Biology subjects

Kulkarni, R.

Publications and source records attributed to Kulkarni, R..

At least 19 recordsLinked to original sources

bioRxiv2026

SPARK: A Systems-level Computational Framework for Reconstructing Transcriptomic State Organisation in Lung Adenocarcinoma

Lung adenocarcinoma (LUAD) exhibits substantial molecular heterogeneity, which complicates tumour stratification and limits the ability of mutation-centric models to capture tumour behaviour and predict patient outcomes. This study investigates whether coordinated transcriptomic programs can provide a systems-level representation of tumour states. Bulk RNA-sequencing data from the TCGA-LUAD cohort were analysed to reconstruct pathway-level transcriptomic organisation using a stability-optimised network framework (SPARK). This analysis identified eight transcriptomic modules representing coordinated biological processes active across tumours. Module activity scores were subsequently used to derive a composite Transcriptomic Risk Score through elastic-net Cox proportional hazards modelling. The resulting risk score showed a significant association with overall survival in the discovery cohort and improved prognostic discrimination beyond clinical variables. An independent evaluation in the CPTAC-LUAD cohort confirmed the prognostic signal and preserved risk stratification across patient groups. Unsupervised clustering of module activity further revealed three transcriptomic patient groups characterised by distinct biological programs, genomic alteration patterns, and survival outcomes. Single-cell analysis also demonstrated that the identified transcriptomic modules reflect coordinated organisation of the tumour-immune-stromal ecosystem across cellular compartments. Together, these findings suggest that LUAD heterogeneity can be organised into coordinated transcriptomic programs with measurable clinical relevance, providing a systems-level framework for representing tumour molecular states.

bioinformatics↗

bioRxiv2025

NELFA-mediated promoter-proximal pausing restrains YAP-driven transcription and shapes context-dependent outcomes in breast cancer

Overexpression of YAP is associated with tumor progression in multiple malignancies. YAP is the key transcriptional effector of Hippo signaling: a conserved pathway from Drosophila (Yki) to humans (YAP). In a Drosophila screen, we identified NELFA, a core component of the promoter-proximal pausing (PPP) complex, as a suppressor of Yki-driven hyperproliferation. We investigated whether PPP-YAP regulatory interaction is conserved in mammalian system. In HEK293T and MDA-MB-231 cells, we demonstrate that NELFA depletion amplifies YAP-driven transcription. Whole-transcriptome analysis of MDA-MB-231 cells revealed widespread reprogramming upon NELFA loss, with strong enrichment of YAP signatures, EMT and TGF-{beta} transcriptional networks--indicating that NELFA regulates a broad YAP-centered gene regulatory module. Clinical analysis of two independent breast cancer cohorts revealed a context-dependent role for NELFA. Low NELFA expression predicted poor disease-free survival in YAP-high tumors--particularly in triple-negative breast cancer (TNBC)--suggesting a tumor-suppressive role. While High NELFA expression correlated with poorer overall survival in all the subtypes. These findings confirm that NELFAs role in YAP-driven transcription is conserved in mammalian system and it manifests in a context-dependent manner in the breast cancer.

cancer biology↗

bioRxiv2025

Spatial transcriptomics of glioblastoma defines biologically and clinically significant reprogramming patterns across unique spatial microenvironments

Intratumoral heterogeneity is thought to hinder targeted therapy in glioblastoma (GBM), but the extent of variation in known targets and tumor cell-intrinsic and extrinsic regulatory mechanisms within tissue remains unclear. In this work, we use Visium spatial transcriptomics to profile 44 tumor slides and 128,176 niche-annotated ST spots, including 14 new slides from 7 GBM specimens, along with spatial annotation from the Ivy Glioblastoma Atlas Project. First, we characterize the differential expression of AVB3, EGFR, VEGF, and PDGFRA pathway activities across space, elucidating the limited success of individual targeted therapies. Second, we identify transcription factor modules driving intratumoral heterogeneity and characterize a novel transcription factor module at the interface between core tumor and the invasive edge. Third, we identify cell type-specific receptor-ligand signaling enriched in specific spatial niches and relate these to specific molecular program alterations. Finally, we identify and characterize transcriptional pathways and their activity across spatial niches through transcription network analysis and demonstrate how these pathways can inform a combined therapeutic approach. Together, through novel insights into the spatial patterning of transcription factor regulation, cellular interactions, and biological pathway activity, our work informs rational combination therapies targeting spatial niche specific vulnerabilities.

