Biology subjects

Mahapatra, A.

Publications and source records attributed to Mahapatra, A..

15 recordsLinked to original sources

bioRxiv2026

Distinct colorectal cancer genotypes shape microbial ecosystems and reveal stage-specific microbiota dependencies

The gut microbiota has emerged as an important modifier of colorectal cancer (CRC), yet how tumor genotype influences host-microbiota interactions and whether microbial signals are required throughout tumor progression remain unclear. Here, we combined genetically engineered mouse models, microbial multi-omics and a germ-free-compatible orthotopic transplantation system to define the functional contribution of the microbiota across distinct stages of CRC evolution. Across multiple CRC genotypes, we identified tumor-associated microbial ecosystem states characterized by distinct taxonomic, functional and metabolic configurations. To directly test their contribution to tumor progression, we established the first orthotopic CRC transplantation platform compatible with long-term experimentation in germ-free mice, enabling side-by-side comparison of genetically identical tumors in the presence or absence of microbiota. Using organoids spanning low-grade adenoma, high-grade adenoma and adenocarcinoma states, we found that the dependence on the presence of microbiota progressively decreases during malignant evolution. Whereas adenoma-derived organoids exhibited profound dependence on microbial exposure and failed or were markedly impaired in establishing tumors under germ-free conditions, adenocarcinoma organoids engrafted and metastasized in both germ-free and specific pathogen-free (SPF) hosts. Unexpectedly, comprehensive histological, immunological and transcriptomic analyses revealed highly similar tumor ecosystem states in advanced tumors arising under both microbial conditions, arguing against broad immune or epithelial defects as a primary explanation for the observed phenotype. Together, our findings demonstrate that distinct oncogenic drivers establish specific microbial ecosystem states and reveal a stage-dependent role of the microbiota during colorectal tumorigenesis. Whereas microbial signals are critical during early stages of tumor progression and may promote malignant transformation, advanced tumors progressively acquire microbiota-independent growth programs and increasingly impose genotype-specific ecological signatures on the surrounding microbial ecosystem. More broadly, we establish a versatile framework for the causal dissection of tumor-microbiota interactions in cancer.

cancer biology↗

bioRxiv2025

Selective Targeting of Kinesin on Lipid Droplets in the Liver Reduces Serum Lipids

The liver controls plasma lipids by secreting lipid-rich very low density lipoproteins (VLDL) into blood. Inside hepatocytes in the liver, Lipid Droplets (LDs) are transported to the smooth Endoplasmic Reticulum (sER) by kinesin-1 motors, and then catabolized in the sER to supply lipids for VLDL assembly. LDs are the only cellular organelle bounded by a phospholipid monolayer, and are thus distinct from all other (bilayer-bounded) organelles. It is therefore plausible that a given protein can bind to the LD membrane using mechanisms that are completely different from all other organelles. Indeed, here we find that kinesin-1 uses its tail domain to bind LDs, but alternative mechanisms to bind other organelles. A peptide corresponding to kinesins tail domain therefore competes with, and removes kinesin-1 selectively from LDs with minimal effect on other organelles. Delivery of lipids for VLDL assembly is consequently reduced, causing a remarkable reduction of [~]50% of secreted lipids (triglycerides and cholesterol) in cell culture. We further develop Orally fed Egg-liposomes as a method to deliver kinesin tail domain peptide to the liver of Zebrafish. The peptide reverses diet-induced hyperlipidaemia in Zebrafish larvae and brings the larvae back to a normolipidaemic state, thus confirming the effectiveness of our method in a physiologically relevant in-vivo situation. Strikingly, the peptide causes no unwanted accumulation of lipids in the liver, no toxicity and no developmental or behavioural defects in Zebrafish. Using a peptide to displace proteins (e.g. kinesin) selectively from LDs provides a conceptually novel and radically different approach against hyperlipidaemia. This monolayer-versus-bilayer strategy can be potentially extended to target other LD-bound proteins that function as key regulators of Lipid metabolism.

cell biology↗

bioRxiv2025

AnnotateAnyCell: Open-Source AI Framework for Efficient Annotation in Digital Pathology

