Biology subjects

Hussain, A.

Publications and source records attributed to Hussain, A..

At least 19 recordsLinked to original sources

bioRxiv2026

RAP2.6 negatively regulates Arabidopsis submergence tolerance through GSNOR1-dependent redox and hormonal signaling

Group VII ETHYLENE RESPONSE FACTORs (ERFVIIs) are central regulators of plant responses to oxygen deprivation. However, the contributions of many other APETALA2 (AP2)/ERF transcription factors to hypoxia and flooding responses remain poorly understood. Here, we identify the group X ERF transcription factor RAP2.6 as a negative regulator of submergence tolerance in Arabidopsis thaliana. RAP2.6 expression declined under hypoxia, and plants overexpressing RAP2.6 exhibited reduced survival following dark submergence, whereas the rap2.6-1 loss-of-function mutant showed enhanced tolerance to submergence, hypoxia, and ethanol treatment. Enhanced tolerance of rap2.6-1 was associated with reduced membrane injury, maintenance of photosynthetic pigments and soluble sugars, and extensive metabolic remodeling. RAP2.6 overexpression altered nitric oxide (NO), S-nitrosothiol (SNO), and ethylene accumulation during submergence and was associated with greater oxidative damage and enhanced abscisic acid (ABA)-responsive gene expression. Genetic analyses using S-NITROSOGLUTATHIONE (GSNO) REDUCTASE 1 (GSNOR1) gain- and loss-of-function backgrounds demonstrated that GSNOR1-dependent GSNO homeostasis strongly modified RAP2.6-dependent submergence responses. Increased GSNOR1 activity suppressed the submergence-sensitive phenotype of RAP2.6-overexpressing plants, reduced nitro-oxidative stress, and restored carbohydrate reserves, whereas loss of GSNOR1 activity abolished the enhanced tolerance of rap2.6-1. GSNOR1 also modified RAP2.6-dependent expression of genes associated with oxygen sensing and ABA signaling, while its protective effect was not explained solely by changes in ethylene accumulation. Together, these findings identify RAP2.6 as a regulatory component of the low-oxygen response and reveal a functional interaction between RAP2.6 and GSNOR1-dependent redox signaling that coordinates plant hormonal, metabolic, and oxidative responses during submergence.

