation predictors on the independent benchmark dataset. This demonstrates that OglyPred-PLM is a powerful and unique computational tool to predict O-linked glycosylation sites in proteins and thus will accelerate the discovery of unknown O-linked glycosylation sites in proteins.

bioinformatics↗

bioRxiv2022

A Photonic Resonator Interferometric Scattering Microscope for Label-free Detection of Nanometer-Scale Objects with Digital Precision in Point-of-Use Environments

Label-free detection and digital counting of nanometer-scaled objects such as nanoparticles, viruses, extracellular vesicles, and protein molecules enable a wide range of applications in cancer diagnostics, pathogen detection, and life science research. The contrast of interferometric scattering microscopy is amplified through a photonic crystal surface, upon which scattered light from an object combines with illumination from a monochromatic plane wave source. The use of a photonic crystal substrate for interference scattering microscopy results in reduced requirements for high-intensity lasers or oil-immersion objectives, thus opening a pathway toward instruments that are more suitable for environments outside the optics laboratory. Here, we report the design, implementation, and characterization of a compact Photonic Resonator Interferometric Scattering Microscope (PRISM) designed for point-of-use environments and applications. The instrument incorporates two innovative elements that facilitate operation on a desktop in ordinary laboratory environments by users that do not have optics expertise. First, because scattering microscopes are extremely sensitive to vibration, we incorporated an inexpensive but effective solution of suspending the instruments main components from a rigid metal framework using elastic bands, resulting in an average of 28.7 dBV reduction in vibration amplitude compared to an office desk. Second, an automated focusing module based on the principle of total internal reflection maintains the stability of image contrast over time and spatial position, facilitating automated data collection. In this work, we characterize the systems performance by measuring the contrast from gold nanoparticles with diameters in the 10-40 nm range and by observing various biological analytes, including HIV virus, SARS-CoV-2 virus, exosomes, and ferritin protein.

bioengineering↗

bioRxiv2022

Net-shaped DNA nanostructure designed for rapid/sensitive detection and potential inhibition of SARS-CoV-2 virus

We present a net-shaped DNA nanostructure (called "DNA Net" herein) design strategy for selective recognition and high-affinity capture of the intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers releases fluorescent signal upon virus binding that is easily read by a hand-held fluorimeter for a rapid (in 10 mins), simple (mix- and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive ([~] $1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1x103-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms.

bioengineering↗

bioRxiv2021

Anisotropy of plasmalemmal sterols and cell mating require StARkin domain proteins Ysp2 and Lam4.

In the budding yeast S. cerevisiae Cdc42 is required for polarized growth and the formation of mating projections (shmoos). Negatively charged lipids including phosphatidylserine and phosphatidylinositol 4,5-bisphosphate support a positive feedback loop that recruits Cdc42 effectors and MAP kinase scaffolds, many of which contain polybasic patches that directly interact with the membrane. Here, using genetically encoded sterol sensor ALOD4 we find that ergosterol is accumulated in the cytosolic leaflet of buds and shmoos. The accumulation of ergosterol in the plasma membrane requires both Osh and Lam proteins however cells lacking Ysp2/Lam2 and Lam4 displayed a reversal in the polarity of ergosterol. The redistribution of ergosterol impairs the polarization of phosphatidylserine and phosphatidylinositol 4,5-bisphophate which further impacts shmoo formation, MAPK signaling and mating efficiency. Our observations demonstrate that the ability of Lam proteins to deliver ergosterol from the plasma membrane to the ER helps maintain a gradient of ergosterol which in turn supports robust cell polarity. SummaryThe sterol sensor ALOD4 is enriched at sites of polarized growth. Elimination of the Osh proteins solubilized the ALOD4 whereas elimination of Ysp2 and Lam4 reversed ALOD4 polarization. Cells lacking Ysp2 and Lam4 have defects in mating and MAP kinase signaling.

cell biology↗

bioRxiv2021

Phosphatidylinositol 3-kinase-independent synthesis of PtdIns(3,4)P2 by a phosphotransferase