bioinformatics↗

bioRxiv2025

Transcriptional and epigenetic repression of hematopoietic stem cells underlies bone marrow failure after spinal cord injury

Spinal cord injury (SCI) triggers systemic pathology beyond the nervous system, including bone marrow failure that can worsen infection risk, anemia, and motor recovery. Here we identify a neuroendocrine mechanism that rapidly imprints long-lasting dysfunction in hematopoietic stem cells (HSCs), which sustain lifelong production of immune cells, red blood cells, and platelets. Rather than mounting a canonical stress-hematopoietic response, SCI HSCs enter a broadly repressed state marked by chromatin closure and suppression of programs required for cell-cycle entry, genome maintenance, and redox defense. This maladaptive state leads to persistent DNA damage, impaired oxidative stress resolution, pancytopenia, and loss of long-term HSC regenerative capacity. Mechanistically, SCI-induced glucocorticoid surges drive glucocorticoid receptor-dependent repression of DNA repair genes, including Lig1 and Fen1. Acute glucocorticoid receptor blockade after SCI restores durable hematopoiesis, revealing an early therapeutic window to preserve hematopoietic integrity after neurotrauma. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/680535v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1627bb3org.highwire.dtl.DTLVardef@a73e19org.highwire.dtl.DTLVardef@1ddf85dorg.highwire.dtl.DTLVardef@1dcd8fe_HPS_FORMAT_FIGEXP M_FIG C_FIG Key FindingsO_LIAcute SCI prevents induction of normal stress-induced repair programs in HSCs. C_LIO_LISCI HSPCs exhibit increased chromatin compaction. C_LIO_LISCI compromises HSC genome-maintenance and redox capabilities. C_LIO_LISCI HSCs have defects in normal cell cycle regulation, are hypersensitive to genotoxic stress, and are deficient in long-term reconstitution. C_LIO_LIEarly glucocorticoid receptor (GR) blockade restores long-term hematopoiesis, supporting a GR-dependent but reversible repression mechanism. C_LI

cell biology↗

bioRxiv2025

A multimodal learning approach for automated detection of wildlife trade on social media

Social media data and machine learning methods for automated content analysis are increasingly being used in ecology and conservation science. A current limitation is the lack of methods for automated multimodal analysis of textual and visual content among other data modalities. In this study, we introduce a multimodal content analysis method applied to the investigation of wildlife trade on YouTube. Our approach consists of analyzing text through transformer based neural networks and video keyframes using convolutional neural networks as part of multimodal filtering followed by classification where a decision fusion module identifies instances of wildlife trade. The decision fusion module achieved an F-score of 0.72 among textual classifiers for trade detection and of 0.77 among visual classifiers for species identification. This multimodal classification helped detect wildlife trade in 3,715 out of 86,321 filtered YouTube posts, featuring 226 species for sale, including 51 Critically Endangered, 62 Endangered, 60 Vulnerable, 25 Near Threatened, and 28 Least Concern species. The proposed multimodal learning methods can be used more broadly for other ecological and biodiversity conservation applications. The bigger pictureThe unsustainable trade in wildlife is a major driver of biodiversity loss, threatening thousands of species across the Tree of Life. While online platforms have become popular spaces for advertising wildlife and exotic pets for sale, monitoring these platforms remains extremely challenging. Traditional surveillance methods are not scalable, and automated tools have typically focused on either text or image analysis in isolation, limiting their effectiveness in identifying nuanced instances of wildlife trade. Our study introduces a multimodal machine learning framework that integrates textual and visual data to detect potential wildlife trade on YouTube. By combining natural language processing with deep learning for image analysis, and filtering millions of posts down to those most relevant, our method significantly improves detection accuracy. This dual-layered approach uncovered thousands of posts featuring hundreds of species, many of which are threatened. This work demonstrates how advances in machine learning can support ecological monitoring and conservation by providing timely, data-driven, insights into online trade networks. In the pursuit of reducing biodiversity loss, this study offers an approach for bridging the gap between online behavior and real-world ecological outcomes. HighlightsO_LIIntroduces a multimodal content analysis approach for detecting wildlife trade on YouTube by integrating textual and visual data. C_LIO_LIA multimodal filtering technique reduces irrelevant text and video content, enhancing analytical efficiency. C_LIO_LIA decision fusion module then combines results from text and video filtering improving wildlife trade detection accuracy. C_LIO_LIThe proposed methods are applicable across multiple online platforms and suitable for diverse tasks in ecology and biodiversity conservation. C_LI

ecology↗

bioRxiv2025

Diabetes mellitus affects urinary tissue tropism of group B streptococci in a sex-dependent manner