plant biology↗

bioRxiv2026

A propensity to hyperinsulinaemia underpins diet-induced diabetes in NODk mice

Aims/hypothesisHeterogeneity in the pathophysiology of type 2 diabetes is increasingly being realised. The currently available rodent models of type 2 diabetes all have limitations and do not accurately reflect all human type 2 diabetes subtypes. NOD.BR-H2k /Wicker mice (NODk), derived from the non-obese diabetic (NOD) mouse, are type 1 diabetes resistant. However, transgene induced beta-cell stress in male NODk mice induces hyperinsulinaemia followed by diabetes. Here we have investigated the propensity of NODk mice to develop a Western-diet (WD) induced hyperinsulinaemic subtype of type 2 diabetes. Comparator mouse strains used were BALB/c and B10.BR-H2k /SgSnJ mice (B10k). MethodsIn the longer-term studies (14-24 weeks), NODk, B10k and BALB/c mice were randomised to receive Chow or WD from 4 weeks of age, followed by serial measurement of body weight and fed-state blood glucose. IPGTT and IPITT tests were conducted at 13 weeks of age. Blood and pancreas were harvested for further analyses at 14 and 24 weeks of age, or sooner if diabetes developed (blood glucose concentrations [≥]20 mmol/l on two consecutive days). In the acute studies, metabolic characteristics of the three strains at 8 weeks of age, continued on Chow or after a 5-day WD challenge (WDC) were assessed, along with harvesting pancreas on day 5 for ex vivo islet insulin secretion, electron microscopy, and bulk islet transcriptomics analyses. ResultsMale WD-fed NODk mice became markedly hyperinsulinaemic, gained excess weight and developed a severe type 2 diabetes phenotype. Emergence of diabetes was associated with islet endocrine cell apoptosis and loss of beta-cell mass, without evidence of insulitis. Insulin resistance on IPITT testing, however, was not evident in Chow-fed NODk mice. In contrast, male B10k mice already had poor glucose tolerance on Chow diet and, despite having a hypoinsulinaemic phenotype, were resistant to WD-induced diabetes. BALB/c mice developed very mild glucose intolerance and hyperinsulinaemia in response to the WD. Female NODk mice were diabetes resistant. At 8 weeks of age, male Chow-fed NODk mice were mildly hyperinsulinaemic despite relative hypoglycaemia compared to the other strains. The acute 5-day WDC markedly increased hyperinsulinaemia in NODk mice. Transcriptomics analyses identified robust strain-specific differences, including altered islet cell differentiation, energy metabolism, endoplasmic reticulum to golgi vesicle transport and insulin processing. Conclusions/interpretationNODk mice, which exhibit mild hyperinsulinaemic hypoglycaemia on Chow diet and rapidly develop marked hyperinsulinaemia on WD, are type 2 diabetes prone. In contrast, B10k mice have poor glucose tolerance on Chow diet and no or limited capacity to increase insulinaemia in response to WD, are diabetes resistant. These findings support the hypothesis that hyperinsulinaemia is upstream to insulin resistance in the pathogenesis of severe insulin resistant subset of type 2 diabetes for which the WD-fed NODk mouse is a suitable new mouse model. Research in ContextO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIWhich of insulin hypersecretion and insulin resistance are upstream in the pathogenesis of the severe insulin resistant subtype of type 2 diabetes continues to be debated C_LIO_LIRodent models of type 2 diabetes do not accurately reflect all human subtypes of type 2 diabetes C_LIO_LINODk mice, derived from the non-obese diabetic (NOD) mouse, are type 1 diabetes resistant, but with transgene induction of islet beta-cell stress develop hyperinsulinaemia, followed by type 2 diabetes C_LI What is the key question?O_LICould Western-diet fed NODk mice be developed as a model of severe insulin resistant type 2 diabetes and shed light on its upstream pathogenesis? C_LI What are the new findings?O_LIMale NODk mice tend to hyperinsulinaemic hypoglycaemia on Chow diet, rapidly develop marked hyperinsulinaemia on Western-diet feeding, and then develop type 2 diabetes C_LIO_LIMale B10k mice (one of two comparator strains (B10k and BALB/c)) have poor glucose tolerance on Chow diet, limited capacity to increase insulinaemia in response to Western-diet feeding, but are resistant to develop Western-diet induced type 2 diabetes C_LIO_LIIsolated islet findings show strain differences that favour intrinsic hyper-responsiveness and hypo-responsiveness of islet beta-cells of NODk and B10k mice, underpinning their respective metabolic phenotypes C_LI How might this impact on clinical practice in the foreseeable future? O_LIThe findings are in support of the insulin hypersecretion hypothesis for severe insulin resistant type 2 diabetes, such that therapies to limit islet beta-cell hyperresponsiveness to prevent and treat this subtype of diabetes warrant investigation C_LI

physiology↗

bioRxiv2026

Dissociable Neural Responses to Conditioned Social Threats are Modulated by Spatial Proximity in PTSD and MDD

The brains response to potential threats is shaped by the egocentric spatiotemporal distance to the threat. While distal threats recruit evaluative, cognitive-fear networks for strategic planning, proximal threats engage evolutionarily conserved reactive-fear circuitry to mount immediate defensive responses. Understanding this dual neural architecture is clinically relevant, as the spatial proximity to a traumatic event predicts subsequent psychiatric symptom severity and recovery. Despite the well-characterized disruptions to threat circuitry in posttraumatic stress disorder (PTSD) and major depressive disorder (MDD), how these networks respond to threats at distinct spatial distances has yet to be investigated in these disorders. Utilizing 3D virtual reality technology, we implemented a spatially-modulated fear conditioning paradigm by presenting human avatars at proximal (peripersonal) and distal (extrapersonal) distances, paired with shock, to trauma-exposed participants (n = 50) during functional MRI (fMRI). We modeled associations between PTSD and MDD symptom severity and task-evoked hemodynamic responses within cognitive-fear and reactive-fear threat networks. Our results support a transdiagnostic disruption of thalamic responses to proximal threats, driven by heightened activation to the safety stimulus and stronger deactivation to the threat stimulus. MDD showed a disorder-specific effect of disrupted activity across cognitive-fear and social cognition regions in response to proximal social threats, and illness severity-by-proximity effects across motor regions. PTSD symptom severity was uniquely associated with hyperactivity of the amygdala to distal threats. Transdiagnostic disruption of connectivity between the dorsal precuneus and several subcortical structures followed a disorder-specific gradient across the anterior-posterior axis. While thalamic disruptions to threats represent a shared transdiagnostic effect, PTSD and MDD are distinguished by differences in amygdala hyperactivation and cognitive-fear network hypoactivation, respectively.

