Biology subjects

Yadav, R.

Publications and source records attributed to Yadav, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Thioesterase modulates antibacterial Type VI secretion system via alteration in oxidative stress responses in Burkholderia

Bacteria utilize specialized protein secretion systems, particularly the type VI secretion system (T6SS), to dominate interbacterial competitions and kill the prey bacteria in a contact-dependent manner. Here, we report that disruption of the thioesterase gene encoded in the gramibactin (a bacterial siderophore) biosynthetic gene cluster activates the T6SS in the Burkholderia gladioli strain NGJ1, even in the absence of prey. The thioesterase mutant exhibits enhanced antibacterial activity, and ectopic expression of the gene complements the phenotype. Notably, thio mutant as well as thioesterase-complement strains show enhanced sensitivity to oxidative stress. The qRT-PCR analysis showed that the thio mutant had upregulated expression of RpoN1, a sigma factor, which positively regulates T6SS functions. We demonstrate that rpoN1 mutant is hypersensitive to oxidative stress and defective in T6SS activation, whereas overexpression of RpoN1 enhances oxidative stress tolerance in NGJ1 and activates T6SS. We propose that, during interbacterial conflicts encountered during plant colonization, NGJ1 faces an oxidative-stress-enriched environment that modulates thioesterase expression, induces RpoN1, and activates T6SS. Overall, our study exemplifies the broader physiological role of Thioesterase in maintaining intracellular ROS homeostasis in bacteria and stimulating antibacterial activity.

microbiology↗

bioRxiv2026

Optical control of membrane mechanics via global and red-light-catalyzed, leaflet-selective photolipid switching

Azobenzene photolipids are versatile actuators of membrane mechanics and protein function, yet long-wavelength control and leaflet-selective perturbations remain difficult to impose. Here, we address both limitations. First, we show that red-light excitation of a lipidated Nile Blue derivative (NB-lipid) catalyzes rapid and reversible cis[->]trans photoisomerization of co-localized azobenzene photolipids without requiring covalent conjugation. Second, we demonstrate that photocatalysis is predominantly intraleaflet, enabling leaflet-selective actuation by incorporating the membrane-targeted chromophore into only one bilayer leaflet. This enables on-demand and rapid writing of transbilayer mechanical asymmetry, which we track via lock-in capacitance signatures. Critically, symmetric and asymmetric leaflet mechanical perturbations can be evoked within the same membrane by illuminating with blue or red light, respectively. Photocatalysis of electron-rich azobenzenes is anticipated to proceed via the singlet excited state of NB-lipid and thus avoids triplet-state phototoxicity. We underscore the biocompatibility of catalysis by demonstrating the effect of leaflet-specific catalyzed perturbations on the ROS-sensitive mechanosensitive peptide ion channel gramicidin A. Our results establish a novel tool for dissecting the role of dynamic leaflet-specific mechanical changes in membrane remodeling and protein function.

biophysics↗

bioRxiv2026

Tissue-resident memory B cells augment local anti-cancer immunity via IgA

Tissue-resident memory B cells (BRM) provide powerful localized protection against microbial infection in barrier tissues. It is unknown if analogous BRM populations survey solid tumors and contribute to anti-cancer immunity. We profiled B cells from patients with colorectal cancer and cutaneous basal cell carcinoma and identified a CD69+ memory B cell population consistent with a tissue-resident phenotype. Integrative analysis of transcriptomic datasets identified an optimized signature enriched across cancer types. Tumor infiltrating BRM-like cells preferentially exhibited autoreactivity and their signature correlated with patient outcomes and response to immunotherapy. Skin and lung targeted vaccination established localized BRM that provided IgA dependent organ specific protection upon tumor challenge in murine models. These findings establish BRM as an active component of anti-cancer immunity via preferential reactivity to tumor associated self-antigens.

