Biology subjects

Mondal, S.

Publications and source records attributed to Mondal, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Genomic characterization of patient derived xenograft models of multiple myeloma reveals selection of multiple pre-existing high risk clones

Multiple myeloma (MM) is a genomically complex malignancy of terminally differentiated plasma cells. Here, we have utilized the SCID-rab patient derived xenograft (PDX) model as a platform to expand scarce primary MM samples across disease stages and major cytogenetic subgroups for comprehensive molecular analysis. The model generated abundant CD138+ cells while retaining key genomic, transcriptomic and proteomic features of corresponding patient tumors. Compared with human myeloma cell lines, PDX cells more closely resembled primary MM in proliferative state and expression of therapeutically relevant targets. WGS and single cell WGS showed that PDXs arose from the selection of pre-existing subclones, including clones harboring high-risk alterations and convergent mechanisms of tumor suppressor inactivation. These findings establish SCID-rab PDX models as a platform for multiomic profiling, studies of clonal evolution, and determining therapeutic response in MM.

cancer biology↗

bioRxiv2026

Root exudates enhance the ecological fitness of a non-native PGPR and reshape rhizosphere microbiome assembly

Root exudates play critical roles in rhizosphere microbiome assembly. Nevertheless, the molecular mechanisms by which plant growth-promoting rhizobacteria (PGPR) perceive these signals, adapt to the rhizosphere, and influence native microbial communities remain poorly understood. Here, using maize (Zea mays cv. Early Golden Bantam) and the rhizobacterium Priestia aryabhattai AB211, we took a multi-omics approach combining metabolomics, bacterial transcriptomics and proteomics, and rhizosphere metagenomics to elucidate the mechanism underlying this process. Maize root exudates were enriched in diverse carbon and nitrogen metabolites that promoted bacterial growth and induced extensive molecular reprogramming of pathways involved in nutrient acquisition, chemotaxis, motility, stress adaptation, and plant growth promotion, thereby enhancing rhizosphere competence. In field-conditioned soil, AB211 persisted as a core member of the maize rhizosphere microbiome, promoted early seedling growth, and reshaped microbial community composition and function. Root exudates-primed (RE-primed) AB211 further enhanced the enrichment of microbial functions associated with nutrient cycling, quorum sensing, plant growth promotion, and rhizosphere fitness, highlighting the role of root exudates in modulating the rhizosphere-adaptative potential of beneficial bacteria. These findings establish a mechanistic framework linking root exudates composition with PGPR adaptation and microbiome assembly, providing a foundation for engineering ecologically adapted microbial inoculants to improve crop productivity and sustainable agriculture.

microbiology↗

bioRxiv2026

Gestational exposure of bisphenol-A limits decidual ECM organization via S100a10-Annexin A2 axis in murine placenta

Environmental exposure to endocrine disrupting chemicals, like bisphenol-A (BPA), can impart detrimental effects on developing feto-placental unit, during pregnancy. Placenta remains a central player maintaining this feto-placental homeostasis for sustenance of a healthy pregnancy. Thus, the bisphenol-A mediated endocrine disruption affects the healthy functioning of placenta by altering key processes, such as tissue remodelling, angiogenesis, and metabolism. However, the underlying mechanism of BPA-altered ECM remodelling remains elusive. Therefore, in this study we investigated the BPA mediated changes in placental tissue remodelling using a bisphenol-A exposed murine model during pregnancy. The results reveal that, the phenotypic changes in feto-placental interface correlates with perturbed placental proteome in response to BPA. Further investigation highlights a S100a10-Annexin A2 axis mediated upregulation of tissue plasminogen activator (tPA), which drives altered extracellular matrix (ECM) degradation in placental decidua. This culminates into functional dysregulation in feto-placental axis, leading to reduced size of fetus and placenta. Therefore, this study provides novel insights of a S100a10-Annexin A2 axis associated mechanism for alteration of ECM remodelling in placental decidua due to BPA exposure, which may lead to toxicity related adverse pregnancy outcome.

