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Biology subjects

Ghosh, S.

Publications and source records attributed to Ghosh, S..

At least 55 records · Page 3Linked to original sources

Unique nasal cell states induced by common pediatric respiratory viruses

Respiratory viral infections in early childhood are major drivers of acute morbidity and long-term airway disease, yet how distinct viruses remodel the pediatric nasal mucosa at cellular resolution remains unresolved. Here, we generated a single-cell RNA sequencing atlas of 335,174 nasal epithelial and immune cells from 132 children under five years of age with SARS-CoV-2, rhinovirus, or respiratory syncytial virus (RSV) infection, alongside uninfected controls. Mapping viral transcripts to individual cells revealed virus-specific infected epithelial states: an NF-kB-responsive ciliated subset in SARS-CoV-2 and a previously undescribed KRT17+ squamous-like subset in RSV. We delineated divergent mucosal response programs, including a robust interferon (IFN) response in SARS-CoV-2, an IL-13-responsive secretory program in rhinovirus, and heightened inflammatory and cytotoxic immune activation in RSV. In RSV, specific immune subsets and elevated IFN-response signatures were associated with disease severity, whereas rhinovirus-induced wheeze was marked by expansion of a CST1+ goblet cell subset. Integration of asthma genome-wide association data with our atlas revealed a KRT13+ hillock-like squamous epithelial subset enriched for expression of childhood-onset asthma risk loci. Finally, we demonstrate that this resource enables high-resolution annotation of independent pediatric cohorts in Kolkata, India and rural Bangladesh. Together, this atlas establishes a comprehensive view of antiviral immunity in the pediatric nasal mucosa and defines virus-specific mucosal immune programs relevant to disease severity and asthma risk in early life.

immunology↗

How the Azadithiolate Ligand Impacts O2-Stability of Group B -Hydrogenase ToHydA

[FeFe]-hydrogenases are metalloenzymes that catalyze the reversible oxidation and production of H2, making them potential candidates for sustainable energy solutions. However, their practical application is restricted by their extreme O2 sensitivity, which leads to irreversible active site degradation. A newly characterized Group B hydrogenase, ToHydA from Thermosediminibacter oceani, has exhibited exceptional O2-stability even after longtime exposure to air. In ToHydA, the highly conserved proton-transporting cysteine (C212) safeguards the H-cluster from O2-induced degradation by formation of the Hinact state. In this study, we investigate the effects of replacing the azadithiolate (ADT) ligand of [2Fe]H with propanedithiolate (PDT), revealing that this substitution prevents the formation of the Hinact and Htrans states observed in ToHydA WT (bearing the ADT ligand). By combining ATR-FTIR spectroscopy and molecular dynamics (MD) simulations, we show that a hydrogen bond between the nitrogen bridgehead of the ADT ligand and the C212 sidechain is crucial for stabilizing these states. The absence of this interaction in ToHydAPDT (bearing the PDT ligand) prevents the C212 sidechain from approaching the Fed center of [2Fe]H, thereby reducing Hinact accumulation. Moreover, as-isolated ToHydAPDT predominantly exhibits the Hhyd state, which is unusual for [FeFe]-hydrogenases with bound PDT ligand. These findings demonstrate how ligand substitution at the [2Fe]H site of ToHydA affects the structural dynamics, offering detailed molecular insights into the ligand-dependent modulation of [FeFe]-hydrogenases.