neuroscience↗

bioRxiv2026

A Nerve-Dependent NGF Receptor Switch Controls Corneal Epithelial Renewal In Neurotrophic Keratopathy

Corneal epithelial integrity depends on continuous epithelial renewal by limbal epithelial stem cells (LESCs), a process tightly linked to sensory innervation. Loss or impairment of innervation causes neurotrophic keratopathy (NK), a sight-threatening degenerative disease for which rhNGF, the only FDA-approved pharmacologic therapy, often has limited efficacy in advanced or refractory disease. The mechanistic basis for this limited response remains unclear. Using surgical, genetic, and pharmacologic approaches in a rodent model of NK with corneal Schwann cell ablation or structural and functional denervation, together with primary human LESCs, we examined how denervation alters NGF receptor signaling during epithelial repair. In innervated corneas, NGF promoted epithelial regeneration through TrkA. Denervation, however, increased expression of a second NGF receptor, anti-regenerative p75NTR, and activation of its effector JNK, and reduced the activity of the TrkA effector AKT in LESCs. In this altered receptor context, denervation-induced elevation of endogenous NGF amplified p75NTR signaling, thereby explaining the failure of topical rhNGF to rescue severely denervated NK phenotype corneas. Conversely, selective TrkA activation, either with the clinical-stage agonist tavilermide, or pharmacologic or genetic inhibition/ablation of p75NTR, restored AKT signaling and rescued epithelial healing in denervated corneas independent of reinnervation. These findings identify a nerve-dependent NGF receptor switch as a key regulator of corneal epithelial renewal and establish receptor-selective modulation as a mechanistically rational therapeutic strategy for treating NK. One Sentence SummaryCorneal denervation shifts limbal epithelial stem cell signaling from pro-regenerative TrkA-AKT toward anti-regenerative p75NTR-JNK, explaining the limited efficacy of recombinant human nerve growth factor (rhNGF; cenegermin), the only approved pharmacologic therapy for neurotrophic keratopathy, in severely denervated corneas and identifying receptor-selective modulation as a mechanistically distinct therapeutic strategy.

cell biology↗

bioRxiv2026

Microbiota-derived TMAO links PM2.5 exposure to cognitive impairment: A gut liver brain axis

Although fine particulate matter (PM2.5) is linked to cognitive impairment, the mechanistic links between pulmonary exposure and neurodegeneration remain poorly understood. This study investigates the role of the gut-liver-brain axis in mediating PM2.5-induced neurotoxicity. We demonstrate that three weeks of intratracheal PM2.5 instillation in mice causes significant memory deficits, impaired hippocampal adult neurogenesis, and reduced synaptic plasticity in both sexes. Metagenomic analysis revealed that PM2.5 alters gut microbiota composition, specifically by upregulating pathways involved in trimethylamine (TMA) synthesis. This microbial shift led to a systemic increase in the metabolite trimethylamine N-oxide (TMAO) and its accumulation in the hippocampus. Mechanistic experiments revealed that TMAO drives neurotoxicity by activating the hippocampal PERK-mediated endoplasmic reticulum (ER) stress pathway. Critically, these deficits were reversed by suppressing hepatic TMAO production via either pharmacological inhibitors or genetic knockdown. Additionally, hippocampal-specific PERK silencing or dietary resveratrol intervention attenuated hippocampal ER stress, thereby protecting against PM2.5-induced cognitive and hippocampal impairments. These results identify the microbial metabolite TMAO as a key mediator of air pollution-related neurotoxicity and highlight the gut-liver-brain axis as a promising therapeutic strategy to counteract the neurological impacts of air pollution.

animal behavior and cognition↗

bioRxiv2026

BK Channels Orchestrate Cardiac Homeostasis Through Mitochondrial Uncoupling Proteins