developmental biology↗

bioRxiv2026

A first-in-class multimodal organomercury compound demonstrates preferential blast reduction with hematopoietic and immune restoration in Acute Lymphoblastic Leukemia

Acute leukemia treatment requires effective blast reduction while improving hematopoietic and immune health. As reported previously, we developed a structurally distinct organomercury derivative of curcumin, -Mercurin, having improved aqueous solubility and intravenous applicability. Here we comprehensively evaluated therapeutic efficacy, pharmacological response, systemic toxicity, blood Hg pharmacokinetics (PK), Hg biodistribution and elimination profile for -Mercurin in a N-nitroso-N-ethylurea (ENU)-induced autochthonous Acute lymphoblastic leukemia (ALL) rat model, comparing with clinical standard cytarabine. Results showed recovery in body-weight, along with longer time-to-humane-endpoint from 13 to 39 days. Treatment successfully reduced immature blast count, while promoting erythroid, myeloid, and megakaryocytic compartments and improving immune mediators across peripheral blood, bone marrow, thymus, spleen, and lymph nodes. Histopathology showed reduced leukemic infiltration with preservation of major organ architecture, while cytarabine produced evident myelosuppression, neurotoxicity, and cardiotoxicity. PK study showed blood Hg reached Tmax at 15 min, followed by urinary and fecal elimination with residual retention in kidney tissue and no detectable Hg in brain. Collectively, -Mercurin demonstrated a promising multimodal therapeutic index, combining cytoreductive activity with improvement in hematopoietic and immune health, along with favorable safety profile for future ALL therapy.

cancer biology↗

bioRxiv2026

Redistribution of codon-optimality effects: measurement strategy alters the division of labor between translation and mRNA decay

Codon optimality promotes efficient translation and, as recent research has shown, also extends mRNA lifetimes. However, how control is distributed between translation and mRNA degradation remains unclear. We show that this relative impact depends strongly on the measurement approach. Using fluorescent protein reporters can underestimate codon-optimality-dependent increases in translation efficiency. Conversely, analyses based on poly(A)-selected RNA overestimate the impact on translation, because stable transcripts undergoing poly(A) shortening are often inefficiently captured, leading to skewed protein-to-mRNA ratios. This technical bias is not offset by the marginal decline in ribosomal association observed as mRNAs age. Estimates based on total RNA measurements redistribute some of the control attributed to translation to mRNA stability, making the contributions comparable for mRNAs with shorter coding sequences. For longer mRNAs, codon optimality increasingly controls elongation speed, with a greater effect on translation efficiency than on degradation. These insights highlight the importance of measurement strategy for accurately quantifying the determinants of mRNA stability and protein synthesis.

biochemistry↗

bioRxiv2026

Translational toolkit for reproducible, cross-study profiling of human ageing hallmarks in human blood and tissue

BackgroundAgeing is a complex, multi-dimensional process, underpinned by interacting biological hallmarks that collectively contribute to functional decline and increased susceptibility to disease. While considerable progress has been made in delineating individual ageing pathways, translation into human studies has been hindered by methodological heterogeneity and a lack of standardised, multi-system approaches. Here, we describe a validated, high-resolution toolkit for the simultaneous quantification of multiple ageing hallmarks in clinically accessible human samples, encompassing cellular senescence, immune ageing, inflammation, mitochondrial function, mTOR signalling, autophagy, genomic instability, and stem cell exhaustion. MethodsBlood (25ml) was obtained from young and aged donors (26-81y). Deep immunophenotyping was performed using a novel 30-colour spectral flow cytometry panel. T-cell mTOR activation and autophagic flux were assessed by flow cytometry. Metabolic flux was measured by Seahorse. From whole blood (4 ml), muscle, and adipose tissue (AT) (obtained during elective hip arthroplasty) RNA, DNA, AT stem cells, and myoblasts were isolated. DNA copy number and senescent cell burden were assessed by q-PCR and SA-{beta}-gal staining, respectively. FindingsUtilising this toolkit, we identified pronounced age-related immune remodelling, increased senescent T-cell burden, diminished mitochondrial capacity and altered mTOR-autophagy signalling between healthy young and aged donors. Furthermore, metabolism was significantly affected by anti-coagulant and freezing sample before analysis. InterpretationThis integrated platform provides a foundation for reproducible, cross-study analyses and facilitates translational investigation of interventions targeting health-span extension. FundingWellcome Leap Dynamic Resilience program (co-funded by Temasek Trust).