AO_SCPLOWBSTRACTC_SCPLOWManual annotation of histopathological whole slide images remains a critical bottleneck for computational pathology and clinical AI deployment, requiring prohibitive expert time at scale. Here we present an open-source semi-supervised framework combining active contrastive learning with iterative human-in-the-loop feedback for efficient cellular annotation and classification. The pipeline integrates Cellpose segmentation, UMAP-based latent space visualization, and contrastive learning with pseudolabel propagation, evaluated on five whole slide images of canine invasive urothelial carcinoma across low, intermediate, and high histological grades at 40x magnification. Latent space clustering-guided annotation required 47 minutes compared to 63 minutes for sequential annotation, a 25% reduction (95% CI 18-32%). Classification accuracy reached 96.3% {+/-} 1.2% for mitotic figures and 98.3% {+/-} 1.4% for nucleoli using 1,075 labeled samples, with nucleoli classification achieving 95.5% {+/-} 1.5% accuracy from only 215 samples. Inter-annotator agreement was high for chromatin ({kappa} = 1.00) and nucleoli ({kappa} = 0.95) but moderate for mitotic figures ({kappa} = 0.58) and nuclear shape ({kappa} = 0.36), reflecting intrinsic morphological ambiguity in these categories. This framework substantially reduces annotation burden while achieving expert-level accuracy for well-defined morphological features, providing a scalable path toward AI-assisted diagnostics in resource-constrained pathology settings.

pathology↗

bioRxiv2025

Tretinoin, a Vitamin A derivative, exerts antiviral effects against Chikungunya virus infection through the nuclear retinoid receptor signaling pathways

Chikungunya virus (CHIKV) has reemerged as a global pathogen causing serious public health threat and socio-economic damage, particularly due to the absence of specific antivirals. Retinoids have been reported to exhibit antiviral potentials against multiple viral infections. In the present study, Tretinoin (TR) or all-trans retinoic acid (ATRA) was evaluated for its anti-CHIKV activity using in vitro, in vivo, and ex vivo models. TR was able to impede CHIKV infection efficiently in Vero and physiologically relevant muscle cells, C2C12, with drastic reduction in the viral RNA, proteins and progeny formation. The IC50 of TR against CHIKV was estimated to be 20.05 {micro}M and 19.71 {micro}M in Vero and C2C12 cells, respectively. In addition, the inhibition was effective during entry as well as in the early stages of post CHIKV-infection. Notably, TR showed remarkable virucidal activity. Next, global transcriptome profile demonstrated that the signaling by Retinoic acid pathway was highly upregulated after CHIKV infection and Retinoic acid receptors (RAR), specifically RAR-{beta} are the key mediators for the anti-CHIKV effect of TR. Further, the drug was also capable to modulate CHIKV-induced inflammatory responses by reducing the phosphorylated MAPKs, NF-{kappa}B and proinflammatory cytokines. Interestingly, TR protected C57BL/6 mice from CHIKV challenge by diminishing viral burden leading to reduced clinical scores and better survival. Similar observation was also noticed in the ex vivo model of CHIKV-infected hPBMC-derived monocyte-macrophage populations. In conclusion, this work demonstrated the repurposing potential of TR against CHIKV infection for the first time, encouraging its clinical validation towards future therapeutics. IMPORTANCECHIKV is an arbovirus causing Chikungunya Fever (CHIKF) leading to debilitating arthralgia and myalgia. The unavailability of licensed antivirals or potent vaccines against CHIKV encourages extensive research to find a therapeutic cure. Retinoids, the derivatives of vitamin A, have been repurposed as antiviral agents against a broad range of viruses; however, their efficacy against alphaviruses remains unexplored. Accordingly, Tretinoin (TR), also known as all-trans retinoic acid (ATRA), was validated for anti-CHIKV efficacy in this investigation. Significant perturbation of CHIKV titer through the modulation of Retinoic acid receptors (RAR) was observed upon drug-treatment. Further, TR reduced major inflammatory markers (MAPKs and proinflammatory cytokines) supporting its anti-inflammatory effect. Further, its anti-CHIKV potential was validated in the mouse model and hPBMC-derived monocyte-macrophage cells, indicating the pre-clinical efficacy. Finally, this is the first study to report the anti-CHIKV property of Tretinoin using in vitro, in vivo, and ex vivo approaches suggesting its repurposing potential.

microbiology↗

bioRxiv2025

DeePhy: A Deep Learning Model to Reconstruct Phylogenetic Tree from Unaligned Nucleotide Sequences