biophysics↗

Gut-derived metabolic reprogramming drives immune aging and tissue degeneration

Aging is characterized by changes in gut microbiome, metabolic imbalance and chronic inflammation, yet how these processes integrate to drive tissue degeneration remains poorly defined. Using age-related macular degeneration (AMD) as a model of tissue aging, we identify a diet-induced metabolic-immune axis that promotes systemic and retinal degeneration. In mice, a high-fat, cholesterol-enriched (HFC) diet induced perturbations in the gut structural integrity and microbiome repertoire, as well as systemic metabolic aging signatures, prominently marked by reduced circulating histidine. Plasma histidine levels were similarly decreased in AMD patients and inversely correlated with body mass index (BMI) in control donors. These diet-induced gut microbiome changes and subsequent metabolic alterations promoted peripheral innate immune reprogramming, with expansion of inflammatory neutrophils and monocytes that infiltrated the outer retina in a mouse model. Mechanistically, the gut-derived IGF1R/AKT2 signaling acts as a central regulator of global epigenetic remodeling and systemic immune aging under high-fat conditions in C. elegans. In a mouse model with an age-dependent dry AMD-like pathology, distinct retinal pigment epithelium (RPE) subpopulations exhibited downregulation of the histidine transporter SLC7A5, linking metabolic stress to activation of MIF/CD74-dependent inflammatory signaling between RPE and infiltrating immune cells. Histidine supplementation or AKT2 phospho-state modulation attenuated systemic immune activation and rescued retinal degeneration. These findings identify histidine-axis dysregulation as a mechanistic bridge between diet-induced microbiome changes, metabolic stress, immune aging, and retinal degeneration.

cell biology↗

Saliva Metabolomics Reveals Distinct Metabolic Signatures in Patients with Chronic Obstructive Pulmonary Disease: A GC-MS-based approach.

Chronic obstructive pulmonary disease (COPD), a chronic lung disease, involves complex metabolic disturbances that remain poorly characterized using non-invasive matrices. The metabolic alterations associated with cigarette smoke (CS), one of the major drivers of disease progression in COPD patients, have not been explored in detail. This study primarily aimed to investigate the metabolic signatures in COPD patients categorized into smoker (n=15), ex-smoker (n=11), and non-smoker (n=3) subgroups. Utilizing saliva as a noninvasive sample, we identified 26 metabolites with differential expression in smokers and 31 in ex-smokers. However, no such significant alteration was observed in the non-smokers subgroup. The multivariate analysis distinctly separated the COPD subgroups from healthy controls. Additionally, pathway enrichment analysis revealed perturbations in key metabolic pathways, including unsaturated fatty acid biosynthesis, arginine biosynthesis, the tricarboxylic acid (TCA) cycle, and pyruvate metabolism. Moreover, univariate Random forest analysis identified four metabolites (cyclopentanone, tetradecane 4-methyl, acetophenone, and scyllo-inositol) as potential biomarkers distinguishing COPD subgroups from healthy controls. This study offers novel molecular insights into the association of smoking with disease progression and provides a mechanistic understanding of COPD in different subgroups for better management of the disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/717654v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1c3be84org.highwire.dtl.DTLVardef@10ce0aorg.highwire.dtl.DTLVardef@1470712org.highwire.dtl.DTLVardef@2163b6_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Community performance curves predict community stability despite interaction effects

Predicting whether aggregate community properties remain stable as environments fluctuate is a central challenge in ecology. We asked how well species' fundamental niches predict this aspect of community stability. We developed community performance (CP) curves by aggregating species-specific performance across environmental conditions and tested whether their variability explains temporal variability in communities. In Lotka-Volterra and mechanistic consumer-resource simulations, CP variability explained, on average, 89% of variation in total abundance variability, and explanatory power remained above 75% across gradients of interaction strength and coexistence conditions. In a purpose-designed microcosm experiment, CP variability explained 67% of variation in total biomass variability. CP curves thus retain substantial predictive information even in strongly interacting systems, providing a tractable basis for forecasting community stability when species interactions are unknown.

ecology↗

Cancer-associated KBTBD4 mutations induce differentiation defects and confer a unique therapeutic vulnerability

Epigenetic regulation governs stem cell fate and perturbations in these mechanisms often lead to tumor development. The CoREST complex, a critical regulator of neural and hematopoietic stem cell differentiation, is recurrently targeted by gain of function mutations in the ubiquitin ligase KBTBD4 in high-risk embryonal brain tumors. However, the tumorigenic potential of these mutations remains unresolved partly due to the challenges in modelling tumors that arise during early brain development. We and others recently demonstrated that small molecule UM171 mimics KBTBD4 mutations by promoting robust CoREST degradation and expansion of hematopoietic stem cells. Leveraging this mechanistic similarity, we modeled KBTBD4 mutations in hematopoietic stem and progenitor cells (HSPCs) and found that mutants induced expansion of immature stem and progenitor populations and impaired lineage differentiation. High-throughput screening identified HDAC inhibitors as specific agents that disrupt mutant KBTBD4 activity, by preventing interaction with the CoREST complex. Using our HSPC model, we demonstrated that the class I HDAC inhibitor mocetinostat alleviated differentiation defects caused by KBTBD4 mutations. Together, these findings reveal the tumorigenic mechanism of KBTBD4 mutations and uncover therapeutic vulnerabilities that may be exploited for clinical applications.