BK channels, coded by the Kcnma1 gene, integrate voltage and intracellular Ca2+ signals and are recognized for their roles in smooth muscle and neuronal excitability. However, their contribution to baseline cardiac physiology remains poorly defined. Here we uncover a fundamental function for BK channels in maintaining normal cardiac performance, independent of pathological stress. Using non-invasive echocardiography, transcriptional profiling, and mechanistic analyses, we demonstrate that Kcnma1 deletion disrupts ventricular function, and remodels metabolic and stress-response pathways. Transcriptomic profiling revealed selective downregulation of mitochondrial uncoupling proteins (UCPs) and suppression of the PGC-1/FOXO3a axis, without broad loss of oxidative phosphorylation components. Enhancing UCP expression restored cardiac performance, indicating that mitochondrial uncoupling and redox control constitute key downstream effectors of BK signaling. Together, these results identify a physiological role for BK channels in maintaining myocardial function and define a mitochondrial BK-UCP axis, critical for cardiac homeostasis.

cell biology↗

bioRxiv2026

Bayesian spatial prediction of three medically important tick species in Illinois

Tick-borne diseases are now reported from nearly every county in Illinois, and three vector tick species (Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis) are of particular concern because these are responsible for most of the tick-borne disease transmission in the state. However, active surveillance is patchy, many counties have little or no sampling, and there is no statewide, quantitative map of relative abundance that can be used to anticipate risk in unsampled areas. To address these gaps, we developed Bayesian hierarchical spatial models to estimate the county-level abundance of these three vector tick species in Illinois. Using active surveillance data from 2019-2022, we modeled county-level abundance as a function of climate, land cover, forest fragmentation, and deer habitat suitability. Spatial dependence was captured using a Besag-York-Mollie 2 (BYM2) prior implemented in INLA, along with spatial 5-fold cross-validation to assess predictive performance. A. americanum showed the highest predicted abundance in southern and central Illinois, D. variabilis was widespread but diffuse, and I. scapularis was concentrated in northern and selected central counties. Together, these models provide the first spatial, statewide, uncertainty-aware assessment of tick abundance in Illinois, highlighting priority counties where surveillance lags disease risk.

ecology↗

bioRxiv2026

Filling surveillance gaps: Bayesian INLA models for predicting tick distributions in data-sparse regions

Fragmented and geographically uneven surveillance limits the ability to target tick monitoring and control in many livestock systems. We evaluated whether heterogeneous published surveillance could be converted into district-level, uncertainty-aware abundance predictions for Rhipicephalus microplus and Hyalomma anatolicum across Punjab and Khyber Pakhtunkhwa, Pakistan. Species-specific tick counts were standardized by the number of animals examined and sampling duration and expressed as ticks per 100,000 animal-months. Environmental covariates were summarized using principal component analysis, with livestock density included separately. Bayesian Gaussian models, with and without a district-level Besag-York-Mollie 2 spatial effect, were fitted in R using Integrated Nested Laplace Approximation (INLA) and compared. Leave-one-district-out validation was performed to assess out-of-sample predictive performance. Spatial models improved model fit for both species. For R. microplus, PC1 and PC4 showed credible negative associations with abundance, whereas no fixed-effect 95% credible interval excluded zero for H. anatolicum. Predicted R. microplus abundance was more spatially heterogeneous, with high but uncertain estimates in several northern districts, whereas H. anatolicum predictions were more homogeneous and relatively higher toward southern Punjab. Mapping posterior uncertainty identified districts where additional standardized surveillance would be most informative. This approach provides a transferable framework for extracting spatial surveillance information from heterogeneous veterinary data while explicitly representing uncertainty.

ecology↗

bioRxiv2026

All-trans retinoic acid recalibrates macrophage transcriptional responses to drug-resistant Mycobacterium tuberculosis through strain-specific immunometabolic reprogramming