O_LIInferring phylogenetic trees for a set of taxa is one of the primary objective in the evolutionary biology. Numerous approaches exist to reconstruct the phylogenetic trees by considering different biological data, such as DNA sequence, protein sequence, protein-protein interaction graph, etc. However, each method has its own strengths and weaknesses. Till date, no existing method guarantees to determine true phylogenetic trees all the times. Various studies identified distinct branch length configurations where the existing methods are inefficient to infer the correct tree topologies. C_LIO_LIHere, we propose a novel deep convolutional neural network (CNN)-based model, DeePhy, to reconstruct the phylogenetic trees from the unaligned sequences. The sequences are repre- sented on a two-dimensional coordinate plane by utilizing a biological semantics-based map- ping. Additionally, to assess the robustness of a method, here we also propose a novel boot- strapping technique to generate replicas from the unaligned sequences. We train the model on the triplet sequences, where the output is a triplet tree topology. C_LIO_LIWe show that the well-trained DeePhy outperforms the state-of-the-art methods in inferring triplet tree topology. We experiment DeePhy on data simulated under numerous critical conditions and various branch length configurations. We conduct the McNemar test for comparing the performance of DeePhy and the state-of-the-art methods. The results exhibit that DeePhy is significantly more accurate and remarkably robust in determining the triplet tree topologies for most of the cases than that of the conventional methods. Again, various comparison metrics show that DeePhy also outperforms the conventional methods in inferring trees. Finally, to analyze the performance of DeePhy on real biological dataset, we apply it on Gadiformes dataset. Reassuringly, DeePhy reconstructs the phylogenetic tree from real biological data with known or widely accepted topologies. C_LIO_LIAlthough various practical challenges still need to be taken care of, the outcomes of our study suggest that the deep learning approaches be a successful endeavour in inferring the accurate phylogenetic trees. C_LI

evolutionary biology↗

bioRxiv2024

Interplay between cortical adhesion and membrane bending regulates microparticle formation

The formation of blebs and microparticle formation requires the bending of the plasma membrane away from the cytosol. There are multiple factors that control the formation of the microparticles including the loss of lipid asymmetry, primarily the exposure of phosphatidylserine on the outer leaflet, detachment of the membrane from the cortical cytoskeleton, and bleb expansion due to pressure. In this work, we develop a biophysical model that accounts for the interaction between these different factors. Our findings reveal that linker attachment is a key determinant of outward budding and lays out the mechanical aspects of outward budding of the plasma membrane. Significance StatementCells release many types of membrane-enclosed vesicles in response to stress, inflammation, or other injuries. Formation of these membrane-enclosed structures is critical for proper function of the coagulation cascade and apoptosis. In many cases, these microparticles are also a part of the long distance intercellular communication and are implicated in chemoresistance. A particular class of vesicles called ectosomes or microparticles are released by the outward budding of the plasma membrane, a process which requires detachment of the membrane from the cortex, exposure of negatively charged, curvature-inducing lipids such as phosphatidylserine from the inner leaflet to the outer leaflet, and pressure-driven expansion of the bleb. Here, we used membrane mechanics coupled with the kinetics of adhesive linker binding-unbinding to investigate how these different factors interact together. Using our models, we predict how linker properties plays an important role in the outward budding of the plasma membrane and identify conditions that can promote or inhibit such curvature generation. These findings have implications not just for conditions that require successful microparticle formation such as the procoagulation cascade but also for inhibiting microparticle formation in cases of chemoresistant drug efflux by tumor cells.

biophysics↗

bioRxiv2023

Liquid-liquid phase separation of alpha-synuclein is highly sensitive to sequence complexity

The Parkinsons-associated protein -synuclein (-syn) can undergo liquid-liquid phase separation (LLPS), which typically leads to the formation of amyloid fibrils. The coincidence of LLPS and amyloid formation has complicated the identification of the molecular determinants unique to LLPS of -syn. Moreover, the lack of strategies to selectively perturb LLPS makes it difficult to dissect the biological roles specific to -syn LLPS, independent of fibrillation. Herein, using a combination of subtle missense mutations, we show that LLPS of -syn is highly sensitive to its sequence complexity. In fact, we find that even a highly conservative mutation (V16I) that increases sequence complexity without perturbing physicochemical and structural properties, is sufficient to reduce LLPS by 75%; this effect can be reversed by an adjacent V-to-I mutation (V15I) that restores the original sequence complexity. A18T, a complexity-enhancing PD-associated mutation, was likewise found to reduce LLPS, implicating sequence complexity in -syn pathogenicity. Furthermore, leveraging the differences in LLPS propensities among different -syn variants, we demonstrate that fibrillation of -syn does not necessarily correlate with its LLPS. In fact, we identify mutations that selectively perturb LLPS or fibrillation of -syn, unlike previously studied mutations. The variants and design principles reported herein should therefore empower future studies to disentangle these two phenomena and distinguish their (patho)biological roles.

biochemistry↗

bioRxiv2023

ADARs employ a neural-specific mechanism to regulate PQM-1 expression and survival from hypoxia