cancer biology↗

Genomic rDNA instabilities in Arabidopsis epigenetic mutants alter location-based rRNA gene expression patterns

The model plant species Arabidopsis thaliana has two nucleolus organizer regions (NORs), each consisting of tandem repeats of 45S rRNA genes on chromosomes 2 (NOR2) and 4 (NOR4). In the ecotype Col-0, the rRNA gene subtypes mapping to NOR2 are mostly silenced during development, whereas those mapping to NOR4 are mostly active. Using molecular and genetic mapping approaches, we demonstrate in multiple epigenetic mutants the occurrence of NOR conversions involving loss of rDNA and the associated telomeres in one NOR and replacement of the lost sequences with the corresponding sequences from the other NOR. We studied mutants of evolutionarily conserved chromatin remodelers DECREASE IN DNA METHYLATION 1 (DDM1) and CHROMATIN ASSEMBLY FACTOR 1 (CAF-1), and plant-specific CHROMOMETHYLASE 2 (CMT2) DNA methyltransferase. We observed NOR conversions in ddm1 and caf-1 mutants, where such NOR conversions altered the rRNA variant expression patterns, which often confound the data pertaining to release of rRNA gene silencing. We delineated the effects of these mutations on the rDNA instability-mediated alterations in rRNA variant expression from their effects on the actual release of rRNA gene silencing. We also show that these mutations release rRNA gene silencing independently of their effect on rDNA genomic instability involving NOR conversions.

plant biology↗

Programmable DNA nanocages to modulate pollen tube growth via active uptake

Delivering biomolecules into pollen tubes that deliver sperm cells for plant fertilization remains technically challenging due to thick cell walls and rapid polarized growth, hindering reproductive engineering. DNA nanotechnology offers a promising alternative over current delivery methods due to their biocompatibility, programmable design, low cytotoxicity, and stimulus-responsive properties, yet their application in plants remains underexplored. Here, we provide the first demonstration of tetrahedral DNA nanostructures (TDNs) as nanocarriers for active, endocytosis-mediated uptake into Arabidopsis pollen tubes, enabling spermidine delivery that shortens pollen tube elongation through actin reorganization and ROS modulation. TDN-treated pollen tubes grew through the Arabidopsis stigma and style, underwent capacitation, and maintained attraction to ovules in a semi-in-vivo assay, preserving reproductive fitness. Furthermore, we demonstrate that functionalization of TDNs with nuclear localization signal peptide significantly enhances nuclear localization. Collectively, these findings establish DNA nanostructures as effective nanocarriers for targeted biomolecule delivery and precise pollen tube modulation, advancing crop reproductive engineering. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/710033v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@a09c01org.highwire.dtl.DTLVardef@623943org.highwire.dtl.DTLVardef@9d954corg.highwire.dtl.DTLVardef@1b4c35b_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

bioengineering↗

Morphological parameters can capture emergent properties of dynamic disordered cytoskeletal networks

The actin cytoskeleton is an inherently disordered active system. the actomyosin cortex and reconstituted actomyosin systems are globally disordered, yet undergo transitions between distinct disordered states as parameters like motor and crosslinker concentration and filament length and rigidity change. In cells these changes are related to genetic mutations or differences in cell state and dictate fundamental biological processes. However, we dont have well established methods to detect and classify differences in disordered polymer networks. Image-based morphology techniques provide a non-invasive, high-throughput method of extracting information about a system. In this work we simulate biopolymer networks under varying conditions and develop and use morphological descriptors to construct trajectories in morphospace. Using statistical analysis we find that morphological descriptors are able to distinguish between different trajectories of the system, including differences not apparent to the eye. However, no single descriptor alone is able to capture all the differences in the simulated trajectories. Nematic order parameters typically perform the worst for our simulations while curvature and texture descriptors can collectively distinguish between dynamic trajectories. This work helps develop quantification of cytoskeleton dynamics for classification and data-driven modeling.