Tuberculosis (TB) caused by Mycobacterium tuberculosis (M.tb) remains the leading infectious cause of death worldwide, with multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains presenting an escalating therapeutic crisis. All-trans retinoic acid (ATRA), an active vitamin A metabolite with established immunomodulatory properties, has emerged as a candidate host-directed therapy, yet its genome-wide transcriptional effects on macrophage across strains of differing drug-resistance profiles remain uncharacterized. We performed RNA sequencing of murine peritoneal macrophages infected with drug-susceptible H37Rv, MDR-2261, or XDR-MCY M.tb strains, with and without ATRA treatment, validated by RT-PCR and flow cytometry. All three strains activated a conserved pro-inflammatory program dominated by Nos2, Il1b, and Acod1 induction with progressive suppression of host translational and mitochondrial machinery. XDR-MCY uniquely induced Ifnb1/IFN-{beta}, suppressed Prdx1 and Gpx4, the latter shared with MDR-2261 and showed selective downregulation of MHC-II processing genes, suggesting a multilayered immune evasion strategy. ATRA activated canonical retinoid signaling across all infection states and consistently induced Arg1-mediated resolution signaling, with Nos2 suppression observed in H37Rv- and MDR-infected macrophages. ATRA selectively restored Epas1/HIF-2 in H37Rv- and MDR-infected macrophages without disrupting the HIF-1-driven antimicrobial program or itaconate biosynthesis. ATRA responsiveness progressively attenuated with drug resistance, with XDR-MCY-infected macrophages largely refractory to transcriptional reprogramming. These findings provide a transcriptional rationale for evaluating ATRA as a host-directed adjunct in drug-resistant TB and identify Gpx4 suppression in drug-resistant strains and XDR-specific Ifnb1 induction as vulnerabilities necessitating further investigation.

microbiology↗

bioRxiv2025

Knowledge, attitudes, and practices of para-veterinary workers about ticks and tick-borne diseases in three provinces of Pakistan

There is a high prevalence of tick infestation in Pakistani livestock, affecting more than 45% of the population of more than 200 million small and large ruminants. Most livestock farmers seek assistance from para-veterinary workers, who fall under the definition of Veterinary Paraprofessionals (VPPs), according to the World Organization for Animal Health (WOAH). There is a shortage of information concerning the awareness of these para-veterinary workers regarding tick control and management. This study aims to bridge this critical knowledge gap by conducting a cross-sectional survey that evaluates the knowledge, attitudes, and practices of para-veterinary workers about tick-borne diseases (TBDs) in Pakistan. Between March and August 2023, we conducted a web-based survey among para-veterinary workers recruited via email, text message, and face-to-face conversations. Poisson regression was used to identify factors associated with knowledge, attitude, and practice (KAP) scores related to TBDs. We received 118 responses from three provinces; only 27.9% (n = 33) responded that they had attended workshops related to ticks and TBDs. Attending workshops was associated with higher KAP scores. All section scores were correlated, and higher knowledge scores were significantly associated with lower odds of tick exposure. Our findings suggest that workshop attendance is important in increasing overall awareness and promoting better practices regarding TBDs.

scientific communication and education↗

bioRxiv2025

Volumetric Differences of Thalamic Nuclei are Associated with Post-Trauma Psychopathology

Previous investigations of whole thalamus and thalamic nuclei volumes in post-trauma psychopathology have been sparse, limited in scope, and yielded inconsistent results. To address this, volumetric estimates of whole thalamus and thalamic nuclei were obtained from structural brain MRI scans from 2,058 participants across 20 worldwide sites in the ENIGMA PTSD working group. Thalamic volumes were compared between trauma-exposed participants with posttraumatic stress disorder (PTSD) (n=238), major depressive disorder (MDD) (n=184), comorbid PTSD+MDD (n=618), and trauma-exposed control participants (n=1,018). PTSD and MDD symptom severity, PTSD symptom clusters, and childhood trauma were similarly examined for associations with thalamic volume. Participants with PTSD only compared to controls had smaller thalamic nuclei volumes in sensorimotor nuclei, including the parafascicular (Pf), ventral anterior magnocellular (VAmc), medial pulvinar (PuM), and anterior pulvinar (PuA) nuclei of the thalamus. MDD only and comorbid PTSD+MDD participants exhibited smaller mediodorsal thalamus volumes compared to controls. Overall PTSD and MDD symptom severity negatively correlated with the volume of the mediodorsal thalamus. A significant interaction between PTSD and MDD severity was found, such that MDD severity was positively associated with thalamic volume only among individuals with high PTSD severity. Avoidance and hyperarousal symptoms of PTSD were positively associated with thalamic volume, while re- experiencing and negative mood/cognition symptoms were negatively associated with thalamic volume. Childhood physical and emotional abuse were positively and negatively associated with thalamic volume, respectively. Whole thalamus volume and volumes of the sensorimotor and limbic thalamus may play an important role in the development of PTSD and MDD in the aftermath of trauma exposure. The interaction between PTSD and MDD symptoms and contrasting effects across PTSD symptom clusters and types of childhood adversity suggests multiple neurobiological mechanisms are involved in shaping thalamic volume post-trauma.