Despite their comparatively low abundance, phosphoinositides play a central role in membrane traffic and signalling. PtdIns(3,4,5)P3 and PtdIns(3,4)P2 are uniquely important, as they promote cell growth, survival, and migration. Pathogenic organisms have developed means to subvert phosphoinositide metabolism to promote successful infection and their survival within host organisms. We demonstrate that PtdIns(3,4)P2 is generated in host cells by effectors of the enteropathogenic bacteria Salmonella and Shigella. Pharmacological, gene silencing and heterologous expression experiments revealed that, remarkably, the biosynthesis of PtdIns(3,4)P2 occurs independently of phosphoinositide 3-kinases. Instead, we found that the Salmonella effector SopB, heretofore believed to be a phosphatase, generates PtdIns(3,4)P2 de novo via a phosphotransferase/phosphoisomerase mechanism. Recombinant SopB is capable of generating PtdIns(3,4)P2 from PtdIns(4,5)P2 in a cell-free system. Through a remarkable instance of convergent evolution, bacterial effectors acquired the ability to synthesize 3-phosphorylated phosphoinositides by an ATP- and kinase-independent mechanism, thereby subverting host signaling to gain entry and even provoke oncogenic transformation.

cell biology↗

bioRxiv2019

Water for sterol: an unusual mechanism of sterol egress from a StARkin domain

Previously we identified a new family of endoplasmic reticulum membrane proteins that possess sterol-binding StARkin domains (Gatta et al. eLife 2015). These Lam/GramD1 proteins are implicated in intracellular sterol homeostasis, a function that requires them to be able to bind sterols. Here we show how these proteins exchange sterol molecules with membranes. An aperture at one end of the StARkin domain enables sterol to enter/exit the binding pocket. Strikingly, the wall of the pocket is fractured along its length, exposing bound sterol to solvent. We considered whether hydration of the pocket could mediate sterol entry/exit. Large-scale atomistic molecular dynamics simulations reveal that sterol egress involves widening of the fracture, penetration of water into the cavity and consequent destabilization of the bound sterol. The simulations also identify polar residues along the fracture that are important for sterol release. Their replacement with alanine affects the ability of the StARkin domain to bind sterol, catalyze inter-vesicular sterol exchange and alleviate the nystatin-sensitivity of lam2{Delta} yeast cells. These data suggest an unprecedented, water-controlled mechanism of sterol acquisition and discharge from a StARkin domain.

biochemistry↗

bioRxiv2019

Integrative Computational Framework for Understanding Metabolic Modulation in Leishmania

The integration of computational and mathematical approaches is used to provide a key insight into the biological systems. Here, we seek to find detailed and more robust information on Leishmanial metabolic network by performing mathematical characterization in terms of Forman/Forman-Ricci curvature measures combined with flux balance analysis (FBA). The model prototype developed largely depends on its structure and topological components. The correlation of curvature measures with various network statistical properties revealed the structural-functional framework. The analyses helped us to identify the importance of several nodes and detect sub-networks. Our results revealed several key high curvature nodes (metabolites) belonging to common yet crucial metabolic, thus, maintaining the integrity of the network which signifies its robustness. Further analysis revealed the presence of some of these metabolites in redox metabolism of the parasite. MGO, an important node, has highly cytotoxic and mutagenic nature that can irreversibly modify DNA, proteins and enzymes, making them nonfunctional, leading to the formation of AGEs and MGO[bullet]-. Being a component in the glyoxalase pathway, we further attempted to study the outcome of the deletion of the key enzyme (GLOI) mainly involved in the neutralization of MGO by utilizing FBA. The model and the objective function both kept as simple as possible, demonstrated an interesting emergent behavior. The nonfunctional GLOI in the model contributed to zero flux which signifies the key role of GLOI as a rate limiting enzyme. This has led to several fold increase production of MGO, thereby, causing an increased level of MGO[bullet]- generation. Hence, the integrated computational approaches has deciphered GLOI as a potential target both from curvature measures as well as FBA which could further be explored for kinetic modeling by implying various redox-dependent constraints on the model. Designing various in vitro experimental perspectives could churn the therapeutic importance of GLOI.\n\nAuthor SummaryLeishmaniasis, one of the most neglected tropical diseases in the world, is of primary concern due to the increased risk of emerging drug resistance. To design novel drugs and search effective molecular drug targets with therapeutic importance, it is important to decipher the relation among the components responsible for leishmanial parasite survival inside the host cell at the metabolic level. Here, we have attempted to get an insight in the leishmanial metabolic network and predict the importance of key metabolites by applying mathematical characterization in terms of curvature measures and flux balance analysis (FBA). Our results identified several metabolites playing significant role in parasites redox homeostasis. Among these MGO (methylglyoxal) caught our interest due to its highly toxic and reactive nature of irreversibly modifying DNA and proteins. FBA results helped us to look into the important role of GLOI (Glyoxalase I), the enzyme that catalyses the detoxification of MGO, in the pathway that, when non-functional, has resulted into increased level production of free radicals and AGEs (advanced glycation end products). Thus, our study has deciphered GLOI as a potential target which could further be explored for future in vitro experiments to design potential GLOI inhibitors.

systems biology↗