Biology subjects

Das, P.

Publications and source records attributed to Das, P..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Mapping Minds to Manage the Tiger of Rivers: A Fuzzy Cognitive Mapping Approach to Understanding Multi-Stakeholder Perspectives on Mahseer Conservation

Conservation of mahseers, a group of charismatic freshwater fishes native to the South, East and South-East Asia, situated at the intersection of complex social, ecological and economic landscapes, necessitates the integration of the knowledge, mental models, and expectation of different stakeholders. Using a Fuzzy Cognitive Mapping approach, this study generated collective mental models of mahseer conservation in two Indian states distinct in their geography, ecology and socio-cultural aspects - Assam and Uttarakhand. Although many core system components were similar in the cognitive map generated for the focal states, notable divergences emerged in the drivers, perceived relationships among the components, etc. indicating regional specificity in socio-cultural governance structures and stakeholder priorities. In both states stakeholder communication emerged as the most central, and the component with highest outdegree, underscoring its shaping effect on system-wide variable interactions. The other influential components were community fishing (destructive and traditional) and human-human conflict (in Assam), and illegal destructive fishing and community involvement in decision-making (in Uttarakhand). The what-if scenario analyses simulating potential interventions, demonstrated that enhancing communication, awareness and education, promoting local identity and cultural significance of community fishing, providing subsistence fishing opportunities for the locals, and community involvement in decision-making could help in reducing human-human conflicts, illegal fishing, and strengthen stakeholder collaboration for mahseer conservation in both states. Our results also indicate that these improvements alone are insufficient to result in measurable mahseer conservation outcomes until cultural revitalisation and governance reforms are integrated with habitat restoration, improved hatchery performance, evidence-based policies and strict law enforcement. We discuss various leverage points that emerged from the FCMs of both focal states and their implication for a broader mahseer conservation policy with a scope for integrating region-specific characteristics.

animal behavior and cognition↗

bioRxiv2025

Biocompatibility assessment of SilkMA-Gelatin ink tuned for 3D extrusion bioprinting

3D bioprinting applications have led to the development of multifunctional scaffolds that are biocompatible, overcoming shear stress to provide structural integrity. We report the isolation of silk fibroin (SF) using calcium chloride (CaCl2), which was further developed into an ink comprising silkMA and gelatin, demonstrating effective cytocompatibility and biocompatibility when 3D printed using an extrusion-based 3D bioprinter. Rheological characterization of SilkMA-Gelatin showed an improved viscosity and printability of the formulation as compared to an unmodified silk-gelatin composition. SilkMA-gelatin was bioprinted with NIH3T3 cells and demonstrated enhanced viability and proliferation, highlighting its cytocompatibility and ability to support a favourable 3D microenvironment. In vivo biocompatibility of the 3D bioprinted SilkMA-Gelatin was evaluated in Wistar rats, where 3D printed scaffolds maintained structural stability for up to 1 month, with no inflammatory response, progressive cell infiltration, and re-epithelialization. Serum biochemistry analysis, including ALP, ALT, LDH, and Urea (BUN), remained within normal physiological ranges, further confirming systemic safety. Based on the findings, the optimized SilkMA-gelatin ink proves to be highly effective in fabricating cell-laden structures that are stable, exhibit enhanced cytocompatibility and biocompatibility, and offer promising potential for advanced tissue regeneration applications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/687334v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1fad3dcorg.highwire.dtl.DTLVardef@6b2d3aorg.highwire.dtl.DTLVardef@6655b8org.highwire.dtl.DTLVardef@85d894_HPS_FORMAT_FIGEXP M_FIG Schematic overview of 3D bioprinting in wound healing and biomedical applications C_FIG

bioengineering↗

bioRxiv2025

Palmitoylation of PSD95 flips the bilayer juxtaposed domain and drives cluster formation on membrane