The ability to alter gene expression programs in response to changes in environmental conditions is central to the ability of an organism to thrive. For most organisms, the nervous system serves as the master regulator in communicating information about the animals surroundings to other tissues. The information relay centers on signaling pathways that cue transcription factors in a given cell type to execute a specific gene expression program, but also provide a means to signal between tissues. The transcription factor PQM-1 is an important mediator of the insulin signaling pathway contributing to longevity and the stress response as well as impacting survival from hypoxia. Herein, we reveal a novel mechanism for regulating PQM-1 expression specifically in neural cells of larval animals. Our studies reveal that the RNA binding protein, ADR-1, binds to pqm-1 mRNA in neural cells. This binding is regulated by the presence of a second RNA binding protein, ADR-2, which when absent leads to reduced expression of both pqm-1 and downstream PQM-1 activated genes. Interestingly, we find that neural pqm-1 expression is sufficient to impact gene expression throughout the animal and affect survival from hypoxia; phenotypes that we also observe in adr mutant animals. Together, these studies reveal an important post-transcriptional gene regulatory mechanism that allows the nervous system to sense and respond to environmental conditions to promote organismal survival from hypoxia.

genetics↗

bioRxiv2023

Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome

Cristae are high curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae-shaping proteins have been defined, analogous mechanisms for lipids have yet to be elucidated. Here we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the IMM against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein-mediated curvatures. The model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that CL is essential in low oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of CL is dependent on the surrounding lipid and protein components of the IMM. SynopsisO_LIcritical lipidic breakpoint for yeast mitochondria phenocopies the loss of cristae-shaping proteins in the IMM. C_LIO_LIsaturation controls membrane mechanical properties and modulates ATP synthase oligomerization. C_LIO_LImitochondrial-specific lipid cardiolipin can functionally compensate for increased phospholipid saturation and is required for cristae formation in low oxygen environments. C_LIO_LImathematical model for cristae membrane tubules predicts a snapthrough instability mediated by both protein and lipid-encoded curvatures. C_LI Synopsis Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/532310v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@196aefforg.highwire.dtl.DTLVardef@1bafcadorg.highwire.dtl.DTLVardef@122f502org.highwire.dtl.DTLVardef@35afd_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

Formation of protein-mediated tubes is governed by a snapthrough transition

Plasma membrane tubes are ubiquitous in cellular membranes and in the membranes of intracellular organelles. They play crucial roles in trafficking, ion transport, and cellular motility. These tubes can be formed due to localized forces acting on the membrane or by the curvature induced by membrane-bound proteins. Here, we present a mathematical framework to model cylindrical tubular protrusions formed by proteins that induce anisotropic spontaneous curvature. Our analysis revealed that the tube radius depends on an effective tension that includes contributions from the bare membrane tension and the protein-induced curvature. We also found that the length of the tube undergoes an abrupt transition from a short, domeshaped membrane to a long cylinder and this transition is characteristic of a snapthrough instability. Finally, we show that the snapthrough instability depends on the different parameters including coat area, bending modulus, and extent of protein-induced curvature. Our findings have implications for tube formation due to BAR-domain proteins in processes such as endocytosis, t-tubule formation in myocytes, and cristae formation in mitochondria.

cell biology↗

bioRxiv2021

Curvature-driven feedback on aggregation-diffusion of proteins in lipid bilayers

AO_SCPLOWBSTRACTC_SCPLOWMembrane bending is an extensively studied problem from both modeling and experimental perspectives because of the wide implications of curvature generation in cell biology. Many of the curvature generating aspects in membranes can be attributed to interactions between proteins and membranes. These interactions include protein diffusion and formation of aggregates due to protein-protein interactions in the plane of the membrane. Recently, we developed a model that couples the in-plane flow of lipids and diffusion of proteins with the out-of-plane bending of the membrane. Building on this work, here, we focus on the role of explicit aggregation of proteins on the surface of the membrane in the presence of membrane bending and diffusion. We develop a comprehensive framework that includes lipid flow, membrane bending energy, the entropy of protein distribution, and an explicit aggregation potential and derive the governing equations. We compare this framework to the Cahn-Hillard formalism to predict the regimes in which the proteins form patterns on the membrane. We demonstrate the utility of this model using numerical simulations to predict how aggregation and diffusion, coupled with curvature generation, can alter the landscape of membrane-protein interactions.

