Biology subjects

Singh, A. P.

Publications and source records attributed to Singh, A. P..

At least 19 recordsLinked to original sources

bioRxiv2026

Iron sensing modules participate in rhizospheric pH perception in rice

Rhizospheric pH has emerged as one of the most important environmental factors regulating plant fitness in almost every aspect of plant physiology and development. Interestingly, the information on how plant perceive rhizospheric pH is still not well understood. In this report we have elucidated the intricate mechanism where rhizospheric pH mediated changes in relative Fe availability are sensed by the plants to initiate complex physiological responses. Using root specific RNA-seq, ICPMS, hormone quantification and physiological validation in rice, the study revealed Fe availability to be a critical determinant of rhizospheric pH where the relative Fe toxicity towards acidic pH and Fe deficiency towards alkaline pH is deduced by the plant in the form of JA-auxin crosstalk regulating the physiological responses against rhizospheric pH.

plant biology↗

bioRxiv2026

Target DNA-Mediated Plasmonic Coupling and Assembly Kinetics of Gold Nanorods for Label-Free Nucleic Acid Detection

DNA-programmed assembly of plasmonic nanostructures provides a powerful route to couple molecular recognition with optical signal generation. Here, we report the sequence-specific assembly of DNA-functionalized gold nanorods using a sesame allergen-derived DNA biomarker as a molecular bridge. Target-induced assembly produces concentration-dependent assembly growth, plasmon coupling, and distinct assembly kinetics that are readily monitored by absorption spectroscopy, enabling label-free detection of the target DNA in the nanomolar concentration range. The assembled nanorods further produce strong surface-enhanced Raman scattering (SERS) signals arising from plasmonic coupling within the assemblies, extending detection to the picomolar regime without the use of Raman reporters. Quantitative analysis reveals that both the extent and rate of assembly formation are governed by target DNA concentration. These results establish a direct relationship between molecular recognition, assembly growth, plasmonic coupling, and spectroscopic response, highlighting DNA-programmed gold nanorod assembly as a versatile platform for investigating hybridization-driven plasmonic self-assembly and nucleic acid detection. Table of Content O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/732610v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@e4fcb9org.highwire.dtl.DTLVardef@18c0d89org.highwire.dtl.DTLVardef@1ccb4bborg.highwire.dtl.DTLVardef@6d84ca_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Soluble Urokinase Plasminogen Activator Receptor Primes Macrophages and Worsens Heart Failure with Preserved Ejection Fraction

BackgroundHeart failure with preserved ejection fraction (HFpEF) is a systemic inflammatory syndrome with few effective therapies. Soluble urokinase plasminogen activator receptor (suPAR), a circulating immune-derived glycoprotein, independently predicts adverse outcomes in HFpEF beyond natriuretic peptides, but whether it is a causal driver or a passive marker of inflammatory burden has remained unresolved. MethodsWe tested the hypothesis that elevated circulating suPAR is sufficient to amplify HFpEF by acting on the innate immune system. suPAR-transgenic (suPAR-Tg) and wild-type mice were subjected to a cardiometabolic two-hit model (high-fat diet plus L-NAME) for 15 weeks. Cardiac structure and diastolic function were assessed by serial echocardiography alongside blood pressure, glucose tolerance, and gravimetric endpoints, and left ventricular tissue was profiled by bulk RNA sequencing with in silico cellular deconvolution. Myeloid populations in the heart, spleen, and peripheral blood were quantified by spectral flow cytometry and corroborated by galectin-3 immunofluorescence, and the direct effect of suPAR on macrophages was tested by priming bone marrow-derived macrophages with recombinant suPAR before LPS and IFN-{gamma} stimulation. ResultsSustained suPAR elevation worsened the established HFpEF phenotype, producing greater diastolic dysfunction (higher E/e' and E/A ratios) and pulmonary congestion without altering blood pressure or ejection fraction, indicating a mechanism downstream of the canonical hemodynamic stimulus. Bulk RNA sequencing of left ventricular tissue revealed a coordinated transcriptional shift, with suppression of mitochondrial oxidative phosphorylation and amplification of innate and adaptive immune programs, including interleukin-1{beta} production, leukocyte chemotaxis, and antigen presentation. Spectral flow cytometry demonstrated stepwise expansion of CCR2 inflammatory monocytes and macrophages across cardiac, splenic, and peripheral compartments, corroborated in situ by increased galectin-3 macrophage density. In vitro, recombinant suPAR was not a stand-alone inflammatory ligand but instead primed bone marrow-derived macrophages to markedly amplify TNF-, IL-1{beta}, IL-6, and NLRP3 responses to LPS and IFN-{gamma}. ConclusionsTogether, these findings establish that elevated suPAR is sufficient to act as an upstream amplifier of HFpEF, identify the CCR2 inflammatory monocyte-macrophage axis as its proximate effector, and convert two decades of epidemiologic association into a mechanistically grounded, therapeutically tractable hypothesis with immediate relevance to clinical-stage anti-suPAR antibodies.