neuroscience↗

bioRxiv2025

Antibody Responses to Salmonella Typhi Antigens among Typhoid Recovered Individuals in an Endemic Region

BackgroundTyphoid fever remains a major public health concern in endemic regions, yet the nature of antibody responses to individual Salmonella Typhi antigens and their potential role in modulating cellular immune functions are not well understood. This gap also applies to the long-term immune response after the vaccination against the disease. ObjectivesTo evaluate the humoral and cellular immune response against the Salmonella Typhi antigens among the Typhoid recovered individuals. MethodsELISA was used to measure antibody responses against five S. Typhi antigens in plasma samples from typhoid-recovered individuals and healthy participants. Vi polysaccharide-specific plasma antibodies were tested for their ability to activate NK cells isolated from healthy donors. Flow cytometry-based assays were performed to analyze T cell and B cell profiles in the peripheral circulation of these individuals. ResultsPolysaccharide antigens mounted better IgA responses among typhoid-recovered individuals compared with healthy participants. Anti-S. Typhi IgM was significantly elevated in the typhoid group for all five antigens (p<0.05), while no significant differences were observed in IgG responses. NK cell activation assays showed comparable levels of activation markers of the NK cells isolated from healthy individuals and treated with the plasma of Typhoid recovered individuals. Analysis of B cell subsets revealed largely comparable distributions between the two groups; however, transitional B cells were elevated among the Typhoid recovered individuals. HlyE-specific memory B cells were detectable in both the groups. CD4 T cell subsets were similar between typhoid-recovered and healthy individuals, whereas differences were observed in CD8 T cell populations, with higher TEMRA cells among recovered individuals and relatively higher central memory CD8 T cells in healthy participants. ConclusionPolysaccharide antigens elicited significantly better IgA response in recovered typhoid participants, possibly reflecting mucosal immune priming from the gut. Persistent IgM antibodies after recovery suggest durable IgM responses following typhoid infection. Similar IgG levels between groups and the presence of antigen-specific memory cells in healthy individuals highlight the influence of repeated exposure in endemic settings. Elevated transitional B cells suggest the reinforcement of the B cells to the peripheral circulation during the disease which remained in the circulation of these individuals. However, elevated TEMRA population of the CD8 T cells has been observed in several other infectious diseases including this study. These findings demonstrate the complexity of humoral and cellular immune responses to S. Typhi in endemic regions.

immunology↗

bioRxiv2025

Lead optimization against drug-resistant Leishmania donovani infection: Semi-synthetic derivatives of ethyl linoleate isolated from Indian edible mushroom Meripilus giganteus.

Visceral leishmaniasis, the most severe form, affects thousands of people annually. Current drugs in practice fail to provide an absolute cure. Globally, treatment relies on a single dose of liposomal amphotericin B, which requires a costly setup and cold chain to maintain. Natural molecules remain the vital sources of therapeutic ingredients in modern medicine. Meripilus giganteus is traditionally consumed by the people of the North-eastern regions of the Himalayas, India. In this study, we planned for the stepwise bioactivity-guided isolation of natural molecules from M. giganteus and to synthesize more potential therapeutic derivatives against the drug-resistant Leishmania infection. HPLC chromatogram of ethyl acetate extract obtained from M. giganteus revealed the presence of ethyl linoleate as the most active anti-leishmanial molecule. Several derivatives of ethyl linoleate were synthesized and evaluated against Leishmania promastigotes. Among them, a single epoxygenated variant of ethyl linoleate, ethyl (Z)-8-(3-(oct-2-en-1-yl) oxiran-2-yl) octanoate (EL3), showed promising anti-leishmanial activity against both drug-sensitive and drug-resistant Leishmania donovani. The lead derivative disrupts the biosynthesis of trypanothione from glutathione and spermidine, making the parasite vulnerable to the oxidative burst inside the host. Interestingly, the lead derivative was found to be more efficient against the drug-resistant L. donovani, in vivo. Besides this, it has almost no toxicity towards host cells. Considering the urgency for new drug development, we propose this novel semi-synthetic derivative as a potent therapeutic lead.