Diabetes mellitus (DM) increases susceptibility to Streptococcus agalactiae (group B Streptococcus or GBS) urinary tract infections (UTI) and their exacerbations such as ascending pyelonephritis and sepsis, although underlying molecular mechanisms have not been fully deciphered. To address our hypothesis that DM mediated alterations in the host urinary immune defenses increase susceptibility to GBS-UTI, we inoculated, via transurethral route, GBS strain 10/84 into the urinary bladders of 8 weeks old, male and female, diabetic (obese, hyperglycemic mice denoted as D) and non-diabetic (ND) mouse littermates. At 24 h post-infection (hpi), compared to their ND littermates, the D-mice showed significantly higher GBS CFUs in the bladder, the kidneys, and the spleen. This was accompanied by a significantly reduced recruitment of CD45+ leukocytes to and suppression of pro-inflammatory cytokine production in GBS-infected D-bladder and D-kidneys compared to their ND counterparts. We also noted sex-dependent differences in GBS urinary tissue tropism. For example, D-females exhibited significantly higher bladder burden compared to ND-females, D-males, and to ND-males, while the bladder burden in ND-females was not significantly different from that in ND-males. In contrast, ND-males showed significantly higher kidney CFUs than ND-females and DM further increased kidney CFU burden in males. GBS-induced recruitment of CD45+ leukocytes was not different between male and female mice within either D or ND cohorts. GBS-UTI induced significantly higher CXCL1 production in male bladders in both D and ND cohorts compared to their female counterparts. These results indicate that DM increases susceptibility to GBS-UTI and the dissemination to spleen by affecting leukocyte recruitment and pro-inflammatory cytokine production in a sex-dependent manner. ImportanceIn this study we sought to understand why diabetic individuals are more susceptible to urinary tract infections (UTI) by Gram positive Streptococcus agalactiae (group B Streptococcus or GBS). We induced UTI by inoculating GBS into the bladders of diabetic (obese, hyperglycemic) and non-diabetic, male and female mice. At 24 hours after infection, compared to the non-diabetic mice, the diabetic mouse urinary tracts showed higher GBS counts and reduced immune defenses. Diabetes also promoted dissemination of GBS to the spleen. Furthermore, female diabetic mice were more susceptible to bladder infection while diabetes worsened the increased overall susceptibility of males to kidney infection, a difficult-to-treat, potentially life threatening exacerbation of GBS-UTI. Overall, our results suggest that both diabetes and sex are important determinants of susceptibility to GBS-UTI and resulting severe outcomes.

microbiology↗

bioRxiv2025

Regulation of hematopoietic stem cell (HSC) proliferation by Epithelial Growth Factor Like-7 (EGFL7)

Understanding the pathways regulating normal and malignant hematopoietic stem cell (HSC) biology is important for improving outcomes for patients with hematologic disorders. Epithelial Growth Factor Like-7 (EGFL7) is [~]30 kDa secreted protein that is highly expressed in adult HSCs. Using Egfl7 genetic knock-out (Egfl7 KO) mice and recombinant EGFL7 (rEGFL7) protein, we examined the role of Egfl7 in regulating normal hematopoiesis. We found that Egfl7 KO mice had decreases in overall BM cellularity resulting in significant reduction in the number of hematopoietic stem and progenitor cells (HSPCs), which was due to dysregulation of normal cell-cycle progression along with a corresponding increase in quiescence. rEGFL7 treatment rescued our observed hematopoietic defects of Egfl7 KO mice and enhanced HSC expansion after genotoxic stress such as 5-FU and irradiation. Furthermore, treatment of WT mice with recombinant EGFL7 (rEGFL7) protein expands functional HSCs evidenced by an increase in transplantation potential. Overall, our data demonstrates a role for EGFL7 in HSC expansion and survival and represents a potential strategy for improving transplant engraftment or recovering bone marrow function after stress.

cell biology↗

bioRxiv2024

scPrediXcan integrates advances in deep learning and single-cell data into a powerful cell-type-specific transcriptome-wide association study framework