Postsynaptic density protein 95 (PSD95) is a highly abundant scaffolding protein at excitatory synapses, where it organizes the molecular architecture of the postsynaptic density (PSD) by anchoring neurotransmitter receptors, ion channels, adhesion molecules, and signaling enzymes. Emerging evidence indicates that PSD95 forms transient "nanodomains" essential for the fidelity of synaptic transmission and plasticity, and disruptions in its clustering are linked to neuropsychiatric disorders. Palmitoylation, a reversible post-translational modification involving the covalent attachment of palmitate to Cysteine residues, has been implicated in the localization and clustering of the PSD95 at the plasma membrane, but its structural and mechanistic role remains unclear. Here, we use a multiscale molecular dynamics approach that combines all-atom and coarse-grained simulations to investigate how palmitoylation regulates PSD95 conformational dynamics, membrane association, and self-assembly. Our results show that palmitoylation promotes an open conformation in solution and stabilizes an extended assembly-primed state at the membrane. In the unmodified state, the PDZ1 domain remains distal while PDZ2 preferentially engages with the membrane; palmitoylation reverses this arrangement, anchoring PDZ1 to the membrane and enhancing clustering propensity. Membrane lipid composition further modulates this behavior, with negatively charged lipids influencing favorable domains orientation through electrostatic interactions. Finally, coarse-grained simulations reveal that palmitoylated PSD95 forms stable dimers on the membrane surface, whereas unmodified molecules fail to associate persistently. Together, these findings provide a mechanistic model for how palmitoylation facilitates the early stages of PSD95 clustering, offering nanoscale insights into synaptic organization that complement experimental observations. Significance StatementPSD95 is a key scaffolding protein that organizes synaptic components essential for neuronal communication. Its ability to cluster at the membrane is critical for postsynaptic architecture, yet the molecular determinants of this process remain unclear. Using multiscale molecular dynamics simulations we reveal how palmitoylation, a reversible lipid modification, acts as a molecular switch that anchors PSD95 to the membrane and reorients its domains to favor self-association. We further demonstrate that membrane lipid composition modulates these effects through electrostatic interactions. Our work offers a mechanistic model for the initial steps of PSD95 clustering, highlighting how post-translational modifications and membrane environment together regulate synaptic protein organization. These insights bridge molecular structure with synaptic function and are not easily accessible through current experimental methods. Graphical Abstract Image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/679381v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1411deaorg.highwire.dtl.DTLVardef@132cddorg.highwire.dtl.DTLVardef@e69aa6org.highwire.dtl.DTLVardef@1b34753_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Modulating p38MAPK recalibrates sensitivity of drug-resistant pancreatic adenoductal carcinoma cells toward chemotherapy and correlate with improved outcome in PDAC patients: Experimental and metadata evidence

Pancreatic cancer is one of the deadliest cancers and has very limited therapeutic options and a dismal prognosis. Among various signaling pathways which are activated during tumor development, hyperactivation of Mitogen-Activated Protein Kinase (MAPK) is responsible for high grade angiogenesis, polarization of Tumor Associated Macrophages, unfolded protein responses and exhaustion of T cells, which together contributes towards this therapeutic resistance. We therefore believe that MAPK targeting is expected to enhance sensitivity of highly resistant PDAC cells toward various cancer directed interventions. In this context, we investigated the impact of modulating p38MAPK on the sensitivity of pancreatic cancer cells towards gemcitabine. Supporting our hypothesis, our results convincely, demonstrated that indeed, p38 inhibition sensitizes both KRAS positive Panc-1 and MiaPaCa2 pancreatic carcinoma cells towards gemcitabine induced death. Interestingly p38MAPK targeting significantly reduced the cell viability, clonogenic potential of these cells and enhanced the early apoptosis. Our in-silico studies, supporting our in vitro data, potentially correlated that that high expression of p38 MAPK14 in PDAC patients is associated with poor prognosis and disease free survival. Deep miming of in silico data further demonstrated that MAPK14, in association with, hypoxia inducible factor-1 alpha and vascular endothelial growth factor signaling pathways promote angiogenic programming of PDAC which render these tumors refractory for cancer directed interventions. Based on our preliminary data, we believe that p38 MAPK based approach is potential approach for changing the faith of PDAC patients toward chemo and immunotherapy and believed to improve PDAC burden effectively in the host. HighlightsO_LIp38 MAPK inhibition enhances the sensitivity of KRAS+ pancreatic cancer cells for Gemcitabine C_LIO_LIP38MAPK knockdown cells are sensitive for Gemcitabine induced death C_LIO_LIMAPK14 (p38) is associated with angiogenesis and poor prognosis in pancreatic cancer C_LIO_LIMAPK14 Regulates Pro-Tumorigenic Pathways and immune infiltration in Pancreatic Cancer C_LI

cancer biology↗

bioRxiv2025

Non-Invasive Diagnostic Evaluation of Urinary Exosomal Let-7c Cluster Expression in Bladder Cancer Using Machine Learning Approaches