immunology↗

bioRxiv2026

Spatiotemporal Decoding of Explore-Exploit Decisions in the Human Brain

Adaptive behavior requires flexibly shifting between exploiting familiar rewards and exploring novel opportunities. These explore-exploit decisions are implemented via a distributed brain network--anchored in frontopolar cortex (FPC) and ventromedial prefrontal cortex (vmPFC)--that computes the total value of a given choice by weighting the immediate value of familiar options against the latent future value of exploration. Capturing the precise temporal dynamics of these neural computations across spatially distributed cortical networks is critical to resolving how the brain manages this tradeoff. Here, we combined magnetoencephalography (MEG) with partially observable Markov decision process (POMDP) modeling during a reinforcement learning task. By decoding POMDP-derived choice policies in MEG source space, we mapped the precise spatiotemporal emergence of explore-exploit decisions across the cortex. We demonstrate that explore-exploit policy implementation unfolds via a hierarchical functional dissociation across the rostral prefrontal cortex. During decision formation, the lateral FPC initiates the strategic shift toward exploration hundreds of milliseconds before choice execution. Conversely, vmPFC and orbitofrontal cortex (OFC) do not exhibit early significant divergence from the baseline exploitative trace on exploration trials, displaying only a delayed, transient peak prior to choice execution. Following feedback, the vmPFC and OFC transition to a sustained representation of the choices empirical value to update reward expectancies and guide future actions. Mapping reinforcement learning variables onto millisecond-resolved neural data reveals how the human brain resolves the explore-exploit dilemma: through early strategic initiation of exploration in the FPC, a delayed exploratory shift in vmPFC and OFC, and sustained outcome evaluation to optimize future actions.

neuroscience↗

bioRxiv2026

Mapping the vRNA Interaction with HIV-1 Integrase

A series of critical interactions within the viral core between the viral RNA (vRNA) and HIV-1 Integrase (IN) has previously been reported. In these studies, contact points between vRNA and IN were identified using RNA-seq and MS-based protein foot-printing approaches. Several IN amino acids located in its C-terminal domain (CTD) were found to be essential for vRNA binding and their alanine substitution severely impacted the correct morphogenesis of the matured viral core. Here, we have extended these studies by performing a comprehensive mapping of the IN-vRNA interaction by deploying RNA crosslinking and NMR methodologies. Together, these approaches were able to identify additional contacts points between the vRNA and IN. Our results reveal several new basic amino acids located in the IN CTD critical for the vRNA-IN interaction, viral replication and correct morphology of the matured viral core.

biochemistry↗

bioRxiv2026

SMARTIE: A Machine-Learning approach for investigating RBP-RNA interactions identified by Editing

RNA-binding proteins (RBPs) play important roles in gene regulation. RNA editing-based approaches, such as TRIBE and STAMP, have gained wider use for identifying RNA targets of RBPs. These methods offer advantages over crosslinking-based approaches in terms of experimental simplicity and in vivo applicability. However, data analysis methods for these approaches remain underdeveloped, limiting sensitivity, and unbiased target prioritization. To address these limitations, we introduce SMARTIE (Systematic Machine-learning Approach for RBP Targets Identified by Editing), a machine-learning-based framework. SMARTIE robustly identifies and ranks RBP target RNAs from editing data by integrating statistical tests with replicate-aware and confidence-weighted features. Reanalysis of multiple published TRIBE datasets demonstrates the effectiveness of SMARTIE. It recovers targets of RBPs like Ataxin-2, TDP-43, Hrp48, Thor, GPATCH8, dFMRP and NonA. Notably, a model trained on TRIBE data generalizes to STAMP datasets, suggesting that SMARTIE learns universal signatures of editing-based RBP targeting there by enabling more accurate inference for RBP-RNA interactions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/726004v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@8b77e5org.highwire.dtl.DTLVardef@6c9416org.highwire.dtl.DTLVardef@6e33a5org.highwire.dtl.DTLVardef@100b7b5_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Environmental impacts of Broiler chicken production in the North Eastern Himalayan region of India: Evaluation using the Life Cycle Assessment approach

The study presents the first comprehensive environmental assessment of broiler chicken production in India, from a cradle-to-farm-gate perspective, using the Life Cycle Assessment (LCA) approach. The objective of the study was to identify environmental hotspots in the broiler production system. All inflows and outflows of the broiler production system were mapped to construct the life-cycle inventory. This study uses a system boundary that extends from the cradle to the farm gate. Inventory data for the broiler chicken farms were collected from six different farms, which is typical of the Indian broiler production system, and background data were sourced from the Ecoinvent 3.0 database. For the LCA study, SimaPro (v 9.3.0.3) was used with the ReCiPe 2016 Midpoint impact assessment methodology. For this study, the functional unit of the "1-kg live weight chicken produced was taken into consideration". The environmental impact categories assessed were mainly Global Warming Potential in hundred years (GWP), stratospheric ozone depletion, freshwater eutrophication, terrestrial ecotoxicity, land use, etc. Results showed that broiler chicken feed was primarily responsible for environmental impacts, followed by transportation and electricity. Broiler chicken production had a total GWP of 3.77 kg CO2-eq per kilogram of live weight. Specifically, the energy component of feed, viz., maize production, was the main source of environmental impact. The process of transporting feed and chicks to the broiler farm also had a significant environmental impact. The broiler production system was found to have moderate environmental impacts compared to other published LCA studies of chicken production. Based on the findings of the present study, we proposed actionable items to further improve the environmental efficiency of broiler chicken production in India.