immunology↗

bioRxiv2026

Mechanistic Insights into TMPyP4 Recognition of the HIV-1 LTR-III G-Quadruplex in Dilute and Protein Condensate Environments Reveal Hidden Dual Binding Modes

G-quadruplex (GQ) structures within the HIV-1 long terminal repeat (LTR) regulate viral transcription and represent promising antiviral targets; however, detailed mechanistic understanding of their ligand recognition at the molecular level remains limited and has largely been investigated under dilute conditions despite the crowded and compartmentalized nature of intracellular environment. Here, we investigate the interaction of the cationic porphyrin TMPyP4 with the HIV-1 LTR-III GQ under dilute conditions and inside protein-rich phase-separated condensates that mimic intracellular biocondensates. Steady-state and time-resolved fluorescence measurements reveal a dual binding behavior that is not discernible from absorption spectroscopy. A high-affinity guanine-rich binding mode leads to efficient fluorescence quenching through electron transfer from ground-state guanine to excited TMPyP4, whereas a weaker non-guanine binding mode gives rise to enhanced and long-lived emission. Nucleotide-specific control experiments validate the origin of these distinct binding environments. Molecular docking and molecular dynamics simulations further support preferential binding of TMPyP4 at the terminal G-quartet together with a secondary binding mode near the quadruplex-duplex junction. Importantly, both TMPyP4 and LTR-III GQ preferentially partition into the condensates, where the hybrid GQ structure, dual binding behavior, and associated excited-state signatures remain preserved despite the crowded and viscous environment. Although a slight reduction in binding affinity is observed inside the condensates, the overall binding mechanism remains largely preserved due to compensatory effects arising from the condensate microenvironment. Overall, this work demonstrates that ligand recognition of viral GQ remains preserved within protein condensates and establishes fluorescence spectroscopy as a sensitive approach for resolving hidden binding heterogeneity in GQ-ligand interactions.

biophysics↗

bioRxiv2026

Biochemical and kinetic properties of a Type III restriction-modification enzyme Mbo45V from the host-adapted pathogen Mycoplasma bovis

Type III restriction-modification (RM) enzymes are prominent bacterial defense against bacteriophage and invading foreign DNA that also modulate the hosts epigenetic landscape. Genome analysis of the host-adapted Mycoplasma bovis PG45 that has a very small genome revealed a Type III RM locus comprising one res and three mod genes. We characterized Mbo45V, a representative enzyme encoded by this locus. The enzyme forms a heterotrimeric complex consisting of two Mod subunits and one Res subunit. Mbo45V recognizes the asymmetric sequence 5'-YAATC-3' (Y = T/C) and cleaves DNA having at least two head-to-head oriented sites [~]26-28 bp away from the recognition site. Methylation of the second adenine of the target site using cofactor S-adenosylmethionine (SAM) protects DNA from restriction, while the SAM analogue sinefungin enhances DNA binding and cleavage. Kinetic studies reveal that Mbo45V exhibits relatively weak DNA binding affinity and an unusually high Km for SAM, indicating low cofactor affinity compared to prototypical enzymes such as EcoP15I. ATPase activity is strongly stimulated by cognate DNA and is inhibited upon methylation of the substrate, suggesting a regulatory interplay between methylation and restriction functions. Comparative analysis indicates that, although Mbo45V shares core mechanistic features with prototypes from Escherichia coli, its kinetic parameters are distinct. These differences likely reflect adaptation to the stable intracellular environment of M. bovis, in contrast to the fluctuating conditions encountered by the enteric bacteria.

biochemistry↗

bioRxiv2026

Searching for a New Home or Rare Dispersal? Habitat Suitability and Landscape Connectivity of the Tibetan Brown Bear across the Indian Cold Deserts and the Tibetan Plateau