BackgroundBladder cancer (BCa) diagnosis typically relies on invasive cystoscopy, which is effective but costly and uncomfortable. Urinary microRNAs (miRNAs), especially exosomal ones, are promising non-invasive biomarkers due to their stability in biological fluids and disease specificity. However, challenges such as population variability, methodological inconsistencies and normalization issues hinder their clinical translation, emphasizing the need for innovative approaches to enhance diagnostic performance. ObjectiveTo evaluate the diagnostic potential of urinary exosomal let-7c cluster (let-7c-5p, miR-99a-5p and miR-125b-5p) in BCa patients by integrating miRNA expression data with Machine Learning (ML) models. MethodsUrine samples were collected from 66 participants, including 50 BCa patients and 16 healthy controls (HC). Exosomal miRNAs were isolated and quantified using Quantitative Real-Time-Polymerase-Chain-Reaction (qRT-PCR). Statistical analysis and hypothesis tests were conducted to explore the nature and diagnostic relevance of individual biomarkers. A logistic regression classifier was applied to evaluate both the combined and differential diagnostic capabilities of the selected biomarkers. Accuracy, precision, recall and AU-ROC scores were used to assess model performance. Bioinformatics analysis was performed to identify pathways associated with the features prioritized by the ML models, ensuring their relevance to BCa. ResultsThe result revealed significant differentiation between BCa patients and HC, with miR-99a-5p (p=0.013, AU-ROC=0.71) and miR-125b-5p (p=0.047, AU-ROC=0.64) demonstrating reliable diagnostic performance (let-7c-5p showed weaker discrimination, AU-ROC=0.65, p>0.1). The logistic regression ML model achieved an accuracy of 80.0% (AU-ROC=0.86, recall=100%) in distinguishing cancer from HC and 53.3% (AU-ROC=0.63) when applied to miRNA-only grade classification. When clinical variables were integrated with miRNA expression, performance improved to 73.3% accuracy (AU-ROC=0.61) for high-versus low-grade differentiation. Across Ta-T2, miR-99a-5p displayed relatively better separation, whereas let-7c-5p and miR-125b-5p showed weak stage-related differences. The integration of bioinformatics analysis confirmed the biological relevance of these miRNAs in BCa-related pathways, including PI3K-Akt, p53, NF-{kappa}B and RAS/MAPK signaling, with hub genes such as TP53, MYC, EGFR, and CCND1 identified, further validating the diagnostic utility of the selected biomarkers. ConclusionUrinary let-7c cluster miRNAs demonstrate promising diagnostic potential when analyzed with ML models, offering a non-invasive alternative to conventional methods. These findings highlight the promise of ML-based approaches alongside molecular markers for advancing clinical diagnostics in BCa.

molecular biology↗

bioRxiv2025

Development of a Stable Human iPSC Line from Peripheral Blood: A Control Resource for Disease Modeling

IntroductionTraditional disease modeling approaches have primarily utilized animal models and immortalized cell lines to investigate disease mechanisms and develop therapeutic strategies. However, previous research indicates that only about 5% of therapeutic interventions tested in animal models eventually receive regulatory approval for human use, highlighting limitations. The discovery of human-induced pluripotent stem cells (iPSCs) by Yamanakas team in 2007 has revolutionized the field with remarkable possibilities for modeling human diseases, drug testing, and regenerative medicine. Differentiated cells derived from iPSCs in two-dimensional (2D) monolayers offer a relatively straightforward system to study disease pathogenesis and underlying molecular mechanisms. ObjectiveThe present study aimed to generate and characterize an induced pluripotent stem cell (iPSC) line from peripheral blood mono-nuclear cells (PBMCs) of a healthy individual intending to serve as an age and gender-matched control for future disease modeling and regenerative medicine research. Materials and MethodsPBMCs were isolated from a healthy 31-year-old male volunteer. Somatic reprogramming was performed using episomal vectors expressing OCT3/4, SOX2, KLF4, and L-MYC. The resulting colonies were cultured and characterized for pluripotency markers by immunocytochemistry demonstrating the ability to differentiate into three germ layers. Karyotype analysis was performed to check the chromosomal abnormalities. InferencesThe resulting iPSC line exhibited pluripotency markers with the differentiation ability into three germ layers. Karyotyping analysis confirmed a normal chromosomal profile in both the donor and the reprogrammed iPSC line. This iPSC line could be a valuable resource as a healthy control for disease modeling and will contribute to advancing stem cell research with potential for regenerative medicine applications.

molecular biology↗

bioRxiv2025

RNA Methylation dynamics regulates cancer stemness through modulation of cell migration and cell proliferation in the spheroidal model of TNBC