ecology↗

bioRxiv2026

Gut microbiota-derived indole-3 acetic acid mitigates key hallmarks of metabolic dysfunction-associated steatotic liver disease (MASLD) in an NLRP3-dependent manner in in vitro and diet-induced mouse models

BackgroundMetabolic-dysfunction associated steatotic liver disease(MASLD) is a global epidemic affecting >30 % global population with no approved therapies till date. Recent reports suggest that activation of NLRP3 inflammasome may be involved in the pathogenesis of MASLD. We, therefore, aimed to identify small molecule inhibitor(s) of NLRP3 inflammasome as a potential therapeutic strategy to manage MASLD and validate their efficacy using in vitro and in vivo models of MASLD. MethodologyWe screened an in-house library of natural products using an in vitro phenotypic assay and identified a gut microbiota derived metabolite of dietary Tryptophan; indole-3 acetic acid (I3A) for its ability to inhibit the levels of IL-1{beta} and IL-18, which are elevated as a result of activation of NLRP3 inflammasome in differentiated THP1 cells. Subsequently, we carried out several in vitro and in vivo studies to confirm the mechanism of action of I3A and its ability to mitigate the key hallmarks of MASLD ResultsOur in vitro data suggest that I3A is an inhibitor of NLRP3 inflammasome. I3A was also found to improve the blood glucose level, plasma lipid profile, hepatic fat, and liver function in high-fat-high-fructose diet induced model of MASLD using C57BL/6 mice. ConclusionOur results show that I3A, which has been previously reported to be a gut microbiota-derived metabolite of dietary tryptophan, mitigates the key hallmarks of MASLD in an NLRP3 dependent manner. A dedicated structure-activity-relationship (SAR) study around the I3A chemotype may be carried out in future to identify novel NLRP3 inhibitors with desirable pharmacological profile.

pharmacology and toxicology↗

bioRxiv2026

LRRK2 I1371V Impairs Astrocytic Glucose Metabolism and Triggers Multi-Organellar Dysfunction in PD

While LRRK2 mutations modulate systemic glucose homeostasis and metabolic dysfunction precedes Parkinsons disease (PD) motor-symptoms, the impact of pathogenic LRRK2-mutations on astrocytic glucose-uptake and organellar function remains unexplored. Here, we demonstrate that LRRK2-I1371V mutation causes profound metabolic and organellar dysfunction in LRRK2-I1371V PD-iPSC-derived astrocytes and U87 cells overexpressing I1371V variant. LRRK2-I1371V astrocytes exhibit significantly reduced GLUT1 expression and plasma membrane localization, resulting in impaired glucose-uptake and decreased lactate-production. This metabolic insufficiency correlates with cascading mitochondrial dysfunction, characterized by membrane depolarization, elevated reactive-oxygen-species, enhanced ubiquitination and reduced proteasomal-activity. Reduced LAMP1/LAMP2 expression, impaired lysosomal-acidification, and selective cathepsin D deficiency were observed. Accumulation of undegraded cargo was confirmed by transmission-electron-microscopy upon -synuclein exposure. ER stress was evident through upregulated GADD34/CHOP, increased phospho-PERK, and reduced nascent protein synthesis. Our results reveal that LRRK2-I1371V induces glucose-uptake deficits, causing energy depletion and multi-organellar dysfunction, identifying astrocytic metabolic restoration as a promising therapeutic target for I1371V-associated PD.

neuroscience↗

bioRxiv2026

Investigating Quinclorac Binding to Human Serum Albumin using Spectroscopy and Molecular Docking