Understanding habitat suitability and landscape connectivity is essential for conserving wide-ranging carnivores in climate-sensitive high-altitude mountain ecosystems. The first occurrence record of the Tibetan brown bear (Ursus arctos pruinosus) from the Changthang region of Ladakh, India, has raised questions about whether this individual represents an isolated dispersal event or reflects functional connectivity with source populations on the Tibetan Plateau. To evaluate potential habitat suitability and transboundary connectivity, we compiled species occurrence records and associated environmental predictors and developed an ensemble species distribution model using biomod2. We then assessed landscape connectivity using circuit theory implemented in Circuitscape to identify potential ecological corridors. Our models indicate that approximately 1,011,818 km{superscript 2} (21.34%) of the combined Ladakh (India) and the Tibetan Plateau landscape is currently suitable for the species, of which only [~]207,000 km{superscript 2} represents highly suitable habitat. Annual precipitation, precipitation of the wettest month, and precipitation of the warmest quarter were the most influential predictors of habitat suitability. Connectivity analysis identified potential corridors linking the eastern Changthang region of Ladakh with suitable habitat on the Tibetan Plateau, suggesting plausible transboundary ecological connectivity. These results indicate that the recent record from Changthang is more likely driven by landscape-scale functional connectivity than by an isolated dispersal event. Although the mapped corridors represent probable connectivity pathways rather than confirmed movement routes, this study provides the first spatially explicit assessment of habitat suitability and potential transboundary connectivity for the Tibetan brown bear across the Ladakh and Tibetan Plateau landscape.

ecology↗

bioRxiv2025

Cellular deconvolution of the brain with topological magnetic resonance image analysis

Magnetic resonance imaging (MRI) is foundational tool in neuroscience, enabling characterization of neuroanatomical markers of disease, behavior, and cognition. However, the precise cellular processes driving the structural and functional readouts provided by MRI remain opaque. Non-invasively assessing cell type, abundance, and location using MRI has the potential to revolutionize both basic science and clinical practice. To this end, we developed SpaTial Representation and Analysis using Topological Architecture (STRATA), an image-based gradient-boosted machine learning framework, which quantifies cell type proportions of neurons, astrocytes, oligodendrocytes, and microglia from MR images. Here we demonstrate and validate STRATA on diverse disease models, species, and regions of interest that together highlight the generalizability of the STRATA framework.

neuroscience↗

bioRxiv2025

Targeting Metabolic Dysfunction and Inflammation with Sotagliflozin Reverses Diastolic Dysfunction in Experimental HFpEF

BackgroundHeart failure with preserved ejection fraction (HFpEF) is increasingly prevalent and strongly associated with cardiometabolic comorbidities including obesity, hypertension, and metabolic dysfunction. While SGLT2 inhibitors have demonstrated clinical benefits in HFpEF, the mechanisms underlying dual SGLT1/2 inhibition remain incompletely understood. MethodsWe utilized a murine model of cardiometabolic HFpEF induced by high-fat diet combined with L-NAME administration. Following disease establishment, mice received sotagliflozin (30 mg/kg) or vehicle for 10 weeks. Comprehensive assessments included echocardiography, indirect calorimetry, cardiac metabolomics, bulk RNA sequencing with cell-type deconvolution, and high-dimensional immune profiling by flow cytometry and CyTOF. ResultsSotagliflozin significantly attenuated weight gain and improved glucose tolerance without normalizing blood pressure. Metabolic cage analyses revealed a sustained reduction in respiratory exchange ratio, indicating enhanced fatty acid oxidation, corroborated by elevated cardiac acylcarnitine intermediates including palmitoylcarnitine and dodecanoylcarnitine. Echocardiography demonstrated that sotagliflozin protected against diastolic dysfunction, normalizing isovolumic relaxation time and E/e ratio while reducing left ventricular mass and myocardial fibrosis. Transcriptomic profiling revealed upregulation of mitochondrial fatty acid {beta}-oxidation pathways and suppression of inflammatory signaling cascades including IL-1 processing and TLR pathways. Flow cytometric analysis demonstrated reduced cardiac infiltration of neutrophils, CCR2+ inflammatory monocytes/macrophages, and IL-1{beta}-expressing immune cells. Splenic immune cell expansion characteristic of systemic inflammation was similarly attenuated. ConclusionsDual SGLT1/2 inhibition with sotagliflozin exerts coordinated cardiometabolic benefits in experimental HFpEF through metabolic reprogramming toward enhanced lipid utilization and suppression of cardiac and systemic inflammation. These findings establish that sotagliflozin targets the intertwined metabolic-inflammatory axis central to HFpEF pathogenesis, providing mechanistic insight into the therapeutic efficacy of dual SGLT inhibition in cardiometabolic heart failure. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/691021v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@146dfbforg.highwire.dtl.DTLVardef@ba784org.highwire.dtl.DTLVardef@122ecfcorg.highwire.dtl.DTLVardef@1f49a1a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