Altered cellular changes in tumors are regulated by a plethora of mechanisms, including post-transcriptional processes such as the reversible m6A RNA methylation which is shown to be involved in multiple steps of RNA processing thus playing a crucial role in gene expression. The individual roles of the writers, erasers and readers is slowly being unravelled and due to their regulatory role at the post transcriptional level, there are reports of both positive and negative modulatory effects on tumorigenesis. In this study, we have studied the role of one of the m6A writer complex proteins, WTAP and the m6A RNA demethylase FTO (fat mass and obesity associated protein) in 2D and 3D culture systems of triple negative breast cancer cells. Genome edited cell lines where WTAP or FTO levels were downregulated show altered cell proliferation through m6A mediated regulation of cell cycle regulators, and altered cell migration properties through modulation of EMT markers. The 3D spheroidal cultures derived from these genome edited lines revealed a role for m6A regulation in CSC marker expression, thus suggesting a potential oncogenic feedback loop between m6A modulators and the major hallmarks of cancer.

cancer biology↗

bioRxiv2025

Formic acid impairs α-synuclein seeding activity in human and mouse brains

-Synuclein (-syn) is an abundant monomeric protein that can aggregate into fibrils and form neuropathological inclusions in the brains of patients with synucleinopathies. New evidence suggests that the mouse-human transmission barrier of -syn is lower than previously reported, emphasizing the need for improved biosafety procedures when working with -syn aggregates. Histopathology of -syn-infected brain represents a significant potential source of occupational exposure, and current methods for tissue fixation do not inactivate the ability of pathologic -syn to seed the conversion of endogenous, monomeric -syn into fibrils. In this study, we tested whether 96% formic acid treatment could reduce the seeding activity of -syn aggregates in paraformaldehyde-fixed brain samples from dementia with Lewy bodies (DLB) patients and -syn pre-formed fibrils (PFF)-injected mouse brains. Using real-time quaking-induced conversion (RT-QuIC), we found that formic acid treatment reduced -syn seeding dose (picograms of -syn seeds per ml of brain homogenate) in DLB and mouse brain by 6 and 8 logarithms, respectively. RT-QuIC reactions seeded with formic acid-treated brain homogenates showed significantly longer lag phase, and decreased total thioflavin T fluorescence compared to untreated samples, indicating that formic acid treatment impairs the ability of pathological -syn to seed monomeric -syn. Importantly, the -syn pathologic features and the immunostaining quality were preserved in formic acid-treated tissues. Our results demonstrate that formic acid treatment is a quick and efficient procedure for reducing -syn seeding activity in fixed brain samples, thereby lowering the risk of accidental exposure in laboratories without compromising the quality of histopathological analysis. SummaryFormic acid treatment drastically reduces -synuclein seeding activity in fixed human and mouse brain samples while preserving histopathological quality.

neuroscience↗

bioRxiv2025

Dietary fatty acids as determinants of cuticular wax profiles in Tribolium castaneum

Cuticular waxes are complex mixtures of hydrocarbons and other lipophilic compounds that form an outer protective layer over the insect cuticle playing a role in ecological interactions as well as physiological processes. While CHC profiles are largely genetically determined, several studies have linked diet to cuticular hydrocarbons and limited research indicates a potential influence of dietary fatty acids. Considering this, the current work investigates the effect of nine cereal flours, i.e., wheat, rice, maize, barley, oat, ragi, sorghum, soybean and gram, each with a distinct fatty acid composition, on the cuticular wax profile of Tribolium castaneum (Coleoptera: Tenebrionidae), a globally significant stored grain insect. Fatty acid compositions of the nine flours and the cuticular waxes from the beetle populations reared on each diet were characterized using gas chromatography mass spectrometry (GC-MS). In all the beetle populations, the most abundant compound was 1-pentadecene, followed by cis-9-tetradecen-1-ol and 1-heptadecene, irrespective of the diet. While no qualitative differences in cuticular wax composition were found, significant quantitative variation in cuticular wax profile was observed across dietary groups. Similarity percentage (SIMPER) analysis revealed a cumulative Bray- Curtis dissimilarity of 47.72 among the flour samples based on their fatty acid profiles, and a dissimilarity of 18.51 among T. castaneum populations reared on these flours based on their cuticular wax composition. Non-metric multidimensional scaling (NMDS) further indicated substantial variation in the cuticular wax profiles of beetle populations raised on different dietary sources. Pearsons correlation analysis between the concentrations of individual cuticular wax components and the fatty acid content of the respective diets demonstrated strong correlations between specific cuticular compounds and dietary fatty acids. Notably, levels of 1-pentadecene in the beetle cuticle were strongly associated with the concentrations of hexadecanoic and octadecanoic acids in the flours. These results support the hypothesis that, alongside endogenous conserved biosynthetic pathways, dietary fatty acid composition contributes to the modulation of insect cuticular chemistry. This dietary influence may have important implications for understanding insect ecological plasticity and diet-mediated changes in surface chemistry.