immunology↗

bioRxiv2025

Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis

The increasing scale and complexity of neuroimaging datasets aggregated from multiple study sites present substantial analytic challenges, as existing statistical analysis tools struggle to handle missing voxel-data, suffer from limited computational speed and inefficient memory allocation, and are restricted in the types of statistical designs they are able to model. We introduce Image-Based Meta- & Mega-Analysis (IBMMA), a novel software package implemented in R and Python that provides a unified framework for analyzing diverse neuroimaging features, efficiently handles large-scale datasets through parallel processing, offers flexible statistical modeling options, and properly manages missing voxel-data commonly encountered in multi-site studies. IBMMA produced stronger effect sizes and revealed findings in brain regions that traditional software overlooked due to missing voxel-data resulting in gaps in brain coverage. IBMMA has the potential to accelerate discoveries in neuroscience and enhance the clinical utility of neuroimaging findings.

neuroscience↗

bioRxiv2025

Enhanced AkaLuc Bioluminescence Imaging for Longitudinal Intravital Monitoring of Minimal Residual Disease in a Murine Model of Triple-negative Breast Cancer

Triple-negative breast cancer (TNBC) is an aggressive form of cancer with poor prognosis. Beyond the absence of targeted therapies, a major challenge is its high recurrence rate, driven by the outgrowth of residual tumor cells that survive chemotherapy and persist during minimal residual disease (MRD). To monitor the therapy response of TNBC by enhanced intravital imaging, we established a clinically relevant combination chemotherapy protocol for the treatment of mouse mammary tumors engrafted from K14cre;Brca1F/F;Trp53F/F (KB1P) organoids engineered to express an mCherry-AkaLuc dual reporter (mCA-KB1P). Reproducible MRD and relapse response patterns with significantly extended relapse-free survivals were achieved with the TAC protocol, consisting of docetaxel, doxorubicin and cyclophosphamide. AkaLuc bioluminescence imaging (AkaBLI) of mCA-KB1P organoids verified the single-cell sensitivity of the system in vitro, and showed a detection limit of approximately 1000 cells in the mammary gland of living mice. Unexpectedly, mCA-KB1P organoids elicited an immune response, which necessitated the use of immunodeficient hosts for the longitudinal intravital monitoring of MRD. AkaBLI and an adapted TAC protocol enabled, for the first time, the non-invasive intravital tracking and an estimation of the number of surviving tumor cells in the MRD state following intensive chemotherapy. Engineering KB1P organoids for Histon2B-mCherry reporter expression (HmC-KB1P) enabled the estimation of tumor cell survival also in syngeneic immunocompetent hosts. Flow cytometry and histological analysis revealed that immunocompetent hosts harbored only a few residual cells at MRD, which exhibited a transient loss of epithelial characteristics, whereas immunodeficient hosts had a greater number of surviving cells with a maintained epithelial phenotype. These findings are consistent with the immune systems role in shaping phenotypic changes influencing survival following chemotherapy Together, the results demonstrate the utility of the AkaBLI system for rare tumor cell tracking and highlight the immune systems role in triggering adaptive responses to chemotherapy.

cancer biology↗

bioRxiv2024

Wnt target IQGAP3 promotes Wnt signaling via disrupting Axin1-CK1α interaction.

The scaffold protein IQGAP3 is highly upregulated in most epithelial cancers. While recent studies have highlighted its pivotal roles in cancer cell proliferation and metastasis, a deeper mechanistic understanding of IQGAP3 is currently lacking. We have here used TurboID to map IQGAP3 proximity partners and identified the Wnt signaling members Axin1 and CK1 as IQGAP3-interacting proteins. Our functional studies demonstrated that overexpression of IQGAP3 increases {beta}-catenin levels, while IQGAP3 depletion reduces {beta}-catenin levels in gastric cancer cells. Mechanistically, IQGAP3 disrupts Axin1-CK1 interaction, thereby inhibiting {beta}-catenin phosphorylation and ultimately leading to its accumulation. Importantly, we discovered that IQGAP3 itself is regulated by Wnt signaling, suggesting its involvement in a positive feedback loop in Wnt/{beta}-catenin signaling through interactions with Axin1 and CK1. These findings identify IQGAP3 as a novel mediator of {beta}-catenin stabilization and underscore its potential as a target for cancer therapy.

cancer biology↗

bioRxiv2024

Benzene metabolites increase vascular permeability by activating heat shock proteins and Rho GTPases