immunology↗

bioRxiv2026

Modeling Multi-Modal Brain Connectomes for Brain Disorder Diagnosis via Graph Diffusion Optimal Transport Network

Network analysis of human brain connectivity provides a fundamental framework for identifying the neurobiological mechanisms that cause cognitive variations and neurological disorders. However, existing diagnostic models often treat structural connectivity (SC) as a fixed or optimal topological scaffold for functional connectivity (FC). This consequently overlooks the higher-order dependencies between brain regions that are critical for characterizing pathological alterations. Moreover, the distinct spatial organizations of SC and FC complicate their direct integration, as naive alignment methods may distort the inherent nonlinear patterns of brain connectivity. To address these limitations, we propose the Graph Diffusion Optimal Transport Network (GDOT-Net), which models disease-related topological evolution and achieves precise alignment between SC and FC. Unlike existing diffusion studies, the proposed model introduces an evolvable brain connectome modeling approach to infer the complex topological structure of brain networks, unveiling higher-order connectivity patterns linked to specific neuropsychiatric disorders. Furthermore, GDOT-Net incorporates a Pattern-Specific Alignment mechanism, leveraging optimal transport to align structural and functional topological representations in a geometry-aware manner. To capture nonlinear topological relationships between brain regions, a Neural Graph Aggregator Module was developed, which adaptively learns complex node interaction patterns in brain networks. By leveraging this module, GDOT-Net generates highly discriminative representations that form a robust basis for the precision diagnosis of brain disorders. Experiments on REST-meta-MDD and ADNI demonstrate that GDOT-Net surpasses SOTA methods in uncovering structural-functional misalignments and disorder-specific subnetworks. The source code is publicly available at this Link.

neuroscience↗

bioRxiv2026

Strategic Segmentation: A Nash Equilibrium based Approach for Weed Segmentation in Agricultural Fields

Weeds present a major challenge to agricultural productivity, competing with crops for critical resources like water, nutrients, and sunlight, resulting in significant yield reductions. Prompt weed identification is essential for enabling effective control strategies, such as the application of herbicides or mechanical removal, to minimize their impact on crop growth. This research focuses on developing a deep learning approach based on game theory for detecting weeds. Using CWFID dataset captured at various times and days, along with multispectral data in the visible and near-infrared spectrum, the study aims to improve early detection methods for more efficient weed management in agricultural settings. A novel segmentation technique for weed regions is introduced, employing a zero-sum game theory model to reconcile conflicting classifications from different weed detectors. These regions are treated as zones of conflict between weeds and crops, with each detector representing a different strategy. By defining an appropriate utility function, the method identifies the Nash equilibrium, effectively minimizing false positive detections of weeds.

plant biology↗

bioRxiv2026

An Indole Dimer Antifungal Metabolite from a Rice Seed Endophyte Inhibits Ergosterol Biosynthesis in Fungal Pathogens