biophysics↗

Multi-dimensional diffusion MRI at ultra-high gradient strength for mapping axonal architecture and microstructure in the primate brain

We present the most comprehensive sampling of the macaque and human brain with diffusion MRI to date. As part of the BRAIN CONNECTS center for Large-scale Imaging of Neural Circuits, we leverage ultra-high-gradient MRI systems, including the first-of-its-kind Connectome 2.0, for post-mortem acquisitions. Each sample is imaged for [~]250 hours at multiple spatial resolutions down to 0.25 mm isotropic for whole macaque brains and 0.4 mm isotropic for human hemispheres. Our optimized protocols allow us to sample both species across [~]50 diffusion shells varying in b-value, diffusion time, and echo time, reaching ultra-high b-values up to 64000 s/mm2 with high signal-to-noise ratio. We demonstrate that these multi-dimensional data resolve not only white matter connectional architecture but also cortical and subcortical cytoarchitectonic boundaries, at a level of detail previously inaccessible in whole-brain noninvasive imaging. As such, these data are an important resource for both technical development and basic and clinical neuroscience.

neuroscience↗

Bistability to Quad-stability: Emergence of Hybrid Phenotypes & Enhanced Spatio-temporal Plasticity in Presence of Host-Circuit Coupling

In the context of multistability-driven diseases, like cancer, spatio-temporal plasticity plays a significant role to achieve a spectrum of phenotypic variations. The interplay between gene regulatory networks and environmental factors, such as resource competition and spatial diffusion, plays a crucial role in determining cellular behaviour and phenotypic heterogeneity. Though reaction-diffusion frameworks have been widely applied in developmental biology, less attention has been paid to the simultaneous effects of resource competition and growth feedback on spatial organization. In this paper, we observed that a bistable genetic circuit under high resource competition due to growth feedback gives rise to multiple emergent phenotypes, as observed in cancer systems. Furthermore, we observed how spatial diffusion coupled with intrinsic nonlinearity can drive the emergence of distinct spatial dynamics over time. The observed spatiotemporal plasticity can also be driven by the comparative stability of the fixed points, diffusivity, and asymmetry of diffusion. Our findings highlight that growth-induced resource competition combined with diffusion can provide deeper insights into metastasis and cancer progression.

cancer biology↗

Spatial pattern formation as a consequence of Protease Competition

Exploring the emergence of spatio-temporal patterns due to nonlinearities in gene expression is a relatively new development. In this work, we explore the effect of resource constraint on gene regulatory motif from both equilibrium and spatio-temporal standpoint, taking into consideration the degradation class of resource, protease. We have demonstrated that protease-tagged degradation can cause an emergent bistability to form in the system in a steady-state scenario. Instead of a graded linear response in protein synthesis, two Saddle-node bifurcations caused by protease competition provide a switch-like response with hysteresis, where two drastically differing protein concentrations can coexist. We next turn our attention to spatio-temporal analysis: we extend our study for a two-dimensional sheet of cells with diffusible protein molecules and report the stationary patterns.To investigate the reasons behind these non-homogeneous stationary patterns, we investigate the traveling wave solution and observe that a stationary pattern is formed by the traveling wave solution. Considering that proteases play a major role in the regulation and expression of genes in a variety of diseased scenarios, the repercussions of this spatial patterning caused by protease competition can be extensive in gene regulatory systems.

synthetic biology↗

Engineering pH-Responsive trans-Ferulic Acid/κ-Carrageenan Beads for On-Demand Micronutrient Delivery in Plants

