Biology subjects

Agrawal, K.

Publications and source records attributed to Agrawal, K..

12 recordsLinked to original sources

bioRxiv2026

Comparative Metabolomic Profiling Reveals Salinity Tolerance Mechanisms in a Rice Introgression Line

Rice (Oryza sativa) is highly sensitive to salinity, yet the metabolic mechanisms underlying salt tolerance remains incompletely understood. In this study, we performed leaf tissue-specific untargeted metabolomic profiling of the salt-tolerant introgression line JN100 (JN), its donor parent Nona Bokra (NB), and its recurrent parent Jupiter (JU) to characterize metabolic responses to salt stress. Comparative analysis identified differentially accumulated metabolites (DAMs) spanning diverse chemical classes, including amino acids, sugars and carbohydrates, lipids, organic acids, cofactors, electron carriers, and nucleotides. Under salt stress (SS), 201 DAMs (89 upregulated and 112 downregulated) were detected in JN relative to JU. Notably, metabolites such as allantoin, glycitin, nicotinamide ribotide, D-arabinono-1,4-lactone, violanthin, L-methionine S-oxide, ribitol, lysine, rutin, glutamine, pantothenic acid, and quinic acid, showed significant differential accumulation. Pathway enrichment analysis revealed significant enrichment of arginine biosynthesis, purine metabolism, and alanine, aspartate, and glutamate metabolism, indicating extensive reprogramming of nitrogen and energy-associated metabolic pathways under salinity stress. Integration of transcriptomic and metabolomic datasets from the SS experiments further identified ten differentially expressed genes (DEGs) associated with the metabolite network in the JN vs. JU comparison. Among these, OsDHQDT/SDH, OsFd-GOGAT, phenylalanyl-tRNA synthetase, OsP5CS1, OsP5CS2, and a pyridoxal phosphate-dependent transferase were linked to metabolites involved in shikimate, amino acid, and proline metabolism. Collectively, these results demonstrate that salinity tolerance in rice is associated with coordinated transcriptional and metabolic reprogramming that supports oxidative stress mitigation and adaptive stress responses.

plant biology↗

bioRxiv2026

Integrated Lipidomics and Nitro-Fatty Acid Profiling Link Adipose Redox Imbalance to Alzheimer's Disease-Related Neurovascular Injury

Alzheimers disease (AD) is increasingly recognized as a systemic disorder in which peripheral metabolic and redox dysfunction affects neurovascular injury and amyloid pathology. However, the lipid-redox mechanisms linking adipose tissue dysfunction to AD are less explored. Here, we applied an integrated multi-omics and imaging approach to investigate adipose lipid remodelling that leads to nitric oxide (NO)-derived nitro-fatty acid modifications and their effects on {beta}-amyloid and VEGF in the hippocampus of APP/PS1 mice. Targeted lipidomics revealed broad suppression of lysophospholipids and membrane phospholipids (LPC, PC, PE, PG) in gonadal white adipose tissue (gWAT), consistent with impaired membrane turnover and mitochondrial lipid deficiency. Untargeted lipidomics demonstrated accumulation of ceramides, triacylglycerols, monoacylglycerols, and phosphatidic acids, indicating lipotoxicity and disrupted lipid flux. Oxidized lipid mediator profiling showed increased 13-HODE, 12-HETE, and 14-HDHA. Further, Raman microscopy mapping revealed a shift from protective nitro-oleic acid toward increased nitration of polyunsaturated fatty acids. These lipid abnormalities coincided with increased adipose expression of redox and inflammatory markers, including NOX4 and TNF-, and impaired mitochondrial redox metabolism assessed by fluorescence lifetime imaging (FLIM). Citrulline and nitrite treatments partially normalized adipose lipid-redox signatures. Citrulline restored phospholipid remodeling and nitro-oleic acid signaling, whereas nitrite preferentially enhanced stress-associated signaling lipids. Importantly, both interventions reduced hippocampal {beta}-amyloid burden and restored VEGF expression, with citrulline producing the strongest neurovascular rescue. These findings identify adipose lipid-redox imbalance as a systemic contributor to neurovascular pathology in AD and highlight NO-directed metabolic modulation as a strategy to mitigate disease-associated lipid dysfunction.

molecular biology↗

bioRxiv2026

Engineering pH-Responsive trans-Ferulic Acid/κ-Carrageenan Beads for On-Demand Micronutrient Delivery in Plants