The increasing prevalence of fungal phytopathogens and the widespread emergence of fungicide resistance necessitate alternative antifungal strategies with reduced environmental impact. Here, we report the isolation and characterization of a novel antifungal metabolite, SM06, produced by the rice seed-associated endophytic bacterium Phytobacter sp. RSE02. SM06 exhibited broad-spectrum antifungal activity against plant and human pathogenic fungi, including Curvularia lunata, Fusarium oxysporum, and Candida albicans. In vitro assays and micromorphological analyses revealed that SM06, an indole dimer, disrupts fungal cell membrane integrity, while in planta experiments demonstrated significant suppression of brown leaf spot disease in tomato and rice. Molecular docking suggested that SM06 binds to lanosterol 14-demethylase (ERG11), a key enzyme in fungal sterol biosynthesis. Consistent with this prediction, LC-MS-based analyses confirmed a significant reduction in ergosterol content in SM06-treated fungal cells. Together, these findings identify SM06 as a biologically active antifungal metabolite produced by a plant-associated bacterium and highlight its potential application in sustainable fungal disease management. IMPORTANCEFungal diseases cause major losses in crop-production and contribute to the growing challenge of antifungal resistance, underscoring the need for sustainable alternatives to chemical fungicides. This study identifies SM06, a novel indole dimer produced by the rice seed endophyte Phytobacter sp. RSE02, with strong antifungal activity against economically important plant pathogens and clinically relevant fungi. Through integrated chemical, cellular, and in planta analyses, we demonstrate that SM06 disrupts fungal membrane integrity by inhibiting ergosterol biosynthesis. The compound is biocompatible, stable, and effective in plant disease suppression, highlighting its translational potential for crop protection. These findings reveal seed endophytes as an important yet underexplored sources of antifungal metabolites and provide a mechanistic foundation for developing eco-friendly biocontrol strategies with implications beyond agriculture. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/697688v1_ufig1.gif" ALT="Figure 1"> View larger version (86K): org.highwire.dtl.DTLVardef@c7da68org.highwire.dtl.DTLVardef@d3f1a1org.highwire.dtl.DTLVardef@9cab82org.highwire.dtl.DTLVardef@1c01141_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Unveiling Differential Epigenetic Regulation of ABC Transporter Genes in Wild and Domestic Rice in Response to Heavy Metal Stress

Plants are continually subjected to heavy metal (HM) stress, which impairs critical physiological and metabolic processes. ATP-binding cassette (ABC) transporters play an important role in heavy metal detoxification, their epigenetic regulation under heavy metal stress remains poorly understood. Epigenetic changes, such as DNA methylation (5mC) and N6-methyladenine (6mA), are emerging as important regulators of stress-responsive genes. We studied the epigenetic regulation of ABC transporter genes in three Oryza species Oryza sativa indica, Oryza rufipogon, and Oryza glaberrima by analysing promoter methylation patterns. Our data show that 5mC is abundant in CHG motifs, whereas 6mA is mostly found at AHCA motifs, indicating sequence-specific methylation preferences across different rice species. Notably, indica rice exhibited higher promoter methylation levels compared to O. rufipogon and O. glaberrima, suggesting a potential link between increased DNA methylation and reduced ABC transporter expression, which may contribute to heightened HM sensitivity in cultivated rice. Phylogenetic analysis further highlighted species-specific variations in methylation patterns, supporting the role of epigenetics in shaping HM stress adaptation. These results provide new insights into the regulatory mechanisms governing heavy metal tolerance in rice and open avenues for epigenetic-based crop improvement strategies.

plant biology↗

bioRxiv2025

Glassy dynamics in active epithelia emerge from an interplay of mechanochemical feedback and crowding.

Glassy dynamics in dense epithelial cells remain a subject of debate, as theory predicts its emergence only at unrealistically low cellular activity, yet experimental studies have shown glassy dynamics at physiologically active conditions. In this study, we address this paradox by integrating experimental observations in epithelial monolayers with an active vertex model. We demonstrate that while crowding is essential, it is not sufficient for glassy dynamics to emerge. A mechanochemical feedback loop (MCFL-1), mediated by cell shape changes through the contractile actomyosin network is required to drive glass transition in dense epithelial tissues. Such mechanochemical feedback is captured experimentally via a crosstalk between actin-based cell clustering and dynamic heterogeneity, as well as via force induced actin reorganization in epithelial cells. Incorporating MCFL into the vertex model reveals contrasting results from those previously predicted by theories-we show that the MCFL can counteract cell division-induced fluidisation and enable glassy dynamics to emerge through active cell-to-cell communication. Furthermore, our analysis reveal, for the first time, the existence of novel collective mechanochemical oscillations that arise from the crosstalk of MCFL-1 with oscillatory MCFL-2, capturing ERK mediated cell shape changes. Together, we demonstrate that an interplay between crowding and active mechanochemical feedback enables the emergence of glass-like traits and collective biochemical oscillations in epithelial tissues with active cell-to-cell contacts.