pH-Sensitive Amino Lipid-Driven Pore Formation Enables Endosomal Escape of Lipid Nanoparticles

Lipid nanoparticles (LNPs) have transformed nucleic acid delivery for vaccines and gene therapies, yet their efficiency remains limited by incomplete endosomal escape. While experimental studies have revealed endosomal membrane disruption facilitating cytosolic release, the molecular basis of this process remains poorly understood. Here, we employ molecular simulations to elucidate how LNPs fuse with the endosomal membrane and release their payloads. We identify multiple fusion pathways, with a dominant stalk-pore mechanism. Our simulations reproduce and rationalize key experimental observations, including the transfer of ionizable lipids from LNPs to the membrane, which promotes nucleic acid reorientation and facilitates stalk formation and expansion. Furthermore, lipid shape, pH sensitivity, membrane tension, and nucleic acid encapsulation emerge as critical molecular determinants of endosomal escape efficiency. These findings advance our mechanistic understanding of intracellular delivery and provide a framework for the rational design of LNPs with improved performance for gene therapies and RNA vaccines.

biophysics↗

bioRxiv2025

Season-specific responses of freshwater ciliate communities to top-down and bottom-up experimental manipulations

In aquatic microbial food webs, ciliates represent an important trophic link in the energy transfer from prokaryotes, algae, and heterotrophic nanoflagellates (HNF) to higher trophic levels. However, the trophic role of abundant small ciliates (< 20 {micro}m) is not clearly understood. To unveil their trophic linkages, we conducted two experiments manipulating both top-down and bottom-up controlling factors, thus modulating the trophic cascading and bacterial prey availability for protists during contrasting spring and summer seasons with samples collected from a freshwater meso-eutrophic reservoir. Water samples were size fractionated, to modify food web complexity, i.e. 10-{micro}m, 20-{micro}m and unfiltered control and amended with bacterial prey additions. The samples were analyzed by morphological and sequencing techniques. The bacterial amendments triggered strong ciliate growth following the peaks of HNF in the 10-{micro}m and 20-{micro}m treatments, reflecting a trophic cascading from HNF to raptorial prostome ciliates (Balanion planctonicum and Urotricha spp.) in spring. In summer, HNF and ciliates peaked simultaneously, suggesting the important trophic cascade from bacteria to bacterivorous scuticociliates (Cyclidium glaucoma and Cinetochilum margaritaceum) and HNF. In spring, unfiltered treatments showed stronger ciliate top-down control by zooplankton than in summer. The sequence analysis revealed season-specific manipulation-induced shifts in ciliate communities and their large cryptic diversity. However, morphological and molecular analyses also revealed considerable discrepancies in the abundance of major ciliate taxa. The ciliate communities responded to our experimental manipulations in season-specific fashion, thereby highlighting the different roles of ciliates as an intermediate trophic link between prokaryotes and higher trophic levels. IMPORTANCECiliates are an important trophic link in aquatic microbial food webs. In this study, we used the food web manipulation techniques to reveal their complex trophic interactions during seasonally different plankton scenarios occurring in spring and summer. Manipulating top-down controlling factors (grazing pressure of micro- and metazooplankton grazers) and bottom-up factors (an availability of bacterial prey) shaped distinctly the complexity and dynamics of natural plankton communities and thus yielded significant changes in ciliate community dynamics. The experimentally simplified plankton and ciliate communities responded to our manipulations in season-specific fashions, reflected in different roles of ciliates as an intermediate trophic link between prokaryotes and higher trophic levels. This study also demonstrates that the combination of morphological and molecular analyses is essential for providing robust and ecologically meaningful results due to the reliability in quantifying the major ciliate taxa and their trophic role.