Micronutrient deficiencies in soils are a critical challenge in agriculture, particularly in acidic soil environments where nutrient availability is strongly limited by fixation, leaching, and altered metal speciation. These constraints contribute to inefficient nutrient uptake and reduced crop yields. Conventional micronutrient supplementation methods are often inefficient, environmentally harmful, and unsustainable, underscoring the need for smarter delivery systems tailored to soil pH conditions. In this study, we developed biodegradable, pH-responsive microbeads from {kappa}-carrageenan ({kappa}-CG) and trans-ferulic acid (TFA) for targeted micronutrient release. The {kappa}-CG-TFA microbeads were synthesized via an eco-friendly process and optimized for size, morphology, stability, and nutrient retention. Characterization confirmed the successful incorporation of functional groups, while swelling, degradation, and release studies demonstrated efficient delivery of essential micronutrients (Mn2+, Zn2+, Cu2+, and Fe3+) under acidic conditions (pH 4.0), mimicking acidic soil environments. The inherent antioxidant activity of TFA conferred strong radical-scavenging capacity, further enhancing its functionality. Soil water and plant growth assays revealed that the microbeads improved micronutrient availability, significantly increased chlorophyll content and leaf area, promoted vigorous seedling growth, and caused no phytotoxic effects. Collectively, these findings establish {kappa}-CG-TFA microbeads as a promising, eco-friendly platform for sustainable micronutrient delivery and stress reduction, thereby improving crop productivity in agriculture.

bioengineering↗

bioRxiv2026

Recombinant Photo-tagging Enables Fluorescent Labelling of Biomolecules and Visualization of Liquid-Liquid Phase Separation

Liquid-liquid phase separation (LLPS) of biomolecules has emerged as a fundamental principle governing biological systems. A key aspect to understand LLPS is the ability to visualize these coacervates, which requires labelling strategies. Fluorescent labelling of biomolecules remains one of the widely adopted techniques involving either small-molecule chemical conjugation or recombinant expression alongside a fluorescent protein. These small-molecule fluorophores are typically employed in excess, which further necessitates additional downstream processing steps, including separation of the conjugated molecules from the unreacted fluorophores. On the other hand, recombinantly appended fluorescent protein affects the functioning of the labelled biomolecule owing to its large size. There is still a need to develop a labelling technique with small molecular weight fluorophores that is also genetically encodable. We previously discovered that the C-terminal peptide fragment (CTPF) released during photo-exposure of a green-to-red photoconvertible fluorescent protein (PhoCl1) displayed red fluorescence. Notably, this chromophore displays broad excitation and emission wavelength profiles, rendering it robust under multiple excitation wavelengths. We leverage this phenomenon to achieve post-expression fluorescent labelling by genetically fusing PhoCl1 to the target peptide or protein to be labelled (TPTL). We successfully demonstrated this approach of conferring fluorescence to silica binding peptide, riboflavin kinase enzyme, TEV protease, Lanthanide Binding Peptide and maltose binding protein, all of which exhibited red fluorescence upon photocleavage. Finally, we demonstrate the applicability of this probe to visualize LLPS of CTPF tagged elastin-like polypeptide in the presence of polymeric crowder. We anticipate that this strategy for inducing red fluorescence in non-fluorescent biomolecules via a photocleavable protein will open new avenues for minimally perturbative fluorescent labelling.

bioengineering↗

bioRxiv2025

Cardiolipin Remodeling as a Regulatory Switch in Osteogenesis: Insights from Multimodal Metabolic Imaging and Molecular Profiling

Cardiolipin (CL), a mitochondria-specific phospholipid, plays a fundamental role in respiratory chain organization and bioenergetic efficiency, yet its contribution to osteogenic differentiation is poorly defined. Here, we used a multimodal approach integrating untargeted LC-MS lipidomics, Raman spectroscopy, fluorescence lifetime imaging microscopy (FLIM), and structural imaging to investigate CL remodeling during human adipose-derived stem cell differentiation. Lipidomics revealed a selective enrichment of highly unsaturated CL species, accompanied by transcriptional upregulation of the cardiolipin biosynthetic and remodeling enzymes CDS1/2, PGS1, CRLS1, TAZ, and HADHA. Lipidomics also revealed a time-dependent increase in membrane-associated lipids including phosphatidylcholine (PC), serine, and phosphatidylinositol (PI). These lipids were implicated in supporting mitochondrial membrane expansion, oxidative phosphorylation, and signaling processes critical for osteoblast maturation. Spatial imaging techniques confirmed cardiolipin accumulation and redistribution in differentiated cells, while Raman-based direct classical least squares (DCLS) analysis provided label-free mapping of lipid species. Gene Ontology (GO) enrichment and protein-protein interaction network analysis further identified biological pathways related to bone remodeling, cardiolipin metabolism, and osteoblast-specific signaling. Fluorescence Lifetime Imaging Microscopy (FLIM) data revealed a metabolic shift from glycolysis to oxidative phosphorylation during differentiation, supported by structural and gene expression evidence. These changes temporally coincided with matrix mineralization and collagen organization, linking CL metabolism to both cellular bioenergetics and extracellular matrix production. Our findings identify cardiolipin remodeling as a metabolic checkpoint in osteogenesis and suggest that targeted modulation of CL pathways may provide new therapeutic strategies for enhancing bone regeneration.