biophysics↗

bioRxiv2025

Recombinant Lactococcus lactis-based multivalent vaccine targeting Campylobacter jejuni colonisation and modulating cecal microbiota in poultry

BackgroundDiarrhoeal diseases remain the second leading cause of preventable death globally, particularly among children under the age of five in developing countries, accounting for an estimated 2-3 million deaths annually. Among the bacterial pathogens causing diarrheal illness, Campylobacter jejuni (C. jejuni) remains one of the major contributors, particularly in LMICs. As a common gut pathogen, C. jejuni expresses several secretory or surface-expressed colonisation proteins, namely Hcp, VgrG, CadF, FlpA, and JlpA. Most of these proteins play pivotal roles in bacterial self-survival, host-cell adhesion, and invasion in avian and non-avian hosts. MethodsTo minimise the C. jejuni adhesion and subsequent colonisation in the avian gut, we explored the potential of a multivalent mucosal vaccine composition using these putative subunits of C. jejuni. For this purpose, we bioengineered a food-grade Lactic Acid-producing Bacterium, Lactococcus lactis (L. lactis), to express three key immunogenic subunits, Hcp, CadF and JlpA. Utilising this live vector-based multi-component mucosal vaccine platform, we investigated the immunoprotective potential of these antigens in chickens. Since the particular strain of L. lactis is non-colonising, we used chitosan as a natural mucoadhesive, biodegradable polymer to microencapsulate the engineered bacteria to increase their gut retention time for optimal interaction with local immune cells. ResultsOur in vivo immunisation study demonstrated that oral administration of this multivalent vaccine formulation elicited a strong local antibody response (sIgA) and upregulated key pro-inflammatory cytokines, leading to robust mucosal immune protection against the cecal colonisation of C. jejuni. Moreover, gut metagenomic analysis of vaccinated birds revealed a marked reduction in the phylum Campylobacterota, accompanied by an increased abundance of the phyla Bacillota and Bacteroidota, as part of a beneficial microbial community. ConclusionsTogether, this study underscores the potential of a live vector-based, multivalent mucosal vaccine as a promising, cost-effective strategy to reduce the risk of foodborne transmission of C. jejuni, particularly in poultry production systems.

immunology↗

bioRxiv2025

Comparative genome analysis of tea rhizosphere dwelling Paenarthrobacter nicotinovorans AB444: Uncovering Physiological Resilience and Ecological Adaptability

Plant growth-promoting rhizobacteria (PGPR) can be considered a promising tool for sustainable agriculture. The recent scenario of growing demand for higher crop yields, with declining soil fertility and impacts of climate change, promotes the global shift towards eco-friendly agricultural practices, emphasising the significance of PGPR as a sustainable solution. In this study, a PGPR Paenarthrobacter sp. AB444 was isolated from the rhizosphere of tea plants at the Longview and Makaibari tea estates in the Darjeeling District of West Bengal. Based on the draft genome sequence along with comprehensive chemotaxonomic analyses, strain AB444 was identified as Paenarthrobacter nicotinovorans. The pangenomic analysis with phylogenetically close strains revealed the gene clusters that are common and unique to the isolate. The plant growth-promoting attributes of AB444 were explored with different assays like phosphate solubilisation, IAA and siderophore production, ACC deaminase, nitrogen fixation, and protease activity. The colonization of the isolate to the plant root and in-planta growth were also assessed. The presence of biosynthetic gene clusters of AB444 related to plant growth was also extensively studied, highlighting the unmapped disposition of Paenarthrobacter nicotinovorans.