Transcriptome-wide association studies (TWAS) help identify disease causing genes, but often fail to pinpoint disease mechanisms at the cellular level because of the limited sample sizes and sparsity of cell-type-specific expression data. Here we propose scPrediXcan which integrates state-of-the-art deep learning approaches that predict epigenetic features from DNA sequences with the canonical TWAS framework. Our prediction approach, ctPred, predicts cell-type-specific expression with high accuracy and captures complex gene regulatory grammar that linear models overlook. Applied to type 2 diabetes and systemic lupus erythematosus, scPrediXcan outperformed the canonical TWAS framework by identifying more candidate causal genes, explaining more genome-wide association studies (GWAS) loci, and providing insights into the cellular specificity of TWAS hits. Overall, our results demonstrate that scPrediXcan represents a significant advance, promising to deepen our understanding of the cellular mechanisms underlying complex diseases.

genetics↗

bioRxiv2024

CIWARS: a web server for waterborne antibiotic resistance surveillance using longitudinal metagenomic data

The rise of antibiotic resistance (AR) is a major global health crisis, exacerbated by the overuse and misuse of antibiotics, leading to the rapid spread of antibiotic resistance genes (ARGs) in bacterial pathogens. This phenomenon poses significant threats to human and animal health, food security, and economic stability. Water bodies, particularly wastewater treatment plants (WWTPs), serve as critical reservoirs for ARGs, creating environments that favor the proliferation of resistant bacteria. Wastewater-based surveillance (WBS) has emerged as a cost-effective strategy for monitoring AR at the population level, providing real-time data to guide public health and policy decisions. Despite advancements in WBS, there are no comprehensive online analytical platforms for continuous environmental AR surveillance. This paper introduces CIWARS, a web server designed for AR analyses of longitudinal metagenomic data. CIWARS offers comprehensive ARG profiling, taxonomic annotation, and anomalous AR risk points detection. We demonstrate its capabilities through an interactive temporal data visualization, showcasing its potential for enhancing AR risk monitoring and guiding effective mitigation strategies. CIWARS is broadly applicable to longitudinal metagenomic data generated from any environment and aims to support global efforts in addressing the AR crisis by providing cyberinfrastructure for continuous AR surveillance. The web server is freely available at https://ciwars.cs.vt.edu/.

bioinformatics↗

bioRxiv2024

circPCMTD1: A protein-coding circular RNA that regulates DNA damage response in BCR/ABL-positive leukemias

Circular RNAs are a novel class of RNA transcripts, which regulate important cellular functions in health and disease. Herein, we report on the functional relevance of the circPCMTD1 transcript in acute leukemias. In screening experiments, we found that circPCMTD1 depletion strongly inhibited the proliferative capacity of leukemic cells with BCR-ABL translocations. Mass cytometry experiments identified the aberrant activation of the DNA damage response as an early downstream event of circPCMTD1 depletion. In in vivo experiments, circPCMTD1 targeting prolonged the survival of mice engrafted with leukemic blasts harboring the Philadelphia chromosome. Mechanistically, we found that circPCMTD1 was enriched in the cytoplasm and associated with the ribosomes of the leukemic cells. We detected a cryptic open reading frame within the circPCMTD1 sequence and found that circPCMTD1 could generate a peptide product. The circPCMTD1-derived peptide interacted with proteins of the BTR complex and enhanced BTR complex formation, thereby increasing tolerance to genotoxic stress.