biophysics↗

bioRxiv2020

Transport Phenomena in Fluid Films with Curvature Elasticity

Cellular membranes are elastic lipid bilayers that contain a variety of proteins, including ion channels, receptors, and scaffolding proteins. These proteins are known to diffuse in the plane of the membrane and to influence the bending of the membrane. Experiments have shown that lipid flow in the plane of the membrane is closely coupled with the diffusion of proteins. Thus there is a need for a comprehensive framework that accounts for the interplay between these processes. Here, we present a theory for the coupled in-plane viscous flow of lipids, diffusion of transmembrane proteins, and curvature elastic deformation of lipid bilayers. The proteins in the membrane are modeled such that they influence membrane bending by inducing a spontaneous curvature. We formulate the free energy of the membrane with a Helfrich-like curvature elastic energy density function modified to account for the chemical potential energy of proteins. We derive the conservation laws and equations of motion for this system. Finally, we present results from dimensional analysis and numerical simulations and demonstrate the effect of coupled transport processes in governing the dynamics of membrane bending and protein diffusion.

biophysics↗

bioRxiv2019

Study of human origin and migration from a novel genomic footprint derived from mitochondrial sequences

The origin of modern human and their migration across the world is one of the most debated topics for the decades. There exist two different hypotheses, recent African origin and multi-regional evolution, based on the genomic studies, haplogroups, archaeological records, cultural behaviors, palaeontology studies, etc. Various studies placed the modern humans in a phylogenetic tree to depict the relationships among them. The debate for determining those regions of Africa which witnessed the first origin of humans still exists. The conflicts between the results obtained from the molecular data and the archaeological and palaeontological reports still exist. We adopt a novel genomic feature derived from the whole mitochondrial sequence, and using a novel distance function the phylogenetic trees are constructed based on the feature which provide a new insight on human migration. We propose a new method to derive the bootstrap replica from the genome sequences by considering the genetic variance to demonstrate the robustness of the obtained trees. The results derived from the genomic feature are more consistent with the archaeological findings based on the time of origin of different communities. We find that west and central African communities are placed at the basal point with a very high bootstrap score. This study roughly estimates the existence of the archaic human at 800-900 kilo years ago and presence of human in Africa at 600-700 kilo years ago. This supports the presence of an ancestor in the west and central Africa much earlier than that of the fossils identified.

evolutionary biology↗

bioRxiv2019

Deformity Index: A semi-reference quality metric of phylogenetic trees based on their clades

Measuring the correctness of a phylogenetic tree is one of the most fundamental tasks in phylogenetic study. A large number of methods have been proposed to measure the correctness of a tree. Such methods completely depend on the reference tree and they compute the distance between reference the tree and the target tree. But it is very difficult to obtain a precise and an accurate reference tree for a selected dataset. As a result, the existing methods for comparing the phylogenetic trees can behave unexpectedly in various scenarios. In this paper, we introduce a scoring function, called the Deformity Index, to measure the correctness of a tree based on the biological knowledge of the clades. The strength of our proposed method is that it does not consider any reference tree. We have also investigated the range and the distributions of the different modules of Deformity Index. Furthermore, we perform different goodness of fit tests to understand its cumulative distribution. We have also examined in detail the robustness as well as the scalability of our measure by different statistical tests under the Yule and the uniform models. Moreover, we show that our proposed scoring function can overcome the limitations of the conventional methods of tree comparing by experimenting on different biological datasets.

bioinformatics↗

bioRxiv2018

GRaphical footprint based Alignment-Free method (GRAFree) for reconstructing evolutionary Traits in Large-Scale Genomic Features

In our study, we attempt to extract novel features from mitochondrial genomic sequences reflecting their evolutionary traits by our proposed method GRAFree (GRaphical footprint based Alignment-Free method). These features are used to build a phylogenetic tree given a set of species from insect, fish, bird, and mammal. A novel distance measure in the feature space is proposed for the purpose of reflecting the proximity of these species in the evolutionary processes. The distance function is found to be a metric. We have proposed a three step technique to select a feature vector from the feature space. We have carried out variations of these selected feature vectors for generating multiple hypothesis of these trees and finally we used a consensus based tree merging algorithm to obtain the phylogeny. Experimentations were carried out with 157 species covering four different classes such as, Insecta, Actinopterygii, Aves, and Mammalia. We also introduce a measure of quality of the inferred tree especially when the reference tree is not present. The performance of the output tree can be measured at each clade by considering the presence of each species at the corresponding clade. GRAFree can be applied on any graphical representation of genome to reconstruct the phylogenetic tree. We apply our proposed distance function on the selected feature vectors for three naive methods of graphical representation of genome. The inferred tree reflects some accepted evolutionary traits with a high bootstrap support. This concludes that our proposed distance function can be applied to capture the evolutionary relationships of a large number of both close and distance species using graphical methods.

evolutionary biology↗