zoology↗

bioRxiv2025

Fluctuations in first passage times and utility of resetting protocol in biochemical systems with two-state toggling

Interesting theoretical problems of target search or threshold crossing, formally known as first passage, often arise in both diffusive transport problems as well as problems of chemical reaction kinetics. We study three systems following different chemical kinetics, and are special as they toggle between two states: (i) a population dynamics of cells with auto-catalytic birth and intermittent toxic chemical-induced forced death, (ii) a bond cluster model representing membrane adhesion to extracellular matrix under a fluctuating load, and (iii) a model of gene transcription with a regulated promoter switching between active and inactive states. Each of these systems has a target state to attain, which defines a first passage problem - namely, population becoming extinct, complete membrane detachment, or mRNA count crossing a threshold. We study the fluctuations in first passage time and show that it is interestingly non-monotonic in all these cases, with increasing strength of bias towards the target. We also study suitable stochastic resetting protocols to expedite first passage for these systems, and show that there is a re-entrant transition of the efficacy of this protocol in all the three cases, as a function of the bias. The exact analytical condition for these transitions predicted in earlier literature is verified here through simulations.

biophysics↗

bioRxiv2025

Using Fiji as a simplified tool for assessing alveolar chord length and septal thickness in neonatal pulmonary disease research

Bronchopulmonary Dysplasia (BPD) is a neonatal condition primarily affecting babies born prematurely, who have been exposed to invasive ventilation and/or oxygen supplementation. These therapies predispose the immature developing lungs to inflammation and injury to the alveolar epithelium resulting in loss of the alveolar epithelium and thickening of alveolar septa, the 2 important hallmarks of the pathology of BPD. The expansion and enlargement of the alveolar sacs gives the characteristic feature of alveolar simplification in BPD. To measure this alveolar abnormality, we have modified and developed a custom-made Chord Length Fiji plugin which can easily measure the Chord Length and Septal Thickness on Hematoxylin-Eosin-stained histological lung sections, thus generating an instant morphometry readout for quick interpretation. We validated this plugin in multiple animal experimental models and human neonatal lungs with BPD. We were able to differentiate the morphology under conditions of ventilation or hyperoxia exposure, when compared with untreated controls. We thus conclude that our Chord Length and Septal Thickness plugin can be used in a simplified manner following a less meticulous automated operation. To facilitate global use, we have created a DOI so that any user can access it without any restrictions to complete the morphometric measurements. This plugin will be useful for smaller research laboratories with limited budgets and require no access to complex software.

pathology↗

bioRxiv2025

'Crafting Fishy News': Framing and Attitudinal Positioning in English Newspaper Articles on Mahseer from Their Endemic Range

With the capacity to influence readers knowledge, emotions, attitudes and behaviours, newspapers play a pivotal role in conservation. We studied framing strategies and attitude positioning in articles published from January 2000 to April 2024 on mahseer, a group of freshwater fishes (56 species), by English-language newspapers from 17 nations that fall within their distribution range. However, we had to restrict our analysis to 6 nations (Bangladesh, Bhutan, Nepal, India, Pakistan and Malaysia) and 6 mahseer species (Tor khudree, T. putitora, T. remadevii, T. tor, N. hexagonolepis, and T. tambroides) due to the limited availability of substantial number of articles from other focal nations. A major share (79%) of the articles came from India, and T. putitora was the species that received the maximum attention from the newspapers (39%). Our result revealed a clear demarcation between the South-East Asian nation of Malaysia and the countries from South Asia, as well as between articles on mahseers native to these two different geographical regions, in terms of headline and text framing, choice of messengers and images, and attitude positioning in the news items. Dailies from South Asia largely employed conservation, environmental challenges and re-stocking efforts frames and promoted nature-centric, ecological and religio-cultural attitudes. By contrast, newspapers from Malaysia and the articles covering mahseer from this nation, T. tambroides reflected utility-centric and recreational framing and attitudes emphasising economic aspects. In general, episodic framing was more common than thematic, and instances of incorporating visual representations (with India as an exception) and positioning information on mahseer in the persuasive sections (exception - Nepal) were limited across focal nations and species. Our study also revealed that GenAI based Large Language Model (LLM ChatGPT 4) and Natural Language Processing (NLP) based tools (Hugging Face transformers) can be utilised as effective complementary or collaborative research tools alongside traditional manual qualitative data analysis to comprehend the framing and attitude positioning in the conservation news. Our results may help contextualise the communication strategies for conserving mahseers in South and South-East Asia, and also elucidate dimensions that need to be made salient for strengthening the connection between media and society for this purpose.