cancer biology↗

bioRxiv2023

Cellular taxonomy of the preleukemic bone marrow niche of acute myeloid leukemia

Mutations in hematopoietic stem/progenitor cells (HSPCs) can remain dormant within the bone marrow (BM) for decades before leukemia onset. Understanding the mechanisms by which these mutant clones eventually slead to full blown leukemia is of critical importance to develop strategies to eliminate these clones before they achieve their full leukemogenic potential. Recent data suggest that leukemic stem cells (LSCs) induce alterations within BM microenvironment (BMM) favoring LSC growth over normal HSCs. However, the cross talk between preleukemic stem cells (pLSC) and BMM is not completely understood. We hypothesize that pLSC induces critical changes within the BMM that are critical for leukemogenesis. To address this question, we are using our previously developed murine model of AML that highly recapitulates the human disease, develops AML sporadically with a preleukemic phase in which mice display normal white blood counts (WBCs) and absence of blasts in the BM. Thus, this is an excellent model to evaluate changes in the BMM that occurs during progression into AML. Using this model we performed single cell RNA-sequencing on cells from the BMM compared to wild-type (WT) controls. Overall, we defined the transcriptional profiles of pre-leukemic BMM cells and observed decreased percentages of normal BMM cells such as LepR+ mesenchymal stem cells (MSCs) and endothelial cells (ECs), known to regulate normal HSC function. Concomitantly, we found increases in CD55+ fibroblasts and NG2+ pericytes, that might play a more important role in regulation of pre-LSCs. Preleukemic CD55+ fibroblasts had a higher proliferation rate and showed significant down-regulation of several collagen genes known for regulating extra cellular matrix (ECM) including: Col1a1, Col1a2, Col3a1, Col4a1, and Col6a1, suggesting that ECM remodeling occurs in the early stages of leukemogenesis. Importantly, co-culture assays found that pre-leukemic CD55+ BM fibroblasts expanded pre-LSCs significantly over normal HSCs. In conclusion, we have identified distinct changes in the preleukemic BMM and identified a novel CD55+ fibroblast population that is expanded in preleukemic BMM that promote the fitness of pre-LSCs over normal HSCs. STATEMENT OF SIGNIFICANCEWe have identified changes in the BMM landscape that define a preleukemic BM niche which includes the expansion of a novel CD55+ fibroblast population. These data suggest that a distinct preleukemic BM niche exists and preferentially supports LSC survival and expansion over normal HSCs to promote leukemogenesis.

cancer biology↗

bioRxiv2023

Genome-wide analysis of Respiratory burst oxidase homolog (Rboh) genes in Aquilaria species and its association with agarwood formation

Respiratory burst oxidase homolog (Rboh), generate reactive oxygen species (ROS) to maintain normal growth and pathogen induced defence responses in plants. In Aquilaria plants, wounding and fungal invasion results in the biosynthesis of secondary metabolites as a defence response which with due course develop into agarwood. During pathogen invasion, Aquilaria tree accumulate ROS species through the action of Rboh enzymes. Although in agarwood formation role of Rboh gene family has been implicated, an comprehensives study on Rboh gene family and information of its role during agarwood formation in missing. In this study, seven Rboh genes were identified from the genomes of two Aquilaria species viz., Aquilaria agallocha and Aquilaria sinensis and phylogenetically classified into five groups. Stress response, hormone regulation, and development related regulatory elements were identified in the promoter regions. The protein sequences comprised of four conserved domains, an EF-hand domain, and a transmembrane region which they probably utilise for MAPK signaling, plant-pathogen interaction and plant hormone signal transduction pathways. Expression analyses revealed that among the seven members, AaRbohA and AaRhobC were involved in generation of ROS species, and also probably play role in agarwood formation. These findings provide valuable information regarding the Rboh members of A. agallocha which can be further used for functional analyses for in-depth understanding of ROS mediated signalling and regulation of agarwood formation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/539809v1_figu1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@169f501org.highwire.dtl.DTLVardef@1541667org.highwire.dtl.DTLVardef@18ad549org.highwire.dtl.DTLVardef@1b8b7b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

NLRP3 inflammasome is dispensable in methicillin resistant Staphylococcus aureus urinary tract infection

NLRP3 inflammasome is a cytoplasmic complex that senses molecular patterns from pathogens or damaged cells to trigger an innate immune defense response marked by the production of proinflammatory cytokines IL-1{beta} and IL-18 and an inflammatory death called pyroptosis. The NLRP3 inflammasome is activated in the urinary tract by a variety of infectious and non-infectious insults. In this study, we investigated the role of NLRP3 inflammasome by inducing methicillin resistant Staphylococcus aureus (MRSA) ascending UTI in WT and Nlrp3-/- mice. At 24 and 72 hpi, compared to the WT, the MRSA-infected Nlrp3-/- showed [~]100-fold lower median CFUs, although this reduction was not statistically significant. The ablation of NLRP3 did not affect MRSA-induced urinary immune defenses as indicated by the similar levels of pro-inflammatory cytokines and chemokines and the similar numbers of granulocytes in the bladder and the kidneys of WT and Nlrp3-/- mice at 24 h after MRSA infection. However, MRSA-infected Nlrp3-/- bladders, but not kidneys, showed significantly higher monocyte infiltration. The histopathological analysis of bladder and kidney sections showed similar inflammation in MRSA-infected Nlrp3-/- and WT mice. Overall, these results suggest that MRSA-induced urinary NLRP3 activity is dispensable to the host. ImportanceIndwelling urinary catheter usage increased susceptibility to methicillin-resistant Staphylococcus aureus (MRSA) urinary tract infections (UTI) which can be difficult to treat and can result in potentially fatal complications such as bacteremia, urosepsis, and shock. In this work, we examined the role of NLRP3 inflammasome in MRSA uropathogenesis. In comparison to the WT, mice deficient in NLRP3 activity showed similar MRSA burden and similar inflammation in the bladder and kidney tissues at 24 h after the experimental induction of ascending UTI. These results suggest that NLRP3 inflammasome is not involved in shaping urinary immune defenses during acute MRSA-UTI.