Benzene is a ubiquitous environmental and occupational pollutant abundant in household products, petrochemicals, and cigarette smoke. It is also a well-known carcinogen and hematopoietic toxin. Population-based studies indicate an increased risk of heart failure in subjects exposed to inhaled benzene, which coincides with the infiltration of immune cells into the myocardium. However, the mechanisms of benzene-induced cardiovascular disease remain unknown. Our data suggests that benzene metabolites trans,trans-muconaldehyde (MA), and hydroquinone (HQ) propagate endothelial activation and apoptosis analyzed by endothelial-specific microparticles in C57BL/6J mice plasma. Subcutaneous injections of MA and HQ increased vascular permeability by 1.54 fold and 1.27 fold correspondingly. In addition, the exposure of primary cardiac microvascular endothelial cells to MA increased vascular permeability detected by transendothelial monolayer resistance and by fluorescently labeled dextrans diffusion. The bulk RNA sequencing of endothelial cells exposed to MA for 2, 6, and 24 hours showed MA-dependent upregulation of heat shock-related pathways at 2 and 6 hours, dysregulation of GTPases at 6 hours, and altered cytoskeleton organization at 24 hours of exposure. We found that the HSP70 protein induced by MA in endothelial cells is colocalized with F-actin foci. HSP70 inhibitor 17AAG and HSP90 inhibitor JG98 attenuated MA-induced endothelial permeability, while HSP activator TRC enhanced endothelial leakage. Moreover, MA induced Rac1 GTPase activity, while Rho GTPase inhibitor Y-27632 attenuated MA-induced endothelial permeability. We showed that benzene metabolites compromised the endothelial barrier by altering HSP- and GTPase-related signaling pathways.

pharmacology and toxicology↗

bioRxiv2024

Comparative genomics studies provide insights into the taxonomic classification and secondary metabolic potential of five bioactive Streptomyces species isolated from the North-Western Himalaya

The linear genome of genus Streptomyces members has the potential to encode diverse and novel biosynthetic gene clusters of invaluable antimicrobial and therapeutic significance. The use of limited taxonomic markers makes the precise identification of these miracle microbes very challenging. In the ongoing omics era, genome sequencing and in-silico analysis of these potential antibiotic producers provide deeper insights into their taxonomy, functional capabilities, and potential for antibiotic production. Here this study presents a multifaceted approach for proper taxonomic identification and genomic and bioinformatic analysis of five bioactive Streptomyces species collected from different sampling sites in the high-altitude oligotrophic North-Western Himalaya, Kashmir, India. We used polyphasic taxonomic classification approaches, such as phylogenetic markers (16S rDNA and gyrase B), average nucleotide identity (ANI) estimation, and digital DNA-DNA hybridization (dDDH), which revealed accurate taxonomic placement of five Streptomyces species, named as, Streptomyces violarus ASQP_29, S. rhizosphaerihabitans ASQP_78, S. fulvoviolaceus ASQP_80, S. mirabilis ASQP_98, and S. thajiwasiensis ASQP_92. Amongst these, one notable finding is the discovery of a novel species proposed as Streptomyces thajiwasiensis sp. nov. ASQP_92. In addition, our study presents the first genome announcement report and analysis for S. rhizosphaerihabitans ASQP_78. Genomic annotation highlighted the presence of an exceptionally high number of poorly characterized genes and hypothetical proteins, indicating their potential for undiscovered biotechnological applications. Clusters of orthologous groups (COG) and gene ontology (GO) analysis provided insights into their varied functional roles in metabolism, signaling, information storage and secondary metabolite biosynthesis. Domain-based functional characterization further detailed their involvement in various biological processes particularly in antibiotic biosynthesis, transport, and resistance. Biosynthetic gene clusters (BGC) analysis demonstrated their diverse metabolite biosynthetic capabilities and identified both unique and conserved BGCs emphasizing the species-specific roles in bioactive metabolite production and the potential of orphan BGCs in novel drug discovery. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/596145v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@15ac69corg.highwire.dtl.DTLVardef@a52f89org.highwire.dtl.DTLVardef@d3f8d6org.highwire.dtl.DTLVardef@75cce7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO Genomic analysis and taxonomic affiliations of five bioactive Streptomyces species isolated from high altitudes of the North Western Himalaya C_FIG

microbiology↗