Human serum albumin (HSA) is the most abundant plasma protein and serves as a major transporter and reservoir for a wide range of endogenous ligands, including fatty acids, heme, bilirubin, prostaglandins, and metal ions, as well as numerous exogenous compounds, such as pharmaceuticals. HSA is a 66 kDa monomeric, multidomain protein containing two principal ligand-binding sites, Sudlow sites I and II. Sudlow site I contains Trp214, the sole tryptophan residue in HSA, whose intrinsic fluorescence provides a sensitive probe for studying ligand-protein interactions. In this study, the interaction between HSA and the persistent organochlorine herbicide quinclorac (QNC) was investigated using steady-state fluorescence spectroscopy and molecular docking. The binding of QNC to HSA is characterized by concentration-dependent quenching of HSAs intrinsic tryptophan fluorescence. Quantitative analysis revealed a high affinity of QNC for HSA, with [~] 1 M dissociation constant (Kd). Temperature-dependent fluorescence quenching experiments indicate a static quenching mechanism. Moreover, a competitive displacement assay using site-specific markers identified Sudlow site I as the primary binding site for QNC in HSA. Induced-fit docking further demonstrated that QNC is accommodated and stabilized by polar interactions, {pi}-stacking, and/or hydrophobic interactions within the Sudlow I binding pocket. Together, these results provide a biochemical and molecular understanding of how QNC, a persistent pesticide, binds to HSA.

biochemistry↗

bioRxiv2025

Combined antagonism of Oncostatin M (OSM) and Interleukin 6 (IL-6) provides both anti-fibrotic and anti-inflammatory benefit in pulmonary fibrosis

Interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF) and systemic sclerosis-associated ILD (SSc-ILD), are irreversible fibrosing diseases with a mean survival time of less than 5 years for IPF. Poorly understood etiology and complex pathogenesis of these diseases have hampered the identification and development of effective therapeutics. Existing treatments can slow progressive fibrosis and lung function decline but do not stop it entirely, resulting in a minimal impact on patient survival. Thus, novel therapeutic interventions are needed. Tocilizumab, an anti-IL-6 receptor antibody, was recently approved by FDA for the treatment of SSc-ILD based on evidence demonstrating a reduction in the rate of lung function decline. In this study, we have characterized an IL-6-driven feed-forward myeloid axis contributing to lung inflammation providing a mechanistic hypothesis for tocilizumab. Concomitantly we have identified an oncostatin M (OSM) orchestrated lung injury response contributing to epithelial and endothelial cell disruption, myofibroblast activation and fibrosis. Despite dysregulated expression of IL11 in IPF, SSc-ILD, and murine models of fibrosis, we found no evidence for a pro-fibrotic role for IL-11 in vitro or in vivo. Instead, in pre-clinical models of IPF we demonstrate that antagonism of OSM alone, or to a greater degree in combination with IL-6, reduced lung fibrosis and inflammation. Translating these observations, we validated gp130:OSMR, rather than gp130:LIFR, as the dominant human receptor complex used by OSM, identifying OSMR as a potential therapeutic target to stall fibrosis.

immunology↗

bioRxiv2025

Targeting Troponin I Phosphorylation for Precision Treatment of Diastolic Dysfunction