immunology↗

bioRxiv2022

Defining the roles of pyruvate oxidation, TCA cycle, and mannitol metabolism in methicillin resistance Staphylococcus aureus urinary tract infection

Methicillin resistant Staphylococcus aureus (MRSA) is an important cause of complicated urinary tract infection (UTI) associated with the use of indwelling urinary catheters. Previous reports have revealed host and pathogen effectors critical for MRSA uropathogenesis. Here, we sought to determine the significance of specific metabolic pathways during MRSA UTI. First, we identified 16 mutants from the Nebraska transposon mutant library in the MRSA JE2 background with significantly reduced growth in pooled human urine (HU). Among these, five genes targeted by transposon mutation also showed significant upregulation upon exposure to HU for 2 h. This prompted us to generate transposon insertion mutants in the uropathogenic MRSA 1369 strain that were defective in TCA cycle ({Delta}sucD, {Delta}fumC), mannitol metabolism ({Delta}mtlD), and pyruvate oxidation and branched chain fatty acid synthesis ({Delta}lpdA). Compared to the WT, the {Delta}lpdA mutant showed a significant defect growth in HU and colonization of the urinary tract and dissemination to spleen in the mouse model of catheter-associated UTI (CAUTI), which may be attributed to its increased membrane hydrophobicity and higher susceptibility to killing in blood. MRSA 1369 {Delta}sucD, {Delta}fumC, and {Delta}mtlD mutants were not defective for in vitro growth in HU but showed significant fitness defects in the CAUTI mouse model. Overall, identification of novel metabolic pathways important for the urinary fitness and survival of MRSA can be used for the development of novel therapeutics. ImportanceWhile Staphylococcus aureus has historically not been considered a uropathogen, S. aureus urinary tract infection (UTI) is clinically significant in certain patient populations, including those with chronic indwelling urinary catheters. Moreover, most S. aureus strains causing catheter-associated UTI (CAUTI) are methicillin-resistant S. aureus (MRSA), which is difficult to treat as it limits treatment options and has the potential to deteriorate into life-threatening bacteremia, urosepsis, and shock. In this study, we found that pathways involved in pyruvate oxidation, TCA cycle, and mannitol metabolism are important for MRSA fitness and survival in the urinary tract. Improved understanding of the metabolic needs of MRSA in the urinary tract may help us develop novel inhibitors of MRSA metabolism that can be used to treat MRSA-CAUTI more effectively.

microbiology↗

bioRxiv2022

Genome-wide investigation of Cytochrome P450 superfamily of Aquilaria agallocha: association with terpenoids and phenylpropanoids biosynthesis

P450 superfamily (CYPs) has been known as contributors to the metabolites diversity and their promiscuous nature has led to the flexibility in substrate specificity and functional diversity. Current study was designed to investigate CYPs in the genome of an agarwood producing plant species named Aquilaria agallocha. Agarwood, the resinous fragrant wood with numerous phytochemicals, produced when an Aquilaria plant respond to wound and microbial infection. These chemicals are of great interest to industries ascribing it a high economic value. However, the pathways for the biosynthesis of these metabolites have not been studied in context of Aquilaria CYPs. We identified 136 A. agallocha CYP proteins from the genome, characterized and classified them into 8 clans and 38 families. Functional analysis unveiled their participation in terpenoids, phenolics, flavonoids and other valuable metabolites biosynthesis. Conserved motifs were detected and evolutionary analysis revealed duplicated and orthologous pairs. Potential members for the biosynthesis of sesquiterpenoids and phenylpropanoids reported in Aquilaria and agarwood were elucidated and validated through expression profiles in stress induced callus tissues and infected Aquilaria tress. This study provides a strong foundation for biochemical characterization of Aquilaria CYPs which will aid heterologous production of valuable phytochemicals and untangle molecular mechanism of agarwood formation.