ecology↗

bioRxiv2025

Allosteric Modulation of MIF-2 Structure, Catalysis, and Biological Signaling via Cysteine Residues and a Small Molecule, Ebselen

The macrophage migration inhibitory factor (MIF) family of cytokines comprised of the MIF and D-dopachrome tautomerase (or MIF-2) paralogs share identical tertiary and quaternary structures that contribute to their overlapping enzymatic and signaling activities. Recent investigations of MIF and MIF-2 have shown them to possess N-to-C-terminal allosteric crosstalk, but despite the similarity of this "allosteric pathway," its regulation of MIF and MIF-2 is not identical. Thus, structure alone does not preserve the precise allosteric mechanism and additional residues that modulate MIF and MIF-2 allosteric function must be characterized. Cysteines have been identified as allosteric switches for the same biochemical functions of MIF and small molecules targeting its N-terminal enzymatic site have affected the structure of three proximal cysteines. Ebselen is a compound that forms covalent selenylsulfide bonds with MIF cysteines and is hypothesized to destabilize and dissociate the MIF trimer into monomers. Ebselen-bound MIF also displays little-to-no catalysis or biological signaling. However, it is unclear whether Ebselen similarly affects the MIF-2 paralog, despite MIF-2 containing two related cysteines (MIF contains three). We used mutagenesis, nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations, in vitro and in vivo biochemistry to investigate the mechanism of Ebselen as an allosteric modulator of MIF-2 via its cysteines. Our findings suggest that Ebselen partially disrupts the MIF-2 homotrimer, though the overall population of such a structure is <35%, even on the timescale of many hours. Ebselen does attenuate the biological functions of MIF-2 and solution structural biology captures the conformational transitions preceding the destabilized MIF-2 trimer. Significance StatementThe nearly identical MIF and MIF-2 structures have been recently shown to contain an N-to-C-terminal crosstalk between non-overlapping functional sites in vitro and in vivo. Small molecule inhibitors designed as therapeutics for the MIF superfamily have primarily targeted the N-terminal active site, while very few allosteric molecules have been reported. Ebselen, however, destabilizes MIF by covalently modifying its distal Cys80 residue and disrupting its obligate trimeric assembly. This unique mechanism has never been evaluated in the MIF-2 paralog, and this study reports the structural, dynamic, and functional impact of Ebselen on MIF-2. We define the essential structural hallmarks preceding trimer dissociation and reveal that Ebselen inhibits MIF-2 function before trimer disruption, leading to destabilized monomer-monomer interfaces that slowly degrade the quaternary assembly.

biophysics↗

bioRxiv2025

Dietary Protein Sources Shape Gut Microbiome: Insights from Meta-analysis and Machine Learning

BackgroundDietary proteins shape gut microbial ecology, yet the taxonomic and functional consequences of plant- versus animal-based proteins remain poorly defined. Although digestibility and fermentation profiles differ by protein type, a systematic evaluation of how these differences influence microbial diversity, community structure, and metabolic capacity is lacking. This meta-analysis integrates taxonomic, machine learning, and functional inference approaches to identify microbial and metabolic signatures associated with dietary protein source in murine models. MethodsFollowing PRISMA guidelines, we analyzed 16S rRNA sequencing data from 10 murine studies (n = 187) comparing plant- and animal-protein diets. Alpha diversity was assessed using Shannon, Inverse Simpson, and Chao1 indices, and beta diversity with Aitchison distances. Differentially abundant taxa were identified using LEfSe and class-weighted Random Forest models. Functional potential was inferred with PICRUSt2, and taxon-pathway relationships were explored using correlation and network analyses. ResultsPlant-protein diets increased gut microbial diversity across all alpha diversity metrics and were associated with higher representation of saccharolytic and nitrogen-recycling genera such as Bacteroides, Muribaculaceae, and Allobaculum. Animal-protein diets favored proteolytic taxa, including Clostridium sensu stricto 1 and Colidextribacter. Microbial community structure differed significantly between diets (ANOSIM R = 0.663, p < 0.001). Random Forest models achieved >88% accuracy (AUC = 0.995) in predicting dietary groups, and LEfSe identified consistent discriminating taxa. Functional profiling showed that plant-based diets enriched pathways linked to short-chain fatty acid and aromatic amino acid metabolism, whereas animal-based diets favored sulfur- and branched-chain amino acid-associated pathways. Network analysis identified Muribaculaceae as a plant-associated hub and Lactobacillus as an animal-associated hub. ConclusionDietary protein source significantly influences gut microbiota composition and functional potential in mice. Plant- and animal-based proteins generate distinct metabolic signatures with implications for nitrogen cycling, sulfur metabolism, and microbial ecology. Future controlled dietary studies that harmonize protein source with other macronutrient variables are needed to isolate protein-specific effects. Statement of SignificanceThis study presents the first standardized meta-analysis of murine protein-intervention microbiome datasets, integrating taxonomic, machine learning, and predicted functional profiling to identify robust microbial and metabolic signatures that differentiate plant- from animal-based protein diets. By harmonizing evidence across diverse studies, it clarifies foundational ecological responses to protein source and provides mechanistic hypotheses that can inform future controlled nutrition and microbiome research