microbiology↗

bioRxiv2025

Multifunctional Roles of Brr6 and Brl1 in Nuclear Envelope Fusion During Nuclear Pore Complex Biogenesis

Brl1 and Brr6 are essential, paralogous integral membrane proteins of the yeast nuclear envelope (NE) that transiently associate with nuclear pore complexes (NPCs) during their assembly to promote fusion of the inner (INM) and outer nuclear membranes (ONM). An amphipathic -helix (AH) in Brl1 is critical for mediating this fusion during NPC biogenesis. However, the exact roles of Brl1 and Brr6 in the molecular mechanisms of NPC assembly are still unclear. Here, we demonstrate that Brr6 operates at both early and late stages of NPC assembly. Its early function is supported by AH mutants that fail to permit nucleoporin recruitment and INM deformation, while mutations in conserved cysteine residues lead to NE herniations and defective membrane fusion. Additionally, the N-terminus of Brl1 interacts with Nic96, likely promoting its recruitment to nascent NPC assembly sites. We further provide evidence that the length of the perinuclear space-spanning region of Brl1 and Brr6 is critical for proper NE fusion during NPC formation. Artificial elongation of this region produces a toxic phenotype marked by Nup82 mislocalisation and severe NE integrity defects. This phenotype supports a model in which Brl1 and Brr6 promote NE fusion following INM deformation, when the distance between the INM and ONM is reduced--a process initiated by nucleoporin assembly on the nuclear side of the INM.

cell biology↗

bioRxiv2025

Comparative evaluation on the fermentative potential of single and assorted fruit and vegetable waste for production of bioethanol

Fruit and vegetable waste (FVW) constitute a large part of municipal solid waste (MSW) and create significant environmental challenges by emitting the greenhouse gas methane. In contrast, these are a big source of fermentable sugar to produce bioenergy. Therefore, in this study, the Scanning Electron Microscopy (SEM), Attenuated total reflectance-fourier-transform infrared spectroscopy (ATR-FTIR), thermogravimetric analysis (TGA), X-ray diffraction (XRD), and biochemical quantification of -cellulose and acid-insoluble lignin contents were carried out to compare fermentative potential between single (potato peel vs. orange peel) and assorted vegetable and fruit wastes. Collectively, the study indicates that assorted vegetable waste holds enormous biofuel potential by having low moisture content (6.78 %), moderately low decomposition temperature (Tmax: 299.36 {degrees}C), low crystallinity index (CrI: 19.12%), and high -cellulose contents (32.35 - 47.73 gm%) yielding high sugar (325.65 mg/g). The study also optimized several key fermentation parameters such as pH, sugar concentration and the time to produce bioethanol. It was observed that maximum production of ethanol (2.14%) was achieved at 28{degrees}C, at pH 6.3 with a higher initial sugar concentration of 200mg/g by using Saccharomyces cerevisiae strain NCIM 3594. This study supports the likely utility of unsorted vegetable waste to obtain bioethanol at a mass scale.

plant biology↗

bioRxiv2025

Mechanisms of microtubule dynamics from single-molecule measurements

Microtubules are dynamic polymers of {beta}-tubulin heterodimers that organize the intracellular space and mediate faithful chromosome segregation. Microtubule function depends on dynamic instability, the apparently random GTPase-dependent switching between growing and shrinking. Microtubule dynamics derive from biochemical properties of individual tubulin subunits and how they interact with the polymer end, a complex environment where individual tubulins can have different numbers of neighbor contacts. A fundamental understanding of microtubule dynamics has been difficult to establish because of challenges measuring the number, strength, and nucleotide-dependence of tubulin binding sites on the microtubule end. We used an improved single-molecule assay to measure tubulin:microtubule interactions. In addition to the two expected classes of binding site (longitudinal and corner), we identified previously unrecognized third binding interaction. We further show that nucleotide state strongly influences the strength of inter-protofilament contacts, with little effect on intra-protofilament contacts, and that a mutation can modulate this nucleotide effect. By uncovering a new tubulin binding state on the microtubule end, clarifying how GDP influences microtubule stability, and demonstrating that the nucleotide effects are allosteric and tunable, these single-molecule measurements and accompanying computational simulations provide rich new biochemical insight into the fundamental mechanisms of microtubule dynamics.