Micronutrient deficiencies in soils are a critical challenge in agriculture, particularly in acidic soil environments where nutrient availability is strongly limited by fixation, leaching, and altered metal speciation. These constraints contribute to inefficient nutrient uptake and reduced crop yields. Conventional micronutrient supplementation methods are often inefficient, environmentally harmful, and unsustainable, underscoring the need for smarter delivery systems tailored to soil pH conditions. In this study, we developed biodegradable, pH-responsive microbeads from {kappa}-carrageenan ({kappa}-CG) and trans-ferulic acid (TFA) for targeted micronutrient release. The {kappa}-CG-TFA microbeads were synthesized via an eco-friendly process and optimized for size, morphology, stability, and nutrient retention. Characterization confirmed the successful incorporation of functional groups, while swelling, degradation, and release studies demonstrated efficient delivery of essential micronutrients (Mn2+, Zn2+, Cu2+, and Fe3+) under acidic conditions (pH 4.0), mimicking acidic soil environments. The inherent antioxidant activity of TFA conferred strong radical-scavenging capacity, further enhancing its functionality. Soil water and plant growth assays revealed that the microbeads improved micronutrient availability, significantly increased chlorophyll content and leaf area, promoted vigorous seedling growth, and caused no phytotoxic effects. Collectively, these findings establish {kappa}-CG-TFA microbeads as a promising, eco-friendly platform for sustainable micronutrient delivery and stress reduction, thereby improving crop productivity in agriculture.

bioengineering↗

An Artificial Intelligence-based framework for protein interaction design with accelerated KAN-based Positive-Unlabeled learning

Protein design seeks optimal amino acid sequences for target structures, but designing stable protein complexes remains challenging. We introduce a protein interaction design pipeline combining Monte-Carlo simulation with Metropolis-criteria (MCM) and Deep-Learning. It uses Protein-Protein-Interaction(PPI) scores from Deep-Learning-based MaTPIP model to form a PPI-score-based-MCM (PMCM). The work-flow integrates PMCM-driven sequence generation, HDBSCAN-clustering-based selection, and validation via AlphaFold2 and Molecular-Dynamics (MD) simulation. Incorporating learned PPI scores enhances efficiency and feature fusion. A Positive-Unlabeled (PU) learning classifier accelerates sequence validation, while the Kolmogorov-Arnold Network (KAN) improves PU learning over Multi-Layer-Perceptron (MLP). AlphaFold2 predictions yield median Root-Mean-Square-Deviation (RMSD) 1.17[A] , predicted-Template-Modelling (pTM) 0.72, and interface pTM 0.88; 73% of complexes remain within 2[A] RMSD after 100 ns MD, confirming stability. Interface mutations reveal altered interactions. The KAN-based PU model improves F1-score, precision, and AUC by 5%, 11%, and 2% over MLP. Overall, our method outperforms traditional and simulation-based methods while remaining competitive with modern Deep-Learning design frameworks.

bioinformatics↗

Laboratory and wild Drosophila sechellia have conserved niche specialization phenotypes

A major challenge to investigating the proximate causes of ecological adaptation is the difficulty of studying the phenotypes of organisms in their natural environments. By necessity, many studies seeking to determine the genetic and cellular basis of adaptation therefore investigate potentially adaptive phenotypes under laboratory conditions where organisms are more easily experimentally manipulated. For laboratory models, it remains unclear if organisms maintained long term under laboratory conditions are representative of relatives in their natural environment. In recent years, Drosophila sechellia, a specialist species endemic to the Seychelles, has emerged as a (neuro)genetic model for studying the molecular basis of ecological adaptation. A multitude of studies have investigated the genetic and cellular basis of various aspects of this species specialization in a laboratory setting. However, the vast majority of these studies use laboratory strains of D. sechellia that were collected many decades ago, and have been maintained under conditions very different from their natural niche. Thus, it remains unclear if and how these strains resemble their wild counterparts. Here, we compare the phenotypes of these laboratory strains with recently-collected wild D. sechellia to ask if laboratory strains display a loss or degradation of phenotypes potentially involved in their specialization resulting from their long-term laboratory maintenance. Across several behavioral and anatomical phenotypes, we find a high degree of similarity between wild-caught and laboratory-maintained strains. Our results suggest that studies of the molecular mechanisms underlying D. sechellias phenotypes associated with specialization are likely representative of the evolution of these flies in the wild.

evolutionary biology↗

Interplay of microRNA-20a and HuR in the regulation of beclin1 during Withaferin-A mediated impaired autophagy in Breast Cancer cell-line, MCF-7