plant biology↗

bioRxiv2022

Ending transmission of SARS-CoV-2: sterilizing immunity using an intranasal subunit vaccine

Immunization programs against SARS-CoV-2 with commercial intramuscular (IM) vaccines prevent disease but not infections. The continued evolution of variants of concern (VOC) like Delta and Omicron has increased infections even in countries with high vaccination coverage. This is due to commercial vaccines being unable to prevent viral infection in the upper airways and exclusively targeting the spike (S) protein that is subject to continuous evolution facilitating immune escape. Here we report a multi-antigen, intranasal vaccine, NanoSTING-NS that yields sterilizing immunity and leads to the rapid and complete elimination of viral loads in both the lungs and the nostrils upon viral challenge with SARS-CoV-2 VOC. We formulated vaccines with the S and nucleocapsid (N) proteins individually to demonstrate that immune responses against S are sufficient to prevent disease whereas combination immune responses against both proteins prevents viral replication in the nasal compartment. Studies with the highly infectious Omicron VOC showed that even in vaccine-naive animals, a single dose of NanoSTING-NS significantly reduced transmission. These observations have two implications: (1) mucosal multi-antigen vaccines present a pathway to preventing transmission and ending the pandemic, and (2) an explanation for why hybrid immunity in humans is superior to vaccine-mediated immunity by current IM vaccines.

immunology↗

bioRxiv2022

CAPG: Comprehensive Allopolyploid Genotyper

MotivationGenotyping by sequencing is a powerful tool for investigating genetic variation in plants, but many economically important plants are allopolyploids, where homoeologous similarity obscures the subgenomic origin of reads and confounds allelic and homoeologous SNPs. Recent polyploid genotyping methods use allelic frequencies, rate of heterozygosity, parental cross or other information to resolve read assignment, but good subgenomic references offer the most direct information. The typical strategy aligns reads to the joint reference, performs diploid genotyping within each subgenome, and filters the results, but persistent read misassignment results in an excess of false heterozygous calls. ResultsWe introduce the Comprehensive Allopolyploid Genotyper (CAPG), which formulates an explicit likelihood to weight read alignments against both subgenomic references and genotype individual allopolyploids from whole genome resequencing (WGS) data. We demonstrate CAPG in allotetraploids, where it performs better than GATKs HaplotypeCaller applied to reads aligned to the combined subgenomic references. AvailabilityCode and tutorials are available at https://github.com/Kkulkarni1/CAPG.git.

bioinformatics↗

bioRxiv2022

An intranasal nanoparticle STING agonist has broad protective immunity against respiratory viruses and variants

Respiratory viral infections, especially Influenza (endemic) or SARS-CoV-2 (pandemic since 2020), cause morbidity and mortality worldwide. Despite remarkable progress in the development and deployment of vaccines, they are clearly impacted by the rapid emergence of viral variants. The development of an off-the-shelf, effective, safe, and low-cost drug for prophylaxis against respiratory viral infections is a major unmet medical need. Here, we developed NanoSTING, a liposomally encapsulated formulation of the endogenous STING agonist, 2-3 cGAMP, to function as an immunoantiviral. NanoSTING rapidly activates the bodys innate immune system to facilitate a broad-spectrum antiviral response against SARS-CoV-2 and influenza variants in hamsters and mice. We demonstrate that a single intranasal dose of NanoSTING can: (1) treat infections throughout the respiratory system and minimize clinical symptoms, (2) protect against highly pathogenic strains of SARS-CoV-2 (alpha and delta), (3) provide durable protection against reinfection from the same strains without the need for retreatment, (4) prevent transmission of the highly infectious SARS-CoV-2 Omicron strain, and (5) provide protection against both oseltamivir-sensitive and resistant strains of influenza. Mechanistically, administration of NanoSTING rapidly upregulated interferon-stimulated and antiviral pathways in both the nasal turbinates and lung. Our results support using NanoSTING as a thermostable, immunoantiviral with broad-spectrum antiviral properties making it appealing as a therapeutic for prophylactic or early post-exposure treatment.

immunology↗