ecology↗

bioRxiv2025

A molecular switch at the yeast mitoribosomal tunnel exit controls cytochrome b synthesis

Mitochondrial gene expression needs to be balanced with cytosolic translation to produce oxidative phosphorylation complexes. In yeast, translational feedback loops involving lowly expressed proteins called translational activators help to achieve this balance. Synthesis of cytochrome b (Cytb or COB), a core subunit of complex III in the respiratory chain, is controlled by three translational activators and the assembly factor Cbp3-Cbp6. However, the molecular interface between the COB translational feedback loop and complex III assembly is yet unknown. Here, using protein-proximity mapping combined with selective mitoribosome profiling, we reveal the components and dynamics of the molecular switch controlling COB translation. Specifically, we demonstrate that Mrx4, a previously uncharacterized ligand of the mitoribosomal polypeptide tunnel exit, interacts with either the assembly factor Cbp3-Cbp6 or with the translational activator Cbs2. These reciprocal interactions determine whether the translational activator complex with bound COB mRNA can interact with the mRNA channel exit on the small ribosomal subunit for translation initiation. Organization of the feedback loop at the tunnel exit therefore orchestrates mitochondrial translation with respiratory chain biogenesis.

molecular biology↗

bioRxiv2024

Genomic Discovery of EF-24 Targets Unveils Antitumorigenic Mechanisms in Leukemia Cells

Curcumin, a polyphenolic compound derived from the plant Curcuma longa L., has demonstrated a wide range of therapeutic properties, including potential anticancer effects. However, its clinical efficacy is limited due to poor bioavailability and stability. To overcome these challenges, curcumin analogs like EF-24 have been developed with improved pharmacological properties. In this study, we used whole-transcriptome profiling to identify the genome-wide functional impacts of EF-24 treatment in leukemia cells to improve our understanding of its potential mechanisms of action. This approach allowed us to establish a model system for associating druggable genes with clinical disease targets. We used the chronic myeloid leukemia (CML) cell line K-562 and acute myeloid leukemia (AML) cell lines HL-60, Kasumi-1, and THP-1 to conduct EF-24 treatment studies. Cell viability was significantly decreased in the EF-24-treated cells as compared to the untreated controls. We discovered that the genes ATF3, CLU, HSPA6, OSGIN1, ZFAND2A, and CXCL8, which are associated with reduced cell viability and proliferation, were consistently upregulated in all EF-24-treated cell lines. Further analysis of the tested cell lines revealed the activation of various signaling pathways, including the STAT1 regulated S100 family signaling pathway, that controlled downstream gene expression in response to EF-24 treatment. Our results elucidate the molecular mechanisms underlying EF-24s antitumor efficacy against leukemia, highlighting its multifaceted impact on signaling pathways and gene networks that regulate cell survival, proliferation, and immune responses in myeloid leukemia cells. SignificanceThis study reveals how EF-24, a curcumin analog, disrupts key signaling pathways in chronic and acute myeloid leukemia cell lines, offering insights to enhance targeted therapies and provide new targets for investigation. Conflict of Interest StatementThe authors declare no potential conflicts of interest.

cancer biology↗

bioRxiv2024

CYP3A5 inhibition causes G1/S blockade and synergizes with CDK4/6 inhibitor to suppress prostate cancer cell growth: Implications in reducing health disparity