biophysics↗

bioRxiv2025

OrganoidChip+: a Microfluidic Platform for Culturing, Staining, Immobilization, and High-Content Imaging of Adult Stem Cell-Derived Organoids

High-content imaging (HCI) and analysis are the keys for advancing our understanding of the science behind organogenesis. To this end, culturing adult stem cell-derived organoids (ASOs) in a platform that also enables live imaging, staining, immobilization, and fast high-resolution imaging is crucial. However, existing platforms only partially satisfy these requirements. In this study, we present the OrganoidChip+, an all-in-one microfluidic device designed to integrate both culturing and HCI of ASOs all within one platform. We previously developed the OrganoidChip as a robust imaging tool. Now, the OrganoidChip+ incorporates several additional features for culturing organoids in addition to fluorescence staining and imaging without the need for sample transfer. The organoids grown within a culture chamber are stained and then transferred to immobilization chambers for blur-free, high-resolution imaging at predetermined locations. We cultured adult stem cell-derived intestinal organoids in the chip for 7 days and tracked growth rates of each organoid using intermittent brightfield images, followed by multiple image-based assays, including viability assay using widefield fluorescence imaging, a redox ratio assay using label-free, two-color, two-photon microscopy, and immunofluorescence assays using confocal microscopy. These assays serve as proof-of-concept to showcase the chips capabilities in HCI of ASOs. Organoids cultured in the chip exhibited superior average growth rates over those in traditional Matrigel dome cultures, off-chip. Viability and redox ratio measurements of on-chip organoids were comparable or slightly better than their off-chip counterparts. Confocal imaging further confirmed that the OrganoidChip+ supports robust organoid culture while enabling detailed, high-resolution analysis. This all-in-one platform holds great potential for advancing ASO-based research, offering a scalable and cost-effective solution for HCI and analysis in organogenesis, drug screening, and disease modeling.

bioengineering↗

bioRxiv2025

Integrating experiments and simulations to unravel coacervate-membrane interactions: Insights into de-mixing and morphology modulation

Intrinsically disordered proteins and polypeptides can undergo liquid-liquid phase separation (LLPS) to form condensates/coacervates, which play numerous regulatory roles in the cell. Recently, the relevance of such LLPS occurring in the vicinity of membranes has been brought to light by several experimental studies. Membrane-adsorbed condensates are crucial for biomolecular localization, and in some cases, phase separation of proteins at the membrane surface induces significant changes in membrane morphology. A detailed microscopic understanding of the mechanisms behind these observations remains incomplete. Here we combine experiments and molecular simulations to unravel structural and dynamic features of the coacervate/membrane interface across scales. We study poly-Lysine/poly-Aspartate (K10/D10) coacervates as a prototype of phase-separated condensates with different unilamellar liposomes. Using a multiscale characterization approach that combines confocal microscopy, hyperspectral imaging, fluorescence recovery after photobleaching, and two complementary coarse-grained approaches, we show that the membrane-condensate affinity can be tuned by the anionic lipid content and quantified through the intrinsic contact angle - a material property derived from system geometry - both in vitro and in silico. We find that the membrane region in contact with the condensate displays a nearly two-fold reduced fluidity compared to the bare membrane. This is attributed to orientational ordering of lipid tails, resulting in decreased area per lipid. Moreover, we observed local lipid de-mixing induced by the coacervate adsorption. This study provides an effective framework for integrating experiment and computation to characterize the properties of coacervate/membrane interfaces that are critical to the functional impacts of these interactions.

biophysics↗