cell biology↗

bioRxiv2025

Multiomics Integration Reveals a Metabolic Myopathy in Cardiometabolic HFpEF

BackgroundSkeletal muscle dysfunction is a major peripheral determinant of exercise intolerance and physical disability in heart failure with preserved ejection fraction (HFpEF). Metabolic and mitochondrial dysfunction are considered to be key components of skeletal muscle dysfunction, but comprehensive profiling of metabolic pathways has not been conducted. Elucidation of dysregulated metabolic pathways is essential to determine viable targets for the treatment of exercise intolerance in HFpEF. MethodsMale ZSF1 Obese rats (HFpEF) and Wistar Kyoto (WKY) lean normotensive controls were studied at 26 weeks of age. Gastrocnemius was subjected to bulk RNA-seq, proteomics, metabolomics, and lipidomics analysis. The R package limma was used to determine differential expression in all omics layers (absolute fold-change>1.5, FDR0.05, unless otherwise indicated). Additional targeted plasma and skeletal muscle (soleus and EDL) metabolomics and lipidomics were performed on HFpEF and control rats. ResultsPathway level analysis for RNA seq and proteomics revealed significant downregulation of oxidative phosphorylation (NES -2.1, p<0.005), electron transport chain (NES -2.0, p<0.005), and TCA cycle (-1.8, p<0.05). The most upregulated pathways were PPAR signaling (NES 2.2, p<0.0001), tryptophan metabolism (NES 1.8, P<0.005), and amino acid oxidation (NES 1.8, p<0.005) pathways. Metabolomics revealed an accumulation of TCA cycle intermediate, isocitrate, and phosphate reduction. Branched-chain amino acids were significantly increased, whereas amino acids related to tryptophan metabolism were reduced and shifted towards increased serotonin accumulation. Phospholipid species were differentially regulated with increased palmitoylated phosphatidylcholines but reduced arachidonoyl-PC species. Phosphatidylethanolamines (PE) species (16:0/16:1-18:0/18:2) were increased. ConclusionOur multiomics analysis of skeletal muscle in HFpEF revealed severe mitochondrial dysfunction that was characterized by reduced complex I and II activity. Mitochondrial and peroxisomal lipid overload results in a shift in membrane phospholipid accumulation and composition. Reduced BCAA oxidation and dysregulation of tryptophan metabolism are key features of amino acid metabolism that reduce anaplerosis and promote the accumulation of toxic metabolites. Comparative analysis of other skeletal muscle disorders suggests that an acquired metabolic myopathy exists in cardiometabolic HFpEF.

physiology↗

bioRxiv2025

Multi-omic Characterization of HIV Effects at Single Cell Level across Human Brain Regions

HIV infection exerts profound and long-lasting neurodegenerative effects on the central nervous system (CNS) that can persist despite antiretroviral therapy (ART). Here, we used single-nucleus multiome sequencing to map the transcriptomic and epigenetic landscapes of postmortem human brains from 13 healthy individuals and 20 individuals with HIV who have a history of treatment with ART. Our study spanned three distinct regions--the prefrontal cortex, insular cortex, and ventral striatum--enabling a comprehensive exploration of region-specific and cross-regional perturbations. We found widespread and persistent HIV-associated transcriptional and epigenetic alterations across multiple cell types. Detailed analyses of microglia revealed state changes marked by immune activation and metabolic dysregulation, while integrative multiomic profiling of astrocytes identified multiple subpopulations, including a reactive subpopulation unique to HIV-infected brains. These findings suggest that cells from people with HIV exhibit molecular shifts that may underlie ongoing neuroinflammation and CNS dysfunction. Furthermore, cell-cell communication analyses uncovered dysregulated and pro-inflammatory interactions among glial populations, underscoring the multifaceted and enduring impact of HIV on the brain milieu. Collectively, our comprehensive atlas of HIV-associated brain changes reveals distinct glial cell states with signatures of pro-inflammatory signaling and metabolic dysregulation, providing a framework for developing targeted therapies for HIV-associated neurological dysfunction.