Prostate cancer (PC) is a leading cause of death in men because of the high incidence and long-term inefficacy of the existing treatment options. Furthermore, it exhibits significant health disparities that affect African-American (AA) men more adversely than others do. Previously, we established CYP3A5, a highly expressed protein in AAs PC, as a positive regulator of androgen receptor (AR) signaling. We examined the impact of CYP3A5 depletion on genome-wide transcriptional output using RNA sequencing to gain deeper mechanistic insights. The data revealed that 561 genes were downregulated and 263 were upregulated upon silencing of CYP3A5 in PC cells. Furthermore, in silico pathway analyses of differentially expressed genes suggested that the cell cycle regulation pathway was most significantly affected by CYP3A5 inhibition. Cell cycle analysis of CYP3A5-silenced cells and those treated with clobetasol, a specific CYP3A5 pharmacological inhibitor, showed G1/S phase blockade. Both CYP3A5-depletion and pharmacological inhibition resulted in the downregulation of cyclin D, cyclin B, and CDK2, along with the upregulation of p27kip1 but had minimal effects on CDK4/6 levels. Combination treatment with clobetasol and the CDK4/6 inhibitor palbociclib exhibited synergy with combination index (CI) values ranging from 0.28-0.78. Our findings support the utility of CYP3A5 as a druggable therapeutic target that works more effectively in combination with CDK4/6 inhibition to limit the progression of PC, especially for AA patients with AA. This combination addresses CDK4/6 inhibitor resistance, which is often linked to CDK2 overexpression, and can potentially be useful in reducing disparities in the clinical outcomes of PC. SignificanceOur study highlights CYP3A5 as a key regulator of the cell cycle in prostate cancer (PC). Its overexpression in African American (AA) patients may be a key molecular driver of disparities in outcomes. The combination of CYP3A5 and CDK4/6 inhibitors shows a synergistic effect on therapeutic outcomes and addresses CDK2-mediated resistance. Thus, targeting both CYP3A5 and CDK4/6 could improve treatment outcomes, especially in AA PC patients.

cancer biology↗

bioRxiv2024

RNA order regulates its interactions with zwitterionic lipid bilayers

RNA-lipid interactions directly influence RNA activity, which plays a crucial role in developing new applications in medicine and biotechnology. However, while specific preferential behaviors between RNA and lipid bilayers have been identified experimentally, their molecular origin remains unexplored. Here we use molecular dynamics simulations to investigate the interaction between RNA and membranes composed of zwitterionic lipids at the atomistic level. Our data reproduce and rationalize previous experimental observations, including that short-chain RNAs rich in guanine have higher affinity for gel-phase membranes compared to RNA sequences rich in other nucleotides and that RNA prefers gel-phase membranes to fluid bilayers. Our simulations reveal that RNA order is a key molecular determinant of RNA-zwitterionic phospholipid interactions. Our data provides a wealth of information at the atomic level that will help accelerating research on RNA-lipid assemblies for task-specific applications such as designing lipid-based nanocarriers for RNA delivery.

biophysics↗

bioRxiv2024

Early life intestinal inflammation alters gut microbiome, impairing gut-brain communication and reproductive behavior in mice

Despite recent advances in understanding the connection between the gut microbiota and the adult brain, there remains a wide knowledge gap in how gut inflammation impacts brain development. We hypothesized that intestinal inflammation in early life would negatively affect neurodevelopment through dysregulation of microbiota communication to the brain. We therefore developed a novel pediatric chemical model of inflammatory bowel disease (IBD), an incurable condition affecting millions of people worldwide. IBD is characterized by chronic intestinal inflammation, and has comorbid symptoms of anxiety, depression and cognitive impairment. Significantly, 25% of patients with IBD are diagnosed during childhood, and the effect of chronic inflammation during this critical period of development is largely unknown. This study investigated the effects of early-life gut inflammation induced by DSS (dextran sulfate sodium) on a range of microbiota, endocrine, and behavioral outcomes, focusing on sex-specific impacts. DSS-treated mice exhibited increased intestinal inflammation, altered microbiota membership, and changes in microbiota-mediated circulating metabolites. The majority of behavioral measures were unaffected, with the exception of impaired mate-seeking behaviors in DSS-treated males. DSS-treated males also showed significantly smaller seminal vesicles, lower circulating androgens, and decreased intestinal hormone-activating enzyme activity. In the brain, microglia morphology was chronically altered with DSS treatment in a sex-specific manner. The results suggest that early-life gut inflammation causes changes in gut microbiota composition, affecting short-chain fatty acid (SCFA) producers and glucuronidase (GUS) activity, correlating with altered SCFA and androgen levels. The findings emphasize the developmental sensitivity to inflammation-induced changes in endocrine signalling and underscore long-lasting physiological and microbiome changes associated with juvenile IBD. HighlightsEarly-life gut inflammation produces sex-specific effects on i) microbiome, ii) sex hormones and iii) behaviour. Both sexes show disrupted gut bacterial members that regulate sex hormone levels. Male mice demonstrate deficits in mate seeking, which may be mediated by reduced androgen levels. Both male and female mice demonstrate shifts in hippocampal microglial morphology.

neuroscience↗

bioRxiv2024

MicroRNA Tae-miR1130p targets wheat ferroportin1 (TaFPN1) in the absence of iron-responsive element/iron-regulatory protein1 module