BackgroundDefective cardiac relaxation (diastolic dysfunction) is prevalent in heart failure, particularly in the context of diabetes, obesity, hypertension, and ageing, and is associated with increased mortality. Yet there is no available treatment that directly targets this abnormal relaxation. Phosphorylation of troponin I by cAMP-dependent protein kinase A (PKA) promotes relaxation, but global PKA activation has widespread, undesirable effects. Here we investigated whether selectively enhancing troponin I phosphorylation could improve relaxation without engaging the broader PKA signalling network. MethodsTo resolve cAMP signalling at subcellular scales, we combined real-time cAMP measurements with FRET-based genetically encoded reporters targeted to defined nanodomains, alongside biochemical and genetic approaches. Protein-protein interaction surfaces were mapped using peptide-array technology, which guided the design of a disruptor peptide to displace specific interactions. The peptides effects on cardiomyocyte function were assessed in vitro using rodent and human cardiomyocytes with biochemical assays, real-time imaging, and work-loop analysis. In vivo effects were evaluated through echocardiography and haemodynamic measurements. ResultsWe identified a previously unrecognized regulatory mechanism in which the cAMP-hydrolyzing enzyme PDE4D9 interacts with troponin I and restricts local cAMP levels within a nanometre-scale domain, thereby selectively controlling troponin I phosphorylation. We found that PDE4D9-troponin I association is markedly increased in cardiac disease in both rodents and humans. A peptide that displaces PDE4D9 from troponin I in a mouse model of heart failure selectively enhances troponin I phosphorylation, accelerates cardiomyocyte relaxation, and prevents diastolic dysfunction, without compromising systolic contractility. ConclusionsThese findings reveal a highly specific regulatory nanodomain governing troponin I phosphorylation and points to a first-in-class, mechanism-based therapeutic strategy with the potential to address a major unmet contributor to heart failure. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIWe identify a previously unrecognized, nanometre-scale regulatory mechanism in which PDE4D9 binds troponin I to locally suppress cAMP, limit troponin I phosphorylation and attenuate relaxation. C_LIO_LIWe demonstrate that this mechanism becomes maladaptive in disease: PDE4D9-troponin I interaction is markedly upregulated in failing hearts in both rodents and humans, which can mechanistically explain the impaired cardiac relaxation. C_LIO_LIWe show that this interaction is druggable: a rationally designed peptide can selectively displace PDE4D9, restore localized cAMP-PKA signalling, and normalize myocardial relaxation without global cAMP perturbation. C_LIO_LIDisplacement of PDE4D9 from TPNI improves relaxation with no impact on the calcium transient amplitude and without adversely affecting systolic output and cardiac reserve. C_LI What Are the Clinical Implications?O_LIDiastolic dysfunction, a major cause of heart failure with no targeted treatments, may be amenable to therapies that modulate cAMP signalling with subcellular precision rather than global pathway modulation. C_LIO_LISelective disruption of PDE4D9-troponin I binding offers a mechanism-based approach with potential to restore diastolic function while minimizing off-target effects typical of GPCR-directed therapies. C_LIO_LIBy enhancing relaxation while preserving systolic function and cardiac reserve, this approach may overcome limitations of myofilament-targeted therapies currently under evaluation for diastolic dysfunction that exhibit negative inotropic effects. C_LIO_LIMore broadly, this work establishes a platform for targeting localized signalling domains, a concept that may extend beyond cardiovascular disease to other pathological conditions in which dysregulated cAMP contributes to dysfunction. C_LI

cell biology↗

bioRxiv2025

Engineered RVG29-Conjugated Chitosan for Enhanced Brain Delivery of Kisspeptin Agonists and Antagonists in Reproductive Health.

Efficient delivery of intact therapeutic peptides across the blood-brain barrier (BBB) remains a central obstacle in translating neuroendocrine modulators to clinical practice. Kisspeptin receptor (KISS1R) agonists and antagonists precisely regulate gonadotropin-releasing hormone (GnRH) pulsatility, thereby controlling luteinizing hormone (LH) release, steroidogenesis, and fertility. While the KISS1R agonist KP10 accelerates GnRH-LH pulses to promote ovulation, the antagonist KP234 suppresses pulse generation, inducing reversible infertility. However, their poor BBB permeability limits clinical application. Here, we engineered a non-invasive brain delivery platform by covalently coupling the rabies virus glycoprotein-derived peptide RVG29 to oxidized chitosan nanoparticles via Schiff base chemistry. Sodium periodate oxidation introduced aldehyde groups, FT-IR confirmed aldehyde formation, and UV-Vis spectroscopy validated RVG29 conjugation through characteristic absorbance shifts. The resulting RVG29 - chitosan carriers demonstrated biocompatibility, enhanced neuronal uptake [~]2.1-fold in vitro, and achieved [~]2.5-fold higher brain accumulation in vivo compared to unconjugated controls. Systemic delivery of RVG29-chitosan-KP10 restored and amplified LH pulsatility in ovariectomized mice, accelerated estrous cycling, increased preovulatory follicle numbers, and enhanced litter size. In contrast, RVG29-chitosan-KP234 abolished LH pulses, maintained animals in persistent diestrus, depleted corpora lutea, and produced complete yet reversible infertility. Longitudinal dosing demonstrated stable neuroendocrine modulation without systemic toxicity, and ovarian histology confirmed ovulatory arrest in antagonist-treated animals. By enabling programmable, bidirectional control of a central hypothalamic circuit through systemic delivery of unmodified peptides, this platform addresses a long-standing barrier in neuroendocrine therapeutics. Beyond fertility regulation, this approach can be adapted to other hypothalamic-driven processes, including metabolic, stress-axis, and circadian control.