bioinformatics↗

bioRxiv2024

The Multiple Roles of Gamma Interferon in Intraepithelial T Cell-Villous Enterocyte Interactions in Active Celiac Disease

We compared duodenal biopsies showing active celiac disease (CeD) to normal controls using single cell RNA sequencing, cyclic immunofluorescence, RNAScope and proximity ligation assays. There is increased infiltration of villous but not crypt epithelium T cells bearing either {beta} or {gamma}{delta} T cell receptors (TCRs) in CeD. Both T cell subsets are activated cytotoxic T lymphocytes (CTLs) and surprisingly are the predominant mucosal source of IFN{gamma}. In response to this IFN{gamma},villous but not crypt enterocytes show an IFN{gamma} signature, including nuclear phospho-STAT1 protein, class II HLA molecules and IFN{gamma}-inducible chemokines known to recruit CTLs (e.g., CCL3, CCL4, CXCL10, and CXCL11) and receptors for these chemokines are expressed on the infiltrating CTLs. Villous enterocytes also display increased HLA-E and HLA-B mRNAs and proteins. Bioinformatic analyses (NICHES) and proximity ligation assays show frequent binding of both {beta} and {gamma}{delta} TCRs with enterocyte HLA-E or HLA-B, but not HLA-DR. In contrast, NKG2C, proposed as an alternative trigger of CTL activation, is infrequently-expressed and shows few interactions with HLA-E. Our data suggest that activated intraepithelial CTLs produce IFN{gamma} which recruits additional CTLs and increases antigen-dependent killing of villous epithelium using either conventional or HLA-E antigen presentation. SignifanceAnalyses of diagnostic biopsies from celiac disease patients reveals critical roles for IFN{gamma} actions on enterocytes and a surprising role of HLA-E in antigen presntation. Activated cytotoxic T lymphocytes (CTLs) that are the primary source of mucosal IFN{gamma}, leading to IFN{gamma} signaling in villous enterocytes, including expression of phospho-STAT1 protein, class II HLA molecules, and chemokines that attract CTLs. Bioinformatic ligand receoptor analyses and proximity ligation assays showed frequent interactions between intraepithelial CTLs and enterocyte HLA-E or HLA-B, indicating that IFN{gamma} production by the CTLs likely promotes further CTL recruitment and antigen-dependent killing of the villous epithelium.

immunology↗

bioRxiv2022

Protein-protein interaction map in pre-eclampsia through the interaction of hub genes, transcription factors and microRNAs

Pre-eclampsia causes complications in pregnancy and characterized by uremia, proteinuria and hypertension in unattended cases. Blood biomarkers for pre-eclampsia are lacking. In this study, microarray gene expression data from peripheral blood of pre-eclampsia women was analyzed. In our study we developed a combined network approach for hub node prediction regulated by transcription factors and microRNAs corresponding to pre-eclampsia. Differentially expressed genes (DEGs) interaction map was constructed using STRING database. JUN, RPL35, NDUFB2, ATP5I, UQCRQ, COX7C, and FN1 were predicted as potential novel hub genes. Pathway analysis showed metabolic pathways, cytokine signaling in the immune system, Wnt, and MAPK signaling pathways involvement in pre-eclampsia. Regulatory network analysis showed that transcription factors JUN and STAT1 were connected with hub nodes, and microRNAs (miRNAs) like hsa-miR-26b-5p and hsa-miR-155-5p. In conclusion, the expression pattern of hub genes, analyzed deciphers a molecular signature for understanding the pathophysiology of pre-eclampsia and prediction of biomarkers for diagnosis.

bioinformatics↗

bioRxiv2022

Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation.