Dysfunctional autophagy is connected to multiple diseases. Withaferin-A, a biologically active withanolide, has been shown to impair autophagy in the breast cancer cell line, MCF-7; however, the underlying mechanism remains unclear. Here while uncovering the mechanism, it was found that treatment of MCF-7 cells with WA declines Beclin1 protein synthesis by restricting association of its mRNA to polysomes with no significant reduction in its mRNA level. Reporter assay established that WA-treatment enhanced the expression level of mature miR-20a which directly interacts with the 3UTR of beclin1 mRNA. RNA affinity chromatography revealed association of mRNA stabilizing protein, HuR with the 3UTR of beclin1 mRNA. Additionally, co-immunoprecipitation assay determined the interactions of GW182, an essential component of GW-body and Ago2, a crucial member of miRNA related silencing complex (RISC) with the 3UTR of beclin1 mRNA. In parallel, it was found that knocking down of HuR eliminates the interaction of GW182 with beclin1 3UTR, while the association of miRNA (Ago2) remains unaffected. These results suggested simultaneous association of HuR, GW182 and microRNA with beclin1 mRNA which could be pivotal for sequestration of beclin1 mRNA in GW-bodies. Thus, our findings culminated in identifying an unconventional mechanism of regulation of Beclin1 expression by the dual interplay between hsa-miR-20a and HuR during WA-induced impaired autophagy in MCF-7 cells.

molecular biology↗

Nucleolar reorganization on stress depends on physicochemical changes due to nascent rRNA synthesis

Successive maturation of ribosomal subunits occurs through multilayered phase-separated structures of the cell nucleolus. The spatio-functional relationship between transcription of rRNA and nucleolar substructures and how this adapts to cellular stress remain incompletely understood. In this study, we resolve the sub nucleolar structures using expansion microscopy to reveal ordered structures of fibrillar center (FC) and dense fibrillar component (DFC) domains as nested shells, which is reorganized upon cellular stress like DNA damage or RNA polymerase I (RNAPI) inhibition. Direct visualization of nascent (5 ETS) and mature (28S) rRNA suggested that rRNA synthesis is the critical regulator of nucleolar size, and organization. Nucleolar reorganization upon stress emerges to be a direct function of nascent rRNA levels. Stress-induced transcription inhibition remodels the sub-nucleolar compartments from a viscoelastic state into solid-like condensates thereby perturbing the nucleolar pH gradient due to the missing rRNA scaffold. We show, that rather than signaling to mediate rDNA repair, nucleolar reorganization naturally arises primarily from reduced rRNA levels and the resultant biophysical restructuring of the nucleolus under cellular stress.

cell biology↗

NRF2-Dependent Anti-Inflammatory Activity of Indole via Cell Surface Receptor Signaling in Murine Macrophages

In this study, we report indoles anti-inflammatory effects to be AhR-independent in RAW 264.7 macrophages. To explore the possibility of indoles surface-receptor mediated signaling, we developed an indole-bovine serum albumin conjugate (I3B), which primarily engage cell surface receptors and has limited intracellular engagement. Treatment with 10 M of I3B led to a comparable reduction of TNF- production in LPS-stimulated RAW 264.7 macrophages to that observed with 500 M of free indole. Transcriptome profiling of I3B-treated LPS-stimulated RAW 264.7 macrophages revealed, I3B blunts pro-inflammatory response and induces gene signatures consistent with NRF2 activation. LPS-stimulated NRF2-/- Bone Marrow-derived Macrophages (BMM) treated with I3B, showed higher levels of pro-inflammatory cytokine production relative to non-treated BMM. To define the upstream pathways responsible for this NRF2-depedent response, we examined GPCR-mediated signaling and found that I3B engages a Gq-coupled receptor to induce PKC{delta} phosphorylation, and subsequent NRF2 phosphorylation. Our results suggest I3B signals through a surface-receptor in a NRF2-dependent manner to reduce inflammation in murine macrophages. TeaserA cell-impermeant indole conjugate inhibits inflammatory signaling in macrophages through an NRF2-dependent mechanism.

cell biology↗