microbiology↗

bioRxiv2025

VEGF-B/NRP1 Signaling Modulates Mitochondrial Homeostasis and Cardiac Function After Myocardial Infarction

BackgroundMyocardial infarction (MI) remains a leading cause of mortality worldwide. Recent studies suggest a cardioprotective role for vascular endothelial growth factor-B (VEGF-B) in MI. However, the molecular mechanisms of VEGF-B-mediated signaling via its co-receptor Neuropilin-1 (NRP1) in MI are poorly understood. In this study, we investigated the intricate signaling mechanisms involving VEGF-B and NRP1 in cardiomyocytes (CMs) using ischemic injury as a model of MI. And secondly, we further validated the protective role of VEFG-B in ischemic heart disease, shedding light on their roles not only in cardiac function but also in its therapeutic potential. MethodsIn this study, we utilized both in vitro and in vivo approaches to elucidate the role of VEGF-B and NRP1 signaling in MI and how it manifests a protective role in mitochondrial functions and cardiac regeneration following ischemic injury. We used two different cardiomyocyte cell lines, H9c2 (rat ventricular cardiomyocytes) and HL-1 (mouse ventricular cardiomyocytes), and induced hypoxia conditions, using either 1% oxygen or 200{micro}M cobalt chloride (CoCl2) to mimic the myocardial infarction-induced ischemic injury in the heart. In addition, we developed a novel heat shock inducible zebrafish model of a cardiomyocyte-specific VEGF-B overexpression system to further examine the protective role of VEGF-B in vivo. ResultsOur findings indicate that both VEGF-B and NRP1 are predominantly expressed in heart tissue compared to other tissues, and their expression is altered in response to hypoxia/ischemic injury. Our results demonstrate that VEGF-B treatment prior to hypoxia enhances cardiomyocyte survival, while NRP1 knockdown abolishes this protective effect, highlighting a prominent role of NRP1 signaling in VEGF-B-mediated cardio protection. Furthermore, we found that VEGF-B promotes cardiomyocyte survival by improving mitochondrial function, as evidenced by reduced oxidative stress and ROS accumulation, decreased oxidative stress, preserved mitochondrial membrane potential, and increased ATP levels. Lastly, using our VEGF-B transgenic zebrafish model, we demonstrated that VEGF-B overexpression in zebrafish cardiomyocytes protects the heart from ischemic injury and enhances cardiac regeneration in an NRP1-dependent manner. ConclusionOur study has uncovered an important role of VEGF-B-NRP1 signaling axis in VEGF-B mediated cell survival and in beneficial mitochondrial functions in the CMs. Importantly, we also demonstrated that VEGF-B is protective against ischemic injury in vivo using a novel zebrafish model Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSO_LIMyocardial infarction (MI) results in mitochondrial dysfunction, cardiomyocyte death, and adverse ventricular remodeling. C_LIO_LIVascular Endothelial Growth Factor B (VEGF-B) is traditionally associated with cardiac metabolism, survival, vascular biology, particularly in angiogenesis and lipid metabolism. C_LIO_LIThe neurophilin-1 (NRP1) receptor, a co-receptor for VEGF-B, is expressed in cardiomyocytes and implicated in mitochondrial signaling pathways. C_LIO_LIEmerging evidence suggests that VEGF-B may influence mitochondrial integrity and function under stress conditions. C_LI What New Information Does This Article Contribute?O_LIVEGF-B exerts a protective effect on cardiomyocyte mitocondria following ischemic injury by preserving mitochondrial function and reducing oxidative stress. C_LIO_LINRP1 receptor as a key mediator of VEGF-B modulates mitochondrial homeostasis in cardiomyocytes. C_LIO_LIVEGF-B signaling can attenuate apoptosis and enhance mitochondrial bioenergetics post-MI, suggesting a novel cardioprotective mechanism. C_LIO_LIClinical Implication: These findings suggest that therapeutic strategies aimed at enhancing VEGF-B/NRP1 signaling may improve mitochondrial function and cardiac recovery after MI, offering a novel avenue for limiting heart failure progression in ischemic heart disease. C_LI