bioengineering↗

bioRxiv2025

CRISPR-engineered deletion of POGZ alters transcription factor binding at promoters of genes involved in synaptic signaling

One of the seminal discoveries from genetic studies of autism spectrum disorder and related neurodevelopmental disorders (NDD) has been that loss-of-function (LoF) mutations in many genes that impact chromatin and transcriptional regulation confer substantial liability to NDD. Haploinsufficiency of the epigenetic regulator POGZ represents one of the strongest such associations; however, little is known about the direct or indirect regulatory targets of POGZ, or the mechanisms by which loss of this chromatin modifier alters early neuronal development and synaptic functions. Here, we created an allelic series of CRISPR-engineered human induced pluripotent stem cell (hiPSC) clones harboring mono- and biallelic POGZ deletions. In hiPSC-derived neural stem cells (NSC) and Neurogenin 2-induced neurons (iN), POGZ LoF altered the expression of genes associated with critical cellular processes and neuronal functions, including synaptic and intracellular signaling and extracellular matrix organization. Our multiomics profiling also showed altered footprinting of critical transcription factors (e.g., activator protein 1 complexes) that were enriched at promoters of differentially expressed genes associated with synaptic function. To further interrogate the shared molecular changes in neuronal development associated with NDD and POGZ regulation, we compared our results to deletions of the transcription factor MEF2C and the sodium channel gene SCN2A that we generated in these same isogenic iN. These analyses revealed strong enrichment of extracellular matrix and intracellular signaling disruption associated with POGZ and MEF2C deletion, whereas POGZ and SCN2A haploinsufficiency exhibited shared transcriptional effects on gene modules enriched for NDD-associated genes with opposing regulatory effects. Notably, we also observed alterations to synaptic firing rate and neurite extension with biallelic deletions, but not heterozygous lines, suggesting subtle effects in neuronal development associated with haploinsufficiency. Overall, these shared molecular consequences suggest key points of convergence that connect epigenetic regulation to neuronal function in the etiology of neurodevelopmental pathologies.

genomics↗

bioRxiv2025

Aberrant recursive splicing in a human disease locus

Recursive splice sites are rare motifs postulated to facilitate splicing across massive introns and shape isoform diversity, especially for long, brain-expressed genes. The necessity of this unique mechanism remains unsubstantiated, as does the role of recursive splicing (RS) in human disease. From analyses of rare copy number variants (CNVs) from almost one million individuals, we previously identified large, heterozygous deletions eliminating an RS site (RS1) in the first intron of CADM2 that conferred substantial risk for attention deficit hyperactivity disorder (ADHD) and other neurobehavioral traits. CADM2 encodes a neuronally expressed cell adhesion molecule that has repeatedly been associated with ADHD and numerous similar traits. To explore the molecular impact of RS ablation in CADM2, we used CRISPR to model patient deletions and to target a smaller region ([~]500 base pairs) containing RS1 in both human induced neurons (iNs) and rats. Transcriptome analyses in unedited iNs provided a catalog of CADM2 transcripts, including novel transcripts that retained RS exons. Intriguingly, ablating RS1 altered the gradient of RNA abundance across the first intron of CADM2, decreased the level of CADM2 expression, and impacted transcript usage. Decreased CADM2 expression was reflected in reduced exon usage downstream of the RS1 site and global alteration to genes involved in neuronal processes including synapse and axon development. Given the scale of our analyses and the widespread association of CADM2 with neurobehavioral traits, we sought to validate these findings using in vivo models and found that rodent models harboring Cadm2 RS1 deletions exhibited significant changes in relevant behaviors and functional brain connectivity. In summary, our analyses demonstrate a functional role for RS as a noncoding regulatory mechanism in a gene associated with a spectrum of neuropsychiatric and behavioral traits. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/666599v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@171156borg.highwire.dtl.DTLVardef@13553baorg.highwire.dtl.DTLVardef@bee7forg.highwire.dtl.DTLVardef@156f19e_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