Ferroportin (FPN) belongs to the Major Facilitator Superfamily of transporters and is a known iron (Fe) exporter in humans, with orthologues also present in plant species. Human FPN is subjected to multi-level regulation at transcriptional, post-transcriptional, and post-translational levels. How plant FPNs are regulated remains to be explored. In the current study, we have characterized wheat FPN1, a plasma-membrane localized protein, for its role in Fe homeostasis. A spatial-temporal expression analysis of wheat FPN1 suggested that its tissue-specific expression is differentially upregulated during Fe deficiency conditions. Unlike human FPN, plant FPN lacks the necessary sites for hepcidin binding, thereby emphasizing the need to explore the transcriptional/post-transcriptional mode of regulation. The lack of Iron Responsive Elements (IRE) in TaFPN1 promoter suggests no direct regulation through the Iron Regulatory Protein (IRP) mechanism like in humans. Further, to explore the miRNA-mediated regulation, we identified Fe-regulated tae-miR1130b-3p capable of targeting TaFPN1 under in-vivo conditions. Transcript expression of tae-miR1130b-3p negatively correlates with the TaFPN1. This alternative regulation pathway suggests a complex network of interactions governing the expression of genes involved in iron homeostasis, highlighting the intricacies of cellular regulatory mechanisms. Altogether, the work will unravel the cellular and physiological role of wheat FPN and contribute to a comprehensive understanding of plant iron homeostasis.

plant biology↗

bioRxiv2023

Dual localization of JA receptor, CaCOI2, explains JA perception dynamics in chickpea

Jasmonates (JAs) form a group of oxylipin-derived phytohormones involved in multiple biotic and abiotic stress responses and regulate plant development. JAs are perceived by the receptor proteins, COI (coronatine insensitive). These JA receptors encoding F-box protein, form SCFCOI ubiquitin ligase complex (Skp, Cullin, F-box) and activate JA signaling by facilitating degradation of the transcriptional repressor (JAZ; Jasmonate associated ZIM domain containing) proteins through 26S proteasomal pathway. However, JA signaling is poorly understood in chickpea, a vital legume plant. Here, we first identified two putative chickpea JA receptor named CaCOI1, CaCOI2 and demonstrated CaCOI2 as a functional JA receptor. Further subcellular localization studies revealed that CaCOI2 is localized to extra-nuclear region and move to the nucleus on JA perception to activate JA signaling. Using domain swapping (between CaCOI1 and CaCOI2) experiments, we have demonstrated that the LRR region of JA receptors, which interact with bioactive JA i.e., JA-Ile, also plays a critical role in regulating subcellular localization of CaCOI proteins. We report that an acidic amino acid in F-box region of COI proteins (AtCOI1T29) stabilizes COI-InsP8 (1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6) tetrakisphosphate) interaction. This interaction is found to be critical for COI-JAZ interaction and therefore, their functionality. Our study thus identified a functional JA receptor in chickpea and revealed novel aspects of JA signaling and perception, which might also have implications in other plants.

plant biology↗

bioRxiv2023

Jasmonates regulate auxin-mediated root growth inhibition in response to rhizospheric pH in Arabidopsis

Rhizospheric pH severely impacts plant growth and fitness through a numerous process and has emerged as a major determinant of crop productivity. Despite numerous attempts, the key questions related to plants response against rhizospheric pH remains largely elusive. The present study provides a mechanistic framework for rhizospheric pH-mediated root growth inhibition (RGI). Utilizing various genetic resources combined with pharmacological agents and high-resolution confocal microscopy, the study provides direct evidences for the involvement of jasmonates and auxin in rhizospheric pH-mediated RGI. We show that auxin maxima at root tip is tightly regulated by the rhizospheric pH. In contrast, jasmonates (JAs) abundance inversely correlates with rhizospheric pH. Further, JA mediated regulation of auxin maxima by GRETCHEN HAGEN 3 (GH3) family genes explains the pattern of RGI observed over the entire range of rhizospheric pH. Our findings revealed auxin as the key regulator of RGI during severe pH conditions, while JAs antagonistically regulate auxin response against rhizospheric pH. HighlightThe current study identifies the mechanistic framework of rhizospheric pH mediated root growth inhibition in model plant Arabidopsis through a prominent crosstalk between two phytohormones i.e. auxin and jasmonates.

plant biology↗