molecular biology↗

bioRxiv2025

SPINK1-COL18A1 Crosstalk Shapes Epigenome and Drives Cancer Stemness in Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a devastating cancer with an increasing incidence and extremely dismal prognosis. Discovery and mechanistic understanding of the genetic and epigenetic drivers of PDAC is therefore of critical importance. Here, we uncover serine protease inhibitor Kazal type 1 (SPINK1) as a putative determinant of clinical progression and demonstrate that it can have a non-canonical function as a regulator of epigenomic states of PDAC cells and associated extensive changes in gene expression. We show that SPINK1 expression, which varies in PDAC, is associated with key aggressive phenotypic cancer states and is correlated with the expression of stemness markers both in vitro and in patient samples. Mechanistically, our results strongly suggest that SPINK1 acts through a new signaling axis, by interacting with COL18A1 in the Golgi apparatus, promoting endostatin release and eventually inducing extensive histone H3 modifications. These results reveal a new function of SPINK1 in PDAC and suggest a potential therapeutic route to combat PDAC aggressiveness by targeting the SPINK1-COL18A1-endostatin signaling.

cancer biology↗

bioRxiv2025

Iron-deplete diet enhances Caenorhabditis elegans lifespan via oxidative stress response pathways

Gut microbes play a crucial role in modulating host lifespan. However, the microbial factors that influence host longevity and their mechanisms of action remain poorly understood. Using the expression of Caenorhabditis elegans FAT-7, a stearoyl-CoA 9-desaturase, as a proxy for lifespan modulation, we conduct a genome-wide bacterial mutant screen and identify 26 Escherichia coli mutants that enhance host lifespan. Transcriptomic and biochemical analyses reveal that these mutant diets induce oxidative stress and activate the mitochondrial unfolded protein response (UPRmt). Antioxidant supplementation abolishes lifespan extension, confirming that oxidative stress drives these effects. The extension of lifespan requires the oxidative stress response regulators SKN-1, SEK-1, and HLH-30. Mechanistically, these effects are linked to reduced iron availability, as iron supplementation restores FAT-7 expression, suppresses UPRmt activation, and abolishes lifespan extension. Iron chelation mimics the pro-longevity effects of the mutant diets, highlighting dietary iron as a key modulator of aging. Our findings reveal a bacterial-host metabolic axis that links oxidative stress, iron homeostasis, and longevity in C. elegans.

physiology↗

bioRxiv2024

Dosage compensation of transposable elements in mammals

In mammals, X-linked dosage compensation involves two processes: X-chromosome inactivation (XCI) to balance X chromosome dosage between males and females, and hyperactivation of the remaining X chromosome (Xa-hyperactivation) to achieve X-autosome balance in both sexes. Studies of both processes have largely focused on coding genes and have not accounted for transposable elements (TEs) which comprise 50% of the X-chromosome, despite TEs being suspected to have numerous epigenetic functions. This oversight is due in part to the technical challenge of capturing repeat RNAs, bioinformatically aligning them, and determining allelic origin. To overcome these challenges, here we develop a new bioinformatic pipeline tailored to repetitive elements with capability for allelic discrimination. We then apply the pipeline to our recent So-Smart-Seq analysis of single embryos to comprehensively interrogate whether X-linked TEs are subject to either XCI or Xa-hyperactivation. With regards to XCI, we observe significant differences in TE silencing in parentally driven "imprinted" XCI versus zygotically driven "random" XCI. Chromosomal positioning and genetic background impact TE silencing. We also find that SINEs may influence 3D organization during XCI. In contrast, TEs do not undergo Xa-hyperactivation. Thus, while coding genes are subject to both forms of dosage compensation, TEs participate only in Xi silencing. Evolutionary and functional implications are discussed.

genetics↗