genomics↗

bioRxiv2025

Forecasting Urban Wastewater Microbiome Dynamics Using a Digital Twin Framework

Urban wastewater microbiomes are complex and temporally dynamic, offering valuable insight into community-scale microbial ecology and potential public health trends. However, existing wastewater-based studies often remain descriptive, lacking tools for predictive modeling. In this study, we introduce a digital twin framework that forecasts microbial abundance trajectories in urban wastewater using an interpretable generative model, Q-net. Trained on a 30-week longitudinal metagenomic dataset from seven wastewater treatment plants, the model captures temporal microbial dynamics with high fidelity (R2 > 0.97 for key taxa; R2 = 0.998 at the final timepoint). Beyond accurate forecasting, Q-net provides transparent model structure through conditional inference trees and enables simulation of realistic microbial trends under hypothetical scenarios. This work demonstrates the potential of digital twins to move wastewater microbiome studies from static snapshots to dynamic, predictive systems, with broad implications for environmental monitoring and microbial ecosystem modeling.

bioinformatics↗

bioRxiv2025

Molecular fingerprints of a convergent mechanism orchestrating diverse ligand recognition and species-specific pharmacology at the complement anaphylatoxin receptors

Complement anaphylatoxin receptors (C3aR and C5aR1) are prototypical G protein-coupled receptors (GPCRs) playing crucial physiological roles in innate immunity by combating pathogenic infections and orchestrating inflammatory responses. They continue to be important therapeutic targets for multiple disorders including autoimmune diseases, acute and chronic inflammation, and allergy-related conditions. Recent structural coverage has provided important insights into their activation and signaling, however, confounding observations in the literature related to ligand efficacy and functional responses, especially in different model systems, present a major challenge for drug discovery efforts. Here, we systematically and comprehensively profile a broad set of natural and synthetic ligands at C3aR and C5aR1 and discover a previously unanticipated level of functional specialization in terms of species-specific pharmacology and receptor activation. Taking a lead from this, we determine seventeen cryo-EM structures of different ligand-receptor-G-protein complexes and uncover distinct orientation of agonists between the human and mouse receptors despite an overlapping positioning in the orthosteric binding pocket. Combined with extensive mutagenesis and functional assays, these structural snapshots allow us to decode and validate a convergent molecular mechanism involving a "Five-Point-Switch" in these receptors that orchestrates the recognition and efficacy of diverse agonists. We also identify species-specific differences at the level of phosphorylation patterns encoded in the carboxyl-terminus of these receptors and directly visualize their impact on {beta}arr binding and activation using cryo-EM structures. Interestingly, we observe that {beta}arrs engage with the mouse C5aR1 using a variation of previously discovered P-X-P-P phosphorylation motif via a "Sliding-Mechanism" and also exhibit distinct oligomeric state for the human vs. mouse receptors. Taken together, this study elucidates functional specialization at the complement anaphylatoxin receptors and underlying molecular mechanisms, offering a previously lacking framework with direct and immediate implications for the development of novel therapeutics.

biochemistry↗

bioRxiv2025

MSH3 is a genetic modifier of somatic repeat instability in X-linked dystonia parkinsonism

X-linked dystonia parkinsonism (XDP) is a progressive adult-onset neurogenerative disorder caused by the insertion of a SINE-VNTR-Alu (SVA) retrotransposon in TAF1 gene. One element of the SVA is a tandem polymorphic CCCTCT repeat tract whose length inversely correlates with the age of disease onset. Previous observations that the repeat exhibits length-dependent somatic expansion and that XDP onset is modified by variation in DNA repair gene MSH3 indicated that somatic repeat expansion is an important disease driver. Here, we sought to uncover genetic modifiers of CCCTCT instability in XDP patients and to provide a mechanistic link between somatic instability and disease. We determined quantitative metrics of both repeat expansion and repeat contraction in blood. Using genetic association analyses of exome sequencing data, as well as directed sequencing of a variant MSH3 repeat, we found that MSH3 modifies repeat expansion and contraction in blood as well as age at onset. MSH3 alleles associated with earlier disease onset were associated with more expansion and less contraction. Conversely, alleles associated with later disease onset were associated with less expansion and more contraction. Notably, MSH3 repeat alleles were also similarly associated with expansion and contraction in brain tissues. Our findings provide key evidence that MSH3s role(s) in CCCTCT repeat dynamics underlies its impact on clinical disease and indicate that therapeutic strategies to lower or inhibit MSH3 are predicted to both slow CCCTCT expansion and promote CCCTCT contraction, impacting the disease course prior to clinical onset.

genetics↗