Ataxin-2 (ATXN2) is a gene implicated in spinocerebellar ataxia type II (SCA2), amyotrophic lateral sclerosis (ALS) and Parkinsonism. The encoded protein is a therapeutic target for ALS and related conditions. ATXN2 (or Atx2 in insects) can function in translational activation, translational repression, mRNA stability and in the assembly of mRNP-granules, a process mediated by intrinsically disordered regions (IDRs). Previous work has shown that the LSm (Like-Sm) domain of Atx2, which can help stimulate mRNA translation, antagonizes mRNP-granule assembly. Here we advance these findings through a series of experiments on Drosophila and human Ataxin-2 proteins. Results of Targets of RNA-Binding Proteins Identified by Editing (TRIBE), co-localization and immunoprecipitation experiments indicate that a polyA-binding protein (PABP) interacting, PAM2 motif of Ataxin-2 may be a major determinant of the mRNA and protein content of Ataxin-2 mRNP granules. Transgenic experiments in Drosophila indicate that while the Atx2-LSm domain may protect against neurodegeneration, structured PAM2- and unstructured IDR- interactions both support Atx2-induced cytotoxicity. Taken together, the data lead to a proposal for how Ataxin-2 interactions are remodelled during translational control and how structured and non-structured interactions contribute differently to the specificity and efficiency of RNP granule condensation as well as to neurodegeneration.

neuroscience↗

bioRxiv2020

ANTAGONISTIC ROLES FOR ATAXIN-2 STRUCTURED AND DISORDEREDDOMAINS IN RNP CONDENSATION

Ataxin-2 is a conserved translational control protein associated with spinocerebellar ataxia type II (SCA2) and amyotrophic lateral sclerosis (ALS) as well as an important target for ALS therapeutics under development. Despite its clinical and biological significance, Ataxin-2s activities, mechanisms and functions are not well understood. While Drosophila Ataxin-2 (Atx2) mediates mRNP condensation via a C-terminal intrinsically disordered domain (cIDR), how Ataxin-2 IDRs work with structured (Lsm, Lsm-AD and PAM2) domains to enable positive and negative regulation of target mRNAs remains unclear. Using TRIBE (Targets of RNA-Binding Proteins Identified by Editing) technology, we identified and analysed Atx-2 target mRNAs in the Drosophila brain. We show that Atx2 preferentially interacts with AU-rich elements (AREs) in 3UTRs and plays a broad role in stabilization of identified target mRNAs. Strikingly, Atx2 interaction with its targets is dependent on the cIDR domain required for neuronal-granule formation. In contrast, Atx2 lacking its Lsm domain not only interacts more efficiently with the target mRNA identified, but also forms larger RNP granules. Providing an extensive dataset of Atx2-interacting brain mRNAs, our results demonstrate that Atx2: (a) interacts with target mRNAs within RNP granules; (b) modulates the turnover of these target mRNAs; (c) has an additional essential role outside of mRNP granules; and (d) contains distinct protein domains that drive or oppose RNP-granule assembly. These findings increase understanding of neuronal translational control mechanisms and inform Ataxin-2-based interventions in development for SCA2 and ALS.

neuroscience↗

bioRxiv2019

An Atlas of Immune Cell Exhaustion in HIV-Infected Individuals Revealed by Single-Cell Transcriptomics

Chronic infection with human immunodeficiency virus (HIV) can cause progressive loss of immune cell function, or exhaustion, which impairs control of virus replication. However, little is known about the development and maintenance, as well as heterogeneity of immune cell exhaustion. Here, we investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from two healthy subjects (15,121 cells) and six HIV-infected donors (28,610 cells). We identified nine immune cell clusters and eight T cell subclusters according to their unique gene expression programs; three of these (exhausted CD4+ and CD8+ T cells and interferon-responsive CD8+ T cells) were detected only in samples from HIV-infected donors. An inhibitory receptor KLRG1 was identified in the exhausted T cell populations and further characterized in HIV infected individuals. We identified a novel HIV-1 specific exhausted CD8+ T cell population expressing KLRG1, TIGIT, and T-betdimEomeshi markers. Ex-vivo antibody blockade of KLRG1 restored the function of HIV-specific exhausted CD8+ T cells demonstrating the contribution of KLRG1+ population to T cell exhaustion and providing a novel target for developing immunotherapy to treat HIV chronic infection. Analysis of gene signatures also revealed impairment of B cell and NK cell function in HIV-infected donors. These data provide a comprehensive analysis of gene signatures associated with immune cell exhaustion during HIV infection, which could be useful in understanding exhaustion mechanisms and developing new cure therapies.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC=\"FIGDIR/small/678763v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@d6291borg.highwire.dtl.DTLVardef@24db3aorg.highwire.dtl.DTLVardef@1b4f65borg.highwire.dtl.DTLVardef@199d243_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